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47469 | <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
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<div class="contentContainer"><a href="#_A_">A</a> <a href="#_B_">B</a> <a href="#_C_">C</a> <a href="#_D_">D</a> <a href="#_E_">E</a> <a href="#_F_">F</a> <a href="#_G_">G</a> <a href="#_H_">H</a> <a href="#_I_">I</a> <a href="#_J_">J</a> <a href="#_K_">K</a> <a href="#_L_">L</a> <a href="#_M_">M</a> <a href="#_N_">N</a> <a href="#_O_">O</a> <a href="#_P_">P</a> <a href="#_Q_">Q</a> <a href="#_R_">R</a> <a href="#_S_">S</a> <a href="#_T_">T</a> <a href="#_U_">U</a> <a href="#_V_">V</a> <a href="#_W_">W</a> <a href="#_X_">X</a> <a href="#_Y_">Y</a> <a href="#_Z_">Z</a> <a href="#___">_</a> <a name="_A_">
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<h2 class="title">A</h2>
<dl>
<dt><span class="strong"><a href="./org/biojava/bio/seq/DNATools.html#a()">a()</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/DNATools.html" title="class in org.biojava.bio.seq">DNATools</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/NucleotideTools.html#a()">a()</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/NucleotideTools.html" title="class in org.biojava.bio.seq">NucleotideTools</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/ProteinTools.html#a()">a()</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/ProteinTools.html" title="class in org.biojava.bio.seq">ProteinTools</a></dt>
<dd>
<div class="block">Returns the <code>AtomicSymbol</code> for the amino acid
Alanine</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/RNATools.html#a()">a()</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/RNATools.html" title="class in org.biojava.bio.seq">RNATools</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/Taxon.html#A_THALIANA">A_THALIANA</a></span> - Static variable in interface org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/Taxon.html" title="interface in org.biojava.bio.program.homologene">Taxon</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOConstants.html#AA">AA</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOConstants.html" title="class in org.biojava.bio.seq.io">SeqIOConstants</a></dt>
<dd>
<div class="block"><code>AA</code> indicates that a sequence contains AA (amino
acid) symbols.</div>
</dd>
<dt><a href="./org/biojava/bio/proteomics/aaindex/AAindex.html" title="class in org.biojava.bio.proteomics.aaindex"><span class="strong">AAindex</span></a> - Class in <a href="./org/biojava/bio/proteomics/aaindex/package-summary.html">org.biojava.bio.proteomics.aaindex</a></dt>
<dd>
<div class="block">Symbol property table based on the Amino Acid Index Database.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/aaindex/AAindex.html#AAindex(java.lang.String)">AAindex(String)</a></span> - Constructor for class org.biojava.bio.proteomics.aaindex.<a href="./org/biojava/bio/proteomics/aaindex/AAindex.html" title="class in org.biojava.bio.proteomics.aaindex">AAindex</a></dt>
<dd>
<div class="block">Initializes the AAindex symbol property table.</div>
</dd>
<dt><a href="./org/biojava/bio/proteomics/aaindex/AAindexStreamReader.html" title="class in org.biojava.bio.proteomics.aaindex"><span class="strong">AAindexStreamReader</span></a> - Class in <a href="./org/biojava/bio/proteomics/aaindex/package-summary.html">org.biojava.bio.proteomics.aaindex</a></dt>
<dd>
<div class="block">Iterator over <a href="./org/biojava/bio/proteomics/aaindex/AAindex.html" title="class in org.biojava.bio.proteomics.aaindex"><code>AAindex</code></a> objects that
are stored in a stream in the AAindex1 file format.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/aaindex/AAindexStreamReader.html#AAindexStreamReader(java.io.Reader)">AAindexStreamReader(Reader)</a></span> - Constructor for class org.biojava.bio.proteomics.aaindex.<a href="./org/biojava/bio/proteomics/aaindex/AAindexStreamReader.html" title="class in org.biojava.bio.proteomics.aaindex">AAindexStreamReader</a></dt>
<dd>
<div class="block">Initializes the iterator.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/aaindex/AAindexStreamReader.html#AAindexStreamReader(java.io.BufferedReader)">AAindexStreamReader(BufferedReader)</a></span> - Constructor for class org.biojava.bio.proteomics.aaindex.<a href="./org/biojava/bio/proteomics/aaindex/AAindexStreamReader.html" title="class in org.biojava.bio.proteomics.aaindex">AAindexStreamReader</a></dt>
<dd>
<div class="block">Initializes the iterator.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.Terms.html#ABBREV_NAME_KEY">ABBREV_NAME_KEY</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.Terms.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat.Terms</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BiblioJournal.html#abbreviation">abbreviation</a></span> - Variable in class org.biojava.bibliography.<a href="./org/biojava/bibliography/BiblioJournal.html" title="class in org.biojava.bibliography">BiblioJournal</a></dt>
<dd>
<div class="block">
An abbreviation of the journal title.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/ChromatogramFactory.html#ABI_MAGIC">ABI_MAGIC</a></span> - Static variable in class org.biojava.bio.chromatogram.<a href="./org/biojava/bio/chromatogram/ChromatogramFactory.html" title="class in org.biojava.bio.chromatogram">ChromatogramFactory</a></dt>
<dd>
<div class="block">The magic number for ABIF files.</div>
</dd>
<dt><a href="./org/biojava/bio/program/abi/ABIFChromatogram.html" title="class in org.biojava.bio.program.abi"><span class="strong">ABIFChromatogram</span></a> - Class in <a href="./org/biojava/bio/program/abi/package-summary.html">org.biojava.bio.program.abi</a></dt>
<dd>
<div class="block">An implementation of <a href="./org/biojava/bio/chromatogram/Chromatogram.html" title="interface in org.biojava.bio.chromatogram"><code>Chromatogram</code></a> to
encapulsulate chromatogram data extracted from the files produced by ABI
sequencers, such as the the 377 and the 3700.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/abi/ABIFChromatogram.html#ABIFChromatogram()">ABIFChromatogram()</a></span> - Constructor for class org.biojava.bio.program.abi.<a href="./org/biojava/bio/program/abi/ABIFChromatogram.html" title="class in org.biojava.bio.program.abi">ABIFChromatogram</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/abi/ABIFChromatogram.Parser.html" title="class in org.biojava.bio.program.abi"><span class="strong">ABIFChromatogram.Parser</span></a> - Class in <a href="./org/biojava/bio/program/abi/package-summary.html">org.biojava.bio.program.abi</a></dt>
<dd>
<div class="block">An extension of <a href="./org/biojava/bio/program/abi/ABIFParser.html" title="class in org.biojava.bio.program.abi"><code>ABIFParser</code></a> that reads the particular fields from
the ABIF that contain the chromatogram data and initializes the fields
in its enclosing <code>ABIFChromatogram</code> instance.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/abi/ABIFChromatogram.Parser.html#ABIFChromatogram.Parser(java.io.InputStream)">ABIFChromatogram.Parser(InputStream)</a></span> - Constructor for class org.biojava.bio.program.abi.<a href="./org/biojava/bio/program/abi/ABIFChromatogram.Parser.html" title="class in org.biojava.bio.program.abi">ABIFChromatogram.Parser</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/abi/ABIFChromatogram.Parser.html#ABIFChromatogram.Parser(java.io.File)">ABIFChromatogram.Parser(File)</a></span> - Constructor for class org.biojava.bio.program.abi.<a href="./org/biojava/bio/program/abi/ABIFChromatogram.Parser.html" title="class in org.biojava.bio.program.abi">ABIFChromatogram.Parser</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/abi/ABIFParser.html" title="class in org.biojava.bio.program.abi"><span class="strong">ABIFParser</span></a> - Class in <a href="./org/biojava/bio/program/abi/package-summary.html">org.biojava.bio.program.abi</a></dt>
<dd>
<div class="block">A general base parser for files produced by ABI software.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/abi/ABIFParser.html#ABIFParser(java.io.File)">ABIFParser(File)</a></span> - Constructor for class org.biojava.bio.program.abi.<a href="./org/biojava/bio/program/abi/ABIFParser.html" title="class in org.biojava.bio.program.abi">ABIFParser</a></dt>
<dd>
<div class="block">Creates a new ABIFParser for a file.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/abi/ABIFParser.html#ABIFParser(java.io.InputStream)">ABIFParser(InputStream)</a></span> - Constructor for class org.biojava.bio.program.abi.<a href="./org/biojava/bio/program/abi/ABIFParser.html" title="class in org.biojava.bio.program.abi">ABIFParser</a></dt>
<dd>
<div class="block">Creates a new ABIFParser for an input stream.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/abi/ABIFParser.html#ABIFParser(org.biojava.bio.program.abi.ABIFParser.DataAccess)">ABIFParser(ABIFParser.DataAccess)</a></span> - Constructor for class org.biojava.bio.program.abi.<a href="./org/biojava/bio/program/abi/ABIFParser.html" title="class in org.biojava.bio.program.abi">ABIFParser</a></dt>
<dd>
<div class="block">Creates a new ABIFParser for the specified <a href="./org/biojava/bio/program/abi/ABIFParser.DataAccess.html" title="interface in org.biojava.bio.program.abi"><code>ABIFParser.DataAccess</code></a> object.</div>
</dd>
<dt><a href="./org/biojava/bio/program/abi/ABIFParser.DataAccess.html" title="interface in org.biojava.bio.program.abi"><span class="strong">ABIFParser.DataAccess</span></a> - Interface in <a href="./org/biojava/bio/program/abi/package-summary.html">org.biojava.bio.program.abi</a></dt>
<dd>
<div class="block">Concatenation of the <a href="./org/biojava/utils/io/Seekable.html" title="interface in org.biojava.utils.io"><code>Seekable</code></a> and <code>DataInput</code> interfaces.</div>
</dd>
<dt><a href="./org/biojava/bio/program/abi/ABIFParser.TaggedDataRecord.html" title="class in org.biojava.bio.program.abi"><span class="strong">ABIFParser.TaggedDataRecord</span></a> - Class in <a href="./org/biojava/bio/program/abi/package-summary.html">org.biojava.bio.program.abi</a></dt>
<dd>
<div class="block">An aggregate immutable type for an ABIF tagged data record.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/abi/ABIFParser.TaggedDataRecord.html#ABIFParser.TaggedDataRecord(org.biojava.bio.program.abi.ABIFParser.DataAccess)">ABIFParser.TaggedDataRecord(ABIFParser.DataAccess)</a></span> - Constructor for class org.biojava.bio.program.abi.<a href="./org/biojava/bio/program/abi/ABIFParser.TaggedDataRecord.html" title="class in org.biojava.bio.program.abi">ABIFParser.TaggedDataRecord</a></dt>
<dd>
<div class="block">Creates a new TaggedDataRecord from the next 28 bytes of
<code>din</code>.</div>
</dd>
<dt><a href="./org/biojava/bio/program/abi/ABITools.html" title="class in org.biojava.bio.program.abi"><span class="strong">ABITools</span></a> - Class in <a href="./org/biojava/bio/program/abi/package-summary.html">org.biojava.bio.program.abi</a></dt>
<dd>
<div class="block">Useful functionality for working with fasta files where the quality of the
DNA is encoded as upper and lower case DNA characters.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/abi/ABITools.html#ABITools()">ABITools()</a></span> - Constructor for class org.biojava.bio.program.abi.<a href="./org/biojava/bio/program/abi/ABITools.html" title="class in org.biojava.bio.program.abi">ABITools</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/abi/ABITrace.html" title="class in org.biojava.bio.program.abi"><span class="strong">ABITrace</span></a> - Class in <a href="./org/biojava/bio/program/abi/package-summary.html">org.biojava.bio.program.abi</a></dt>
<dd>
<div class="block">Title: ABITrace<br><br>
ABITrace is a class for managing ABI file information,
it is capable of opening an ABI file and storing
the most important fields, which can be recalled as simple java types.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/abi/ABITrace.html#ABITrace(java.io.File)">ABITrace(File)</a></span> - Constructor for class org.biojava.bio.program.abi.<a href="./org/biojava/bio/program/abi/ABITrace.html" title="class in org.biojava.bio.program.abi">ABITrace</a></dt>
<dd>
<div class="block">The File constructor opens a local ABI file and parses the content.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/abi/ABITrace.html#ABITrace(java.net.URL)">ABITrace(URL)</a></span> - Constructor for class org.biojava.bio.program.abi.<a href="./org/biojava/bio/program/abi/ABITrace.html" title="class in org.biojava.bio.program.abi">ABITrace</a></dt>
<dd>
<div class="block">The URL constructor opens an ABI file from any URL.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/abi/ABITrace.html#ABITrace(byte[])">ABITrace(byte[])</a></span> - Constructor for class org.biojava.bio.program.abi.<a href="./org/biojava/bio/program/abi/ABITrace.html" title="class in org.biojava.bio.program.abi">ABITrace</a></dt>
<dd>
<div class="block">The <code>byte[]</code> constructor parses an ABI file represented as a byte array.</div>
</dd>
<dt><a href="./org/biojava/bio/gui/sequence/AbiTraceRenderer.html" title="class in org.biojava.bio.gui.sequence"><span class="strong">AbiTraceRenderer</span></a> - Class in <a href="./org/biojava/bio/gui/sequence/package-summary.html">org.biojava.bio.gui.sequence</a></dt>
<dd>
<div class="block">Renders an ABI trace file as a chromatogram graph.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/AbiTraceRenderer.html#AbiTraceRenderer()">AbiTraceRenderer()</a></span> - Constructor for class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/AbiTraceRenderer.html" title="class in org.biojava.bio.gui.sequence">AbiTraceRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFErrorHandler.html#ABORT_PARSING">ABORT_PARSING</a></span> - Static variable in interface org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFErrorHandler.html" title="interface in org.biojava.bio.program.gff">GFFErrorHandler</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/blast2html/AbstractAlignmentStyler.html" title="class in org.biojava.bio.program.blast2html"><span class="strong">AbstractAlignmentStyler</span></a> - Class in <a href="./org/biojava/bio/program/blast2html/package-summary.html">org.biojava.bio.program.blast2html</a></dt>
<dd>
<div class="block">
Abstract implementation of <code>AlignmentStyler</code>, contains
utility methods for generating a set of HTML styles from a list of
RGB colours.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/blast2html/AbstractAlignmentStyler.html#AbstractAlignmentStyler()">AbstractAlignmentStyler()</a></span> - Constructor for class org.biojava.bio.program.blast2html.<a href="./org/biojava/bio/program/blast2html/AbstractAlignmentStyler.html" title="class in org.biojava.bio.program.blast2html">AbstractAlignmentStyler</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/symbol/AbstractAlphabet.html" title="class in org.biojava.bio.symbol"><span class="strong">AbstractAlphabet</span></a> - Class in <a href="./org/biojava/bio/symbol/package-summary.html">org.biojava.bio.symbol</a></dt>
<dd>
<div class="block">
An abstract implementation of <code>Alphabet</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AbstractAlphabet.html#AbstractAlphabet()">AbstractAlphabet()</a></span> - Constructor for class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AbstractAlphabet.html" title="class in org.biojava.bio.symbol">AbstractAlphabet</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/AbstractAnnotation.html" title="class in org.biojava.bio"><span class="strong">AbstractAnnotation</span></a> - Class in <a href="./org/biojava/bio/package-summary.html">org.biojava.bio</a></dt>
<dd>
<div class="block">A utility class to ease the problem of implementing an Annotation to that of
providing an apropreate implementation of Map.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/AbstractAnnotation.html#AbstractAnnotation()">AbstractAnnotation()</a></span> - Constructor for class org.biojava.bio.<a href="./org/biojava/bio/AbstractAnnotation.html" title="class in org.biojava.bio">AbstractAnnotation</a></dt>
<dd>
<div class="block">Protected no-args constructor intended for sub-classes.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/AbstractAnnotation.html#AbstractAnnotation(org.biojava.bio.Annotation)">AbstractAnnotation(Annotation)</a></span> - Constructor for class org.biojava.bio.<a href="./org/biojava/bio/AbstractAnnotation.html" title="class in org.biojava.bio">AbstractAnnotation</a></dt>
<dd>
<div class="block">Copy-constructor.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/AbstractAnnotation.html#AbstractAnnotation(java.util.Map)">AbstractAnnotation(Map)</a></span> - Constructor for class org.biojava.bio.<a href="./org/biojava/bio/AbstractAnnotation.html" title="class in org.biojava.bio">AbstractAnnotation</a></dt>
<dd>
<div class="block">Create a new Annotation by copying the key-value pairs from a map.</div>
</dd>
<dt><a href="./org/biojava/bio/gui/sequence/AbstractBeadRenderer.html" title="class in org.biojava.bio.gui.sequence"><span class="strong">AbstractBeadRenderer</span></a> - Class in <a href="./org/biojava/bio/gui/sequence/package-summary.html">org.biojava.bio.gui.sequence</a></dt>
<dd>
<div class="block"><code>AbstractBeadRenderer</code> is a an abstract base class
for the creation of <code>FeatureRenderer</code>s which use a
'string of beads' metaphor for displaying features.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/AbstractBeadRenderer.html#AbstractBeadRenderer()">AbstractBeadRenderer()</a></span> - Constructor for class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/AbstractBeadRenderer.html" title="class in org.biojava.bio.gui.sequence">AbstractBeadRenderer</a></dt>
<dd>
<div class="block">Creates a new <code>AbstractBeadRenderer</code> with no
delegates.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/AbstractBeadRenderer.html#AbstractBeadRenderer(double, double, java.awt.Paint, java.awt.Paint, java.awt.Stroke)">AbstractBeadRenderer(double, double, Paint, Paint, Stroke)</a></span> - Constructor for class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/AbstractBeadRenderer.html" title="class in org.biojava.bio.gui.sequence">AbstractBeadRenderer</a></dt>
<dd>
<div class="block">Creates a new <code>AbstractBeadRenderer</code> object.</div>
</dd>
<dt><a href="./org/biojava/bio/structure/io/mmcif/model/AbstractBean.html" title="class in org.biojava.bio.structure.io.mmcif.model"><span class="strong">AbstractBean</span></a> - Class in <a href="./org/biojava/bio/structure/io/mmcif/model/package-summary.html">org.biojava.bio.structure.io.mmcif.model</a></dt>
<dd>
<div class="block">a generic class that implements the toString method for a bean</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/AbstractBean.html#AbstractBean()">AbstractBean()</a></span> - Constructor for class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/AbstractBean.html" title="class in org.biojava.bio.structure.io.mmcif.model">AbstractBean</a></dt>
<dd> </dd>
<dt><a href="./org/biojavax/bio/db/AbstractBioEntryDB.html" title="class in org.biojavax.bio.db"><span class="strong">AbstractBioEntryDB</span></a> - Class in <a href="./org/biojavax/bio/db/package-summary.html">org.biojavax.bio.db</a></dt>
<dd>
<div class="block">An abstract implementation of BioEntryDB that provides the getBioEntryIterator
method.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/AbstractBioEntryDB.html#AbstractBioEntryDB()">AbstractBioEntryDB()</a></span> - Constructor for class org.biojavax.bio.db.<a href="./org/biojavax/bio/db/AbstractBioEntryDB.html" title="class in org.biojavax.bio.db">AbstractBioEntryDB</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/utils/AbstractChangeable.html" title="class in org.biojava.utils"><span class="strong">AbstractChangeable</span></a> - Class in <a href="./org/biojava/utils/package-summary.html">org.biojava.utils</a></dt>
<dd>
<div class="block">Useful base-class for objects implementing Changeable</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/AbstractChangeable.html#AbstractChangeable()">AbstractChangeable()</a></span> - Constructor for class org.biojava.utils.<a href="./org/biojava/utils/AbstractChangeable.html" title="class in org.biojava.utils">AbstractChangeable</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/chromatogram/AbstractChromatogram.html" title="class in org.biojava.bio.chromatogram"><span class="strong">AbstractChromatogram</span></a> - Class in <a href="./org/biojava/bio/chromatogram/package-summary.html">org.biojava.bio.chromatogram</a></dt>
<dd>
<div class="block">A basic, abstract implementation of <a href="./org/biojava/bio/chromatogram/Chromatogram.html" title="interface in org.biojava.bio.chromatogram"><code>Chromatogram</code></a>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/AbstractChromatogram.html#AbstractChromatogram()">AbstractChromatogram()</a></span> - Constructor for class org.biojava.bio.chromatogram.<a href="./org/biojava/bio/chromatogram/AbstractChromatogram.html" title="class in org.biojava.bio.chromatogram">AbstractChromatogram</a></dt>
<dd>
<div class="block">Create a new AbstractChromatogram.</div>
</dd>
<dt><a href="./org/biojavax/ga/functions/AbstractCrossOverFunction.html" title="class in org.biojavax.ga.functions"><span class="strong">AbstractCrossOverFunction</span></a> - Class in <a href="./org/biojavax/ga/functions/package-summary.html">org.biojavax.ga.functions</a></dt>
<dd>
<div class="block">Abstract implementation of <code>CrossOverFunction</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ga/functions/AbstractCrossOverFunction.html#AbstractCrossOverFunction()">AbstractCrossOverFunction()</a></span> - Constructor for class org.biojavax.ga.functions.<a href="./org/biojavax/ga/functions/AbstractCrossOverFunction.html" title="class in org.biojavax.ga.functions">AbstractCrossOverFunction</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/dist/AbstractDistribution.html" title="class in org.biojava.bio.dist"><span class="strong">AbstractDistribution</span></a> - Class in <a href="./org/biojava/bio/dist/package-summary.html">org.biojava.bio.dist</a></dt>
<dd>
<div class="block">An abstract implementation of Distribution.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/AbstractDistribution.html#AbstractDistribution()">AbstractDistribution()</a></span> - Constructor for class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/AbstractDistribution.html" title="class in org.biojava.bio.dist">AbstractDistribution</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/AbstractFeatureHolder.html" title="class in org.biojava.bio.seq"><span class="strong">AbstractFeatureHolder</span></a> - Class in <a href="./org/biojava/bio/seq/package-summary.html">org.biojava.bio.seq</a></dt>
<dd>
<div class="block">An abstract implementation of FeatureHolder.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/AbstractFeatureHolder.html#AbstractFeatureHolder()">AbstractFeatureHolder()</a></span> - Constructor for class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/AbstractFeatureHolder.html" title="class in org.biojava.bio.seq">AbstractFeatureHolder</a></dt>
<dd> </dd>
<dt><a href="./org/biojavax/ga/impl/AbstractGeneticAlgorithm.html" title="class in org.biojavax.ga.impl"><span class="strong">AbstractGeneticAlgorithm</span></a> - Class in <a href="./org/biojavax/ga/impl/package-summary.html">org.biojavax.ga.impl</a></dt>
<dd>
<div class="block">Base class from which most implementations of GeneticAlgorithm will inherit.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ga/impl/AbstractGeneticAlgorithm.html#AbstractGeneticAlgorithm()">AbstractGeneticAlgorithm()</a></span> - Constructor for class org.biojavax.ga.impl.<a href="./org/biojavax/ga/impl/AbstractGeneticAlgorithm.html" title="class in org.biojavax.ga.impl">AbstractGeneticAlgorithm</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/symbol/AbstractLocation.html" title="class in org.biojava.bio.symbol"><span class="strong">AbstractLocation</span></a> - Class in <a href="./org/biojava/bio/symbol/package-summary.html">org.biojava.bio.symbol</a></dt>
<dd>
<div class="block">An abstract implementation of <code>Location</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AbstractLocation.html#AbstractLocation()">AbstractLocation()</a></span> - Constructor for class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AbstractLocation.html" title="class in org.biojava.bio.symbol">AbstractLocation</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/symbol/AbstractLocationDecorator.html" title="class in org.biojava.bio.symbol"><span class="strong">AbstractLocationDecorator</span></a> - Class in <a href="./org/biojava/bio/symbol/package-summary.html">org.biojava.bio.symbol</a></dt>
<dd>
<div class="block">Abstract <code>Location</code> decorator (wrapper).</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AbstractLocationDecorator.html#AbstractLocationDecorator(org.biojava.bio.symbol.Location)">AbstractLocationDecorator(Location)</a></span> - Constructor for class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AbstractLocationDecorator.html" title="class in org.biojava.bio.symbol">AbstractLocationDecorator</a></dt>
<dd>
<div class="block">Construct a new decorator wrapping the specified Location.</div>
</dd>
<dt><a href="./org/biojava/bio/symbol/AbstractManyToOneTranslationTable.html" title="class in org.biojava.bio.symbol"><span class="strong">AbstractManyToOneTranslationTable</span></a> - Class in <a href="./org/biojava/bio/symbol/package-summary.html">org.biojava.bio.symbol</a></dt>
<dd>
<div class="block">an abstract class implementing basic functionality
of a translation table that translates Symbols from
one Alphabet to another.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AbstractManyToOneTranslationTable.html#AbstractManyToOneTranslationTable()">AbstractManyToOneTranslationTable()</a></span> - Constructor for class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AbstractManyToOneTranslationTable.html" title="class in org.biojava.bio.symbol">AbstractManyToOneTranslationTable</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/dp/twohead/AbstractMatrixPairDPCursor.html" title="class in org.biojava.bio.dp.twohead"><span class="strong">AbstractMatrixPairDPCursor</span></a> - Class in <a href="./org/biojava/bio/dp/twohead/package-summary.html">org.biojava.bio.dp.twohead</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/twohead/AbstractMatrixPairDPCursor.html#AbstractMatrixPairDPCursor(org.biojava.bio.symbol.SymbolList, org.biojava.bio.symbol.SymbolList, int, int, int, int, org.biojava.bio.dp.twohead.PairDPMatrix, org.biojava.bio.dp.twohead.EmissionCache)">AbstractMatrixPairDPCursor(SymbolList, SymbolList, int, int, int, int, PairDPMatrix, EmissionCache)</a></span> - Constructor for class org.biojava.bio.dp.twohead.<a href="./org/biojava/bio/dp/twohead/AbstractMatrixPairDPCursor.html" title="class in org.biojava.bio.dp.twohead">AbstractMatrixPairDPCursor</a></dt>
<dd> </dd>
<dt><a href="./org/biojavax/ga/functions/AbstractMutationFunction.html" title="class in org.biojavax.ga.functions"><span class="strong">AbstractMutationFunction</span></a> - Class in <a href="./org/biojavax/ga/functions/package-summary.html">org.biojavax.ga.functions</a></dt>
<dd>
<div class="block">Abstract implementation of <code>MutationFunction</code> all custom
implementations should inherit from here.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ga/functions/AbstractMutationFunction.html#AbstractMutationFunction()">AbstractMutationFunction()</a></span> - Constructor for class org.biojavax.ga.functions.<a href="./org/biojavax/ga/functions/AbstractMutationFunction.html" title="class in org.biojavax.ga.functions">AbstractMutationFunction</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/dist/AbstractOrderNDistribution.html" title="class in org.biojava.bio.dist"><span class="strong">AbstractOrderNDistribution</span></a> - Class in <a href="./org/biojava/bio/dist/package-summary.html">org.biojava.bio.dist</a></dt>
<dd>
<div class="block">Simple base class for OrderNDistributions.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/AbstractOrderNDistribution.html#AbstractOrderNDistribution(org.biojava.bio.symbol.Alphabet)">AbstractOrderNDistribution(Alphabet)</a></span> - Constructor for class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/AbstractOrderNDistribution.html" title="class in org.biojava.bio.dist">AbstractOrderNDistribution</a></dt>
<dd>
<div class="block">Construct a new NthOrderDistribution.</div>
</dd>
<dt><a href="./org/biojavax/ga/impl/AbstractOrganism.html" title="class in org.biojavax.ga.impl"><span class="strong">AbstractOrganism</span></a> - Class in <a href="./org/biojavax/ga/impl/package-summary.html">org.biojavax.ga.impl</a></dt>
<dd>
<div class="block">Abstract implementation of Organism.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ga/impl/AbstractOrganism.html#AbstractOrganism()">AbstractOrganism()</a></span> - Constructor for class org.biojavax.ga.impl.<a href="./org/biojavax/ga/impl/AbstractOrganism.html" title="class in org.biojavax.ga.impl">AbstractOrganism</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/impl/AbstractOrganism.html#AbstractOrganism(org.biojavax.ga.Organism, java.lang.String)">AbstractOrganism(Organism, String)</a></span> - Constructor for class org.biojavax.ga.impl.<a href="./org/biojavax/ga/impl/AbstractOrganism.html" title="class in org.biojavax.ga.impl">AbstractOrganism</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/homologene/AbstractOrthologueSet.html" title="class in org.biojava.bio.program.homologene"><span class="strong">AbstractOrthologueSet</span></a> - Class in <a href="./org/biojava/bio/program/homologene/package-summary.html">org.biojava.bio.program.homologene</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/AbstractOrthologueSet.html#AbstractOrthologueSet()">AbstractOrthologueSet()</a></span> - Constructor for class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/AbstractOrthologueSet.html" title="class in org.biojava.bio.program.homologene">AbstractOrthologueSet</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/homologene/AbstractOrthoPairCollection.html" title="class in org.biojava.bio.program.homologene"><span class="strong">AbstractOrthoPairCollection</span></a> - Class in <a href="./org/biojava/bio/program/homologene/package-summary.html">org.biojava.bio.program.homologene</a></dt>
<dd>
<div class="block">An abstract implementation of the OrthoPairCollection
interface.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/AbstractOrthoPairCollection.html#AbstractOrthoPairCollection()">AbstractOrthoPairCollection()</a></span> - Constructor for class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/AbstractOrthoPairCollection.html" title="class in org.biojava.bio.program.homologene">AbstractOrthoPairCollection</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/homologene/AbstractOrthoPairSet.html" title="class in org.biojava.bio.program.homologene"><span class="strong">AbstractOrthoPairSet</span></a> - Class in <a href="./org/biojava/bio/program/homologene/package-summary.html">org.biojava.bio.program.homologene</a></dt>
<dd>
<div class="block">represents the Homologene Group.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/AbstractOrthoPairSet.html#AbstractOrthoPairSet()">AbstractOrthoPairSet()</a></span> - Constructor for class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/AbstractOrthoPairSet.html" title="class in org.biojava.bio.program.homologene">AbstractOrthoPairSet</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/gui/sequence/AbstractPeptideDigestRenderer.html" title="class in org.biojava.bio.gui.sequence"><span class="strong">AbstractPeptideDigestRenderer</span></a> - Class in <a href="./org/biojava/bio/gui/sequence/package-summary.html">org.biojava.bio.gui.sequence</a></dt>
<dd>
<div class="block">A SequenceRenderer that renders a set of Features that match a FeatureFilter in such a way that
they do not overlap in the display.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/AbstractPeptideDigestRenderer.html#AbstractPeptideDigestRenderer()">AbstractPeptideDigestRenderer()</a></span> - Constructor for class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/AbstractPeptideDigestRenderer.html" title="class in org.biojava.bio.gui.sequence">AbstractPeptideDigestRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/AbstractPeptideDigestRenderer.html#AbstractPeptideDigestRenderer(org.biojava.bio.gui.sequence.FeatureSource)">AbstractPeptideDigestRenderer(FeatureSource)</a></span> - Constructor for class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/AbstractPeptideDigestRenderer.html" title="class in org.biojava.bio.gui.sequence">AbstractPeptideDigestRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/AbstractPeptideDigestRenderer.html#AbstractPeptideDigestRenderer(org.biojava.bio.gui.sequence.FeatureSource, org.biojava.bio.seq.FeatureFilter)">AbstractPeptideDigestRenderer(FeatureSource, FeatureFilter)</a></span> - Constructor for class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/AbstractPeptideDigestRenderer.html" title="class in org.biojava.bio.gui.sequence">AbstractPeptideDigestRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/AbstractPeptideDigestRenderer.html#AbstractPeptideDigestRenderer(org.biojava.bio.gui.sequence.FeatureSource, org.biojava.bio.seq.FeatureFilter, int)">AbstractPeptideDigestRenderer(FeatureSource, FeatureFilter, int)</a></span> - Constructor for class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/AbstractPeptideDigestRenderer.html" title="class in org.biojava.bio.gui.sequence">AbstractPeptideDigestRenderer</a></dt>
<dd> </dd>
<dt><a href="./org/biojavax/ga/impl/AbstractPopulation.html" title="class in org.biojavax.ga.impl"><span class="strong">AbstractPopulation</span></a> - Class in <a href="./org/biojavax/ga/impl/package-summary.html">org.biojavax.ga.impl</a></dt>
<dd>
<div class="block">Most Population implementations will want to inherit from here.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ga/impl/AbstractPopulation.html#AbstractPopulation()">AbstractPopulation()</a></span> - Constructor for class org.biojavax.ga.impl.<a href="./org/biojavax/ga/impl/AbstractPopulation.html" title="class in org.biojavax.ga.impl">AbstractPopulation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/impl/AbstractPopulation.html#AbstractPopulation(java.lang.String)">AbstractPopulation(String)</a></span> - Constructor for class org.biojavax.ga.impl.<a href="./org/biojavax/ga/impl/AbstractPopulation.html" title="class in org.biojavax.ga.impl">AbstractPopulation</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/symbol/AbstractRangeLocation.html" title="class in org.biojava.bio.symbol"><span class="strong">AbstractRangeLocation</span></a> - Class in <a href="./org/biojava/bio/symbol/package-summary.html">org.biojava.bio.symbol</a></dt>
<dd>
<div class="block">Base class for simple contiguous Location implementations.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AbstractRangeLocation.html#AbstractRangeLocation()">AbstractRangeLocation()</a></span> - Constructor for class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AbstractRangeLocation.html" title="class in org.biojava.bio.symbol">AbstractRangeLocation</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/symbol/AbstractReversibleTranslationTable.html" title="class in org.biojava.bio.symbol"><span class="strong">AbstractReversibleTranslationTable</span></a> - Class in <a href="./org/biojava/bio/symbol/package-summary.html">org.biojava.bio.symbol</a></dt>
<dd>
<div class="block">an abstract class implementing basic functionality
of a translation table that translates Symbols from
one Alphabet to another.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AbstractReversibleTranslationTable.html#AbstractReversibleTranslationTable()">AbstractReversibleTranslationTable()</a></span> - Constructor for class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AbstractReversibleTranslationTable.html" title="class in org.biojava.bio.symbol">AbstractReversibleTranslationTable</a></dt>
<dd> </dd>
<dt><a href="./org/biojavax/bio/db/AbstractRichSequenceDB.html" title="class in org.biojavax.bio.db"><span class="strong">AbstractRichSequenceDB</span></a> - Class in <a href="./org/biojavax/bio/db/package-summary.html">org.biojavax.bio.db</a></dt>
<dd>
<div class="block">An abstract implementation of RichSequenceDB that provides the getRichSequenceIterator
method.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/AbstractRichSequenceDB.html#AbstractRichSequenceDB()">AbstractRichSequenceDB()</a></span> - Constructor for class org.biojavax.bio.db.<a href="./org/biojavax/bio/db/AbstractRichSequenceDB.html" title="class in org.biojavax.bio.db">AbstractRichSequenceDB</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/db/AbstractSequenceDB.html" title="class in org.biojava.bio.seq.db"><span class="strong">AbstractSequenceDB</span></a> - Class in <a href="./org/biojava/bio/seq/db/package-summary.html">org.biojava.bio.seq.db</a></dt>
<dd>
<div class="block">An abstract implementation of SequenceDB that provides the sequenceIterator
method.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/AbstractSequenceDB.html#AbstractSequenceDB()">AbstractSequenceDB()</a></span> - Constructor for class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/AbstractSequenceDB.html" title="class in org.biojava.bio.seq.db">AbstractSequenceDB</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/stats/svm/AbstractSVMClassifierModel.html" title="class in org.biojava.stats.svm"><span class="strong">AbstractSVMClassifierModel</span></a> - Class in <a href="./org/biojava/stats/svm/package-summary.html">org.biojava.stats.svm</a></dt>
<dd>
<div class="block">
Abstract implementation of SVMClassifierModel.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/AbstractSVMClassifierModel.html#AbstractSVMClassifierModel()">AbstractSVMClassifierModel()</a></span> - Constructor for class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/AbstractSVMClassifierModel.html" title="class in org.biojava.stats.svm">AbstractSVMClassifierModel</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/stats/svm/AbstractSVMTarget.html" title="class in org.biojava.stats.svm"><span class="strong">AbstractSVMTarget</span></a> - Class in <a href="./org/biojava/stats/svm/package-summary.html">org.biojava.stats.svm</a></dt>
<dd>
<div class="block">
An abstract implementation of an SVMModel.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/AbstractSVMTarget.html#AbstractSVMTarget()">AbstractSVMTarget()</a></span> - Constructor for class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/AbstractSVMTarget.html" title="class in org.biojava.stats.svm">AbstractSVMTarget</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/symbol/AbstractSymbol.html" title="class in org.biojava.bio.symbol"><span class="strong">AbstractSymbol</span></a> - Class in <a href="./org/biojava/bio/symbol/package-summary.html">org.biojava.bio.symbol</a></dt>
<dd>
<div class="block">The base-class for Symbol implementations.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AbstractSymbol.html#AbstractSymbol()">AbstractSymbol()</a></span> - Constructor for class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AbstractSymbol.html" title="class in org.biojava.bio.symbol">AbstractSymbol</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/symbol/AbstractSymbolList.html" title="class in org.biojava.bio.symbol"><span class="strong">AbstractSymbolList</span></a> - Class in <a href="./org/biojava/bio/symbol/package-summary.html">org.biojava.bio.symbol</a></dt>
<dd>
<div class="block">
Abstract helper implementation of the SymbolList core interface.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AbstractSymbolList.html#AbstractSymbolList()">AbstractSymbolList()</a></span> - Constructor for class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AbstractSymbolList.html" title="class in org.biojava.bio.symbol">AbstractSymbolList</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/symbol/AbstractSymbolList.EditScreener.html" title="class in org.biojava.bio.symbol"><span class="strong">AbstractSymbolList.EditScreener</span></a> - Class in <a href="./org/biojava/bio/symbol/package-summary.html">org.biojava.bio.symbol</a></dt>
<dd>
<div class="block">This adapter screens all edit events to see if they overlap with a window
of interest.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AbstractSymbolList.EditScreener.html#AbstractSymbolList.EditScreener(java.lang.Object, org.biojava.utils.ChangeSupport, int, int)">AbstractSymbolList.EditScreener(Object, ChangeSupport, int, int)</a></span> - Constructor for class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AbstractSymbolList.EditScreener.html" title="class in org.biojava.bio.symbol">AbstractSymbolList.EditScreener</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/symbol/AbstractSymbolList.EditTranslater.html" title="class in org.biojava.bio.symbol"><span class="strong">AbstractSymbolList.EditTranslater</span></a> - Class in <a href="./org/biojava/bio/symbol/package-summary.html">org.biojava.bio.symbol</a></dt>
<dd>
<div class="block">This translates edit events that fall within a window into window co-ordinates.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AbstractSymbolList.EditTranslater.html#AbstractSymbolList.EditTranslater(java.lang.Object, org.biojava.utils.ChangeSupport, int, int)">AbstractSymbolList.EditTranslater(Object, ChangeSupport, int, int)</a></span> - Constructor for class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AbstractSymbolList.EditTranslater.html" title="class in org.biojava.bio.symbol">AbstractSymbolList.EditTranslater</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/taxa/AbstractTaxon.html" title="class in org.biojava.bio.taxa"><span class="strong">AbstractTaxon</span></a> - Class in <a href="./org/biojava/bio/taxa/package-summary.html">org.biojava.bio.taxa</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>replaced by classes in <a href="./org/biojavax/bio/taxa/package-summary.html"><code>org.biojavax.bio.taxa</code></a></i></div>
</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/taxa/AbstractTaxon.html#AbstractTaxon()">AbstractTaxon()</a></span> - Constructor for class org.biojava.bio.taxa.<a href="./org/biojava/bio/taxa/AbstractTaxon.html" title="class in org.biojava.bio.taxa">AbstractTaxon</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/taxa/AbstractTaxon.html#AbstractTaxon(java.lang.String, java.lang.String)">AbstractTaxon(String, String)</a></span> - Constructor for class org.biojava.bio.taxa.<a href="./org/biojava/bio/taxa/AbstractTaxon.html" title="class in org.biojava.bio.taxa">AbstractTaxon</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><a href="./org/biojava/ontology/AbstractTerm.html" title="class in org.biojava.ontology"><span class="strong">AbstractTerm</span></a> - Class in <a href="./org/biojava/ontology/package-summary.html">org.biojava.ontology</a></dt>
<dd>
<div class="block">Abstract implementation of term
This provides basic change-forwarding functionality from
the annotation and ontology properties.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/AbstractTerm.html#AbstractTerm()">AbstractTerm()</a></span> - Constructor for class org.biojava.ontology.<a href="./org/biojava/ontology/AbstractTerm.html" title="class in org.biojava.ontology">AbstractTerm</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/dp/AbstractTrainer.html" title="class in org.biojava.bio.dp"><span class="strong">AbstractTrainer</span></a> - Class in <a href="./org/biojava/bio/dp/package-summary.html">org.biojava.bio.dp</a></dt>
<dd>
<div class="block">An abstract implementation of TrainingAlgorithm that provides a framework
for plugging in per-cycle code for parameter optimization.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/AbstractTrainer.html#AbstractTrainer(org.biojava.bio.dp.DP)">AbstractTrainer(DP)</a></span> - Constructor for class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/AbstractTrainer.html" title="class in org.biojava.bio.dp">AbstractTrainer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/AbstractTrainer.html#AbstractTrainer()">AbstractTrainer()</a></span> - Constructor for class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/AbstractTrainer.html" title="class in org.biojava.bio.dp">AbstractTrainer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BiblioDescription.html#abstractType">abstractType</a></span> - Variable in class org.biojava.bibliography.<a href="./org/biojava/bibliography/BiblioDescription.html" title="class in org.biojava.bibliography">BiblioDescription</a></dt>
<dd>
<div class="block">
It specifies how <a href="./org/biojava/bibliography/BiblioDescription.html#theAbstract"><code>BiblioDescription.theAbstract</code></a> is coded.</div>
</dd>
<dt><a href="./org/biojava/bio/alignment/AbstractULAlignment.html" title="class in org.biojava.bio.alignment"><span class="strong">AbstractULAlignment</span></a> - Class in <a href="./org/biojava/bio/alignment/package-summary.html">org.biojava.bio.alignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/AbstractULAlignment.html#AbstractULAlignment()">AbstractULAlignment()</a></span> - Constructor for class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/AbstractULAlignment.html" title="class in org.biojava.bio.alignment">AbstractULAlignment</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/alignment/AbstractULAlignment.LeftRightLocationComparator.html" title="class in org.biojava.bio.alignment"><span class="strong">AbstractULAlignment.LeftRightLocationComparator</span></a> - Class in <a href="./org/biojava/bio/alignment/package-summary.html">org.biojava.bio.alignment</a></dt>
<dd>
<div class="block">Orders by location left to right.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/AbstractULAlignment.LeftRightLocationComparator.html#AbstractULAlignment.LeftRightLocationComparator()">AbstractULAlignment.LeftRightLocationComparator()</a></span> - Constructor for class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/AbstractULAlignment.LeftRightLocationComparator.html" title="class in org.biojava.bio.alignment">AbstractULAlignment.LeftRightLocationComparator</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/alignment/AbstractULAlignment.SubULAlignment.html" title="class in org.biojava.bio.alignment"><span class="strong">AbstractULAlignment.SubULAlignment</span></a> - Class in <a href="./org/biojava/bio/alignment/package-summary.html">org.biojava.bio.alignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/AbstractULAlignment.SubULAlignment.html#AbstractULAlignment.SubULAlignment(java.util.Set, org.biojava.bio.symbol.Location)">AbstractULAlignment.SubULAlignment(Set, Location)</a></span> - Constructor for class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/AbstractULAlignment.SubULAlignment.html" title="class in org.biojava.bio.alignment">AbstractULAlignment.SubULAlignment</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/tagvalue/AbstractWrapper.html" title="class in org.biojava.bio.program.tagvalue"><span class="strong">AbstractWrapper</span></a> - Class in <a href="./org/biojava/bio/program/tagvalue/package-summary.html">org.biojava.bio.program.tagvalue</a></dt>
<dd>
<div class="block">
An abstract TagValueWrapper that does nothing!</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/AbstractWrapper.html#AbstractWrapper()">AbstractWrapper()</a></span> - Constructor for class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/AbstractWrapper.html" title="class in org.biojava.bio.program.tagvalue">AbstractWrapper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/INSDseqFormat.html#ACC_VERSION_TAG">ACC_VERSION_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/INSDseqFormat.html" title="class in org.biojavax.bio.seq.io">INSDseqFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/CollectionConstraint.html#accept(java.lang.Object)">accept(Object)</a></span> - Method in interface org.biojava.bio.<a href="./org/biojava/bio/CollectionConstraint.html" title="interface in org.biojava.bio">CollectionConstraint</a></dt>
<dd>
<div class="block"><code>accept</code> returns true if the value fulfills the
constraint.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/CollectionConstraint.AllValuesIn.html#accept(java.lang.Object)">accept(Object)</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/CollectionConstraint.AllValuesIn.html" title="class in org.biojava.bio">CollectionConstraint.AllValuesIn</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/CollectionConstraint.And.html#accept(java.lang.Object)">accept(Object)</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/CollectionConstraint.And.html" title="class in org.biojava.bio">CollectionConstraint.And</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/CollectionConstraint.Contains.html#accept(java.lang.Object)">accept(Object)</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/CollectionConstraint.Contains.html" title="class in org.biojava.bio">CollectionConstraint.Contains</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/CollectionConstraint.Or.html#accept(java.lang.Object)">accept(Object)</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/CollectionConstraint.Or.html" title="class in org.biojava.bio">CollectionConstraint.Or</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFRecordFilter.html#accept(org.biojava.bio.program.gff.GFFRecord)">accept(GFFRecord)</a></span> - Method in interface org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFRecordFilter.html" title="interface in org.biojava.bio.program.gff">GFFRecordFilter</a></dt>
<dd>
<div class="block">Return whether or not to accept <span class="arg">record</span>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFRecordFilter.AcceptAll.html#accept(org.biojava.bio.program.gff.GFFRecord)">accept(GFFRecord)</a></span> - Method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFRecordFilter.AcceptAll.html" title="class in org.biojava.bio.program.gff">GFFRecordFilter.AcceptAll</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFRecordFilter.FeatureFilter.html#accept(org.biojava.bio.program.gff.GFFRecord)">accept(GFFRecord)</a></span> - Method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFRecordFilter.FeatureFilter.html" title="class in org.biojava.bio.program.gff">GFFRecordFilter.FeatureFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFRecordFilter.FrameFilter.html#accept(org.biojava.bio.program.gff.GFFRecord)">accept(GFFRecord)</a></span> - Method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFRecordFilter.FrameFilter.html" title="class in org.biojava.bio.program.gff">GFFRecordFilter.FrameFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFRecordFilter.NotFilter.html#accept(org.biojava.bio.program.gff.GFFRecord)">accept(GFFRecord)</a></span> - Method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFRecordFilter.NotFilter.html" title="class in org.biojava.bio.program.gff">GFFRecordFilter.NotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFRecordFilter.SequenceFilter.html#accept(org.biojava.bio.program.gff.GFFRecord)">accept(GFFRecord)</a></span> - Method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFRecordFilter.SequenceFilter.html" title="class in org.biojava.bio.program.gff">GFFRecordFilter.SequenceFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFRecordFilter.SourceFilter.html#accept(org.biojava.bio.program.gff.GFFRecord)">accept(GFFRecord)</a></span> - Method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFRecordFilter.SourceFilter.html" title="class in org.biojava.bio.program.gff">GFFRecordFilter.SourceFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFRecordFilter.StrandFilter.html#accept(org.biojava.bio.program.gff.GFFRecord)">accept(GFFRecord)</a></span> - Method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFRecordFilter.StrandFilter.html" title="class in org.biojava.bio.program.gff">GFFRecordFilter.StrandFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/OrthologueFilter.html#accept(org.biojava.bio.program.homologene.Orthologue)">accept(Orthologue)</a></span> - Method in interface org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/OrthologueFilter.html" title="interface in org.biojava.bio.program.homologene">OrthologueFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/OrthologueFilter.AcceptAll.html#accept(org.biojava.bio.program.homologene.Orthologue)">accept(Orthologue)</a></span> - Method in class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/OrthologueFilter.AcceptAll.html" title="class in org.biojava.bio.program.homologene">OrthologueFilter.AcceptAll</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/OrthologueFilter.And.html#accept(org.biojava.bio.program.homologene.Orthologue)">accept(Orthologue)</a></span> - Method in class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/OrthologueFilter.And.html" title="class in org.biojava.bio.program.homologene">OrthologueFilter.And</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/OrthologueFilter.ByAccession.html#accept(org.biojava.bio.program.homologene.Orthologue)">accept(Orthologue)</a></span> - Method in class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/OrthologueFilter.ByAccession.html" title="class in org.biojava.bio.program.homologene">OrthologueFilter.ByAccession</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/OrthologueFilter.ByHomologeneID.html#accept(org.biojava.bio.program.homologene.Orthologue)">accept(Orthologue)</a></span> - Method in class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/OrthologueFilter.ByHomologeneID.html" title="class in org.biojava.bio.program.homologene">OrthologueFilter.ByHomologeneID</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/OrthologueFilter.ByLocusID.html#accept(org.biojava.bio.program.homologene.Orthologue)">accept(Orthologue)</a></span> - Method in class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/OrthologueFilter.ByLocusID.html" title="class in org.biojava.bio.program.homologene">OrthologueFilter.ByLocusID</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/OrthologueFilter.ByTaxon.html#accept(org.biojava.bio.program.homologene.Orthologue)">accept(Orthologue)</a></span> - Method in class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/OrthologueFilter.ByTaxon.html" title="class in org.biojava.bio.program.homologene">OrthologueFilter.ByTaxon</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/OrthologueFilter.ByTaxonID.html#accept(org.biojava.bio.program.homologene.Orthologue)">accept(Orthologue)</a></span> - Method in class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/OrthologueFilter.ByTaxonID.html" title="class in org.biojava.bio.program.homologene">OrthologueFilter.ByTaxonID</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/OrthologueFilter.ByTitle.html#accept(org.biojava.bio.program.homologene.Orthologue)">accept(Orthologue)</a></span> - Method in class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/OrthologueFilter.ByTitle.html" title="class in org.biojava.bio.program.homologene">OrthologueFilter.ByTitle</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/OrthologueFilter.Not.html#accept(org.biojava.bio.program.homologene.Orthologue)">accept(Orthologue)</a></span> - Method in class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/OrthologueFilter.Not.html" title="class in org.biojava.bio.program.homologene">OrthologueFilter.Not</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/OrthologueFilter.Or.html#accept(org.biojava.bio.program.homologene.Orthologue)">accept(Orthologue)</a></span> - Method in class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/OrthologueFilter.Or.html" title="class in org.biojava.bio.program.homologene">OrthologueFilter.Or</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/OrthologueFilter.Xor.html#accept(org.biojava.bio.program.homologene.Orthologue)">accept(Orthologue)</a></span> - Method in class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/OrthologueFilter.Xor.html" title="class in org.biojava.bio.program.homologene">OrthologueFilter.Xor</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/OrthoPairFilter.html#accept(org.biojava.bio.program.homologene.OrthoPair)">accept(OrthoPair)</a></span> - Method in interface org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/OrthoPairFilter.html" title="interface in org.biojava.bio.program.homologene">OrthoPairFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/OrthoPairFilter.AcceptAll.html#accept(org.biojava.bio.program.homologene.OrthoPair)">accept(OrthoPair)</a></span> - Method in class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/OrthoPairFilter.AcceptAll.html" title="class in org.biojava.bio.program.homologene">OrthoPairFilter.AcceptAll</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/OrthoPairFilter.And.html#accept(org.biojava.bio.program.homologene.OrthoPair)">accept(OrthoPair)</a></span> - Method in class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/OrthoPairFilter.And.html" title="class in org.biojava.bio.program.homologene">OrthoPairFilter.And</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/OrthoPairFilter.ByMaxIdentity.html#accept(org.biojava.bio.program.homologene.OrthoPair)">accept(OrthoPair)</a></span> - Method in class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/OrthoPairFilter.ByMaxIdentity.html" title="class in org.biojava.bio.program.homologene">OrthoPairFilter.ByMaxIdentity</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/OrthoPairFilter.ByMinIdentity.html#accept(org.biojava.bio.program.homologene.OrthoPair)">accept(OrthoPair)</a></span> - Method in class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/OrthoPairFilter.ByMinIdentity.html" title="class in org.biojava.bio.program.homologene">OrthoPairFilter.ByMinIdentity</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/OrthoPairFilter.ByRef.html#accept(org.biojava.bio.program.homologene.OrthoPair)">accept(OrthoPair)</a></span> - Method in class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/OrthoPairFilter.ByRef.html" title="class in org.biojava.bio.program.homologene">OrthoPairFilter.ByRef</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/OrthoPairFilter.BySimilarityType.html#accept(org.biojava.bio.program.homologene.OrthoPair)">accept(OrthoPair)</a></span> - Method in class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/OrthoPairFilter.BySimilarityType.html" title="class in org.biojava.bio.program.homologene">OrthoPairFilter.BySimilarityType</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/OrthoPairFilter.Not.html#accept(org.biojava.bio.program.homologene.OrthoPair)">accept(OrthoPair)</a></span> - Method in class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/OrthoPairFilter.Not.html" title="class in org.biojava.bio.program.homologene">OrthoPairFilter.Not</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/OrthoPairFilter.Or.html#accept(org.biojava.bio.program.homologene.OrthoPair)">accept(OrthoPair)</a></span> - Method in class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/OrthoPairFilter.Or.html" title="class in org.biojava.bio.program.homologene">OrthoPairFilter.Or</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/OrthoPairFilter.Xor.html#accept(org.biojava.bio.program.homologene.OrthoPair)">accept(OrthoPair)</a></span> - Method in class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/OrthoPairFilter.Xor.html" title="class in org.biojava.bio.program.homologene">OrthoPairFilter.Xor</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/OrthoPairSetFilter.html#accept(org.biojava.bio.program.homologene.OrthoPairSet)">accept(OrthoPairSet)</a></span> - Method in interface org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/OrthoPairSetFilter.html" title="interface in org.biojava.bio.program.homologene">OrthoPairSetFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/OrthoPairSetFilter.AcceptAll.html#accept(org.biojava.bio.program.homologene.OrthoPairSet)">accept(OrthoPairSet)</a></span> - Method in class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/OrthoPairSetFilter.AcceptAll.html" title="class in org.biojava.bio.program.homologene">OrthoPairSetFilter.AcceptAll</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/OrthoPairSetFilter.AllPairsInCollection.html#accept(org.biojava.bio.program.homologene.OrthoPairSet)">accept(OrthoPairSet)</a></span> - Method in class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/OrthoPairSetFilter.AllPairsInCollection.html" title="class in org.biojava.bio.program.homologene">OrthoPairSetFilter.AllPairsInCollection</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/OrthoPairSetFilter.And.html#accept(org.biojava.bio.program.homologene.OrthoPairSet)">accept(OrthoPairSet)</a></span> - Method in class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/OrthoPairSetFilter.And.html" title="class in org.biojava.bio.program.homologene">OrthoPairSetFilter.And</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/OrthoPairSetFilter.ByMinIdentity.html#accept(org.biojava.bio.program.homologene.OrthoPairSet)">accept(OrthoPairSet)</a></span> - Method in class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/OrthoPairSetFilter.ByMinIdentity.html" title="class in org.biojava.bio.program.homologene">OrthoPairSetFilter.ByMinIdentity</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/OrthoPairSetFilter.ByTaxon.html#accept(org.biojava.bio.program.homologene.OrthoPairSet)">accept(OrthoPairSet)</a></span> - Method in class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/OrthoPairSetFilter.ByTaxon.html" title="class in org.biojava.bio.program.homologene">OrthoPairSetFilter.ByTaxon</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/OrthoPairSetFilter.Not.html#accept(org.biojava.bio.program.homologene.OrthoPairSet)">accept(OrthoPairSet)</a></span> - Method in class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/OrthoPairSetFilter.Not.html" title="class in org.biojava.bio.program.homologene">OrthoPairSetFilter.Not</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/OrthoPairSetFilter.Or.html#accept(org.biojava.bio.program.homologene.OrthoPairSet)">accept(OrthoPairSet)</a></span> - Method in class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/OrthoPairSetFilter.Or.html" title="class in org.biojava.bio.program.homologene">OrthoPairSetFilter.Or</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/OrthoPairSetFilter.SomePairsInCollection.html#accept(org.biojava.bio.program.homologene.OrthoPairSet)">accept(OrthoPairSet)</a></span> - Method in class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/OrthoPairSetFilter.SomePairsInCollection.html" title="class in org.biojava.bio.program.homologene">OrthoPairSetFilter.SomePairsInCollection</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/OrthoPairSetFilter.Xor.html#accept(org.biojava.bio.program.homologene.OrthoPairSet)">accept(OrthoPairSet)</a></span> - Method in class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/OrthoPairSetFilter.Xor.html" title="class in org.biojava.bio.program.homologene">OrthoPairSetFilter.Xor</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/PropertyConstraint.html#accept(java.lang.Object)">accept(Object)</a></span> - Method in interface org.biojava.bio.<a href="./org/biojava/bio/PropertyConstraint.html" title="interface in org.biojava.bio">PropertyConstraint</a></dt>
<dd>
<div class="block"><code>accept</code> returns true if the value fulfills the
constraint.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/PropertyConstraint.And.html#accept(java.lang.Object)">accept(Object)</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/PropertyConstraint.And.html" title="class in org.biojava.bio">PropertyConstraint.And</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/PropertyConstraint.ByAnnotationType.html#accept(java.lang.Object)">accept(Object)</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/PropertyConstraint.ByAnnotationType.html" title="class in org.biojava.bio">PropertyConstraint.ByAnnotationType</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/PropertyConstraint.ByClass.html#accept(java.lang.Object)">accept(Object)</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/PropertyConstraint.ByClass.html" title="class in org.biojava.bio">PropertyConstraint.ByClass</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/PropertyConstraint.Enumeration.html#accept(java.lang.Object)">accept(Object)</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/PropertyConstraint.Enumeration.html" title="class in org.biojava.bio">PropertyConstraint.Enumeration</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/PropertyConstraint.ExactValue.html#accept(java.lang.Object)">accept(Object)</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/PropertyConstraint.ExactValue.html" title="class in org.biojava.bio">PropertyConstraint.ExactValue</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/PropertyConstraint.Or.html#accept(java.lang.Object)">accept(Object)</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/PropertyConstraint.Or.html" title="class in org.biojava.bio">PropertyConstraint.Or</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/BlastLikeSearchFilter.AbstractBlastLikeSearchFilter.html#accept()">accept()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/BlastLikeSearchFilter.AbstractBlastLikeSearchFilter.html" title="class in org.biojava.bio.search">BlastLikeSearchFilter.AbstractBlastLikeSearchFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/BlastLikeSearchFilter.html#accept()">accept()</a></span> - Method in interface org.biojava.bio.search.<a href="./org/biojava/bio/search/BlastLikeSearchFilter.html" title="interface in org.biojava.bio.search">BlastLikeSearchFilter</a></dt>
<dd>
<div class="block">returns a TriState indicating the current outcome
of evaluating this filter.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/BlastLikeSearchFilter.And.html#accept()">accept()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/BlastLikeSearchFilter.And.html" title="class in org.biojava.bio.search">BlastLikeSearchFilter.And</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/BlastLikeSearchFilter.Not.html#accept()">accept()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/BlastLikeSearchFilter.Not.html" title="class in org.biojava.bio.search">BlastLikeSearchFilter.Not</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/BlastLikeSearchFilter.Or.html#accept()">accept()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/BlastLikeSearchFilter.Or.html" title="class in org.biojava.bio.search">BlastLikeSearchFilter.Or</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/FilterTest.html#accept(java.lang.Object)">accept(Object)</a></span> - Method in interface org.biojava.bio.search.<a href="./org/biojava/bio/search/FilterTest.html" title="interface in org.biojava.bio.search">FilterTest</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/FilterTest.Equals.html#accept(java.lang.Object)">accept(Object)</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/FilterTest.Equals.html" title="class in org.biojava.bio.search">FilterTest.Equals</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/FilterTest.FindRegex.html#accept(java.lang.Object)">accept(Object)</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/FilterTest.FindRegex.html" title="class in org.biojava.bio.search">FilterTest.FindRegex</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/FilterTest.GreaterThan.html#accept(java.lang.Object)">accept(Object)</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/FilterTest.GreaterThan.html" title="class in org.biojava.bio.search">FilterTest.GreaterThan</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/FilterTest.LessThan.html#accept(java.lang.Object)">accept(Object)</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/FilterTest.LessThan.html" title="class in org.biojava.bio.search">FilterTest.LessThan</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/FilterTest.MatchRegex.html#accept(java.lang.Object)">accept(Object)</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/FilterTest.MatchRegex.html" title="class in org.biojava.bio.search">FilterTest.MatchRegex</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.html#accept(org.biojava.bio.seq.Feature)">accept(Feature)</a></span> - Method in interface org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.html" title="interface in org.biojava.bio.seq">FeatureFilter</a></dt>
<dd>
<div class="block">This method determines whether a feature is to be accepted.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.And.html#accept(org.biojava.bio.seq.Feature)">accept(Feature)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.And.html" title="class in org.biojava.bio.seq">FeatureFilter.And</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ByAncestor.html#accept(org.biojava.bio.seq.Feature)">accept(Feature)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ByAncestor.html" title="class in org.biojava.bio.seq">FeatureFilter.ByAncestor</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ByAnnotationType.html#accept(org.biojava.bio.seq.Feature)">accept(Feature)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ByAnnotationType.html" title="class in org.biojava.bio.seq">FeatureFilter.ByAnnotationType</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ByChild.html#accept(org.biojava.bio.seq.Feature)">accept(Feature)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ByChild.html" title="class in org.biojava.bio.seq">FeatureFilter.ByChild</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ByClass.html#accept(org.biojava.bio.seq.Feature)">accept(Feature)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ByClass.html" title="class in org.biojava.bio.seq">FeatureFilter.ByClass</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ByComponentName.html#accept(org.biojava.bio.seq.Feature)">accept(Feature)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ByComponentName.html" title="class in org.biojava.bio.seq">FeatureFilter.ByComponentName</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ByDescendant.html#accept(org.biojava.bio.seq.Feature)">accept(Feature)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ByDescendant.html" title="class in org.biojava.bio.seq">FeatureFilter.ByDescendant</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ByFeature.html#accept(org.biojava.bio.seq.Feature)">accept(Feature)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ByFeature.html" title="class in org.biojava.bio.seq">FeatureFilter.ByFeature</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ByPairwiseScore.html#accept(org.biojava.bio.seq.Feature)">accept(Feature)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ByPairwiseScore.html" title="class in org.biojava.bio.seq">FeatureFilter.ByPairwiseScore</a></dt>
<dd>
<div class="block">Accept a Feature if it is an instance of
SimilarityPairFeature and its score is <= filter's minimum
score and >= filter's maximum score.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ByParent.html#accept(org.biojava.bio.seq.Feature)">accept(Feature)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ByParent.html" title="class in org.biojava.bio.seq">FeatureFilter.ByParent</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.BySequenceName.html#accept(org.biojava.bio.seq.Feature)">accept(Feature)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.BySequenceName.html" title="class in org.biojava.bio.seq">FeatureFilter.BySequenceName</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.BySource.html#accept(org.biojava.bio.seq.Feature)">accept(Feature)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.BySource.html" title="class in org.biojava.bio.seq">FeatureFilter.BySource</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ByType.html#accept(org.biojava.bio.seq.Feature)">accept(Feature)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ByType.html" title="class in org.biojava.bio.seq">FeatureFilter.ByType</a></dt>
<dd>
<div class="block">Returns true if the feature has a matching type property.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ContainedByLocation.html#accept(org.biojava.bio.seq.Feature)">accept(Feature)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ContainedByLocation.html" title="class in org.biojava.bio.seq">FeatureFilter.ContainedByLocation</a></dt>
<dd>
<div class="block">Returns true if the feature is within this filter's location.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.FrameFilter.html#accept(org.biojava.bio.seq.Feature)">accept(Feature)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.FrameFilter.html" title="class in org.biojava.bio.seq">FeatureFilter.FrameFilter</a></dt>
<dd>
<div class="block">Accept the Feature if it is an instance of FramedFeature and matches
the value of getFrame().</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.Not.html#accept(org.biojava.bio.seq.Feature)">accept(Feature)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.Not.html" title="class in org.biojava.bio.seq">FeatureFilter.Not</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.OnlyChildren.html#accept(org.biojava.bio.seq.Feature)">accept(Feature)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.OnlyChildren.html" title="class in org.biojava.bio.seq">FeatureFilter.OnlyChildren</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.OnlyDescendants.html#accept(org.biojava.bio.seq.Feature)">accept(Feature)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.OnlyDescendants.html" title="class in org.biojava.bio.seq">FeatureFilter.OnlyDescendants</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.Or.html#accept(org.biojava.bio.seq.Feature)">accept(Feature)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.Or.html" title="class in org.biojava.bio.seq">FeatureFilter.Or</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.OverlapsLocation.html#accept(org.biojava.bio.seq.Feature)">accept(Feature)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.OverlapsLocation.html" title="class in org.biojava.bio.seq">FeatureFilter.OverlapsLocation</a></dt>
<dd>
<div class="block">Returns true if the feature overlaps this filter's location.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ShadowContainedByLocation.html#accept(org.biojava.bio.seq.Feature)">accept(Feature)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ShadowContainedByLocation.html" title="class in org.biojava.bio.seq">FeatureFilter.ShadowContainedByLocation</a></dt>
<dd>
<div class="block">Returns true if the feature is within this filter's location.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ShadowOverlapsLocation.html#accept(org.biojava.bio.seq.Feature)">accept(Feature)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ShadowOverlapsLocation.html" title="class in org.biojava.bio.seq">FeatureFilter.ShadowOverlapsLocation</a></dt>
<dd>
<div class="block">Returns true if the feature overlaps this filter's location.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.StrandFilter.html#accept(org.biojava.bio.seq.Feature)">accept(Feature)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.StrandFilter.html" title="class in org.biojava.bio.seq">FeatureFilter.StrandFilter</a></dt>
<dd>
<div class="block">Accept the Feature if it is an instance of StrandedFeature and matches
the value of getStrand().</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/server/PDBFilter.html#accept(org.biojava.bio.structure.PDBHeader)">accept(PDBHeader)</a></span> - Method in interface org.biojava.bio.structure.server.<a href="./org/biojava/bio/structure/server/PDBFilter.html" title="interface in org.biojava.bio.structure.server">PDBFilter</a></dt>
<dd>
<div class="block">return true if this PDBHeader is passing this filter.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLAcceptAllFilter.html#accept(org.biojava.bio.seq.Feature)">accept(Feature)</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLAcceptAllFilter.html" title="class in org.biojavax.bio.db.biosql">BioSQLAcceptAllFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLAcceptNoneFilter.html#accept(org.biojava.bio.seq.Feature)">accept(Feature)</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLAcceptNoneFilter.html" title="class in org.biojavax.bio.db.biosql">BioSQLAcceptNoneFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.And.html#accept(org.biojava.bio.seq.Feature)">accept(Feature)</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.And.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.And</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByName.html#accept(org.biojava.bio.seq.Feature)">accept(Feature)</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByName.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.ByName</a></dt>
<dd>
<div class="block">Returns true if the feature has a matching type property.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByNote.html#accept(org.biojava.bio.seq.Feature)">accept(Feature)</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByNote.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.ByNote</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByNoteTermOnly.html#accept(org.biojava.bio.seq.Feature)">accept(Feature)</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByNoteTermOnly.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.ByNoteTermOnly</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByRank.html#accept(org.biojava.bio.seq.Feature)">accept(Feature)</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByRank.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.ByRank</a></dt>
<dd>
<div class="block">Returns true if the feature has a matching type property.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.BySequenceName.html#accept(org.biojava.bio.seq.Feature)">accept(Feature)</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.BySequenceName.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.BySequenceName</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.BySourceTerm.html#accept(org.biojava.bio.seq.Feature)">accept(Feature)</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.BySourceTerm.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.BySourceTerm</a></dt>
<dd>
<div class="block">Returns true if the feature has a matching source property.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.BySourceTermName.html#accept(org.biojava.bio.seq.Feature)">accept(Feature)</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.BySourceTermName.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.BySourceTermName</a></dt>
<dd>
<div class="block">Returns true if the feature has a matching source property.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByStrand.html#accept(org.biojava.bio.seq.Feature)">accept(Feature)</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByStrand.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.ByStrand</a></dt>
<dd>
<div class="block">Returns true if the feature overlaps this filter's location.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByTypeTerm.html#accept(org.biojava.bio.seq.Feature)">accept(Feature)</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByTypeTerm.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.ByTypeTerm</a></dt>
<dd>
<div class="block">Returns true if the feature has a matching type property.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByTypeTermName.html#accept(org.biojava.bio.seq.Feature)">accept(Feature)</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByTypeTermName.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.ByTypeTermName</a></dt>
<dd>
<div class="block">Returns true if the feature has a matching type property.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ContainedByRichLocation.html#accept(org.biojava.bio.seq.Feature)">accept(Feature)</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ContainedByRichLocation.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.ContainedByRichLocation</a></dt>
<dd>
<div class="block">Returns true if the feature is within this filter's location.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.Not.html#accept(org.biojava.bio.seq.Feature)">accept(Feature)</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.Not.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.Not</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.Or.html#accept(org.biojava.bio.seq.Feature)">accept(Feature)</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.Or.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.Or</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.OverlapsRichLocation.html#accept(org.biojava.bio.seq.Feature)">accept(Feature)</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.OverlapsRichLocation.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.OverlapsRichLocation</a></dt>
<dd>
<div class="block">Returns true if the feature overlaps this filter's location.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFRecordFilter.html#ACCEPT_ALL">ACCEPT_ALL</a></span> - Static variable in interface org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFRecordFilter.html" title="interface in org.biojava.bio.program.gff">GFFRecordFilter</a></dt>
<dd>
<div class="block">A <span class="type">GFFRecordFilter</span> that accepts everything.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/HomologeneBuilder.html#ACCESSION">ACCESSION</a></span> - Static variable in interface org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/HomologeneBuilder.html" title="interface in org.biojava.bio.program.homologene">HomologeneBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/EmblLikeFormat.html#ACCESSION_TAG">ACCESSION_TAG</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/EmblLikeFormat.html" title="class in org.biojava.bio.seq.io">EmblLikeFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/GenbankFormat.html#ACCESSION_TAG">ACCESSION_TAG</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/GenbankFormat.html" title="class in org.biojava.bio.seq.io">GenbankFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLFormat.html#ACCESSION_TAG">ACCESSION_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLFormat.html" title="class in org.biojavax.bio.seq.io">EMBLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/GenbankFormat.html#ACCESSION_TAG">ACCESSION_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/GenbankFormat.html" title="class in org.biojavax.bio.seq.io">GenbankFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/INSDseqFormat.html#ACCESSION_TAG">ACCESSION_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/INSDseqFormat.html" title="class in org.biojavax.bio.seq.io">INSDseqFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtFormat.html#ACCESSION_TAG">ACCESSION_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtFormat.html" title="class in org.biojavax.bio.seq.io">UniProtFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#ACCESSION_TAG">ACCESSION_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/aaindex/AAindex.html#accessionNumber()">accessionNumber()</a></span> - Method in class org.biojava.bio.proteomics.aaindex.<a href="./org/biojava/bio/proteomics/aaindex/AAindex.html" title="class in org.biojava.bio.proteomics.aaindex">AAindex</a></dt>
<dd>
<div class="block">Gets the accession number of the AAindex entry.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/db/emblcd/AcnumHitReader.html" title="class in org.biojava.bio.seq.db.emblcd"><span class="strong">AcnumHitReader</span></a> - Class in <a href="./org/biojava/bio/seq/db/emblcd/package-summary.html">org.biojava.bio.seq.db.emblcd</a></dt>
<dd>
<div class="block"><code>AcnumHitReader</code> reads the "acnum.hit" file of an EMBL
CD-ROM format binary index.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/emblcd/AcnumHitReader.html#AcnumHitReader(java.io.InputStream)">AcnumHitReader(InputStream)</a></span> - Constructor for class org.biojava.bio.seq.db.emblcd.<a href="./org/biojava/bio/seq/db/emblcd/AcnumHitReader.html" title="class in org.biojava.bio.seq.db.emblcd">AcnumHitReader</a></dt>
<dd>
<div class="block">Creates a new <code>AcnumHitReader</code>.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/db/emblcd/AcnumTrgReader.html" title="class in org.biojava.bio.seq.db.emblcd"><span class="strong">AcnumTrgReader</span></a> - Class in <a href="./org/biojava/bio/seq/db/emblcd/package-summary.html">org.biojava.bio.seq.db.emblcd</a></dt>
<dd>
<div class="block"><code>AcnumTrgReader</code> reads the "acnum.trg" file of an EMBL
CD-ROM format binary index.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/emblcd/AcnumTrgReader.html#AcnumTrgReader(java.io.InputStream)">AcnumTrgReader(InputStream)</a></span> - Constructor for class org.biojava.bio.seq.db.emblcd.<a href="./org/biojava/bio/seq/db/emblcd/AcnumTrgReader.html" title="class in org.biojava.bio.seq.db.emblcd">AcnumTrgReader</a></dt>
<dd>
<div class="block">Creates a new <code>AcnumTrgReader</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/taxa/NCBITaxon.html#ACRONYM">ACRONYM</a></span> - Static variable in interface org.biojavax.bio.taxa.<a href="./org/biojavax/bio/taxa/NCBITaxon.html" title="interface in org.biojavax.bio.taxa">NCBITaxon</a></dt>
<dd>
<div class="block">Use this to define acronyms for things.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/Namespace.html#ACRONYM">ACRONYM</a></span> - Static variable in interface org.biojavax.<a href="./org/biojavax/Namespace.html" title="interface in org.biojavax">Namespace</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/RasmolCommandListener.html#actionPerformed(java.awt.event.ActionEvent)">actionPerformed(ActionEvent)</a></span> - Method in class org.biojava.bio.structure.gui.<a href="./org/biojava/bio/structure/gui/RasmolCommandListener.html" title="class in org.biojava.bio.structure.gui">RasmolCommandListener</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ActivityListener.html#activityFailed(java.lang.Object, java.lang.Exception)">activityFailed(Object, Exception)</a></span> - Method in interface org.biojava.utils.<a href="./org/biojava/utils/ActivityListener.html" title="interface in org.biojava.utils">ActivityListener</a></dt>
<dd>
<div class="block">Notification of errors behind the scenes.</div>
</dd>
<dt><a href="./org/biojava/utils/ActivityListener.html" title="interface in org.biojava.utils"><span class="strong">ActivityListener</span></a> - Interface in <a href="./org/biojava/utils/package-summary.html">org.biojava.utils</a></dt>
<dd>
<div class="block">Interface for object which monitor long-running activities.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/DAS.html#activityProgress(java.lang.Object, int, int)">activityProgress(Object, int, int)</a></span> - Static method in class org.biojava.bio.program.das.<a href="./org/biojava/bio/program/das/DAS.html" title="class in org.biojava.bio.program.das">DAS</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ActivityListener.html#activityProgress(java.lang.Object, int, int)">activityProgress(Object, int, int)</a></span> - Method in interface org.biojava.utils.<a href="./org/biojava/utils/ActivityListener.html" title="interface in org.biojava.utils">ActivityListener</a></dt>
<dd>
<div class="block">Estimated progress of an activity.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/BiojavaJmol.html#adapter">adapter</a></span> - Static variable in class org.biojava.bio.structure.gui.<a href="./org/biojava/bio/structure/gui/BiojavaJmol.html" title="class in org.biojava.bio.structure.gui">BiojavaJmol</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFEntrySet.html#add(java.lang.String)">add(String)</a></span> - Method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFEntrySet.html" title="class in org.biojava.bio.program.gff">GFFEntrySet</a></dt>
<dd>
<div class="block">Add a comment to the end of this set.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFEntrySet.html#add(org.biojava.bio.program.gff.GFFRecord)">add(GFFRecord)</a></span> - Method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFEntrySet.html" title="class in org.biojava.bio.program.gff">GFFEntrySet</a></dt>
<dd>
<div class="block">Add a <span class="type">GFFRecord</span> to the end of this set.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/AbstractOrthoPairCollection.html#add(org.biojava.bio.program.homologene.OrthoPairSet)">add(OrthoPairSet)</a></span> - Method in class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/AbstractOrthoPairCollection.html" title="class in org.biojava.bio.program.homologene">AbstractOrthoPairCollection</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/OrthoPairCollection.html#add(org.biojava.bio.program.homologene.OrthoPairSet)">add(OrthoPairSet)</a></span> - Method in interface org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/OrthoPairCollection.html" title="interface in org.biojava.bio.program.homologene">OrthoPairCollection</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/SimpleOrthoPairCollection.html#add(org.biojava.bio.program.homologene.OrthoPairSet)">add(OrthoPairSet)</a></span> - Method in class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/SimpleOrthoPairCollection.html" title="class in org.biojava.bio.program.homologene">SimpleOrthoPairCollection</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/helper/JointFragments.html#add(int, int, int, int)">add(int, int, int, int)</a></span> - Method in class org.biojava.bio.structure.align.helper.<a href="./org/biojava/bio/structure/align/helper/JointFragments.html" title="class in org.biojava.bio.structure.align.helper">JointFragments</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Calc.html#add(org.biojava.bio.structure.Atom, org.biojava.bio.structure.Atom)">add(Atom, Atom)</a></span> - Static method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Calc.html" title="class in org.biojava.bio.structure">Calc</a></dt>
<dd>
<div class="block">add two atoms ( a + b).</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/FileAsList.html#add(java.lang.Object)">add(Object)</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/FileAsList.html" title="class in org.biojava.utils">FileAsList</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/MergingSet.html#add(java.lang.Object)">add(Object)</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/MergingSet.html" title="class in org.biojava.utils">MergingSet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/SmallSet.html#add(java.lang.Object)">add(Object)</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/SmallSet.html" title="class in org.biojava.utils">SmallSet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/util/WeightedSet.html#add(java.lang.Object)">add(Object)</a></span> - Method in class org.biojavax.ga.util.<a href="./org/biojavax/ga/util/WeightedSet.html" title="class in org.biojavax.ga.util">WeightedSet</a></dt>
<dd>
<div class="block">Adds a new <code>Object</code> with a weight of zero.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/ARAlignment.html#ADD_LABEL">ADD_LABEL</a></span> - Static variable in interface org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/ARAlignment.html" title="interface in org.biojava.bio.alignment">ARAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/DAS.html#addActivityListener(org.biojava.utils.ActivityListener)">addActivityListener(ActivityListener)</a></span> - Static method in class org.biojava.bio.program.das.<a href="./org/biojava/bio/program/das/DAS.html" title="class in org.biojava.bio.program.das">DAS</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/SequenceDisplay.html#addAlignmentPositionListener(org.biojava.bio.structure.gui.events.AlignmentPositionListener)">addAlignmentPositionListener(AlignmentPositionListener)</a></span> - Method in class org.biojava.bio.structure.gui.<a href="./org/biojava/bio/structure/gui/SequenceDisplay.html" title="class in org.biojava.bio.structure.gui">SequenceDisplay</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/util/SequenceMouseListener.html#addAlignmentPositionListener(org.biojava.bio.structure.gui.events.AlignmentPositionListener)">addAlignmentPositionListener(AlignmentPositionListener)</a></span> - Method in class org.biojava.bio.structure.gui.util.<a href="./org/biojava/bio/structure/gui/util/SequenceMouseListener.html" title="class in org.biojava.bio.structure.gui.util">SequenceMouseListener</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/util/WeightedSet.html#addAll(java.util.Collection)">addAll(Collection)</a></span> - Method in class org.biojavax.ga.util.<a href="./org/biojavax/ga/util/WeightedSet.html" title="class in org.biojavax.ga.util">WeightedSet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/SequenceTools.html#addAllFeatures(org.biojava.bio.seq.Sequence, org.biojava.bio.seq.FeatureHolder)">addAllFeatures(Sequence, FeatureHolder)</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/SequenceTools.html" title="class in org.biojava.bio.seq">SequenceTools</a></dt>
<dd>
<div class="block">Add features to a sequence that contain the same information as all
those in a feature holder.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/MergeAnnotation.html#addAnnotation(org.biojava.bio.Annotation)">addAnnotation(Annotation)</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/MergeAnnotation.html" title="class in org.biojava.bio">MergeAnnotation</a></dt>
<dd>
<div class="block">Add a new Annotation to to the end of the list to be merged.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/annodb/MergingAnnotationDB.html#addAnnotationDB(org.biojava.bio.annodb.AnnotationDB)">addAnnotationDB(AnnotationDB)</a></span> - Method in class org.biojava.bio.annodb.<a href="./org/biojava/bio/annodb/MergingAnnotationDB.html" title="class in org.biojava.bio.annodb">MergingAnnotationDB</a></dt>
<dd>
<div class="block">Add a DB to be merged in this view.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/DASSequence.html#addAnnotationSource(java.net.URL)">addAnnotationSource(URL)</a></span> - Method in class org.biojava.bio.program.das.<a href="./org/biojava/bio/program/das/DASSequence.html" title="class in org.biojava.bio.program.das">DASSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Group.html#addAtom(org.biojava.bio.structure.Atom)">addAtom(Atom)</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Group.html" title="interface in org.biojava.bio.structure">Group</a></dt>
<dd>
<div class="block">add an atom to this group.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/HetatomImpl.html#addAtom(org.biojava.bio.structure.Atom)">addAtom(Atom)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/HetatomImpl.html" title="class in org.biojava.bio.structure">HetatomImpl</a></dt>
<dd>
<div class="block">add an atom to this group.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/AbstractBioEntryDB.html#addBioEntry(org.biojavax.bio.BioEntry)">addBioEntry(BioEntry)</a></span> - Method in class org.biojavax.bio.db.<a href="./org/biojavax/bio/db/AbstractBioEntryDB.html" title="class in org.biojavax.bio.db">AbstractBioEntryDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/AbstractRichSequenceDB.html#addBioEntry(org.biojavax.bio.BioEntry)">addBioEntry(BioEntry)</a></span> - Method in class org.biojavax.bio.db.<a href="./org/biojavax/bio/db/AbstractRichSequenceDB.html" title="class in org.biojavax.bio.db">AbstractRichSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/BioEntryDBLite.html#addBioEntry(org.biojavax.bio.BioEntry)">addBioEntry(BioEntry)</a></span> - Method in interface org.biojavax.bio.db.<a href="./org/biojavax/bio/db/BioEntryDBLite.html" title="interface in org.biojavax.bio.db">BioEntryDBLite</a></dt>
<dd>
<div class="block">Adds a sequence to the database.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLBioEntryDB.html#addBioEntry(org.biojavax.bio.BioEntry)">addBioEntry(BioEntry)</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLBioEntryDB.html" title="class in org.biojavax.bio.db.biosql">BioSQLBioEntryDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/HashBioEntryDB.html#addBioEntry(org.biojavax.bio.BioEntry)">addBioEntry(BioEntry)</a></span> - Method in class org.biojavax.bio.db.<a href="./org/biojavax/bio/db/HashBioEntryDB.html" title="class in org.biojavax.bio.db">HashBioEntryDB</a></dt>
<dd>
<div class="block">Add a BioEntry, the name of the BioEntry will be used as the ID</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/HashBioEntryDB.html#addBioEntry(java.lang.String, org.biojavax.bio.BioEntry)">addBioEntry(String, BioEntry)</a></span> - Method in class org.biojavax.bio.db.<a href="./org/biojavax/bio/db/HashBioEntryDB.html" title="class in org.biojavax.bio.db">HashBioEntryDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/dasalignment/Alignment.html#addBlock(org.biojava.bio.Annotation)">addBlock(Annotation)</a></span> - Method in class org.biojava.bio.program.das.dasalignment.<a href="./org/biojava/bio/program/das/dasalignment/Alignment.html" title="class in org.biojava.bio.program.das.dasalignment">Alignment</a></dt>
<dd>
<div class="block">Add a "Block" Annotation.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/directory/RegistryConfiguration.Composite.html#addBottomConfig(org.biojava.directory.RegistryConfiguration)">addBottomConfig(RegistryConfiguration)</a></span> - Method in class org.biojava.directory.<a href="./org/biojava/directory/RegistryConfiguration.Composite.html" title="class in org.biojava.directory">RegistryConfiguration.Composite</a></dt>
<dd>
<div class="block">Add a configuration as the most default place to look.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Compound.html#addChain(org.biojava.bio.structure.Chain)">addChain(Chain)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure">Compound</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Structure.html#addChain(org.biojava.bio.structure.Chain)">addChain(Chain)</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Structure.html" title="interface in org.biojava.bio.structure">Structure</a></dt>
<dd>
<div class="block">add a new chain.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Structure.html#addChain(org.biojava.bio.structure.Chain, int)">addChain(Chain, int)</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Structure.html" title="interface in org.biojava.bio.structure">Structure</a></dt>
<dd>
<div class="block">add a new chain, if several models are available.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/StructureImpl.html#addChain(org.biojava.bio.structure.Chain)">addChain(Chain)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/StructureImpl.html" title="class in org.biojava.bio.structure">StructureImpl</a></dt>
<dd>
<div class="block">add a new chain.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/StructureImpl.html#addChain(org.biojava.bio.structure.Chain, int)">addChain(Chain, int)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/StructureImpl.html" title="class in org.biojava.bio.structure">StructureImpl</a></dt>
<dd>
<div class="block">add a new chain, if several models are available.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PairwiseSequencePanel.html#addChangeListener(org.biojava.utils.ChangeListener)">addChangeListener(ChangeListener)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PairwiseSequencePanel.html" title="class in org.biojava.bio.gui.sequence">PairwiseSequencePanel</a></dt>
<dd>
<div class="block"><code>addChangeListener</code> adds a listener for all types of
change.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PairwiseSequencePanel.html#addChangeListener(org.biojava.utils.ChangeListener, org.biojava.utils.ChangeType)">addChangeListener(ChangeListener, ChangeType)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PairwiseSequencePanel.html" title="class in org.biojava.bio.gui.sequence">PairwiseSequencePanel</a></dt>
<dd>
<div class="block"><code>addChangeListener</code> adds a listener for specific
types of change.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePanel.html#addChangeListener(org.biojava.utils.ChangeListener)">addChangeListener(ChangeListener)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePanel.html" title="class in org.biojava.bio.gui.sequence">SequencePanel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePanel.html#addChangeListener(org.biojava.utils.ChangeListener, org.biojava.utils.ChangeType)">addChangeListener(ChangeListener, ChangeType)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePanel.html" title="class in org.biojava.bio.gui.sequence">SequencePanel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePoster.html#addChangeListener(org.biojava.utils.ChangeListener)">addChangeListener(ChangeListener)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePoster.html" title="class in org.biojava.bio.gui.sequence">SequencePoster</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePoster.html#addChangeListener(org.biojava.utils.ChangeListener, org.biojava.utils.ChangeType)">addChangeListener(ChangeListener, ChangeType)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePoster.html" title="class in org.biojava.bio.gui.sequence">SequencePoster</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/TranslatedSequencePanel.html#addChangeListener(org.biojava.utils.ChangeListener)">addChangeListener(ChangeListener)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/TranslatedSequencePanel.html" title="class in org.biojava.bio.gui.sequence">TranslatedSequencePanel</a></dt>
<dd>
<div class="block"><code>addChangeListener</code> adds a listener for all types of
change.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/TranslatedSequencePanel.html#addChangeListener(org.biojava.utils.ChangeListener, org.biojava.utils.ChangeType)">addChangeListener(ChangeListener, ChangeType)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/TranslatedSequencePanel.html" title="class in org.biojava.bio.gui.sequence">TranslatedSequencePanel</a></dt>
<dd>
<div class="block"><code>addChangeListener</code> adds a listener for specific
types of change.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/ReferenceServer.html#addChangeListener(org.biojava.utils.ChangeListener)">addChangeListener(ChangeListener)</a></span> - Method in class org.biojava.bio.program.das.<a href="./org/biojava/bio/program/das/ReferenceServer.html" title="class in org.biojava.bio.program.das">ReferenceServer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/ReferenceServer.html#addChangeListener(org.biojava.utils.ChangeListener, org.biojava.utils.ChangeType)">addChangeListener(ChangeListener, ChangeType)</a></span> - Method in class org.biojava.bio.program.das.<a href="./org/biojava/bio/program/das/ReferenceServer.html" title="class in org.biojava.bio.program.das">ReferenceServer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/LazyFilterFeatureHolder.html#addChangeListener(org.biojava.utils.ChangeListener)">addChangeListener(ChangeListener)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/LazyFilterFeatureHolder.html" title="class in org.biojava.bio.seq.impl">LazyFilterFeatureHolder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/LazyFilterFeatureHolder.html#addChangeListener(org.biojava.utils.ChangeListener, org.biojava.utils.ChangeType)">addChangeListener(ChangeListener, ChangeType)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/LazyFilterFeatureHolder.html" title="class in org.biojava.bio.seq.impl">LazyFilterFeatureHolder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SubSequence.html#addChangeListener(org.biojava.utils.ChangeListener, org.biojava.utils.ChangeType)">addChangeListener(ChangeListener, ChangeType)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SubSequence.html" title="class in org.biojava.bio.seq.impl">SubSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SubSequence.html#addChangeListener(org.biojava.utils.ChangeListener)">addChangeListener(ChangeListener)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SubSequence.html" title="class in org.biojava.bio.seq.impl">SubSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/projection/ProjectedFeature.html#addChangeListener(org.biojava.utils.ChangeListener)">addChangeListener(ChangeListener)</a></span> - Method in class org.biojava.bio.seq.projection.<a href="./org/biojava/bio/seq/projection/ProjectedFeature.html" title="class in org.biojava.bio.seq.projection">ProjectedFeature</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/projection/ProjectedFeature.html#addChangeListener(org.biojava.utils.ChangeListener, org.biojava.utils.ChangeType)">addChangeListener(ChangeListener, ChangeType)</a></span> - Method in class org.biojava.bio.seq.projection.<a href="./org/biojava/bio/seq/projection/ProjectedFeature.html" title="class in org.biojava.bio.seq.projection">ProjectedFeature</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/projection/ProjectionContext.html#addChangeListener(org.biojava.bio.seq.Feature, org.biojava.utils.ChangeListener, org.biojava.utils.ChangeType)">addChangeListener(Feature, ChangeListener, ChangeType)</a></span> - Method in interface org.biojava.bio.seq.projection.<a href="./org/biojava/bio/seq/projection/ProjectionContext.html" title="interface in org.biojava.bio.seq.projection">ProjectionContext</a></dt>
<dd>
<div class="block">Add a ChangeListener to a projected feature.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/projection/ReparentContext.html#addChangeListener(org.biojava.bio.seq.Feature, org.biojava.utils.ChangeListener, org.biojava.utils.ChangeType)">addChangeListener(Feature, ChangeListener, ChangeType)</a></span> - Method in class org.biojava.bio.seq.projection.<a href="./org/biojava/bio/seq/projection/ReparentContext.html" title="class in org.biojava.bio.seq.projection">ReparentContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/AbstractChangeable.html#addChangeListener(org.biojava.utils.ChangeListener)">addChangeListener(ChangeListener)</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/AbstractChangeable.html" title="class in org.biojava.utils">AbstractChangeable</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/AbstractChangeable.html#addChangeListener(org.biojava.utils.ChangeListener, org.biojava.utils.ChangeType)">addChangeListener(ChangeListener, ChangeType)</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/AbstractChangeable.html" title="class in org.biojava.utils">AbstractChangeable</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/Changeable.html#addChangeListener(org.biojava.utils.ChangeListener)">addChangeListener(ChangeListener)</a></span> - Method in interface org.biojava.utils.<a href="./org/biojava/utils/Changeable.html" title="interface in org.biojava.utils">Changeable</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>use addChangeListener(cl, ChangeType.UNKNOWN)</i></div>
</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/Changeable.html#addChangeListener(org.biojava.utils.ChangeListener, org.biojava.utils.ChangeType)">addChangeListener(ChangeListener, ChangeType)</a></span> - Method in interface org.biojava.utils.<a href="./org/biojava/utils/Changeable.html" title="interface in org.biojava.utils">Changeable</a></dt>
<dd>
<div class="block">Add a listener that will be informed of changes of a given type.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/ChangeSupport.html#addChangeListener(org.biojava.utils.ChangeListener)">addChangeListener(ChangeListener)</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/ChangeSupport.html" title="class in org.biojava.utils">ChangeSupport</a></dt>
<dd>
<div class="block">Add a listener that will be informed of all changes.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/ChangeSupport.html#addChangeListener(org.biojava.utils.ChangeListener, org.biojava.utils.ChangeType)">addChangeListener(ChangeListener, ChangeType)</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/ChangeSupport.html" title="class in org.biojava.utils">ChangeSupport</a></dt>
<dd>
<div class="block">Add a listener that will be informed of changes of a given type (and it's subtypes)</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/Unchangeable.html#addChangeListener(org.biojava.utils.ChangeListener)">addChangeListener(ChangeListener)</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/Unchangeable.html" title="class in org.biojava.utils">Unchangeable</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/Unchangeable.html#addChangeListener(org.biojava.utils.ChangeListener, org.biojava.utils.ChangeType)">addChangeListener(ChangeListener, ChangeType)</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/Unchangeable.html" title="class in org.biojava.utils">Unchangeable</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/InfinitelyAmbiguousSymbolList.html#addChangeListener(org.biojava.utils.ChangeListener)">addChangeListener(ChangeListener)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/InfinitelyAmbiguousSymbolList.html" title="class in org.biojavax.bio.seq">InfinitelyAmbiguousSymbolList</a></dt>
<dd>
<div class="block">Add a listener that will be informed of all changes.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/InfinitelyAmbiguousSymbolList.html#addChangeListener(org.biojava.utils.ChangeListener, org.biojava.utils.ChangeType)">addChangeListener(ChangeListener, ChangeType)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/InfinitelyAmbiguousSymbolList.html" title="class in org.biojavax.bio.seq">InfinitelyAmbiguousSymbolList</a></dt>
<dd>
<div class="block">Add a listener that will be informed of changes of a given type.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ga/functions/CrossOverFunction.NoCross.html#addChangeListener(org.biojava.utils.ChangeListener)">addChangeListener(ChangeListener)</a></span> - Method in class org.biojavax.ga.functions.<a href="./org/biojavax/ga/functions/CrossOverFunction.NoCross.html" title="class in org.biojavax.ga.functions">CrossOverFunction.NoCross</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/functions/CrossOverFunction.NoCross.html#addChangeListener(org.biojava.utils.ChangeListener, org.biojava.utils.ChangeType)">addChangeListener(ChangeListener, ChangeType)</a></span> - Method in class org.biojavax.ga.functions.<a href="./org/biojavax/ga/functions/CrossOverFunction.NoCross.html" title="class in org.biojavax.ga.functions">CrossOverFunction.NoCross</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/functions/MutationFunction.NoMutation.html#addChangeListener(org.biojava.utils.ChangeListener)">addChangeListener(ChangeListener)</a></span> - Method in class org.biojavax.ga.functions.<a href="./org/biojavax/ga/functions/MutationFunction.NoMutation.html" title="class in org.biojavax.ga.functions">MutationFunction.NoMutation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/functions/MutationFunction.NoMutation.html#addChangeListener(org.biojava.utils.ChangeListener, org.biojava.utils.ChangeType)">addChangeListener(ChangeListener, ChangeType)</a></span> - Method in class org.biojavax.ga.functions.<a href="./org/biojavax/ga/functions/MutationFunction.NoMutation.html" title="class in org.biojavax.ga.functions">MutationFunction.NoMutation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/ChemicalComponentDictionary.html#addChemComp(org.biojava.bio.structure.io.mmcif.model.ChemComp)">addChemComp(ChemComp)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/ChemicalComponentDictionary.html" title="class in org.biojava.bio.structure.io.mmcif">ChemicalComponentDictionary</a></dt>
<dd>
<div class="block">add a new component to the dictionary</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/taxa/SimpleTaxonFactory.html#addChild(org.biojava.bio.taxa.Taxon, org.biojava.bio.taxa.Taxon)">addChild(Taxon, Taxon)</a></span> - Method in class org.biojava.bio.taxa.<a href="./org/biojava/bio/taxa/SimpleTaxonFactory.html" title="class in org.biojava.bio.taxa">SimpleTaxonFactory</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/taxa/TaxonFactory.html#addChild(org.biojava.bio.taxa.Taxon, org.biojava.bio.taxa.Taxon)">addChild(Taxon, Taxon)</a></span> - Method in interface org.biojava.bio.taxa.<a href="./org/biojava/bio/taxa/TaxonFactory.html" title="interface in org.biojava.bio.taxa">TaxonFactory</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Add a taxon as a child to a parent.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/taxa/WeakTaxonFactory.html#addChild(org.biojava.bio.taxa.Taxon, org.biojava.bio.taxa.Taxon)">addChild(Taxon, Taxon)</a></span> - Method in class org.biojava.bio.taxa.<a href="./org/biojava/bio/taxa/WeakTaxonFactory.html" title="class in org.biojava.bio.taxa">WeakTaxonFactory</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/unigene/UnigeneDB.html#addCluster(org.biojava.bio.program.unigene.UnigeneCluster)">addCluster(UnigeneCluster)</a></span> - Method in interface org.biojava.bio.program.unigene.<a href="./org/biojava/bio/program/unigene/UnigeneDB.html" title="interface in org.biojava.bio.program.unigene">UnigeneDB</a></dt>
<dd>
<div class="block">Add a cluster to a database.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/BioEntry.html#addComment(org.biojavax.Comment)">addComment(Comment)</a></span> - Method in interface org.biojavax.bio.<a href="./org/biojavax/bio/BioEntry.html" title="interface in org.biojavax.bio">BioEntry</a></dt>
<dd>
<div class="block">Adds a comment instance to this bioentry.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/SimpleBioEntry.html#addComment(org.biojavax.Comment)">addComment(Comment)</a></span> - Method in class org.biojavax.bio.<a href="./org/biojavax/bio/SimpleBioEntry.html" title="class in org.biojavax.bio">SimpleBioEntry</a></dt>
<dd>
<div class="block">Adds a comment instance to this bioentry.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SimpleAssemblyBuilder.html#addComponentSequence(org.biojava.bio.seq.ComponentFeature.Template)">addComponentSequence(ComponentFeature.Template)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SimpleAssemblyBuilder.html" title="class in org.biojava.bio.seq.io">SimpleAssemblyBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/DistributionTrainer.html#addCount(org.biojava.bio.dist.DistributionTrainerContext, org.biojava.bio.symbol.AtomicSymbol, double)">addCount(DistributionTrainerContext, AtomicSymbol, double)</a></span> - Method in interface org.biojava.bio.dist.<a href="./org/biojava/bio/dist/DistributionTrainer.html" title="interface in org.biojava.bio.dist">DistributionTrainer</a></dt>
<dd>
<div class="block">
Registers that sym was counted in this state.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/DistributionTrainerContext.html#addCount(org.biojava.bio.dist.Distribution, org.biojava.bio.symbol.Symbol, double)">addCount(Distribution, Symbol, double)</a></span> - Method in interface org.biojava.bio.dist.<a href="./org/biojava/bio/dist/DistributionTrainerContext.html" title="interface in org.biojava.bio.dist">DistributionTrainerContext</a></dt>
<dd>
<div class="block">
Registers that sym was counted in this state.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/IgnoreCountsTrainer.html#addCount(org.biojava.bio.dist.DistributionTrainerContext, org.biojava.bio.symbol.AtomicSymbol, double)">addCount(DistributionTrainerContext, AtomicSymbol, double)</a></span> - Method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/IgnoreCountsTrainer.html" title="class in org.biojava.bio.dist">IgnoreCountsTrainer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/SimpleDistribution.Trainer.html#addCount(org.biojava.bio.dist.DistributionTrainerContext, org.biojava.bio.symbol.AtomicSymbol, double)">addCount(DistributionTrainerContext, AtomicSymbol, double)</a></span> - Method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/SimpleDistribution.Trainer.html" title="class in org.biojava.bio.dist">SimpleDistribution.Trainer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/SimpleDistributionTrainer.html#addCount(org.biojava.bio.dist.DistributionTrainerContext, org.biojava.bio.symbol.AtomicSymbol, double)">addCount(DistributionTrainerContext, AtomicSymbol, double)</a></span> - Method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/SimpleDistributionTrainer.html" title="class in org.biojava.bio.dist">SimpleDistributionTrainer</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/SimpleDistributionTrainerContext.html#addCount(org.biojava.bio.dist.Distribution, org.biojava.bio.symbol.Symbol, double)">addCount(Distribution, Symbol, double)</a></span> - Method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/SimpleDistributionTrainerContext.html" title="class in org.biojava.bio.dist">SimpleDistributionTrainerContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/TransitionTrainer.html#addCount(org.biojava.bio.dp.State, org.biojava.bio.dp.State, double)">addCount(State, State, double)</a></span> - Method in interface org.biojava.bio.dp.<a href="./org/biojava/bio/dp/TransitionTrainer.html" title="interface in org.biojava.bio.dp">TransitionTrainer</a></dt>
<dd>
<div class="block">Add 'count' to the transition from->to.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/DAS.html#addDasURL(java.net.URL)">addDasURL(URL)</a></span> - Method in class org.biojava.bio.program.das.<a href="./org/biojava/bio/program/das/DAS.html" title="class in org.biojava.bio.program.das">DAS</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/distributed/DistributedSequenceDB.html#addDataSource(org.biojava.bio.seq.distributed.DistDataSource)">addDataSource(DistDataSource)</a></span> - Method in class org.biojava.bio.seq.distributed.<a href="./org/biojava/bio/seq/distributed/DistributedSequenceDB.html" title="class in org.biojava.bio.seq.distributed">DistributedSequenceDB</a></dt>
<dd>
<div class="block">Add a distributed data source.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEAltIdsPropHandler.html#addDbId(org.biojava.bio.seq.io.agave.AGAVEDbId)">addDbId(AGAVEDbId)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEAltIdsPropHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEAltIdsPropHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEDbIdCallbackItf.html#addDbId(org.biojava.bio.seq.io.agave.AGAVEDbId)">addDbId(AGAVEDbId)</a></span> - Method in interface org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEDbIdCallbackItf.html" title="interface in org.biojava.bio.seq.io.agave">AGAVEDbIdCallbackItf</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEMapPosition.html#addDbId(org.biojava.bio.seq.io.agave.AGAVEDbId)">addDbId(AGAVEDbId)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEMapPosition.html" title="class in org.biojava.bio.seq.io.agave">AGAVEMapPosition</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEMapPositionPropHandler.html#addDbId(org.biojava.bio.seq.io.agave.AGAVEDbId)">addDbId(AGAVEDbId)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEMapPositionPropHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEMapPositionPropHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEMatchRegionPropHandler.html#addDbId(org.biojava.bio.seq.io.agave.AGAVEDbId)">addDbId(AGAVEDbId)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEMatchRegionPropHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEMatchRegionPropHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEQueryRegionPropHandler.html#addDbId(org.biojava.bio.seq.io.agave.AGAVEDbId)">addDbId(AGAVEDbId)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEQueryRegionPropHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEQueryRegionPropHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEXrefPropHandler.html#addDbId(org.biojava.bio.seq.io.agave.AGAVEDbId)">addDbId(AGAVEDbId)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEXrefPropHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEXrefPropHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEXrefs.html#addDbId(org.biojava.bio.seq.io.agave.AGAVEDbId)">addDbId(AGAVEDbId)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEXrefs.html" title="class in org.biojava.bio.seq.io.agave">AGAVEXrefs</a></dt>
<dd>
<div class="block">add @param id</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEXrefsPropHandler.html#addDbId(org.biojava.bio.seq.io.agave.AGAVEDbId)">addDbId(AGAVEDbId)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEXrefsPropHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEXrefsPropHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ontology/ComparableTriple.html#addDescriptor(org.biojavax.ontology.ComparableTerm)">addDescriptor(ComparableTerm)</a></span> - Method in interface org.biojavax.ontology.<a href="./org/biojavax/ontology/ComparableTriple.html" title="interface in org.biojavax.ontology">ComparableTriple</a></dt>
<dd>
<div class="block">Adds a descriptor.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ontology/SimpleComparableTriple.html#addDescriptor(org.biojavax.ontology.ComparableTerm)">addDescriptor(ComparableTerm)</a></span> - Method in class org.biojavax.ontology.<a href="./org/biojavax/ontology/SimpleComparableTriple.html" title="class in org.biojavax.ontology">SimpleComparableTriple</a></dt>
<dd>
<div class="block">Adds a descriptor.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/xff/XFFFeatureSetHandler.html#addDetailHandler(org.biojava.bio.program.xff.ElementRecognizer, org.biojava.bio.program.xff.XFFPartHandlerFactory)">addDetailHandler(ElementRecognizer, XFFPartHandlerFactory)</a></span> - Method in class org.biojava.bio.program.xff.<a href="./org/biojava/bio/program/xff/XFFFeatureSetHandler.html" title="class in org.biojava.bio.program.xff">XFFFeatureSetHandler</a></dt>
<dd>
<div class="block">Extend this FeatureSetHandler to delegate certain detail elements
to the specified handler type.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/Digest.html#addDigestFeatures()">addDigestFeatures()</a></span> - Method in class org.biojava.bio.proteomics.<a href="./org/biojava/bio/proteomics/Digest.html" title="class in org.biojava.bio.proteomics">Digest</a></dt>
<dd>
<div class="block">Adds peptides as features to the Sequence in this class.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEEvidenceCallbackItf.html#addElementId(java.lang.String)">addElementId(String)</a></span> - Method in interface org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEEvidenceCallbackItf.html" title="interface in org.biojava.bio.seq.io.agave">AGAVEEvidenceCallbackItf</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEEvidenceHandler.html#addElementId(java.lang.String)">addElementId(String)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEEvidenceHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEEvidenceHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEMatchRegionPropHandler.html#addElementId(java.lang.String)">addElementId(String)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEMatchRegionPropHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEMatchRegionPropHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVERelatedAnnot.html#addElementId(java.lang.String)">addElementId(String)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVERelatedAnnot.html" title="class in org.biojava.bio.seq.io.agave">AGAVERelatedAnnot</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVERelatedAnnotPropHandler.html#addElementId(java.lang.String)">addElementId(String)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVERelatedAnnotPropHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVERelatedAnnotPropHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVETranscriptHandler.html#addElementId(java.lang.String)">addElementId(String)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVETranscriptHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVETranscriptHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/molbio/RestrictionMapper.html#addEnzyme(org.biojava.bio.molbio.RestrictionEnzyme)">addEnzyme(RestrictionEnzyme)</a></span> - Method in class org.biojava.bio.molbio.<a href="./org/biojava/bio/molbio/RestrictionMapper.html" title="class in org.biojava.bio.molbio">RestrictionMapper</a></dt>
<dd>
<div class="block"><code>addEnzyme</code> adds an enzyme to be searched for in the
<code>Sequence</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/automata/Nfa.html#addEpsilonTransition(org.biojava.utils.automata.FiniteAutomaton.Node, org.biojava.utils.automata.FiniteAutomaton.Node)">addEpsilonTransition(FiniteAutomaton.Node, FiniteAutomaton.Node)</a></span> - Method in class org.biojava.utils.automata.<a href="./org/biojava/utils/automata/Nfa.html" title="class in org.biojava.utils.automata">Nfa</a></dt>
<dd>
<div class="block">Add a silent optimisable transition to instance.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/automata/NfaBuilder.html#addEpsilonTransition(org.biojava.utils.automata.FiniteAutomaton.Node, org.biojava.utils.automata.FiniteAutomaton.Node)">addEpsilonTransition(FiniteAutomaton.Node, FiniteAutomaton.Node)</a></span> - Method in interface org.biojava.utils.automata.<a href="./org/biojava/utils/automata/NfaBuilder.html" title="interface in org.biojava.utils.automata">NfaBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/automata/NfaSubModel.html#addEpsilonTransition(org.biojava.utils.automata.FiniteAutomaton.Node, org.biojava.utils.automata.FiniteAutomaton.Node)">addEpsilonTransition(FiniteAutomaton.Node, FiniteAutomaton.Node)</a></span> - Method in class org.biojava.utils.automata.<a href="./org/biojava/utils/automata/NfaSubModel.html" title="class in org.biojava.utils.automata">NfaSubModel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/MMCIFFileReader.html#addExtension(java.lang.String)">addExtension(String)</a></span> - Method in class org.biojava.bio.structure.io.<a href="./org/biojava/bio/structure/io/MMCIFFileReader.html" title="class in org.biojava.bio.structure.io">MMCIFFileReader</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/PDBFileReader.html#addExtension(java.lang.String)">addExtension(String)</a></span> - Method in class org.biojava.bio.structure.io.<a href="./org/biojava/bio/structure/io/PDBFileReader.html" title="class in org.biojava.bio.structure.io">PDBFileReader</a></dt>
<dd>
<div class="block">define supported file extensions
compressed extensions .Z,.gz do not need to be specified
they are dealt with automatically.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/StructureIOFile.html#addExtension(java.lang.String)">addExtension(String)</a></span> - Method in interface org.biojava.bio.structure.io.<a href="./org/biojava/bio/structure/io/StructureIOFile.html" title="interface in org.biojava.bio.structure.io">StructureIOFile</a></dt>
<dd>
<div class="block">add a known File extension.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/SimpleFeatureHolder.html#addFeature(org.biojava.bio.seq.Feature)">addFeature(Feature)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/SimpleFeatureHolder.html" title="class in org.biojava.bio.seq">SimpleFeatureHolder</a></dt>
<dd>
<div class="block">Add a feature to the featureholder</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/xff/XFFFeatureSetHandler.html#addFeatureHandler(org.biojava.bio.program.xff.ElementRecognizer, org.biojava.bio.program.xff.XFFPartHandlerFactory)">addFeatureHandler(ElementRecognizer, XFFPartHandlerFactory)</a></span> - Method in class org.biojava.bio.program.xff.<a href="./org/biojava/bio/program/xff/XFFFeatureSetHandler.html" title="class in org.biojava.bio.program.xff">XFFFeatureSetHandler</a></dt>
<dd>
<div class="block">Extend this FeatureSetHandler to delegate certain feature elements
to the specified handler type.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/MergeFeatureHolder.html#addFeatureHolder(org.biojava.bio.seq.FeatureHolder)">addFeatureHolder(FeatureHolder)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/MergeFeatureHolder.html" title="class in org.biojava.bio.seq">MergeFeatureHolder</a></dt>
<dd>
<div class="block">Add an extra FeatureHolder to the set of FeatureHolders which
are merged.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/EmblFileFormer.html#addFeatureProperty(java.lang.Object, java.lang.Object)">addFeatureProperty(Object, Object)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/EmblFileFormer.html" title="class in org.biojava.bio.seq.io">EmblFileFormer</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/GenbankFileFormer.html#addFeatureProperty(java.lang.Object, java.lang.Object)">addFeatureProperty(Object, Object)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/GenbankFileFormer.html" title="class in org.biojava.bio.seq.io">GenbankFileFormer</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOAdapter.html#addFeatureProperty(java.lang.Object, java.lang.Object)">addFeatureProperty(Object, Object)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOAdapter.html" title="class in org.biojava.bio.seq.io">SeqIOAdapter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOFilter.html#addFeatureProperty(java.lang.Object, java.lang.Object)">addFeatureProperty(Object, Object)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOFilter.html" title="class in org.biojava.bio.seq.io">SeqIOFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOListener.html#addFeatureProperty(java.lang.Object, java.lang.Object)">addFeatureProperty(Object, Object)</a></span> - Method in interface org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOListener.html" title="interface in org.biojava.bio.seq.io">SeqIOListener</a></dt>
<dd>
<div class="block">Notify the listener of a feature property.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SequenceBuilderBase.html#addFeatureProperty(java.lang.Object, java.lang.Object)">addFeatureProperty(Object, Object)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SequenceBuilderBase.html" title="class in org.biojava.bio.seq.io">SequenceBuilderBase</a></dt>
<dd>
<div class="block">Add an annotation-bundle entry to the feature.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SequenceBuilderFilter.html#addFeatureProperty(java.lang.Object, java.lang.Object)">addFeatureProperty(Object, Object)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SequenceBuilderFilter.html" title="class in org.biojava.bio.seq.io">SequenceBuilderFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SwissprotFileFormer.html#addFeatureProperty(java.lang.Object, java.lang.Object)">addFeatureProperty(Object, Object)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SwissprotFileFormer.html" title="class in org.biojava.bio.seq.io">SwissprotFileFormer</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Null implementation</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/DebuggingRichSeqIOListener.html#addFeatureProperty(java.lang.Object, java.lang.Object)">addFeatureProperty(Object, Object)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/DebuggingRichSeqIOListener.html" title="class in org.biojavax.bio.seq.io">DebuggingRichSeqIOListener</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/RichSeqIOAdapter.html#addFeatureProperty(java.lang.Object, java.lang.Object)">addFeatureProperty(Object, Object)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/RichSeqIOAdapter.html" title="class in org.biojavax.bio.seq.io">RichSeqIOAdapter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/SimpleRichSequenceBuilder.html#addFeatureProperty(java.lang.Object, java.lang.Object)">addFeatureProperty(Object, Object)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/SimpleRichSequenceBuilder.html" title="class in org.biojavax.bio.seq.io">SimpleRichSequenceBuilder</a></dt>
<dd>
<div class="block">Notify the listener of a feature property.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichFeatureRelationshipHolder.html#addFeatureRelationship(org.biojavax.bio.seq.RichFeatureRelationship)">addFeatureRelationship(RichFeatureRelationship)</a></span> - Method in interface org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichFeatureRelationshipHolder.html" title="interface in org.biojavax.bio.seq">RichFeatureRelationshipHolder</a></dt>
<dd>
<div class="block">Adds a relationship to this feature holder.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichFeature.html#addFeatureRelationship(org.biojavax.bio.seq.RichFeatureRelationship)">addFeatureRelationship(RichFeatureRelationship)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichFeature.html" title="class in org.biojavax.bio.seq">SimpleRichFeature</a></dt>
<dd>
<div class="block">Adds a relationship to this feature holder.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/StAXFeatureHandler.html#addFeatureToSequence(org.biojava.bio.seq.Sequence)">addFeatureToSequence(Sequence)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/StAXFeatureHandler.html" title="class in org.biojava.bio.seq.io.agave">StAXFeatureHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/IndexedSequenceDB.html#addFile(java.io.File)">addFile(File)</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/IndexedSequenceDB.html" title="class in org.biojava.bio.seq.db">IndexedSequenceDB</a></dt>
<dd>
<div class="block">Add sequences from a file to the sequence database.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/TabIndexStore.html#addFile(java.io.File)">addFile(File)</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/TabIndexStore.html" title="class in org.biojava.bio.seq.db">TabIndexStore</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/GlyphFeatureRenderer.html#addFilterAndGlyph(org.biojava.bio.seq.FeatureFilter, org.biojava.bio.gui.glyph.Glyph)">addFilterAndGlyph(FeatureFilter, Glyph)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/GlyphFeatureRenderer.html" title="class in org.biojava.bio.gui.sequence">GlyphFeatureRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/Unchangeable.html#addForwarder(org.biojava.utils.ChangeForwarder, org.biojava.utils.ChangeType)">addForwarder(ChangeForwarder, ChangeType)</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/Unchangeable.html" title="class in org.biojava.utils">Unchangeable</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/GappedSymbolList.html#addGapInSource(int)">addGapInSource(int)</a></span> - Method in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/GappedSymbolList.html" title="interface in org.biojava.bio.symbol">GappedSymbolList</a></dt>
<dd>
<div class="block">Add a gap at pos within the source coordinates.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleGappedSymbolList.html#addGapInSource(int)">addGapInSource(int)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleGappedSymbolList.html" title="class in org.biojava.bio.symbol">SimpleGappedSymbolList</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/GappedSymbolList.html#addGapInView(int)">addGapInView(int)</a></span> - Method in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/GappedSymbolList.html" title="interface in org.biojava.bio.symbol">GappedSymbolList</a></dt>
<dd>
<div class="block">Add a single gap at pos within the view coordintates.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleGappedSymbolList.html#addGapInView(int)">addGapInView(int)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleGappedSymbolList.html" title="class in org.biojava.bio.symbol">SimpleGappedSymbolList</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/GappedSymbolList.html#addGapsInSource(int, int)">addGapsInSource(int, int)</a></span> - Method in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/GappedSymbolList.html" title="interface in org.biojava.bio.symbol">GappedSymbolList</a></dt>
<dd>
<div class="block">Add length gaps at pos within the source coordinates.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleGappedSymbolList.html#addGapsInSource(int, int)">addGapsInSource(int, int)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleGappedSymbolList.html" title="class in org.biojava.bio.symbol">SimpleGappedSymbolList</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/GappedSymbolList.html#addGapsInView(int, int)">addGapsInView(int, int)</a></span> - Method in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/GappedSymbolList.html" title="interface in org.biojava.bio.symbol">GappedSymbolList</a></dt>
<dd>
<div class="block">Add length gaps at pos within the view coordinates.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleGappedSymbolList.html#addGapsInView(int, int)">addGapsInView(int, int)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleGappedSymbolList.html" title="class in org.biojava.bio.symbol">SimpleGappedSymbolList</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Chain.html#addGroup(org.biojava.bio.structure.Group)">addGroup(Group)</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Chain.html" title="interface in org.biojava.bio.structure">Chain</a></dt>
<dd>
<div class="block">add a group to the list of ATOM record group of this chain.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/ChainImpl.html#addGroup(org.biojava.bio.structure.Group)">addGroup(Group)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/ChainImpl.html" title="class in org.biojava.bio.structure">ChainImpl</a></dt>
<dd>
<div class="block">add a group to the list of ATOM record group of this chain.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/SeqSimilarityStAXHandler.html#addHandler(org.biojava.bio.program.xff.ElementRecognizer, org.biojava.bio.program.ssbind.StAXHandlerFactory)">addHandler(ElementRecognizer, StAXHandlerFactory)</a></span> - Method in class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/SeqSimilarityStAXHandler.html" title="class in org.biojava.bio.program.ssbind">SeqSimilarityStAXHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/StAXFeatureHandler.html#addHandler(org.biojava.bio.seq.io.agave.ElementRecognizer, org.biojava.bio.seq.io.agave.StAXHandlerFactory)">addHandler(ElementRecognizer, StAXHandlerFactory)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/StAXFeatureHandler.html" title="class in org.biojava.bio.seq.io.agave">StAXFeatureHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/StAXPropertyHandler.html#addHandler(org.biojava.bio.seq.io.agave.ElementRecognizer, org.biojava.bio.seq.io.agave.StAXHandlerFactory)">addHandler(ElementRecognizer, StAXHandlerFactory)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/StAXPropertyHandler.html" title="class in org.biojava.bio.seq.io.agave">StAXPropertyHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game/StAXFeatureHandler.html#addHandler(org.biojava.bio.seq.io.game.ElementRecognizer, org.biojava.bio.seq.io.game.StAXHandlerFactory)">addHandler(ElementRecognizer, StAXHandlerFactory)</a></span> - Method in class org.biojava.bio.seq.io.game.<a href="./org/biojava/bio/seq/io/game/StAXFeatureHandler.html" title="class in org.biojava.bio.seq.io.game">StAXFeatureHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game/StAXPropertyHandler.html#addHandler(org.biojava.bio.seq.io.game.ElementRecognizer, org.biojava.bio.seq.io.game.StAXHandlerFactory)">addHandler(ElementRecognizer, StAXHandlerFactory)</a></span> - Method in class org.biojava.bio.seq.io.game.<a href="./org/biojava/bio/seq/io/game/StAXPropertyHandler.html" title="class in org.biojava.bio.seq.io.game">StAXPropertyHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game12/StAXFeatureHandler.html#addHandler(org.biojava.bio.seq.io.game.ElementRecognizer, org.biojava.bio.seq.io.game12.StAXHandlerFactory)">addHandler(ElementRecognizer, StAXHandlerFactory)</a></span> - Method in class org.biojava.bio.seq.io.game12.<a href="./org/biojava/bio/seq/io/game12/StAXFeatureHandler.html" title="class in org.biojava.bio.seq.io.game12">StAXFeatureHandler</a></dt>
<dd>
<div class="block">Adds a feature to the Handler attribute of the StAXFeatureHandler object</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/sax/FastaSearchSAXParser.html#addHitProperty(java.lang.Object, java.lang.Object)">addHitProperty(Object, Object)</a></span> - Method in class org.biojava.bio.program.sax.<a href="./org/biojava/bio/program/sax/FastaSearchSAXParser.html" title="class in org.biojava.bio.program.sax">FastaSearchSAXParser</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/BlastLikeHomologyBuilder.html#addHitProperty(java.lang.Object, java.lang.Object)">addHitProperty(Object, Object)</a></span> - Method in class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/BlastLikeHomologyBuilder.html" title="class in org.biojava.bio.program.ssbind">BlastLikeHomologyBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/BlastLikeSearchBuilder.html#addHitProperty(java.lang.Object, java.lang.Object)">addHitProperty(Object, Object)</a></span> - Method in class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/BlastLikeSearchBuilder.html" title="class in org.biojava.bio.program.ssbind">BlastLikeSearchBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/SimilarityPairBuilder.html#addHitProperty(java.lang.Object, java.lang.Object)">addHitProperty(Object, Object)</a></span> - Method in class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/SimilarityPairBuilder.html" title="class in org.biojava.bio.program.ssbind">SimilarityPairBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/FilteringContentHandler.html#addHitProperty(java.lang.Object, java.lang.Object)">addHitProperty(Object, Object)</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/FilteringContentHandler.html" title="class in org.biojava.bio.search">FilteringContentHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SearchContentAdapter.html#addHitProperty(java.lang.Object, java.lang.Object)">addHitProperty(Object, Object)</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SearchContentAdapter.html" title="class in org.biojava.bio.search">SearchContentAdapter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SearchContentFilter.html#addHitProperty(java.lang.Object, java.lang.Object)">addHitProperty(Object, Object)</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SearchContentFilter.html" title="class in org.biojava.bio.search">SearchContentFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SearchContentHandler.html#addHitProperty(java.lang.Object, java.lang.Object)">addHitProperty(Object, Object)</a></span> - Method in interface org.biojava.bio.search.<a href="./org/biojava/bio/search/SearchContentHandler.html" title="interface in org.biojava.bio.search">SearchContentHandler</a></dt>
<dd>
<div class="block">The <code>addHitProperty</code> method adds a key/value pair
containing some property of a particular hit.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SearchContentHandlerDebugger.html#addHitProperty(java.lang.Object, java.lang.Object)">addHitProperty(Object, Object)</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SearchContentHandlerDebugger.html" title="class in org.biojava.bio.search">SearchContentHandlerDebugger</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/ImageMap.html#addHotSpot(org.biojava.bio.gui.sequence.ImageMap.HotSpot)">addHotSpot(ImageMap.HotSpot)</a></span> - Method in interface org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/ImageMap.html" title="interface in org.biojava.bio.gui.sequence">ImageMap</a></dt>
<dd>
<div class="block"><code>addHotSpot</code> adds a hotspot to the map.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/ImageMap.ClientSide.html#addHotSpot(org.biojava.bio.gui.sequence.ImageMap.HotSpot)">addHotSpot(ImageMap.HotSpot)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/ImageMap.ClientSide.html" title="class in org.biojava.bio.gui.sequence">ImageMap.ClientSide</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/ImageMap.ServerSide.html#addHotSpot(org.biojava.bio.gui.sequence.ImageMap.HotSpot)">addHotSpot(ImageMap.HotSpot)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/ImageMap.ServerSide.html" title="class in org.biojava.bio.gui.sequence">ImageMap.ServerSide</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEClassificationHandler.html#addIdAlias(org.biojava.bio.seq.io.agave.AGAVEIdAlias)">addIdAlias(AGAVEIdAlias)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEClassificationHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEClassificationHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEIdAliasCallbackItf.html#addIdAlias(org.biojava.bio.seq.io.agave.AGAVEIdAlias)">addIdAlias(AGAVEIdAlias)</a></span> - Method in interface org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEIdAliasCallbackItf.html" title="interface in org.biojava.bio.seq.io.agave">AGAVEIdAliasCallbackItf</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/SimpleFeatureRealizer.html#addImplementation(java.lang.Class, java.lang.Class)">addImplementation(Class, Class)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/SimpleFeatureRealizer.html" title="class in org.biojava.bio.seq">SimpleFeatureRealizer</a></dt>
<dd>
<div class="block">Install a new mapping from a class of Feature.Template to
a class of Feature implementations.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/AbstractSVMClassifierModel.html#addItem(java.lang.Object)">addItem(Object)</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/AbstractSVMClassifierModel.html" title="class in org.biojava.stats.svm">AbstractSVMClassifierModel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/AbstractSVMTarget.html#addItem(java.lang.Object)">addItem(Object)</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/AbstractSVMTarget.html" title="class in org.biojava.stats.svm">AbstractSVMTarget</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/SimpleSVMClassifierModel.html#addItem(java.lang.Object)">addItem(Object)</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/SimpleSVMClassifierModel.html" title="class in org.biojava.stats.svm">SimpleSVMClassifierModel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/SimpleSVMTarget.html#addItem(java.lang.Object)">addItem(Object)</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/SimpleSVMTarget.html" title="class in org.biojava.stats.svm">SimpleSVMTarget</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/SVMClassifierModel.html#addItem(java.lang.Object)">addItem(Object)</a></span> - Method in interface org.biojava.stats.svm.<a href="./org/biojava/stats/svm/SVMClassifierModel.html" title="interface in org.biojava.stats.svm">SVMClassifierModel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/SVMTarget.html#addItem(java.lang.Object)">addItem(Object)</a></span> - Method in interface org.biojava.stats.svm.<a href="./org/biojava/stats/svm/SVMTarget.html" title="interface in org.biojava.stats.svm">SVMTarget</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/AbstractSVMClassifierModel.html#addItemAlpha(java.lang.Object, double)">addItemAlpha(Object, double)</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/AbstractSVMClassifierModel.html" title="class in org.biojava.stats.svm">AbstractSVMClassifierModel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/SimpleSVMClassifierModel.html#addItemAlpha(java.lang.Object, double)">addItemAlpha(Object, double)</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/SimpleSVMClassifierModel.html" title="class in org.biojava.stats.svm">SimpleSVMClassifierModel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/SVMClassifierModel.html#addItemAlpha(java.lang.Object, double)">addItemAlpha(Object, double)</a></span> - Method in interface org.biojava.stats.svm.<a href="./org/biojava/stats/svm/SVMClassifierModel.html" title="interface in org.biojava.stats.svm">SVMClassifierModel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/AbstractSVMTarget.html#addItemTarget(java.lang.Object, double)">addItemTarget(Object, double)</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/AbstractSVMTarget.html" title="class in org.biojava.stats.svm">AbstractSVMTarget</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/SimpleSVMTarget.html#addItemTarget(java.lang.Object, double)">addItemTarget(Object, double)</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/SimpleSVMTarget.html" title="class in org.biojava.stats.svm">SimpleSVMTarget</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/SVMTarget.html#addItemTarget(java.lang.Object, double)">addItemTarget(Object, double)</a></span> - Method in interface org.biojava.stats.svm.<a href="./org/biojava/stats/svm/SVMTarget.html" title="interface in org.biojava.stats.svm">SVMTarget</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/indexdb/BioStoreFactory.html#addKey(java.lang.String, int)">addKey(String, int)</a></span> - Method in class org.biojava.bio.program.indexdb.<a href="./org/biojava/bio/program/indexdb/BioStoreFactory.html" title="class in org.biojava.bio.program.indexdb">BioStoreFactory</a></dt>
<dd>
<div class="block"><code>addKey</code> adds a new identifier namespace.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/Index2Model.html#addKeyPath(java.lang.String, java.lang.Object[])">addKeyPath(String, Object[])</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/Index2Model.html" title="class in org.biojava.bio.program.tagvalue">Index2Model</a></dt>
<dd>
<div class="block">
Add a key and a path to that key in the tag-value hierachy.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/LabelledSequenceRenderer.html#addLabelString(java.lang.String)">addLabelString(String)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/LabelledSequenceRenderer.html" title="class in org.biojava.bio.gui.sequence">LabelledSequenceRenderer</a></dt>
<dd>
<div class="block">Add a piece of text to this renderer's label</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/automata/Nfa.html#addLambdaTransition(org.biojava.utils.automata.FiniteAutomaton.Node, org.biojava.utils.automata.FiniteAutomaton.Node)">addLambdaTransition(FiniteAutomaton.Node, FiniteAutomaton.Node)</a></span> - Method in class org.biojava.utils.automata.<a href="./org/biojava/utils/automata/Nfa.html" title="class in org.biojava.utils.automata">Nfa</a></dt>
<dd>
<div class="block">Add a silent persistent transition to instance.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/automata/NfaBuilder.html#addLambdaTransition(org.biojava.utils.automata.FiniteAutomaton.Node, org.biojava.utils.automata.FiniteAutomaton.Node)">addLambdaTransition(FiniteAutomaton.Node, FiniteAutomaton.Node)</a></span> - Method in interface org.biojava.utils.automata.<a href="./org/biojava/utils/automata/NfaBuilder.html" title="interface in org.biojava.utils.automata">NfaBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/automata/NfaSubModel.html#addLambdaTransition(org.biojava.utils.automata.FiniteAutomaton.Node, org.biojava.utils.automata.FiniteAutomaton.Node)">addLambdaTransition(FiniteAutomaton.Node, FiniteAutomaton.Node)</a></span> - Method in class org.biojava.utils.automata.<a href="./org/biojava/utils/automata/NfaSubModel.html" title="class in org.biojava.utils.automata">NfaSubModel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ChangeHub.html#addListener(java.lang.Object, org.biojava.utils.ChangeListener, org.biojava.utils.ChangeType)">addListener(Object, ChangeListener, ChangeType)</a></span> - Method in interface org.biojava.utils.<a href="./org/biojava/utils/ChangeHub.html" title="interface in org.biojava.utils">ChangeHub</a></dt>
<dd>
<div class="block">add a ChangeListener associated with given key.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/IndexedChangeHub.html#addListener(java.lang.Object, org.biojava.utils.ChangeListener, org.biojava.utils.ChangeType)">addListener(Object, ChangeListener, ChangeType)</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/IndexedChangeHub.html" title="class in org.biojava.utils">IndexedChangeHub</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEMapLocationPropHandler.html#addMapPosition(org.biojava.bio.seq.io.agave.AGAVEMapPosition)">addMapPosition(AGAVEMapPosition)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEMapLocationPropHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEMapLocationPropHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/dasalignment/Alignment.html#addMatrix(org.biojava.bio.Annotation)">addMatrix(Annotation)</a></span> - Method in class org.biojava.bio.program.das.dasalignment.<a href="./org/biojava/bio/program/das/dasalignment/Alignment.html" title="class in org.biojava.bio.program.das.dasalignment">Alignment</a></dt>
<dd>
<div class="block">add Annotation of DAS alignment "matrix" type.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/MMcifParser.html#addMMcifConsumer(org.biojava.bio.structure.io.mmcif.MMcifConsumer)">addMMcifConsumer(MMcifConsumer)</a></span> - Method in interface org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/MMcifParser.html" title="interface in org.biojava.bio.structure.io.mmcif">MMcifParser</a></dt>
<dd>
<div class="block">Add a MMcifConsumer that listens to even being triggered by the parser and processes the data into a backend provided by the Consumer.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/SimpleMMcifParser.html#addMMcifConsumer(org.biojava.bio.structure.io.mmcif.MMcifConsumer)">addMMcifConsumer(MMcifConsumer)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/SimpleMMcifParser.html" title="class in org.biojava.bio.structure.io.mmcif">SimpleMMcifParser</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Structure.html#addModel(java.util.List)">addModel(List<Chain>)</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Structure.html" title="interface in org.biojava.bio.structure">Structure</a></dt>
<dd>
<div class="block">add a new model.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/StructureImpl.html#addModel(java.util.List)">addModel(List<Chain>)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/StructureImpl.html" title="class in org.biojava.bio.structure">StructureImpl</a></dt>
<dd>
<div class="block">add a new model.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/biosql/TaxonSQL.html#addName(java.sql.Connection, org.biojava.bio.taxa.Taxon, java.lang.String, java.lang.String)">addName(Connection, Taxon, String, String)</a></span> - Static method in class org.biojava.bio.seq.db.biosql.<a href="./org/biojava/bio/seq/db/biosql/TaxonSQL.html" title="class in org.biojava.bio.seq.db.biosql">TaxonSQL</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Adds a new name of the given <code>nameClass</code> to the taxon.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/taxa/NCBITaxon.html#addName(java.lang.String, java.lang.String)">addName(String, String)</a></span> - Method in interface org.biojavax.bio.taxa.<a href="./org/biojavax/bio/taxa/NCBITaxon.html" title="interface in org.biojavax.bio.taxa">NCBITaxon</a></dt>
<dd>
<div class="block">Adds the name to this taxon in the given name class.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/taxa/SimpleNCBITaxon.html#addName(java.lang.String, java.lang.String)">addName(String, String)</a></span> - Method in class org.biojavax.bio.taxa.<a href="./org/biojavax/bio/taxa/SimpleNCBITaxon.html" title="class in org.biojavax.bio.taxa">SimpleNCBITaxon</a></dt>
<dd>
<div class="block">Adds the name to this taxon in the given name class.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/DiagonalAddKernel.html#addNeg(java.lang.Object)">addNeg(Object)</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/DiagonalAddKernel.html" title="class in org.biojava.stats.svm">DiagonalAddKernel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/automata/FiniteAutomaton.html#addNode(boolean)">addNode(boolean)</a></span> - Method in class org.biojava.utils.automata.<a href="./org/biojava/utils/automata/FiniteAutomaton.html" title="class in org.biojava.utils.automata">FiniteAutomaton</a></dt>
<dd>
<div class="block">Add a node to the FA.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/automata/NfaBuilder.html#addNode(boolean)">addNode(boolean)</a></span> - Method in interface org.biojava.utils.automata.<a href="./org/biojava/utils/automata/NfaBuilder.html" title="interface in org.biojava.utils.automata">NfaBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/automata/NfaSubModel.html#addNode(boolean)">addNode(boolean)</a></span> - Method in class org.biojava.utils.automata.<a href="./org/biojava/utils/automata/NfaSubModel.html" title="class in org.biojava.utils.automata">NfaSubModel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/EmptyRichAnnotation.html#addNote(org.biojavax.Note)">addNote(Note)</a></span> - Method in class org.biojavax.<a href="./org/biojavax/EmptyRichAnnotation.html" title="class in org.biojavax">EmptyRichAnnotation</a></dt>
<dd>
<div class="block">Adds a note to this annotation.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/RichAnnotation.html#addNote(org.biojavax.Note)">addNote(Note)</a></span> - Method in interface org.biojavax.<a href="./org/biojavax/RichAnnotation.html" title="interface in org.biojavax">RichAnnotation</a></dt>
<dd>
<div class="block">Adds a note to this annotation.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleRichAnnotation.html#addNote(org.biojavax.Note)">addNote(Note)</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleRichAnnotation.html" title="class in org.biojavax">SimpleRichAnnotation</a></dt>
<dd>
<div class="block">Adds a note to this annotation.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/dasalignment/Alignment.html#addObject(org.biojava.bio.Annotation)">addObject(Annotation)</a></span> - Method in class org.biojava.bio.program.das.dasalignment.<a href="./org/biojava/bio/program/das/dasalignment/Alignment.html" title="class in org.biojava.bio.program.das.dasalignment">Alignment</a></dt>
<dd>
<div class="block">add Annotation of DAS alignment "object" type.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/obo/OboFileParser.html#addOboFileEventListener(org.biojava.ontology.obo.OboFileEventListener)">addOboFileEventListener(OboFileEventListener)</a></span> - Method in class org.biojava.ontology.obo.<a href="./org/biojava/ontology/obo/OboFileParser.html" title="class in org.biojava.ontology.obo">OboFileParser</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/biosql/BioSQLSequenceDB.html#addOntology(org.biojava.ontology.Ontology)">addOntology(Ontology)</a></span> - Method in class org.biojava.bio.seq.db.biosql.<a href="./org/biojava/bio/seq/db/biosql/BioSQLSequenceDB.html" title="class in org.biojava.bio.seq.db.biosql">BioSQLSequenceDB</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ga/impl/AbstractPopulation.html#addOrganism(org.biojavax.ga.Organism)">addOrganism(Organism)</a></span> - Method in class org.biojavax.ga.impl.<a href="./org/biojavax/ga/impl/AbstractPopulation.html" title="class in org.biojavax.ga.impl">AbstractPopulation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/Population.html#addOrganism(org.biojavax.ga.Organism)">addOrganism(Organism)</a></span> - Method in interface org.biojavax.ga.<a href="./org/biojavax/ga/Population.html" title="interface in org.biojavax.ga">Population</a></dt>
<dd>
<div class="block">Adds an Organism to the Population</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ga/impl/AbstractPopulation.html#addOrganismImpl(org.biojavax.ga.Organism)">addOrganismImpl(Organism)</a></span> - Method in class org.biojavax.ga.impl.<a href="./org/biojavax/ga/impl/AbstractPopulation.html" title="class in org.biojavax.ga.impl">AbstractPopulation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/impl/SimplePopulation.html#addOrganismImpl(org.biojavax.ga.Organism)">addOrganismImpl(Organism)</a></span> - Method in class org.biojavax.ga.impl.<a href="./org/biojavax/ga/impl/SimplePopulation.html" title="class in org.biojavax.ga.impl">SimplePopulation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/impl/AbstractPopulation.html#addOrganisms(org.biojavax.ga.Organism[])">addOrganisms(Organism[])</a></span> - Method in class org.biojavax.ga.impl.<a href="./org/biojavax/ga/impl/AbstractPopulation.html" title="class in org.biojavax.ga.impl">AbstractPopulation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/impl/AbstractPopulation.html#addOrganisms(java.util.Set)">addOrganisms(Set)</a></span> - Method in class org.biojavax.ga.impl.<a href="./org/biojavax/ga/impl/AbstractPopulation.html" title="class in org.biojavax.ga.impl">AbstractPopulation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/impl/AbstractPopulation.html#addOrganisms(org.biojavax.ga.Population)">addOrganisms(Population)</a></span> - Method in class org.biojavax.ga.impl.<a href="./org/biojavax/ga/impl/AbstractPopulation.html" title="class in org.biojavax.ga.impl">AbstractPopulation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/Population.html#addOrganisms(org.biojavax.ga.Organism[])">addOrganisms(Organism[])</a></span> - Method in interface org.biojavax.ga.<a href="./org/biojavax/ga/Population.html" title="interface in org.biojavax.ga">Population</a></dt>
<dd>
<div class="block">Adds several organisms to the population</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ga/Population.html#addOrganisms(java.util.Set)">addOrganisms(Set)</a></span> - Method in interface org.biojavax.ga.<a href="./org/biojavax/ga/Population.html" title="interface in org.biojavax.ga">Population</a></dt>
<dd>
<div class="block">Adds several organisms to the population</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ga/Population.html#addOrganisms(org.biojavax.ga.Population)">addOrganisms(Population)</a></span> - Method in interface org.biojavax.ga.<a href="./org/biojavax/ga/Population.html" title="interface in org.biojavax.ga">Population</a></dt>
<dd>
<div class="block">Adds the residents of one population to this one</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/OrthologueSet.html#addOrthologue(org.biojava.bio.program.homologene.Orthologue)">addOrthologue(Orthologue)</a></span> - Method in interface org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/OrthologueSet.html" title="interface in org.biojava.bio.program.homologene">OrthologueSet</a></dt>
<dd>
<div class="block">Add an orthologue to the set.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/SimpleOrthologueSet.html#addOrthologue(org.biojava.bio.program.homologene.Orthologue)">addOrthologue(Orthologue)</a></span> - Method in class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/SimpleOrthologueSet.html" title="class in org.biojava.bio.program.homologene">SimpleOrthologueSet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/HomologeneBuilder.html#addOrthologueProperty(java.lang.String, java.lang.String)">addOrthologueProperty(String, String)</a></span> - Method in interface org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/HomologeneBuilder.html" title="interface in org.biojava.bio.program.homologene">HomologeneBuilder</a></dt>
<dd>
<div class="block">add a property to the current Orthologue</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/SimpleHomologeneBuilder.html#addOrthologueProperty(java.lang.String, java.lang.String)">addOrthologueProperty(String, String)</a></span> - Method in class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/SimpleHomologeneBuilder.html" title="class in org.biojava.bio.program.homologene">SimpleHomologeneBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/OrthoPairSet.html#addOrthoPair(org.biojava.bio.program.homologene.OrthoPair)">addOrthoPair(OrthoPair)</a></span> - Method in interface org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/OrthoPairSet.html" title="interface in org.biojava.bio.program.homologene">OrthoPairSet</a></dt>
<dd>
<div class="block">adds a specified OrthoPair relationship
to this group.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/SimpleOrthoPairSet.html#addOrthoPair(org.biojava.bio.program.homologene.OrthoPair)">addOrthoPair(OrthoPair)</a></span> - Method in class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/SimpleOrthoPairSet.html" title="class in org.biojava.bio.program.homologene">SimpleOrthoPairSet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/HomologeneBuilder.html#addOrthoPairProperty(java.lang.String, java.lang.String)">addOrthoPairProperty(String, String)</a></span> - Method in interface org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/HomologeneBuilder.html" title="interface in org.biojava.bio.program.homologene">HomologeneBuilder</a></dt>
<dd>
<div class="block">add a property to the current OrthoPair</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/SimpleHomologeneBuilder.html#addOrthoPairProperty(java.lang.String, java.lang.String)">addOrthoPairProperty(String, String)</a></span> - Method in class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/SimpleHomologeneBuilder.html" title="class in org.biojava.bio.program.homologene">SimpleHomologeneBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/phred/PhredFormat.html#addParseErrorListener(org.biojava.utils.ParseErrorListener)">addParseErrorListener(ParseErrorListener)</a></span> - Method in class org.biojava.bio.program.phred.<a href="./org/biojava/bio/program/phred/PhredFormat.html" title="class in org.biojava.bio.program.phred">PhredFormat</a></dt>
<dd>
<div class="block">Adds a parse error listener to the list of listeners if it isn't already
included.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/EmblLikeFormat.html#addParseErrorListener(org.biojava.utils.ParseErrorListener)">addParseErrorListener(ParseErrorListener)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/EmblLikeFormat.html" title="class in org.biojava.bio.seq.io">EmblLikeFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Adds a parse error listener to the list of listeners if it isn't already
included.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/EmblProcessor.html#addParseErrorListener(org.biojava.utils.ParseErrorListener)">addParseErrorListener(ParseErrorListener)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/EmblProcessor.html" title="class in org.biojava.bio.seq.io">EmblProcessor</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Adds a parse error listener to the list of listeners if it isn't already
included.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/FastaFormat.html#addParseErrorListener(org.biojava.utils.ParseErrorListener)">addParseErrorListener(ParseErrorListener)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/FastaFormat.html" title="class in org.biojava.bio.seq.io">FastaFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Adds a parse error listener to the list of listeners if it isn't already
included.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/GenbankFormat.html#addParseErrorListener(org.biojava.utils.ParseErrorListener)">addParseErrorListener(ParseErrorListener)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/GenbankFormat.html" title="class in org.biojava.bio.seq.io">GenbankFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Adds a parse error listener to the list of listeners if it isn't already
included.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/GenbankProcessor.html#addParseErrorListener(org.biojava.utils.ParseErrorListener)">addParseErrorListener(ParseErrorListener)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/GenbankProcessor.html" title="class in org.biojava.bio.seq.io">GenbankProcessor</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Adds a parse error listener to the list of listeners if it isn't already
included.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SwissprotProcessor.html#addParseErrorListener(org.biojava.utils.ParseErrorListener)">addParseErrorListener(ParseErrorListener)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SwissprotProcessor.html" title="class in org.biojava.bio.seq.io">SwissprotProcessor</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Adds a parse error listener to the list of listeners if it isn't already
included.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/ParseErrorSource.html#addParseErrorListener(org.biojava.utils.ParseErrorListener)">addParseErrorListener(ParseErrorListener)</a></span> - Method in interface org.biojava.utils.<a href="./org/biojava/utils/ParseErrorSource.html" title="interface in org.biojava.utils">ParseErrorSource</a></dt>
<dd>
<div class="block">Adds a parse error listener to the list of listeners.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/automata/PatternBlitz.html#addPattern(java.lang.String)">addPattern(String)</a></span> - Method in class org.biojava.utils.automata.<a href="./org/biojava/utils/automata/PatternBlitz.html" title="class in org.biojava.utils.automata">PatternBlitz</a></dt>
<dd>
<div class="block">add the specified regex to the patterns
used for searching.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/regex/Search.html#addPattern(java.lang.String, boolean)">addPattern(String, boolean)</a></span> - Method in class org.biojava.utils.regex.<a href="./org/biojava/utils/regex/Search.html" title="class in org.biojava.utils.regex">Search</a></dt>
<dd>
<div class="block">add a search pattern to the searches to be conducted
by this object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/regex/Search.html#addPattern(java.lang.String, java.lang.String, boolean)">addPattern(String, String, boolean)</a></span> - Method in class org.biojava.utils.regex.<a href="./org/biojava/utils/regex/Search.html" title="class in org.biojava.utils.regex">Search</a></dt>
<dd>
<div class="block">add a search pattern to the searches to be conducted
by this object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/server/FlatFileInstallation.html#addPDBFilter(org.biojava.bio.structure.server.PDBFilter)">addPDBFilter(PDBFilter)</a></span> - Method in class org.biojava.bio.structure.server.<a href="./org/biojava/bio/structure/server/FlatFileInstallation.html" title="class in org.biojava.bio.structure.server">FlatFileInstallation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/server/MMCIFFileInstallation.html#addPDBFilter(org.biojava.bio.structure.server.PDBFilter)">addPDBFilter(PDBFilter)</a></span> - Method in class org.biojava.bio.structure.server.<a href="./org/biojava/bio/structure/server/MMCIFFileInstallation.html" title="class in org.biojava.bio.structure.server">MMCIFFileInstallation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/server/PDBInstallation.html#addPDBFilter(org.biojava.bio.structure.server.PDBFilter)">addPDBFilter(PDBFilter)</a></span> - Method in interface org.biojava.bio.structure.server.<a href="./org/biojava/bio/structure/server/PDBInstallation.html" title="interface in org.biojava.bio.structure.server">PDBInstallation</a></dt>
<dd>
<div class="block">add a filter for PDB files.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/DiagonalAddKernel.html#addPos(java.lang.Object)">addPos(Object)</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/DiagonalAddKernel.html" title="class in org.biojava.stats.svm">DiagonalAddKernel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEMapLocation.html#addPosition(org.biojava.bio.seq.io.agave.AGAVEMapPosition)">addPosition(AGAVEMapPosition)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEMapLocation.html" title="class in org.biojava.bio.seq.io.agave">AGAVEMapLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVERelatedAnnot.html#addProp(org.biojava.bio.seq.io.agave.AGAVEProperty)">addProp(AGAVEProperty)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVERelatedAnnot.html" title="class in org.biojava.bio.seq.io.agave">AGAVERelatedAnnot</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEXref.html#addProp(org.biojava.bio.seq.io.agave.AGAVEProperty)">addProp(AGAVEProperty)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEXref.html" title="class in org.biojava.bio.seq.io.agave">AGAVEXref</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/AnnotationType.Abstract.html#addProperty(org.biojava.bio.Annotation, java.lang.Object, java.lang.Object)">addProperty(Annotation, Object, Object)</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/AnnotationType.Abstract.html" title="class in org.biojava.bio">AnnotationType.Abstract</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/AnnotationType.html#addProperty(org.biojava.bio.Annotation, java.lang.Object, java.lang.Object)">addProperty(Annotation, Object, Object)</a></span> - Method in interface org.biojava.bio.<a href="./org/biojava/bio/AnnotationType.html" title="interface in org.biojava.bio">AnnotationType</a></dt>
<dd>
<div class="block">Add a value to the specified property slot.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVECompResultHandler.html#addProperty(org.biojava.bio.seq.io.agave.AGAVEProperty)">addProperty(AGAVEProperty)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVECompResultHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVECompResultHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEDbIdPropCallbackItf.html#addProperty(org.biojava.bio.seq.io.agave.AGAVEProperty)">addProperty(AGAVEProperty)</a></span> - Method in interface org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEDbIdPropCallbackItf.html" title="interface in org.biojava.bio.seq.io.agave">AGAVEDbIdPropCallbackItf</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEGeneHandler.html#addProperty(org.biojava.bio.seq.io.agave.AGAVEProperty)">addProperty(AGAVEProperty)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEGeneHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEGeneHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVERelatedAnnotPropHandler.html#addProperty(org.biojava.bio.seq.io.agave.AGAVEProperty)">addProperty(AGAVEProperty)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVERelatedAnnotPropHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVERelatedAnnotPropHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVESeqFeatureHandler.html#addProperty(org.biojava.bio.seq.io.agave.AGAVEProperty)">addProperty(AGAVEProperty)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVESeqFeatureHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVESeqFeatureHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEXrefPropHandler.html#addProperty(org.biojava.bio.seq.io.agave.AGAVEProperty)">addProperty(AGAVEProperty)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEXrefPropHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEXrefPropHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SequenceBuilderBase.html#addProperty(org.biojava.bio.Annotation, java.lang.Object, java.lang.Object)">addProperty(Annotation, Object, Object)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SequenceBuilderBase.html" title="class in org.biojava.bio.seq.io">SequenceBuilderBase</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePanel.Border.html#addPropertyChangeListener(java.beans.PropertyChangeListener)">addPropertyChangeListener(PropertyChangeListener)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePanel.Border.html" title="class in org.biojava.bio.gui.sequence">SequencePanel.Border</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePoster.Border.html#addPropertyChangeListener(java.beans.PropertyChangeListener)">addPropertyChangeListener(PropertyChangeListener)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePoster.Border.html" title="class in org.biojava.bio.gui.sequence">SequencePoster.Border</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/StackedLogoPainter.html#addPropertyChangeListener(java.beans.PropertyChangeListener)">addPropertyChangeListener(PropertyChangeListener)</a></span> - Method in class org.biojava.bio.gui.<a href="./org/biojava/bio/gui/StackedLogoPainter.html" title="class in org.biojava.bio.gui">StackedLogoPainter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/StackedLogoPainter.html#addPropertyChangeListener(java.lang.String, java.beans.PropertyChangeListener)">addPropertyChangeListener(String, PropertyChangeListener)</a></span> - Method in class org.biojava.bio.gui.<a href="./org/biojava/bio/gui/StackedLogoPainter.html" title="class in org.biojava.bio.gui">StackedLogoPainter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/TextLogoPainter.html#addPropertyChangeListener(java.beans.PropertyChangeListener)">addPropertyChangeListener(PropertyChangeListener)</a></span> - Method in class org.biojava.bio.gui.<a href="./org/biojava/bio/gui/TextLogoPainter.html" title="class in org.biojava.bio.gui">TextLogoPainter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/TextLogoPainter.html#addPropertyChangeListener(java.lang.String, java.beans.PropertyChangeListener)">addPropertyChangeListener(String, PropertyChangeListener)</a></span> - Method in class org.biojava.bio.gui.<a href="./org/biojava/bio/gui/TextLogoPainter.html" title="class in org.biojava.bio.gui">TextLogoPainter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichFeature.html#addRankedCrossRef(org.biojavax.RankedCrossRef)">addRankedCrossRef(RankedCrossRef)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichFeature.html" title="class in org.biojavax.bio.seq">SimpleRichFeature</a></dt>
<dd>
<div class="block">Adds a ranked cross reference to the existing set.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/SimpleBioEntry.html#addRankedCrossRef(org.biojavax.RankedCrossRef)">addRankedCrossRef(RankedCrossRef)</a></span> - Method in class org.biojavax.bio.<a href="./org/biojavax/bio/SimpleBioEntry.html" title="class in org.biojavax.bio">SimpleBioEntry</a></dt>
<dd>
<div class="block">Adds a ranked cross reference to the existing set.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ontology/SimpleComparableTerm.html#addRankedCrossRef(org.biojavax.RankedCrossRef)">addRankedCrossRef(RankedCrossRef)</a></span> - Method in class org.biojavax.ontology.<a href="./org/biojavax/ontology/SimpleComparableTerm.html" title="class in org.biojavax.ontology">SimpleComparableTerm</a></dt>
<dd>
<div class="block">Adds a ranked cross reference to the existing set.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/RankedCrossRefable.html#addRankedCrossRef(org.biojavax.RankedCrossRef)">addRankedCrossRef(RankedCrossRef)</a></span> - Method in interface org.biojavax.<a href="./org/biojavax/RankedCrossRefable.html" title="interface in org.biojavax">RankedCrossRefable</a></dt>
<dd>
<div class="block">Adds a ranked cross reference to the existing set.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/BioEntry.html#addRankedDocRef(org.biojavax.RankedDocRef)">addRankedDocRef(RankedDocRef)</a></span> - Method in interface org.biojavax.bio.<a href="./org/biojavax/bio/BioEntry.html" title="interface in org.biojavax.bio">BioEntry</a></dt>
<dd>
<div class="block">Adds a ranked docref instance to this bioentry.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/SimpleBioEntry.html#addRankedDocRef(org.biojavax.RankedDocRef)">addRankedDocRef(RankedDocRef)</a></span> - Method in class org.biojavax.bio.<a href="./org/biojavax/bio/SimpleBioEntry.html" title="class in org.biojavax.bio">SimpleBioEntry</a></dt>
<dd>
<div class="block">Adds a ranked docref instance to this bioentry.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVECompResultHandler.html#addRelatedAnnot(org.biojava.bio.seq.io.agave.AGAVERelatedAnnot)">addRelatedAnnot(AGAVERelatedAnnot)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVECompResultHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVECompResultHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEGeneHandler.html#addRelatedAnnot(org.biojava.bio.seq.io.agave.AGAVERelatedAnnot)">addRelatedAnnot(AGAVERelatedAnnot)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEGeneHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEGeneHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVESeqFeatureHandler.html#addRelatedAnnot(org.biojava.bio.seq.io.agave.AGAVERelatedAnnot)">addRelatedAnnot(AGAVERelatedAnnot)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVESeqFeatureHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVESeqFeatureHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/BioEntry.html#addRelationship(org.biojavax.bio.BioEntryRelationship)">addRelationship(BioEntryRelationship)</a></span> - Method in interface org.biojavax.bio.<a href="./org/biojavax/bio/BioEntry.html" title="interface in org.biojavax.bio">BioEntry</a></dt>
<dd>
<div class="block">Adds a relation instance to this bioentry.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/SimpleBioEntry.html#addRelationship(org.biojavax.bio.BioEntryRelationship)">addRelationship(BioEntryRelationship)</a></span> - Method in class org.biojavax.bio.<a href="./org/biojavax/bio/SimpleBioEntry.html" title="class in org.biojavax.bio">SimpleBioEntry</a></dt>
<dd>
<div class="block">Adds a relation instance to this bioentry.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/CircularMLR.html#addRenderer(org.biojava.bio.gui.sequence.CircularRenderer)">addRenderer(CircularRenderer)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/CircularMLR.html" title="class in org.biojava.bio.gui.sequence">CircularMLR</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/MultiLineRenderer.html#addRenderer(org.biojava.bio.gui.sequence.SequenceRenderer)">addRenderer(SequenceRenderer)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/MultiLineRenderer.html" title="class in org.biojava.bio.gui.sequence">MultiLineRenderer</a></dt>
<dd>
<div class="block"><code>addRenderer</code> adds a renderer as a new track.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PairwiseOverlayRenderer.html#addRenderer(org.biojava.bio.gui.sequence.PairwiseSequenceRenderer)">addRenderer(PairwiseSequenceRenderer)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PairwiseOverlayRenderer.html" title="class in org.biojava.bio.gui.sequence">PairwiseOverlayRenderer</a></dt>
<dd>
<div class="block"><code>addRenderer</code> adds a renderer.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/StackedFeatureRenderer.html#addRenderer(org.biojava.bio.gui.sequence.FeatureRenderer)">addRenderer(FeatureRenderer)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/StackedFeatureRenderer.html" title="class in org.biojava.bio.gui.sequence">StackedFeatureRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureTypes.html#addRepository(org.biojava.bio.seq.FeatureTypes.Repository)">addRepository(FeatureTypes.Repository)</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureTypes.html" title="class in org.biojava.bio.seq">FeatureTypes</a></dt>
<dd>
<div class="block">Add a repository to FeatureTypes.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/SimpleThreadPool.html#addRequest(java.lang.Runnable)">addRequest(Runnable)</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/SimpleThreadPool.html" title="class in org.biojava.utils">SimpleThreadPool</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ThreadPool.html#addRequest(java.lang.Runnable)">addRequest(Runnable)</a></span> - Method in interface org.biojava.utils.<a href="./org/biojava/utils/ThreadPool.html" title="interface in org.biojava.utils">ThreadPool</a></dt>
<dd>
<div class="block"><code>addRequest</code> requests that a <code>Runnable</code>
be scheduled to be run by one of the threads in the pool.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/AbstractRichSequenceDB.html#addRichSequence(org.biojavax.bio.seq.RichSequence)">addRichSequence(RichSequence)</a></span> - Method in class org.biojavax.bio.db.<a href="./org/biojavax/bio/db/AbstractRichSequenceDB.html" title="class in org.biojavax.bio.db">AbstractRichSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLRichSequenceDB.html#addRichSequence(org.biojavax.bio.seq.RichSequence)">addRichSequence(RichSequence)</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLRichSequenceDB.html" title="class in org.biojavax.bio.db.biosql">BioSQLRichSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/HashRichSequenceDB.html#addRichSequence(org.biojavax.bio.seq.RichSequence)">addRichSequence(RichSequence)</a></span> - Method in class org.biojavax.bio.db.<a href="./org/biojavax/bio/db/HashRichSequenceDB.html" title="class in org.biojavax.bio.db">HashRichSequenceDB</a></dt>
<dd>
<div class="block">Add a sequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/HashRichSequenceDB.html#addRichSequence(java.lang.String, org.biojavax.bio.seq.RichSequence)">addRichSequence(String, RichSequence)</a></span> - Method in class org.biojavax.bio.db.<a href="./org/biojavax/bio/db/HashRichSequenceDB.html" title="class in org.biojavax.bio.db">HashRichSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/RichSequenceDBLite.html#addRichSequence(org.biojavax.bio.seq.RichSequence)">addRichSequence(RichSequence)</a></span> - Method in interface org.biojavax.bio.db.<a href="./org/biojavax/bio/db/RichSequenceDBLite.html" title="interface in org.biojavax.bio.db">RichSequenceDBLite</a></dt>
<dd>
<div class="block">Adds a sequence to the database.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/dasalignment/Alignment.html#addScore(org.biojava.bio.Annotation)">addScore(Annotation)</a></span> - Method in class org.biojava.bio.program.das.dasalignment.<a href="./org/biojava/bio/program/das/dasalignment/Alignment.html" title="class in org.biojava.bio.program.das.dasalignment">Alignment</a></dt>
<dd>
<div class="block">adds a "Score" Annotation.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/sax/FastaSearchSAXParser.html#addSearchProperty(java.lang.Object, java.lang.Object)">addSearchProperty(Object, Object)</a></span> - Method in class org.biojava.bio.program.sax.<a href="./org/biojava/bio/program/sax/FastaSearchSAXParser.html" title="class in org.biojava.bio.program.sax">FastaSearchSAXParser</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/BlastLikeHomologyBuilder.html#addSearchProperty(java.lang.Object, java.lang.Object)">addSearchProperty(Object, Object)</a></span> - Method in class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/BlastLikeHomologyBuilder.html" title="class in org.biojava.bio.program.ssbind">BlastLikeHomologyBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/BlastLikeSearchBuilder.html#addSearchProperty(java.lang.Object, java.lang.Object)">addSearchProperty(Object, Object)</a></span> - Method in class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/BlastLikeSearchBuilder.html" title="class in org.biojava.bio.program.ssbind">BlastLikeSearchBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/SimilarityPairBuilder.html#addSearchProperty(java.lang.Object, java.lang.Object)">addSearchProperty(Object, Object)</a></span> - Method in class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/SimilarityPairBuilder.html" title="class in org.biojava.bio.program.ssbind">SimilarityPairBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/FilteringContentHandler.html#addSearchProperty(java.lang.Object, java.lang.Object)">addSearchProperty(Object, Object)</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/FilteringContentHandler.html" title="class in org.biojava.bio.search">FilteringContentHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SearchContentAdapter.html#addSearchProperty(java.lang.Object, java.lang.Object)">addSearchProperty(Object, Object)</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SearchContentAdapter.html" title="class in org.biojava.bio.search">SearchContentAdapter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SearchContentFilter.html#addSearchProperty(java.lang.Object, java.lang.Object)">addSearchProperty(Object, Object)</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SearchContentFilter.html" title="class in org.biojava.bio.search">SearchContentFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SearchContentHandler.html#addSearchProperty(java.lang.Object, java.lang.Object)">addSearchProperty(Object, Object)</a></span> - Method in interface org.biojava.bio.search.<a href="./org/biojava/bio/search/SearchContentHandler.html" title="interface in org.biojava.bio.search">SearchContentHandler</a></dt>
<dd>
<div class="block">The <code>addSearchProperty</code> method adds a key/value pair
containing some property of the overall search result.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SearchContentHandlerDebugger.html#addSearchProperty(java.lang.Object, java.lang.Object)">addSearchProperty(Object, Object)</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SearchContentHandlerDebugger.html" title="class in org.biojava.bio.search">SearchContentHandlerDebugger</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/Indexer.html#addSecondaryKey(java.lang.String)">addSecondaryKey(String)</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/Indexer.html" title="class in org.biojava.bio.program.tagvalue">Indexer</a></dt>
<dd>
<div class="block">
Add a secondary key.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/ARAlignment.html#addSequence(org.biojava.bio.alignment.AlignmentElement)">addSequence(AlignmentElement)</a></span> - Method in interface org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/ARAlignment.html" title="interface in org.biojava.bio.alignment">ARAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/FlexibleAlignment.html#addSequence(org.biojava.bio.alignment.AlignmentElement)">addSequence(AlignmentElement)</a></span> - Method in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/FlexibleAlignment.html" title="class in org.biojava.bio.alignment">FlexibleAlignment</a></dt>
<dd>
<div class="block">add a new a alignment usings a location to the reference sequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/DASSequenceDB.html#addSequence(org.biojava.bio.seq.Sequence)">addSequence(Sequence)</a></span> - Method in class org.biojava.bio.program.das.<a href="./org/biojava/bio/program/das/DASSequenceDB.html" title="class in org.biojava.bio.program.das">DASSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/AbstractSequenceDB.html#addSequence(org.biojava.bio.seq.Sequence)">addSequence(Sequence)</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/AbstractSequenceDB.html" title="class in org.biojava.bio.seq.db">AbstractSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/biofetch/BioFetchSequenceDB.html#addSequence(org.biojava.bio.seq.Sequence)">addSequence(Sequence)</a></span> - Method in class org.biojava.bio.seq.db.biofetch.<a href="./org/biojava/bio/seq/db/biofetch/BioFetchSequenceDB.html" title="class in org.biojava.bio.seq.db.biofetch">BioFetchSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/biosql/BioSQLSequenceDB.html#addSequence(org.biojava.bio.seq.Sequence)">addSequence(Sequence)</a></span> - Method in class org.biojava.bio.seq.db.biosql.<a href="./org/biojava/bio/seq/db/biosql/BioSQLSequenceDB.html" title="class in org.biojava.bio.seq.db.biosql">BioSQLSequenceDB</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/DummySequenceDB.html#addSequence(org.biojava.bio.seq.Sequence)">addSequence(Sequence)</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/DummySequenceDB.html" title="class in org.biojava.bio.seq.db">DummySequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/flat/FlatSequenceDB.html#addSequence(org.biojava.bio.seq.Sequence)">addSequence(Sequence)</a></span> - Method in class org.biojava.bio.seq.db.flat.<a href="./org/biojava/bio/seq/db/flat/FlatSequenceDB.html" title="class in org.biojava.bio.seq.db.flat">FlatSequenceDB</a></dt>
<dd>
<div class="block"><code>addSequence</code> always throws a
<code>ChangeVetoException</code> as this implementation is
immutable.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/HashSequenceDB.html#addSequence(java.lang.String, org.biojava.bio.seq.Sequence)">addSequence(String, Sequence)</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/HashSequenceDB.html" title="class in org.biojava.bio.seq.db">HashSequenceDB</a></dt>
<dd>
<div class="block">Add a sequence under a particular id.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/HashSequenceDB.html#addSequence(org.biojava.bio.seq.Sequence)">addSequence(Sequence)</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/HashSequenceDB.html" title="class in org.biojava.bio.seq.db">HashSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/SequenceDBLite.html#addSequence(org.biojava.bio.seq.Sequence)">addSequence(Sequence)</a></span> - Method in interface org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/SequenceDBLite.html" title="interface in org.biojava.bio.seq.db">SequenceDBLite</a></dt>
<dd>
<div class="block">Adds a sequence to the database.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/WebSequenceDB.html#addSequence(org.biojava.bio.seq.Sequence)">addSequence(Sequence)</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/WebSequenceDB.html" title="class in org.biojava.bio.seq.db">WebSequenceDB</a></dt>
<dd>
<div class="block">Not supported, You can't add sequences to a WebDB!</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/distributed/DistributedSequenceDB.html#addSequence(org.biojava.bio.seq.Sequence)">addSequence(Sequence)</a></span> - Method in class org.biojava.bio.seq.distributed.<a href="./org/biojava/bio/seq/distributed/DistributedSequenceDB.html" title="class in org.biojava.bio.seq.distributed">DistributedSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/UkkonenSuffixTree.html#addSequence(java.lang.String, java.lang.String, boolean)">addSequence(String, String, boolean)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/UkkonenSuffixTree.html" title="class in org.biojava.bio.symbol">UkkonenSuffixTree</a></dt>
<dd>
<div class="block">Add a sequence into the tree.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/AbstractRichSequenceDB.html#addSequence(org.biojava.bio.seq.Sequence)">addSequence(Sequence)</a></span> - Method in class org.biojavax.bio.db.<a href="./org/biojavax/bio/db/AbstractRichSequenceDB.html" title="class in org.biojavax.bio.db">AbstractRichSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/DummySequenceDBInstallation.html#addSequenceDB(org.biojava.bio.seq.db.SequenceDBLite, java.util.Set)">addSequenceDB(SequenceDBLite, Set)</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/DummySequenceDBInstallation.html" title="class in org.biojava.bio.seq.db">DummySequenceDBInstallation</a></dt>
<dd>
<div class="block">As this is a dummy implementation adding a sequenceDB doesn't do anything</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/SequenceDBInstallation.html#addSequenceDB(org.biojava.bio.seq.db.SequenceDBLite, java.util.Set)">addSequenceDB(SequenceDBLite, Set)</a></span> - Method in interface org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/SequenceDBInstallation.html" title="interface in org.biojava.bio.seq.db">SequenceDBInstallation</a></dt>
<dd>
<div class="block"><code>addSequenceDB</code> adds a new <code>SequenceDB</code>
under its own identifier which will additionally be recognised
by the set of other identifiers.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/SimpleSequenceDBInstallation.html#addSequenceDB(java.lang.String, java.util.Set)">addSequenceDB(String, Set)</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/SimpleSequenceDBInstallation.html" title="class in org.biojava.bio.seq.db">SimpleSequenceDBInstallation</a></dt>
<dd>
<div class="block">This method creates a new (and empty) HashSequenceDB with the
given name that will be accessible through this sequence db
installation through this name and all given other identifiers.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/SimpleSequenceDBInstallation.html#addSequenceDB(org.biojava.bio.seq.db.SequenceDBLite, java.util.Set)">addSequenceDB(SequenceDBLite, Set)</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/SimpleSequenceDBInstallation.html" title="class in org.biojava.bio.seq.db">SimpleSequenceDBInstallation</a></dt>
<dd>
<div class="block"><code>addSequenceDB</code> adds a new SequenceDB which will be
accessible via the name returned by its getName() method and
via all other given identifiers.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/EmblFileFormer.html#addSequenceProperty(java.lang.Object, java.lang.Object)">addSequenceProperty(Object, Object)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/EmblFileFormer.html" title="class in org.biojava.bio.seq.io">EmblFileFormer</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/EmblProcessor.html#addSequenceProperty(java.lang.Object, java.lang.Object)">addSequenceProperty(Object, Object)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/EmblProcessor.html" title="class in org.biojava.bio.seq.io">EmblProcessor</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/FastaDescriptionLineParser.html#addSequenceProperty(java.lang.Object, java.lang.Object)">addSequenceProperty(Object, Object)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/FastaDescriptionLineParser.html" title="class in org.biojava.bio.seq.io">FastaDescriptionLineParser</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/GenbankFileFormer.html#addSequenceProperty(java.lang.Object, java.lang.Object)">addSequenceProperty(Object, Object)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/GenbankFileFormer.html" title="class in org.biojava.bio.seq.io">GenbankFileFormer</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/GenbankProcessor.html#addSequenceProperty(java.lang.Object, java.lang.Object)">addSequenceProperty(Object, Object)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/GenbankProcessor.html" title="class in org.biojava.bio.seq.io">GenbankProcessor</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/OrganismParser.html#addSequenceProperty(java.lang.Object, java.lang.Object)">addSequenceProperty(Object, Object)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/OrganismParser.html" title="class in org.biojava.bio.seq.io">OrganismParser</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOAdapter.html#addSequenceProperty(java.lang.Object, java.lang.Object)">addSequenceProperty(Object, Object)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOAdapter.html" title="class in org.biojava.bio.seq.io">SeqIOAdapter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOFilter.html#addSequenceProperty(java.lang.Object, java.lang.Object)">addSequenceProperty(Object, Object)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOFilter.html" title="class in org.biojava.bio.seq.io">SeqIOFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOListener.html#addSequenceProperty(java.lang.Object, java.lang.Object)">addSequenceProperty(Object, Object)</a></span> - Method in interface org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOListener.html" title="interface in org.biojava.bio.seq.io">SeqIOListener</a></dt>
<dd>
<div class="block">Notify the listener of a sequence-wide property.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SequenceBuilderBase.html#addSequenceProperty(java.lang.Object, java.lang.Object)">addSequenceProperty(Object, Object)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SequenceBuilderBase.html" title="class in org.biojava.bio.seq.io">SequenceBuilderBase</a></dt>
<dd>
<div class="block">Add an annotation-bundle entry to the sequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SequenceBuilderFilter.html#addSequenceProperty(java.lang.Object, java.lang.Object)">addSequenceProperty(Object, Object)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SequenceBuilderFilter.html" title="class in org.biojava.bio.seq.io">SequenceBuilderFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SwissprotFileFormer.html#addSequenceProperty(java.lang.Object, java.lang.Object)">addSequenceProperty(Object, Object)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SwissprotFileFormer.html" title="class in org.biojava.bio.seq.io">SwissprotFileFormer</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Notify the listener of a sequence-wide property.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SwissprotProcessor.html#addSequenceProperty(java.lang.Object, java.lang.Object)">addSequenceProperty(Object, Object)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SwissprotProcessor.html" title="class in org.biojava.bio.seq.io">SwissprotProcessor</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/DebuggingRichSeqIOListener.html#addSequenceProperty(java.lang.Object, java.lang.Object)">addSequenceProperty(Object, Object)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/DebuggingRichSeqIOListener.html" title="class in org.biojavax.bio.seq.io">DebuggingRichSeqIOListener</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/RichSeqIOAdapter.html#addSequenceProperty(java.lang.Object, java.lang.Object)">addSequenceProperty(Object, Object)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/RichSeqIOAdapter.html" title="class in org.biojavax.bio.seq.io">RichSeqIOAdapter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/SimpleRichSequenceBuilder.html#addSequenceProperty(java.lang.Object, java.lang.Object)">addSequenceProperty(Object, Object)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/SimpleRichSequenceBuilder.html" title="class in org.biojavax.bio.seq.io">SimpleRichSequenceBuilder</a></dt>
<dd>
<div class="block">Notify the listener of a sequence-wide property.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PairwiseSequencePanel.html#addSequenceViewerListener(org.biojava.bio.gui.sequence.SequenceViewerListener)">addSequenceViewerListener(SequenceViewerListener)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PairwiseSequencePanel.html" title="class in org.biojava.bio.gui.sequence">PairwiseSequencePanel</a></dt>
<dd>
<div class="block"><code>addSequenceViewerListener</code> adds a listener for
mouse click <code>SequenceViewerEvent</code>s.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePanel.html#addSequenceViewerListener(org.biojava.bio.gui.sequence.SequenceViewerListener)">addSequenceViewerListener(SequenceViewerListener)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePanel.html" title="class in org.biojava.bio.gui.sequence">SequencePanel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePanelWrapper.html#addSequenceViewerListener(org.biojava.bio.gui.sequence.SequenceViewerListener)">addSequenceViewerListener(SequenceViewerListener)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePanelWrapper.html" title="class in org.biojava.bio.gui.sequence">SequencePanelWrapper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePoster.html#addSequenceViewerListener(org.biojava.bio.gui.sequence.SequenceViewerListener)">addSequenceViewerListener(SequenceViewerListener)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePoster.html" title="class in org.biojava.bio.gui.sequence">SequencePoster</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequenceViewerSupport.html#addSequenceViewerListener(org.biojava.bio.gui.sequence.SequenceViewerListener)">addSequenceViewerListener(SequenceViewerListener)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequenceViewerSupport.html" title="class in org.biojava.bio.gui.sequence">SequenceViewerSupport</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/TranslatedSequencePanel.html#addSequenceViewerListener(org.biojava.bio.gui.sequence.SequenceViewerListener)">addSequenceViewerListener(SequenceViewerListener)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/TranslatedSequencePanel.html" title="class in org.biojava.bio.gui.sequence">TranslatedSequencePanel</a></dt>
<dd>
<div class="block"><code>addSequenceViewerListener</code> adds a listener for
mouse click <code>SequenceViewerEvent</code>s.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PairwiseSequencePanel.html#addSequenceViewerMotionListener(org.biojava.bio.gui.sequence.SequenceViewerMotionListener)">addSequenceViewerMotionListener(SequenceViewerMotionListener)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PairwiseSequencePanel.html" title="class in org.biojava.bio.gui.sequence">PairwiseSequencePanel</a></dt>
<dd>
<div class="block"><code>addSequenceViewerMotionListener</code> adds a listener for
mouse motion <code>SequenceViewerEvent</code>s.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePanel.html#addSequenceViewerMotionListener(org.biojava.bio.gui.sequence.SequenceViewerMotionListener)">addSequenceViewerMotionListener(SequenceViewerMotionListener)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePanel.html" title="class in org.biojava.bio.gui.sequence">SequencePanel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePanelWrapper.html#addSequenceViewerMotionListener(org.biojava.bio.gui.sequence.SequenceViewerMotionListener)">addSequenceViewerMotionListener(SequenceViewerMotionListener)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePanelWrapper.html" title="class in org.biojava.bio.gui.sequence">SequencePanelWrapper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePoster.html#addSequenceViewerMotionListener(org.biojava.bio.gui.sequence.SequenceViewerMotionListener)">addSequenceViewerMotionListener(SequenceViewerMotionListener)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePoster.html" title="class in org.biojava.bio.gui.sequence">SequencePoster</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequenceViewerMotionSupport.html#addSequenceViewerMotionListener(org.biojava.bio.gui.sequence.SequenceViewerMotionListener)">addSequenceViewerMotionListener(SequenceViewerMotionListener)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequenceViewerMotionSupport.html" title="class in org.biojava.bio.gui.sequence">SequenceViewerMotionSupport</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/TranslatedSequencePanel.html#addSequenceViewerMotionListener(org.biojava.bio.gui.sequence.SequenceViewerMotionListener)">addSequenceViewerMotionListener(SequenceViewerMotionListener)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/TranslatedSequencePanel.html" title="class in org.biojava.bio.gui.sequence">TranslatedSequencePanel</a></dt>
<dd>
<div class="block"><code>addSequenceViewerMotionListener</code> adds a listener for
mouse motion <code>SequenceViewerEvent</code>s.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/MergingSet.html#addSet(java.util.Set)">addSet(Set)</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/MergingSet.html" title="class in org.biojava.utils">MergingSet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Structure.html#addSSBond(org.biojava.bio.structure.SSBond)">addSSBond(SSBond)</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Structure.html" title="interface in org.biojava.bio.structure">Structure</a></dt>
<dd>
<div class="block">add a single SSBond to this structure</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/StructureImpl.html#addSSBond(org.biojava.bio.structure.SSBond)">addSSBond(SSBond)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/StructureImpl.html" title="class in org.biojava.bio.structure">StructureImpl</a></dt>
<dd>
<div class="block">add a single SSBond to this structure</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/MarkovModel.html#addState(org.biojava.bio.dp.State)">addState(State)</a></span> - Method in interface org.biojava.bio.dp.<a href="./org/biojava/bio/dp/MarkovModel.html" title="interface in org.biojava.bio.dp">MarkovModel</a></dt>
<dd>
<div class="block">Adds a state to the model.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/SimpleMarkovModel.html#addState(org.biojava.bio.dp.State)">addState(State)</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/SimpleMarkovModel.html" title="class in org.biojava.bio.dp">SimpleMarkovModel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/WMAsMM.html#addState(org.biojava.bio.dp.State)">addState(State)</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/WMAsMM.html" title="class in org.biojava.bio.dp">WMAsMM</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/server/SimpleStructureServer.html#addStructureListener(org.biojava.bio.structure.server.StructureListener)">addStructureListener(StructureListener)</a></span> - Method in class org.biojava.bio.structure.server.<a href="./org/biojava/bio/structure/server/SimpleStructureServer.html" title="class in org.biojava.bio.structure.server">SimpleStructureServer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/server/StructureFetcherRunnable.html#addStructureListener(org.biojava.bio.structure.server.StructureListener)">addStructureListener(StructureListener)</a></span> - Method in class org.biojava.bio.structure.server.<a href="./org/biojava/bio/structure/server/StructureFetcherRunnable.html" title="class in org.biojava.bio.structure.server">StructureFetcherRunnable</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/server/StructureServer.html#addStructureListener(org.biojava.bio.structure.server.StructureListener)">addStructureListener(StructureListener)</a></span> - Method in interface org.biojava.bio.structure.server.<a href="./org/biojava/bio/structure/server/StructureServer.html" title="interface in org.biojava.bio.structure.server">StructureServer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/blast2html/AbstractAlignmentStyler.html#addStyle(java.lang.String, java.lang.String)">addStyle(String, String)</a></span> - Method in class org.biojava.bio.program.blast2html.<a href="./org/biojava/bio/program/blast2html/AbstractAlignmentStyler.html" title="class in org.biojava.bio.program.blast2html">AbstractAlignmentStyler</a></dt>
<dd>
<div class="block">Add a colour style to this Styler.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/sax/FastaSearchSAXParser.html#addSubHitProperty(java.lang.Object, java.lang.Object)">addSubHitProperty(Object, Object)</a></span> - Method in class org.biojava.bio.program.sax.<a href="./org/biojava/bio/program/sax/FastaSearchSAXParser.html" title="class in org.biojava.bio.program.sax">FastaSearchSAXParser</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/BlastLikeHomologyBuilder.html#addSubHitProperty(java.lang.Object, java.lang.Object)">addSubHitProperty(Object, Object)</a></span> - Method in class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/BlastLikeHomologyBuilder.html" title="class in org.biojava.bio.program.ssbind">BlastLikeHomologyBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/BlastLikeSearchBuilder.html#addSubHitProperty(java.lang.Object, java.lang.Object)">addSubHitProperty(Object, Object)</a></span> - Method in class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/BlastLikeSearchBuilder.html" title="class in org.biojava.bio.program.ssbind">BlastLikeSearchBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/SimilarityPairBuilder.html#addSubHitProperty(java.lang.Object, java.lang.Object)">addSubHitProperty(Object, Object)</a></span> - Method in class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/SimilarityPairBuilder.html" title="class in org.biojava.bio.program.ssbind">SimilarityPairBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/FilteringContentHandler.html#addSubHitProperty(java.lang.Object, java.lang.Object)">addSubHitProperty(Object, Object)</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/FilteringContentHandler.html" title="class in org.biojava.bio.search">FilteringContentHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SearchContentAdapter.html#addSubHitProperty(java.lang.Object, java.lang.Object)">addSubHitProperty(Object, Object)</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SearchContentAdapter.html" title="class in org.biojava.bio.search">SearchContentAdapter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SearchContentFilter.html#addSubHitProperty(java.lang.Object, java.lang.Object)">addSubHitProperty(Object, Object)</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SearchContentFilter.html" title="class in org.biojava.bio.search">SearchContentFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SearchContentHandler.html#addSubHitProperty(java.lang.Object, java.lang.Object)">addSubHitProperty(Object, Object)</a></span> - Method in interface org.biojava.bio.search.<a href="./org/biojava/bio/search/SearchContentHandler.html" title="interface in org.biojava.bio.search">SearchContentHandler</a></dt>
<dd>
<div class="block">The <code>addSubHitProperty</code> method adds a key/value pair
containing some property of a particular subhit.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SearchContentHandlerDebugger.html#addSubHitProperty(java.lang.Object, java.lang.Object)">addSubHitProperty(Object, Object)</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SearchContentHandlerDebugger.html" title="class in org.biojava.bio.search">SearchContentHandlerDebugger</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AbstractAlphabet.html#addSymbol(org.biojava.bio.symbol.Symbol)">addSymbol(Symbol)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AbstractAlphabet.html" title="class in org.biojava.bio.symbol">AbstractAlphabet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/FiniteAlphabet.html#addSymbol(org.biojava.bio.symbol.Symbol)">addSymbol(Symbol)</a></span> - Method in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/FiniteAlphabet.html" title="interface in org.biojava.bio.symbol">FiniteAlphabet</a></dt>
<dd>
<div class="block">Adds a symbol to this alphabet.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleSymbolList.html#addSymbol(org.biojava.bio.symbol.Symbol)">addSymbol(Symbol)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleSymbolList.html" title="class in org.biojava.bio.symbol">SimpleSymbolList</a></dt>
<dd>
<div class="block">Add a new Symbol to the end of this list.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SoftMaskedAlphabet.html#addSymbol(org.biojava.bio.symbol.Symbol)">addSymbol(Symbol)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SoftMaskedAlphabet.html" title="class in org.biojava.bio.symbol">SoftMaskedAlphabet</a></dt>
<dd>
<div class="block"><code>SoftMaskedAlphabet</code>s cannot add new <code>Symbol</code>s.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AbstractAlphabet.html#addSymbolImpl(org.biojava.bio.symbol.AtomicSymbol)">addSymbolImpl(AtomicSymbol)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AbstractAlphabet.html" title="class in org.biojava.bio.symbol">AbstractAlphabet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/IntegerAlphabet.SubIntegerAlphabet.html#addSymbolImpl(org.biojava.bio.symbol.AtomicSymbol)">addSymbolImpl(AtomicSymbol)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/IntegerAlphabet.SubIntegerAlphabet.html" title="class in org.biojava.bio.symbol">IntegerAlphabet.SubIntegerAlphabet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleAlphabet.html#addSymbolImpl(org.biojava.bio.symbol.AtomicSymbol)">addSymbolImpl(AtomicSymbol)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleAlphabet.html" title="class in org.biojava.bio.symbol">SimpleAlphabet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SingletonAlphabet.html#addSymbolImpl(org.biojava.bio.symbol.AtomicSymbol)">addSymbolImpl(AtomicSymbol)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SingletonAlphabet.html" title="class in org.biojava.bio.symbol">SingletonAlphabet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/UkkonenSuffixTree.html#addSymbolList(org.biojava.bio.symbol.SymbolList, java.lang.String, boolean)">addSymbolList(SymbolList, String, boolean)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/UkkonenSuffixTree.html" title="class in org.biojava.bio.symbol">UkkonenSuffixTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/ChunkedSymbolListFactory.html#addSymbols(org.biojava.bio.symbol.Alphabet, org.biojava.bio.symbol.Symbol[], int, int)">addSymbols(Alphabet, Symbol[], int, int)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/ChunkedSymbolListFactory.html" title="class in org.biojava.bio.seq.io">ChunkedSymbolListFactory</a></dt>
<dd>
<div class="block">tool to construct the SymbolList by adding Symbols.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/EmblFileFormer.html#addSymbols(org.biojava.bio.symbol.Alphabet, org.biojava.bio.symbol.Symbol[], int, int)">addSymbols(Alphabet, Symbol[], int, int)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/EmblFileFormer.html" title="class in org.biojava.bio.seq.io">EmblFileFormer</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/GenbankFileFormer.html#addSymbols(org.biojava.bio.symbol.Alphabet, org.biojava.bio.symbol.Symbol[], int, int)">addSymbols(Alphabet, Symbol[], int, int)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/GenbankFileFormer.html" title="class in org.biojava.bio.seq.io">GenbankFileFormer</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/ProteinRefSeqFileFormer.html#addSymbols(org.biojava.bio.symbol.Alphabet, org.biojava.bio.symbol.Symbol[], int, int)">addSymbols(Alphabet, Symbol[], int, int)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/ProteinRefSeqFileFormer.html" title="class in org.biojava.bio.seq.io">ProteinRefSeqFileFormer</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOAdapter.html#addSymbols(org.biojava.bio.symbol.Alphabet, org.biojava.bio.symbol.Symbol[], int, int)">addSymbols(Alphabet, Symbol[], int, int)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOAdapter.html" title="class in org.biojava.bio.seq.io">SeqIOAdapter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOFilter.html#addSymbols(org.biojava.bio.symbol.Alphabet, org.biojava.bio.symbol.Symbol[], int, int)">addSymbols(Alphabet, Symbol[], int, int)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOFilter.html" title="class in org.biojava.bio.seq.io">SeqIOFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOListener.html#addSymbols(org.biojava.bio.symbol.Alphabet, org.biojava.bio.symbol.Symbol[], int, int)">addSymbols(Alphabet, Symbol[], int, int)</a></span> - Method in interface org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOListener.html" title="interface in org.biojava.bio.seq.io">SeqIOListener</a></dt>
<dd>
<div class="block">Notify the listener of symbol data.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SequenceBuilderBase.html#addSymbols(org.biojava.bio.symbol.Alphabet, org.biojava.bio.symbol.Symbol[], int, int)">addSymbols(Alphabet, Symbol[], int, int)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SequenceBuilderBase.html" title="class in org.biojava.bio.seq.io">SequenceBuilderBase</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SequenceBuilderFilter.html#addSymbols(org.biojava.bio.symbol.Alphabet, org.biojava.bio.symbol.Symbol[], int, int)">addSymbols(Alphabet, Symbol[], int, int)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SequenceBuilderFilter.html" title="class in org.biojava.bio.seq.io">SequenceBuilderFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SequenceDBSequenceBuilder.html#addSymbols(org.biojava.bio.symbol.Alphabet, org.biojava.bio.symbol.Symbol[], int, int)">addSymbols(Alphabet, Symbol[], int, int)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SequenceDBSequenceBuilder.html" title="class in org.biojava.bio.seq.io">SequenceDBSequenceBuilder</a></dt>
<dd>
<div class="block">does nothing for now.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SimpleAssemblyBuilder.html#addSymbols(org.biojava.bio.symbol.Alphabet, org.biojava.bio.symbol.Symbol[], int, int)">addSymbols(Alphabet, Symbol[], int, int)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SimpleAssemblyBuilder.html" title="class in org.biojava.bio.seq.io">SimpleAssemblyBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SimpleSequenceBuilder.html#addSymbols(org.biojava.bio.symbol.Alphabet, org.biojava.bio.symbol.Symbol[], int, int)">addSymbols(Alphabet, Symbol[], int, int)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SimpleSequenceBuilder.html" title="class in org.biojava.bio.seq.io">SimpleSequenceBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SmartSequenceBuilder.html#addSymbols(org.biojava.bio.symbol.Alphabet, org.biojava.bio.symbol.Symbol[], int, int)">addSymbols(Alphabet, Symbol[], int, int)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SmartSequenceBuilder.html" title="class in org.biojava.bio.seq.io">SmartSequenceBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SwissprotFileFormer.html#addSymbols(org.biojava.bio.symbol.Alphabet, org.biojava.bio.symbol.Symbol[], int, int)">addSymbols(Alphabet, Symbol[], int, int)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SwissprotFileFormer.html" title="class in org.biojava.bio.seq.io">SwissprotFileFormer</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Prints out the sequences properties in order.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SuffixTree.html#addSymbols(org.biojava.bio.symbol.SymbolList, int)">addSymbols(SymbolList, int)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SuffixTree.html" title="class in org.biojava.bio.symbol">SuffixTree</a></dt>
<dd>
<div class="block">Add a count for all motifs with length of up to <code>window</code>
to this tree.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/DebuggingRichSeqIOListener.html#addSymbols(org.biojava.bio.symbol.Alphabet, org.biojava.bio.symbol.Symbol[], int, int)">addSymbols(Alphabet, Symbol[], int, int)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/DebuggingRichSeqIOListener.html" title="class in org.biojavax.bio.seq.io">DebuggingRichSeqIOListener</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/RichSeqIOAdapter.html#addSymbols(org.biojava.bio.symbol.Alphabet, org.biojava.bio.symbol.Symbol[], int, int)">addSymbols(Alphabet, Symbol[], int, int)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/RichSeqIOAdapter.html" title="class in org.biojavax.bio.seq.io">RichSeqIOAdapter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/SimpleRichSequenceBuilder.html#addSymbols(org.biojava.bio.symbol.Alphabet, org.biojava.bio.symbol.Symbol[], int, int)">addSymbols(Alphabet, Symbol[], int, int)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/SimpleRichSequenceBuilder.html" title="class in org.biojavax.bio.seq.io">SimpleRichSequenceBuilder</a></dt>
<dd>
<div class="block">Notify the listener of symbol data.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/IntegerOntology.IntTerm.html#addSynonym(java.lang.Object)">addSynonym(Object)</a></span> - Method in class org.biojava.ontology.<a href="./org/biojava/ontology/IntegerOntology.IntTerm.html" title="class in org.biojava.ontology">IntegerOntology.IntTerm</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/OntologyTerm.Impl.html#addSynonym(java.lang.Object)">addSynonym(Object)</a></span> - Method in class org.biojava.ontology.<a href="./org/biojava/ontology/OntologyTerm.Impl.html" title="class in org.biojava.ontology">OntologyTerm.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/RemoteTerm.Impl.html#addSynonym(java.lang.Object)">addSynonym(Object)</a></span> - Method in class org.biojava.ontology.<a href="./org/biojava/ontology/RemoteTerm.Impl.html" title="class in org.biojava.ontology">RemoteTerm.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/Term.html#addSynonym(java.lang.Object)">addSynonym(Object)</a></span> - Method in interface org.biojava.ontology.<a href="./org/biojava/ontology/Term.html" title="interface in org.biojava.ontology">Term</a></dt>
<dd>
<div class="block">Add a synonym for this term.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/Term.Impl.html#addSynonym(java.lang.Object)">addSynonym(Object)</a></span> - Method in class org.biojava.ontology.<a href="./org/biojava/ontology/Term.Impl.html" title="class in org.biojava.ontology">Term.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/Triple.Impl.html#addSynonym(java.lang.Object)">addSynonym(Object)</a></span> - Method in class org.biojava.ontology.<a href="./org/biojava/ontology/Triple.Impl.html" title="class in org.biojava.ontology">Triple.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ontology/SimpleComparableTerm.html#addSynonym(java.lang.Object)">addSynonym(Object)</a></span> - Method in class org.biojavax.ontology.<a href="./org/biojavax/ontology/SimpleComparableTerm.html" title="class in org.biojavax.ontology">SimpleComparableTerm</a></dt>
<dd>
<div class="block">Add a synonym for this term.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ontology/SimpleComparableTriple.html#addSynonym(java.lang.Object)">addSynonym(Object)</a></span> - Method in class org.biojavax.ontology.<a href="./org/biojavax/ontology/SimpleComparableTriple.html" title="class in org.biojavax.ontology">SimpleComparableTriple</a></dt>
<dd>
<div class="block">Add a synonym for this term.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/aaindex/SimpleSymbolPropertyTableDB.html#addTable(org.biojava.bio.symbol.SymbolPropertyTable)">addTable(SymbolPropertyTable)</a></span> - Method in class org.biojava.bio.proteomics.aaindex.<a href="./org/biojava/bio/proteomics/aaindex/SimpleSymbolPropertyTableDB.html" title="class in org.biojava.bio.proteomics.aaindex">SimpleSymbolPropertyTableDB</a></dt>
<dd>
<div class="block">Adds a symbol property table to the database.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/TagDropper.html#addTag(java.lang.Object)">addTag(Object)</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/TagDropper.html" title="class in org.biojava.bio.program.tagvalue">TagDropper</a></dt>
<dd>
<div class="block">Add a tag to retain.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/HomologeneBuilder.html#addTitle(int, java.lang.String, java.lang.String)">addTitle(int, String, String)</a></span> - Method in interface org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/HomologeneBuilder.html" title="interface in org.biojava.bio.program.homologene">HomologeneBuilder</a></dt>
<dd>
<div class="block">add title information to an Orthologue
(this is not in enclosed in the Orthologue element
because it comes completely separate in the Homologene
data files.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/SimpleHomologeneBuilder.html#addTitle(int, java.lang.String, java.lang.String)">addTitle(int, String, String)</a></span> - Method in class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/SimpleHomologeneBuilder.html" title="class in org.biojava.bio.program.homologene">SimpleHomologeneBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/naming/ObdaContext.html#addToEnvironment(java.lang.String, java.lang.Object)">addToEnvironment(String, Object)</a></span> - Method in class org.biojava.naming.<a href="./org/biojava/naming/ObdaContext.html" title="class in org.biojava.naming">ObdaContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/directory/RegistryConfiguration.Composite.html#addTopConfig(org.biojava.directory.RegistryConfiguration)">addTopConfig(RegistryConfiguration)</a></span> - Method in class org.biojava.directory.<a href="./org/biojava/directory/RegistryConfiguration.Composite.html" title="class in org.biojava.directory">RegistryConfiguration.Composite</a></dt>
<dd>
<div class="block">Add a configuration as the most authoritative place to look.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/automata/FiniteAutomaton.html#addTransition(org.biojava.utils.automata.FiniteAutomaton.Node, org.biojava.utils.automata.FiniteAutomaton.Node, org.biojava.bio.symbol.Symbol)">addTransition(FiniteAutomaton.Node, FiniteAutomaton.Node, Symbol)</a></span> - Method in class org.biojava.utils.automata.<a href="./org/biojava/utils/automata/FiniteAutomaton.html" title="class in org.biojava.utils.automata">FiniteAutomaton</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/automata/NfaBuilder.html#addTransition(org.biojava.utils.automata.FiniteAutomaton.Node, org.biojava.utils.automata.FiniteAutomaton.Node, org.biojava.bio.symbol.Symbol)">addTransition(FiniteAutomaton.Node, FiniteAutomaton.Node, Symbol)</a></span> - Method in interface org.biojava.utils.automata.<a href="./org/biojava/utils/automata/NfaBuilder.html" title="interface in org.biojava.utils.automata">NfaBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/automata/NfaSubModel.html#addTransition(org.biojava.utils.automata.FiniteAutomaton.Node, org.biojava.utils.automata.FiniteAutomaton.Node, org.biojava.bio.symbol.Symbol)">addTransition(FiniteAutomaton.Node, FiniteAutomaton.Node, Symbol)</a></span> - Method in class org.biojava.utils.automata.<a href="./org/biojava/utils/automata/NfaSubModel.html" title="class in org.biojava.utils.automata">NfaSubModel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/walker/WalkerFactory.html#addTypeWithParent(java.lang.Class)">addTypeWithParent(Class)</a></span> - Method in class org.biojava.utils.walker.<a href="./org/biojava/utils/walker/WalkerFactory.html" title="class in org.biojava.utils.walker">WalkerFactory</a></dt>
<dd>
<div class="block">Register a type as being a 'container' class.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/MassCalc.html#addVariableModification(char, double[])">addVariableModification(char, double[])</a></span> - Method in class org.biojava.bio.proteomics.<a href="./org/biojava/bio/proteomics/MassCalc.html" title="class in org.biojava.bio.proteomics">MassCalc</a></dt>
<dd>
<div class="block">Add Variable modifications.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/MassCalc.html#addVariableModification(org.biojava.bio.symbol.Symbol, double[])">addVariableModification(Symbol, double[])</a></span> - Method in class org.biojava.bio.proteomics.<a href="./org/biojava/bio/proteomics/MassCalc.html" title="class in org.biojava.bio.proteomics">MassCalc</a></dt>
<dd>
<div class="block">Add Variable modifications.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/dasalignment/Alignment.html#addVector(org.biojava.bio.Annotation)">addVector(Annotation)</a></span> - Method in class org.biojava.bio.program.das.dasalignment.<a href="./org/biojava/bio/program/das/dasalignment/Alignment.html" title="class in org.biojava.bio.program.das.dasalignment">Alignment</a></dt>
<dd>
<div class="block">add Annotation of DAS alignment "vector" type.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/SVMRegressionModel.html#addVector(java.lang.Object, double, double)">addVector(Object, double, double)</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/SVMRegressionModel.html" title="class in org.biojava.stats.svm">SVMRegressionModel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/SVMRegressionModel.html#addVector(java.lang.Object)">addVector(Object)</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/SVMRegressionModel.html" title="class in org.biojava.stats.svm">SVMRegressionModel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/filterxml/XMLAnnotationTypeWriter.html#addXMLCollectionConstraintWriter(java.lang.Class, org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeWriter.XMLCollectionConstraintWriter)">addXMLCollectionConstraintWriter(Class, XMLAnnotationTypeWriter.XMLCollectionConstraintWriter)</a></span> - Method in class org.biojava.bio.seq.io.filterxml.<a href="./org/biojava/bio/seq/io/filterxml/XMLAnnotationTypeWriter.html" title="class in org.biojava.bio.seq.io.filterxml">XMLAnnotationTypeWriter</a></dt>
<dd>
<div class="block">Register a writer for the specified class of collection constraint</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/filterxml/XMLAnnotationTypeWriter.html#addXMLCollectionConstraintWriter(org.biojava.bio.CollectionConstraint, org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeWriter.XMLCollectionConstraintWriter)">addXMLCollectionConstraintWriter(CollectionConstraint, XMLAnnotationTypeWriter.XMLCollectionConstraintWriter)</a></span> - Method in class org.biojava.bio.seq.io.filterxml.<a href="./org/biojava/bio/seq/io/filterxml/XMLAnnotationTypeWriter.html" title="class in org.biojava.bio.seq.io.filterxml">XMLAnnotationTypeWriter</a></dt>
<dd>
<div class="block">Register a writer for a singleton property constraint.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/filterxml/XMLFilterWriter.html#addXMLFilterWriter(java.lang.Class, org.biojava.bio.seq.io.filterxml.XMLFilterWriter.FilterWriter)">addXMLFilterWriter(Class, XMLFilterWriter.FilterWriter)</a></span> - Method in class org.biojava.bio.seq.io.filterxml.<a href="./org/biojava/bio/seq/io/filterxml/XMLFilterWriter.html" title="class in org.biojava.bio.seq.io.filterxml">XMLFilterWriter</a></dt>
<dd>
<div class="block">Add a writer for the specified class of filters</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/filterxml/XMLFilterWriter.html#addXMLFilterWriter(org.biojava.bio.seq.FeatureFilter, org.biojava.bio.seq.io.filterxml.XMLFilterWriter.FilterWriter)">addXMLFilterWriter(FeatureFilter, XMLFilterWriter.FilterWriter)</a></span> - Method in class org.biojava.bio.seq.io.filterxml.<a href="./org/biojava/bio/seq/io/filterxml/XMLFilterWriter.html" title="class in org.biojava.bio.seq.io.filterxml">XMLFilterWriter</a></dt>
<dd>
<div class="block">Add a writer for a singleton filter.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/filterxml/XMLAnnotationTypeWriter.html#addXMLPropertyConstraintWriter(java.lang.Class, org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeWriter.XMLPropertyConstraintWriter)">addXMLPropertyConstraintWriter(Class, XMLAnnotationTypeWriter.XMLPropertyConstraintWriter)</a></span> - Method in class org.biojava.bio.seq.io.filterxml.<a href="./org/biojava/bio/seq/io/filterxml/XMLAnnotationTypeWriter.html" title="class in org.biojava.bio.seq.io.filterxml">XMLAnnotationTypeWriter</a></dt>
<dd>
<div class="block">Register a writer for the specified class of property constraint</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/filterxml/XMLAnnotationTypeWriter.html#addXMLPropertyConstraintWriter(org.biojava.bio.PropertyConstraint, org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeWriter.XMLPropertyConstraintWriter)">addXMLPropertyConstraintWriter(PropertyConstraint, XMLAnnotationTypeWriter.XMLPropertyConstraintWriter)</a></span> - Method in class org.biojava.bio.seq.io.filterxml.<a href="./org/biojava/bio/seq/io/filterxml/XMLAnnotationTypeWriter.html" title="class in org.biojava.bio.seq.io.filterxml">XMLAnnotationTypeWriter</a></dt>
<dd>
<div class="block">Register a writer for a singleton property constraint.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEXrefCallbackItf.html#addXref(org.biojava.bio.seq.io.agave.AGAVEXref)">addXref(AGAVEXref)</a></span> - Method in interface org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEXrefCallbackItf.html" title="interface in org.biojava.bio.seq.io.agave">AGAVEXrefCallbackItf</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEXrefs.html#addXref(org.biojava.bio.seq.io.agave.AGAVEXref)">addXref(AGAVEXref)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEXrefs.html" title="class in org.biojava.bio.seq.io.agave">AGAVEXrefs</a></dt>
<dd>
<div class="block">add @param xref</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEXrefsPropHandler.html#addXref(org.biojava.bio.seq.io.agave.AGAVEXref)">addXref(AGAVEXref)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEXrefsPropHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEXrefsPropHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/EmissionState.html#ADVANCE">ADVANCE</a></span> - Static variable in interface org.biojava.bio.dp.<a href="./org/biojava/bio/dp/EmissionState.html" title="interface in org.biojava.bio.dp">EmissionState</a></dt>
<dd>
<div class="block">
This signals that the advance array has been altered.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/MarkovModel.html#advance()">advance()</a></span> - Method in interface org.biojava.bio.dp.<a href="./org/biojava/bio/dp/MarkovModel.html" title="interface in org.biojava.bio.dp">MarkovModel</a></dt>
<dd>
<div class="block">The maximum advance for this model.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/onehead/DPCursor.html#advance()">advance()</a></span> - Method in interface org.biojava.bio.dp.onehead.<a href="./org/biojava/bio/dp/onehead/DPCursor.html" title="interface in org.biojava.bio.dp.onehead">DPCursor</a></dt>
<dd>
<div class="block">Advance.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/onehead/SmallCursor.html#advance()">advance()</a></span> - Method in class org.biojava.bio.dp.onehead.<a href="./org/biojava/bio/dp/onehead/SmallCursor.html" title="class in org.biojava.bio.dp.onehead">SmallCursor</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/SimpleMarkovModel.html#advance()">advance()</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/SimpleMarkovModel.html" title="class in org.biojava.bio.dp">SimpleMarkovModel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/WMAsMM.html#advance()">advance()</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/WMAsMM.html" title="class in org.biojava.bio.dp">WMAsMM</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BiblioPerson.html#affiliation">affiliation</a></span> - Variable in class org.biojava.bibliography.<a href="./org/biojava/bibliography/BiblioPerson.html" title="class in org.biojava.bibliography">BiblioPerson</a></dt>
<dd>
<div class="block">Their affiliation.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/agave/Agave2AgaveAnnotFilter.html" title="class in org.biojava.bio.seq.io.agave"><span class="strong">Agave2AgaveAnnotFilter</span></a> - Class in <a href="./org/biojava/bio/seq/io/agave/package-summary.html">org.biojava.bio.seq.io.agave</a></dt>
<dd>
<div class="block">Dumping the data from biojava with source of agave into agave format</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/Agave2AgaveAnnotFilter.html#AGAVE_AGAVE_ANNOT_FILTER_FACTORY">AGAVE_AGAVE_ANNOT_FILTER_FACTORY</a></span> - Static variable in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/Agave2AgaveAnnotFilter.html" title="class in org.biojava.bio.seq.io.agave">Agave2AgaveAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEAltIdsPropHandler.html#AGAVE_ALT_IDS_PROP_HANDLER_FACTORY">AGAVE_ALT_IDS_PROP_HANDLER_FACTORY</a></span> - Static variable in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEAltIdsPropHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEAltIdsPropHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEAnnotationsHandler.html#AGAVE_ANNOTATIONS_HANDLER_FACTORY">AGAVE_ANNOTATIONS_HANDLER_FACTORY</a></span> - Static variable in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEAnnotationsHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEAnnotationsHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEAssemblyHandler.html#AGAVE_ASSEMBLY_HANDLER_FACTORY">AGAVE_ASSEMBLY_HANDLER_FACTORY</a></span> - Static variable in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEAssemblyHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEAssemblyHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEBioSeqHandler.html#AGAVE_BIO_SEQ_HANDLER_FACTORY">AGAVE_BIO_SEQ_HANDLER_FACTORY</a></span> - Static variable in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEBioSeqHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEBioSeqHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEBioSequenceHandler.html#AGAVE_BIO_SEQUENCE_HANDLER_FACTORY">AGAVE_BIO_SEQUENCE_HANDLER_FACTORY</a></span> - Static variable in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEBioSequenceHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEBioSequenceHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVECdsHandler.html#AGAVE_CDS_HANDLER_FACTORY">AGAVE_CDS_HANDLER_FACTORY</a></span> - Static variable in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVECdsHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVECdsHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEChromosomeHandler.html#AGAVE_CHROMOSOME_HANDLER_FACTORY">AGAVE_CHROMOSOME_HANDLER_FACTORY</a></span> - Static variable in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEChromosomeHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEChromosomeHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEClassificationHandler.html#AGAVE_CLASSIFICATION_HANDLER_FACTORY">AGAVE_CLASSIFICATION_HANDLER_FACTORY</a></span> - Static variable in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEClassificationHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEClassificationHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVECompResultHandler.html#AGAVE_COMP_RESULT_HANDLER_FACTORY">AGAVE_COMP_RESULT_HANDLER_FACTORY</a></span> - Static variable in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVECompResultHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVECompResultHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEComputationHandler.html#AGAVE_COMPUTATION_HANDLER_FACTORY">AGAVE_COMPUTATION_HANDLER_FACTORY</a></span> - Static variable in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEComputationHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEComputationHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEContigHandler.html#AGAVE_CONTIG_HANDLER_FACTORY">AGAVE_CONTIG_HANDLER_FACTORY</a></span> - Static variable in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEContigHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEContigHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEDbIdPropHandler.html#AGAVE_DBID_PROP_HANDLER_FACTORY">AGAVE_DBID_PROP_HANDLER_FACTORY</a></span> - Static variable in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEDbIdPropHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEDbIdPropHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEDescPropHandler.html#AGAVE_DESC_PROP_HANDLER_FACTORY">AGAVE_DESC_PROP_HANDLER_FACTORY</a></span> - Static variable in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEDescPropHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEDescPropHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEElementIdPropHandler.html#AGAVE_ELEMENT_ID_PROP_HANDLER_FACTORY">AGAVE_ELEMENT_ID_PROP_HANDLER_FACTORY</a></span> - Static variable in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEElementIdPropHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEElementIdPropHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEEvidenceHandler.html#AGAVE_EVIDENCE_HANDLER_FACTORY">AGAVE_EVIDENCE_HANDLER_FACTORY</a></span> - Static variable in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEEvidenceHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEEvidenceHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEExonsPropHandler.html#AGAVE_EXONS_PROP_HANDLER_FACTORY">AGAVE_EXONS_PROP_HANDLER_FACTORY</a></span> - Static variable in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEExonsPropHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEExonsPropHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEFragmentOrderHandler.html#AGAVE_FRAGMENT_ORDER_HANDLER_FACTORY">AGAVE_FRAGMENT_ORDER_HANDLER_FACTORY</a></span> - Static variable in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEFragmentOrderHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEFragmentOrderHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEFragmentOrientationHandler.html#AGAVE_FRAGMENT_ORIENTATION_HANDLER_FACTORY">AGAVE_FRAGMENT_ORIENTATION_HANDLER_FACTORY</a></span> - Static variable in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEFragmentOrientationHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEFragmentOrientationHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEGeneHandler.html#AGAVE_GENE_HANDLER_FACTORY">AGAVE_GENE_HANDLER_FACTORY</a></span> - Static variable in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEGeneHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEGeneHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEIdAliasPropHandler.html#AGAVE_ID_ALIAS_PROP_HANDLER_FACTORY">AGAVE_ID_ALIAS_PROP_HANDLER_FACTORY</a></span> - Static variable in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEIdAliasPropHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEIdAliasPropHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEKeywordPropHandler.html#AGAVE_KEYWORD_PROP_HANDLER_FACTORY">AGAVE_KEYWORD_PROP_HANDLER_FACTORY</a></span> - Static variable in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEKeywordPropHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEKeywordPropHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEMapLocationPropHandler.html#AGAVE_MAP_LOCATION_PROP_HANDLER_FACTORY">AGAVE_MAP_LOCATION_PROP_HANDLER_FACTORY</a></span> - Static variable in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEMapLocationPropHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEMapLocationPropHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEMapPositionPropHandler.html#AGAVE_MAP_POSITION_PROP_HANDLER_FACTORY">AGAVE_MAP_POSITION_PROP_HANDLER_FACTORY</a></span> - Static variable in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEMapPositionPropHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEMapPositionPropHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEMatchAlignPropHandler.html#AGAVE_MATCH_ALIGN_PROP_HANDLER_FACTORY">AGAVE_MATCH_ALIGN_PROP_HANDLER_FACTORY</a></span> - Static variable in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEMatchAlignPropHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEMatchAlignPropHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEMatchDescPropHandler.html#AGAVE_MATCH_DESC_PROP_HANDLER_FACTORY">AGAVE_MATCH_DESC_PROP_HANDLER_FACTORY</a></span> - Static variable in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEMatchDescPropHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEMatchDescPropHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEMatchRegionPropHandler.html#AGAVE_MATCH_REGION_PROP_HANDLER_FACTORY">AGAVE_MATCH_REGION_PROP_HANDLER_FACTORY</a></span> - Static variable in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEMatchRegionPropHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEMatchRegionPropHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEMrnaHandler.html#AGAVE_MRNA_HANDLER_FACTORY">AGAVE_MRNA_HANDLER_FACTORY</a></span> - Static variable in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEMrnaHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEMrnaHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVENotePropHandler.html#AGAVE_NOTE_PROP_HANDLER_FACTORY">AGAVE_NOTE_PROP_HANDLER_FACTORY</a></span> - Static variable in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVENotePropHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVENotePropHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEPredictedProteinHandler.html#AGAVE_PREDICTED_PROTEIN_HANDLER_FACTORY">AGAVE_PREDICTED_PROTEIN_HANDLER_FACTORY</a></span> - Static variable in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEPredictedProteinHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEPredictedProteinHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEQualifierPropHandler.html#AGAVE_QUALIFIER_PROP_HANDLER_FACTORY">AGAVE_QUALIFIER_PROP_HANDLER_FACTORY</a></span> - Static variable in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEQualifierPropHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEQualifierPropHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEQueryRegionPropHandler.html#AGAVE_QUERY_REGION_PROP_HANDLER_FACTORY">AGAVE_QUERY_REGION_PROP_HANDLER_FACTORY</a></span> - Static variable in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEQueryRegionPropHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEQueryRegionPropHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVERelatedAnnotPropHandler.html#AGAVE_RELATED_ANNOT_PROP_HANDLER_FACTORY">AGAVE_RELATED_ANNOT_PROP_HANDLER_FACTORY</a></span> - Static variable in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVERelatedAnnotPropHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVERelatedAnnotPropHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEResultGroupHandler.html#AGAVE_RESULT_GROUP_HANDLER_FACTORY">AGAVE_RESULT_GROUP_HANDLER_FACTORY</a></span> - Static variable in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEResultGroupHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEResultGroupHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEResultPropertyPropHandler.html#AGAVE_RESULT_PROPERTY_PROP_HANDLER_FACTORY">AGAVE_RESULT_PROPERTY_PROP_HANDLER_FACTORY</a></span> - Static variable in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEResultPropertyPropHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEResultPropertyPropHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVESciPropertyPropHandler.html#AGAVE_SCI_PROPERTY_PROP_HANDLER_FACTORY">AGAVE_SCI_PROPERTY_PROP_HANDLER_FACTORY</a></span> - Static variable in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVESciPropertyPropHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVESciPropertyPropHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVESeqFeatureHandler.html#AGAVE_SEQ_FEATURE_HANDLER_FACTORY">AGAVE_SEQ_FEATURE_HANDLER_FACTORY</a></span> - Static variable in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVESeqFeatureHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVESeqFeatureHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVESeqLocationPropHandler.html#AGAVE_SEQ_LOCATION_PROP_HANDLER_FACTORY">AGAVE_SEQ_LOCATION_PROP_HANDLER_FACTORY</a></span> - Static variable in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVESeqLocationPropHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVESeqLocationPropHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVESeqMapHandler.html#AGAVE_SEQ_MAP_HANDLER_FACTORY">AGAVE_SEQ_MAP_HANDLER_FACTORY</a></span> - Static variable in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVESeqMapHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVESeqMapHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVESeqPropHandler.html#AGAVE_SEQ_PROP_HANDLER_FACTORY">AGAVE_SEQ_PROP_HANDLER_FACTORY</a></span> - Static variable in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVESeqPropHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVESeqPropHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVETranscriptHandler.html#AGAVE_TRANSCRIPT_HANDLER_FACTORY">AGAVE_TRANSCRIPT_HANDLER_FACTORY</a></span> - Static variable in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVETranscriptHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVETranscriptHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEUnorderedFragmentsHandler.html#AGAVE_UNORDERED_FRAGMENTS_HANDLER_FACTORY">AGAVE_UNORDERED_FRAGMENTS_HANDLER_FACTORY</a></span> - Static variable in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEUnorderedFragmentsHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEUnorderedFragmentsHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEViewPropHandler.html#AGAVE_VIEW_PROP_HANDLER_FACTORY">AGAVE_VIEW_PROP_HANDLER_FACTORY</a></span> - Static variable in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEViewPropHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEViewPropHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEXrefPropHandler.html#AGAVE_XREF_PROP_HANDLER_FACTORY">AGAVE_XREF_PROP_HANDLER_FACTORY</a></span> - Static variable in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEXrefPropHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEXrefPropHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEXrefPropPropHandler.html#AGAVE_XREF_PROP_PROP_HANDLER_FACTORY">AGAVE_XREF_PROP_PROP_HANDLER_FACTORY</a></span> - Static variable in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEXrefPropPropHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEXrefPropPropHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEXrefsPropHandler.html#AGAVE_XREFS_PROP_HANDLER_FACTORY">AGAVE_XREFS_PROP_HANDLER_FACTORY</a></span> - Static variable in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEXrefsPropHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEXrefsPropHandler</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/io/agave/AGAVEAltIdsPropHandler.html" title="class in org.biojava.bio.seq.io.agave"><span class="strong">AGAVEAltIdsPropHandler</span></a> - Class in <a href="./org/biojava/bio/seq/io/agave/package-summary.html">org.biojava.bio.seq.io.agave</a></dt>
<dd>
<div class="block">Deals with alternate sequence IDs</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/agave/AGAVEAnnotationsHandler.html" title="class in org.biojava.bio.seq.io.agave"><span class="strong">AGAVEAnnotationsHandler</span></a> - Class in <a href="./org/biojava/bio/seq/io/agave/package-summary.html">org.biojava.bio.seq.io.agave</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/io/agave/AGAVEAnnotFilter.html" title="interface in org.biojava.bio.seq.io.agave"><span class="strong">AGAVEAnnotFilter</span></a> - Interface in <a href="./org/biojava/bio/seq/io/agave/package-summary.html">org.biojava.bio.seq.io.agave</a></dt>
<dd>
<div class="block">This interface defines mapping from BioJava into AGAVE format.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/agave/AGAVEAnnotFilterFactory.html" title="interface in org.biojava.bio.seq.io.agave"><span class="strong">AGAVEAnnotFilterFactory</span></a> - Interface in <a href="./org/biojava/bio/seq/io/agave/package-summary.html">org.biojava.bio.seq.io.agave</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/io/agave/AGAVEAssemblyHandler.html" title="class in org.biojava.bio.seq.io.agave"><span class="strong">AGAVEAssemblyHandler</span></a> - Class in <a href="./org/biojava/bio/seq/io/agave/package-summary.html">org.biojava.bio.seq.io.agave</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/io/agave/AGAVEBioSeqCallbackItf.html" title="interface in org.biojava.bio.seq.io.agave"><span class="strong">AGAVEBioSeqCallbackItf</span></a> - Interface in <a href="./org/biojava/bio/seq/io/agave/package-summary.html">org.biojava.bio.seq.io.agave</a></dt>
<dd>
<div class="block">An interface that can be tested for by nested handlers
when trying to do a callback.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/agave/AGAVEBioSeqHandler.html" title="class in org.biojava.bio.seq.io.agave"><span class="strong">AGAVEBioSeqHandler</span></a> - Class in <a href="./org/biojava/bio/seq/io/agave/package-summary.html">org.biojava.bio.seq.io.agave</a></dt>
<dd>
<div class="block">Handles the AGAVE <bio_sequence> element</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/agave/AGAVEBioSequenceHandler.html" title="class in org.biojava.bio.seq.io.agave"><span class="strong">AGAVEBioSequenceHandler</span></a> - Class in <a href="./org/biojava/bio/seq/io/agave/package-summary.html">org.biojava.bio.seq.io.agave</a></dt>
<dd>
<div class="block">Handles the AGAVE <bio_sequence> element</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/agave/AGAVECallbackItf.html" title="interface in org.biojava.bio.seq.io.agave"><span class="strong">AGAVECallbackItf</span></a> - Interface in <a href="./org/biojava/bio/seq/io/agave/package-summary.html">org.biojava.bio.seq.io.agave</a></dt>
<dd>
<div class="block">An interface that can be tested for by nested handlers
when trying to do a callback.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/agave/AGAVECdsHandler.html" title="class in org.biojava.bio.seq.io.agave"><span class="strong">AGAVECdsHandler</span></a> - Class in <a href="./org/biojava/bio/seq/io/agave/package-summary.html">org.biojava.bio.seq.io.agave</a></dt>
<dd>
<div class="block">Handles the AGAVE <cds> element</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/agave/AGAVEChromosomeCallbackItf.html" title="interface in org.biojava.bio.seq.io.agave"><span class="strong">AGAVEChromosomeCallbackItf</span></a> - Interface in <a href="./org/biojava/bio/seq/io/agave/package-summary.html">org.biojava.bio.seq.io.agave</a></dt>
<dd>
<div class="block">An interface that can be tested for by nested handlers
when trying to do a callback.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/agave/AGAVEChromosomeHandler.html" title="class in org.biojava.bio.seq.io.agave"><span class="strong">AGAVEChromosomeHandler</span></a> - Class in <a href="./org/biojava/bio/seq/io/agave/package-summary.html">org.biojava.bio.seq.io.agave</a></dt>
<dd>
<div class="block">Handles the AGAVE <chromosome> element</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/agave/AGAVEClassificationHandler.html" title="class in org.biojava.bio.seq.io.agave"><span class="strong">AGAVEClassificationHandler</span></a> - Class in <a href="./org/biojava/bio/seq/io/agave/package-summary.html">org.biojava.bio.seq.io.agave</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/io/agave/AGAVECompResultHandler.html" title="class in org.biojava.bio.seq.io.agave"><span class="strong">AGAVECompResultHandler</span></a> - Class in <a href="./org/biojava/bio/seq/io/agave/package-summary.html">org.biojava.bio.seq.io.agave</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/io/agave/AGAVEComputationHandler.html" title="class in org.biojava.bio.seq.io.agave"><span class="strong">AGAVEComputationHandler</span></a> - Class in <a href="./org/biojava/bio/seq/io/agave/package-summary.html">org.biojava.bio.seq.io.agave</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/io/agave/AGAVEContigCallbackItf.html" title="interface in org.biojava.bio.seq.io.agave"><span class="strong">AGAVEContigCallbackItf</span></a> - Interface in <a href="./org/biojava/bio/seq/io/agave/package-summary.html">org.biojava.bio.seq.io.agave</a></dt>
<dd>
<div class="block">An interface that can be tested for by nested handlers
when trying to do a callback.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/agave/AGAVEContigHandler.html" title="class in org.biojava.bio.seq.io.agave"><span class="strong">AGAVEContigHandler</span></a> - Class in <a href="./org/biojava/bio/seq/io/agave/package-summary.html">org.biojava.bio.seq.io.agave</a></dt>
<dd>
<div class="block">Handles the AGAVE <contig> element</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/agave/AGAVEDbId.html" title="class in org.biojava.bio.seq.io.agave"><span class="strong">AGAVEDbId</span></a> - Class in <a href="./org/biojava/bio/seq/io/agave/package-summary.html">org.biojava.bio.seq.io.agave</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEDbId.html#AGAVEDbId()">AGAVEDbId()</a></span> - Constructor for class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEDbId.html" title="class in org.biojava.bio.seq.io.agave">AGAVEDbId</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/io/agave/AGAVEDbIdCallbackItf.html" title="interface in org.biojava.bio.seq.io.agave"><span class="strong">AGAVEDbIdCallbackItf</span></a> - Interface in <a href="./org/biojava/bio/seq/io/agave/package-summary.html">org.biojava.bio.seq.io.agave</a></dt>
<dd>
<div class="block">this is the interface implemented by several classes</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/agave/AGAVEDbIdPropCallbackItf.html" title="interface in org.biojava.bio.seq.io.agave"><span class="strong">AGAVEDbIdPropCallbackItf</span></a> - Interface in <a href="./org/biojava/bio/seq/io/agave/package-summary.html">org.biojava.bio.seq.io.agave</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/io/agave/AGAVEDbIdPropHandler.html" title="class in org.biojava.bio.seq.io.agave"><span class="strong">AGAVEDbIdPropHandler</span></a> - Class in <a href="./org/biojava/bio/seq/io/agave/package-summary.html">org.biojava.bio.seq.io.agave</a></dt>
<dd>
<div class="block">Deals with database crossreferences</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/agave/AGAVEDescPropHandler.html" title="class in org.biojava.bio.seq.io.agave"><span class="strong">AGAVEDescPropHandler</span></a> - Class in <a href="./org/biojava/bio/seq/io/agave/package-summary.html">org.biojava.bio.seq.io.agave</a></dt>
<dd>
<div class="block">Deals with database crossreferences</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/agave/AGAVEElementIdPropHandler.html" title="class in org.biojava.bio.seq.io.agave"><span class="strong">AGAVEElementIdPropHandler</span></a> - Class in <a href="./org/biojava/bio/seq/io/agave/package-summary.html">org.biojava.bio.seq.io.agave</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/io/agave/AGAVEEvidenceCallbackItf.html" title="interface in org.biojava.bio.seq.io.agave"><span class="strong">AGAVEEvidenceCallbackItf</span></a> - Interface in <a href="./org/biojava/bio/seq/io/agave/package-summary.html">org.biojava.bio.seq.io.agave</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/io/agave/AGAVEEvidenceHandler.html" title="class in org.biojava.bio.seq.io.agave"><span class="strong">AGAVEEvidenceHandler</span></a> - Class in <a href="./org/biojava/bio/seq/io/agave/package-summary.html">org.biojava.bio.seq.io.agave</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/io/agave/AGAVEExonsPropHandler.html" title="class in org.biojava.bio.seq.io.agave"><span class="strong">AGAVEExonsPropHandler</span></a> - Class in <a href="./org/biojava/bio/seq/io/agave/package-summary.html">org.biojava.bio.seq.io.agave</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/io/agave/AGAVEFeatureCallbackItf.html" title="interface in org.biojava.bio.seq.io.agave"><span class="strong">AGAVEFeatureCallbackItf</span></a> - Interface in <a href="./org/biojava/bio/seq/io/agave/package-summary.html">org.biojava.bio.seq.io.agave</a></dt>
<dd>
<div class="block">An interface that can be tested for by nested handlers
when trying to do a callback.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/agave/AGAVEFragmentOrderHandler.html" title="class in org.biojava.bio.seq.io.agave"><span class="strong">AGAVEFragmentOrderHandler</span></a> - Class in <a href="./org/biojava/bio/seq/io/agave/package-summary.html">org.biojava.bio.seq.io.agave</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/io/agave/AGAVEFragmentOrientationHandler.html" title="class in org.biojava.bio.seq.io.agave"><span class="strong">AGAVEFragmentOrientationHandler</span></a> - Class in <a href="./org/biojava/bio/seq/io/agave/package-summary.html">org.biojava.bio.seq.io.agave</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/io/agave/AGAVEGeneHandler.html" title="class in org.biojava.bio.seq.io.agave"><span class="strong">AGAVEGeneHandler</span></a> - Class in <a href="./org/biojava/bio/seq/io/agave/package-summary.html">org.biojava.bio.seq.io.agave</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/io/agave/AGAVEHandler.html" title="class in org.biojava.bio.seq.io.agave"><span class="strong">AGAVEHandler</span></a> - Class in <a href="./org/biojava/bio/seq/io/agave/package-summary.html">org.biojava.bio.seq.io.agave</a></dt>
<dd>
<div class="block">Handles the root AGAVE element
modified for agave format</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEHandler.html#AGAVEHandler()">AGAVEHandler()</a></span> - Constructor for class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEHandler</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/io/agave/AGAVEIdAlias.html" title="class in org.biojava.bio.seq.io.agave"><span class="strong">AGAVEIdAlias</span></a> - Class in <a href="./org/biojava/bio/seq/io/agave/package-summary.html">org.biojava.bio.seq.io.agave</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/io/agave/AGAVEIdAliasCallbackItf.html" title="interface in org.biojava.bio.seq.io.agave"><span class="strong">AGAVEIdAliasCallbackItf</span></a> - Interface in <a href="./org/biojava/bio/seq/io/agave/package-summary.html">org.biojava.bio.seq.io.agave</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/io/agave/AGAVEIdAliasPropHandler.html" title="class in org.biojava.bio.seq.io.agave"><span class="strong">AGAVEIdAliasPropHandler</span></a> - Class in <a href="./org/biojava/bio/seq/io/agave/package-summary.html">org.biojava.bio.seq.io.agave</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/io/agave/AGAVEKeywordPropHandler.html" title="class in org.biojava.bio.seq.io.agave"><span class="strong">AGAVEKeywordPropHandler</span></a> - Class in <a href="./org/biojava/bio/seq/io/agave/package-summary.html">org.biojava.bio.seq.io.agave</a></dt>
<dd>
<div class="block">Deals with AGAVE keywords</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/agave/AGAVEMapLocation.html" title="class in org.biojava.bio.seq.io.agave"><span class="strong">AGAVEMapLocation</span></a> - Class in <a href="./org/biojava/bio/seq/io/agave/package-summary.html">org.biojava.bio.seq.io.agave</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEMapLocation.html#AGAVEMapLocation()">AGAVEMapLocation()</a></span> - Constructor for class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEMapLocation.html" title="class in org.biojava.bio.seq.io.agave">AGAVEMapLocation</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/io/agave/AGAVEMapLocationPropHandler.html" title="class in org.biojava.bio.seq.io.agave"><span class="strong">AGAVEMapLocationPropHandler</span></a> - Class in <a href="./org/biojava/bio/seq/io/agave/package-summary.html">org.biojava.bio.seq.io.agave</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/io/agave/AGAVEMapPosition.html" title="class in org.biojava.bio.seq.io.agave"><span class="strong">AGAVEMapPosition</span></a> - Class in <a href="./org/biojava/bio/seq/io/agave/package-summary.html">org.biojava.bio.seq.io.agave</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEMapPosition.html#AGAVEMapPosition()">AGAVEMapPosition()</a></span> - Constructor for class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEMapPosition.html" title="class in org.biojava.bio.seq.io.agave">AGAVEMapPosition</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/io/agave/AGAVEMapPositionPropHandler.html" title="class in org.biojava.bio.seq.io.agave"><span class="strong">AGAVEMapPositionPropHandler</span></a> - Class in <a href="./org/biojava/bio/seq/io/agave/package-summary.html">org.biojava.bio.seq.io.agave</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/io/agave/AGAVEMatchAlignPropHandler.html" title="class in org.biojava.bio.seq.io.agave"><span class="strong">AGAVEMatchAlignPropHandler</span></a> - Class in <a href="./org/biojava/bio/seq/io/agave/package-summary.html">org.biojava.bio.seq.io.agave</a></dt>
<dd>
<div class="block">Deals with match_align</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/agave/AGAVEMatchDescPropHandler.html" title="class in org.biojava.bio.seq.io.agave"><span class="strong">AGAVEMatchDescPropHandler</span></a> - Class in <a href="./org/biojava/bio/seq/io/agave/package-summary.html">org.biojava.bio.seq.io.agave</a></dt>
<dd>
<div class="block">Deals with match_desc</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/agave/AGAVEMatchRegion.html" title="class in org.biojava.bio.seq.io.agave"><span class="strong">AGAVEMatchRegion</span></a> - Class in <a href="./org/biojava/bio/seq/io/agave/package-summary.html">org.biojava.bio.seq.io.agave</a></dt>
<dd>
<div class="block">match_region</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEMatchRegion.html#AGAVEMatchRegion()">AGAVEMatchRegion()</a></span> - Constructor for class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEMatchRegion.html" title="class in org.biojava.bio.seq.io.agave">AGAVEMatchRegion</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/io/agave/AGAVEMatchRegionPropHandler.html" title="class in org.biojava.bio.seq.io.agave"><span class="strong">AGAVEMatchRegionPropHandler</span></a> - Class in <a href="./org/biojava/bio/seq/io/agave/package-summary.html">org.biojava.bio.seq.io.agave</a></dt>
<dd>
<div class="block">Deals with match_region</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/agave/AGAVEMrnaHandler.html" title="class in org.biojava.bio.seq.io.agave"><span class="strong">AGAVEMrnaHandler</span></a> - Class in <a href="./org/biojava/bio/seq/io/agave/package-summary.html">org.biojava.bio.seq.io.agave</a></dt>
<dd>
<div class="block">Handles the AGAVE <mrna> element</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/agave/AGAVENotePropHandler.html" title="class in org.biojava.bio.seq.io.agave"><span class="strong">AGAVENotePropHandler</span></a> - Class in <a href="./org/biojava/bio/seq/io/agave/package-summary.html">org.biojava.bio.seq.io.agave</a></dt>
<dd>
<div class="block">Deals with note</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/agave/AGAVEPredictedProteinHandler.html" title="class in org.biojava.bio.seq.io.agave"><span class="strong">AGAVEPredictedProteinHandler</span></a> - Class in <a href="./org/biojava/bio/seq/io/agave/package-summary.html">org.biojava.bio.seq.io.agave</a></dt>
<dd>
<div class="block">Handles the AGAVE <predicted_protein> element</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/agave/AGAVEProperty.html" title="class in org.biojava.bio.seq.io.agave"><span class="strong">AGAVEProperty</span></a> - Class in <a href="./org/biojava/bio/seq/io/agave/package-summary.html">org.biojava.bio.seq.io.agave</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEProperty.html#AGAVEProperty(java.lang.String, java.lang.String, java.lang.String, java.lang.String)">AGAVEProperty(String, String, String, String)</a></span> - Constructor for class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEProperty.html" title="class in org.biojava.bio.seq.io.agave">AGAVEProperty</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/io/agave/AGAVEQualifierPropHandler.html" title="class in org.biojava.bio.seq.io.agave"><span class="strong">AGAVEQualifierPropHandler</span></a> - Class in <a href="./org/biojava/bio/seq/io/agave/package-summary.html">org.biojava.bio.seq.io.agave</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/io/agave/AGAVEQueryRegion.html" title="class in org.biojava.bio.seq.io.agave"><span class="strong">AGAVEQueryRegion</span></a> - Class in <a href="./org/biojava/bio/seq/io/agave/package-summary.html">org.biojava.bio.seq.io.agave</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEQueryRegion.html#AGAVEQueryRegion()">AGAVEQueryRegion()</a></span> - Constructor for class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEQueryRegion.html" title="class in org.biojava.bio.seq.io.agave">AGAVEQueryRegion</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/io/agave/AGAVEQueryRegionPropHandler.html" title="class in org.biojava.bio.seq.io.agave"><span class="strong">AGAVEQueryRegionPropHandler</span></a> - Class in <a href="./org/biojava/bio/seq/io/agave/package-summary.html">org.biojava.bio.seq.io.agave</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/io/agave/AGAVERelatedAnnot.html" title="class in org.biojava.bio.seq.io.agave"><span class="strong">AGAVERelatedAnnot</span></a> - Class in <a href="./org/biojava/bio/seq/io/agave/package-summary.html">org.biojava.bio.seq.io.agave</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVERelatedAnnot.html#AGAVERelatedAnnot()">AGAVERelatedAnnot()</a></span> - Constructor for class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVERelatedAnnot.html" title="class in org.biojava.bio.seq.io.agave">AGAVERelatedAnnot</a></dt>
<dd>
<div class="block">construct..</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/agave/AGAVERelatedAnnotPropHandler.html" title="class in org.biojava.bio.seq.io.agave"><span class="strong">AGAVERelatedAnnotPropHandler</span></a> - Class in <a href="./org/biojava/bio/seq/io/agave/package-summary.html">org.biojava.bio.seq.io.agave</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/io/agave/AGAVEResultGroupHandler.html" title="class in org.biojava.bio.seq.io.agave"><span class="strong">AGAVEResultGroupHandler</span></a> - Class in <a href="./org/biojava/bio/seq/io/agave/package-summary.html">org.biojava.bio.seq.io.agave</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/io/agave/AGAVEResultPropertyPropHandler.html" title="class in org.biojava.bio.seq.io.agave"><span class="strong">AGAVEResultPropertyPropHandler</span></a> - Class in <a href="./org/biojava/bio/seq/io/agave/package-summary.html">org.biojava.bio.seq.io.agave</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/io/agave/AGAVESciPropertyPropHandler.html" title="class in org.biojava.bio.seq.io.agave"><span class="strong">AGAVESciPropertyPropHandler</span></a> - Class in <a href="./org/biojava/bio/seq/io/agave/package-summary.html">org.biojava.bio.seq.io.agave</a></dt>
<dd>
<div class="block">sci_property</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/agave/AGAVESeqFeatureHandler.html" title="class in org.biojava.bio.seq.io.agave"><span class="strong">AGAVESeqFeatureHandler</span></a> - Class in <a href="./org/biojava/bio/seq/io/agave/package-summary.html">org.biojava.bio.seq.io.agave</a></dt>
<dd>
<div class="block">seq_feature</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/agave/AGAVESeqLocationPropHandler.html" title="class in org.biojava.bio.seq.io.agave"><span class="strong">AGAVESeqLocationPropHandler</span></a> - Class in <a href="./org/biojava/bio/seq/io/agave/package-summary.html">org.biojava.bio.seq.io.agave</a></dt>
<dd>
<div class="block">seq_location</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/agave/AGAVESeqMapHandler.html" title="class in org.biojava.bio.seq.io.agave"><span class="strong">AGAVESeqMapHandler</span></a> - Class in <a href="./org/biojava/bio/seq/io/agave/package-summary.html">org.biojava.bio.seq.io.agave</a></dt>
<dd>
<div class="block">sequence_map</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/agave/AGAVESeqPropHandler.html" title="class in org.biojava.bio.seq.io.agave"><span class="strong">AGAVESeqPropHandler</span></a> - Class in <a href="./org/biojava/bio/seq/io/agave/package-summary.html">org.biojava.bio.seq.io.agave</a></dt>
<dd>
<div class="block">Deals with sequence code</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/agave/AGAVETranscriptHandler.html" title="class in org.biojava.bio.seq.io.agave"><span class="strong">AGAVETranscriptHandler</span></a> - Class in <a href="./org/biojava/bio/seq/io/agave/package-summary.html">org.biojava.bio.seq.io.agave</a></dt>
<dd>
<div class="block">transcript</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/agave/AGAVEUnorderedFragmentsHandler.html" title="class in org.biojava.bio.seq.io.agave"><span class="strong">AGAVEUnorderedFragmentsHandler</span></a> - Class in <a href="./org/biojava/bio/seq/io/agave/package-summary.html">org.biojava.bio.seq.io.agave</a></dt>
<dd>
<div class="block">unordered_fragments</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/agave/AGAVEViewPropHandler.html" title="class in org.biojava.bio.seq.io.agave"><span class="strong">AGAVEViewPropHandler</span></a> - Class in <a href="./org/biojava/bio/seq/io/agave/package-summary.html">org.biojava.bio.seq.io.agave</a></dt>
<dd>
<div class="block">Moves view attributes into annotation properties.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/agave/AgaveWriter.html" title="class in org.biojava.bio.seq.io.agave"><span class="strong">AgaveWriter</span></a> - Class in <a href="./org/biojava/bio/seq/io/agave/package-summary.html">org.biojava.bio.seq.io.agave</a></dt>
<dd>
<div class="block">Writes Sequence into AGAVE XML document.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AgaveWriter.html#AgaveWriter()">AgaveWriter()</a></span> - Constructor for class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AgaveWriter.html" title="class in org.biojava.bio.seq.io.agave">AgaveWriter</a></dt>
<dd>
<div class="block">Default constructor uses generic annotation to attribute mapping.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AgaveWriter.html#AgaveWriter(org.biojava.bio.seq.io.agave.AGAVEAnnotFilter)">AgaveWriter(AGAVEAnnotFilter)</a></span> - Constructor for class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AgaveWriter.html" title="class in org.biojava.bio.seq.io.agave">AgaveWriter</a></dt>
<dd>
<div class="block">Construct with data source specific annotation to attribute
mapping.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/agave/AgaveWriter.Indent.html" title="class in org.biojava.bio.seq.io.agave"><span class="strong">AgaveWriter.Indent</span></a> - Class in <a href="./org/biojava/bio/seq/io/agave/package-summary.html">org.biojava.bio.seq.io.agave</a></dt>
<dd>
<div class="block">Implements indenting for elements.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AgaveWriter.Indent.html#AgaveWriter.Indent()">AgaveWriter.Indent()</a></span> - Constructor for class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AgaveWriter.Indent.html" title="class in org.biojava.bio.seq.io.agave">AgaveWriter.Indent</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/io/agave/AGAVEXref.html" title="class in org.biojava.bio.seq.io.agave"><span class="strong">AGAVEXref</span></a> - Class in <a href="./org/biojava/bio/seq/io/agave/package-summary.html">org.biojava.bio.seq.io.agave</a></dt>
<dd>
<div class="block">xref</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEXref.html#AGAVEXref()">AGAVEXref()</a></span> - Constructor for class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEXref.html" title="class in org.biojava.bio.seq.io.agave">AGAVEXref</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/io/agave/AGAVEXrefCallbackItf.html" title="interface in org.biojava.bio.seq.io.agave"><span class="strong">AGAVEXrefCallbackItf</span></a> - Interface in <a href="./org/biojava/bio/seq/io/agave/package-summary.html">org.biojava.bio.seq.io.agave</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/io/agave/AGAVEXrefPropHandler.html" title="class in org.biojava.bio.seq.io.agave"><span class="strong">AGAVEXrefPropHandler</span></a> - Class in <a href="./org/biojava/bio/seq/io/agave/package-summary.html">org.biojava.bio.seq.io.agave</a></dt>
<dd>
<div class="block">handle AGAVE xref</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/agave/AGAVEXrefPropPropHandler.html" title="class in org.biojava.bio.seq.io.agave"><span class="strong">AGAVEXrefPropPropHandler</span></a> - Class in <a href="./org/biojava/bio/seq/io/agave/package-summary.html">org.biojava.bio.seq.io.agave</a></dt>
<dd>
<div class="block">xref_property</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/agave/AGAVEXrefs.html" title="class in org.biojava.bio.seq.io.agave"><span class="strong">AGAVEXrefs</span></a> - Class in <a href="./org/biojava/bio/seq/io/agave/package-summary.html">org.biojava.bio.seq.io.agave</a></dt>
<dd>
<div class="block">xrefs</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEXrefs.html#AGAVEXrefs()">AGAVEXrefs()</a></span> - Constructor for class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEXrefs.html" title="class in org.biojava.bio.seq.io.agave">AGAVEXrefs</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/io/agave/AGAVEXrefsPropHandler.html" title="class in org.biojava.bio.seq.io.agave"><span class="strong">AGAVEXrefsPropHandler</span></a> - Class in <a href="./org/biojava/bio/seq/io/agave/package-summary.html">org.biojava.bio.seq.io.agave</a></dt>
<dd>
<div class="block">Deals with database crossreferences (xrefs)</div>
</dd>
<dt><a href="./org/biojava/bio/program/tagvalue/Aggregator.html" title="class in org.biojava.bio.program.tagvalue"><span class="strong">Aggregator</span></a> - Class in <a href="./org/biojava/bio/program/tagvalue/package-summary.html">org.biojava.bio.program.tagvalue</a></dt>
<dd>
<div class="block">Joins multipel values into single values.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/Aggregator.html#Aggregator(org.biojava.bio.program.tagvalue.TagValueListener, org.biojava.bio.program.tagvalue.BoundaryFinder, java.lang.String)">Aggregator(TagValueListener, BoundaryFinder, String)</a></span> - Constructor for class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/Aggregator.html" title="class in org.biojava.bio.program.tagvalue">Aggregator</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/ProteinTools.html#ala()">ala()</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/ProteinTools.html" title="class in org.biojava.bio.seq">ProteinTools</a></dt>
<dd>
<div class="block">Returns the <code>AtomicSymbol</code> for the amino acid Alanine
(A)</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/Gotoh.html#ALIGFACTOR">ALIGFACTOR</a></span> - Static variable in class org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/Gotoh.html" title="class in org.biojava.bio.structure.align.pairwise">Gotoh</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/structure/align/helper/AligMatEl.html" title="class in org.biojava.bio.structure.align.helper"><span class="strong">AligMatEl</span></a> - Class in <a href="./org/biojava/bio/structure/align/helper/package-summary.html">org.biojava.bio.structure.align.helper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/helper/AligMatEl.html#AligMatEl()">AligMatEl()</a></span> - Constructor for class org.biojava.bio.structure.align.helper.<a href="./org/biojava/bio/structure/align/helper/AligMatEl.html" title="class in org.biojava.bio.structure.align.helper">AligMatEl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/StructurePairAligner.html#align(org.biojava.bio.structure.Structure, org.biojava.bio.structure.Structure)">align(Structure, Structure)</a></span> - Method in class org.biojava.bio.structure.align.<a href="./org/biojava/bio/structure/align/StructurePairAligner.html" title="class in org.biojava.bio.structure.align">StructurePairAligner</a></dt>
<dd>
<div class="block">calculate the alignment between the two full structures with default parameters</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/StructurePairAligner.html#align(org.biojava.bio.structure.Structure, org.biojava.bio.structure.Structure, org.biojava.bio.structure.align.StrucAligParameters)">align(Structure, Structure, StrucAligParameters)</a></span> - Method in class org.biojava.bio.structure.align.<a href="./org/biojava/bio/structure/align/StructurePairAligner.html" title="class in org.biojava.bio.structure.align">StructurePairAligner</a></dt>
<dd>
<div class="block">calculate the alignment between the two full structures with user provided parameters</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/StructurePairAligner.html#align(org.biojava.bio.structure.Atom[], org.biojava.bio.structure.Atom[], org.biojava.bio.structure.align.StrucAligParameters)">align(Atom[], Atom[], StrucAligParameters)</a></span> - Method in class org.biojava.bio.structure.align.<a href="./org/biojava/bio/structure/align/StructurePairAligner.html" title="class in org.biojava.bio.structure.align">StructurePairAligner</a></dt>
<dd>
<div class="block">calculate the protein structure superimposition, between two sets of atoms.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/SeqRes2AtomAligner.html#align(org.biojava.bio.structure.Structure, java.util.List)">align(Structure, List<Chain>)</a></span> - Method in class org.biojava.bio.structure.io.<a href="./org/biojava/bio/structure/io/SeqRes2AtomAligner.html" title="class in org.biojava.bio.structure.io">SeqRes2AtomAligner</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/SeqRes2AtomAligner.html#align(java.util.List, java.util.List)">align(List<Group>, List<Group>)</a></span> - Method in class org.biojava.bio.structure.io.<a href="./org/biojava/bio/structure/io/SeqRes2AtomAligner.html" title="class in org.biojava.bio.structure.io">SeqRes2AtomAligner</a></dt>
<dd>
<div class="block">aligns two chains of groups, where the first chain is representing the
list of amino acids as obtained from the SEQRES records, and the second chain
represents the groups obtained from the ATOM records (and containing the actual ATOM information).</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/AligNPE.html#align_NPE(org.biojava.bio.structure.jama.Matrix, org.biojava.bio.structure.align.StrucAligParameters)">align_NPE(Matrix, StrucAligParameters)</a></span> - Static method in class org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/AligNPE.html" title="class in org.biojava.bio.structure.align.pairwise">AligNPE</a></dt>
<dd>
<div class="block">Align w/o penalizing endpags.</div>
</dd>
<dt><a href="./org/biojava/bio/structure/align/pairwise/Alignable.html" title="interface in org.biojava.bio.structure.align.pairwise"><span class="strong">Alignable</span></a> - Interface in <a href="./org/biojava/bio/structure/align/pairwise/package-summary.html">org.biojava.bio.structure.align.pairwise</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/NeedlemanWunsch.html#alignAll(org.biojava.bio.seq.SequenceIterator, org.biojava.bio.seq.db.SequenceDB)">alignAll(SequenceIterator, SequenceDB)</a></span> - Method in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/NeedlemanWunsch.html" title="class in org.biojava.bio.alignment">NeedlemanWunsch</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/SequenceAlignment.html#alignAll(org.biojava.bio.seq.SequenceIterator, org.biojava.bio.seq.db.SequenceDB)">alignAll(SequenceIterator, SequenceDB)</a></span> - Method in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/SequenceAlignment.html" title="class in org.biojava.bio.alignment">SequenceAlignment</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/structure/gui/util/AlignedPosition.html" title="class in org.biojava.bio.structure.gui.util"><span class="strong">AlignedPosition</span></a> - Class in <a href="./org/biojava/bio/structure/gui/util/package-summary.html">org.biojava.bio.structure.gui.util</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/util/AlignedPosition.html#AlignedPosition()">AlignedPosition()</a></span> - Constructor for class org.biojava.bio.structure.gui.util.<a href="./org/biojava/bio/structure/gui/util/AlignedPosition.html" title="class in org.biojava.bio.structure.gui.util">AlignedPosition</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/io/AlignIOConstants.html" title="class in org.biojava.bio.seq.io"><span class="strong">AlignIOConstants</span></a> - Class in <a href="./org/biojava/bio/seq/io/package-summary.html">org.biojava.bio.seq.io</a></dt>
<dd>
<div class="block"><code>AlignIOConstants</code> contains constants used to identify
sequence formats, alphabets etc, in the context of reading and
writing alignments.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/AlignIOConstants.html#AlignIOConstants()">AlignIOConstants()</a></span> - Constructor for class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/AlignIOConstants.html" title="class in org.biojava.bio.seq.io">AlignIOConstants</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/NeedlemanWunsch.html#alignment">alignment</a></span> - Variable in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/NeedlemanWunsch.html" title="class in org.biojava.bio.alignment">NeedlemanWunsch</a></dt>
<dd>
<div class="block">The result of a successful alignment as a simple String.</div>
</dd>
<dt><a href="./org/biojava/bio/program/das/dasalignment/Alignment.html" title="class in org.biojava.bio.program.das.dasalignment"><span class="strong">Alignment</span></a> - Class in <a href="./org/biojava/bio/program/das/dasalignment/package-summary.html">org.biojava.bio.program.das.dasalignment</a></dt>
<dd>
<div class="block">Alignment object to contain/manage a DAS alignment.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/dasalignment/Alignment.html#Alignment()">Alignment()</a></span> - Constructor for class org.biojava.bio.program.das.dasalignment.<a href="./org/biojava/bio/program/das/dasalignment/Alignment.html" title="class in org.biojava.bio.program.das.dasalignment">Alignment</a></dt>
<dd>
<div class="block">Construct a new empty Alignment object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/homol/Homology.html#ALIGNMENT">ALIGNMENT</a></span> - Static variable in interface org.biojava.bio.seq.homol.<a href="./org/biojava/bio/seq/homol/Homology.html" title="interface in org.biojava.bio.seq.homol">Homology</a></dt>
<dd>
<div class="block">Signals that the alignment describing the homologous sequences
has changed.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/homol/SimilarityPairFeature.Template.html#alignment">alignment</a></span> - Variable in class org.biojava.bio.seq.homol.<a href="./org/biojava/bio/seq/homol/SimilarityPairFeature.Template.html" title="class in org.biojava.bio.seq.homol">SimilarityPairFeature.Template</a></dt>
<dd>
<div class="block"><code>alignment</code> <code>Alignment</code> field.</div>
</dd>
<dt><a href="./org/biojava/bio/symbol/Alignment.html" title="interface in org.biojava.bio.symbol"><span class="strong">Alignment</span></a> - Interface in <a href="./org/biojava/bio/symbol/package-summary.html">org.biojava.bio.symbol</a></dt>
<dd>
<div class="block">An alignment containing multiple <span class="type">SymbolList</span>s.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SymbolListViews.html#alignment(java.util.Map)">alignment(Map)</a></span> - Static method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SymbolListViews.html" title="class in org.biojava.bio.symbol">SymbolListViews</a></dt>
<dd>
<div class="block">Construct an alignment of the SymbolLists contained in the values collection
of <code>labelToSymList</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SymbolListViews.html#alignment(java.util.List, org.biojava.bio.symbol.SymbolList)">alignment(List, SymbolList)</a></span> - Static method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SymbolListViews.html" title="class in org.biojava.bio.symbol">SymbolListViews</a></dt>
<dd>
<div class="block">View a SymbolList over a cross-product Alphabet as an Alignment.</div>
</dd>
<dt><a href="./org/biojava/bio/symbol/Alignment.SymbolListIterator.html" title="class in org.biojava.bio.symbol"><span class="strong">Alignment.SymbolListIterator</span></a> - Class in <a href="./org/biojava/bio/symbol/package-summary.html">org.biojava.bio.symbol</a></dt>
<dd>
<div class="block">Iterator implementation looping over symbol lists in an alignment using
the labels.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/Alignment.SymbolListIterator.html#Alignment.SymbolListIterator(org.biojava.bio.symbol.Alignment)">Alignment.SymbolListIterator(Alignment)</a></span> - Constructor for class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/Alignment.SymbolListIterator.html" title="class in org.biojava.bio.symbol">Alignment.SymbolListIterator</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/AlignmentStAXHandler.html#ALIGNMENT_HANDLER_FACTORY">ALIGNMENT_HANDLER_FACTORY</a></span> - Static variable in class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/AlignmentStAXHandler.html" title="class in org.biojava.bio.program.ssbind">AlignmentStAXHandler</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/structure/gui/util/AlignmentCalc.html" title="class in org.biojava.bio.structure.gui.util"><span class="strong">AlignmentCalc</span></a> - Class in <a href="./org/biojava/bio/structure/gui/util/package-summary.html">org.biojava.bio.structure.gui.util</a></dt>
<dd>
<div class="block">A class that obtains two structures via DAS and aligns them
This is done in a separate thread.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/util/AlignmentCalc.html#AlignmentCalc(org.biojava.bio.structure.gui.AlignmentGui, org.biojava.bio.structure.Structure, org.biojava.bio.structure.Structure)">AlignmentCalc(AlignmentGui, Structure, Structure)</a></span> - Constructor for class org.biojava.bio.structure.gui.util.<a href="./org/biojava/bio/structure/gui/util/AlignmentCalc.html" title="class in org.biojava.bio.structure.gui.util">AlignmentCalc</a></dt>
<dd>
<div class="block">requests an alignment of pdb1 vs pdb 2.</div>
</dd>
<dt><a href="./org/biojava/bio/alignment/AlignmentElement.html" title="interface in org.biojava.bio.alignment"><span class="strong">AlignmentElement</span></a> - Interface in <a href="./org/biojava/bio/alignment/package-summary.html">org.biojava.bio.alignment</a></dt>
<dd>
<div class="block">AlignmentElement is a class which represents a SymbolList and its
location within an Alignment This is for use in
UnequalLengthAlignments and ARAlignments.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/AlignmentFormat.html" title="interface in org.biojava.bio.seq.io"><span class="strong">AlignmentFormat</span></a> - Interface in <a href="./org/biojava/bio/seq/io/package-summary.html">org.biojava.bio.seq.io</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/structure/gui/AlignmentGui.html" title="class in org.biojava.bio.structure.gui"><span class="strong">AlignmentGui</span></a> - Class in <a href="./org/biojava/bio/structure/gui/package-summary.html">org.biojava.bio.structure.gui</a></dt>
<dd>
<div class="block">A JFrame that allows to trigger a pairwise structure alignment,
either from files in a directory,
or after manual upload.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/AlignmentGui.html#AlignmentGui()">AlignmentGui()</a></span> - Constructor for class org.biojava.bio.structure.gui.<a href="./org/biojava/bio/structure/gui/AlignmentGui.html" title="class in org.biojava.bio.structure.gui">AlignmentGui</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/blast2html/AlignmentMarker.html" title="class in org.biojava.bio.program.blast2html"><span class="strong">AlignmentMarker</span></a> - Class in <a href="./org/biojava/bio/program/blast2html/package-summary.html">org.biojava.bio.program.blast2html</a></dt>
<dd>
<div class="block">
Class to do simple HTML colouring of sequence alignments.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/blast2html/AlignmentMarker.html#AlignmentMarker(org.biojava.bio.program.blast2html.ColourCommand, org.biojava.bio.program.blast2html.AlignmentStyler)">AlignmentMarker(ColourCommand, AlignmentStyler)</a></span> - Constructor for class org.biojava.bio.program.blast2html.<a href="./org/biojava/bio/program/blast2html/AlignmentMarker.html" title="class in org.biojava.bio.program.blast2html">AlignmentMarker</a></dt>
<dd>
<div class="block">Creates a new <code>AlignmentMarker</code> instance.</div>
</dd>
<dt><a href="./org/biojava/bio/structure/gui/events/AlignmentPositionListener.html" title="interface in org.biojava.bio.structure.gui.events"><span class="strong">AlignmentPositionListener</span></a> - Interface in <a href="./org/biojava/bio/structure/gui/events/package-summary.html">org.biojava.bio.structure.gui.events</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/FlexibleAlignment.html#alignmentRange">alignmentRange</a></span> - Variable in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/FlexibleAlignment.html" title="class in org.biojava.bio.alignment">FlexibleAlignment</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/gui/sequence/AlignmentRenderer.html" title="class in org.biojava.bio.gui.sequence"><span class="strong">AlignmentRenderer</span></a> - Class in <a href="./org/biojava/bio/gui/sequence/package-summary.html">org.biojava.bio.gui.sequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/AlignmentRenderer.html#AlignmentRenderer()">AlignmentRenderer()</a></span> - Constructor for class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/AlignmentRenderer.html" title="class in org.biojava.bio.gui.sequence">AlignmentRenderer</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/ssbind/AlignmentStAXHandler.html" title="class in org.biojava.bio.program.ssbind"><span class="strong">AlignmentStAXHandler</span></a> - Class in <a href="./org/biojava/bio/program/ssbind/package-summary.html">org.biojava.bio.program.ssbind</a></dt>
<dd>
<div class="block"><code>AlignmentStAXHandler</code> handles the BlastLikeAlignment
element of BioJava BlastLike XML.</div>
</dd>
<dt><a href="./org/biojava/bio/structure/align/pairwise/AligNPE.html" title="class in org.biojava.bio.structure.align.pairwise"><span class="strong">AligNPE</span></a> - Class in <a href="./org/biojava/bio/structure/align/pairwise/package-summary.html">org.biojava.bio.structure.align.pairwise</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/AligNPE.html#AligNPE()">AligNPE()</a></span> - Constructor for class org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/AligNPE.html" title="class in org.biojava.bio.structure.align.pairwise">AligNPE</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/structure/align/helper/AlignTools.html" title="class in org.biojava.bio.structure.align.helper"><span class="strong">AlignTools</span></a> - Class in <a href="./org/biojava/bio/structure/align/helper/package-summary.html">org.biojava.bio.structure.align.helper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/helper/AlignTools.html#AlignTools()">AlignTools()</a></span> - Constructor for class org.biojava.bio.structure.align.helper.<a href="./org/biojava/bio/structure/align/helper/AlignTools.html" title="class in org.biojava.bio.structure.align.helper">AlignTools</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/xff/ElementRecognizer.html#ALL">ALL</a></span> - Static variable in interface org.biojava.bio.program.xff.<a href="./org/biojava/bio/program/xff/ElementRecognizer.html" title="interface in org.biojava.bio.program.xff">ElementRecognizer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.html#all">all</a></span> - Static variable in interface org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.html" title="interface in org.biojava.bio.seq">FeatureFilter</a></dt>
<dd>
<div class="block">All features are selected by this filter.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FilterUtils.html#all()">all()</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FilterUtils.html" title="class in org.biojava.bio.seq">FilterUtils</a></dt>
<dd>
<div class="block">Return a filter which matches all features.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/ElementRecognizer.html#ALL">ALL</a></span> - Static variable in interface org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/ElementRecognizer.html" title="interface in org.biojava.bio.seq.io.agave">ElementRecognizer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game/ElementRecognizer.html#ALL">ALL</a></span> - Static variable in interface org.biojava.bio.seq.io.game.<a href="./org/biojava/bio/seq/io/game/ElementRecognizer.html" title="interface in org.biojava.bio.seq.io.game">ElementRecognizer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.html#all">all</a></span> - Static variable in interface org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.html" title="interface in org.biojavax.bio.db.biosql">BioSQLFeatureFilter</a></dt>
<dd>
<div class="block">All features are selected by this filter.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/chem/PolymerType.html#ALL_POLYMER_TYPES">ALL_POLYMER_TYPES</a></span> - Static variable in enum org.biojava.bio.structure.io.mmcif.chem.<a href="./org/biojava/bio/structure/io/mmcif/chem/PolymerType.html" title="enum in org.biojava.bio.structure.io.mmcif.chem">PolymerType</a></dt>
<dd>
<div class="block">Convenience <tt>Set</tt> of all polymer types.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/DASSequenceDB.html#allEntryPointsDB()">allEntryPointsDB()</a></span> - Method in class org.biojava.bio.program.das.<a href="./org/biojava/bio/program/das/DASSequenceDB.html" title="class in org.biojava.bio.program.das">DASSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/FlexibleAlignment.html#allGaps(org.biojava.bio.symbol.SymbolList, int, int)">allGaps(SymbolList, int, int)</a></span> - Method in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/FlexibleAlignment.html" title="class in org.biojava.bio.alignment">FlexibleAlignment</a></dt>
<dd>
<div class="block">make sure that all Symbols in this range are gaps</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/AnnotationTools.html#allIn(org.biojava.bio.Annotation, org.biojava.bio.AnnotationType)">allIn(Annotation, AnnotationType)</a></span> - Static method in class org.biojava.bio.<a href="./org/biojava/bio/AnnotationTools.html" title="class in org.biojava.bio">AnnotationTools</a></dt>
<dd>
<div class="block">
Destructive down-cast an annotation to a type.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/AnnotationTools.html#allOut(org.biojava.bio.Annotation, org.biojava.bio.AnnotationType)">allOut(Annotation, AnnotationType)</a></span> - Static method in class org.biojava.bio.<a href="./org/biojava/bio/AnnotationTools.html" title="class in org.biojava.bio">AnnotationTools</a></dt>
<dd>
<div class="block"><code>allOut</code> returns a new <code>Annotation</code>
containing only those values in the <code>Annotation</code>
argument which are <strong>not</strong> of a type specified by
the <code>AnnotationType</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/hmmer/HmmerProfileParser.html#alph">alph</a></span> - Variable in class org.biojava.bio.program.hmmer.<a href="./org/biojava/bio/program/hmmer/HmmerProfileParser.html" title="class in org.biojava.bio.program.hmmer">HmmerProfileParser</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/AbstractULAlignment.html#alphabet">alphabet</a></span> - Variable in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/AbstractULAlignment.html" title="class in org.biojava.bio.alignment">AbstractULAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/SubstitutionMatrix.html#alphabet">alphabet</a></span> - Variable in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/SubstitutionMatrix.html" title="class in org.biojava.bio.alignment">SubstitutionMatrix</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/symbol/Alphabet.html" title="interface in org.biojava.bio.symbol"><span class="strong">Alphabet</span></a> - Interface in <a href="./org/biojava/bio/symbol/package-summary.html">org.biojava.bio.symbol</a></dt>
<dd>
<div class="block">
The set of AtomicSymbols which can be concatenated together to make a
SymbolList.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AlphabetManager.html#alphabetForName(java.lang.String)">alphabetForName(String)</a></span> - Static method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AlphabetManager.html" title="class in org.biojava.bio.symbol">AlphabetManager</a></dt>
<dd>
<div class="block">Retrieve the alphabet for a specific name.</div>
</dd>
<dt><a href="./org/biojava/bio/symbol/AlphabetIndex.html" title="interface in org.biojava.bio.symbol"><span class="strong">AlphabetIndex</span></a> - Interface in <a href="./org/biojava/bio/symbol/package-summary.html">org.biojava.bio.symbol</a></dt>
<dd>
<div class="block">
Map between Symbols and index numbers.</div>
</dd>
<dt><a href="./org/biojava/bio/symbol/AlphabetManager.html" title="class in org.biojava.bio.symbol"><span class="strong">AlphabetManager</span></a> - Class in <a href="./org/biojava/bio/symbol/package-summary.html">org.biojava.bio.symbol</a></dt>
<dd>
<div class="block">Utility methods for working with Alphabets.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AlphabetManager.html#AlphabetManager()">AlphabetManager()</a></span> - Constructor for class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AlphabetManager.html" title="class in org.biojava.bio.symbol">AlphabetManager</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/ssbind/AlphabetResolver.html" title="class in org.biojava.bio.program.ssbind"><span class="strong">AlphabetResolver</span></a> - Class in <a href="./org/biojava/bio/program/ssbind/package-summary.html">org.biojava.bio.program.ssbind</a></dt>
<dd>
<div class="block"><code>AlphabetResolver</code>s are helpers which determine which
type of sequence <code>Alphabet</code> to expect from a search
result.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/AlphabetResolver.html#AlphabetResolver()">AlphabetResolver()</a></span> - Constructor for class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/AlphabetResolver.html" title="class in org.biojava.bio.program.ssbind">AlphabetResolver</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AlphabetManager.html#alphabets()">alphabets()</a></span> - Static method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AlphabetManager.html" title="class in org.biojava.bio.symbol">AlphabetManager</a></dt>
<dd>
<div class="block">Get an iterator over all alphabets known.</div>
</dd>
<dt><a href="./org/biojava/bio/structure/AlphaCTools.html" title="class in org.biojava.bio.structure"><span class="strong">AlphaCTools</span></a> - Class in <a href="./org/biojava/bio/structure/package-summary.html">org.biojava.bio.structure</a></dt>
<dd>
<div class="block">AlphaCTools is a collection of static convenience methods for dealing with
Alpha Carbon Backbone Phi / Psi angles.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/AlphaCTools.html#AlphaCTools()">AlphaCTools()</a></span> - Constructor for class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/AlphaCTools.html" title="class in org.biojava.bio.structure">AlphaCTools</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/automata/FiniteAutomaton.html#alphaIndex(org.biojava.bio.symbol.Symbol)">alphaIndex(Symbol)</a></span> - Method in class org.biojava.utils.automata.<a href="./org/biojava/utils/automata/FiniteAutomaton.html" title="class in org.biojava.utils.automata">FiniteAutomaton</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/automata/Nfa.html#alphaIndex(org.biojava.bio.symbol.Symbol)">alphaIndex(Symbol)</a></span> - Method in class org.biojava.utils.automata.<a href="./org/biojava/utils/automata/Nfa.html" title="class in org.biojava.utils.automata">Nfa</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/ontology/AlreadyExistsException.html" title="class in org.biojava.ontology"><span class="strong">AlreadyExistsException</span></a> - Exception in <a href="./org/biojava/ontology/package-summary.html">org.biojava.ontology</a></dt>
<dd>
<div class="block">Thrown to indicate that a term or triple can't be added to an ontology
because it is already present.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/AlreadyExistsException.html#AlreadyExistsException()">AlreadyExistsException()</a></span> - Constructor for exception org.biojava.ontology.<a href="./org/biojava/ontology/AlreadyExistsException.html" title="class in org.biojava.ontology">AlreadyExistsException</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/AlreadyExistsException.html#AlreadyExistsException(java.lang.String)">AlreadyExistsException(String)</a></span> - Constructor for exception org.biojava.ontology.<a href="./org/biojava/ontology/AlreadyExistsException.html" title="class in org.biojava.ontology">AlreadyExistsException</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/obo/OboFileHandler.html#ALT_ID">ALT_ID</a></span> - Static variable in class org.biojava.ontology.obo.<a href="./org/biojava/ontology/obo/OboFileHandler.html" title="class in org.biojava.ontology.obo">OboFileHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/TranslationTable.html#ALT_YEAST_NUC">ALT_YEAST_NUC</a></span> - Static variable in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/TranslationTable.html" title="interface in org.biojava.bio.symbol">TranslationTable</a></dt>
<dd>
<div class="block">Translation table name for the alternative yeast nuclear
genetic code.</div>
</dd>
<dt><a href="./org/biojava/bio/structure/align/pairwise/AltAligComparator.html" title="class in org.biojava.bio.structure.align.pairwise"><span class="strong">AltAligComparator</span></a> - Class in <a href="./org/biojava/bio/structure/align/pairwise/package-summary.html">org.biojava.bio.structure.align.pairwise</a></dt>
<dd>
<div class="block">a comparator to sort AlternativeAlignments based on their number of equivalent residues
and RMSD.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/AltAligComparator.html#AltAligComparator()">AltAligComparator()</a></span> - Constructor for class org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/AltAligComparator.html" title="class in org.biojava.bio.structure.align.pairwise">AltAligComparator</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/io/AlternateTokenization.html" title="class in org.biojava.bio.seq.io"><span class="strong">AlternateTokenization</span></a> - Class in <a href="./org/biojava/bio/seq/io/package-summary.html">org.biojava.bio.seq.io</a></dt>
<dd>
<div class="block">Implementation of SymbolTokenization which binds symbols to
strings of characters.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/AlternateTokenization.html#AlternateTokenization(org.biojava.bio.symbol.Alphabet, boolean)">AlternateTokenization(Alphabet, boolean)</a></span> - Constructor for class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/AlternateTokenization.html" title="class in org.biojava.bio.seq.io">AlternateTokenization</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html#ALTERNATIVE_PRODUCTS">ALTERNATIVE_PRODUCTS</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html" title="class in org.biojavax.bio.seq.io">UniProtCommentParser</a></dt>
<dd>
<div class="block">A name for a comment type.</div>
</dd>
<dt><a href="./org/biojava/bio/structure/align/pairwise/AlternativeAlignment.html" title="class in org.biojava.bio.structure.align.pairwise"><span class="strong">AlternativeAlignment</span></a> - Class in <a href="./org/biojava/bio/structure/align/pairwise/package-summary.html">org.biojava.bio.structure.align.pairwise</a></dt>
<dd>
<div class="block">Implements a class which handles one possible (alternative) solution.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/AlternativeAlignment.html#AlternativeAlignment()">AlternativeAlignment()</a></span> - Constructor for class org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/AlternativeAlignment.html" title="class in org.biojava.bio.structure.align.pairwise">AlternativeAlignment</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/structure/gui/util/AlternativeAlignmentFrame.html" title="class in org.biojava.bio.structure.gui.util"><span class="strong">AlternativeAlignmentFrame</span></a> - Class in <a href="./org/biojava/bio/structure/gui/util/package-summary.html">org.biojava.bio.structure.gui.util</a></dt>
<dd>
<div class="block">a frame showing the alternative alignments, which are the result of a structure superimposition</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/util/AlternativeAlignmentFrame.html#AlternativeAlignmentFrame(org.biojava.bio.structure.Structure, org.biojava.bio.structure.Structure)">AlternativeAlignmentFrame(Structure, Structure)</a></span> - Constructor for class org.biojava.bio.structure.gui.util.<a href="./org/biojava/bio/structure/gui/util/AlternativeAlignmentFrame.html" title="class in org.biojava.bio.structure.gui.util">AlternativeAlignmentFrame</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ChangeListener.html#ALWAYS_VETO">ALWAYS_VETO</a></span> - Static variable in interface org.biojava.utils.<a href="./org/biojava/utils/ChangeListener.html" title="interface in org.biojava.utils">ChangeListener</a></dt>
<dd>
<div class="block">Convenience implementation which vetoes every change of which it is
notified.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOConstants.html#AMBIGUOUS">AMBIGUOUS</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOConstants.html" title="class in org.biojava.bio.seq.io">SeqIOConstants</a></dt>
<dd>
<div class="block"><code>AMBIGUOUS</code> indicates that a sequence contains
ambiguity symbols.</div>
</dd>
<dt><a href="./org/biojava/bio/structure/AminoAcid.html" title="interface in org.biojava.bio.structure"><span class="strong">AminoAcid</span></a> - Interface in <a href="./org/biojava/bio/structure/package-summary.html">org.biojava.bio.structure</a></dt>
<dd>
<div class="block">
A <a href="./org/biojava/bio/structure/Group.html" title="interface in org.biojava.bio.structure"><code>Group</code></a> that represents an AminoAcid.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/GroupType.html#AMINOACID">AMINOACID</a></span> - Static variable in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/GroupType.html" title="class in org.biojava.bio.structure">GroupType</a></dt>
<dd>
<div class="block">the type for amino acids</div>
</dd>
<dt><a href="./org/biojava/bio/structure/AminoAcidImpl.html" title="class in org.biojava.bio.structure"><span class="strong">AminoAcidImpl</span></a> - Class in <a href="./org/biojava/bio/structure/package-summary.html">org.biojava.bio.structure</a></dt>
<dd>
<div class="block">AminoAcid inherits most from Hetatom.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/AminoAcidImpl.html#AminoAcidImpl()">AminoAcidImpl()</a></span> - Constructor for class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/AminoAcidImpl.html" title="class in org.biojava.bio.structure">AminoAcidImpl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/FastaFormat.html#aminoAcids">aminoAcids</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/FastaFormat.html" title="class in org.biojavax.bio.seq.io">FastaFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Calc.html#amount(org.biojava.bio.structure.Atom)">amount(Atom)</a></span> - Static method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Calc.html" title="class in org.biojava.bio.structure">Calc</a></dt>
<dd>
<div class="block">amount.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/filter/FilterTransformer.html#and(org.biojava.bio.seq.FeatureFilter.And, org.biojava.bio.seq.FeatureFilter, org.biojava.bio.seq.FeatureFilter)">and(FeatureFilter.And, FeatureFilter, FeatureFilter)</a></span> - Method in class org.biojava.bio.seq.filter.<a href="./org/biojava/bio/seq/filter/FilterTransformer.html" title="class in org.biojava.bio.seq.filter">FilterTransformer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FilterUtils.html#and(org.biojava.bio.seq.FeatureFilter, org.biojava.bio.seq.FeatureFilter)">and(FeatureFilter, FeatureFilter)</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FilterUtils.html" title="class in org.biojava.bio.seq">FilterUtils</a></dt>
<dd>
<div class="block">Construct a new filter which matches the intersection of two other
filters.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FilterUtils.html#and(org.biojava.bio.seq.FeatureFilter[])">and(FeatureFilter[])</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FilterUtils.html" title="class in org.biojava.bio.seq">FilterUtils</a></dt>
<dd>
<div class="block">Constructs a new filter which matches the intersection of a set of filters.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.HibernateFeatureFilter.html#and">and</a></span> - Variable in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.HibernateFeatureFilter.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.HibernateFeatureFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Calc.html#angle(org.biojava.bio.structure.Atom, org.biojava.bio.structure.Atom)">angle(Atom, Atom)</a></span> - Static method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Calc.html" title="class in org.biojava.bio.structure">Calc</a></dt>
<dd>
<div class="block">angle.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/StAXFeatureHandler.html#annot">annot</a></span> - Variable in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/StAXFeatureHandler.html" title="class in org.biojava.bio.seq.io.agave">StAXFeatureHandler</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/Annotatable.html" title="interface in org.biojava.bio"><span class="strong">Annotatable</span></a> - Interface in <a href="./org/biojava/bio/package-summary.html">org.biojava.bio</a></dt>
<dd>
<div class="block">Indicates that an object has an associated annotation.</div>
</dd>
<dt><a href="./org/biojava/bio/Annotatable.AnnotationForwarder.html" title="class in org.biojava.bio"><span class="strong">Annotatable.AnnotationForwarder</span></a> - Class in <a href="./org/biojava/bio/package-summary.html">org.biojava.bio</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>use
<code>new ChangeForwarder.Retyper(source, cs, Annotation.PROPERTY)</code>
instead</i></div>
</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/Annotatable.AnnotationForwarder.html#Annotatable.AnnotationForwarder(java.lang.Object, org.biojava.utils.ChangeSupport)">Annotatable.AnnotationForwarder(Object, ChangeSupport)</a></span> - Constructor for class org.biojava.bio.<a href="./org/biojava/bio/Annotatable.AnnotationForwarder.html" title="class in org.biojava.bio">Annotatable.AnnotationForwarder</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Create a new AnnotationForwarder that will forward events for a source
using a change support.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/WeightMatrixAnnotator.html#annotate(org.biojava.bio.seq.Sequence)">annotate(Sequence)</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/WeightMatrixAnnotator.html" title="class in org.biojava.bio.dp">WeightMatrixAnnotator</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/molbio/RestrictionMapper.html#annotate(org.biojava.bio.seq.Sequence)">annotate(Sequence)</a></span> - Method in class org.biojava.bio.molbio.<a href="./org/biojava/bio/molbio/RestrictionMapper.html" title="class in org.biojava.bio.molbio">RestrictionMapper</a></dt>
<dd>
<div class="block"><code>annotate</code> adds <code>Feature</code>s which
represent restriction sites.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/SequenceAnnotator.html#annotate(org.biojava.bio.seq.Sequence)">annotate(Sequence)</a></span> - Method in interface org.biojava.bio.seq.<a href="./org/biojava/bio/seq/SequenceAnnotator.html" title="interface in org.biojava.bio.seq">SequenceAnnotator</a></dt>
<dd>
<div class="block">Return an annotated version of a sequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SequenceDBSequenceBuilder.html#ANNOTATE_EXISTING">ANNOTATE_EXISTING</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SequenceDBSequenceBuilder.html" title="class in org.biojava.bio.seq.io">SequenceDBSequenceBuilder</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/db/AnnotatedSequenceDB.html" title="class in org.biojava.bio.seq.db"><span class="strong">AnnotatedSequenceDB</span></a> - Class in <a href="./org/biojava/bio/seq/db/package-summary.html">org.biojava.bio.seq.db</a></dt>
<dd>
<div class="block">SequenceDB implementation which lazily applies a SequenceAnnotator
to sequences retrieved from a SequenceDB.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/AnnotatedSequenceDB.html#AnnotatedSequenceDB(org.biojava.bio.seq.db.SequenceDB, org.biojava.bio.seq.SequenceAnnotator)">AnnotatedSequenceDB(SequenceDB, SequenceAnnotator)</a></span> - Constructor for class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/AnnotatedSequenceDB.html" title="class in org.biojava.bio.seq.db">AnnotatedSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFTools.html#annotateSequence(org.biojava.bio.seq.Sequence, org.biojava.bio.program.gff.GFFEntrySet)">annotateSequence(Sequence, GFFEntrySet)</a></span> - Static method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFTools.html" title="class in org.biojava.bio.program.gff">GFFTools</a></dt>
<dd>
<div class="block">Annotates a sequence with the features from a GFF entry set with sequence
name matching this sequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFTools.html#annotateSequence(org.biojava.bio.seq.Sequence, org.biojava.bio.program.gff.GFFEntrySet, boolean)">annotateSequence(Sequence, GFFEntrySet, boolean)</a></span> - Static method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFTools.html" title="class in org.biojava.bio.program.gff">GFFTools</a></dt>
<dd>
<div class="block">Annotates a sequence with the features from a GFF entry set.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFTools.html#annotateSequences(org.biojava.bio.seq.db.SequenceDB, org.biojava.bio.program.gff.GFFEntrySet)">annotateSequences(SequenceDB, GFFEntrySet)</a></span> - Static method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFTools.html" title="class in org.biojava.bio.program.gff">GFFTools</a></dt>
<dd>
<div class="block">Annotates all sequences in a sequence DB with features from a GFF entry set.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/xff/XFFTools.html#annotateXFF(java.io.File, org.biojava.bio.seq.Sequence)">annotateXFF(File, Sequence)</a></span> - Static method in class org.biojava.bio.program.xff.<a href="./org/biojava/bio/program/xff/XFFTools.html" title="class in org.biojava.bio.program.xff">XFFTools</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/xff/XFFTools.html#annotateXFF(java.io.File, org.biojava.bio.seq.Sequence, org.biojava.bio.Annotation)">annotateXFF(File, Sequence, Annotation)</a></span> - Static method in class org.biojava.bio.program.xff.<a href="./org/biojava/bio/program/xff/XFFTools.html" title="class in org.biojava.bio.program.xff">XFFTools</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/Annotatable.html#ANNOTATION">ANNOTATION</a></span> - Static variable in interface org.biojava.bio.<a href="./org/biojava/bio/Annotatable.html" title="interface in org.biojava.bio">Annotatable</a></dt>
<dd>
<div class="block">Signals that the associated Annotation has altered in some way.</div>
</dd>
<dt><a href="./org/biojava/bio/Annotation.html" title="interface in org.biojava.bio"><span class="strong">Annotation</span></a> - Interface in <a href="./org/biojava/bio/package-summary.html">org.biojava.bio</a></dt>
<dd>
<div class="block">
Arbitrary annotation associated with one or more objects.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/Feature.Template.html#annotation">annotation</a></span> - Variable in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/Feature.Template.html" title="class in org.biojava.bio.seq">Feature.Template</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SequenceBuilderBase.html#annotation">annotation</a></span> - Variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SequenceBuilderBase.html" title="class in org.biojava.bio.seq.io">SequenceBuilderBase</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/MergeAnnotation.html#ANNOTATION_ADD">ANNOTATION_ADD</a></span> - Static variable in class org.biojava.bio.<a href="./org/biojava/bio/MergeAnnotation.html" title="class in org.biojava.bio">MergeAnnotation</a></dt>
<dd>
<div class="block">ChangeType of ChangeEvent fired before and after an annotation is added
to MergeAnnotation.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/MergeAnnotation.html#ANNOTATION_CHANGED">ANNOTATION_CHANGED</a></span> - Static variable in class org.biojava.bio.<a href="./org/biojava/bio/MergeAnnotation.html" title="class in org.biojava.bio">MergeAnnotation</a></dt>
<dd>
<div class="block">ChangeType of ChangeEvent fired before and after an annotation is added
to MergeAnnotation.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/MergeAnnotation.html#ANNOTATION_REMOVE">ANNOTATION_REMOVE</a></span> - Static variable in class org.biojava.bio.<a href="./org/biojava/bio/MergeAnnotation.html" title="class in org.biojava.bio">MergeAnnotation</a></dt>
<dd>
<div class="block">ChangeType of ChangeEvent fired before and after an annotation is added
to MergeAnnotation.</div>
</dd>
<dt><a href="./org/biojava/bio/program/tagvalue/AnnotationBuilder.html" title="class in org.biojava.bio.program.tagvalue"><span class="strong">AnnotationBuilder</span></a> - Class in <a href="./org/biojava/bio/program/tagvalue/package-summary.html">org.biojava.bio.program.tagvalue</a></dt>
<dd>
<div class="block">
Builds an Annotation tree from TagValue events using an AnnotationType to
work out which fields are of what type.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/AnnotationBuilder.html#AnnotationBuilder(org.biojava.bio.AnnotationType)">AnnotationBuilder(AnnotationType)</a></span> - Constructor for class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/AnnotationBuilder.html" title="class in org.biojava.bio.program.tagvalue">AnnotationBuilder</a></dt>
<dd>
<div class="block">
Make a new AnnotationBuilder that will build Annotation instances of a
given type.</div>
</dd>
<dt><a href="./org/biojava/bio/AnnotationChanger.html" title="class in org.biojava.bio"><span class="strong">AnnotationChanger</span></a> - Class in <a href="./org/biojava/bio/package-summary.html">org.biojava.bio</a></dt>
<dd>
<div class="block"><code>AnnotationChanger</code> remaps the values of an
<code>Annotation</code> to new values specified by a
<code>ValueChanger</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/AnnotationChanger.html#AnnotationChanger(org.biojava.bio.Annotation, org.biojava.bio.program.tagvalue.ChangeTable)">AnnotationChanger(Annotation, ChangeTable)</a></span> - Constructor for class org.biojava.bio.<a href="./org/biojava/bio/AnnotationChanger.html" title="class in org.biojava.bio">AnnotationChanger</a></dt>
<dd>
<div class="block">Creates a new <code>AnnotationChanger</code> using the
specified <code>ValueChanger</code> to remap its values.</div>
</dd>
<dt><a href="./org/biojava/bio/annodb/AnnotationDB.html" title="interface in org.biojava.bio.annodb"><span class="strong">AnnotationDB</span></a> - Interface in <a href="./org/biojava/bio/annodb/package-summary.html">org.biojava.bio.annodb</a></dt>
<dd>
<div class="block">A database of Annotation instances.</div>
</dd>
<dt><a href="./org/biojava/bio/program/ssbind/AnnotationFactory.html" title="class in org.biojava.bio.program.ssbind"><span class="strong">AnnotationFactory</span></a> - Class in <a href="./org/biojava/bio/program/ssbind/package-summary.html">org.biojava.bio.program.ssbind</a></dt>
<dd>
<div class="block"><code>AnnotationFactory</code> is a utility class for making
<code>Annotation</code>s from <code>Map</code>s.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/AnnotationFactory.html#AnnotationFactory()">AnnotationFactory()</a></span> - Constructor for class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/AnnotationFactory.html" title="class in org.biojava.bio.program.ssbind">AnnotationFactory</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/SimpleEmissionState.html#annotationForwarder">annotationForwarder</a></span> - Variable in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/SimpleEmissionState.html" title="class in org.biojava.bio.dp">SimpleEmissionState</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/DASSequence.html#annotationForwarder">annotationForwarder</a></span> - Variable in class org.biojava.bio.program.das.<a href="./org/biojava/bio/program/das/DASSequence.html" title="class in org.biojava.bio.program.das">DASSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SequenceDBSearchHit.html#annotationForwarder">annotationForwarder</a></span> - Variable in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SequenceDBSearchHit.html" title="class in org.biojava.bio.search">SequenceDBSearchHit</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SequenceDBSearchResult.html#annotationForwarder">annotationForwarder</a></span> - Variable in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SequenceDBSearchResult.html" title="class in org.biojava.bio.search">SequenceDBSearchResult</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SequenceDBSearchSubHit.html#annotationForwarder">annotationForwarder</a></span> - Variable in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SequenceDBSearchSubHit.html" title="class in org.biojava.bio.search">SequenceDBSearchSubHit</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SimpleSeqSimilaritySearchHit.html#annotationForwarder">annotationForwarder</a></span> - Variable in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SimpleSeqSimilaritySearchHit.html" title="class in org.biojava.bio.search">SimpleSeqSimilaritySearchHit</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SimpleSeqSimilaritySearchResult.html#annotationForwarder">annotationForwarder</a></span> - Variable in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SimpleSeqSimilaritySearchResult.html" title="class in org.biojava.bio.search">SimpleSeqSimilaritySearchResult</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SimpleSeqSimilaritySearchSubHit.html#annotationForwarder">annotationForwarder</a></span> - Variable in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SimpleSeqSimilaritySearchSubHit.html" title="class in org.biojava.bio.search">SimpleSeqSimilaritySearchSubHit</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SubSequence.html#annotationForwarder">annotationForwarder</a></span> - Variable in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SubSequence.html" title="class in org.biojava.bio.seq.impl">SubSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/NewSimpleAssembly.html#annotationForwarder">annotationForwarder</a></span> - Variable in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/NewSimpleAssembly.html" title="class in org.biojava.bio.seq">NewSimpleAssembly</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/SimpleAssembly.html#annotationForwarder">annotationForwarder</a></span> - Variable in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/SimpleAssembly.html" title="class in org.biojava.bio.seq">SimpleAssembly</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AbstractSymbol.html#annotationForwarder">annotationForwarder</a></span> - Variable in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AbstractSymbol.html" title="class in org.biojava.bio.symbol">AbstractSymbol</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleAlphabet.html#annotationForwarder">annotationForwarder</a></span> - Variable in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleAlphabet.html" title="class in org.biojava.bio.symbol">SimpleAlphabet</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/AnnotationRenamer.html" title="class in org.biojava.bio"><span class="strong">AnnotationRenamer</span></a> - Class in <a href="./org/biojava/bio/package-summary.html">org.biojava.bio</a></dt>
<dd>
<div class="block"><code>AnnotationRenamer</code> remaps the keys of an
<code>Annotation</code> to new keys specified by a
<code>TagMapper</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/AnnotationRenamer.html#AnnotationRenamer(org.biojava.bio.Annotation, org.biojava.bio.program.tagvalue.PropertyChanger)">AnnotationRenamer(Annotation, PropertyChanger)</a></span> - Constructor for class org.biojava.bio.<a href="./org/biojava/bio/AnnotationRenamer.html" title="class in org.biojava.bio">AnnotationRenamer</a></dt>
<dd>
<div class="block">Creates a new <code>AnnotationRenamer</code> using the
specified <code>TagMapper</code> to remap its keys.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/DASSequence.html#ANNOTATIONS">ANNOTATIONS</a></span> - Static variable in class org.biojava.bio.program.das.<a href="./org/biojava/bio/program/das/DASSequence.html" title="class in org.biojava.bio.program.das">DASSequence</a></dt>
<dd>
<div class="block">Change type which indicates that the set of annotation servers used
by this DASSequence has been changed.</div>
</dd>
<dt><a href="./org/biojava/bio/AnnotationTools.html" title="class in org.biojava.bio"><span class="strong">AnnotationTools</span></a> - Class in <a href="./org/biojava/bio/package-summary.html">org.biojava.bio</a></dt>
<dd>
<div class="block"><code>AnnotationTools</code> is a set of static utility methods for
manipulating <code>Annotation</code>s and <code>AnnotationType</code>s.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/AnnotationTools.html#AnnotationTools()">AnnotationTools()</a></span> - Constructor for class org.biojava.bio.<a href="./org/biojava/bio/AnnotationTools.html" title="class in org.biojava.bio">AnnotationTools</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/AnnotationType.html" title="interface in org.biojava.bio"><span class="strong">AnnotationType</span></a> - Interface in <a href="./org/biojava/bio/package-summary.html">org.biojava.bio</a></dt>
<dd>
<div class="block">A set of constraints on the data contained in an <code>Annotation</code>.</div>
</dd>
<dt><a href="./org/biojava/bio/AnnotationType.Abstract.html" title="class in org.biojava.bio"><span class="strong">AnnotationType.Abstract</span></a> - Class in <a href="./org/biojava/bio/package-summary.html">org.biojava.bio</a></dt>
<dd>
<div class="block">An abstract base class useful for implementing AnnotationType
instances.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/AnnotationType.Abstract.html#AnnotationType.Abstract()">AnnotationType.Abstract()</a></span> - Constructor for class org.biojava.bio.<a href="./org/biojava/bio/AnnotationType.Abstract.html" title="class in org.biojava.bio">AnnotationType.Abstract</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/AnnotationType.Impl.html" title="class in org.biojava.bio"><span class="strong">AnnotationType.Impl</span></a> - Class in <a href="./org/biojava/bio/package-summary.html">org.biojava.bio</a></dt>
<dd>
<div class="block">An implementation of <code>AnnotationType</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/AnnotationType.Impl.html#AnnotationType.Impl()">AnnotationType.Impl()</a></span> - Constructor for class org.biojava.bio.<a href="./org/biojava/bio/AnnotationType.Impl.html" title="class in org.biojava.bio">AnnotationType.Impl</a></dt>
<dd>
<div class="block">Create a new Impl with no constraints.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/AnnotationType.Impl.html#AnnotationType.Impl(org.biojava.bio.PropertyConstraint, org.biojava.bio.symbol.Location)">AnnotationType.Impl(PropertyConstraint, Location)</a></span> - Constructor for class org.biojava.bio.<a href="./org/biojava/bio/AnnotationType.Impl.html" title="class in org.biojava.bio">AnnotationType.Impl</a></dt>
<dd>
<div class="block">Create a new Impl with a default property and cardinality constraint.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/AnnotationType.Impl.html#AnnotationType.Impl(org.biojava.bio.CollectionConstraint)">AnnotationType.Impl(CollectionConstraint)</a></span> - Constructor for class org.biojava.bio.<a href="./org/biojava/bio/AnnotationType.Impl.html" title="class in org.biojava.bio">AnnotationType.Impl</a></dt>
<dd>
<div class="block">Create a new Impl with a default collection constraint.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/ReferenceServer.html#ANNOTATOR">ANNOTATOR</a></span> - Static variable in class org.biojava.bio.program.das.<a href="./org/biojava/bio/program/das/ReferenceServer.html" title="class in org.biojava.bio.program.das">ReferenceServer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/AnnotationType.html#ANY">ANY</a></span> - Static variable in interface org.biojava.bio.<a href="./org/biojava/bio/AnnotationType.html" title="interface in org.biojava.bio">AnnotationType</a></dt>
<dd>
<div class="block">The type that accepts all annotations and is the supertype of all
other annotations.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/CardinalityConstraint.html#ANY">ANY</a></span> - Static variable in class org.biojava.bio.<a href="./org/biojava/bio/CardinalityConstraint.html" title="class in org.biojava.bio">CardinalityConstraint</a></dt>
<dd>
<div class="block">The property can have any number of values, including none.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/CollectionConstraint.html#ANY">ANY</a></span> - Static variable in interface org.biojava.bio.<a href="./org/biojava/bio/CollectionConstraint.html" title="interface in org.biojava.bio">CollectionConstraint</a></dt>
<dd>
<div class="block"><code>ANY</code> is a constraint which accepts a property for
addition under all conditions.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/PropertyConstraint.html#ANY">ANY</a></span> - Static variable in interface org.biojava.bio.<a href="./org/biojava/bio/PropertyConstraint.html" title="interface in org.biojava.bio">PropertyConstraint</a></dt>
<dd>
<div class="block"><code>ANY</code> is a constraint which accepts a property for
addition under all conditions.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/OntoTools.html#ANY">ANY</a></span> - Static variable in class org.biojava.ontology.<a href="./org/biojava/ontology/OntoTools.html" title="class in org.biojava.ontology">OntoTools</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/AlternativeAlignment.html#apairs_from_idxlst(org.biojava.bio.structure.align.helper.JointFragments)">apairs_from_idxlst(JointFragments)</a></span> - Method in class org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/AlternativeAlignment.html" title="class in org.biojava.bio.structure.align.pairwise">AlternativeAlignment</a></dt>
<dd>
<div class="block">Set apairs according to a list of (i,j) tuples.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/AlternativeAlignment.html#apairs_from_seed(int, int, int)">apairs_from_seed(int, int, int)</a></span> - Method in class org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/AlternativeAlignment.html" title="class in org.biojava.bio.structure.align.pairwise">AlternativeAlignment</a></dt>
<dd>
<div class="block">Set apairs according to a seed position.</div>
</dd>
<dt><a href="./org/biojava/utils/xml/AppBeanRunner.html" title="class in org.biojava.utils.xml"><span class="strong">AppBeanRunner</span></a> - Class in <a href="./org/biojava/utils/xml/package-summary.html">org.biojava.utils.xml</a></dt>
<dd>
<div class="block">Create a bean from an XML file, then attempt to enter it.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/xml/AppBeanRunner.html#AppBeanRunner()">AppBeanRunner()</a></span> - Constructor for class org.biojava.utils.xml.<a href="./org/biojava/utils/xml/AppBeanRunner.html" title="class in org.biojava.utils.xml">AppBeanRunner</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/fastq/FastqWriter.html#append(T, org.biojava.bio.program.fastq.Fastq...)">append(T, Fastq...)</a></span> - Method in interface org.biojava.bio.program.fastq.<a href="./org/biojava/bio/program/fastq/FastqWriter.html" title="interface in org.biojava.bio.program.fastq">FastqWriter</a></dt>
<dd>
<div class="block">Append the specified FASTQ formatted sequences to the specified appendable.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/fastq/FastqWriter.html#append(T, java.lang.Iterable)">append(T, Iterable<Fastq>)</a></span> - Method in interface org.biojava.bio.program.fastq.<a href="./org/biojava/bio/program/fastq/FastqWriter.html" title="interface in org.biojava.bio.program.fastq">FastqWriter</a></dt>
<dd>
<div class="block">Append the specified FASTQ formatted sequences to the specified appendable.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/automata/NfaSubModel.html#append(org.biojava.utils.automata.NfaSubModel)">append(NfaSubModel)</a></span> - Method in class org.biojava.utils.automata.<a href="./org/biojava/utils/automata/NfaSubModel.html" title="class in org.biojava.utils.automata">NfaSubModel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/fastq/FastqBuilder.html#appendQuality(java.lang.String)">appendQuality(String)</a></span> - Method in class org.biojava.bio.program.fastq.<a href="./org/biojava/bio/program/fastq/FastqBuilder.html" title="class in org.biojava.bio.program.fastq">FastqBuilder</a></dt>
<dd>
<div class="block">Return this FASTQ formatted sequence builder configured with the specified quality scores
appended to its current quality scores.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/fastq/FastqBuilder.html#appendSequence(java.lang.String)">appendSequence(String)</a></span> - Method in class org.biojava.bio.program.fastq.<a href="./org/biojava/bio/program/fastq/FastqBuilder.html" title="class in org.biojava.bio.program.fastq">FastqBuilder</a></dt>
<dd>
<div class="block">Return this FASTQ formatted sequence builder configured with the specified sequence
appended to its current sequence.</div>
</dd>
<dt><a href="./org/biojava/utils/xml/AppEntry.html" title="interface in org.biojava.utils.xml"><span class="strong">AppEntry</span></a> - Interface in <a href="./org/biojava/utils/xml/package-summary.html">org.biojava.utils.xml</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/utils/xml/AppException.html" title="class in org.biojava.utils.xml"><span class="strong">AppException</span></a> - Exception in <a href="./org/biojava/utils/xml/package-summary.html">org.biojava.utils.xml</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/xml/AppException.html#AppException(java.lang.String)">AppException(String)</a></span> - Constructor for exception org.biojava.utils.xml.<a href="./org/biojava/utils/xml/AppException.html" title="class in org.biojava.utils.xml">AppException</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BiblioPatent.html#applicants">applicants</a></span> - Variable in class org.biojava.bibliography.<a href="./org/biojava/bibliography/BiblioPatent.html" title="class in org.biojava.bibliography">BiblioPatent</a></dt>
<dd>
<div class="block">Array of applicants.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/server/FlatFileInstallation.html#applyFilters()">applyFilters()</a></span> - Method in class org.biojava.bio.structure.server.<a href="./org/biojava/bio/structure/server/FlatFileInstallation.html" title="class in org.biojava.bio.structure.server">FlatFileInstallation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/FragmentJoiner.html#approach_ap3(org.biojava.bio.structure.Atom[], org.biojava.bio.structure.Atom[], org.biojava.bio.structure.align.pairwise.FragmentPair[], org.biojava.bio.structure.align.StrucAligParameters)">approach_ap3(Atom[], Atom[], FragmentPair[], StrucAligParameters)</a></span> - Method in class org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/FragmentJoiner.html" title="class in org.biojava.bio.structure.align.pairwise">FragmentJoiner</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/alignment/ARAlignment.html" title="interface in org.biojava.bio.alignment"><span class="strong">ARAlignment</span></a> - Interface in <a href="./org/biojava/bio/alignment/package-summary.html">org.biojava.bio.alignment</a></dt>
<dd>
<div class="block">ARAlignment is an interface that defines methods for adding and
removing seqeunces from an Alignment.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/RoundRectangularBeadRenderer.html#arcHeight">arcHeight</a></span> - Variable in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/RoundRectangularBeadRenderer.html" title="class in org.biojava.bio.gui.sequence">RoundRectangularBeadRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/MarkovModel.html#ARCHITECTURE">ARCHITECTURE</a></span> - Static variable in interface org.biojava.bio.dp.<a href="./org/biojava/bio/dp/MarkovModel.html" title="interface in org.biojava.bio.dp">MarkovModel</a></dt>
<dd>
<div class="block">Signals that the architecture of the model is changing.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/RoundRectangularBeadRenderer.html#arcWidth">arcWidth</a></span> - Variable in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/RoundRectangularBeadRenderer.html" title="class in org.biojava.bio.gui.sequence">RoundRectangularBeadRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FilterUtils.html#areDisjoint(org.biojava.bio.seq.FeatureFilter, org.biojava.bio.seq.FeatureFilter)">areDisjoint(FeatureFilter, FeatureFilter)</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FilterUtils.html" title="class in org.biojava.bio.seq">FilterUtils</a></dt>
<dd>
<div class="block">Determines if two queries can be proven to be disjoint.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/DistributionTools.html#areEmissionSpectraEqual(org.biojava.bio.dist.Distribution, org.biojava.bio.dist.Distribution)">areEmissionSpectraEqual(Distribution, Distribution)</a></span> - Static method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/DistributionTools.html" title="class in org.biojava.bio.dist">DistributionTools</a></dt>
<dd>
<div class="block">Compares the emission spectra of two distributions.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/DistributionTools.html#areEmissionSpectraEqual(org.biojava.bio.dist.Distribution[], org.biojava.bio.dist.Distribution[])">areEmissionSpectraEqual(Distribution[], Distribution[])</a></span> - Static method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/DistributionTools.html" title="class in org.biojava.bio.dist">DistributionTools</a></dt>
<dd>
<div class="block">Compares the emission spectra of two distribution arrays.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FilterUtils.html#areEqual(org.biojava.bio.seq.FeatureFilter, org.biojava.bio.seq.FeatureFilter)">areEqual(FeatureFilter, FeatureFilter)</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FilterUtils.html" title="class in org.biojava.bio.seq">FilterUtils</a></dt>
<dd>
<div class="block">Decide if two feature filters accept exactly the same set of features.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/LocationTools.html#areEqual(org.biojava.bio.symbol.Location, org.biojava.bio.symbol.Location)">areEqual(Location, Location)</a></span> - Static method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/LocationTools.html" title="class in org.biojava.bio.symbol">LocationTools</a></dt>
<dd>
<div class="block">Return whether two locations are equal.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FilterUtils.html#areProperSubset(org.biojava.bio.seq.FeatureFilter, org.biojava.bio.seq.FeatureFilter)">areProperSubset(FeatureFilter, FeatureFilter)</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FilterUtils.html" title="class in org.biojava.bio.seq">FilterUtils</a></dt>
<dd>
<div class="block">Determines if the set of features matched by sub can be <code>proven</code> to be a
proper subset of the features matched by sup.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/ProteinTools.html#arg()">arg()</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/ProteinTools.html" title="class in org.biojava.bio.seq">ProteinTools</a></dt>
<dd>
<div class="block">Returns the <code>AtomicSymbol</code> for the amino acid
Arginine (R)</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/Protease.html#ARG_C">ARG_C</a></span> - Static variable in class org.biojava.bio.proteomics.<a href="./org/biojava/bio/proteomics/Protease.html" title="class in org.biojava.bio.proteomics">Protease</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/ProteaseManager.html#ARG_C">ARG_C</a></span> - Static variable in class org.biojava.bio.proteomics.<a href="./org/biojava/bio/proteomics/ProteaseManager.html" title="class in org.biojava.bio.proteomics">ProteaseManager</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/jama/Matrix.html#arrayLeftDivide(org.biojava.bio.structure.jama.Matrix)">arrayLeftDivide(Matrix)</a></span> - Method in class org.biojava.bio.structure.jama.<a href="./org/biojava/bio/structure/jama/Matrix.html" title="class in org.biojava.bio.structure.jama">Matrix</a></dt>
<dd>
<div class="block">Element-by-element left division, C = A.\B</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/jama/Matrix.html#arrayLeftDivideEquals(org.biojava.bio.structure.jama.Matrix)">arrayLeftDivideEquals(Matrix)</a></span> - Method in class org.biojava.bio.structure.jama.<a href="./org/biojava/bio/structure/jama/Matrix.html" title="class in org.biojava.bio.structure.jama">Matrix</a></dt>
<dd>
<div class="block">Element-by-element left division in place, A = A.\B</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/jama/Matrix.html#arrayRightDivide(org.biojava.bio.structure.jama.Matrix)">arrayRightDivide(Matrix)</a></span> - Method in class org.biojava.bio.structure.jama.<a href="./org/biojava/bio/structure/jama/Matrix.html" title="class in org.biojava.bio.structure.jama">Matrix</a></dt>
<dd>
<div class="block">Element-by-element right division, C = A./B</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/jama/Matrix.html#arrayRightDivideEquals(org.biojava.bio.structure.jama.Matrix)">arrayRightDivideEquals(Matrix)</a></span> - Method in class org.biojava.bio.structure.jama.<a href="./org/biojava/bio/structure/jama/Matrix.html" title="class in org.biojava.bio.structure.jama">Matrix</a></dt>
<dd>
<div class="block">Element-by-element right division in place, A = A./B</div>
</dd>
<dt><a href="./org/biojava/utils/automata/ArrayStateMachineToolkit.html" title="class in org.biojava.utils.automata"><span class="strong">ArrayStateMachineToolkit</span></a> - Class in <a href="./org/biojava/utils/automata/package-summary.html">org.biojava.utils.automata</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/jama/Matrix.html#arrayTimes(org.biojava.bio.structure.jama.Matrix)">arrayTimes(Matrix)</a></span> - Method in class org.biojava.bio.structure.jama.<a href="./org/biojava/bio/structure/jama/Matrix.html" title="class in org.biojava.bio.structure.jama">Matrix</a></dt>
<dd>
<div class="block">Element-by-element multiplication, C = A.*B</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/jama/Matrix.html#arrayTimesEquals(org.biojava.bio.structure.jama.Matrix)">arrayTimesEquals(Matrix)</a></span> - Method in class org.biojava.bio.structure.jama.<a href="./org/biojava/bio/structure/jama/Matrix.html" title="class in org.biojava.bio.structure.jama">Matrix</a></dt>
<dd>
<div class="block">Element-by-element multiplication in place, A = A.*B</div>
</dd>
<dt><a href="./org/biojava/bio/gui/sequence/ArrowedFeatureRenderer.html" title="class in org.biojava.bio.gui.sequence"><span class="strong">ArrowedFeatureRenderer</span></a> - Class in <a href="./org/biojava/bio/gui/sequence/package-summary.html">org.biojava.bio.gui.sequence</a></dt>
<dd>
<div class="block">A Feature Renderer that paints the Feature as a right facing arrow Based heavily on
BasicFeatureRenderer</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/ArrowedFeatureRenderer.html#ArrowedFeatureRenderer()">ArrowedFeatureRenderer()</a></span> - Constructor for class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/ArrowedFeatureRenderer.html" title="class in org.biojava.bio.gui.sequence">ArrowedFeatureRenderer</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/gui/glyph/ArrowGlyph.html" title="class in org.biojava.bio.gui.glyph"><span class="strong">ArrowGlyph</span></a> - Class in <a href="./org/biojava/bio/gui/glyph/package-summary.html">org.biojava.bio.gui.glyph</a></dt>
<dd>
<div class="block">A Glyph that paints an arrow shape within the bounds.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/glyph/ArrowGlyph.html#ArrowGlyph()">ArrowGlyph()</a></span> - Constructor for class org.biojava.bio.gui.glyph.<a href="./org/biojava/bio/gui/glyph/ArrowGlyph.html" title="class in org.biojava.bio.gui.glyph">ArrowGlyph</a></dt>
<dd>
<div class="block">Creates a new <code>ArrowGlyph</code>, which is filled with the color
blue by default.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/glyph/ArrowGlyph.html#ArrowGlyph(java.awt.Paint, java.awt.Paint)">ArrowGlyph(Paint, Paint)</a></span> - Constructor for class org.biojava.bio.gui.glyph.<a href="./org/biojava/bio/gui/glyph/ArrowGlyph.html" title="class in org.biojava.bio.gui.glyph">ArrowGlyph</a></dt>
<dd>
<div class="block">Creates a new <code>ArrowGlyph</code>, which is filled with the given
color.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/glyph/ArrowGlyph.html#ArrowGlyph(java.awt.geom.Rectangle2D.Float)">ArrowGlyph(Rectangle2D.Float)</a></span> - Constructor for class org.biojava.bio.gui.glyph.<a href="./org/biojava/bio/gui/glyph/ArrowGlyph.html" title="class in org.biojava.bio.gui.glyph">ArrowGlyph</a></dt>
<dd>
<div class="block">This constructs an arrow in the given bounds, which is colored blue.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/glyph/ArrowGlyph.html#ArrowGlyph(java.awt.geom.Rectangle2D.Float, java.awt.Paint, java.awt.Paint)">ArrowGlyph(Rectangle2D.Float, Paint, Paint)</a></span> - Constructor for class org.biojava.bio.gui.glyph.<a href="./org/biojava/bio/gui/glyph/ArrowGlyph.html" title="class in org.biojava.bio.gui.glyph">ArrowGlyph</a></dt>
<dd>
<div class="block">Constructor which sets both the size of this arrow and its color.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/TranslationTable.html#ASCID_MITO">ASCID_MITO</a></span> - Static variable in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/TranslationTable.html" title="interface in org.biojava.bio.symbol">TranslationTable</a></dt>
<dd>
<div class="block">Translation table name for the ascidian mitochondrial genetic
code.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLAcceptAllFilter.html#asCriterion()">asCriterion()</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLAcceptAllFilter.html" title="class in org.biojavax.bio.db.biosql">BioSQLAcceptAllFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLAcceptNoneFilter.html#asCriterion()">asCriterion()</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLAcceptNoneFilter.html" title="class in org.biojavax.bio.db.biosql">BioSQLAcceptNoneFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.And.html#asCriterion()">asCriterion()</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.And.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.And</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.html#asCriterion()">asCriterion()</a></span> - Method in interface org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.html" title="interface in org.biojavax.bio.db.biosql">BioSQLFeatureFilter</a></dt>
<dd>
<div class="block">This method returns a Hibernate Criterion object that can be used to
query the database.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByName.html#asCriterion()">asCriterion()</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByName.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.ByName</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByNote.html#asCriterion()">asCriterion()</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByNote.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.ByNote</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByNoteTermOnly.html#asCriterion()">asCriterion()</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByNoteTermOnly.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.ByNoteTermOnly</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByRank.html#asCriterion()">asCriterion()</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByRank.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.ByRank</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.BySequenceName.html#asCriterion()">asCriterion()</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.BySequenceName.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.BySequenceName</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.BySourceTerm.html#asCriterion()">asCriterion()</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.BySourceTerm.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.BySourceTerm</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.BySourceTermName.html#asCriterion()">asCriterion()</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.BySourceTermName.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.BySourceTermName</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByStrand.html#asCriterion()">asCriterion()</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByStrand.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.ByStrand</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByTypeTerm.html#asCriterion()">asCriterion()</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByTypeTerm.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.ByTypeTerm</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByTypeTermName.html#asCriterion()">asCriterion()</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByTypeTermName.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.ByTypeTermName</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ContainedByRichLocation.html#asCriterion()">asCriterion()</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ContainedByRichLocation.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.ContainedByRichLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.Not.html#asCriterion()">asCriterion()</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.Not.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.Not</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.Or.html#asCriterion()">asCriterion()</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.Or.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.Or</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.OverlapsRichLocation.html#asCriterion()">asCriterion()</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.OverlapsRichLocation.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.OverlapsRichLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/AbstractAnnotation.html#asMap()">asMap()</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/AbstractAnnotation.html" title="class in org.biojava.bio">AbstractAnnotation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/Annotation.html#asMap()">asMap()</a></span> - Method in interface org.biojava.bio.<a href="./org/biojava/bio/Annotation.html" title="interface in org.biojava.bio">Annotation</a></dt>
<dd>
<div class="block">Return a map that contains the same key/values as this Annotation.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/MergeAnnotation.html#asMap()">asMap()</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/MergeAnnotation.html" title="class in org.biojava.bio">MergeAnnotation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/OverlayAnnotation.html#asMap()">asMap()</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/OverlayAnnotation.html" title="class in org.biojava.bio">OverlayAnnotation</a></dt>
<dd>
<div class="block">Return a <code>Map</code> view onto this annotation.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/EmptyRichAnnotation.html#asMap()">asMap()</a></span> - Method in class org.biojavax.<a href="./org/biojavax/EmptyRichAnnotation.html" title="class in org.biojavax">EmptyRichAnnotation</a></dt>
<dd>
<div class="block">Return a map that contains the same key/values as this Annotation.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ga/util/WeightedSet.html#asMap()">asMap()</a></span> - Method in class org.biojavax.ga.util.<a href="./org/biojavax/ga/util/WeightedSet.html" title="class in org.biojavax.ga.util">WeightedSet</a></dt>
<dd>
<div class="block">Converts the Set to a map from key <code>Objects</code> to <code>Double</code>
weights.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleRichAnnotation.html#asMap()">asMap()</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleRichAnnotation.html" title="class in org.biojavax">SimpleRichAnnotation</a></dt>
<dd>
<div class="block">Return a map that contains the same key/values as this Annotation.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/ProteinTools.html#asn()">asn()</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/ProteinTools.html" title="class in org.biojava.bio.seq">ProteinTools</a></dt>
<dd>
<div class="block">Returns the <code>AtomicSymbol</code> for the amino acid
Asparagine (N)</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/ProteinTools.html#asp()">asp()</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/ProteinTools.html" title="class in org.biojava.bio.seq">ProteinTools</a></dt>
<dd>
<div class="block">Returns the <code>AtomicSymbol</code> for the amino acid
Aspartic Acid (D)</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/Protease.html#ASP_N">ASP_N</a></span> - Static variable in class org.biojava.bio.proteomics.<a href="./org/biojava/bio/proteomics/Protease.html" title="class in org.biojava.bio.proteomics">Protease</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/ProteaseManager.html#ASP_N">ASP_N</a></span> - Static variable in class org.biojava.bio.proteomics.<a href="./org/biojava/bio/proteomics/ProteaseManager.html" title="class in org.biojava.bio.proteomics">ProteaseManager</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/impl/AssembledSymbolList.html" title="class in org.biojava.bio.seq.impl"><span class="strong">AssembledSymbolList</span></a> - Class in <a href="./org/biojava/bio/seq/impl/package-summary.html">org.biojava.bio.seq.impl</a></dt>
<dd>
<div class="block">Support class for applications which need to patch together sections
of sequence into a single SymbolList.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/AssembledSymbolList.html#AssembledSymbolList()">AssembledSymbolList()</a></span> - Constructor for class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/AssembledSymbolList.html" title="class in org.biojava.bio.seq.impl">AssembledSymbolList</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/utils/AssertionFailure.html" title="class in org.biojava.utils"><span class="strong">AssertionFailure</span></a> - Error in <a href="./org/biojava/utils/package-summary.html">org.biojava.utils</a></dt>
<dd>
<div class="block">An unchecked exception representing an Assertion failure.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/AssertionFailure.html#AssertionFailure(java.lang.String)">AssertionFailure(String)</a></span> - Constructor for error org.biojava.utils.<a href="./org/biojava/utils/AssertionFailure.html" title="class in org.biojava.utils">AssertionFailure</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/AssertionFailure.html#AssertionFailure(java.lang.Throwable)">AssertionFailure(Throwable)</a></span> - Constructor for error org.biojava.utils.<a href="./org/biojava/utils/AssertionFailure.html" title="class in org.biojava.utils">AssertionFailure</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/AssertionFailure.html#AssertionFailure(java.lang.String, java.lang.Throwable)">AssertionFailure(String, Throwable)</a></span> - Constructor for error org.biojava.utils.<a href="./org/biojava/utils/AssertionFailure.html" title="class in org.biojava.utils">AssertionFailure</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/structure/Atom.html" title="interface in org.biojava.bio.structure"><span class="strong">Atom</span></a> - Interface in <a href="./org/biojava/bio/structure/package-summary.html">org.biojava.bio.structure</a></dt>
<dd>
<div class="block">A simple interface for an Atom.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/PDBFileParser.html#ATOM_CA_THRESHOLD">ATOM_CA_THRESHOLD</a></span> - Static variable in class org.biojava.bio.structure.io.<a href="./org/biojava/bio/structure/io/PDBFileParser.html" title="class in org.biojava.bio.structure.io">PDBFileParser</a></dt>
<dd>
<div class="block">the maximum number of atoms that will be parsed before the parser switches to a CA-only
representation of the PDB file.</div>
</dd>
<dt><a href="./org/biojava/bio/symbol/AtomicSymbol.html" title="interface in org.biojava.bio.symbol"><span class="strong">AtomicSymbol</span></a> - Interface in <a href="./org/biojava/bio/symbol/package-summary.html">org.biojava.bio.symbol</a></dt>
<dd>
<div class="block">
A symbol that is not ambiguous.</div>
</dd>
<dt><a href="./org/biojava/bio/structure/AtomImpl.html" title="class in org.biojava.bio.structure"><span class="strong">AtomImpl</span></a> - Class in <a href="./org/biojava/bio/structure/package-summary.html">org.biojava.bio.structure</a></dt>
<dd>
<div class="block">Implementation of an Atom of a PDB file.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/AtomImpl.html#AtomImpl()">AtomImpl()</a></span> - Constructor for class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/AtomImpl.html" title="class in org.biojava.bio.structure">AtomImpl</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/structure/AtomIterator.html" title="class in org.biojava.bio.structure"><span class="strong">AtomIterator</span></a> - Class in <a href="./org/biojava/bio/structure/package-summary.html">org.biojava.bio.structure</a></dt>
<dd>
<div class="block">an iterator over all atoms of a structure / group.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/AtomIterator.html#AtomIterator(org.biojava.bio.structure.Structure)">AtomIterator(Structure)</a></span> - Constructor for class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/AtomIterator.html" title="class in org.biojava.bio.structure">AtomIterator</a></dt>
<dd>
<div class="block">Constructs an AtomIterator object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/AtomIterator.html#AtomIterator(org.biojava.bio.structure.Group)">AtomIterator(Group)</a></span> - Constructor for class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/AtomIterator.html" title="class in org.biojava.bio.structure">AtomIterator</a></dt>
<dd>
<div class="block">Constructs an AtomIterator object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/AminoAcid.html#ATOMRECORD">ATOMRECORD</a></span> - Static variable in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/AminoAcid.html" title="interface in org.biojava.bio.structure">AminoAcid</a></dt>
<dd>
<div class="block">Field to distribguish AminoAcids that have been created from SEQRES records and ATOM records.</div>
</dd>
<dt><a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html" title="class in org.biojava.bio.structure.io.mmcif.model"><span class="strong">AtomSite</span></a> - Class in <a href="./org/biojava/bio/structure/io/mmcif/model/package-summary.html">org.biojava.bio.structure.io.mmcif.model</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html#AtomSite()">AtomSite()</a></span> - Constructor for class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html" title="class in org.biojava.bio.structure.io.mmcif.model">AtomSite</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/biosql/TaxonSQL.html#attemptClose(java.sql.Statement)">attemptClose(Statement)</a></span> - Static method in class org.biojava.bio.seq.db.biosql.<a href="./org/biojava/bio/seq/db/biosql/TaxonSQL.html" title="class in org.biojava.bio.seq.db.biosql">TaxonSQL</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Attempt to close the Statement.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/biosql/TaxonSQL.html#attemptClose(java.sql.ResultSet)">attemptClose(ResultSet)</a></span> - Static method in class org.biojava.bio.seq.db.biosql.<a href="./org/biojava/bio/seq/db/biosql/TaxonSQL.html" title="class in org.biojava.bio.seq.db.biosql">TaxonSQL</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Attempt to close the ResultSet.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BibRefSupport.html#ATTR_FORMAT">ATTR_FORMAT</a></span> - Static variable in interface org.biojava.bibliography.<a href="./org/biojava/bibliography/BibRefSupport.html" title="interface in org.biojava.bibliography">BibRefSupport</a></dt>
<dd>
<div class="block">A vocabulary name, or a part of a vocabulary name.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BibRefSupport.html#ATTR_PROPERTIES">ATTR_PROPERTIES</a></span> - Static variable in interface org.biojava.bibliography.<a href="./org/biojava/bibliography/BibRefSupport.html" title="interface in org.biojava.bibliography">BibRefSupport</a></dt>
<dd>
<div class="block">
A part of a vocabulary name.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BibRefSupport.html#ATTR_SCOPE">ATTR_SCOPE</a></span> - Static variable in interface org.biojava.bibliography.<a href="./org/biojava/bibliography/BibRefSupport.html" title="interface in org.biojava.bibliography">BibRefSupport</a></dt>
<dd>
<div class="block">A vocabulary name, or a part of a vocabulary name.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/xml/FastXMLWriter.html#attribute(java.lang.String, java.lang.String)">attribute(String, String)</a></span> - Method in class org.biojava.utils.xml.<a href="./org/biojava/utils/xml/FastXMLWriter.html" title="class in org.biojava.utils.xml">FastXMLWriter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/xml/PrettyXMLWriter.html#attribute(java.lang.String, java.lang.String, java.lang.String)">attribute(String, String, String)</a></span> - Method in class org.biojava.utils.xml.<a href="./org/biojava/utils/xml/PrettyXMLWriter.html" title="class in org.biojava.utils.xml">PrettyXMLWriter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/xml/PrettyXMLWriter.html#attribute(java.lang.String, java.lang.String)">attribute(String, String)</a></span> - Method in class org.biojava.utils.xml.<a href="./org/biojava/utils/xml/PrettyXMLWriter.html" title="class in org.biojava.utils.xml">PrettyXMLWriter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/xml/XMLWriter.html#attribute(java.lang.String, java.lang.String, java.lang.String)">attribute(String, String, String)</a></span> - Method in interface org.biojava.utils.xml.<a href="./org/biojava/utils/xml/XMLWriter.html" title="interface in org.biojava.utils.xml">XMLWriter</a></dt>
<dd>
<div class="block">Add an attribute to an element.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/xml/XMLWriter.html#attribute(java.lang.String, java.lang.String)">attribute(String, String)</a></span> - Method in interface org.biojava.utils.xml.<a href="./org/biojava/utils/xml/XMLWriter.html" title="interface in org.biojava.utils.xml">XMLWriter</a></dt>
<dd>
<div class="block">Add an un-qualified attribute to an element.</div>
</dd>
<dt><a href="./org/biojava/bio/structure/Author.html" title="class in org.biojava.bio.structure"><span class="strong">Author</span></a> - Class in <a href="./org/biojava/bio/structure/package-summary.html">org.biojava.bio.structure</a></dt>
<dd>
<div class="block">Describes author attributes for author information in a PDB file.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Author.html#Author()">Author()</a></span> - Constructor for class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Author.html" title="class in org.biojava.bio.structure">Author</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#AUTHOR_LIST_TAG">AUTHOR_LIST_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html#AUTHOR_TAG">AUTHOR_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html" title="class in org.biojavax.bio.seq.io">EMBLxmlFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/INSDseqFormat.html#AUTHOR_TAG">AUTHOR_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/INSDseqFormat.html" title="class in org.biojavax.bio.seq.io">INSDseqFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/Namespace.html#AUTHORITY">AUTHORITY</a></span> - Static variable in interface org.biojavax.<a href="./org/biojavax/Namespace.html" title="interface in org.biojavax">Namespace</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BibRef.html#authors">authors</a></span> - Variable in class org.biojava.bibliography.<a href="./org/biojava/bibliography/BibRef.html" title="class in org.biojava.bibliography">BibRef</a></dt>
<dd>
<div class="block">
The authors and contributors are responsible for creating the contents of the cited resource.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/INSDseqFormat.html#AUTHORS_GROUP_TAG">AUTHORS_GROUP_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/INSDseqFormat.html" title="class in org.biojavax.bio.seq.io">INSDseqFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/EmblLikeFormat.html#AUTHORS_TAG">AUTHORS_TAG</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/EmblLikeFormat.html" title="class in org.biojava.bio.seq.io">EmblLikeFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/GenbankFormat.html#AUTHORS_TAG">AUTHORS_TAG</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/GenbankFormat.html" title="class in org.biojava.bio.seq.io">GenbankFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLFormat.html#AUTHORS_TAG">AUTHORS_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLFormat.html" title="class in org.biojavax.bio.seq.io">EMBLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/GenbankFormat.html#AUTHORS_TAG">AUTHORS_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/GenbankFormat.html" title="class in org.biojavax.bio.seq.io">GenbankFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtFormat.html#AUTHORS_TAG">AUTHORS_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtFormat.html" title="class in org.biojavax.bio.seq.io">UniProtFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/biosql/TaxonSQL.html#automaticUpdate(java.sql.Connection, org.biojava.bio.seq.db.biosql.DBHelper, org.biojava.bio.taxa.TaxonFactory, java.io.File, java.io.File)">automaticUpdate(Connection, DBHelper, TaxonFactory, File, File)</a></span> - Static method in class org.biojava.bio.seq.db.biosql.<a href="./org/biojava/bio/seq/db/biosql/TaxonSQL.html" title="class in org.biojava.bio.seq.db.biosql">TaxonSQL</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">This method tries to perform a complete update according to the given
<code>TaxonFactory</code>, which already contains the newes taxa and the files
available at the NCBI-FTP-Site.</div>
</dd>
<dt><a href="./org/biojava/utils/automata/AutomatonException.html" title="class in org.biojava.utils.automata"><span class="strong">AutomatonException</span></a> - Exception in <a href="./org/biojava/utils/automata/package-summary.html">org.biojava.utils.automata</a></dt>
<dd>
<div class="block">An exception thrown by classes of this package.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/automata/AutomatonException.html#AutomatonException(java.lang.String)">AutomatonException(String)</a></span> - Constructor for exception org.biojava.utils.automata.<a href="./org/biojava/utils/automata/AutomatonException.html" title="class in org.biojava.utils.automata">AutomatonException</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/automata/AutomatonException.html#AutomatonException(java.lang.Throwable)">AutomatonException(Throwable)</a></span> - Constructor for exception org.biojava.utils.automata.<a href="./org/biojava/utils/automata/AutomatonException.html" title="class in org.biojava.utils.automata">AutomatonException</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/automata/AutomatonException.html#AutomatonException(java.lang.Throwable, java.lang.String)">AutomatonException(Throwable, String)</a></span> - Constructor for exception org.biojava.utils.automata.<a href="./org/biojava/utils/automata/AutomatonException.html" title="class in org.biojava.utils.automata">AutomatonException</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/io/UncompressInputStream.html#available()">available()</a></span> - Method in class org.biojava.utils.io.<a href="./org/biojava/utils/io/UncompressInputStream.html" title="class in org.biojava.utils.io">UncompressInputStream</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/DistributionTools.html#average(org.biojava.bio.dist.Distribution[])">average(Distribution[])</a></span> - Static method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/DistributionTools.html" title="class in org.biojava.bio.dist">DistributionTools</a></dt>
<dd>
<div class="block">Averages two or more distributions.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SymbolPropertyTable.html#AVG_MASS">AVG_MASS</a></span> - Static variable in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SymbolPropertyTable.html" title="interface in org.biojava.bio.symbol">SymbolPropertyTable</a></dt>
<dd> </dd>
</dl>
<a name="_B_">
<!-- -->
</a>
<h2 class="title">B</h2>
<dl>
<dt><span class="strong"><a href="./org/biojava/bio/seq/DNATools.html#b()">b()</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/DNATools.html" title="class in org.biojava.bio.seq">DNATools</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/NucleotideTools.html#b()">b()</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/NucleotideTools.html" title="class in org.biojava.bio.seq">NucleotideTools</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/Taxon.html#B_TAURUS">B_TAURUS</a></span> - Static variable in interface org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/Taxon.html" title="interface in org.biojava.bio.program.homologene">Taxon</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/BackPointer.html#back">back</a></span> - Variable in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/BackPointer.html" title="class in org.biojava.bio.dp">BackPointer</a></dt>
<dd>
<div class="block">The previous backpointer (towards origin of DP matrix) in traceback.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/StructureTools.html#backboneAtomNames">backboneAtomNames</a></span> - Static variable in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/StructureTools.html" title="class in org.biojava.bio.structure">StructureTools</a></dt>
<dd>
<div class="block">The names of the Atoms that form the backbone.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/util/SequenceScalePanel.html#BACKGROUND_COLOR">BACKGROUND_COLOR</a></span> - Static variable in class org.biojava.bio.structure.gui.util.<a href="./org/biojava/bio/structure/gui/util/SequenceScalePanel.html" title="class in org.biojava.bio.structure.gui.util">SequenceScalePanel</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/dp/twohead/BackMatrixPairDPCursor.html" title="class in org.biojava.bio.dp.twohead"><span class="strong">BackMatrixPairDPCursor</span></a> - Class in <a href="./org/biojava/bio/dp/twohead/package-summary.html">org.biojava.bio.dp.twohead</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/twohead/BackMatrixPairDPCursor.html#BackMatrixPairDPCursor(org.biojava.bio.symbol.SymbolList, org.biojava.bio.symbol.SymbolList, int, int, org.biojava.bio.dp.twohead.PairDPMatrix, org.biojava.bio.dp.twohead.EmissionCache)">BackMatrixPairDPCursor(SymbolList, SymbolList, int, int, PairDPMatrix, EmissionCache)</a></span> - Constructor for class org.biojava.bio.dp.twohead.<a href="./org/biojava/bio/dp/twohead/BackMatrixPairDPCursor.html" title="class in org.biojava.bio.dp.twohead">BackMatrixPairDPCursor</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/dp/BackPointer.html" title="class in org.biojava.bio.dp"><span class="strong">BackPointer</span></a> - Class in <a href="./org/biojava/bio/dp/package-summary.html">org.biojava.bio.dp</a></dt>
<dd>
<div class="block">A backpointer.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/BackPointer.html#BackPointer(org.biojava.bio.dp.State, org.biojava.bio.dp.BackPointer, double)">BackPointer(State, BackPointer, double)</a></span> - Constructor for class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/BackPointer.html" title="class in org.biojava.bio.dp">BackPointer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/BackPointer.html#BackPointer(org.biojava.bio.dp.State)">BackPointer(State)</a></span> - Constructor for class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/BackPointer.html" title="class in org.biojava.bio.dp">BackPointer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/twohead/Cell.html#backPointers">backPointers</a></span> - Variable in class org.biojava.bio.dp.twohead.<a href="./org/biojava/bio/dp/twohead/Cell.html" title="class in org.biojava.bio.dp.twohead">Cell</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/DP.html#backward(org.biojava.bio.symbol.SymbolList[], org.biojava.bio.dp.ScoreType)">backward(SymbolList[], ScoreType)</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/DP.html" title="class in org.biojava.bio.dp">DP</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/onehead/SingleDP.html#backward(org.biojava.bio.symbol.SymbolList[], org.biojava.bio.dp.ScoreType)">backward(SymbolList[], ScoreType)</a></span> - Method in class org.biojava.bio.dp.onehead.<a href="./org/biojava/bio/dp/onehead/SingleDP.html" title="class in org.biojava.bio.dp.onehead">SingleDP</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/onehead/SingleDP.html#backward(org.biojava.bio.dp.onehead.DPCursor, org.biojava.bio.dp.ScoreType)">backward(DPCursor, ScoreType)</a></span> - Method in class org.biojava.bio.dp.onehead.<a href="./org/biojava/bio/dp/onehead/SingleDP.html" title="class in org.biojava.bio.dp.onehead">SingleDP</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/twohead/PairwiseDP.html#backward(org.biojava.bio.symbol.SymbolList[], org.biojava.bio.dp.ScoreType)">backward(SymbolList[], ScoreType)</a></span> - Method in class org.biojava.bio.dp.twohead.<a href="./org/biojava/bio/dp/twohead/PairwiseDP.html" title="class in org.biojava.bio.dp.twohead">PairwiseDP</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/onehead/SingleDP.html#backward_initialize(org.biojava.bio.dp.onehead.DPCursor, org.biojava.bio.dp.ScoreType)">backward_initialize(DPCursor, ScoreType)</a></span> - Method in class org.biojava.bio.dp.onehead.<a href="./org/biojava/bio/dp/onehead/SingleDP.html" title="class in org.biojava.bio.dp.onehead">SingleDP</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/onehead/SingleDP.html#backward_recurse(org.biojava.bio.dp.onehead.DPCursor, org.biojava.bio.dp.ScoreType)">backward_recurse(DPCursor, ScoreType)</a></span> - Method in class org.biojava.bio.dp.onehead.<a href="./org/biojava/bio/dp/onehead/SingleDP.html" title="class in org.biojava.bio.dp.onehead">SingleDP</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/onehead/SingleDP.html#backward_termination(org.biojava.bio.dp.onehead.DPCursor, org.biojava.bio.dp.ScoreType)">backward_termination(DPCursor, ScoreType)</a></span> - Method in class org.biojava.bio.dp.onehead.<a href="./org/biojava/bio/dp/onehead/SingleDP.html" title="class in org.biojava.bio.dp.onehead">SingleDP</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/DP.html#backwardMatrix(org.biojava.bio.symbol.SymbolList[], org.biojava.bio.dp.ScoreType)">backwardMatrix(SymbolList[], ScoreType)</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/DP.html" title="class in org.biojava.bio.dp">DP</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/DP.html#backwardMatrix(org.biojava.bio.symbol.SymbolList[], org.biojava.bio.dp.DPMatrix, org.biojava.bio.dp.ScoreType)">backwardMatrix(SymbolList[], DPMatrix, ScoreType)</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/DP.html" title="class in org.biojava.bio.dp">DP</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/onehead/SingleDP.html#backwardMatrix(org.biojava.bio.symbol.SymbolList[], org.biojava.bio.dp.ScoreType)">backwardMatrix(SymbolList[], ScoreType)</a></span> - Method in class org.biojava.bio.dp.onehead.<a href="./org/biojava/bio/dp/onehead/SingleDP.html" title="class in org.biojava.bio.dp.onehead">SingleDP</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/onehead/SingleDP.html#backwardMatrix(org.biojava.bio.symbol.SymbolList[], org.biojava.bio.dp.DPMatrix, org.biojava.bio.dp.ScoreType)">backwardMatrix(SymbolList[], DPMatrix, ScoreType)</a></span> - Method in class org.biojava.bio.dp.onehead.<a href="./org/biojava/bio/dp/onehead/SingleDP.html" title="class in org.biojava.bio.dp.onehead">SingleDP</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/twohead/PairwiseDP.html#backwardMatrix(org.biojava.bio.symbol.SymbolList[], org.biojava.bio.dp.ScoreType)">backwardMatrix(SymbolList[], ScoreType)</a></span> - Method in class org.biojava.bio.dp.twohead.<a href="./org/biojava/bio/dp/twohead/PairwiseDP.html" title="class in org.biojava.bio.dp.twohead">PairwiseDP</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/twohead/PairwiseDP.html#backwardMatrix(org.biojava.bio.symbol.SymbolList[], org.biojava.bio.dp.DPMatrix, org.biojava.bio.dp.ScoreType)">backwardMatrix(SymbolList[], DPMatrix, ScoreType)</a></span> - Method in class org.biojava.bio.dp.twohead.<a href="./org/biojava/bio/dp/twohead/PairwiseDP.html" title="class in org.biojava.bio.dp.twohead">PairwiseDP</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/twohead/CellCalculatorFactory.html#backwards(org.biojava.bio.dp.ScoreType)">backwards(ScoreType)</a></span> - Method in interface org.biojava.bio.dp.twohead.<a href="./org/biojava/bio/dp/twohead/CellCalculatorFactory.html" title="interface in org.biojava.bio.dp.twohead">CellCalculatorFactory</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/twohead/DPInterpreter.html#backwards(org.biojava.bio.dp.ScoreType)">backwards(ScoreType)</a></span> - Method in class org.biojava.bio.dp.twohead.<a href="./org/biojava/bio/dp/twohead/DPInterpreter.html" title="class in org.biojava.bio.dp.twohead">DPInterpreter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/DP.html#backwardTransitions(org.biojava.bio.dp.MarkovModel, org.biojava.bio.dp.State[])">backwardTransitions(MarkovModel, State[])</a></span> - Static method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/DP.html" title="class in org.biojava.bio.dp">DP</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/DP.html#backwardTransitionScores(org.biojava.bio.dp.MarkovModel, org.biojava.bio.dp.State[], int[][], org.biojava.bio.dp.ScoreType)">backwardTransitionScores(MarkovModel, State[], int[][], ScoreType)</a></span> - Static method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/DP.html" title="class in org.biojava.bio.dp">DP</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/TranslationTable.html#BACTERIAL">BACTERIAL</a></span> - Static variable in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/TranslationTable.html" title="interface in org.biojava.bio.symbol">TranslationTable</a></dt>
<dd>
<div class="block">Translation table name for the bacterial and plant plastid genetic code.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/phred/PhredFormat.html#BadLineParsed(org.biojava.utils.ParseErrorEvent)">BadLineParsed(ParseErrorEvent)</a></span> - Method in class org.biojava.bio.program.phred.<a href="./org/biojava/bio/program/phred/PhredFormat.html" title="class in org.biojava.bio.program.phred">PhredFormat</a></dt>
<dd>
<div class="block">This method determines the behaviour when a bad line is processed.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/EmblLikeFormat.html#BadLineParsed(org.biojava.utils.ParseErrorEvent)">BadLineParsed(ParseErrorEvent)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/EmblLikeFormat.html" title="class in org.biojava.bio.seq.io">EmblLikeFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">
This method determines the behaviour when a bad line is processed.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/FastaFormat.html#BadLineParsed(org.biojava.utils.ParseErrorEvent)">BadLineParsed(ParseErrorEvent)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/FastaFormat.html" title="class in org.biojava.bio.seq.io">FastaFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">This method determines the behaviour when a bad line is processed.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/GenbankFormat.html#BadLineParsed(org.biojava.utils.ParseErrorEvent)">BadLineParsed(ParseErrorEvent)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/GenbankFormat.html" title="class in org.biojava.bio.seq.io">GenbankFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">This method determines the behaviour when a bad line is processed.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/StreamReader.html#BadLineParsed(org.biojava.utils.ParseErrorEvent)">BadLineParsed(ParseErrorEvent)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/StreamReader.html" title="class in org.biojava.bio.seq.io">StreamReader</a></dt>
<dd>
<div class="block">This method determines the behaviour when a bad line is processed.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/ParseErrorListener.html#BadLineParsed(org.biojava.utils.ParseErrorEvent)">BadLineParsed(ParseErrorEvent)</a></span> - Method in interface org.biojava.utils.<a href="./org/biojava/utils/ParseErrorListener.html" title="interface in org.biojava.utils">ParseErrorListener</a></dt>
<dd>
<div class="block">Method called when the parser encounters a bad line.</div>
</dd>
<dt><a href="./org/biojava/bio/gui/BarLogoPainter.html" title="class in org.biojava.bio.gui"><span class="strong">BarLogoPainter</span></a> - Class in <a href="./org/biojava/bio/gui/package-summary.html">org.biojava.bio.gui</a></dt>
<dd>
<div class="block">A logo painter that paints in bars.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/BarLogoPainter.html#BarLogoPainter()">BarLogoPainter()</a></span> - Constructor for class org.biojava.bio.gui.<a href="./org/biojava/bio/gui/BarLogoPainter.html" title="class in org.biojava.bio.gui">BarLogoPainter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/GenbankFormat.html#BASE_COUNT_TAG">BASE_COUNT_TAG</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/GenbankFormat.html" title="class in org.biojava.bio.seq.io">GenbankFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/GenbankFormat.html#BASE_COUNT_TAG">BASE_COUNT_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/GenbankFormat.html" title="class in org.biojavax.bio.seq.io">GenbankFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/GenbankFormat.html#BASE_COUNT_TAG_FULL">BASE_COUNT_TAG_FULL</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/GenbankFormat.html" title="class in org.biojavax.bio.seq.io">GenbankFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html#BASEPOSITION_TAG">BASEPOSITION_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html" title="class in org.biojavax.bio.seq.io">EMBLxmlFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html#BASEPOSITION_TYPE_ATTR">BASEPOSITION_TYPE_ATTR</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html" title="class in org.biojavax.bio.seq.io">EMBLxmlFormat</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/xml/BaseXMLWriter.html" title="class in org.biojava.bio.program.xml"><span class="strong">BaseXMLWriter</span></a> - Class in <a href="./org/biojava/bio/program/xml/package-summary.html">org.biojava.bio.program.xml</a></dt>
<dd>
<div class="block">Base XMLWriter class for writing XML representations of Java Value
Objects with bespoke architectures.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/xml/BaseXMLWriter.html#BaseXMLWriter()">BaseXMLWriter()</a></span> - Constructor for class org.biojava.bio.program.xml.<a href="./org/biojava/bio/program/xml/BaseXMLWriter.html" title="class in org.biojava.bio.program.xml">BaseXMLWriter</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/gui/sequence/BasicFeatureRenderer.html" title="class in org.biojava.bio.gui.sequence"><span class="strong">BasicFeatureRenderer</span></a> - Class in <a href="./org/biojava/bio/gui/sequence/package-summary.html">org.biojava.bio.gui.sequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/BasicFeatureRenderer.html#BasicFeatureRenderer()">BasicFeatureRenderer()</a></span> - Constructor for class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/BasicFeatureRenderer.html" title="class in org.biojava.bio.gui.sequence">BasicFeatureRenderer</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/gui/sequence/BasicImapRenderer.html" title="class in org.biojava.bio.gui.sequence"><span class="strong">BasicImapRenderer</span></a> - Class in <a href="./org/biojava/bio/gui/sequence/package-summary.html">org.biojava.bio.gui.sequence</a></dt>
<dd>
<div class="block"><code>BasicImapRenderer</code> is a decorator for
<code>BasicFeatureRenderer</code> which adds the ability to create
HTML image map coordinates which correspond to the feature
rendering produced by the <code>BasicFeatureRenderer</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/BasicImapRenderer.html#BasicImapRenderer(org.biojava.bio.gui.sequence.BasicFeatureRenderer, org.biojava.bio.gui.sequence.ImageMap, org.biojava.utils.net.URLFactory)">BasicImapRenderer(BasicFeatureRenderer, ImageMap, URLFactory)</a></span> - Constructor for class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/BasicImapRenderer.html" title="class in org.biojava.bio.gui.sequence">BasicImapRenderer</a></dt>
<dd>
<div class="block">Creates a new <code>BasicImapRenderer</code>.</div>
</dd>
<dt><a href="./org/biojava/bio/program/xff/BasicXFFHelper.html" title="class in org.biojava.bio.program.xff"><span class="strong">BasicXFFHelper</span></a> - Class in <a href="./org/biojava/bio/program/xff/package-summary.html">org.biojava.bio.program.xff</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/xff/BasicXFFHelper.html#BasicXFFHelper()">BasicXFFHelper()</a></span> - Constructor for class org.biojava.bio.program.xff.<a href="./org/biojava/bio/program/xff/BasicXFFHelper.html" title="class in org.biojava.bio.program.xff">BasicXFFHelper</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/symbol/BasisSymbol.html" title="interface in org.biojava.bio.symbol"><span class="strong">BasisSymbol</span></a> - Interface in <a href="./org/biojava/bio/symbol/package-summary.html">org.biojava.bio.symbol</a></dt>
<dd>
<div class="block">
A symbol that can be represented as a string of Symbols.</div>
</dd>
<dt><a href="./org/biojava/bio/dp/BaumWelchSampler.html" title="class in org.biojava.bio.dp"><span class="strong">BaumWelchSampler</span></a> - Class in <a href="./org/biojava/bio/dp/package-summary.html">org.biojava.bio.dp</a></dt>
<dd>
<div class="block">
Train a hidden markov model using a sampling algorithm.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/BaumWelchSampler.html#BaumWelchSampler(org.biojava.bio.dp.DP)">BaumWelchSampler(DP)</a></span> - Constructor for class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/BaumWelchSampler.html" title="class in org.biojava.bio.dp">BaumWelchSampler</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/dp/BaumWelchTrainer.html" title="class in org.biojava.bio.dp"><span class="strong">BaumWelchTrainer</span></a> - Class in <a href="./org/biojava/bio/dp/package-summary.html">org.biojava.bio.dp</a></dt>
<dd>
<div class="block">
Train a hidden markov model using maximum likelihood.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/BaumWelchTrainer.html#BaumWelchTrainer(org.biojava.bio.dp.DP)">BaumWelchTrainer(DP)</a></span> - Constructor for class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/BaumWelchTrainer.html" title="class in org.biojava.bio.dp">BaumWelchTrainer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/AbstractBeadRenderer.html#beadDepth">beadDepth</a></span> - Variable in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/AbstractBeadRenderer.html" title="class in org.biojava.bio.gui.sequence">AbstractBeadRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/AbstractBeadRenderer.html#beadDisplacement">beadDisplacement</a></span> - Variable in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/AbstractBeadRenderer.html" title="class in org.biojava.bio.gui.sequence">AbstractBeadRenderer</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/gui/sequence/BeadFeatureRenderer.html" title="interface in org.biojava.bio.gui.sequence"><span class="strong">BeadFeatureRenderer</span></a> - Interface in <a href="./org/biojava/bio/gui/sequence/package-summary.html">org.biojava.bio.gui.sequence</a></dt>
<dd>
<div class="block"><code>BeadFeatureRenderer</code>s use a 'string of beads'
metaphor for displaying features.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/AbstractBeadRenderer.html#beadFill">beadFill</a></span> - Variable in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/AbstractBeadRenderer.html" title="class in org.biojava.bio.gui.sequence">AbstractBeadRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/AbstractBeadRenderer.html#beadOutline">beadOutline</a></span> - Variable in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/AbstractBeadRenderer.html" title="class in org.biojava.bio.gui.sequence">AbstractBeadRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/AbstractBeadRenderer.html#beadStroke">beadStroke</a></span> - Variable in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/AbstractBeadRenderer.html" title="class in org.biojava.bio.gui.sequence">AbstractBeadRenderer</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/BeanAsAnnotation.html" title="class in org.biojava.bio"><span class="strong">BeanAsAnnotation</span></a> - Class in <a href="./org/biojava/bio/package-summary.html">org.biojava.bio</a></dt>
<dd>
<div class="block">Create an Annotation with properties matching those of a JavaBean instance.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/BeanAsAnnotation.html#BeanAsAnnotation(java.lang.Object)">BeanAsAnnotation(Object)</a></span> - Constructor for class org.biojava.bio.<a href="./org/biojava/bio/BeanAsAnnotation.html" title="class in org.biojava.bio">BeanAsAnnotation</a></dt>
<dd>
<div class="block">Create a new BeanAsAnnotation for a bean.</div>
</dd>
<dt><a href="./org/biojava/utils/BeanAsMap.html" title="class in org.biojava.utils"><span class="strong">BeanAsMap</span></a> - Class in <a href="./org/biojava/utils/package-summary.html">org.biojava.utils</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/BeanAsMap.html#BeanAsMap(java.lang.Object)">BeanAsMap(Object)</a></span> - Constructor for class org.biojava.utils.<a href="./org/biojava/utils/BeanAsMap.html" title="class in org.biojava.utils">BeanAsMap</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html#beginWriting()">beginWriting()</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html" title="class in org.biojavax.bio.seq.io">EMBLxmlFormat</a></dt>
<dd>
<div class="block">Informs the writer that we want to start writing.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/INSDseqFormat.html#beginWriting()">beginWriting()</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/INSDseqFormat.html" title="class in org.biojavax.bio.seq.io">INSDseqFormat</a></dt>
<dd>
<div class="block">Informs the writer that we want to start writing.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/RichSequenceFormat.html#beginWriting()">beginWriting()</a></span> - Method in interface org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/RichSequenceFormat.html" title="interface in org.biojavax.bio.seq.io">RichSequenceFormat</a></dt>
<dd>
<div class="block">Informs the writer that we want to start writing.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/RichSequenceFormat.HeaderlessFormat.html#beginWriting()">beginWriting()</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/RichSequenceFormat.HeaderlessFormat.html" title="class in org.biojavax.bio.seq.io">RichSequenceFormat.HeaderlessFormat</a></dt>
<dd>
<div class="block">Informs the writer that we want to start writing.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#beginWriting()">beginWriting()</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd>
<div class="block">Informs the writer that we want to start writing.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/Position.html#BETWEEN_BASES">BETWEEN_BASES</a></span> - Static variable in interface org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/Position.html" title="interface in org.biojavax.bio.seq">Position</a></dt>
<dd>
<div class="block">A symbol representing a position that falls in between two bases,
eg.</div>
</dd>
<dt><a href="./org/biojava/bio/symbol/BetweenLocation.html" title="class in org.biojava.bio.symbol"><span class="strong">BetweenLocation</span></a> - Class in <a href="./org/biojava/bio/symbol/package-summary.html">org.biojava.bio.symbol</a></dt>
<dd>
<div class="block">Between view onto an underlying Location instance.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/BetweenLocation.html#BetweenLocation(org.biojava.bio.symbol.Location)">BetweenLocation(Location)</a></span> - Constructor for class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/BetweenLocation.html" title="class in org.biojava.bio.symbol">BetweenLocation</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bibliography/BiblioArticle.html" title="class in org.biojava.bibliography"><span class="strong">BiblioArticle</span></a> - Class in <a href="./org/biojava/bibliography/package-summary.html">org.biojava.bibliography</a></dt>
<dd>
<div class="block">
It represents an article.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BiblioArticle.html#BiblioArticle()">BiblioArticle()</a></span> - Constructor for class org.biojava.bibliography.<a href="./org/biojava/bibliography/BiblioArticle.html" title="class in org.biojava.bibliography">BiblioArticle</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bibliography/BiblioBook.html" title="class in org.biojava.bibliography"><span class="strong">BiblioBook</span></a> - Class in <a href="./org/biojava/bibliography/package-summary.html">org.biojava.bibliography</a></dt>
<dd>
<div class="block">It represents a book.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BiblioBook.html#BiblioBook()">BiblioBook()</a></span> - Constructor for class org.biojava.bibliography.<a href="./org/biojava/bibliography/BiblioBook.html" title="class in org.biojava.bibliography">BiblioBook</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bibliography/BiblioBookArticle.html" title="class in org.biojava.bibliography"><span class="strong">BiblioBookArticle</span></a> - Class in <a href="./org/biojava/bibliography/package-summary.html">org.biojava.bibliography</a></dt>
<dd>
<div class="block">It represents a book article.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BiblioBookArticle.html#BiblioBookArticle()">BiblioBookArticle()</a></span> - Constructor for class org.biojava.bibliography.<a href="./org/biojava/bibliography/BiblioBookArticle.html" title="class in org.biojava.bibliography">BiblioBookArticle</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bibliography/BiblioCriterion.html" title="class in org.biojava.bibliography"><span class="strong">BiblioCriterion</span></a> - Class in <a href="./org/biojava/bibliography/package-summary.html">org.biojava.bibliography</a></dt>
<dd>
<div class="block">The criteria define how the matching or ordering should be done
during queries.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BiblioCriterion.html#BiblioCriterion()">BiblioCriterion()</a></span> - Constructor for class org.biojava.bibliography.<a href="./org/biojava/bibliography/BiblioCriterion.html" title="class in org.biojava.bibliography">BiblioCriterion</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bibliography/BiblioDescription.html" title="class in org.biojava.bibliography"><span class="strong">BiblioDescription</span></a> - Class in <a href="./org/biojava/bibliography/package-summary.html">org.biojava.bibliography</a></dt>
<dd>
<div class="block">
It represents an account of the content of the cited resource.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BiblioDescription.html#BiblioDescription()">BiblioDescription()</a></span> - Constructor for class org.biojava.bibliography.<a href="./org/biojava/bibliography/BiblioDescription.html" title="class in org.biojava.bibliography">BiblioDescription</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bibliography/BiblioEntryStatus.html" title="class in org.biojava.bibliography"><span class="strong">BiblioEntryStatus</span></a> - Class in <a href="./org/biojava/bibliography/package-summary.html">org.biojava.bibliography</a></dt>
<dd>
<div class="block">
It defines information related to the citation itself rather than to the cited resource.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BiblioEntryStatus.html#BiblioEntryStatus()">BiblioEntryStatus()</a></span> - Constructor for class org.biojava.bibliography.<a href="./org/biojava/bibliography/BiblioEntryStatus.html" title="class in org.biojava.bibliography">BiblioEntryStatus</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bibliography/BiblioJournal.html" title="class in org.biojava.bibliography"><span class="strong">BiblioJournal</span></a> - Class in <a href="./org/biojava/bibliography/package-summary.html">org.biojava.bibliography</a></dt>
<dd>
<div class="block">
A class describing journals.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BiblioJournal.html#BiblioJournal()">BiblioJournal()</a></span> - Constructor for class org.biojava.bibliography.<a href="./org/biojava/bibliography/BiblioJournal.html" title="class in org.biojava.bibliography">BiblioJournal</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bibliography/BiblioJournalArticle.html" title="class in org.biojava.bibliography"><span class="strong">BiblioJournalArticle</span></a> - Class in <a href="./org/biojava/bibliography/package-summary.html">org.biojava.bibliography</a></dt>
<dd>
<div class="block">
It represents a journal article.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BiblioJournalArticle.html#BiblioJournalArticle()">BiblioJournalArticle()</a></span> - Constructor for class org.biojava.bibliography.<a href="./org/biojava/bibliography/BiblioJournalArticle.html" title="class in org.biojava.bibliography">BiblioJournalArticle</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bibliography/BiblioOrganisation.html" title="class in org.biojava.bibliography"><span class="strong">BiblioOrganisation</span></a> - Class in <a href="./org/biojava/bibliography/package-summary.html">org.biojava.bibliography</a></dt>
<dd>
<div class="block">
It represents an organisation dealing with the bibliographic
resources.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BiblioOrganisation.html#BiblioOrganisation()">BiblioOrganisation()</a></span> - Constructor for class org.biojava.bibliography.<a href="./org/biojava/bibliography/BiblioOrganisation.html" title="class in org.biojava.bibliography">BiblioOrganisation</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bibliography/BiblioPatent.html" title="class in org.biojava.bibliography"><span class="strong">BiblioPatent</span></a> - Class in <a href="./org/biojava/bibliography/package-summary.html">org.biojava.bibliography</a></dt>
<dd>
<div class="block">
It represents a patent.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BiblioPatent.html#BiblioPatent()">BiblioPatent()</a></span> - Constructor for class org.biojava.bibliography.<a href="./org/biojava/bibliography/BiblioPatent.html" title="class in org.biojava.bibliography">BiblioPatent</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bibliography/BiblioPerson.html" title="class in org.biojava.bibliography"><span class="strong">BiblioPerson</span></a> - Class in <a href="./org/biojava/bibliography/package-summary.html">org.biojava.bibliography</a></dt>
<dd>
<div class="block">
It represents a person dealing with the bibliographic resources.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BiblioPerson.html#BiblioPerson()">BiblioPerson()</a></span> - Constructor for class org.biojava.bibliography.<a href="./org/biojava/bibliography/BiblioPerson.html" title="class in org.biojava.bibliography">BiblioPerson</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bibliography/BiblioProceeding.html" title="class in org.biojava.bibliography"><span class="strong">BiblioProceeding</span></a> - Class in <a href="./org/biojava/bibliography/package-summary.html">org.biojava.bibliography</a></dt>
<dd>
<div class="block">
It represents a conference proceeding.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BiblioProceeding.html#BiblioProceeding()">BiblioProceeding()</a></span> - Constructor for class org.biojava.bibliography.<a href="./org/biojava/bibliography/BiblioProceeding.html" title="class in org.biojava.bibliography">BiblioProceeding</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bibliography/BiblioProvider.html" title="class in org.biojava.bibliography"><span class="strong">BiblioProvider</span></a> - Class in <a href="./org/biojava/bibliography/package-summary.html">org.biojava.bibliography</a></dt>
<dd>
<div class="block">
This class and its sub-classes define active participants of the process
of creation and dissemination of the bibliographic resources.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BiblioProvider.html#BiblioProvider()">BiblioProvider()</a></span> - Constructor for class org.biojava.bibliography.<a href="./org/biojava/bibliography/BiblioProvider.html" title="class in org.biojava.bibliography">BiblioProvider</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bibliography/BiblioScope.html" title="class in org.biojava.bibliography"><span class="strong">BiblioScope</span></a> - Class in <a href="./org/biojava/bibliography/package-summary.html">org.biojava.bibliography</a></dt>
<dd>
<div class="block">
It represent an extent or scope of the content of the cited resource.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BiblioScope.html#BiblioScope()">BiblioScope()</a></span> - Constructor for class org.biojava.bibliography.<a href="./org/biojava/bibliography/BiblioScope.html" title="class in org.biojava.bibliography">BiblioScope</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bibliography/BiblioService.html" title="class in org.biojava.bibliography"><span class="strong">BiblioService</span></a> - Class in <a href="./org/biojava/bibliography/package-summary.html">org.biojava.bibliography</a></dt>
<dd>
<div class="block">
It represents a service dealing with the bibliographic
resources.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BiblioService.html#BiblioService()">BiblioService()</a></span> - Constructor for class org.biojava.bibliography.<a href="./org/biojava/bibliography/BiblioService.html" title="class in org.biojava.bibliography">BiblioService</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bibliography/BiblioSubject.html" title="class in org.biojava.bibliography"><span class="strong">BiblioSubject</span></a> - Class in <a href="./org/biojava/bibliography/package-summary.html">org.biojava.bibliography</a></dt>
<dd>
<div class="block">
It represents the topic of the content of the cited resource.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BiblioSubject.html#BiblioSubject()">BiblioSubject()</a></span> - Constructor for class org.biojava.bibliography.<a href="./org/biojava/bibliography/BiblioSubject.html" title="class in org.biojava.bibliography">BiblioSubject</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bibliography/BiblioTechReport.html" title="class in org.biojava.bibliography"><span class="strong">BiblioTechReport</span></a> - Class in <a href="./org/biojava/bibliography/package-summary.html">org.biojava.bibliography</a></dt>
<dd>
<div class="block">
It represents a technical report.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BiblioTechReport.html#BiblioTechReport()">BiblioTechReport()</a></span> - Constructor for class org.biojava.bibliography.<a href="./org/biojava/bibliography/BiblioTechReport.html" title="class in org.biojava.bibliography">BiblioTechReport</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bibliography/BiblioThesis.html" title="class in org.biojava.bibliography"><span class="strong">BiblioThesis</span></a> - Class in <a href="./org/biojava/bibliography/package-summary.html">org.biojava.bibliography</a></dt>
<dd>
<div class="block">
It represents a thesis.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BiblioThesis.html#BiblioThesis()">BiblioThesis()</a></span> - Constructor for class org.biojava.bibliography.<a href="./org/biojava/bibliography/BiblioThesis.html" title="class in org.biojava.bibliography">BiblioThesis</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bibliography/BiblioWebResource.html" title="class in org.biojava.bibliography"><span class="strong">BiblioWebResource</span></a> - Class in <a href="./org/biojava/bibliography/package-summary.html">org.biojava.bibliography</a></dt>
<dd>
<div class="block">
It represents a WWW resource.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BiblioWebResource.html#BiblioWebResource()">BiblioWebResource()</a></span> - Constructor for class org.biojava.bibliography.<a href="./org/biojava/bibliography/BiblioWebResource.html" title="class in org.biojava.bibliography">BiblioWebResource</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bibliography/BibRef.html" title="class in org.biojava.bibliography"><span class="strong">BibRef</span></a> - Class in <a href="./org/biojava/bibliography/package-summary.html">org.biojava.bibliography</a></dt>
<dd>
<div class="block">
This class is a core class of the bibliographic data model - it
represents a bibliographic reference, a citation.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BibRef.html#BibRef()">BibRef()</a></span> - Constructor for class org.biojava.bibliography.<a href="./org/biojava/bibliography/BibRef.html" title="class in org.biojava.bibliography">BibRef</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bibliography/BibRefException.html" title="class in org.biojava.bibliography"><span class="strong">BibRefException</span></a> - Exception in <a href="./org/biojava/bibliography/package-summary.html">org.biojava.bibliography</a></dt>
<dd>
<div class="block">An exception raised when communciation with the BibRef APIs fails.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BibRefException.html#BibRefException(java.lang.String)">BibRefException(String)</a></span> - Constructor for exception org.biojava.bibliography.<a href="./org/biojava/bibliography/BibRefException.html" title="class in org.biojava.bibliography">BibRefException</a></dt>
<dd>
<div class="block">Create a new BibRefException with a message.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BibRefException.html#BibRefException(java.lang.Throwable)">BibRefException(Throwable)</a></span> - Constructor for exception org.biojava.bibliography.<a href="./org/biojava/bibliography/BibRefException.html" title="class in org.biojava.bibliography">BibRefException</a></dt>
<dd>
<div class="block">Create a new BibRefException with a root cause.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BibRefException.html#BibRefException(java.lang.String, java.lang.Throwable)">BibRefException(String, Throwable)</a></span> - Constructor for exception org.biojava.bibliography.<a href="./org/biojava/bibliography/BibRefException.html" title="class in org.biojava.bibliography">BibRefException</a></dt>
<dd>
<div class="block">Create a nw BibRefException with a message and a root cause.</div>
</dd>
<dt><a href="./org/biojava/bibliography/BibRefQuery.html" title="interface in org.biojava.bibliography"><span class="strong">BibRefQuery</span></a> - Interface in <a href="./org/biojava/bibliography/package-summary.html">org.biojava.bibliography</a></dt>
<dd>
<div class="block">
The interface <em>BibRefQuery</em> is a fundamental part of the Bibliographic Query
Service.</div>
</dd>
<dt><a href="./org/biojava/bibliography/BibRefSupport.html" title="interface in org.biojava.bibliography"><span class="strong">BibRefSupport</span></a> - Interface in <a href="./org/biojava/bibliography/package-summary.html">org.biojava.bibliography</a></dt>
<dd>
<div class="block">
This interface defines supporting utilities for working with
bibliographic repositories.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/PackingFactory.html#binary(long)">binary(long)</a></span> - Static method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/PackingFactory.html" title="class in org.biojava.bio.symbol">PackingFactory</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/PackingFactory.html#binary(int)">binary(int)</a></span> - Static method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/PackingFactory.html" title="class in org.biojava.bio.symbol">PackingFactory</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/utils/math/BinarySearch.html" title="class in org.biojava.utils.math"><span class="strong">BinarySearch</span></a> - Class in <a href="./org/biojava/utils/math/package-summary.html">org.biojava.utils.math</a></dt>
<dd>
<div class="block">solves y = f(x) = 0 by binary search.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/math/BinarySearch.html#BinarySearch()">BinarySearch()</a></span> - Constructor for class org.biojava.utils.math.<a href="./org/biojava/utils/math/BinarySearch.html" title="class in org.biojava.utils.math">BinarySearch</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/naming/ObdaContext.html#bind(javax.naming.Name, java.lang.Object)">bind(Name, Object)</a></span> - Method in class org.biojava.naming.<a href="./org/biojava/naming/ObdaContext.html" title="class in org.biojava.naming">ObdaContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/naming/ObdaContext.html#bind(javax.naming.Name, java.lang.Object, javax.naming.directory.Attributes)">bind(Name, Object, Attributes)</a></span> - Method in class org.biojava.naming.<a href="./org/biojava/naming/ObdaContext.html" title="class in org.biojava.naming">ObdaContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/naming/ObdaContext.html#bind(java.lang.String, java.lang.Object)">bind(String, Object)</a></span> - Method in class org.biojava.naming.<a href="./org/biojava/naming/ObdaContext.html" title="class in org.biojava.naming">ObdaContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/naming/ObdaContext.html#bind(java.lang.String, java.lang.Object, javax.naming.directory.Attributes)">bind(String, Object, Attributes)</a></span> - Method in class org.biojava.naming.<a href="./org/biojava/naming/ObdaContext.html" title="class in org.biojava.naming">ObdaContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/AlternateTokenization.html#bindSymbol(org.biojava.bio.symbol.Symbol, java.lang.String)">bindSymbol(Symbol, String)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/AlternateTokenization.html" title="class in org.biojava.bio.seq.io">AlternateTokenization</a></dt>
<dd>
<div class="block">Bind a Symbol to a string.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/CharacterTokenization.html#bindSymbol(org.biojava.bio.symbol.Symbol, char)">bindSymbol(Symbol, char)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/CharacterTokenization.html" title="class in org.biojava.bio.seq.io">CharacterTokenization</a></dt>
<dd>
<div class="block">
Bind a Symbol to a character.</div>
</dd>
<dt><a href="./org/biojavax/bio/BioEntry.html" title="interface in org.biojavax.bio"><span class="strong">BioEntry</span></a> - Interface in <a href="./org/biojavax/bio/package-summary.html">org.biojavax.bio</a></dt>
<dd>
<div class="block">This class relates to the bioentry table in BioSQL.</div>
</dd>
<dt><a href="./org/biojavax/bio/db/BioEntryDB.html" title="interface in org.biojavax.bio.db"><span class="strong">BioEntryDB</span></a> - Interface in <a href="./org/biojavax/bio/db/package-summary.html">org.biojavax.bio.db</a></dt>
<dd>
<div class="block">.</div>
</dd>
<dt><a href="./org/biojavax/bio/db/BioEntryDBLite.html" title="interface in org.biojavax.bio.db"><span class="strong">BioEntryDBLite</span></a> - Interface in <a href="./org/biojavax/bio/db/package-summary.html">org.biojavax.bio.db</a></dt>
<dd>
<div class="block">A database of BioEntrys.</div>
</dd>
<dt><a href="./org/biojavax/bio/BioEntryIterator.html" title="interface in org.biojavax.bio"><span class="strong">BioEntryIterator</span></a> - Interface in <a href="./org/biojavax/bio/package-summary.html">org.biojavax.bio</a></dt>
<dd>
<div class="block">Essentially the same as SequenceIterator.</div>
</dd>
<dt><a href="./org/biojavax/bio/BioEntryRelationship.html" title="interface in org.biojavax.bio"><span class="strong">BioEntryRelationship</span></a> - Interface in <a href="./org/biojavax/bio/package-summary.html">org.biojavax.bio</a></dt>
<dd>
<div class="block">Represents the relation between two bioentries.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/BioEntryDBLite.html#BIOENTRYS">BIOENTRYS</a></span> - Static variable in interface org.biojavax.bio.db.<a href="./org/biojavax/bio/db/BioEntryDBLite.html" title="interface in org.biojavax.bio.db">BioEntryDBLite</a></dt>
<dd>
<div class="block">Signals that sequences are being added to or remove from the database.</div>
</dd>
<dt><a href="./org/biojava/bio/BioError.html" title="class in org.biojava.bio"><span class="strong">BioError</span></a> - Error in <a href="./org/biojava/bio/package-summary.html">org.biojava.bio</a></dt>
<dd>
<div class="block">A nestable biological error.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/BioError.html#BioError(java.lang.String)">BioError(String)</a></span> - Constructor for error org.biojava.bio.<a href="./org/biojava/bio/BioError.html" title="class in org.biojava.bio">BioError</a></dt>
<dd>
<div class="block">Create a new BioError with a message.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/BioError.html#BioError(java.lang.Throwable)">BioError(Throwable)</a></span> - Constructor for error org.biojava.bio.<a href="./org/biojava/bio/BioError.html" title="class in org.biojava.bio">BioError</a></dt>
<dd>
<div class="block">Create a new BioError with a cause.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/BioError.html#BioError(java.lang.Throwable, java.lang.String)">BioError(Throwable, String)</a></span> - Constructor for error org.biojava.bio.<a href="./org/biojava/bio/BioError.html" title="class in org.biojava.bio">BioError</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>Use BioError(message, ex) instead.</i></div>
</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/BioError.html#BioError(java.lang.String, java.lang.Throwable)">BioError(String, Throwable)</a></span> - Constructor for error org.biojava.bio.<a href="./org/biojava/bio/BioError.html" title="class in org.biojava.bio">BioError</a></dt>
<dd>
<div class="block">Create a new BioError with a cause and a message.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/BioError.html#BioError()">BioError()</a></span> - Constructor for error org.biojava.bio.<a href="./org/biojava/bio/BioError.html" title="class in org.biojava.bio">BioError</a></dt>
<dd>
<div class="block">Create a new BioError.</div>
</dd>
<dt><a href="./org/biojava/bio/BioException.html" title="class in org.biojava.bio"><span class="strong">BioException</span></a> - Exception in <a href="./org/biojava/bio/package-summary.html">org.biojava.bio</a></dt>
<dd>
<div class="block">A nestable biological exception.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/BioException.html#BioException(java.lang.String)">BioException(String)</a></span> - Constructor for exception org.biojava.bio.<a href="./org/biojava/bio/BioException.html" title="class in org.biojava.bio">BioException</a></dt>
<dd>
<div class="block">Create a new BioException with a message.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/BioException.html#BioException(java.lang.Throwable)">BioException(Throwable)</a></span> - Constructor for exception org.biojava.bio.<a href="./org/biojava/bio/BioException.html" title="class in org.biojava.bio">BioException</a></dt>
<dd>
<div class="block">Create a new BioException with a cause.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/BioException.html#BioException(java.lang.Throwable, java.lang.String)">BioException(Throwable, String)</a></span> - Constructor for exception org.biojava.bio.<a href="./org/biojava/bio/BioException.html" title="class in org.biojava.bio">BioException</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>use new BioException(message, ex) instead</i></div>
</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/BioException.html#BioException(java.lang.String, java.lang.Throwable)">BioException(String, Throwable)</a></span> - Constructor for exception org.biojava.bio.<a href="./org/biojava/bio/BioException.html" title="class in org.biojava.bio">BioException</a></dt>
<dd>
<div class="block">Create a new BioException with a cause and a message.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/BioException.html#BioException()">BioException()</a></span> - Constructor for exception org.biojava.bio.<a href="./org/biojava/bio/BioException.html" title="class in org.biojava.bio">BioException</a></dt>
<dd>
<div class="block">Create a new BioException.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/db/biofetch/BioFetchSequenceDB.html" title="class in org.biojava.bio.seq.db.biofetch"><span class="strong">BioFetchSequenceDB</span></a> - Class in <a href="./org/biojava/bio/seq/db/biofetch/package-summary.html">org.biojava.bio.seq.db.biofetch</a></dt>
<dd>
<div class="block">Simple SequenceDB implementation backed by a BioFetch (HTTP)
server.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/biofetch/BioFetchSequenceDB.html#BioFetchSequenceDB(java.lang.String, java.lang.String)">BioFetchSequenceDB(String, String)</a></span> - Constructor for class org.biojava.bio.seq.db.biofetch.<a href="./org/biojava/bio/seq/db/biofetch/BioFetchSequenceDB.html" title="class in org.biojava.bio.seq.db.biofetch">BioFetchSequenceDB</a></dt>
<dd>
<div class="block">Construct a BioFetchSequenceDB which connects to the specified
BioFetch server.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/db/biofetch/BioFetchSequenceDBProvider.html" title="class in org.biojava.bio.seq.db.biofetch"><span class="strong">BioFetchSequenceDBProvider</span></a> - Class in <a href="./org/biojava/bio/seq/db/biofetch/package-summary.html">org.biojava.bio.seq.db.biofetch</a></dt>
<dd>
<div class="block">Directory-services plugin for biofetch databases.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/biofetch/BioFetchSequenceDBProvider.html#BioFetchSequenceDBProvider()">BioFetchSequenceDBProvider()</a></span> - Constructor for class org.biojava.bio.seq.db.biofetch.<a href="./org/biojava/bio/seq/db/biofetch/BioFetchSequenceDBProvider.html" title="class in org.biojava.bio.seq.db.biofetch">BioFetchSequenceDBProvider</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/db/BioIndex.html" title="class in org.biojava.bio.seq.db"><span class="strong">BioIndex</span></a> - Class in <a href="./org/biojava/bio/seq/db/package-summary.html">org.biojava.bio.seq.db</a></dt>
<dd>
<div class="block">The original object for indexing sequence files.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/BioIndex.html#BioIndex(java.io.File, java.lang.String, int)">BioIndex(File, String, int)</a></span> - Constructor for class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/BioIndex.html" title="class in org.biojava.bio.seq.db">BioIndex</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/BioIndex.html#BioIndex(java.io.File)">BioIndex(File)</a></span> - Constructor for class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/BioIndex.html" title="class in org.biojava.bio.seq.db">BioIndex</a></dt>
<dd>
<div class="block">Load an existing index file.</div>
</dd>
<dt><a href="./org/biojava/bio/structure/gui/BiojavaJmol.html" title="class in org.biojava.bio.structure.gui"><span class="strong">BiojavaJmol</span></a> - Class in <a href="./org/biojava/bio/structure/gui/package-summary.html">org.biojava.bio.structure.gui</a></dt>
<dd>
<div class="block">A class that provides a simple GUI for Jmol</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/BiojavaJmol.html#BiojavaJmol()">BiojavaJmol()</a></span> - Constructor for class org.biojava.bio.structure.gui.<a href="./org/biojava/bio/structure/gui/BiojavaJmol.html" title="class in org.biojava.bio.structure.gui">BiojavaJmol</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOTools.html#biojavaToFile(java.lang.String, java.lang.String, java.io.OutputStream, java.lang.Object)">biojavaToFile(String, String, OutputStream, Object)</a></span> - Static method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOTools.html" title="class in org.biojava.bio.seq.io">SeqIOTools</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Writes a Biojava <code>SequenceIterator</code>,
<code>SequenceDB</code>, <code>Sequence</code> or <code>Aligment</code>
to an <code>OutputStream</code></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOTools.html#biojavaToFile(int, java.io.OutputStream, java.lang.Object)">biojavaToFile(int, OutputStream, Object)</a></span> - Static method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOTools.html" title="class in org.biojava.bio.seq.io">SeqIOTools</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Converts a Biojava object to the given filetype.</div>
</dd>
<dt><a href="./org/biojava/bio/search/BioMatcher.html" title="interface in org.biojava.bio.search"><span class="strong">BioMatcher</span></a> - Interface in <a href="./org/biojava/bio/search/package-summary.html">org.biojava.bio.search</a></dt>
<dd>
<div class="block">Interface for things that perform matches.</div>
</dd>
<dt><a href="./org/biojava/bio/search/BioPattern.html" title="interface in org.biojava.bio.search"><span class="strong">BioPattern</span></a> - Interface in <a href="./org/biojava/bio/search/package-summary.html">org.biojava.bio.search</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html#BIOPHYSICOCHEMICAL_PROPERTIES">BIOPHYSICOCHEMICAL_PROPERTIES</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html" title="class in org.biojavax.bio.seq.io">UniProtCommentParser</a></dt>
<dd>
<div class="block">A name for a comment type.</div>
</dd>
<dt><a href="./org/biojava/bio/BioRuntimeException.html" title="class in org.biojava.bio"><span class="strong">BioRuntimeException</span></a> - Exception in <a href="./org/biojava/bio/package-summary.html">org.biojava.bio</a></dt>
<dd>
<div class="block">A nestable biological exception.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/BioRuntimeException.html#BioRuntimeException(java.lang.String)">BioRuntimeException(String)</a></span> - Constructor for exception org.biojava.bio.<a href="./org/biojava/bio/BioRuntimeException.html" title="class in org.biojava.bio">BioRuntimeException</a></dt>
<dd>
<div class="block">Create a new BioRuntimeException with a message.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/BioRuntimeException.html#BioRuntimeException(java.lang.Throwable)">BioRuntimeException(Throwable)</a></span> - Constructor for exception org.biojava.bio.<a href="./org/biojava/bio/BioRuntimeException.html" title="class in org.biojava.bio">BioRuntimeException</a></dt>
<dd>
<div class="block">Create a new BioRuntimeException with a cause.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/BioRuntimeException.html#BioRuntimeException(java.lang.Throwable, java.lang.String)">BioRuntimeException(Throwable, String)</a></span> - Constructor for exception org.biojava.bio.<a href="./org/biojava/bio/BioRuntimeException.html" title="class in org.biojava.bio">BioRuntimeException</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>use new BioRuntimeException(message, ex) instead</i></div>
</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/BioRuntimeException.html#BioRuntimeException(java.lang.String, java.lang.Throwable)">BioRuntimeException(String, Throwable)</a></span> - Constructor for exception org.biojava.bio.<a href="./org/biojava/bio/BioRuntimeException.html" title="class in org.biojava.bio">BioRuntimeException</a></dt>
<dd>
<div class="block">Create a new BioRuntimeException with a cause and a message.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/BioRuntimeException.html#BioRuntimeException()">BioRuntimeException()</a></span> - Constructor for exception org.biojava.bio.<a href="./org/biojava/bio/BioRuntimeException.html" title="class in org.biojava.bio">BioRuntimeException</a></dt>
<dd>
<div class="block">Create a new BioRuntimeException.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/biosql/DBHelper.html#BIOSEQUENCE_GENERIC">BIOSEQUENCE_GENERIC</a></span> - Static variable in class org.biojava.bio.seq.db.biosql.<a href="./org/biojava/bio/seq/db/biosql/DBHelper.html" title="class in org.biojava.bio.seq.db.biosql">DBHelper</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/biosql/DBHelper.html#BIOSEQUENCE_ORACLECLOB">BIOSEQUENCE_ORACLECLOB</a></span> - Static variable in class org.biojava.bio.seq.db.biosql.<a href="./org/biojava/bio/seq/db/biosql/DBHelper.html" title="class in org.biojava.bio.seq.db.biosql">DBHelper</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><a href="./org/biojavax/bio/db/biosql/BioSQLAcceptAllFilter.html" title="class in org.biojavax.bio.db.biosql"><span class="strong">BioSQLAcceptAllFilter</span></a> - Class in <a href="./org/biojavax/bio/db/biosql/package-summary.html">org.biojavax.bio.db.biosql</a></dt>
<dd>
<div class="block">The class that accepts all features.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLAcceptAllFilter.html#BioSQLAcceptAllFilter()">BioSQLAcceptAllFilter()</a></span> - Constructor for class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLAcceptAllFilter.html" title="class in org.biojavax.bio.db.biosql">BioSQLAcceptAllFilter</a></dt>
<dd> </dd>
<dt><a href="./org/biojavax/bio/db/biosql/BioSQLAcceptNoneFilter.html" title="class in org.biojavax.bio.db.biosql"><span class="strong">BioSQLAcceptNoneFilter</span></a> - Class in <a href="./org/biojavax/bio/db/biosql/package-summary.html">org.biojavax.bio.db.biosql</a></dt>
<dd>
<div class="block">The class that accepts no features.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLAcceptNoneFilter.html#BioSQLAcceptNoneFilter()">BioSQLAcceptNoneFilter()</a></span> - Constructor for class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLAcceptNoneFilter.html" title="class in org.biojavax.bio.db.biosql">BioSQLAcceptNoneFilter</a></dt>
<dd> </dd>
<dt><a href="./org/biojavax/bio/db/biosql/BioSQLBioEntryDB.html" title="class in org.biojavax.bio.db.biosql"><span class="strong">BioSQLBioEntryDB</span></a> - Class in <a href="./org/biojavax/bio/db/biosql/package-summary.html">org.biojavax.bio.db.biosql</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLBioEntryDB.html#BioSQLBioEntryDB(java.lang.Object)">BioSQLBioEntryDB(Object)</a></span> - Constructor for class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLBioEntryDB.html" title="class in org.biojavax.bio.db.biosql">BioSQLBioEntryDB</a></dt>
<dd>
<div class="block">Creates a new instance of BioSQLBioEntryDB</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLBioEntryDB.html#BioSQLBioEntryDB(java.lang.String, java.lang.Object)">BioSQLBioEntryDB(String, Object)</a></span> - Constructor for class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLBioEntryDB.html" title="class in org.biojavax.bio.db.biosql">BioSQLBioEntryDB</a></dt>
<dd>
<div class="block">Creates a new instance of BioSQLBioEntryDB</div>
</dd>
<dt><a href="./org/biojavax/bio/db/biosql/BioSQLCrossReferenceResolver.html" title="class in org.biojavax.bio.db.biosql"><span class="strong">BioSQLCrossReferenceResolver</span></a> - Class in <a href="./org/biojavax/bio/db/biosql/package-summary.html">org.biojavax.bio.db.biosql</a></dt>
<dd>
<div class="block">A simple implementation of CrossReferenceResolver</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLCrossReferenceResolver.html#BioSQLCrossReferenceResolver(java.lang.Object)">BioSQLCrossReferenceResolver(Object)</a></span> - Constructor for class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLCrossReferenceResolver.html" title="class in org.biojavax.bio.db.biosql">BioSQLCrossReferenceResolver</a></dt>
<dd>
<div class="block">Requires a Hibernate session to work correctly.</div>
</dd>
<dt><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.html" title="interface in org.biojavax.bio.db.biosql"><span class="strong">BioSQLFeatureFilter</span></a> - Interface in <a href="./org/biojavax/bio/db/biosql/package-summary.html">org.biojavax.bio.db.biosql</a></dt>
<dd>
<div class="block">A filter for accepting or rejecting a feature.</div>
</dd>
<dt><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.And.html" title="class in org.biojavax.bio.db.biosql"><span class="strong">BioSQLFeatureFilter.And</span></a> - Class in <a href="./org/biojavax/bio/db/biosql/package-summary.html">org.biojavax.bio.db.biosql</a></dt>
<dd>
<div class="block">A filter that returns all features accepted by both child filter.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.And.html#BioSQLFeatureFilter.And(org.biojavax.bio.db.biosql.BioSQLFeatureFilter, org.biojavax.bio.db.biosql.BioSQLFeatureFilter)">BioSQLFeatureFilter.And(BioSQLFeatureFilter, BioSQLFeatureFilter)</a></span> - Constructor for class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.And.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.And</a></dt>
<dd> </dd>
<dt><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByName.html" title="class in org.biojavax.bio.db.biosql"><span class="strong">BioSQLFeatureFilter.ByName</span></a> - Class in <a href="./org/biojavax/bio/db/biosql/package-summary.html">org.biojavax.bio.db.biosql</a></dt>
<dd>
<div class="block">Construct one of these to filter features by display name.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByName.html#BioSQLFeatureFilter.ByName(java.lang.String)">BioSQLFeatureFilter.ByName(String)</a></span> - Constructor for class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByName.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.ByName</a></dt>
<dd>
<div class="block">Create a ByType filter that filters in all features with type fields
equal to type.</div>
</dd>
<dt><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByNote.html" title="class in org.biojavax.bio.db.biosql"><span class="strong">BioSQLFeatureFilter.ByNote</span></a> - Class in <a href="./org/biojavax/bio/db/biosql/package-summary.html">org.biojavax.bio.db.biosql</a></dt>
<dd>
<div class="block">A filter that returns all features that have the given note, and
the value and rank is checked as well.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByNote.html#BioSQLFeatureFilter.ByNote(org.biojavax.Note)">BioSQLFeatureFilter.ByNote(Note)</a></span> - Constructor for class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByNote.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.ByNote</a></dt>
<dd> </dd>
<dt><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByNoteTermOnly.html" title="class in org.biojavax.bio.db.biosql"><span class="strong">BioSQLFeatureFilter.ByNoteTermOnly</span></a> - Class in <a href="./org/biojavax/bio/db/biosql/package-summary.html">org.biojavax.bio.db.biosql</a></dt>
<dd>
<div class="block">A filter that returns all features that have a note with the given term.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByNoteTermOnly.html#BioSQLFeatureFilter.ByNoteTermOnly(org.biojavax.ontology.ComparableTerm)">BioSQLFeatureFilter.ByNoteTermOnly(ComparableTerm)</a></span> - Constructor for class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByNoteTermOnly.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.ByNoteTermOnly</a></dt>
<dd> </dd>
<dt><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByRank.html" title="class in org.biojavax.bio.db.biosql"><span class="strong">BioSQLFeatureFilter.ByRank</span></a> - Class in <a href="./org/biojavax/bio/db/biosql/package-summary.html">org.biojavax.bio.db.biosql</a></dt>
<dd>
<div class="block">Construct one of these to filter features by rank.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByRank.html#BioSQLFeatureFilter.ByRank(int)">BioSQLFeatureFilter.ByRank(int)</a></span> - Constructor for class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByRank.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.ByRank</a></dt>
<dd>
<div class="block">Create a Rank filter that filters in all features with rank fields
equal to rank.</div>
</dd>
<dt><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.BySequenceName.html" title="class in org.biojavax.bio.db.biosql"><span class="strong">BioSQLFeatureFilter.BySequenceName</span></a> - Class in <a href="./org/biojavax/bio/db/biosql/package-summary.html">org.biojavax.bio.db.biosql</a></dt>
<dd>
<div class="block">Accept features that reside on a sequence with a particular name.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.BySequenceName.html#BioSQLFeatureFilter.BySequenceName(java.lang.String)">BioSQLFeatureFilter.BySequenceName(String)</a></span> - Constructor for class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.BySequenceName.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.BySequenceName</a></dt>
<dd> </dd>
<dt><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.BySourceTerm.html" title="class in org.biojavax.bio.db.biosql"><span class="strong">BioSQLFeatureFilter.BySourceTerm</span></a> - Class in <a href="./org/biojavax/bio/db/biosql/package-summary.html">org.biojavax.bio.db.biosql</a></dt>
<dd>
<div class="block">Construct one of these to filter features by source.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.BySourceTerm.html#BioSQLFeatureFilter.BySourceTerm(org.biojavax.ontology.ComparableTerm)">BioSQLFeatureFilter.BySourceTerm(ComparableTerm)</a></span> - Constructor for class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.BySourceTerm.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.BySourceTerm</a></dt>
<dd>
<div class="block">Create a BySourceTerm filter that filters in all features with sourceTerm fields
equal to source.</div>
</dd>
<dt><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.BySourceTermName.html" title="class in org.biojavax.bio.db.biosql"><span class="strong">BioSQLFeatureFilter.BySourceTermName</span></a> - Class in <a href="./org/biojavax/bio/db/biosql/package-summary.html">org.biojavax.bio.db.biosql</a></dt>
<dd>
<div class="block">Construct one of these to filter features by source (name only - parent ontology
is ignored).</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.BySourceTermName.html#BioSQLFeatureFilter.BySourceTermName(java.lang.String)">BioSQLFeatureFilter.BySourceTermName(String)</a></span> - Constructor for class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.BySourceTermName.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.BySourceTermName</a></dt>
<dd>
<div class="block">Create a BySourceTerm filter that filters in all features with sourceTerm fields
having name equal to sourceTermName.</div>
</dd>
<dt><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByStrand.html" title="class in org.biojavax.bio.db.biosql"><span class="strong">BioSQLFeatureFilter.ByStrand</span></a> - Class in <a href="./org/biojavax/bio/db/biosql/package-summary.html">org.biojavax.bio.db.biosql</a></dt>
<dd>
<div class="block">A filter that returns all features having locations on a given strand.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByStrand.html#BioSQLFeatureFilter.ByStrand(org.biojavax.bio.seq.RichLocation.Strand)">BioSQLFeatureFilter.ByStrand(RichLocation.Strand)</a></span> - Constructor for class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByStrand.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.ByStrand</a></dt>
<dd>
<div class="block">Creates a filter that returns everything on strand str.</div>
</dd>
<dt><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByTypeTerm.html" title="class in org.biojavax.bio.db.biosql"><span class="strong">BioSQLFeatureFilter.ByTypeTerm</span></a> - Class in <a href="./org/biojavax/bio/db/biosql/package-summary.html">org.biojavax.bio.db.biosql</a></dt>
<dd>
<div class="block">Construct one of these to filter features by type.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByTypeTerm.html#BioSQLFeatureFilter.ByTypeTerm(org.biojavax.ontology.ComparableTerm)">BioSQLFeatureFilter.ByTypeTerm(ComparableTerm)</a></span> - Constructor for class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByTypeTerm.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.ByTypeTerm</a></dt>
<dd>
<div class="block">Create a ByTypeTerm filter that filters in all features with typeTerm fields
equal to typeTerm.</div>
</dd>
<dt><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByTypeTermName.html" title="class in org.biojavax.bio.db.biosql"><span class="strong">BioSQLFeatureFilter.ByTypeTermName</span></a> - Class in <a href="./org/biojavax/bio/db/biosql/package-summary.html">org.biojavax.bio.db.biosql</a></dt>
<dd>
<div class="block">Construct one of these to filter features by type (name only - parent ontology
is ignored).</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByTypeTermName.html#BioSQLFeatureFilter.ByTypeTermName(java.lang.String)">BioSQLFeatureFilter.ByTypeTermName(String)</a></span> - Constructor for class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByTypeTermName.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.ByTypeTermName</a></dt>
<dd>
<div class="block">Create a ByTypeTermName filter that filters in all features with typeTerm fields
having name equal to typeTermName.</div>
</dd>
<dt><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ContainedByRichLocation.html" title="class in org.biojavax.bio.db.biosql"><span class="strong">BioSQLFeatureFilter.ContainedByRichLocation</span></a> - Class in <a href="./org/biojavax/bio/db/biosql/package-summary.html">org.biojavax.bio.db.biosql</a></dt>
<dd>
<div class="block">A filter that returns all features contained within a location.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ContainedByRichLocation.html#BioSQLFeatureFilter.ContainedByRichLocation(org.biojavax.bio.seq.RichLocation)">BioSQLFeatureFilter.ContainedByRichLocation(RichLocation)</a></span> - Constructor for class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ContainedByRichLocation.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.ContainedByRichLocation</a></dt>
<dd>
<div class="block">Creates a filter that returns everything contained within loc.</div>
</dd>
<dt><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.HibernateFeatureFilter.html" title="class in org.biojavax.bio.db.biosql"><span class="strong">BioSQLFeatureFilter.HibernateFeatureFilter</span></a> - Class in <a href="./org/biojavax/bio/db/biosql/package-summary.html">org.biojavax.bio.db.biosql</a></dt>
<dd>
<div class="block">A filter for Hibernate-BioSQL filters to extend.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.HibernateFeatureFilter.html#BioSQLFeatureFilter.HibernateFeatureFilter()">BioSQLFeatureFilter.HibernateFeatureFilter()</a></span> - Constructor for class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.HibernateFeatureFilter.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.HibernateFeatureFilter</a></dt>
<dd> </dd>
<dt><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.Not.html" title="class in org.biojavax.bio.db.biosql"><span class="strong">BioSQLFeatureFilter.Not</span></a> - Class in <a href="./org/biojavax/bio/db/biosql/package-summary.html">org.biojavax.bio.db.biosql</a></dt>
<dd>
<div class="block">A filter that returns all features not accepted by a child filter.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.Not.html#BioSQLFeatureFilter.Not(org.biojavax.bio.db.biosql.BioSQLFeatureFilter)">BioSQLFeatureFilter.Not(BioSQLFeatureFilter)</a></span> - Constructor for class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.Not.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.Not</a></dt>
<dd> </dd>
<dt><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.Or.html" title="class in org.biojavax.bio.db.biosql"><span class="strong">BioSQLFeatureFilter.Or</span></a> - Class in <a href="./org/biojavax/bio/db/biosql/package-summary.html">org.biojavax.bio.db.biosql</a></dt>
<dd>
<div class="block">A filter that returns all features accepted by at least one child filter.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.Or.html#BioSQLFeatureFilter.Or(org.biojavax.bio.db.biosql.BioSQLFeatureFilter, org.biojavax.bio.db.biosql.BioSQLFeatureFilter)">BioSQLFeatureFilter.Or(BioSQLFeatureFilter, BioSQLFeatureFilter)</a></span> - Constructor for class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.Or.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.Or</a></dt>
<dd> </dd>
<dt><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.OverlapsRichLocation.html" title="class in org.biojavax.bio.db.biosql"><span class="strong">BioSQLFeatureFilter.OverlapsRichLocation</span></a> - Class in <a href="./org/biojavax/bio/db/biosql/package-summary.html">org.biojavax.bio.db.biosql</a></dt>
<dd>
<div class="block">A filter that returns all features overlapping a location.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.OverlapsRichLocation.html#BioSQLFeatureFilter.OverlapsRichLocation(org.biojavax.bio.seq.RichLocation)">BioSQLFeatureFilter.OverlapsRichLocation(RichLocation)</a></span> - Constructor for class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.OverlapsRichLocation.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.OverlapsRichLocation</a></dt>
<dd>
<div class="block">Creates a filter that returns everything overlapping loc.</div>
</dd>
<dt><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.Tools.html" title="class in org.biojavax.bio.db.biosql"><span class="strong">BioSQLFeatureFilter.Tools</span></a> - Class in <a href="./org/biojavax/bio/db/biosql/package-summary.html">org.biojavax.bio.db.biosql</a></dt>
<dd>
<div class="block">A class representing some useful stuff you can do with BioSQLFeatureFilters,
for instance converting plain FeatureFilters into a their BioSQLFeatureFilter
equivalents (where possible).</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.Tools.html#BioSQLFeatureFilter.Tools()">BioSQLFeatureFilter.Tools()</a></span> - Constructor for class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.Tools.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.Tools</a></dt>
<dd> </dd>
<dt><a href="./org/biojavax/bio/db/biosql/BioSQLRichObjectBuilder.html" title="class in org.biojavax.bio.db.biosql"><span class="strong">BioSQLRichObjectBuilder</span></a> - Class in <a href="./org/biojavax/bio/db/biosql/package-summary.html">org.biojavax.bio.db.biosql</a></dt>
<dd>
<div class="block">Takes requests for RichObjects and sees if it can load them from a Hibernate
database.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLRichObjectBuilder.html#BioSQLRichObjectBuilder(java.lang.Object)">BioSQLRichObjectBuilder(Object)</a></span> - Constructor for class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLRichObjectBuilder.html" title="class in org.biojavax.bio.db.biosql">BioSQLRichObjectBuilder</a></dt>
<dd>
<div class="block">Creates a new instance of SimpleRichObjectBuilder.</div>
</dd>
<dt><a href="./org/biojavax/bio/db/biosql/BioSQLRichSequenceDB.html" title="class in org.biojavax.bio.db.biosql"><span class="strong">BioSQLRichSequenceDB</span></a> - Class in <a href="./org/biojavax/bio/db/biosql/package-summary.html">org.biojavax.bio.db.biosql</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLRichSequenceDB.html#BioSQLRichSequenceDB(java.lang.Object)">BioSQLRichSequenceDB(Object)</a></span> - Constructor for class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLRichSequenceDB.html" title="class in org.biojavax.bio.db.biosql">BioSQLRichSequenceDB</a></dt>
<dd>
<div class="block">Creates a new instance of BioSQLRichSequenceDB</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLRichSequenceDB.html#BioSQLRichSequenceDB(java.lang.String, java.lang.Object)">BioSQLRichSequenceDB(String, Object)</a></span> - Constructor for class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLRichSequenceDB.html" title="class in org.biojavax.bio.db.biosql">BioSQLRichSequenceDB</a></dt>
<dd>
<div class="block">Creates a new instance of BioSQLRichSequenceDB</div>
</dd>
<dt><a href="./org/biojavax/bio/db/biosql/BioSQLRichSequenceHandler.html" title="class in org.biojavax.bio.db.biosql"><span class="strong">BioSQLRichSequenceHandler</span></a> - Class in <a href="./org/biojavax/bio/db/biosql/package-summary.html">org.biojavax.bio.db.biosql</a></dt>
<dd>
<div class="block">A handler which loads sequence data from a BioSQL database, caching it where possible.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLRichSequenceHandler.html#BioSQLRichSequenceHandler(java.lang.Object)">BioSQLRichSequenceHandler(Object)</a></span> - Constructor for class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLRichSequenceHandler.html" title="class in org.biojavax.bio.db.biosql">BioSQLRichSequenceHandler</a></dt>
<dd>
<div class="block">Requires a Hibernate session to work correctly.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/db/biosql/BioSQLSequenceDB.html" title="class in org.biojava.bio.seq.db.biosql"><span class="strong">BioSQLSequenceDB</span></a> - Class in <a href="./org/biojava/bio/seq/db/biosql/package-summary.html">org.biojava.bio.seq.db.biosql</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>Use hibernate and org.biojavax.bio.db.*</i></div>
</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/biosql/BioSQLSequenceDB.html#BioSQLSequenceDB(java.lang.String, java.lang.String, java.lang.String, java.lang.String, java.lang.String, boolean)">BioSQLSequenceDB(String, String, String, String, String, boolean)</a></span> - Constructor for class org.biojava.bio.seq.db.biosql.<a href="./org/biojava/bio/seq/db/biosql/BioSQLSequenceDB.html" title="class in org.biojava.bio.seq.db.biosql">BioSQLSequenceDB</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Connect to a BioSQL database.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/biosql/BioSQLSequenceDB.html#BioSQLSequenceDB(java.lang.String, java.lang.String, java.lang.String, java.lang.String, boolean)">BioSQLSequenceDB(String, String, String, String, boolean)</a></span> - Constructor for class org.biojava.bio.seq.db.biosql.<a href="./org/biojava/bio/seq/db/biosql/BioSQLSequenceDB.html" title="class in org.biojava.bio.seq.db.biosql">BioSQLSequenceDB</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Connect to a BioSQL database.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/biosql/BioSQLSequenceDB.html#BioSQLSequenceDB(javax.sql.DataSource, java.lang.String, boolean)">BioSQLSequenceDB(DataSource, String, boolean)</a></span> - Constructor for class org.biojava.bio.seq.db.biosql.<a href="./org/biojava/bio/seq/db/biosql/BioSQLSequenceDB.html" title="class in org.biojava.bio.seq.db.biosql">BioSQLSequenceDB</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><a href="./org/biojava/bio/seq/db/biosql/BioSQLSequenceDBProvider.html" title="class in org.biojava.bio.seq.db.biosql"><span class="strong">BioSQLSequenceDBProvider</span></a> - Class in <a href="./org/biojava/bio/seq/db/biosql/package-summary.html">org.biojava.bio.seq.db.biosql</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>Use hibernate and org.biojavax.bio.db.*</i></div>
</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/biosql/BioSQLSequenceDBProvider.html#BioSQLSequenceDBProvider()">BioSQLSequenceDBProvider()</a></span> - Constructor for class org.biojava.bio.seq.db.biosql.<a href="./org/biojava/bio/seq/db/biosql/BioSQLSequenceDBProvider.html" title="class in org.biojava.bio.seq.db.biosql">BioSQLSequenceDBProvider</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><a href="./org/biojava/bio/program/indexdb/BioStore.html" title="class in org.biojava.bio.program.indexdb"><span class="strong">BioStore</span></a> - Class in <a href="./org/biojava/bio/program/indexdb/package-summary.html">org.biojava.bio.program.indexdb</a></dt>
<dd>
<div class="block"><code>BioStore</code>s represent directory and file structures
which index flat files according to the OBDA specification.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/indexdb/BioStore.html#BioStore(java.io.File, boolean)">BioStore(File, boolean)</a></span> - Constructor for class org.biojava.bio.program.indexdb.<a href="./org/biojava/bio/program/indexdb/BioStore.html" title="class in org.biojava.bio.program.indexdb">BioStore</a></dt>
<dd>
<div class="block">Creates a new <code>BioStore</code> flatfile index at the
specified location with the specified caching behaviour.</div>
</dd>
<dt><a href="./org/biojava/bio/program/indexdb/BioStoreFactory.html" title="class in org.biojava.bio.program.indexdb"><span class="strong">BioStoreFactory</span></a> - Class in <a href="./org/biojava/bio/program/indexdb/package-summary.html">org.biojava.bio.program.indexdb</a></dt>
<dd>
<div class="block"><code>BioStoreFactory</code> creates <code>BioStore</code>
instances.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/indexdb/BioStoreFactory.html#BioStoreFactory()">BioStoreFactory()</a></span> - Constructor for class org.biojava.bio.program.indexdb.<a href="./org/biojava/bio/program/indexdb/BioStoreFactory.html" title="class in org.biojava.bio.program.indexdb">BioStoreFactory</a></dt>
<dd>
<div class="block">Creates a new <code>BioStoreFactory</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SmartSequenceBuilder.html#BIT_PACKED">BIT_PACKED</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SmartSequenceBuilder.html" title="class in org.biojava.bio.seq.io">SmartSequenceBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/DistributionTools.html#bitsOfInformation(org.biojava.bio.dist.Distribution)">bitsOfInformation(Distribution)</a></span> - Static method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/DistributionTools.html" title="class in org.biojava.bio.dist">DistributionTools</a></dt>
<dd>
<div class="block">Calculates the total bits of information for a distribution.</div>
</dd>
<dt><a href="./org/biojava/bio/program/blast2html/Blast2HTMLHandler.html" title="class in org.biojava.bio.program.blast2html"><span class="strong">Blast2HTMLHandler</span></a> - Class in <a href="./org/biojava/bio/program/blast2html/package-summary.html">org.biojava.bio.program.blast2html</a></dt>
<dd>
<div class="block">Takes a SAX event stream and a HTMLRenderer to produce
a HTML Blast like program report.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/blast2html/Blast2HTMLHandler.html#Blast2HTMLHandler(org.biojava.bio.program.blast2html.HTMLRenderer)">Blast2HTMLHandler(HTMLRenderer)</a></span> - Constructor for class org.biojava.bio.program.blast2html.<a href="./org/biojava/bio/program/blast2html/Blast2HTMLHandler.html" title="class in org.biojava.bio.program.blast2html">Blast2HTMLHandler</a></dt>
<dd>
<div class="block">A content handler for rendering blast like outputs into
HTML.</div>
</dd>
<dt><a href="./org/biojava/bio/program/ssbind/BlastLikeHomologyBuilder.html" title="class in org.biojava.bio.program.ssbind"><span class="strong">BlastLikeHomologyBuilder</span></a> - Class in <a href="./org/biojava/bio/program/ssbind/package-summary.html">org.biojava.bio.program.ssbind</a></dt>
<dd>
<div class="block"><code>BlastLikeHomologyBuilder</code> populates a
<code>List</code> with <code>Homology</code> instances created from
SAX events supplied via a <code>SeqSimilarityAdapter</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/BlastLikeHomologyBuilder.html#BlastLikeHomologyBuilder(java.util.List)">BlastLikeHomologyBuilder(List)</a></span> - Constructor for class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/BlastLikeHomologyBuilder.html" title="class in org.biojava.bio.program.ssbind">BlastLikeHomologyBuilder</a></dt>
<dd>
<div class="block">Creates a new <code>BlastLikeHomologyBuilder</code> which will
instantiate <code>Homology</code> objects into the
<code>List</code> target.</div>
</dd>
<dt><a href="./org/biojava/bio/program/sax/BlastLikeSAXParser.html" title="class in org.biojava.bio.program.sax"><span class="strong">BlastLikeSAXParser</span></a> - Class in <a href="./org/biojava/bio/program/sax/package-summary.html">org.biojava.bio.program.sax</a></dt>
<dd>
<div class="block">A facade class allowing for direct SAX2-like parsing of the native
output from Blast-like bioinformatics software.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/sax/BlastLikeSAXParser.html#BlastLikeSAXParser()">BlastLikeSAXParser()</a></span> - Constructor for class org.biojava.bio.program.sax.<a href="./org/biojava/bio/program/sax/BlastLikeSAXParser.html" title="class in org.biojava.bio.program.sax">BlastLikeSAXParser</a></dt>
<dd>
<div class="block">Initialises SAXParser, and sets default namespace prefix
to "biojava".</div>
</dd>
<dt><a href="./org/biojava/bio/program/ssbind/BlastLikeSearchBuilder.html" title="class in org.biojava.bio.program.ssbind"><span class="strong">BlastLikeSearchBuilder</span></a> - Class in <a href="./org/biojava/bio/program/ssbind/package-summary.html">org.biojava.bio.program.ssbind</a></dt>
<dd>
<div class="block"><code>BlastLikeSearchBuilder</code> will create
<code>SeqSimilaritySearchResult</code>s from SAX events via a
<code>SeqSimilarityAdapter</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/BlastLikeSearchBuilder.html#BlastLikeSearchBuilder(java.util.List)">BlastLikeSearchBuilder(List)</a></span> - Constructor for class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/BlastLikeSearchBuilder.html" title="class in org.biojava.bio.program.ssbind">BlastLikeSearchBuilder</a></dt>
<dd>
<div class="block">Creates a new <code>BlastLikeSearchBuilder</code> which will
instantiate results into the <code>List</code> target.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/BlastLikeSearchBuilder.html#BlastLikeSearchBuilder(java.util.List, org.biojava.bio.seq.db.SequenceDB, org.biojava.bio.seq.db.SequenceDBInstallation)">BlastLikeSearchBuilder(List, SequenceDB, SequenceDBInstallation)</a></span> - Constructor for class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/BlastLikeSearchBuilder.html" title="class in org.biojava.bio.program.ssbind">BlastLikeSearchBuilder</a></dt>
<dd>
<div class="block">Creates a new <code>BlastLikeSearchBuilder</code> which will
instantiate results into the <code>List</code> target.</div>
</dd>
<dt><a href="./org/biojava/bio/search/BlastLikeSearchFilter.html" title="interface in org.biojava.bio.search"><span class="strong">BlastLikeSearchFilter</span></a> - Interface in <a href="./org/biojava/bio/search/package-summary.html">org.biojava.bio.search</a></dt>
<dd>
<div class="block">A SearchContentHandler class that implements filtering
in chains of SearchContentHandler instances.</div>
</dd>
<dt><a href="./org/biojava/bio/search/BlastLikeSearchFilter.AbstractBlastLikeSearchFilter.html" title="class in org.biojava.bio.search"><span class="strong">BlastLikeSearchFilter.AbstractBlastLikeSearchFilter</span></a> - Class in <a href="./org/biojava/bio/search/package-summary.html">org.biojava.bio.search</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/search/BlastLikeSearchFilter.And.html" title="class in org.biojava.bio.search"><span class="strong">BlastLikeSearchFilter.And</span></a> - Class in <a href="./org/biojava/bio/search/package-summary.html">org.biojava.bio.search</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/BlastLikeSearchFilter.And.html#BlastLikeSearchFilter.And(org.biojava.bio.search.BlastLikeSearchFilter.AbstractBlastLikeSearchFilter, org.biojava.bio.search.BlastLikeSearchFilter.AbstractBlastLikeSearchFilter)">BlastLikeSearchFilter.And(BlastLikeSearchFilter.AbstractBlastLikeSearchFilter, BlastLikeSearchFilter.AbstractBlastLikeSearchFilter)</a></span> - Constructor for class org.biojava.bio.search.<a href="./org/biojava/bio/search/BlastLikeSearchFilter.And.html" title="class in org.biojava.bio.search">BlastLikeSearchFilter.And</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/search/BlastLikeSearchFilter.ByHitProperty.html" title="class in org.biojava.bio.search"><span class="strong">BlastLikeSearchFilter.ByHitProperty</span></a> - Class in <a href="./org/biojava/bio/search/package-summary.html">org.biojava.bio.search</a></dt>
<dd>
<div class="block">Applies test to the value specified by the key in hit properties.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/BlastLikeSearchFilter.ByHitProperty.html#BlastLikeSearchFilter.ByHitProperty(java.lang.String, org.biojava.bio.search.FilterTest)">BlastLikeSearchFilter.ByHitProperty(String, FilterTest)</a></span> - Constructor for class org.biojava.bio.search.<a href="./org/biojava/bio/search/BlastLikeSearchFilter.ByHitProperty.html" title="class in org.biojava.bio.search">BlastLikeSearchFilter.ByHitProperty</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/search/BlastLikeSearchFilter.BySearchProperty.html" title="class in org.biojava.bio.search"><span class="strong">BlastLikeSearchFilter.BySearchProperty</span></a> - Class in <a href="./org/biojava/bio/search/package-summary.html">org.biojava.bio.search</a></dt>
<dd>
<div class="block">Applies test to the value specified by the key in search properties.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/BlastLikeSearchFilter.BySearchProperty.html#BlastLikeSearchFilter.BySearchProperty(java.lang.String, org.biojava.bio.search.FilterTest)">BlastLikeSearchFilter.BySearchProperty(String, FilterTest)</a></span> - Constructor for class org.biojava.bio.search.<a href="./org/biojava/bio/search/BlastLikeSearchFilter.BySearchProperty.html" title="class in org.biojava.bio.search">BlastLikeSearchFilter.BySearchProperty</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/search/BlastLikeSearchFilter.BySubHitProperty.html" title="class in org.biojava.bio.search"><span class="strong">BlastLikeSearchFilter.BySubHitProperty</span></a> - Class in <a href="./org/biojava/bio/search/package-summary.html">org.biojava.bio.search</a></dt>
<dd>
<div class="block">Applies test to the value specified by the key in subhit properties.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/BlastLikeSearchFilter.BySubHitProperty.html#BlastLikeSearchFilter.BySubHitProperty(java.lang.String, org.biojava.bio.search.FilterTest)">BlastLikeSearchFilter.BySubHitProperty(String, FilterTest)</a></span> - Constructor for class org.biojava.bio.search.<a href="./org/biojava/bio/search/BlastLikeSearchFilter.BySubHitProperty.html" title="class in org.biojava.bio.search">BlastLikeSearchFilter.BySubHitProperty</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/search/BlastLikeSearchFilter.Node.html" title="interface in org.biojava.bio.search"><span class="strong">BlastLikeSearchFilter.Node</span></a> - Interface in <a href="./org/biojava/bio/search/package-summary.html">org.biojava.bio.search</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/search/BlastLikeSearchFilter.Not.html" title="class in org.biojava.bio.search"><span class="strong">BlastLikeSearchFilter.Not</span></a> - Class in <a href="./org/biojava/bio/search/package-summary.html">org.biojava.bio.search</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/BlastLikeSearchFilter.Not.html#BlastLikeSearchFilter.Not(org.biojava.bio.search.BlastLikeSearchFilter.AbstractBlastLikeSearchFilter)">BlastLikeSearchFilter.Not(BlastLikeSearchFilter.AbstractBlastLikeSearchFilter)</a></span> - Constructor for class org.biojava.bio.search.<a href="./org/biojava/bio/search/BlastLikeSearchFilter.Not.html" title="class in org.biojava.bio.search">BlastLikeSearchFilter.Not</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/search/BlastLikeSearchFilter.Or.html" title="class in org.biojava.bio.search"><span class="strong">BlastLikeSearchFilter.Or</span></a> - Class in <a href="./org/biojava/bio/search/package-summary.html">org.biojava.bio.search</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/BlastLikeSearchFilter.Or.html#BlastLikeSearchFilter.Or(org.biojava.bio.search.BlastLikeSearchFilter.AbstractBlastLikeSearchFilter, org.biojava.bio.search.BlastLikeSearchFilter.AbstractBlastLikeSearchFilter)">BlastLikeSearchFilter.Or(BlastLikeSearchFilter.AbstractBlastLikeSearchFilter, BlastLikeSearchFilter.AbstractBlastLikeSearchFilter)</a></span> - Constructor for class org.biojava.bio.search.<a href="./org/biojava/bio/search/BlastLikeSearchFilter.Or.html" title="class in org.biojava.bio.search">BlastLikeSearchFilter.Or</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/BlastLikeToXMLConverter.html" title="class in org.biojava.bio.program"><span class="strong">BlastLikeToXMLConverter</span></a> - Class in <a href="./org/biojava/bio/program/package-summary.html">org.biojava.bio.program</a></dt>
<dd>
<div class="block">
A class that converts the raw output from a variety of bioinformatics
software and converts it to XML that will validate against the
biojava:BlastLikeDataSetCollection DTD.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/BlastLikeToXMLConverter.html#BlastLikeToXMLConverter(java.lang.String)">BlastLikeToXMLConverter(String)</a></span> - Constructor for class org.biojava.bio.program.<a href="./org/biojava/bio/program/BlastLikeToXMLConverter.html" title="class in org.biojava.bio.program">BlastLikeToXMLConverter</a></dt>
<dd>
<div class="block">Creates a new <code>BlastToXMLConverter</code> instance.</div>
</dd>
<dt><a href="./org/biojava/bio/program/sax/blastxml/BlastXMLParser.html" title="class in org.biojava.bio.program.sax.blastxml"><span class="strong">BlastXMLParser</span></a> - Class in <a href="./org/biojava/bio/program/sax/blastxml/package-summary.html">org.biojava.bio.program.sax.blastxml</a></dt>
<dd>
<div class="block">This class parses NCBI Blast XML output.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/sax/blastxml/BlastXMLParser.html#BlastXMLParser()">BlastXMLParser()</a></span> - Constructor for class org.biojava.bio.program.sax.blastxml.<a href="./org/biojava/bio/program/sax/blastxml/BlastXMLParser.html" title="class in org.biojava.bio.program.sax.blastxml">BlastXMLParser</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/sax/blastxml/BlastXMLParserFacade.html" title="class in org.biojava.bio.program.sax.blastxml"><span class="strong">BlastXMLParserFacade</span></a> - Class in <a href="./org/biojava/bio/program/sax/blastxml/package-summary.html">org.biojava.bio.program.sax.blastxml</a></dt>
<dd>
<div class="block">A facade class that wraps the NCBI Blast XML
parsing framework in a more user-friendly form.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/sax/blastxml/BlastXMLParserFacade.html#BlastXMLParserFacade()">BlastXMLParserFacade()</a></span> - Constructor for class org.biojava.bio.program.sax.blastxml.<a href="./org/biojava/bio/program/sax/blastxml/BlastXMLParserFacade.html" title="class in org.biojava.bio.program.sax.blastxml">BlastXMLParserFacade</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/TranslationTable.html#BLEPH_MNUC">BLEPH_MNUC</a></span> - Static variable in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/TranslationTable.html" title="interface in org.biojava.bio.symbol">TranslationTable</a></dt>
<dd>
<div class="block">Translation table name for the blepharisma macronuclear genetic
code.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/LocationTools.html#blockCount(org.biojava.bio.symbol.Location)">blockCount(Location)</a></span> - Static method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/LocationTools.html" title="class in org.biojava.bio.symbol">LocationTools</a></dt>
<dd>
<div class="block">Return the number of contiguous blocks in a location.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AbstractLocationDecorator.html#blockIterator()">blockIterator()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AbstractLocationDecorator.html" title="class in org.biojava.bio.symbol">AbstractLocationDecorator</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AbstractRangeLocation.html#blockIterator()">blockIterator()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AbstractRangeLocation.html" title="class in org.biojava.bio.symbol">AbstractRangeLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/FuzzyPointLocation.html#blockIterator()">blockIterator()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/FuzzyPointLocation.html" title="class in org.biojava.bio.symbol">FuzzyPointLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/Location.html#blockIterator()">blockIterator()</a></span> - Method in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/Location.html" title="interface in org.biojava.bio.symbol">Location</a></dt>
<dd>
<div class="block">Return an Iterator over the set of maximal contiguous sub-locations.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleGappedSymbolList.html#BlockIterator()">BlockIterator()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleGappedSymbolList.html" title="class in org.biojava.bio.symbol">SimpleGappedSymbolList</a></dt>
<dd>
<div class="block">Get list of the un-gapped region of the SymbolList.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/CompoundRichLocation.html#blockIterator()">blockIterator()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/CompoundRichLocation.html" title="class in org.biojavax.bio.seq">CompoundRichLocation</a></dt>
<dd>
<div class="block">Return an Iterator over the set of maximal contiguous sub-locations.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/EmptyRichLocation.html#blockIterator()">blockIterator()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/EmptyRichLocation.html" title="class in org.biojavax.bio.seq">EmptyRichLocation</a></dt>
<dd>
<div class="block">Return an Iterator over the set of maximal contiguous sub-locations.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichLocation.html#blockIterator()">blockIterator()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichLocation.html" title="class in org.biojavax.bio.seq">SimpleRichLocation</a></dt>
<dd>
<div class="block">Return an Iterator over the set of maximal contiguous sub-locations.</div>
</dd>
<dt><a href="./org/biojava/bio/gui/BlockPainter.html" title="interface in org.biojava.bio.gui"><span class="strong">BlockPainter</span></a> - Interface in <a href="./org/biojava/bio/gui/package-summary.html">org.biojava.bio.gui</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/molbio/RestrictionEnzyme.html#BLUNT">BLUNT</a></span> - Static variable in class org.biojava.bio.molbio.<a href="./org/biojava/bio/molbio/RestrictionEnzyme.html" title="class in org.biojava.bio.molbio">RestrictionEnzyme</a></dt>
<dd>
<div class="block"><code>BLUNT</code> the end type created by enzymes which leave
a blunt end.</div>
</dd>
<dt><a href="./org/biojava/utils/stax/BooleanElementHandlerBase.html" title="class in org.biojava.utils.stax"><span class="strong">BooleanElementHandlerBase</span></a> - Class in <a href="./org/biojava/utils/stax/package-summary.html">org.biojava.utils.stax</a></dt>
<dd>
<div class="block">
StAX handler for any element which just contains a string representation of
an boolean.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/stax/BooleanElementHandlerBase.html#BooleanElementHandlerBase()">BooleanElementHandlerBase()</a></span> - Constructor for class org.biojava.utils.stax.<a href="./org/biojava/utils/stax/BooleanElementHandlerBase.html" title="class in org.biojava.utils.stax">BooleanElementHandlerBase</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEAnnotFilter.html#BOTH_FORWARD_COMPLEMENT">BOTH_FORWARD_COMPLEMENT</a></span> - Static variable in interface org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEAnnotFilter.html" title="interface in org.biojava.bio.seq.io.agave">AGAVEAnnotFilter</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/tagvalue/BoundaryFinder.html" title="interface in org.biojava.bio.program.tagvalue"><span class="strong">BoundaryFinder</span></a> - Interface in <a href="./org/biojava/bio/program/tagvalue/package-summary.html">org.biojava.bio.program.tagvalue</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/twohead/AbstractMatrixPairDPCursor.html#bPointers">bPointers</a></span> - Variable in class org.biojava.bio.dp.twohead.<a href="./org/biojava/bio/dp/twohead/AbstractMatrixPairDPCursor.html" title="class in org.biojava.bio.dp.twohead">AbstractMatrixPairDPCursor</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/twohead/LightPairDPCursor.html#bPointers">bPointers</a></span> - Variable in class org.biojava.bio.dp.twohead.<a href="./org/biojava/bio/dp/twohead/LightPairDPCursor.html" title="class in org.biojava.bio.dp.twohead">LightPairDPCursor</a></dt>
<dd>
<div class="block">Description of the Field</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/ProteinRefSeqFileFormer.html#breakSymbolArray(org.biojava.bio.symbol.Alphabet, org.biojava.bio.symbol.Symbol[], int, int)">breakSymbolArray(Alphabet, Symbol[], int, int)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/ProteinRefSeqFileFormer.html" title="class in org.biojava.bio.seq.io">ProteinRefSeqFileFormer</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Converts the symbol list passed in into an array of strings.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SwissprotFileFormer.html#breakSymbolArray(org.biojava.bio.symbol.Alphabet, org.biojava.bio.symbol.Symbol[], int, int)">breakSymbolArray(Alphabet, Symbol[], int, int)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SwissprotFileFormer.html" title="class in org.biojava.bio.seq.io">SwissprotFileFormer</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Converts the symbol list passed in into an array of strings.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/obo/OboFileHandler.html#BROAD_SYNONYM">BROAD_SYNONYM</a></span> - Static variable in class org.biojava.ontology.obo.<a href="./org/biojava/ontology/obo/OboFileHandler.html" title="class in org.biojava.ontology.obo">OboFileHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/Synonym.html#BROAD_SYNONYM">BROAD_SYNONYM</a></span> - Static variable in class org.biojava.ontology.<a href="./org/biojava/ontology/Synonym.html" title="class in org.biojava.ontology">Synonym</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/fastq/FastqBuilder.html#build()">build()</a></span> - Method in class org.biojava.bio.program.fastq.<a href="./org/biojava/bio/program/fastq/FastqBuilder.html" title="class in org.biojava.bio.program.fastq">FastqBuilder</a></dt>
<dd>
<div class="block">Build and return a new FASTQ formatted sequence configured from the properties of this builder.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/unigene/UnigeneTools.html#buildDataParser(org.biojava.bio.program.tagvalue.TagValueListener)">buildDataParser(TagValueListener)</a></span> - Static method in class org.biojava.bio.program.unigene.<a href="./org/biojava/bio/program/unigene/UnigeneTools.html" title="class in org.biojava.bio.program.unigene">UnigeneTools</a></dt>
<dd>
<div class="block">Generate a tag-value parser for unigene data files that will pass all
parsing events on to your listener.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssaha/CompactedDataStoreFactory.html#buildDataStore(java.io.File, org.biojava.bio.seq.db.SequenceDB, org.biojava.bio.symbol.Packing, int, int)">buildDataStore(File, SequenceDB, Packing, int, int)</a></span> - Method in class org.biojava.bio.program.ssaha.<a href="./org/biojava/bio/program/ssaha/CompactedDataStoreFactory.html" title="class in org.biojava.bio.program.ssaha">CompactedDataStoreFactory</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssaha/CompactedDataStoreFactory.html#buildDataStore(java.io.File, org.biojava.bio.program.ssaha.SequenceStreamer, org.biojava.bio.symbol.Packing, int, int, int)">buildDataStore(File, SequenceStreamer, Packing, int, int, int)</a></span> - Method in class org.biojava.bio.program.ssaha.<a href="./org/biojava/bio/program/ssaha/CompactedDataStoreFactory.html" title="class in org.biojava.bio.program.ssaha">CompactedDataStoreFactory</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssaha/DataStoreFactory.html#buildDataStore(java.io.File, org.biojava.bio.seq.db.SequenceDB, org.biojava.bio.symbol.Packing, int, int)">buildDataStore(File, SequenceDB, Packing, int, int)</a></span> - Method in interface org.biojava.bio.program.ssaha.<a href="./org/biojava/bio/program/ssaha/DataStoreFactory.html" title="interface in org.biojava.bio.program.ssaha">DataStoreFactory</a></dt>
<dd>
<div class="block">Build a new DataStore.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssaha/MappedDataStoreFactory.html#buildDataStore(java.io.File, org.biojava.bio.seq.db.SequenceDB, org.biojava.bio.symbol.Packing, int, int)">buildDataStore(File, SequenceDB, Packing, int, int)</a></span> - Method in class org.biojava.bio.program.ssaha.<a href="./org/biojava/bio/program/ssaha/MappedDataStoreFactory.html" title="class in org.biojava.bio.program.ssaha">MappedDataStoreFactory</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssaha/NIODataStoreFactory.html#buildDataStore(java.io.File, org.biojava.bio.seq.db.SequenceDB, org.biojava.bio.symbol.Packing, int, int)">buildDataStore(File, SequenceDB, Packing, int, int)</a></span> - Method in class org.biojava.bio.program.ssaha.<a href="./org/biojava/bio/program/ssaha/NIODataStoreFactory.html" title="class in org.biojava.bio.program.ssaha">NIODataStoreFactory</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/unigene/UnigeneTools.html#buildLibInfoParser(org.biojava.bio.program.tagvalue.TagValueListener)">buildLibInfoParser(TagValueListener)</a></span> - Static method in class org.biojava.bio.program.unigene.<a href="./org/biojava/bio/program/unigene/UnigeneTools.html" title="class in org.biojava.bio.program.unigene">UnigeneTools</a></dt>
<dd>
<div class="block">Generate a tag-value parser for the library info unigene files.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLRichObjectBuilder.html#buildObject(java.lang.Class, java.util.List)">buildObject(Class, List)</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLRichObjectBuilder.html" title="class in org.biojavax.bio.db.biosql">BioSQLRichObjectBuilder</a></dt>
<dd>
<div class="block">This method takes a class name and some parameters, and uses that
information to construct and return an equivalent object, usually by
calling the constructor on the class with the supplied parameters.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/RichObjectBuilder.html#buildObject(java.lang.Class, java.util.List)">buildObject(Class, List)</a></span> - Method in interface org.biojavax.<a href="./org/biojavax/RichObjectBuilder.html" title="interface in org.biojavax">RichObjectBuilder</a></dt>
<dd>
<div class="block">This method takes a class name and some parameters, and uses that
information to construct and return an equivalent object, usually by
calling the constructor on the class with the supplied parameters.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleRichObjectBuilder.html#buildObject(java.lang.Class, java.util.List)">buildObject(Class, List)</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleRichObjectBuilder.html" title="class in org.biojavax">SimpleRichObjectBuilder</a></dt>
<dd>
<div class="block">This method takes a class name and some parameters, and uses that
information to construct and return an equivalent object, usually by
calling the constructor on the class with the supplied parameters.</div>
</dd>
<dt><a href="./org/biojava/bio/gui/sequence/BumpedRenderer.html" title="class in org.biojava.bio.gui.sequence"><span class="strong">BumpedRenderer</span></a> - Class in <a href="./org/biojava/bio/gui/sequence/package-summary.html">org.biojava.bio.gui.sequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/BumpedRenderer.html#BumpedRenderer()">BumpedRenderer()</a></span> - Constructor for class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/BumpedRenderer.html" title="class in org.biojava.bio.gui.sequence">BumpedRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/BumpedRenderer.html#BumpedRenderer(org.biojava.bio.gui.sequence.SequenceRenderer)">BumpedRenderer(SequenceRenderer)</a></span> - Constructor for class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/BumpedRenderer.html" title="class in org.biojava.bio.gui.sequence">BumpedRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/BumpedRenderer.html#BumpedRenderer(org.biojava.bio.gui.sequence.SequenceRenderer, int, int)">BumpedRenderer(SequenceRenderer, int, int)</a></span> - Constructor for class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/BumpedRenderer.html" title="class in org.biojava.bio.gui.sequence">BumpedRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/filter/FilterTransformer.html#byAncestor(org.biojava.bio.seq.FeatureFilter.ByAncestor, org.biojava.bio.seq.FeatureFilter)">byAncestor(FeatureFilter.ByAncestor, FeatureFilter)</a></span> - Method in class org.biojava.bio.seq.filter.<a href="./org/biojava/bio/seq/filter/FilterTransformer.html" title="class in org.biojava.bio.seq.filter">FilterTransformer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FilterUtils.html#byAncestor(org.biojava.bio.seq.FeatureFilter)">byAncestor(FeatureFilter)</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FilterUtils.html" title="class in org.biojava.bio.seq">FilterUtils</a></dt>
<dd>
<div class="block">Match features where at least one of the ancestors matches the specified
filter.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FilterUtils.html#byAnnotation(java.lang.Object, java.lang.Object)">byAnnotation(Object, Object)</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FilterUtils.html" title="class in org.biojava.bio.seq">FilterUtils</a></dt>
<dd>
<div class="block">Match features where the annotation property named <code>key</code> is
equal to <code>value</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FilterUtils.html#byAnnotationType(org.biojava.bio.AnnotationType)">byAnnotationType(AnnotationType)</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FilterUtils.html" title="class in org.biojava.bio.seq">FilterUtils</a></dt>
<dd>
<div class="block">Match features with annotations matching the specified <code>AnnotationType</code></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FilterUtils.html#byAnnotationType(java.lang.Object, java.lang.Class)">byAnnotationType(Object, Class)</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FilterUtils.html" title="class in org.biojava.bio.seq">FilterUtils</a></dt>
<dd>
<div class="block">Match features where the annotation property named <code>key</code> is
an instance of <code>valClass</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/filter/FilterTransformer.html#byChild(org.biojava.bio.seq.FeatureFilter.ByChild, org.biojava.bio.seq.FeatureFilter)">byChild(FeatureFilter.ByChild, FeatureFilter)</a></span> - Method in class org.biojava.bio.seq.filter.<a href="./org/biojava/bio/seq/filter/FilterTransformer.html" title="class in org.biojava.bio.seq.filter">FilterTransformer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FilterUtils.html#byChild(org.biojava.bio.seq.FeatureFilter)">byChild(FeatureFilter)</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FilterUtils.html" title="class in org.biojava.bio.seq">FilterUtils</a></dt>
<dd>
<div class="block">Match features where at least one child feature matches the supplied filter.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FilterUtils.html#byClass(java.lang.Class)">byClass(Class)</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FilterUtils.html" title="class in org.biojava.bio.seq">FilterUtils</a></dt>
<dd>
<div class="block">Construct a filter which matches features which are assignable to the
specified class or interface.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FilterUtils.html#byComponentName(java.lang.String)">byComponentName(String)</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FilterUtils.html" title="class in org.biojava.bio.seq">FilterUtils</a></dt>
<dd>
<div class="block">Construct a filter which matches all features which implement the
<code>ComponentFeature</code> interface and have a <code>componentName</code>
property equal to the specified value</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/filter/FilterTransformer.html#byDescendant(org.biojava.bio.seq.FeatureFilter.ByDescendant, org.biojava.bio.seq.FeatureFilter)">byDescendant(FeatureFilter.ByDescendant, FeatureFilter)</a></span> - Method in class org.biojava.bio.seq.filter.<a href="./org/biojava/bio/seq/filter/FilterTransformer.html" title="class in org.biojava.bio.seq.filter">FilterTransformer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FilterUtils.html#byDescendant(org.biojava.bio.seq.FeatureFilter)">byDescendant(FeatureFilter)</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FilterUtils.html" title="class in org.biojava.bio.seq">FilterUtils</a></dt>
<dd>
<div class="block">Match features where at least one decendant feature -- possibly but not necessarily an
immediate child -- matches the specified filter.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FilterUtils.html#byFrame(org.biojava.bio.seq.FramedFeature.ReadingFrame)">byFrame(FramedFeature.ReadingFrame)</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FilterUtils.html" title="class in org.biojava.bio.seq">FilterUtils</a></dt>
<dd>
<div class="block">Construct a filter which matches FramedFeatures with the specified reading
frame.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/FilteringContentHandler.FilterVisitor.html#byHitProperty(org.biojava.bio.search.BlastLikeSearchFilter.ByHitProperty)">byHitProperty(BlastLikeSearchFilter.ByHitProperty)</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/FilteringContentHandler.FilterVisitor.html" title="class in org.biojava.bio.search">FilteringContentHandler.FilterVisitor</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/ByLocationMinMaxComparator.html" title="class in org.biojava.bio.seq"><span class="strong">ByLocationMinMaxComparator</span></a> - Class in <a href="./org/biojava/bio/seq/package-summary.html">org.biojava.bio.seq</a></dt>
<dd>
<div class="block">A Comparator similar to Feature.ByLocationComparator except that the min and max positions of
the location are both compared</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/ByLocationMinMaxComparator.html#ByLocationMinMaxComparator()">ByLocationMinMaxComparator()</a></span> - Constructor for class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/ByLocationMinMaxComparator.html" title="class in org.biojava.bio.seq">ByLocationMinMaxComparator</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/ByLocationMinMaxFeatureComparator.html" title="class in org.biojava.bio.seq"><span class="strong">ByLocationMinMaxFeatureComparator</span></a> - Class in <a href="./org/biojava/bio/seq/package-summary.html">org.biojava.bio.seq</a></dt>
<dd>
<div class="block">Comparator that compares the min and max positions of Features
Required by org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer instances.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/ByLocationMinMaxFeatureComparator.html#ByLocationMinMaxFeatureComparator()">ByLocationMinMaxFeatureComparator()</a></span> - Constructor for class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/ByLocationMinMaxFeatureComparator.html" title="class in org.biojava.bio.seq">ByLocationMinMaxFeatureComparator</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/Feature.html#byLocationOrder">byLocationOrder</a></span> - Static variable in interface org.biojava.bio.seq.<a href="./org/biojava/bio/seq/Feature.html" title="interface in org.biojava.bio.seq">Feature</a></dt>
<dd>
<div class="block"><code>byLocationOrder</code> contains a <code>Feature</code>
comparator which compares by the minimum base position of their
<code>Location</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/IDMaker.html#byName">byName</a></span> - Static variable in interface org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/IDMaker.html" title="interface in org.biojava.bio.seq.db">IDMaker</a></dt>
<dd>
<div class="block">A simple implementation of IDMaker that hashes by sequence name.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FilterUtils.html#byPairwiseScore(double, double)">byPairwiseScore(double, double)</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FilterUtils.html" title="class in org.biojava.bio.seq">FilterUtils</a></dt>
<dd>
<div class="block">Match SeqSimilaritiy features with scores in the specified range.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/filter/FilterTransformer.html#byParent(org.biojava.bio.seq.FeatureFilter.ByParent, org.biojava.bio.seq.FeatureFilter)">byParent(FeatureFilter.ByParent, FeatureFilter)</a></span> - Method in class org.biojava.bio.seq.filter.<a href="./org/biojava/bio/seq/filter/FilterTransformer.html" title="class in org.biojava.bio.seq.filter">FilterTransformer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FilterUtils.html#byParent(org.biojava.bio.seq.FeatureFilter)">byParent(FeatureFilter)</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FilterUtils.html" title="class in org.biojava.bio.seq">FilterUtils</a></dt>
<dd>
<div class="block">Match features where the parent feature matches the specified filter.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SeqSimilaritySearchHit.html#byScore">byScore</a></span> - Static variable in interface org.biojava.bio.search.<a href="./org/biojava/bio/search/SeqSimilaritySearchHit.html" title="interface in org.biojava.bio.search">SeqSimilaritySearchHit</a></dt>
<dd>
<div class="block"><code>byScore</code> contains a
<code>SeqSimilaritySearchHit</code> comparator which
compares by their score.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SeqSimilaritySearchSubHit.html#byScore">byScore</a></span> - Static variable in interface org.biojava.bio.search.<a href="./org/biojava/bio/search/SeqSimilaritySearchSubHit.html" title="interface in org.biojava.bio.search">SeqSimilaritySearchSubHit</a></dt>
<dd>
<div class="block"><code>byScore</code> contains a
<code>SeqSimilaritySearchSubHit</code> comparator which
compares by the score of the sub-hit.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/FilteringContentHandler.FilterVisitor.html#bySearchProperty(org.biojava.bio.search.BlastLikeSearchFilter.BySearchProperty)">bySearchProperty(BlastLikeSearchFilter.BySearchProperty)</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/FilteringContentHandler.FilterVisitor.html" title="class in org.biojava.bio.search">FilteringContentHandler.FilterVisitor</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FilterUtils.html#bySequenceName(java.lang.String)">bySequenceName(String)</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FilterUtils.html" title="class in org.biojava.bio.seq">FilterUtils</a></dt>
<dd>
<div class="block">Match features attached to sequences with a specified name.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FilterUtils.html#bySource(java.lang.String)">bySource(String)</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FilterUtils.html" title="class in org.biojava.bio.seq">FilterUtils</a></dt>
<dd>
<div class="block">Construct a filter which matches features with a specific <code>source</code>
value.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FilterUtils.html#byStrand(org.biojava.bio.seq.StrandedFeature.Strand)">byStrand(StrandedFeature.Strand)</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FilterUtils.html" title="class in org.biojava.bio.seq">FilterUtils</a></dt>
<dd>
<div class="block">Match StrandedFeatures on the specified strand.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SeqSimilaritySearchHit.html#bySubHitCount">bySubHitCount</a></span> - Static variable in interface org.biojava.bio.search.<a href="./org/biojava/bio/search/SeqSimilaritySearchHit.html" title="interface in org.biojava.bio.search">SeqSimilaritySearchHit</a></dt>
<dd>
<div class="block"><code>bySubHitCount</code> contains a
<code>SeqSimilaritySearchHit</code> comparator which
compares by their number of sub-hits.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/FilteringContentHandler.FilterVisitor.html#bySubHitProperty(org.biojava.bio.search.BlastLikeSearchFilter.BySubHitProperty)">bySubHitProperty(BlastLikeSearchFilter.BySubHitProperty)</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/FilteringContentHandler.FilterVisitor.html" title="class in org.biojava.bio.search">FilteringContentHandler.FilterVisitor</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SeqSimilaritySearchSubHit.html#bySubjectStart">bySubjectStart</a></span> - Static variable in interface org.biojava.bio.search.<a href="./org/biojava/bio/search/SeqSimilaritySearchSubHit.html" title="interface in org.biojava.bio.search">SeqSimilaritySearchSubHit</a></dt>
<dd>
<div class="block"><code>bySubjectStart</code> contains a
<code>SeqSimilaritySearchSubHit</code> comparator which
compares by the start position of the sub-hit on the subject
sequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/scf/SCF.html#BYTE_MAX_VALUE">BYTE_MAX_VALUE</a></span> - Static variable in class org.biojava.bio.program.scf.<a href="./org/biojava/bio/program/scf/SCF.html" title="class in org.biojava.bio.program.scf">SCF</a></dt>
<dd>
<div class="block">Represents the maximum unsigned value
of a byte for wrapping purposes</div>
</dd>
<dt><a href="./org/biojava/utils/stax/ByteElementHandlerBase.html" title="class in org.biojava.utils.stax"><span class="strong">ByteElementHandlerBase</span></a> - Class in <a href="./org/biojava/utils/stax/package-summary.html">org.biojava.utils.stax</a></dt>
<dd>
<div class="block">
StAX handler for any element which just contains a string representation of
a byte.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/stax/ByteElementHandlerBase.html#ByteElementHandlerBase()">ByteElementHandlerBase()</a></span> - Constructor for class org.biojava.utils.stax.<a href="./org/biojava/utils/stax/ByteElementHandlerBase.html" title="class in org.biojava.utils.stax">ByteElementHandlerBase</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/Constants.html#BYTES_IN_BYTE">BYTES_IN_BYTE</a></span> - Static variable in class org.biojava.utils.<a href="./org/biojava/utils/Constants.html" title="class in org.biojava.utils">Constants</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/Constants.html#BYTES_IN_CHAR">BYTES_IN_CHAR</a></span> - Static variable in class org.biojava.utils.<a href="./org/biojava/utils/Constants.html" title="class in org.biojava.utils">Constants</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/Constants.html#BYTES_IN_DOUBLE">BYTES_IN_DOUBLE</a></span> - Static variable in class org.biojava.utils.<a href="./org/biojava/utils/Constants.html" title="class in org.biojava.utils">Constants</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/Constants.html#BYTES_IN_FLOAT">BYTES_IN_FLOAT</a></span> - Static variable in class org.biojava.utils.<a href="./org/biojava/utils/Constants.html" title="class in org.biojava.utils">Constants</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/Constants.html#BYTES_IN_INT">BYTES_IN_INT</a></span> - Static variable in class org.biojava.utils.<a href="./org/biojava/utils/Constants.html" title="class in org.biojava.utils">Constants</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/Constants.html#BYTES_IN_LONG">BYTES_IN_LONG</a></span> - Static variable in class org.biojava.utils.<a href="./org/biojava/utils/Constants.html" title="class in org.biojava.utils">Constants</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/Constants.html#BYTES_IN_SHORT">BYTES_IN_SHORT</a></span> - Static variable in class org.biojava.utils.<a href="./org/biojava/utils/Constants.html" title="class in org.biojava.utils">Constants</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/obo/OboFileParser.html#bytesRead">bytesRead</a></span> - Variable in class org.biojava.ontology.obo.<a href="./org/biojava/ontology/obo/OboFileParser.html" title="class in org.biojava.ontology.obo">OboFileParser</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FilterUtils.html#byType(java.lang.String)">byType(String)</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FilterUtils.html" title="class in org.biojava.bio.seq">FilterUtils</a></dt>
<dd>
<div class="block">Construct a filter which matches features with a specific <code>type</code>
value.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/IDMaker.html#byURN">byURN</a></span> - Static variable in interface org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/IDMaker.html" title="interface in org.biojava.bio.seq.db">IDMaker</a></dt>
<dd>
<div class="block">A simple implementation of IDMaker that hashes by URN.</div>
</dd>
</dl>
<a name="_C_">
<!-- -->
</a>
<h2 class="title">C</h2>
<dl>
<dt><span class="strong"><a href="./org/biojava/bio/seq/DNATools.html#c()">c()</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/DNATools.html" title="class in org.biojava.bio.seq">DNATools</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/NucleotideTools.html#c()">c()</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/NucleotideTools.html" title="class in org.biojava.bio.seq">NucleotideTools</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/ProteinTools.html#c()">c()</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/ProteinTools.html" title="class in org.biojava.bio.seq">ProteinTools</a></dt>
<dd>
<div class="block">Returns the <code>AtomicSymbol</code> for the amino acid
Cysteine</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/RNATools.html#c()">c()</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/RNATools.html" title="class in org.biojava.bio.seq">RNATools</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/Taxon.html#C_ELEGANS">C_ELEGANS</a></span> - Static variable in interface org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/Taxon.html" title="interface in org.biojava.bio.program.homologene">Taxon</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/StructureTools.html#caAtomName">caAtomName</a></span> - Static variable in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/StructureTools.html" title="class in org.biojava.bio.structure">StructureTools</a></dt>
<dd>
<div class="block">The Atom name of C-alpha atoms.</div>
</dd>
<dt><a href="./org/biojava/utils/cache/Cache.html" title="interface in org.biojava.utils.cache"><span class="strong">Cache</span></a> - Interface in <a href="./org/biojava/utils/cache/package-summary.html">org.biojava.utils.cache</a></dt>
<dd>
<div class="block">Interface for managing caches of objects.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/io/CachingInputStream.html#cache">cache</a></span> - Variable in class org.biojava.utils.io.<a href="./org/biojava/utils/io/CachingInputStream.html" title="class in org.biojava.utils.io">CachingInputStream</a></dt>
<dd>
<div class="block">The byte cache itself.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/BlastLikeSearchFilter.AbstractBlastLikeSearchFilter.html#cachedOutcome">cachedOutcome</a></span> - Variable in class org.biojava.bio.search.<a href="./org/biojava/bio/search/BlastLikeSearchFilter.AbstractBlastLikeSearchFilter.html" title="class in org.biojava.bio.search">BlastLikeSearchFilter.AbstractBlastLikeSearchFilter</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/utils/cache/CacheMap.html" title="interface in org.biojava.utils.cache"><span class="strong">CacheMap</span></a> - Interface in <a href="./org/biojava/utils/cache/package-summary.html">org.biojava.utils.cache</a></dt>
<dd>
<div class="block">
Interface for managing caches of objects fetchable by key.</div>
</dd>
<dt><a href="./org/biojava/utils/cache/CacheReference.html" title="interface in org.biojava.utils.cache"><span class="strong">CacheReference</span></a> - Interface in <a href="./org/biojava/utils/cache/package-summary.html">org.biojava.utils.cache</a></dt>
<dd>
<div class="block">Interface for a reference to an object, analogous to
<code>java.lang.ref.Referencce</code>, but more flexible.</div>
</dd>
<dt><a href="./org/biojava/utils/io/CachingInputStream.html" title="class in org.biojava.utils.io"><span class="strong">CachingInputStream</span></a> - Class in <a href="./org/biojava/utils/io/package-summary.html">org.biojava.utils.io</a></dt>
<dd>
<div class="block">A wrapper around <code>InputStream</code> that provides in-memory
caching of the input data.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/io/CachingInputStream.html#CachingInputStream(java.io.InputStream)">CachingInputStream(InputStream)</a></span> - Constructor for class org.biojava.utils.io.<a href="./org/biojava/utils/io/CachingInputStream.html" title="class in org.biojava.utils.io">CachingInputStream</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/stats/svm/CachingKernel.html" title="class in org.biojava.stats.svm"><span class="strong">CachingKernel</span></a> - Class in <a href="./org/biojava/stats/svm/package-summary.html">org.biojava.stats.svm</a></dt>
<dd>
<div class="block">
Caches the results of a nested kernel so that k(a, b) need only be calculated
once.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/CachingKernel.html#CachingKernel()">CachingKernel()</a></span> - Constructor for class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/CachingKernel.html" title="class in org.biojava.stats.svm">CachingKernel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/CachingKernel.html#CachingKernel(org.biojava.stats.svm.SVMKernel)">CachingKernel(SVMKernel)</a></span> - Constructor for class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/CachingKernel.html" title="class in org.biojava.stats.svm">CachingKernel</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/db/CachingSequenceDB.html" title="class in org.biojava.bio.seq.db"><span class="strong">CachingSequenceDB</span></a> - Class in <a href="./org/biojava/bio/seq/db/package-summary.html">org.biojava.bio.seq.db</a></dt>
<dd>
<div class="block">SequenceDB implementation that caches the results of another SequenceDB.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/CachingSequenceDB.html#CachingSequenceDB(org.biojava.bio.seq.db.SequenceDB)">CachingSequenceDB(SequenceDB)</a></span> - Constructor for class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/CachingSequenceDB.html" title="class in org.biojava.bio.seq.db">CachingSequenceDB</a></dt>
<dd>
<div class="block">Create a new CachingSequenceDB that caches the sequences in parent.</div>
</dd>
<dt><a href="./org/biojava/bio/structure/io/CAConverter.html" title="class in org.biojava.bio.structure.io"><span class="strong">CAConverter</span></a> - Class in <a href="./org/biojava/bio/structure/io/package-summary.html">org.biojava.bio.structure.io</a></dt>
<dd>
<div class="block">Converts full atom representations to Calpha only ones.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/CAConverter.html#CAConverter()">CAConverter()</a></span> - Constructor for class org.biojava.bio.structure.io.<a href="./org/biojava/bio/structure/io/CAConverter.html" title="class in org.biojava.bio.structure.io">CAConverter</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/structure/Calc.html" title="class in org.biojava.bio.structure"><span class="strong">Calc</span></a> - Class in <a href="./org/biojava/bio/structure/package-summary.html">org.biojava.bio.structure</a></dt>
<dd>
<div class="block">utility operations on Atoms, AminoAcids, etc.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Calc.html#Calc()">Calc()</a></span> - Constructor for class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Calc.html" title="class in org.biojava.bio.structure">Calc</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/twohead/CellCalculator.html#calcCell(org.biojava.bio.dp.twohead.Cell[][])">calcCell(Cell[][])</a></span> - Method in interface org.biojava.bio.dp.twohead.<a href="./org/biojava/bio/dp/twohead/CellCalculator.html" title="interface in org.biojava.bio.dp.twohead">CellCalculator</a></dt>
<dd>
<div class="block">
Calculate the 'scores' array in the cell at cells[0][0].</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePanel.html#calcDist()">calcDist()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePanel.html" title="class in org.biojava.bio.gui.sequence">SequencePanel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/IDMaker.ByName.html#calcID(org.biojava.bio.seq.Sequence)">calcID(Sequence)</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/IDMaker.ByName.html" title="class in org.biojava.bio.seq.db">IDMaker.ByName</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/IDMaker.ByURN.html#calcID(org.biojava.bio.seq.Sequence)">calcID(Sequence)</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/IDMaker.ByURN.html" title="class in org.biojava.bio.seq.db">IDMaker.ByURN</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/IDMaker.html#calcID(org.biojava.bio.seq.Sequence)">calcID(Sequence)</a></span> - Method in interface org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/IDMaker.html" title="interface in org.biojava.bio.seq.db">IDMaker</a></dt>
<dd>
<div class="block">Calculate the id for a sequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/SVMRegressionModel.html#calcKernel()">calcKernel()</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/SVMRegressionModel.html" title="class in org.biojava.stats.svm">SVMRegressionModel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePoster.html#calcLineExtent(java.awt.event.MouseEvent)">calcLineExtent(MouseEvent)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePoster.html" title="class in org.biojava.bio.gui.sequence">SequencePoster</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/SequenceDisplay.html#calcScale(int)">calcScale(int)</a></span> - Method in class org.biojava.bio.structure.gui.<a href="./org/biojava/bio/structure/gui/SequenceDisplay.html" title="class in org.biojava.bio.structure.gui">SequenceDisplay</a></dt>
<dd>
<div class="block">a value of 100 means that the whole sequence should be displayed in the current visible window
a factor of 1 means that one amino acid shoud be drawn as big as possible</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/AlternativeAlignment.html#calcScores(org.biojava.bio.structure.Atom[], org.biojava.bio.structure.Atom[])">calcScores(Atom[], Atom[])</a></span> - Method in class org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/AlternativeAlignment.html" title="class in org.biojava.bio.structure.align.pairwise">AlternativeAlignment</a></dt>
<dd>
<div class="block">calculates scores for this alignment ( %id )</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/indexdb/BioStoreFactory.html#calculatePrimRecLen(int)">calculatePrimRecLen(int)</a></span> - Static method in class org.biojava.bio.program.indexdb.<a href="./org/biojava/bio/program/indexdb/BioStoreFactory.html" title="class in org.biojava.bio.program.indexdb">BioStoreFactory</a></dt>
<dd>
<div class="block"><code>calculatePrimRecLen</code> calculates the byte length of
primary namespace records.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/ScoreType.html#calculateScore(org.biojava.bio.dist.Distribution, org.biojava.bio.symbol.Symbol)">calculateScore(Distribution, Symbol)</a></span> - Method in interface org.biojava.bio.dp.<a href="./org/biojava/bio/dp/ScoreType.html" title="interface in org.biojava.bio.dp">ScoreType</a></dt>
<dd>
<div class="block">Calculates the score associated with a distribution and a symbol.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/ScoreType.NullModel.html#calculateScore(org.biojava.bio.dist.Distribution, org.biojava.bio.symbol.Symbol)">calculateScore(Distribution, Symbol)</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/ScoreType.NullModel.html" title="class in org.biojava.bio.dp">ScoreType.NullModel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/ScoreType.Odds.html#calculateScore(org.biojava.bio.dist.Distribution, org.biojava.bio.symbol.Symbol)">calculateScore(Distribution, Symbol)</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/ScoreType.Odds.html" title="class in org.biojava.bio.dp">ScoreType.Odds</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/ScoreType.Probability.html#calculateScore(org.biojava.bio.dist.Distribution, org.biojava.bio.symbol.Symbol)">calculateScore(Distribution, Symbol)</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/ScoreType.Probability.html" title="class in org.biojava.bio.dp">ScoreType.Probability</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/indexdb/BioStoreFactory.html#calculateSecRecLen(int, java.lang.String, java.util.Map)">calculateSecRecLen(int, String, Map)</a></span> - Static method in class org.biojava.bio.program.indexdb.<a href="./org/biojava/bio/program/indexdb/BioStoreFactory.html" title="class in org.biojava.bio.program.indexdb">BioStoreFactory</a></dt>
<dd>
<div class="block"><code>calculateSecRecLen</code> calculates the byte length of
secondary namespace records.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/AlternativeAlignment.html#calculateSuperpositionByIdx(org.biojava.bio.structure.Atom[], org.biojava.bio.structure.Atom[])">calculateSuperpositionByIdx(Atom[], Atom[])</a></span> - Method in class org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/AlternativeAlignment.html" title="class in org.biojava.bio.structure.align.pairwise">AlternativeAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/StAXFeatureHandler.html#callbackStack">callbackStack</a></span> - Variable in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/StAXFeatureHandler.html" title="class in org.biojava.bio.seq.io.agave">StAXFeatureHandler</a></dt>
<dd>
<div class="block">this is the stack of handler objects for the current feature.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game/StAXFeatureHandler.html#callbackStack">callbackStack</a></span> - Variable in class org.biojava.bio.seq.io.game.<a href="./org/biojava/bio/seq/io/game/StAXFeatureHandler.html" title="class in org.biojava.bio.seq.io.game">StAXFeatureHandler</a></dt>
<dd>
<div class="block">this is the stack of handler objects for the current feature.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.html#callboxesValid">callboxesValid</a></span> - Variable in class org.biojava.bio.chromatogram.graphic.<a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.html" title="class in org.biojava.bio.chromatogram.graphic">ChromatogramGraphic</a></dt>
<dd>
<div class="block">Flag for call boxes.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/unigene/FlatFileUnigeneFactory.html#canAccept(java.net.URL)">canAccept(URL)</a></span> - Method in class org.biojava.bio.program.unigene.<a href="./org/biojava/bio/program/unigene/FlatFileUnigeneFactory.html" title="class in org.biojava.bio.program.unigene">FlatFileUnigeneFactory</a></dt>
<dd>
<div class="block">Accepts all URLs that are of the file protocol.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/unigene/SQLUnigeneFactory.html#canAccept(java.net.URL)">canAccept(URL)</a></span> - Method in class org.biojava.bio.program.unigene.<a href="./org/biojava/bio/program/unigene/SQLUnigeneFactory.html" title="class in org.biojava.bio.program.unigene">SQLUnigeneFactory</a></dt>
<dd>
<div class="block">Accepts all URLs that are of the jdbc protocol.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/unigene/UnigeneFactory.html#canAccept(java.net.URL)">canAccept(URL)</a></span> - Method in interface org.biojava.bio.program.unigene.<a href="./org/biojava/bio/program/unigene/UnigeneFactory.html" title="interface in org.biojava.bio.program.unigene">UnigeneFactory</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/onehead/DPCursor.html#canAdvance()">canAdvance()</a></span> - Method in interface org.biojava.bio.dp.onehead.<a href="./org/biojava/bio/dp/onehead/DPCursor.html" title="interface in org.biojava.bio.dp.onehead">DPCursor</a></dt>
<dd>
<div class="block">Can we advance?</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/candy/CandyVocabulary.html#CANDIES_NOT_SORTED">CANDIES_NOT_SORTED</a></span> - Static variable in interface org.biojava.utils.candy.<a href="./org/biojava/utils/candy/CandyVocabulary.html" title="interface in org.biojava.utils.candy">CandyVocabulary</a></dt>
<dd>
<div class="block">
A property name.</div>
</dd>
<dt><a href="./org/biojava/utils/candy/CandyEntry.html" title="class in org.biojava.utils.candy"><span class="strong">CandyEntry</span></a> - Class in <a href="./org/biojava/utils/candy/package-summary.html">org.biojava.utils.candy</a></dt>
<dd>
<div class="block">
This is a basic container for a vocabulary entry.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/candy/CandyEntry.html#CandyEntry()">CandyEntry()</a></span> - Constructor for class org.biojava.utils.candy.<a href="./org/biojava/utils/candy/CandyEntry.html" title="class in org.biojava.utils.candy">CandyEntry</a></dt>
<dd>
<div class="block">An empty constructor.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/candy/CandyEntry.html#CandyEntry(java.lang.String)">CandyEntry(String)</a></span> - Constructor for class org.biojava.utils.candy.<a href="./org/biojava/utils/candy/CandyEntry.html" title="class in org.biojava.utils.candy">CandyEntry</a></dt>
<dd>
<div class="block">It creates an entry instance with given name and empty value.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/candy/CandyEntry.html#CandyEntry(java.lang.String, java.lang.String)">CandyEntry(String, String)</a></span> - Constructor for class org.biojava.utils.candy.<a href="./org/biojava/utils/candy/CandyEntry.html" title="class in org.biojava.utils.candy">CandyEntry</a></dt>
<dd>
<div class="block">It creates an entry instance with given name and value.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/candy/CandyEntry.html#CandyEntry(java.lang.String, java.lang.String, java.util.Hashtable)">CandyEntry(String, String, Hashtable)</a></span> - Constructor for class org.biojava.utils.candy.<a href="./org/biojava/utils/candy/CandyEntry.html" title="class in org.biojava.utils.candy">CandyEntry</a></dt>
<dd>
<div class="block">It creates an entry instance with given name, value and
additional properties.</div>
</dd>
<dt><a href="./org/biojava/utils/candy/CandyException.html" title="class in org.biojava.utils.candy"><span class="strong">CandyException</span></a> - Exception in <a href="./org/biojava/utils/candy/package-summary.html">org.biojava.utils.candy</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/candy/CandyException.html#CandyException(java.lang.String)">CandyException(String)</a></span> - Constructor for exception org.biojava.utils.candy.<a href="./org/biojava/utils/candy/CandyException.html" title="class in org.biojava.utils.candy">CandyException</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/candy/CandyException.html#CandyException(java.lang.Throwable)">CandyException(Throwable)</a></span> - Constructor for exception org.biojava.utils.candy.<a href="./org/biojava/utils/candy/CandyException.html" title="class in org.biojava.utils.candy">CandyException</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/candy/CandyException.html#CandyException(java.lang.String, java.lang.Throwable)">CandyException(String, Throwable)</a></span> - Constructor for exception org.biojava.utils.candy.<a href="./org/biojava/utils/candy/CandyException.html" title="class in org.biojava.utils.candy">CandyException</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/utils/candy/CandyFinder.html" title="interface in org.biojava.utils.candy"><span class="strong">CandyFinder</span></a> - Interface in <a href="./org/biojava/utils/candy/package-summary.html">org.biojava.utils.candy</a></dt>
<dd>
<div class="block">
This interface is a main entry point to a set of controlled
vocabularies.</div>
</dd>
<dt><a href="./org/biojava/utils/candy/CandyVocabulary.html" title="interface in org.biojava.utils.candy"><span class="strong">CandyVocabulary</span></a> - Interface in <a href="./org/biojava/utils/candy/package-summary.html">org.biojava.utils.candy</a></dt>
<dd>
<div class="block">
This interface defines functionality of a controlled vocabulary.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/LocationTools.html#canMerge(org.biojava.bio.symbol.Location, org.biojava.bio.symbol.Location)">canMerge(Location, Location)</a></span> - Static method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/LocationTools.html" title="class in org.biojava.bio.symbol">LocationTools</a></dt>
<dd>
<div class="block">Determines whether the locations are touching or not (if they could be
merged in a single Location.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLFormat.html#canRead(java.io.File)">canRead(File)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLFormat.html" title="class in org.biojavax.bio.seq.io">EMBLFormat</a></dt>
<dd>
<div class="block">Check to see if a given file is in our format.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLFormat.html#canRead(java.io.BufferedInputStream)">canRead(BufferedInputStream)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLFormat.html" title="class in org.biojavax.bio.seq.io">EMBLFormat</a></dt>
<dd>
<div class="block">Check to see if a given stream is in our format.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html#canRead(java.io.File)">canRead(File)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html" title="class in org.biojavax.bio.seq.io">EMBLxmlFormat</a></dt>
<dd>
<div class="block">Check to see if a given file is in our format.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html#canRead(java.io.BufferedInputStream)">canRead(BufferedInputStream)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html" title="class in org.biojavax.bio.seq.io">EMBLxmlFormat</a></dt>
<dd>
<div class="block">Check to see if a given stream is in our format.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/FastaFormat.html#canRead(java.io.File)">canRead(File)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/FastaFormat.html" title="class in org.biojavax.bio.seq.io">FastaFormat</a></dt>
<dd>
<div class="block">Check to see if a given file is in our format.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/FastaFormat.html#canRead(java.io.BufferedInputStream)">canRead(BufferedInputStream)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/FastaFormat.html" title="class in org.biojavax.bio.seq.io">FastaFormat</a></dt>
<dd>
<div class="block">Check to see if a given stream is in our format.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/GenbankFormat.html#canRead(java.io.File)">canRead(File)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/GenbankFormat.html" title="class in org.biojavax.bio.seq.io">GenbankFormat</a></dt>
<dd>
<div class="block">Check to see if a given file is in our format.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/GenbankFormat.html#canRead(java.io.BufferedInputStream)">canRead(BufferedInputStream)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/GenbankFormat.html" title="class in org.biojavax.bio.seq.io">GenbankFormat</a></dt>
<dd>
<div class="block">Check to see if a given stream is in our format.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/INSDseqFormat.html#canRead(java.io.File)">canRead(File)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/INSDseqFormat.html" title="class in org.biojavax.bio.seq.io">INSDseqFormat</a></dt>
<dd>
<div class="block">Check to see if a given file is in our format.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/INSDseqFormat.html#canRead(java.io.BufferedInputStream)">canRead(BufferedInputStream)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/INSDseqFormat.html" title="class in org.biojavax.bio.seq.io">INSDseqFormat</a></dt>
<dd>
<div class="block">Check to see if a given stream is in our format.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/RichSequenceFormat.BasicFormat.html#canRead(java.io.File)">canRead(File)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/RichSequenceFormat.BasicFormat.html" title="class in org.biojavax.bio.seq.io">RichSequenceFormat.BasicFormat</a></dt>
<dd>
<div class="block">Check to see if a given file is in our format.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/RichSequenceFormat.html#canRead(java.io.File)">canRead(File)</a></span> - Method in interface org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/RichSequenceFormat.html" title="interface in org.biojavax.bio.seq.io">RichSequenceFormat</a></dt>
<dd>
<div class="block">Check to see if a given file is in our format.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/RichSequenceFormat.html#canRead(java.io.BufferedInputStream)">canRead(BufferedInputStream)</a></span> - Method in interface org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/RichSequenceFormat.html" title="interface in org.biojavax.bio.seq.io">RichSequenceFormat</a></dt>
<dd>
<div class="block">Check to see if a given stream is in our format.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtFormat.html#canRead(java.io.File)">canRead(File)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtFormat.html" title="class in org.biojavax.bio.seq.io">UniProtFormat</a></dt>
<dd>
<div class="block">Check to see if a given file is in our format.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtFormat.html#canRead(java.io.BufferedInputStream)">canRead(BufferedInputStream)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtFormat.html" title="class in org.biojavax.bio.seq.io">UniProtFormat</a></dt>
<dd>
<div class="block">Check to see if a given stream is in our format.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#canRead(java.io.File)">canRead(File)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd>
<div class="block">Check to see if a given file is in our format.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#canRead(java.io.BufferedInputStream)">canRead(BufferedInputStream)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd>
<div class="block">Check to see if a given stream is in our format.</div>
</dd>
<dt><a href="./org/biojava/bio/CardinalityConstraint.html" title="class in org.biojava.bio"><span class="strong">CardinalityConstraint</span></a> - Class in <a href="./org/biojava/bio/package-summary.html">org.biojava.bio</a></dt>
<dd>
<div class="block">A constraint on the number of values a property can have.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/MassCalc.html#Cavg">Cavg</a></span> - Static variable in class org.biojava.bio.proteomics.<a href="./org/biojava/bio/proteomics/MassCalc.html" title="class in org.biojava.bio.proteomics">MassCalc</a></dt>
<dd>
<div class="block">Constant value of Carbon average mass</div>
</dd>
<dt><a href="./org/biojava/bio/dp/twohead/Cell.html" title="class in org.biojava.bio.dp.twohead"><span class="strong">Cell</span></a> - Class in <a href="./org/biojava/bio/dp/twohead/package-summary.html">org.biojava.bio.dp.twohead</a></dt>
<dd>
<div class="block">
A single cell in the DP matrix.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/twohead/Cell.html#Cell()">Cell()</a></span> - Constructor for class org.biojava.bio.dp.twohead.<a href="./org/biojava/bio/dp/twohead/Cell.html" title="class in org.biojava.bio.dp.twohead">Cell</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/dp/twohead/CellCalculator.html" title="interface in org.biojava.bio.dp.twohead"><span class="strong">CellCalculator</span></a> - Interface in <a href="./org/biojava/bio/dp/twohead/package-summary.html">org.biojava.bio.dp.twohead</a></dt>
<dd>
<div class="block">
The interface for all functions that can calculate the 'scores' array for
a given cell.</div>
</dd>
<dt><a href="./org/biojava/bio/dp/twohead/CellCalculatorFactory.html" title="interface in org.biojava.bio.dp.twohead"><span class="strong">CellCalculatorFactory</span></a> - Interface in <a href="./org/biojava/bio/dp/twohead/package-summary.html">org.biojava.bio.dp.twohead</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/dp/twohead/CellCalculatorFactoryMaker.html" title="interface in org.biojava.bio.dp.twohead"><span class="strong">CellCalculatorFactoryMaker</span></a> - Interface in <a href="./org/biojava/bio/dp/twohead/package-summary.html">org.biojava.bio.dp.twohead</a></dt>
<dd>
<div class="block">The interface for all functions that can calculate the 'scores' array for
a given cell.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Calc.html#centerAtoms(org.biojava.bio.structure.Atom[])">centerAtoms(Atom[])</a></span> - Static method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Calc.html" title="class in org.biojava.bio.structure">Calc</a></dt>
<dd>
<div class="block">Center the atoms at the Centroid.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/CodonPrefTools.html#CEREVISIAE_NUCLEAR">CEREVISIAE_NUCLEAR</a></span> - Static variable in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/CodonPrefTools.html" title="class in org.biojava.bio.symbol">CodonPrefTools</a></dt>
<dd>
<div class="block">Saccharomyces cerevisiae codon preferences</div>
</dd>
<dt><a href="./org/biojava/bio/structure/Chain.html" title="interface in org.biojava.bio.structure"><span class="strong">Chain</span></a> - Interface in <a href="./org/biojava/bio/structure/package-summary.html">org.biojava.bio.structure</a></dt>
<dd>
<div class="block">
Defines the interface for a Chain.</div>
</dd>
<dt><a href="./org/biojava/bio/structure/ChainImpl.html" title="class in org.biojava.bio.structure"><span class="strong">ChainImpl</span></a> - Class in <a href="./org/biojava/bio/structure/package-summary.html">org.biojava.bio.structure</a></dt>
<dd>
<div class="block">A Chain in a PDB file.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/ChainImpl.html#ChainImpl()">ChainImpl()</a></span> - Constructor for class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/ChainImpl.html" title="class in org.biojava.bio.structure">ChainImpl</a></dt>
<dd>
<div class="block">Constructs a ChainImpl object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/ChangeTable.ChainedChanger.html#change(java.lang.Object)">change(Object)</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/ChangeTable.ChainedChanger.html" title="class in org.biojava.bio.program.tagvalue">ChangeTable.ChainedChanger</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/ChangeTable.html#change(java.lang.Object, java.lang.Object)">change(Object, Object)</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/ChangeTable.html" title="class in org.biojava.bio.program.tagvalue">ChangeTable</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/ChangeTable.Changer.html#change(java.lang.Object)">change(Object)</a></span> - Method in interface org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/ChangeTable.Changer.html" title="interface in org.biojava.bio.program.tagvalue">ChangeTable.Changer</a></dt>
<dd>
<div class="block">
Produce a modified value from an old value.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/RegexChanger.html#change(java.lang.Object)">change(Object)</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/RegexChanger.html" title="class in org.biojava.bio.program.tagvalue">RegexChanger</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/taxa/Taxon.html#CHANGE_COMMON_NAME">CHANGE_COMMON_NAME</a></span> - Static variable in interface org.biojava.bio.taxa.<a href="./org/biojava/bio/taxa/Taxon.html" title="interface in org.biojava.bio.taxa">Taxon</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Change type to indicate that the common name of this Taxon is
changing.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/taxa/Taxon.html#CHANGE_SCIENTIFIC_NAME">CHANGE_SCIENTIFIC_NAME</a></span> - Static variable in interface org.biojava.bio.taxa.<a href="./org/biojava/bio/taxa/Taxon.html" title="interface in org.biojava.bio.taxa">Taxon</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Change type to indicate that the scientific name of this Taxon is
changing.</div>
</dd>
<dt><a href="./org/biojava/utils/Changeable.html" title="interface in org.biojava.utils"><span class="strong">Changeable</span></a> - Interface in <a href="./org/biojava/utils/package-summary.html">org.biojava.utils</a></dt>
<dd>
<div class="block">This is a flag interface that defines the common add/remove listener methods
for classes and interfaces that wish to indicate that they are sources of
ChangeEvents.</div>
</dd>
<dt><a href="./org/biojava/utils/cache/ChangeableCache.html" title="class in org.biojava.utils.cache"><span class="strong">ChangeableCache</span></a> - Class in <a href="./org/biojava/utils/cache/package-summary.html">org.biojava.utils.cache</a></dt>
<dd>
<div class="block">A cache that clears values as the keys fire ChangeEvents of a given type.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/cache/ChangeableCache.html#ChangeableCache(org.biojava.utils.ChangeType)">ChangeableCache(ChangeType)</a></span> - Constructor for class org.biojava.utils.cache.<a href="./org/biojava/utils/cache/ChangeableCache.html" title="class in org.biojava.utils.cache">ChangeableCache</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/utils/ChangeAdapter.html" title="class in org.biojava.utils"><span class="strong">ChangeAdapter</span></a> - Class in <a href="./org/biojava/utils/package-summary.html">org.biojava.utils</a></dt>
<dd>
<div class="block">This is a ChangeListener that ignores everything.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/ChangeAdapter.html#ChangeAdapter()">ChangeAdapter()</a></span> - Constructor for class org.biojava.utils.<a href="./org/biojava/utils/ChangeAdapter.html" title="class in org.biojava.utils">ChangeAdapter</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/utils/ChangeEvent.html" title="class in org.biojava.utils"><span class="strong">ChangeEvent</span></a> - Class in <a href="./org/biojava/utils/package-summary.html">org.biojava.utils</a></dt>
<dd>
<div class="block">Event which encapsulates a change in any mutable BioJava object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/ChangeEvent.html#ChangeEvent(java.lang.Object, org.biojava.utils.ChangeType)">ChangeEvent(Object, ChangeType)</a></span> - Constructor for class org.biojava.utils.<a href="./org/biojava/utils/ChangeEvent.html" title="class in org.biojava.utils">ChangeEvent</a></dt>
<dd>
<div class="block">Construct a ChangeEvent with no change details.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/ChangeEvent.html#ChangeEvent(java.lang.Object, org.biojava.utils.ChangeType, java.lang.Object)">ChangeEvent(Object, ChangeType, Object)</a></span> - Constructor for class org.biojava.utils.<a href="./org/biojava/utils/ChangeEvent.html" title="class in org.biojava.utils">ChangeEvent</a></dt>
<dd>
<div class="block">Construct a ChangeEvent specifying a new value for
a property, or an object to be added to a collection.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/ChangeEvent.html#ChangeEvent(java.lang.Object, org.biojava.utils.ChangeType, java.lang.Object, java.lang.Object)">ChangeEvent(Object, ChangeType, Object, Object)</a></span> - Constructor for class org.biojava.utils.<a href="./org/biojava/utils/ChangeEvent.html" title="class in org.biojava.utils">ChangeEvent</a></dt>
<dd>
<div class="block">Construct a ChangeEvent specifying a new value for
a property, and giving the previous value.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/ChangeEvent.html#ChangeEvent(java.lang.Object, org.biojava.utils.ChangeType, java.lang.Object, java.lang.Object, org.biojava.utils.ChangeEvent)">ChangeEvent(Object, ChangeType, Object, Object, ChangeEvent)</a></span> - Constructor for class org.biojava.utils.<a href="./org/biojava/utils/ChangeEvent.html" title="class in org.biojava.utils">ChangeEvent</a></dt>
<dd>
<div class="block">Construct a ChangeEvent to be fired because another ChangeEvent has
been received from a property object.</div>
</dd>
<dt><a href="./org/biojava/utils/ChangeForwarder.html" title="class in org.biojava.utils"><span class="strong">ChangeForwarder</span></a> - Class in <a href="./org/biojava/utils/package-summary.html">org.biojava.utils</a></dt>
<dd>
<div class="block">This is a ChangeListener that is designed to adapt events of one type from
one source to events of another type emitted by another source.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/ChangeForwarder.html#ChangeForwarder(java.lang.Object, org.biojava.utils.ChangeSupport)">ChangeForwarder(Object, ChangeSupport)</a></span> - Constructor for class org.biojava.utils.<a href="./org/biojava/utils/ChangeForwarder.html" title="class in org.biojava.utils">ChangeForwarder</a></dt>
<dd>
<div class="block">Create a new ChangeForwarder for forwarding events.</div>
</dd>
<dt><a href="./org/biojava/utils/ChangeForwarder.Retyper.html" title="class in org.biojava.utils"><span class="strong">ChangeForwarder.Retyper</span></a> - Class in <a href="./org/biojava/utils/package-summary.html">org.biojava.utils</a></dt>
<dd>
<div class="block">A ChangeForwarder that systematically uses a given type and wraps the old
event.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/ChangeForwarder.Retyper.html#ChangeForwarder.Retyper(java.lang.Object, org.biojava.utils.ChangeSupport, org.biojava.utils.ChangeType)">ChangeForwarder.Retyper(Object, ChangeSupport, ChangeType)</a></span> - Constructor for class org.biojava.utils.<a href="./org/biojava/utils/ChangeForwarder.Retyper.html" title="class in org.biojava.utils">ChangeForwarder.Retyper</a></dt>
<dd>
<div class="block">Create a new Retyper for forwarding events.</div>
</dd>
<dt><a href="./org/biojava/utils/ChangeHub.html" title="interface in org.biojava.utils"><span class="strong">ChangeHub</span></a> - Interface in <a href="./org/biojava/utils/package-summary.html">org.biojava.utils</a></dt>
<dd>
<div class="block">Interface implemented by ChangeHubs, i.e.</div>
</dd>
<dt><a href="./org/biojava/utils/ChangeListener.html" title="interface in org.biojava.utils"><span class="strong">ChangeListener</span></a> - Interface in <a href="./org/biojava/utils/package-summary.html">org.biojava.utils</a></dt>
<dd>
<div class="block">Interface for objects which listen to ChangeEvents.</div>
</dd>
<dt><a href="./org/biojava/utils/ChangeListener.AlwaysVetoListener.html" title="class in org.biojava.utils"><span class="strong">ChangeListener.AlwaysVetoListener</span></a> - Class in <a href="./org/biojava/utils/package-summary.html">org.biojava.utils</a></dt>
<dd>
<div class="block">An implementation that always vetoes everything.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/ChangeListener.AlwaysVetoListener.html#ChangeListener.AlwaysVetoListener()">ChangeListener.AlwaysVetoListener()</a></span> - Constructor for class org.biojava.utils.<a href="./org/biojava/utils/ChangeListener.AlwaysVetoListener.html" title="class in org.biojava.utils">ChangeListener.AlwaysVetoListener</a></dt>
<dd>
<div class="block">Private constructor.</div>
</dd>
<dt><a href="./org/biojava/utils/ChangeListener.ChangeEventRecorder.html" title="class in org.biojava.utils"><span class="strong">ChangeListener.ChangeEventRecorder</span></a> - Class in <a href="./org/biojava/utils/package-summary.html">org.biojava.utils</a></dt>
<dd>
<div class="block">A listener that remembers the ChangeEvent of the last change.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/ChangeListener.ChangeEventRecorder.html#ChangeListener.ChangeEventRecorder()">ChangeListener.ChangeEventRecorder()</a></span> - Constructor for class org.biojava.utils.<a href="./org/biojava/utils/ChangeListener.ChangeEventRecorder.html" title="class in org.biojava.utils">ChangeListener.ChangeEventRecorder</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/utils/ChangeListener.LoggingListener.html" title="class in org.biojava.utils"><span class="strong">ChangeListener.LoggingListener</span></a> - Class in <a href="./org/biojava/utils/package-summary.html">org.biojava.utils</a></dt>
<dd>
<div class="block">A listener that writes information about the event stream to a PrintStream.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/ChangeListener.LoggingListener.html#ChangeListener.LoggingListener(java.io.PrintStream)">ChangeListener.LoggingListener(PrintStream)</a></span> - Constructor for class org.biojava.utils.<a href="./org/biojava/utils/ChangeListener.LoggingListener.html" title="class in org.biojava.utils">ChangeListener.LoggingListener</a></dt>
<dd>
<div class="block">Create a LoggingListener that will log all events to 'out'.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/ChangeListener.LoggingListener.html#ChangeListener.LoggingListener(java.io.PrintStream, java.lang.String)">ChangeListener.LoggingListener(PrintStream, String)</a></span> - Constructor for class org.biojava.utils.<a href="./org/biojava/utils/ChangeListener.LoggingListener.html" title="class in org.biojava.utils">ChangeListener.LoggingListener</a></dt>
<dd>
<div class="block">Create a LoggingListener that will log all events to 'out' with a prefix.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/ChangeForwarder.html#changeSupport()">changeSupport()</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/ChangeForwarder.html" title="class in org.biojava.utils">ChangeForwarder</a></dt>
<dd>
<div class="block">Return the underlying <code>ChangeSupport</code> instance that can be used to
fire <code>ChangeEvent</code>s and mannage listeners.</div>
</dd>
<dt><a href="./org/biojava/utils/ChangeSupport.html" title="class in org.biojava.utils"><span class="strong">ChangeSupport</span></a> - Class in <a href="./org/biojava/utils/package-summary.html">org.biojava.utils</a></dt>
<dd>
<div class="block">
A utility class to provide management for informing ChangeListeners of
ChangeEvents.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/ChangeSupport.html#ChangeSupport()">ChangeSupport()</a></span> - Constructor for class org.biojava.utils.<a href="./org/biojava/utils/ChangeSupport.html" title="class in org.biojava.utils">ChangeSupport</a></dt>
<dd>
<div class="block">Generate a new ChangeSupport instance.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/ChangeSupport.html#ChangeSupport(int)">ChangeSupport(int)</a></span> - Constructor for class org.biojava.utils.<a href="./org/biojava/utils/ChangeSupport.html" title="class in org.biojava.utils">ChangeSupport</a></dt>
<dd>
<div class="block">Generate a new ChangeSupport instance which has room for initialSize
listeners before it needs to grow any resources.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/ChangeSupport.html#ChangeSupport(int, int)">ChangeSupport(int, int)</a></span> - Constructor for class org.biojava.utils.<a href="./org/biojava/utils/ChangeSupport.html" title="class in org.biojava.utils">ChangeSupport</a></dt>
<dd>
<div class="block">Generate a new ChangeSupport instance which has room for initialSize
listeners before it needs to grow any resources, and which will grow by
delta each time.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/ChangeSupport.html#ChangeSupport(java.util.Set)">ChangeSupport(Set)</a></span> - Constructor for class org.biojava.utils.<a href="./org/biojava/utils/ChangeSupport.html" title="class in org.biojava.utils">ChangeSupport</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ChangeSupport.html#ChangeSupport(java.util.Set, int, int)">ChangeSupport(Set, int, int)</a></span> - Constructor for class org.biojava.utils.<a href="./org/biojava/utils/ChangeSupport.html" title="class in org.biojava.utils">ChangeSupport</a></dt>
<dd>
<div class="block">Generate a new ChangeSupport instance which has room for initialSize
listeners before it needs to grow any resources, and which will grow by
delta each time.</div>
</dd>
<dt><a href="./org/biojava/bio/program/tagvalue/ChangeTable.html" title="class in org.biojava.bio.program.tagvalue"><span class="strong">ChangeTable</span></a> - Class in <a href="./org/biojava/bio/program/tagvalue/package-summary.html">org.biojava.bio.program.tagvalue</a></dt>
<dd>
<div class="block">
A mapping between keys and actions to turn old values into new values.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/ChangeTable.html#ChangeTable()">ChangeTable()</a></span> - Constructor for class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/ChangeTable.html" title="class in org.biojava.bio.program.tagvalue">ChangeTable</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/tagvalue/ChangeTable.ChainedChanger.html" title="class in org.biojava.bio.program.tagvalue"><span class="strong">ChangeTable.ChainedChanger</span></a> - Class in <a href="./org/biojava/bio/program/tagvalue/package-summary.html">org.biojava.bio.program.tagvalue</a></dt>
<dd>
<div class="block">An implementation of Changer that applies a list of Changer instances to
the value in turn.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/ChangeTable.ChainedChanger.html#ChangeTable.ChainedChanger(org.biojava.bio.program.tagvalue.ChangeTable.Changer[])">ChangeTable.ChainedChanger(ChangeTable.Changer[])</a></span> - Constructor for class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/ChangeTable.ChainedChanger.html" title="class in org.biojava.bio.program.tagvalue">ChangeTable.ChainedChanger</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/tagvalue/ChangeTable.Changer.html" title="interface in org.biojava.bio.program.tagvalue"><span class="strong">ChangeTable.Changer</span></a> - Interface in <a href="./org/biojava/bio/program/tagvalue/package-summary.html">org.biojava.bio.program.tagvalue</a></dt>
<dd>
<div class="block">Callback used to produce a new value from an old one.</div>
</dd>
<dt><a href="./org/biojava/bio/program/tagvalue/ChangeTable.Splitter.html" title="interface in org.biojava.bio.program.tagvalue"><span class="strong">ChangeTable.Splitter</span></a> - Interface in <a href="./org/biojava/bio/program/tagvalue/package-summary.html">org.biojava.bio.program.tagvalue</a></dt>
<dd>
<div class="block">Callback used to produce a list of values from a single old one.</div>
</dd>
<dt><a href="./org/biojava/utils/ChangeType.html" title="class in org.biojava.utils"><span class="strong">ChangeType</span></a> - Class in <a href="./org/biojava/utils/package-summary.html">org.biojava.utils</a></dt>
<dd>
<div class="block">Class for all constants which are used to indicate change
types.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/ChangeType.html#ChangeType(java.lang.String, java.lang.reflect.Field, org.biojava.utils.ChangeType)">ChangeType(String, Field, ChangeType)</a></span> - Constructor for class org.biojava.utils.<a href="./org/biojava/utils/ChangeType.html" title="class in org.biojava.utils">ChangeType</a></dt>
<dd>
<div class="block">Construct a new ChangeType.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/ChangeType.html#ChangeType(java.lang.String, java.lang.reflect.Field)">ChangeType(String, Field)</a></span> - Constructor for class org.biojava.utils.<a href="./org/biojava/utils/ChangeType.html" title="class in org.biojava.utils">ChangeType</a></dt>
<dd>
<div class="block">Construct a new ChangeType with superType UNKNOWN.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/ChangeType.html#ChangeType(java.lang.String, java.lang.Class, java.lang.String)">ChangeType(String, Class, String)</a></span> - Constructor for class org.biojava.utils.<a href="./org/biojava/utils/ChangeType.html" title="class in org.biojava.utils">ChangeType</a></dt>
<dd>
<div class="block">Construct a new ChangeType with supertype UNKNOWN.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/ChangeType.html#ChangeType(java.lang.String, java.lang.Class, java.lang.String, org.biojava.utils.ChangeType)">ChangeType(String, Class, String, ChangeType)</a></span> - Constructor for class org.biojava.utils.<a href="./org/biojava/utils/ChangeType.html" title="class in org.biojava.utils">ChangeType</a></dt>
<dd>
<div class="block">Construct a new ChangeType.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/ChangeType.html#ChangeType(java.lang.String, java.lang.String, java.lang.String, org.biojava.utils.ChangeType)">ChangeType(String, String, String, ChangeType)</a></span> - Constructor for class org.biojava.utils.<a href="./org/biojava/utils/ChangeType.html" title="class in org.biojava.utils">ChangeType</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ChangeType.html#ChangeType(java.lang.String, java.lang.String, java.lang.String)">ChangeType(String, String, String)</a></span> - Constructor for class org.biojava.utils.<a href="./org/biojava/utils/ChangeType.html" title="class in org.biojava.utils">ChangeType</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/utils/ChangeVetoException.html" title="class in org.biojava.utils"><span class="strong">ChangeVetoException</span></a> - Exception in <a href="./org/biojava/utils/package-summary.html">org.biojava.utils</a></dt>
<dd>
<div class="block">Exception which is thrown when a ChangeListener does not
wish a change to take place.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/ChangeVetoException.html#ChangeVetoException()">ChangeVetoException()</a></span> - Constructor for exception org.biojava.utils.<a href="./org/biojava/utils/ChangeVetoException.html" title="class in org.biojava.utils">ChangeVetoException</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ChangeVetoException.html#ChangeVetoException(org.biojava.utils.ChangeEvent)">ChangeVetoException(ChangeEvent)</a></span> - Constructor for exception org.biojava.utils.<a href="./org/biojava/utils/ChangeVetoException.html" title="class in org.biojava.utils">ChangeVetoException</a></dt>
<dd>
<div class="block">Construct an exception to veto a change without explanation.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/ChangeVetoException.html#ChangeVetoException(java.lang.String)">ChangeVetoException(String)</a></span> - Constructor for exception org.biojava.utils.<a href="./org/biojava/utils/ChangeVetoException.html" title="class in org.biojava.utils">ChangeVetoException</a></dt>
<dd>
<div class="block">Create an exception with a detail message</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/ChangeVetoException.html#ChangeVetoException(org.biojava.utils.ChangeEvent, java.lang.String)">ChangeVetoException(ChangeEvent, String)</a></span> - Constructor for exception org.biojava.utils.<a href="./org/biojava/utils/ChangeVetoException.html" title="class in org.biojava.utils">ChangeVetoException</a></dt>
<dd>
<div class="block">Construct an exception to veto a change for a specified reason.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/ChangeVetoException.html#ChangeVetoException(java.lang.Throwable, org.biojava.utils.ChangeEvent)">ChangeVetoException(Throwable, ChangeEvent)</a></span> - Constructor for exception org.biojava.utils.<a href="./org/biojava/utils/ChangeVetoException.html" title="class in org.biojava.utils">ChangeVetoException</a></dt>
<dd>
<div class="block">Propogate an exception without (additional) explanation.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/ChangeVetoException.html#ChangeVetoException(java.lang.Throwable, java.lang.String)">ChangeVetoException(Throwable, String)</a></span> - Constructor for exception org.biojava.utils.<a href="./org/biojava/utils/ChangeVetoException.html" title="class in org.biojava.utils">ChangeVetoException</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>use new ChangeVetoException(reason, ex);</i></div>
</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/ChangeVetoException.html#ChangeVetoException(java.lang.String, java.lang.Throwable)">ChangeVetoException(String, Throwable)</a></span> - Constructor for exception org.biojava.utils.<a href="./org/biojava/utils/ChangeVetoException.html" title="class in org.biojava.utils">ChangeVetoException</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ChangeVetoException.html#ChangeVetoException(java.lang.Throwable, org.biojava.utils.ChangeEvent, java.lang.String)">ChangeVetoException(Throwable, ChangeEvent, String)</a></span> - Constructor for exception org.biojava.utils.<a href="./org/biojava/utils/ChangeVetoException.html" title="class in org.biojava.utils">ChangeVetoException</a></dt>
<dd>
<div class="block">Propogate an exception, giving a detail message</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SymbolTokenization.html#CHARACTER">CHARACTER</a></span> - Static variable in interface org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SymbolTokenization.html" title="interface in org.biojava.bio.seq.io">SymbolTokenization</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/blast2html/Blast2HTMLHandler.html#characters(char[], int, int)">characters(char[], int, int)</a></span> - Method in class org.biojava.bio.program.blast2html.<a href="./org/biojava/bio/program/blast2html/Blast2HTMLHandler.html" title="class in org.biojava.bio.program.blast2html">Blast2HTMLHandler</a></dt>
<dd>
<div class="block">Describe <code>characters</code> method here.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/dasalignment/DASAlignmentXMLResponseParser.html#characters(char[], int, int)">characters(char[], int, int)</a></span> - Method in class org.biojava.bio.program.das.dasalignment.<a href="./org/biojava/bio/program/das/dasalignment/DASAlignmentXMLResponseParser.html" title="class in org.biojava.bio.program.das.dasalignment">DASAlignmentXMLResponseParser</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/dasstructure/DASStructureXMLResponseParser.html#characters(char[], int, int)">characters(char[], int, int)</a></span> - Method in class org.biojava.bio.program.das.dasstructure.<a href="./org/biojava/bio/program/das/dasstructure/DASStructureXMLResponseParser.html" title="class in org.biojava.bio.program.das.dasstructure">DASStructureXMLResponseParser</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/SeqSimilarityAdapter.html#characters(char[], int, int)">characters(char[], int, int)</a></span> - Method in class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/SeqSimilarityAdapter.html" title="class in org.biojava.bio.program.ssbind">SeqSimilarityAdapter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/xml/SimpleXMLEmitter.html#characters(char[], int, int)">characters(char[], int, int)</a></span> - Method in class org.biojava.bio.program.xml.<a href="./org/biojava/bio/program/xml/SimpleXMLEmitter.html" title="class in org.biojava.bio.program.xml">SimpleXMLEmitter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEDescPropHandler.html#characters(char[], int, int)">characters(char[], int, int)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEDescPropHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEDescPropHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEKeywordPropHandler.html#characters(char[], int, int)">characters(char[], int, int)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEKeywordPropHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEKeywordPropHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEMatchAlignPropHandler.html#characters(char[], int, int)">characters(char[], int, int)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEMatchAlignPropHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEMatchAlignPropHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEMatchDescPropHandler.html#characters(char[], int, int)">characters(char[], int, int)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEMatchDescPropHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEMatchDescPropHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVENotePropHandler.html#characters(char[], int, int)">characters(char[], int, int)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVENotePropHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVENotePropHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEQualifierPropHandler.html#characters(char[], int, int)">characters(char[], int, int)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEQualifierPropHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEQualifierPropHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEResultPropertyPropHandler.html#characters(char[], int, int)">characters(char[], int, int)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEResultPropertyPropHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEResultPropertyPropHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVESciPropertyPropHandler.html#characters(char[], int, int)">characters(char[], int, int)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVESciPropertyPropHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVESciPropertyPropHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVESeqPropHandler.html#characters(char[], int, int)">characters(char[], int, int)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVESeqPropHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVESeqPropHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEXrefPropPropHandler.html#characters(char[], int, int)">characters(char[], int, int)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEXrefPropPropHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEXrefPropPropHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/SAX2StAXAdaptor.html#characters(char[], int, int)">characters(char[], int, int)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/SAX2StAXAdaptor.html" title="class in org.biojava.bio.seq.io.agave">SAX2StAXAdaptor</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/StAXContentHandler.html#characters(char[], int, int)">characters(char[], int, int)</a></span> - Method in interface org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/StAXContentHandler.html" title="interface in org.biojava.bio.seq.io.agave">StAXContentHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/StAXContentHandlerBase.html#characters(char[], int, int)">characters(char[], int, int)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/StAXContentHandlerBase.html" title="class in org.biojava.bio.seq.io.agave">StAXContentHandlerBase</a></dt>
<dd>
<div class="block">Signal a span of character data in the XML input.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game/SequenceContentHandlerBase.html#characters(char[], int, int)">characters(char[], int, int)</a></span> - Method in class org.biojava.bio.seq.io.game.<a href="./org/biojava/bio/seq/io/game/SequenceContentHandlerBase.html" title="class in org.biojava.bio.seq.io.game">SequenceContentHandlerBase</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/StreamParser.html#characters(char[], int, int)">characters(char[], int, int)</a></span> - Method in interface org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/StreamParser.html" title="interface in org.biojava.bio.seq.io">StreamParser</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/stax/BooleanElementHandlerBase.html#characters(char[], int, int)">characters(char[], int, int)</a></span> - Method in class org.biojava.utils.stax.<a href="./org/biojava/utils/stax/BooleanElementHandlerBase.html" title="class in org.biojava.utils.stax">BooleanElementHandlerBase</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/stax/ByteElementHandlerBase.html#characters(char[], int, int)">characters(char[], int, int)</a></span> - Method in class org.biojava.utils.stax.<a href="./org/biojava/utils/stax/ByteElementHandlerBase.html" title="class in org.biojava.utils.stax">ByteElementHandlerBase</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/stax/CharElementHandlerBase.html#characters(char[], int, int)">characters(char[], int, int)</a></span> - Method in class org.biojava.utils.stax.<a href="./org/biojava/utils/stax/CharElementHandlerBase.html" title="class in org.biojava.utils.stax">CharElementHandlerBase</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/stax/DoubleElementHandlerBase.html#characters(char[], int, int)">characters(char[], int, int)</a></span> - Method in class org.biojava.utils.stax.<a href="./org/biojava/utils/stax/DoubleElementHandlerBase.html" title="class in org.biojava.utils.stax">DoubleElementHandlerBase</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/stax/FloatElementHandlerBase.html#characters(char[], int, int)">characters(char[], int, int)</a></span> - Method in class org.biojava.utils.stax.<a href="./org/biojava/utils/stax/FloatElementHandlerBase.html" title="class in org.biojava.utils.stax">FloatElementHandlerBase</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/stax/IntElementHandlerBase.html#characters(char[], int, int)">characters(char[], int, int)</a></span> - Method in class org.biojava.utils.stax.<a href="./org/biojava/utils/stax/IntElementHandlerBase.html" title="class in org.biojava.utils.stax">IntElementHandlerBase</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/stax/LongElementHandlerBase.html#characters(char[], int, int)">characters(char[], int, int)</a></span> - Method in class org.biojava.utils.stax.<a href="./org/biojava/utils/stax/LongElementHandlerBase.html" title="class in org.biojava.utils.stax">LongElementHandlerBase</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/stax/SAX2StAXAdaptor.html#characters(char[], int, int)">characters(char[], int, int)</a></span> - Method in class org.biojava.utils.stax.<a href="./org/biojava/utils/stax/SAX2StAXAdaptor.html" title="class in org.biojava.utils.stax">SAX2StAXAdaptor</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/stax/StAXContentHandler.html#characters(char[], int, int)">characters(char[], int, int)</a></span> - Method in interface org.biojava.utils.stax.<a href="./org/biojava/utils/stax/StAXContentHandler.html" title="interface in org.biojava.utils.stax">StAXContentHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/stax/StAXContentHandlerBase.html#characters(char[], int, int)">characters(char[], int, int)</a></span> - Method in class org.biojava.utils.stax.<a href="./org/biojava/utils/stax/StAXContentHandlerBase.html" title="class in org.biojava.utils.stax">StAXContentHandlerBase</a></dt>
<dd>
<div class="block">Signal a span of character data in the XML input.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/stax/StringElementHandlerBase.html#characters(char[], int, int)">characters(char[], int, int)</a></span> - Method in class org.biojava.utils.stax.<a href="./org/biojava/utils/stax/StringElementHandlerBase.html" title="class in org.biojava.utils.stax">StringElementHandlerBase</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/io/CharacterTokenization.html" title="class in org.biojava.bio.seq.io"><span class="strong">CharacterTokenization</span></a> - Class in <a href="./org/biojava/bio/seq/io/package-summary.html">org.biojava.bio.seq.io</a></dt>
<dd>
<div class="block">Implementation of SymbolTokenization which binds symbols to
single unicode characters.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/CharacterTokenization.html#CharacterTokenization(org.biojava.bio.symbol.Alphabet, boolean)">CharacterTokenization(Alphabet, boolean)</a></span> - Constructor for class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/CharacterTokenization.html" title="class in org.biojava.bio.seq.io">CharacterTokenization</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SymbolListCharSequence.html#charAt(int)">charAt(int)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SymbolListCharSequence.html" title="class in org.biojava.bio.seq.io">SymbolListCharSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/RepeatedCharSequence.html#charAt(int)">charAt(int)</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/RepeatedCharSequence.html" title="class in org.biojava.utils">RepeatedCharSequence</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/utils/stax/CharElementHandlerBase.html" title="class in org.biojava.utils.stax"><span class="strong">CharElementHandlerBase</span></a> - Class in <a href="./org/biojava/utils/stax/package-summary.html">org.biojava.utils.stax</a></dt>
<dd>
<div class="block">
StAX handler for any element which just contains a string representation of
a char.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/stax/CharElementHandlerBase.html#CharElementHandlerBase()">CharElementHandlerBase()</a></span> - Constructor for class org.biojava.utils.stax.<a href="./org/biojava/utils/stax/CharElementHandlerBase.html" title="class in org.biojava.utils.stax">CharElementHandlerBase</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/regex/PatternFactory.html#charValue(org.biojava.bio.symbol.Symbol)">charValue(Symbol)</a></span> - Method in class org.biojava.utils.regex.<a href="./org/biojava/utils/regex/PatternFactory.html" title="class in org.biojava.utils.regex">PatternFactory</a></dt>
<dd>
<div class="block">Returns the character that represents the specified Symbol in
the Alphabet that this PatternFactory was defined for.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/regex/Search.html#charValue(org.biojava.bio.symbol.Symbol)">charValue(Symbol)</a></span> - Method in class org.biojava.utils.regex.<a href="./org/biojava/utils/regex/Search.html" title="class in org.biojava.utils.regex">Search</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/GenbankSequenceDB.html#checkException()">checkException()</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/GenbankSequenceDB.html" title="class in org.biojava.bio.seq.db">GenbankSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/GenpeptSequenceDB.html#checkException()">checkException()</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/GenpeptSequenceDB.html" title="class in org.biojava.bio.seq.db">GenpeptSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/GenbankSequenceDB.html#checkIOException()">checkIOException()</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/GenbankSequenceDB.html" title="class in org.biojava.bio.seq.db">GenbankSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/GenpeptSequenceDB.html#checkIOException()">checkIOException()</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/GenpeptSequenceDB.html" title="class in org.biojava.bio.seq.db">GenpeptSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/SwissprotSequenceDB.html#checkIOException()">checkIOException()</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/SwissprotSequenceDB.html" title="class in org.biojava.bio.seq.db">SwissprotSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/chem/ResidueType.html#chem_comp_type">chem_comp_type</a></span> - Variable in enum org.biojava.bio.structure.io.mmcif.chem.<a href="./org/biojava/bio/structure/io/mmcif/chem/ResidueType.html" title="enum in org.biojava.bio.structure.io.mmcif.chem">ResidueType</a></dt>
<dd>
<div class="block">String value of the type</div>
</dd>
<dt><a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html" title="class in org.biojava.bio.structure.io.mmcif.model"><span class="strong">ChemComp</span></a> - Class in <a href="./org/biojava/bio/structure/io/mmcif/model/package-summary.html">org.biojava.bio.structure.io.mmcif.model</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html#ChemComp()">ChemComp()</a></span> - Constructor for class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html" title="class in org.biojava.bio.structure.io.mmcif.model">ChemComp</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/structure/io/mmcif/ChemCompConsumer.html" title="class in org.biojava.bio.structure.io.mmcif"><span class="strong">ChemCompConsumer</span></a> - Class in <a href="./org/biojava/bio/structure/io/mmcif/package-summary.html">org.biojava.bio.structure.io.mmcif</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/ChemCompConsumer.html#ChemCompConsumer()">ChemCompConsumer()</a></span> - Constructor for class org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/ChemCompConsumer.html" title="class in org.biojava.bio.structure.io.mmcif">ChemCompConsumer</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/structure/io/mmcif/chem/ChemCompTools.html" title="class in org.biojava.bio.structure.io.mmcif.chem"><span class="strong">ChemCompTools</span></a> - Class in <a href="./org/biojava/bio/structure/io/mmcif/chem/package-summary.html">org.biojava.bio.structure.io.mmcif.chem</a></dt>
<dd>
<div class="block">Some tools for working with chemical compounds.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/chem/ChemCompTools.html#ChemCompTools()">ChemCompTools()</a></span> - Constructor for class org.biojava.bio.structure.io.mmcif.chem.<a href="./org/biojava/bio/structure/io/mmcif/chem/ChemCompTools.html" title="class in org.biojava.bio.structure.io.mmcif.chem">ChemCompTools</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/structure/io/mmcif/ChemicalComponentDictionary.html" title="class in org.biojava.bio.structure.io.mmcif"><span class="strong">ChemicalComponentDictionary</span></a> - Class in <a href="./org/biojava/bio/structure/io/mmcif/package-summary.html">org.biojava.bio.structure.io.mmcif</a></dt>
<dd>
<div class="block">A representation of the Chemical Component Dictionary.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/ChemicalComponentDictionary.html#ChemicalComponentDictionary()">ChemicalComponentDictionary()</a></span> - Constructor for class org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/ChemicalComponentDictionary.html" title="class in org.biojava.bio.structure.io.mmcif">ChemicalComponentDictionary</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/taxa/SimpleTaxon.html#children">children</a></span> - Variable in class org.biojava.bio.taxa.<a href="./org/biojava/bio/taxa/SimpleTaxon.html" title="class in org.biojava.bio.taxa">SimpleTaxon</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/TranslationTable.html#CHLORO_MITO">CHLORO_MITO</a></span> - Static variable in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/TranslationTable.html" title="interface in org.biojava.bio.symbol">TranslationTable</a></dt>
<dd>
<div class="block">Translation table name for the chlorophycean mitochondrial genetic
code.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/jama/Matrix.html#chol()">chol()</a></span> - Method in class org.biojava.bio.structure.jama.<a href="./org/biojava/bio/structure/jama/Matrix.html" title="class in org.biojava.bio.structure.jama">Matrix</a></dt>
<dd>
<div class="block">Cholesky Decomposition</div>
</dd>
<dt><a href="./org/biojava/bio/structure/jama/CholeskyDecomposition.html" title="class in org.biojava.bio.structure.jama"><span class="strong">CholeskyDecomposition</span></a> - Class in <a href="./org/biojava/bio/structure/jama/package-summary.html">org.biojava.bio.structure.jama</a></dt>
<dd>
<div class="block">Cholesky Decomposition.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/jama/CholeskyDecomposition.html#CholeskyDecomposition(org.biojava.bio.structure.jama.Matrix)">CholeskyDecomposition(Matrix)</a></span> - Constructor for class org.biojava.bio.structure.jama.<a href="./org/biojava/bio/structure/jama/CholeskyDecomposition.html" title="class in org.biojava.bio.structure.jama">CholeskyDecomposition</a></dt>
<dd>
<div class="block">Cholesky algorithm for symmetric and positive definite matrix.</div>
</dd>
<dt><a href="./org/biojava/bio/chromatogram/Chromatogram.html" title="interface in org.biojava.bio.chromatogram"><span class="strong">Chromatogram</span></a> - Interface in <a href="./org/biojava/bio/chromatogram/package-summary.html">org.biojava.bio.chromatogram</a></dt>
<dd>
<div class="block">Encapsulates the basic information you would want from a chromatogram.</div>
</dd>
<dt><a href="./org/biojava/bio/chromatogram/ChromatogramFactory.html" title="class in org.biojava.bio.chromatogram"><span class="strong">ChromatogramFactory</span></a> - Class in <a href="./org/biojava/bio/chromatogram/package-summary.html">org.biojava.bio.chromatogram</a></dt>
<dd>
<div class="block">A factory that creates <a href="./org/biojava/bio/chromatogram/Chromatogram.html" title="interface in org.biojava.bio.chromatogram"><code>Chromatogram</code></a> objects from files or streams.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/ChromatogramFactory.html#ChromatogramFactory()">ChromatogramFactory()</a></span> - Constructor for class org.biojava.bio.chromatogram.<a href="./org/biojava/bio/chromatogram/ChromatogramFactory.html" title="class in org.biojava.bio.chromatogram">ChromatogramFactory</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.html" title="class in org.biojava.bio.chromatogram.graphic"><span class="strong">ChromatogramGraphic</span></a> - Class in <a href="./org/biojava/bio/chromatogram/graphic/package-summary.html">org.biojava.bio.chromatogram.graphic</a></dt>
<dd>
<div class="block">Encapsulates a configurable method for drawing a <a href="./org/biojava/bio/chromatogram/Chromatogram.html" title="interface in org.biojava.bio.chromatogram"><code>Chromatogram</code></a>
into a graphics context.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.html#ChromatogramGraphic()">ChromatogramGraphic()</a></span> - Constructor for class org.biojava.bio.chromatogram.graphic.<a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.html" title="class in org.biojava.bio.chromatogram.graphic">ChromatogramGraphic</a></dt>
<dd>
<div class="block">Default constructor with no Chromatogram.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.html#ChromatogramGraphic(org.biojava.bio.chromatogram.Chromatogram)">ChromatogramGraphic(Chromatogram)</a></span> - Constructor for class org.biojava.bio.chromatogram.graphic.<a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.html" title="class in org.biojava.bio.chromatogram.graphic">ChromatogramGraphic</a></dt>
<dd>
<div class="block">Creates a new <code>ChromatogramGraphic</code>, initially displaying
the given chromatogram.</div>
</dd>
<dt><a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.Option.html" title="class in org.biojava.bio.chromatogram.graphic"><span class="strong">ChromatogramGraphic.Option</span></a> - Class in <a href="./org/biojava/bio/chromatogram/graphic/package-summary.html">org.biojava.bio.chromatogram.graphic</a></dt>
<dd>
<div class="block">A typesafe enumeration of the options available for configuring
the behavior of a <a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.html" title="class in org.biojava.bio.chromatogram.graphic"><code>ChromatogramGraphic</code></a> instance.</div>
</dd>
<dt><a href="./org/biojava/bio/chromatogram/graphic/ChromatogramNonlinearScaler.html" title="interface in org.biojava.bio.chromatogram.graphic"><span class="strong">ChromatogramNonlinearScaler</span></a> - Interface in <a href="./org/biojava/bio/chromatogram/graphic/package-summary.html">org.biojava.bio.chromatogram.graphic</a></dt>
<dd>
<div class="block">Provides the mechanism whereby a ChromatogramGraphic can display
a Chromatogram with a non-linear horizontal scale.</div>
</dd>
<dt><a href="./org/biojava/bio/chromatogram/graphic/ChromatogramNonlinearScaler.Identity.html" title="class in org.biojava.bio.chromatogram.graphic"><span class="strong">ChromatogramNonlinearScaler.Identity</span></a> - Class in <a href="./org/biojava/bio/chromatogram/graphic/package-summary.html">org.biojava.bio.chromatogram.graphic</a></dt>
<dd>
<div class="block">The default scaler that displays the chromatogram 1:1.</div>
</dd>
<dt><a href="./org/biojava/bio/chromatogram/ChromatogramTools.html" title="class in org.biojava.bio.chromatogram"><span class="strong">ChromatogramTools</span></a> - Class in <a href="./org/biojava/bio/chromatogram/package-summary.html">org.biojava.bio.chromatogram</a></dt>
<dd>
<div class="block">Utility class for dealing with <a href="./org/biojava/bio/chromatogram/Chromatogram.html" title="interface in org.biojava.bio.chromatogram"><code>Chromatogram</code></a>s.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ga/impl/AbstractOrganism.html#chromosomes">chromosomes</a></span> - Variable in class org.biojavax.ga.impl.<a href="./org/biojavax/ga/impl/AbstractOrganism.html" title="class in org.biojavax.ga.impl">AbstractOrganism</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/Organism.html#CHROMOSOMES">CHROMOSOMES</a></span> - Static variable in interface org.biojavax.ga.<a href="./org/biojavax/ga/Organism.html" title="interface in org.biojavax.ga">Organism</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/symbol/ChunkedSymbolList.html" title="class in org.biojava.bio.symbol"><span class="strong">ChunkedSymbolList</span></a> - Class in <a href="./org/biojava/bio/symbol/package-summary.html">org.biojava.bio.symbol</a></dt>
<dd>
<div class="block">SymbolList implementation using constant-size chunks.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/ChunkedSymbolList.html#ChunkedSymbolList(org.biojava.bio.symbol.SymbolList[], int, int, org.biojava.bio.symbol.Alphabet)">ChunkedSymbolList(SymbolList[], int, int, Alphabet)</a></span> - Constructor for class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/ChunkedSymbolList.html" title="class in org.biojava.bio.symbol">ChunkedSymbolList</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/io/ChunkedSymbolListFactory.html" title="class in org.biojava.bio.seq.io"><span class="strong">ChunkedSymbolListFactory</span></a> - Class in <a href="./org/biojava/bio/seq/io/package-summary.html">org.biojava.bio.seq.io</a></dt>
<dd>
<div class="block">class that makes ChunkedSymbolLists with the chunks
implemented as SymbolLists themselves.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/ChunkedSymbolListFactory.html#ChunkedSymbolListFactory(org.biojava.bio.symbol.SymbolListFactory)">ChunkedSymbolListFactory(SymbolListFactory)</a></span> - Constructor for class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/ChunkedSymbolListFactory.html" title="class in org.biojava.bio.seq.io">ChunkedSymbolListFactory</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/ChunkedSymbolListFactory.html#ChunkedSymbolListFactory(org.biojava.bio.symbol.SymbolListFactory, int)">ChunkedSymbolListFactory(SymbolListFactory, int)</a></span> - Constructor for class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/ChunkedSymbolListFactory.html" title="class in org.biojava.bio.seq.io">ChunkedSymbolListFactory</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/Protease.html#CHYMOTRYP">CHYMOTRYP</a></span> - Static variable in class org.biojava.bio.proteomics.<a href="./org/biojava/bio/proteomics/Protease.html" title="class in org.biojava.bio.proteomics">Protease</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/ProteaseManager.html#CHYMOTRYP">CHYMOTRYP</a></span> - Static variable in class org.biojava.bio.proteomics.<a href="./org/biojava/bio/proteomics/ProteaseManager.html" title="class in org.biojava.bio.proteomics">ProteaseManager</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/TranslationTable.html#CILIATE_NUC">CILIATE_NUC</a></span> - Static variable in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/TranslationTable.html" title="interface in org.biojava.bio.symbol">TranslationTable</a></dt>
<dd>
<div class="block">Translation table name for the ciliate nuclear genetic code.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/ImageMap.html#CIRCLE">CIRCLE</a></span> - Static variable in interface org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/ImageMap.html" title="interface in org.biojava.bio.gui.sequence">ImageMap</a></dt>
<dd>
<div class="block"><code>CIRCLE</code> indicates a circular image map hotspot.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichLocation.html#CIRCULAR">CIRCULAR</a></span> - Static variable in interface org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichLocation.html" title="interface in org.biojavax.bio.seq">RichLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.html#CIRCULAR">CIRCULAR</a></span> - Static variable in interface org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.html" title="interface in org.biojavax.bio.seq">RichSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/EmblLikeFormat.html#CIRCULAR_TAG">CIRCULAR_TAG</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/EmblLikeFormat.html" title="class in org.biojava.bio.seq.io">EmblLikeFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/GenbankFormat.html#CIRCULAR_TAG">CIRCULAR_TAG</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/GenbankFormat.html" title="class in org.biojava.bio.seq.io">GenbankFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><a href="./org/biojava/bio/gui/sequence/CircularFeatureFilteringRenderer.html" title="class in org.biojava.bio.gui.sequence"><span class="strong">CircularFeatureFilteringRenderer</span></a> - Class in <a href="./org/biojava/bio/gui/sequence/package-summary.html">org.biojava.bio.gui.sequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/CircularFeatureFilteringRenderer.html#CircularFeatureFilteringRenderer(org.biojava.bio.gui.sequence.CircularRenderer, org.biojava.bio.seq.FeatureFilter, boolean)">CircularFeatureFilteringRenderer(CircularRenderer, FeatureFilter, boolean)</a></span> - Constructor for class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/CircularFeatureFilteringRenderer.html" title="class in org.biojava.bio.gui.sequence">CircularFeatureFilteringRenderer</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/gui/sequence/CircularFeatureRenderer.html" title="interface in org.biojava.bio.gui.sequence"><span class="strong">CircularFeatureRenderer</span></a> - Interface in <a href="./org/biojava/bio/gui/sequence/package-summary.html">org.biojava.bio.gui.sequence</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/gui/sequence/CircularFeaturesRenderer.html" title="class in org.biojava.bio.gui.sequence"><span class="strong">CircularFeaturesRenderer</span></a> - Class in <a href="./org/biojava/bio/gui/sequence/package-summary.html">org.biojava.bio.gui.sequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/CircularFeaturesRenderer.html#CircularFeaturesRenderer()">CircularFeaturesRenderer()</a></span> - Constructor for class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/CircularFeaturesRenderer.html" title="class in org.biojava.bio.gui.sequence">CircularFeaturesRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/CircularFeaturesRenderer.html#CircularFeaturesRenderer(org.biojava.bio.gui.sequence.CircularFeatureRenderer)">CircularFeaturesRenderer(CircularFeatureRenderer)</a></span> - Constructor for class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/CircularFeaturesRenderer.html" title="class in org.biojava.bio.gui.sequence">CircularFeaturesRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichLocation.html#circularLength">circularLength</a></span> - Variable in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichLocation.html" title="class in org.biojavax.bio.seq">SimpleRichLocation</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/symbol/CircularLocation.html" title="class in org.biojava.bio.symbol"><span class="strong">CircularLocation</span></a> - Class in <a href="./org/biojava/bio/symbol/package-summary.html">org.biojava.bio.symbol</a></dt>
<dd>
<div class="block">Circular view onto an underlying Location instance.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/CircularLocation.html#CircularLocation(org.biojava.bio.symbol.Location, int)">CircularLocation(Location, int)</a></span> - Constructor for class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/CircularLocation.html" title="class in org.biojava.bio.symbol">CircularLocation</a></dt>
<dd>
<div class="block">Constructs a CircularLocation by wrapping another Location
<strong>It is preferable to use LocationTools to make CircularLocations</strong></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/CircularLocation.html#CircularLocation(org.biojava.bio.symbol.Location, int, int)">CircularLocation(Location, int, int)</a></span> - Constructor for class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/CircularLocation.html" title="class in org.biojava.bio.symbol">CircularLocation</a></dt>
<dd>
<div class="block">Makes a CircularLocation where the 5' end of the Location is specified.</div>
</dd>
<dt><a href="./org/biojava/bio/gui/sequence/CircularMLR.html" title="class in org.biojava.bio.gui.sequence"><span class="strong">CircularMLR</span></a> - Class in <a href="./org/biojava/bio/gui/sequence/package-summary.html">org.biojava.bio.gui.sequence</a></dt>
<dd>
<div class="block">Renders multiple renderers, each in their own concentric rings.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/CircularMLR.html#CircularMLR()">CircularMLR()</a></span> - Constructor for class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/CircularMLR.html" title="class in org.biojava.bio.gui.sequence">CircularMLR</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/gui/sequence/CircularPaddedRenderer.html" title="class in org.biojava.bio.gui.sequence"><span class="strong">CircularPaddedRenderer</span></a> - Class in <a href="./org/biojava/bio/gui/sequence/package-summary.html">org.biojava.bio.gui.sequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/CircularPaddedRenderer.html#CircularPaddedRenderer()">CircularPaddedRenderer()</a></span> - Constructor for class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/CircularPaddedRenderer.html" title="class in org.biojava.bio.gui.sequence">CircularPaddedRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/CircularPaddedRenderer.html#CircularPaddedRenderer(org.biojava.bio.gui.sequence.CircularRenderer)">CircularPaddedRenderer(CircularRenderer)</a></span> - Constructor for class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/CircularPaddedRenderer.html" title="class in org.biojava.bio.gui.sequence">CircularPaddedRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/CircularPaddedRenderer.html#CircularPaddedRenderer(double, double)">CircularPaddedRenderer(double, double)</a></span> - Constructor for class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/CircularPaddedRenderer.html" title="class in org.biojava.bio.gui.sequence">CircularPaddedRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/CircularPaddedRenderer.html#CircularPaddedRenderer(org.biojava.bio.gui.sequence.CircularRenderer, double, double)">CircularPaddedRenderer(CircularRenderer, double, double)</a></span> - Constructor for class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/CircularPaddedRenderer.html" title="class in org.biojava.bio.gui.sequence">CircularPaddedRenderer</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/taxa/CircularReferenceException.html" title="class in org.biojava.bio.taxa"><span class="strong">CircularReferenceException</span></a> - Exception in <a href="./org/biojava/bio/taxa/package-summary.html">org.biojava.bio.taxa</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>replaced by classes in <a href="./org/biojavax/bio/taxa/package-summary.html"><code>org.biojavax.bio.taxa</code></a></i></div>
</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/taxa/CircularReferenceException.html#CircularReferenceException()">CircularReferenceException()</a></span> - Constructor for exception org.biojava.bio.taxa.<a href="./org/biojava/bio/taxa/CircularReferenceException.html" title="class in org.biojava.bio.taxa">CircularReferenceException</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/taxa/CircularReferenceException.html#CircularReferenceException(java.lang.Throwable)">CircularReferenceException(Throwable)</a></span> - Constructor for exception org.biojava.bio.taxa.<a href="./org/biojava/bio/taxa/CircularReferenceException.html" title="class in org.biojava.bio.taxa">CircularReferenceException</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/taxa/CircularReferenceException.html#CircularReferenceException(java.lang.String)">CircularReferenceException(String)</a></span> - Constructor for exception org.biojava.bio.taxa.<a href="./org/biojava/bio/taxa/CircularReferenceException.html" title="class in org.biojava.bio.taxa">CircularReferenceException</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/taxa/CircularReferenceException.html#CircularReferenceException(java.lang.Throwable, java.lang.String)">CircularReferenceException(Throwable, String)</a></span> - Constructor for exception org.biojava.bio.taxa.<a href="./org/biojava/bio/taxa/CircularReferenceException.html" title="class in org.biojava.bio.taxa">CircularReferenceException</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><a href="./org/biojava/bio/gui/sequence/CircularRenderer.html" title="interface in org.biojava.bio.gui.sequence"><span class="strong">CircularRenderer</span></a> - Interface in <a href="./org/biojava/bio/gui/sequence/package-summary.html">org.biojava.bio.gui.sequence</a></dt>
<dd>
<div class="block">Render information from a CircularRendererContext onto a graphics context.</div>
</dd>
<dt><a href="./org/biojava/bio/gui/sequence/CircularRendererContext.html" title="interface in org.biojava.bio.gui.sequence"><span class="strong">CircularRendererContext</span></a> - Interface in <a href="./org/biojava/bio/gui/sequence/package-summary.html">org.biojava.bio.gui.sequence</a></dt>
<dd>
<div class="block">A context providing information for rendering sequences into circular coordinate systems.</div>
</dd>
<dt><a href="./org/biojava/bio/gui/sequence/CircularRendererPanel.html" title="class in org.biojava.bio.gui.sequence"><span class="strong">CircularRendererPanel</span></a> - Class in <a href="./org/biojava/bio/gui/sequence/package-summary.html">org.biojava.bio.gui.sequence</a></dt>
<dd>
<div class="block">Renders a sequence as a circle using a CircularRenderer.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/CircularRendererPanel.html#CircularRendererPanel()">CircularRendererPanel()</a></span> - Constructor for class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/CircularRendererPanel.html" title="class in org.biojava.bio.gui.sequence">CircularRendererPanel</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/CircularView.html" title="class in org.biojava.bio.seq"><span class="strong">CircularView</span></a> - Class in <a href="./org/biojava/bio/seq/package-summary.html">org.biojava.bio.seq</a></dt>
<dd>
<div class="block">
A circular view onto another Sequence object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/CircularView.html#CircularView(org.biojava.bio.seq.Sequence, org.biojava.bio.seq.FeatureRealizer)">CircularView(Sequence, FeatureRealizer)</a></span> - Constructor for class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/CircularView.html" title="class in org.biojava.bio.seq">CircularView</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/CircularView.html#CircularView(org.biojava.bio.seq.Sequence)">CircularView(Sequence)</a></span> - Constructor for class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/CircularView.html" title="class in org.biojava.bio.seq">CircularView</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html#CITATION_DATE_ATTR">CITATION_DATE_ATTR</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html" title="class in org.biojavax.bio.seq.io">EMBLxmlFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html#CITATION_FIRST_ATTR">CITATION_FIRST_ATTR</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html" title="class in org.biojavax.bio.seq.io">EMBLxmlFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html#CITATION_ID_ATTR">CITATION_ID_ATTR</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html" title="class in org.biojavax.bio.seq.io">EMBLxmlFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html#CITATION_INSTITUTE_ATTR">CITATION_INSTITUTE_ATTR</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html" title="class in org.biojavax.bio.seq.io">EMBLxmlFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html#CITATION_ISSUE_ATTR">CITATION_ISSUE_ATTR</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html" title="class in org.biojavax.bio.seq.io">EMBLxmlFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html#CITATION_LAST_ATTR">CITATION_LAST_ATTR</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html" title="class in org.biojavax.bio.seq.io">EMBLxmlFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html#CITATION_LOCATION_TAG">CITATION_LOCATION_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html" title="class in org.biojavax.bio.seq.io">EMBLxmlFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html#CITATION_NAME_ATTR">CITATION_NAME_ATTR</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html" title="class in org.biojavax.bio.seq.io">EMBLxmlFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html#CITATION_PATENT_ATTR">CITATION_PATENT_ATTR</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html" title="class in org.biojavax.bio.seq.io">EMBLxmlFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html#CITATION_PUB_ATTR">CITATION_PUB_ATTR</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html" title="class in org.biojavax.bio.seq.io">EMBLxmlFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html#CITATION_TAG">CITATION_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html" title="class in org.biojavax.bio.seq.io">EMBLxmlFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#CITATION_TAG">CITATION_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html#CITATION_TYPE_ATTR">CITATION_TYPE_ATTR</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html" title="class in org.biojavax.bio.seq.io">EMBLxmlFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html#CITATION_VOL_ATTR">CITATION_VOL_ATTR</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html" title="class in org.biojavax.bio.seq.io">EMBLxmlFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html#CITATION_YEAR_ATTR">CITATION_YEAR_ATTR</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html" title="class in org.biojavax.bio.seq.io">EMBLxmlFormat</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/stats/svm/tools/ClassifierExample.html" title="class in org.biojava.stats.svm.tools"><span class="strong">ClassifierExample</span></a> - Class in <a href="./org/biojava/stats/svm/tools/package-summary.html">org.biojava.stats.svm.tools</a></dt>
<dd>
<div class="block">A simple toy example that allows you to put points on a canvas, and find a
polynomial hyperplane to seperate them.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/tools/ClassifierExample.html#ClassifierExample()">ClassifierExample()</a></span> - Constructor for class org.biojava.stats.svm.tools.<a href="./org/biojava/stats/svm/tools/ClassifierExample.html" title="class in org.biojava.stats.svm.tools">ClassifierExample</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/stats/svm/tools/ClassifierExample.PointClassifier.html" title="class in org.biojava.stats.svm.tools"><span class="strong">ClassifierExample.PointClassifier</span></a> - Class in <a href="./org/biojava/stats/svm/tools/package-summary.html">org.biojava.stats.svm.tools</a></dt>
<dd>
<div class="block">An extention of JComponent that contains the points & encapsulates the
classifier.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/tools/ClassifierExample.PointClassifier.html#ClassifierExample.PointClassifier()">ClassifierExample.PointClassifier()</a></span> - Constructor for class org.biojava.stats.svm.tools.<a href="./org/biojava/stats/svm/tools/ClassifierExample.PointClassifier.html" title="class in org.biojava.stats.svm.tools">ClassifierExample.PointClassifier</a></dt>
<dd>
<div class="block">Make a new PointClassifier.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/AbstractSVMClassifierModel.html#classify(java.lang.Object)">classify(Object)</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/AbstractSVMClassifierModel.html" title="class in org.biojava.stats.svm">AbstractSVMClassifierModel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/SVMClassifierModel.html#classify(java.lang.Object)">classify(Object)</a></span> - Method in interface org.biojava.stats.svm.<a href="./org/biojava/stats/svm/SVMClassifierModel.html" title="interface in org.biojava.stats.svm">SVMClassifierModel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/SVMRegressionModel.html#classify(java.lang.Object)">classify(Object)</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/SVMRegressionModel.html" title="class in org.biojava.stats.svm">SVMRegressionModel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/tools/ClassifierExample.PointClassifier.html#classify()">classify()</a></span> - Method in class org.biojava.stats.svm.tools.<a href="./org/biojava/stats/svm/tools/ClassifierExample.PointClassifier.html" title="class in org.biojava.stats.svm.tools">ClassifierExample.PointClassifier</a></dt>
<dd>
<div class="block">Learn a model from the current points.</div>
</dd>
<dt><a href="./org/biojava/stats/svm/tools/Classify.html" title="class in org.biojava.stats.svm.tools"><span class="strong">Classify</span></a> - Class in <a href="./org/biojava/stats/svm/tools/package-summary.html">org.biojava.stats.svm.tools</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/tools/Classify.html#Classify()">Classify()</a></span> - Constructor for class org.biojava.stats.svm.tools.<a href="./org/biojava/stats/svm/tools/Classify.html" title="class in org.biojava.stats.svm.tools">Classify</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/utils/ClassTools.html" title="class in org.biojava.utils"><span class="strong">ClassTools</span></a> - Class in <a href="./org/biojava/utils/package-summary.html">org.biojava.utils</a></dt>
<dd>
<div class="block">Utility methods for manipulating class objects and resources.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/AlignmentGui.html#cleanUp()">cleanUp()</a></span> - Method in class org.biojava.bio.structure.gui.<a href="./org/biojava/bio/structure/gui/AlignmentGui.html" title="class in org.biojava.bio.structure.gui">AlignmentGui</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/util/AlignmentCalc.html#cleanup()">cleanup()</a></span> - Method in class org.biojava.bio.structure.gui.util.<a href="./org/biojava/bio/structure/gui/util/AlignmentCalc.html" title="class in org.biojava.bio.structure.gui.util">AlignmentCalc</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/twohead/EmissionCache.html#clear()">clear()</a></span> - Method in class org.biojava.bio.dp.twohead.<a href="./org/biojava/bio/dp/twohead/EmissionCache.html" title="class in org.biojava.bio.dp.twohead">EmissionCache</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/AbstractSVMClassifierModel.html#clear()">clear()</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/AbstractSVMClassifierModel.html" title="class in org.biojava.stats.svm">AbstractSVMClassifierModel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/AbstractSVMTarget.html#clear()">clear()</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/AbstractSVMTarget.html" title="class in org.biojava.stats.svm">AbstractSVMTarget</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/SimpleSVMClassifierModel.html#clear()">clear()</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/SimpleSVMClassifierModel.html" title="class in org.biojava.stats.svm">SimpleSVMClassifierModel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/SimpleSVMTarget.html#clear()">clear()</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/SimpleSVMTarget.html" title="class in org.biojava.stats.svm">SimpleSVMTarget</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/SVMClassifierModel.html#clear()">clear()</a></span> - Method in interface org.biojava.stats.svm.<a href="./org/biojava/stats/svm/SVMClassifierModel.html" title="interface in org.biojava.stats.svm">SVMClassifierModel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/SVMTarget.html#clear()">clear()</a></span> - Method in interface org.biojava.stats.svm.<a href="./org/biojava/stats/svm/SVMTarget.html" title="interface in org.biojava.stats.svm">SVMTarget</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/tools/ClassifierExample.PointClassifier.html#clear()">clear()</a></span> - Method in class org.biojava.stats.svm.tools.<a href="./org/biojava/stats/svm/tools/ClassifierExample.PointClassifier.html" title="class in org.biojava.stats.svm.tools">ClassifierExample.PointClassifier</a></dt>
<dd>
<div class="block">Remove all points from the canvas, and discard any model.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/cache/CacheReference.html#clear()">clear()</a></span> - Method in interface org.biojava.utils.cache.<a href="./org/biojava/utils/cache/CacheReference.html" title="interface in org.biojava.utils.cache">CacheReference</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/FileAsList.html#clear()">clear()</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/FileAsList.html" title="class in org.biojava.utils">FileAsList</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/EmptyRichAnnotation.html#clear()">clear()</a></span> - Method in class org.biojavax.<a href="./org/biojavax/EmptyRichAnnotation.html" title="class in org.biojavax">EmptyRichAnnotation</a></dt>
<dd>
<div class="block">Removes all notes from this annotation object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ga/util/WeightedSet.html#clear()">clear()</a></span> - Method in class org.biojavax.ga.util.<a href="./org/biojavax/ga/util/WeightedSet.html" title="class in org.biojavax.ga.util">WeightedSet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/RichAnnotation.html#clear()">clear()</a></span> - Method in interface org.biojavax.<a href="./org/biojavax/RichAnnotation.html" title="interface in org.biojavax">RichAnnotation</a></dt>
<dd>
<div class="block">Removes all notes from this annotation object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleRichAnnotation.html#clear()">clear()</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleRichAnnotation.html" title="class in org.biojavax">SimpleRichAnnotation</a></dt>
<dd>
<div class="block">Removes all notes from this annotation object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Group.html#clearAtoms()">clearAtoms()</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Group.html" title="interface in org.biojava.bio.structure">Group</a></dt>
<dd>
<div class="block">Remove all atoms from this group.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/HetatomImpl.html#clearAtoms()">clearAtoms()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/HetatomImpl.html" title="class in org.biojava.bio.structure">HetatomImpl</a></dt>
<dd>
<div class="block">remove all atoms</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/MMcifParser.html#clearConsumers()">clearConsumers()</a></span> - Method in interface org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/MMcifParser.html" title="interface in org.biojava.bio.structure.io.mmcif">MMcifParser</a></dt>
<dd>
<div class="block">Remove all consumers from the parser.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/SimpleMMcifParser.html#clearConsumers()">clearConsumers()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/SimpleMMcifParser.html" title="class in org.biojava.bio.structure.io.mmcif">SimpleMMcifParser</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/DistributionTrainer.html#clearCounts(org.biojava.bio.dist.DistributionTrainerContext)">clearCounts(DistributionTrainerContext)</a></span> - Method in interface org.biojava.bio.dist.<a href="./org/biojava/bio/dist/DistributionTrainer.html" title="interface in org.biojava.bio.dist">DistributionTrainer</a></dt>
<dd>
<div class="block">Clears all of the counts to zero.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/DistributionTrainerContext.html#clearCounts()">clearCounts()</a></span> - Method in interface org.biojava.bio.dist.<a href="./org/biojava/bio/dist/DistributionTrainerContext.html" title="interface in org.biojava.bio.dist">DistributionTrainerContext</a></dt>
<dd>
<div class="block">Clears all of the counts to zero.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/IgnoreCountsTrainer.html#clearCounts(org.biojava.bio.dist.DistributionTrainerContext)">clearCounts(DistributionTrainerContext)</a></span> - Method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/IgnoreCountsTrainer.html" title="class in org.biojava.bio.dist">IgnoreCountsTrainer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/SimpleDistribution.Trainer.html#clearCounts(org.biojava.bio.dist.DistributionTrainerContext)">clearCounts(DistributionTrainerContext)</a></span> - Method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/SimpleDistribution.Trainer.html" title="class in org.biojava.bio.dist">SimpleDistribution.Trainer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/SimpleDistributionTrainer.html#clearCounts(org.biojava.bio.dist.DistributionTrainerContext)">clearCounts(DistributionTrainerContext)</a></span> - Method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/SimpleDistributionTrainer.html" title="class in org.biojava.bio.dist">SimpleDistributionTrainer</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/SimpleDistributionTrainerContext.html#clearCounts()">clearCounts()</a></span> - Method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/SimpleDistributionTrainerContext.html" title="class in org.biojava.bio.dist">SimpleDistributionTrainerContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/TransitionTrainer.html#clearCounts()">clearCounts()</a></span> - Method in interface org.biojava.bio.dp.<a href="./org/biojava/bio/dp/TransitionTrainer.html" title="interface in org.biojava.bio.dp">TransitionTrainer</a></dt>
<dd>
<div class="block">Clears all of the counts to zero.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/molbio/RestrictionMapper.html#clearEnzymes()">clearEnzymes()</a></span> - Method in class org.biojava.bio.molbio.<a href="./org/biojava/bio/molbio/RestrictionMapper.html" title="class in org.biojava.bio.molbio">RestrictionMapper</a></dt>
<dd>
<div class="block"><code>clearEnzymes</code> removes all enzymes from those to be
searched for in the <code>Sequence</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/MMCIFFileReader.html#clearExtensions()">clearExtensions()</a></span> - Method in class org.biojava.bio.structure.io.<a href="./org/biojava/bio/structure/io/MMCIFFileReader.html" title="class in org.biojava.bio.structure.io">MMCIFFileReader</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/PDBFileReader.html#clearExtensions()">clearExtensions()</a></span> - Method in class org.biojava.bio.structure.io.<a href="./org/biojava/bio/structure/io/PDBFileReader.html" title="class in org.biojava.bio.structure.io">PDBFileReader</a></dt>
<dd>
<div class="block">clear the supported file extensions</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/StructureIOFile.html#clearExtensions()">clearExtensions()</a></span> - Method in interface org.biojava.bio.structure.io.<a href="./org/biojava/bio/structure/io/StructureIOFile.html" title="interface in org.biojava.bio.structure.io">StructureIOFile</a></dt>
<dd>
<div class="block">clear all file extensions</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/server/FlatFileInstallation.html#clearFilters()">clearFilters()</a></span> - Method in class org.biojava.bio.structure.server.<a href="./org/biojava/bio/structure/server/FlatFileInstallation.html" title="class in org.biojava.bio.structure.server">FlatFileInstallation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/server/MMCIFFileInstallation.html#clearFilters()">clearFilters()</a></span> - Method in class org.biojava.bio.structure.server.<a href="./org/biojava/bio/structure/server/MMCIFFileInstallation.html" title="class in org.biojava.bio.structure.server">MMCIFFileInstallation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/server/PDBInstallation.html#clearFilters()">clearFilters()</a></span> - Method in interface org.biojava.bio.structure.server.<a href="./org/biojava/bio/structure/server/PDBInstallation.html" title="interface in org.biojava.bio.structure.server">PDBInstallation</a></dt>
<dd>
<div class="block">remove all filters, next time getAll is called, it will return all available PDBs</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/SequenceDisplay.html#clearListeners()">clearListeners()</a></span> - Method in class org.biojava.bio.structure.gui.<a href="./org/biojava/bio/structure/gui/SequenceDisplay.html" title="class in org.biojava.bio.structure.gui">SequenceDisplay</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/util/SequenceMouseListener.html#clearListeners()">clearListeners()</a></span> - Method in class org.biojava.bio.structure.gui.util.<a href="./org/biojava/bio/structure/gui/util/SequenceMouseListener.html" title="class in org.biojava.bio.structure.gui.util">SequenceMouseListener</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/server/StructureFetcherRunnable.html#clearListeners()">clearListeners()</a></span> - Method in class org.biojava.bio.structure.server.<a href="./org/biojava/bio/structure/server/StructureFetcherRunnable.html" title="class in org.biojava.bio.structure.server">StructureFetcherRunnable</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/RichObjectFactory.html#clearLRUCache()">clearLRUCache()</a></span> - Static method in class org.biojavax.<a href="./org/biojavax/RichObjectFactory.html" title="class in org.biojavax">RichObjectFactory</a></dt>
<dd>
<div class="block">Removes all objects from the LRU cache.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/RichObjectFactory.html#clearLRUCache(java.lang.Class)">clearLRUCache(Class)</a></span> - Static method in class org.biojavax.<a href="./org/biojavax/RichObjectFactory.html" title="class in org.biojavax">RichObjectFactory</a></dt>
<dd>
<div class="block">Removes all objects of the specified class from the LRU cache.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/regex/Search.html#clearPatterns()">clearPatterns()</a></span> - Method in class org.biojava.utils.regex.<a href="./org/biojava/utils/regex/Search.html" title="class in org.biojava.utils.regex">Search</a></dt>
<dd>
<div class="block">remove all patterns from the pattern cache.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/MultiLineRenderer.html#clearRenderers()">clearRenderers()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/MultiLineRenderer.html" title="class in org.biojava.bio.gui.sequence">MultiLineRenderer</a></dt>
<dd>
<div class="block"><code>clearRenderers</code> removes all renderers from this
renderer.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PairwiseOverlayRenderer.html#clearRenderers()">clearRenderers()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PairwiseOverlayRenderer.html" title="class in org.biojava.bio.gui.sequence">PairwiseOverlayRenderer</a></dt>
<dd>
<div class="block"><code>clearRenderers</code> removes all the renderers.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/server/SimpleStructureServer.html#clearStructureListeners()">clearStructureListeners()</a></span> - Method in class org.biojava.bio.structure.server.<a href="./org/biojava/bio/structure/server/SimpleStructureServer.html" title="class in org.biojava.bio.structure.server">SimpleStructureServer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/server/StructureServer.html#clearStructureListeners()">clearStructureListeners()</a></span> - Method in interface org.biojava.bio.structure.server.<a href="./org/biojava/bio/structure/server/StructureServer.html" title="interface in org.biojava.bio.structure.server">StructureServer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/AbstractChromatogram.html#clearTraces()">clearTraces()</a></span> - Method in class org.biojava.bio.chromatogram.<a href="./org/biojava/bio/chromatogram/AbstractChromatogram.html" title="class in org.biojava.bio.chromatogram">AbstractChromatogram</a></dt>
<dd>
<div class="block">Sets the trace data structures to null.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/SimpleChromatogram.html#clearTraceValues()">clearTraceValues()</a></span> - Method in class org.biojava.bio.chromatogram.<a href="./org/biojava/bio/chromatogram/SimpleChromatogram.html" title="class in org.biojava.bio.chromatogram">SimpleChromatogram</a></dt>
<dd>
<div class="block">Sets all the traces to null.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/biosql/OracleDBHelper.html#clobToString(java.sql.Connection, java.sql.ResultSet, int)">clobToString(Connection, ResultSet, int)</a></span> - Method in class org.biojava.bio.seq.db.biosql.<a href="./org/biojava/bio/seq/db/biosql/OracleDBHelper.html" title="class in org.biojava.bio.seq.db.biosql">OracleDBHelper</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.html#clone()">clone()</a></span> - Method in class org.biojava.bio.chromatogram.graphic.<a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.html" title="class in org.biojava.bio.chromatogram.graphic">ChromatogramGraphic</a></dt>
<dd>
<div class="block">Performs a partial deep copy and invalidates regenerable structures.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/LineSplitParser.html#clone()">clone()</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/LineSplitParser.html" title="class in org.biojava.bio.program.tagvalue">LineSplitParser</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/Feature.Template.html#clone()">clone()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/Feature.Template.html" title="class in org.biojava.bio.seq">Feature.Template</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/RevCompSequence.html#clone()">clone()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/RevCompSequence.html" title="class in org.biojava.bio.seq.impl">RevCompSequence</a></dt>
<dd>
<div class="block">clone() should make a complete copy of the Sequence with all features (and children) and return
a SimpleSequence that is unconnected from the original sequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/FragmentPair.html#clone()">clone()</a></span> - Method in class org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/FragmentPair.html" title="class in org.biojava.bio.structure.align.pairwise">FragmentPair</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/AminoAcidImpl.html#clone()">clone()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/AminoAcidImpl.html" title="class in org.biojava.bio.structure">AminoAcidImpl</a></dt>
<dd>
<div class="block">returns and identical copy of this Group object .</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Atom.html#clone()">clone()</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Atom.html" title="interface in org.biojava.bio.structure">Atom</a></dt>
<dd>
<div class="block">returns and identical copy of this object .</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/AtomImpl.html#clone()">clone()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/AtomImpl.html" title="class in org.biojava.bio.structure">AtomImpl</a></dt>
<dd>
<div class="block">returns and identical copy of this object .</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Chain.html#clone()">clone()</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Chain.html" title="interface in org.biojava.bio.structure">Chain</a></dt>
<dd>
<div class="block">returns an identical copy of this Chain.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/ChainImpl.html#clone()">clone()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/ChainImpl.html" title="class in org.biojava.bio.structure">ChainImpl</a></dt>
<dd>
<div class="block">Returns an identical copy of this Chain .</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Compound.html#clone()">clone()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure">Compound</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Group.html#clone()">clone()</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Group.html" title="interface in org.biojava.bio.structure">Group</a></dt>
<dd>
<div class="block">returns and identical copy of this Group object .</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/GroupIterator.html#clone()">clone()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/GroupIterator.html" title="class in org.biojava.bio.structure">GroupIterator</a></dt>
<dd>
<div class="block">Creates and returns a copy of this object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/HetatomImpl.html#clone()">clone()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/HetatomImpl.html" title="class in org.biojava.bio.structure">HetatomImpl</a></dt>
<dd>
<div class="block">returns and identical copy of this Group object .</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/jama/Matrix.html#clone()">clone()</a></span> - Method in class org.biojava.bio.structure.jama.<a href="./org/biojava/bio/structure/jama/Matrix.html" title="class in org.biojava.bio.structure.jama">Matrix</a></dt>
<dd>
<div class="block">Clone the Matrix object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/NucleotideImpl.html#clone()">clone()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/NucleotideImpl.html" title="class in org.biojava.bio.structure">NucleotideImpl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/SSBond.html#clone()">clone()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/SSBond.html" title="class in org.biojava.bio.structure">SSBond</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Structure.html#clone()">clone()</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Structure.html" title="interface in org.biojava.bio.structure">Structure</a></dt>
<dd>
<div class="block">returns an identical copy of this Structure object</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/StructureImpl.html#clone()">clone()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/StructureImpl.html" title="class in org.biojava.bio.structure">StructureImpl</a></dt>
<dd>
<div class="block">returns an identical copy of this structure .</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/ExecRunner.html#clone()">clone()</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/ExecRunner.html" title="class in org.biojava.utils">ExecRunner</a></dt>
<dd>
<div class="block">We override the <code>clone</code> method here to prevent cloning of our class.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/TypedProperties.html#clone()">clone()</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/TypedProperties.html" title="class in org.biojava.utils">TypedProperties</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/emblcd/EmblCDROMIndexReader.html#close()">close()</a></span> - Method in class org.biojava.bio.seq.db.emblcd.<a href="./org/biojava/bio/seq/db/emblcd/EmblCDROMIndexReader.html" title="class in org.biojava.bio.seq.db.emblcd">EmblCDROMIndexReader</a></dt>
<dd>
<div class="block"><code>close</code> closes the underlying
<code>InputStream</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/emblcd/EmblCDROMRandomAccess.html#close()">close()</a></span> - Method in class org.biojava.bio.seq.db.emblcd.<a href="./org/biojava/bio/seq/db/emblcd/EmblCDROMRandomAccess.html" title="class in org.biojava.bio.seq.db.emblcd">EmblCDROMRandomAccess</a></dt>
<dd>
<div class="block"><code>close</code> closes the underlying
<code>RandomAccessFile</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/EmblCDROMIndexStore.html#close()">close()</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/EmblCDROMIndexStore.html" title="class in org.biojava.bio.seq.db">EmblCDROMIndexStore</a></dt>
<dd>
<div class="block"><code>close</code> closes the underlying
<code>EntryNamRandomAccess</code> which in turn closes the
lower level <code>RandomAccessFile</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/StreamParser.html#close()">close()</a></span> - Method in interface org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/StreamParser.html" title="interface in org.biojava.bio.seq.io">StreamParser</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/CodonPrefFilter.EverythingToXML.html#close()">close()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/CodonPrefFilter.EverythingToXML.html" title="class in org.biojava.bio.symbol">CodonPrefFilter.EverythingToXML</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/naming/ObdaContext.html#close()">close()</a></span> - Method in class org.biojava.naming.<a href="./org/biojava/naming/ObdaContext.html" title="class in org.biojava.naming">ObdaContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/io/CountedBufferedReader.html#close()">close()</a></span> - Method in class org.biojava.utils.io.<a href="./org/biojava/utils/io/CountedBufferedReader.html" title="class in org.biojava.utils.io">CountedBufferedReader</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/io/RandomAccessReader.html#close()">close()</a></span> - Method in class org.biojava.utils.io.<a href="./org/biojava/utils/io/RandomAccessReader.html" title="class in org.biojava.utils.io">RandomAccessReader</a></dt>
<dd>
<div class="block"><code>close</code> closes the underlying
<code>RandomAccessFile</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/xml/PrettyXMLWriter.html#close()">close()</a></span> - Method in class org.biojava.utils.xml.<a href="./org/biojava/utils/xml/PrettyXMLWriter.html" title="class in org.biojava.utils.xml">PrettyXMLWriter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/xml/XMLWriter.html#close()">close()</a></span> - Method in interface org.biojava.utils.xml.<a href="./org/biojava/utils/xml/XMLWriter.html" title="interface in org.biojava.utils.xml">XMLWriter</a></dt>
<dd>
<div class="block">Close this XMLWriter, and it's underlying stream.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/xml/FastXMLWriter.html#closeTag(java.lang.String)">closeTag(String)</a></span> - Method in class org.biojava.utils.xml.<a href="./org/biojava/utils/xml/FastXMLWriter.html" title="class in org.biojava.utils.xml">FastXMLWriter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/xml/PrettyXMLWriter.html#closeTag(java.lang.String, java.lang.String)">closeTag(String, String)</a></span> - Method in class org.biojava.utils.xml.<a href="./org/biojava/utils/xml/PrettyXMLWriter.html" title="class in org.biojava.utils.xml">PrettyXMLWriter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/xml/PrettyXMLWriter.html#closeTag(java.lang.String)">closeTag(String)</a></span> - Method in class org.biojava.utils.xml.<a href="./org/biojava/utils/xml/PrettyXMLWriter.html" title="class in org.biojava.utils.xml">PrettyXMLWriter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/xml/XMLWriter.html#closeTag(java.lang.String, java.lang.String)">closeTag(String, String)</a></span> - Method in interface org.biojava.utils.xml.<a href="./org/biojava/utils/xml/XMLWriter.html" title="interface in org.biojava.utils.xml">XMLWriter</a></dt>
<dd>
<div class="block">Closes an element</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/xml/XMLWriter.html#closeTag(java.lang.String)">closeTag(String)</a></span> - Method in interface org.biojava.utils.xml.<a href="./org/biojava/utils/xml/XMLWriter.html" title="interface in org.biojava.utils.xml">XMLWriter</a></dt>
<dd>
<div class="block">Closes an un-qualified element.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/AlignIOConstants.html#CLUSTAL">CLUSTAL</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/AlignIOConstants.html" title="class in org.biojava.bio.seq.io">AlignIOConstants</a></dt>
<dd>
<div class="block"><code>CLUSTAL</code> indicates that the alignment format is
Clustal.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/AlignIOConstants.html#CLUSTAL_AA">CLUSTAL_AA</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/AlignIOConstants.html" title="class in org.biojava.bio.seq.io">AlignIOConstants</a></dt>
<dd>
<div class="block"><code>CLUSTAL_AA</code> premade CLUSTAL | AA;</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/AlignIOConstants.html#CLUSTAL_DNA">CLUSTAL_DNA</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/AlignIOConstants.html" title="class in org.biojava.bio.seq.io">AlignIOConstants</a></dt>
<dd>
<div class="block"><code>CLUSTAL_DNA</code> premade CLUSTAL | DNA;</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/AlignIOConstants.html#CLUSTAL_RNA">CLUSTAL_RNA</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/AlignIOConstants.html" title="class in org.biojava.bio.seq.io">AlignIOConstants</a></dt>
<dd>
<div class="block"><code>CLUSTAL_RNA</code> premade CLUSTAL | RNA;</div>
</dd>
<dt><a href="./org/biojava/bio/program/sax/ClustalWAlignmentSAXParser.html" title="class in org.biojava.bio.program.sax"><span class="strong">ClustalWAlignmentSAXParser</span></a> - Class in <a href="./org/biojava/bio/program/sax/package-summary.html">org.biojava.bio.program.sax</a></dt>
<dd>
<div class="block">A SAX2 parser for dealing with a multiple sequence
alignment as produced by ClustalW outputing .aln format.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/sax/ClustalWAlignmentSAXParser.html#ClustalWAlignmentSAXParser()">ClustalWAlignmentSAXParser()</a></span> - Constructor for class org.biojava.bio.program.sax.<a href="./org/biojava/bio/program/sax/ClustalWAlignmentSAXParser.html" title="class in org.biojava.bio.program.sax">ClustalWAlignmentSAXParser</a></dt>
<dd>
<div class="block">Initialises internal state
Sets namespace prefix to "biojava"</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/ClusterAltAligs.html#cluster(org.biojava.bio.structure.align.pairwise.AlternativeAlignment[])">cluster(AlternativeAlignment[])</a></span> - Static method in class org.biojava.bio.structure.align.<a href="./org/biojava/bio/structure/align/ClusterAltAligs.html" title="class in org.biojava.bio.structure.align">ClusterAltAligs</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/ClusterAltAligs.html#cluster(org.biojava.bio.structure.align.pairwise.AlternativeAlignment[], int)">cluster(AlternativeAlignment[], int)</a></span> - Static method in class org.biojava.bio.structure.align.<a href="./org/biojava/bio/structure/align/ClusterAltAligs.html" title="class in org.biojava.bio.structure.align">ClusterAltAligs</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/structure/align/ClusterAltAligs.html" title="class in org.biojava.bio.structure.align"><span class="strong">ClusterAltAligs</span></a> - Class in <a href="./org/biojava/bio/structure/align/package-summary.html">org.biojava.bio.structure.align</a></dt>
<dd>
<div class="block">A class that clusters alternative alignments according to their
similarity.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/ClusterAltAligs.html#ClusterAltAligs()">ClusterAltAligs()</a></span> - Constructor for class org.biojava.bio.structure.align.<a href="./org/biojava/bio/structure/align/ClusterAltAligs.html" title="class in org.biojava.bio.structure.align">ClusterAltAligs</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/MassCalc.html#Cmono">Cmono</a></span> - Static variable in class org.biojava.bio.proteomics.<a href="./org/biojava/bio/proteomics/MassCalc.html" title="class in org.biojava.bio.proteomics">MassCalc</a></dt>
<dd>
<div class="block">Constant value of Carbon monoisotopic mass</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/Protease.html#CNBr">CNBr</a></span> - Static variable in class org.biojava.bio.proteomics.<a href="./org/biojava/bio/proteomics/Protease.html" title="class in org.biojava.bio.proteomics">Protease</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/ProteaseManager.html#CNBr">CNBr</a></span> - Static variable in class org.biojava.bio.proteomics.<a href="./org/biojava/bio/proteomics/ProteaseManager.html" title="class in org.biojava.bio.proteomics">ProteaseManager</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BiblioSubject.html#codes">codes</a></span> - Variable in class org.biojava.bibliography.<a href="./org/biojava/bibliography/BiblioSubject.html" title="class in org.biojava.bibliography">BiblioSubject</a></dt>
<dd>
<div class="block">
Classification code (call number) is usually either Dewey decimal or
Congress classification.</div>
</dd>
<dt><a href="./org/biojava/bio/symbol/CodonPref.html" title="interface in org.biojava.bio.symbol"><span class="strong">CodonPref</span></a> - Interface in <a href="./org/biojava/bio/symbol/package-summary.html">org.biojava.bio.symbol</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/symbol/CodonPrefFilter.html" title="interface in org.biojava.bio.symbol"><span class="strong">CodonPrefFilter</span></a> - Interface in <a href="./org/biojava/bio/symbol/package-summary.html">org.biojava.bio.symbol</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/symbol/CodonPrefFilter.AcceptAll.html" title="class in org.biojava.bio.symbol"><span class="strong">CodonPrefFilter.AcceptAll</span></a> - Class in <a href="./org/biojava/bio/symbol/package-summary.html">org.biojava.bio.symbol</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/CodonPrefFilter.AcceptAll.html#CodonPrefFilter.AcceptAll()">CodonPrefFilter.AcceptAll()</a></span> - Constructor for class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/CodonPrefFilter.AcceptAll.html" title="class in org.biojava.bio.symbol">CodonPrefFilter.AcceptAll</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/symbol/CodonPrefFilter.ByName.html" title="class in org.biojava.bio.symbol"><span class="strong">CodonPrefFilter.ByName</span></a> - Class in <a href="./org/biojava/bio/symbol/package-summary.html">org.biojava.bio.symbol</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/CodonPrefFilter.ByName.html#CodonPrefFilter.ByName(java.lang.String)">CodonPrefFilter.ByName(String)</a></span> - Constructor for class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/CodonPrefFilter.ByName.html" title="class in org.biojava.bio.symbol">CodonPrefFilter.ByName</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/symbol/CodonPrefFilter.EverythingToXML.html" title="class in org.biojava.bio.symbol"><span class="strong">CodonPrefFilter.EverythingToXML</span></a> - Class in <a href="./org/biojava/bio/symbol/package-summary.html">org.biojava.bio.symbol</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/CodonPrefFilter.EverythingToXML.html#CodonPrefFilter.EverythingToXML(java.io.PrintWriter)">CodonPrefFilter.EverythingToXML(PrintWriter)</a></span> - Constructor for class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/CodonPrefFilter.EverythingToXML.html" title="class in org.biojava.bio.symbol">CodonPrefFilter.EverythingToXML</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/symbol/CodonPrefTools.html" title="class in org.biojava.bio.symbol"><span class="strong">CodonPrefTools</span></a> - Class in <a href="./org/biojava/bio/symbol/package-summary.html">org.biojava.bio.symbol</a></dt>
<dd>
<div class="block">An utility class for codon preferences</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/CodonPrefTools.html#CodonPrefTools()">CodonPrefTools()</a></span> - Constructor for class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/CodonPrefTools.html" title="class in org.biojava.bio.symbol">CodonPrefTools</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/CollectionConstraint.html" title="interface in org.biojava.bio"><span class="strong">CollectionConstraint</span></a> - Interface in <a href="./org/biojava/bio/package-summary.html">org.biojava.bio</a></dt>
<dd>
<div class="block">Used by <code>AnnotationType</code> to represent the constraint on
the collection of values in a property-slot.</div>
</dd>
<dt><a href="./org/biojava/bio/CollectionConstraint.AllValuesIn.html" title="class in org.biojava.bio"><span class="strong">CollectionConstraint.AllValuesIn</span></a> - Class in <a href="./org/biojava/bio/package-summary.html">org.biojava.bio</a></dt>
<dd>
<div class="block">CollectionConstraint which validates all members of a Collection.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/CollectionConstraint.AllValuesIn.html#CollectionConstraint.AllValuesIn(org.biojava.bio.PropertyConstraint, org.biojava.bio.symbol.Location)">CollectionConstraint.AllValuesIn(PropertyConstraint, Location)</a></span> - Constructor for class org.biojava.bio.<a href="./org/biojava/bio/CollectionConstraint.AllValuesIn.html" title="class in org.biojava.bio">CollectionConstraint.AllValuesIn</a></dt>
<dd>
<div class="block">Create an AllValuesIn based upon a PropertyConstraint and a
cardinality.</div>
</dd>
<dt><a href="./org/biojava/bio/CollectionConstraint.And.html" title="class in org.biojava.bio"><span class="strong">CollectionConstraint.And</span></a> - Class in <a href="./org/biojava/bio/package-summary.html">org.biojava.bio</a></dt>
<dd>
<div class="block">A collection constraint that accpepts collections iff they are accepted by both
child constraints.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/CollectionConstraint.And.html#CollectionConstraint.And(org.biojava.bio.CollectionConstraint, org.biojava.bio.CollectionConstraint)">CollectionConstraint.And(CollectionConstraint, CollectionConstraint)</a></span> - Constructor for class org.biojava.bio.<a href="./org/biojava/bio/CollectionConstraint.And.html" title="class in org.biojava.bio">CollectionConstraint.And</a></dt>
<dd>
<div class="block">Create a new <code>And</code> from two child constraints.</div>
</dd>
<dt><a href="./org/biojava/bio/CollectionConstraint.Contains.html" title="class in org.biojava.bio"><span class="strong">CollectionConstraint.Contains</span></a> - Class in <a href="./org/biojava/bio/package-summary.html">org.biojava.bio</a></dt>
<dd>
<div class="block">CollectionConstraint which validates a portion of a Collection.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/CollectionConstraint.Contains.html#CollectionConstraint.Contains(org.biojava.bio.PropertyConstraint, org.biojava.bio.symbol.Location)">CollectionConstraint.Contains(PropertyConstraint, Location)</a></span> - Constructor for class org.biojava.bio.<a href="./org/biojava/bio/CollectionConstraint.Contains.html" title="class in org.biojava.bio">CollectionConstraint.Contains</a></dt>
<dd>
<div class="block">Create a Contains based upon a PropertyConstraint and a
cardinality.</div>
</dd>
<dt><a href="./org/biojava/bio/CollectionConstraint.Or.html" title="class in org.biojava.bio"><span class="strong">CollectionConstraint.Or</span></a> - Class in <a href="./org/biojava/bio/package-summary.html">org.biojava.bio</a></dt>
<dd>
<div class="block">A collection constraint that accepts items iff they are accepted by either
child constraints.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/CollectionConstraint.Or.html#CollectionConstraint.Or(org.biojava.bio.CollectionConstraint, org.biojava.bio.CollectionConstraint)">CollectionConstraint.Or(CollectionConstraint, CollectionConstraint)</a></span> - Constructor for class org.biojava.bio.<a href="./org/biojava/bio/CollectionConstraint.Or.html" title="class in org.biojava.bio">CollectionConstraint.Or</a></dt>
<dd>
<div class="block">Create a new <code>Or</code> from two child constraints.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.html#colors">colors</a></span> - Variable in class org.biojava.bio.chromatogram.graphic.<a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.html" title="class in org.biojava.bio.chromatogram.graphic">ChromatogramGraphic</a></dt>
<dd>
<div class="block">The map containing the colors for drawing traces.</div>
</dd>
<dt><a href="./org/biojava/bio/program/blast2html/ColourCommand.html" title="interface in org.biojava.bio.program.blast2html"><span class="strong">ColourCommand</span></a> - Interface in <a href="./org/biojava/bio/program/blast2html/package-summary.html">org.biojava.bio.program.blast2html</a></dt>
<dd>
<div class="block">
Interface for specifying whether a particular pair
of residues/bases should be coloured.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/SubstitutionMatrix.html#colSymbols">colSymbols</a></span> - Variable in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/SubstitutionMatrix.html" title="class in org.biojava.bio.alignment">SubstitutionMatrix</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/ProfileHMM.html#columns()">columns()</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/ProfileHMM.html" title="class in org.biojava.bio.dp">ProfileHMM</a></dt>
<dd>
<div class="block">Retrieve the number of columns in the model.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/SimpleWeightMatrix.html#columns()">columns()</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/SimpleWeightMatrix.html" title="class in org.biojava.bio.dp">SimpleWeightMatrix</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/twohead/AbstractMatrixPairDPCursor.html#columns">columns</a></span> - Variable in class org.biojava.bio.dp.twohead.<a href="./org/biojava/bio/dp/twohead/AbstractMatrixPairDPCursor.html" title="class in org.biojava.bio.dp.twohead">AbstractMatrixPairDPCursor</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/WeightMatrix.html#columns()">columns()</a></span> - Method in interface org.biojava.bio.dp.<a href="./org/biojava/bio/dp/WeightMatrix.html" title="interface in org.biojava.bio.dp">WeightMatrix</a></dt>
<dd>
<div class="block">The number of columns modeled by the weight matrix.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/obo/OboFileHandler.html#COMMENT">COMMENT</a></span> - Static variable in class org.biojava.ontology.obo.<a href="./org/biojava/ontology/obo/OboFileHandler.html" title="class in org.biojava.ontology.obo">OboFileHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/BioEntry.html#COMMENT">COMMENT</a></span> - Static variable in interface org.biojavax.bio.<a href="./org/biojavax/bio/BioEntry.html" title="interface in org.biojavax.bio">BioEntry</a></dt>
<dd> </dd>
<dt><a href="./org/biojavax/Comment.html" title="interface in org.biojavax"><span class="strong">Comment</span></a> - Interface in <a href="./org/biojavax/package-summary.html">org.biojavax</a></dt>
<dd>
<div class="block">A simple ranked comment designed to be used for BioEntry comments
in BioSQL.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#COMMENT_ABS_MAX_TAG">COMMENT_ABS_MAX_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#COMMENT_ABSORPTION_TAG">COMMENT_ABSORPTION_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#COMMENT_ERROR_ATTR">COMMENT_ERROR_ATTR</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#COMMENT_EVENT_TAG">COMMENT_EVENT_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#COMMENT_EXPERIMENTS_TAG">COMMENT_EXPERIMENTS_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#COMMENT_INTERACT_INTACT_ATTR">COMMENT_INTERACT_INTACT_ATTR</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#COMMENT_INTERACT_LABEL_TAG">COMMENT_INTERACT_LABEL_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#COMMENT_INTERACTANT_TAG">COMMENT_INTERACTANT_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#COMMENT_ISOFORM_TAG">COMMENT_ISOFORM_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#COMMENT_KIN_KM_TAG">COMMENT_KIN_KM_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#COMMENT_KIN_VMAX_TAG">COMMENT_KIN_VMAX_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#COMMENT_KINETICS_TAG">COMMENT_KINETICS_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#COMMENT_LINK_TAG">COMMENT_LINK_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#COMMENT_LINK_URI_ATTR">COMMENT_LINK_URI_ATTR</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#COMMENT_LOCTYPE_ATTR">COMMENT_LOCTYPE_ATTR</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#COMMENT_MASS_ATTR">COMMENT_MASS_ATTR</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#COMMENT_METHOD_ATTR">COMMENT_METHOD_ATTR</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#COMMENT_ORGANISMS_TAG">COMMENT_ORGANISMS_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#COMMENT_PH_TAG">COMMENT_PH_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#COMMENT_REDOX_TAG">COMMENT_REDOX_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/EmblLikeFormat.html#COMMENT_TAG">COMMENT_TAG</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/EmblLikeFormat.html" title="class in org.biojava.bio.seq.io">EmblLikeFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/GenbankFormat.html#COMMENT_TAG">COMMENT_TAG</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/GenbankFormat.html" title="class in org.biojava.bio.seq.io">GenbankFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLFormat.html#COMMENT_TAG">COMMENT_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLFormat.html" title="class in org.biojavax.bio.seq.io">EMBLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html#COMMENT_TAG">COMMENT_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html" title="class in org.biojavax.bio.seq.io">EMBLxmlFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/GenbankFormat.html#COMMENT_TAG">COMMENT_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/GenbankFormat.html" title="class in org.biojavax.bio.seq.io">GenbankFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/INSDseqFormat.html#COMMENT_TAG">COMMENT_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/INSDseqFormat.html" title="class in org.biojavax.bio.seq.io">INSDseqFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtFormat.html#COMMENT_TAG">COMMENT_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtFormat.html" title="class in org.biojavax.bio.seq.io">UniProtFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#COMMENT_TAG">COMMENT_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#COMMENT_TEMPERATURE_TAG">COMMENT_TEMPERATURE_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFDocumentHandler.html#commentLine(java.lang.String)">commentLine(String)</a></span> - Method in interface org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFDocumentHandler.html" title="interface in org.biojava.bio.program.gff">GFFDocumentHandler</a></dt>
<dd>
<div class="block">A comment line has been encountered.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFFilterer.html#commentLine(java.lang.String)">commentLine(String)</a></span> - Method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFFilterer.html" title="class in org.biojava.bio.program.gff">GFFFilterer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFWriter.html#commentLine(java.lang.String)">commentLine(String)</a></span> - Method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFWriter.html" title="class in org.biojava.bio.program.gff">GFFWriter</a></dt>
<dd>
<div class="block">Prints the comment directly to the <span class="type">PrintWriter</span>
after adding a leading '<code>#</code>'.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff3/GFF3DocumentHandler.html#commentLine(java.lang.String)">commentLine(String)</a></span> - Method in interface org.biojava.bio.program.gff3.<a href="./org/biojava/bio/program/gff3/GFF3DocumentHandler.html" title="interface in org.biojava.bio.program.gff3">GFF3DocumentHandler</a></dt>
<dd>
<div class="block">A comment line has been encountered.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/indexdb/BioStore.html#commit()">commit()</a></span> - Method in class org.biojava.bio.program.indexdb.<a href="./org/biojava/bio/program/indexdb/BioStore.html" title="class in org.biojava.bio.program.indexdb">BioStore</a></dt>
<dd>
<div class="block"><code>commit</code> writes an index to disk.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/BioIndex.html#commit()">commit()</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/BioIndex.html" title="class in org.biojava.bio.seq.db">BioIndex</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/EmblCDROMIndexStore.html#commit()">commit()</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/EmblCDROMIndexStore.html" title="class in org.biojava.bio.seq.db">EmblCDROMIndexStore</a></dt>
<dd>
<div class="block"><code>commit</code> commits changes.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/IndexStore.html#commit()">commit()</a></span> - Method in interface org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/IndexStore.html" title="interface in org.biojava.bio.seq.db">IndexStore</a></dt>
<dd>
<div class="block">Commit the stored indices to permanent storage.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/TabIndexStore.html#commit()">commit()</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/TabIndexStore.html" title="class in org.biojava.bio.seq.db">TabIndexStore</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/Commitable.html#commit()">commit()</a></span> - Method in interface org.biojava.utils.<a href="./org/biojava/utils/Commitable.html" title="interface in org.biojava.utils">Commitable</a></dt>
<dd>
<div class="block"><code>commit</code> commits pending changes.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/FileAsList.html#commit()">commit()</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/FileAsList.html" title="class in org.biojava.utils">FileAsList</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/utils/Commitable.html" title="interface in org.biojava.utils"><span class="strong">Commitable</span></a> - Interface in <a href="./org/biojava/utils/package-summary.html">org.biojava.utils</a></dt>
<dd>
<div class="block">Implementations of <code>Commitable</code> support atomic changes
from one known state to another via commit/rollback semantics.</div>
</dd>
<dt><a href="./org/biojava/utils/CommitFailure.html" title="class in org.biojava.utils"><span class="strong">CommitFailure</span></a> - Exception in <a href="./org/biojava/utils/package-summary.html">org.biojava.utils</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/CommitFailure.html#CommitFailure(java.lang.String)">CommitFailure(String)</a></span> - Constructor for exception org.biojava.utils.<a href="./org/biojava/utils/CommitFailure.html" title="class in org.biojava.utils">CommitFailure</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/CommitFailure.html#CommitFailure(java.lang.Throwable)">CommitFailure(Throwable)</a></span> - Constructor for exception org.biojava.utils.<a href="./org/biojava/utils/CommitFailure.html" title="class in org.biojava.utils">CommitFailure</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/CommitFailure.html#CommitFailure(java.lang.String, java.lang.Throwable)">CommitFailure(String, Throwable)</a></span> - Constructor for exception org.biojava.utils.<a href="./org/biojava/utils/CommitFailure.html" title="class in org.biojava.utils">CommitFailure</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/TabIndexStore.html#commitStore()">commitStore()</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/TabIndexStore.html" title="class in org.biojava.bio.seq.db">TabIndexStore</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/taxa/NCBITaxon.html#COMMON">COMMON</a></span> - Static variable in interface org.biojavax.bio.taxa.<a href="./org/biojavax/bio/taxa/NCBITaxon.html" title="interface in org.biojavax.bio.taxa">NCBITaxon</a></dt>
<dd>
<div class="block">Use this to define common names for things.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.Terms.html#COMMON_NAME_KEY">COMMON_NAME_KEY</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.Terms.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat.Terms</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html#COMNAME_TAG">COMNAME_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html" title="class in org.biojavax.bio.seq.io">EMBLxmlFormat</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/ssaha/CompactedDataStore.html" title="class in org.biojava.bio.program.ssaha"><span class="strong">CompactedDataStore</span></a> - Class in <a href="./org/biojava/bio/program/ssaha/package-summary.html">org.biojava.bio.program.ssaha</a></dt>
<dd>
<div class="block">An implementation of DataStore that will map onto a file using the NIO
constructs.</div>
</dd>
<dt><a href="./org/biojava/bio/program/ssaha/CompactedDataStoreFactory.html" title="class in org.biojava.bio.program.ssaha"><span class="strong">CompactedDataStoreFactory</span></a> - Class in <a href="./org/biojava/bio/program/ssaha/package-summary.html">org.biojava.bio.program.ssaha</a></dt>
<dd>
<div class="block">
Builder for a data store that is backed by a java.nio.MappedByteBuffer.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssaha/CompactedDataStoreFactory.html#CompactedDataStoreFactory()">CompactedDataStoreFactory()</a></span> - Constructor for class org.biojava.bio.program.ssaha.<a href="./org/biojava/bio/program/ssaha/CompactedDataStoreFactory.html" title="class in org.biojava.bio.program.ssaha">CompactedDataStoreFactory</a></dt>
<dd> </dd>
<dt><a href="./org/biojavax/ontology/ComparableOntology.html" title="interface in org.biojavax.ontology"><span class="strong">ComparableOntology</span></a> - Interface in <a href="./org/biojavax/ontology/package-summary.html">org.biojavax.ontology</a></dt>
<dd>
<div class="block">An Ontology that can be compared to another.</div>
</dd>
<dt><a href="./org/biojavax/ontology/ComparableTerm.html" title="interface in org.biojavax.ontology"><span class="strong">ComparableTerm</span></a> - Interface in <a href="./org/biojavax/ontology/package-summary.html">org.biojavax.ontology</a></dt>
<dd>
<div class="block">Makes Term objects comparable properly and adds some extra features to them.</div>
</dd>
<dt><a href="./org/biojavax/ontology/ComparableTriple.html" title="interface in org.biojavax.ontology"><span class="strong">ComparableTriple</span></a> - Interface in <a href="./org/biojavax/ontology/package-summary.html">org.biojavax.ontology</a></dt>
<dd>
<div class="block">Comparable triples, obviously.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/ByLocationMinMaxComparator.html#comparator()">comparator()</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/ByLocationMinMaxComparator.html" title="class in org.biojava.bio.seq">ByLocationMinMaxComparator</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/Synonym.html#COMPARATOR">COMPARATOR</a></span> - Static variable in class org.biojava.ontology.<a href="./org/biojava/ontology/Synonym.html" title="class in org.biojava.ontology">Synonym</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/AbstractULAlignment.LeftRightLocationComparator.html#compare(java.lang.Object, java.lang.Object)">compare(Object, Object)</a></span> - Method in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/AbstractULAlignment.LeftRightLocationComparator.html" title="class in org.biojava.bio.alignment">AbstractULAlignment.LeftRightLocationComparator</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SeqSimilaritySearchHit.ByScoreComparator.html#compare(java.lang.Object, java.lang.Object)">compare(Object, Object)</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SeqSimilaritySearchHit.ByScoreComparator.html" title="class in org.biojava.bio.search">SeqSimilaritySearchHit.ByScoreComparator</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SeqSimilaritySearchHit.BySubHitCountComparator.html#compare(java.lang.Object, java.lang.Object)">compare(Object, Object)</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SeqSimilaritySearchHit.BySubHitCountComparator.html" title="class in org.biojava.bio.search">SeqSimilaritySearchHit.BySubHitCountComparator</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SeqSimilaritySearchSubHit.ByScoreComparator.html#compare(java.lang.Object, java.lang.Object)">compare(Object, Object)</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SeqSimilaritySearchSubHit.ByScoreComparator.html" title="class in org.biojava.bio.search">SeqSimilaritySearchSubHit.ByScoreComparator</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SeqSimilaritySearchSubHit.BySubjectStartComparator.html#compare(java.lang.Object, java.lang.Object)">compare(Object, Object)</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SeqSimilaritySearchSubHit.BySubjectStartComparator.html" title="class in org.biojava.bio.search">SeqSimilaritySearchSubHit.BySubjectStartComparator</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/ByLocationMinMaxComparator.html#compare(java.lang.Object, java.lang.Object)">compare(Object, Object)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/ByLocationMinMaxComparator.html" title="class in org.biojava.bio.seq">ByLocationMinMaxComparator</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/ByLocationMinMaxFeatureComparator.html#compare(java.lang.Object, java.lang.Object)">compare(Object, Object)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/ByLocationMinMaxFeatureComparator.html" title="class in org.biojava.bio.seq">ByLocationMinMaxFeatureComparator</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/Feature.ByLocationComparator.html#compare(java.lang.Object, java.lang.Object)">compare(Object, Object)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/Feature.ByLocationComparator.html" title="class in org.biojava.bio.seq">Feature.ByLocationComparator</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/EmblReferenceComparator.html#compare(java.lang.Object, java.lang.Object)">compare(Object, Object)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/EmblReferenceComparator.html" title="class in org.biojava.bio.seq.io">EmblReferenceComparator</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/GenEmblFeatureComparator.html#compare(java.lang.Object, java.lang.Object)">compare(Object, Object)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/GenEmblFeatureComparator.html" title="class in org.biojava.bio.seq.io">GenEmblFeatureComparator</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/GenEmblPropertyComparator.html#compare(java.lang.Object, java.lang.Object)">compare(Object, Object)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/GenEmblPropertyComparator.html" title="class in org.biojava.bio.seq.io">GenEmblPropertyComparator</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/AltAligComparator.html#compare(org.biojava.bio.structure.align.pairwise.AlternativeAlignment, org.biojava.bio.structure.align.pairwise.AlternativeAlignment)">compare(AlternativeAlignment, AlternativeAlignment)</a></span> - Method in class org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/AltAligComparator.html" title="class in org.biojava.bio.structure.align.pairwise">AltAligComparator</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/Synonym.html#compareTo(org.biojava.ontology.Synonym)">compareTo(Synonym)</a></span> - Method in class org.biojava.ontology.<a href="./org/biojava/ontology/Synonym.html" title="class in org.biojava.ontology">Synonym</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/CompoundRichLocation.html#compareTo(java.lang.Object)">compareTo(Object)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/CompoundRichLocation.html" title="class in org.biojavax.bio.seq">CompoundRichLocation</a></dt>
<dd>
<div class="block">
Locations are sorted first by rank, then crossref, then
strand, then term, then min, then max.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/EmptyRichLocation.html#compareTo(java.lang.Object)">compareTo(Object)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/EmptyRichLocation.html" title="class in org.biojavax.bio.seq">EmptyRichLocation</a></dt>
<dd>
<div class="block">
Empty Rich Locations return 0 when compared to other Empty ones,
or -1 otherwise.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichLocation.Strand.html#compareTo(java.lang.Object)">compareTo(Object)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichLocation.Strand.html" title="class in org.biojavax.bio.seq">RichLocation.Strand</a></dt>
<dd>
<div class="block"> Strands are compared first by symbol, then by number.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichFeature.html#compareTo(java.lang.Object)">compareTo(Object)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichFeature.html" title="class in org.biojavax.bio.seq">SimpleRichFeature</a></dt>
<dd>
<div class="block">
Features are sorted first by rank, then parent, type, and source.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichFeatureRelationship.html#compareTo(java.lang.Object)">compareTo(Object)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichFeatureRelationship.html" title="class in org.biojavax.bio.seq">SimpleRichFeatureRelationship</a></dt>
<dd>
<div class="block">
Relations are compared first by rank, then object, subject, then finally term.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichLocation.html#compareTo(java.lang.Object)">compareTo(Object)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichLocation.html" title="class in org.biojavax.bio.seq">SimpleRichLocation</a></dt>
<dd>
<div class="block">
Locations are sorted first by rank, then crossref, then
strand, then term, then min, then max.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/SimpleBioEntry.html#compareTo(java.lang.Object)">compareTo(Object)</a></span> - Method in class org.biojavax.bio.<a href="./org/biojavax/bio/SimpleBioEntry.html" title="class in org.biojavax.bio">SimpleBioEntry</a></dt>
<dd>
<div class="block">
Bioentries are ordered first by namespace, then name, accession, and
finally version.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/SimpleBioEntryRelationship.html#compareTo(java.lang.Object)">compareTo(Object)</a></span> - Method in class org.biojavax.bio.<a href="./org/biojavax/bio/SimpleBioEntryRelationship.html" title="class in org.biojavax.bio">SimpleBioEntryRelationship</a></dt>
<dd>
<div class="block">
A relationship is compared first by rank, then object, subject, and term.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/taxa/SimpleNCBITaxon.html#compareTo(java.lang.Object)">compareTo(Object)</a></span> - Method in class org.biojavax.bio.taxa.<a href="./org/biojavax/bio/taxa/SimpleNCBITaxon.html" title="class in org.biojavax.bio.taxa">SimpleNCBITaxon</a></dt>
<dd>
<div class="block">
NCBITaxon objects are compared only by their NCBITaxID fields.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/taxa/SimpleNCBITaxonName.html#compareTo(java.lang.Object)">compareTo(Object)</a></span> - Method in class org.biojavax.bio.taxa.<a href="./org/biojavax/bio/taxa/SimpleNCBITaxonName.html" title="class in org.biojavax.bio.taxa">SimpleNCBITaxonName</a></dt>
<dd>
<div class="block">
Taxon names are sorted by class first, then name.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ontology/SimpleComparableOntology.html#compareTo(java.lang.Object)">compareTo(Object)</a></span> - Method in class org.biojavax.ontology.<a href="./org/biojavax/ontology/SimpleComparableOntology.html" title="class in org.biojavax.ontology">SimpleComparableOntology</a></dt>
<dd>
<div class="block">
Ontologies are compared only by name.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ontology/SimpleComparableTerm.html#compareTo(java.lang.Object)">compareTo(Object)</a></span> - Method in class org.biojavax.ontology.<a href="./org/biojavax/ontology/SimpleComparableTerm.html" title="class in org.biojavax.ontology">SimpleComparableTerm</a></dt>
<dd>
<div class="block">
Terms are sorted by ontology first, then name.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ontology/SimpleComparableTriple.html#compareTo(java.lang.Object)">compareTo(Object)</a></span> - Method in class org.biojavax.ontology.<a href="./org/biojavax/ontology/SimpleComparableTriple.html" title="class in org.biojavax.ontology">SimpleComparableTriple</a></dt>
<dd>
<div class="block">
Triples are sorted in order of ontology, subject, object, and finally
predicate.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleComment.html#compareTo(java.lang.Object)">compareTo(Object)</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleComment.html" title="class in org.biojavax">SimpleComment</a></dt>
<dd>
<div class="block">
Comments are ordered first by their rank, then by a string
comparison of their text values.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleCrossRef.html#compareTo(java.lang.Object)">compareTo(Object)</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleCrossRef.html" title="class in org.biojavax">SimpleCrossRef</a></dt>
<dd>
<div class="block">
Compares cross references first by database name, then by accession,
then by version.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleDocRef.html#compareTo(java.lang.Object)">compareTo(Object)</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleDocRef.html" title="class in org.biojavax">SimpleDocRef</a></dt>
<dd>
<div class="block">
Document references are compared first by author, then by location, then
by title.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleDocRefAuthor.html#compareTo(java.lang.Object)">compareTo(Object)</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleDocRefAuthor.html" title="class in org.biojavax">SimpleDocRefAuthor</a></dt>
<dd>
<div class="block">
Document authors are compared first by name, then consortium status, then editor status.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleNamespace.html#compareTo(java.lang.Object)">compareTo(Object)</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleNamespace.html" title="class in org.biojavax">SimpleNamespace</a></dt>
<dd>
<div class="block">
Namespaces are compared only by name.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleNote.html#compareTo(java.lang.Object)">compareTo(Object)</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleNote.html" title="class in org.biojavax">SimpleNote</a></dt>
<dd>
<div class="block">
Notes are compared first by rank, then by the term.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleRankedCrossRef.html#compareTo(java.lang.Object)">compareTo(Object)</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleRankedCrossRef.html" title="class in org.biojavax">SimpleRankedCrossRef</a></dt>
<dd>
<div class="block">
Ranked cross references are sorted first by rank, then by cross reference.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleRankedDocRef.html#compareTo(java.lang.Object)">compareTo(Object)</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleRankedDocRef.html" title="class in org.biojavax">SimpleRankedDocRef</a></dt>
<dd>
<div class="block">
Ranked document references are sorted first by rank then location
then by actual document reference.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/regex/PatternFactory.html#compile(java.lang.String)">compile(String)</a></span> - Method in class org.biojava.utils.regex.<a href="./org/biojava/utils/regex/PatternFactory.html" title="class in org.biojava.utils.regex">PatternFactory</a></dt>
<dd>
<div class="block">Returns a Pattern object that applies the specified regex
against SymbolLists in the Alphabet that this PatternFactory
was defined against.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/regex/PatternFactory.html#compile(java.lang.String, java.lang.String)">compile(String, String)</a></span> - Method in class org.biojava.utils.regex.<a href="./org/biojava/utils/regex/PatternFactory.html" title="class in org.biojava.utils.regex">PatternFactory</a></dt>
<dd>
<div class="block">Returns a Pattern object that applies the specified regex
against SymbolLists in the Alphabet that this PatternFactory
was defined against.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/DNATools.html#complement(org.biojava.bio.symbol.Symbol)">complement(Symbol)</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/DNATools.html" title="class in org.biojava.bio.seq">DNATools</a></dt>
<dd>
<div class="block">Complement the symbol.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/DNATools.html#complement(org.biojava.bio.symbol.SymbolList)">complement(SymbolList)</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/DNATools.html" title="class in org.biojava.bio.seq">DNATools</a></dt>
<dd>
<div class="block">Retrieve a complement view of list.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEAnnotFilter.html#COMPLEMENT">COMPLEMENT</a></span> - Static variable in interface org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEAnnotFilter.html" title="interface in org.biojava.bio.seq.io.agave">AGAVEAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/NucleotideTools.html#complement(org.biojava.bio.symbol.Symbol)">complement(Symbol)</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/NucleotideTools.html" title="class in org.biojava.bio.seq">NucleotideTools</a></dt>
<dd>
<div class="block">Complement the symbol.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/NucleotideTools.html#complement(org.biojava.bio.symbol.SymbolList)">complement(SymbolList)</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/NucleotideTools.html" title="class in org.biojava.bio.seq">NucleotideTools</a></dt>
<dd>
<div class="block">Retrieve a complement view of list.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/RNATools.html#complement(org.biojava.bio.symbol.Symbol)">complement(Symbol)</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/RNATools.html" title="class in org.biojava.bio.seq">RNATools</a></dt>
<dd>
<div class="block">Complement the symbol.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/RNATools.html#complement(org.biojava.bio.symbol.SymbolList)">complement(SymbolList)</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/RNATools.html" title="class in org.biojava.bio.seq">RNATools</a></dt>
<dd>
<div class="block">Retrieve a complement view of list.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/DNATools.html#complementTable()">complementTable()</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/DNATools.html" title="class in org.biojava.bio.seq">DNATools</a></dt>
<dd>
<div class="block">Get a translation table for complementing DNA symbols.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/NucleotideTools.html#complementTable()">complementTable()</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/NucleotideTools.html" title="class in org.biojava.bio.seq">NucleotideTools</a></dt>
<dd>
<div class="block">Get a translation table for complementing Nucleotide symbols.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/RNATools.html#complementTable()">complementTable()</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/RNATools.html" title="class in org.biojava.bio.seq">RNATools</a></dt>
<dd>
<div class="block">Get a translation table for complementing DNA symbols.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/HMMTrainer.html#completeCycle()">completeCycle()</a></span> - Method in interface org.biojava.bio.dp.<a href="./org/biojava/bio/dp/HMMTrainer.html" title="interface in org.biojava.bio.dp">HMMTrainer</a></dt>
<dd>
<div class="block">indicate that a cycle of training is completed and the
emission/transition matrices should be updated.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/SimpleHMMTrainer.html#completeCycle()">completeCycle()</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/SimpleHMMTrainer.html" title="class in org.biojava.bio.dp">SimpleHMMTrainer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/DAS.html#completedActivity(java.lang.Object)">completedActivity(Object)</a></span> - Static method in class org.biojava.bio.program.das.<a href="./org/biojava/bio/program/das/DAS.html" title="class in org.biojava.bio.program.das">DAS</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ActivityListener.html#completedActivity(java.lang.Object)">completedActivity(Object)</a></span> - Method in interface org.biojava.utils.<a href="./org/biojava/utils/ActivityListener.html" title="interface in org.biojava.utils">ActivityListener</a></dt>
<dd>
<div class="block">Notification that an activity is complete.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#COMPONENT_TAG">COMPONENT_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/ComponentFeature.html" title="interface in org.biojava.bio.seq"><span class="strong">ComponentFeature</span></a> - Interface in <a href="./org/biojava/bio/seq/package-summary.html">org.biojava.bio.seq</a></dt>
<dd>
<div class="block">Feature which represents a component in an assembly (contig).</div>
</dd>
<dt><a href="./org/biojava/bio/seq/ComponentFeature.Template.html" title="class in org.biojava.bio.seq"><span class="strong">ComponentFeature.Template</span></a> - Class in <a href="./org/biojava/bio/seq/package-summary.html">org.biojava.bio.seq</a></dt>
<dd>
<div class="block">Template for constructing a new ComponentFeature.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/ComponentFeature.Template.html#ComponentFeature.Template()">ComponentFeature.Template()</a></span> - Constructor for class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/ComponentFeature.Template.html" title="class in org.biojava.bio.seq">ComponentFeature.Template</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/ComponentFeature.Template.html#componentLocation">componentLocation</a></span> - Variable in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/ComponentFeature.Template.html" title="class in org.biojava.bio.seq">ComponentFeature.Template</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/MergeLocation.html#componentLocationIterator()">componentLocationIterator()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/MergeLocation.html" title="class in org.biojava.bio.symbol">MergeLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/ComponentFeature.Template.html#componentSequence">componentSequence</a></span> - Variable in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/ComponentFeature.Template.html" title="class in org.biojava.bio.seq">ComponentFeature.Template</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/ComponentFeature.Template.html#componentSequenceName">componentSequenceName</a></span> - Variable in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/ComponentFeature.Template.html" title="class in org.biojava.bio.seq">ComponentFeature.Template</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/naming/ObdaContext.html#composeName(javax.naming.Name, javax.naming.Name)">composeName(Name, Name)</a></span> - Method in class org.biojava.naming.<a href="./org/biojava/naming/ObdaContext.html" title="class in org.biojava.naming">ObdaContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/naming/ObdaContext.html#composeName(java.lang.String, java.lang.String)">composeName(String, String)</a></span> - Method in class org.biojava.naming.<a href="./org/biojava/naming/ObdaContext.html" title="class in org.biojava.naming">ObdaContext</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/molbio/Composition.html" title="class in org.biojava.bio.molbio"><span class="strong">Composition</span></a> - Class in <a href="./org/biojava/bio/molbio/package-summary.html">org.biojava.bio.molbio</a></dt>
<dd>
<div class="block">Computes composition statistics about a <code>SymbolList</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/molbio/Composition.html#Composition()">Composition()</a></span> - Constructor for class org.biojava.bio.molbio.<a href="./org/biojava/bio/molbio/Composition.html" title="class in org.biojava.bio.molbio">Composition</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure"><span class="strong">Compound</span></a> - Class in <a href="./org/biojava/bio/structure/package-summary.html">org.biojava.bio.structure</a></dt>
<dd>
<div class="block">Created by IntelliJ IDEA.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Compound.html#Compound()">Compound()</a></span> - Constructor for class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure">Compound</a></dt>
<dd> </dd>
<dt><a href="./org/biojavax/bio/seq/CompoundRichLocation.html" title="class in org.biojavax.bio.seq"><span class="strong">CompoundRichLocation</span></a> - Class in <a href="./org/biojavax/bio/seq/package-summary.html">org.biojavax.bio.seq</a></dt>
<dd>
<div class="block">An implementation of RichLocation which covers multiple locations,
but on the same strand of the same (optionally circular) sequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/CompoundRichLocation.html#CompoundRichLocation(java.util.Collection)">CompoundRichLocation(Collection)</a></span> - Constructor for class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/CompoundRichLocation.html" title="class in org.biojavax.bio.seq">CompoundRichLocation</a></dt>
<dd>
<div class="block">Constructs a CompoundRichLocation from the given set of members, with
the default term of "join".</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/CompoundRichLocation.html#CompoundRichLocation(org.biojavax.ontology.ComparableTerm, java.util.Collection)">CompoundRichLocation(ComparableTerm, Collection)</a></span> - Constructor for class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/CompoundRichLocation.html" title="class in org.biojavax.bio.seq">CompoundRichLocation</a></dt>
<dd>
<div class="block">Constructs a CompoundRichLocation from the given set of members.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/CompoundRichLocation.html#CompoundRichLocation()">CompoundRichLocation()</a></span> - Constructor for class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/CompoundRichLocation.html" title="class in org.biojavax.bio.seq">CompoundRichLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/IsoelectricPointCalc.ChargeCalculator.html#compute(double)">compute(double)</a></span> - Method in class org.biojava.bio.proteomics.<a href="./org/biojava/bio/proteomics/IsoelectricPointCalc.ChargeCalculator.html" title="class in org.biojava.bio.proteomics">IsoelectricPointCalc.ChargeCalculator</a></dt>
<dd>
<div class="block">computes charge at given pH</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/math/ComputeObject.html#compute(double)">compute(double)</a></span> - Method in interface org.biojava.utils.math.<a href="./org/biojava/utils/math/ComputeObject.html" title="interface in org.biojava.utils.math">ComputeObject</a></dt>
<dd>
<div class="block">workhorse method for this class.</div>
</dd>
<dt><a href="./org/biojava/utils/math/ComputeObject.html" title="interface in org.biojava.utils.math"><span class="strong">ComputeObject</span></a> - Interface in <a href="./org/biojava/utils/math/package-summary.html">org.biojava.utils.math</a></dt>
<dd>
<div class="block">interface for classes that return a single
double precision value for a single double
precision argument.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/jama/Matrix.html#cond()">cond()</a></span> - Method in class org.biojava.bio.structure.jama.<a href="./org/biojava/bio/structure/jama/Matrix.html" title="class in org.biojava.bio.structure.jama">Matrix</a></dt>
<dd>
<div class="block">Matrix condition (2 norm)</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/jama/SingularValueDecomposition.html#cond()">cond()</a></span> - Method in class org.biojava.bio.structure.jama.<a href="./org/biojava/bio/structure/jama/SingularValueDecomposition.html" title="class in org.biojava.bio.structure.jama">SingularValueDecomposition</a></dt>
<dd>
<div class="block">Two norm condition number</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/OrderNDistribution.html#conditionedDistributions()">conditionedDistributions()</a></span> - Method in interface org.biojava.bio.dist.<a href="./org/biojava/bio/dist/OrderNDistribution.html" title="interface in org.biojava.bio.dist">OrderNDistribution</a></dt>
<dd>
<div class="block">Get the conditioned distributions.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/directory/SystemRegistry.html#CONFIG_FILE">CONFIG_FILE</a></span> - Static variable in class org.biojava.directory.<a href="./org/biojava/directory/SystemRegistry.html" title="class in org.biojava.directory">SystemRegistry</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/directory/SystemRegistry.html#CONFIG_LOCATOR">CONFIG_LOCATOR</a></span> - Static variable in class org.biojava.directory.<a href="./org/biojava/directory/SystemRegistry.html" title="class in org.biojava.directory">SystemRegistry</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.HibernateFeatureFilter.html#conjunctAdd">conjunctAdd</a></span> - Variable in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.HibernateFeatureFilter.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.HibernateFeatureFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.HibernateFeatureFilter.html#conjunction">conjunction</a></span> - Variable in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.HibernateFeatureFilter.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.HibernateFeatureFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BibRefQuery.html#connect()">connect()</a></span> - Method in interface org.biojava.bibliography.<a href="./org/biojava/bibliography/BibRefQuery.html" title="interface in org.biojava.bibliography">BibRefQuery</a></dt>
<dd>
<div class="block">
It creates a connection to a bibliographic repository, or/and it makes
all necessary initialization steps needed for further communication.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BibRefQuery.html#connect(byte[])">connect(byte[])</a></span> - Method in interface org.biojava.bibliography.<a href="./org/biojava/bibliography/BibRefQuery.html" title="interface in org.biojava.bibliography">BibRefQuery</a></dt>
<dd>
<div class="block">
It creates a connection to a bibliographic repository, or/and it makes
all necessary initialization steps needed for further communication,
and it makes the collection described by <tt>collectionId</tt>
the current collection.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BibRefSupport.html#connect()">connect()</a></span> - Method in interface org.biojava.bibliography.<a href="./org/biojava/bibliography/BibRefSupport.html" title="interface in org.biojava.bibliography">BibRefSupport</a></dt>
<dd>
<div class="block">
It creates a connection to an object providing the supporting
utilities, or/and it makes all necessary initialization steps
needed for further communication.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/candy/CandyFinder.html#connect()">connect()</a></span> - Method in interface org.biojava.utils.candy.<a href="./org/biojava/utils/candy/CandyFinder.html" title="interface in org.biojava.utils.candy">CandyFinder</a></dt>
<dd>
<div class="block">
It creates a connection to an object representing a vocabulary
finder, or/and it makes all necessary initialization steps
needed for further communication.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/ProfileHMM.html#connectModel()">connectModel()</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/ProfileHMM.html" title="class in org.biojava.bio.dp">ProfileHMM</a></dt>
<dd>
<div class="block">This is called by constructor in setting up the allowed transitions in the model</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/hmmer/HmmerProfileHMM.html#connectModel()">connectModel()</a></span> - Method in class org.biojava.bio.program.hmmer.<a href="./org/biojava/bio/program/hmmer/HmmerProfileHMM.html" title="class in org.biojava.bio.program.hmmer">HmmerProfileHMM</a></dt>
<dd>
<div class="block">This is called by constructor in setting up the allowed transitions in the model</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/RichObjectFactory.html#connectToBioSQL(java.lang.Object)">connectToBioSQL(Object)</a></span> - Static method in class org.biojavax.<a href="./org/biojavax/RichObjectFactory.html" title="class in org.biojavax">RichObjectFactory</a></dt>
<dd>
<div class="block">A utility method that configures the RichObjectFactory for use with a Hibernate session.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLFormat.html#CONSORTIUM_TAG">CONSORTIUM_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLFormat.html" title="class in org.biojavax.bio.seq.io">EMBLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html#CONSORTIUM_TAG">CONSORTIUM_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html" title="class in org.biojavax.bio.seq.io">EMBLxmlFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/GenbankFormat.html#CONSORTIUM_TAG">CONSORTIUM_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/GenbankFormat.html" title="class in org.biojavax.bio.seq.io">GenbankFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/INSDseqFormat.html#CONSORTIUM_TAG">CONSORTIUM_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/INSDseqFormat.html" title="class in org.biojavax.bio.seq.io">INSDseqFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtFormat.html#CONSORTIUM_TAG">CONSORTIUM_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtFormat.html" title="class in org.biojavax.bio.seq.io">UniProtFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#CONSORTIUM_TAG">CONSORTIUM_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/utils/Constants.html" title="class in org.biojava.utils"><span class="strong">Constants</span></a> - Class in <a href="./org/biojava/utils/package-summary.html">org.biojava.utils</a></dt>
<dd>
<div class="block">Some usefull constants for working with binary files.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/Constants.html#Constants()">Constants()</a></span> - Constructor for class org.biojava.utils.<a href="./org/biojava/utils/Constants.html" title="class in org.biojava.utils">Constants</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichLocation.Tools.html#construct(java.util.Collection)">construct(Collection<Location>)</a></span> - Static method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichLocation.Tools.html" title="class in org.biojavax.bio.seq">RichLocation.Tools</a></dt>
<dd>
<div class="block">Constructs a RichLocation object based on the given collection of
members.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/automata/DfaBuilder.html#constructSubsets()">constructSubsets()</a></span> - Method in class org.biojava.utils.automata.<a href="./org/biojava/utils/automata/DfaBuilder.html" title="class in org.biojava.utils.automata">DfaBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/jama/Matrix.html#constructWithCopy(double[][])">constructWithCopy(double[][])</a></span> - Static method in class org.biojava.bio.structure.jama.<a href="./org/biojava/bio/structure/jama/Matrix.html" title="class in org.biojava.bio.structure.jama">Matrix</a></dt>
<dd>
<div class="block">Construct a matrix from a copy of a 2-D array.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FilterUtils.html#containedByLocation(org.biojava.bio.symbol.Location)">containedByLocation(Location)</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FilterUtils.html" title="class in org.biojava.bio.seq">FilterUtils</a></dt>
<dd>
<div class="block">Construct a filter which matches features with locations wholly contained
by the specified <code>Location</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/AbstractOrthoPairCollection.html#contains(org.biojava.bio.program.homologene.OrthoPairSet)">contains(OrthoPairSet)</a></span> - Method in class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/AbstractOrthoPairCollection.html" title="class in org.biojava.bio.program.homologene">AbstractOrthoPairCollection</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/OrthoPairCollection.html#contains(org.biojava.bio.program.homologene.OrthoPairSet)">contains(OrthoPairSet)</a></span> - Method in interface org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/OrthoPairCollection.html" title="interface in org.biojava.bio.program.homologene">OrthoPairCollection</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/SimpleOrthoPairCollection.html#contains(org.biojava.bio.program.homologene.OrthoPairSet)">contains(OrthoPairSet)</a></span> - Method in class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/SimpleOrthoPairCollection.html" title="class in org.biojava.bio.program.homologene">SimpleOrthoPairCollection</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AbstractAlphabet.html#contains(org.biojava.bio.symbol.Symbol)">contains(Symbol)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AbstractAlphabet.html" title="class in org.biojava.bio.symbol">AbstractAlphabet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AbstractLocation.html#contains(org.biojava.bio.symbol.Location)">contains(Location)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AbstractLocation.html" title="class in org.biojava.bio.symbol">AbstractLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AbstractLocationDecorator.html#contains(org.biojava.bio.symbol.Location)">contains(Location)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AbstractLocationDecorator.html" title="class in org.biojava.bio.symbol">AbstractLocationDecorator</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AbstractLocationDecorator.html#contains(int)">contains(int)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AbstractLocationDecorator.html" title="class in org.biojava.bio.symbol">AbstractLocationDecorator</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AbstractRangeLocation.html#contains(int)">contains(int)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AbstractRangeLocation.html" title="class in org.biojava.bio.symbol">AbstractRangeLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/Alphabet.html#contains(org.biojava.bio.symbol.Symbol)">contains(Symbol)</a></span> - Method in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/Alphabet.html" title="interface in org.biojava.bio.symbol">Alphabet</a></dt>
<dd>
<div class="block">
Returns whether or not this Alphabet contains the symbol.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/CircularLocation.html#contains(int)">contains(int)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/CircularLocation.html" title="class in org.biojava.bio.symbol">CircularLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/CircularLocation.html#contains(org.biojava.bio.symbol.Location)">contains(Location)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/CircularLocation.html" title="class in org.biojava.bio.symbol">CircularLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/DoubleAlphabet.html#contains(org.biojava.bio.symbol.Symbol)">contains(Symbol)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/DoubleAlphabet.html" title="class in org.biojava.bio.symbol">DoubleAlphabet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/DoubleAlphabet.SubDoubleAlphabet.html#contains(org.biojava.bio.symbol.Symbol)">contains(Symbol)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/DoubleAlphabet.SubDoubleAlphabet.html" title="class in org.biojava.bio.symbol">DoubleAlphabet.SubDoubleAlphabet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/FuzzyPointLocation.html#contains(org.biojava.bio.symbol.Location)">contains(Location)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/FuzzyPointLocation.html" title="class in org.biojava.bio.symbol">FuzzyPointLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/FuzzyPointLocation.html#contains(int)">contains(int)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/FuzzyPointLocation.html" title="class in org.biojava.bio.symbol">FuzzyPointLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/IntegerAlphabet.html#contains(org.biojava.bio.symbol.Symbol)">contains(Symbol)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/IntegerAlphabet.html" title="class in org.biojava.bio.symbol">IntegerAlphabet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/Location.html#contains(org.biojava.bio.symbol.Location)">contains(Location)</a></span> - Method in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/Location.html" title="interface in org.biojava.bio.symbol">Location</a></dt>
<dd>
<div class="block">Checks if this location contains the other.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/Location.html#contains(int)">contains(int)</a></span> - Method in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/Location.html" title="interface in org.biojava.bio.symbol">Location</a></dt>
<dd>
<div class="block">Checks if this location contains a point.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/LocationTools.html#contains(org.biojava.bio.symbol.Location, org.biojava.bio.symbol.Location)">contains(Location, Location)</a></span> - Static method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/LocationTools.html" title="class in org.biojava.bio.symbol">LocationTools</a></dt>
<dd>
<div class="block">Return <code>true</code> iff all indices in <code>locB</code> are also contained
by <code>locA</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/PointLocation.html#contains(int)">contains(int)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/PointLocation.html" title="class in org.biojava.bio.symbol">PointLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SoftMaskedAlphabet.html#contains(org.biojava.bio.symbol.Symbol)">contains(Symbol)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SoftMaskedAlphabet.html" title="class in org.biojava.bio.symbol">SoftMaskedAlphabet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/candy/CandyVocabulary.html#contains(java.lang.String)">contains(String)</a></span> - Method in interface org.biojava.utils.candy.<a href="./org/biojava/utils/candy/CandyVocabulary.html" title="interface in org.biojava.utils.candy">CandyVocabulary</a></dt>
<dd>
<div class="block">It checks if a given entry exists in this vocabulary.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/MergingSet.html#contains(java.lang.Object)">contains(Object)</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/MergingSet.html" title="class in org.biojava.utils">MergingSet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/SmallSet.html#contains(java.lang.Object)">contains(Object)</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/SmallSet.html" title="class in org.biojava.utils">SmallSet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/CompoundRichLocation.html#contains(int)">contains(int)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/CompoundRichLocation.html" title="class in org.biojavax.bio.seq">CompoundRichLocation</a></dt>
<dd>
<div class="block">Checks if this location contains a point.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/CompoundRichLocation.html#contains(org.biojava.bio.symbol.Location)">contains(Location)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/CompoundRichLocation.html" title="class in org.biojavax.bio.seq">CompoundRichLocation</a></dt>
<dd>
<div class="block">Checks if this location contains the other.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/EmptyRichLocation.html#contains(int)">contains(int)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/EmptyRichLocation.html" title="class in org.biojavax.bio.seq">EmptyRichLocation</a></dt>
<dd>
<div class="block">Checks if this location contains a point.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/EmptyRichLocation.html#contains(org.biojava.bio.symbol.Location)">contains(Location)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/EmptyRichLocation.html" title="class in org.biojavax.bio.seq">EmptyRichLocation</a></dt>
<dd>
<div class="block">Checks if this location contains the other.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichLocation.html#contains(int)">contains(int)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichLocation.html" title="class in org.biojavax.bio.seq">SimpleRichLocation</a></dt>
<dd>
<div class="block">Checks if this location contains a point.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichLocation.html#contains(org.biojava.bio.symbol.Location)">contains(Location)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichLocation.html" title="class in org.biojavax.bio.seq">SimpleRichLocation</a></dt>
<dd>
<div class="block">Checks if this location contains the other.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/EmptyRichAnnotation.html#contains(org.biojavax.Note)">contains(Note)</a></span> - Method in class org.biojavax.<a href="./org/biojavax/EmptyRichAnnotation.html" title="class in org.biojavax">EmptyRichAnnotation</a></dt>
<dd>
<div class="block">Returns true if the given note exists in this annotation.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ga/util/WeightedSet.html#contains(java.lang.Object)">contains(Object)</a></span> - Method in class org.biojavax.ga.util.<a href="./org/biojavax/ga/util/WeightedSet.html" title="class in org.biojavax.ga.util">WeightedSet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/RichAnnotation.html#contains(org.biojavax.Note)">contains(Note)</a></span> - Method in interface org.biojavax.<a href="./org/biojavax/RichAnnotation.html" title="interface in org.biojavax">RichAnnotation</a></dt>
<dd>
<div class="block">Returns true if the given note exists in this annotation.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleRichAnnotation.html#contains(org.biojavax.Note)">contains(Note)</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleRichAnnotation.html" title="class in org.biojavax">SimpleRichAnnotation</a></dt>
<dd>
<div class="block">Returns true if the given note exists in this annotation.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.Terms.html#CONTAINS_PREFIX">CONTAINS_PREFIX</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.Terms.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat.Terms</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/util/WeightedSet.html#containsAll(java.util.Collection)">containsAll(Collection)</a></span> - Method in class org.biojavax.ga.util.<a href="./org/biojavax/ga/util/WeightedSet.html" title="class in org.biojavax.ga.util">WeightedSet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/DASSequence.html#containsFeature(org.biojava.bio.seq.Feature)">containsFeature(Feature)</a></span> - Method in class org.biojava.bio.program.das.<a href="./org/biojava/bio/program/das/DASSequence.html" title="class in org.biojava.bio.program.das">DASSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureHolder.html#containsFeature(org.biojava.bio.seq.Feature)">containsFeature(Feature)</a></span> - Method in interface org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureHolder.html" title="interface in org.biojava.bio.seq">FeatureHolder</a></dt>
<dd>
<div class="block">Check if the feature is present in this holder.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureHolder.EmptyFeatureHolder.html#containsFeature(org.biojava.bio.seq.Feature)">containsFeature(Feature)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureHolder.EmptyFeatureHolder.html" title="class in org.biojava.bio.seq">FeatureHolder.EmptyFeatureHolder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/DummySequence.html#containsFeature(org.biojava.bio.seq.Feature)">containsFeature(Feature)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/DummySequence.html" title="class in org.biojava.bio.seq.impl">DummySequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/LazyFilterFeatureHolder.html#containsFeature(org.biojava.bio.seq.Feature)">containsFeature(Feature)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/LazyFilterFeatureHolder.html" title="class in org.biojava.bio.seq.impl">LazyFilterFeatureHolder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/RevCompSequence.html#containsFeature(org.biojava.bio.seq.Feature)">containsFeature(Feature)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/RevCompSequence.html" title="class in org.biojava.bio.seq.impl">RevCompSequence</a></dt>
<dd>
<div class="block">containsFeature() will return true if this seq contains the feature in question, or
if if the original (non reverse complement) sequence contains the feature;</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleFeature.html#containsFeature(org.biojava.bio.seq.Feature)">containsFeature(Feature)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleFeature.html" title="class in org.biojava.bio.seq.impl">SimpleFeature</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleGappedSequence.html#containsFeature(org.biojava.bio.seq.Feature)">containsFeature(Feature)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleGappedSequence.html" title="class in org.biojava.bio.seq.impl">SimpleGappedSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleSequence.html#containsFeature(org.biojava.bio.seq.Feature)">containsFeature(Feature)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleSequence.html" title="class in org.biojava.bio.seq.impl">SimpleSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SubSequence.html#containsFeature(org.biojava.bio.seq.Feature)">containsFeature(Feature)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SubSequence.html" title="class in org.biojava.bio.seq.impl">SubSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/ViewSequence.html#containsFeature(org.biojava.bio.seq.Feature)">containsFeature(Feature)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/ViewSequence.html" title="class in org.biojava.bio.seq.impl">ViewSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/LazyFeatureHolder.html#containsFeature(org.biojava.bio.seq.Feature)">containsFeature(Feature)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/LazyFeatureHolder.html" title="class in org.biojava.bio.seq">LazyFeatureHolder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/MergeFeatureHolder.html#containsFeature(org.biojava.bio.seq.Feature)">containsFeature(Feature)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/MergeFeatureHolder.html" title="class in org.biojava.bio.seq">MergeFeatureHolder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/NewSimpleAssembly.html#containsFeature(org.biojava.bio.seq.Feature)">containsFeature(Feature)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/NewSimpleAssembly.html" title="class in org.biojava.bio.seq">NewSimpleAssembly</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/projection/ProjectedFeature.html#containsFeature(org.biojava.bio.seq.Feature)">containsFeature(Feature)</a></span> - Method in class org.biojava.bio.seq.projection.<a href="./org/biojava/bio/seq/projection/ProjectedFeature.html" title="class in org.biojava.bio.seq.projection">ProjectedFeature</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/projection/ProjectedFeatureHolder.html#containsFeature(org.biojava.bio.seq.Feature)">containsFeature(Feature)</a></span> - Method in class org.biojava.bio.seq.projection.<a href="./org/biojava/bio/seq/projection/ProjectedFeatureHolder.html" title="class in org.biojava.bio.seq.projection">ProjectedFeatureHolder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/SimpleAssembly.html#containsFeature(org.biojava.bio.seq.Feature)">containsFeature(Feature)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/SimpleAssembly.html" title="class in org.biojava.bio.seq">SimpleAssembly</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/SimpleFeatureHolder.html#containsFeature(org.biojava.bio.seq.Feature)">containsFeature(Feature)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/SimpleFeatureHolder.html" title="class in org.biojava.bio.seq">SimpleFeatureHolder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichFeature.html#containsFeature(org.biojava.bio.seq.Feature)">containsFeature(Feature)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichFeature.html" title="class in org.biojavax.bio.seq">SimpleRichFeature</a></dt>
<dd>
<div class="block">Check if the feature is present in this holder.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/ThinRichSequence.html#containsFeature(org.biojava.bio.seq.Feature)">containsFeature(Feature)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/ThinRichSequence.html" title="class in org.biojavax.bio.seq">ThinRichSequence</a></dt>
<dd>
<div class="block">Check if the feature is present in this holder.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/GlyphFeatureRenderer.html#containsFilter(org.biojava.bio.seq.FeatureFilter)">containsFilter(FeatureFilter)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/GlyphFeatureRenderer.html" title="class in org.biojava.bio.gui.sequence">GlyphFeatureRenderer</a></dt>
<dd>
<div class="block">Returns true if the given <a href="./org/biojava/bio/seq/FeatureFilter.html" title="interface in org.biojava.bio.seq"><code>FeatureFilter</code></a> is already contained in this
renderer.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AbstractAlphabet.html#containsImpl(org.biojava.bio.symbol.AtomicSymbol)">containsImpl(AtomicSymbol)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AbstractAlphabet.html" title="class in org.biojava.bio.symbol">AbstractAlphabet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/IntegerAlphabet.SubIntegerAlphabet.html#containsImpl(org.biojava.bio.symbol.AtomicSymbol)">containsImpl(AtomicSymbol)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/IntegerAlphabet.SubIntegerAlphabet.html" title="class in org.biojava.bio.symbol">IntegerAlphabet.SubIntegerAlphabet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleAlphabet.html#containsImpl(org.biojava.bio.symbol.AtomicSymbol)">containsImpl(AtomicSymbol)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleAlphabet.html" title="class in org.biojava.bio.symbol">SimpleAlphabet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SingletonAlphabet.html#containsImpl(org.biojava.bio.symbol.AtomicSymbol)">containsImpl(AtomicSymbol)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SingletonAlphabet.html" title="class in org.biojava.bio.symbol">SingletonAlphabet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/cache/WeakValueHashMap.html#containsKey(java.lang.Object)">containsKey(Object)</a></span> - Method in class org.biojava.utils.cache.<a href="./org/biojava/utils/cache/WeakValueHashMap.html" title="class in org.biojava.utils.cache">WeakValueHashMap</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/OverlayMap.html#containsKey(java.lang.Object)">containsKey(Object)</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/OverlayMap.html" title="class in org.biojava.utils">OverlayMap</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/SmallMap.html#containsKey(java.lang.Object)">containsKey(Object)</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/SmallMap.html" title="class in org.biojava.utils">SmallMap</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/taxa/NCBITaxon.html#containsName(java.lang.String, java.lang.String)">containsName(String, String)</a></span> - Method in interface org.biojavax.bio.taxa.<a href="./org/biojavax/bio/taxa/NCBITaxon.html" title="interface in org.biojavax.bio.taxa">NCBITaxon</a></dt>
<dd>
<div class="block">Tests for the presence of a name in a given class.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/taxa/SimpleNCBITaxon.html#containsName(java.lang.String, java.lang.String)">containsName(String, String)</a></span> - Method in class org.biojavax.bio.taxa.<a href="./org/biojavax/bio/taxa/SimpleNCBITaxon.html" title="class in org.biojavax.bio.taxa">SimpleNCBITaxon</a></dt>
<dd>
<div class="block">Tests for the presence of a name in a given class.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/automata/Nfa.html#containsNode(org.biojava.utils.automata.FiniteAutomaton.Node)">containsNode(FiniteAutomaton.Node)</a></span> - Method in class org.biojava.utils.automata.<a href="./org/biojava/utils/automata/Nfa.html" title="class in org.biojava.utils.automata">Nfa</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/AbstractAnnotation.html#containsProperty(java.lang.Object)">containsProperty(Object)</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/AbstractAnnotation.html" title="class in org.biojava.bio">AbstractAnnotation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/Annotation.html#containsProperty(java.lang.Object)">containsProperty(Object)</a></span> - Method in interface org.biojava.bio.<a href="./org/biojava/bio/Annotation.html" title="interface in org.biojava.bio">Annotation</a></dt>
<dd>
<div class="block">Returns whether there the property is defined.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/MergeAnnotation.html#containsProperty(java.lang.Object)">containsProperty(Object)</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/MergeAnnotation.html" title="class in org.biojava.bio">MergeAnnotation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/OverlayAnnotation.html#containsProperty(java.lang.Object)">containsProperty(Object)</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/OverlayAnnotation.html" title="class in org.biojava.bio">OverlayAnnotation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/EmptyRichAnnotation.html#containsProperty(java.lang.Object)">containsProperty(Object)</a></span> - Method in class org.biojavax.<a href="./org/biojavax/EmptyRichAnnotation.html" title="class in org.biojavax">EmptyRichAnnotation</a></dt>
<dd>
<div class="block">Returns whether there the property is defined.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleRichAnnotation.html#containsProperty(java.lang.Object)">containsProperty(Object)</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleRichAnnotation.html" title="class in org.biojavax">SimpleRichAnnotation</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span> </div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/biosql/DBHelper.html#containsTable(javax.sql.DataSource, java.lang.String)">containsTable(DataSource, String)</a></span> - Method in class org.biojava.bio.seq.db.biosql.<a href="./org/biojava/bio/seq/db/biosql/DBHelper.html" title="class in org.biojava.bio.seq.db.biosql">DBHelper</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Detects whether a particular table is present in the database.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/biosql/HypersonicDBHelper.html#containsTable(javax.sql.DataSource, java.lang.String)">containsTable(DataSource, String)</a></span> - Method in class org.biojava.bio.seq.db.biosql.<a href="./org/biojava/bio/seq/db/biosql/HypersonicDBHelper.html" title="class in org.biojava.bio.seq.db.biosql">HypersonicDBHelper</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/biosql/OracleDBHelper.html#containsTable(javax.sql.DataSource, java.lang.String)">containsTable(DataSource, String)</a></span> - Method in class org.biojava.bio.seq.db.biosql.<a href="./org/biojava/bio/seq/db/biosql/OracleDBHelper.html" title="class in org.biojava.bio.seq.db.biosql">OracleDBHelper</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/IntegerOntology.html#containsTerm(java.lang.String)">containsTerm(String)</a></span> - Method in class org.biojava.ontology.<a href="./org/biojava/ontology/IntegerOntology.html" title="class in org.biojava.ontology">IntegerOntology</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/Ontology.html#containsTerm(java.lang.String)">containsTerm(String)</a></span> - Method in interface org.biojava.ontology.<a href="./org/biojava/ontology/Ontology.html" title="interface in org.biojava.ontology">Ontology</a></dt>
<dd>
<div class="block">Determines if this ontology currently contains a term named <code>name</code></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/Ontology.Impl.html#containsTerm(java.lang.String)">containsTerm(String)</a></span> - Method in class org.biojava.ontology.<a href="./org/biojava/ontology/Ontology.Impl.html" title="class in org.biojava.ontology">Ontology.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ontology/SimpleComparableOntology.html#containsTerm(java.lang.String)">containsTerm(String)</a></span> - Method in class org.biojavax.ontology.<a href="./org/biojavax/ontology/SimpleComparableOntology.html" title="class in org.biojavax.ontology">SimpleComparableOntology</a></dt>
<dd>
<div class="block">Determines if this ontology currently contains a term named <code>name</code></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/MarkovModel.html#containsTransition(org.biojava.bio.dp.State, org.biojava.bio.dp.State)">containsTransition(State, State)</a></span> - Method in interface org.biojava.bio.dp.<a href="./org/biojava/bio/dp/MarkovModel.html" title="interface in org.biojava.bio.dp">MarkovModel</a></dt>
<dd>
<div class="block">Returns wether a transition exists or not.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/SimpleMarkovModel.html#containsTransition(org.biojava.bio.dp.State, org.biojava.bio.dp.State)">containsTransition(State, State)</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/SimpleMarkovModel.html" title="class in org.biojava.bio.dp">SimpleMarkovModel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/WMAsMM.html#containsTransition(org.biojava.bio.dp.State, org.biojava.bio.dp.State)">containsTransition(State, State)</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/WMAsMM.html" title="class in org.biojava.bio.dp">WMAsMM</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/IntegerOntology.html#containsTriple(org.biojava.ontology.Term, org.biojava.ontology.Term, org.biojava.ontology.Term)">containsTriple(Term, Term, Term)</a></span> - Method in class org.biojava.ontology.<a href="./org/biojava/ontology/IntegerOntology.html" title="class in org.biojava.ontology">IntegerOntology</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/Ontology.html#containsTriple(org.biojava.ontology.Term, org.biojava.ontology.Term, org.biojava.ontology.Term)">containsTriple(Term, Term, Term)</a></span> - Method in interface org.biojava.ontology.<a href="./org/biojava/ontology/Ontology.html" title="interface in org.biojava.ontology">Ontology</a></dt>
<dd>
<div class="block">See if a triple exists in this ontology</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/Ontology.Impl.html#containsTriple(org.biojava.ontology.Term, org.biojava.ontology.Term, org.biojava.ontology.Term)">containsTriple(Term, Term, Term)</a></span> - Method in class org.biojava.ontology.<a href="./org/biojava/ontology/Ontology.Impl.html" title="class in org.biojava.ontology">Ontology.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ontology/SimpleComparableOntology.html#containsTriple(org.biojava.ontology.Term, org.biojava.ontology.Term, org.biojava.ontology.Term)">containsTriple(Term, Term, Term)</a></span> - Method in class org.biojavax.ontology.<a href="./org/biojavax/ontology/SimpleComparableOntology.html" title="class in org.biojavax.ontology">SimpleComparableOntology</a></dt>
<dd>
<div class="block">See if a triple exists in this ontology</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/Alignment.html#CONTENT">CONTENT</a></span> - Static variable in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/Alignment.html" title="interface in org.biojava.bio.symbol">Alignment</a></dt>
<dd>
<div class="block">Signals that SymbolLists will be added to or removed from an alignment.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/AlignmentRenderer.html#contextForLabel(org.biojava.bio.gui.sequence.SequenceRenderContext, java.lang.Object)">contextForLabel(SequenceRenderContext, Object)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/AlignmentRenderer.html" title="class in org.biojava.bio.gui.sequence">AlignmentRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLFormat.html#CONTIG_TAG">CONTIG_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLFormat.html" title="class in org.biojavax.bio.seq.io">EMBLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html#CONTIG_TAG">CONTIG_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html" title="class in org.biojavax.bio.seq.io">EMBLxmlFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/INSDseqFormat.html#CONTIG_TAG">CONTIG_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/INSDseqFormat.html" title="class in org.biojavax.bio.seq.io">INSDseqFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BibRef.html#contributors">contributors</a></span> - Variable in class org.biojava.bibliography.<a href="./org/biojava/bibliography/BibRef.html" title="class in org.biojava.bibliography">BibRef</a></dt>
<dd>
<div class="block">
The authors and contributors are responsible for creating the contents of the cited resource.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/BlastLikeToXMLConverter.html#convert()">convert()</a></span> - Method in class org.biojava.bio.program.<a href="./org/biojava/bio/program/BlastLikeToXMLConverter.html" title="class in org.biojava.bio.program">BlastLikeToXMLConverter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/PdbToXMLConverter.html#convert()">convert()</a></span> - Method in class org.biojava.bio.program.<a href="./org/biojava/bio/program/PdbToXMLConverter.html" title="class in org.biojava.bio.program">PdbToXMLConverter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.Tools.html#convert(org.biojava.bio.seq.FeatureFilter)">convert(FeatureFilter)</a></span> - Static method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.Tools.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.Tools</a></dt>
<dd>
<div class="block">Convert a non-BioSQL FeatureFilter into a BioSQL one.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/StructureTools.html#convert_3code_1code(java.lang.String)">convert_3code_1code(String)</a></span> - Static method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/StructureTools.html" title="class in org.biojava.bio.structure">StructureTools</a></dt>
<dd>
<div class="block">convert three character amino acid codes into single character
e.g.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/FeatureTree.html#convertValueToText(java.lang.Object, boolean, boolean, boolean, int, boolean)">convertValueToText(Object, boolean, boolean, boolean, int, boolean)</a></span> - Method in class org.biojava.bio.gui.<a href="./org/biojava/bio/gui/FeatureTree.html" title="class in org.biojava.bio.gui">FeatureTree</a></dt>
<dd>
<div class="block">Labels <code>Sequence</code> objects with their name, <code>Annotations</code> with
the tag Annotations, <code>Features</code> with the tag Features and other objects
with the <code>toString</code> value.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/EmblLikeFormat.html#COORDINATE_TAG">COORDINATE_TAG</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/EmblLikeFormat.html" title="class in org.biojava.bio.seq.io">EmblLikeFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/GenbankFormat.html#COORDINATE_TAG">COORDINATE_TAG</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/GenbankFormat.html" title="class in org.biojava.bio.seq.io">GenbankFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/CrosshairRenderer.html#coordinateDisplayOn(boolean)">coordinateDisplayOn(boolean)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/CrosshairRenderer.html" title="class in org.biojava.bio.gui.sequence">CrosshairRenderer</a></dt>
<dd>
<div class="block"><code>coordinateDisplayOn</code> toggles the display of
sequence coordinates.</div>
</dd>
<dt><a href="./org/biojava/bio/structure/gui/util/CoordManager.html" title="class in org.biojava.bio.structure.gui.util"><span class="strong">CoordManager</span></a> - Class in <a href="./org/biojava/bio/structure/gui/util/package-summary.html">org.biojava.bio.structure.gui.util</a></dt>
<dd>
<div class="block">a class that manages the conversion of sequence coordinate system to
JPanel drawing coordinates</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/util/CoordManager.html#CoordManager()">CoordManager()</a></span> - Constructor for class org.biojava.bio.structure.gui.util.<a href="./org/biojava/bio/structure/gui/util/CoordManager.html" title="class in org.biojava.bio.structure.gui.util">CoordManager</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/jama/Matrix.html#copy()">copy()</a></span> - Method in class org.biojava.bio.structure.jama.<a href="./org/biojava/bio/structure/jama/Matrix.html" title="class in org.biojava.bio.structure.jama">Matrix</a></dt>
<dd>
<div class="block">Make a deep copy of a matrix</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#COPYRIGHT_TAG">COPYRIGHT_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BiblioWebResource.html#cost">cost</a></span> - Variable in class org.biojava.bibliography.<a href="./org/biojava/bibliography/BiblioWebResource.html" title="class in org.biojava.bibliography">BiblioWebResource</a></dt>
<dd>
<div class="block">The cost of accessing the resource.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/NeedlemanWunsch.html#CostMatrix">CostMatrix</a></span> - Variable in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/NeedlemanWunsch.html" title="class in org.biojava.bio.alignment">NeedlemanWunsch</a></dt>
<dd>
<div class="block">A matrix with the size length(sequence1) times length(sequence2)</div>
</dd>
<dt><a href="./org/biojava/bio/dist/Count.html" title="interface in org.biojava.bio.dist"><span class="strong">Count</span></a> - Interface in <a href="./org/biojava/bio/dist/package-summary.html">org.biojava.bio.dist</a></dt>
<dd>
<div class="block">
An encapsulation of a count over the Symbols within an alphabet.</div>
</dd>
<dt><a href="./org/biojava/utils/io/CountedBufferedReader.html" title="class in org.biojava.utils.io"><span class="strong">CountedBufferedReader</span></a> - Class in <a href="./org/biojava/utils/io/package-summary.html">org.biojava.utils.io</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/io/CountedBufferedReader.html#CountedBufferedReader(java.io.Reader)">CountedBufferedReader(Reader)</a></span> - Constructor for class org.biojava.utils.io.<a href="./org/biojava/utils/io/CountedBufferedReader.html" title="class in org.biojava.utils.io">CountedBufferedReader</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/DASSequence.html#countFeatures()">countFeatures()</a></span> - Method in class org.biojava.bio.program.das.<a href="./org/biojava/bio/program/das/DASSequence.html" title="class in org.biojava.bio.program.das">DASSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureHolder.html#countFeatures()">countFeatures()</a></span> - Method in interface org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureHolder.html" title="interface in org.biojava.bio.seq">FeatureHolder</a></dt>
<dd>
<div class="block">Count how many features are contained.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureHolder.EmptyFeatureHolder.html#countFeatures()">countFeatures()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureHolder.EmptyFeatureHolder.html" title="class in org.biojava.bio.seq">FeatureHolder.EmptyFeatureHolder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/DummySequence.html#countFeatures()">countFeatures()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/DummySequence.html" title="class in org.biojava.bio.seq.impl">DummySequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/LazyFilterFeatureHolder.html#countFeatures()">countFeatures()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/LazyFilterFeatureHolder.html" title="class in org.biojava.bio.seq.impl">LazyFilterFeatureHolder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/RevCompSequence.html#countFeatures()">countFeatures()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/RevCompSequence.html" title="class in org.biojava.bio.seq.impl">RevCompSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleFeature.html#countFeatures()">countFeatures()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleFeature.html" title="class in org.biojava.bio.seq.impl">SimpleFeature</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleGappedSequence.html#countFeatures()">countFeatures()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleGappedSequence.html" title="class in org.biojava.bio.seq.impl">SimpleGappedSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleSequence.html#countFeatures()">countFeatures()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleSequence.html" title="class in org.biojava.bio.seq.impl">SimpleSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SubSequence.html#countFeatures()">countFeatures()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SubSequence.html" title="class in org.biojava.bio.seq.impl">SubSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/ViewSequence.html#countFeatures()">countFeatures()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/ViewSequence.html" title="class in org.biojava.bio.seq.impl">ViewSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/LazyFeatureHolder.html#countFeatures()">countFeatures()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/LazyFeatureHolder.html" title="class in org.biojava.bio.seq">LazyFeatureHolder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/MergeFeatureHolder.html#countFeatures()">countFeatures()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/MergeFeatureHolder.html" title="class in org.biojava.bio.seq">MergeFeatureHolder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/NewSimpleAssembly.html#countFeatures()">countFeatures()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/NewSimpleAssembly.html" title="class in org.biojava.bio.seq">NewSimpleAssembly</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/projection/ProjectedFeature.html#countFeatures()">countFeatures()</a></span> - Method in class org.biojava.bio.seq.projection.<a href="./org/biojava/bio/seq/projection/ProjectedFeature.html" title="class in org.biojava.bio.seq.projection">ProjectedFeature</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/projection/ProjectedFeatureHolder.html#countFeatures()">countFeatures()</a></span> - Method in class org.biojava.bio.seq.projection.<a href="./org/biojava/bio/seq/projection/ProjectedFeatureHolder.html" title="class in org.biojava.bio.seq.projection">ProjectedFeatureHolder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/SimpleAssembly.html#countFeatures()">countFeatures()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/SimpleAssembly.html" title="class in org.biojava.bio.seq">SimpleAssembly</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/SimpleFeatureHolder.html#countFeatures()">countFeatures()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/SimpleFeatureHolder.html" title="class in org.biojava.bio.seq">SimpleFeatureHolder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichFeature.html#countFeatures()">countFeatures()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichFeature.html" title="class in org.biojavax.bio.seq">SimpleRichFeature</a></dt>
<dd>
<div class="block">Count how many features are contained.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/ThinRichSequence.html#countFeatures()">countFeatures()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/ThinRichSequence.html" title="class in org.biojavax.bio.seq">ThinRichSequence</a></dt>
<dd>
<div class="block">Count how many features are contained.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/Count.html#COUNTS">COUNTS</a></span> - Static variable in interface org.biojava.bio.dist.<a href="./org/biojava/bio/dist/Count.html" title="interface in org.biojava.bio.dist">Count</a></dt>
<dd>
<div class="block">
Whenever a component count changes the values that would be returned by
getCount, they should fire a ChangeEvent with this object as the type.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/DistributionTools.html#countToDistribution(org.biojava.bio.dist.Count)">countToDistribution(Count)</a></span> - Static method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/DistributionTools.html" title="class in org.biojava.bio.dist">DistributionTools</a></dt>
<dd>
<div class="block">Make a distribution from a count.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BibRef.html#coverage">coverage</a></span> - Variable in class org.biojava.bibliography.<a href="./org/biojava/bibliography/BibRef.html" title="class in org.biojava.bibliography">BibRef</a></dt>
<dd>
<div class="block">It defines an extent or scope of the content of the cited resource.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/LocationTools.html#coverage(org.biojava.bio.symbol.Location)">coverage(Location)</a></span> - Static method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/LocationTools.html" title="class in org.biojava.bio.symbol">LocationTools</a></dt>
<dd>
<div class="block">Return the number of positions which are covered by a <code>Location</code></div>
</dd>
<dt><a href="./org/biojavax/utils/CRC64Checksum.html" title="class in org.biojavax.utils"><span class="strong">CRC64Checksum</span></a> - Class in <a href="./org/biojavax/utils/package-summary.html">org.biojavax.utils</a></dt>
<dd>
<div class="block">Utility class that calculates a CRC64 checksum on a stream of bytes.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/utils/CRC64Checksum.html#CRC64Checksum()">CRC64Checksum()</a></span> - Constructor for class org.biojavax.utils.<a href="./org/biojavax/utils/CRC64Checksum.html" title="class in org.biojavax.utils">CRC64Checksum</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/ChromatogramFactory.html#create(java.io.File)">create(File)</a></span> - Static method in class org.biojava.bio.chromatogram.<a href="./org/biojava/bio/chromatogram/ChromatogramFactory.html" title="class in org.biojava.bio.chromatogram">ChromatogramFactory</a></dt>
<dd>
<div class="block">Creates a new <code>Chromatogram</code> object from the named file.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/ChromatogramFactory.html#create(java.io.InputStream)">create(InputStream)</a></span> - Static method in class org.biojava.bio.chromatogram.<a href="./org/biojava/bio/chromatogram/ChromatogramFactory.html" title="class in org.biojava.bio.chromatogram">ChromatogramFactory</a></dt>
<dd>
<div class="block">Creates a new <code>Chromatogram</code> object from the supplied stream.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/abi/ABIFChromatogram.html#create(java.io.File)">create(File)</a></span> - Static method in class org.biojava.bio.program.abi.<a href="./org/biojava/bio/program/abi/ABIFChromatogram.html" title="class in org.biojava.bio.program.abi">ABIFChromatogram</a></dt>
<dd>
<div class="block">Create a new ABIF object from a file.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/abi/ABIFChromatogram.html#create(java.io.InputStream)">create(InputStream)</a></span> - Static method in class org.biojava.bio.program.abi.<a href="./org/biojava/bio/program/abi/ABIFChromatogram.html" title="class in org.biojava.bio.program.abi">ABIFChromatogram</a></dt>
<dd>
<div class="block">Create a new ABIF object from a stream of bytes.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/scf/SCF.html#create(java.io.File)">create(File)</a></span> - Static method in class org.biojava.bio.program.scf.<a href="./org/biojava/bio/program/scf/SCF.html" title="class in org.biojava.bio.program.scf">SCF</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/scf/SCF.html#create(java.io.InputStream, long)">create(InputStream, long)</a></span> - Static method in class org.biojava.bio.program.scf.<a href="./org/biojava/bio/program/scf/SCF.html" title="class in org.biojava.bio.program.scf">SCF</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/INSDseqFormat.html#CREATE_DATE_TAG">CREATE_DATE_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/INSDseqFormat.html" title="class in org.biojavax.bio.seq.io">INSDseqFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SequenceDBSequenceBuilder.html#CREATE_DUMMYSEQ">CREATE_DUMMYSEQ</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SequenceDBSequenceBuilder.html" title="class in org.biojava.bio.seq.io">SequenceDBSequenceBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SequenceDBSequenceBuilder.html#CREATE_REALSEQ">CREATE_REALSEQ</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SequenceDBSequenceBuilder.html" title="class in org.biojava.bio.seq.io">SequenceDBSequenceBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/INSDseqFormat.html#CREATE_REL_TAG">CREATE_REL_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/INSDseqFormat.html" title="class in org.biojavax.bio.seq.io">INSDseqFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/util/GATools.html#createBinary(java.lang.String)">createBinary(String)</a></span> - Static method in class org.biojavax.ga.util.<a href="./org/biojavax/ga/util/GATools.html" title="class in org.biojavax.ga.util">GATools</a></dt>
<dd>
<div class="block">Creates a <code>SymbolList</code> in the GABinary <code>Alphabet</code></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/indexdb/BioStoreFactory.html#createBioStore()">createBioStore()</a></span> - Method in class org.biojava.bio.program.indexdb.<a href="./org/biojava/bio/program/indexdb/BioStoreFactory.html" title="class in org.biojava.bio.program.indexdb">BioStoreFactory</a></dt>
<dd>
<div class="block"><code>createBioStore</code> creates a <code>BioStore</code>
reflecting the current state of the factory and returns a
reference to it.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/DistributionFactory.html#createDistribution(org.biojava.bio.symbol.Alphabet)">createDistribution(Alphabet)</a></span> - Method in interface org.biojava.bio.dist.<a href="./org/biojava/bio/dist/DistributionFactory.html" title="interface in org.biojava.bio.dist">DistributionFactory</a></dt>
<dd>
<div class="block">Generate a new Distribution as requested.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/DistributionFactory.DefaultDistributionFactory.html#createDistribution(org.biojava.bio.symbol.Alphabet)">createDistribution(Alphabet)</a></span> - Method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/DistributionFactory.DefaultDistributionFactory.html" title="class in org.biojava.bio.dist">DistributionFactory.DefaultDistributionFactory</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/OrderNDistributionFactory.html#createDistribution(org.biojava.bio.symbol.Alphabet)">createDistribution(Alphabet)</a></span> - Method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/OrderNDistributionFactory.html" title="class in org.biojava.bio.dist">OrderNDistributionFactory</a></dt>
<dd>
<div class="block">Creates an OrderNDistribution of the appropriate type.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/DNATools.html#createDNA(java.lang.String)">createDNA(String)</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/DNATools.html" title="class in org.biojava.bio.seq">DNATools</a></dt>
<dd>
<div class="block">Return a new DNA <span class="type">SymbolList</span> for
<span class="arg">dna</span>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/DNATools.html#createDNASequence(java.lang.String, java.lang.String)">createDNASequence(String, String)</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/DNATools.html" title="class in org.biojava.bio.seq">DNATools</a></dt>
<dd>
<div class="block">Return a new DNA <span class="type">Sequence</span> for
<span class="arg">dna</span>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/DPFactory.html#createDP(org.biojava.bio.dp.MarkovModel)">createDP(MarkovModel)</a></span> - Method in interface org.biojava.bio.dp.<a href="./org/biojava/bio/dp/DPFactory.html" title="interface in org.biojava.bio.dp">DPFactory</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/DPFactory.DefaultFactory.html#createDP(org.biojava.bio.dp.MarkovModel)">createDP(MarkovModel)</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/DPFactory.DefaultFactory.html" title="class in org.biojava.bio.dp">DPFactory.DefaultFactory</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/SequenceTools.html#createDummy(java.lang.String, java.lang.String)">createDummy(String, String)</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/SequenceTools.html" title="class in org.biojava.bio.seq">SequenceTools</a></dt>
<dd>
<div class="block">Create a new Sequence that has no annotation, no features and a zero-length
symbol list.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/SequenceTools.html#createDummy(org.biojava.bio.symbol.Alphabet, int, org.biojava.bio.symbol.Symbol, java.lang.String, java.lang.String)">createDummy(Alphabet, int, Symbol, String, String)</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/SequenceTools.html" title="class in org.biojava.bio.seq">SequenceTools</a></dt>
<dd>
<div class="block">Create a new Sequence that contains a single symbol repeated over and over.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/biosql/BioSQLSequenceDB.html#createDummySequence(java.lang.String, org.biojava.bio.symbol.Alphabet, int)">createDummySequence(String, Alphabet, int)</a></span> - Method in class org.biojava.bio.seq.db.biosql.<a href="./org/biojava/bio/seq/db/biosql/BioSQLSequenceDB.html" title="class in org.biojava.bio.seq.db.biosql">BioSQLSequenceDB</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/Formats.html#createEmblParserListener(org.biojava.bio.program.tagvalue.TagValueListener)">createEmblParserListener(TagValueListener)</a></span> - Static method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/Formats.html" title="class in org.biojava.bio.program.tagvalue">Formats</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/DASSequence.html#createFeature(org.biojava.bio.seq.Feature.Template)">createFeature(Feature.Template)</a></span> - Method in class org.biojava.bio.program.das.<a href="./org/biojava/bio/program/das/DASSequence.html" title="class in org.biojava.bio.program.das">DASSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/AbstractFeatureHolder.html#createFeature(org.biojava.bio.seq.Feature.Template)">createFeature(Feature.Template)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/AbstractFeatureHolder.html" title="class in org.biojava.bio.seq">AbstractFeatureHolder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/CircularView.html#createFeature(org.biojava.bio.seq.Feature.Template)">createFeature(Feature.Template)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/CircularView.html" title="class in org.biojava.bio.seq">CircularView</a></dt>
<dd>
<div class="block">Over rides ViewSequence to allow the use of locations that have
coordinates outside of the sequence length (which are needed to
describe locations that overlap the origin of a circular sequence).</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureHolder.html#createFeature(org.biojava.bio.seq.Feature.Template)">createFeature(Feature.Template)</a></span> - Method in interface org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureHolder.html" title="interface in org.biojava.bio.seq">FeatureHolder</a></dt>
<dd>
<div class="block">Create a new Feature, and add it to this FeatureHolder.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureHolder.EmptyFeatureHolder.html#createFeature(org.biojava.bio.seq.Feature.Template)">createFeature(Feature.Template)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureHolder.EmptyFeatureHolder.html" title="class in org.biojava.bio.seq">FeatureHolder.EmptyFeatureHolder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/DummySequence.html#createFeature(org.biojava.bio.seq.Feature.Template)">createFeature(Feature.Template)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/DummySequence.html" title="class in org.biojava.bio.seq.impl">DummySequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/LazyFilterFeatureHolder.html#createFeature(org.biojava.bio.seq.Feature.Template)">createFeature(Feature.Template)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/LazyFilterFeatureHolder.html" title="class in org.biojava.bio.seq.impl">LazyFilterFeatureHolder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/RevCompSequence.html#createFeature(org.biojava.bio.seq.Feature.Template)">createFeature(Feature.Template)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/RevCompSequence.html" title="class in org.biojava.bio.seq.impl">RevCompSequence</a></dt>
<dd>
<div class="block">createFeature() will call createFeature() on the underlying Sequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleFeature.html#createFeature(org.biojava.bio.seq.Feature.Template)">createFeature(Feature.Template)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleFeature.html" title="class in org.biojava.bio.seq.impl">SimpleFeature</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleGappedSequence.html#createFeature(org.biojava.bio.seq.Feature.Template)">createFeature(Feature.Template)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleGappedSequence.html" title="class in org.biojava.bio.seq.impl">SimpleGappedSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleSequence.html#createFeature(org.biojava.bio.seq.Feature.Template)">createFeature(Feature.Template)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleSequence.html" title="class in org.biojava.bio.seq.impl">SimpleSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleSequence.html#createFeature(org.biojava.bio.seq.FeatureHolder, org.biojava.bio.seq.Feature.Template)">createFeature(FeatureHolder, Feature.Template)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleSequence.html" title="class in org.biojava.bio.seq.impl">SimpleSequence</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>Please use new 1-arg createFeature instead.</i></div>
</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SubSequence.html#createFeature(org.biojava.bio.seq.Feature.Template)">createFeature(Feature.Template)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SubSequence.html" title="class in org.biojava.bio.seq.impl">SubSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/ViewSequence.html#createFeature(org.biojava.bio.seq.Feature.Template)">createFeature(Feature.Template)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/ViewSequence.html" title="class in org.biojava.bio.seq.impl">ViewSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/LazyFeatureHolder.html#createFeature(org.biojava.bio.seq.Feature.Template)">createFeature(Feature.Template)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/LazyFeatureHolder.html" title="class in org.biojava.bio.seq">LazyFeatureHolder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/NewSimpleAssembly.html#createFeature(org.biojava.bio.seq.Feature.Template)">createFeature(Feature.Template)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/NewSimpleAssembly.html" title="class in org.biojava.bio.seq">NewSimpleAssembly</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/projection/ProjectedFeature.html#createFeature(org.biojava.bio.seq.Feature.Template)">createFeature(Feature.Template)</a></span> - Method in class org.biojava.bio.seq.projection.<a href="./org/biojava/bio/seq/projection/ProjectedFeature.html" title="class in org.biojava.bio.seq.projection">ProjectedFeature</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/projection/ProjectedFeatureHolder.html#createFeature(org.biojava.bio.seq.Feature.Template)">createFeature(Feature.Template)</a></span> - Method in class org.biojava.bio.seq.projection.<a href="./org/biojava/bio/seq/projection/ProjectedFeatureHolder.html" title="class in org.biojava.bio.seq.projection">ProjectedFeatureHolder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/projection/ProjectionContext.html#createFeature(org.biojava.bio.seq.Feature.Template)">createFeature(Feature.Template)</a></span> - Method in interface org.biojava.bio.seq.projection.<a href="./org/biojava/bio/seq/projection/ProjectionContext.html" title="interface in org.biojava.bio.seq.projection">ProjectionContext</a></dt>
<dd>
<div class="block">Create a projected feature with properties matching the template.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/projection/ProjectionContext.html#createFeature(org.biojava.bio.seq.Feature, org.biojava.bio.seq.Feature.Template)">createFeature(Feature, Feature.Template)</a></span> - Method in interface org.biojava.bio.seq.projection.<a href="./org/biojava/bio/seq/projection/ProjectionContext.html" title="interface in org.biojava.bio.seq.projection">ProjectionContext</a></dt>
<dd>
<div class="block">Create a new projected feature.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/projection/ReparentContext.html#createFeature(org.biojava.bio.seq.Feature.Template)">createFeature(Feature.Template)</a></span> - Method in class org.biojava.bio.seq.projection.<a href="./org/biojava/bio/seq/projection/ReparentContext.html" title="class in org.biojava.bio.seq.projection">ReparentContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/projection/ReparentContext.html#createFeature(org.biojava.bio.seq.Feature, org.biojava.bio.seq.Feature.Template)">createFeature(Feature, Feature.Template)</a></span> - Method in class org.biojava.bio.seq.projection.<a href="./org/biojava/bio/seq/projection/ReparentContext.html" title="class in org.biojava.bio.seq.projection">ReparentContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/SimpleAssembly.html#createFeature(org.biojava.bio.seq.Feature.Template)">createFeature(Feature.Template)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/SimpleAssembly.html" title="class in org.biojava.bio.seq">SimpleAssembly</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichFeature.html#createFeature(org.biojava.bio.seq.Feature.Template)">createFeature(Feature.Template)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichFeature.html" title="class in org.biojavax.bio.seq">SimpleRichFeature</a></dt>
<dd>
<div class="block">Create a new Feature, and add it to this FeatureHolder.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/ThinRichSequence.html#createFeature(org.biojava.bio.seq.Feature.Template)">createFeature(Feature.Template)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/ThinRichSequence.html" title="class in org.biojavax.bio.seq">ThinRichSequence</a></dt>
<dd>
<div class="block">Create a new Feature, and add it to this FeatureHolder.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/LazyFeatureHolder.html#createFeatureHolder()">createFeatureHolder()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/LazyFeatureHolder.html" title="class in org.biojava.bio.seq">LazyFeatureHolder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/xff/FeatureHandler.html#createFeatureTemplate()">createFeatureTemplate()</a></span> - Method in class org.biojava.bio.program.xff.<a href="./org/biojava/bio/program/xff/FeatureHandler.html" title="class in org.biojava.bio.program.xff">FeatureHandler</a></dt>
<dd>
<div class="block">Create a new template of the appropriate type.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/xff/StrandedFeatureHandler.html#createFeatureTemplate()">createFeatureTemplate()</a></span> - Method in class org.biojava.bio.program.xff.<a href="./org/biojava/bio/program/xff/StrandedFeatureHandler.html" title="class in org.biojava.bio.program.xff">StrandedFeatureHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/DNATools.html#createGappedDNASequence(java.lang.String, java.lang.String)">createGappedDNASequence(String, String)</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/DNATools.html" title="class in org.biojava.bio.seq">DNATools</a></dt>
<dd>
<div class="block">Get a new dna as a GappedSequence</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/ProteinTools.html#createGappedProteinSequence(java.lang.String, java.lang.String)">createGappedProteinSequence(String, String)</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/ProteinTools.html" title="class in org.biojava.bio.seq">ProteinTools</a></dt>
<dd>
<div class="block">Get a new protein as a GappedSequence</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/SequencesAsGFF.html#createGFFRecord(org.biojava.bio.seq.Feature, java.lang.String)">createGFFRecord(Feature, String)</a></span> - Method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/SequencesAsGFF.html" title="class in org.biojava.bio.program.gff">SequencesAsGFF</a></dt>
<dd>
<div class="block">Internal method to create a <span class="type">GFFRecord</span>
from an individual <span class="type">Feature</span>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/AbstractChromatogram.html#createImmutableAlignment(java.util.Map)">createImmutableAlignment(Map)</a></span> - Method in class org.biojava.bio.chromatogram.<a href="./org/biojava/bio/chromatogram/AbstractChromatogram.html" title="class in org.biojava.bio.chromatogram">AbstractChromatogram</a></dt>
<dd>
<div class="block">A factory method for creating new immutable alignments, particularly
for use as base call alignments.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/AbstractChromatogram.html#createImmutableSymbolList(org.biojava.bio.symbol.Alphabet, java.util.List)">createImmutableSymbolList(Alphabet, List)</a></span> - Method in class org.biojava.bio.chromatogram.<a href="./org/biojava/bio/chromatogram/AbstractChromatogram.html" title="class in org.biojava.bio.chromatogram">AbstractChromatogram</a></dt>
<dd>
<div class="block">A factory method for creating new symbol lists with a given alphabet.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/GUITools.html#createInnerBounds(org.biojava.bio.gui.sequence.CircularRendererContext)">createInnerBounds(CircularRendererContext)</a></span> - Static method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/GUITools.html" title="class in org.biojava.bio.gui.sequence">GUITools</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ListTools.html#createList(java.util.List)">createList(List)</a></span> - Static method in class org.biojava.utils.<a href="./org/biojava/utils/ListTools.html" title="class in org.biojava.utils">ListTools</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ListTools.html#createList(java.lang.Object[])">createList(Object[])</a></span> - Static method in class org.biojava.utils.<a href="./org/biojava/utils/ListTools.html" title="class in org.biojava.utils">ListTools</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleAtomicSymbol.html#createMatches()">createMatches()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleAtomicSymbol.html" title="class in org.biojava.bio.symbol">SimpleAtomicSymbol</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/server/PrepareMMcifIndexFile.html#createMMcifInfoList(java.io.File[], java.io.File, java.io.File)">createMMcifInfoList(File[], File, File)</a></span> - Method in class org.biojava.bio.structure.server.<a href="./org/biojava/bio/structure/server/PrepareMMcifIndexFile.html" title="class in org.biojava.bio.structure.server">PrepareMMcifIndexFile</a></dt>
<dd>
<div class="block">parses a set of PDB files and writes info into a file
the file is tab separated and has the following columns:
name length resolution depositionDate modificationDate technique title classification filename
binaryDirectory: a directory in which binary files containing the atoms will be places, to provide a speedup
This method needs to be run, before a DBSearch can be performed, since the files created by this method
are required for the DBSearch</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/automata/FiniteAutomaton.html#createNodeSet()">createNodeSet()</a></span> - Method in class org.biojava.utils.automata.<a href="./org/biojava/utils/automata/FiniteAutomaton.html" title="class in org.biojava.utils.automata">FiniteAutomaton</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/automata/NfaBuilder.html#createNodeSet()">createNodeSet()</a></span> - Method in interface org.biojava.utils.automata.<a href="./org/biojava/utils/automata/NfaBuilder.html" title="interface in org.biojava.utils.automata">NfaBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/automata/NfaSubModel.html#createNodeSet()">createNodeSet()</a></span> - Method in class org.biojava.utils.automata.<a href="./org/biojava/utils/automata/NfaSubModel.html" title="class in org.biojava.utils.automata">NfaSubModel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/NucleotideTools.html#createNucleotide(java.lang.String)">createNucleotide(String)</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/NucleotideTools.html" title="class in org.biojava.bio.seq">NucleotideTools</a></dt>
<dd>
<div class="block">Return a new Nucleotide <span class="type">SymbolList</span> for
<span class="arg">nucleotide</span>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/NucleotideTools.html#createNucleotideSequence(java.lang.String, java.lang.String)">createNucleotideSequence(String, String)</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/NucleotideTools.html" title="class in org.biojava.bio.seq">NucleotideTools</a></dt>
<dd>
<div class="block">Return a new Nucleotide <span class="type">Sequence</span> for
<span class="arg">nucleotide</span>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/biosql/BioSQLSequenceDB.html#createOntology(java.lang.String, java.lang.String)">createOntology(String, String)</a></span> - Method in class org.biojava.bio.seq.db.biosql.<a href="./org/biojava/bio/seq/db/biosql/BioSQLSequenceDB.html" title="class in org.biojava.bio.seq.db.biosql">BioSQLSequenceDB</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/OntologyFactory.html#createOntology(java.lang.String, java.lang.String)">createOntology(String, String)</a></span> - Method in interface org.biojava.ontology.<a href="./org/biojava/ontology/OntologyFactory.html" title="interface in org.biojava.ontology">OntologyFactory</a></dt>
<dd>
<div class="block">Creates a new Ontology</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/Ontology.Impl.html#createOntologyTerm(org.biojava.ontology.Ontology)">createOntologyTerm(Ontology)</a></span> - Method in class org.biojava.ontology.<a href="./org/biojava/ontology/Ontology.Impl.html" title="class in org.biojava.ontology">Ontology.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/HomologeneDB.html#createOrthologue(org.biojava.bio.program.homologene.Taxon, java.lang.String, java.lang.String, java.lang.String)">createOrthologue(Taxon, String, String, String)</a></span> - Method in interface org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/HomologeneDB.html" title="interface in org.biojava.bio.program.homologene">HomologeneDB</a></dt>
<dd>
<div class="block">Create an orthologue.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/HomologeneDB.html#createOrthologue(int, java.lang.String, java.lang.String, java.lang.String)">createOrthologue(int, String, String, String)</a></span> - Method in interface org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/HomologeneDB.html" title="interface in org.biojava.bio.program.homologene">HomologeneDB</a></dt>
<dd>
<div class="block">Create an orthologue.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/SimpleHomologeneDB.html#createOrthologue(org.biojava.bio.program.homologene.Taxon, java.lang.String, java.lang.String, java.lang.String)">createOrthologue(Taxon, String, String, String)</a></span> - Method in class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/SimpleHomologeneDB.html" title="class in org.biojava.bio.program.homologene">SimpleHomologeneDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/SimpleHomologeneDB.html#createOrthologue(int, java.lang.String, java.lang.String, java.lang.String)">createOrthologue(int, String, String, String)</a></span> - Method in class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/SimpleHomologeneDB.html" title="class in org.biojava.bio.program.homologene">SimpleHomologeneDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/HomologeneDB.html#createOrthoPair(org.biojava.bio.program.homologene.Orthologue, org.biojava.bio.program.homologene.Orthologue, org.biojava.bio.program.homologene.SimilarityType, double)">createOrthoPair(Orthologue, Orthologue, SimilarityType, double)</a></span> - Method in interface org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/HomologeneDB.html" title="interface in org.biojava.bio.program.homologene">HomologeneDB</a></dt>
<dd>
<div class="block">Create a computed orthology entry.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/HomologeneDB.html#createOrthoPair(org.biojava.bio.program.homologene.Orthologue, org.biojava.bio.program.homologene.Orthologue, java.lang.String)">createOrthoPair(Orthologue, Orthologue, String)</a></span> - Method in interface org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/HomologeneDB.html" title="interface in org.biojava.bio.program.homologene">HomologeneDB</a></dt>
<dd>
<div class="block">Create a curated orthology entry.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/SimpleHomologeneDB.html#createOrthoPair(org.biojava.bio.program.homologene.Orthologue, org.biojava.bio.program.homologene.Orthologue, org.biojava.bio.program.homologene.SimilarityType, double)">createOrthoPair(Orthologue, Orthologue, SimilarityType, double)</a></span> - Method in class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/SimpleHomologeneDB.html" title="class in org.biojava.bio.program.homologene">SimpleHomologeneDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/SimpleHomologeneDB.html#createOrthoPair(org.biojava.bio.program.homologene.Orthologue, org.biojava.bio.program.homologene.Orthologue, java.lang.String)">createOrthoPair(Orthologue, Orthologue, String)</a></span> - Method in class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/SimpleHomologeneDB.html" title="class in org.biojava.bio.program.homologene">SimpleHomologeneDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/HomologeneDB.html#createOrthoPairSet()">createOrthoPairSet()</a></span> - Method in interface org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/HomologeneDB.html" title="interface in org.biojava.bio.program.homologene">HomologeneDB</a></dt>
<dd>
<div class="block">Create a Homologene Group.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/SimpleHomologeneDB.html#createOrthoPairSet()">createOrthoPairSet()</a></span> - Method in class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/SimpleHomologeneDB.html" title="class in org.biojava.bio.program.homologene">SimpleHomologeneDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/GUITools.html#createOuterBounds(org.biojava.bio.gui.sequence.CircularRendererContext, double)">createOuterBounds(CircularRendererContext, double)</a></span> - Static method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/GUITools.html" title="class in org.biojava.bio.gui.sequence">GUITools</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/server/PrepareIndexFile.html#createPDBInfoList(java.io.File[], java.io.File, java.io.File)">createPDBInfoList(File[], File, File)</a></span> - Method in class org.biojava.bio.structure.server.<a href="./org/biojava/bio/structure/server/PrepareIndexFile.html" title="class in org.biojava.bio.structure.server">PrepareIndexFile</a></dt>
<dd>
<div class="block">parses a set of PDB files and writes info into a file
the file is tab separated and has the following columns:
name length resolution depositionDate modificationDate technique title classification filename
binaryDirectory: a directory in which binary files containing the atoms will be places, to provide a speedup
This method needs to be run, before a DBSearch can be performed, since the files created by this method
are required for the DBSearch</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/phred/PhredTools.html#createPhred(org.biojava.bio.symbol.SymbolList, org.biojava.bio.symbol.SymbolList)">createPhred(SymbolList, SymbolList)</a></span> - Static method in class org.biojava.bio.program.phred.<a href="./org/biojava/bio/program/phred/PhredTools.html" title="class in org.biojava.bio.program.phred">PhredTools</a></dt>
<dd>
<div class="block">Merges a Symbol List from the DNA alphabet with a SymbolList from the
[0..99] subset of the IntegerAlphabet into a SymbolList from
the PHRED alphabet.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/ProteaseManager.html#createProtease(org.biojava.bio.symbol.SymbolList, boolean, org.biojava.bio.symbol.SymbolList, java.lang.String)">createProtease(SymbolList, boolean, SymbolList, String)</a></span> - Static method in class org.biojava.bio.proteomics.<a href="./org/biojava/bio/proteomics/ProteaseManager.html" title="class in org.biojava.bio.proteomics">ProteaseManager</a></dt>
<dd>
<div class="block">Creates and registers a new Protease.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/ProteaseManager.html#createProtease(org.biojava.bio.symbol.SymbolList, boolean, java.lang.String)">createProtease(SymbolList, boolean, String)</a></span> - Static method in class org.biojava.bio.proteomics.<a href="./org/biojava/bio/proteomics/ProteaseManager.html" title="class in org.biojava.bio.proteomics">ProteaseManager</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/ProteaseManager.html#createProtease(java.lang.String, boolean, java.lang.String, java.lang.String)">createProtease(String, boolean, String, String)</a></span> - Static method in class org.biojava.bio.proteomics.<a href="./org/biojava/bio/proteomics/ProteaseManager.html" title="class in org.biojava.bio.proteomics">ProteaseManager</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/ProteaseManager.html#createProtease(java.lang.String, boolean, java.lang.String)">createProtease(String, boolean, String)</a></span> - Static method in class org.biojava.bio.proteomics.<a href="./org/biojava/bio/proteomics/ProteaseManager.html" title="class in org.biojava.bio.proteomics">ProteaseManager</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/ProteinTools.html#createProtein(java.lang.String)">createProtein(String)</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/ProteinTools.html" title="class in org.biojava.bio.seq">ProteinTools</a></dt>
<dd>
<div class="block">Return a new Protein <span class="type">SymbolList</span> for <span
class="arg">protein</span>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/ProteinTools.html#createProteinSequence(java.lang.String, java.lang.String)">createProteinSequence(String, String)</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/ProteinTools.html" title="class in org.biojava.bio.seq">ProteinTools</a></dt>
<dd>
<div class="block">Return a new PROTEIN <span class="type">Sequence</span> for
<span class="arg">protein</span>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFParser.html#createRecord(org.biojava.bio.program.gff.GFFDocumentHandler, java.util.List, java.lang.String, java.lang.String)">createRecord(GFFDocumentHandler, List, String, String)</a></span> - Method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFParser.html" title="class in org.biojava.bio.program.gff">GFFParser</a></dt>
<dd>
<div class="block">Actually turns a list of tokens, some value string and a comment into a
<span class="type">GFFRecord</span> and informs
<span class="arg">handler</span>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff3/GFF3Parser.html#createRecord(org.biojava.bio.program.gff3.GFF3DocumentHandler, java.util.List, java.lang.String, java.lang.String, org.biojava.ontology.Ontology, org.biojava.ontology.Ontology)">createRecord(GFF3DocumentHandler, List, String, String, Ontology, Ontology)</a></span> - Method in class org.biojava.bio.program.gff3.<a href="./org/biojava/bio/program/gff3/GFF3Parser.html" title="class in org.biojava.bio.program.gff3">GFF3Parser</a></dt>
<dd>
<div class="block">Actually turns a list of tokens, some value string and a comment into a
<span class="type">GFF3Record</span> and informs
<span class="arg">handler</span>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/MotifTools.html#createRegex(org.biojava.bio.symbol.SymbolList)">createRegex(SymbolList)</a></span> - Static method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/MotifTools.html" title="class in org.biojava.bio.symbol">MotifTools</a></dt>
<dd>
<div class="block"><code>createRegex</code> creates a regular expression which
matches the <code>SymbolList</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/AbstractPeptideDigestRenderer.html#createRenderer(int)">createRenderer(int)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/AbstractPeptideDigestRenderer.html" title="class in org.biojava.bio.gui.sequence">AbstractPeptideDigestRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PeptideDigestRenderer.html#createRenderer(int)">createRenderer(int)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PeptideDigestRenderer.html" title="class in org.biojava.bio.gui.sequence">PeptideDigestRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.Tools.html#createRichSequence(java.lang.String, java.lang.String, org.biojava.bio.symbol.Alphabet)">createRichSequence(String, String, Alphabet)</a></span> - Static method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.Tools.html" title="class in org.biojavax.bio.seq">RichSequence.Tools</a></dt>
<dd>
<div class="block">Create a new RichSequence in the default namespace.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.Tools.html#createRichSequence(java.lang.String, java.lang.String, java.lang.String, org.biojava.bio.symbol.Alphabet)">createRichSequence(String, String, String, Alphabet)</a></span> - Static method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.Tools.html" title="class in org.biojavax.bio.seq">RichSequence.Tools</a></dt>
<dd>
<div class="block">Create a new RichSequence in the specified namespace.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.Tools.html#createRichSequence(org.biojavax.Namespace, java.lang.String, java.lang.String, org.biojava.bio.symbol.Alphabet)">createRichSequence(Namespace, String, String, Alphabet)</a></span> - Static method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.Tools.html" title="class in org.biojavax.bio.seq">RichSequence.Tools</a></dt>
<dd>
<div class="block">Create a new RichSequence in the specified namespace.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.Tools.html#createRichSequence(java.lang.String, org.biojava.bio.symbol.SymbolList)">createRichSequence(String, SymbolList)</a></span> - Static method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.Tools.html" title="class in org.biojavax.bio.seq">RichSequence.Tools</a></dt>
<dd>
<div class="block">Create a new RichSequence in the default namespace.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.Tools.html#createRichSequence(org.biojavax.Namespace, java.lang.String, org.biojava.bio.symbol.SymbolList)">createRichSequence(Namespace, String, SymbolList)</a></span> - Static method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.Tools.html" title="class in org.biojavax.bio.seq">RichSequence.Tools</a></dt>
<dd>
<div class="block">Create a new RichSequence in the specified namespace.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/RNATools.html#createRNA(java.lang.String)">createRNA(String)</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/RNATools.html" title="class in org.biojava.bio.seq">RNATools</a></dt>
<dd>
<div class="block">Return a new RNA <span class="type">SymbolList</span> for
<span class="arg">rna</span>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/RNATools.html#createRNASequence(java.lang.String, java.lang.String)">createRNASequence(String, String)</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/RNATools.html" title="class in org.biojava.bio.seq">RNATools</a></dt>
<dd>
<div class="block">Return a new RNA <span class="type">Sequence</span> for
<span class="arg">rna</span>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleSequenceFactory.html#createSequence(org.biojava.bio.symbol.SymbolList, java.lang.String, java.lang.String, org.biojava.bio.Annotation)">createSequence(SymbolList, String, String, Annotation)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleSequenceFactory.html" title="class in org.biojava.bio.seq.impl">SimpleSequenceFactory</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/SequenceFactory.html#createSequence(org.biojava.bio.symbol.SymbolList, java.lang.String, java.lang.String, org.biojava.bio.Annotation)">createSequence(SymbolList, String, String, Annotation)</a></span> - Method in interface org.biojava.bio.seq.<a href="./org/biojava/bio/seq/SequenceFactory.html" title="interface in org.biojava.bio.seq">SequenceFactory</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Creates a sequence using these parameters.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/SequenceTools.html#createSequence(org.biojava.bio.symbol.SymbolList, java.lang.String, java.lang.String, org.biojava.bio.Annotation)">createSequence(SymbolList, String, String, Annotation)</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/SequenceTools.html" title="class in org.biojava.bio.seq">SequenceTools</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ListTools.html#createSeriesList(java.lang.String, java.lang.String, int)">createSeriesList(String, String, int)</a></span> - Static method in class org.biojava.utils.<a href="./org/biojava/utils/ListTools.html" title="class in org.biojava.utils">ListTools</a></dt>
<dd>
<div class="block">Create a new SeriesList with the given leader, trailer and size.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/StateMachine.html#createState(java.lang.String)">createState(String)</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/StateMachine.html" title="class in org.biojava.bio.program.tagvalue">StateMachine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/naming/ObdaContext.html#createSubcontext(javax.naming.Name)">createSubcontext(Name)</a></span> - Method in class org.biojava.naming.<a href="./org/biojava/naming/ObdaContext.html" title="class in org.biojava.naming">ObdaContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/naming/ObdaContext.html#createSubcontext(javax.naming.Name, javax.naming.directory.Attributes)">createSubcontext(Name, Attributes)</a></span> - Method in class org.biojava.naming.<a href="./org/biojava/naming/ObdaContext.html" title="class in org.biojava.naming">ObdaContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/naming/ObdaContext.html#createSubcontext(java.lang.String)">createSubcontext(String)</a></span> - Method in class org.biojava.naming.<a href="./org/biojava/naming/ObdaContext.html" title="class in org.biojava.naming">ObdaContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/naming/ObdaContext.html#createSubcontext(java.lang.String, javax.naming.directory.Attributes)">createSubcontext(String, Attributes)</a></span> - Method in class org.biojava.naming.<a href="./org/biojava/naming/ObdaContext.html" title="class in org.biojava.naming">ObdaContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/Formats.html#createSwissprotParserListener(org.biojava.bio.program.tagvalue.TagValueListener)">createSwissprotParserListener(TagValueListener)</a></span> - Static method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/Formats.html" title="class in org.biojava.bio.program.tagvalue">Formats</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AlphabetManager.html#createSymbol(java.lang.String, org.biojava.bio.Annotation)">createSymbol(String, Annotation)</a></span> - Static method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AlphabetManager.html" title="class in org.biojava.bio.symbol">AlphabetManager</a></dt>
<dd>
<div class="block">
Generate a new AtomicSymbol instance with a name and Annotation.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AlphabetManager.html#createSymbol(java.lang.String)">createSymbol(String)</a></span> - Static method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AlphabetManager.html" title="class in org.biojava.bio.symbol">AlphabetManager</a></dt>
<dd>
<div class="block">
Generate a new AtomicSymbol instance with a name and an Empty Annotation.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AlphabetManager.html#createSymbol(char, java.lang.String, org.biojava.bio.Annotation)">createSymbol(char, String, Annotation)</a></span> - Static method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AlphabetManager.html" title="class in org.biojava.bio.symbol">AlphabetManager</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>Use the two-arg version of this method instead.</i></div>
</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AlphabetManager.html#createSymbol(char, org.biojava.bio.Annotation, java.util.List, org.biojava.bio.symbol.Alphabet)">createSymbol(char, Annotation, List, Alphabet)</a></span> - Static method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AlphabetManager.html" title="class in org.biojava.bio.symbol">AlphabetManager</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>use the new version, without the token argument</i></div>
</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AlphabetManager.html#createSymbol(org.biojava.bio.Annotation, java.util.List, org.biojava.bio.symbol.Alphabet)">createSymbol(Annotation, List, Alphabet)</a></span> - Static method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AlphabetManager.html" title="class in org.biojava.bio.symbol">AlphabetManager</a></dt>
<dd>
<div class="block">
Generates a new Symbol instance that represents the tuple of Symbols in
symList.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AlphabetManager.html#createSymbol(char, org.biojava.bio.Annotation, java.util.Set, org.biojava.bio.symbol.Alphabet)">createSymbol(char, Annotation, Set, Alphabet)</a></span> - Static method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AlphabetManager.html" title="class in org.biojava.bio.symbol">AlphabetManager</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>use the three-arg version of this method instead.</i></div>
</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AlphabetManager.html#createSymbol(org.biojava.bio.Annotation, java.util.Set, org.biojava.bio.symbol.Alphabet)">createSymbol(Annotation, Set, Alphabet)</a></span> - Static method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AlphabetManager.html" title="class in org.biojava.bio.symbol">AlphabetManager</a></dt>
<dd>
<div class="block">
Generates a new Symbol instance that represents the tuple of Symbols in
symList.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/HomologeneTools.html#createTaxon(int, java.lang.String)">createTaxon(int, String)</a></span> - Static method in class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/HomologeneTools.html" title="class in org.biojava.bio.program.homologene">HomologeneTools</a></dt>
<dd>
<div class="block">add a Taxon</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/taxa/SimpleTaxonFactory.html#createTaxon(java.lang.String, java.lang.String)">createTaxon(String, String)</a></span> - Method in class org.biojava.bio.taxa.<a href="./org/biojava/bio/taxa/SimpleTaxonFactory.html" title="class in org.biojava.bio.taxa">SimpleTaxonFactory</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/taxa/TaxonFactory.html#createTaxon(java.lang.String, java.lang.String)">createTaxon(String, String)</a></span> - Method in interface org.biojava.bio.taxa.<a href="./org/biojava/bio/taxa/TaxonFactory.html" title="interface in org.biojava.bio.taxa">TaxonFactory</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Create a new orphan Taxon with a given scientific and common
name.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/taxa/WeakTaxonFactory.html#createTaxon(java.lang.String, java.lang.String)">createTaxon(String, String)</a></span> - Method in class org.biojava.bio.taxa.<a href="./org/biojava/bio/taxa/WeakTaxonFactory.html" title="class in org.biojava.bio.taxa">WeakTaxonFactory</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/StAXFeatureHandler.html#createTemplate()">createTemplate()</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/StAXFeatureHandler.html" title="class in org.biojava.bio.seq.io.agave">StAXFeatureHandler</a></dt>
<dd>
<div class="block">generates a very basic Template for the feature with
SmallAnnotation in the annotation field.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game/GAMEAnnotationHandler.html#createTemplate()">createTemplate()</a></span> - Method in class org.biojava.bio.seq.io.game.<a href="./org/biojava/bio/seq/io/game/GAMEAnnotationHandler.html" title="class in org.biojava.bio.seq.io.game">GAMEAnnotationHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game/GAMEFeatureSetHandler.html#createTemplate()">createTemplate()</a></span> - Method in class org.biojava.bio.seq.io.game.<a href="./org/biojava/bio/seq/io/game/GAMEFeatureSetHandler.html" title="class in org.biojava.bio.seq.io.game">GAMEFeatureSetHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game/GAMEFeatureSpanHandler.html#createTemplate()">createTemplate()</a></span> - Method in class org.biojava.bio.seq.io.game.<a href="./org/biojava/bio/seq/io/game/GAMEFeatureSpanHandler.html" title="class in org.biojava.bio.seq.io.game">GAMEFeatureSpanHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game/StAXFeatureHandler.html#createTemplate()">createTemplate()</a></span> - Method in class org.biojava.bio.seq.io.game.<a href="./org/biojava/bio/seq/io/game/StAXFeatureHandler.html" title="class in org.biojava.bio.seq.io.game">StAXFeatureHandler</a></dt>
<dd>
<div class="block">generates a very basic Template for the feature with
SmallAnnotation in the annotation field.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/IntegerOntology.html#createTerm(java.lang.String)">createTerm(String)</a></span> - Method in class org.biojava.ontology.<a href="./org/biojava/ontology/IntegerOntology.html" title="class in org.biojava.ontology">IntegerOntology</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/IntegerOntology.html#createTerm(java.lang.String, java.lang.String)">createTerm(String, String)</a></span> - Method in class org.biojava.ontology.<a href="./org/biojava/ontology/IntegerOntology.html" title="class in org.biojava.ontology">IntegerOntology</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/IntegerOntology.html#createTerm(java.lang.String, java.lang.String, java.lang.Object[])">createTerm(String, String, Object[])</a></span> - Method in class org.biojava.ontology.<a href="./org/biojava/ontology/IntegerOntology.html" title="class in org.biojava.ontology">IntegerOntology</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/Ontology.html#createTerm(java.lang.String)">createTerm(String)</a></span> - Method in interface org.biojava.ontology.<a href="./org/biojava/ontology/Ontology.html" title="interface in org.biojava.ontology">Ontology</a></dt>
<dd>
<div class="block">Create a new term in this ontology.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/Ontology.html#createTerm(java.lang.String, java.lang.String)">createTerm(String, String)</a></span> - Method in interface org.biojava.ontology.<a href="./org/biojava/ontology/Ontology.html" title="interface in org.biojava.ontology">Ontology</a></dt>
<dd>
<div class="block">Create a new term in this ontology.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/Ontology.html#createTerm(java.lang.String, java.lang.String, java.lang.Object[])">createTerm(String, String, Object[])</a></span> - Method in interface org.biojava.ontology.<a href="./org/biojava/ontology/Ontology.html" title="interface in org.biojava.ontology">Ontology</a></dt>
<dd>
<div class="block">Create a new term in this ontology.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/Ontology.Impl.html#createTerm(java.lang.String)">createTerm(String)</a></span> - Method in class org.biojava.ontology.<a href="./org/biojava/ontology/Ontology.Impl.html" title="class in org.biojava.ontology">Ontology.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/Ontology.Impl.html#createTerm(java.lang.String, java.lang.String)">createTerm(String, String)</a></span> - Method in class org.biojava.ontology.<a href="./org/biojava/ontology/Ontology.Impl.html" title="class in org.biojava.ontology">Ontology.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/Ontology.Impl.html#createTerm(java.lang.String, java.lang.String, java.lang.Object[])">createTerm(String, String, Object[])</a></span> - Method in class org.biojava.ontology.<a href="./org/biojava/ontology/Ontology.Impl.html" title="class in org.biojava.ontology">Ontology.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ontology/SimpleComparableOntology.html#createTerm(java.lang.String, java.lang.String, java.lang.Object[])">createTerm(String, String, Object[])</a></span> - Method in class org.biojavax.ontology.<a href="./org/biojavax/ontology/SimpleComparableOntology.html" title="class in org.biojavax.ontology">SimpleComparableOntology</a></dt>
<dd>
<div class="block">Create a new term in this ontology.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ontology/SimpleComparableOntology.html#createTerm(java.lang.String)">createTerm(String)</a></span> - Method in class org.biojavax.ontology.<a href="./org/biojavax/ontology/SimpleComparableOntology.html" title="class in org.biojavax.ontology">SimpleComparableOntology</a></dt>
<dd>
<div class="block">Create a new term in this ontology.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ontology/SimpleComparableOntology.html#createTerm(java.lang.String, java.lang.String)">createTerm(String, String)</a></span> - Method in class org.biojavax.ontology.<a href="./org/biojavax/ontology/SimpleComparableOntology.html" title="class in org.biojavax.ontology">SimpleComparableOntology</a></dt>
<dd>
<div class="block">Create a new term in this ontology.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/MarkovModel.html#createTransition(org.biojava.bio.dp.State, org.biojava.bio.dp.State)">createTransition(State, State)</a></span> - Method in interface org.biojava.bio.dp.<a href="./org/biojava/bio/dp/MarkovModel.html" title="interface in org.biojava.bio.dp">MarkovModel</a></dt>
<dd>
<div class="block">Makes a transition between two states legal.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/SimpleMarkovModel.html#createTransition(org.biojava.bio.dp.State, org.biojava.bio.dp.State)">createTransition(State, State)</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/SimpleMarkovModel.html" title="class in org.biojava.bio.dp">SimpleMarkovModel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/WMAsMM.html#createTransition(org.biojava.bio.dp.State, org.biojava.bio.dp.State)">createTransition(State, State)</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/WMAsMM.html" title="class in org.biojava.bio.dp">WMAsMM</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/StateMachine.html#createTransitionTable()">createTransitionTable()</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/StateMachine.html" title="class in org.biojava.bio.program.tagvalue">StateMachine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/IntegerOntology.html#createTriple(org.biojava.ontology.Term, org.biojava.ontology.Term, org.biojava.ontology.Term, java.lang.String, java.lang.String)">createTriple(Term, Term, Term, String, String)</a></span> - Method in class org.biojava.ontology.<a href="./org/biojava/ontology/IntegerOntology.html" title="class in org.biojava.ontology">IntegerOntology</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/Ontology.html#createTriple(org.biojava.ontology.Term, org.biojava.ontology.Term, org.biojava.ontology.Term, java.lang.String, java.lang.String)">createTriple(Term, Term, Term, String, String)</a></span> - Method in interface org.biojava.ontology.<a href="./org/biojava/ontology/Ontology.html" title="interface in org.biojava.ontology">Ontology</a></dt>
<dd>
<div class="block">Creates a new Triple.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/Ontology.Impl.html#createTriple(org.biojava.ontology.Term, org.biojava.ontology.Term, org.biojava.ontology.Term, java.lang.String, java.lang.String)">createTriple(Term, Term, Term, String, String)</a></span> - Method in class org.biojava.ontology.<a href="./org/biojava/ontology/Ontology.Impl.html" title="class in org.biojava.ontology">Ontology.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ontology/SimpleComparableOntology.html#createTriple(org.biojava.ontology.Term, org.biojava.ontology.Term, org.biojava.ontology.Term, java.lang.String, java.lang.String)">createTriple(Term, Term, Term, String, String)</a></span> - Method in class org.biojavax.ontology.<a href="./org/biojavax/ontology/SimpleComparableOntology.html" title="class in org.biojavax.ontology">SimpleComparableOntology</a></dt>
<dd>
<div class="block">Creates a new Triple.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureTypes.RepositoryImpl.html#createType(java.lang.String, org.biojava.bio.seq.FeatureFilter, java.util.Set)">createType(String, FeatureFilter, Set)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureTypes.RepositoryImpl.html" title="class in org.biojava.bio.seq">FeatureTypes.RepositoryImpl</a></dt>
<dd>
<div class="block">Create a new type in this repository.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/unigene/FlatFileUnigeneFactory.html#createUnigene(java.net.URL)">createUnigene(URL)</a></span> - Method in class org.biojava.bio.program.unigene.<a href="./org/biojava/bio/program/unigene/FlatFileUnigeneFactory.html" title="class in org.biojava.bio.program.unigene">FlatFileUnigeneFactory</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/unigene/SQLUnigeneFactory.html#createUnigene(java.net.URL)">createUnigene(URL)</a></span> - Method in class org.biojava.bio.program.unigene.<a href="./org/biojava/bio/program/unigene/SQLUnigeneFactory.html" title="class in org.biojava.bio.program.unigene">SQLUnigeneFactory</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/unigene/UnigeneFactory.html#createUnigene(java.net.URL)">createUnigene(URL)</a></span> - Method in interface org.biojava.bio.program.unigene.<a href="./org/biojava/bio/program/unigene/UnigeneFactory.html" title="interface in org.biojava.bio.program.unigene">UnigeneFactory</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/unigene/UnigeneTools.html#createUnigene(java.net.URL)">createUnigene(URL)</a></span> - Static method in class org.biojava.bio.program.unigene.<a href="./org/biojava/bio/program/unigene/UnigeneTools.html" title="class in org.biojava.bio.program.unigene">UnigeneTools</a></dt>
<dd>
<div class="block">Create a new UnigeneDB instance referred to by a URL.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/net/URLFactory.html#createURL(java.lang.Object)">createURL(Object)</a></span> - Method in interface org.biojava.utils.net.<a href="./org/biojava/utils/net/URLFactory.html" title="interface in org.biojava.utils.net">URLFactory</a></dt>
<dd>
<div class="block"><code>createURL</code> returns a URL which is relevant to the
object in a way specified by the implementation.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/IntegerOntology.html#createVariable(java.lang.String, java.lang.String)">createVariable(String, String)</a></span> - Method in class org.biojava.ontology.<a href="./org/biojava/ontology/IntegerOntology.html" title="class in org.biojava.ontology">IntegerOntology</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/Ontology.html#createVariable(java.lang.String, java.lang.String)">createVariable(String, String)</a></span> - Method in interface org.biojava.ontology.<a href="./org/biojava/ontology/Ontology.html" title="interface in org.biojava.ontology">Ontology</a></dt>
<dd>
<div class="block">Create a new term in this ontology that is used as a variable.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/Ontology.Impl.html#createVariable(java.lang.String, java.lang.String)">createVariable(String, String)</a></span> - Method in class org.biojava.ontology.<a href="./org/biojava/ontology/Ontology.Impl.html" title="class in org.biojava.ontology">Ontology.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ontology/SimpleComparableOntology.html#createVariable(java.lang.String, java.lang.String)">createVariable(String, String)</a></span> - Method in class org.biojavax.ontology.<a href="./org/biojavax/ontology/SimpleComparableOntology.html" title="class in org.biojavax.ontology">SimpleComparableOntology</a></dt>
<dd>
<div class="block">Create a new term in this ontology that is used as a variable.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Calc.html#createVirtualCBAtom(org.biojava.bio.structure.AminoAcid)">createVirtualCBAtom(AminoAcid)</a></span> - Static method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Calc.html" title="class in org.biojava.bio.structure">Calc</a></dt>
<dd>
<div class="block">creates a virtual C-beta atom.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLAcceptAllFilter.html#criterionAliasMap()">criterionAliasMap()</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLAcceptAllFilter.html" title="class in org.biojavax.bio.db.biosql">BioSQLAcceptAllFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLAcceptNoneFilter.html#criterionAliasMap()">criterionAliasMap()</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLAcceptNoneFilter.html" title="class in org.biojavax.bio.db.biosql">BioSQLAcceptNoneFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.And.html#criterionAliasMap()">criterionAliasMap()</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.And.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.And</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByNote.html#criterionAliasMap()">criterionAliasMap()</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByNote.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.ByNote</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByNoteTermOnly.html#criterionAliasMap()">criterionAliasMap()</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByNoteTermOnly.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.ByNoteTermOnly</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.BySequenceName.html#criterionAliasMap()">criterionAliasMap()</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.BySequenceName.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.BySequenceName</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.BySourceTermName.html#criterionAliasMap()">criterionAliasMap()</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.BySourceTermName.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.BySourceTermName</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByStrand.html#criterionAliasMap()">criterionAliasMap()</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByStrand.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.ByStrand</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByTypeTermName.html#criterionAliasMap()">criterionAliasMap()</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByTypeTermName.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.ByTypeTermName</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ContainedByRichLocation.html#criterionAliasMap()">criterionAliasMap()</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ContainedByRichLocation.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.ContainedByRichLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.html#criterionAliasMap()">criterionAliasMap()</a></span> - Method in interface org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.html" title="interface in org.biojavax.bio.db.biosql">BioSQLFeatureFilter</a></dt>
<dd>
<div class="block">Returns a map of property names (keys) to aliases (values), if the criterion
returned by asCriterion() uses aliases at all.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.HibernateFeatureFilter.html#criterionAliasMap()">criterionAliasMap()</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.HibernateFeatureFilter.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.HibernateFeatureFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.Not.html#criterionAliasMap()">criterionAliasMap()</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.Not.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.Not</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.Or.html#criterionAliasMap()">criterionAliasMap()</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.Or.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.Or</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.OverlapsRichLocation.html#criterionAliasMap()">criterionAliasMap()</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.OverlapsRichLocation.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.OverlapsRichLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/GeneticAlgorithm.html#CROSS_OVER_FUNCTION">CROSS_OVER_FUNCTION</a></span> - Static variable in interface org.biojavax.ga.<a href="./org/biojavax/ga/GeneticAlgorithm.html" title="interface in org.biojavax.ga">GeneticAlgorithm</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/functions/CrossOverFunction.html#CROSS_PROB">CROSS_PROB</a></span> - Static variable in interface org.biojavax.ga.functions.<a href="./org/biojavax/ga/functions/CrossOverFunction.html" title="interface in org.biojavax.ga.functions">CrossOverFunction</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/gui/sequence/CrosshairRenderer.html" title="class in org.biojava.bio.gui.sequence"><span class="strong">CrosshairRenderer</span></a> - Class in <a href="./org/biojava/bio/gui/sequence/package-summary.html">org.biojava.bio.gui.sequence</a></dt>
<dd>
<div class="block">
<code>CrosshairRenderer</code> draws a crosshair, optionally
with coordinates.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/CrosshairRenderer.html#CrosshairRenderer()">CrosshairRenderer()</a></span> - Constructor for class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/CrosshairRenderer.html" title="class in org.biojava.bio.gui.sequence">CrosshairRenderer</a></dt>
<dd>
<div class="block">Creates a new <code>CrosshairRenderer</code> in light grey with
coordinates displayed.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/CrosshairRenderer.html#CrosshairRenderer(java.awt.Paint)">CrosshairRenderer(Paint)</a></span> - Constructor for class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/CrosshairRenderer.html" title="class in org.biojava.bio.gui.sequence">CrosshairRenderer</a></dt>
<dd>
<div class="block">Creates a new <code>CrosshairRenderer</code> of the specified
colour, with coordinates displayed.</div>
</dd>
<dt><a href="./org/biojavax/ga/functions/CrossOverFunction.html" title="interface in org.biojavax.ga.functions"><span class="strong">CrossOverFunction</span></a> - Interface in <a href="./org/biojavax/ga/functions/package-summary.html">org.biojavax.ga.functions</a></dt>
<dd>
<div class="block">Crosses two chromosomes.</div>
</dd>
<dt><a href="./org/biojavax/ga/functions/CrossOverFunction.NoCross.html" title="class in org.biojavax.ga.functions"><span class="strong">CrossOverFunction.NoCross</span></a> - Class in <a href="./org/biojavax/ga/functions/package-summary.html">org.biojavax.ga.functions</a></dt>
<dd>
<div class="block">A place holder CrossOverFunction that doesn't perform cross overs</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ga/functions/CrossOverFunction.NoCross.html#CrossOverFunction.NoCross()">CrossOverFunction.NoCross()</a></span> - Constructor for class org.biojavax.ga.functions.<a href="./org/biojavax/ga/functions/CrossOverFunction.NoCross.html" title="class in org.biojavax.ga.functions">CrossOverFunction.NoCross</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/io/CrossProductTokenization.html" title="class in org.biojava.bio.seq.io"><span class="strong">CrossProductTokenization</span></a> - Class in <a href="./org/biojava/bio/seq/io/package-summary.html">org.biojava.bio.seq.io</a></dt>
<dd>
<div class="block">Tokenization for cross-product alphabets.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/CrossProductTokenization.html#CrossProductTokenization(org.biojava.bio.symbol.Alphabet)">CrossProductTokenization(Alphabet)</a></span> - Constructor for class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/CrossProductTokenization.html" title="class in org.biojava.bio.seq.io">CrossProductTokenization</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/CrossProductTokenization.html#CrossProductTokenization(org.biojava.bio.symbol.Alphabet, java.util.List)">CrossProductTokenization(Alphabet, List)</a></span> - Constructor for class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/CrossProductTokenization.html" title="class in org.biojava.bio.seq.io">CrossProductTokenization</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichFeature.html#CROSSREF">CROSSREF</a></span> - Static variable in interface org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichFeature.html" title="interface in org.biojavax.bio.seq">RichFeature</a></dt>
<dd> </dd>
<dt><a href="./org/biojavax/CrossRef.html" title="interface in org.biojavax"><span class="strong">CrossRef</span></a> - Interface in <a href="./org/biojavax/package-summary.html">org.biojavax</a></dt>
<dd>
<div class="block">Represents a cross reference to another database.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/DocRef.html#CROSSREF">CROSSREF</a></span> - Static variable in interface org.biojavax.<a href="./org/biojavax/DocRef.html" title="interface in org.biojavax">DocRef</a></dt>
<dd> </dd>
<dt><a href="./org/biojavax/CrossReferenceResolutionException.html" title="class in org.biojavax"><span class="strong">CrossReferenceResolutionException</span></a> - Exception in <a href="./org/biojavax/package-summary.html">org.biojavax</a></dt>
<dd>
<div class="block">An exception that indicates that an attempt to resolve a <code>CrossRef</code>
has failed.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/CrossReferenceResolutionException.html#CrossReferenceResolutionException()">CrossReferenceResolutionException()</a></span> - Constructor for exception org.biojavax.<a href="./org/biojavax/CrossReferenceResolutionException.html" title="class in org.biojavax">CrossReferenceResolutionException</a></dt>
<dd>
<div class="block">Creates a new instance of CrossReferenceResolutionException</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/CrossReferenceResolutionException.html#CrossReferenceResolutionException(java.lang.String)">CrossReferenceResolutionException(String)</a></span> - Constructor for exception org.biojavax.<a href="./org/biojavax/CrossReferenceResolutionException.html" title="class in org.biojavax">CrossReferenceResolutionException</a></dt>
<dd>
<div class="block">Creates a new instance of CrossReferenceResolutionException with a
message.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/CrossReferenceResolutionException.html#CrossReferenceResolutionException(java.lang.String, java.lang.Throwable)">CrossReferenceResolutionException(String, Throwable)</a></span> - Constructor for exception org.biojavax.<a href="./org/biojavax/CrossReferenceResolutionException.html" title="class in org.biojavax">CrossReferenceResolutionException</a></dt>
<dd>
<div class="block">Creates a new instance of CrossReferenceResolutionException with a
message and a cause.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/CrossReferenceResolutionException.html#CrossReferenceResolutionException(java.lang.Throwable)">CrossReferenceResolutionException(Throwable)</a></span> - Constructor for exception org.biojavax.<a href="./org/biojavax/CrossReferenceResolutionException.html" title="class in org.biojavax">CrossReferenceResolutionException</a></dt>
<dd>
<div class="block">Creates a new instance of CrossReferenceResolutionException with a
cause.</div>
</dd>
<dt><a href="./org/biojavax/CrossReferenceResolver.html" title="interface in org.biojavax"><span class="strong">CrossReferenceResolver</span></a> - Interface in <a href="./org/biojavax/package-summary.html">org.biojavax</a></dt>
<dd>
<div class="block">This interface returns symbols or sequence for a given cross-reference.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BibRef.html#crossReferences">crossReferences</a></span> - Variable in class org.biojava.bibliography.<a href="./org/biojava/bibliography/BibRef.html" title="class in org.biojava.bibliography">BibRef</a></dt>
<dd>
<div class="block">
It is an array of identifiers, all of them pointing to <em>the same cited source</em>
but usually stored in different bibliographic repositories.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/abi/ABIFParser.TaggedDataRecord.html#crypticVariable">crypticVariable</a></span> - Variable in class org.biojava.bio.program.abi.<a href="./org/biojava/bio/program/abi/ABIFParser.TaggedDataRecord.html" title="class in org.biojava.bio.program.abi">ABIFParser.TaggedDataRecord</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/hmmer/FullHmmerProfileHMM.html#cState()">cState()</a></span> - Method in class org.biojava.bio.program.hmmer.<a href="./org/biojava/bio/program/hmmer/FullHmmerProfileHMM.html" title="class in org.biojava.bio.program.hmmer">FullHmmerProfileHMM</a></dt>
<dd>
<div class="block">Gets the c loop state</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/HomologeneBuilder.html#CURATED">CURATED</a></span> - Static variable in interface org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/HomologeneBuilder.html" title="interface in org.biojava.bio.program.homologene">HomologeneBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/SimilarityType.html#CURATED">CURATED</a></span> - Static variable in interface org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/SimilarityType.html" title="interface in org.biojava.bio.program.homologene">SimilarityType</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/onehead/DPCursor.html#currentCol()">currentCol()</a></span> - Method in interface org.biojava.bio.dp.onehead.<a href="./org/biojava/bio/dp/onehead/DPCursor.html" title="interface in org.biojava.bio.dp.onehead">DPCursor</a></dt>
<dd>
<div class="block">The current column of the matrix.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/onehead/SmallCursor.html#currentCol()">currentCol()</a></span> - Method in class org.biojava.bio.dp.onehead.<a href="./org/biojava/bio/dp/onehead/SmallCursor.html" title="class in org.biojava.bio.dp.onehead">SmallCursor</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/onehead/DPCursor.html#currentRes()">currentRes()</a></span> - Method in interface org.biojava.bio.dp.onehead.<a href="./org/biojava/bio/dp/onehead/DPCursor.html" title="interface in org.biojava.bio.dp.onehead">DPCursor</a></dt>
<dd>
<div class="block">The current symbol.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/molbio/RestrictionEnzyme.html#CUT_COMPOUND">CUT_COMPOUND</a></span> - Static variable in class org.biojava.bio.molbio.<a href="./org/biojava/bio/molbio/RestrictionEnzyme.html" title="class in org.biojava.bio.molbio">RestrictionEnzyme</a></dt>
<dd>
<div class="block"><code>CUT_COMPOUND</code> a cut type where the enzyme cuts in
two positions relative to the recognition site.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/molbio/RestrictionEnzyme.html#CUT_SIMPLE">CUT_SIMPLE</a></span> - Static variable in class org.biojava.bio.molbio.<a href="./org/biojava/bio/molbio/RestrictionEnzyme.html" title="class in org.biojava.bio.molbio">RestrictionEnzyme</a></dt>
<dd>
<div class="block"><code>CUT_SIMPLE</code> a cut type where the enzyme cuts in one
position relative to the recognition site.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/molbio/RestrictionEnzyme.html#cutType">cutType</a></span> - Variable in class org.biojava.bio.molbio.<a href="./org/biojava/bio/molbio/RestrictionEnzyme.html" title="class in org.biojava.bio.molbio">RestrictionEnzyme</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/ProteinTools.html#cys()">cys()</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/ProteinTools.html" title="class in org.biojava.bio.seq">ProteinTools</a></dt>
<dd>
<div class="block">Returns the <code>AtomicSymbol</code> for the amino acid
Cysteine (C)</div>
</dd>
</dl>
<a name="_D_">
<!-- -->
</a>
<h2 class="title">D</h2>
<dl>
<dt><span class="strong"><a href="./org/biojava/bio/seq/DNATools.html#d()">d()</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/DNATools.html" title="class in org.biojava.bio.seq">DNATools</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/NucleotideTools.html#d()">d()</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/NucleotideTools.html" title="class in org.biojava.bio.seq">NucleotideTools</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/ProteinTools.html#d()">d()</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/ProteinTools.html" title="class in org.biojava.bio.seq">ProteinTools</a></dt>
<dd>
<div class="block">Returns the <code>AtomicSymbol</code> for the amino acid
Aspartic Acid</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/Taxon.html#D_MELANOGASTER">D_MELANOGASTER</a></span> - Static variable in interface org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/Taxon.html" title="interface in org.biojava.bio.program.homologene">Taxon</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/Taxon.html#D_RERIO">D_RERIO</a></span> - Static variable in interface org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/Taxon.html" title="interface in org.biojava.bio.program.homologene">Taxon</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/das/DAS.html" title="class in org.biojava.bio.program.das"><span class="strong">DAS</span></a> - Class in <a href="./org/biojava/bio/program/das/package-summary.html">org.biojava.bio.program.das</a></dt>
<dd>
<div class="block">A collection of DAS datasources.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/DAS.html#DAS()">DAS()</a></span> - Constructor for class org.biojava.bio.program.das.<a href="./org/biojava/bio/program/das/DAS.html" title="class in org.biojava.bio.program.das">DAS</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/das/dasalignment/DASAlignmentCall.html" title="class in org.biojava.bio.program.das.dasalignment"><span class="strong">DASAlignmentCall</span></a> - Class in <a href="./org/biojava/bio/program/das/dasalignment/package-summary.html">org.biojava.bio.program.das.dasalignment</a></dt>
<dd>
<div class="block">takes care of the communication with a DAS Alignment service.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/dasalignment/DASAlignmentCall.html#DASAlignmentCall()">DASAlignmentCall()</a></span> - Constructor for class org.biojava.bio.program.das.dasalignment.<a href="./org/biojava/bio/program/das/dasalignment/DASAlignmentCall.html" title="class in org.biojava.bio.program.das.dasalignment">DASAlignmentCall</a></dt>
<dd>
<div class="block">Constructs a DASAlignmentCall object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/dasalignment/DASAlignmentCall.html#DASAlignmentCall(java.lang.String)">DASAlignmentCall(String)</a></span> - Constructor for class org.biojava.bio.program.das.dasalignment.<a href="./org/biojava/bio/program/das/dasalignment/DASAlignmentCall.html" title="class in org.biojava.bio.program.das.dasalignment">DASAlignmentCall</a></dt>
<dd>
<div class="block">Constructs a DASAlignmentCall object.</div>
</dd>
<dt><a href="./org/biojava/bio/program/das/dasalignment/DASAlignmentClient.html" title="class in org.biojava.bio.program.das.dasalignment"><span class="strong">DASAlignmentClient</span></a> - Class in <a href="./org/biojava/bio/program/das/dasalignment/package-summary.html">org.biojava.bio.program.das.dasalignment</a></dt>
<dd>
<div class="block">A DAS client that connects to a DAS aligmnent service and
returns a Biojava Alignment object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/dasalignment/DASAlignmentClient.html#DASAlignmentClient()">DASAlignmentClient()</a></span> - Constructor for class org.biojava.bio.program.das.dasalignment.<a href="./org/biojava/bio/program/das/dasalignment/DASAlignmentClient.html" title="class in org.biojava.bio.program.das.dasalignment">DASAlignmentClient</a></dt>
<dd>
<div class="block">Constructs a DASAlignmentClient object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/dasalignment/DASAlignmentClient.html#DASAlignmentClient(java.lang.String)">DASAlignmentClient(String)</a></span> - Constructor for class org.biojava.bio.program.das.dasalignment.<a href="./org/biojava/bio/program/das/dasalignment/DASAlignmentClient.html" title="class in org.biojava.bio.program.das.dasalignment">DASAlignmentClient</a></dt>
<dd>
<div class="block">Constructs a DASAlignmentClient object.</div>
</dd>
<dt><a href="./org/biojava/bio/program/das/dasalignment/DASAlignmentXMLResponseParser.html" title="class in org.biojava.bio.program.das.dasalignment"><span class="strong">DASAlignmentXMLResponseParser</span></a> - Class in <a href="./org/biojava/bio/program/das/dasalignment/package-summary.html">org.biojava.bio.program.das.dasalignment</a></dt>
<dd>
<div class="block">A class to Parse the XML response of a DAS Alignment service.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/dasalignment/DASAlignmentXMLResponseParser.html#DASAlignmentXMLResponseParser()">DASAlignmentXMLResponseParser()</a></span> - Constructor for class org.biojava.bio.program.das.dasalignment.<a href="./org/biojava/bio/program/das/dasalignment/DASAlignmentXMLResponseParser.html" title="class in org.biojava.bio.program.das.dasalignment">DASAlignmentXMLResponseParser</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/das/dasalignment/DASException.html" title="class in org.biojava.bio.program.das.dasalignment"><span class="strong">DASException</span></a> - Exception in <a href="./org/biojava/bio/program/das/dasalignment/package-summary.html">org.biojava.bio.program.das.dasalignment</a></dt>
<dd>
<div class="block">An exception of one of the DAS classes.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/dasalignment/DASException.html#DASException(java.lang.String)">DASException(String)</a></span> - Constructor for exception org.biojava.bio.program.das.dasalignment.<a href="./org/biojava/bio/program/das/dasalignment/DASException.html" title="class in org.biojava.bio.program.das.dasalignment">DASException</a></dt>
<dd>
<div class="block">Constructs a DASException object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/dasalignment/DASException.html#DASException(java.lang.Throwable, java.lang.String)">DASException(Throwable, String)</a></span> - Constructor for exception org.biojava.bio.program.das.dasalignment.<a href="./org/biojava/bio/program/das/dasalignment/DASException.html" title="class in org.biojava.bio.program.das.dasalignment">DASException</a></dt>
<dd>
<div class="block">Constructs a DASException object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/dasalignment/DASException.html#DASException(java.lang.Throwable)">DASException(Throwable)</a></span> - Constructor for exception org.biojava.bio.program.das.dasalignment.<a href="./org/biojava/bio/program/das/dasalignment/DASException.html" title="class in org.biojava.bio.program.das.dasalignment">DASException</a></dt>
<dd>
<div class="block">Constructs a DASException object.</div>
</dd>
<dt><a href="./org/biojava/bio/program/das/DASLink.html" title="class in org.biojava.bio.program.das"><span class="strong">DASLink</span></a> - Class in <a href="./org/biojava/bio/program/das/package-summary.html">org.biojava.bio.program.das</a></dt>
<dd>
<div class="block">A memento class for storing a link.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/DASLink.html#DASLink(java.lang.String, java.lang.String)">DASLink(String, String)</a></span> - Constructor for class org.biojava.bio.program.das.<a href="./org/biojava/bio/program/das/DASLink.html" title="class in org.biojava.bio.program.das">DASLink</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/das/DASSequence.html" title="class in org.biojava.bio.program.das"><span class="strong">DASSequence</span></a> - Class in <a href="./org/biojava/bio/program/das/package-summary.html">org.biojava.bio.program.das</a></dt>
<dd>
<div class="block">Sequence reflecting a DAS reference sequence, possibly
decorated with one of more annotation sets.</div>
</dd>
<dt><a href="./org/biojava/bio/program/das/DASSequenceDB.html" title="class in org.biojava.bio.program.das"><span class="strong">DASSequenceDB</span></a> - Class in <a href="./org/biojava/bio/program/das/package-summary.html">org.biojava.bio.program.das</a></dt>
<dd>
<div class="block">
Collection of sequences retrieved from the DAS network.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/DASSequenceDB.html#DASSequenceDB(java.net.URL)">DASSequenceDB(URL)</a></span> - Constructor for class org.biojava.bio.program.das.<a href="./org/biojava/bio/program/das/DASSequenceDB.html" title="class in org.biojava.bio.program.das">DASSequenceDB</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/das/DASSequenceDBProvider.html" title="class in org.biojava.bio.program.das"><span class="strong">DASSequenceDBProvider</span></a> - Class in <a href="./org/biojava/bio/program/das/package-summary.html">org.biojava.bio.program.das</a></dt>
<dd>
<div class="block">Hook DAS into the OBDA directory system.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/DASSequenceDBProvider.html#DASSequenceDBProvider()">DASSequenceDBProvider()</a></span> - Constructor for class org.biojava.bio.program.das.<a href="./org/biojava/bio/program/das/DASSequenceDBProvider.html" title="class in org.biojava.bio.program.das">DASSequenceDBProvider</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/das/dasstructure/DASStructureCall.html" title="class in org.biojava.bio.program.das.dasstructure"><span class="strong">DASStructureCall</span></a> - Class in <a href="./org/biojava/bio/program/das/dasstructure/package-summary.html">org.biojava.bio.program.das.dasstructure</a></dt>
<dd>
<div class="block">Calls a DAS - Structure server.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/dasstructure/DASStructureCall.html#DASStructureCall()">DASStructureCall()</a></span> - Constructor for class org.biojava.bio.program.das.dasstructure.<a href="./org/biojava/bio/program/das/dasstructure/DASStructureCall.html" title="class in org.biojava.bio.program.das.dasstructure">DASStructureCall</a></dt>
<dd>
<div class="block">Constructs a DASStructureCall object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/dasstructure/DASStructureCall.html#DASStructureCall(java.lang.String)">DASStructureCall(String)</a></span> - Constructor for class org.biojava.bio.program.das.dasstructure.<a href="./org/biojava/bio/program/das/dasstructure/DASStructureCall.html" title="class in org.biojava.bio.program.das.dasstructure">DASStructureCall</a></dt>
<dd>
<div class="block">Constructs a DASStructureCall object.</div>
</dd>
<dt><a href="./org/biojava/bio/structure/io/DASStructureClient.html" title="class in org.biojava.bio.structure.io"><span class="strong">DASStructureClient</span></a> - Class in <a href="./org/biojava/bio/structure/io/package-summary.html">org.biojava.bio.structure.io</a></dt>
<dd>
<div class="block">A DAS client that connects to a DAS structure service and
returns a Biojava structure class.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/DASStructureClient.html#DASStructureClient(java.lang.String)">DASStructureClient(String)</a></span> - Constructor for class org.biojava.bio.structure.io.<a href="./org/biojava/bio/structure/io/DASStructureClient.html" title="class in org.biojava.bio.structure.io">DASStructureClient</a></dt>
<dd>
<div class="block">Constructs a DASStructureClient object.</div>
</dd>
<dt><a href="./org/biojava/bio/program/das/dasstructure/DASStructureXMLResponseParser.html" title="class in org.biojava.bio.program.das.dasstructure"><span class="strong">DASStructureXMLResponseParser</span></a> - Class in <a href="./org/biojava/bio/program/das/dasstructure/package-summary.html">org.biojava.bio.program.das.dasstructure</a></dt>
<dd>
<div class="block">a class to Parse the XML response of a DAS structure service.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/dasstructure/DASStructureXMLResponseParser.html#DASStructureXMLResponseParser()">DASStructureXMLResponseParser()</a></span> - Constructor for class org.biojava.bio.program.das.dasstructure.<a href="./org/biojava/bio/program/das/dasstructure/DASStructureXMLResponseParser.html" title="class in org.biojava.bio.program.das.dasstructure">DASStructureXMLResponseParser</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/FlexibleAlignment.html#data">data</a></span> - Variable in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/FlexibleAlignment.html" title="class in org.biojava.bio.alignment">FlexibleAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/abi/ABIFParser.TaggedDataRecord.html#DATA_TYPE_ASCII_ARRAY">DATA_TYPE_ASCII_ARRAY</a></span> - Static variable in class org.biojava.bio.program.abi.<a href="./org/biojava/bio/program/abi/ABIFParser.TaggedDataRecord.html" title="class in org.biojava.bio.program.abi">ABIFParser.TaggedDataRecord</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/abi/ABIFParser.TaggedDataRecord.html#DATA_TYPE_DATE">DATA_TYPE_DATE</a></span> - Static variable in class org.biojava.bio.program.abi.<a href="./org/biojava/bio/program/abi/ABIFParser.TaggedDataRecord.html" title="class in org.biojava.bio.program.abi">ABIFParser.TaggedDataRecord</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/abi/ABIFParser.TaggedDataRecord.html#DATA_TYPE_FLOAT">DATA_TYPE_FLOAT</a></span> - Static variable in class org.biojava.bio.program.abi.<a href="./org/biojava/bio/program/abi/ABIFParser.TaggedDataRecord.html" title="class in org.biojava.bio.program.abi">ABIFParser.TaggedDataRecord</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/abi/ABIFParser.TaggedDataRecord.html#DATA_TYPE_INTEGER">DATA_TYPE_INTEGER</a></span> - Static variable in class org.biojava.bio.program.abi.<a href="./org/biojava/bio/program/abi/ABIFParser.TaggedDataRecord.html" title="class in org.biojava.bio.program.abi">ABIFParser.TaggedDataRecord</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/abi/ABIFParser.TaggedDataRecord.html#DATA_TYPE_PSTRING">DATA_TYPE_PSTRING</a></span> - Static variable in class org.biojava.bio.program.abi.<a href="./org/biojava/bio/program/abi/ABIFParser.TaggedDataRecord.html" title="class in org.biojava.bio.program.abi">ABIFParser.TaggedDataRecord</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/abi/ABIFParser.TaggedDataRecord.html#DATA_TYPE_TIME">DATA_TYPE_TIME</a></span> - Static variable in class org.biojava.bio.program.abi.<a href="./org/biojava/bio/program/abi/ABIFParser.TaggedDataRecord.html" title="class in org.biojava.bio.program.abi">ABIFParser.TaggedDataRecord</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html#DATABASE">DATABASE</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html" title="class in org.biojavax.bio.seq.io">UniProtCommentParser</a></dt>
<dd>
<div class="block">A name for a comment type.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLFormat.html#DATABASE_XREF_TAG">DATABASE_XREF_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLFormat.html" title="class in org.biojavax.bio.seq.io">EMBLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/INSDseqFormat.html#DATABASE_XREF_TAG">DATABASE_XREF_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/INSDseqFormat.html" title="class in org.biojavax.bio.seq.io">INSDseqFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtFormat.html#DATABASE_XREF_TAG">DATABASE_XREF_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtFormat.html" title="class in org.biojavax.bio.seq.io">UniProtFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/ViewSequenceFactory.html#databaseID">databaseID</a></span> - Variable in class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/ViewSequenceFactory.html" title="class in org.biojava.bio.program.ssbind">ViewSequenceFactory</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/structure/io/mmcif/model/DatabasePDBremark.html" title="class in org.biojava.bio.structure.io.mmcif.model"><span class="strong">DatabasePDBremark</span></a> - Class in <a href="./org/biojava/bio/structure/io/mmcif/model/package-summary.html">org.biojava.bio.structure.io.mmcif.model</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/DatabasePDBremark.html#DatabasePDBremark()">DatabasePDBremark()</a></span> - Constructor for class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/DatabasePDBremark.html" title="class in org.biojava.bio.structure.io.mmcif.model">DatabasePDBremark</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/structure/io/mmcif/model/DatabasePDBrev.html" title="class in org.biojava.bio.structure.io.mmcif.model"><span class="strong">DatabasePDBrev</span></a> - Class in <a href="./org/biojava/bio/structure/io/mmcif/model/package-summary.html">org.biojava.bio.structure.io.mmcif.model</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/DatabasePDBrev.html#DatabasePDBrev()">DatabasePDBrev()</a></span> - Constructor for class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/DatabasePDBrev.html" title="class in org.biojava.bio.structure.io.mmcif.model">DatabasePDBrev</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/blast2html/DatabaseURLGenerator.html" title="interface in org.biojava.bio.program.blast2html"><span class="strong">DatabaseURLGenerator</span></a> - Interface in <a href="./org/biojava/bio/program/blast2html/package-summary.html">org.biojava.bio.program.blast2html</a></dt>
<dd>
<div class="block">Takes a database ID and some configuration properties
( such as base URL ) and returns either a URL or
a full anchor tag.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/abi/ABIFParser.TaggedDataRecord.html#dataRecord">dataRecord</a></span> - Variable in class org.biojava.bio.program.abi.<a href="./org/biojava/bio/program/abi/ABIFParser.TaggedDataRecord.html" title="class in org.biojava.bio.program.abi">ABIFParser.TaggedDataRecord</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/das/DataSource.html" title="class in org.biojava.bio.program.das"><span class="strong">DataSource</span></a> - Class in <a href="./org/biojava/bio/program/das/package-summary.html">org.biojava.bio.program.das</a></dt>
<dd>
<div class="block">Reflect a datasource (reference or annotation) in the DAS1 network.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/distributed/DistributedSequenceDB.html#DATASOURCE">DATASOURCE</a></span> - Static variable in class org.biojava.bio.seq.distributed.<a href="./org/biojava/bio/seq/distributed/DistributedSequenceDB.html" title="class in org.biojava.bio.seq.distributed">DistributedSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/PDBMSDReader.html#dataSource">dataSource</a></span> - Variable in class org.biojava.bio.structure.io.<a href="./org/biojava/bio/structure/io/PDBMSDReader.html" title="class in org.biojava.bio.structure.io">PDBMSDReader</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/distributed/DistributedSequenceDB.html#DATASOURCE_SELECTION">DATASOURCE_SELECTION</a></span> - Static variable in class org.biojava.bio.seq.distributed.<a href="./org/biojava/bio/seq/distributed/DistributedSequenceDB.html" title="class in org.biojava.bio.seq.distributed">DistributedSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/DASSequence.html#dataSourceURLs()">dataSourceURLs()</a></span> - Method in class org.biojava.bio.program.das.<a href="./org/biojava/bio/program/das/DASSequence.html" title="class in org.biojava.bio.program.das">DASSequence</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/ssaha/DataStore.html" title="interface in org.biojava.bio.program.ssaha"><span class="strong">DataStore</span></a> - Interface in <a href="./org/biojava/bio/program/ssaha/package-summary.html">org.biojava.bio.program.ssaha</a></dt>
<dd>
<div class="block">A repository that can be searched with a sequence.</div>
</dd>
<dt><a href="./org/biojava/bio/program/ssaha/DataStoreFactory.html" title="interface in org.biojava.bio.program.ssaha"><span class="strong">DataStoreFactory</span></a> - Interface in <a href="./org/biojava/bio/program/ssaha/package-summary.html">org.biojava.bio.program.ssaha</a></dt>
<dd>
<div class="block">
Builder for a data store.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/abi/ABIFParser.TaggedDataRecord.html#dataType">dataType</a></span> - Variable in class org.biojava.bio.program.abi.<a href="./org/biojava/bio/program/abi/ABIFParser.TaggedDataRecord.html" title="class in org.biojava.bio.program.abi">ABIFParser.TaggedDataRecord</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BibRef.html#date">date</a></span> - Variable in class org.biojava.bibliography.<a href="./org/biojava/bibliography/BibRef.html" title="class in org.biojava.bibliography">BibRef</a></dt>
<dd>
<div class="block">
Defines a date associated with an event in the life cycle of the cited resource
when this resource became available.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/EmblLikeFormat.html#DATE_TAG">DATE_TAG</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/EmblLikeFormat.html" title="class in org.biojava.bio.seq.io">EmblLikeFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/GenbankFormat.html#DATE_TAG">DATE_TAG</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/GenbankFormat.html" title="class in org.biojava.bio.seq.io">GenbankFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLFormat.html#DATE_TAG">DATE_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLFormat.html" title="class in org.biojavax.bio.seq.io">EMBLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtFormat.html#DATE_TAG">DATE_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtFormat.html" title="class in org.biojavax.bio.seq.io">UniProtFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/server/FlatFileInstallation.html#dateFormat">dateFormat</a></span> - Static variable in class org.biojava.bio.structure.server.<a href="./org/biojava/bio/structure/server/FlatFileInstallation.html" title="class in org.biojava.bio.structure.server">FlatFileInstallation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/obo/OboFileParser.html#dateFormat">dateFormat</a></span> - Variable in class org.biojava.ontology.obo.<a href="./org/biojava/ontology/obo/OboFileParser.html" title="class in org.biojava.ontology.obo">OboFileParser</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/NCBISequenceDB.html#DB_NUCLEOTIDE">DB_NUCLEOTIDE</a></span> - Static variable in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/NCBISequenceDB.html" title="class in org.biojava.bio.seq.db">NCBISequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/NCBISequenceDB.html#DB_PROTEIN">DB_PROTEIN</a></span> - Static variable in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/NCBISequenceDB.html" title="class in org.biojava.bio.seq.db">NCBISequenceDB</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/db/biosql/DBHelper.html" title="class in org.biojava.bio.seq.db.biosql"><span class="strong">DBHelper</span></a> - Class in <a href="./org/biojava/bio/seq/db/biosql/package-summary.html">org.biojava.bio.seq.db.biosql</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>Use hibernate and org.biojavax.bio.db.*</i></div>
</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/biosql/DBHelper.html#DBHelper()">DBHelper()</a></span> - Constructor for class org.biojava.bio.seq.db.biosql.<a href="./org/biojava/bio/seq/db/biosql/DBHelper.html" title="class in org.biojava.bio.seq.db.biosql">DBHelper</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><a href="./org/biojava/bio/seq/db/biosql/DBHelper.BioSequenceStyle.html" title="class in org.biojava.bio.seq.db.biosql"><span class="strong">DBHelper.BioSequenceStyle</span></a> - Class in <a href="./org/biojava/bio/seq/db/biosql/package-summary.html">org.biojava.bio.seq.db.biosql</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><a href="./org/biojava/bio/seq/db/biosql/DBHelper.DeleteStyle.html" title="class in org.biojava.bio.seq.db.biosql"><span class="strong">DBHelper.DeleteStyle</span></a> - Class in <a href="./org/biojava/bio/seq/db/biosql/package-summary.html">org.biojava.bio.seq.db.biosql</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><a href="./org/biojava/bio/seq/db/biosql/DBHelper.JoinStyle.html" title="class in org.biojava.bio.seq.db.biosql"><span class="strong">DBHelper.JoinStyle</span></a> - Class in <a href="./org/biojava/bio/seq/db/biosql/package-summary.html">org.biojava.bio.seq.db.biosql</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><a href="./org/biojava/bio/structure/DBRef.html" title="class in org.biojava.bio.structure"><span class="strong">DBRef</span></a> - Class in <a href="./org/biojava/bio/structure/package-summary.html">org.biojava.bio.structure</a></dt>
<dd>
<div class="block">A class to represent database cross references.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/DBRef.html#DBRef()">DBRef()</a></span> - Constructor for class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/DBRef.html" title="class in org.biojava.bio.structure">DBRef</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html#DBREF_DB_ATTR">DBREF_DB_ATTR</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html" title="class in org.biojavax.bio.seq.io">EMBLxmlFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html#DBREF_PRIMARY_ATTR">DBREF_PRIMARY_ATTR</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html" title="class in org.biojavax.bio.seq.io">EMBLxmlFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html#DBREF_SEC_ATTR">DBREF_SEC_ATTR</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html" title="class in org.biojavax.bio.seq.io">EMBLxmlFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html#DBREFERENCE_TAG">DBREFERENCE_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html" title="class in org.biojavax.bio.seq.io">EMBLxmlFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLFormat.html#dbxp">dbxp</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLFormat.html" title="class in org.biojavax.bio.seq.io">EMBLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/GenbankFormat.html#dbxp">dbxp</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/GenbankFormat.html" title="class in org.biojavax.bio.seq.io">GenbankFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/INSDseqFormat.html#dbxp">dbxp</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/INSDseqFormat.html" title="class in org.biojavax.bio.seq.io">INSDseqFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#DBXREF_TAG">DBXREF_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/AbstractULAlignment.html#debug(java.lang.String)">debug(String)</a></span> - Method in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/AbstractULAlignment.html" title="class in org.biojava.bio.alignment">AbstractULAlignment</a></dt>
<dd> </dd>
<dt><a href="./org/biojavax/bio/seq/io/DebuggingRichSeqIOListener.html" title="class in org.biojavax.bio.seq.io"><span class="strong">DebuggingRichSeqIOListener</span></a> - Class in <a href="./org/biojavax/bio/seq/io/package-summary.html">org.biojavax.bio.seq.io</a></dt>
<dd>
<div class="block">This is purely for debugging purposes.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/DebuggingRichSeqIOListener.html#DebuggingRichSeqIOListener(java.io.InputStream)">DebuggingRichSeqIOListener(InputStream)</a></span> - Constructor for class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/DebuggingRichSeqIOListener.html" title="class in org.biojavax.bio.seq.io">DebuggingRichSeqIOListener</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/xml/PrettyXMLWriter.html#declareNamespace(java.lang.String, java.lang.String)">declareNamespace(String, String)</a></span> - Method in class org.biojava.utils.xml.<a href="./org/biojava/utils/xml/PrettyXMLWriter.html" title="class in org.biojava.utils.xml">PrettyXMLWriter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/xml/XMLWriter.html#declareNamespace(java.lang.String, java.lang.String)">declareNamespace(String, String)</a></span> - Method in interface org.biojava.utils.xml.<a href="./org/biojava/utils/xml/XMLWriter.html" title="interface in org.biojava.utils.xml">XMLWriter</a></dt>
<dd>
<div class="block">Hints that a namespace is going to be used in a sub-tree.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/abi/ABIFParser.html#decodeDNAToken(char)">decodeDNAToken(char)</a></span> - Static method in class org.biojava.bio.program.abi.<a href="./org/biojava/bio/program/abi/ABIFParser.html" title="class in org.biojava.bio.program.abi">ABIFParser</a></dt>
<dd>
<div class="block">Decodes a character into a <a href="./org/biojava/bio/symbol/Symbol.html" title="interface in org.biojava.bio.symbol"><code>Symbol</code></a> in the DNA alphabet.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AbstractLocationDecorator.html#decorate(org.biojava.bio.symbol.Location)">decorate(Location)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AbstractLocationDecorator.html" title="class in org.biojava.bio.symbol">AbstractLocationDecorator</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/BetweenLocation.html#decorate(org.biojava.bio.symbol.Location)">decorate(Location)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/BetweenLocation.html" title="class in org.biojava.bio.symbol">BetweenLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/CircularLocation.html#decorate(org.biojava.bio.symbol.Location)">decorate(Location)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/CircularLocation.html" title="class in org.biojava.bio.symbol">CircularLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/obo/OboFileHandler.html#DEF">DEF</a></span> - Static variable in class org.biojava.ontology.obo.<a href="./org/biojava/ontology/obo/OboFileHandler.html" title="class in org.biojava.ontology.obo">OboFileHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/server/FlatFileInstallation.html#DEFAUL_CHAIN_FILE">DEFAUL_CHAIN_FILE</a></span> - Static variable in class org.biojava.bio.structure.server.<a href="./org/biojava/bio/structure/server/FlatFileInstallation.html" title="class in org.biojava.bio.structure.server">FlatFileInstallation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/DistributionFactory.html#DEFAULT">DEFAULT</a></span> - Static variable in interface org.biojava.bio.dist.<a href="./org/biojava/bio/dist/DistributionFactory.html" title="interface in org.biojava.bio.dist">DistributionFactory</a></dt>
<dd>
<div class="block">
The default DistributionFactory object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/OrderNDistributionFactory.html#DEFAULT">DEFAULT</a></span> - Static variable in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/OrderNDistributionFactory.html" title="class in org.biojava.bio.dist">OrderNDistributionFactory</a></dt>
<dd>
<div class="block">Factory which used DistributionFactory.DEFAULT to create conditioned
distributions.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/DPFactory.html#DEFAULT">DEFAULT</a></span> - Static variable in interface org.biojava.bio.dp.<a href="./org/biojava/bio/dp/DPFactory.html" title="interface in org.biojava.bio.dp">DPFactory</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/phred/PhredFormat.html#DEFAULT">DEFAULT</a></span> - Static variable in class org.biojava.bio.program.phred.<a href="./org/biojava/bio/program/phred/PhredFormat.html" title="class in org.biojava.bio.program.phred">PhredFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/FeatureImpl.html#DEFAULT">DEFAULT</a></span> - Static variable in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/FeatureImpl.html" title="class in org.biojava.bio.seq.impl">FeatureImpl</a></dt>
<dd>
<div class="block">Default implementation of FeatureRealizer, which wraps simple
implementations of Feature and StrandedFeature.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/EmblLikeFormat.html#DEFAULT">DEFAULT</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/EmblLikeFormat.html" title="class in org.biojava.bio.seq.io">EmblLikeFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/FastaFormat.html#DEFAULT">DEFAULT</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/FastaFormat.html" title="class in org.biojava.bio.seq.io">FastaFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/GAMEFormat.html#DEFAULT">DEFAULT</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/GAMEFormat.html" title="class in org.biojava.bio.seq.io">GAMEFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/GenbankFormat.html#DEFAULT">DEFAULT</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/GenbankFormat.html" title="class in org.biojava.bio.seq.io">GenbankFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/projection/ProjectionEngine.html#DEFAULT">DEFAULT</a></span> - Static variable in class org.biojava.bio.seq.projection.<a href="./org/biojava/bio/seq/projection/ProjectionEngine.html" title="class in org.biojava.bio.seq.projection">ProjectionEngine</a></dt>
<dd>
<div class="block">The standard projection engine object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SoftMaskedAlphabet.MaskingDetector.html#DEFAULT">DEFAULT</a></span> - Static variable in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SoftMaskedAlphabet.MaskingDetector.html" title="interface in org.biojava.bio.symbol">SoftMaskedAlphabet.MaskingDetector</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/functions/SelectionFunction.html#DEFAULT">DEFAULT</a></span> - Static variable in interface org.biojavax.ga.functions.<a href="./org/biojavax/ga/functions/SelectionFunction.html" title="interface in org.biojavax.ga.functions">SelectionFunction</a></dt>
<dd>
<div class="block">Selects all members of a population for replication</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/ChainImpl.html#DEFAULT_CHAIN_ID">DEFAULT_CHAIN_ID</a></span> - Static variable in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/ChainImpl.html" title="class in org.biojava.bio.structure">ChainImpl</a></dt>
<dd>
<div class="block">The default chain identifier is an empty space.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/ClusterAltAligs.html#DEFAULT_CLUSTER_CUTOFF">DEFAULT_CLUSTER_CUTOFF</a></span> - Static variable in class org.biojava.bio.structure.align.<a href="./org/biojava/bio/structure/align/ClusterAltAligs.html" title="class in org.biojava.bio.structure.align">ClusterAltAligs</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/functions/CrossOverFunction.html#DEFAULT_CROSS_PROB">DEFAULT_CROSS_PROB</a></span> - Static variable in interface org.biojavax.ga.functions.<a href="./org/biojavax/ga/functions/CrossOverFunction.html" title="interface in org.biojavax.ga.functions">CrossOverFunction</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/TypedProperties.html#DEFAULT_DELIMITERS">DEFAULT_DELIMITERS</a></span> - Static variable in class org.biojava.utils.<a href="./org/biojava/utils/TypedProperties.html" title="class in org.biojava.utils">TypedProperties</a></dt>
<dd>
<div class="block">the default string of delimiter characters used by getAsStringList()</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/candy/CandyFinder.html#DEFAULT_FINDER_NAME">DEFAULT_FINDER_NAME</a></span> - Static variable in interface org.biojava.utils.candy.<a href="./org/biojava/utils/candy/CandyFinder.html" title="interface in org.biojava.utils.candy">CandyFinder</a></dt>
<dd>
<div class="block">A default name of this (and any) finder.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/server/FlatFileInstallation.html#DEFAULT_INDEX_FILE">DEFAULT_INDEX_FILE</a></span> - Static variable in class org.biojava.bio.structure.server.<a href="./org/biojava/bio/structure/server/FlatFileInstallation.html" title="class in org.biojava.bio.structure.server">FlatFileInstallation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/functions/CrossOverFunction.html#DEFAULT_MAX_CROSS">DEFAULT_MAX_CROSS</a></span> - Static variable in interface org.biojavax.ga.functions.<a href="./org/biojavax/ga/functions/CrossOverFunction.html" title="interface in org.biojavax.ga.functions">CrossOverFunction</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/functions/MutationFunction.html#DEFAULT_MUTATION_PROBS">DEFAULT_MUTATION_PROBS</a></span> - Static variable in interface org.biojavax.ga.functions.<a href="./org/biojavax/ga/functions/MutationFunction.html" title="interface in org.biojavax.ga.functions">MutationFunction</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/PDBHeader.html#DEFAULT_RESOLUTION">DEFAULT_RESOLUTION</a></span> - Static variable in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/PDBHeader.html" title="class in org.biojava.bio.structure">PDBHeader</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/UkkonenSuffixTree.html#DEFAULT_TERM_CHAR">DEFAULT_TERM_CHAR</a></span> - Static variable in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/UkkonenSuffixTree.html" title="class in org.biojava.bio.symbol">UkkonenSuffixTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/fastq/FastqBuilder.html#DEFAULT_VARIANT">DEFAULT_VARIANT</a></span> - Static variable in class org.biojava.bio.program.fastq.<a href="./org/biojava/bio/program/fastq/FastqBuilder.html" title="class in org.biojava.bio.program.fastq">FastqBuilder</a></dt>
<dd>
<div class="block">Default FASTQ sequence format variant, <code>FastqVariant.FASTQ_SANGER</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/util/SequenceScalePanel.html#DEFAULT_X_RIGHT_BORDER">DEFAULT_X_RIGHT_BORDER</a></span> - Static variable in class org.biojava.bio.structure.gui.util.<a href="./org/biojava/bio/structure/gui/util/SequenceScalePanel.html" title="class in org.biojava.bio.structure.gui.util">SequenceScalePanel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/util/SequenceScalePanel.html#DEFAULT_X_START">DEFAULT_X_START</a></span> - Static variable in class org.biojava.bio.structure.gui.util.<a href="./org/biojava/bio/structure/gui/util/SequenceScalePanel.html" title="class in org.biojava.bio.structure.gui.util">SequenceScalePanel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/util/SequenceScalePanel.html#DEFAULT_Y_BOTTOM">DEFAULT_Y_BOTTOM</a></span> - Static variable in class org.biojava.bio.structure.gui.util.<a href="./org/biojava/bio/structure/gui/util/SequenceScalePanel.html" title="class in org.biojava.bio.structure.gui.util">SequenceScalePanel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/util/SequenceScalePanel.html#DEFAULT_Y_HEIGHT">DEFAULT_Y_HEIGHT</a></span> - Static variable in class org.biojava.bio.structure.gui.util.<a href="./org/biojava/bio/structure/gui/util/SequenceScalePanel.html" title="class in org.biojava.bio.structure.gui.util">SequenceScalePanel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/util/SequenceScalePanel.html#DEFAULT_Y_START">DEFAULT_Y_START</a></span> - Static variable in class org.biojava.bio.structure.gui.util.<a href="./org/biojava/bio/structure/gui/util/SequenceScalePanel.html" title="class in org.biojava.bio.structure.gui.util">SequenceScalePanel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/util/SequenceScalePanel.html#DEFAULT_Y_STEP">DEFAULT_Y_STEP</a></span> - Static variable in class org.biojava.bio.structure.gui.util.<a href="./org/biojava/bio/structure/gui/util/SequenceScalePanel.html" title="class in org.biojava.bio.structure.gui.util">SequenceScalePanel</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/ontology/DefaultOps.html" title="class in org.biojava.ontology"><span class="strong">DefaultOps</span></a> - Class in <a href="./org/biojava/ontology/package-summary.html">org.biojava.ontology</a></dt>
<dd>
<div class="block">Default implementation of OntologyOps.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/DefaultOps.html#DefaultOps()">DefaultOps()</a></span> - Constructor for class org.biojava.ontology.<a href="./org/biojava/ontology/DefaultOps.html" title="class in org.biojava.ontology">DefaultOps</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/blast2html/DefaultURLGeneratorFactory.html" title="class in org.biojava.bio.program.blast2html"><span class="strong">DefaultURLGeneratorFactory</span></a> - Class in <a href="./org/biojava/bio/program/blast2html/package-summary.html">org.biojava.bio.program.blast2html</a></dt>
<dd>
<div class="block">A simple default <code>URLGeneratorFactory</code> which returns
a single <code>NcbiDatabaseURLGenerator</code> instance.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/blast2html/DefaultURLGeneratorFactory.html#DefaultURLGeneratorFactory()">DefaultURLGeneratorFactory()</a></span> - Constructor for class org.biojava.bio.program.blast2html.<a href="./org/biojava/bio/program/blast2html/DefaultURLGeneratorFactory.html" title="class in org.biojava.bio.program.blast2html">DefaultURLGeneratorFactory</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/EmblLikeFormat.html#DEFINITION_TAG">DEFINITION_TAG</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/EmblLikeFormat.html" title="class in org.biojava.bio.seq.io">EmblLikeFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/GenbankFormat.html#DEFINITION_TAG">DEFINITION_TAG</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/GenbankFormat.html" title="class in org.biojava.bio.seq.io">GenbankFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLFormat.html#DEFINITION_TAG">DEFINITION_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLFormat.html" title="class in org.biojavax.bio.seq.io">EMBLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/GenbankFormat.html#DEFINITION_TAG">DEFINITION_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/GenbankFormat.html" title="class in org.biojavax.bio.seq.io">GenbankFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/INSDseqFormat.html#DEFINITION_TAG">DEFINITION_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/INSDseqFormat.html" title="class in org.biojavax.bio.seq.io">INSDseqFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtFormat.html#DEFINITION_TAG">DEFINITION_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtFormat.html" title="class in org.biojavax.bio.seq.io">UniProtFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Calc.html#degreesPerRadian">degreesPerRadian</a></span> - Static variable in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Calc.html" title="class in org.biojava.bio.structure">Calc</a></dt>
<dd>
<div class="block">Degrees per radian.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/StateMachine.html#delegate">delegate</a></span> - Variable in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/StateMachine.html" title="class in org.biojava.bio.program.tagvalue">StateMachine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/DelegationManager.html#delegate(org.biojava.bio.seq.io.agave.StAXContentHandler)">delegate(StAXContentHandler)</a></span> - Method in interface org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/DelegationManager.html" title="interface in org.biojava.bio.seq.io.agave">DelegationManager</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/stax/DelegationManager.html#delegate(org.biojava.utils.stax.StAXContentHandler)">delegate(StAXContentHandler)</a></span> - Method in interface org.biojava.utils.stax.<a href="./org/biojava/utils/stax/DelegationManager.html" title="interface in org.biojava.utils.stax">DelegationManager</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/AbstractBeadRenderer.html#delegates">delegates</a></span> - Variable in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/AbstractBeadRenderer.html" title="class in org.biojava.bio.gui.sequence">AbstractBeadRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/AbstractBeadRenderer.html#delegationCache">delegationCache</a></span> - Variable in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/AbstractBeadRenderer.html" title="class in org.biojava.bio.gui.sequence">AbstractBeadRenderer</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/io/agave/DelegationManager.html" title="interface in org.biojava.bio.seq.io.agave"><span class="strong">DelegationManager</span></a> - Interface in <a href="./org/biojava/bio/seq/io/agave/package-summary.html">org.biojava.bio.seq.io.agave</a></dt>
<dd>
<div class="block">Interface which exposes delegation services offered by a StAX
event source.</div>
</dd>
<dt><a href="./org/biojava/utils/stax/DelegationManager.html" title="interface in org.biojava.utils.stax"><span class="strong">DelegationManager</span></a> - Interface in <a href="./org/biojava/utils/stax/package-summary.html">org.biojava.utils.stax</a></dt>
<dd>
<div class="block">Interface which exposes delegation services offered by a StAX
event source.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/biosql/DBHelper.html#DELETE_GENERIC">DELETE_GENERIC</a></span> - Static variable in class org.biojava.bio.seq.db.biosql.<a href="./org/biojava/bio/seq/db/biosql/DBHelper.html" title="class in org.biojava.bio.seq.db.biosql">DBHelper</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/biosql/DBHelper.html#DELETE_MYSQL4">DELETE_MYSQL4</a></span> - Static variable in class org.biojava.bio.seq.db.biosql.<a href="./org/biojava/bio/seq/db/biosql/DBHelper.html" title="class in org.biojava.bio.seq.db.biosql">DBHelper</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/biosql/DBHelper.html#DELETE_POSTGRESQL">DELETE_POSTGRESQL</a></span> - Static variable in class org.biojava.bio.seq.db.biosql.<a href="./org/biojava/bio/seq/db/biosql/DBHelper.html" title="class in org.biojava.bio.seq.db.biosql">DBHelper</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/IntegerOntology.html#deleteTerm(org.biojava.ontology.Term)">deleteTerm(Term)</a></span> - Method in class org.biojava.ontology.<a href="./org/biojava/ontology/IntegerOntology.html" title="class in org.biojava.ontology">IntegerOntology</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/Ontology.html#deleteTerm(org.biojava.ontology.Term)">deleteTerm(Term)</a></span> - Method in interface org.biojava.ontology.<a href="./org/biojava/ontology/Ontology.html" title="interface in org.biojava.ontology">Ontology</a></dt>
<dd>
<div class="block">Remove a term from an ontology, together with all triples which refer to it.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/Ontology.Impl.html#deleteTerm(org.biojava.ontology.Term)">deleteTerm(Term)</a></span> - Method in class org.biojava.ontology.<a href="./org/biojava/ontology/Ontology.Impl.html" title="class in org.biojava.ontology">Ontology.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ontology/SimpleComparableOntology.html#deleteTerm(org.biojava.ontology.Term)">deleteTerm(Term)</a></span> - Method in class org.biojavax.ontology.<a href="./org/biojavax/ontology/SimpleComparableOntology.html" title="class in org.biojavax.ontology">SimpleComparableOntology</a></dt>
<dd>
<div class="block">Remove a term from an ontology, together with all triples which refer to it.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLFormat.html#DELIMITER_TAG">DELIMITER_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLFormat.html" title="class in org.biojavax.bio.seq.io">EMBLFormat</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/structure/server/DemoStructureServer.html" title="class in org.biojava.bio.structure.server"><span class="strong">DemoStructureServer</span></a> - Class in <a href="./org/biojava/bio/structure/server/package-summary.html">org.biojava.bio.structure.server</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/server/DemoStructureServer.html#DemoStructureServer()">DemoStructureServer()</a></span> - Constructor for class org.biojava.bio.structure.server.<a href="./org/biojava/bio/structure/server/DemoStructureServer.html" title="class in org.biojava.bio.structure.server">DemoStructureServer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/twohead/AbstractMatrixPairDPCursor.html#depth">depth</a></span> - Variable in class org.biojava.bio.dp.twohead.<a href="./org/biojava/bio/dp/twohead/AbstractMatrixPairDPCursor.html" title="class in org.biojava.bio.dp.twohead">AbstractMatrixPairDPCursor</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/twohead/LightPairDPCursor.html#depth">depth</a></span> - Variable in class org.biojava.bio.dp.twohead.<a href="./org/biojava/bio/dp/twohead/LightPairDPCursor.html" title="class in org.biojava.bio.dp.twohead">LightPairDPCursor</a></dt>
<dd>
<div class="block">Description of the Field</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/AbiTraceRenderer.html#DEPTH">DEPTH</a></span> - Static variable in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/AbiTraceRenderer.html" title="class in org.biojava.bio.gui.sequence">AbiTraceRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/AbstractBeadRenderer.html#DEPTH">DEPTH</a></span> - Static variable in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/AbstractBeadRenderer.html" title="class in org.biojava.bio.gui.sequence">AbstractBeadRenderer</a></dt>
<dd>
<div class="block">Constant <code>DEPTH</code> indicating a change to the depth of
the renderer.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/TickFeatureRenderer.html#DEPTH">DEPTH</a></span> - Static variable in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/TickFeatureRenderer.html" title="class in org.biojava.bio.gui.sequence">TickFeatureRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html#DESC_TAG">DESC_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html" title="class in org.biojavax.bio.seq.io">EMBLxmlFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/phred/PhredFormat.html#describeSequence(org.biojava.bio.seq.Sequence)">describeSequence(Sequence)</a></span> - Method in class org.biojava.bio.program.phred.<a href="./org/biojava/bio/program/phred/PhredFormat.html" title="class in org.biojava.bio.program.phred">PhredFormat</a></dt>
<dd>
<div class="block">Return a suitable description line for a Sequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/FastaFormat.html#describeSequence(org.biojava.bio.seq.Sequence)">describeSequence(Sequence)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/FastaFormat.html" title="class in org.biojava.bio.seq.io">FastaFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Return a suitable description line for a Sequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BibRef.html#description">description</a></span> - Variable in class org.biojava.bibliography.<a href="./org/biojava/bibliography/BibRef.html" title="class in org.biojava.bibliography">BibRef</a></dt>
<dd>
<div class="block">An account of the content of the cited resource.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/SubstitutionMatrix.html#description">description</a></span> - Variable in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/SubstitutionMatrix.html" title="class in org.biojava.bio.alignment">SubstitutionMatrix</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/AbstractTerm.html#description">description</a></span> - Variable in class org.biojava.ontology.<a href="./org/biojava/ontology/AbstractTerm.html" title="class in org.biojava.ontology">AbstractTerm</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/candy/CandyEntry.html#description">description</a></span> - Variable in class org.biojava.utils.candy.<a href="./org/biojava/utils/candy/CandyEntry.html" title="class in org.biojava.utils.candy">CandyEntry</a></dt>
<dd>
<div class="block">A value of this entry.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/BioEntry.html#DESCRIPTION">DESCRIPTION</a></span> - Static variable in interface org.biojavax.bio.<a href="./org/biojavax/bio/BioEntry.html" title="interface in org.biojavax.bio">BioEntry</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/Namespace.html#DESCRIPTION">DESCRIPTION</a></span> - Static variable in interface org.biojavax.<a href="./org/biojavax/Namespace.html" title="interface in org.biojavax">Namespace</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ontology/ComparableOntology.html#DESCRIPTION">DESCRIPTION</a></span> - Static variable in interface org.biojavax.ontology.<a href="./org/biojavax/ontology/ComparableOntology.html" title="interface in org.biojavax.ontology">ComparableOntology</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ontology/ComparableTerm.html#DESCRIPTION">DESCRIPTION</a></span> - Static variable in interface org.biojavax.ontology.<a href="./org/biojavax/ontology/ComparableTerm.html" title="interface in org.biojavax.ontology">ComparableTerm</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ontology/ComparableTriple.html#DESCRIPTOR">DESCRIPTOR</a></span> - Static variable in interface org.biojavax.ontology.<a href="./org/biojavax/ontology/ComparableTriple.html" title="interface in org.biojavax.ontology">ComparableTriple</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/StateMachine.Transition.html#destination">destination</a></span> - Variable in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/StateMachine.Transition.html" title="class in org.biojava.bio.program.tagvalue">StateMachine.Transition</a></dt>
<dd>
<div class="block">the terminus of this Transition</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BibRefQuery.html#destroy()">destroy()</a></span> - Method in interface org.biojava.bibliography.<a href="./org/biojava/bibliography/BibRefQuery.html" title="interface in org.biojava.bibliography">BibRefQuery</a></dt>
<dd>
<div class="block">
It frees all resources related to this query collection.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/candy/CandyVocabulary.html#destroy()">destroy()</a></span> - Method in interface org.biojava.utils.candy.<a href="./org/biojava/utils/candy/CandyVocabulary.html" title="interface in org.biojava.utils.candy">CandyVocabulary</a></dt>
<dd>
<div class="block">It frees all resources related to this vocabulary.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/naming/ObdaContext.html#destroySubcontext(javax.naming.Name)">destroySubcontext(Name)</a></span> - Method in class org.biojava.naming.<a href="./org/biojava/naming/ObdaContext.html" title="class in org.biojava.naming">ObdaContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/naming/ObdaContext.html#destroySubcontext(java.lang.String)">destroySubcontext(String)</a></span> - Method in class org.biojava.naming.<a href="./org/biojava/naming/ObdaContext.html" title="class in org.biojava.naming">ObdaContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/MarkovModel.html#destroyTransition(org.biojava.bio.dp.State, org.biojava.bio.dp.State)">destroyTransition(State, State)</a></span> - Method in interface org.biojava.bio.dp.<a href="./org/biojava/bio/dp/MarkovModel.html" title="interface in org.biojava.bio.dp">MarkovModel</a></dt>
<dd>
<div class="block">Breaks a transition between two states legal.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/SimpleMarkovModel.html#destroyTransition(org.biojava.bio.dp.State, org.biojava.bio.dp.State)">destroyTransition(State, State)</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/SimpleMarkovModel.html" title="class in org.biojava.bio.dp">SimpleMarkovModel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/WMAsMM.html#destroyTransition(org.biojava.bio.dp.State, org.biojava.bio.dp.State)">destroyTransition(State, State)</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/WMAsMM.html" title="class in org.biojava.bio.dp">WMAsMM</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/jama/LUDecomposition.html#det()">det()</a></span> - Method in class org.biojava.bio.structure.jama.<a href="./org/biojava/bio/structure/jama/LUDecomposition.html" title="class in org.biojava.bio.structure.jama">LUDecomposition</a></dt>
<dd>
<div class="block">Determinant</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/jama/Matrix.html#det()">det()</a></span> - Method in class org.biojava.bio.structure.jama.<a href="./org/biojava/bio/structure/jama/Matrix.html" title="class in org.biojava.bio.structure.jama">Matrix</a></dt>
<dd>
<div class="block">Matrix determinant</div>
</dd>
<dt><a href="./org/biojava/utils/automata/DfaBuilder.html" title="class in org.biojava.utils.automata"><span class="strong">DfaBuilder</span></a> - Class in <a href="./org/biojava/utils/automata/package-summary.html">org.biojava.utils.automata</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/stats/svm/DiagonalAddKernel.html" title="class in org.biojava.stats.svm"><span class="strong">DiagonalAddKernel</span></a> - Class in <a href="./org/biojava/stats/svm/package-summary.html">org.biojava.stats.svm</a></dt>
<dd>
<div class="block">Adds a class specific constant to k(x, x).</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/DiagonalAddKernel.html#DiagonalAddKernel()">DiagonalAddKernel()</a></span> - Constructor for class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/DiagonalAddKernel.html" title="class in org.biojava.stats.svm">DiagonalAddKernel</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/stats/svm/DiagonalCachingKernel.html" title="class in org.biojava.stats.svm"><span class="strong">DiagonalCachingKernel</span></a> - Class in <a href="./org/biojava/stats/svm/package-summary.html">org.biojava.stats.svm</a></dt>
<dd>
<div class="block">Caches the leading diagonal of a kernel matrix.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/DiagonalCachingKernel.html#DiagonalCachingKernel()">DiagonalCachingKernel()</a></span> - Constructor for class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/DiagonalCachingKernel.html" title="class in org.biojava.stats.svm">DiagonalCachingKernel</a></dt>
<dd>
<div class="block">Create a new CachingKernel.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/DiagonalCachingKernel.html#DiagonalCachingKernel(org.biojava.stats.svm.SVMKernel)">DiagonalCachingKernel(SVMKernel)</a></span> - Constructor for class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/DiagonalCachingKernel.html" title="class in org.biojava.stats.svm">DiagonalCachingKernel</a></dt>
<dd>
<div class="block">Creates a new DiagonalCachingKernel that nests k.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/IndexedChangeHub.html#diddleQueue()">diddleQueue()</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/IndexedChangeHub.html" title="class in org.biojava.utils">IndexedChangeHub</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/AbstractPeptideDigestRenderer.html#DIGEST">DIGEST</a></span> - Static variable in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/AbstractPeptideDigestRenderer.html" title="class in org.biojava.bio.gui.sequence">AbstractPeptideDigestRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PeptideDigestRenderer.html#DIGEST">DIGEST</a></span> - Static variable in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PeptideDigestRenderer.html" title="class in org.biojava.bio.gui.sequence">PeptideDigestRenderer</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/proteomics/Digest.html" title="class in org.biojava.bio.proteomics"><span class="strong">Digest</span></a> - Class in <a href="./org/biojava/bio/proteomics/package-summary.html">org.biojava.bio.proteomics</a></dt>
<dd>
<div class="block">This class contains methods for calculating the results of proteolytic digestion
of a protein sequence
<b> this class is not designed to be thread safe </b></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/Digest.html#Digest()">Digest()</a></span> - Constructor for class org.biojava.bio.proteomics.<a href="./org/biojava/bio/proteomics/Digest.html" title="class in org.biojava.bio.proteomics">Digest</a></dt>
<dd>
<div class="block">Creates a new Digest Bean</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/EllipticalBeadRenderer.html#dimensionRatio">dimensionRatio</a></span> - Variable in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/EllipticalBeadRenderer.html" title="class in org.biojava.bio.gui.sequence">EllipticalBeadRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BibRefQuery.html#disconnect()">disconnect()</a></span> - Method in interface org.biojava.bibliography.<a href="./org/biojava/bibliography/BibRefQuery.html" title="interface in org.biojava.bibliography">BibRefQuery</a></dt>
<dd>
<div class="block">
It disconnects from the repository.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BibRefSupport.html#disconnect()">disconnect()</a></span> - Method in interface org.biojava.bibliography.<a href="./org/biojava/bibliography/BibRefSupport.html" title="interface in org.biojava.bibliography">BibRefSupport</a></dt>
<dd>
<div class="block">It closes connection with a utility object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/candy/CandyFinder.html#disconnect()">disconnect()</a></span> - Method in interface org.biojava.utils.candy.<a href="./org/biojava/utils/candy/CandyFinder.html" title="interface in org.biojava.utils.candy">CandyFinder</a></dt>
<dd>
<div class="block">It closes connection with the finder object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/obo/OboFileHandler.html#DISJOINT_FROM">DISJOINT_FROM</a></span> - Static variable in class org.biojava.ontology.obo.<a href="./org/biojava/ontology/obo/OboFileHandler.html" title="class in org.biojava.ontology.obo">OboFileHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.HibernateFeatureFilter.html#disjunctAdd">disjunctAdd</a></span> - Variable in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.HibernateFeatureFilter.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.HibernateFeatureFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.HibernateFeatureFilter.html#disjunction">disjunction</a></span> - Variable in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.HibernateFeatureFilter.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.HibernateFeatureFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/AbstractBeadRenderer.html#DISPLACEMENT">DISPLACEMENT</a></span> - Static variable in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/AbstractBeadRenderer.html" title="class in org.biojava.bio.gui.sequence">AbstractBeadRenderer</a></dt>
<dd>
<div class="block">Constant <code>DISPLACEMENT</code> indicating a change to the
Y-axis displacement of the features.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/ChangeSupport.html#displayString()">displayString()</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/ChangeSupport.html" title="class in org.biojava.utils">ChangeSupport</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/distributed/DistDataSource.html" title="interface in org.biojava.bio.seq.distributed"><span class="strong">DistDataSource</span></a> - Interface in <a href="./org/biojava/bio/seq/distributed/package-summary.html">org.biojava.bio.seq.distributed</a></dt>
<dd>
<div class="block">Object which contributes data to a DistributedSequenceDB.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/SimpleEmissionState.html#distForwarder">distForwarder</a></span> - Variable in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/SimpleEmissionState.html" title="class in org.biojava.bio.dp">SimpleEmissionState</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/DistributionTools.html#distOverAlignment(org.biojava.bio.symbol.Alignment)">distOverAlignment(Alignment)</a></span> - Static method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/DistributionTools.html" title="class in org.biojava.bio.dist">DistributionTools</a></dt>
<dd>
<div class="block">Equivalent to distOverAlignment(a, false, 0.0).</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/DistributionTools.html#distOverAlignment(org.biojava.bio.symbol.Alignment, boolean, double)">distOverAlignment(Alignment, boolean, double)</a></span> - Static method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/DistributionTools.html" title="class in org.biojava.bio.dist">DistributionTools</a></dt>
<dd>
<div class="block">Creates an array of distributions, one for each column of the alignment.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/DistributionTools.html#distOverAlignment(org.biojava.bio.symbol.Alignment, boolean)">distOverAlignment(Alignment, boolean)</a></span> - Static method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/DistributionTools.html" title="class in org.biojava.bio.dist">DistributionTools</a></dt>
<dd>
<div class="block">Creates an array of distributions, one for each column of the alignment.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/distributed/DistributedSequenceDB.html" title="class in org.biojava.bio.seq.distributed"><span class="strong">DistributedSequenceDB</span></a> - Class in <a href="./org/biojava/bio/seq/distributed/package-summary.html">org.biojava.bio.seq.distributed</a></dt>
<dd>
<div class="block">Sequence database from the meta-DAS system.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/distributed/DistributedSequenceDB.html#DistributedSequenceDB()">DistributedSequenceDB()</a></span> - Constructor for class org.biojava.bio.seq.distributed.<a href="./org/biojava/bio/seq/distributed/DistributedSequenceDB.html" title="class in org.biojava.bio.seq.distributed">DistributedSequenceDB</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/dist/Distribution.html" title="interface in org.biojava.bio.dist"><span class="strong">Distribution</span></a> - Interface in <a href="./org/biojava/bio/dist/package-summary.html">org.biojava.bio.dist</a></dt>
<dd>
<div class="block">
An encapsulation of a probability distribution over the Symbols within an
alphabet.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/EmissionState.html#DISTRIBUTION">DISTRIBUTION</a></span> - Static variable in interface org.biojava.bio.dp.<a href="./org/biojava/bio/dp/EmissionState.html" title="interface in org.biojava.bio.dp">EmissionState</a></dt>
<dd>
<div class="block">
This signals that the distribution associate with an EmissionState has
been altered.</div>
</dd>
<dt><a href="./org/biojava/bio/dist/Distribution.NullModelForwarder.html" title="class in org.biojava.bio.dist"><span class="strong">Distribution.NullModelForwarder</span></a> - Class in <a href="./org/biojava/bio/dist/package-summary.html">org.biojava.bio.dist</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>use
<code>new ChangeForwarder.Retyper(this, cs, Annotation.PROPERTY)</code>
instead</i></div>
</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/Distribution.NullModelForwarder.html#Distribution.NullModelForwarder(java.lang.Object, org.biojava.utils.ChangeSupport)">Distribution.NullModelForwarder(Object, ChangeSupport)</a></span> - Constructor for class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/Distribution.NullModelForwarder.html" title="class in org.biojava.bio.dist">Distribution.NullModelForwarder</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Create a new forwarder.</div>
</dd>
<dt><a href="./org/biojava/bio/dist/DistributionFactory.html" title="interface in org.biojava.bio.dist"><span class="strong">DistributionFactory</span></a> - Interface in <a href="./org/biojava/bio/dist/package-summary.html">org.biojava.bio.dist</a></dt>
<dd>
<div class="block">
A thing that can make Distributions.</div>
</dd>
<dt><a href="./org/biojava/bio/dist/DistributionFactory.DefaultDistributionFactory.html" title="class in org.biojava.bio.dist"><span class="strong">DistributionFactory.DefaultDistributionFactory</span></a> - Class in <a href="./org/biojava/bio/dist/package-summary.html">org.biojava.bio.dist</a></dt>
<dd>
<div class="block">
The default DistributionFactory implementation.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/DistributionFactory.DefaultDistributionFactory.html#DistributionFactory.DefaultDistributionFactory()">DistributionFactory.DefaultDistributionFactory()</a></span> - Constructor for class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/DistributionFactory.DefaultDistributionFactory.html" title="class in org.biojava.bio.dist">DistributionFactory.DefaultDistributionFactory</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/gui/DistributionLogo.html" title="class in org.biojava.bio.gui"><span class="strong">DistributionLogo</span></a> - Class in <a href="./org/biojava/bio/gui/package-summary.html">org.biojava.bio.gui</a></dt>
<dd>
<div class="block">The GUI component for rendering a DistributionLogo.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/DistributionLogo.html#DistributionLogo()">DistributionLogo()</a></span> - Constructor for class org.biojava.bio.gui.<a href="./org/biojava/bio/gui/DistributionLogo.html" title="class in org.biojava.bio.gui">DistributionLogo</a></dt>
<dd>
<div class="block">Create a new DistributionLogo object.</div>
</dd>
<dt><a href="./org/biojava/bio/dist/DistributionTools.html" title="class in org.biojava.bio.dist"><span class="strong">DistributionTools</span></a> - Class in <a href="./org/biojava/bio/dist/package-summary.html">org.biojava.bio.dist</a></dt>
<dd>
<div class="block">A class to hold static methods for calculations and manipulations using
Distributions.</div>
</dd>
<dt><a href="./org/biojava/bio/dist/DistributionTrainer.html" title="interface in org.biojava.bio.dist"><span class="strong">DistributionTrainer</span></a> - Interface in <a href="./org/biojava/bio/dist/package-summary.html">org.biojava.bio.dist</a></dt>
<dd>
<div class="block">
An object that can be used to train a distribution up.</div>
</dd>
<dt><a href="./org/biojava/bio/dist/DistributionTrainerContext.html" title="interface in org.biojava.bio.dist"><span class="strong">DistributionTrainerContext</span></a> - Interface in <a href="./org/biojava/bio/dist/package-summary.html">org.biojava.bio.dist</a></dt>
<dd>
<div class="block">A context within a group of DistributionTrainers can be trained together.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/BioEntry.html#DIVISION">DIVISION</a></span> - Static variable in interface org.biojavax.bio.<a href="./org/biojavax/bio/BioEntry.html" title="interface in org.biojavax.bio">BioEntry</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/EmblLikeFormat.html#DIVISION_TAG">DIVISION_TAG</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/EmblLikeFormat.html" title="class in org.biojava.bio.seq.io">EmblLikeFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/GenbankFormat.html#DIVISION_TAG">DIVISION_TAG</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/GenbankFormat.html" title="class in org.biojava.bio.seq.io">GenbankFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/INSDseqFormat.html#DIVISION_TAG">DIVISION_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/INSDseqFormat.html" title="class in org.biojavax.bio.seq.io">INSDseqFormat</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/db/emblcd/DivisionLkpReader.html" title="class in org.biojava.bio.seq.db.emblcd"><span class="strong">DivisionLkpReader</span></a> - Class in <a href="./org/biojava/bio/seq/db/emblcd/package-summary.html">org.biojava.bio.seq.db.emblcd</a></dt>
<dd>
<div class="block"><code>DivisionLkpReader</code> reads the "division.lkp" file of an
EMBL CD-ROM format binary index.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/emblcd/DivisionLkpReader.html#DivisionLkpReader(java.io.InputStream)">DivisionLkpReader(InputStream)</a></span> - Constructor for class org.biojava.bio.seq.db.emblcd.<a href="./org/biojava/bio/seq/db/emblcd/DivisionLkpReader.html" title="class in org.biojava.bio.seq.db.emblcd">DivisionLkpReader</a></dt>
<dd>
<div class="block">Creates a new <code>DivisionLkpReader</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/Chromatogram.html#DNA">DNA</a></span> - Static variable in interface org.biojava.bio.chromatogram.<a href="./org/biojava/bio/chromatogram/Chromatogram.html" title="interface in org.biojava.bio.chromatogram">Chromatogram</a></dt>
<dd>
<div class="block">The sequence label for the list of called bases.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/FastaAlignmentFormat.html#DNA">DNA</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/FastaAlignmentFormat.html" title="class in org.biojava.bio.seq.io">FastaAlignmentFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOConstants.html#DNA">DNA</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOConstants.html" title="class in org.biojava.bio.seq.io">SeqIOConstants</a></dt>
<dd>
<div class="block"><code>DNA</code> indicates that a sequence contains DNA
(deoxyribonucleic acid) symbols.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/chem/PolymerType.html#DNA_ONLY">DNA_ONLY</a></span> - Static variable in enum org.biojava.bio.structure.io.mmcif.chem.<a href="./org/biojava/bio/structure/io/mmcif/chem/PolymerType.html" title="enum in org.biojava.bio.structure.io.mmcif.chem">PolymerType</a></dt>
<dd>
<div class="block">Convenience <tt>Set</tt> of polymer types classified as DNA.</div>
</dd>
<dt><a href="./org/biojava/bio/symbol/DNAAmbPack.html" title="class in org.biojava.bio.symbol"><span class="strong">DNAAmbPack</span></a> - Class in <a href="./org/biojava/bio/symbol/package-summary.html">org.biojava.bio.symbol</a></dt>
<dd>
<div class="block">Packing utility class for DNA.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/DNAAmbPack.html#DNAAmbPack()">DNAAmbPack()</a></span> - Constructor for class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/DNAAmbPack.html" title="class in org.biojava.bio.symbol">DNAAmbPack</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/molbio/DNAComposition.html" title="class in org.biojava.bio.molbio"><span class="strong">DNAComposition</span></a> - Class in <a href="./org/biojava/bio/molbio/package-summary.html">org.biojava.bio.molbio</a></dt>
<dd>
<div class="block">Computes composition statistics about a DNA <code>SymbolList</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/molbio/DNAComposition.html#DNAComposition()">DNAComposition()</a></span> - Constructor for class org.biojava.bio.molbio.<a href="./org/biojava/bio/molbio/DNAComposition.html" title="class in org.biojava.bio.molbio">DNAComposition</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/symbol/DNANoAmbPack.html" title="class in org.biojava.bio.symbol"><span class="strong">DNANoAmbPack</span></a> - Class in <a href="./org/biojava/bio/symbol/package-summary.html">org.biojava.bio.symbol</a></dt>
<dd>
<div class="block">A <code>Packing</code> implementation which handles the DNA alphabet, without any
support for ambiguity symbols.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/DNANoAmbPack.html#DNANoAmbPack(byte)">DNANoAmbPack(byte)</a></span> - Constructor for class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/DNANoAmbPack.html" title="class in org.biojava.bio.symbol">DNANoAmbPack</a></dt>
<dd>
<div class="block">Construct a new packing which returns the specified byte value for unknown Symbols
(such as ambiguity symbols).</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/DNANoAmbPack.html#DNANoAmbPack(org.biojava.bio.symbol.Symbol)">DNANoAmbPack(Symbol)</a></span> - Constructor for class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/DNANoAmbPack.html" title="class in org.biojava.bio.symbol">DNANoAmbPack</a></dt>
<dd>
<div class="block">Construct a new packing which translates unknown symbols into
the specified symbol.</div>
</dd>
<dt><a href="./org/biojava/bio/gui/DNAStyle.html" title="class in org.biojava.bio.gui"><span class="strong">DNAStyle</span></a> - Class in <a href="./org/biojava/bio/gui/package-summary.html">org.biojava.bio.gui</a></dt>
<dd>
<div class="block">A simple implementation of SymbolStyle optimized for DNA.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/DNAStyle.html#DNAStyle()">DNAStyle()</a></span> - Constructor for class org.biojava.bio.gui.<a href="./org/biojava/bio/gui/DNAStyle.html" title="class in org.biojava.bio.gui">DNAStyle</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/phred/PhredTools.html#dnaSymbolFromPhred(org.biojava.bio.symbol.Symbol)">dnaSymbolFromPhred(Symbol)</a></span> - Static method in class org.biojava.bio.program.phred.<a href="./org/biojava/bio/program/phred/PhredTools.html" title="class in org.biojava.bio.program.phred">PhredTools</a></dt>
<dd>
<div class="block">Retrives the DNA symbol component of the Phred BasisSymbol from the
PHRED alphabet.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/DNATools.html#dnaToken(org.biojava.bio.symbol.Symbol)">dnaToken(Symbol)</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/DNATools.html" title="class in org.biojava.bio.seq">DNATools</a></dt>
<dd>
<div class="block">Get a single-character token for a DNA symbol</div>
</dd>
<dt><a href="./org/biojava/bio/seq/DNATools.html" title="class in org.biojava.bio.seq"><span class="strong">DNATools</span></a> - Class in <a href="./org/biojava/bio/seq/package-summary.html">org.biojava.bio.seq</a></dt>
<dd>
<div class="block">Useful functionality for processing DNA sequences.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/AnnotatedSequenceDB.html#doAnnotation(org.biojava.bio.seq.Sequence)">doAnnotation(Sequence)</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/AnnotatedSequenceDB.html" title="class in org.biojava.bio.seq.db">AnnotatedSequenceDB</a></dt>
<dd>
<div class="block">Apply the annotation to a sequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BiblioPatent.html#docNumber">docNumber</a></span> - Variable in class org.biojava.bibliography.<a href="./org/biojava/bibliography/BiblioPatent.html" title="class in org.biojava.bibliography">BiblioPatent</a></dt>
<dd>
<div class="block">The document number.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BiblioPatent.html#docOffice">docOffice</a></span> - Variable in class org.biojava.bibliography.<a href="./org/biojava/bibliography/BiblioPatent.html" title="class in org.biojava.bibliography">BiblioPatent</a></dt>
<dd>
<div class="block">Document office.</div>
</dd>
<dt><a href="./org/biojavax/DocRef.html" title="interface in org.biojavax"><span class="strong">DocRef</span></a> - Interface in <a href="./org/biojavax/package-summary.html">org.biojavax</a></dt>
<dd>
<div class="block">Represents a documentary reference.</div>
</dd>
<dt><a href="./org/biojavax/DocRefAuthor.html" title="interface in org.biojavax"><span class="strong">DocRefAuthor</span></a> - Interface in <a href="./org/biojavax/package-summary.html">org.biojavax</a></dt>
<dd>
<div class="block">Represents an author of a documentary reference.</div>
</dd>
<dt><a href="./org/biojavax/DocRefAuthor.Tools.html" title="class in org.biojavax"><span class="strong">DocRefAuthor.Tools</span></a> - Class in <a href="./org/biojavax/package-summary.html">org.biojavax</a></dt>
<dd>
<div class="block">Useful tools for working with authors.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BiblioPatent.html#docType">docType</a></span> - Variable in class org.biojava.bibliography.<a href="./org/biojava/bibliography/BiblioPatent.html" title="class in org.biojava.bibliography">BiblioPatent</a></dt>
<dd>
<div class="block">Document type.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/ChemCompConsumer.html#documentEnd()">documentEnd()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/ChemCompConsumer.html" title="class in org.biojava.bio.structure.io.mmcif">ChemCompConsumer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/MMcifConsumer.html#documentEnd()">documentEnd()</a></span> - Method in interface org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/MMcifConsumer.html" title="interface in org.biojava.bio.structure.io.mmcif">MMcifConsumer</a></dt>
<dd>
<div class="block">called at end of document</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/SimpleMMcifConsumer.html#documentEnd()">documentEnd()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/SimpleMMcifConsumer.html" title="class in org.biojava.bio.structure.io.mmcif">SimpleMMcifConsumer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/obo/OboFileEventListener.html#documentEnd()">documentEnd()</a></span> - Method in interface org.biojava.ontology.obo.<a href="./org/biojava/ontology/obo/OboFileEventListener.html" title="interface in org.biojava.ontology.obo">OboFileEventListener</a></dt>
<dd>
<div class="block">end of parsing a new OBO file</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/obo/OboFileHandler.html#documentEnd()">documentEnd()</a></span> - Method in class org.biojava.ontology.obo.<a href="./org/biojava/ontology/obo/OboFileHandler.html" title="class in org.biojava.ontology.obo">OboFileHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/ChemCompConsumer.html#documentStart()">documentStart()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/ChemCompConsumer.html" title="class in org.biojava.bio.structure.io.mmcif">ChemCompConsumer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/MMcifConsumer.html#documentStart()">documentStart()</a></span> - Method in interface org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/MMcifConsumer.html" title="interface in org.biojava.bio.structure.io.mmcif">MMcifConsumer</a></dt>
<dd>
<div class="block">called at start of document</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/SimpleMMcifConsumer.html#documentStart()">documentStart()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/SimpleMMcifConsumer.html" title="class in org.biojava.bio.structure.io.mmcif">SimpleMMcifConsumer</a></dt>
<dd>
<div class="block">Start the parsing</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/obo/OboFileEventListener.html#documentStart()">documentStart()</a></span> - Method in interface org.biojava.ontology.obo.<a href="./org/biojava/ontology/obo/OboFileEventListener.html" title="interface in org.biojava.ontology.obo">OboFileEventListener</a></dt>
<dd>
<div class="block">starting to parse a new OBO file</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/obo/OboFileHandler.html#documentStart()">documentStart()</a></span> - Method in class org.biojava.ontology.obo.<a href="./org/biojava/ontology/obo/OboFileHandler.html" title="class in org.biojava.ontology.obo">OboFileHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.Terms.html#DOI_KEY">DOI_KEY</a></span> - Static variable in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.Terms.html" title="class in org.biojavax.bio.seq">RichSequence.Terms</a></dt>
<dd>
<div class="block">Holds a reference to the key that must be used to store DOI
references.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/BumpedRenderer.html#doLayer(org.biojava.bio.gui.sequence.SequenceRenderContext, org.biojava.bio.seq.FeatureFilter)">doLayer(SequenceRenderContext, FeatureFilter)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/BumpedRenderer.html" title="class in org.biojava.bio.gui.sequence">BumpedRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/hmmer/HmmerProfileParser.html#domain1">domain1</a></span> - Variable in class org.biojava.bio.program.hmmer.<a href="./org/biojava/bio/program/hmmer/HmmerProfileParser.html" title="class in org.biojava.bio.program.hmmer">HmmerProfileParser</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#DOMAIN_TAG">DOMAIN_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/SequencesAsGFF.html#doPreProcessSequence(org.biojava.bio.seq.Sequence, org.biojava.bio.program.gff.GFFDocumentHandler, java.lang.String)">doPreProcessSequence(Sequence, GFFDocumentHandler, String)</a></span> - Method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/SequencesAsGFF.html" title="class in org.biojava.bio.program.gff">SequencesAsGFF</a></dt>
<dd>
<div class="block">Emit any per-sequence header information.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/FileConvert.html#doPrintConnections()">doPrintConnections()</a></span> - Method in class org.biojava.bio.structure.io.<a href="./org/biojava/bio/structure/io/FileConvert.html" title="class in org.biojava.bio.structure.io">FileConvert</a></dt>
<dd>
<div class="block">returns if the Connections should be added
default is true;</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/SequencesAsGFF.html#doProcessFeature(org.biojava.bio.seq.Feature, org.biojava.bio.program.gff.GFFDocumentHandler, java.lang.String)">doProcessFeature(Feature, GFFDocumentHandler, String)</a></span> - Method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/SequencesAsGFF.html" title="class in org.biojava.bio.program.gff">SequencesAsGFF</a></dt>
<dd>
<div class="block">Internal method to process an individual <span class="type">Feature</span>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/SequencesAsGFF.html#doProcessSequence(org.biojava.bio.seq.Sequence, org.biojava.bio.program.gff.GFFDocumentHandler, java.lang.String)">doProcessSequence(Sequence, GFFDocumentHandler, String)</a></span> - Method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/SequencesAsGFF.html" title="class in org.biojava.bio.program.gff">SequencesAsGFF</a></dt>
<dd>
<div class="block">Internal method to process an individual <span class="type">Sequence</span>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/AbstractPeptideDigestRenderer.html#doRefreshRenderers()">doRefreshRenderers()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/AbstractPeptideDigestRenderer.html" title="class in org.biojava.bio.gui.sequence">AbstractPeptideDigestRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/TagDropper.html#doRetain()">doRetain()</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/TagDropper.html" title="class in org.biojava.bio.program.tagvalue">TagDropper</a></dt>
<dd>
<div class="block">Find out if known tags are retained or dropped.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/AbstractPeptideDigestRenderer.html#doSortPeptides()">doSortPeptides()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/AbstractPeptideDigestRenderer.html" title="class in org.biojava.bio.gui.sequence">AbstractPeptideDigestRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleManyToOneTranslationTable.html#doTranslate(org.biojava.bio.symbol.Symbol)">doTranslate(Symbol)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleManyToOneTranslationTable.html" title="class in org.biojava.bio.symbol">SimpleManyToOneTranslationTable</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleReversibleTranslationTable.html#doTranslate(org.biojava.bio.symbol.Symbol)">doTranslate(Symbol)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleReversibleTranslationTable.html" title="class in org.biojava.bio.symbol">SimpleReversibleTranslationTable</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleTranslationTable.html#doTranslate(org.biojava.bio.symbol.Symbol)">doTranslate(Symbol)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleTranslationTable.html" title="class in org.biojava.bio.symbol">SimpleTranslationTable</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/dp/DotState.html" title="interface in org.biojava.bio.dp"><span class="strong">DotState</span></a> - Interface in <a href="./org/biojava/bio/dp/package-summary.html">org.biojava.bio.dp</a></dt>
<dd>
<div class="block">
A Dot state.</div>
</dd>
<dt><a href="./org/biojava/bio/symbol/DoubleAlphabet.html" title="class in org.biojava.bio.symbol"><span class="strong">DoubleAlphabet</span></a> - Class in <a href="./org/biojava/bio/symbol/package-summary.html">org.biojava.bio.symbol</a></dt>
<dd>
<div class="block">
An efficient implementation of an Alphabet over the infinite set of double
values.</div>
</dd>
<dt><a href="./org/biojava/bio/symbol/DoubleAlphabet.DoubleRange.html" title="class in org.biojava.bio.symbol"><span class="strong">DoubleAlphabet.DoubleRange</span></a> - Class in <a href="./org/biojava/bio/symbol/package-summary.html">org.biojava.bio.symbol</a></dt>
<dd>
<div class="block">A range of double values.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/DoubleAlphabet.DoubleRange.html#DoubleAlphabet.DoubleRange(double, double)">DoubleAlphabet.DoubleRange(double, double)</a></span> - Constructor for class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/DoubleAlphabet.DoubleRange.html" title="class in org.biojava.bio.symbol">DoubleAlphabet.DoubleRange</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/symbol/DoubleAlphabet.DoubleSymbol.html" title="class in org.biojava.bio.symbol"><span class="strong">DoubleAlphabet.DoubleSymbol</span></a> - Class in <a href="./org/biojava/bio/symbol/package-summary.html">org.biojava.bio.symbol</a></dt>
<dd>
<div class="block">A single double value.</div>
</dd>
<dt><a href="./org/biojava/bio/symbol/DoubleAlphabet.SubDoubleAlphabet.html" title="class in org.biojava.bio.symbol"><span class="strong">DoubleAlphabet.SubDoubleAlphabet</span></a> - Class in <a href="./org/biojava/bio/symbol/package-summary.html">org.biojava.bio.symbol</a></dt>
<dd>
<div class="block">A class to represent a contiguous range of double symbols.</div>
</dd>
<dt><a href="./org/biojava/utils/stax/DoubleElementHandlerBase.html" title="class in org.biojava.utils.stax"><span class="strong">DoubleElementHandlerBase</span></a> - Class in <a href="./org/biojava/utils/stax/package-summary.html">org.biojava.utils.stax</a></dt>
<dd>
<div class="block">
StAX handler for any element which just contains a string representation of
a double.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/stax/DoubleElementHandlerBase.html#DoubleElementHandlerBase()">DoubleElementHandlerBase()</a></span> - Constructor for class org.biojava.utils.stax.<a href="./org/biojava/utils/stax/DoubleElementHandlerBase.html" title="class in org.biojava.utils.stax">DoubleElementHandlerBase</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/io/DoubleTokenization.html" title="class in org.biojava.bio.seq.io"><span class="strong">DoubleTokenization</span></a> - Class in <a href="./org/biojava/bio/seq/io/package-summary.html">org.biojava.bio.seq.io</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/DoubleTokenization.html#DoubleTokenization()">DoubleTokenization()</a></span> - Constructor for class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/DoubleTokenization.html" title="class in org.biojava.bio.seq.io">DoubleTokenization</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/DoubleAlphabet.DoubleSymbol.html#doubleValue()">doubleValue()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/DoubleAlphabet.DoubleSymbol.html" title="class in org.biojava.bio.symbol">DoubleAlphabet.DoubleSymbol</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AbstractManyToOneTranslationTable.html#doUntranslate(org.biojava.bio.symbol.Symbol)">doUntranslate(Symbol)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AbstractManyToOneTranslationTable.html" title="class in org.biojava.bio.symbol">AbstractManyToOneTranslationTable</a></dt>
<dd>
<div class="block">this method is expected to reverse-translate any symbol
in the source alphabet.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AbstractReversibleTranslationTable.html#doUntranslate(org.biojava.bio.symbol.Symbol)">doUntranslate(Symbol)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AbstractReversibleTranslationTable.html" title="class in org.biojava.bio.symbol">AbstractReversibleTranslationTable</a></dt>
<dd>
<div class="block">this method is expected to reverse-translate any symbol
in the source alphabet.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleManyToOneTranslationTable.html#doUntranslate(org.biojava.bio.symbol.Symbol)">doUntranslate(Symbol)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleManyToOneTranslationTable.html" title="class in org.biojava.bio.symbol">SimpleManyToOneTranslationTable</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleReversibleTranslationTable.html#doUntranslate(org.biojava.bio.symbol.Symbol)">doUntranslate(Symbol)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleReversibleTranslationTable.html" title="class in org.biojava.bio.symbol">SimpleReversibleTranslationTable</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/server/MMCIFFileInstallation.html#downloadCIF(java.lang.String)">downloadCIF(String)</a></span> - Method in class org.biojava.bio.structure.server.<a href="./org/biojava/bio/structure/server/MMCIFFileInstallation.html" title="class in org.biojava.bio.structure.server">MMCIFFileInstallation</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/dp/DP.html" title="class in org.biojava.bio.dp"><span class="strong">DP</span></a> - Class in <a href="./org/biojava/bio/dp/package-summary.html">org.biojava.bio.dp</a></dt>
<dd>
<div class="block">
Objects that can perform dymamic programming operations upon sequences with
HMMs.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/DP.html#DP(org.biojava.bio.dp.MarkovModel)">DP(MarkovModel)</a></span> - Constructor for class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/DP.html" title="class in org.biojava.bio.dp">DP</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/DP.html#DP()">DP()</a></span> - Constructor for class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/DP.html" title="class in org.biojava.bio.dp">DP</a></dt>
<dd>
<div class="block">This method will result in a DP with no model.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLFormat.html#dp">dp</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLFormat.html" title="class in org.biojavax.bio.seq.io">EMBLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/FastaFormat.html#dp">dp</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/FastaFormat.html" title="class in org.biojavax.bio.seq.io">FastaFormat</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/dp/DP.ReverseIterator.html" title="class in org.biojava.bio.dp"><span class="strong">DP.ReverseIterator</span></a> - Class in <a href="./org/biojava/bio/dp/package-summary.html">org.biojava.bio.dp</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/DP.ReverseIterator.html#DP.ReverseIterator(org.biojava.bio.symbol.SymbolList)">DP.ReverseIterator(SymbolList)</a></span> - Constructor for class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/DP.ReverseIterator.html" title="class in org.biojava.bio.dp">DP.ReverseIterator</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtFormat.html#dp_ipi">dp_ipi</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtFormat.html" title="class in org.biojavax.bio.seq.io">UniProtFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtFormat.html#dp_uniprot">dp_uniprot</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtFormat.html" title="class in org.biojavax.bio.seq.io">UniProtFormat</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/dp/twohead/DPCompiler.html" title="class in org.biojava.bio.dp.twohead"><span class="strong">DPCompiler</span></a> - Class in <a href="./org/biojava/bio/dp/twohead/package-summary.html">org.biojava.bio.dp.twohead</a></dt>
<dd>
<div class="block">This is an implementation of CellCalculatorFactoryMaker that compiles the
HMM object down to Java byte-code that is equivalent in behaviour to the
interpreter.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/twohead/DPCompiler.html#DPCompiler(boolean)">DPCompiler(boolean)</a></span> - Constructor for class org.biojava.bio.dp.twohead.<a href="./org/biojava/bio/dp/twohead/DPCompiler.html" title="class in org.biojava.bio.dp.twohead">DPCompiler</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/dp/onehead/DPCursor.html" title="interface in org.biojava.bio.dp.onehead"><span class="strong">DPCursor</span></a> - Interface in <a href="./org/biojava/bio/dp/onehead/package-summary.html">org.biojava.bio.dp.onehead</a></dt>
<dd>
<div class="block">Encapsulates the dynamic programmming matrix, and the context within algorithms work.</div>
</dd>
<dt><a href="./org/biojava/bio/dp/DPFactory.html" title="interface in org.biojava.bio.dp"><span class="strong">DPFactory</span></a> - Interface in <a href="./org/biojava/bio/dp/package-summary.html">org.biojava.bio.dp</a></dt>
<dd>
<div class="block">The interface for objects that can generate a DP object for a MarkovModel.</div>
</dd>
<dt><a href="./org/biojava/bio/dp/DPFactory.DefaultFactory.html" title="class in org.biojava.bio.dp"><span class="strong">DPFactory.DefaultFactory</span></a> - Class in <a href="./org/biojava/bio/dp/package-summary.html">org.biojava.bio.dp</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/DPFactory.DefaultFactory.html#DPFactory.DefaultFactory(org.biojava.bio.dp.twohead.CellCalculatorFactoryMaker)">DPFactory.DefaultFactory(CellCalculatorFactoryMaker)</a></span> - Constructor for class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/DPFactory.DefaultFactory.html" title="class in org.biojava.bio.dp">DPFactory.DefaultFactory</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/dp/twohead/DPInterpreter.html" title="class in org.biojava.bio.dp.twohead"><span class="strong">DPInterpreter</span></a> - Class in <a href="./org/biojava/bio/dp/twohead/package-summary.html">org.biojava.bio.dp.twohead</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/twohead/DPInterpreter.html#DPInterpreter(org.biojava.bio.dp.DP)">DPInterpreter(DP)</a></span> - Constructor for class org.biojava.bio.dp.twohead.<a href="./org/biojava/bio/dp/twohead/DPInterpreter.html" title="class in org.biojava.bio.dp.twohead">DPInterpreter</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/dp/twohead/DPInterpreter.Maker.html" title="class in org.biojava.bio.dp.twohead"><span class="strong">DPInterpreter.Maker</span></a> - Class in <a href="./org/biojava/bio/dp/twohead/package-summary.html">org.biojava.bio.dp.twohead</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/twohead/DPInterpreter.Maker.html#DPInterpreter.Maker()">DPInterpreter.Maker()</a></span> - Constructor for class org.biojava.bio.dp.twohead.<a href="./org/biojava/bio/dp/twohead/DPInterpreter.Maker.html" title="class in org.biojava.bio.dp.twohead">DPInterpreter.Maker</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/dp/DPMatrix.html" title="interface in org.biojava.bio.dp"><span class="strong">DPMatrix</span></a> - Interface in <a href="./org/biojava/bio/dp/package-summary.html">org.biojava.bio.dp</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/EmblLikeFormat.html#DR_TAG">DR_TAG</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/EmblLikeFormat.html" title="class in org.biojava.bio.seq.io">EmblLikeFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.Option.html#DRAW_CALL_A">DRAW_CALL_A</a></span> - Static variable in class org.biojava.bio.chromatogram.graphic.<a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.Option.html" title="class in org.biojava.bio.chromatogram.graphic">ChromatogramGraphic.Option</a></dt>
<dd>
<div class="block">Option indicating whether to fill in the callboxes for calls of
nucleotide A.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.Option.html#DRAW_CALL_C">DRAW_CALL_C</a></span> - Static variable in class org.biojava.bio.chromatogram.graphic.<a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.Option.html" title="class in org.biojava.bio.chromatogram.graphic">ChromatogramGraphic.Option</a></dt>
<dd>
<div class="block">Option indicating whether to fill in the callboxes for calls of
nucleotide C.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.Option.html#DRAW_CALL_G">DRAW_CALL_G</a></span> - Static variable in class org.biojava.bio.chromatogram.graphic.<a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.Option.html" title="class in org.biojava.bio.chromatogram.graphic">ChromatogramGraphic.Option</a></dt>
<dd>
<div class="block">Option indicating whether to fill in the callboxes for calls of
nucleotide G.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.Option.html#DRAW_CALL_OTHER">DRAW_CALL_OTHER</a></span> - Static variable in class org.biojava.bio.chromatogram.graphic.<a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.Option.html" title="class in org.biojava.bio.chromatogram.graphic">ChromatogramGraphic.Option</a></dt>
<dd>
<div class="block">Option indicating whether to fill in the callboxes for non-base calls
(gaps, ambiguities).</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.Option.html#DRAW_CALL_SEPARATORS">DRAW_CALL_SEPARATORS</a></span> - Static variable in class org.biojava.bio.chromatogram.graphic.<a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.Option.html" title="class in org.biojava.bio.chromatogram.graphic">ChromatogramGraphic.Option</a></dt>
<dd>
<div class="block">Option indicating whether to draw vertical lines separating
the calls.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.Option.html#DRAW_CALL_T">DRAW_CALL_T</a></span> - Static variable in class org.biojava.bio.chromatogram.graphic.<a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.Option.html" title="class in org.biojava.bio.chromatogram.graphic">ChromatogramGraphic.Option</a></dt>
<dd>
<div class="block">Option indicating whether to fill in the callboxes for calls of
nucleotide T.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.Option.html#DRAW_TRACE_A">DRAW_TRACE_A</a></span> - Static variable in class org.biojava.bio.chromatogram.graphic.<a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.Option.html" title="class in org.biojava.bio.chromatogram.graphic">ChromatogramGraphic.Option</a></dt>
<dd>
<div class="block">Option indicating whether to draw the chromatogram trace for
nucleotide A.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.Option.html#DRAW_TRACE_C">DRAW_TRACE_C</a></span> - Static variable in class org.biojava.bio.chromatogram.graphic.<a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.Option.html" title="class in org.biojava.bio.chromatogram.graphic">ChromatogramGraphic.Option</a></dt>
<dd>
<div class="block">Option indicating whether to draw the chromatogram trace for
nucleotide C.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.Option.html#DRAW_TRACE_G">DRAW_TRACE_G</a></span> - Static variable in class org.biojava.bio.chromatogram.graphic.<a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.Option.html" title="class in org.biojava.bio.chromatogram.graphic">ChromatogramGraphic.Option</a></dt>
<dd>
<div class="block">Option indicating whether to draw the chromatogram trace for
nucleotide G.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.Option.html#DRAW_TRACE_T">DRAW_TRACE_T</a></span> - Static variable in class org.biojava.bio.chromatogram.graphic.<a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.Option.html" title="class in org.biojava.bio.chromatogram.graphic">ChromatogramGraphic.Option</a></dt>
<dd>
<div class="block">Option indicating whether to draw the chromatogram trace for
nucleotide T.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.html#drawableCallboxesValid">drawableCallboxesValid</a></span> - Variable in class org.biojava.bio.chromatogram.graphic.<a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.html" title="class in org.biojava.bio.chromatogram.graphic">ChromatogramGraphic</a></dt>
<dd>
<div class="block">Flag for drawable call boxes.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/JMatrixPanel.html#drawBoxes(java.awt.Graphics)">drawBoxes(Graphics)</a></span> - Method in class org.biojava.bio.structure.gui.<a href="./org/biojava/bio/structure/gui/JMatrixPanel.html" title="class in org.biojava.bio.structure.gui">JMatrixPanel</a></dt>
<dd>
<div class="block">draw high scoring fragments that are used for the initial alignment seed
selection</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/JMatrixPanel.html#drawDistances(java.awt.Graphics)">drawDistances(Graphics)</a></span> - Method in class org.biojava.bio.structure.gui.<a href="./org/biojava/bio/structure/gui/JMatrixPanel.html" title="class in org.biojava.bio.structure.gui">JMatrixPanel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/util/SequenceScalePanel.html#drawIdx(java.awt.Graphics2D, int)">drawIdx(Graphics2D, int)</a></span> - Method in class org.biojava.bio.structure.gui.util.<a href="./org/biojava/bio/structure/gui/util/SequenceScalePanel.html" title="class in org.biojava.bio.structure.gui.util">SequenceScalePanel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SixFrameRenderer.html#drawLine(java.awt.Graphics2D, org.biojava.bio.gui.sequence.SequenceRenderContext, int, org.biojava.bio.seq.StrandedFeature.Strand)">drawLine(Graphics2D, SequenceRenderContext, int, StrandedFeature.Strand)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SixFrameRenderer.html" title="class in org.biojava.bio.gui.sequence">SixFrameRenderer</a></dt>
<dd>
<div class="block">draws required bar in correct translation frame.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/JMatrixPanel.html#drawPairs(java.awt.Graphics)">drawPairs(Graphics)</a></span> - Method in class org.biojava.bio.structure.gui.<a href="./org/biojava/bio/structure/gui/JMatrixPanel.html" title="class in org.biojava.bio.structure.gui">JMatrixPanel</a></dt>
<dd>
<div class="block">draw alternative alignments</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/util/SequenceScalePanel.html#drawScale(java.awt.Graphics2D, int)">drawScale(Graphics2D, int)</a></span> - Method in class org.biojava.bio.structure.gui.util.<a href="./org/biojava/bio/structure/gui/util/SequenceScalePanel.html" title="class in org.biojava.bio.structure.gui.util">SequenceScalePanel</a></dt>
<dd>
<div class="block">draw the Scale</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/util/SequenceScalePanel.html#drawSequence(java.awt.Graphics2D, int)">drawSequence(Graphics2D, int)</a></span> - Method in class org.biojava.bio.structure.gui.util.<a href="./org/biojava/bio/structure/gui/util/SequenceScalePanel.html" title="class in org.biojava.bio.structure.gui.util">SequenceScalePanel</a></dt>
<dd>
<div class="block">draw the Amino acid sequence</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.html#drawTo(java.awt.Graphics2D)">drawTo(Graphics2D)</a></span> - Method in class org.biojava.bio.chromatogram.graphic.<a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.html" title="class in org.biojava.bio.chromatogram.graphic">ChromatogramGraphic</a></dt>
<dd>
<div class="block">Draws the chromatogram onto the provided graphics context.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/BoundaryFinder.html#dropBoundaryValues()">dropBoundaryValues()</a></span> - Method in interface org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/BoundaryFinder.html" title="interface in org.biojava.bio.program.tagvalue">BoundaryFinder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/CodonPrefTools.html#DROSOPHILA_MELANOGASTER_NUCLEAR">DROSOPHILA_MELANOGASTER_NUCLEAR</a></span> - Static variable in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/CodonPrefTools.html" title="class in org.biojava.bio.symbol">CodonPrefTools</a></dt>
<dd>
<div class="block">Drosophila melanogaster codon preferences</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/molbio/RestrictionEnzyme.html#dsCutPositions">dsCutPositions</a></span> - Variable in class org.biojava.bio.molbio.<a href="./org/biojava/bio/molbio/RestrictionEnzyme.html" title="class in org.biojava.bio.molbio">RestrictionEnzyme</a></dt>
<dd> </dd>
<dt><a href="./org/biojavax/DummyCrossReferenceResolver.html" title="class in org.biojavax"><span class="strong">DummyCrossReferenceResolver</span></a> - Class in <a href="./org/biojavax/package-summary.html">org.biojavax</a></dt>
<dd>
<div class="block">A simple implementation of CrossReferenceResolver.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/DummyCrossReferenceResolver.html#DummyCrossReferenceResolver()">DummyCrossReferenceResolver()</a></span> - Constructor for class org.biojavax.<a href="./org/biojavax/DummyCrossReferenceResolver.html" title="class in org.biojavax">DummyCrossReferenceResolver</a></dt>
<dd> </dd>
<dt><a href="./org/biojavax/bio/seq/DummyRichSequenceHandler.html" title="class in org.biojavax.bio.seq"><span class="strong">DummyRichSequenceHandler</span></a> - Class in <a href="./org/biojavax/bio/seq/package-summary.html">org.biojavax.bio.seq</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/DummyRichSequenceHandler.html#DummyRichSequenceHandler()">DummyRichSequenceHandler()</a></span> - Constructor for class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/DummyRichSequenceHandler.html" title="class in org.biojavax.bio.seq">DummyRichSequenceHandler</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/impl/DummySequence.html" title="class in org.biojava.bio.seq.impl"><span class="strong">DummySequence</span></a> - Class in <a href="./org/biojava/bio/seq/impl/package-summary.html">org.biojava.bio.seq.impl</a></dt>
<dd>
<div class="block">A Sequence implementation that has a name and URI but no features,
and a zero length symbol list.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/DummySequence.html#DummySequence(java.lang.String, java.lang.String)">DummySequence(String, String)</a></span> - Constructor for class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/DummySequence.html" title="class in org.biojava.bio.seq.impl">DummySequence</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/db/DummySequenceDB.html" title="class in org.biojava.bio.seq.db"><span class="strong">DummySequenceDB</span></a> - Class in <a href="./org/biojava/bio/seq/db/package-summary.html">org.biojava.bio.seq.db</a></dt>
<dd>
<div class="block"><code>DummySequenceDB</code> is an implementation which contains
only a <code>DummySequence</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/DummySequenceDB.html#DummySequenceDB(java.lang.String)">DummySequenceDB(String)</a></span> - Constructor for class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/DummySequenceDB.html" title="class in org.biojava.bio.seq.db">DummySequenceDB</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/db/DummySequenceDBInstallation.html" title="class in org.biojava.bio.seq.db"><span class="strong">DummySequenceDBInstallation</span></a> - Class in <a href="./org/biojava/bio/seq/db/package-summary.html">org.biojava.bio.seq.db</a></dt>
<dd>
<div class="block"><code>DummySequenceDBInstallation</code> is an implementation which
returns the same <code>DummySequenceDB</code> instance regardless
of the identifier used to retrieve a database.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/DummySequenceDBInstallation.html#DummySequenceDBInstallation()">DummySequenceDBInstallation()</a></span> - Constructor for class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/DummySequenceDBInstallation.html" title="class in org.biojava.bio.seq.db">DummySequenceDBInstallation</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/symbol/DummySymbolList.html" title="class in org.biojava.bio.symbol"><span class="strong">DummySymbolList</span></a> - Class in <a href="./org/biojava/bio/symbol/package-summary.html">org.biojava.bio.symbol</a></dt>
<dd>
<div class="block">Symbol list which just consists of non-informative symbols.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/DummySymbolList.html#DummySymbolList(org.biojava.bio.symbol.FiniteAlphabet, int)">DummySymbolList(FiniteAlphabet, int)</a></span> - Constructor for class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/DummySymbolList.html" title="class in org.biojava.bio.symbol">DummySymbolList</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/DummySymbolList.html#DummySymbolList(org.biojava.bio.symbol.Alphabet, int, org.biojava.bio.symbol.Symbol)">DummySymbolList(Alphabet, int, Symbol)</a></span> - Constructor for class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/DummySymbolList.html" title="class in org.biojava.bio.symbol">DummySymbolList</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleGappedSymbolList.html#dumpBlocks()">dumpBlocks()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleGappedSymbolList.html" title="class in org.biojava.bio.symbol">SimpleGappedSymbolList</a></dt>
<dd>
<div class="block">Debugging method</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/automata/NfaSubModel.html#duplicate()">duplicate()</a></span> - Method in class org.biojava.utils.automata.<a href="./org/biojava/utils/automata/NfaSubModel.html" title="class in org.biojava.utils.automata">NfaSubModel</a></dt>
<dd>
<div class="block">Makes a deep clone of this instance.</div>
</dd>
<dt><a href="./org/biojava/bio/program/homologene/DuplicateTaxonException.html" title="class in org.biojava.bio.program.homologene"><span class="strong">DuplicateTaxonException</span></a> - Exception in <a href="./org/biojava/bio/program/homologene/package-summary.html">org.biojava.bio.program.homologene</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/DuplicateTaxonException.html#DuplicateTaxonException()">DuplicateTaxonException()</a></span> - Constructor for exception org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/DuplicateTaxonException.html" title="class in org.biojava.bio.program.homologene">DuplicateTaxonException</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/DuplicateTaxonException.html#DuplicateTaxonException(java.lang.String)">DuplicateTaxonException(String)</a></span> - Constructor for exception org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/DuplicateTaxonException.html" title="class in org.biojava.bio.program.homologene">DuplicateTaxonException</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/DuplicateTaxonException.html#DuplicateTaxonException(java.lang.Throwable)">DuplicateTaxonException(Throwable)</a></span> - Constructor for exception org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/DuplicateTaxonException.html" title="class in org.biojava.bio.program.homologene">DuplicateTaxonException</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/DuplicateTaxonException.html#DuplicateTaxonException(java.lang.Throwable, java.lang.String)">DuplicateTaxonException(Throwable, String)</a></span> - Constructor for exception org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/DuplicateTaxonException.html" title="class in org.biojava.bio.program.homologene">DuplicateTaxonException</a></dt>
<dd> </dd>
</dl>
<a name="_E_">
<!-- -->
</a>
<h2 class="title">E</h2>
<dl>
<dt><span class="strong"><a href="./org/biojava/bio/seq/ProteinTools.html#e()">e()</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/ProteinTools.html" title="class in org.biojava.bio.seq">ProteinTools</a></dt>
<dd>
<div class="block">Returns the <code>AtomicSymbol</code> for the amino acid
Glutamic Acid</div>
</dd>
<dt><a href="./org/biojava/bio/program/blast2html/EbiDatabaseURLGenerator.html" title="class in org.biojava.bio.program.blast2html"><span class="strong">EbiDatabaseURLGenerator</span></a> - Class in <a href="./org/biojava/bio/program/blast2html/package-summary.html">org.biojava.bio.program.blast2html</a></dt>
<dd>
<div class="block">Simple URL generator for EMBL at the EBI.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/blast2html/EbiDatabaseURLGenerator.html#EbiDatabaseURLGenerator()">EbiDatabaseURLGenerator()</a></span> - Constructor for class org.biojava.bio.program.blast2html.<a href="./org/biojava/bio/program/blast2html/EbiDatabaseURLGenerator.html" title="class in org.biojava.bio.program.blast2html">EbiDatabaseURLGenerator</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/taxa/EbiFormat.html" title="class in org.biojava.bio.taxa"><span class="strong">EbiFormat</span></a> - Class in <a href="./org/biojava/bio/taxa/package-summary.html">org.biojava.bio.taxa</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>replaced by classes in <a href="./org/biojavax/bio/taxa/package-summary.html"><code>org.biojavax.bio.taxa</code></a></i></div>
</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/taxa/EbiFormat.html#EbiFormat()">EbiFormat()</a></span> - Constructor for class org.biojava.bio.taxa.<a href="./org/biojava/bio/taxa/EbiFormat.html" title="class in org.biojava.bio.taxa">EbiFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/formats/FormatTools.html#EC_FROM_STRING">EC_FROM_STRING</a></span> - Static variable in class org.biojava.bio.program.formats.<a href="./org/biojava/bio/program/formats/FormatTools.html" title="class in org.biojava.bio.program.formats">FormatTools</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/EcNumber.html#EC_PATTERN">EC_PATTERN</a></span> - Static variable in interface org.biojava.bio.<a href="./org/biojava/bio/EcNumber.html" title="interface in org.biojava.bio">EcNumber</a></dt>
<dd>
<div class="block">A Pattern that can be used to parse EC strings into the indiidual numbers.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/twohead/AbstractMatrixPairDPCursor.html#eCache">eCache</a></span> - Variable in class org.biojava.bio.dp.twohead.<a href="./org/biojava/bio/dp/twohead/AbstractMatrixPairDPCursor.html" title="class in org.biojava.bio.dp.twohead">AbstractMatrixPairDPCursor</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/twohead/LightPairDPCursor.html#eCache">eCache</a></span> - Variable in class org.biojava.bio.dp.twohead.<a href="./org/biojava/bio/dp/twohead/LightPairDPCursor.html" title="class in org.biojava.bio.dp.twohead">LightPairDPCursor</a></dt>
<dd>
<div class="block">Description of the Field</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/TranslationTable.html#ECHIN_MITO">ECHIN_MITO</a></span> - Static variable in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/TranslationTable.html" title="interface in org.biojava.bio.symbol">TranslationTable</a></dt>
<dd>
<div class="block">Translation table name for the echinoderm mitochondrial genetic
code.</div>
</dd>
<dt><a href="./org/biojava/bio/program/tagvalue/Echo.html" title="class in org.biojava.bio.program.tagvalue"><span class="strong">Echo</span></a> - Class in <a href="./org/biojava/bio/program/tagvalue/package-summary.html">org.biojava.bio.program.tagvalue</a></dt>
<dd>
<div class="block">
A simple listener that just echoes events back to the console.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/Echo.html#Echo()">Echo()</a></span> - Constructor for class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/Echo.html" title="class in org.biojava.bio.program.tagvalue">Echo</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/EcNumber.html" title="interface in org.biojava.bio"><span class="strong">EcNumber</span></a> - Interface in <a href="./org/biojava/bio/package-summary.html">org.biojava.bio</a></dt>
<dd>
<div class="block">An ec (enzyme classification) number.</div>
</dd>
<dt><a href="./org/biojava/bio/EcNumber.Impl.html" title="class in org.biojava.bio"><span class="strong">EcNumber.Impl</span></a> - Class in <a href="./org/biojava/bio/package-summary.html">org.biojava.bio</a></dt>
<dd>
<div class="block">A simple implementation of EcNumber.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/EcNumber.Impl.html#EcNumber.Impl(int, int, int, int)">EcNumber.Impl(int, int, int, int)</a></span> - Constructor for class org.biojava.bio.<a href="./org/biojava/bio/EcNumber.Impl.html" title="class in org.biojava.bio">EcNumber.Impl</a></dt>
<dd>
<div class="block">Make a new EcNumber.Impl with the data provided.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/CodonPrefTools.html#ECOLI">ECOLI</a></span> - Static variable in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/CodonPrefTools.html" title="class in org.biojava.bio.symbol">CodonPrefTools</a></dt>
<dd>
<div class="block">Escherichia coli codon preferences</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/EditableAlignment.html#edit(java.lang.Object, org.biojava.bio.symbol.Edit)">edit(Object, Edit)</a></span> - Method in interface org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/EditableAlignment.html" title="interface in org.biojava.bio.alignment">EditableAlignment</a></dt>
<dd>
<div class="block"> edit() allows edits on an individual sequence, they should be reflected back
to the underlying SymbolList.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/FlexibleAlignment.html#edit(java.lang.Object, org.biojava.bio.symbol.Edit)">edit(Object, Edit)</a></span> - Method in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/FlexibleAlignment.html" title="class in org.biojava.bio.alignment">FlexibleAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/SimpleStatePath.html#edit(org.biojava.bio.symbol.Edit)">edit(Edit)</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/SimpleStatePath.html" title="class in org.biojava.bio.dp">SimpleStatePath</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/DASSequence.html#edit(org.biojava.bio.symbol.Edit)">edit(Edit)</a></span> - Method in class org.biojava.bio.program.das.<a href="./org/biojava/bio/program/das/DASSequence.html" title="class in org.biojava.bio.program.das">DASSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/homol/SimilarityPairFeature.EmptyPairwiseAlignment.html#edit(org.biojava.bio.symbol.Edit)">edit(Edit)</a></span> - Method in class org.biojava.bio.seq.homol.<a href="./org/biojava/bio/seq/homol/SimilarityPairFeature.EmptyPairwiseAlignment.html" title="class in org.biojava.bio.seq.homol">SimilarityPairFeature.EmptyPairwiseAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/DummySequence.html#edit(org.biojava.bio.symbol.Edit)">edit(Edit)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/DummySequence.html" title="class in org.biojava.bio.seq.impl">DummySequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/RevCompSequence.html#edit(org.biojava.bio.symbol.Edit)">edit(Edit)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/RevCompSequence.html" title="class in org.biojava.bio.seq.impl">RevCompSequence</a></dt>
<dd>
<div class="block">edit() will try to edit the underlying Sequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleSequence.html#edit(org.biojava.bio.symbol.Edit)">edit(Edit)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleSequence.html" title="class in org.biojava.bio.seq.impl">SimpleSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SubSequence.html#edit(org.biojava.bio.symbol.Edit)">edit(Edit)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SubSequence.html" title="class in org.biojava.bio.seq.impl">SubSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/ViewSequence.html#edit(org.biojava.bio.symbol.Edit)">edit(Edit)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/ViewSequence.html" title="class in org.biojava.bio.seq.impl">ViewSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/NewSimpleAssembly.html#edit(org.biojava.bio.symbol.Edit)">edit(Edit)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/NewSimpleAssembly.html" title="class in org.biojava.bio.seq">NewSimpleAssembly</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/SimpleAssembly.html#edit(org.biojava.bio.symbol.Edit)">edit(Edit)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/SimpleAssembly.html" title="class in org.biojava.bio.seq">SimpleAssembly</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AbstractSymbolList.html#edit(org.biojava.bio.symbol.Edit)">edit(Edit)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AbstractSymbolList.html" title="class in org.biojava.bio.symbol">AbstractSymbolList</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/symbol/Edit.html" title="class in org.biojava.bio.symbol"><span class="strong">Edit</span></a> - Class in <a href="./org/biojava/bio/symbol/package-summary.html">org.biojava.bio.symbol</a></dt>
<dd>
<div class="block">
Encapsulates an edit operation on a SymbolList.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/Edit.html#Edit(int, int, org.biojava.bio.symbol.SymbolList)">Edit(int, int, SymbolList)</a></span> - Constructor for class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/Edit.html" title="class in org.biojava.bio.symbol">Edit</a></dt>
<dd>
<div class="block">Create a new Edit.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/Edit.html#Edit(int, org.biojava.bio.symbol.Alphabet, org.biojava.bio.symbol.Symbol)">Edit(int, Alphabet, Symbol)</a></span> - Constructor for class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/Edit.html" title="class in org.biojava.bio.symbol">Edit</a></dt>
<dd>
<div class="block">Convenience construtor for making single residue changes</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/RelabeledAlignment.html#edit(org.biojava.bio.symbol.Edit)">edit(Edit)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/RelabeledAlignment.html" title="class in org.biojava.bio.symbol">RelabeledAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleSymbolList.html#edit(org.biojava.bio.symbol.Edit)">edit(Edit)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleSymbolList.html" title="class in org.biojava.bio.symbol">SimpleSymbolList</a></dt>
<dd>
<div class="block">Apply and edit to the SymbolList as specified by Edit.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SymbolList.html#EDIT">EDIT</a></span> - Static variable in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SymbolList.html" title="interface in org.biojava.bio.symbol">SymbolList</a></dt>
<dd>
<div class="block">Signals that the SymbolList is being edited.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SymbolList.html#edit(org.biojava.bio.symbol.Edit)">edit(Edit)</a></span> - Method in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SymbolList.html" title="interface in org.biojava.bio.symbol">SymbolList</a></dt>
<dd>
<div class="block">Apply an edit to the SymbolList as specified by the edit object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLRichSequenceHandler.html#edit(org.biojavax.bio.seq.RichSequence, org.biojava.bio.symbol.Edit)">edit(RichSequence, Edit)</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLRichSequenceHandler.html" title="class in org.biojavax.bio.db.biosql">BioSQLRichSequenceHandler</a></dt>
<dd>
<div class="block">Apply an edit to the Sequence as specified by the edit object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/DummyRichSequenceHandler.html#edit(org.biojavax.bio.seq.RichSequence, org.biojava.bio.symbol.Edit)">edit(RichSequence, Edit)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/DummyRichSequenceHandler.html" title="class in org.biojavax.bio.seq">DummyRichSequenceHandler</a></dt>
<dd>
<div class="block">Apply an edit to the Sequence as specified by the edit object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/InfinitelyAmbiguousSymbolList.html#edit(org.biojava.bio.symbol.Edit)">edit(Edit)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/InfinitelyAmbiguousSymbolList.html" title="class in org.biojavax.bio.seq">InfinitelyAmbiguousSymbolList</a></dt>
<dd>
<div class="block">Apply an edit to the SymbolList as specified by the edit object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequenceHandler.html#edit(org.biojavax.bio.seq.RichSequence, org.biojava.bio.symbol.Edit)">edit(RichSequence, Edit)</a></span> - Method in interface org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequenceHandler.html" title="interface in org.biojavax.bio.seq">RichSequenceHandler</a></dt>
<dd>
<div class="block">Apply an edit to the Sequence as specified by the edit object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/ThinRichSequence.html#edit(org.biojava.bio.symbol.Edit)">edit(Edit)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/ThinRichSequence.html" title="class in org.biojavax.bio.seq">ThinRichSequence</a></dt>
<dd>
<div class="block">Apply an edit to the SymbolList as specified by the edit object.</div>
</dd>
<dt><a href="./org/biojava/bio/alignment/EditableAlignment.html" title="interface in org.biojava.bio.alignment"><span class="strong">EditableAlignment</span></a> - Interface in <a href="./org/biojava/bio/alignment/package-summary.html">org.biojava.bio.alignment</a></dt>
<dd>
<div class="block">EditableAlignment is an interface that defines methods for
shifting bases within an Alignment.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BiblioBook.html#edition">edition</a></span> - Variable in class org.biojava.bibliography.<a href="./org/biojava/bibliography/BiblioBook.html" title="class in org.biojava.bibliography">BiblioBook</a></dt>
<dd>
<div class="block">Edition.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BiblioBook.html#editor">editor</a></span> - Variable in class org.biojava.bibliography.<a href="./org/biojava/bibliography/BiblioBook.html" title="class in org.biojava.bibliography">BiblioBook</a></dt>
<dd>
<div class="block">Editor.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#EDITOR_LIST_TAG">EDITOR_LIST_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html#EDITOR_TAG">EDITOR_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html" title="class in org.biojavax.bio.seq.io">EMBLxmlFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/jama/Matrix.html#eig()">eig()</a></span> - Method in class org.biojava.bio.structure.jama.<a href="./org/biojava/bio/structure/jama/Matrix.html" title="class in org.biojava.bio.structure.jama">Matrix</a></dt>
<dd>
<div class="block">Eigenvalue Decomposition</div>
</dd>
<dt><a href="./org/biojava/bio/structure/jama/EigenvalueDecomposition.html" title="class in org.biojava.bio.structure.jama"><span class="strong">EigenvalueDecomposition</span></a> - Class in <a href="./org/biojava/bio/structure/jama/package-summary.html">org.biojava.bio.structure.jama</a></dt>
<dd>
<div class="block">Eigenvalues and eigenvectors of a real matrix.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/jama/EigenvalueDecomposition.html#EigenvalueDecomposition(org.biojava.bio.structure.jama.Matrix)">EigenvalueDecomposition(Matrix)</a></span> - Constructor for class org.biojava.bio.structure.jama.<a href="./org/biojava/bio/structure/jama/EigenvalueDecomposition.html" title="class in org.biojava.bio.structure.jama">EigenvalueDecomposition</a></dt>
<dd>
<div class="block">Check for symmetry, then construct the eigenvalue decomposition
provides a way to access D and V.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/abi/ABIFParser.TaggedDataRecord.html#elementLength">elementLength</a></span> - Variable in class org.biojava.bio.program.abi.<a href="./org/biojava/bio/program/abi/ABIFParser.TaggedDataRecord.html" title="class in org.biojava.bio.program.abi">ABIFParser.TaggedDataRecord</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/xff/ElementRecognizer.html" title="interface in org.biojava.bio.program.xff"><span class="strong">ElementRecognizer</span></a> - Interface in <a href="./org/biojava/bio/program/xff/package-summary.html">org.biojava.bio.program.xff</a></dt>
<dd>
<div class="block">Simple interface for filtering SAX/StAX startElement events.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/agave/ElementRecognizer.html" title="interface in org.biojava.bio.seq.io.agave"><span class="strong">ElementRecognizer</span></a> - Interface in <a href="./org/biojava/bio/seq/io/agave/package-summary.html">org.biojava.bio.seq.io.agave</a></dt>
<dd>
<div class="block">This class is copied to agave package
Simple interface for filtering SAX/StAX startElement events</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/game/ElementRecognizer.html" title="interface in org.biojava.bio.seq.io.game"><span class="strong">ElementRecognizer</span></a> - Interface in <a href="./org/biojava/bio/seq/io/game/package-summary.html">org.biojava.bio.seq.io.game</a></dt>
<dd>
<div class="block">Simple interface for filtering SAX/StAX startElement events</div>
</dd>
<dt><a href="./org/biojava/bio/program/xff/ElementRecognizer.AllElementRecognizer.html" title="class in org.biojava.bio.program.xff"><span class="strong">ElementRecognizer.AllElementRecognizer</span></a> - Class in <a href="./org/biojava/bio/program/xff/package-summary.html">org.biojava.bio.program.xff</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/xff/ElementRecognizer.AllElementRecognizer.html#ElementRecognizer.AllElementRecognizer()">ElementRecognizer.AllElementRecognizer()</a></span> - Constructor for class org.biojava.bio.program.xff.<a href="./org/biojava/bio/program/xff/ElementRecognizer.AllElementRecognizer.html" title="class in org.biojava.bio.program.xff">ElementRecognizer.AllElementRecognizer</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/io/agave/ElementRecognizer.AllElementRecognizer.html" title="class in org.biojava.bio.seq.io.agave"><span class="strong">ElementRecognizer.AllElementRecognizer</span></a> - Class in <a href="./org/biojava/bio/seq/io/agave/package-summary.html">org.biojava.bio.seq.io.agave</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/ElementRecognizer.AllElementRecognizer.html#ElementRecognizer.AllElementRecognizer()">ElementRecognizer.AllElementRecognizer()</a></span> - Constructor for class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/ElementRecognizer.AllElementRecognizer.html" title="class in org.biojava.bio.seq.io.agave">ElementRecognizer.AllElementRecognizer</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/io/game/ElementRecognizer.AllElementRecognizer.html" title="class in org.biojava.bio.seq.io.game"><span class="strong">ElementRecognizer.AllElementRecognizer</span></a> - Class in <a href="./org/biojava/bio/seq/io/game/package-summary.html">org.biojava.bio.seq.io.game</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game/ElementRecognizer.AllElementRecognizer.html#ElementRecognizer.AllElementRecognizer()">ElementRecognizer.AllElementRecognizer()</a></span> - Constructor for class org.biojava.bio.seq.io.game.<a href="./org/biojava/bio/seq/io/game/ElementRecognizer.AllElementRecognizer.html" title="class in org.biojava.bio.seq.io.game">ElementRecognizer.AllElementRecognizer</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/xff/ElementRecognizer.ByLocalName.html" title="class in org.biojava.bio.program.xff"><span class="strong">ElementRecognizer.ByLocalName</span></a> - Class in <a href="./org/biojava/bio/program/xff/package-summary.html">org.biojava.bio.program.xff</a></dt>
<dd>
<div class="block">Filter elements by local name (not recommended).</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/xff/ElementRecognizer.ByLocalName.html#ElementRecognizer.ByLocalName(java.lang.String)">ElementRecognizer.ByLocalName(String)</a></span> - Constructor for class org.biojava.bio.program.xff.<a href="./org/biojava/bio/program/xff/ElementRecognizer.ByLocalName.html" title="class in org.biojava.bio.program.xff">ElementRecognizer.ByLocalName</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/io/agave/ElementRecognizer.ByLocalName.html" title="class in org.biojava.bio.seq.io.agave"><span class="strong">ElementRecognizer.ByLocalName</span></a> - Class in <a href="./org/biojava/bio/seq/io/agave/package-summary.html">org.biojava.bio.seq.io.agave</a></dt>
<dd>
<div class="block">Filter elements by local name (not recommended).</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/ElementRecognizer.ByLocalName.html#ElementRecognizer.ByLocalName(java.lang.String)">ElementRecognizer.ByLocalName(String)</a></span> - Constructor for class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/ElementRecognizer.ByLocalName.html" title="class in org.biojava.bio.seq.io.agave">ElementRecognizer.ByLocalName</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/io/game/ElementRecognizer.ByLocalName.html" title="class in org.biojava.bio.seq.io.game"><span class="strong">ElementRecognizer.ByLocalName</span></a> - Class in <a href="./org/biojava/bio/seq/io/game/package-summary.html">org.biojava.bio.seq.io.game</a></dt>
<dd>
<div class="block">Filter elements by local name (not recommended).</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game/ElementRecognizer.ByLocalName.html#ElementRecognizer.ByLocalName(java.lang.String)">ElementRecognizer.ByLocalName(String)</a></span> - Constructor for class org.biojava.bio.seq.io.game.<a href="./org/biojava/bio/seq/io/game/ElementRecognizer.ByLocalName.html" title="class in org.biojava.bio.seq.io.game">ElementRecognizer.ByLocalName</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/xff/ElementRecognizer.ByNSName.html" title="class in org.biojava.bio.program.xff"><span class="strong">ElementRecognizer.ByNSName</span></a> - Class in <a href="./org/biojava/bio/program/xff/package-summary.html">org.biojava.bio.program.xff</a></dt>
<dd>
<div class="block">Filter elements by name and namespace.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/xff/ElementRecognizer.ByNSName.html#ElementRecognizer.ByNSName(java.lang.String, java.lang.String)">ElementRecognizer.ByNSName(String, String)</a></span> - Constructor for class org.biojava.bio.program.xff.<a href="./org/biojava/bio/program/xff/ElementRecognizer.ByNSName.html" title="class in org.biojava.bio.program.xff">ElementRecognizer.ByNSName</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/io/agave/ElementRecognizer.ByNSName.html" title="class in org.biojava.bio.seq.io.agave"><span class="strong">ElementRecognizer.ByNSName</span></a> - Class in <a href="./org/biojava/bio/seq/io/agave/package-summary.html">org.biojava.bio.seq.io.agave</a></dt>
<dd>
<div class="block">Filter elements by name and namespace.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/ElementRecognizer.ByNSName.html#ElementRecognizer.ByNSName(java.lang.String, java.lang.String)">ElementRecognizer.ByNSName(String, String)</a></span> - Constructor for class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/ElementRecognizer.ByNSName.html" title="class in org.biojava.bio.seq.io.agave">ElementRecognizer.ByNSName</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/io/game/ElementRecognizer.ByNSName.html" title="class in org.biojava.bio.seq.io.game"><span class="strong">ElementRecognizer.ByNSName</span></a> - Class in <a href="./org/biojava/bio/seq/io/game/package-summary.html">org.biojava.bio.seq.io.game</a></dt>
<dd>
<div class="block">Filter elements by name and namespace.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game/ElementRecognizer.ByNSName.html#ElementRecognizer.ByNSName(java.lang.String, java.lang.String)">ElementRecognizer.ByNSName(String, String)</a></span> - Constructor for class org.biojava.bio.seq.io.game.<a href="./org/biojava/bio/seq/io/game/ElementRecognizer.ByNSName.html" title="class in org.biojava.bio.seq.io.game">ElementRecognizer.ByNSName</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/xff/ElementRecognizer.HasAttribute.html" title="class in org.biojava.bio.program.xff"><span class="strong">ElementRecognizer.HasAttribute</span></a> - Class in <a href="./org/biojava/bio/program/xff/package-summary.html">org.biojava.bio.program.xff</a></dt>
<dd>
<div class="block">Filter elements on the existence of a specified attribute.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/xff/ElementRecognizer.HasAttribute.html#ElementRecognizer.HasAttribute(java.lang.String)">ElementRecognizer.HasAttribute(String)</a></span> - Constructor for class org.biojava.bio.program.xff.<a href="./org/biojava/bio/program/xff/ElementRecognizer.HasAttribute.html" title="class in org.biojava.bio.program.xff">ElementRecognizer.HasAttribute</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/io/agave/ElementRecognizer.HasAttribute.html" title="class in org.biojava.bio.seq.io.agave"><span class="strong">ElementRecognizer.HasAttribute</span></a> - Class in <a href="./org/biojava/bio/seq/io/agave/package-summary.html">org.biojava.bio.seq.io.agave</a></dt>
<dd>
<div class="block">Filter elements on the existence of a specified attribute.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/ElementRecognizer.HasAttribute.html#ElementRecognizer.HasAttribute(java.lang.String)">ElementRecognizer.HasAttribute(String)</a></span> - Constructor for class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/ElementRecognizer.HasAttribute.html" title="class in org.biojava.bio.seq.io.agave">ElementRecognizer.HasAttribute</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/io/game/ElementRecognizer.HasAttribute.html" title="class in org.biojava.bio.seq.io.game"><span class="strong">ElementRecognizer.HasAttribute</span></a> - Class in <a href="./org/biojava/bio/seq/io/game/package-summary.html">org.biojava.bio.seq.io.game</a></dt>
<dd>
<div class="block">Filter elements on the existence of a specified attribute.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game/ElementRecognizer.HasAttribute.html#ElementRecognizer.HasAttribute(java.lang.String)">ElementRecognizer.HasAttribute(String)</a></span> - Constructor for class org.biojava.bio.seq.io.game.<a href="./org/biojava/bio/seq/io/game/ElementRecognizer.HasAttribute.html" title="class in org.biojava.bio.seq.io.game">ElementRecognizer.HasAttribute</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/gui/sequence/EllipticalBeadRenderer.html" title="class in org.biojava.bio.gui.sequence"><span class="strong">EllipticalBeadRenderer</span></a> - Class in <a href="./org/biojava/bio/gui/sequence/package-summary.html">org.biojava.bio.gui.sequence</a></dt>
<dd>
<div class="block"><code>EllipticalBeadRenderer</code> renders features as simple
ellipses.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/EllipticalBeadRenderer.html#EllipticalBeadRenderer()">EllipticalBeadRenderer()</a></span> - Constructor for class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/EllipticalBeadRenderer.html" title="class in org.biojava.bio.gui.sequence">EllipticalBeadRenderer</a></dt>
<dd>
<div class="block">Creates a new <code>EllipticalBeadRenderer</code> object
with the default settings.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/EllipticalBeadRenderer.html#EllipticalBeadRenderer(double, double, java.awt.Paint, java.awt.Paint, java.awt.Stroke, double)">EllipticalBeadRenderer(double, double, Paint, Paint, Stroke, double)</a></span> - Constructor for class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/EllipticalBeadRenderer.html" title="class in org.biojava.bio.gui.sequence">EllipticalBeadRenderer</a></dt>
<dd>
<div class="block">Creates a new <code>EllipticalBeadRenderer</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BiblioPerson.html#email">email</a></span> - Variable in class org.biojava.bibliography.<a href="./org/biojava/bibliography/BiblioPerson.html" title="class in org.biojava.bibliography">BiblioPerson</a></dt>
<dd>
<div class="block">Their e-mail address.</div>
</dd>
<dt><a href="./org/biojava/bio/program/formats/Embl.html" title="class in org.biojava.bio.program.formats"><span class="strong">Embl</span></a> - Class in <a href="./org/biojava/bio/program/formats/package-summary.html">org.biojava.bio.program.formats</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/formats/Embl.html#Embl()">Embl()</a></span> - Constructor for class org.biojava.bio.program.formats.<a href="./org/biojava/bio/program/formats/Embl.html" title="class in org.biojava.bio.program.formats">Embl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/LineSplitParser.html#EMBL">EMBL</a></span> - Static variable in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/LineSplitParser.html" title="class in org.biojava.bio.program.tagvalue">LineSplitParser</a></dt>
<dd>
<div class="block">A LineSplitParser pre-configured to process EMBL-style flat files.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOConstants.html#EMBL">EMBL</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOConstants.html" title="class in org.biojava.bio.seq.io">SeqIOConstants</a></dt>
<dd>
<div class="block"><code>EMBL</code> indicates that the sequence format is EMBL.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/agave/Embl2AgaveAnnotFilter.html" title="class in org.biojava.bio.seq.io.agave"><span class="strong">Embl2AgaveAnnotFilter</span></a> - Class in <a href="./org/biojava/bio/seq/io/agave/package-summary.html">org.biojava.bio.seq.io.agave</a></dt>
<dd>
<div class="block">Map EMBL data into AGAVE format</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOConstants.html#EMBL_AA">EMBL_AA</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOConstants.html" title="class in org.biojava.bio.seq.io">SeqIOConstants</a></dt>
<dd>
<div class="block"><code>EMBL_AA</code> premade EMBL | AA.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/Embl2AgaveAnnotFilter.html#EMBL_AGAVE_ANNOT_FILTER_FACTORY">EMBL_AGAVE_ANNOT_FILTER_FACTORY</a></span> - Static variable in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/Embl2AgaveAnnotFilter.html" title="class in org.biojava.bio.seq.io.agave">Embl2AgaveAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOConstants.html#EMBL_DNA">EMBL_DNA</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOConstants.html" title="class in org.biojava.bio.seq.io">SeqIOConstants</a></dt>
<dd>
<div class="block"><code>EMBL_DNA</code> premade EMBL | DNA.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLFormat.html#EMBL_FORMAT">EMBL_FORMAT</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLFormat.html" title="class in org.biojavax.bio.seq.io">EMBLFormat</a></dt>
<dd>
<div class="block">The name of the current format</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/Formats.html#EMBL_GENBANK_FEATURE_TABLE_TYPE">EMBL_GENBANK_FEATURE_TABLE_TYPE</a></span> - Static variable in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/Formats.html" title="class in org.biojava.bio.program.tagvalue">Formats</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLFormat.html#EMBL_PRE87_FORMAT">EMBL_PRE87_FORMAT</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLFormat.html" title="class in org.biojavax.bio.seq.io">EMBLFormat</a></dt>
<dd>
<div class="block">The name of the Pre-87 format</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOConstants.html#EMBL_RNA">EMBL_RNA</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOConstants.html" title="class in org.biojava.bio.seq.io">SeqIOConstants</a></dt>
<dd>
<div class="block"><code>EMBL_RNA</code> premade EMBL | RNA.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/Formats.html#EMBL_TYPE">EMBL_TYPE</a></span> - Static variable in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/Formats.html" title="class in org.biojava.bio.program.tagvalue">Formats</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/db/emblcd/EmblCDROMIndexReader.html" title="class in org.biojava.bio.seq.db.emblcd"><span class="strong">EmblCDROMIndexReader</span></a> - Class in <a href="./org/biojava/bio/seq/db/emblcd/package-summary.html">org.biojava.bio.seq.db.emblcd</a></dt>
<dd>
<div class="block"><code>EmblCDROMIndexReader</code> is an abstract class whose
concrete subclasses read EMBL CD-ROM format indices from an
underlying <code>InputStream</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/emblcd/EmblCDROMIndexReader.html#EmblCDROMIndexReader(java.io.InputStream)">EmblCDROMIndexReader(InputStream)</a></span> - Constructor for class org.biojava.bio.seq.db.emblcd.<a href="./org/biojava/bio/seq/db/emblcd/EmblCDROMIndexReader.html" title="class in org.biojava.bio.seq.db.emblcd">EmblCDROMIndexReader</a></dt>
<dd>
<div class="block">Creates a new <code>EmblCDROMIndexReader</code> instance.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/db/EmblCDROMIndexStore.html" title="class in org.biojava.bio.seq.db"><span class="strong">EmblCDROMIndexStore</span></a> - Class in <a href="./org/biojava/bio/seq/db/package-summary.html">org.biojava.bio.seq.db</a></dt>
<dd>
<div class="block"><code>EmblCDROMIndexStore</code>s implement a read-only
<code>IndexStore</code> backed by EMBL CD-ROM format binary
indices.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/EmblCDROMIndexStore.html#EmblCDROMIndexStore(java.io.File, java.io.File, org.biojava.bio.seq.io.SequenceFormat, org.biojava.bio.seq.io.SequenceBuilderFactory, org.biojava.bio.seq.io.SymbolTokenization)">EmblCDROMIndexStore(File, File, SequenceFormat, SequenceBuilderFactory, SymbolTokenization)</a></span> - Constructor for class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/EmblCDROMIndexStore.html" title="class in org.biojava.bio.seq.db">EmblCDROMIndexStore</a></dt>
<dd>
<div class="block">Creates a new <code>EmblCDROMIndexStore</code> backed by a
random access binary index.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/EmblCDROMIndexStore.html#EmblCDROMIndexStore(java.io.File, java.io.File, java.io.File, org.biojava.bio.seq.io.SequenceFormat, org.biojava.bio.seq.io.SequenceBuilderFactory, org.biojava.bio.seq.io.SymbolTokenization)">EmblCDROMIndexStore(File, File, File, SequenceFormat, SequenceBuilderFactory, SymbolTokenization)</a></span> - Constructor for class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/EmblCDROMIndexStore.html" title="class in org.biojava.bio.seq.db">EmblCDROMIndexStore</a></dt>
<dd>
<div class="block">Creates a new <code>EmblCDROMIndexStore</code> backed by a
random access binary index.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/db/emblcd/EmblCDROMRandomAccess.html" title="class in org.biojava.bio.seq.db.emblcd"><span class="strong">EmblCDROMRandomAccess</span></a> - Class in <a href="./org/biojava/bio/seq/db/emblcd/package-summary.html">org.biojava.bio.seq.db.emblcd</a></dt>
<dd>
<div class="block"><code>EmblCDROMRandomAccess</code> is an abstract class whose
concrete subclasses can perform fast lookups in EMBL CD-ROM format
index files.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/emblcd/EmblCDROMRandomAccess.html#EmblCDROMRandomAccess(java.io.File, int, int, long)">EmblCDROMRandomAccess(File, int, int, long)</a></span> - Constructor for class org.biojava.bio.seq.db.emblcd.<a href="./org/biojava/bio/seq/db/emblcd/EmblCDROMRandomAccess.html" title="class in org.biojava.bio.seq.db.emblcd">EmblCDROMRandomAccess</a></dt>
<dd>
<div class="block">Creates a new <code>EmblCDROMRandomAccess</code> object.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/EmblFileFormer.html" title="class in org.biojava.bio.seq.io"><span class="strong">EmblFileFormer</span></a> - Class in <a href="./org/biojava/bio/seq/io/package-summary.html">org.biojava.bio.seq.io</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>Use org.biojavax.bio.seq.io framework instead</i></div>
</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/EmblFileFormer.html#EmblFileFormer()">EmblFileFormer()</a></span> - Constructor for class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/EmblFileFormer.html" title="class in org.biojava.bio.seq.io">EmblFileFormer</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Creates a new <code>EmblFileFormer</code> using
<code>System.out</code> stream.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/EmblFileFormer.html#EmblFileFormer(java.io.PrintStream)">EmblFileFormer(PrintStream)</a></span> - Constructor for class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/EmblFileFormer.html" title="class in org.biojava.bio.seq.io">EmblFileFormer</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Creates a new <code>EmblFileFormer</code> using the specified
stream.</div>
</dd>
<dt><a href="./org/biojavax/bio/seq/io/EMBLFormat.html" title="class in org.biojavax.bio.seq.io"><span class="strong">EMBLFormat</span></a> - Class in <a href="./org/biojavax/bio/seq/io/package-summary.html">org.biojavax.bio.seq.io</a></dt>
<dd>
<div class="block">Format reader for EMBL files.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLFormat.html#EMBLFormat()">EMBLFormat()</a></span> - Constructor for class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLFormat.html" title="class in org.biojavax.bio.seq.io">EMBLFormat</a></dt>
<dd> </dd>
<dt><a href="./org/biojavax/bio/seq/io/EMBLFormat.Terms.html" title="class in org.biojavax.bio.seq.io"><span class="strong">EMBLFormat.Terms</span></a> - Class in <a href="./org/biojavax/bio/seq/io/package-summary.html">org.biojavax.bio.seq.io</a></dt>
<dd>
<div class="block">Implements some EMBL-specific terms.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLFormat.Terms.html#EMBLFormat.Terms()">EMBLFormat.Terms()</a></span> - Constructor for class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLFormat.Terms.html" title="class in org.biojavax.bio.seq.io">EMBLFormat.Terms</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/io/EmblLikeFormat.html" title="class in org.biojava.bio.seq.io"><span class="strong">EmblLikeFormat</span></a> - Class in <a href="./org/biojava/bio/seq/io/package-summary.html">org.biojava.bio.seq.io</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>Use org.biojavax.bio.seq.io.EMBLFormat instead</i></div>
</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/EmblLikeFormat.html#EmblLikeFormat()">EmblLikeFormat()</a></span> - Constructor for class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/EmblLikeFormat.html" title="class in org.biojava.bio.seq.io">EmblLikeFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/EmblLikeLocationParser.html" title="class in org.biojava.bio.seq.io"><span class="strong">EmblLikeLocationParser</span></a> - Class in <a href="./org/biojava/bio/seq/io/package-summary.html">org.biojava.bio.seq.io</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>Use org.biojavax.bio.seq.io framework instead</i></div>
</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/EmblProcessor.html" title="class in org.biojava.bio.seq.io"><span class="strong">EmblProcessor</span></a> - Class in <a href="./org/biojava/bio/seq/io/package-summary.html">org.biojava.bio.seq.io</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>Use org.biojavax.bio.seq.io framework instead</i></div>
</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/EmblProcessor.html#EmblProcessor(org.biojava.bio.seq.io.SequenceBuilder)">EmblProcessor(SequenceBuilder)</a></span> - Constructor for class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/EmblProcessor.html" title="class in org.biojava.bio.seq.io">EmblProcessor</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/EmblProcessor.Factory.html" title="class in org.biojava.bio.seq.io"><span class="strong">EmblProcessor.Factory</span></a> - Class in <a href="./org/biojava/bio/seq/io/package-summary.html">org.biojava.bio.seq.io</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Factory which wraps SequenceBuilders in an EmblProcessor</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/EmblProcessor.Factory.html#EmblProcessor.Factory(org.biojava.bio.seq.io.SequenceBuilderFactory)">EmblProcessor.Factory(SequenceBuilderFactory)</a></span> - Constructor for class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/EmblProcessor.Factory.html" title="class in org.biojava.bio.seq.io">EmblProcessor.Factory</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/EmblReferenceComparator.html" title="class in org.biojava.bio.seq.io"><span class="strong">EmblReferenceComparator</span></a> - Class in <a href="./org/biojava/bio/seq/io/package-summary.html">org.biojava.bio.seq.io</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/EmblReferenceComparator.html#EmblReferenceComparator()">EmblReferenceComparator()</a></span> - Constructor for class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/EmblReferenceComparator.html" title="class in org.biojava.bio.seq.io">EmblReferenceComparator</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html#EMBLXML_FORMAT">EMBLXML_FORMAT</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html" title="class in org.biojavax.bio.seq.io">EMBLxmlFormat</a></dt>
<dd>
<div class="block">The name of this format</div>
</dd>
<dt><a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html" title="class in org.biojavax.bio.seq.io"><span class="strong">EMBLxmlFormat</span></a> - Class in <a href="./org/biojavax/bio/seq/io/package-summary.html">org.biojavax.bio.seq.io</a></dt>
<dd>
<div class="block">Format reader for EMBLxml files.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html#EMBLxmlFormat()">EMBLxmlFormat()</a></span> - Constructor for class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html" title="class in org.biojavax.bio.seq.io">EMBLxmlFormat</a></dt>
<dd> </dd>
<dt><a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.Terms.html" title="class in org.biojavax.bio.seq.io"><span class="strong">EMBLxmlFormat.Terms</span></a> - Class in <a href="./org/biojavax/bio/seq/io/package-summary.html">org.biojavax.bio.seq.io</a></dt>
<dd>
<div class="block">Implements some EMBLxml-specific terms.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.Terms.html#EMBLxmlFormat.Terms()">EMBLxmlFormat.Terms()</a></span> - Constructor for class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.Terms.html" title="class in org.biojavax.bio.seq.io">EMBLxmlFormat.Terms</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/MarkovModel.html#emissionAlphabet()">emissionAlphabet()</a></span> - Method in interface org.biojava.bio.dp.<a href="./org/biojava/bio/dp/MarkovModel.html" title="interface in org.biojava.bio.dp">MarkovModel</a></dt>
<dd>
<div class="block">Alphabet that is emitted by the emission states.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/SimpleMarkovModel.html#emissionAlphabet()">emissionAlphabet()</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/SimpleMarkovModel.html" title="class in org.biojava.bio.dp">SimpleMarkovModel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/WMAsMM.html#emissionAlphabet()">emissionAlphabet()</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/WMAsMM.html" title="class in org.biojava.bio.dp">WMAsMM</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/dp/twohead/EmissionCache.html" title="class in org.biojava.bio.dp.twohead"><span class="strong">EmissionCache</span></a> - Class in <a href="./org/biojava/bio/dp/twohead/package-summary.html">org.biojava.bio.dp.twohead</a></dt>
<dd>
<div class="block">Cache for columns of emission probabilities in pair-wise alignment
algorithms.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/twohead/EmissionCache.html#EmissionCache(org.biojava.bio.symbol.Alphabet, org.biojava.bio.dp.State[], int, org.biojava.bio.dp.ScoreType)">EmissionCache(Alphabet, State[], int, ScoreType)</a></span> - Constructor for class org.biojava.bio.dp.twohead.<a href="./org/biojava/bio/dp/twohead/EmissionCache.html" title="class in org.biojava.bio.dp.twohead">EmissionCache</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/twohead/AbstractMatrixPairDPCursor.html#emissions">emissions</a></span> - Variable in class org.biojava.bio.dp.twohead.<a href="./org/biojava/bio/dp/twohead/AbstractMatrixPairDPCursor.html" title="class in org.biojava.bio.dp.twohead">AbstractMatrixPairDPCursor</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/twohead/Cell.html#emissions">emissions</a></span> - Variable in class org.biojava.bio.dp.twohead.<a href="./org/biojava/bio/dp/twohead/Cell.html" title="class in org.biojava.bio.dp.twohead">Cell</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/onehead/SingleDP.html#emissionsNull">emissionsNull</a></span> - Variable in class org.biojava.bio.dp.onehead.<a href="./org/biojava/bio/dp/onehead/SingleDP.html" title="class in org.biojava.bio.dp.onehead">SingleDP</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/onehead/SingleDP.html#emissionsOdds">emissionsOdds</a></span> - Variable in class org.biojava.bio.dp.onehead.<a href="./org/biojava/bio/dp/onehead/SingleDP.html" title="class in org.biojava.bio.dp.onehead">SingleDP</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/onehead/SingleDP.html#emissionsProb">emissionsProb</a></span> - Variable in class org.biojava.bio.dp.onehead.<a href="./org/biojava/bio/dp/onehead/SingleDP.html" title="class in org.biojava.bio.dp.onehead">SingleDP</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/dp/EmissionState.html" title="interface in org.biojava.bio.dp"><span class="strong">EmissionState</span></a> - Interface in <a href="./org/biojava/bio/dp/package-summary.html">org.biojava.bio.dp</a></dt>
<dd>
<div class="block">
A state in a markov process that has an emission spectrum.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/annodb/AnnotationDB.html#EMPTY">EMPTY</a></span> - Static variable in interface org.biojava.bio.annodb.<a href="./org/biojava/bio/annodb/AnnotationDB.html" title="interface in org.biojava.bio.annodb">AnnotationDB</a></dt>
<dd>
<div class="block">An AnnotationDB that is always empty.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/CollectionConstraint.html#EMPTY">EMPTY</a></span> - Static variable in interface org.biojava.bio.<a href="./org/biojava/bio/CollectionConstraint.html" title="interface in org.biojava.bio">CollectionConstraint</a></dt>
<dd>
<div class="block"><code>EMPTY</code> is a constraint which only accepts the empty
set.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/Location.html#empty">empty</a></span> - Static variable in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/Location.html" title="interface in org.biojava.bio.symbol">Location</a></dt>
<dd>
<div class="block">The <code>Location</code> which contains no points.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/Alphabet.html#EMPTY_ALPHABET">EMPTY_ALPHABET</a></span> - Static variable in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/Alphabet.html" title="interface in org.biojava.bio.symbol">Alphabet</a></dt>
<dd>
<div class="block">A really useful static alphabet that is always empty.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/Annotation.html#EMPTY_ANNOTATION">EMPTY_ANNOTATION</a></span> - Static variable in interface org.biojava.bio.<a href="./org/biojava/bio/Annotation.html" title="interface in org.biojava.bio">Annotation</a></dt>
<dd>
<div class="block">
A really useful empty and immutable annotation object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/RichAnnotation.html#EMPTY_ANNOTATION">EMPTY_ANNOTATION</a></span> - Static variable in interface org.biojavax.<a href="./org/biojavax/RichAnnotation.html" title="interface in org.biojavax">RichAnnotation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureHolder.html#EMPTY_FEATURE_HOLDER">EMPTY_FEATURE_HOLDER</a></span> - Static variable in interface org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureHolder.html" title="interface in org.biojava.bio.seq">FeatureHolder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/TagValueParser.html#EMPTY_LINE_EOR">EMPTY_LINE_EOR</a></span> - Static variable in interface org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/TagValueParser.html" title="interface in org.biojava.bio.program.tagvalue">TagValueParser</a></dt>
<dd>
<div class="block"><code>EMPTY_LINE_EOR</code> is a special EOR value which
allows an empty line to be used as a record separator.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SymbolList.html#EMPTY_LIST">EMPTY_LIST</a></span> - Static variable in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SymbolList.html" title="interface in org.biojava.bio.symbol">SymbolList</a></dt>
<dd>
<div class="block">A useful object that represents an empty symbol list, to avoid returning
null.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichLocation.html#EMPTY_LOCATION">EMPTY_LOCATION</a></span> - Static variable in interface org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichLocation.html" title="interface in org.biojavax.bio.seq">RichLocation</a></dt>
<dd>
<div class="block">The empty location matches nothing.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/homol/SimilarityPairFeature.html#EMPTY_PAIRWISE">EMPTY_PAIRWISE</a></span> - Static variable in interface org.biojava.bio.seq.homol.<a href="./org/biojava/bio/seq/homol/SimilarityPairFeature.html" title="interface in org.biojava.bio.seq.homol">SimilarityPairFeature</a></dt>
<dd>
<div class="block">Constant <code>EMPTY_PAIRWISE</code> is an empty alignment for
situations where there is no available alignment data or the
implementation does not want to create one.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/Position.html#EMPTY_POSITION">EMPTY_POSITION</a></span> - Static variable in interface org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/Position.html" title="interface in org.biojavax.bio.seq">Position</a></dt>
<dd>
<div class="block">The empty position lies nowhere.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/twohead/AbstractMatrixPairDPCursor.html#emptyBP">emptyBP</a></span> - Variable in class org.biojava.bio.dp.twohead.<a href="./org/biojava/bio/dp/twohead/AbstractMatrixPairDPCursor.html" title="class in org.biojava.bio.dp.twohead">AbstractMatrixPairDPCursor</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/twohead/LightPairDPCursor.html#emptyBP">emptyBP</a></span> - Variable in class org.biojava.bio.dp.twohead.<a href="./org/biojava/bio/dp/twohead/LightPairDPCursor.html" title="class in org.biojava.bio.dp.twohead">LightPairDPCursor</a></dt>
<dd>
<div class="block">Description of the Field</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/RichSeqIOAdapter.html#emptyFeature">emptyFeature</a></span> - Variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/RichSeqIOAdapter.html" title="class in org.biojavax.bio.seq.io">RichSeqIOAdapter</a></dt>
<dd>
<div class="block">This is a dummy feature.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SymbolListViews.html#emptyList(org.biojava.bio.symbol.Alphabet)">emptyList(Alphabet)</a></span> - Static method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SymbolListViews.html" title="class in org.biojava.bio.symbol">SymbolListViews</a></dt>
<dd>
<div class="block">Get a new immutable, empty symbol list with the given alphabet.</div>
</dd>
<dt><a href="./org/biojavax/EmptyRichAnnotation.html" title="class in org.biojavax"><span class="strong">EmptyRichAnnotation</span></a> - Class in <a href="./org/biojavax/package-summary.html">org.biojavax</a></dt>
<dd>
<div class="block">A place holder for a RichAnnotation that prevents null having to be used</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/EmptyRichAnnotation.html#EmptyRichAnnotation()">EmptyRichAnnotation()</a></span> - Constructor for class org.biojavax.<a href="./org/biojavax/EmptyRichAnnotation.html" title="class in org.biojavax">EmptyRichAnnotation</a></dt>
<dd> </dd>
<dt><a href="./org/biojavax/bio/seq/EmptyRichLocation.html" title="class in org.biojavax.bio.seq"><span class="strong">EmptyRichLocation</span></a> - Class in <a href="./org/biojavax/bio/seq/package-summary.html">org.biojavax.bio.seq</a></dt>
<dd>
<div class="block">An Empty implementation of RichLocation.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/EmptyRichLocation.html#EmptyRichLocation()">EmptyRichLocation()</a></span> - Constructor for class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/EmptyRichLocation.html" title="class in org.biojavax.bio.seq">EmptyRichLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/BioMatcher.html#end()">end()</a></span> - Method in interface org.biojava.bio.search.<a href="./org/biojava/bio/search/BioMatcher.html" title="interface in org.biojava.bio.search">BioMatcher</a></dt>
<dd>
<div class="block">Get the last symbol index that matches the pattern.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/MaxMismatchMatcher.html#end()">end()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/MaxMismatchMatcher.html" title="class in org.biojava.bio.search">MaxMismatchMatcher</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/automata/FiniteAutomaton.html#end">end</a></span> - Variable in class org.biojava.utils.automata.<a href="./org/biojava/utils/automata/FiniteAutomaton.html" title="class in org.biojava.utils.automata">FiniteAutomaton</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/regex/Matcher.html#end()">end()</a></span> - Method in class org.biojava.utils.regex.<a href="./org/biojava/utils/regex/Matcher.html" title="class in org.biojava.utils.regex">Matcher</a></dt>
<dd>
<div class="block">Returns the index of the last character matched, plus one.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/regex/Matcher.html#end(int)">end(int)</a></span> - Method in class org.biojava.utils.regex.<a href="./org/biojava/utils/regex/Matcher.html" title="class in org.biojava.utils.regex">Matcher</a></dt>
<dd>
<div class="block">Returns the index of the last Symbol, plus one,
of the subsequence captured by the given group during the previous match operation.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/StateMachine.html#END_RECORD_TAG">END_RECORD_TAG</a></span> - Static variable in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/StateMachine.html" title="class in org.biojava.bio.program.tagvalue">StateMachine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/EmblLikeFormat.html#END_SEQUENCE_TAG">END_SEQUENCE_TAG</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/EmblLikeFormat.html" title="class in org.biojava.bio.seq.io">EmblLikeFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/GenbankFormat.html#END_SEQUENCE_TAG">END_SEQUENCE_TAG</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/GenbankFormat.html" title="class in org.biojava.bio.seq.io">GenbankFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLFormat.html#END_SEQUENCE_TAG">END_SEQUENCE_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLFormat.html" title="class in org.biojavax.bio.seq.io">EMBLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/GenbankFormat.html#END_SEQUENCE_TAG">END_SEQUENCE_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/GenbankFormat.html" title="class in org.biojavax.bio.seq.io">GenbankFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtFormat.html#END_SEQUENCE_TAG">END_SEQUENCE_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtFormat.html" title="class in org.biojavax.bio.seq.io">UniProtFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/StateMachine.html#END_TAG">END_TAG</a></span> - Static variable in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/StateMachine.html" title="class in org.biojava.bio.program.tagvalue">StateMachine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/HomologeneBuilder.html#endDB()">endDB()</a></span> - Method in interface org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/HomologeneBuilder.html" title="interface in org.biojava.bio.program.homologene">HomologeneBuilder</a></dt>
<dd>
<div class="block">end of data for DB</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/SimpleHomologeneBuilder.html#endDB()">endDB()</a></span> - Method in class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/SimpleHomologeneBuilder.html" title="class in org.biojava.bio.program.homologene">SimpleHomologeneBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/dasalignment/DASAlignmentXMLResponseParser.html#endDocument()">endDocument()</a></span> - Method in class org.biojava.bio.program.das.dasalignment.<a href="./org/biojava/bio/program/das/dasalignment/DASAlignmentXMLResponseParser.html" title="class in org.biojava.bio.program.das.dasalignment">DASAlignmentXMLResponseParser</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/dasstructure/DASStructureXMLResponseParser.html#endDocument()">endDocument()</a></span> - Method in class org.biojava.bio.program.das.dasstructure.<a href="./org/biojava/bio/program/das/dasstructure/DASStructureXMLResponseParser.html" title="class in org.biojava.bio.program.das.dasstructure">DASStructureXMLResponseParser</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFDocumentHandler.html#endDocument()">endDocument()</a></span> - Method in interface org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFDocumentHandler.html" title="interface in org.biojava.bio.program.gff">GFFDocumentHandler</a></dt>
<dd>
<div class="block">Indicates that the current GFF document has now ended.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFFilterer.html#endDocument()">endDocument()</a></span> - Method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFFilterer.html" title="class in org.biojava.bio.program.gff">GFFFilterer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFWriter.html#endDocument()">endDocument()</a></span> - Method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFWriter.html" title="class in org.biojava.bio.program.gff">GFFWriter</a></dt>
<dd>
<div class="block">Flushes the <span class="type">PrintWriter</span> to make sure that everything is written.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff3/GFF3DocumentHandler.html#endDocument()">endDocument()</a></span> - Method in interface org.biojava.bio.program.gff3.<a href="./org/biojava/bio/program/gff3/GFF3DocumentHandler.html" title="interface in org.biojava.bio.program.gff3">GFF3DocumentHandler</a></dt>
<dd>
<div class="block">Indicates that the current GFF document has now ended.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/SeqSimilarityAdapter.html#endDocument()">endDocument()</a></span> - Method in class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/SeqSimilarityAdapter.html" title="class in org.biojava.bio.program.ssbind">SeqSimilarityAdapter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/SAX2StAXAdaptor.html#endDocument()">endDocument()</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/SAX2StAXAdaptor.html" title="class in org.biojava.bio.seq.io.agave">SAX2StAXAdaptor</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/stax/SAX2StAXAdaptor.html#endDocument()">endDocument()</a></span> - Method in class org.biojava.utils.stax.<a href="./org/biojava/utils/stax/SAX2StAXAdaptor.html" title="class in org.biojava.utils.stax">SAX2StAXAdaptor</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/blast2html/Blast2HTMLHandler.html#endElement(java.lang.String, java.lang.String, java.lang.String)">endElement(String, String, String)</a></span> - Method in class org.biojava.bio.program.blast2html.<a href="./org/biojava/bio/program/blast2html/Blast2HTMLHandler.html" title="class in org.biojava.bio.program.blast2html">Blast2HTMLHandler</a></dt>
<dd>
<div class="block">Called when the end of an element is reached.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/dasalignment/DASAlignmentXMLResponseParser.html#endElement(java.lang.String, java.lang.String, java.lang.String)">endElement(String, String, String)</a></span> - Method in class org.biojava.bio.program.das.dasalignment.<a href="./org/biojava/bio/program/das/dasalignment/DASAlignmentXMLResponseParser.html" title="class in org.biojava.bio.program.das.dasalignment">DASAlignmentXMLResponseParser</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/dasstructure/DASStructureXMLResponseParser.html#endElement(java.lang.String, java.lang.String, java.lang.String)">endElement(String, String, String)</a></span> - Method in class org.biojava.bio.program.das.dasstructure.<a href="./org/biojava/bio/program/das/dasstructure/DASStructureXMLResponseParser.html" title="class in org.biojava.bio.program.das.dasstructure">DASStructureXMLResponseParser</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/SeqSimilarityAdapter.html#endElement(java.lang.String, java.lang.String, java.lang.String)">endElement(String, String, String)</a></span> - Method in class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/SeqSimilarityAdapter.html" title="class in org.biojava.bio.program.ssbind">SeqSimilarityAdapter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/SeqSimilarityStAXAdapter.html#endElement(java.lang.String, java.lang.String, java.lang.String, org.biojava.utils.stax.StAXContentHandler)">endElement(String, String, String, StAXContentHandler)</a></span> - Method in class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/SeqSimilarityStAXAdapter.html" title="class in org.biojava.bio.program.ssbind">SeqSimilarityStAXAdapter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/SeqSimilarityStAXHandler.html#endElement(java.lang.String, java.lang.String, java.lang.String, org.biojava.utils.stax.StAXContentHandler)">endElement(String, String, String, StAXContentHandler)</a></span> - Method in class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/SeqSimilarityStAXHandler.html" title="class in org.biojava.bio.program.ssbind">SeqSimilarityStAXHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/xff/FeatureHandler.html#endElement(java.lang.String, java.lang.String, java.lang.String, org.biojava.utils.stax.StAXContentHandler)">endElement(String, String, String, StAXContentHandler)</a></span> - Method in class org.biojava.bio.program.xff.<a href="./org/biojava/bio/program/xff/FeatureHandler.html" title="class in org.biojava.bio.program.xff">FeatureHandler</a></dt>
<dd>
<div class="block">StAX callback for element ends.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/xff/LocationHandlerBase.html#endElement(java.lang.String, java.lang.String, java.lang.String, org.biojava.utils.stax.StAXContentHandler)">endElement(String, String, String, StAXContentHandler)</a></span> - Method in class org.biojava.bio.program.xff.<a href="./org/biojava/bio/program/xff/LocationHandlerBase.html" title="class in org.biojava.bio.program.xff">LocationHandlerBase</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/xff/XFFFeatureSetHandler.html#endElement(java.lang.String, java.lang.String, java.lang.String, org.biojava.utils.stax.StAXContentHandler)">endElement(String, String, String, StAXContentHandler)</a></span> - Method in class org.biojava.bio.program.xff.<a href="./org/biojava/bio/program/xff/XFFFeatureSetHandler.html" title="class in org.biojava.bio.program.xff">XFFFeatureSetHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/xml/BaseXMLWriter.html#endElement()">endElement()</a></span> - Method in class org.biojava.bio.program.xml.<a href="./org/biojava/bio/program/xml/BaseXMLWriter.html" title="class in org.biojava.bio.program.xml">BaseXMLWriter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/xml/SimpleXMLEmitter.html#endElement(java.lang.String, java.lang.String, java.lang.String)">endElement(String, String, String)</a></span> - Method in class org.biojava.bio.program.xml.<a href="./org/biojava/bio/program/xml/SimpleXMLEmitter.html" title="class in org.biojava.bio.program.xml">SimpleXMLEmitter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/SAX2StAXAdaptor.html#endElement(java.lang.String, java.lang.String, java.lang.String)">endElement(String, String, String)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/SAX2StAXAdaptor.html" title="class in org.biojava.bio.seq.io.agave">SAX2StAXAdaptor</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/StAXContentHandler.html#endElement(java.lang.String, java.lang.String, java.lang.String, org.biojava.bio.seq.io.agave.StAXContentHandler)">endElement(String, String, String, StAXContentHandler)</a></span> - Method in interface org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/StAXContentHandler.html" title="interface in org.biojava.bio.seq.io.agave">StAXContentHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/StAXContentHandlerBase.html#endElement(java.lang.String, java.lang.String, java.lang.String, org.biojava.bio.seq.io.agave.StAXContentHandler)">endElement(String, String, String, StAXContentHandler)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/StAXContentHandlerBase.html" title="class in org.biojava.bio.seq.io.agave">StAXContentHandlerBase</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/StAXFeatureHandler.html#endElement(java.lang.String, java.lang.String, java.lang.String, org.biojava.bio.seq.io.agave.StAXContentHandler)">endElement(String, String, String, StAXContentHandler)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/StAXFeatureHandler.html" title="class in org.biojava.bio.seq.io.agave">StAXFeatureHandler</a></dt>
<dd>
<div class="block">Handles basic exit processing.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/StAXPropertyHandler.html#endElement(java.lang.String, java.lang.String, java.lang.String, org.biojava.bio.seq.io.agave.StAXContentHandler)">endElement(String, String, String, StAXContentHandler)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/StAXPropertyHandler.html" title="class in org.biojava.bio.seq.io.agave">StAXPropertyHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/filterxml/XMLAnnotationTypeHandler.html#endElement(java.lang.String, java.lang.String, java.lang.String, org.biojava.utils.stax.StAXContentHandler)">endElement(String, String, String, StAXContentHandler)</a></span> - Method in class org.biojava.bio.seq.io.filterxml.<a href="./org/biojava/bio/seq/io/filterxml/XMLAnnotationTypeHandler.html" title="class in org.biojava.bio.seq.io.filterxml">XMLAnnotationTypeHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game/SequenceContentHandlerBase.html#endElement(java.lang.String, java.lang.String, java.lang.String, org.biojava.utils.stax.StAXContentHandler)">endElement(String, String, String, StAXContentHandler)</a></span> - Method in class org.biojava.bio.seq.io.game.<a href="./org/biojava/bio/seq/io/game/SequenceContentHandlerBase.html" title="class in org.biojava.bio.seq.io.game">SequenceContentHandlerBase</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game/StAXFeatureHandler.html#endElement(java.lang.String, java.lang.String, java.lang.String, org.biojava.utils.stax.StAXContentHandler)">endElement(String, String, String, StAXContentHandler)</a></span> - Method in class org.biojava.bio.seq.io.game.<a href="./org/biojava/bio/seq/io/game/StAXFeatureHandler.html" title="class in org.biojava.bio.seq.io.game">StAXFeatureHandler</a></dt>
<dd>
<div class="block">Handles basic exit processing.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game/StAXPropertyHandler.html#endElement(java.lang.String, java.lang.String, java.lang.String, org.biojava.utils.stax.StAXContentHandler)">endElement(String, String, String, StAXContentHandler)</a></span> - Method in class org.biojava.bio.seq.io.game.<a href="./org/biojava/bio/seq/io/game/StAXPropertyHandler.html" title="class in org.biojava.bio.seq.io.game">StAXPropertyHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game12/StAXFeatureHandler.html#endElement(java.lang.String, java.lang.String, java.lang.String, org.biojava.utils.stax.StAXContentHandler)">endElement(String, String, String, StAXContentHandler)</a></span> - Method in class org.biojava.bio.seq.io.game12.<a href="./org/biojava/bio/seq/io/game12/StAXFeatureHandler.html" title="class in org.biojava.bio.seq.io.game12">StAXFeatureHandler</a></dt>
<dd>
<div class="block">Handles basic exit processing.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/stax/BooleanElementHandlerBase.html#endElement(java.lang.String, java.lang.String, java.lang.String, org.biojava.utils.stax.StAXContentHandler)">endElement(String, String, String, StAXContentHandler)</a></span> - Method in class org.biojava.utils.stax.<a href="./org/biojava/utils/stax/BooleanElementHandlerBase.html" title="class in org.biojava.utils.stax">BooleanElementHandlerBase</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/stax/ByteElementHandlerBase.html#endElement(java.lang.String, java.lang.String, java.lang.String, org.biojava.utils.stax.StAXContentHandler)">endElement(String, String, String, StAXContentHandler)</a></span> - Method in class org.biojava.utils.stax.<a href="./org/biojava/utils/stax/ByteElementHandlerBase.html" title="class in org.biojava.utils.stax">ByteElementHandlerBase</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/stax/CharElementHandlerBase.html#endElement(java.lang.String, java.lang.String, java.lang.String, org.biojava.utils.stax.StAXContentHandler)">endElement(String, String, String, StAXContentHandler)</a></span> - Method in class org.biojava.utils.stax.<a href="./org/biojava/utils/stax/CharElementHandlerBase.html" title="class in org.biojava.utils.stax">CharElementHandlerBase</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/stax/DoubleElementHandlerBase.html#endElement(java.lang.String, java.lang.String, java.lang.String, org.biojava.utils.stax.StAXContentHandler)">endElement(String, String, String, StAXContentHandler)</a></span> - Method in class org.biojava.utils.stax.<a href="./org/biojava/utils/stax/DoubleElementHandlerBase.html" title="class in org.biojava.utils.stax">DoubleElementHandlerBase</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/stax/FloatElementHandlerBase.html#endElement(java.lang.String, java.lang.String, java.lang.String, org.biojava.utils.stax.StAXContentHandler)">endElement(String, String, String, StAXContentHandler)</a></span> - Method in class org.biojava.utils.stax.<a href="./org/biojava/utils/stax/FloatElementHandlerBase.html" title="class in org.biojava.utils.stax">FloatElementHandlerBase</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/stax/IntElementHandlerBase.html#endElement(java.lang.String, java.lang.String, java.lang.String, org.biojava.utils.stax.StAXContentHandler)">endElement(String, String, String, StAXContentHandler)</a></span> - Method in class org.biojava.utils.stax.<a href="./org/biojava/utils/stax/IntElementHandlerBase.html" title="class in org.biojava.utils.stax">IntElementHandlerBase</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/stax/LongElementHandlerBase.html#endElement(java.lang.String, java.lang.String, java.lang.String, org.biojava.utils.stax.StAXContentHandler)">endElement(String, String, String, StAXContentHandler)</a></span> - Method in class org.biojava.utils.stax.<a href="./org/biojava/utils/stax/LongElementHandlerBase.html" title="class in org.biojava.utils.stax">LongElementHandlerBase</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/stax/SAX2StAXAdaptor.html#endElement(java.lang.String, java.lang.String, java.lang.String)">endElement(String, String, String)</a></span> - Method in class org.biojava.utils.stax.<a href="./org/biojava/utils/stax/SAX2StAXAdaptor.html" title="class in org.biojava.utils.stax">SAX2StAXAdaptor</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/stax/StAXContentHandler.html#endElement(java.lang.String, java.lang.String, java.lang.String, org.biojava.utils.stax.StAXContentHandler)">endElement(String, String, String, StAXContentHandler)</a></span> - Method in interface org.biojava.utils.stax.<a href="./org/biojava/utils/stax/StAXContentHandler.html" title="interface in org.biojava.utils.stax">StAXContentHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/stax/StAXContentHandlerBase.html#endElement(java.lang.String, java.lang.String, java.lang.String, org.biojava.utils.stax.StAXContentHandler)">endElement(String, String, String, StAXContentHandler)</a></span> - Method in class org.biojava.utils.stax.<a href="./org/biojava/utils/stax/StAXContentHandlerBase.html" title="class in org.biojava.utils.stax">StAXContentHandlerBase</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/stax/StringElementHandlerBase.html#endElement(java.lang.String, java.lang.String, java.lang.String, org.biojava.utils.stax.StAXContentHandler)">endElement(String, String, String, StAXContentHandler)</a></span> - Method in class org.biojava.utils.stax.<a href="./org/biojava/utils/stax/StringElementHandlerBase.html" title="class in org.biojava.utils.stax">StringElementHandlerBase</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/sax/blastxml/BlastXMLParser.html#endElementHandler(java.lang.String, java.lang.String, java.lang.String, org.biojava.utils.stax.StAXContentHandler)">endElementHandler(String, String, String, StAXContentHandler)</a></span> - Method in class org.biojava.bio.program.sax.blastxml.<a href="./org/biojava/bio/program/sax/blastxml/BlastXMLParser.html" title="class in org.biojava.bio.program.sax.blastxml">BlastXMLParser</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEBioSeqHandler.html#endElementHandler(java.lang.String, java.lang.String, java.lang.String, org.biojava.bio.seq.io.agave.StAXContentHandler)">endElementHandler(String, String, String, StAXContentHandler)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEBioSeqHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEBioSeqHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEChromosomeHandler.html#endElementHandler(java.lang.String, java.lang.String, java.lang.String, org.biojava.bio.seq.io.agave.StAXContentHandler)">endElementHandler(String, String, String, StAXContentHandler)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEChromosomeHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEChromosomeHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEClassificationHandler.html#endElementHandler(java.lang.String, java.lang.String, java.lang.String, org.biojava.bio.seq.io.agave.StAXContentHandler)">endElementHandler(String, String, String, StAXContentHandler)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEClassificationHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEClassificationHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEContigHandler.html#endElementHandler(java.lang.String, java.lang.String, java.lang.String, org.biojava.bio.seq.io.agave.StAXContentHandler)">endElementHandler(String, String, String, StAXContentHandler)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEContigHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEContigHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEDbIdPropHandler.html#endElementHandler(java.lang.String, java.lang.String, java.lang.String, org.biojava.bio.seq.io.agave.StAXContentHandler)">endElementHandler(String, String, String, StAXContentHandler)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEDbIdPropHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEDbIdPropHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEElementIdPropHandler.html#endElementHandler(java.lang.String, java.lang.String, java.lang.String, org.biojava.bio.seq.io.agave.StAXContentHandler)">endElementHandler(String, String, String, StAXContentHandler)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEElementIdPropHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEElementIdPropHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEEvidenceHandler.html#endElementHandler(java.lang.String, java.lang.String, java.lang.String, org.biojava.bio.seq.io.agave.StAXContentHandler)">endElementHandler(String, String, String, StAXContentHandler)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEEvidenceHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEEvidenceHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEIdAliasPropHandler.html#endElementHandler(java.lang.String, java.lang.String, java.lang.String, org.biojava.bio.seq.io.agave.StAXContentHandler)">endElementHandler(String, String, String, StAXContentHandler)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEIdAliasPropHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEIdAliasPropHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEMapLocationPropHandler.html#endElementHandler(java.lang.String, java.lang.String, java.lang.String, org.biojava.bio.seq.io.agave.StAXContentHandler)">endElementHandler(String, String, String, StAXContentHandler)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEMapLocationPropHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEMapLocationPropHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEMapPositionPropHandler.html#endElementHandler(java.lang.String, java.lang.String, java.lang.String, org.biojava.bio.seq.io.agave.StAXContentHandler)">endElementHandler(String, String, String, StAXContentHandler)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEMapPositionPropHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEMapPositionPropHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEMatchRegionPropHandler.html#endElementHandler(java.lang.String, java.lang.String, java.lang.String, org.biojava.bio.seq.io.agave.StAXContentHandler)">endElementHandler(String, String, String, StAXContentHandler)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEMatchRegionPropHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEMatchRegionPropHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEQualifierPropHandler.html#endElementHandler(java.lang.String, java.lang.String, java.lang.String, org.biojava.bio.seq.io.agave.StAXContentHandler)">endElementHandler(String, String, String, StAXContentHandler)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEQualifierPropHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEQualifierPropHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEQueryRegionPropHandler.html#endElementHandler(java.lang.String, java.lang.String, java.lang.String, org.biojava.bio.seq.io.agave.StAXContentHandler)">endElementHandler(String, String, String, StAXContentHandler)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEQueryRegionPropHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEQueryRegionPropHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVERelatedAnnotPropHandler.html#endElementHandler(java.lang.String, java.lang.String, java.lang.String, org.biojava.bio.seq.io.agave.StAXContentHandler)">endElementHandler(String, String, String, StAXContentHandler)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVERelatedAnnotPropHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVERelatedAnnotPropHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEResultPropertyPropHandler.html#endElementHandler(java.lang.String, java.lang.String, java.lang.String, org.biojava.bio.seq.io.agave.StAXContentHandler)">endElementHandler(String, String, String, StAXContentHandler)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEResultPropertyPropHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEResultPropertyPropHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVESciPropertyPropHandler.html#endElementHandler(java.lang.String, java.lang.String, java.lang.String, org.biojava.bio.seq.io.agave.StAXContentHandler)">endElementHandler(String, String, String, StAXContentHandler)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVESciPropertyPropHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVESciPropertyPropHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVESeqLocationPropHandler.html#endElementHandler(java.lang.String, java.lang.String, java.lang.String, org.biojava.bio.seq.io.agave.StAXContentHandler)">endElementHandler(String, String, String, StAXContentHandler)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVESeqLocationPropHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVESeqLocationPropHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVESeqPropHandler.html#endElementHandler(java.lang.String, java.lang.String, java.lang.String, org.biojava.bio.seq.io.agave.StAXContentHandler)">endElementHandler(String, String, String, StAXContentHandler)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVESeqPropHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVESeqPropHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEXrefPropHandler.html#endElementHandler(java.lang.String, java.lang.String, java.lang.String, org.biojava.bio.seq.io.agave.StAXContentHandler)">endElementHandler(String, String, String, StAXContentHandler)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEXrefPropHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEXrefPropHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEXrefPropPropHandler.html#endElementHandler(java.lang.String, java.lang.String, java.lang.String, org.biojava.bio.seq.io.agave.StAXContentHandler)">endElementHandler(String, String, String, StAXContentHandler)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEXrefPropPropHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEXrefPropPropHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEXrefsPropHandler.html#endElementHandler(java.lang.String, java.lang.String, java.lang.String, org.biojava.bio.seq.io.agave.StAXContentHandler)">endElementHandler(String, String, String, StAXContentHandler)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEXrefsPropHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEXrefsPropHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/StAXFeatureHandler.html#endElementHandler(java.lang.String, java.lang.String, java.lang.String, org.biojava.bio.seq.io.agave.StAXContentHandler)">endElementHandler(String, String, String, StAXContentHandler)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/StAXFeatureHandler.html" title="class in org.biojava.bio.seq.io.agave">StAXFeatureHandler</a></dt>
<dd>
<div class="block">Element specific exit handler
Subclass to do anything useful.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/StAXPropertyHandler.html#endElementHandler(java.lang.String, java.lang.String, java.lang.String, org.biojava.bio.seq.io.agave.StAXContentHandler)">endElementHandler(String, String, String, StAXContentHandler)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/StAXPropertyHandler.html" title="class in org.biojava.bio.seq.io.agave">StAXPropertyHandler</a></dt>
<dd>
<div class="block">Element specific exit handler
Subclass to do anything useful.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game/GAMEAnnotationHandler.html#endElementHandler(java.lang.String, java.lang.String, java.lang.String, org.biojava.utils.stax.StAXContentHandler)">endElementHandler(String, String, String, StAXContentHandler)</a></span> - Method in class org.biojava.bio.seq.io.game.<a href="./org/biojava/bio/seq/io/game/GAMEAnnotationHandler.html" title="class in org.biojava.bio.seq.io.game">GAMEAnnotationHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game/GAMEDbxrefPropHandler.html#endElementHandler(java.lang.String, java.lang.String, java.lang.String, org.biojava.utils.stax.StAXContentHandler)">endElementHandler(String, String, String, StAXContentHandler)</a></span> - Method in class org.biojava.bio.seq.io.game.<a href="./org/biojava/bio/seq/io/game/GAMEDbxrefPropHandler.html" title="class in org.biojava.bio.seq.io.game">GAMEDbxrefPropHandler</a></dt>
<dd>
<div class="block">when exiting, put the DbXrefElement into the annotation bundle</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game/GAMEFeatureSetHandler.html#endElementHandler(java.lang.String, java.lang.String, java.lang.String, org.biojava.utils.stax.StAXContentHandler)">endElementHandler(String, String, String, StAXContentHandler)</a></span> - Method in class org.biojava.bio.seq.io.game.<a href="./org/biojava/bio/seq/io/game/GAMEFeatureSetHandler.html" title="class in org.biojava.bio.seq.io.game">GAMEFeatureSetHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game/GAMEFeatureSpanHandler.html#endElementHandler(java.lang.String, java.lang.String, java.lang.String, org.biojava.utils.stax.StAXContentHandler)">endElementHandler(String, String, String, StAXContentHandler)</a></span> - Method in class org.biojava.bio.seq.io.game.<a href="./org/biojava/bio/seq/io/game/GAMEFeatureSpanHandler.html" title="class in org.biojava.bio.seq.io.game">GAMEFeatureSpanHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game/GAMESpanPropHandler.html#endElementHandler(java.lang.String, java.lang.String, java.lang.String, org.biojava.utils.stax.StAXContentHandler)">endElementHandler(String, String, String, StAXContentHandler)</a></span> - Method in class org.biojava.bio.seq.io.game.<a href="./org/biojava/bio/seq/io/game/GAMESpanPropHandler.html" title="class in org.biojava.bio.seq.io.game">GAMESpanPropHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game/StAXFeatureHandler.html#endElementHandler(java.lang.String, java.lang.String, java.lang.String, org.biojava.utils.stax.StAXContentHandler)">endElementHandler(String, String, String, StAXContentHandler)</a></span> - Method in class org.biojava.bio.seq.io.game.<a href="./org/biojava/bio/seq/io/game/StAXFeatureHandler.html" title="class in org.biojava.bio.seq.io.game">StAXFeatureHandler</a></dt>
<dd>
<div class="block">Element specific exit handler
Subclass to do anything useful.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game/StAXPropertyHandler.html#endElementHandler(java.lang.String, java.lang.String, java.lang.String, org.biojava.utils.stax.StAXContentHandler)">endElementHandler(String, String, String, StAXContentHandler)</a></span> - Method in class org.biojava.bio.seq.io.game.<a href="./org/biojava/bio/seq/io/game/StAXPropertyHandler.html" title="class in org.biojava.bio.seq.io.game">StAXPropertyHandler</a></dt>
<dd>
<div class="block">Element specific exit handler
Subclass to do anything useful.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game12/GAMEAnnotationHandler.html#endElementHandler(java.lang.String, java.lang.String, java.lang.String, org.biojava.utils.stax.StAXContentHandler)">endElementHandler(String, String, String, StAXContentHandler)</a></span> - Method in class org.biojava.bio.seq.io.game12.<a href="./org/biojava/bio/seq/io/game12/GAMEAnnotationHandler.html" title="class in org.biojava.bio.seq.io.game12">GAMEAnnotationHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game12/GAMEAspectHandler.html#endElementHandler(java.lang.String, java.lang.String, java.lang.String, org.biojava.utils.stax.StAXContentHandler)">endElementHandler(String, String, String, StAXContentHandler)</a></span> - Method in class org.biojava.bio.seq.io.game12.<a href="./org/biojava/bio/seq/io/game12/GAMEAspectHandler.html" title="class in org.biojava.bio.seq.io.game12">GAMEAspectHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game12/GAMEDbxrefHandler.html#endElementHandler(java.lang.String, java.lang.String, java.lang.String, org.biojava.utils.stax.StAXContentHandler)">endElementHandler(String, String, String, StAXContentHandler)</a></span> - Method in class org.biojava.bio.seq.io.game12.<a href="./org/biojava/bio/seq/io/game12/GAMEDbxrefHandler.html" title="class in org.biojava.bio.seq.io.game12">GAMEDbxrefHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game12/GAMEFeatureSetHandler.html#endElementHandler(java.lang.String, java.lang.String, java.lang.String, org.biojava.utils.stax.StAXContentHandler)">endElementHandler(String, String, String, StAXContentHandler)</a></span> - Method in class org.biojava.bio.seq.io.game12.<a href="./org/biojava/bio/seq/io/game12/GAMEFeatureSetHandler.html" title="class in org.biojava.bio.seq.io.game12">GAMEFeatureSetHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game12/GAMEFeatureSpanHandler.html#endElementHandler(java.lang.String, java.lang.String, java.lang.String, org.biojava.utils.stax.StAXContentHandler)">endElementHandler(String, String, String, StAXContentHandler)</a></span> - Method in class org.biojava.bio.seq.io.game12.<a href="./org/biojava/bio/seq/io/game12/GAMEFeatureSpanHandler.html" title="class in org.biojava.bio.seq.io.game12">GAMEFeatureSpanHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game12/GAMEFeatureSpanHandler.SeqRelHandler.html#endElementHandler(java.lang.String, java.lang.String, java.lang.String, org.biojava.utils.stax.StAXContentHandler)">endElementHandler(String, String, String, StAXContentHandler)</a></span> - Method in class org.biojava.bio.seq.io.game12.<a href="./org/biojava/bio/seq/io/game12/GAMEFeatureSpanHandler.SeqRelHandler.html" title="class in org.biojava.bio.seq.io.game12">GAMEFeatureSpanHandler.SeqRelHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game12/GAMEGeneHandler.html#endElementHandler(java.lang.String, java.lang.String, java.lang.String, org.biojava.utils.stax.StAXContentHandler)">endElementHandler(String, String, String, StAXContentHandler)</a></span> - Method in class org.biojava.bio.seq.io.game12.<a href="./org/biojava/bio/seq/io/game12/GAMEGeneHandler.html" title="class in org.biojava.bio.seq.io.game12">GAMEGeneHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game12/GAMEHandler.html#endElementHandler(java.lang.String, java.lang.String, java.lang.String, org.biojava.utils.stax.StAXContentHandler)">endElementHandler(String, String, String, StAXContentHandler)</a></span> - Method in class org.biojava.bio.seq.io.game12.<a href="./org/biojava/bio/seq/io/game12/GAMEHandler.html" title="class in org.biojava.bio.seq.io.game12">GAMEHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game12/GAMEPropertyHandler.html#endElementHandler(java.lang.String, java.lang.String, java.lang.String, org.biojava.utils.stax.StAXContentHandler)">endElementHandler(String, String, String, StAXContentHandler)</a></span> - Method in class org.biojava.bio.seq.io.game12.<a href="./org/biojava/bio/seq/io/game12/GAMEPropertyHandler.html" title="class in org.biojava.bio.seq.io.game12">GAMEPropertyHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game12/GAMESeqHandler.html#endElementHandler(java.lang.String, java.lang.String, java.lang.String, org.biojava.utils.stax.StAXContentHandler)">endElementHandler(String, String, String, StAXContentHandler)</a></span> - Method in class org.biojava.bio.seq.io.game12.<a href="./org/biojava/bio/seq/io/game12/GAMESeqHandler.html" title="class in org.biojava.bio.seq.io.game12">GAMESeqHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game12/GAMESeqRelHandler.html#endElementHandler(java.lang.String, java.lang.String, java.lang.String, org.biojava.utils.stax.StAXContentHandler)">endElementHandler(String, String, String, StAXContentHandler)</a></span> - Method in class org.biojava.bio.seq.io.game12.<a href="./org/biojava/bio/seq/io/game12/GAMESeqRelHandler.html" title="class in org.biojava.bio.seq.io.game12">GAMESeqRelHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game12/GAMESpanHandler.html#endElementHandler(java.lang.String, java.lang.String, java.lang.String, org.biojava.utils.stax.StAXContentHandler)">endElementHandler(String, String, String, StAXContentHandler)</a></span> - Method in class org.biojava.bio.seq.io.game12.<a href="./org/biojava/bio/seq/io/game12/GAMESpanHandler.html" title="class in org.biojava.bio.seq.io.game12">GAMESpanHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game12/StAXFeatureHandler.html#endElementHandler(java.lang.String, java.lang.String, java.lang.String, org.biojava.utils.stax.StAXContentHandler)">endElementHandler(String, String, String, StAXContentHandler)</a></span> - Method in class org.biojava.bio.seq.io.game12.<a href="./org/biojava/bio/seq/io/game12/StAXFeatureHandler.html" title="class in org.biojava.bio.seq.io.game12">StAXFeatureHandler</a></dt>
<dd>
<div class="block">Element specific exit handler Subclass to do anything useful.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/EmblFileFormer.html#endFeature()">endFeature()</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/EmblFileFormer.html" title="class in org.biojava.bio.seq.io">EmblFileFormer</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/FeatureTableParser.html#endFeature()">endFeature()</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/FeatureTableParser.html" title="class in org.biojava.bio.seq.io">FeatureTableParser</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/GenbankFileFormer.html#endFeature()">endFeature()</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/GenbankFileFormer.html" title="class in org.biojava.bio.seq.io">GenbankFileFormer</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOAdapter.html#endFeature()">endFeature()</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOAdapter.html" title="class in org.biojava.bio.seq.io">SeqIOAdapter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOFilter.html#endFeature()">endFeature()</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOFilter.html" title="class in org.biojava.bio.seq.io">SeqIOFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOListener.html#endFeature()">endFeature()</a></span> - Method in interface org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOListener.html" title="interface in org.biojava.bio.seq.io">SeqIOListener</a></dt>
<dd>
<div class="block">Mark the end of data associated with one specific feature.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SequenceBuilderBase.html#endFeature()">endFeature()</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SequenceBuilderBase.html" title="class in org.biojava.bio.seq.io">SequenceBuilderBase</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SequenceBuilderFilter.html#endFeature()">endFeature()</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SequenceBuilderFilter.html" title="class in org.biojava.bio.seq.io">SequenceBuilderFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SwissprotFileFormer.html#endFeature()">endFeature()</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SwissprotFileFormer.html" title="class in org.biojava.bio.seq.io">SwissprotFileFormer</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Null implementation.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/DebuggingRichSeqIOListener.html#endFeature()">endFeature()</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/DebuggingRichSeqIOListener.html" title="class in org.biojavax.bio.seq.io">DebuggingRichSeqIOListener</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/RichSeqIOAdapter.html#endFeature()">endFeature()</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/RichSeqIOAdapter.html" title="class in org.biojavax.bio.seq.io">RichSeqIOAdapter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/SimpleRichSequenceBuilder.html#endFeature()">endFeature()</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/SimpleRichSequenceBuilder.html" title="class in org.biojavax.bio.seq.io">SimpleRichSequenceBuilder</a></dt>
<dd>
<div class="block">Mark the end of data associated with one specific feature.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/phylo/io/phylip/PHYLIPFileBuilder.html#endFile()">endFile()</a></span> - Method in class org.biojavax.bio.phylo.io.phylip.<a href="./org/biojavax/bio/phylo/io/phylip/PHYLIPFileBuilder.html" title="class in org.biojavax.bio.phylo.io.phylip">PHYLIPFileBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/phylo/io/phylip/PHYLIPFileListener.html#endFile()">endFile()</a></span> - Method in interface org.biojavax.bio.phylo.io.phylip.<a href="./org/biojavax/bio/phylo/io/phylip/PHYLIPFileListener.html" title="interface in org.biojavax.bio.phylo.io.phylip">PHYLIPFileListener</a></dt>
<dd>
<div class="block">Finished reading a file.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/HomologeneBuilder.html#endGroup()">endGroup()</a></span> - Method in interface org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/HomologeneBuilder.html" title="interface in org.biojava.bio.program.homologene">HomologeneBuilder</a></dt>
<dd>
<div class="block">end of data for group</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/SimpleHomologeneBuilder.html#endGroup()">endGroup()</a></span> - Method in class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/SimpleHomologeneBuilder.html" title="class in org.biojava.bio.program.homologene">SimpleHomologeneBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/sax/FastaSearchSAXParser.html#endHeader()">endHeader()</a></span> - Method in class org.biojava.bio.program.sax.<a href="./org/biojava/bio/program/sax/FastaSearchSAXParser.html" title="class in org.biojava.bio.program.sax">FastaSearchSAXParser</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/BlastLikeHomologyBuilder.html#endHeader()">endHeader()</a></span> - Method in class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/BlastLikeHomologyBuilder.html" title="class in org.biojava.bio.program.ssbind">BlastLikeHomologyBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/BlastLikeSearchBuilder.html#endHeader()">endHeader()</a></span> - Method in class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/BlastLikeSearchBuilder.html" title="class in org.biojava.bio.program.ssbind">BlastLikeSearchBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/SimilarityPairBuilder.html#endHeader()">endHeader()</a></span> - Method in class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/SimilarityPairBuilder.html" title="class in org.biojava.bio.program.ssbind">SimilarityPairBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/FilteringContentHandler.html#endHeader()">endHeader()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/FilteringContentHandler.html" title="class in org.biojava.bio.search">FilteringContentHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SearchContentAdapter.html#endHeader()">endHeader()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SearchContentAdapter.html" title="class in org.biojava.bio.search">SearchContentAdapter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SearchContentFilter.html#endHeader()">endHeader()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SearchContentFilter.html" title="class in org.biojava.bio.search">SearchContentFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SearchContentHandler.html#endHeader()">endHeader()</a></span> - Method in interface org.biojava.bio.search.<a href="./org/biojava/bio/search/SearchContentHandler.html" title="interface in org.biojava.bio.search">SearchContentHandler</a></dt>
<dd>
<div class="block">The <code>endHeader</code> method indicates the end of a
formatted header.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SearchContentHandlerDebugger.html#endHeader()">endHeader()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SearchContentHandlerDebugger.html" title="class in org.biojava.bio.search">SearchContentHandlerDebugger</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/sax/FastaSearchSAXParser.html#endHit()">endHit()</a></span> - Method in class org.biojava.bio.program.sax.<a href="./org/biojava/bio/program/sax/FastaSearchSAXParser.html" title="class in org.biojava.bio.program.sax">FastaSearchSAXParser</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/BlastLikeHomologyBuilder.html#endHit()">endHit()</a></span> - Method in class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/BlastLikeHomologyBuilder.html" title="class in org.biojava.bio.program.ssbind">BlastLikeHomologyBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/BlastLikeSearchBuilder.html#endHit()">endHit()</a></span> - Method in class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/BlastLikeSearchBuilder.html" title="class in org.biojava.bio.program.ssbind">BlastLikeSearchBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/SimilarityPairBuilder.html#endHit()">endHit()</a></span> - Method in class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/SimilarityPairBuilder.html" title="class in org.biojava.bio.program.ssbind">SimilarityPairBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/FilteringContentHandler.html#endHit()">endHit()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/FilteringContentHandler.html" title="class in org.biojava.bio.search">FilteringContentHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SearchContentAdapter.html#endHit()">endHit()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SearchContentAdapter.html" title="class in org.biojava.bio.search">SearchContentAdapter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SearchContentFilter.html#endHit()">endHit()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SearchContentFilter.html" title="class in org.biojava.bio.search">SearchContentFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SearchContentHandler.html#endHit()">endHit()</a></span> - Method in interface org.biojava.bio.search.<a href="./org/biojava/bio/search/SearchContentHandler.html" title="interface in org.biojava.bio.search">SearchContentHandler</a></dt>
<dd>
<div class="block">The <code>endHit</code> method indicates the end of a formatted
hit.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SearchContentHandlerDebugger.html#endHit()">endHit()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SearchContentHandlerDebugger.html" title="class in org.biojava.bio.search">SearchContentHandlerDebugger</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/obo/OboFileParser.SOPair.html#endIndex">endIndex</a></span> - Variable in class org.biojava.ontology.obo.<a href="./org/biojava/ontology/obo/OboFileParser.SOPair.html" title="class in org.biojava.ontology.obo">OboFileParser.SOPair</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/StAXFeatureHandler.html#endLoc">endLoc</a></span> - Variable in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/StAXFeatureHandler.html" title="class in org.biojava.bio.seq.io.agave">StAXFeatureHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game/StAXFeatureHandler.html#endLoc">endLoc</a></span> - Variable in class org.biojava.bio.seq.io.game.<a href="./org/biojava/bio/seq/io/game/StAXFeatureHandler.html" title="class in org.biojava.bio.seq.io.game">StAXFeatureHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/HomologeneBuilder.html#endOrthologue()">endOrthologue()</a></span> - Method in interface org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/HomologeneBuilder.html" title="interface in org.biojava.bio.program.homologene">HomologeneBuilder</a></dt>
<dd>
<div class="block">end of data for this Orthologue</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/SimpleHomologeneBuilder.html#endOrthologue()">endOrthologue()</a></span> - Method in class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/SimpleHomologeneBuilder.html" title="class in org.biojava.bio.program.homologene">SimpleHomologeneBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/HomologeneBuilder.html#endOrthoPair()">endOrthoPair()</a></span> - Method in interface org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/HomologeneBuilder.html" title="interface in org.biojava.bio.program.homologene">HomologeneBuilder</a></dt>
<dd>
<div class="block">end of data for this OrthoPair</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/SimpleHomologeneBuilder.html#endOrthoPair()">endOrthoPair()</a></span> - Method in class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/SimpleHomologeneBuilder.html" title="class in org.biojava.bio.program.homologene">SimpleHomologeneBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/SeqSimilarityAdapter.html#endPrefixMapping(java.lang.String)">endPrefixMapping(String)</a></span> - Method in class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/SeqSimilarityAdapter.html" title="class in org.biojava.bio.program.ssbind">SeqSimilarityAdapter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/SAX2StAXAdaptor.html#endPrefixMapping(java.lang.String)">endPrefixMapping(String)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/SAX2StAXAdaptor.html" title="class in org.biojava.bio.seq.io.agave">SAX2StAXAdaptor</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/StAXContentHandler.html#endPrefixMapping(java.lang.String)">endPrefixMapping(String)</a></span> - Method in interface org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/StAXContentHandler.html" title="interface in org.biojava.bio.seq.io.agave">StAXContentHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/StAXContentHandlerBase.html#endPrefixMapping(java.lang.String)">endPrefixMapping(String)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/StAXContentHandlerBase.html" title="class in org.biojava.bio.seq.io.agave">StAXContentHandlerBase</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/stax/SAX2StAXAdaptor.html#endPrefixMapping(java.lang.String)">endPrefixMapping(String)</a></span> - Method in class org.biojava.utils.stax.<a href="./org/biojava/utils/stax/SAX2StAXAdaptor.html" title="class in org.biojava.utils.stax">SAX2StAXAdaptor</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/stax/StAXContentHandler.html#endPrefixMapping(java.lang.String)">endPrefixMapping(String)</a></span> - Method in interface org.biojava.utils.stax.<a href="./org/biojava/utils/stax/StAXContentHandler.html" title="interface in org.biojava.utils.stax">StAXContentHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/stax/StAXContentHandlerBase.html#endPrefixMapping(java.lang.String)">endPrefixMapping(String)</a></span> - Method in class org.biojava.utils.stax.<a href="./org/biojava/utils/stax/StAXContentHandlerBase.html" title="class in org.biojava.utils.stax">StAXContentHandlerBase</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/AbstractWrapper.html#endRecord()">endRecord()</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/AbstractWrapper.html" title="class in org.biojava.bio.program.tagvalue">AbstractWrapper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/AnnotationBuilder.html#endRecord()">endRecord()</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/AnnotationBuilder.html" title="class in org.biojava.bio.program.tagvalue">AnnotationBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/Echo.html#endRecord()">endRecord()</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/Echo.html" title="class in org.biojava.bio.program.tagvalue">Echo</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/Indexer.html#endRecord()">endRecord()</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/Indexer.html" title="class in org.biojava.bio.program.tagvalue">Indexer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/Indexer2.html#endRecord()">endRecord()</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/Indexer2.html" title="class in org.biojava.bio.program.tagvalue">Indexer2</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/SimpleTagValueWrapper.html#endRecord()">endRecord()</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/SimpleTagValueWrapper.html" title="class in org.biojava.bio.program.tagvalue">SimpleTagValueWrapper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/StateMachine.html#endRecord()">endRecord()</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/StateMachine.html" title="class in org.biojava.bio.program.tagvalue">StateMachine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/StateMachine.SimpleStateListener.html#endRecord()">endRecord()</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/StateMachine.SimpleStateListener.html" title="class in org.biojava.bio.program.tagvalue">StateMachine.SimpleStateListener</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/TagValueListener.html#endRecord()">endRecord()</a></span> - Method in interface org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/TagValueListener.html" title="interface in org.biojava.bio.program.tagvalue">TagValueListener</a></dt>
<dd>
<div class="block">The current record has ended.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/sax/FastaSearchSAXParser.html#endSearch()">endSearch()</a></span> - Method in class org.biojava.bio.program.sax.<a href="./org/biojava/bio/program/sax/FastaSearchSAXParser.html" title="class in org.biojava.bio.program.sax">FastaSearchSAXParser</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssaha/HitMerger.html#endSearch(java.lang.String)">endSearch(String)</a></span> - Method in class org.biojava.bio.program.ssaha.<a href="./org/biojava/bio/program/ssaha/HitMerger.html" title="class in org.biojava.bio.program.ssaha">HitMerger</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssaha/SearchListener.Echo.html#endSearch(java.lang.String)">endSearch(String)</a></span> - Method in class org.biojava.bio.program.ssaha.<a href="./org/biojava/bio/program/ssaha/SearchListener.Echo.html" title="class in org.biojava.bio.program.ssaha">SearchListener.Echo</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssaha/SearchListener.html#endSearch(java.lang.String)">endSearch(String)</a></span> - Method in interface org.biojava.bio.program.ssaha.<a href="./org/biojava/bio/program/ssaha/SearchListener.html" title="interface in org.biojava.bio.program.ssaha">SearchListener</a></dt>
<dd>
<div class="block">Indicates that a sequence has been searched against a DataStore.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssaha/SearchListener.Tee.html#endSearch(java.lang.String)">endSearch(String)</a></span> - Method in class org.biojava.bio.program.ssaha.<a href="./org/biojava/bio/program/ssaha/SearchListener.Tee.html" title="class in org.biojava.bio.program.ssaha">SearchListener.Tee</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssaha/SearchListener.Wrapper.html#endSearch(java.lang.String)">endSearch(String)</a></span> - Method in class org.biojava.bio.program.ssaha.<a href="./org/biojava/bio/program/ssaha/SearchListener.Wrapper.html" title="class in org.biojava.bio.program.ssaha">SearchListener.Wrapper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/BlastLikeHomologyBuilder.html#endSearch()">endSearch()</a></span> - Method in class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/BlastLikeHomologyBuilder.html" title="class in org.biojava.bio.program.ssbind">BlastLikeHomologyBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/BlastLikeSearchBuilder.html#endSearch()">endSearch()</a></span> - Method in class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/BlastLikeSearchBuilder.html" title="class in org.biojava.bio.program.ssbind">BlastLikeSearchBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/SimilarityPairBuilder.html#endSearch()">endSearch()</a></span> - Method in class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/SimilarityPairBuilder.html" title="class in org.biojava.bio.program.ssbind">SimilarityPairBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/FilteringContentHandler.html#endSearch()">endSearch()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/FilteringContentHandler.html" title="class in org.biojava.bio.search">FilteringContentHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SearchContentAdapter.html#endSearch()">endSearch()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SearchContentAdapter.html" title="class in org.biojava.bio.search">SearchContentAdapter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SearchContentFilter.html#endSearch()">endSearch()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SearchContentFilter.html" title="class in org.biojava.bio.search">SearchContentFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SearchContentHandler.html#endSearch()">endSearch()</a></span> - Method in interface org.biojava.bio.search.<a href="./org/biojava/bio/search/SearchContentHandler.html" title="interface in org.biojava.bio.search">SearchContentHandler</a></dt>
<dd>
<div class="block">The <code>endSearch</code> method indicates the end of useful
search information.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SearchContentHandlerDebugger.html#endSearch()">endSearch()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SearchContentHandlerDebugger.html" title="class in org.biojava.bio.search">SearchContentHandlerDebugger</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/EmblFileFormer.html#endSequence()">endSequence()</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/EmblFileFormer.html" title="class in org.biojava.bio.seq.io">EmblFileFormer</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/EmblProcessor.html#endSequence()">endSequence()</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/EmblProcessor.html" title="class in org.biojava.bio.seq.io">EmblProcessor</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/GenbankFileFormer.html#endSequence()">endSequence()</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/GenbankFileFormer.html" title="class in org.biojava.bio.seq.io">GenbankFileFormer</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/GenbankProcessor.html#endSequence()">endSequence()</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/GenbankProcessor.html" title="class in org.biojava.bio.seq.io">GenbankProcessor</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/OrganismParser.html#endSequence()">endSequence()</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/OrganismParser.html" title="class in org.biojava.bio.seq.io">OrganismParser</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOAdapter.html#endSequence()">endSequence()</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOAdapter.html" title="class in org.biojava.bio.seq.io">SeqIOAdapter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOFilter.html#endSequence()">endSequence()</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOFilter.html" title="class in org.biojava.bio.seq.io">SeqIOFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOListener.html#endSequence()">endSequence()</a></span> - Method in interface org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOListener.html" title="interface in org.biojava.bio.seq.io">SeqIOListener</a></dt>
<dd>
<div class="block">Notify the listener that processing of the sequence is complete.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SequenceBuilderBase.html#endSequence()">endSequence()</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SequenceBuilderBase.html" title="class in org.biojava.bio.seq.io">SequenceBuilderBase</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SequenceBuilderFilter.html#endSequence()">endSequence()</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SequenceBuilderFilter.html" title="class in org.biojava.bio.seq.io">SequenceBuilderFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SwissprotFileFormer.html#endSequence()">endSequence()</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SwissprotFileFormer.html" title="class in org.biojava.bio.seq.io">SwissprotFileFormer</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Notify the listener that processing of the sequence is complete.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SwissprotProcessor.html#endSequence()">endSequence()</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SwissprotProcessor.html" title="class in org.biojava.bio.seq.io">SwissprotProcessor</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/DebuggingRichSeqIOListener.html#endSequence()">endSequence()</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/DebuggingRichSeqIOListener.html" title="class in org.biojavax.bio.seq.io">DebuggingRichSeqIOListener</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/RichSeqIOAdapter.html#endSequence()">endSequence()</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/RichSeqIOAdapter.html" title="class in org.biojavax.bio.seq.io">RichSeqIOAdapter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/SimpleRichSequenceBuilder.html#endSequence()">endSequence()</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/SimpleRichSequenceBuilder.html" title="class in org.biojavax.bio.seq.io">SimpleRichSequenceBuilder</a></dt>
<dd>
<div class="block">Notify the listener that processing of the sequence is complete.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/sax/FastaSearchSAXParser.html#endSubHit()">endSubHit()</a></span> - Method in class org.biojava.bio.program.sax.<a href="./org/biojava/bio/program/sax/FastaSearchSAXParser.html" title="class in org.biojava.bio.program.sax">FastaSearchSAXParser</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/BlastLikeHomologyBuilder.html#endSubHit()">endSubHit()</a></span> - Method in class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/BlastLikeHomologyBuilder.html" title="class in org.biojava.bio.program.ssbind">BlastLikeHomologyBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/BlastLikeSearchBuilder.html#endSubHit()">endSubHit()</a></span> - Method in class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/BlastLikeSearchBuilder.html" title="class in org.biojava.bio.program.ssbind">BlastLikeSearchBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/SimilarityPairBuilder.html#endSubHit()">endSubHit()</a></span> - Method in class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/SimilarityPairBuilder.html" title="class in org.biojava.bio.program.ssbind">SimilarityPairBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/FilteringContentHandler.html#endSubHit()">endSubHit()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/FilteringContentHandler.html" title="class in org.biojava.bio.search">FilteringContentHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SearchContentAdapter.html#endSubHit()">endSubHit()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SearchContentAdapter.html" title="class in org.biojava.bio.search">SearchContentAdapter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SearchContentFilter.html#endSubHit()">endSubHit()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SearchContentFilter.html" title="class in org.biojava.bio.search">SearchContentFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SearchContentHandler.html#endSubHit()">endSubHit()</a></span> - Method in interface org.biojava.bio.search.<a href="./org/biojava/bio/search/SearchContentHandler.html" title="interface in org.biojava.bio.search">SearchContentHandler</a></dt>
<dd>
<div class="block">The <code>endSubHit</code> method indicates the end of a
formatted subhit.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SearchContentHandlerDebugger.html#endSubHit()">endSubHit()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SearchContentHandlerDebugger.html" title="class in org.biojava.bio.search">SearchContentHandlerDebugger</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/AbstractWrapper.html#endTag()">endTag()</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/AbstractWrapper.html" title="class in org.biojava.bio.program.tagvalue">AbstractWrapper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/Aggregator.html#endTag()">endTag()</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/Aggregator.html" title="class in org.biojava.bio.program.tagvalue">Aggregator</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/AnnotationBuilder.html#endTag()">endTag()</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/AnnotationBuilder.html" title="class in org.biojava.bio.program.tagvalue">AnnotationBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/Echo.html#endTag()">endTag()</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/Echo.html" title="class in org.biojava.bio.program.tagvalue">Echo</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/Indexer.html#endTag()">endTag()</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/Indexer.html" title="class in org.biojava.bio.program.tagvalue">Indexer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/Indexer2.html#endTag()">endTag()</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/Indexer2.html" title="class in org.biojava.bio.program.tagvalue">Indexer2</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/MultiTagger.html#endTag()">endTag()</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/MultiTagger.html" title="class in org.biojava.bio.program.tagvalue">MultiTagger</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/RegexFieldFinder.html#endTag()">endTag()</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/RegexFieldFinder.html" title="class in org.biojava.bio.program.tagvalue">RegexFieldFinder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/SimpleTagValueWrapper.html#endTag()">endTag()</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/SimpleTagValueWrapper.html" title="class in org.biojava.bio.program.tagvalue">SimpleTagValueWrapper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/StateMachine.html#endTag()">endTag()</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/StateMachine.html" title="class in org.biojava.bio.program.tagvalue">StateMachine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/StateMachine.SimpleStateListener.html#endTag()">endTag()</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/StateMachine.SimpleStateListener.html" title="class in org.biojava.bio.program.tagvalue">StateMachine.SimpleStateListener</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/TagDelegator.html#endTag()">endTag()</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/TagDelegator.html" title="class in org.biojava.bio.program.tagvalue">TagDelegator</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/TagDropper.html#endTag()">endTag()</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/TagDropper.html" title="class in org.biojava.bio.program.tagvalue">TagDropper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/TagValueListener.html#endTag()">endTag()</a></span> - Method in interface org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/TagValueListener.html" title="interface in org.biojava.bio.program.tagvalue">TagValueListener</a></dt>
<dd>
<div class="block">End the current tag.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/StAXContentHandler.html#endTree()">endTree()</a></span> - Method in interface org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/StAXContentHandler.html" title="interface in org.biojava.bio.seq.io.agave">StAXContentHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/StAXContentHandlerBase.html#endTree()">endTree()</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/StAXContentHandlerBase.html" title="class in org.biojava.bio.seq.io.agave">StAXContentHandlerBase</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/stax/StAXContentHandler.html#endTree()">endTree()</a></span> - Method in interface org.biojava.utils.stax.<a href="./org/biojava/utils/stax/StAXContentHandler.html" title="interface in org.biojava.utils.stax">StAXContentHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/stax/StAXContentHandlerBase.html#endTree()">endTree()</a></span> - Method in class org.biojava.utils.stax.<a href="./org/biojava/utils/stax/StAXContentHandlerBase.html" title="class in org.biojava.utils.stax">StAXContentHandlerBase</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichFeature.Tools.html#enrich(org.biojava.bio.seq.Feature)">enrich(Feature)</a></span> - Static method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichFeature.Tools.html" title="class in org.biojavax.bio.seq">RichFeature.Tools</a></dt>
<dd>
<div class="block">Takes a normal Feature and attempts to convert it into a RichFeature.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichLocation.Tools.html#enrich(org.biojava.bio.symbol.Location)">enrich(Location)</a></span> - Static method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichLocation.Tools.html" title="class in org.biojavax.bio.seq">RichLocation.Tools</a></dt>
<dd>
<div class="block">Attempts to convert a plain Location into a RichLocation.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.Tools.html#enrich(org.biojava.bio.seq.Sequence)">enrich(Sequence)</a></span> - Static method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.Tools.html" title="class in org.biojavax.bio.seq">RichSequence.Tools</a></dt>
<dd>
<div class="block">Boldly attempts to convert a <CODE>Sequence</CODE> into a
<CODE>RichSequence</CODE>.</div>
</dd>
<dt><a href="./org/biojava/bio/structure/io/mmcif/model/Entity.html" title="class in org.biojava.bio.structure.io.mmcif.model"><span class="strong">Entity</span></a> - Class in <a href="./org/biojava/bio/structure/io/mmcif/model/package-summary.html">org.biojava.bio.structure.io.mmcif.model</a></dt>
<dd>
<div class="block">A simple class to represent Entity records in mmCif files</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Entity.html#Entity()">Entity()</a></span> - Constructor for class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Entity.html" title="class in org.biojava.bio.structure.io.mmcif.model">Entity</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/chem/PolymerType.html#entity_poly_type">entity_poly_type</a></span> - Variable in enum org.biojava.bio.structure.io.mmcif.chem.<a href="./org/biojava/bio/structure/io/mmcif/chem/PolymerType.html" title="enum in org.biojava.bio.structure.io.mmcif.chem">PolymerType</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/structure/io/mmcif/model/EntityPolySeq.html" title="class in org.biojava.bio.structure.io.mmcif.model"><span class="strong">EntityPolySeq</span></a> - Class in <a href="./org/biojava/bio/structure/io/mmcif/model/package-summary.html">org.biojava.bio.structure.io.mmcif.model</a></dt>
<dd>
<div class="block">Container for _entity_poly_seq records</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/EntityPolySeq.html#EntityPolySeq()">EntityPolySeq()</a></span> - Constructor for class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/EntityPolySeq.html" title="class in org.biojava.bio.structure.io.mmcif.model">EntityPolySeq</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/DistributionLogo.html#entropy(org.biojava.bio.dist.Distribution, org.biojava.bio.symbol.Symbol)">entropy(Distribution, Symbol)</a></span> - Static method in class org.biojava.bio.gui.<a href="./org/biojava/bio/gui/DistributionLogo.html" title="class in org.biojava.bio.gui">DistributionLogo</a></dt>
<dd>
<div class="block">Calculate the information content of a symbol in bits.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/candy/CandyEntry.html#entry">entry</a></span> - Variable in class org.biojava.utils.candy.<a href="./org/biojava/utils/candy/CandyEntry.html" title="class in org.biojava.utils.candy">CandyEntry</a></dt>
<dd>
<div class="block">A unique identifier of this entry.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html#ENTRY_ACCESSION_ATTR">ENTRY_ACCESSION_ATTR</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html" title="class in org.biojavax.bio.seq.io">EMBLxmlFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html#ENTRY_CREATED_ATTR">ENTRY_CREATED_ATTR</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html" title="class in org.biojavax.bio.seq.io">EMBLxmlFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#ENTRY_CREATED_ATTR">ENTRY_CREATED_ATTR</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html#ENTRY_DATACLASS_ATTR">ENTRY_DATACLASS_ATTR</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html" title="class in org.biojavax.bio.seq.io">EMBLxmlFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html#ENTRY_GROUP_TAG">ENTRY_GROUP_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html" title="class in org.biojavax.bio.seq.io">EMBLxmlFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#ENTRY_GROUP_TAG">ENTRY_GROUP_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#ENTRY_NAMESPACE_ATTR">ENTRY_NAMESPACE_ATTR</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BibRefSupport.html#ENTRY_PROPERTIES">ENTRY_PROPERTIES</a></span> - Static variable in interface org.biojava.bibliography.<a href="./org/biojava/bibliography/BibRefSupport.html" title="interface in org.biojava.bibliography">BibRefSupport</a></dt>
<dd>
<div class="block">A vocabulary name.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html#ENTRY_RELCREATED_ATTR">ENTRY_RELCREATED_ATTR</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html" title="class in org.biojavax.bio.seq.io">EMBLxmlFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html#ENTRY_RELUPDATED_ATTR">ENTRY_RELUPDATED_ATTR</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html" title="class in org.biojavax.bio.seq.io">EMBLxmlFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html#ENTRY_STATUS_ATTR">ENTRY_STATUS_ATTR</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html" title="class in org.biojavax.bio.seq.io">EMBLxmlFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html#ENTRY_STATUS_DATE_ATTR">ENTRY_STATUS_DATE_ATTR</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html" title="class in org.biojavax.bio.seq.io">EMBLxmlFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html#ENTRY_SUBACC_ATTR">ENTRY_SUBACC_ATTR</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html" title="class in org.biojavax.bio.seq.io">EMBLxmlFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html#ENTRY_SUBVER_ATTR">ENTRY_SUBVER_ATTR</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html" title="class in org.biojavax.bio.seq.io">EMBLxmlFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html#ENTRY_SUBWGSVER_ATTR">ENTRY_SUBWGSVER_ATTR</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html" title="class in org.biojavax.bio.seq.io">EMBLxmlFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html#ENTRY_TAG">ENTRY_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html" title="class in org.biojavax.bio.seq.io">EMBLxmlFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#ENTRY_TAG">ENTRY_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html#ENTRY_TAX_DIVISION_ATTR">ENTRY_TAX_DIVISION_ATTR</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html" title="class in org.biojavax.bio.seq.io">EMBLxmlFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html#ENTRY_UPDATED_ATTR">ENTRY_UPDATED_ATTR</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html" title="class in org.biojavax.bio.seq.io">EMBLxmlFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#ENTRY_UPDATED_ATTR">ENTRY_UPDATED_ATTR</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html#ENTRY_VER_ATTR">ENTRY_VER_ATTR</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html" title="class in org.biojavax.bio.seq.io">EMBLxmlFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#ENTRY_VERSION_ATTR">ENTRY_VERSION_ATTR</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/db/emblcd/EntryNamIdxReader.html" title="class in org.biojava.bio.seq.db.emblcd"><span class="strong">EntryNamIdxReader</span></a> - Class in <a href="./org/biojava/bio/seq/db/emblcd/package-summary.html">org.biojava.bio.seq.db.emblcd</a></dt>
<dd>
<div class="block"><code>EntryNamIdxReader</code> reads the "entrynam.idx" file of an
EMBL CD-ROM format binary index.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/emblcd/EntryNamIdxReader.html#EntryNamIdxReader(java.io.InputStream)">EntryNamIdxReader(InputStream)</a></span> - Constructor for class org.biojava.bio.seq.db.emblcd.<a href="./org/biojava/bio/seq/db/emblcd/EntryNamIdxReader.html" title="class in org.biojava.bio.seq.db.emblcd">EntryNamIdxReader</a></dt>
<dd>
<div class="block">Creates a new <code>EntryNamIdxReader</code>.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/db/emblcd/EntryNamRandomAccess.html" title="class in org.biojava.bio.seq.db.emblcd"><span class="strong">EntryNamRandomAccess</span></a> - Class in <a href="./org/biojava/bio/seq/db/emblcd/package-summary.html">org.biojava.bio.seq.db.emblcd</a></dt>
<dd>
<div class="block"><code>EntryNamRandomAccess</code> objects provide random access to
records within the "entrynam.idx" file of an EMBL CD-ROM format
binary index.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/emblcd/EntryNamRandomAccess.html#EntryNamRandomAccess(java.io.File, int, int, long)">EntryNamRandomAccess(File, int, int, long)</a></span> - Constructor for class org.biojava.bio.seq.db.emblcd.<a href="./org/biojava/bio/seq/db/emblcd/EntryNamRandomAccess.html" title="class in org.biojava.bio.seq.db.emblcd">EntryNamRandomAccess</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/BeanAsMap.html#entrySet()">entrySet()</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/BeanAsMap.html" title="class in org.biojava.utils">BeanAsMap</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/cache/WeakValueHashMap.html#entrySet()">entrySet()</a></span> - Method in class org.biojava.utils.cache.<a href="./org/biojava/utils/cache/WeakValueHashMap.html" title="class in org.biojava.utils.cache">WeakValueHashMap</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/OverlayMap.html#entrySet()">entrySet()</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/OverlayMap.html" title="class in org.biojava.utils">OverlayMap</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/SmallMap.html#entrySet()">entrySet()</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/SmallMap.html" title="class in org.biojava.utils">SmallMap</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BibRef.html#entryStatus">entryStatus</a></span> - Variable in class org.biojava.bibliography.<a href="./org/biojava/bibliography/BibRef.html" title="class in org.biojava.bibliography">BibRef</a></dt>
<dd>
<div class="block">It defines information related to the citation itself rather than to the cited resource.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/molbio/RestrictionSite.Template.html#enzyme">enzyme</a></span> - Variable in class org.biojava.bio.molbio.<a href="./org/biojava/bio/molbio/RestrictionSite.Template.html" title="class in org.biojava.bio.molbio">RestrictionSite.Template</a></dt>
<dd>
<div class="block"><code>enzyme</code> <code>RestrictionEnzyme</code> field.</div>
</dd>
<dt><a href="./org/biojava/bio/program/formats/Enzyme.html" title="class in org.biojava.bio.program.formats"><span class="strong">Enzyme</span></a> - Class in <a href="./org/biojava/bio/program/formats/package-summary.html">org.biojava.bio.program.formats</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/formats/Enzyme.html#Enzyme()">Enzyme()</a></span> - Constructor for class org.biojava.bio.program.formats.<a href="./org/biojava/bio/program/formats/Enzyme.html" title="class in org.biojava.bio.program.formats">Enzyme</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/aaindex/AAindexStreamReader.html#eof()">eof()</a></span> - Method in class org.biojava.bio.proteomics.aaindex.<a href="./org/biojava/bio/proteomics/aaindex/AAindexStreamReader.html" title="class in org.biojava.bio.proteomics.aaindex">AAindexStreamReader</a></dt>
<dd>
<div class="block">Checks if the end of the file or stream is reached.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.HibernateFeatureFilter.html#eq">eq</a></span> - Variable in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.HibernateFeatureFilter.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.HibernateFeatureFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/AbstractAnnotation.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/AbstractAnnotation.html" title="class in org.biojava.bio">AbstractAnnotation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/CollectionConstraint.AllValuesIn.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/CollectionConstraint.AllValuesIn.html" title="class in org.biojava.bio">CollectionConstraint.AllValuesIn</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/CollectionConstraint.Contains.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/CollectionConstraint.Contains.html" title="class in org.biojava.bio">CollectionConstraint.Contains</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/AbstractDistribution.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/AbstractDistribution.html" title="class in org.biojava.bio.dist">AbstractDistribution</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/SimpleWeightMatrix.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/SimpleWeightMatrix.html" title="class in org.biojava.bio.dp">SimpleWeightMatrix</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/TrainerTransition.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/TrainerTransition.html" title="class in org.biojava.bio.dp">TrainerTransition</a></dt>
<dd>
<div class="block">Two transitions are equal if they have the same trainer, from and to states.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/Transition.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/Transition.html" title="class in org.biojava.bio.dp">Transition</a></dt>
<dd>
<div class="block">Two transitions are equal if they have the same from and to states.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/EcNumber.Impl.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/EcNumber.Impl.html" title="class in org.biojava.bio">EcNumber.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePanel.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePanel.html" title="class in org.biojava.bio.gui.sequence">SequencePanel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/molbio/RestrictionEnzyme.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in class org.biojava.bio.molbio.<a href="./org/biojava/bio/molbio/RestrictionEnzyme.html" title="class in org.biojava.bio.molbio">RestrictionEnzyme</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/DataSource.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in class org.biojava.bio.program.das.<a href="./org/biojava/bio/program/das/DataSource.html" title="class in org.biojava.bio.program.das">DataSource</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/SimpleOrthologue.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/SimpleOrthologue.html" title="class in org.biojava.bio.program.homologene">SimpleOrthologue</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/SimpleOrthoPair.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/SimpleOrthoPair.html" title="class in org.biojava.bio.program.homologene">SimpleOrthoPair</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SequenceDBSearchHit.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SequenceDBSearchHit.html" title="class in org.biojava.bio.search">SequenceDBSearchHit</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SequenceDBSearchResult.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SequenceDBSearchResult.html" title="class in org.biojava.bio.search">SequenceDBSearchResult</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SequenceDBSearchSubHit.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SequenceDBSearchSubHit.html" title="class in org.biojava.bio.search">SequenceDBSearchSubHit</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SimpleSeqSimilaritySearchHit.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SimpleSeqSimilaritySearchHit.html" title="class in org.biojava.bio.search">SimpleSeqSimilaritySearchHit</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SimpleSeqSimilaritySearchResult.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SimpleSeqSimilaritySearchResult.html" title="class in org.biojava.bio.search">SimpleSeqSimilaritySearchResult</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SimpleSeqSimilaritySearchSubHit.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SimpleSeqSimilaritySearchSubHit.html" title="class in org.biojava.bio.search">SimpleSeqSimilaritySearchSubHit</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/SimpleSequenceDBInstallation.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/SimpleSequenceDBInstallation.html" title="class in org.biojava.bio.seq.db">SimpleSequenceDBInstallation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/Feature.Template.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/Feature.Template.html" title="class in org.biojava.bio.seq">Feature.Template</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.And.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.And.html" title="class in org.biojava.bio.seq">FeatureFilter.And</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ByAncestor.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ByAncestor.html" title="class in org.biojava.bio.seq">FeatureFilter.ByAncestor</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ByAnnotationType.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ByAnnotationType.html" title="class in org.biojava.bio.seq">FeatureFilter.ByAnnotationType</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ByChild.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ByChild.html" title="class in org.biojava.bio.seq">FeatureFilter.ByChild</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ByClass.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ByClass.html" title="class in org.biojava.bio.seq">FeatureFilter.ByClass</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ByComponentName.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ByComponentName.html" title="class in org.biojava.bio.seq">FeatureFilter.ByComponentName</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ByDescendant.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ByDescendant.html" title="class in org.biojava.bio.seq">FeatureFilter.ByDescendant</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ByFeature.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ByFeature.html" title="class in org.biojava.bio.seq">FeatureFilter.ByFeature</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ByPairwiseScore.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ByPairwiseScore.html" title="class in org.biojava.bio.seq">FeatureFilter.ByPairwiseScore</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ByParent.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ByParent.html" title="class in org.biojava.bio.seq">FeatureFilter.ByParent</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.BySequenceName.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.BySequenceName.html" title="class in org.biojava.bio.seq">FeatureFilter.BySequenceName</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.BySource.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.BySource.html" title="class in org.biojava.bio.seq">FeatureFilter.BySource</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ByType.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ByType.html" title="class in org.biojava.bio.seq">FeatureFilter.ByType</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ContainedByLocation.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ContainedByLocation.html" title="class in org.biojava.bio.seq">FeatureFilter.ContainedByLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.FrameFilter.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.FrameFilter.html" title="class in org.biojava.bio.seq">FeatureFilter.FrameFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.Not.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.Not.html" title="class in org.biojava.bio.seq">FeatureFilter.Not</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.OnlyChildren.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.OnlyChildren.html" title="class in org.biojava.bio.seq">FeatureFilter.OnlyChildren</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.OnlyDescendants.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.OnlyDescendants.html" title="class in org.biojava.bio.seq">FeatureFilter.OnlyDescendants</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.Or.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.Or.html" title="class in org.biojava.bio.seq">FeatureFilter.Or</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.OverlapsLocation.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.OverlapsLocation.html" title="class in org.biojava.bio.seq">FeatureFilter.OverlapsLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ShadowContainedByLocation.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ShadowContainedByLocation.html" title="class in org.biojava.bio.seq">FeatureFilter.ShadowContainedByLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ShadowOverlapsLocation.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ShadowOverlapsLocation.html" title="class in org.biojava.bio.seq">FeatureFilter.ShadowOverlapsLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.StrandFilter.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.StrandFilter.html" title="class in org.biojava.bio.seq">FeatureFilter.StrandFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleFeature.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleFeature.html" title="class in org.biojava.bio.seq.impl">SimpleFeature</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/projection/ProjectedFeature.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in class org.biojava.bio.seq.projection.<a href="./org/biojava/bio/seq/projection/ProjectedFeature.html" title="class in org.biojava.bio.seq.projection">ProjectedFeature</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Author.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Author.html" title="class in org.biojava.bio.structure">Author</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/PDBHeader.html#equals(org.biojava.bio.structure.PDBHeader)">equals(PDBHeader)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/PDBHeader.html" title="class in org.biojava.bio.structure">PDBHeader</a></dt>
<dd>
<div class="block">Compare two PDBHeader objects</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AbstractLocation.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AbstractLocation.html" title="class in org.biojava.bio.symbol">AbstractLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AbstractLocationDecorator.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AbstractLocationDecorator.html" title="class in org.biojava.bio.symbol">AbstractLocationDecorator</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AbstractSymbolList.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AbstractSymbolList.html" title="class in org.biojava.bio.symbol">AbstractSymbolList</a></dt>
<dd>
<div class="block">Provides logical equality for two SymbolLists that share the same list
of canonical symbols</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/CircularLocation.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/CircularLocation.html" title="class in org.biojava.bio.symbol">CircularLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/FuzzyPointLocation.html#equals(org.biojava.bio.symbol.Location)">equals(Location)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/FuzzyPointLocation.html" title="class in org.biojava.bio.symbol">FuzzyPointLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/IntegerAlphabet.IntegerSymbol.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/IntegerAlphabet.IntegerSymbol.html" title="class in org.biojava.bio.symbol">IntegerAlphabet.IntegerSymbol</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/Location.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/Location.html" title="interface in org.biojava.bio.symbol">Location</a></dt>
<dd>
<div class="block">Checks if this location is equivalent to the other.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/taxa/AbstractTaxon.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in class org.biojava.bio.taxa.<a href="./org/biojava/bio/taxa/AbstractTaxon.html" title="class in org.biojava.bio.taxa">AbstractTaxon</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/taxa/Taxon.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in interface org.biojava.bio.taxa.<a href="./org/biojava/bio/taxa/Taxon.html" title="interface in org.biojava.bio.taxa">Taxon</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Two taxa are equal if they have equivalent children, common
and scientific names.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/Term.Impl.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in class org.biojava.ontology.<a href="./org/biojava/ontology/Term.Impl.html" title="class in org.biojava.ontology">Term.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/Triple.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in interface org.biojava.ontology.<a href="./org/biojava/ontology/Triple.html" title="interface in org.biojava.ontology">Triple</a></dt>
<dd>
<div class="block">Check to see if an object is an equivalent Triple.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/Triple.Impl.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in class org.biojava.ontology.<a href="./org/biojava/ontology/Triple.Impl.html" title="class in org.biojava.ontology">Triple.Impl</a></dt>
<dd>
<div class="block">Two triples are equal if all their fields are identical.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/ListTools.Doublet.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/ListTools.Doublet.html" title="class in org.biojava.utils">ListTools.Doublet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ListTools.Triplet.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/ListTools.Triplet.html" title="class in org.biojava.utils">ListTools.Triplet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/lsid/LifeScienceIdentifier.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in class org.biojava.utils.lsid.<a href="./org/biojava/utils/lsid/LifeScienceIdentifier.html" title="class in org.biojava.utils.lsid">LifeScienceIdentifier</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ObjectUtil.html#equals(boolean, boolean)">equals(boolean, boolean)</a></span> - Static method in class org.biojava.utils.<a href="./org/biojava/utils/ObjectUtil.html" title="class in org.biojava.utils">ObjectUtil</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ObjectUtil.html#equals(int, int)">equals(int, int)</a></span> - Static method in class org.biojava.utils.<a href="./org/biojava/utils/ObjectUtil.html" title="class in org.biojava.utils">ObjectUtil</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ObjectUtil.html#equals(long, long)">equals(long, long)</a></span> - Static method in class org.biojava.utils.<a href="./org/biojava/utils/ObjectUtil.html" title="class in org.biojava.utils">ObjectUtil</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ObjectUtil.html#equals(float, float)">equals(float, float)</a></span> - Static method in class org.biojava.utils.<a href="./org/biojava/utils/ObjectUtil.html" title="class in org.biojava.utils">ObjectUtil</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ObjectUtil.html#equals(double, double)">equals(double, double)</a></span> - Static method in class org.biojava.utils.<a href="./org/biojava/utils/ObjectUtil.html" title="class in org.biojava.utils">ObjectUtil</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ObjectUtil.html#equals(boolean[], boolean[])">equals(boolean[], boolean[])</a></span> - Static method in class org.biojava.utils.<a href="./org/biojava/utils/ObjectUtil.html" title="class in org.biojava.utils">ObjectUtil</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ObjectUtil.html#equals(int[], int[])">equals(int[], int[])</a></span> - Static method in class org.biojava.utils.<a href="./org/biojava/utils/ObjectUtil.html" title="class in org.biojava.utils">ObjectUtil</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ObjectUtil.html#equals(long[], long[])">equals(long[], long[])</a></span> - Static method in class org.biojava.utils.<a href="./org/biojava/utils/ObjectUtil.html" title="class in org.biojava.utils">ObjectUtil</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ObjectUtil.html#equals(float[], float[])">equals(float[], float[])</a></span> - Static method in class org.biojava.utils.<a href="./org/biojava/utils/ObjectUtil.html" title="class in org.biojava.utils">ObjectUtil</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ObjectUtil.html#equals(double[], double[])">equals(double[], double[])</a></span> - Static method in class org.biojava.utils.<a href="./org/biojava/utils/ObjectUtil.html" title="class in org.biojava.utils">ObjectUtil</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ObjectUtil.html#equals(java.lang.Object[], java.lang.Object[])">equals(Object[], Object[])</a></span> - Static method in class org.biojava.utils.<a href="./org/biojava/utils/ObjectUtil.html" title="class in org.biojava.utils">ObjectUtil</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ObjectUtil.html#equals(java.lang.Object, java.lang.Object)">equals(Object, Object)</a></span> - Static method in class org.biojava.utils.<a href="./org/biojava/utils/ObjectUtil.html" title="class in org.biojava.utils">ObjectUtil</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/TypedProperties.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/TypedProperties.html" title="class in org.biojava.utils">TypedProperties</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLAcceptAllFilter.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLAcceptAllFilter.html" title="class in org.biojavax.bio.db.biosql">BioSQLAcceptAllFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLAcceptNoneFilter.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLAcceptNoneFilter.html" title="class in org.biojavax.bio.db.biosql">BioSQLAcceptNoneFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.And.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.And.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.And</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByName.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByName.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.ByName</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByNote.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByNote.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.ByNote</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByNoteTermOnly.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByNoteTermOnly.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.ByNoteTermOnly</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByRank.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByRank.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.ByRank</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.BySequenceName.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.BySequenceName.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.BySequenceName</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.BySourceTerm.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.BySourceTerm.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.BySourceTerm</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.BySourceTermName.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.BySourceTermName.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.BySourceTermName</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByStrand.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByStrand.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.ByStrand</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByTypeTerm.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByTypeTerm.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.ByTypeTerm</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByTypeTermName.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByTypeTermName.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.ByTypeTermName</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ContainedByRichLocation.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ContainedByRichLocation.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.ContainedByRichLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.Not.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.Not.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.Not</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.Or.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.Or.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.Or</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.OverlapsRichLocation.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.OverlapsRichLocation.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.OverlapsRichLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/CompoundRichLocation.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/CompoundRichLocation.html" title="class in org.biojavax.bio.seq">CompoundRichLocation</a></dt>
<dd>
<div class="block">Checks if this location is equivalent to the other.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/EmptyRichLocation.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/EmptyRichLocation.html" title="class in org.biojavax.bio.seq">EmptyRichLocation</a></dt>
<dd>
<div class="block">Checks if this location is equivalent to the other.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichLocation.Strand.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichLocation.Strand.html" title="class in org.biojavax.bio.seq">RichLocation.Strand</a></dt>
<dd>
<div class="block"> Strands are equal if their numbers and symbols match.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimplePosition.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimplePosition.html" title="class in org.biojavax.bio.seq">SimplePosition</a></dt>
<dd>
<div class="block">
Two positions are equal if they share all parameters in common,
eg.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichFeature.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichFeature.html" title="class in org.biojavax.bio.seq">SimpleRichFeature</a></dt>
<dd>
<div class="block">
Features are equal when they have the same rank, parent, type, and source.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichFeatureRelationship.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichFeatureRelationship.html" title="class in org.biojavax.bio.seq">SimpleRichFeatureRelationship</a></dt>
<dd>
<div class="block">
Relations are equal if their objects, subjects and terms are equal.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichLocation.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichLocation.html" title="class in org.biojavax.bio.seq">SimpleRichLocation</a></dt>
<dd>
<div class="block">Checks if this location is equivalent to the other.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/SimpleBioEntry.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in class org.biojavax.bio.<a href="./org/biojavax/bio/SimpleBioEntry.html" title="class in org.biojavax.bio">SimpleBioEntry</a></dt>
<dd>
<div class="block">
Two bioentries are equal if they share the same namespace, name,
accession and version.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/SimpleBioEntryRelationship.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in class org.biojavax.bio.<a href="./org/biojavax/bio/SimpleBioEntryRelationship.html" title="class in org.biojavax.bio">SimpleBioEntryRelationship</a></dt>
<dd>
<div class="block">
Relationships are equal if they share the same rank, object, subject and term.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/taxa/SimpleNCBITaxon.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in class org.biojavax.bio.taxa.<a href="./org/biojavax/bio/taxa/SimpleNCBITaxon.html" title="class in org.biojavax.bio.taxa">SimpleNCBITaxon</a></dt>
<dd>
<div class="block">
NCBITaxon objects are equal if their NCBITaxID fields match.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/taxa/SimpleNCBITaxonName.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in class org.biojavax.bio.taxa.<a href="./org/biojavax/bio/taxa/SimpleNCBITaxonName.html" title="class in org.biojavax.bio.taxa">SimpleNCBITaxonName</a></dt>
<dd>
<div class="block">
Two taxon names are equal if their name and class match.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/EmptyRichAnnotation.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in class org.biojavax.<a href="./org/biojavax/EmptyRichAnnotation.html" title="class in org.biojavax">EmptyRichAnnotation</a></dt>
<dt><span class="strong"><a href="./org/biojavax/ontology/SimpleComparableOntology.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in class org.biojavax.ontology.<a href="./org/biojavax/ontology/SimpleComparableOntology.html" title="class in org.biojavax.ontology">SimpleComparableOntology</a></dt>
<dd>
<div class="block">
Ontologies are equal if their names are equal.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ontology/SimpleComparableTerm.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in class org.biojavax.ontology.<a href="./org/biojavax/ontology/SimpleComparableTerm.html" title="class in org.biojavax.ontology">SimpleComparableTerm</a></dt>
<dd>
<div class="block">
Two terms are equal if they are in the same ontology and
share the same name.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ontology/SimpleComparableTriple.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in class org.biojavax.ontology.<a href="./org/biojavax/ontology/SimpleComparableTriple.html" title="class in org.biojavax.ontology">SimpleComparableTriple</a></dt>
<dd>
<div class="block">Check to see if an object is an equivalent Triple.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleComment.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleComment.html" title="class in org.biojavax">SimpleComment</a></dt>
<dd>
<div class="block">
Two comments are defined as equal if their text values and
rankings are identical.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleCrossRef.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleCrossRef.html" title="class in org.biojavax">SimpleCrossRef</a></dt>
<dd>
<div class="block">
Equality is defined as having the same database name, accession and
version.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleDocRef.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleDocRef.html" title="class in org.biojavax">SimpleDocRef</a></dt>
<dd>
<div class="block">
Document references are equal if they have the same author and location and title.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleDocRefAuthor.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleDocRefAuthor.html" title="class in org.biojavax">SimpleDocRefAuthor</a></dt>
<dd>
<div class="block">
Document references are equal if they have all fields the same.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleNamespace.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleNamespace.html" title="class in org.biojavax">SimpleNamespace</a></dt>
<dd>
<div class="block">
Namespaces are equal only by name.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleNote.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleNote.html" title="class in org.biojavax">SimpleNote</a></dt>
<dd>
<div class="block">
Notes are equal if they have the same rank and term.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleRankedCrossRef.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleRankedCrossRef.html" title="class in org.biojavax">SimpleRankedCrossRef</a></dt>
<dd>
<div class="block">
Ranked cross references are the same if they have the same rank and
refer to the same cross reference (cross references are equal).</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleRankedDocRef.html#equals(java.lang.Object)">equals(Object)</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleRankedDocRef.html" title="class in org.biojavax">SimpleRankedDocRef</a></dt>
<dd>
<div class="block">
Two ranked document references are equal if they have the same rank
and refer to the same location and same document reference.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/OntoTools.html#EQUIVALENCE">EQUIVALENCE</a></span> - Static variable in class org.biojava.ontology.<a href="./org/biojava/ontology/OntoTools.html" title="class in org.biojava.ontology">OntoTools</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/util/AlignedPosition.html#EQUIVALENT">EQUIVALENT</a></span> - Static variable in class org.biojava.bio.structure.gui.util.<a href="./org/biojava/bio/structure/gui/util/AlignedPosition.html" title="class in org.biojava.bio.structure.gui.util">AlignedPosition</a></dt>
<dd>
<div class="block">flag if this position is equivalent</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/taxa/NCBITaxon.html#EQUIVALENT">EQUIVALENT</a></span> - Static variable in interface org.biojavax.bio.taxa.<a href="./org/biojavax/bio/taxa/NCBITaxon.html" title="interface in org.biojavax.bio.taxa">NCBITaxon</a></dt>
<dd>
<div class="block">Use this to define equivalent names for things.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SequenceBuilderBase.html#ERROR_FEATURES_PROPERTY">ERROR_FEATURES_PROPERTY</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SequenceBuilderBase.html" title="class in org.biojava.bio.seq.io">SequenceBuilderBase</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/obo/OboFileParser.html#escape(java.lang.String, boolean)">escape(String, boolean)</a></span> - Static method in class org.biojava.ontology.obo.<a href="./org/biojava/ontology/obo/OboFileParser.html" title="class in org.biojava.ontology.obo">OboFileParser</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/obo/OboFileParser.html#escapeChars">escapeChars</a></span> - Static variable in class org.biojava.ontology.obo.<a href="./org/biojava/ontology/obo/OboFileParser.html" title="class in org.biojava.ontology.obo">OboFileParser</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BiblioWebResource.html#estimatedSize">estimatedSize</a></span> - Variable in class org.biojava.bibliography.<a href="./org/biojava/bibliography/BiblioWebResource.html" title="class in org.biojava.bibliography">BiblioWebResource</a></dt>
<dd>
<div class="block">An estomated size in kilobytes.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/TranslationTable.html#EUPL_NUC">EUPL_NUC</a></span> - Static variable in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/TranslationTable.html" title="interface in org.biojava.bio.symbol">TranslationTable</a></dt>
<dd>
<div class="block">Translation table name for the euplotid nuclear genetic code.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/BiojavaJmol.html#evalString(java.lang.String)">evalString(String)</a></span> - Method in class org.biojava.bio.structure.gui.<a href="./org/biojava/bio/structure/gui/BiojavaJmol.html" title="class in org.biojava.bio.structure.gui">BiojavaJmol</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/BlastLikeSearchFilter.AbstractBlastLikeSearchFilter.html#evaluate(org.biojava.bio.search.BlastLikeSearchFilter.Node)">evaluate(BlastLikeSearchFilter.Node)</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/BlastLikeSearchFilter.AbstractBlastLikeSearchFilter.html" title="class in org.biojava.bio.search">BlastLikeSearchFilter.AbstractBlastLikeSearchFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/BlastLikeSearchFilter.ByHitProperty.html#evaluate(org.biojava.bio.search.BlastLikeSearchFilter.Node)">evaluate(BlastLikeSearchFilter.Node)</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/BlastLikeSearchFilter.ByHitProperty.html" title="class in org.biojava.bio.search">BlastLikeSearchFilter.ByHitProperty</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/BlastLikeSearchFilter.BySearchProperty.html#evaluate(org.biojava.bio.search.BlastLikeSearchFilter.Node)">evaluate(BlastLikeSearchFilter.Node)</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/BlastLikeSearchFilter.BySearchProperty.html" title="class in org.biojava.bio.search">BlastLikeSearchFilter.BySearchProperty</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/BlastLikeSearchFilter.BySubHitProperty.html#evaluate(org.biojava.bio.search.BlastLikeSearchFilter.Node)">evaluate(BlastLikeSearchFilter.Node)</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/BlastLikeSearchFilter.BySubHitProperty.html" title="class in org.biojava.bio.search">BlastLikeSearchFilter.BySubHitProperty</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/BlastLikeSearchFilter.html#evaluate(org.biojava.bio.search.BlastLikeSearchFilter.Node)">evaluate(BlastLikeSearchFilter.Node)</a></span> - Method in interface org.biojava.bio.search.<a href="./org/biojava/bio/search/BlastLikeSearchFilter.html" title="interface in org.biojava.bio.search">BlastLikeSearchFilter</a></dt>
<dd>
<div class="block">computes the outcome of this filter on the
specified node and stores it.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/BlastLikeSearchFilter.Not.html#evaluate(org.biojava.bio.search.BlastLikeSearchFilter.Node)">evaluate(BlastLikeSearchFilter.Node)</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/BlastLikeSearchFilter.Not.html" title="class in org.biojava.bio.search">BlastLikeSearchFilter.Not</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/CachingKernel.html#evaluate(java.lang.Object, java.lang.Object)">evaluate(Object, Object)</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/CachingKernel.html" title="class in org.biojava.stats.svm">CachingKernel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/DiagonalAddKernel.html#evaluate(java.lang.Object, java.lang.Object)">evaluate(Object, Object)</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/DiagonalAddKernel.html" title="class in org.biojava.stats.svm">DiagonalAddKernel</a></dt>
<dd>
<div class="block">Return the dot product of a, b.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/DiagonalCachingKernel.html#evaluate(java.lang.Object, java.lang.Object)">evaluate(Object, Object)</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/DiagonalCachingKernel.html" title="class in org.biojava.stats.svm">DiagonalCachingKernel</a></dt>
<dd>
<div class="block">
Returns the kernel product of two Objects.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/LinearKernel.html#evaluate(java.lang.Object, java.lang.Object)">evaluate(Object, Object)</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/LinearKernel.html" title="class in org.biojava.stats.svm">LinearKernel</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">The linear kernel is equal to the dot product of a and b.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/ListSumKernel.html#evaluate(java.lang.Object, java.lang.Object)">evaluate(Object, Object)</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/ListSumKernel.html" title="class in org.biojava.stats.svm">ListSumKernel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/NormalizingKernel.html#evaluate(java.lang.Object, java.lang.Object)">evaluate(Object, Object)</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/NormalizingKernel.html" title="class in org.biojava.stats.svm">NormalizingKernel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/PolynomialKernel.html#evaluate(java.lang.Object, java.lang.Object)">evaluate(Object, Object)</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/PolynomialKernel.html" title="class in org.biojava.stats.svm">PolynomialKernel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/RadialBaseKernel.html#evaluate(java.lang.Object, java.lang.Object)">evaluate(Object, Object)</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/RadialBaseKernel.html" title="class in org.biojava.stats.svm">RadialBaseKernel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/SigmoidKernel.html#evaluate(java.lang.Object, java.lang.Object)">evaluate(Object, Object)</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/SigmoidKernel.html" title="class in org.biojava.stats.svm">SigmoidKernel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/SparseVector.NormalizingKernel.html#evaluate(java.lang.Object, java.lang.Object)">evaluate(Object, Object)</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/SparseVector.NormalizingKernel.html" title="class in org.biojava.stats.svm">SparseVector.NormalizingKernel</a></dt>
<dd>
<div class="block">Evaluate the kernel function between two SparseVectors.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/SVMKernel.html#evaluate(java.lang.Object, java.lang.Object)">evaluate(Object, Object)</a></span> - Method in interface org.biojava.stats.svm.<a href="./org/biojava/stats/svm/SVMKernel.html" title="interface in org.biojava.stats.svm">SVMKernel</a></dt>
<dd>
<div class="block">Return the dot product of two vectors in an arbitrary
feature space.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/tools/SuffixTreeKernel.html#evaluate(java.lang.Object, java.lang.Object)">evaluate(Object, Object)</a></span> - Method in class org.biojava.stats.svm.tools.<a href="./org/biojava/stats/svm/tools/SuffixTreeKernel.html" title="class in org.biojava.stats.svm.tools">SuffixTreeKernel</a></dt>
<dd>
<div class="block">Calculate the dot product between the
<span class="type">SuffixTree</span>s <span class="arg">a</span> and
<span class="arg">b</span>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#EVIDENCE_ATTR">EVIDENCE_ATTR</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#EVIDENCE_ATTRIBUTE_ATTR">EVIDENCE_ATTRIBUTE_ATTR</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#EVIDENCE_CATEGORY_ATTR">EVIDENCE_CATEGORY_ATTR</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#EVIDENCE_DATE_ATTR">EVIDENCE_DATE_ATTR</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#EVIDENCE_TAG">EVIDENCE_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/obo/OboFileHandler.html#EXACT_SYNONYM">EXACT_SYNONYM</a></span> - Static variable in class org.biojava.ontology.obo.<a href="./org/biojava/ontology/obo/OboFileHandler.html" title="class in org.biojava.ontology.obo">OboFileHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/Synonym.html#EXACT_SYNONYM">EXACT_SYNONYM</a></span> - Static variable in class org.biojava.ontology.<a href="./org/biojava/ontology/Synonym.html" title="class in org.biojava.ontology">Synonym</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/GenbankSequenceDB.html#ExceptionFound">ExceptionFound</a></span> - Variable in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/GenbankSequenceDB.html" title="class in org.biojava.bio.seq.db">GenbankSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ExecRunner.html#exec(java.lang.String)">exec(String)</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/ExecRunner.html" title="class in org.biojava.utils">ExecRunner</a></dt>
<dd>
<div class="block">The <B>exec(String)</B> method runs a process inside of a watched thread.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/ExecRunner.html#exec(java.lang.String, java.lang.String[])">exec(String, String[])</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/ExecRunner.html" title="class in org.biojava.utils">ExecRunner</a></dt>
<dd>
<div class="block">Sometimes special cases may occur that the arguments of an external program
are Strings containing white spaces.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/ExecRunner.html#exec(java.lang.String, java.io.OutputStream, java.io.OutputStream)">exec(String, OutputStream, OutputStream)</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/ExecRunner.html" title="class in org.biojava.utils">ExecRunner</a></dt>
<dd>
<div class="block">Convenience method for calling exec with OutputStreams.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/ExecRunner.html#exec(java.lang.String, java.lang.String[], java.io.OutputStream, java.io.OutputStream)">exec(String, String[], OutputStream, OutputStream)</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/ExecRunner.html" title="class in org.biojava.utils">ExecRunner</a></dt>
<dd>
<div class="block">Convenience method for calling exec with OutputStreams.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/ExecRunner.html#exec(java.lang.String, java.io.PrintWriter, java.io.PrintWriter)">exec(String, PrintWriter, PrintWriter)</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/ExecRunner.html" title="class in org.biojava.utils">ExecRunner</a></dt>
<dd>
<div class="block">The <code>exec(String, PrintWriter, PrintWriter)</code> method runs
a process inside of a watched thread.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/ExecRunner.html#exec(java.lang.String, java.lang.String[], java.io.PrintWriter, java.io.PrintWriter)">exec(String, String[], PrintWriter, PrintWriter)</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/ExecRunner.html" title="class in org.biojava.utils">ExecRunner</a></dt>
<dd>
<div class="block">The <code>exec(String, PrintWriter, PrintWriter)</code> method runs
a process inside of a watched thread.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/ProcessTools.html#exec(java.lang.String[], java.io.Reader, java.io.Writer, java.io.Writer)">exec(String[], Reader, Writer, Writer)</a></span> - Static method in class org.biojava.utils.<a href="./org/biojava/utils/ProcessTools.html" title="class in org.biojava.utils">ProcessTools</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Execute the specified command and wait for it to return.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/ProcessTools.html#exec(java.lang.String[], java.lang.String[], java.io.File, java.io.Reader, java.io.Writer, java.io.Writer, long)">exec(String[], String[], File, Reader, Writer, Writer, long)</a></span> - Static method in class org.biojava.utils.<a href="./org/biojava/utils/ProcessTools.html" title="class in org.biojava.utils">ProcessTools</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Execute the specified command and wait for it to return, or kill
it if the specified timeout expires first.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/ProcessTools.html#exec(java.lang.String, java.io.Reader, java.io.Writer, java.io.Writer)">exec(String, Reader, Writer, Writer)</a></span> - Static method in class org.biojava.utils.<a href="./org/biojava/utils/ProcessTools.html" title="class in org.biojava.utils">ProcessTools</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Execute the specified command and wait for it to return.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/ProcessTools.html#exec(java.lang.String, java.lang.String[], java.io.File, java.io.Reader, java.io.Writer, java.io.Writer, long)">exec(String, String[], File, Reader, Writer, Writer, long)</a></span> - Static method in class org.biojava.utils.<a href="./org/biojava/utils/ProcessTools.html" title="class in org.biojava.utils">ProcessTools</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Execute the specified command and wait for it to return.</div>
</dd>
<dt><a href="./org/biojava/utils/ExecRunner.html" title="class in org.biojava.utils"><span class="strong">ExecRunner</span></a> - Class in <a href="./org/biojava/utils/package-summary.html">org.biojava.utils</a></dt>
<dd>
<div class="block">Makes running external executables easier, optionally under a watched thread.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/ExecRunner.html#ExecRunner()">ExecRunner()</a></span> - Constructor for class org.biojava.utils.<a href="./org/biojava/utils/ExecRunner.html" title="class in org.biojava.utils">ExecRunner</a></dt>
<dd>
<div class="block">Basic ExecRunner constructor.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/ExecRunner.html#ExecRunner(java.lang.String)">ExecRunner(String)</a></span> - Constructor for class org.biojava.utils.<a href="./org/biojava/utils/ExecRunner.html" title="class in org.biojava.utils">ExecRunner</a></dt>
<dd>
<div class="block">ExecRunner constructor which also conveniently runs exec(String).</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/ExecRunner.html#ExecRunner(java.lang.String, java.lang.String[])">ExecRunner(String, String[])</a></span> - Constructor for class org.biojava.utils.<a href="./org/biojava/utils/ExecRunner.html" title="class in org.biojava.utils">ExecRunner</a></dt>
<dd>
<div class="block">ExecRunner constructor which also conveniently runs exec(String).</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/process/ExternalProcess.html#execute(java.lang.String)">execute(String)</a></span> - Static method in class org.biojava.utils.process.<a href="./org/biojava/utils/process/ExternalProcess.html" title="class in org.biojava.utils.process">ExternalProcess</a></dt>
<dd>
<div class="block">Executes an external program.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/process/ExternalProcess.html#execute(java.lang.String, java.lang.String, java.io.StringWriter, java.io.StringWriter)">execute(String, String, StringWriter, StringWriter)</a></span> - Static method in class org.biojava.utils.process.<a href="./org/biojava/utils/process/ExternalProcess.html" title="class in org.biojava.utils.process">ExternalProcess</a></dt>
<dd>
<div class="block">Executes an external program.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/process/ExternalProcess.html#execute()">execute()</a></span> - Method in class org.biojava.utils.process.<a href="./org/biojava/utils/process/ExternalProcess.html" title="class in org.biojava.utils.process">ExternalProcess</a></dt>
<dd>
<div class="block">Executes the external process and waits for its termination.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/process/ExternalProcess.html#execute(java.util.Properties)">execute(Properties)</a></span> - Method in class org.biojava.utils.process.<a href="./org/biojava/utils/process/ExternalProcess.html" title="class in org.biojava.utils.process">ExternalProcess</a></dt>
<dd>
<div class="block">Executes the external process and waits for its termination.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/io/CachingInputStream.html#expandCache(int)">expandCache(int)</a></span> - Method in class org.biojava.utils.io.<a href="./org/biojava/utils/io/CachingInputStream.html" title="class in org.biojava.utils.io">CachingInputStream</a></dt>
<dd>
<div class="block">Expands the cache to hold some number of <code>additionalBytes</code>.</div>
</dd>
<dt><a href="./org/biojava/bio/structure/io/mmcif/model/Exptl.html" title="class in org.biojava.bio.structure.io.mmcif.model"><span class="strong">Exptl</span></a> - Class in <a href="./org/biojava/bio/structure/io/mmcif/model/package-summary.html">org.biojava.bio.structure.io.mmcif.model</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Exptl.html#Exptl()">Exptl()</a></span> - Constructor for class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Exptl.html" title="class in org.biojava.bio.structure.io.mmcif.model">Exptl</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/utils/process/ExternalProcess.html" title="class in org.biojava.utils.process"><span class="strong">ExternalProcess</span></a> - Class in <a href="./org/biojava/utils/process/package-summary.html">org.biojava.utils.process</a></dt>
<dd>
<div class="block">Utility class to execute an external process and to handle
the <code>STDOUT</code>, <code>STDERR</code> and <code>STDIN</code> streams
in multiple threads managed by a thread pool.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/process/ExternalProcess.html#ExternalProcess()">ExternalProcess()</a></span> - Constructor for class org.biojava.utils.process.<a href="./org/biojava/utils/process/ExternalProcess.html" title="class in org.biojava.utils.process">ExternalProcess</a></dt>
<dd>
<div class="block">Initializes the external process.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/process/ExternalProcess.html#ExternalProcess(org.biojava.utils.ThreadPool)">ExternalProcess(ThreadPool)</a></span> - Constructor for class org.biojava.utils.process.<a href="./org/biojava/utils/process/ExternalProcess.html" title="class in org.biojava.utils.process">ExternalProcess</a></dt>
<dd>
<div class="block">Initializes the external process.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FilterUtils.html#extractOverlappingLocation(org.biojava.bio.seq.FeatureFilter)">extractOverlappingLocation(FeatureFilter)</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FilterUtils.html" title="class in org.biojava.bio.seq">FilterUtils</a></dt>
<dd>
<div class="block">Try to determine the minimal location which all features matching a given
filter must overlap.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/candy/CandyEntry.html#extras">extras</a></span> - Variable in class org.biojava.utils.candy.<a href="./org/biojava/utils/candy/CandyEntry.html" title="class in org.biojava.utils.candy">CandyEntry</a></dt>
<dd>
<div class="block">A container for the additional properties represented by this entry.</div>
</dd>
</dl>
<a name="_F_">
<!-- -->
</a>
<h2 class="title">F</h2>
<dl>
<dt><span class="strong"><a href="./org/biojava/bio/seq/ProteinTools.html#f()">f()</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/ProteinTools.html" title="class in org.biojava.bio.seq">ProteinTools</a></dt>
<dd>
<div class="block">Returns the <code>AtomicSymbol</code> for the amino acid
Phenylalanine</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AlphabetManager.html#factorize(org.biojava.bio.symbol.Alphabet, java.util.Set)">factorize(Alphabet, Set)</a></span> - Static method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AlphabetManager.html" title="class in org.biojava.bio.symbol">AlphabetManager</a></dt>
<dd>
<div class="block">
Return a list of BasisSymbol instances that uniquely sum up all
AtomicSymbol
instances in symSet.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SimpleAssemblyBuilder.html#FACTORY">FACTORY</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SimpleAssemblyBuilder.html" title="class in org.biojava.bio.seq.io">SimpleAssemblyBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SimpleSequenceBuilder.html#FACTORY">FACTORY</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SimpleSequenceBuilder.html" title="class in org.biojava.bio.seq.io">SimpleSequenceBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SmartSequenceBuilder.html#FACTORY">FACTORY</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SmartSequenceBuilder.html" title="class in org.biojava.bio.seq.io">SmartSequenceBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/RichSequenceBuilderFactory.html#FACTORY">FACTORY</a></span> - Static variable in interface org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/RichSequenceBuilderFactory.html" title="interface in org.biojavax.bio.seq.io">RichSequenceBuilderFactory</a></dt>
<dd>
<div class="block">Accessor for the default factory.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/TriState.html#FALSE">FALSE</a></span> - Static variable in class org.biojava.utils.<a href="./org/biojava/utils/TriState.html" title="class in org.biojava.utils">TriState</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/AlignIOConstants.html#FASTA">FASTA</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/AlignIOConstants.html" title="class in org.biojava.bio.seq.io">AlignIOConstants</a></dt>
<dd>
<div class="block"><code>FASTA</code> indicates that the alignment format is
Fasta.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOConstants.html#FASTA">FASTA</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOConstants.html" title="class in org.biojava.bio.seq.io">SeqIOConstants</a></dt>
<dd>
<div class="block"><code>FASTA</code> indicates that the sequence format is Fasta.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/AlignIOConstants.html#FASTA_AA">FASTA_AA</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/AlignIOConstants.html" title="class in org.biojava.bio.seq.io">AlignIOConstants</a></dt>
<dd>
<div class="block"><code>FASTA_AA</code> premade FASTA | AA;</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOConstants.html#FASTA_AA">FASTA_AA</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOConstants.html" title="class in org.biojava.bio.seq.io">SeqIOConstants</a></dt>
<dd>
<div class="block"><code>FASTA_AA</code> premade FASTA | AA.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/AlignIOConstants.html#FASTA_DNA">FASTA_DNA</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/AlignIOConstants.html" title="class in org.biojava.bio.seq.io">AlignIOConstants</a></dt>
<dd>
<div class="block"><code>FASTA_DNA</code> premade FASTA | DNA;</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOConstants.html#FASTA_DNA">FASTA_DNA</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOConstants.html" title="class in org.biojava.bio.seq.io">SeqIOConstants</a></dt>
<dd>
<div class="block"><code>FASTA_DNA</code> premade FASTA | DNA.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/FastaFormat.html#FASTA_FORMAT">FASTA_FORMAT</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/FastaFormat.html" title="class in org.biojavax.bio.seq.io">FastaFormat</a></dt>
<dd>
<div class="block">The name of this format</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/AlignIOConstants.html#FASTA_RNA">FASTA_RNA</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/AlignIOConstants.html" title="class in org.biojava.bio.seq.io">AlignIOConstants</a></dt>
<dd>
<div class="block"><code>FASTA_RNA</code> premade FASTA | RNA;</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOConstants.html#FASTA_RNA">FASTA_RNA</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOConstants.html" title="class in org.biojava.bio.seq.io">SeqIOConstants</a></dt>
<dd>
<div class="block"><code>FASTA_RNA</code> premade FASTA | RNA.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/FastaAlignmentFormat.html" title="class in org.biojava.bio.seq.io"><span class="strong">FastaAlignmentFormat</span></a> - Class in <a href="./org/biojava/bio/seq/io/package-summary.html">org.biojava.bio.seq.io</a></dt>
<dd>
<div class="block">This class implements the AlignmentFormat interface to read FASTA alignments.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/FastaAlignmentFormat.html#FastaAlignmentFormat()">FastaAlignmentFormat()</a></span> - Constructor for class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/FastaAlignmentFormat.html" title="class in org.biojava.bio.seq.io">FastaAlignmentFormat</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/io/FastaDescriptionLineParser.html" title="class in org.biojava.bio.seq.io"><span class="strong">FastaDescriptionLineParser</span></a> - Class in <a href="./org/biojava/bio/seq/io/package-summary.html">org.biojava.bio.seq.io</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>Use org.biojavax.bio.seq.io.FastaFormat</i></div>
</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/FastaDescriptionLineParser.html#FastaDescriptionLineParser(org.biojava.bio.seq.io.SequenceBuilder)">FastaDescriptionLineParser(SequenceBuilder)</a></span> - Constructor for class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/FastaDescriptionLineParser.html" title="class in org.biojava.bio.seq.io">FastaDescriptionLineParser</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/FastaDescriptionLineParser.Factory.html" title="class in org.biojava.bio.seq.io"><span class="strong">FastaDescriptionLineParser.Factory</span></a> - Class in <a href="./org/biojava/bio/seq/io/package-summary.html">org.biojava.bio.seq.io</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Factory which wraps SequenceBuilders in a FastaDescriptionLineParser</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/FastaDescriptionLineParser.Factory.html#FastaDescriptionLineParser.Factory(org.biojava.bio.seq.io.SequenceBuilderFactory)">FastaDescriptionLineParser.Factory(SequenceBuilderFactory)</a></span> - Constructor for class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/FastaDescriptionLineParser.Factory.html" title="class in org.biojava.bio.seq.io">FastaDescriptionLineParser.Factory</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/FastaFormat.html" title="class in org.biojava.bio.seq.io"><span class="strong">FastaFormat</span></a> - Class in <a href="./org/biojava/bio/seq/io/package-summary.html">org.biojava.bio.seq.io</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>Use org.biojavax.bio.seq.io.FastaFormat</i></div>
</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/FastaFormat.html#FastaFormat()">FastaFormat()</a></span> - Constructor for class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/FastaFormat.html" title="class in org.biojava.bio.seq.io">FastaFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><a href="./org/biojavax/bio/seq/io/FastaFormat.html" title="class in org.biojavax.bio.seq.io"><span class="strong">FastaFormat</span></a> - Class in <a href="./org/biojavax/bio/seq/io/package-summary.html">org.biojavax.bio.seq.io</a></dt>
<dd>
<div class="block">Format object representing FASTA files.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/FastaFormat.html#FastaFormat()">FastaFormat()</a></span> - Constructor for class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/FastaFormat.html" title="class in org.biojavax.bio.seq.io">FastaFormat</a></dt>
<dd> </dd>
<dt><a href="./org/biojavax/bio/seq/io/FastaHeader.html" title="class in org.biojavax.bio.seq.io"><span class="strong">FastaHeader</span></a> - Class in <a href="./org/biojavax/bio/seq/io/package-summary.html">org.biojavax.bio.seq.io</a></dt>
<dd>
<div class="block">This class is used by <code>FastaFormat</code> to determine which fields are in the
fasta header.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/FastaHeader.html#FastaHeader()">FastaHeader()</a></span> - Constructor for class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/FastaHeader.html" title="class in org.biojavax.bio.seq.io">FastaHeader</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/sax/FastaSearchSAXParser.html" title="class in org.biojava.bio.program.sax"><span class="strong">FastaSearchSAXParser</span></a> - Class in <a href="./org/biojava/bio/program/sax/package-summary.html">org.biojava.bio.program.sax</a></dt>
<dd>
<div class="block"><code>FastaSearchSAXParser</code> is a SAX2 compliant parser for
'-m 10' format output from the the Fasta search program (see the
Fasta documentation for details of this format).</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/sax/FastaSearchSAXParser.html#FastaSearchSAXParser()">FastaSearchSAXParser()</a></span> - Constructor for class org.biojava.bio.program.sax.<a href="./org/biojava/bio/program/sax/FastaSearchSAXParser.html" title="class in org.biojava.bio.program.sax">FastaSearchSAXParser</a></dt>
<dd>
<div class="block">Creates a new <code>FastaSearchSAXParser</code> instance.</div>
</dd>
<dt><a href="./org/biojava/bio/program/sax/FastaSequenceSAXParser.html" title="class in org.biojava.bio.program.sax"><span class="strong">FastaSequenceSAXParser</span></a> - Class in <a href="./org/biojava/bio/program/sax/package-summary.html">org.biojava.bio.program.sax</a></dt>
<dd>
<div class="block">A SAX2 parser for dealing with multiple sequences in
FASTA format.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/sax/FastaSequenceSAXParser.html#FastaSequenceSAXParser()">FastaSequenceSAXParser()</a></span> - Constructor for class org.biojava.bio.program.sax.<a href="./org/biojava/bio/program/sax/FastaSequenceSAXParser.html" title="class in org.biojava.bio.program.sax">FastaSequenceSAXParser</a></dt>
<dd>
<div class="block">Initialises internal state
Sets namespace prefix to "biojava"</div>
</dd>
<dt><a href="./org/biojava/bio/program/fastq/Fastq.html" title="class in org.biojava.bio.program.fastq"><span class="strong">Fastq</span></a> - Class in <a href="./org/biojava/bio/program/fastq/package-summary.html">org.biojava.bio.program.fastq</a></dt>
<dd>
<div class="block">FASTQ formatted sequence.</div>
</dd>
<dt><a href="./org/biojava/bio/program/fastq/FastqBuilder.html" title="class in org.biojava.bio.program.fastq"><span class="strong">FastqBuilder</span></a> - Class in <a href="./org/biojava/bio/program/fastq/package-summary.html">org.biojava.bio.program.fastq</a></dt>
<dd>
<div class="block">Fluent builder API for creating FASTQ formatted sequences.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/fastq/FastqBuilder.html#FastqBuilder()">FastqBuilder()</a></span> - Constructor for class org.biojava.bio.program.fastq.<a href="./org/biojava/bio/program/fastq/FastqBuilder.html" title="class in org.biojava.bio.program.fastq">FastqBuilder</a></dt>
<dd>
<div class="block">Create a new FASTQ formatted sequence builder.</div>
</dd>
<dt><a href="./org/biojava/bio/program/fastq/FastqReader.html" title="interface in org.biojava.bio.program.fastq"><span class="strong">FastqReader</span></a> - Interface in <a href="./org/biojava/bio/program/fastq/package-summary.html">org.biojava.bio.program.fastq</a></dt>
<dd>
<div class="block">Reader for FASTQ formatted sequences.</div>
</dd>
<dt><a href="./org/biojava/bio/program/fastq/FastqVariant.html" title="enum in org.biojava.bio.program.fastq"><span class="strong">FastqVariant</span></a> - Enum in <a href="./org/biojava/bio/program/fastq/package-summary.html">org.biojava.bio.program.fastq</a></dt>
<dd>
<div class="block">FASTQ sequence format variant.</div>
</dd>
<dt><a href="./org/biojava/bio/program/fastq/FastqWriter.html" title="interface in org.biojava.bio.program.fastq"><span class="strong">FastqWriter</span></a> - Interface in <a href="./org/biojava/bio/program/fastq/package-summary.html">org.biojava.bio.program.fastq</a></dt>
<dd>
<div class="block">Writer for FASTQ formatted sequences.</div>
</dd>
<dt><a href="./org/biojava/utils/xml/FastXMLWriter.html" title="class in org.biojava.utils.xml"><span class="strong">FastXMLWriter</span></a> - Class in <a href="./org/biojava/utils/xml/package-summary.html">org.biojava.utils.xml</a></dt>
<dd>
<div class="block">Simple implementation of XMLWriter, optimized for speed.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/xml/FastXMLWriter.html#FastXMLWriter(java.io.PrintWriter)">FastXMLWriter(PrintWriter)</a></span> - Constructor for class org.biojava.utils.xml.<a href="./org/biojava/utils/xml/FastXMLWriter.html" title="class in org.biojava.utils.xml">FastXMLWriter</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/Feature.html" title="interface in org.biojava.bio.seq"><span class="strong">Feature</span></a> - Interface in <a href="./org/biojava/bio/seq/package-summary.html">org.biojava.bio.seq</a></dt>
<dd>
<div class="block">A feature within a sequence, or nested within another feature.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichLocation.html#FEATURE">FEATURE</a></span> - Static variable in interface org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichLocation.html" title="interface in org.biojavax.bio.seq">RichLocation</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/Feature.ByLocationComparator.html" title="class in org.biojava.bio.seq"><span class="strong">Feature.ByLocationComparator</span></a> - Class in <a href="./org/biojava/bio/seq/package-summary.html">org.biojava.bio.seq</a></dt>
<dd>
<div class="block"><code>ByLocationComparator</code> compares
<code>Feature</code>s by the minimum base position of their
<code>Location</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/Feature.ByLocationComparator.html#Feature.ByLocationComparator()">Feature.ByLocationComparator()</a></span> - Constructor for class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/Feature.ByLocationComparator.html" title="class in org.biojava.bio.seq">Feature.ByLocationComparator</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/Feature.Template.html" title="class in org.biojava.bio.seq"><span class="strong">Feature.Template</span></a> - Class in <a href="./org/biojava/bio/seq/package-summary.html">org.biojava.bio.seq</a></dt>
<dd>
<div class="block">Template class for a plain feature.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/Feature.Template.html#Feature.Template()">Feature.Template()</a></span> - Constructor for class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/Feature.Template.html" title="class in org.biojava.bio.seq">Feature.Template</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/INSDseqFormat.html#FEATURE_ACCESSION_TAG">FEATURE_ACCESSION_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/INSDseqFormat.html" title="class in org.biojavax.bio.seq.io">INSDseqFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/FeatureBlockSequenceRenderer.html#FEATURE_COLLAPSING">FEATURE_COLLAPSING</a></span> - Static variable in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/FeatureBlockSequenceRenderer.html" title="class in org.biojava.bio.gui.sequence">FeatureBlockSequenceRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#FEATURE_DESC_ATTR">FEATURE_DESC_ATTR</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/GenbankFormat.html#FEATURE_FLAG">FEATURE_FLAG</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/GenbankFormat.html" title="class in org.biojava.bio.seq.io">GenbankFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/INSDseqFormat.html#FEATURE_FROM_TAG">FEATURE_FROM_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/INSDseqFormat.html" title="class in org.biojavax.bio.seq.io">INSDseqFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/xff/FeatureHandler.html#FEATURE_HANDLER_FACTORY">FEATURE_HANDLER_FACTORY</a></span> - Static variable in class org.biojava.bio.program.xff.<a href="./org/biojava/bio/program/xff/FeatureHandler.html" title="class in org.biojava.bio.program.xff">FeatureHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLFormat.html#FEATURE_HEADER_TAG">FEATURE_HEADER_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLFormat.html" title="class in org.biojavax.bio.seq.io">EMBLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/INSDseqFormat.html#FEATURE_INTERBP_TAG">FEATURE_INTERBP_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/INSDseqFormat.html" title="class in org.biojavax.bio.seq.io">INSDseqFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/INSDseqFormat.html#FEATURE_INTERVAL_TAG">FEATURE_INTERVAL_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/INSDseqFormat.html" title="class in org.biojavax.bio.seq.io">INSDseqFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/INSDseqFormat.html#FEATURE_INTERVALS_GROUP_TAG">FEATURE_INTERVALS_GROUP_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/INSDseqFormat.html" title="class in org.biojavax.bio.seq.io">INSDseqFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/INSDseqFormat.html#FEATURE_ISCOMP_TAG">FEATURE_ISCOMP_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/INSDseqFormat.html" title="class in org.biojavax.bio.seq.io">INSDseqFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/INSDseqFormat.html#FEATURE_KEY_TAG">FEATURE_KEY_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/INSDseqFormat.html" title="class in org.biojavax.bio.seq.io">INSDseqFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/GenbankFormat.html#FEATURE_LINE_PREFIX">FEATURE_LINE_PREFIX</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/GenbankFormat.html" title="class in org.biojava.bio.seq.io">GenbankFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/INSDseqFormat.html#FEATURE_LOC_TAG">FEATURE_LOC_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/INSDseqFormat.html" title="class in org.biojavax.bio.seq.io">INSDseqFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html#FEATURE_NAME_ATTR">FEATURE_NAME_ATTR</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html" title="class in org.biojavax.bio.seq.io">EMBLxmlFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/INSDseqFormat.html#FEATURE_OPERATOR_TAG">FEATURE_OPERATOR_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/INSDseqFormat.html" title="class in org.biojavax.bio.seq.io">INSDseqFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#FEATURE_ORIGINAL_TAG">FEATURE_ORIGINAL_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/INSDseqFormat.html#FEATURE_PARTIAL3_TAG">FEATURE_PARTIAL3_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/INSDseqFormat.html" title="class in org.biojavax.bio.seq.io">INSDseqFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/INSDseqFormat.html#FEATURE_PARTIAL5_TAG">FEATURE_PARTIAL5_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/INSDseqFormat.html" title="class in org.biojavax.bio.seq.io">INSDseqFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/INSDseqFormat.html#FEATURE_POINT_TAG">FEATURE_POINT_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/INSDseqFormat.html" title="class in org.biojavax.bio.seq.io">INSDseqFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/FeatureBlockSequenceRenderer.html#FEATURE_RENDERER">FEATURE_RENDERER</a></span> - Static variable in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/FeatureBlockSequenceRenderer.html" title="class in org.biojava.bio.gui.sequence">FeatureBlockSequenceRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/EmblLikeFormat.html#FEATURE_TABLE_TAG">FEATURE_TABLE_TAG</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/EmblLikeFormat.html" title="class in org.biojava.bio.seq.io">EmblLikeFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/EmblLikeFormat.html#FEATURE_TAG">FEATURE_TAG</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/EmblLikeFormat.html" title="class in org.biojava.bio.seq.io">EmblLikeFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/GenbankFormat.html#FEATURE_TAG">FEATURE_TAG</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/GenbankFormat.html" title="class in org.biojava.bio.seq.io">GenbankFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLFormat.html#FEATURE_TAG">FEATURE_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLFormat.html" title="class in org.biojavax.bio.seq.io">EMBLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html#FEATURE_TAG">FEATURE_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html" title="class in org.biojavax.bio.seq.io">EMBLxmlFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/GenbankFormat.html#FEATURE_TAG">FEATURE_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/GenbankFormat.html" title="class in org.biojavax.bio.seq.io">GenbankFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/INSDseqFormat.html#FEATURE_TAG">FEATURE_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/INSDseqFormat.html" title="class in org.biojavax.bio.seq.io">INSDseqFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtFormat.html#FEATURE_TAG">FEATURE_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtFormat.html" title="class in org.biojavax.bio.seq.io">UniProtFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#FEATURE_TAG">FEATURE_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/INSDseqFormat.html#FEATURE_TO_TAG">FEATURE_TO_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/INSDseqFormat.html" title="class in org.biojavax.bio.seq.io">INSDseqFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#FEATURE_VARIATION_TAG">FEATURE_VARIATION_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/gui/sequence/FeatureBlockSequenceRenderer.html" title="class in org.biojava.bio.gui.sequence"><span class="strong">FeatureBlockSequenceRenderer</span></a> - Class in <a href="./org/biojava/bio/gui/sequence/package-summary.html">org.biojava.bio.gui.sequence</a></dt>
<dd>
<div class="block"><code>FeatureBlockSequenceRenderer</code> forms a bridge between
<code>Sequence</code> rendering and <code>Feature</code>
rendering.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/FeatureBlockSequenceRenderer.html#FeatureBlockSequenceRenderer()">FeatureBlockSequenceRenderer()</a></span> - Constructor for class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/FeatureBlockSequenceRenderer.html" title="class in org.biojava.bio.gui.sequence">FeatureBlockSequenceRenderer</a></dt>
<dd>
<div class="block">Creates a new <code>FeatureBlockSequenceRenderer</code> which
uses a <code>BasicFeatureRenderer</code> as its renderer.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/FeatureBlockSequenceRenderer.html#FeatureBlockSequenceRenderer(org.biojava.bio.gui.sequence.FeatureRenderer)">FeatureBlockSequenceRenderer(FeatureRenderer)</a></span> - Constructor for class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/FeatureBlockSequenceRenderer.html" title="class in org.biojava.bio.gui.sequence">FeatureBlockSequenceRenderer</a></dt>
<dd>
<div class="block">Creates a new <code>FeatureBlockSequenceRenderer</code> which
uses the specified <code>FeatureRenderer</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/FeatureTableParser.html#featureData(java.lang.String)">featureData(String)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/FeatureTableParser.html" title="class in org.biojava.bio.seq.io">FeatureTableParser</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><a href="./org/biojava/bio/seq/FeatureFilter.html" title="interface in org.biojava.bio.seq"><span class="strong">FeatureFilter</span></a> - Interface in <a href="./org/biojava/bio/seq/package-summary.html">org.biojava.bio.seq</a></dt>
<dd>
<div class="block">A filter for accepting or rejecting a feature.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/filter/FilterTransformer.html#featureFilter(org.biojava.bio.seq.FeatureFilter)">featureFilter(FeatureFilter)</a></span> - Method in class org.biojava.bio.seq.filter.<a href="./org/biojava/bio/seq/filter/FilterTransformer.html" title="class in org.biojava.bio.seq.filter">FilterTransformer</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/FeatureFilter.And.html" title="class in org.biojava.bio.seq"><span class="strong">FeatureFilter.And</span></a> - Class in <a href="./org/biojava/bio/seq/package-summary.html">org.biojava.bio.seq</a></dt>
<dd>
<div class="block">A filter that returns all features accepted by both child filter.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.And.html#FeatureFilter.And(org.biojava.bio.seq.FeatureFilter, org.biojava.bio.seq.FeatureFilter)">FeatureFilter.And(FeatureFilter, FeatureFilter)</a></span> - Constructor for class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.And.html" title="class in org.biojava.bio.seq">FeatureFilter.And</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/FeatureFilter.AnnotationContains.html" title="class in org.biojava.bio.seq"><span class="strong">FeatureFilter.AnnotationContains</span></a> - Class in <a href="./org/biojava/bio/seq/package-summary.html">org.biojava.bio.seq</a></dt>
<dd>
<div class="block">Retrieve features that contain a given annotation, and that the set of values
contains the value given.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.AnnotationContains.html#FeatureFilter.AnnotationContains(java.lang.Object, java.lang.Object)">FeatureFilter.AnnotationContains(Object, Object)</a></span> - Constructor for class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.AnnotationContains.html" title="class in org.biojava.bio.seq">FeatureFilter.AnnotationContains</a></dt>
<dd>
<div class="block">Make a new AnnotationContains that will accept features with an annotation
bundle where the value-set assosiated with the property <code>key</code>
contains a member equal to <code>value</code>.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/FeatureFilter.ByAncestor.html" title="class in org.biojava.bio.seq"><span class="strong">FeatureFilter.ByAncestor</span></a> - Class in <a href="./org/biojava/bio/seq/package-summary.html">org.biojava.bio.seq</a></dt>
<dd>
<div class="block">Filter by applying a nested <code>FeatureFilter</code> to all
ancestor features.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ByAncestor.html#FeatureFilter.ByAncestor(org.biojava.bio.seq.FeatureFilter)">FeatureFilter.ByAncestor(FeatureFilter)</a></span> - Constructor for class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ByAncestor.html" title="class in org.biojava.bio.seq">FeatureFilter.ByAncestor</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/FeatureFilter.ByAnnotation.html" title="class in org.biojava.bio.seq"><span class="strong">FeatureFilter.ByAnnotation</span></a> - Class in <a href="./org/biojava/bio/seq/package-summary.html">org.biojava.bio.seq</a></dt>
<dd>
<div class="block">Retrieve features that contain a given annotation with a given value.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ByAnnotation.html#FeatureFilter.ByAnnotation(java.lang.Object, java.lang.Object)">FeatureFilter.ByAnnotation(Object, Object)</a></span> - Constructor for class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ByAnnotation.html" title="class in org.biojava.bio.seq">FeatureFilter.ByAnnotation</a></dt>
<dd>
<div class="block">Make a new ByAnnotation that will accept features with an annotation
bundle containing 'value' associated with 'key'.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/FeatureFilter.ByAnnotationType.html" title="class in org.biojava.bio.seq"><span class="strong">FeatureFilter.ByAnnotationType</span></a> - Class in <a href="./org/biojava/bio/seq/package-summary.html">org.biojava.bio.seq</a></dt>
<dd>
<div class="block">A filter that returns all features that have an annotation bundle that is of a given
annotation type.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ByAnnotationType.html#FeatureFilter.ByAnnotationType()">FeatureFilter.ByAnnotationType()</a></span> - Constructor for class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ByAnnotationType.html" title="class in org.biojava.bio.seq">FeatureFilter.ByAnnotationType</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ByAnnotationType.html#FeatureFilter.ByAnnotationType(org.biojava.bio.AnnotationType)">FeatureFilter.ByAnnotationType(AnnotationType)</a></span> - Constructor for class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ByAnnotationType.html" title="class in org.biojava.bio.seq">FeatureFilter.ByAnnotationType</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/FeatureFilter.ByChild.html" title="class in org.biojava.bio.seq"><span class="strong">FeatureFilter.ByChild</span></a> - Class in <a href="./org/biojava/bio/seq/package-summary.html">org.biojava.bio.seq</a></dt>
<dd>
<div class="block">Filter by applying a nested <code>FeatureFilter</code> to the
child features.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ByChild.html#FeatureFilter.ByChild(org.biojava.bio.seq.FeatureFilter)">FeatureFilter.ByChild(FeatureFilter)</a></span> - Constructor for class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ByChild.html" title="class in org.biojava.bio.seq">FeatureFilter.ByChild</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/FeatureFilter.ByClass.html" title="class in org.biojava.bio.seq"><span class="strong">FeatureFilter.ByClass</span></a> - Class in <a href="./org/biojava/bio/seq/package-summary.html">org.biojava.bio.seq</a></dt>
<dd>
<div class="block">Filter which accepts only those filters which are an instance
of a specific Java class</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ByClass.html#FeatureFilter.ByClass(java.lang.Class)">FeatureFilter.ByClass(Class)</a></span> - Constructor for class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ByClass.html" title="class in org.biojava.bio.seq">FeatureFilter.ByClass</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/FeatureFilter.ByComponentName.html" title="class in org.biojava.bio.seq"><span class="strong">FeatureFilter.ByComponentName</span></a> - Class in <a href="./org/biojava/bio/seq/package-summary.html">org.biojava.bio.seq</a></dt>
<dd>
<div class="block">Accepts features which are ComponentFeatures and have a <code>componentSequenceName</code>
property of the specified value.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ByComponentName.html#FeatureFilter.ByComponentName(java.lang.String)">FeatureFilter.ByComponentName(String)</a></span> - Constructor for class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ByComponentName.html" title="class in org.biojava.bio.seq">FeatureFilter.ByComponentName</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/FeatureFilter.ByDescendant.html" title="class in org.biojava.bio.seq"><span class="strong">FeatureFilter.ByDescendant</span></a> - Class in <a href="./org/biojava/bio/seq/package-summary.html">org.biojava.bio.seq</a></dt>
<dd>
<div class="block">Filter by applying a nested <code>FeatureFilter</code> to all
descendant features.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ByDescendant.html#FeatureFilter.ByDescendant(org.biojava.bio.seq.FeatureFilter)">FeatureFilter.ByDescendant(FeatureFilter)</a></span> - Constructor for class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ByDescendant.html" title="class in org.biojava.bio.seq">FeatureFilter.ByDescendant</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/FeatureFilter.ByFeature.html" title="class in org.biojava.bio.seq"><span class="strong">FeatureFilter.ByFeature</span></a> - Class in <a href="./org/biojava/bio/seq/package-summary.html">org.biojava.bio.seq</a></dt>
<dd>
<div class="block">Accept only features which are equal to the specified feature</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ByFeature.html#FeatureFilter.ByFeature(org.biojava.bio.seq.Feature)">FeatureFilter.ByFeature(Feature)</a></span> - Constructor for class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ByFeature.html" title="class in org.biojava.bio.seq">FeatureFilter.ByFeature</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/FeatureFilter.ByPairwiseScore.html" title="class in org.biojava.bio.seq"><span class="strong">FeatureFilter.ByPairwiseScore</span></a> - Class in <a href="./org/biojava/bio/seq/package-summary.html">org.biojava.bio.seq</a></dt>
<dd>
<div class="block"><code>ByPairwiseScore</code> is used to filter
<code>SimilarityPairFeature</code>s by their score.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ByPairwiseScore.html#FeatureFilter.ByPairwiseScore(double, double)">FeatureFilter.ByPairwiseScore(double, double)</a></span> - Constructor for class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ByPairwiseScore.html" title="class in org.biojava.bio.seq">FeatureFilter.ByPairwiseScore</a></dt>
<dd>
<div class="block">Creates a new <code>ByPairwiseScore</code>.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/FeatureFilter.ByParent.html" title="class in org.biojava.bio.seq"><span class="strong">FeatureFilter.ByParent</span></a> - Class in <a href="./org/biojava/bio/seq/package-summary.html">org.biojava.bio.seq</a></dt>
<dd>
<div class="block">Filter by applying a nested <code>FeatureFilter</code> to the
parent feature.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ByParent.html#FeatureFilter.ByParent(org.biojava.bio.seq.FeatureFilter)">FeatureFilter.ByParent(FeatureFilter)</a></span> - Constructor for class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ByParent.html" title="class in org.biojava.bio.seq">FeatureFilter.ByParent</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/FeatureFilter.BySequenceName.html" title="class in org.biojava.bio.seq"><span class="strong">FeatureFilter.BySequenceName</span></a> - Class in <a href="./org/biojava/bio/seq/package-summary.html">org.biojava.bio.seq</a></dt>
<dd>
<div class="block">Accept features that reside on a sequence with a particular name.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.BySequenceName.html#FeatureFilter.BySequenceName(java.lang.String)">FeatureFilter.BySequenceName(String)</a></span> - Constructor for class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.BySequenceName.html" title="class in org.biojava.bio.seq">FeatureFilter.BySequenceName</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/FeatureFilter.BySource.html" title="class in org.biojava.bio.seq"><span class="strong">FeatureFilter.BySource</span></a> - Class in <a href="./org/biojava/bio/seq/package-summary.html">org.biojava.bio.seq</a></dt>
<dd>
<div class="block">Construct one of these to filter features by source.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.BySource.html#FeatureFilter.BySource(java.lang.String)">FeatureFilter.BySource(String)</a></span> - Constructor for class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.BySource.html" title="class in org.biojava.bio.seq">FeatureFilter.BySource</a></dt>
<dd>
<div class="block">Create a BySource filter that filters in all features which have sources
equal to source.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/FeatureFilter.ByType.html" title="class in org.biojava.bio.seq"><span class="strong">FeatureFilter.ByType</span></a> - Class in <a href="./org/biojava/bio/seq/package-summary.html">org.biojava.bio.seq</a></dt>
<dd>
<div class="block">Construct one of these to filter features by type.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ByType.html#FeatureFilter.ByType(java.lang.String)">FeatureFilter.ByType(String)</a></span> - Constructor for class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ByType.html" title="class in org.biojava.bio.seq">FeatureFilter.ByType</a></dt>
<dd>
<div class="block">Create a ByType filter that filters in all features with type fields
equal to type.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/FeatureFilter.ContainedByLocation.html" title="class in org.biojava.bio.seq"><span class="strong">FeatureFilter.ContainedByLocation</span></a> - Class in <a href="./org/biojava/bio/seq/package-summary.html">org.biojava.bio.seq</a></dt>
<dd>
<div class="block">A filter that returns all features contained within a location.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ContainedByLocation.html#FeatureFilter.ContainedByLocation(org.biojava.bio.symbol.Location)">FeatureFilter.ContainedByLocation(Location)</a></span> - Constructor for class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ContainedByLocation.html" title="class in org.biojava.bio.seq">FeatureFilter.ContainedByLocation</a></dt>
<dd>
<div class="block">Creates a filter that returns everything contained within loc.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/FeatureFilter.FrameFilter.html" title="class in org.biojava.bio.seq"><span class="strong">FeatureFilter.FrameFilter</span></a> - Class in <a href="./org/biojava/bio/seq/package-summary.html">org.biojava.bio.seq</a></dt>
<dd>
<div class="block">Accept features with a given reading frame.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.FrameFilter.html#FeatureFilter.FrameFilter(org.biojava.bio.seq.FramedFeature.ReadingFrame)">FeatureFilter.FrameFilter(FramedFeature.ReadingFrame)</a></span> - Constructor for class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.FrameFilter.html" title="class in org.biojava.bio.seq">FeatureFilter.FrameFilter</a></dt>
<dd>
<div class="block">Build a new filter that matches all features of a reading frame.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/FeatureFilter.HasAnnotation.html" title="class in org.biojava.bio.seq"><span class="strong">FeatureFilter.HasAnnotation</span></a> - Class in <a href="./org/biojava/bio/seq/package-summary.html">org.biojava.bio.seq</a></dt>
<dd>
<div class="block">Retrieve features that contain a given annotation with any value.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.HasAnnotation.html#FeatureFilter.HasAnnotation(java.lang.Object)">FeatureFilter.HasAnnotation(Object)</a></span> - Constructor for class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.HasAnnotation.html" title="class in org.biojava.bio.seq">FeatureFilter.HasAnnotation</a></dt>
<dd>
<div class="block">Make a new ByAnnotation that will accept features with an annotation
bundle containing any value associated with 'key'.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/FeatureFilter.Not.html" title="class in org.biojava.bio.seq"><span class="strong">FeatureFilter.Not</span></a> - Class in <a href="./org/biojava/bio/seq/package-summary.html">org.biojava.bio.seq</a></dt>
<dd>
<div class="block">A filter that returns all features not accepted by a child filter.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.Not.html#FeatureFilter.Not(org.biojava.bio.seq.FeatureFilter)">FeatureFilter.Not(FeatureFilter)</a></span> - Constructor for class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.Not.html" title="class in org.biojava.bio.seq">FeatureFilter.Not</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/FeatureFilter.OnlyChildren.html" title="class in org.biojava.bio.seq"><span class="strong">FeatureFilter.OnlyChildren</span></a> - Class in <a href="./org/biojava/bio/seq/package-summary.html">org.biojava.bio.seq</a></dt>
<dd>
<div class="block">Accepts features where all immediate children meet the supplied filter.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.OnlyChildren.html#FeatureFilter.OnlyChildren(org.biojava.bio.seq.FeatureFilter)">FeatureFilter.OnlyChildren(FeatureFilter)</a></span> - Constructor for class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.OnlyChildren.html" title="class in org.biojava.bio.seq">FeatureFilter.OnlyChildren</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/FeatureFilter.OnlyDescendants.html" title="class in org.biojava.bio.seq"><span class="strong">FeatureFilter.OnlyDescendants</span></a> - Class in <a href="./org/biojava/bio/seq/package-summary.html">org.biojava.bio.seq</a></dt>
<dd>
<div class="block">Accepts features where all descendants meet the supplied filter.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.OnlyDescendants.html#FeatureFilter.OnlyDescendants(org.biojava.bio.seq.FeatureFilter)">FeatureFilter.OnlyDescendants(FeatureFilter)</a></span> - Constructor for class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.OnlyDescendants.html" title="class in org.biojava.bio.seq">FeatureFilter.OnlyDescendants</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/FeatureFilter.Or.html" title="class in org.biojava.bio.seq"><span class="strong">FeatureFilter.Or</span></a> - Class in <a href="./org/biojava/bio/seq/package-summary.html">org.biojava.bio.seq</a></dt>
<dd>
<div class="block">A filter that returns all features accepted by at least one child filter.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.Or.html#FeatureFilter.Or(org.biojava.bio.seq.FeatureFilter, org.biojava.bio.seq.FeatureFilter)">FeatureFilter.Or(FeatureFilter, FeatureFilter)</a></span> - Constructor for class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.Or.html" title="class in org.biojava.bio.seq">FeatureFilter.Or</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/FeatureFilter.OverlapsLocation.html" title="class in org.biojava.bio.seq"><span class="strong">FeatureFilter.OverlapsLocation</span></a> - Class in <a href="./org/biojava/bio/seq/package-summary.html">org.biojava.bio.seq</a></dt>
<dd>
<div class="block">A filter that returns all features overlapping a location.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.OverlapsLocation.html#FeatureFilter.OverlapsLocation(org.biojava.bio.symbol.Location)">FeatureFilter.OverlapsLocation(Location)</a></span> - Constructor for class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.OverlapsLocation.html" title="class in org.biojava.bio.seq">FeatureFilter.OverlapsLocation</a></dt>
<dd>
<div class="block">Creates a filter that returns everything overlapping loc.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/FeatureFilter.ShadowContainedByLocation.html" title="class in org.biojava.bio.seq"><span class="strong">FeatureFilter.ShadowContainedByLocation</span></a> - Class in <a href="./org/biojava/bio/seq/package-summary.html">org.biojava.bio.seq</a></dt>
<dd>
<div class="block">A filter that accepts all features whose shadow is contained by a specified
<code>Location</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ShadowContainedByLocation.html#FeatureFilter.ShadowContainedByLocation(org.biojava.bio.symbol.Location)">FeatureFilter.ShadowContainedByLocation(Location)</a></span> - Constructor for class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ShadowContainedByLocation.html" title="class in org.biojava.bio.seq">FeatureFilter.ShadowContainedByLocation</a></dt>
<dd>
<div class="block">Creates a filter that returns everything contained within loc.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/FeatureFilter.ShadowOverlapsLocation.html" title="class in org.biojava.bio.seq"><span class="strong">FeatureFilter.ShadowOverlapsLocation</span></a> - Class in <a href="./org/biojava/bio/seq/package-summary.html">org.biojava.bio.seq</a></dt>
<dd>
<div class="block">A filter that accepts all features whose shadow overlaps a specified
<code>Location</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ShadowOverlapsLocation.html#FeatureFilter.ShadowOverlapsLocation(org.biojava.bio.symbol.Location)">FeatureFilter.ShadowOverlapsLocation(Location)</a></span> - Constructor for class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ShadowOverlapsLocation.html" title="class in org.biojava.bio.seq">FeatureFilter.ShadowOverlapsLocation</a></dt>
<dd>
<div class="block">Creates a filter that returns everything overlapping loc.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/FeatureFilter.StrandFilter.html" title="class in org.biojava.bio.seq"><span class="strong">FeatureFilter.StrandFilter</span></a> - Class in <a href="./org/biojava/bio/seq/package-summary.html">org.biojava.bio.seq</a></dt>
<dd>
<div class="block">Accept features with a given strandedness.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.StrandFilter.html#FeatureFilter.StrandFilter(org.biojava.bio.seq.StrandedFeature.Strand)">FeatureFilter.StrandFilter(StrandedFeature.Strand)</a></span> - Constructor for class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.StrandFilter.html" title="class in org.biojava.bio.seq">FeatureFilter.StrandFilter</a></dt>
<dd>
<div class="block">Build a new filter that matches all features of a given strand.</div>
</dd>
<dt><a href="./org/biojava/bio/program/xff/FeatureHandler.html" title="class in org.biojava.bio.program.xff"><span class="strong">FeatureHandler</span></a> - Class in <a href="./org/biojava/bio/program/xff/package-summary.html">org.biojava.bio.program.xff</a></dt>
<dd>
<div class="block">StAX handler for the basic <code>feature</code> type of XFF.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/xff/FeatureHandler.html#FeatureHandler(org.biojava.bio.program.xff.XFFFeatureSetHandler)">FeatureHandler(XFFFeatureSetHandler)</a></span> - Constructor for class org.biojava.bio.program.xff.<a href="./org/biojava/bio/program/xff/FeatureHandler.html" title="class in org.biojava.bio.program.xff">FeatureHandler</a></dt>
<dd>
<div class="block">Construct a new Feature handler, passing in an XFF-parsing environment.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/FeatureHolder.html" title="interface in org.biojava.bio.seq"><span class="strong">FeatureHolder</span></a> - Interface in <a href="./org/biojava/bio/seq/package-summary.html">org.biojava.bio.seq</a></dt>
<dd>
<div class="block">The interface for objects that contain features.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/FeatureHolder.EmptyFeatureHolder.html" title="class in org.biojava.bio.seq"><span class="strong">FeatureHolder.EmptyFeatureHolder</span></a> - Class in <a href="./org/biojava/bio/seq/package-summary.html">org.biojava.bio.seq</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureHolder.EmptyFeatureHolder.html#FeatureHolder.EmptyFeatureHolder()">FeatureHolder.EmptyFeatureHolder()</a></span> - Constructor for class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureHolder.EmptyFeatureHolder.html" title="class in org.biojava.bio.seq">FeatureHolder.EmptyFeatureHolder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleFeature.html#featureHolderAllocated()">featureHolderAllocated()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleFeature.html" title="class in org.biojava.bio.seq.impl">SimpleFeature</a></dt>
<dd>
<div class="block">A utility function to find out if the feature holder delegate has been
instantiated yet.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleSequence.html#featureHolderAllocated()">featureHolderAllocated()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleSequence.html" title="class in org.biojava.bio.seq.impl">SimpleSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureHolderUtils.html#featureHolderAsSet(org.biojava.bio.seq.FeatureHolder)">featureHolderAsSet(FeatureHolder)</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureHolderUtils.html" title="class in org.biojava.bio.seq">FeatureHolderUtils</a></dt>
<dd>
<div class="block">Returns a FeatureHolder as a Set of Features</div>
</dd>
<dt><a href="./org/biojava/bio/seq/FeatureHolderUtils.html" title="class in org.biojava.bio.seq"><span class="strong">FeatureHolderUtils</span></a> - Class in <a href="./org/biojava/bio/seq/package-summary.html">org.biojava.bio.seq</a></dt>
<dd>
<div class="block">This class intendes to provide some FeatureHolder utilities.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureHolderUtils.html#FeatureHolderUtils()">FeatureHolderUtils()</a></span> - Constructor for class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureHolderUtils.html" title="class in org.biojava.bio.seq">FeatureHolderUtils</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/impl/FeatureImpl.html" title="class in org.biojava.bio.seq.impl"><span class="strong">FeatureImpl</span></a> - Class in <a href="./org/biojava/bio/seq/impl/package-summary.html">org.biojava.bio.seq.impl</a></dt>
<dd>
<div class="block">Wrap up default sets of Feature implementations.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/FeatureImpl.html#FeatureImpl()">FeatureImpl()</a></span> - Constructor for class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/FeatureImpl.html" title="class in org.biojava.bio.seq.impl">FeatureImpl</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/gui/sequence/FeatureLabelRenderer.html" title="class in org.biojava.bio.gui.sequence"><span class="strong">FeatureLabelRenderer</span></a> - Class in <a href="./org/biojava/bio/gui/sequence/package-summary.html">org.biojava.bio.gui.sequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/FeatureLabelRenderer.html#FeatureLabelRenderer()">FeatureLabelRenderer()</a></span> - Constructor for class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/FeatureLabelRenderer.html" title="class in org.biojava.bio.gui.sequence">FeatureLabelRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/FeatureLabelRenderer.html#FeatureLabelRenderer(org.biojava.bio.gui.sequence.FeatureLabelRenderer.LabelMaker)">FeatureLabelRenderer(FeatureLabelRenderer.LabelMaker)</a></span> - Constructor for class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/FeatureLabelRenderer.html" title="class in org.biojava.bio.gui.sequence">FeatureLabelRenderer</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/gui/sequence/FeatureLabelRenderer.AnnotationLabelMaker.html" title="class in org.biojava.bio.gui.sequence"><span class="strong">FeatureLabelRenderer.AnnotationLabelMaker</span></a> - Class in <a href="./org/biojava/bio/gui/sequence/package-summary.html">org.biojava.bio.gui.sequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/FeatureLabelRenderer.AnnotationLabelMaker.html#FeatureLabelRenderer.AnnotationLabelMaker()">FeatureLabelRenderer.AnnotationLabelMaker()</a></span> - Constructor for class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/FeatureLabelRenderer.AnnotationLabelMaker.html" title="class in org.biojava.bio.gui.sequence">FeatureLabelRenderer.AnnotationLabelMaker</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/FeatureLabelRenderer.AnnotationLabelMaker.html#FeatureLabelRenderer.AnnotationLabelMaker(java.lang.Object)">FeatureLabelRenderer.AnnotationLabelMaker(Object)</a></span> - Constructor for class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/FeatureLabelRenderer.AnnotationLabelMaker.html" title="class in org.biojava.bio.gui.sequence">FeatureLabelRenderer.AnnotationLabelMaker</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/gui/sequence/FeatureLabelRenderer.LabelMaker.html" title="interface in org.biojava.bio.gui.sequence"><span class="strong">FeatureLabelRenderer.LabelMaker</span></a> - Interface in <a href="./org/biojava/bio/gui/sequence/package-summary.html">org.biojava.bio.gui.sequence</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/gui/sequence/FeatureLabelRenderer.SourceLabelMaker.html" title="class in org.biojava.bio.gui.sequence"><span class="strong">FeatureLabelRenderer.SourceLabelMaker</span></a> - Class in <a href="./org/biojava/bio/gui/sequence/package-summary.html">org.biojava.bio.gui.sequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/FeatureLabelRenderer.SourceLabelMaker.html#FeatureLabelRenderer.SourceLabelMaker()">FeatureLabelRenderer.SourceLabelMaker()</a></span> - Constructor for class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/FeatureLabelRenderer.SourceLabelMaker.html" title="class in org.biojava.bio.gui.sequence">FeatureLabelRenderer.SourceLabelMaker</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/gui/sequence/FeatureLabelRenderer.TypeLabelMaker.html" title="class in org.biojava.bio.gui.sequence"><span class="strong">FeatureLabelRenderer.TypeLabelMaker</span></a> - Class in <a href="./org/biojava/bio/gui/sequence/package-summary.html">org.biojava.bio.gui.sequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/FeatureLabelRenderer.TypeLabelMaker.html#FeatureLabelRenderer.TypeLabelMaker()">FeatureLabelRenderer.TypeLabelMaker()</a></span> - Constructor for class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/FeatureLabelRenderer.TypeLabelMaker.html" title="class in org.biojava.bio.gui.sequence">FeatureLabelRenderer.TypeLabelMaker</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/StAXFeatureHandler.html#featureListener">featureListener</a></span> - Variable in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/StAXFeatureHandler.html" title="class in org.biojava.bio.seq.io.agave">StAXFeatureHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/StAXPropertyHandler.html#featureListener">featureListener</a></span> - Variable in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/StAXPropertyHandler.html" title="class in org.biojava.bio.seq.io.agave">StAXPropertyHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game/StAXFeatureHandler.html#featureListener">featureListener</a></span> - Variable in class org.biojava.bio.seq.io.game.<a href="./org/biojava/bio/seq/io/game/StAXFeatureHandler.html" title="class in org.biojava.bio.seq.io.game">StAXFeatureHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game/StAXPropertyHandler.html#featureListener">featureListener</a></span> - Variable in class org.biojava.bio.seq.io.game.<a href="./org/biojava/bio/seq/io/game/StAXPropertyHandler.html" title="class in org.biojava.bio.seq.io.game">StAXPropertyHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/INSDseqFormat.html#FEATUREQUAL_NAME_TAG">FEATUREQUAL_NAME_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/INSDseqFormat.html" title="class in org.biojavax.bio.seq.io">INSDseqFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/INSDseqFormat.html#FEATUREQUAL_TAG">FEATUREQUAL_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/INSDseqFormat.html" title="class in org.biojavax.bio.seq.io">INSDseqFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/INSDseqFormat.html#FEATUREQUAL_VALUE_TAG">FEATUREQUAL_VALUE_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/INSDseqFormat.html" title="class in org.biojavax.bio.seq.io">INSDseqFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/INSDseqFormat.html#FEATUREQUALS_GROUP_TAG">FEATUREQUALS_GROUP_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/INSDseqFormat.html" title="class in org.biojavax.bio.seq.io">INSDseqFormat</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/FeatureRealizer.html" title="interface in org.biojava.bio.seq"><span class="strong">FeatureRealizer</span></a> - Interface in <a href="./org/biojava/bio/seq/package-summary.html">org.biojava.bio.seq</a></dt>
<dd>
<div class="block">Interface for translators which map from Feature.Template
instances to real Feature objects.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichFeature.Template.html#featureRelationshipSet">featureRelationshipSet</a></span> - Variable in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichFeature.Template.html" title="class in org.biojavax.bio.seq">RichFeature.Template</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/gui/sequence/FeatureRenderer.html" title="interface in org.biojava.bio.gui.sequence"><span class="strong">FeatureRenderer</span></a> - Interface in <a href="./org/biojava/bio/gui/sequence/package-summary.html">org.biojava.bio.gui.sequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/DASSequence.html#features()">features()</a></span> - Method in class org.biojava.bio.program.das.<a href="./org/biojava/bio/program/das/DASSequence.html" title="class in org.biojava.bio.program.das">DASSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/Feature.html#features()">features()</a></span> - Method in interface org.biojava.bio.seq.<a href="./org/biojava/bio/seq/Feature.html" title="interface in org.biojava.bio.seq">Feature</a></dt>
<dd>
<div class="block">Iterate over any child features which are held by this
feature.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureHolder.EmptyFeatureHolder.html#features()">features()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureHolder.EmptyFeatureHolder.html" title="class in org.biojava.bio.seq">FeatureHolder.EmptyFeatureHolder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureHolder.html#FEATURES">FEATURES</a></span> - Static variable in interface org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureHolder.html" title="interface in org.biojava.bio.seq">FeatureHolder</a></dt>
<dd>
<div class="block">Signals that features have been added or removed directly within this
FeatureHolder.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureHolder.html#features()">features()</a></span> - Method in interface org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureHolder.html" title="interface in org.biojava.bio.seq">FeatureHolder</a></dt>
<dd>
<div class="block">Iterate over the features in no well defined order.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/DummySequence.html#features()">features()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/DummySequence.html" title="class in org.biojava.bio.seq.impl">DummySequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/LazyFilterFeatureHolder.html#features()">features()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/LazyFilterFeatureHolder.html" title="class in org.biojava.bio.seq.impl">LazyFilterFeatureHolder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/RevCompSequence.html#features()">features()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/RevCompSequence.html" title="class in org.biojava.bio.seq.impl">RevCompSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleFeature.html#features()">features()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleFeature.html" title="class in org.biojava.bio.seq.impl">SimpleFeature</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleGappedSequence.html#features()">features()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleGappedSequence.html" title="class in org.biojava.bio.seq.impl">SimpleGappedSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleSequence.html#features()">features()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleSequence.html" title="class in org.biojava.bio.seq.impl">SimpleSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SubSequence.html#features()">features()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SubSequence.html" title="class in org.biojava.bio.seq.impl">SubSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/ViewSequence.html#features()">features()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/ViewSequence.html" title="class in org.biojava.bio.seq.impl">ViewSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/GenbankProcessor.html#features">features</a></span> - Variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/GenbankProcessor.html" title="class in org.biojava.bio.seq.io">GenbankProcessor</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/LazyFeatureHolder.html#features()">features()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/LazyFeatureHolder.html" title="class in org.biojava.bio.seq">LazyFeatureHolder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/MergeFeatureHolder.html#features()">features()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/MergeFeatureHolder.html" title="class in org.biojava.bio.seq">MergeFeatureHolder</a></dt>
<dd>
<div class="block">Iterate over all the features in all child FeatureHolders.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/NewSimpleAssembly.html#features()">features()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/NewSimpleAssembly.html" title="class in org.biojava.bio.seq">NewSimpleAssembly</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/projection/ProjectedFeature.html#features()">features()</a></span> - Method in class org.biojava.bio.seq.projection.<a href="./org/biojava/bio/seq/projection/ProjectedFeature.html" title="class in org.biojava.bio.seq.projection">ProjectedFeature</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/projection/ProjectedFeatureHolder.html#features()">features()</a></span> - Method in class org.biojava.bio.seq.projection.<a href="./org/biojava/bio/seq/projection/ProjectedFeatureHolder.html" title="class in org.biojava.bio.seq.projection">ProjectedFeatureHolder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/SimpleAssembly.html#features()">features()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/SimpleAssembly.html" title="class in org.biojava.bio.seq">SimpleAssembly</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/SimpleFeatureHolder.html#features()">features()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/SimpleFeatureHolder.html" title="class in org.biojava.bio.seq">SimpleFeatureHolder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichFeature.html#features()">features()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichFeature.html" title="class in org.biojavax.bio.seq">SimpleRichFeature</a></dt>
<dd>
<div class="block">Iterate over any child features which are held by this
feature.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/ThinRichSequence.html#features()">features()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/ThinRichSequence.html" title="class in org.biojavax.bio.seq">ThinRichSequence</a></dt>
<dd>
<div class="block">Iterate over the features in no well defined order.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/INSDseqFormat.html#FEATURES_GROUP_TAG">FEATURES_GROUP_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/INSDseqFormat.html" title="class in org.biojavax.bio.seq.io">INSDseqFormat</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/gui/sequence/FeatureSource.html" title="interface in org.biojava.bio.gui.sequence"><span class="strong">FeatureSource</span></a> - Interface in <a href="./org/biojava/bio/gui/sequence/package-summary.html">org.biojava.bio.gui.sequence</a></dt>
<dd>
<div class="block">A closure that allows AbstractPeptideDigestRenderer implementations to obtain the features of the rendered sequence.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/FeatureTableParser.html" title="class in org.biojava.bio.seq.io"><span class="strong">FeatureTableParser</span></a> - Class in <a href="./org/biojava/bio/seq/io/package-summary.html">org.biojava.bio.seq.io</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>Use org.biojavax.bio.seq.io framework instead</i></div>
</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/StAXFeatureHandler.html#featureTemplate">featureTemplate</a></span> - Variable in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/StAXFeatureHandler.html" title="class in org.biojava.bio.seq.io.agave">StAXFeatureHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game/StAXFeatureHandler.html#featureTemplate">featureTemplate</a></span> - Variable in class org.biojava.bio.seq.io.game.<a href="./org/biojava/bio/seq/io/game/StAXFeatureHandler.html" title="class in org.biojava.bio.seq.io.game">StAXFeatureHandler</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/gui/FeatureTree.html" title="class in org.biojava.bio.gui"><span class="strong">FeatureTree</span></a> - Class in <a href="./org/biojava/bio/gui/package-summary.html">org.biojava.bio.gui</a></dt>
<dd>
<div class="block">FeatureTree is GUI tree to display the features and annotations
of the sequences in a <code>SequenceDB</code> Nested Features are
displayed as expandable leaves.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/FeatureTree.html#FeatureTree()">FeatureTree()</a></span> - Constructor for class org.biojava.bio.gui.<a href="./org/biojava/bio/gui/FeatureTree.html" title="class in org.biojava.bio.gui">FeatureTree</a></dt>
<dd>
<div class="block">Create a new FeatureTree</div>
</dd>
<dt><a href="./org/biojava/bio/seq/FeatureTypes.html" title="class in org.biojava.bio.seq"><span class="strong">FeatureTypes</span></a> - Class in <a href="./org/biojava/bio/seq/package-summary.html">org.biojava.bio.seq</a></dt>
<dd>
<div class="block">Registry of known types of features.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureTypes.html#FeatureTypes()">FeatureTypes()</a></span> - Constructor for class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureTypes.html" title="class in org.biojava.bio.seq">FeatureTypes</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/FeatureTypes.Repository.html" title="interface in org.biojava.bio.seq"><span class="strong">FeatureTypes.Repository</span></a> - Interface in <a href="./org/biojava/bio/seq/package-summary.html">org.biojava.bio.seq</a></dt>
<dd>
<div class="block">A named collection of Types.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/FeatureTypes.RepositoryImpl.html" title="class in org.biojava.bio.seq"><span class="strong">FeatureTypes.RepositoryImpl</span></a> - Class in <a href="./org/biojava/bio/seq/package-summary.html">org.biojava.bio.seq</a></dt>
<dd>
<div class="block">A simple implementation of a Repository.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureTypes.RepositoryImpl.html#FeatureTypes.RepositoryImpl(java.lang.String)">FeatureTypes.RepositoryImpl(String)</a></span> - Constructor for class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureTypes.RepositoryImpl.html" title="class in org.biojava.bio.seq">FeatureTypes.RepositoryImpl</a></dt>
<dd>
<div class="block">Create a named repository.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/FeatureTypes.Type.html" title="interface in org.biojava.bio.seq"><span class="strong">FeatureTypes.Type</span></a> - Interface in <a href="./org/biojava/bio/seq/package-summary.html">org.biojava.bio.seq</a></dt>
<dd>
<div class="block">A type of feature.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/BioIndex.html#fetch(java.lang.String)">fetch(String)</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/BioIndex.html" title="class in org.biojava.bio.seq.db">BioIndex</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/EmblCDROMIndexStore.html#fetch(java.lang.String)">fetch(String)</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/EmblCDROMIndexStore.html" title="class in org.biojava.bio.seq.db">EmblCDROMIndexStore</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/IndexStore.html#fetch(java.lang.String)">fetch(String)</a></span> - Method in interface org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/IndexStore.html" title="interface in org.biojava.bio.seq.db">IndexStore</a></dt>
<dd>
<div class="block">Fetch an Index based upon an ID.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/TabIndexStore.html#fetch(java.lang.String)">fetch(String)</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/TabIndexStore.html" title="class in org.biojava.bio.seq.db">TabIndexStore</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/db/FetchURL.html" title="class in org.biojava.bio.seq.db"><span class="strong">FetchURL</span></a> - Class in <a href="./org/biojava/bio/seq/db/package-summary.html">org.biojava.bio.seq.db</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/FetchURL.html#FetchURL(java.lang.String, java.lang.String)">FetchURL(String, String)</a></span> - Constructor for class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/FetchURL.html" title="class in org.biojava.bio.seq.db">FetchURL</a></dt>
<dd>
<div class="block">Constructs a fetchURL object based on the database name
and specified return format of sequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/SimpleMMcifParser.html#FIELD_LINE">FIELD_LINE</a></span> - Static variable in class org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/SimpleMMcifParser.html" title="class in org.biojava.bio.structure.io.mmcif">SimpleMMcifParser</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/utils/FileAsList.html" title="class in org.biojava.utils"><span class="strong">FileAsList</span></a> - Class in <a href="./org/biojava/utils/package-summary.html">org.biojava.utils</a></dt>
<dd>
<div class="block"><code>FileAsList</code> creates a writable <code>List</code>
implementation backed by a random access file.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/FileAsList.html#FileAsList(java.io.File, int)">FileAsList(File, int)</a></span> - Constructor for class org.biojava.utils.<a href="./org/biojava/utils/FileAsList.html" title="class in org.biojava.utils">FileAsList</a></dt>
<dd>
<div class="block">Creates a new <code>FileAsList</code> and corresponding backing
file.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/FileAsList.html#FileAsList(java.io.File, boolean)">FileAsList(File, boolean)</a></span> - Constructor for class org.biojava.utils.<a href="./org/biojava/utils/FileAsList.html" title="class in org.biojava.utils">FileAsList</a></dt>
<dd>
<div class="block">Creates a new <code>FileAsList</code> instance from an existing
backing file.</div>
</dd>
<dt><a href="./org/biojava/bio/structure/io/FileConvert.html" title="class in org.biojava.bio.structure.io"><span class="strong">FileConvert</span></a> - Class in <a href="./org/biojava/bio/structure/io/package-summary.html">org.biojava.bio.structure.io</a></dt>
<dd>
<div class="block">Methods to convert a structure object into different file formats.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/FileConvert.html#FileConvert(org.biojava.bio.structure.Structure)">FileConvert(Structure)</a></span> - Constructor for class org.biojava.bio.structure.io.<a href="./org/biojava/bio/structure/io/FileConvert.html" title="class in org.biojava.bio.structure.io">FileConvert</a></dt>
<dd>
<div class="block">Constructs a FileConvert object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOTools.html#fileToBiojava(java.lang.String, java.lang.String, java.io.BufferedReader)">fileToBiojava(String, String, BufferedReader)</a></span> - Static method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOTools.html" title="class in org.biojava.bio.seq.io">SeqIOTools</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Reads a file with the specified format and alphabet</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOTools.html#fileToBiojava(int, java.io.BufferedReader)">fileToBiojava(int, BufferedReader)</a></span> - Static method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOTools.html" title="class in org.biojava.bio.seq.io">SeqIOTools</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Reads a file and returns the corresponding Biojava object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/AbstractBeadRenderer.html#FILL">FILL</a></span> - Static variable in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/AbstractBeadRenderer.html" title="class in org.biojava.bio.gui.sequence">AbstractBeadRenderer</a></dt>
<dd>
<div class="block">Constant <code>FILL</code> indicating a change to the fill of
the features.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/BasicFeatureRenderer.html#FILL">FILL</a></span> - Static variable in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/BasicFeatureRenderer.html" title="class in org.biojava.bio.gui.sequence">BasicFeatureRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/TickFeatureRenderer.html#FILL">FILL</a></span> - Static variable in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/TickFeatureRenderer.html" title="class in org.biojava.bio.gui.sequence">TickFeatureRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SwissprotFileFormer.html#fillBuffer(java.lang.StringBuffer, int)">fillBuffer(StringBuffer, int)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SwissprotFileFormer.html" title="class in org.biojava.bio.seq.io">SwissprotFileFormer</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Simple method that adds spaces onto the buffer passed in.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.html#fillColors">fillColors</a></span> - Variable in class org.biojava.bio.chromatogram.graphic.<a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.html" title="class in org.biojava.bio.chromatogram.graphic">ChromatogramGraphic</a></dt>
<dd>
<div class="block">The map containing the fill colors for callboxes.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/DNAStyle.html#fillPaint(org.biojava.bio.symbol.Symbol)">fillPaint(Symbol)</a></span> - Method in class org.biojava.bio.gui.<a href="./org/biojava/bio/gui/DNAStyle.html" title="class in org.biojava.bio.gui">DNAStyle</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/PlainStyle.html#fillPaint(org.biojava.bio.symbol.Symbol)">fillPaint(Symbol)</a></span> - Method in class org.biojava.bio.gui.<a href="./org/biojava/bio/gui/PlainStyle.html" title="class in org.biojava.bio.gui">PlainStyle</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/SimpleSymbolStyle.html#fillPaint(org.biojava.bio.symbol.Symbol)">fillPaint(Symbol)</a></span> - Method in class org.biojava.bio.gui.<a href="./org/biojava/bio/gui/SimpleSymbolStyle.html" title="class in org.biojava.bio.gui">SimpleSymbolStyle</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/SymbolStyle.html#fillPaint(org.biojava.bio.symbol.Symbol)">fillPaint(Symbol)</a></span> - Method in interface org.biojava.bio.gui.<a href="./org/biojava/bio/gui/SymbolStyle.html" title="interface in org.biojava.bio.gui">SymbolStyle</a></dt>
<dd>
<div class="block">Return the fill paint for a symbol.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleFeature.html#fillTemplate(org.biojava.bio.seq.Feature.Template)">fillTemplate(Feature.Template)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleFeature.html" title="class in org.biojava.bio.seq.impl">SimpleFeature</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleFramedFeature.html#fillTemplate(org.biojava.bio.seq.FramedFeature.Template)">fillTemplate(FramedFeature.Template)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleFramedFeature.html" title="class in org.biojava.bio.seq.impl">SimpleFramedFeature</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleHomologyFeature.html#fillTemplate(org.biojava.bio.seq.homol.HomologyFeature.Template)">fillTemplate(HomologyFeature.Template)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleHomologyFeature.html" title="class in org.biojava.bio.seq.impl">SimpleHomologyFeature</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleRemoteFeature.html#fillTemplate(org.biojava.bio.seq.RemoteFeature.Template)">fillTemplate(RemoteFeature.Template)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleRemoteFeature.html" title="class in org.biojava.bio.seq.impl">SimpleRemoteFeature</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleSimilarityPairFeature.html#fillTemplate(org.biojava.bio.seq.homol.SimilarityPairFeature.Template)">fillTemplate(SimilarityPairFeature.Template)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleSimilarityPairFeature.html" title="class in org.biojava.bio.seq.impl">SimpleSimilarityPairFeature</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleStrandedFeature.html#fillTemplate(org.biojava.bio.seq.StrandedFeature.Template)">fillTemplate(StrandedFeature.Template)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleStrandedFeature.html" title="class in org.biojava.bio.seq.impl">SimpleStrandedFeature</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/annodb/AnnotationDB.html#filter(org.biojava.bio.AnnotationType)">filter(AnnotationType)</a></span> - Method in interface org.biojava.bio.annodb.<a href="./org/biojava/bio/annodb/AnnotationDB.html" title="interface in org.biojava.bio.annodb">AnnotationDB</a></dt>
<dd>
<div class="block">Find all Annotation instances in this DB that are of a particular type.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/annodb/IndexedAnnotationDB.html#filter(org.biojava.bio.AnnotationType)">filter(AnnotationType)</a></span> - Method in class org.biojava.bio.annodb.<a href="./org/biojava/bio/annodb/IndexedAnnotationDB.html" title="class in org.biojava.bio.annodb">IndexedAnnotationDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/annodb/LazyFilteredAnnotationDB.html#filter(org.biojava.bio.AnnotationType)">filter(AnnotationType)</a></span> - Method in class org.biojava.bio.annodb.<a href="./org/biojava/bio/annodb/LazyFilteredAnnotationDB.html" title="class in org.biojava.bio.annodb">LazyFilteredAnnotationDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/annodb/LazySearchedAnnotationDB.html#filter(org.biojava.bio.AnnotationType)">filter(AnnotationType)</a></span> - Method in class org.biojava.bio.annodb.<a href="./org/biojava/bio/annodb/LazySearchedAnnotationDB.html" title="class in org.biojava.bio.annodb">LazySearchedAnnotationDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/annodb/MergingAnnotationDB.html#filter(org.biojava.bio.AnnotationType)">filter(AnnotationType)</a></span> - Method in class org.biojava.bio.annodb.<a href="./org/biojava/bio/annodb/MergingAnnotationDB.html" title="class in org.biojava.bio.annodb">MergingAnnotationDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/annodb/SimpleAnnotationDB.html#filter(org.biojava.bio.AnnotationType)">filter(AnnotationType)</a></span> - Method in class org.biojava.bio.annodb.<a href="./org/biojava/bio/annodb/SimpleAnnotationDB.html" title="class in org.biojava.bio.annodb">SimpleAnnotationDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/FilteringRenderer.html#FILTER">FILTER</a></span> - Static variable in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/FilteringRenderer.html" title="class in org.biojava.bio.gui.sequence">FilteringRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/FilteringRenderer.html#filter">filter</a></span> - Variable in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/FilteringRenderer.html" title="class in org.biojava.bio.gui.sequence">FilteringRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PairwiseFilteringRenderer.html#FILTER">FILTER</a></span> - Static variable in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PairwiseFilteringRenderer.html" title="class in org.biojava.bio.gui.sequence">PairwiseFilteringRenderer</a></dt>
<dd>
<div class="block">Constant <code>FILTER</code> indicating a change to the
renderer's filter.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PairwiseFilteringRenderer.html#filter">filter</a></span> - Variable in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PairwiseFilteringRenderer.html" title="class in org.biojava.bio.gui.sequence">PairwiseFilteringRenderer</a></dt>
<dd>
<div class="block"><code>filter</code> is the filter applied to both
<code>FeatureHolder</code>s.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/DASSequence.html#filter(org.biojava.bio.seq.FeatureFilter)">filter(FeatureFilter)</a></span> - Method in class org.biojava.bio.program.das.<a href="./org/biojava/bio/program/das/DASSequence.html" title="class in org.biojava.bio.program.das">DASSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/DASSequence.html#filter(org.biojava.bio.seq.FeatureFilter, boolean)">filter(FeatureFilter, boolean)</a></span> - Method in class org.biojava.bio.program.das.<a href="./org/biojava/bio/program/das/DASSequence.html" title="class in org.biojava.bio.program.das">DASSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/DASSequenceDB.html#filter(org.biojava.bio.seq.FeatureFilter)">filter(FeatureFilter)</a></span> - Method in class org.biojava.bio.program.das.<a href="./org/biojava/bio/program/das/DASSequenceDB.html" title="class in org.biojava.bio.program.das">DASSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFEntrySet.html#filter(org.biojava.bio.program.gff.GFFRecordFilter)">filter(GFFRecordFilter)</a></span> - Method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFEntrySet.html" title="class in org.biojava.bio.program.gff">GFFEntrySet</a></dt>
<dd>
<div class="block">Filter this entry set into another set.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/AbstractOrthologueSet.html#filter(org.biojava.bio.program.homologene.OrthologueFilter)">filter(OrthologueFilter)</a></span> - Method in class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/AbstractOrthologueSet.html" title="class in org.biojava.bio.program.homologene">AbstractOrthologueSet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/AbstractOrthoPairCollection.html#filter(org.biojava.bio.program.homologene.OrthoPairSetFilter)">filter(OrthoPairSetFilter)</a></span> - Method in class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/AbstractOrthoPairCollection.html" title="class in org.biojava.bio.program.homologene">AbstractOrthoPairCollection</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/AbstractOrthoPairSet.html#filter(org.biojava.bio.program.homologene.OrthoPairFilter)">filter(OrthoPairFilter)</a></span> - Method in class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/AbstractOrthoPairSet.html" title="class in org.biojava.bio.program.homologene">AbstractOrthoPairSet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/HomologeneDB.html#filter(org.biojava.bio.program.homologene.OrthoPairSetFilter)">filter(OrthoPairSetFilter)</a></span> - Method in interface org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/HomologeneDB.html" title="interface in org.biojava.bio.program.homologene">HomologeneDB</a></dt>
<dd>
<div class="block">Filter the database for a specified group.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/OrthologueSet.html#filter(org.biojava.bio.program.homologene.OrthologueFilter)">filter(OrthologueFilter)</a></span> - Method in interface org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/OrthologueSet.html" title="interface in org.biojava.bio.program.homologene">OrthologueSet</a></dt>
<dd>
<div class="block">Filter the contents of a set.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/OrthoPairCollection.html#filter(org.biojava.bio.program.homologene.OrthoPairSetFilter)">filter(OrthoPairSetFilter)</a></span> - Method in interface org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/OrthoPairCollection.html" title="interface in org.biojava.bio.program.homologene">OrthoPairCollection</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/OrthoPairSet.html#filter(org.biojava.bio.program.homologene.OrthoPairFilter)">filter(OrthoPairFilter)</a></span> - Method in interface org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/OrthoPairSet.html" title="interface in org.biojava.bio.program.homologene">OrthoPairSet</a></dt>
<dd>
<div class="block">filter an OrthoPairSet</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/AbstractFeatureHolder.html#filter(org.biojava.bio.seq.FeatureFilter)">filter(FeatureFilter)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/AbstractFeatureHolder.html" title="class in org.biojava.bio.seq">AbstractFeatureHolder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/AbstractFeatureHolder.html#filter(org.biojava.bio.seq.FeatureFilter, boolean)">filter(FeatureFilter, boolean)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/AbstractFeatureHolder.html" title="class in org.biojava.bio.seq">AbstractFeatureHolder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/AbstractSequenceDB.html#filter(org.biojava.bio.seq.FeatureFilter)">filter(FeatureFilter)</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/AbstractSequenceDB.html" title="class in org.biojava.bio.seq.db">AbstractSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/biosql/BioSQLSequenceDB.html#filter(org.biojava.bio.seq.FeatureFilter)">filter(FeatureFilter)</a></span> - Method in class org.biojava.bio.seq.db.biosql.<a href="./org/biojava/bio/seq/db/biosql/BioSQLSequenceDB.html" title="class in org.biojava.bio.seq.db.biosql">BioSQLSequenceDB</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/SequenceDB.html#filter(org.biojava.bio.seq.FeatureFilter)">filter(FeatureFilter)</a></span> - Method in interface org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/SequenceDB.html" title="interface in org.biojava.bio.seq.db">SequenceDB</a></dt>
<dd>
<div class="block">Query features attached to all sequences in this database.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureHolder.EmptyFeatureHolder.html#filter(org.biojava.bio.seq.FeatureFilter, boolean)">filter(FeatureFilter, boolean)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureHolder.EmptyFeatureHolder.html" title="class in org.biojava.bio.seq">FeatureHolder.EmptyFeatureHolder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureHolder.EmptyFeatureHolder.html#filter(org.biojava.bio.seq.FeatureFilter)">filter(FeatureFilter)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureHolder.EmptyFeatureHolder.html" title="class in org.biojava.bio.seq">FeatureHolder.EmptyFeatureHolder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureHolder.html#filter(org.biojava.bio.seq.FeatureFilter, boolean)">filter(FeatureFilter, boolean)</a></span> - Method in interface org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureHolder.html" title="interface in org.biojava.bio.seq">FeatureHolder</a></dt>
<dd>
<div class="block">Return a new FeatureHolder that contains all of the children of this one
that passed the filter fc.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureHolder.html#filter(org.biojava.bio.seq.FeatureFilter)">filter(FeatureFilter)</a></span> - Method in interface org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureHolder.html" title="interface in org.biojava.bio.seq">FeatureHolder</a></dt>
<dd>
<div class="block">Query this set of features using a supplied <code>FeatureFilter</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/DummySequence.html#filter(org.biojava.bio.seq.FeatureFilter, boolean)">filter(FeatureFilter, boolean)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/DummySequence.html" title="class in org.biojava.bio.seq.impl">DummySequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/DummySequence.html#filter(org.biojava.bio.seq.FeatureFilter)">filter(FeatureFilter)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/DummySequence.html" title="class in org.biojava.bio.seq.impl">DummySequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/LazyFilterFeatureHolder.html#filter(org.biojava.bio.seq.FeatureFilter)">filter(FeatureFilter)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/LazyFilterFeatureHolder.html" title="class in org.biojava.bio.seq.impl">LazyFilterFeatureHolder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/LazyFilterFeatureHolder.html#filter(org.biojava.bio.seq.FeatureFilter, boolean)">filter(FeatureFilter, boolean)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/LazyFilterFeatureHolder.html" title="class in org.biojava.bio.seq.impl">LazyFilterFeatureHolder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/RevCompSequence.html#filter(org.biojava.bio.seq.FeatureFilter)">filter(FeatureFilter)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/RevCompSequence.html" title="class in org.biojava.bio.seq.impl">RevCompSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/RevCompSequence.html#filter(org.biojava.bio.seq.FeatureFilter, boolean)">filter(FeatureFilter, boolean)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/RevCompSequence.html" title="class in org.biojava.bio.seq.impl">RevCompSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleFeature.html#filter(org.biojava.bio.seq.FeatureFilter)">filter(FeatureFilter)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleFeature.html" title="class in org.biojava.bio.seq.impl">SimpleFeature</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleFeature.html#filter(org.biojava.bio.seq.FeatureFilter, boolean)">filter(FeatureFilter, boolean)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleFeature.html" title="class in org.biojava.bio.seq.impl">SimpleFeature</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleGappedSequence.html#filter(org.biojava.bio.seq.FeatureFilter)">filter(FeatureFilter)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleGappedSequence.html" title="class in org.biojava.bio.seq.impl">SimpleGappedSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleGappedSequence.html#filter(org.biojava.bio.seq.FeatureFilter, boolean)">filter(FeatureFilter, boolean)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleGappedSequence.html" title="class in org.biojava.bio.seq.impl">SimpleGappedSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleSequence.html#filter(org.biojava.bio.seq.FeatureFilter)">filter(FeatureFilter)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleSequence.html" title="class in org.biojava.bio.seq.impl">SimpleSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleSequence.html#filter(org.biojava.bio.seq.FeatureFilter, boolean)">filter(FeatureFilter, boolean)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleSequence.html" title="class in org.biojava.bio.seq.impl">SimpleSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SubSequence.html#filter(org.biojava.bio.seq.FeatureFilter, boolean)">filter(FeatureFilter, boolean)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SubSequence.html" title="class in org.biojava.bio.seq.impl">SubSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SubSequence.html#filter(org.biojava.bio.seq.FeatureFilter)">filter(FeatureFilter)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SubSequence.html" title="class in org.biojava.bio.seq.impl">SubSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/ViewSequence.html#filter(org.biojava.bio.seq.FeatureFilter, boolean)">filter(FeatureFilter, boolean)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/ViewSequence.html" title="class in org.biojava.bio.seq.impl">ViewSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/ViewSequence.html#filter(org.biojava.bio.seq.FeatureFilter)">filter(FeatureFilter)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/ViewSequence.html" title="class in org.biojava.bio.seq.impl">ViewSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/LazyFeatureHolder.html#filter(org.biojava.bio.seq.FeatureFilter)">filter(FeatureFilter)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/LazyFeatureHolder.html" title="class in org.biojava.bio.seq">LazyFeatureHolder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/LazyFeatureHolder.html#filter(org.biojava.bio.seq.FeatureFilter, boolean)">filter(FeatureFilter, boolean)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/LazyFeatureHolder.html" title="class in org.biojava.bio.seq">LazyFeatureHolder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/MergeFeatureHolder.html#filter(org.biojava.bio.seq.FeatureFilter, boolean)">filter(FeatureFilter, boolean)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/MergeFeatureHolder.html" title="class in org.biojava.bio.seq">MergeFeatureHolder</a></dt>
<dd>
<div class="block">When applied to a MergeFeatureHolder, this filters each child
FeatureHolder independently.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/NewSimpleAssembly.html#filter(org.biojava.bio.seq.FeatureFilter, boolean)">filter(FeatureFilter, boolean)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/NewSimpleAssembly.html" title="class in org.biojava.bio.seq">NewSimpleAssembly</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/NewSimpleAssembly.html#filter(org.biojava.bio.seq.FeatureFilter)">filter(FeatureFilter)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/NewSimpleAssembly.html" title="class in org.biojava.bio.seq">NewSimpleAssembly</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/projection/ProjectedFeature.html#filter(org.biojava.bio.seq.FeatureFilter)">filter(FeatureFilter)</a></span> - Method in class org.biojava.bio.seq.projection.<a href="./org/biojava/bio/seq/projection/ProjectedFeature.html" title="class in org.biojava.bio.seq.projection">ProjectedFeature</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/projection/ProjectedFeature.html#filter(org.biojava.bio.seq.FeatureFilter, boolean)">filter(FeatureFilter, boolean)</a></span> - Method in class org.biojava.bio.seq.projection.<a href="./org/biojava/bio/seq/projection/ProjectedFeature.html" title="class in org.biojava.bio.seq.projection">ProjectedFeature</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/projection/ProjectedFeatureHolder.html#filter(org.biojava.bio.seq.FeatureFilter)">filter(FeatureFilter)</a></span> - Method in class org.biojava.bio.seq.projection.<a href="./org/biojava/bio/seq/projection/ProjectedFeatureHolder.html" title="class in org.biojava.bio.seq.projection">ProjectedFeatureHolder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/projection/ProjectedFeatureHolder.html#filter(org.biojava.bio.seq.FeatureFilter, boolean)">filter(FeatureFilter, boolean)</a></span> - Method in class org.biojava.bio.seq.projection.<a href="./org/biojava/bio/seq/projection/ProjectedFeatureHolder.html" title="class in org.biojava.bio.seq.projection">ProjectedFeatureHolder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/SimpleAssembly.html#filter(org.biojava.bio.seq.FeatureFilter, boolean)">filter(FeatureFilter, boolean)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/SimpleAssembly.html" title="class in org.biojava.bio.seq">SimpleAssembly</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/SimpleAssembly.html#filter(org.biojava.bio.seq.FeatureFilter)">filter(FeatureFilter)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/SimpleAssembly.html" title="class in org.biojava.bio.seq">SimpleAssembly</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/AbstractRichSequenceDB.html#filter(org.biojava.bio.seq.FeatureFilter)">filter(FeatureFilter)</a></span> - Method in class org.biojavax.bio.db.<a href="./org/biojavax/bio/db/AbstractRichSequenceDB.html" title="class in org.biojavax.bio.db">AbstractRichSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLRichSequenceDB.html#filter(org.biojava.bio.seq.FeatureFilter)">filter(FeatureFilter)</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLRichSequenceDB.html" title="class in org.biojavax.bio.db.biosql">BioSQLRichSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichFeature.html#filter(org.biojava.bio.seq.FeatureFilter)">filter(FeatureFilter)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichFeature.html" title="class in org.biojavax.bio.seq">SimpleRichFeature</a></dt>
<dd>
<div class="block">Query this set of features using a supplied <code>FeatureFilter</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichFeature.html#filter(org.biojava.bio.seq.FeatureFilter, boolean)">filter(FeatureFilter, boolean)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichFeature.html" title="class in org.biojavax.bio.seq">SimpleRichFeature</a></dt>
<dd>
<div class="block">Return a new FeatureHolder that contains all of the children of this one
that passed the filter fc.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/ThinRichSequence.html#filter(org.biojava.bio.seq.FeatureFilter, boolean)">filter(FeatureFilter, boolean)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/ThinRichSequence.html" title="class in org.biojavax.bio.seq">ThinRichSequence</a></dt>
<dd>
<div class="block">Return a new FeatureHolder that contains all of the children of this one
that passed the filter fc.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/ThinRichSequence.html#filter(org.biojava.bio.seq.FeatureFilter)">filter(FeatureFilter)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/ThinRichSequence.html" title="class in org.biojavax.bio.seq">ThinRichSequence</a></dt>
<dd>
<div class="block">Query this set of features using a supplied <code>FeatureFilter</code>.</div>
</dd>
<dt><a href="./org/biojava/bio/search/FilteringContentHandler.html" title="class in org.biojava.bio.search"><span class="strong">FilteringContentHandler</span></a> - Class in <a href="./org/biojava/bio/search/package-summary.html">org.biojava.bio.search</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/FilteringContentHandler.html#FilteringContentHandler(org.biojava.bio.search.BlastLikeSearchFilter, org.biojava.bio.search.SearchContentHandler)">FilteringContentHandler(BlastLikeSearchFilter, SearchContentHandler)</a></span> - Constructor for class org.biojava.bio.search.<a href="./org/biojava/bio/search/FilteringContentHandler.html" title="class in org.biojava.bio.search">FilteringContentHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/FilteringContentHandler.html#FilteringContentHandler(org.biojava.bio.search.BlastLikeSearchFilter)">FilteringContentHandler(BlastLikeSearchFilter)</a></span> - Constructor for class org.biojava.bio.search.<a href="./org/biojava/bio/search/FilteringContentHandler.html" title="class in org.biojava.bio.search">FilteringContentHandler</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/search/FilteringContentHandler.FilterVisitor.html" title="class in org.biojava.bio.search"><span class="strong">FilteringContentHandler.FilterVisitor</span></a> - Class in <a href="./org/biojava/bio/search/package-summary.html">org.biojava.bio.search</a></dt>
<dd>
<div class="block">Visitor class that parses the filter tree</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/FilteringContentHandler.FilterVisitor.html#FilteringContentHandler.FilterVisitor()">FilteringContentHandler.FilterVisitor()</a></span> - Constructor for class org.biojava.bio.search.<a href="./org/biojava/bio/search/FilteringContentHandler.FilterVisitor.html" title="class in org.biojava.bio.search">FilteringContentHandler.FilterVisitor</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/gui/sequence/FilteringRenderer.html" title="class in org.biojava.bio.gui.sequence"><span class="strong">FilteringRenderer</span></a> - Class in <a href="./org/biojava/bio/gui/sequence/package-summary.html">org.biojava.bio.gui.sequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/FilteringRenderer.html#FilteringRenderer()">FilteringRenderer()</a></span> - Constructor for class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/FilteringRenderer.html" title="class in org.biojava.bio.gui.sequence">FilteringRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/FilteringRenderer.html#FilteringRenderer(org.biojava.bio.gui.sequence.SequenceRenderer, org.biojava.bio.seq.FeatureFilter, boolean)">FilteringRenderer(SequenceRenderer, FeatureFilter, boolean)</a></span> - Constructor for class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/FilteringRenderer.html" title="class in org.biojava.bio.gui.sequence">FilteringRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/xff/ElementRecognizer.AllElementRecognizer.html#filterStartElement(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes)">filterStartElement(String, String, String, Attributes)</a></span> - Method in class org.biojava.bio.program.xff.<a href="./org/biojava/bio/program/xff/ElementRecognizer.AllElementRecognizer.html" title="class in org.biojava.bio.program.xff">ElementRecognizer.AllElementRecognizer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/xff/ElementRecognizer.ByLocalName.html#filterStartElement(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes)">filterStartElement(String, String, String, Attributes)</a></span> - Method in class org.biojava.bio.program.xff.<a href="./org/biojava/bio/program/xff/ElementRecognizer.ByLocalName.html" title="class in org.biojava.bio.program.xff">ElementRecognizer.ByLocalName</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/xff/ElementRecognizer.ByNSName.html#filterStartElement(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes)">filterStartElement(String, String, String, Attributes)</a></span> - Method in class org.biojava.bio.program.xff.<a href="./org/biojava/bio/program/xff/ElementRecognizer.ByNSName.html" title="class in org.biojava.bio.program.xff">ElementRecognizer.ByNSName</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/xff/ElementRecognizer.html#filterStartElement(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes)">filterStartElement(String, String, String, Attributes)</a></span> - Method in interface org.biojava.bio.program.xff.<a href="./org/biojava/bio/program/xff/ElementRecognizer.html" title="interface in org.biojava.bio.program.xff">ElementRecognizer</a></dt>
<dd>
<div class="block">Recognize an element based upon the start element parameters.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/xff/ElementRecognizer.HasAttribute.html#filterStartElement(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes)">filterStartElement(String, String, String, Attributes)</a></span> - Method in class org.biojava.bio.program.xff.<a href="./org/biojava/bio/program/xff/ElementRecognizer.HasAttribute.html" title="class in org.biojava.bio.program.xff">ElementRecognizer.HasAttribute</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/ElementRecognizer.AllElementRecognizer.html#filterStartElement(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes)">filterStartElement(String, String, String, Attributes)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/ElementRecognizer.AllElementRecognizer.html" title="class in org.biojava.bio.seq.io.agave">ElementRecognizer.AllElementRecognizer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/ElementRecognizer.ByLocalName.html#filterStartElement(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes)">filterStartElement(String, String, String, Attributes)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/ElementRecognizer.ByLocalName.html" title="class in org.biojava.bio.seq.io.agave">ElementRecognizer.ByLocalName</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/ElementRecognizer.ByNSName.html#filterStartElement(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes)">filterStartElement(String, String, String, Attributes)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/ElementRecognizer.ByNSName.html" title="class in org.biojava.bio.seq.io.agave">ElementRecognizer.ByNSName</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/ElementRecognizer.html#filterStartElement(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes)">filterStartElement(String, String, String, Attributes)</a></span> - Method in interface org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/ElementRecognizer.html" title="interface in org.biojava.bio.seq.io.agave">ElementRecognizer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/ElementRecognizer.HasAttribute.html#filterStartElement(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes)">filterStartElement(String, String, String, Attributes)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/ElementRecognizer.HasAttribute.html" title="class in org.biojava.bio.seq.io.agave">ElementRecognizer.HasAttribute</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game/ElementRecognizer.AllElementRecognizer.html#filterStartElement(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes)">filterStartElement(String, String, String, Attributes)</a></span> - Method in class org.biojava.bio.seq.io.game.<a href="./org/biojava/bio/seq/io/game/ElementRecognizer.AllElementRecognizer.html" title="class in org.biojava.bio.seq.io.game">ElementRecognizer.AllElementRecognizer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game/ElementRecognizer.ByLocalName.html#filterStartElement(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes)">filterStartElement(String, String, String, Attributes)</a></span> - Method in class org.biojava.bio.seq.io.game.<a href="./org/biojava/bio/seq/io/game/ElementRecognizer.ByLocalName.html" title="class in org.biojava.bio.seq.io.game">ElementRecognizer.ByLocalName</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game/ElementRecognizer.ByNSName.html#filterStartElement(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes)">filterStartElement(String, String, String, Attributes)</a></span> - Method in class org.biojava.bio.seq.io.game.<a href="./org/biojava/bio/seq/io/game/ElementRecognizer.ByNSName.html" title="class in org.biojava.bio.seq.io.game">ElementRecognizer.ByNSName</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game/ElementRecognizer.html#filterStartElement(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes)">filterStartElement(String, String, String, Attributes)</a></span> - Method in interface org.biojava.bio.seq.io.game.<a href="./org/biojava/bio/seq/io/game/ElementRecognizer.html" title="interface in org.biojava.bio.seq.io.game">ElementRecognizer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game/ElementRecognizer.HasAttribute.html#filterStartElement(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes)">filterStartElement(String, String, String, Attributes)</a></span> - Method in class org.biojava.bio.seq.io.game.<a href="./org/biojava/bio/seq/io/game/ElementRecognizer.HasAttribute.html" title="class in org.biojava.bio.seq.io.game">ElementRecognizer.HasAttribute</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/search/FilterTest.html" title="interface in org.biojava.bio.search"><span class="strong">FilterTest</span></a> - Interface in <a href="./org/biojava/bio/search/package-summary.html">org.biojava.bio.search</a></dt>
<dd>
<div class="block">Class for implementing tests with BlastLikeSearchFilter
objects.</div>
</dd>
<dt><a href="./org/biojava/bio/search/FilterTest.Equals.html" title="class in org.biojava.bio.search"><span class="strong">FilterTest.Equals</span></a> - Class in <a href="./org/biojava/bio/search/package-summary.html">org.biojava.bio.search</a></dt>
<dd>
<div class="block">Tests that the value associated with the specified
key is equal to the value supplied here by whatever
criterion of equality appropriate to those objects.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/FilterTest.Equals.html#FilterTest.Equals(java.lang.Object)">FilterTest.Equals(Object)</a></span> - Constructor for class org.biojava.bio.search.<a href="./org/biojava/bio/search/FilterTest.Equals.html" title="class in org.biojava.bio.search">FilterTest.Equals</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/search/FilterTest.FindRegex.html" title="class in org.biojava.bio.search"><span class="strong">FilterTest.FindRegex</span></a> - Class in <a href="./org/biojava/bio/search/package-summary.html">org.biojava.bio.search</a></dt>
<dd>
<div class="block">Tests that the value associated with the specified
key contains a part matched by the supplied regex.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/FilterTest.FindRegex.html#FilterTest.FindRegex(java.lang.String)">FilterTest.FindRegex(String)</a></span> - Constructor for class org.biojava.bio.search.<a href="./org/biojava/bio/search/FilterTest.FindRegex.html" title="class in org.biojava.bio.search">FilterTest.FindRegex</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/search/FilterTest.GreaterThan.html" title="class in org.biojava.bio.search"><span class="strong">FilterTest.GreaterThan</span></a> - Class in <a href="./org/biojava/bio/search/package-summary.html">org.biojava.bio.search</a></dt>
<dd>
<div class="block">Tests that the value associated with the specified
key is greater than the specified threshold.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/FilterTest.GreaterThan.html#FilterTest.GreaterThan(double)">FilterTest.GreaterThan(double)</a></span> - Constructor for class org.biojava.bio.search.<a href="./org/biojava/bio/search/FilterTest.GreaterThan.html" title="class in org.biojava.bio.search">FilterTest.GreaterThan</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/search/FilterTest.LessThan.html" title="class in org.biojava.bio.search"><span class="strong">FilterTest.LessThan</span></a> - Class in <a href="./org/biojava/bio/search/package-summary.html">org.biojava.bio.search</a></dt>
<dd>
<div class="block">Tests that the value associated with the specified
key is less than the specified threshold.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/FilterTest.LessThan.html#FilterTest.LessThan(double)">FilterTest.LessThan(double)</a></span> - Constructor for class org.biojava.bio.search.<a href="./org/biojava/bio/search/FilterTest.LessThan.html" title="class in org.biojava.bio.search">FilterTest.LessThan</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/search/FilterTest.MatchRegex.html" title="class in org.biojava.bio.search"><span class="strong">FilterTest.MatchRegex</span></a> - Class in <a href="./org/biojava/bio/search/package-summary.html">org.biojava.bio.search</a></dt>
<dd>
<div class="block">Tests that the value associated with the specified
key is matched in its entirety by the supplied regex.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/FilterTest.MatchRegex.html#FilterTest.MatchRegex(java.lang.String)">FilterTest.MatchRegex(String)</a></span> - Constructor for class org.biojava.bio.search.<a href="./org/biojava/bio/search/FilterTest.MatchRegex.html" title="class in org.biojava.bio.search">FilterTest.MatchRegex</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/filter/FilterTransformer.html" title="class in org.biojava.bio.seq.filter"><span class="strong">FilterTransformer</span></a> - Class in <a href="./org/biojava/bio/seq/filter/package-summary.html">org.biojava.bio.seq.filter</a></dt>
<dd>
<div class="block">Base-class for visitors that re-write a filter tree.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/filter/FilterTransformer.html#FilterTransformer()">FilterTransformer()</a></span> - Constructor for class org.biojava.bio.seq.filter.<a href="./org/biojava/bio/seq/filter/FilterTransformer.html" title="class in org.biojava.bio.seq.filter">FilterTransformer</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/FilterUtils.html" title="class in org.biojava.bio.seq"><span class="strong">FilterUtils</span></a> - Class in <a href="./org/biojava/bio/seq/package-summary.html">org.biojava.bio.seq</a></dt>
<dd>
<div class="block">A set of FeatureFilter algebraic operations.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/FilterUtils.DelegatingTransformer.html" title="class in org.biojava.bio.seq"><span class="strong">FilterUtils.DelegatingTransformer</span></a> - Class in <a href="./org/biojava/bio/seq/package-summary.html">org.biojava.bio.seq</a></dt>
<dd>
<div class="block">An implementation of FilterTransformer that attempts to transform by one transformer,
and if that fails, by another.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FilterUtils.DelegatingTransformer.html#FilterUtils.DelegatingTransformer(org.biojava.bio.seq.FilterUtils.FilterTransformer, org.biojava.bio.seq.FilterUtils.FilterTransformer)">FilterUtils.DelegatingTransformer(FilterUtils.FilterTransformer, FilterUtils.FilterTransformer)</a></span> - Constructor for class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FilterUtils.DelegatingTransformer.html" title="class in org.biojava.bio.seq">FilterUtils.DelegatingTransformer</a></dt>
<dd>
<div class="block">Create a new DelegatingTransformer that will apply t1 and then t2 if t1 fails.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/FilterUtils.FilterTransformer.html" title="interface in org.biojava.bio.seq"><span class="strong">FilterUtils.FilterTransformer</span></a> - Interface in <a href="./org/biojava/bio/seq/package-summary.html">org.biojava.bio.seq</a></dt>
<dd>
<div class="block">An object able to transform some FeatureFilter instances sytematically into others.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/NameTokenization.html#finalize()">finalize()</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/NameTokenization.html" title="class in org.biojava.bio.seq.io">NameTokenization</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/ChunkedSymbolList.html#finalize()">finalize()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/ChunkedSymbolList.html" title="class in org.biojava.bio.symbol">ChunkedSymbolList</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleAlignment.html#finalize()">finalize()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleAlignment.html" title="class in org.biojava.bio.symbol">SimpleAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleSymbolList.html#finalize()">finalize()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleSymbolList.html" title="class in org.biojava.bio.symbol">SimpleSymbolList</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/process/ExternalProcess.html#finalize()">finalize()</a></span> - Method in class org.biojava.utils.process.<a href="./org/biojava/utils/process/ExternalProcess.html" title="class in org.biojava.utils.process">ExternalProcess</a></dt>
<dt><span class="strong"><a href="./org/biojava/bibliography/BibRefQuery.html#find(java.lang.String[], java.lang.String[], java.util.Hashtable)">find(String[], String[], Hashtable)</a></span> - Method in interface org.biojava.bibliography.<a href="./org/biojava/bibliography/BibRefQuery.html" title="interface in org.biojava.bibliography">BibRefQuery</a></dt>
<dd>
<div class="block">
The easiest direct method for querying a repository.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/BioMatcher.html#find()">find()</a></span> - Method in interface org.biojava.bio.search.<a href="./org/biojava/bio/search/BioMatcher.html" title="interface in org.biojava.bio.search">BioMatcher</a></dt>
<dd>
<div class="block">Attempt to find the next match.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/MaxMismatchMatcher.html#find()">find()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/MaxMismatchMatcher.html" title="class in org.biojava.bio.search">MaxMismatchMatcher</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/regex/Matcher.html#find()">find()</a></span> - Method in class org.biojava.utils.regex.<a href="./org/biojava/utils/regex/Matcher.html" title="class in org.biojava.utils.regex">Matcher</a></dt>
<dd>
<div class="block">Attempts to find the next subsequence of the input sequence that matches the pattern.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/regex/Matcher.html#find(int)">find(int)</a></span> - Method in class org.biojava.utils.regex.<a href="./org/biojava/utils/regex/Matcher.html" title="class in org.biojava.utils.regex">Matcher</a></dt>
<dd>
<div class="block">Resets this matcher and then attempts to find the next subsequence
of the input sequence that matches the pattern, starting at the specified index.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BibRefQuery.html#findByAuthor(org.biojava.bibliography.BiblioProvider, java.util.Hashtable)">findByAuthor(BiblioProvider, Hashtable)</a></span> - Method in interface org.biojava.bibliography.<a href="./org/biojava/bibliography/BibRefQuery.html" title="interface in org.biojava.bibliography">BibRefQuery</a></dt>
<dd>
<div class="block">
This is a convenient method for a common query.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BibRefQuery.html#findById(java.lang.String)">findById(String)</a></span> - Method in interface org.biojava.bibliography.<a href="./org/biojava/bibliography/BibRefQuery.html" title="interface in org.biojava.bibliography">BibRefQuery</a></dt>
<dd>
<div class="block">
This is a convenient method returning just one citation.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BibRefQuery.html#findById(java.lang.String, java.lang.String[])">findById(String, String[])</a></span> - Method in interface org.biojava.bibliography.<a href="./org/biojava/bibliography/BibRefQuery.html" title="interface in org.biojava.bibliography">BibRefQuery</a></dt>
<dd>
<div class="block">
This is a convenient method returning just one citation, perhaps with
a limited number of attributes.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Structure.html#findChain(java.lang.String)">findChain(String)</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Structure.html" title="interface in org.biojava.bio.structure">Structure</a></dt>
<dd>
<div class="block">request a particular chain from a structure.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Structure.html#findChain(java.lang.String, int)">findChain(String, int)</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Structure.html" title="interface in org.biojava.bio.structure">Structure</a></dt>
<dd>
<div class="block">request a particular chain from a particular model</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/StructureImpl.html#findChain(java.lang.String, int)">findChain(String, int)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/StructureImpl.html" title="class in org.biojava.bio.structure">StructureImpl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/StructureImpl.html#findChain(java.lang.String)">findChain(String)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/StructureImpl.html" title="class in org.biojava.bio.structure">StructureImpl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/unigene/UnigeneTools.html#findFactory(java.net.URL)">findFactory(URL)</a></span> - Static method in class org.biojava.bio.program.unigene.<a href="./org/biojava/bio/program/unigene/UnigeneTools.html" title="class in org.biojava.bio.program.unigene">UnigeneTools</a></dt>
<dd>
<div class="block">Find the UnigeneFactory that can accept a URL.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Structure.html#findGroup(java.lang.String, java.lang.String)">findGroup(String, String)</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Structure.html" title="interface in org.biojava.bio.structure">Structure</a></dt>
<dd>
<div class="block">request a particular group from a structure.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Structure.html#findGroup(java.lang.String, java.lang.String, int)">findGroup(String, String, int)</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Structure.html" title="interface in org.biojava.bio.structure">Structure</a></dt>
<dd>
<div class="block">request a particular group from a structure.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/StructureImpl.html#findGroup(java.lang.String, java.lang.String, int)">findGroup(String, String, int)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/StructureImpl.html" title="class in org.biojava.bio.structure">StructureImpl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/StructureImpl.html#findGroup(java.lang.String, java.lang.String)">findGroup(String, String)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/StructureImpl.html" title="class in org.biojava.bio.structure">StructureImpl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/KnuthMorrisPrattSearch.html#findMatches(org.biojava.bio.symbol.SymbolList)">findMatches(SymbolList)</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/KnuthMorrisPrattSearch.html" title="class in org.biojava.bio.search">KnuthMorrisPrattSearch</a></dt>
<dd>
<div class="block">This will return an int[] giving the offsets of the matches in <code>text</code>
(ie the location of the first symbol of each match in the <code>text</code>).</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/emblcd/EmblCDROMRandomAccess.html#findRecord(java.lang.String)">findRecord(String)</a></span> - Method in class org.biojava.bio.seq.db.emblcd.<a href="./org/biojava/bio/seq/db/emblcd/EmblCDROMRandomAccess.html" title="class in org.biojava.bio.seq.db.emblcd">EmblCDROMRandomAccess</a></dt>
<dd>
<div class="block"><code>findRecord</code> performs a binary search within the
file for a record specified by an identifier String.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleGappedSymbolList.html#findSourceBlock(int)">findSourceBlock(int)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleGappedSymbolList.html" title="class in org.biojava.bio.symbol">SimpleGappedSymbolList</a></dt>
<dd>
<div class="block">Finds the index of the block containing the source coordinate indx.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleGappedSymbolList.html#findSourceGap(int)">findSourceGap(int)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleGappedSymbolList.html" title="class in org.biojava.bio.symbol">SimpleGappedSymbolList</a></dt>
<dd>
<div class="block">Finds the index of the Block before the gap at indx within the following gap.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/taxa/io/SimpleNCBITaxonomyLoader.html#findTaxon(java.lang.Object[])">findTaxon(Object[])</a></span> - Method in class org.biojavax.bio.taxa.io.<a href="./org/biojavax/bio/taxa/io/SimpleNCBITaxonomyLoader.html" title="class in org.biojavax.bio.taxa.io">SimpleNCBITaxonomyLoader</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/obo/OboFileParser.html#findUnescaped(java.lang.String, char)">findUnescaped(String, char)</a></span> - Static method in class org.biojava.ontology.obo.<a href="./org/biojava/ontology/obo/OboFileParser.html" title="class in org.biojava.ontology.obo">OboFileParser</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/obo/OboFileParser.html#findUnescaped(java.lang.String, char, int, int)">findUnescaped(String, char, int, int)</a></span> - Static method in class org.biojava.ontology.obo.<a href="./org/biojava/ontology/obo/OboFileParser.html" title="class in org.biojava.ontology.obo">OboFileParser</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/obo/OboFileParser.html#findUnescaped(java.lang.String, char, int, int, boolean)">findUnescaped(String, char, int, int, boolean)</a></span> - Static method in class org.biojava.ontology.obo.<a href="./org/biojava/ontology/obo/OboFileParser.html" title="class in org.biojava.ontology.obo">OboFileParser</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleGappedSymbolList.html#findViewBlock(int)">findViewBlock(int)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleGappedSymbolList.html" title="class in org.biojava.bio.symbol">SimpleGappedSymbolList</a></dt>
<dd>
<div class="block">Finds the index of the Block containing indx within the view ranges.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleGappedSymbolList.html#findViewGap(int)">findViewGap(int)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleGappedSymbolList.html" title="class in org.biojava.bio.symbol">SimpleGappedSymbolList</a></dt>
<dd>
<div class="block">Finds the index of the Block before the gap at indx within the view range.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/AlternativeAlignment.html#finish(org.biojava.bio.structure.align.StrucAligParameters, org.biojava.bio.structure.Atom[], org.biojava.bio.structure.Atom[])">finish(StrucAligParameters, Atom[], Atom[])</a></span> - Method in class org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/AlternativeAlignment.html" title="class in org.biojava.bio.structure.align.pairwise">AlternativeAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/abi/ABIFParser.DataAccess.html#finishedReading()">finishedReading()</a></span> - Method in interface org.biojava.bio.program.abi.<a href="./org/biojava/bio/program/abi/ABIFParser.DataAccess.html" title="interface in org.biojava.bio.program.abi">ABIFParser.DataAccess</a></dt>
<dd>
<div class="block">Called when the parser has finished reading.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html#finishWriting()">finishWriting()</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html" title="class in org.biojavax.bio.seq.io">EMBLxmlFormat</a></dt>
<dd>
<div class="block">Informs the writer that are done writing.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/INSDseqFormat.html#finishWriting()">finishWriting()</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/INSDseqFormat.html" title="class in org.biojavax.bio.seq.io">INSDseqFormat</a></dt>
<dd>
<div class="block">Informs the writer that are done writing.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/RichSequenceFormat.html#finishWriting()">finishWriting()</a></span> - Method in interface org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/RichSequenceFormat.html" title="interface in org.biojavax.bio.seq.io">RichSequenceFormat</a></dt>
<dd>
<div class="block">Informs the writer that are done writing.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/RichSequenceFormat.HeaderlessFormat.html#finishWriting()">finishWriting()</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/RichSequenceFormat.HeaderlessFormat.html" title="class in org.biojavax.bio.seq.io">RichSequenceFormat.HeaderlessFormat</a></dt>
<dd>
<div class="block">Informs the writer that are done writing.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#finishWriting()">finishWriting()</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd>
<div class="block">Informs the writer that are done writing.</div>
</dd>
<dt><a href="./org/biojava/bio/symbol/FiniteAlphabet.html" title="interface in org.biojava.bio.symbol"><span class="strong">FiniteAlphabet</span></a> - Interface in <a href="./org/biojava/bio/symbol/package-summary.html">org.biojava.bio.symbol</a></dt>
<dd>
<div class="block">An alphabet over a finite set of Symbols.</div>
</dd>
<dt><a href="./org/biojava/utils/automata/FiniteAutomaton.html" title="class in org.biojava.utils.automata"><span class="strong">FiniteAutomaton</span></a> - Class in <a href="./org/biojava/utils/automata/package-summary.html">org.biojava.utils.automata</a></dt>
<dd>
<div class="block">Class for modelling finite automata.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/xff/FeatureHandler.html#fireEndFeature()">fireEndFeature()</a></span> - Method in class org.biojava.bio.program.xff.<a href="./org/biojava/bio/program/xff/FeatureHandler.html" title="class in org.biojava.bio.program.xff">FeatureHandler</a></dt>
<dd>
<div class="block">Fire the endFeature event.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssaha/CompactedDataStore.html#fireHits(int, int, org.biojava.bio.program.ssaha.SearchListener)">fireHits(int, int, SearchListener)</a></span> - Method in class org.biojava.bio.program.ssaha.<a href="./org/biojava/bio/program/ssaha/CompactedDataStore.html" title="class in org.biojava.bio.program.ssaha">CompactedDataStore</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequenceViewerSupport.html#fireMouseClicked(org.biojava.bio.gui.sequence.SequenceViewerEvent)">fireMouseClicked(SequenceViewerEvent)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequenceViewerSupport.html" title="class in org.biojava.bio.gui.sequence">SequenceViewerSupport</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequenceViewerMotionSupport.html#fireMouseDragged(org.biojava.bio.gui.sequence.SequenceViewerEvent)">fireMouseDragged(SequenceViewerEvent)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequenceViewerMotionSupport.html" title="class in org.biojava.bio.gui.sequence">SequenceViewerMotionSupport</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequenceViewerMotionSupport.html#fireMouseMoved(org.biojava.bio.gui.sequence.SequenceViewerEvent)">fireMouseMoved(SequenceViewerEvent)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequenceViewerMotionSupport.html" title="class in org.biojava.bio.gui.sequence">SequenceViewerMotionSupport</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequenceViewerSupport.html#fireMousePressed(org.biojava.bio.gui.sequence.SequenceViewerEvent)">fireMousePressed(SequenceViewerEvent)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequenceViewerSupport.html" title="class in org.biojava.bio.gui.sequence">SequenceViewerSupport</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequenceViewerSupport.html#fireMouseReleased(org.biojava.bio.gui.sequence.SequenceViewerEvent)">fireMouseReleased(SequenceViewerEvent)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequenceViewerSupport.html" title="class in org.biojava.bio.gui.sequence">SequenceViewerSupport</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ChangeHub.html#firePostChange(java.lang.Object, org.biojava.utils.ChangeEvent)">firePostChange(Object, ChangeEvent)</a></span> - Method in interface org.biojava.utils.<a href="./org/biojava/utils/ChangeHub.html" title="interface in org.biojava.utils">ChangeHub</a></dt>
<dd>
<div class="block">invoke the firePostChangeEvent on all ChangeListeners associated with
a specific key.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/IndexedChangeHub.html#firePostChange(java.lang.Object, org.biojava.utils.ChangeEvent)">firePostChange(Object, ChangeEvent)</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/IndexedChangeHub.html" title="class in org.biojava.utils">IndexedChangeHub</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ChangeSupport.html#firePostChangeEvent(org.biojava.utils.ChangeEvent)">firePostChangeEvent(ChangeEvent)</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/ChangeSupport.html" title="class in org.biojava.utils">ChangeSupport</a></dt>
<dd>
<div class="block">
Inform the listeners that a change has taken place using their
firePostChangeEvent methods.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/ChangeHub.html#firePreChange(java.lang.Object, org.biojava.utils.ChangeEvent)">firePreChange(Object, ChangeEvent)</a></span> - Method in interface org.biojava.utils.<a href="./org/biojava/utils/ChangeHub.html" title="interface in org.biojava.utils">ChangeHub</a></dt>
<dd>
<div class="block">invoke the firePreChangeEvent on all ChangeListeners associated with
a specific key.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/IndexedChangeHub.html#firePreChange(java.lang.Object, org.biojava.utils.ChangeEvent)">firePreChange(Object, ChangeEvent)</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/IndexedChangeHub.html" title="class in org.biojava.utils">IndexedChangeHub</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ChangeSupport.html#firePreChangeEvent(org.biojava.utils.ChangeEvent)">firePreChangeEvent(ChangeEvent)</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/ChangeSupport.html" title="class in org.biojava.utils">ChangeSupport</a></dt>
<dd>
<div class="block">
Inform the listeners that a change is about to take place using their
firePreChangeEvent methods.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/StackedLogoPainter.html#firePropertyChange(java.lang.String, java.lang.Object, java.lang.Object)">firePropertyChange(String, Object, Object)</a></span> - Method in class org.biojava.bio.gui.<a href="./org/biojava/bio/gui/StackedLogoPainter.html" title="class in org.biojava.bio.gui">StackedLogoPainter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/StackedLogoPainter.html#firePropertyChange(java.lang.String, int, int)">firePropertyChange(String, int, int)</a></span> - Method in class org.biojava.bio.gui.<a href="./org/biojava/bio/gui/StackedLogoPainter.html" title="class in org.biojava.bio.gui">StackedLogoPainter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/StackedLogoPainter.html#firePropertyChange(java.lang.String, boolean, boolean)">firePropertyChange(String, boolean, boolean)</a></span> - Method in class org.biojava.bio.gui.<a href="./org/biojava/bio/gui/StackedLogoPainter.html" title="class in org.biojava.bio.gui">StackedLogoPainter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/StackedLogoPainter.html#firePropertyChange(java.beans.PropertyChangeEvent)">firePropertyChange(PropertyChangeEvent)</a></span> - Method in class org.biojava.bio.gui.<a href="./org/biojava/bio/gui/StackedLogoPainter.html" title="class in org.biojava.bio.gui">StackedLogoPainter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/TextLogoPainter.html#firePropertyChange(java.lang.String, java.lang.Object, java.lang.Object)">firePropertyChange(String, Object, Object)</a></span> - Method in class org.biojava.bio.gui.<a href="./org/biojava/bio/gui/TextLogoPainter.html" title="class in org.biojava.bio.gui">TextLogoPainter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/TextLogoPainter.html#firePropertyChange(java.lang.String, int, int)">firePropertyChange(String, int, int)</a></span> - Method in class org.biojava.bio.gui.<a href="./org/biojava/bio/gui/TextLogoPainter.html" title="class in org.biojava.bio.gui">TextLogoPainter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/TextLogoPainter.html#firePropertyChange(java.lang.String, boolean, boolean)">firePropertyChange(String, boolean, boolean)</a></span> - Method in class org.biojava.bio.gui.<a href="./org/biojava/bio/gui/TextLogoPainter.html" title="class in org.biojava.bio.gui">TextLogoPainter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/TextLogoPainter.html#firePropertyChange(java.beans.PropertyChangeEvent)">firePropertyChange(PropertyChangeEvent)</a></span> - Method in class org.biojava.bio.gui.<a href="./org/biojava/bio/gui/TextLogoPainter.html" title="class in org.biojava.bio.gui">TextLogoPainter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/xff/FeatureHandler.html#fireStartFeature()">fireStartFeature()</a></span> - Method in class org.biojava.bio.program.xff.<a href="./org/biojava/bio/program/xff/FeatureHandler.html" title="class in org.biojava.bio.program.xff">FeatureHandler</a></dt>
<dd>
<div class="block">Fire the startFeature event.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BiblioPerson.html#firstName">firstName</a></span> - Variable in class org.biojava.bibliography.<a href="./org/biojava/bibliography/BiblioPerson.html" title="class in org.biojava.bibliography">BiblioPerson</a></dt>
<dd>
<div class="block">The person's christian name (first name).</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/GappedSymbolList.html#firstNonGap()">firstNonGap()</a></span> - Method in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/GappedSymbolList.html" title="interface in org.biojava.bio.symbol">GappedSymbolList</a></dt>
<dd>
<div class="block">Return the index of the first Symbol that is not a Gap character.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleGappedSymbolList.html#firstNonGap()">firstNonGap()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleGappedSymbolList.html" title="class in org.biojava.bio.symbol">SimpleGappedSymbolList</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BiblioArticle.html#firstPage">firstPage</a></span> - Variable in class org.biojava.bibliography.<a href="./org/biojava/bibliography/BiblioArticle.html" title="class in org.biojava.bibliography">BiblioArticle</a></dt>
<dd>
<div class="block">First page of the article.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/tools/SVM_Light.html#firstToken(java.lang.String)">firstToken(String)</a></span> - Static method in class org.biojava.stats.svm.tools.<a href="./org/biojava/stats/svm/tools/SVM_Light.html" title="class in org.biojava.stats.svm.tools">SVM_Light</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/functions/FitnessFunction.html#fitness(org.biojavax.ga.Organism, org.biojavax.ga.Population, org.biojavax.ga.GeneticAlgorithm)">fitness(Organism, Population, GeneticAlgorithm)</a></span> - Method in interface org.biojavax.ga.functions.<a href="./org/biojavax/ga/functions/FitnessFunction.html" title="interface in org.biojavax.ga.functions">FitnessFunction</a></dt>
<dd>
<div class="block">Calculates the fitness of <code>org</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ga/GeneticAlgorithm.html#FITNESS_FUNCTION">FITNESS_FUNCTION</a></span> - Static variable in interface org.biojavax.ga.<a href="./org/biojavax/ga/GeneticAlgorithm.html" title="interface in org.biojavax.ga">GeneticAlgorithm</a></dt>
<dd> </dd>
<dt><a href="./org/biojavax/ga/functions/FitnessFunction.html" title="interface in org.biojavax.ga.functions"><span class="strong">FitnessFunction</span></a> - Interface in <a href="./org/biojavax/ga/functions/package-summary.html">org.biojavax.ga.functions</a></dt>
<dd>
<div class="block">Calculates the fitness of an <code>Organism</code> in a
<code>Population</code> of <code>Organisms</code></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/CircularLocation.html#fivePrimeBlockIterator()">fivePrimeBlockIterator()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/CircularLocation.html" title="class in org.biojava.bio.symbol">CircularLocation</a></dt>
<dd>
<div class="block">Iterates over the location blocks in order starting with the most 5'</div>
</dd>
<dt><a href="./org/biojava/bio/chromatogram/graphic/FixedBaseWidthScaler.html" title="class in org.biojava.bio.chromatogram.graphic"><span class="strong">FixedBaseWidthScaler</span></a> - Class in <a href="./org/biojava/bio/chromatogram/graphic/package-summary.html">org.biojava.bio.chromatogram.graphic</a></dt>
<dd>
<div class="block">A <a href="./org/biojava/bio/chromatogram/graphic/ChromatogramNonlinearScaler.html" title="interface in org.biojava.bio.chromatogram.graphic"><code>ChromatogramNonlinearScaler</code></a> that scales all the
base calls in a chromatogram to the same width in pixels,
optionally biasing the peak of the call to the center.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/graphic/FixedBaseWidthScaler.html#FixedBaseWidthScaler(float)">FixedBaseWidthScaler(float)</a></span> - Constructor for class org.biojava.bio.chromatogram.graphic.<a href="./org/biojava/bio/chromatogram/graphic/FixedBaseWidthScaler.html" title="class in org.biojava.bio.chromatogram.graphic">FixedBaseWidthScaler</a></dt>
<dd>
<div class="block">Creates a new scaler that will scale bases to the specified width
without attempting to center their peaks.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/graphic/FixedBaseWidthScaler.html#FixedBaseWidthScaler(float, boolean)">FixedBaseWidthScaler(float, boolean)</a></span> - Constructor for class org.biojava.bio.chromatogram.graphic.<a href="./org/biojava/bio/chromatogram/graphic/FixedBaseWidthScaler.html" title="class in org.biojava.bio.chromatogram.graphic">FixedBaseWidthScaler</a></dt>
<dd>
<div class="block">Creates a new scaler that will scale bases to the specified width
and may or may not bias the peaks to the center.</div>
</dd>
<dt><a href="./org/biojava/utils/cache/FixedSizeCache.html" title="class in org.biojava.utils.cache"><span class="strong">FixedSizeCache</span></a> - Class in <a href="./org/biojava/utils/cache/package-summary.html">org.biojava.utils.cache</a></dt>
<dd>
<div class="block">Cache which stores up to <code>limit</code> Objects.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/cache/FixedSizeCache.html#FixedSizeCache(int)">FixedSizeCache(int)</a></span> - Constructor for class org.biojava.utils.cache.<a href="./org/biojava/utils/cache/FixedSizeCache.html" title="class in org.biojava.utils.cache">FixedSizeCache</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/utils/cache/FixedSizeMap.html" title="class in org.biojava.utils.cache"><span class="strong">FixedSizeMap</span></a> - Class in <a href="./org/biojava/utils/cache/package-summary.html">org.biojava.utils.cache</a></dt>
<dd>
<div class="block">A cache that only remembers a given number of keys.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/cache/FixedSizeMap.html#FixedSizeMap(int)">FixedSizeMap(int)</a></span> - Constructor for class org.biojava.utils.cache.<a href="./org/biojava/utils/cache/FixedSizeMap.html" title="class in org.biojava.utils.cache">FixedSizeMap</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SymbolTokenization.html#FIXEDWIDTH">FIXEDWIDTH</a></span> - Static variable in interface org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SymbolTokenization.html" title="interface in org.biojava.bio.seq.io">SymbolTokenization</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/structure/server/FlatFileInstallation.html" title="class in org.biojava.bio.structure.server"><span class="strong">FlatFileInstallation</span></a> - Class in <a href="./org/biojava/bio/structure/server/package-summary.html">org.biojava.bio.structure.server</a></dt>
<dd>
<div class="block">a PDB installation that reads all files from one directory in the file system.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/server/FlatFileInstallation.html#FlatFileInstallation(java.io.File)">FlatFileInstallation(File)</a></span> - Constructor for class org.biojava.bio.structure.server.<a href="./org/biojava/bio/structure/server/FlatFileInstallation.html" title="class in org.biojava.bio.structure.server">FlatFileInstallation</a></dt>
<dd>
<div class="block">create a new FlatFile Installation and point it to the directory that contains all PDB files</div>
</dd>
<dt><a href="./org/biojava/bio/program/unigene/FlatFileUnigeneFactory.html" title="class in org.biojava.bio.program.unigene"><span class="strong">FlatFileUnigeneFactory</span></a> - Class in <a href="./org/biojava/bio/program/unigene/package-summary.html">org.biojava.bio.program.unigene</a></dt>
<dd>
<div class="block">A UnigeneFactory that will use flat-file indexing of the unigene ascii-art
files.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/unigene/FlatFileUnigeneFactory.html#FlatFileUnigeneFactory()">FlatFileUnigeneFactory()</a></span> - Constructor for class org.biojava.bio.program.unigene.<a href="./org/biojava/bio/program/unigene/FlatFileUnigeneFactory.html" title="class in org.biojava.bio.program.unigene">FlatFileUnigeneFactory</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/db/flat/FlatSequenceDB.html" title="class in org.biojava.bio.seq.db.flat"><span class="strong">FlatSequenceDB</span></a> - Class in <a href="./org/biojava/bio/seq/db/flat/package-summary.html">org.biojava.bio.seq.db.flat</a></dt>
<dd>
<div class="block"><code>FlatSequenceDB</code> is an OBDA flatfile sequence databank
implementation.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/flat/FlatSequenceDB.html#FlatSequenceDB(java.lang.String, java.lang.String)">FlatSequenceDB(String, String)</a></span> - Constructor for class org.biojava.bio.seq.db.flat.<a href="./org/biojava/bio/seq/db/flat/FlatSequenceDB.html" title="class in org.biojava.bio.seq.db.flat">FlatSequenceDB</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/db/flat/FlatSequenceDBProvider.html" title="class in org.biojava.bio.seq.db.flat"><span class="strong">FlatSequenceDBProvider</span></a> - Class in <a href="./org/biojava/bio/seq/db/flat/package-summary.html">org.biojava.bio.seq.db.flat</a></dt>
<dd>
<div class="block"><code>FlatSequenceDBProvider</code> directory-services plugin for
flatfile databases.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/flat/FlatSequenceDBProvider.html#FlatSequenceDBProvider()">FlatSequenceDBProvider()</a></span> - Constructor for class org.biojava.bio.seq.db.flat.<a href="./org/biojava/bio/seq/db/flat/FlatSequenceDBProvider.html" title="class in org.biojava.bio.seq.db.flat">FlatSequenceDBProvider</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichLocation.Tools.html#flatten(org.biojavax.bio.seq.RichLocation)">flatten(RichLocation)</a></span> - Static method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichLocation.Tools.html" title="class in org.biojavax.bio.seq">RichLocation.Tools</a></dt>
<dd>
<div class="block">Takes a location and returns the set of all members.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichLocation.Tools.html#flatten(java.util.Collection)">flatten(Collection<Location>)</a></span> - Static method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichLocation.Tools.html" title="class in org.biojavax.bio.seq">RichLocation.Tools</a></dt>
<dd>
<div class="block">Takes a set of locations and returns the set of all members.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/DP.html#flatView(org.biojava.bio.dp.MarkovModel)">flatView(MarkovModel)</a></span> - Static method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/DP.html" title="class in org.biojava.bio.dp">DP</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/alignment/FlexibleAlignment.html" title="class in org.biojava.bio.alignment"><span class="strong">FlexibleAlignment</span></a> - Class in <a href="./org/biojava/bio/alignment/package-summary.html">org.biojava.bio.alignment</a></dt>
<dd>
<div class="block">FlexibleAlignment is a class which implements
UnequalLengthAlignment, ARAlignment and EditableAlignment <b>It
places no restriction on where any sequence can be in the alignment
so there could be gaps in the alignment.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/FlexibleAlignment.html#FlexibleAlignment(java.util.List)">FlexibleAlignment(List)</a></span> - Constructor for class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/FlexibleAlignment.html" title="class in org.biojava.bio.alignment">FlexibleAlignment</a></dt>
<dd>
<div class="block">construct this object with the reference sequence which can either be a gappedSymbolList or not
label in all cases refers to an object that holds the display name (generally just a String).</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/DNATools.html#flip(org.biojava.bio.symbol.SymbolList, org.biojava.bio.seq.StrandedFeature.Strand)">flip(SymbolList, StrandedFeature.Strand)</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/DNATools.html" title="class in org.biojava.bio.seq">DNATools</a></dt>
<dd>
<div class="block">Returns a SymbolList that is reverse complemented if the strand is
negative, and the origninal one if it is not.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/StrandedFeature.Strand.html#flip()">flip()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/StrandedFeature.Strand.html" title="class in org.biojava.bio.seq">StrandedFeature.Strand</a></dt>
<dd>
<div class="block">Return a strand that represents flipping this onto the opposite strand.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/LocationTools.html#flip(org.biojava.bio.symbol.Location, int)">flip(Location, int)</a></span> - Static method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/LocationTools.html" title="class in org.biojava.bio.symbol">LocationTools</a></dt>
<dd>
<div class="block">Flips a location relative to a length.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/projection/ProjectionUtils.html#flipLocation(org.biojava.bio.symbol.Location, int)">flipLocation(Location, int)</a></span> - Static method in class org.biojava.bio.seq.projection.<a href="./org/biojava/bio/seq/projection/ProjectionUtils.html" title="class in org.biojava.bio.seq.projection">ProjectionUtils</a></dt>
<dd>
<div class="block">Flip a location.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/projection/ProjectionUtils.html#flipStrand(org.biojava.bio.seq.StrandedFeature.Strand)">flipStrand(StrandedFeature.Strand)</a></span> - Static method in class org.biojava.bio.seq.projection.<a href="./org/biojava/bio/seq/projection/ProjectionUtils.html" title="class in org.biojava.bio.seq.projection">ProjectionUtils</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/GlyphFeatureRenderer.html#fList">fList</a></span> - Variable in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/GlyphFeatureRenderer.html" title="class in org.biojava.bio.gui.sequence">GlyphFeatureRenderer</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/utils/stax/FloatElementHandlerBase.html" title="class in org.biojava.utils.stax"><span class="strong">FloatElementHandlerBase</span></a> - Class in <a href="./org/biojava/utils/stax/package-summary.html">org.biojava.utils.stax</a></dt>
<dd>
<div class="block">StAX handler for any element which just contains a string representation of
a float.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/stax/FloatElementHandlerBase.html#FloatElementHandlerBase()">FloatElementHandlerBase()</a></span> - Constructor for class org.biojava.utils.stax.<a href="./org/biojava/utils/stax/FloatElementHandlerBase.html" title="class in org.biojava.utils.stax">FloatElementHandlerBase</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/RepeatedCharSequence.html#flush()">flush()</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/RepeatedCharSequence.html" title="class in org.biojava.utils">RepeatedCharSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/LazyFeatureHolder.html#flushFeatures()">flushFeatures()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/LazyFeatureHolder.html" title="class in org.biojava.bio.seq">LazyFeatureHolder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/io/LargeBuffer.html#force()">force()</a></span> - Method in class org.biojava.utils.io.<a href="./org/biojava/utils/io/LargeBuffer.html" title="class in org.biojava.utils.io">LargeBuffer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/DNATools.html#forIndex(int)">forIndex(int)</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/DNATools.html" title="class in org.biojava.bio.seq">DNATools</a></dt>
<dd>
<div class="block">Return the symbol for an index - compatible with <code>index</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/NucleotideTools.html#forIndex(int)">forIndex(int)</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/NucleotideTools.html" title="class in org.biojava.bio.seq">NucleotideTools</a></dt>
<dd>
<div class="block">Return the symbol for an index - compatible with <code>index</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/RNATools.html#forIndex(int)">forIndex(int)</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/RNATools.html" title="class in org.biojava.bio.seq">RNATools</a></dt>
<dd>
<div class="block">Return the symbol for an index - compatible with index.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BibRef.html#format">format</a></span> - Variable in class org.biojava.bibliography.<a href="./org/biojava/bibliography/BibRef.html" title="class in org.biojava.bibliography">BibRef</a></dt>
<dd>
<div class="block">It describes the physical or digital manifestation of the cited
resource.</div>
</dd>
<dt><a href="./org/biojava/bio/program/formats/Format.html" title="interface in org.biojava.bio.program.formats"><span class="strong">Format</span></a> - Interface in <a href="./org/biojava/bio/program/formats/package-summary.html">org.biojava.bio.program.formats</a></dt>
<dd>
<div class="block">A file format supported by the tag-value event-based parsing system.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqFileFormer.html#formatLocation(java.lang.StringBuffer, org.biojava.bio.symbol.Location, org.biojava.bio.seq.StrandedFeature.Strand)">formatLocation(StringBuffer, Location, StrandedFeature.Strand)</a></span> - Method in interface org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqFileFormer.html" title="interface in org.biojava.bio.seq.io">SeqFileFormer</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block"><code>formatLocation</code> creates a String representation of
a <code>Location</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqFileFormer.html#formatLocation(org.biojava.bio.seq.Feature)">formatLocation(Feature)</a></span> - Method in interface org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqFileFormer.html" title="interface in org.biojava.bio.seq.io">SeqFileFormer</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Formats the location of a feature.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SwissprotFileFormer.html#formatLocation(java.lang.StringBuffer, org.biojava.bio.symbol.Location, org.biojava.bio.seq.StrandedFeature.Strand)">formatLocation(StringBuffer, Location, StrandedFeature.Strand)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SwissprotFileFormer.html" title="class in org.biojava.bio.seq.io">SwissprotFileFormer</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block"><code>formatLocation</code> creates a String representation of
a <code>Location</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SwissprotFileFormer.html#formatLocation(org.biojava.bio.seq.Feature)">formatLocation(Feature)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SwissprotFileFormer.html" title="class in org.biojava.bio.seq.io">SwissprotFileFormer</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Creates a string representation of the location of a feature</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SwissprotFileFormer.html#formatLocation(java.lang.StringBuffer, org.biojava.bio.symbol.Location)">formatLocation(StringBuffer, Location)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SwissprotFileFormer.html" title="class in org.biojava.bio.seq.io">SwissprotFileFormer</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block"><code>formatLocation</code> creates a String representation of
a <code>Location</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/SequenceAlignment.html#formatOutput(java.lang.String, java.lang.String, java.lang.String[], java.lang.String, int, int, long, int, int, long, int, long)">formatOutput(String, String, String[], String, int, int, long, int, int, long, int, long)</a></span> - Static method in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/SequenceAlignment.html" title="class in org.biojava.bio.alignment">SequenceAlignment</a></dt>
<dd>
<div class="block">This method provides a BLAST-like formated alignment from the given
<code>String</code>s, in which the sequence coordinates and the
information "Query" or "Target", respectively is added to each line.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SwissprotFileFormer.html#formatPoint(int, int, boolean)">formatPoint(int, int, boolean)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SwissprotFileFormer.html" title="class in org.biojava.bio.seq.io">SwissprotFileFormer</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Formats the points from fuzzy locations.</div>
</dd>
<dt><a href="./org/biojava/bio/program/tagvalue/Formats.html" title="class in org.biojava.bio.program.tagvalue"><span class="strong">Formats</span></a> - Class in <a href="./org/biojava/bio/program/tagvalue/package-summary.html">org.biojava.bio.program.tagvalue</a></dt>
<dd>
<div class="block">This is intended as a repository for tag-value and AnnotationType information
about common file formats.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/Formats.html#Formats()">Formats()</a></span> - Constructor for class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/Formats.html" title="class in org.biojava.bio.program.tagvalue">Formats</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOTools.html#formatToFactory(org.biojava.bio.seq.io.SequenceFormat, org.biojava.bio.symbol.Alphabet)">formatToFactory(SequenceFormat, Alphabet)</a></span> - Static method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOTools.html" title="class in org.biojava.bio.seq.io">SeqIOTools</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>as this essentially duplicates the operation
available in the method <code>identifyBuilderFactory</code>.</i></div>
</div>
</dd>
<dt><a href="./org/biojava/bio/program/formats/FormatTools.html" title="class in org.biojava.bio.program.formats"><span class="strong">FormatTools</span></a> - Class in <a href="./org/biojava/bio/program/formats/package-summary.html">org.biojava.bio.program.formats</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichLocation.Strand.html#forName(java.lang.String)">forName(String)</a></span> - Static method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichLocation.Strand.html" title="class in org.biojavax.bio.seq">RichLocation.Strand</a></dt>
<dd>
<div class="block">Returns the strand object that matches the symbol given.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BiblioCriterion.html#forSubset">forSubset</a></span> - Variable in class org.biojava.bibliography.<a href="./org/biojava/bibliography/BiblioCriterion.html" title="class in org.biojava.bibliography">BiblioCriterion</a></dt>
<dd>
<div class="block">A name of a repository subset which this criterion is valid/used for.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/DNATools.html#forSymbol(char)">forSymbol(char)</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/DNATools.html" title="class in org.biojava.bio.seq">DNATools</a></dt>
<dd>
<div class="block">Retrieve the symbol for a symbol.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/NucleotideTools.html#forSymbol(char)">forSymbol(char)</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/NucleotideTools.html" title="class in org.biojava.bio.seq">NucleotideTools</a></dt>
<dd>
<div class="block">Retrieve the symbol for a symbol.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/RNATools.html#forSymbol(char)">forSymbol(char)</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/RNATools.html" title="class in org.biojava.bio.seq">RNATools</a></dt>
<dd>
<div class="block">Retrieve the symbol for a symbol.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichLocation.Strand.html#forValue(int)">forValue(int)</a></span> - Static method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichLocation.Strand.html" title="class in org.biojavax.bio.seq">RichLocation.Strand</a></dt>
<dd>
<div class="block">Returns the strand object that matches the number given.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/DP.html#forward(org.biojava.bio.symbol.SymbolList[], org.biojava.bio.dp.ScoreType)">forward(SymbolList[], ScoreType)</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/DP.html" title="class in org.biojava.bio.dp">DP</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/onehead/SingleDP.html#forward(org.biojava.bio.symbol.SymbolList[], org.biojava.bio.dp.ScoreType)">forward(SymbolList[], ScoreType)</a></span> - Method in class org.biojava.bio.dp.onehead.<a href="./org/biojava/bio/dp/onehead/SingleDP.html" title="class in org.biojava.bio.dp.onehead">SingleDP</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/onehead/SingleDP.html#forward(org.biojava.bio.dp.onehead.DPCursor, org.biojava.bio.dp.ScoreType)">forward(DPCursor, ScoreType)</a></span> - Method in class org.biojava.bio.dp.onehead.<a href="./org/biojava/bio/dp/onehead/SingleDP.html" title="class in org.biojava.bio.dp.onehead">SingleDP</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/twohead/PairwiseDP.html#forward(org.biojava.bio.symbol.SymbolList[], org.biojava.bio.dp.ScoreType)">forward(SymbolList[], ScoreType)</a></span> - Method in class org.biojava.bio.dp.twohead.<a href="./org/biojava/bio/dp/twohead/PairwiseDP.html" title="class in org.biojava.bio.dp.twohead">PairwiseDP</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEAnnotFilter.html#FORWARD">FORWARD</a></span> - Static variable in interface org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEAnnotFilter.html" title="interface in org.biojava.bio.seq.io.agave">AGAVEAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/onehead/SingleDP.html#forward_initialize(org.biojava.bio.dp.onehead.DPCursor, org.biojava.bio.dp.ScoreType)">forward_initialize(DPCursor, ScoreType)</a></span> - Method in class org.biojava.bio.dp.onehead.<a href="./org/biojava/bio/dp/onehead/SingleDP.html" title="class in org.biojava.bio.dp.onehead">SingleDP</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/projection/ProjectedFeatureHolder.html#forwardChangeEvent(org.biojava.utils.ChangeEvent)">forwardChangeEvent(ChangeEvent)</a></span> - Method in class org.biojava.bio.seq.projection.<a href="./org/biojava/bio/seq/projection/ProjectedFeatureHolder.html" title="class in org.biojava.bio.seq.projection">ProjectedFeatureHolder</a></dt>
<dd>
<div class="block">Called internally to generate a forwarded version of a ChangeEvent from our
underlying FeatureHolder</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/DP.html#forwardMatrix(org.biojava.bio.symbol.SymbolList[], org.biojava.bio.dp.ScoreType)">forwardMatrix(SymbolList[], ScoreType)</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/DP.html" title="class in org.biojava.bio.dp">DP</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/DP.html#forwardMatrix(org.biojava.bio.symbol.SymbolList[], org.biojava.bio.dp.DPMatrix, org.biojava.bio.dp.ScoreType)">forwardMatrix(SymbolList[], DPMatrix, ScoreType)</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/DP.html" title="class in org.biojava.bio.dp">DP</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/onehead/SingleDP.html#forwardMatrix(org.biojava.bio.symbol.SymbolList[], org.biojava.bio.dp.ScoreType)">forwardMatrix(SymbolList[], ScoreType)</a></span> - Method in class org.biojava.bio.dp.onehead.<a href="./org/biojava/bio/dp/onehead/SingleDP.html" title="class in org.biojava.bio.dp.onehead">SingleDP</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/onehead/SingleDP.html#forwardMatrix(org.biojava.bio.symbol.SymbolList[], org.biojava.bio.dp.DPMatrix, org.biojava.bio.dp.ScoreType)">forwardMatrix(SymbolList[], DPMatrix, ScoreType)</a></span> - Method in class org.biojava.bio.dp.onehead.<a href="./org/biojava/bio/dp/onehead/SingleDP.html" title="class in org.biojava.bio.dp.onehead">SingleDP</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/twohead/PairwiseDP.html#forwardMatrix(org.biojava.bio.symbol.SymbolList[], org.biojava.bio.dp.ScoreType)">forwardMatrix(SymbolList[], ScoreType)</a></span> - Method in class org.biojava.bio.dp.twohead.<a href="./org/biojava/bio/dp/twohead/PairwiseDP.html" title="class in org.biojava.bio.dp.twohead">PairwiseDP</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/twohead/PairwiseDP.html#forwardMatrix(org.biojava.bio.symbol.SymbolList[], org.biojava.bio.dp.DPMatrix, org.biojava.bio.dp.ScoreType)">forwardMatrix(SymbolList[], DPMatrix, ScoreType)</a></span> - Method in class org.biojava.bio.dp.twohead.<a href="./org/biojava/bio/dp/twohead/PairwiseDP.html" title="class in org.biojava.bio.dp.twohead">PairwiseDP</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/molbio/RestrictionEnzyme.html#forwardRegex">forwardRegex</a></span> - Variable in class org.biojava.bio.molbio.<a href="./org/biojava/bio/molbio/RestrictionEnzyme.html" title="class in org.biojava.bio.molbio">RestrictionEnzyme</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/twohead/CellCalculatorFactory.html#forwards(org.biojava.bio.dp.ScoreType)">forwards(ScoreType)</a></span> - Method in interface org.biojava.bio.dp.twohead.<a href="./org/biojava/bio/dp/twohead/CellCalculatorFactory.html" title="interface in org.biojava.bio.dp.twohead">CellCalculatorFactory</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/twohead/DPInterpreter.html#forwards(org.biojava.bio.dp.ScoreType)">forwards(ScoreType)</a></span> - Method in class org.biojava.bio.dp.twohead.<a href="./org/biojava/bio/dp/twohead/DPInterpreter.html" title="class in org.biojava.bio.dp.twohead">DPInterpreter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/DP.html#forwardsBackwards(org.biojava.bio.symbol.SymbolList[], org.biojava.bio.dp.ScoreType)">forwardsBackwards(SymbolList[], ScoreType)</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/DP.html" title="class in org.biojava.bio.dp">DP</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/DP.html#forwardTransitions(org.biojava.bio.dp.MarkovModel, org.biojava.bio.dp.State[])">forwardTransitions(MarkovModel, State[])</a></span> - Static method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/DP.html" title="class in org.biojava.bio.dp">DP</a></dt>
<dd>
<div class="block">Returns a matrix for the specified States describing all
valid Transitions between those States.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/DP.html#forwardTransitionScores(org.biojava.bio.dp.MarkovModel, org.biojava.bio.dp.State[], int[][], org.biojava.bio.dp.ScoreType)">forwardTransitionScores(MarkovModel, State[], int[][], ScoreType)</a></span> - Static method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/DP.html" title="class in org.biojava.bio.dp">DP</a></dt>
<dd>
<div class="block">Compute the log(score) of all transitions
between the specified States.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtFormat.html#fp">fp</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtFormat.html" title="class in org.biojavax.bio.seq.io">UniProtFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/FragmentJoiner.html#frag_pairwise_compat(org.biojava.bio.structure.align.pairwise.FragmentPair[], int, float, int)">frag_pairwise_compat(FragmentPair[], int, float, int)</a></span> - Method in class org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/FragmentJoiner.html" title="class in org.biojava.bio.structure.align.pairwise">FragmentJoiner</a></dt>
<dd>
<div class="block">Calculate the pairwise compatibility of fpairs.</div>
</dd>
<dt><a href="./org/biojava/bio/structure/align/pairwise/FragmentJoiner.html" title="class in org.biojava.bio.structure.align.pairwise"><span class="strong">FragmentJoiner</span></a> - Class in <a href="./org/biojava/bio/structure/align/pairwise/package-summary.html">org.biojava.bio.structure.align.pairwise</a></dt>
<dd>
<div class="block">Joins the initial Fragments together to larger Fragments</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/FragmentJoiner.html#FragmentJoiner()">FragmentJoiner()</a></span> - Constructor for class org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/FragmentJoiner.html" title="class in org.biojava.bio.structure.align.pairwise">FragmentJoiner</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/structure/align/pairwise/FragmentPair.html" title="class in org.biojava.bio.structure.align.pairwise"><span class="strong">FragmentPair</span></a> - Class in <a href="./org/biojava/bio/structure/align/pairwise/package-summary.html">org.biojava.bio.structure.align.pairwise</a></dt>
<dd>
<div class="block">a pair of fragments of two protein structures</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/FragmentPair.html#FragmentPair(int, int, int)">FragmentPair(int, int, int)</a></span> - Constructor for class org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/FragmentPair.html" title="class in org.biojava.bio.structure.align.pairwise">FragmentPair</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/Frame.html" title="interface in org.biojava.bio.seq"><span class="strong">Frame</span></a> - Interface in <a href="./org/biojava/bio/seq/package-summary.html">org.biojava.bio.seq</a></dt>
<dd>
<div class="block">Title: Frame.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/Frame.html#FRAME_0">FRAME_0</a></span> - Static variable in interface org.biojava.bio.seq.<a href="./org/biojava/bio/seq/Frame.html" title="interface in org.biojava.bio.seq">Frame</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FramedFeature.html#FRAME_0">FRAME_0</a></span> - Static variable in interface org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FramedFeature.html" title="interface in org.biojava.bio.seq">FramedFeature</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/Frame.html#FRAME_1">FRAME_1</a></span> - Static variable in interface org.biojava.bio.seq.<a href="./org/biojava/bio/seq/Frame.html" title="interface in org.biojava.bio.seq">Frame</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FramedFeature.html#FRAME_1">FRAME_1</a></span> - Static variable in interface org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FramedFeature.html" title="interface in org.biojava.bio.seq">FramedFeature</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/Frame.html#FRAME_2">FRAME_2</a></span> - Static variable in interface org.biojava.bio.seq.<a href="./org/biojava/bio/seq/Frame.html" title="interface in org.biojava.bio.seq">Frame</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FramedFeature.html#FRAME_2">FRAME_2</a></span> - Static variable in interface org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FramedFeature.html" title="interface in org.biojava.bio.seq">FramedFeature</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/FramedFeature.html" title="interface in org.biojava.bio.seq"><span class="strong">FramedFeature</span></a> - Interface in <a href="./org/biojava/bio/seq/package-summary.html">org.biojava.bio.seq</a></dt>
<dd>
<div class="block">Title: FramedFeature.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/FramedFeature.ReadingFrame.html" title="class in org.biojava.bio.seq"><span class="strong">FramedFeature.ReadingFrame</span></a> - Class in <a href="./org/biojava/bio/seq/package-summary.html">org.biojava.bio.seq</a></dt>
<dd>
<div class="block">A singleton to hold the frame information</div>
</dd>
<dt><a href="./org/biojava/bio/seq/FramedFeature.Template.html" title="class in org.biojava.bio.seq"><span class="strong">FramedFeature.Template</span></a> - Class in <a href="./org/biojava/bio/seq/package-summary.html">org.biojava.bio.seq</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FramedFeature.Template.html#FramedFeature.Template()">FramedFeature.Template()</a></span> - Constructor for class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FramedFeature.Template.html" title="class in org.biojava.bio.seq">FramedFeature.Template</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SuffixTree.html#frequency(int)">frequency(int)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SuffixTree.html" title="class in org.biojava.bio.symbol">SuffixTree</a></dt>
<dd>
<div class="block">Return the number of motifs of a given length encoded
in this SuffixTree.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/TrainerTransition.html#from">from</a></span> - Variable in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/TrainerTransition.html" title="class in org.biojava.bio.dp">TrainerTransition</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/Transition.html#from">from</a></span> - Variable in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/Transition.html" title="class in org.biojava.bio.dp">Transition</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.Option.html#FROM_TRACE_SAMPLE">FROM_TRACE_SAMPLE</a></span> - Static variable in class org.biojava.bio.chromatogram.graphic.<a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.Option.html" title="class in org.biojava.bio.chromatogram.graphic">ChromatogramGraphic.Option</a></dt>
<dd>
<div class="block">Option indicating the lowest (leftmost) trace sample that should be
drawn.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/DoubleAlphabet.html#fromArray(double[])">fromArray(double[])</a></span> - Static method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/DoubleAlphabet.html" title="class in org.biojava.bio.symbol">DoubleAlphabet</a></dt>
<dd>
<div class="block">
Retrieve a SymbolList view of an array of doubles.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/IntegerAlphabet.html#fromArray(int[])">fromArray(int[])</a></span> - Static method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/IntegerAlphabet.html" title="class in org.biojava.bio.symbol">IntegerAlphabet</a></dt>
<dd>
<div class="block">Retrieve a SymbolList view of an array of integers.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BiblioBookArticle.html#fromBook">fromBook</a></span> - Variable in class org.biojava.bibliography.<a href="./org/biojava/bibliography/BiblioBookArticle.html" title="class in org.biojava.bibliography">BiblioBookArticle</a></dt>
<dd>
<div class="block">Book this is from.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BiblioJournalArticle.html#fromJournal">fromJournal</a></span> - Variable in class org.biojava.bibliography.<a href="./org/biojava/bibliography/BiblioJournalArticle.html" title="class in org.biojava.bibliography">BiblioJournalArticle</a></dt>
<dd>
<div class="block">The journal that this article is in.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/CodonPrefTools.html#FUGU_NUCLEAR">FUGU_NUCLEAR</a></span> - Static variable in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/CodonPrefTools.html" title="class in org.biojava.bio.symbol">CodonPrefTools</a></dt>
<dd>
<div class="block">Takifugu rubripes codon preferences</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/Location.html#full">full</a></span> - Static variable in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/Location.html" title="interface in org.biojava.bio.symbol">Location</a></dt>
<dd>
<div class="block">The <code>Location</code> which contains all points.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.Terms.html#FULL_NAME_KEY">FULL_NAME_KEY</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.Terms.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat.Terms</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/hmmer/FullHmmerProfileHMM.html" title="class in org.biojava.bio.program.hmmer"><span class="strong">FullHmmerProfileHMM</span></a> - Class in <a href="./org/biojava/bio/program/hmmer/package-summary.html">org.biojava.bio.program.hmmer</a></dt>
<dd>
<div class="block">This is a class for representing the full HMMER generated Profile HMM (including loop
states N and C terminal looping states).</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLRichSequenceDB.html#fullyLoadRichSequence(org.biojavax.bio.seq.RichSequence)">fullyLoadRichSequence(RichSequence)</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLRichSequenceDB.html" title="class in org.biojavax.bio.db.biosql">BioSQLRichSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/GeneticAlgorithm.html#FUNCTION">FUNCTION</a></span> - Static variable in interface org.biojavax.ga.<a href="./org/biojavax/ga/GeneticAlgorithm.html" title="interface in org.biojavax.ga">GeneticAlgorithm</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/symbol/FundamentalAtomicSymbol.html" title="class in org.biojava.bio.symbol"><span class="strong">FundamentalAtomicSymbol</span></a> - Class in <a href="./org/biojava/bio/symbol/package-summary.html">org.biojava.bio.symbol</a></dt>
<dd>
<div class="block">An atomic symbol consisting only of itself.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/FundamentalAtomicSymbol.html#FundamentalAtomicSymbol(java.lang.String, org.biojava.bio.Annotation)">FundamentalAtomicSymbol(String, Annotation)</a></span> - Constructor for class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/FundamentalAtomicSymbol.html" title="class in org.biojava.bio.symbol">FundamentalAtomicSymbol</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/symbol/FuzzyLocation.html" title="class in org.biojava.bio.symbol"><span class="strong">FuzzyLocation</span></a> - Class in <a href="./org/biojava/bio/symbol/package-summary.html">org.biojava.bio.symbol</a></dt>
<dd>
<div class="block">A 'fuzzy' location a-la Embl fuzzy locations.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/FuzzyLocation.html#FuzzyLocation(int, int, int, int, org.biojava.bio.symbol.FuzzyLocation.RangeResolver)">FuzzyLocation(int, int, int, int, FuzzyLocation.RangeResolver)</a></span> - Constructor for class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/FuzzyLocation.html" title="class in org.biojava.bio.symbol">FuzzyLocation</a></dt>
<dd>
<div class="block">Create a new FuzzyLocation with endpoints (outerMin.innerMin) and (innerMax.outerMax).</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/FuzzyLocation.html#FuzzyLocation(int, int, int, int, boolean, boolean, org.biojava.bio.symbol.FuzzyLocation.RangeResolver)">FuzzyLocation(int, int, int, int, boolean, boolean, FuzzyLocation.RangeResolver)</a></span> - Constructor for class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/FuzzyLocation.html" title="class in org.biojava.bio.symbol">FuzzyLocation</a></dt>
<dd>
<div class="block">Create a new FuzzyLocation with endpoints (outerMin.innerMin) and
(innerMax.outerMax).</div>
</dd>
<dt><a href="./org/biojava/bio/symbol/FuzzyLocation.RangeResolver.html" title="interface in org.biojava.bio.symbol"><span class="strong">FuzzyLocation.RangeResolver</span></a> - Interface in <a href="./org/biojava/bio/symbol/package-summary.html">org.biojava.bio.symbol</a></dt>
<dd>
<div class="block">Determines how a <code>FuzzyLocation</code> should be treated when used
as a normal <code>Location</code>.</div>
</dd>
<dt><a href="./org/biojava/bio/symbol/FuzzyPointLocation.html" title="class in org.biojava.bio.symbol"><span class="strong">FuzzyPointLocation</span></a> - Class in <a href="./org/biojava/bio/symbol/package-summary.html">org.biojava.bio.symbol</a></dt>
<dd>
<div class="block"><code>FuzzyPointLocation</code> represents two types of EMBL-style
partially-defined locations.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/FuzzyPointLocation.html#FuzzyPointLocation(int, int, org.biojava.bio.symbol.FuzzyPointLocation.PointResolver)">FuzzyPointLocation(int, int, FuzzyPointLocation.PointResolver)</a></span> - Constructor for class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/FuzzyPointLocation.html" title="class in org.biojava.bio.symbol">FuzzyPointLocation</a></dt>
<dd>
<div class="block">Creates a new <code>FuzzyPointLocation</code> object.</div>
</dd>
<dt><a href="./org/biojava/bio/symbol/FuzzyPointLocation.PointResolver.html" title="interface in org.biojava.bio.symbol"><span class="strong">FuzzyPointLocation.PointResolver</span></a> - Interface in <a href="./org/biojava/bio/symbol/package-summary.html">org.biojava.bio.symbol</a></dt>
<dd>
<div class="block">Determines how a <code>FuzzyPointLocation</code> should be treated when used
as a normal <code>Location</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/TranslationTable.html#FWORM_MITO">FWORM_MITO</a></span> - Static variable in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/TranslationTable.html" title="interface in org.biojava.bio.symbol">TranslationTable</a></dt>
<dd>
<div class="block">Translation table name for the flatworm mitochondrial genetic
code.</div>
</dd>
</dl>
<a name="_G_">
<!-- -->
</a>
<h2 class="title">G</h2>
<dl>
<dt><span class="strong"><a href="./org/biojava/bio/seq/DNATools.html#g()">g()</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/DNATools.html" title="class in org.biojava.bio.seq">DNATools</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/NucleotideTools.html#g()">g()</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/NucleotideTools.html" title="class in org.biojava.bio.seq">NucleotideTools</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/ProteinTools.html#g()">g()</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/ProteinTools.html" title="class in org.biojava.bio.seq">ProteinTools</a></dt>
<dd>
<div class="block">Returns the <code>AtomicSymbol</code> for the amino acid
Glycine</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/RNATools.html#g()">g()</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/RNATools.html" title="class in org.biojava.bio.seq">RNATools</a></dt>
<dd> </dd>
<dt><a href="./org/biojavax/ga/functions/GACross.html" title="interface in org.biojavax.ga.functions"><span class="strong">GACross</span></a> - Interface in <a href="./org/biojavax/ga/functions/package-summary.html">org.biojavax.ga.functions</a></dt>
<dd>
<div class="block">Holds the results of a CrossOver event, objects of this type are made by
<code>CrossOverFunctions</code></div>
</dd>
<dt><a href="./org/biojavax/ga/functions/GACrossResult.html" title="interface in org.biojavax.ga.functions"><span class="strong">GACrossResult</span></a> - Interface in <a href="./org/biojavax/ga/functions/package-summary.html">org.biojavax.ga.functions</a></dt>
<dd>
<div class="block">Holds the results of a CrossOver event, objects of this type are made by
<code>CrossOverFunctions</code></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game/GAMEAnnotationHandler.html#GAME_ANNOTATION_HANDLER_FACTORY">GAME_ANNOTATION_HANDLER_FACTORY</a></span> - Static variable in class org.biojava.bio.seq.io.game.<a href="./org/biojava/bio/seq/io/game/GAMEAnnotationHandler.html" title="class in org.biojava.bio.seq.io.game">GAMEAnnotationHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game12/GAMEAnnotationHandler.html#GAME_ANNOTATION_HANDLER_FACTORY">GAME_ANNOTATION_HANDLER_FACTORY</a></span> - Static variable in class org.biojava.bio.seq.io.game12.<a href="./org/biojava/bio/seq/io/game12/GAMEAnnotationHandler.html" title="class in org.biojava.bio.seq.io.game12">GAMEAnnotationHandler</a></dt>
<dd>
<div class="block">Description of the Field</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game12/GAMEAspectHandler.html#GAME_ASPECT_HANDLER_FACTORY">GAME_ASPECT_HANDLER_FACTORY</a></span> - Static variable in class org.biojava.bio.seq.io.game12.<a href="./org/biojava/bio/seq/io/game12/GAMEAspectHandler.html" title="class in org.biojava.bio.seq.io.game12">GAMEAspectHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game/GAMEAspectPropHandler.html#GAME_ASPECT_PROP_HANDLER_FACTORY">GAME_ASPECT_PROP_HANDLER_FACTORY</a></span> - Static variable in class org.biojava.bio.seq.io.game.<a href="./org/biojava/bio/seq/io/game/GAMEAspectPropHandler.html" title="class in org.biojava.bio.seq.io.game">GAMEAspectPropHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game12/GAMEDbxrefHandler.html#GAME_DBXREF_HANDLER_FACTORY">GAME_DBXREF_HANDLER_FACTORY</a></span> - Static variable in class org.biojava.bio.seq.io.game12.<a href="./org/biojava/bio/seq/io/game12/GAMEDbxrefHandler.html" title="class in org.biojava.bio.seq.io.game12">GAMEDbxrefHandler</a></dt>
<dd>
<div class="block">Description of the Field</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game/GAMEDbxrefPropHandler.html#GAME_DBXREF_PROP_HANDLER_FACTORY">GAME_DBXREF_PROP_HANDLER_FACTORY</a></span> - Static variable in class org.biojava.bio.seq.io.game.<a href="./org/biojava/bio/seq/io/game/GAMEDbxrefPropHandler.html" title="class in org.biojava.bio.seq.io.game">GAMEDbxrefPropHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game/GAMEDescriptionPropHandler.html#GAME_DESCRIPTION_PROP_HANDLER_FACTORY">GAME_DESCRIPTION_PROP_HANDLER_FACTORY</a></span> - Static variable in class org.biojava.bio.seq.io.game.<a href="./org/biojava/bio/seq/io/game/GAMEDescriptionPropHandler.html" title="class in org.biojava.bio.seq.io.game">GAMEDescriptionPropHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game12/GAMEFeatureSetHandler.html#GAME_FEATURE_SET_HANDLER_FACTORY">GAME_FEATURE_SET_HANDLER_FACTORY</a></span> - Static variable in class org.biojava.bio.seq.io.game12.<a href="./org/biojava/bio/seq/io/game12/GAMEFeatureSetHandler.html" title="class in org.biojava.bio.seq.io.game12">GAMEFeatureSetHandler</a></dt>
<dd>
<div class="block">Description of the Field</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game12/GAMEFeatureSpanHandler.html#GAME_FEATURE_SPAN_HANDLER_FACTORY">GAME_FEATURE_SPAN_HANDLER_FACTORY</a></span> - Static variable in class org.biojava.bio.seq.io.game12.<a href="./org/biojava/bio/seq/io/game12/GAMEFeatureSpanHandler.html" title="class in org.biojava.bio.seq.io.game12">GAMEFeatureSpanHandler</a></dt>
<dd>
<div class="block">Description of the Field</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game/GAMEFeatureSetHandler.html#GAME_FEATURESET_HANDLER_FACTORY">GAME_FEATURESET_HANDLER_FACTORY</a></span> - Static variable in class org.biojava.bio.seq.io.game.<a href="./org/biojava/bio/seq/io/game/GAMEFeatureSetHandler.html" title="class in org.biojava.bio.seq.io.game">GAMEFeatureSetHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game/GAMEFeatureSetPropHandler.html#GAME_FEATURESET_PROP_HANDLER_FACTORY">GAME_FEATURESET_PROP_HANDLER_FACTORY</a></span> - Static variable in class org.biojava.bio.seq.io.game.<a href="./org/biojava/bio/seq/io/game/GAMEFeatureSetPropHandler.html" title="class in org.biojava.bio.seq.io.game">GAMEFeatureSetPropHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game/GAMEFeatureSpanHandler.html#GAME_FEATURESPAN_HANDLER_FACTORY">GAME_FEATURESPAN_HANDLER_FACTORY</a></span> - Static variable in class org.biojava.bio.seq.io.game.<a href="./org/biojava/bio/seq/io/game/GAMEFeatureSpanHandler.html" title="class in org.biojava.bio.seq.io.game">GAMEFeatureSpanHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game12/GAMEGeneHandler.html#GAME_GENE_HANDLER_FACTORY">GAME_GENE_HANDLER_FACTORY</a></span> - Static variable in class org.biojava.bio.seq.io.game12.<a href="./org/biojava/bio/seq/io/game12/GAMEGeneHandler.html" title="class in org.biojava.bio.seq.io.game12">GAMEGeneHandler</a></dt>
<dd>
<div class="block">Description of the Field</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game/GAMEGenePropHandler.html#GAME_GENE_PROP_HANDLER_FACTORY">GAME_GENE_PROP_HANDLER_FACTORY</a></span> - Static variable in class org.biojava.bio.seq.io.game.<a href="./org/biojava/bio/seq/io/game/GAMEGenePropHandler.html" title="class in org.biojava.bio.seq.io.game">GAMEGenePropHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game/GAMEMapPosPropHandler.html#GAME_MAP_POS_PROP_HANDLER_FACTORY">GAME_MAP_POS_PROP_HANDLER_FACTORY</a></span> - Static variable in class org.biojava.bio.seq.io.game.<a href="./org/biojava/bio/seq/io/game/GAMEMapPosPropHandler.html" title="class in org.biojava.bio.seq.io.game">GAMEMapPosPropHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game/GAMENamePropHandler.html#GAME_NAME_PROP_HANDLER_FACTORY">GAME_NAME_PROP_HANDLER_FACTORY</a></span> - Static variable in class org.biojava.bio.seq.io.game.<a href="./org/biojava/bio/seq/io/game/GAMENamePropHandler.html" title="class in org.biojava.bio.seq.io.game">GAMENamePropHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game12/GAMEPropertyHandler.html#GAME_PROPERTY_HANDLER_FACTORY">GAME_PROPERTY_HANDLER_FACTORY</a></span> - Static variable in class org.biojava.bio.seq.io.game12.<a href="./org/biojava/bio/seq/io/game12/GAMEPropertyHandler.html" title="class in org.biojava.bio.seq.io.game12">GAMEPropertyHandler</a></dt>
<dd>
<div class="block">Description of the Field</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game/GAMEResiduesPropHandler.html#GAME_RESIDUES_PROP_HANDLER_FACTORY">GAME_RESIDUES_PROP_HANDLER_FACTORY</a></span> - Static variable in class org.biojava.bio.seq.io.game.<a href="./org/biojava/bio/seq/io/game/GAMEResiduesPropHandler.html" title="class in org.biojava.bio.seq.io.game">GAMEResiduesPropHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game12/GAMESeqHandler.html#GAME_SEQ_HANDLER_FACTORY">GAME_SEQ_HANDLER_FACTORY</a></span> - Static variable in class org.biojava.bio.seq.io.game12.<a href="./org/biojava/bio/seq/io/game12/GAMESeqHandler.html" title="class in org.biojava.bio.seq.io.game12">GAMESeqHandler</a></dt>
<dd>
<div class="block">Description of the Field</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game/GAMESeqPropHandler.html#GAME_SEQ_PROP_HANDLER_FACTORY">GAME_SEQ_PROP_HANDLER_FACTORY</a></span> - Static variable in class org.biojava.bio.seq.io.game.<a href="./org/biojava/bio/seq/io/game/GAMESeqPropHandler.html" title="class in org.biojava.bio.seq.io.game">GAMESeqPropHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game12/GAMESeqRelHandler.html#GAME_SEQ_REL_HANDLER_FACTORY">GAME_SEQ_REL_HANDLER_FACTORY</a></span> - Static variable in class org.biojava.bio.seq.io.game12.<a href="./org/biojava/bio/seq/io/game12/GAMESeqRelHandler.html" title="class in org.biojava.bio.seq.io.game12">GAMESeqRelHandler</a></dt>
<dd>
<div class="block">Description of the Field</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game/GAMESeqRelPropHandler.html#GAME_SEQREL_PROP_HANDLER_FACTORY">GAME_SEQREL_PROP_HANDLER_FACTORY</a></span> - Static variable in class org.biojava.bio.seq.io.game.<a href="./org/biojava/bio/seq/io/game/GAMESeqRelPropHandler.html" title="class in org.biojava.bio.seq.io.game">GAMESeqRelPropHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game12/GAMESpanHandler.html#GAME_SPAN_HANDLER_FACTORY">GAME_SPAN_HANDLER_FACTORY</a></span> - Static variable in class org.biojava.bio.seq.io.game12.<a href="./org/biojava/bio/seq/io/game12/GAMESpanHandler.html" title="class in org.biojava.bio.seq.io.game12">GAMESpanHandler</a></dt>
<dd>
<div class="block">Description of the Field</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game/GAMESpanPropHandler.html#GAME_SPAN_PROP_HANDLER_FACTORY">GAME_SPAN_PROP_HANDLER_FACTORY</a></span> - Static variable in class org.biojava.bio.seq.io.game.<a href="./org/biojava/bio/seq/io/game/GAMESpanPropHandler.html" title="class in org.biojava.bio.seq.io.game">GAMESpanPropHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game/GAMETypePropHandler.html#GAME_TYPE_PROP_HANDLER_FACTORY">GAME_TYPE_PROP_HANDLER_FACTORY</a></span> - Static variable in class org.biojava.bio.seq.io.game.<a href="./org/biojava/bio/seq/io/game/GAMETypePropHandler.html" title="class in org.biojava.bio.seq.io.game">GAMETypePropHandler</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/io/game/GAMEAnnotationHandler.html" title="class in org.biojava.bio.seq.io.game"><span class="strong">GAMEAnnotationHandler</span></a> - Class in <a href="./org/biojava/bio/seq/io/game/package-summary.html">org.biojava.bio.seq.io.game</a></dt>
<dd>
<div class="block">Handles the GAME <annotation> element</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/game12/GAMEAnnotationHandler.html" title="class in org.biojava.bio.seq.io.game12"><span class="strong">GAMEAnnotationHandler</span></a> - Class in <a href="./org/biojava/bio/seq/io/game12/package-summary.html">org.biojava.bio.seq.io.game12</a></dt>
<dd>
<div class="block">Handles the GAME <annotation> element</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/game12/GAMEAspectHandler.html" title="class in org.biojava.bio.seq.io.game12"><span class="strong">GAMEAspectHandler</span></a> - Class in <a href="./org/biojava/bio/seq/io/game12/package-summary.html">org.biojava.bio.seq.io.game12</a></dt>
<dd>
<div class="block">Handles the GAME <aspect> element</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/game/GAMEAspectPropHandler.html" title="class in org.biojava.bio.seq.io.game"><span class="strong">GAMEAspectPropHandler</span></a> - Class in <a href="./org/biojava/bio/seq/io/game/package-summary.html">org.biojava.bio.seq.io.game</a></dt>
<dd>
<div class="block">Handles the GAME <aspect> element</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/game12/GAMEDbxrefHandler.html" title="class in org.biojava.bio.seq.io.game12"><span class="strong">GAMEDbxrefHandler</span></a> - Class in <a href="./org/biojava/bio/seq/io/game12/package-summary.html">org.biojava.bio.seq.io.game12</a></dt>
<dd>
<div class="block">Handles the GAME <dbxref> element</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/game/GAMEDbxrefPropHandler.html" title="class in org.biojava.bio.seq.io.game"><span class="strong">GAMEDbxrefPropHandler</span></a> - Class in <a href="./org/biojava/bio/seq/io/game/package-summary.html">org.biojava.bio.seq.io.game</a></dt>
<dd>
<div class="block">Deals with database crossreferences</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/game/GAMEDbxrefPropHandler.DbXrefElement.html" title="class in org.biojava.bio.seq.io.game"><span class="strong">GAMEDbxrefPropHandler.DbXrefElement</span></a> - Class in <a href="./org/biojava/bio/seq/io/game/package-summary.html">org.biojava.bio.seq.io.game</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/io/game/GAMEDescriptionPropHandler.html" title="class in org.biojava.bio.seq.io.game"><span class="strong">GAMEDescriptionPropHandler</span></a> - Class in <a href="./org/biojava/bio/seq/io/game/package-summary.html">org.biojava.bio.seq.io.game</a></dt>
<dd>
<div class="block">StAX handler for GAME <description> elements.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game/GAMEDescriptionPropHandler.html#GAMEDescriptionPropHandler(org.biojava.bio.seq.io.game.StAXFeatureHandler)">GAMEDescriptionPropHandler(StAXFeatureHandler)</a></span> - Constructor for class org.biojava.bio.seq.io.game.<a href="./org/biojava/bio/seq/io/game/GAMEDescriptionPropHandler.html" title="class in org.biojava.bio.seq.io.game">GAMEDescriptionPropHandler</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/io/game/GAMEFeatureCallbackItf.html" title="interface in org.biojava.bio.seq.io.game"><span class="strong">GAMEFeatureCallbackItf</span></a> - Interface in <a href="./org/biojava/bio/seq/io/game/package-summary.html">org.biojava.bio.seq.io.game</a></dt>
<dd>
<div class="block">An interface that can be tested for by nested handlers
when trying to do a callback.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/game/GAMEFeatureSetHandler.html" title="class in org.biojava.bio.seq.io.game"><span class="strong">GAMEFeatureSetHandler</span></a> - Class in <a href="./org/biojava/bio/seq/io/game/package-summary.html">org.biojava.bio.seq.io.game</a></dt>
<dd>
<div class="block">Handles the <feature_set> element</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/game12/GAMEFeatureSetHandler.html" title="class in org.biojava.bio.seq.io.game12"><span class="strong">GAMEFeatureSetHandler</span></a> - Class in <a href="./org/biojava/bio/seq/io/game12/package-summary.html">org.biojava.bio.seq.io.game12</a></dt>
<dd>
<div class="block">Handles the GAME <feature_set> element
this element is used to represent transcripts.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/game/GAMEFeatureSetPropHandler.html" title="class in org.biojava.bio.seq.io.game"><span class="strong">GAMEFeatureSetPropHandler</span></a> - Class in <a href="./org/biojava/bio/seq/io/game/package-summary.html">org.biojava.bio.seq.io.game</a></dt>
<dd>
<div class="block">Handles the GAME <feature_set> element</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/game/GAMEFeatureSpanHandler.html" title="class in org.biojava.bio.seq.io.game"><span class="strong">GAMEFeatureSpanHandler</span></a> - Class in <a href="./org/biojava/bio/seq/io/game/package-summary.html">org.biojava.bio.seq.io.game</a></dt>
<dd>
<div class="block">Handles the <feature_span> element</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/game12/GAMEFeatureSpanHandler.html" title="class in org.biojava.bio.seq.io.game12"><span class="strong">GAMEFeatureSpanHandler</span></a> - Class in <a href="./org/biojava/bio/seq/io/game12/package-summary.html">org.biojava.bio.seq.io.game12</a></dt>
<dd>
<div class="block">Handles the GAME <feature_span> element</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/game12/GAMEFeatureSpanHandler.SeqRelHandler.html" title="class in org.biojava.bio.seq.io.game12"><span class="strong">GAMEFeatureSpanHandler.SeqRelHandler</span></a> - Class in <a href="./org/biojava/bio/seq/io/game12/package-summary.html">org.biojava.bio.seq.io.game12</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/io/GAMEFormat.html" title="class in org.biojava.bio.seq.io"><span class="strong">GAMEFormat</span></a> - Class in <a href="./org/biojava/bio/seq/io/package-summary.html">org.biojava.bio.seq.io</a></dt>
<dd>
<div class="block">A rudimentary read-only GAME 1.2 Format object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/GAMEFormat.html#GAMEFormat()">GAMEFormat()</a></span> - Constructor for class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/GAMEFormat.html" title="class in org.biojava.bio.seq.io">GAMEFormat</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/io/game12/GAMEGeneHandler.html" title="class in org.biojava.bio.seq.io.game12"><span class="strong">GAMEGeneHandler</span></a> - Class in <a href="./org/biojava/bio/seq/io/game12/package-summary.html">org.biojava.bio.seq.io.game12</a></dt>
<dd>
<div class="block">Handles the GAME <annotation> element</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/game/GAMEGenePropHandler.html" title="class in org.biojava.bio.seq.io.game"><span class="strong">GAMEGenePropHandler</span></a> - Class in <a href="./org/biojava/bio/seq/io/game/package-summary.html">org.biojava.bio.seq.io.game</a></dt>
<dd>
<div class="block">Handles the GAME <gene> element</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/game/GAMEHandler.html" title="class in org.biojava.bio.seq.io.game"><span class="strong">GAMEHandler</span></a> - Class in <a href="./org/biojava/bio/seq/io/game/package-summary.html">org.biojava.bio.seq.io.game</a></dt>
<dd>
<div class="block">Handles the root GAME element</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game/GAMEHandler.html#GAMEHandler()">GAMEHandler()</a></span> - Constructor for class org.biojava.bio.seq.io.game.<a href="./org/biojava/bio/seq/io/game/GAMEHandler.html" title="class in org.biojava.bio.seq.io.game">GAMEHandler</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/io/game12/GAMEHandler.html" title="class in org.biojava.bio.seq.io.game12"><span class="strong">GAMEHandler</span></a> - Class in <a href="./org/biojava/bio/seq/io/game12/package-summary.html">org.biojava.bio.seq.io.game12</a></dt>
<dd>
<div class="block">Handles the root GAME element</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game12/GAMEHandler.html#GAMEHandler(org.biojava.bio.seq.io.SeqIOListener)">GAMEHandler(SeqIOListener)</a></span> - Constructor for class org.biojava.bio.seq.io.game12.<a href="./org/biojava/bio/seq/io/game12/GAMEHandler.html" title="class in org.biojava.bio.seq.io.game12">GAMEHandler</a></dt>
<dd>
<div class="block">Constructor for the GAMEHandler object</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/game/GAMEMapPosPropHandler.html" title="class in org.biojava.bio.seq.io.game"><span class="strong">GAMEMapPosPropHandler</span></a> - Class in <a href="./org/biojava/bio/seq/io/game/package-summary.html">org.biojava.bio.seq.io.game</a></dt>
<dd>
<div class="block">Handles the GAME <map_position> element
Currently, it just ignores it!</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/game/GAMENameCallbackItf.html" title="interface in org.biojava.bio.seq.io.game"><span class="strong">GAMENameCallbackItf</span></a> - Interface in <a href="./org/biojava/bio/seq/io/game/package-summary.html">org.biojava.bio.seq.io.game</a></dt>
<dd>
<div class="block">An interface that can be tested for by nested handlers
when trying to do a callback.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/game/GAMENamePropHandler.html" title="class in org.biojava.bio.seq.io.game"><span class="strong">GAMENamePropHandler</span></a> - Class in <a href="./org/biojava/bio/seq/io/game/package-summary.html">org.biojava.bio.seq.io.game</a></dt>
<dd>
<div class="block">StAX handler for the GAME <name> element.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game/GAMENamePropHandler.html#GAMENamePropHandler(org.biojava.bio.seq.io.game.StAXFeatureHandler)">GAMENamePropHandler(StAXFeatureHandler)</a></span> - Constructor for class org.biojava.bio.seq.io.game.<a href="./org/biojava/bio/seq/io/game/GAMENamePropHandler.html" title="class in org.biojava.bio.seq.io.game">GAMENamePropHandler</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/io/game12/GAMEPropertyHandler.html" title="class in org.biojava.bio.seq.io.game12"><span class="strong">GAMEPropertyHandler</span></a> - Class in <a href="./org/biojava/bio/seq/io/game12/package-summary.html">org.biojava.bio.seq.io.game12</a></dt>
<dd>
<div class="block">Handles the GAME <dbxref> element</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/game/GAMEResiduesPropHandler.html" title="class in org.biojava.bio.seq.io.game"><span class="strong">GAMEResiduesPropHandler</span></a> - Class in <a href="./org/biojava/bio/seq/io/game/package-summary.html">org.biojava.bio.seq.io.game</a></dt>
<dd>
<div class="block">StAX handler for GAME <residues> elements.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game/GAMEResiduesPropHandler.html#GAMEResiduesPropHandler(org.biojava.bio.seq.io.game.StAXFeatureHandler)">GAMEResiduesPropHandler(StAXFeatureHandler)</a></span> - Constructor for class org.biojava.bio.seq.io.game.<a href="./org/biojava/bio/seq/io/game/GAMEResiduesPropHandler.html" title="class in org.biojava.bio.seq.io.game">GAMEResiduesPropHandler</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/io/game12/GAMESeqHandler.html" title="class in org.biojava.bio.seq.io.game12"><span class="strong">GAMESeqHandler</span></a> - Class in <a href="./org/biojava/bio/seq/io/game12/package-summary.html">org.biojava.bio.seq.io.game12</a></dt>
<dd>
<div class="block">Handles the GAME <seq> element</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/game/GAMESeqPropHandler.html" title="class in org.biojava.bio.seq.io.game"><span class="strong">GAMESeqPropHandler</span></a> - Class in <a href="./org/biojava/bio/seq/io/game/package-summary.html">org.biojava.bio.seq.io.game</a></dt>
<dd>
<div class="block">Handles the GAME <seq> element</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/game12/GAMESeqRelHandler.html" title="class in org.biojava.bio.seq.io.game12"><span class="strong">GAMESeqRelHandler</span></a> - Class in <a href="./org/biojava/bio/seq/io/game12/package-summary.html">org.biojava.bio.seq.io.game12</a></dt>
<dd>
<div class="block">Handles the GAME <<seq_relationship>> element</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/game/GAMESeqRelPropHandler.html" title="class in org.biojava.bio.seq.io.game"><span class="strong">GAMESeqRelPropHandler</span></a> - Class in <a href="./org/biojava/bio/seq/io/game/package-summary.html">org.biojava.bio.seq.io.game</a></dt>
<dd>
<div class="block">Handles the GAME <aspect> element</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/game12/GAMESpanHandler.html" title="class in org.biojava.bio.seq.io.game12"><span class="strong">GAMESpanHandler</span></a> - Class in <a href="./org/biojava/bio/seq/io/game12/package-summary.html">org.biojava.bio.seq.io.game12</a></dt>
<dd>
<div class="block">Handles the GAME <<span>> element.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/game/GAMESpanPropHandler.html" title="class in org.biojava.bio.seq.io.game"><span class="strong">GAMESpanPropHandler</span></a> - Class in <a href="./org/biojava/bio/seq/io/game/package-summary.html">org.biojava.bio.seq.io.game</a></dt>
<dd>
<div class="block">Handles the GAME <span> element
Currently, it just ignores it!</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/game/GAMETranscriptCallbackItf.html" title="interface in org.biojava.bio.seq.io.game"><span class="strong">GAMETranscriptCallbackItf</span></a> - Interface in <a href="./org/biojava/bio/seq/io/game/package-summary.html">org.biojava.bio.seq.io.game</a></dt>
<dd>
<div class="block">An interface that can be tested for by nested handlers
when trying to do a callback.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/game/GAMETypePropHandler.html" title="class in org.biojava.bio.seq.io.game"><span class="strong">GAMETypePropHandler</span></a> - Class in <a href="./org/biojava/bio/seq/io/game/package-summary.html">org.biojava.bio.seq.io.game</a></dt>
<dd>
<div class="block">StAX handler for GAME <type> elements.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game/GAMETypePropHandler.html#GAMETypePropHandler(org.biojava.bio.seq.io.game.StAXFeatureHandler)">GAMETypePropHandler(StAXFeatureHandler)</a></span> - Constructor for class org.biojava.bio.seq.io.game.<a href="./org/biojava/bio/seq/io/game/GAMETypePropHandler.html" title="class in org.biojava.bio.seq.io.game">GAMETypePropHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/util/SequenceScalePanel.html#GAP_COLOR">GAP_COLOR</a></span> - Static variable in class org.biojava.bio.structure.gui.util.<a href="./org/biojava/bio/structure/gui/util/SequenceScalePanel.html" title="class in org.biojava.bio.structure.gui.util">SequenceScalePanel</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/structure/align/helper/GapArray.html" title="class in org.biojava.bio.structure.align.helper"><span class="strong">GapArray</span></a> - Class in <a href="./org/biojava/bio/structure/align/helper/package-summary.html">org.biojava.bio.structure.align.helper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/helper/GapArray.html#GapArray()">GapArray()</a></span> - Constructor for class org.biojava.bio.structure.align.helper.<a href="./org/biojava/bio/structure/align/helper/GapArray.html" title="class in org.biojava.bio.structure.align.helper">GapArray</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/dist/GapDistribution.html" title="class in org.biojava.bio.dist"><span class="strong">GapDistribution</span></a> - Class in <a href="./org/biojava/bio/dist/package-summary.html">org.biojava.bio.dist</a></dt>
<dd>
<div class="block">This distribution emits gap symbols.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/GapDistribution.html#GapDistribution(org.biojava.bio.symbol.Alphabet)">GapDistribution(Alphabet)</a></span> - Constructor for class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/GapDistribution.html" title="class in org.biojava.bio.dist">GapDistribution</a></dt>
<dd>
<div class="block">Get a GapDistribution for an alphabet.</div>
</dd>
<dt><a href="./org/biojava/bio/gui/sequence/GappedRenderer.html" title="class in org.biojava.bio.gui.sequence"><span class="strong">GappedRenderer</span></a> - Class in <a href="./org/biojava/bio/gui/sequence/package-summary.html">org.biojava.bio.gui.sequence</a></dt>
<dd>
<div class="block">A renderer that will display a gapped sequence as a discontinuous series of
regions.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/GappedRenderer.html#GappedRenderer()">GappedRenderer()</a></span> - Constructor for class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/GappedRenderer.html" title="class in org.biojava.bio.gui.sequence">GappedRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/GappedRenderer.html#GappedRenderer(org.biojava.bio.gui.sequence.SequenceRenderer)">GappedRenderer(SequenceRenderer)</a></span> - Constructor for class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/GappedRenderer.html" title="class in org.biojava.bio.gui.sequence">GappedRenderer</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/GappedSequence.html" title="interface in org.biojava.bio.seq"><span class="strong">GappedSequence</span></a> - Interface in <a href="./org/biojava/bio/seq/package-summary.html">org.biojava.bio.seq</a></dt>
<dd>
<div class="block">Extension of GappedSymbolList which also projects features
into the gapped coordinate system.</div>
</dd>
<dt><a href="./org/biojava/bio/symbol/GappedSymbolList.html" title="interface in org.biojava.bio.symbol"><span class="strong">GappedSymbolList</span></a> - Interface in <a href="./org/biojava/bio/symbol/package-summary.html">org.biojava.bio.symbol</a></dt>
<dd>
<div class="block">This extends SymbolList with API for manipulating, inserting and deleting
gaps.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleGappedSymbolList.html#gappedToLocation(org.biojava.bio.symbol.Location)">gappedToLocation(Location)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleGappedSymbolList.html" title="class in org.biojava.bio.symbol">SimpleGappedSymbolList</a></dt>
<dd>
<div class="block">Translates a Location from the gapped view into the underlying sequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/SequenceTools.html#gappedView(org.biojava.bio.seq.Sequence)">gappedView(Sequence)</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/SequenceTools.html" title="class in org.biojava.bio.seq">SequenceTools</a></dt>
<dd>
<div class="block">Create a new gapped sequence for a sequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/EditableAlignment.html#GAPS">GAPS</a></span> - Static variable in interface org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/EditableAlignment.html" title="interface in org.biojava.bio.alignment">EditableAlignment</a></dt>
<dd> </dd>
<dt><a href="./org/biojavax/ga/GAStoppingCriteria.html" title="interface in org.biojavax.ga"><span class="strong">GAStoppingCriteria</span></a> - Interface in <a href="./org/biojavax/ga/package-summary.html">org.biojavax.ga</a></dt>
<dd>
<div class="block">Used by a <code>GeneticAlgorithm.run()</code> method
to determine when the algorithm should stop</div>
</dd>
<dt><a href="./org/biojavax/ga/GAStoppingCriteria.MaximumGeneration.html" title="class in org.biojavax.ga"><span class="strong">GAStoppingCriteria.MaximumGeneration</span></a> - Class in <a href="./org/biojavax/ga/package-summary.html">org.biojavax.ga</a></dt>
<dd>
<div class="block">Simple Implementation of GAStoppingCriteria, signals
a <code>GeneticAlgorithm</code> to stop after n generations</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ga/GAStoppingCriteria.MaximumGeneration.html#GAStoppingCriteria.MaximumGeneration(int)">GAStoppingCriteria.MaximumGeneration(int)</a></span> - Constructor for class org.biojavax.ga.<a href="./org/biojavax/ga/GAStoppingCriteria.MaximumGeneration.html" title="class in org.biojavax.ga">GAStoppingCriteria.MaximumGeneration</a></dt>
<dd>
<div class="block">Public Constructer</div>
</dd>
<dt><a href="./org/biojavax/ga/util/GATools.html" title="class in org.biojavax.ga.util"><span class="strong">GATools</span></a> - Class in <a href="./org/biojavax/ga/util/package-summary.html">org.biojavax.ga.util</a></dt>
<dd>
<div class="block"> Utility methods for the GA library</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ga/util/GATools.html#GATools()">GATools()</a></span> - Constructor for class org.biojavax.ga.util.<a href="./org/biojavax/ga/util/GATools.html" title="class in org.biojavax.ga.util">GATools</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOConstants.html#GCG">GCG</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOConstants.html" title="class in org.biojava.bio.seq.io">SeqIOConstants</a></dt>
<dd>
<div class="block"><code>GCG</code> indicates that the sequence format is GCG.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.HibernateFeatureFilter.html#ge">ge</a></span> - Variable in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.HibernateFeatureFilter.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.HibernateFeatureFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/LineSplitParser.html#GENBANK">GENBANK</a></span> - Static variable in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/LineSplitParser.html" title="class in org.biojava.bio.program.tagvalue">LineSplitParser</a></dt>
<dd>
<div class="block">A LineSplitParser pre-configured to process GENBANK-style flat files.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOConstants.html#GENBANK">GENBANK</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOConstants.html" title="class in org.biojava.bio.seq.io">SeqIOConstants</a></dt>
<dd>
<div class="block"><code>GENBANK</code> indicates that the sequence format is
GENBANK.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOConstants.html#GENBANK_AA">GENBANK_AA</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOConstants.html" title="class in org.biojava.bio.seq.io">SeqIOConstants</a></dt>
<dd>
<div class="block"><code>GENBANK_DNA</code> premade GENBANK | AA.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOConstants.html#GENBANK_DNA">GENBANK_DNA</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOConstants.html" title="class in org.biojava.bio.seq.io">SeqIOConstants</a></dt>
<dd>
<div class="block"><code>GENBANK_DNA</code> premade GENBANK | DNA.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/GenbankFormat.html#GENBANK_FORMAT">GENBANK_FORMAT</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/GenbankFormat.html" title="class in org.biojavax.bio.seq.io">GenbankFormat</a></dt>
<dd>
<div class="block">The name of this format</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOConstants.html#GENBANK_RNA">GENBANK_RNA</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOConstants.html" title="class in org.biojava.bio.seq.io">SeqIOConstants</a></dt>
<dd>
<div class="block"><code>GENBANK_DNA</code> premade GENBANK | RNA.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/GenbankFileFormer.html" title="class in org.biojava.bio.seq.io"><span class="strong">GenbankFileFormer</span></a> - Class in <a href="./org/biojava/bio/seq/io/package-summary.html">org.biojava.bio.seq.io</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>Use org.biojavax.bio.seq.io framework instead</i></div>
</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/GenbankFileFormer.html#GenbankFileFormer()">GenbankFileFormer()</a></span> - Constructor for class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/GenbankFileFormer.html" title="class in org.biojava.bio.seq.io">GenbankFileFormer</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Creates a new <code>GenbankFileFormer</code> using
<code>System.out</code> stream.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/GenbankFileFormer.html#GenbankFileFormer(java.io.PrintStream)">GenbankFileFormer(PrintStream)</a></span> - Constructor for class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/GenbankFileFormer.html" title="class in org.biojava.bio.seq.io">GenbankFileFormer</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Creates a new <code>GenbankFileFormer</code> using the
specified stream.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/GenbankFormat.html" title="class in org.biojava.bio.seq.io"><span class="strong">GenbankFormat</span></a> - Class in <a href="./org/biojava/bio/seq/io/package-summary.html">org.biojava.bio.seq.io</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>Use org.biojavax.bio.seq.io.GenbankFormat</i></div>
</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/GenbankFormat.html#GenbankFormat()">GenbankFormat()</a></span> - Constructor for class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/GenbankFormat.html" title="class in org.biojava.bio.seq.io">GenbankFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><a href="./org/biojavax/bio/seq/io/GenbankFormat.html" title="class in org.biojavax.bio.seq.io"><span class="strong">GenbankFormat</span></a> - Class in <a href="./org/biojavax/bio/seq/io/package-summary.html">org.biojavax.bio.seq.io</a></dt>
<dd>
<div class="block">Format reader for GenBank files.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/GenbankFormat.html#GenbankFormat()">GenbankFormat()</a></span> - Constructor for class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/GenbankFormat.html" title="class in org.biojavax.bio.seq.io">GenbankFormat</a></dt>
<dd> </dd>
<dt><a href="./org/biojavax/bio/seq/io/GenbankFormat.Terms.html" title="class in org.biojavax.bio.seq.io"><span class="strong">GenbankFormat.Terms</span></a> - Class in <a href="./org/biojavax/bio/seq/io/package-summary.html">org.biojavax.bio.seq.io</a></dt>
<dd>
<div class="block">Implements some GenBank-specific terms.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/GenbankFormat.Terms.html#GenbankFormat.Terms()">GenbankFormat.Terms()</a></span> - Constructor for class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/GenbankFormat.Terms.html" title="class in org.biojavax.bio.seq.io">GenbankFormat.Terms</a></dt>
<dd> </dd>
<dt><a href="./org/biojavax/bio/seq/io/GenbankLocationParser.html" title="class in org.biojavax.bio.seq.io"><span class="strong">GenbankLocationParser</span></a> - Class in <a href="./org/biojavax/bio/seq/io/package-summary.html">org.biojavax.bio.seq.io</a></dt>
<dd>
<div class="block">Parses Genbank location strings into RichLocation objects.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/GenbankProcessor.html" title="class in org.biojava.bio.seq.io"><span class="strong">GenbankProcessor</span></a> - Class in <a href="./org/biojava/bio/seq/io/package-summary.html">org.biojava.bio.seq.io</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>Use org.biojavax.bio.seq.io framework instead</i></div>
</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/GenbankProcessor.html#GenbankProcessor(org.biojava.bio.seq.io.SequenceBuilder, java.lang.String)">GenbankProcessor(SequenceBuilder, String)</a></span> - Constructor for class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/GenbankProcessor.html" title="class in org.biojava.bio.seq.io">GenbankProcessor</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/GenbankProcessor.html#GenbankProcessor(org.biojava.bio.seq.io.SequenceBuilder)">GenbankProcessor(SequenceBuilder)</a></span> - Constructor for class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/GenbankProcessor.html" title="class in org.biojava.bio.seq.io">GenbankProcessor</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/GenbankProcessor.Factory.html" title="class in org.biojava.bio.seq.io"><span class="strong">GenbankProcessor.Factory</span></a> - Class in <a href="./org/biojava/bio/seq/io/package-summary.html">org.biojava.bio.seq.io</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Factory which wraps sequence builders in a GenbankProcessor</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/GenbankProcessor.Factory.html#GenbankProcessor.Factory(org.biojava.bio.seq.io.SequenceBuilderFactory)">GenbankProcessor.Factory(SequenceBuilderFactory)</a></span> - Constructor for class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/GenbankProcessor.Factory.html" title="class in org.biojava.bio.seq.io">GenbankProcessor.Factory</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><a href="./org/biojavax/bio/db/ncbi/GenbankRichSequenceDB.html" title="class in org.biojavax.bio.db.ncbi"><span class="strong">GenbankRichSequenceDB</span></a> - Class in <a href="./org/biojavax/bio/db/ncbi/package-summary.html">org.biojavax.bio.db.ncbi</a></dt>
<dd>
<div class="block">This class contains functions accessing DNA sequences in Genbank format.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/ncbi/GenbankRichSequenceDB.html#GenbankRichSequenceDB()">GenbankRichSequenceDB()</a></span> - Constructor for class org.biojavax.bio.db.ncbi.<a href="./org/biojavax/bio/db/ncbi/GenbankRichSequenceDB.html" title="class in org.biojavax.bio.db.ncbi">GenbankRichSequenceDB</a></dt>
<dd>
<div class="block">The default constructor delegates to the parent class.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/db/GenbankSequenceDB.html" title="class in org.biojava.bio.seq.db"><span class="strong">GenbankSequenceDB</span></a> - Class in <a href="./org/biojava/bio/seq/db/package-summary.html">org.biojava.bio.seq.db</a></dt>
<dd>
<div class="block">This class contains functions accessing DNA sequences in Genbank format.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/GenbankSequenceDB.html#GenbankSequenceDB()">GenbankSequenceDB()</a></span> - Constructor for class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/GenbankSequenceDB.html" title="class in org.biojava.bio.seq.db">GenbankSequenceDB</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/io/GenbankXmlFormat.html" title="class in org.biojava.bio.seq.io"><span class="strong">GenbankXmlFormat</span></a> - Class in <a href="./org/biojava/bio/seq/io/package-summary.html">org.biojava.bio.seq.io</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>Use org.biojavax.bio.seq.io.INSDseqFormat</i></div>
</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/GenbankXmlFormat.html#GenbankXmlFormat()">GenbankXmlFormat()</a></span> - Constructor for class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/GenbankXmlFormat.html" title="class in org.biojava.bio.seq.io">GenbankXmlFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtFormat.html#GENE_TAG">GENE_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtFormat.html" title="class in org.biojavax.bio.seq.io">UniProtFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#GENE_TAG">GENE_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#GENELOCATION_NAME_TAG">GENELOCATION_NAME_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#GENELOCATION_TAG">GENELOCATION_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/io/GenEmblFeatureComparator.html" title="class in org.biojava.bio.seq.io"><span class="strong">GenEmblFeatureComparator</span></a> - Class in <a href="./org/biojava/bio/seq/io/package-summary.html">org.biojava.bio.seq.io</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>Use org.biojavax.bio.seq.io framework instead</i></div>
</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/GenEmblPropertyComparator.html" title="class in org.biojava.bio.seq.io"><span class="strong">GenEmblPropertyComparator</span></a> - Class in <a href="./org/biojava/bio/seq/io/package-summary.html">org.biojava.bio.seq.io</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>Use org.biojavax.bio.seq.io framework instead</i></div>
</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.Terms.html#GENENAME_KEY">GENENAME_KEY</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.Terms.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat.Terms</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/DP.html#generate(int)">generate(int)</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/DP.html" title="class in org.biojava.bio.dp">DP</a></dt>
<dd>
<div class="block">
Generates an alignment from a model.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html#generate()">generate()</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html" title="class in org.biojavax.bio.seq.io">UniProtCommentParser</a></dt>
<dd>
<div class="block">Generates a comment string based on the current values of the
internal fields.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/DocRefAuthor.Tools.html#generateAuthorString(java.util.List, boolean)">generateAuthorString(List, boolean)</a></span> - Static method in class org.biojavax.<a href="./org/biojavax/DocRefAuthor.Tools.html" title="class in org.biojavax">DocRefAuthor.Tools</a></dt>
<dd>
<div class="block">Takes a set of authors and creates a comma-separated string.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/twohead/DPCompiler.html#generateBackwardClass(org.biojava.bio.dp.DP)">generateBackwardClass(DP)</a></span> - Method in class org.biojava.bio.dp.twohead.<a href="./org/biojava/bio/dp/twohead/DPCompiler.html" title="class in org.biojava.bio.dp.twohead">DPCompiler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.html#generateCallboxes()">generateCallboxes()</a></span> - Method in class org.biojava.bio.chromatogram.graphic.<a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.html" title="class in org.biojava.bio.chromatogram.graphic">ChromatogramGraphic</a></dt>
<dd>
<div class="block">Precomputes the <code>Rectangle2D</code>s that are the in-memory
representation of the callboxes.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/LabelledSequenceRenderer.html#generateChangeSupport()">generateChangeSupport()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/LabelledSequenceRenderer.html" title="class in org.biojava.bio.gui.sequence">LabelledSequenceRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/AbstractChangeable.html#generateChangeSupport()">generateChangeSupport()</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/AbstractChangeable.html" title="class in org.biojava.utils">AbstractChangeable</a></dt>
<dd>
<div class="block">Called the first time a ChangeSupport object is needed.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AlphabetManager.html#generateCrossProductAlphaFromName(java.lang.String)">generateCrossProductAlphaFromName(String)</a></span> - Static method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AlphabetManager.html" title="class in org.biojava.bio.symbol">AlphabetManager</a></dt>
<dd>
<div class="block">Generates a new CrossProductAlphabet from the give name.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.html#generateDrawableCallboxes(java.awt.geom.AffineTransform)">generateDrawableCallboxes(AffineTransform)</a></span> - Method in class org.biojava.bio.chromatogram.graphic.<a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.html" title="class in org.biojava.bio.chromatogram.graphic">ChromatogramGraphic</a></dt>
<dd>
<div class="block">Precomputes the callboxes in screen coordinates.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/Annotatable.AnnotationForwarder.html#generateEvent(org.biojava.utils.ChangeEvent)">generateEvent(ChangeEvent)</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/Annotatable.AnnotationForwarder.html" title="class in org.biojava.bio">Annotatable.AnnotationForwarder</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/Distribution.NullModelForwarder.html#generateEvent(org.biojava.utils.ChangeEvent)">generateEvent(ChangeEvent)</a></span> - Method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/Distribution.NullModelForwarder.html" title="class in org.biojava.bio.dist">Distribution.NullModelForwarder</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PairwiseSequenceRenderer.PairwiseRendererForwarder.html#generateEvent(org.biojava.utils.ChangeEvent)">generateEvent(ChangeEvent)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PairwiseSequenceRenderer.PairwiseRendererForwarder.html" title="class in org.biojava.bio.gui.sequence">PairwiseSequenceRenderer.PairwiseRendererForwarder</a></dt>
<dd>
<div class="block"><code>generateEvent</code> generates events in response to
layout change and repaint requests.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequenceRenderer.RendererForwarder.html#generateEvent(org.biojava.utils.ChangeEvent)">generateEvent(ChangeEvent)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequenceRenderer.RendererForwarder.html" title="class in org.biojava.bio.gui.sequence">SequenceRenderer.RendererForwarder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/MergeAnnotation.PropertyForwarder.html#generateEvent(org.biojava.utils.ChangeEvent)">generateEvent(ChangeEvent)</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/MergeAnnotation.PropertyForwarder.html" title="class in org.biojava.bio">MergeAnnotation.PropertyForwarder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/OverlayAnnotation.PropertyForwarder.html#generateEvent(org.biojava.utils.ChangeEvent)">generateEvent(ChangeEvent)</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/OverlayAnnotation.PropertyForwarder.html" title="class in org.biojava.bio">OverlayAnnotation.PropertyForwarder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/SequenceDBWrapper.SequencesForwarder.html#generateEvent(org.biojava.utils.ChangeEvent)">generateEvent(ChangeEvent)</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/SequenceDBWrapper.SequencesForwarder.html" title="class in org.biojava.bio.seq.db">SequenceDBWrapper.SequencesForwarder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AbstractSymbolList.EditScreener.html#generateEvent(org.biojava.utils.ChangeEvent)">generateEvent(ChangeEvent)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AbstractSymbolList.EditScreener.html" title="class in org.biojava.bio.symbol">AbstractSymbolList.EditScreener</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AbstractSymbolList.EditTranslater.html#generateEvent(org.biojava.utils.ChangeEvent)">generateEvent(ChangeEvent)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AbstractSymbolList.EditTranslater.html" title="class in org.biojava.bio.symbol">AbstractSymbolList.EditTranslater</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ChangeForwarder.html#generateEvent(org.biojava.utils.ChangeEvent)">generateEvent(ChangeEvent)</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/ChangeForwarder.html" title="class in org.biojava.utils">ChangeForwarder</a></dt>
<dd>
<div class="block">
Return the new event to represent the originating event ce.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/ChangeForwarder.Retyper.html#generateEvent(org.biojava.utils.ChangeEvent)">generateEvent(ChangeEvent)</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/ChangeForwarder.Retyper.html" title="class in org.biojava.utils">ChangeForwarder.Retyper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/twohead/DPCompiler.html#generateForardClass(org.biojava.bio.dp.DP)">generateForardClass(DP)</a></span> - Method in class org.biojava.bio.dp.twohead.<a href="./org/biojava/bio/dp/twohead/DPCompiler.html" title="class in org.biojava.bio.dp.twohead">DPCompiler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/DistributionTools.html#generateOrderNSequence(java.lang.String, org.biojava.bio.dist.OrderNDistribution, int)">generateOrderNSequence(String, OrderNDistribution, int)</a></span> - Static method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/DistributionTools.html" title="class in org.biojava.bio.dist">DistributionTools</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>use generateSequence() or generateSymbolList() instead.</i></div>
</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/FileAsList.html#generateRecord(byte[], java.lang.Object)">generateRecord(byte[], Object)</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/FileAsList.html" title="class in org.biojava.utils">FileAsList</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/DistributionTools.html#generateSequence(java.lang.String, org.biojava.bio.dist.Distribution, int)">generateSequence(String, Distribution, int)</a></span> - Static method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/DistributionTools.html" title="class in org.biojava.bio.dist">DistributionTools</a></dt>
<dd>
<div class="block">Produces a sequence by randomly sampling the Distribution.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.html#generateSubpaths()">generateSubpaths()</a></span> - Method in class org.biojava.bio.chromatogram.graphic.<a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.html" title="class in org.biojava.bio.chromatogram.graphic">ChromatogramGraphic</a></dt>
<dd>
<div class="block">Precomputes the <code>GeneralPath</code>s used to draw the
traces.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/DistributionTools.html#generateSymbolList(org.biojava.bio.dist.Distribution, int)">generateSymbolList(Distribution, int)</a></span> - Static method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/DistributionTools.html" title="class in org.biojava.bio.dist">DistributionTools</a></dt>
<dd>
<div class="block">Produces a <code>SymbolList</code> by randomly sampling a Distribution.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/twohead/DPCompiler.html#generateViterbiClass(org.biojava.bio.dp.DP)">generateViterbiClass(DP)</a></span> - Method in class org.biojava.bio.dp.twohead.<a href="./org/biojava/bio/dp/twohead/DPCompiler.html" title="class in org.biojava.bio.dp.twohead">DPCompiler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BibRefSupport.html#GENERIC_PROVIDER">GENERIC_PROVIDER</a></span> - Static variable in interface org.biojava.bibliography.<a href="./org/biojava/bibliography/BibRefSupport.html" title="interface in org.biojava.bibliography">BibRefSupport</a></dt>
<dd>
<div class="block">A name of a provider type.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.Terms.html#GENESYNONYM_KEY">GENESYNONYM_KEY</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.Terms.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat.Terms</a></dt>
<dd> </dd>
<dt><a href="./org/biojavax/ga/GeneticAlgorithm.html" title="interface in org.biojavax.ga"><span class="strong">GeneticAlgorithm</span></a> - Interface in <a href="./org/biojavax/ga/package-summary.html">org.biojavax.ga</a></dt>
<dd>
<div class="block">The class that runs the cycles of reproduction, evolution and selection,
potentially on multiple <code>Population</code>s</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/taxa/NCBITaxon.html#GENETICCODE">GENETICCODE</a></span> - Static variable in interface org.biojavax.bio.taxa.<a href="./org/biojavax/bio/taxa/NCBITaxon.html" title="interface in org.biojavax.bio.taxa">NCBITaxon</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/GeneticCodes.html" title="class in org.biojava.bio.seq"><span class="strong">GeneticCodes</span></a> - Class in <a href="./org/biojava/bio/seq/package-summary.html">org.biojava.bio.seq</a></dt>
<dd>
<div class="block">Collects the references to translation methods in one place.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOConstants.html#GENPEPT">GENPEPT</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOConstants.html" title="class in org.biojava.bio.seq.io">SeqIOConstants</a></dt>
<dd>
<div class="block"><code>GENPEPT</code> indicates that the sequence format is
GENPEPT.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/GenpeptFormat.html" title="class in org.biojava.bio.seq.io"><span class="strong">GenpeptFormat</span></a> - Class in <a href="./org/biojava/bio/seq/io/package-summary.html">org.biojava.bio.seq.io</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>Use org.biojavax.bio.seq.io framework instead</i></div>
</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/GenpeptFormat.html#GenpeptFormat()">GenpeptFormat()</a></span> - Constructor for class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/GenpeptFormat.html" title="class in org.biojava.bio.seq.io">GenpeptFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><a href="./org/biojavax/bio/db/ncbi/GenpeptRichSequenceDB.html" title="class in org.biojavax.bio.db.ncbi"><span class="strong">GenpeptRichSequenceDB</span></a> - Class in <a href="./org/biojavax/bio/db/ncbi/package-summary.html">org.biojavax.bio.db.ncbi</a></dt>
<dd>
<div class="block">This class contains functions accessing Peptide sequences in Genpept format.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/ncbi/GenpeptRichSequenceDB.html#GenpeptRichSequenceDB()">GenpeptRichSequenceDB()</a></span> - Constructor for class org.biojavax.bio.db.ncbi.<a href="./org/biojavax/bio/db/ncbi/GenpeptRichSequenceDB.html" title="class in org.biojavax.bio.db.ncbi">GenpeptRichSequenceDB</a></dt>
<dd>
<div class="block">The default constructor delegates to the parent class.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/db/GenpeptSequenceDB.html" title="class in org.biojava.bio.seq.db"><span class="strong">GenpeptSequenceDB</span></a> - Class in <a href="./org/biojava/bio/seq/db/package-summary.html">org.biojava.bio.seq.db</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/GenpeptSequenceDB.html#GenpeptSequenceDB()">GenpeptSequenceDB()</a></span> - Constructor for class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/GenpeptSequenceDB.html" title="class in org.biojava.bio.seq.db">GenpeptSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/indexdb/BioStore.html#get(java.lang.String)">get(String)</a></span> - Method in class org.biojava.bio.program.indexdb.<a href="./org/biojava/bio/program/indexdb/BioStore.html" title="class in org.biojava.bio.program.indexdb">BioStore</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/indexdb/BioStore.html#get(java.lang.String, java.lang.String)">get(String, String)</a></span> - Method in class org.biojava.bio.program.indexdb.<a href="./org/biojava/bio/program/indexdb/BioStore.html" title="class in org.biojava.bio.program.indexdb">BioStore</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/indexdb/IndexStore.html#get(java.lang.String)">get(String)</a></span> - Method in interface org.biojava.bio.program.indexdb.<a href="./org/biojava/bio/program/indexdb/IndexStore.html" title="interface in org.biojava.bio.program.indexdb">IndexStore</a></dt>
<dd>
<div class="block"><code>get</code> returns a record specified by a primary
identifier.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/indexdb/IndexStore.html#get(java.lang.String, java.lang.String)">get(String, String)</a></span> - Method in interface org.biojava.bio.program.indexdb.<a href="./org/biojava/bio/program/indexdb/IndexStore.html" title="interface in org.biojava.bio.program.indexdb">IndexStore</a></dt>
<dd>
<div class="block"><code>get</code> returns a list of <code>Record</code>s by
searching against the primary identifiers if the namespace
argument is equal to the primary namespace or otherwise by
searching the secondary namespaces.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/StateMachine.TransitionTable.html#get(java.lang.Object)">get(Object)</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/StateMachine.TransitionTable.html" title="class in org.biojava.bio.program.tagvalue">StateMachine.TransitionTable</a></dt>
<dd>
<div class="block">get the Transition associated with the specified tag.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/jama/Matrix.html#get(int, int)">get(int, int)</a></span> - Method in class org.biojava.bio.structure.jama.<a href="./org/biojava/bio/structure/jama/Matrix.html" title="class in org.biojava.bio.structure.jama">Matrix</a></dt>
<dd>
<div class="block">Get a single element.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/SparseVector.html#get(int)">get(int)</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/SparseVector.html" title="class in org.biojava.stats.svm">SparseVector</a></dt>
<dd>
<div class="block">Retrieve the value at dimension dim.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/cache/CacheMap.html#get(java.lang.Object)">get(Object)</a></span> - Method in interface org.biojava.utils.cache.<a href="./org/biojava/utils/cache/CacheMap.html" title="interface in org.biojava.utils.cache">CacheMap</a></dt>
<dd>
<div class="block">Retrieve the Object associated with the key, or null if either no value has
been associated or if the key's value has been cleared by the cache.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/cache/CacheReference.html#get()">get()</a></span> - Method in interface org.biojava.utils.cache.<a href="./org/biojava/utils/cache/CacheReference.html" title="interface in org.biojava.utils.cache">CacheReference</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/cache/ChangeableCache.html#get(java.lang.Object)">get(Object)</a></span> - Method in class org.biojava.utils.cache.<a href="./org/biojava/utils/cache/ChangeableCache.html" title="class in org.biojava.utils.cache">ChangeableCache</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/cache/FixedSizeMap.html#get(java.lang.Object)">get(Object)</a></span> - Method in class org.biojava.utils.cache.<a href="./org/biojava/utils/cache/FixedSizeMap.html" title="class in org.biojava.utils.cache">FixedSizeMap</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/cache/WeakCacheMap.html#get(java.lang.Object)">get(Object)</a></span> - Method in class org.biojava.utils.cache.<a href="./org/biojava/utils/cache/WeakCacheMap.html" title="class in org.biojava.utils.cache">WeakCacheMap</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/cache/WeakValueHashMap.html#get(java.lang.Object)">get(Object)</a></span> - Method in class org.biojava.utils.cache.<a href="./org/biojava/utils/cache/WeakValueHashMap.html" title="class in org.biojava.utils.cache">WeakValueHashMap</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/FileAsList.html#get(int)">get(int)</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/FileAsList.html" title="class in org.biojava.utils">FileAsList</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/io/LargeBuffer.html#get(long)">get(long)</a></span> - Method in class org.biojava.utils.io.<a href="./org/biojava/utils/io/LargeBuffer.html" title="class in org.biojava.utils.io">LargeBuffer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/io/LargeBuffer.html#get()">get()</a></span> - Method in class org.biojava.utils.io.<a href="./org/biojava/utils/io/LargeBuffer.html" title="class in org.biojava.utils.io">LargeBuffer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ListTools.Doublet.html#get(int)">get(int)</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/ListTools.Doublet.html" title="class in org.biojava.utils">ListTools.Doublet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ListTools.SeriesList.html#get(int)">get(int)</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/ListTools.SeriesList.html" title="class in org.biojava.utils">ListTools.SeriesList</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ListTools.Triplet.html#get(int)">get(int)</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/ListTools.Triplet.html" title="class in org.biojava.utils">ListTools.Triplet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/OverlayMap.html#get(java.lang.Object)">get(Object)</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/OverlayMap.html" title="class in org.biojava.utils">OverlayMap</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/SingletonList.html#get(int)">get(int)</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/SingletonList.html" title="class in org.biojava.utils">SingletonList</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/SmallMap.html#get(java.lang.Object)">get(Object)</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/SmallMap.html" title="class in org.biojava.utils">SmallMap</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/StructureTools.html#get1LetterCode(java.lang.String)">get1LetterCode(String)</a></span> - Static method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/StructureTools.html" title="class in org.biojava.bio.structure">StructureTools</a></dt>
<dd>
<div class="block">convert a three letter code into single character.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/CircularLocation.html#get3PrimeEnd()">get3PrimeEnd()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/CircularLocation.html" title="class in org.biojava.bio.symbol">CircularLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/CircularLocation.html#get5PrimeEnd()">get5PrimeEnd()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/CircularLocation.html" title="class in org.biojava.bio.symbol">CircularLocation</a></dt>
<dd>
<div class="block">The point at which indicates the 5' end of the Location.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/StructureTools.html#get_()">get_()</a></span> - Method in class org.biojava.bio.proteomics.<a href="./org/biojava/bio/proteomics/StructureTools.html" title="class in org.biojava.bio.proteomics">StructureTools</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/dasstructure/DASStructureXMLResponseParser.html#get_structure()">get_structure()</a></span> - Method in class org.biojava.bio.program.das.dasstructure.<a href="./org/biojava/bio/program/das/dasstructure/DASStructureXMLResponseParser.html" title="class in org.biojava.bio.program.das.dasstructure">DASStructureXMLResponseParser</a></dt>
<dd>
<div class="block">returns the Structure object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/molbio/DNAComposition.html#getA()">getA()</a></span> - Method in class org.biojava.bio.molbio.<a href="./org/biojava/bio/molbio/DNAComposition.html" title="class in org.biojava.bio.molbio">DNAComposition</a></dt>
<dd>
<div class="block">Get the relative compositon of 'A'.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/ListTools.Doublet.html#getA()">getA()</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/ListTools.Doublet.html" title="class in org.biojava.utils">ListTools.Doublet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ListTools.Triplet.html#getA()">getA()</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/ListTools.Triplet.html" title="class in org.biojava.utils">ListTools.Triplet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Exptl.html#getAbsorpt_coefficient_mu()">getAbsorpt_coefficient_mu()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Exptl.html" title="class in org.biojava.bio.structure.io.mmcif.model">Exptl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Exptl.html#getAbsorpt_correction_T_max()">getAbsorpt_correction_T_max()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Exptl.html" title="class in org.biojava.bio.structure.io.mmcif.model">Exptl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Exptl.html#getAbsorpt_correction_T_min()">getAbsorpt_correction_T_min()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Exptl.html" title="class in org.biojava.bio.structure.io.mmcif.model">Exptl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Exptl.html#getAbsorpt_correction_type()">getAbsorpt_correction_type()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Exptl.html" title="class in org.biojava.bio.structure.io.mmcif.model">Exptl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Exptl.html#getAbsorpt_process_details()">getAbsorpt_process_details()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Exptl.html" title="class in org.biojava.bio.structure.io.mmcif.model">Exptl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html#getAbsorptionMax()">getAbsorptionMax()</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html" title="class in org.biojavax.bio.seq.io">UniProtCommentParser</a></dt>
<dd>
<div class="block">Getter for property absorptionMax.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html#getAbsorptionNote()">getAbsorptionNote()</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html" title="class in org.biojavax.bio.seq.io">UniProtCommentParser</a></dt>
<dd>
<div class="block">Getter for property absorptionNote.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/Orthologue.html#getAccession()">getAccession()</a></span> - Method in interface org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/Orthologue.html" title="interface in org.biojava.bio.program.homologene">Orthologue</a></dt>
<dd>
<div class="block">get the Accession ID associated with this orthologue.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/SimpleOrthologue.html#getAccession()">getAccession()</a></span> - Method in class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/SimpleOrthologue.html" title="class in org.biojava.bio.program.homologene">SimpleOrthologue</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/Agave2AgaveAnnotFilter.html#getAccession(org.biojava.bio.Annotation)">getAccession(Annotation)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/Agave2AgaveAnnotFilter.html" title="class in org.biojava.bio.seq.io.agave">Agave2AgaveAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEAnnotFilter.html#getAccession(org.biojava.bio.Annotation)">getAccession(Annotation)</a></span> - Method in interface org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEAnnotFilter.html" title="interface in org.biojava.bio.seq.io.agave">AGAVEAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/Embl2AgaveAnnotFilter.html#getAccession(org.biojava.bio.Annotation)">getAccession(Annotation)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/Embl2AgaveAnnotFilter.html" title="class in org.biojava.bio.seq.io.agave">Embl2AgaveAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/SimpleAnnotFilter.html#getAccession(org.biojava.bio.Annotation)">getAccession(Annotation)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/SimpleAnnotFilter.html" title="class in org.biojava.bio.seq.io.agave">SimpleAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/BioEntry.html#getAccession()">getAccession()</a></span> - Method in interface org.biojavax.bio.<a href="./org/biojavax/bio/BioEntry.html" title="interface in org.biojavax.bio">BioEntry</a></dt>
<dd>
<div class="block">Returns the accession of this bioentry.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/SimpleBioEntry.html#getAccession()">getAccession()</a></span> - Method in class org.biojavax.bio.<a href="./org/biojavax/bio/SimpleBioEntry.html" title="class in org.biojavax.bio">SimpleBioEntry</a></dt>
<dd>
<div class="block">Returns the accession of this bioentry.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/CrossRef.html#getAccession()">getAccession()</a></span> - Method in interface org.biojavax.<a href="./org/biojavax/CrossRef.html" title="interface in org.biojavax">CrossRef</a></dt>
<dd>
<div class="block">Returns the accession of the object that the crossref refers to.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleCrossRef.html#getAccession()">getAccession()</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleCrossRef.html" title="class in org.biojavax">SimpleCrossRef</a></dt>
<dd>
<div class="block">Returns the accession of the object that the crossref refers to.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/Namespace.html#getAcronym()">getAcronym()</a></span> - Method in interface org.biojavax.<a href="./org/biojavax/Namespace.html" title="interface in org.biojavax">Namespace</a></dt>
<dd>
<div class="block">If the namespace has an acronym, this will return it.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleNamespace.html#getAcronym()">getAcronym()</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleNamespace.html" title="class in org.biojavax">SimpleNamespace</a></dt>
<dd>
<div class="block">If the namespace has an acronym, this will return it.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/ViewSequence.html#getAddedFeatures()">getAddedFeatures()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/ViewSequence.html" title="class in org.biojava.bio.seq.impl">ViewSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFEntrySet.html#getAddHandler()">getAddHandler()</a></span> - Method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFEntrySet.html" title="class in org.biojava.bio.program.gff">GFFEntrySet</a></dt>
<dd>
<div class="block">Get the <span class="type">GFFDocumentHandler</span> for adding to this
set.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.Terms.html#getAdditionalAccessionTerm()">getAdditionalAccessionTerm()</a></span> - Static method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.Terms.html" title="class in org.biojavax.bio.seq">RichSequence.Terms</a></dt>
<dd>
<div class="block">Getter for the secondary/tertiary/additional accession term</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/tools/ClassifierExample.PointClassifier.html#getAddPos()">getAddPos()</a></span> - Method in class org.biojava.stats.svm.tools.<a href="./org/biojava/stats/svm/tools/ClassifierExample.PointClassifier.html" title="class in org.biojava.stats.svm.tools">ClassifierExample.PointClassifier</a></dt>
<dd>
<div class="block">Retrieve the current value of addPos.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/GenbankSequenceDB.html#getAddress(java.lang.String)">getAddress(String)</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/GenbankSequenceDB.html" title="class in org.biojava.bio.seq.db">GenbankSequenceDB</a></dt>
<dd>
<div class="block">Get the URL object for locating sequence object using eutils.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/GenbankSequenceDB.html#getAddress(java.lang.String, java.lang.String)">getAddress(String, String)</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/GenbankSequenceDB.html" title="class in org.biojava.bio.seq.db">GenbankSequenceDB</a></dt>
<dd>
<div class="block">Get the URL object for locating sequence object using eutils.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/GenpeptSequenceDB.html#getAddress(java.lang.String)">getAddress(String)</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/GenpeptSequenceDB.html" title="class in org.biojava.bio.seq.db">GenpeptSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/GenpeptSequenceDB.html#getAddress(java.lang.String, java.lang.String)">getAddress(String, String)</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/GenpeptSequenceDB.html" title="class in org.biojava.bio.seq.db">GenpeptSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/NCBISequenceDB.html#getAddress(java.lang.String)">getAddress(String)</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/NCBISequenceDB.html" title="class in org.biojava.bio.seq.db">NCBISequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/SwissprotSequenceDB.html#getAddress(java.lang.String)">getAddress(String)</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/SwissprotSequenceDB.html" title="class in org.biojava.bio.seq.db">SwissprotSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/WebSequenceDB.html#getAddress(java.lang.String)">getAddress(String)</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/WebSequenceDB.html" title="class in org.biojava.bio.seq.db">WebSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/ncbi/GenbankRichSequenceDB.html#getAddress(java.lang.String)">getAddress(String)</a></span> - Method in class org.biojavax.bio.db.ncbi.<a href="./org/biojavax/bio/db/ncbi/GenbankRichSequenceDB.html" title="class in org.biojavax.bio.db.ncbi">GenbankRichSequenceDB</a></dt>
<dd>
<div class="block">Get the URL object for locating sequence object using eutils.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/ncbi/GenpeptRichSequenceDB.html#getAddress(java.lang.String)">getAddress(String)</a></span> - Method in class org.biojavax.bio.db.ncbi.<a href="./org/biojavax/bio/db/ncbi/GenpeptRichSequenceDB.html" title="class in org.biojavax.bio.db.ncbi">GenpeptRichSequenceDB</a></dt>
<dd>
<div class="block">Get the URL object for locating sequence object using eutils.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/EmissionState.html#getAdvance()">getAdvance()</a></span> - Method in interface org.biojava.bio.dp.<a href="./org/biojava/bio/dp/EmissionState.html" title="interface in org.biojava.bio.dp">EmissionState</a></dt>
<dd>
<div class="block">Determine the number of symbols this state advances along
one or more symbol lists.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/SimpleEmissionState.html#getAdvance()">getAdvance()</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/SimpleEmissionState.html" title="class in org.biojava.bio.dp">SimpleEmissionState</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/FlexibleAlignment.html#getAE(java.lang.Object)">getAE(Object)</a></span> - Method in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/FlexibleAlignment.html" title="class in org.biojava.bio.alignment">FlexibleAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/SequenceDisplay.html#getAligMap()">getAligMap()</a></span> - Method in class org.biojava.bio.structure.gui.<a href="./org/biojava/bio/structure/gui/SequenceDisplay.html" title="class in org.biojava.bio.structure.gui">SequenceDisplay</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/Alignable.html#getAligMat()">getAligMat()</a></span> - Method in interface org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/Alignable.html" title="interface in org.biojava.bio.structure.align.pairwise">Alignable</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/StrCompAlignment.html#getAligMat(int, int)">getAligMat(int, int)</a></span> - Method in class org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/StrCompAlignment.html" title="class in org.biojava.bio.structure.align.pairwise">StrCompAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/StrCompAlignment.html#getAligMat()">getAligMat()</a></span> - Method in class org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/StrCompAlignment.html" title="class in org.biojava.bio.structure.align.pairwise">StrCompAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/StructRefSeq.html#getAlign_id()">getAlign_id()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/StructRefSeq.html" title="class in org.biojava.bio.structure.io.mmcif.model">StructRefSeq</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/AlternativeAlignment.html#getAlignedStructure(org.biojava.bio.structure.Structure, org.biojava.bio.structure.Structure)">getAlignedStructure(Structure, Structure)</a></span> - Method in class org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/AlternativeAlignment.html" title="class in org.biojava.bio.structure.align.pairwise">AlternativeAlignment</a></dt>
<dd>
<div class="block">create an artifical Structure object that contains the two
structures superimposed onto each other.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEAnnotFilter.html#getAlignLength(org.biojava.bio.Annotation)">getAlignLength(Annotation)</a></span> - Method in interface org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEAnnotFilter.html" title="interface in org.biojava.bio.seq.io.agave">AGAVEAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/SimpleAnnotFilter.html#getAlignLength(org.biojava.bio.Annotation)">getAlignLength(Annotation)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/SimpleAnnotFilter.html" title="class in org.biojava.bio.seq.io.agave">SimpleAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/NeedlemanWunsch.html#getAlignment(org.biojava.bio.symbol.SymbolList, org.biojava.bio.symbol.SymbolList)">getAlignment(SymbolList, SymbolList)</a></span> - Method in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/NeedlemanWunsch.html" title="class in org.biojava.bio.alignment">NeedlemanWunsch</a></dt>
<dd>
<div class="block">This method is good if one wants to reuse the alignment calculated by this
class in another BioJava class.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/SequenceAlignment.html#getAlignment(org.biojava.bio.symbol.SymbolList, org.biojava.bio.symbol.SymbolList)">getAlignment(SymbolList, SymbolList)</a></span> - Method in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/SequenceAlignment.html" title="class in org.biojava.bio.alignment">SequenceAlignment</a></dt>
<dd>
<div class="block">This method also performs a sequence alignment of the two given sequences
but it returns an Alignment object instead of the score.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePanel.Border.html#getAlignment()">getAlignment()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePanel.Border.html" title="class in org.biojava.bio.gui.sequence">SequencePanel.Border</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePoster.Border.html#getAlignment()">getAlignment()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePoster.Border.html" title="class in org.biojava.bio.gui.sequence">SequencePoster.Border</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequenceRenderContext.Border.html#getAlignment()">getAlignment()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequenceRenderContext.Border.html" title="class in org.biojava.bio.gui.sequence">SequenceRenderContext.Border</a></dt>
<dd>
<div class="block">Gets the Alignment - one of LEADING, TRAILING or CENTER.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/abi/ABITools.html#getAlignment(org.biojava.bio.symbol.SymbolList)">getAlignment(SymbolList)</a></span> - Static method in class org.biojava.bio.program.abi.<a href="./org/biojava/bio/program/abi/ABITools.html" title="class in org.biojava.bio.program.abi">ABITools</a></dt>
<dd>
<div class="block">
View a symbol list over the QUALITY alphabet as an alignment.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/dasalignment/DASAlignmentXMLResponseParser.html#getAlignment(int)">getAlignment(int)</a></span> - Method in class org.biojava.bio.program.das.dasalignment.<a href="./org/biojava/bio/program/das/dasalignment/DASAlignmentXMLResponseParser.html" title="class in org.biojava.bio.program.das.dasalignment">DASAlignmentXMLResponseParser</a></dt>
<dd>
<div class="block">Returns Alignment at position ...</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SeqSimilaritySearchSubHit.html#getAlignment()">getAlignment()</a></span> - Method in interface org.biojava.bio.search.<a href="./org/biojava/bio/search/SeqSimilaritySearchSubHit.html" title="interface in org.biojava.bio.search">SeqSimilaritySearchSubHit</a></dt>
<dd>
<div class="block">Return an alignment of (possibly part of) the query sequence
against (possibly part of) this hit sequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SequenceDBSearchSubHit.html#getAlignment()">getAlignment()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SequenceDBSearchSubHit.html" title="class in org.biojava.bio.search">SequenceDBSearchSubHit</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SimpleSeqSimilaritySearchSubHit.html#getAlignment()">getAlignment()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SimpleSeqSimilaritySearchSubHit.html" title="class in org.biojava.bio.search">SimpleSeqSimilaritySearchSubHit</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/homol/Homology.html#getAlignment()">getAlignment()</a></span> - Method in interface org.biojava.bio.seq.homol.<a href="./org/biojava/bio/seq/homol/Homology.html" title="interface in org.biojava.bio.seq.homol">Homology</a></dt>
<dd>
<div class="block">Retrieve the Alignment that specifies how the homologous regions are
aligned.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/homol/SimilarityPairFeature.html#getAlignment()">getAlignment()</a></span> - Method in interface org.biojava.bio.seq.homol.<a href="./org/biojava/bio/seq/homol/SimilarityPairFeature.html" title="interface in org.biojava.bio.seq.homol">SimilarityPairFeature</a></dt>
<dd>
<div class="block"><code>getAlignment</code> returns the <code>Alignment</code> of
two similar features.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/homol/SimpleHomology.html#getAlignment()">getAlignment()</a></span> - Method in class org.biojava.bio.seq.homol.<a href="./org/biojava/bio/seq/homol/SimpleHomology.html" title="class in org.biojava.bio.seq.homol">SimpleHomology</a></dt>
<dd>
<div class="block"><code>getAlignment</code> returns the alignment, which uses the
<code>HomologyFeature</code>s as keys.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleSimilarityPairFeature.html#getAlignment()">getAlignment()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleSimilarityPairFeature.html" title="class in org.biojava.bio.seq.impl">SimpleSimilarityPairFeature</a></dt>
<dd>
<div class="block"><code>getAlignment</code> returns the alignment between the two
features.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/phylo/io/phylip/PHYLIPFileBuilder.html#getAlignment()">getAlignment()</a></span> - Method in class org.biojavax.bio.phylo.io.phylip.<a href="./org/biojavax/bio/phylo/io/phylip/PHYLIPFileBuilder.html" title="class in org.biojavax.bio.phylo.io.phylip">PHYLIPFileBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/StructurePairAligner.html#getAlignmentAtoms(org.biojava.bio.structure.Structure)">getAlignmentAtoms(Structure)</a></span> - Method in class org.biojava.bio.structure.align.<a href="./org/biojava/bio/structure/align/StructurePairAligner.html" title="class in org.biojava.bio.structure.align">StructurePairAligner</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/dasalignment/DASAlignmentCall.html#getAlignments()">getAlignments()</a></span> - Method in class org.biojava.bio.program.das.dasalignment.<a href="./org/biojava/bio/program/das/dasalignment/DASAlignmentCall.html" title="class in org.biojava.bio.program.das.dasalignment">DASAlignmentCall</a></dt>
<dd>
<div class="block">connect to a DAS alignment service and retreive alignments.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/dasalignment/DASAlignmentCall.html#getAlignments(java.lang.String)">getAlignments(String)</a></span> - Method in class org.biojava.bio.program.das.dasalignment.<a href="./org/biojava/bio/program/das/dasalignment/DASAlignmentCall.html" title="class in org.biojava.bio.program.das.dasalignment">DASAlignmentCall</a></dt>
<dd>
<div class="block">connect to a DAS alignment service and retreive data.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/dasalignment/DASAlignmentClient.html#getAlignments(java.lang.String)">getAlignments(String)</a></span> - Method in class org.biojava.bio.program.das.dasalignment.<a href="./org/biojava/bio/program/das/dasalignment/DASAlignmentClient.html" title="class in org.biojava.bio.program.das.dasalignment">DASAlignmentClient</a></dt>
<dd>
<div class="block">Returns the alignments.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/dasalignment/DASAlignmentClient.html#getAlignments()">getAlignments()</a></span> - Method in class org.biojava.bio.program.das.dasalignment.<a href="./org/biojava/bio/program/das/dasalignment/DASAlignmentClient.html" title="class in org.biojava.bio.program.das.dasalignment">DASAlignmentClient</a></dt>
<dd>
<div class="block">Returns the alignments.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/dasalignment/DASAlignmentXMLResponseParser.html#getAlignments()">getAlignments()</a></span> - Method in class org.biojava.bio.program.das.dasalignment.<a href="./org/biojava/bio/program/das/dasalignment/DASAlignmentXMLResponseParser.html" title="class in org.biojava.bio.program.das.dasalignment">DASAlignmentXMLResponseParser</a></dt>
<dd>
<div class="block">Returns the alignments.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/StructurePairAligner.html#getAlignments()">getAlignments()</a></span> - Method in class org.biojava.bio.structure.align.<a href="./org/biojava/bio/structure/align/StructurePairAligner.html" title="class in org.biojava.bio.structure.align">StructurePairAligner</a></dt>
<dd>
<div class="block">return the alternative alignments that can be found for the two structures</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/NeedlemanWunsch.html#getAlignmentString()">getAlignmentString()</a></span> - Method in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/NeedlemanWunsch.html" title="class in org.biojava.bio.alignment">NeedlemanWunsch</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/SequenceAlignment.html#getAlignmentString()">getAlignmentString()</a></span> - Method in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/SequenceAlignment.html" title="class in org.biojava.bio.alignment">SequenceAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/SeqRes2AtomAligner.html#getAlignmentString()">getAlignmentString()</a></span> - Method in class org.biojava.bio.structure.io.<a href="./org/biojava/bio/structure/io/SeqRes2AtomAligner.html" title="class in org.biojava.bio.structure.io">SeqRes2AtomAligner</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/blast2html/AbstractAlignmentStyler.html#getAlignmentStyles()">getAlignmentStyles()</a></span> - Method in class org.biojava.bio.program.blast2html.<a href="./org/biojava/bio/program/blast2html/AbstractAlignmentStyler.html" title="class in org.biojava.bio.program.blast2html">AbstractAlignmentStyler</a></dt>
<dd>
<div class="block">
Returns a fragment of HTML that defines the FONT
styles to be used in the alignment markup.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/Agave2AgaveAnnotFilter.html#getAlignUnits(org.biojava.bio.Annotation)">getAlignUnits(Annotation)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/Agave2AgaveAnnotFilter.html" title="class in org.biojava.bio.seq.io.agave">Agave2AgaveAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEAnnotFilter.html#getAlignUnits(org.biojava.bio.Annotation)">getAlignUnits(Annotation)</a></span> - Method in interface org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEAnnotFilter.html" title="interface in org.biojava.bio.seq.io.agave">AGAVEAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/SimpleAnnotFilter.html#getAlignUnits(org.biojava.bio.Annotation)">getAlignUnits(Annotation)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/SimpleAnnotFilter.html" title="class in org.biojava.bio.seq.io.agave">SimpleAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/unigene/UnigeneCluster.html#getAll()">getAll()</a></span> - Method in interface org.biojava.bio.program.unigene.<a href="./org/biojava/bio/program/unigene/UnigeneCluster.html" title="interface in org.biojava.bio.program.unigene">UnigeneCluster</a></dt>
<dd>
<div class="block">All sequences that map to this cluster.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/server/FlatFileInstallation.html#getAll()">getAll()</a></span> - Method in class org.biojava.bio.structure.server.<a href="./org/biojava/bio/structure/server/FlatFileInstallation.html" title="class in org.biojava.bio.structure.server">FlatFileInstallation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/server/MMCIFFileInstallation.html#getAll()">getAll()</a></span> - Method in class org.biojava.bio.structure.server.<a href="./org/biojava/bio/structure/server/MMCIFFileInstallation.html" title="class in org.biojava.bio.structure.server">MMCIFFileInstallation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/server/PDBInstallation.html#getAll()">getAll()</a></span> - Method in interface org.biojava.bio.structure.server.<a href="./org/biojava/bio/structure/server/PDBInstallation.html" title="interface in org.biojava.bio.structure.server">PDBInstallation</a></dt>
<dd>
<div class="block">get all PDBHeaders that pass the added Filters, if no filters have been added returns all available PDBs</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AlphabetManager.html#getAllAmbiguitySymbol(org.biojava.bio.symbol.FiniteAlphabet)">getAllAmbiguitySymbol(FiniteAlphabet)</a></span> - Static method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AlphabetManager.html" title="class in org.biojava.bio.symbol">AlphabetManager</a></dt>
<dd>
<div class="block">Return the ambiguity symbol which matches all symbols in
a given alphabet.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BibRefQuery.html#getAllBibRefs()">getAllBibRefs()</a></span> - Method in interface org.biojava.bibliography.<a href="./org/biojava/bibliography/BibRefQuery.html" title="interface in org.biojava.bibliography">BibRefQuery</a></dt>
<dd>
<div class="block">
It returns all citations from the current collection as a
(possibly big) array.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BibRefQuery.html#getAllBibRefs(java.lang.String[])">getAllBibRefs(String[])</a></span> - Method in interface org.biojava.bibliography.<a href="./org/biojava/bibliography/BibRefQuery.html" title="interface in org.biojava.bibliography">BibRefQuery</a></dt>
<dd>
<div class="block">
It returns all citations from the current collection as a
(possibly big) array, perhaps with a limited number of attributes.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BibRefQuery.html#getAllBibRefsAsXML()">getAllBibRefsAsXML()</a></span> - Method in interface org.biojava.bibliography.<a href="./org/biojava/bibliography/BibRefQuery.html" title="interface in org.biojava.bibliography">BibRefQuery</a></dt>
<dd>
<div class="block">
It returns all citations from the current collection as an XML stream.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/abi/ABIFParser.html#getAllDataRecords()">getAllDataRecords()</a></span> - Method in class org.biojava.bio.program.abi.<a href="./org/biojava/bio/program/abi/ABIFParser.html" title="class in org.biojava.bio.program.abi">ABIFParser</a></dt>
<dd>
<div class="block">Obtain all data records.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/candy/CandyVocabulary.html#getAllEntries()">getAllEntries()</a></span> - Method in interface org.biojava.utils.candy.<a href="./org/biojava/utils/candy/CandyVocabulary.html" title="interface in org.biojava.utils.candy">CandyVocabulary</a></dt>
<dd>
<div class="block">It returns all available vocabulary entries.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/molbio/RestrictionEnzymeManager.html#getAllEnzymes()">getAllEnzymes()</a></span> - Static method in class org.biojava.bio.molbio.<a href="./org/biojava/bio/molbio/RestrictionEnzymeManager.html" title="class in org.biojava.bio.molbio">RestrictionEnzymeManager</a></dt>
<dd>
<div class="block"><code>getAllEnzymes</code> returns an unmodifable set of all
available enzymes.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BibRefQuery.html#getAllIDs()">getAllIDs()</a></span> - Method in interface org.biojava.bibliography.<a href="./org/biojava/bibliography/BibRefQuery.html" title="interface in org.biojava.bibliography">BibRefQuery</a></dt>
<dd>
<div class="block">
A convenient method returning just identifiers of all current citations.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/server/PrepareMMcifIndexFile.html#getAllMMcif(java.io.File)">getAllMMcif(File)</a></span> - Method in class org.biojava.bio.structure.server.<a href="./org/biojava/bio/structure/server/PrepareMMcifIndexFile.html" title="class in org.biojava.bio.structure.server">PrepareMMcifIndexFile</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/candy/CandyVocabulary.html#getAllNames()">getAllNames()</a></span> - Method in interface org.biojava.utils.candy.<a href="./org/biojava/utils/candy/CandyVocabulary.html" title="interface in org.biojava.utils.candy">CandyVocabulary</a></dt>
<dd>
<div class="block">It return all names (entry identifiers) available in this vocabulary.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/UkkonenSuffixTree.html#getAllNodes(org.biojava.bio.symbol.UkkonenSuffixTree.SuffixNode, java.util.ArrayList, boolean)">getAllNodes(UkkonenSuffixTree.SuffixNode, ArrayList, boolean)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/UkkonenSuffixTree.html" title="class in org.biojava.bio.symbol">UkkonenSuffixTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/server/PrepareIndexFile.html#getAllPDB(java.io.File)">getAllPDB(File)</a></span> - Method in class org.biojava.bio.structure.server.<a href="./org/biojava/bio/structure/server/PrepareIndexFile.html" title="class in org.biojava.bio.structure.server">PrepareIndexFile</a></dt>
<dd>
<div class="block">get all PDBfiles from a directory</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/ProteaseManager.html#getAllProteases()">getAllProteases()</a></span> - Static method in class org.biojava.bio.proteomics.<a href="./org/biojava/bio/proteomics/ProteaseManager.html" title="class in org.biojava.bio.proteomics">ProteaseManager</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/biosql/TaxonSQL.html#getAllScientificNames(java.sql.Connection)">getAllScientificNames(Connection)</a></span> - Static method in class org.biojava.bio.seq.db.biosql.<a href="./org/biojava/bio/seq/db/biosql/TaxonSQL.html" title="class in org.biojava.bio.seq.db.biosql">TaxonSQL</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Returns all the <code>scientific name</code>s, which are currently stored in the
database.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AlphabetManager.html#getAllSymbols(org.biojava.bio.symbol.FiniteAlphabet)">getAllSymbols(FiniteAlphabet)</a></span> - Static method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AlphabetManager.html" title="class in org.biojava.bio.symbol">AlphabetManager</a></dt>
<dd>
<div class="block">Return a set containing all possible symbols which can be
considered members of a given alphabet, including ambiguous
symbols.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/candy/CandyFinder.html#getAllVocabularies()">getAllVocabularies()</a></span> - Method in interface org.biojava.utils.candy.<a href="./org/biojava/utils/candy/CandyFinder.html" title="interface in org.biojava.utils.candy">CandyFinder</a></dt>
<dd>
<div class="block">It returns all available vocabularies.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/candy/CandyFinder.html#getAllVocabularyNames()">getAllVocabularyNames()</a></span> - Method in interface org.biojava.utils.candy.<a href="./org/biojava/utils/candy/CandyFinder.html" title="interface in org.biojava.utils.candy">CandyFinder</a></dt>
<dd>
<div class="block">
It returns names of all vocabularies known to this vocabulary
finder.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/SimpleSVMClassifierModel.html#getAlpha(java.lang.Object)">getAlpha(Object)</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/SimpleSVMClassifierModel.html" title="class in org.biojava.stats.svm">SimpleSVMClassifierModel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/SVMClassifierModel.html#getAlpha(java.lang.Object)">getAlpha(Object)</a></span> - Method in interface org.biojava.stats.svm.<a href="./org/biojava/stats/svm/SVMClassifierModel.html" title="interface in org.biojava.stats.svm">SVMClassifierModel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/SVMRegressionModel.html#getAlpha(int)">getAlpha(int)</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/SVMRegressionModel.html" title="class in org.biojava.stats.svm">SVMRegressionModel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/AbstractULAlignment.SubULAlignment.html#getAlphabet()">getAlphabet()</a></span> - Method in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/AbstractULAlignment.SubULAlignment.html" title="class in org.biojava.bio.alignment">AbstractULAlignment.SubULAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/FlexibleAlignment.html#getAlphabet()">getAlphabet()</a></span> - Method in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/FlexibleAlignment.html" title="class in org.biojava.bio.alignment">FlexibleAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/SubstitutionMatrix.html#getAlphabet()">getAlphabet()</a></span> - Method in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/SubstitutionMatrix.html" title="class in org.biojava.bio.alignment">SubstitutionMatrix</a></dt>
<dd>
<div class="block">Gives the alphabet used by this matrix.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/AbstractOrderNDistribution.html#getAlphabet()">getAlphabet()</a></span> - Method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/AbstractOrderNDistribution.html" title="class in org.biojava.bio.dist">AbstractOrderNDistribution</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/Count.html#getAlphabet()">getAlphabet()</a></span> - Method in interface org.biojava.bio.dist.<a href="./org/biojava/bio/dist/Count.html" title="interface in org.biojava.bio.dist">Count</a></dt>
<dd>
<div class="block">The alphabet from which this Count is over.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/Distribution.html#getAlphabet()">getAlphabet()</a></span> - Method in interface org.biojava.bio.dist.<a href="./org/biojava/bio/dist/Distribution.html" title="interface in org.biojava.bio.dist">Distribution</a></dt>
<dd>
<div class="block">The alphabet from which this spectrum emits symbols.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/GapDistribution.html#getAlphabet()">getAlphabet()</a></span> - Method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/GapDistribution.html" title="class in org.biojava.bio.dist">GapDistribution</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/IndexedCount.html#getAlphabet()">getAlphabet()</a></span> - Method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/IndexedCount.html" title="class in org.biojava.bio.dist">IndexedCount</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/PairDistribution.html#getAlphabet()">getAlphabet()</a></span> - Method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/PairDistribution.html" title="class in org.biojava.bio.dist">PairDistribution</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/SimpleDistribution.html#getAlphabet()">getAlphabet()</a></span> - Method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/SimpleDistribution.html" title="class in org.biojava.bio.dist">SimpleDistribution</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/TranslatedDistribution.html#getAlphabet()">getAlphabet()</a></span> - Method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/TranslatedDistribution.html" title="class in org.biojava.bio.dist">TranslatedDistribution</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/UniformDistribution.html#getAlphabet()">getAlphabet()</a></span> - Method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/UniformDistribution.html" title="class in org.biojava.bio.dist">UniformDistribution</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/SimpleStatePath.html#getAlphabet()">getAlphabet()</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/SimpleStatePath.html" title="class in org.biojava.bio.dp">SimpleStatePath</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/SimpleWeightMatrix.html#getAlphabet()">getAlphabet()</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/SimpleWeightMatrix.html" title="class in org.biojava.bio.dp">SimpleWeightMatrix</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/WeightMatrix.html#getAlphabet()">getAlphabet()</a></span> - Method in interface org.biojava.bio.dp.<a href="./org/biojava/bio/dp/WeightMatrix.html" title="interface in org.biojava.bio.dp">WeightMatrix</a></dt>
<dd>
<div class="block">The alphabet for the sequences that this weight matrix models.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/SimpleSymbolStyle.html#getAlphabet()">getAlphabet()</a></span> - Method in class org.biojava.bio.gui.<a href="./org/biojava/bio/gui/SimpleSymbolStyle.html" title="class in org.biojava.bio.gui">SimpleSymbolStyle</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/DASSequence.html#getAlphabet()">getAlphabet()</a></span> - Method in class org.biojava.bio.program.das.<a href="./org/biojava/bio/program/das/DASSequence.html" title="class in org.biojava.bio.program.das">DASSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssaha/CompactedDataStore.html#getAlphabet()">getAlphabet()</a></span> - Method in class org.biojava.bio.program.ssaha.<a href="./org/biojava/bio/program/ssaha/CompactedDataStore.html" title="class in org.biojava.bio.program.ssaha">CompactedDataStore</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssaha/DataStore.html#getAlphabet()">getAlphabet()</a></span> - Method in interface org.biojava.bio.program.ssaha.<a href="./org/biojava/bio/program/ssaha/DataStore.html" title="interface in org.biojava.bio.program.ssaha">DataStore</a></dt>
<dd>
<div class="block">The alphabet of symbol lists that can be searched against this
DataStore.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/GenbankSequenceDB.html#getAlphabet()">getAlphabet()</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/GenbankSequenceDB.html" title="class in org.biojava.bio.seq.db">GenbankSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/GenpeptSequenceDB.html#getAlphabet()">getAlphabet()</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/GenpeptSequenceDB.html" title="class in org.biojava.bio.seq.db">GenpeptSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/NCBISequenceDB.html#getAlphabet()">getAlphabet()</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/NCBISequenceDB.html" title="class in org.biojava.bio.seq.db">NCBISequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/SwissprotSequenceDB.html#getAlphabet()">getAlphabet()</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/SwissprotSequenceDB.html" title="class in org.biojava.bio.seq.db">SwissprotSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/WebSequenceDB.html#getAlphabet()">getAlphabet()</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/WebSequenceDB.html" title="class in org.biojava.bio.seq.db">WebSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/homol/SimilarityPairFeature.EmptyPairwiseAlignment.html#getAlphabet()">getAlphabet()</a></span> - Method in class org.biojava.bio.seq.homol.<a href="./org/biojava/bio/seq/homol/SimilarityPairFeature.EmptyPairwiseAlignment.html" title="class in org.biojava.bio.seq.homol">SimilarityPairFeature.EmptyPairwiseAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/AssembledSymbolList.html#getAlphabet()">getAlphabet()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/AssembledSymbolList.html" title="class in org.biojava.bio.seq.impl">AssembledSymbolList</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/DummySequence.html#getAlphabet()">getAlphabet()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/DummySequence.html" title="class in org.biojava.bio.seq.impl">DummySequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/NewAssembledSymbolList.html#getAlphabet()">getAlphabet()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/NewAssembledSymbolList.html" title="class in org.biojava.bio.seq.impl">NewAssembledSymbolList</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleSequence.html#getAlphabet()">getAlphabet()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleSequence.html" title="class in org.biojava.bio.seq.impl">SimpleSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SubSequence.html#getAlphabet()">getAlphabet()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SubSequence.html" title="class in org.biojava.bio.seq.impl">SubSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/ViewSequence.html#getAlphabet()">getAlphabet()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/ViewSequence.html" title="class in org.biojava.bio.seq.impl">ViewSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/AlternateTokenization.html#getAlphabet()">getAlphabet()</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/AlternateTokenization.html" title="class in org.biojava.bio.seq.io">AlternateTokenization</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/CharacterTokenization.html#getAlphabet()">getAlphabet()</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/CharacterTokenization.html" title="class in org.biojava.bio.seq.io">CharacterTokenization</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOTools.html#getAlphabet(int)">getAlphabet(int)</a></span> - Static method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOTools.html" title="class in org.biojava.bio.seq.io">SeqIOTools</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block"><code>getAlphabet</code> accepts a value which represents a
sequence format and returns the relevant
<code>FiniteAlphabet</code> object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SymbolReader.html#getAlphabet()">getAlphabet()</a></span> - Method in interface org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SymbolReader.html" title="interface in org.biojava.bio.seq.io">SymbolReader</a></dt>
<dd>
<div class="block">Find the alphabet of all symbols which may be returned by
this SymbolReader.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SymbolTokenization.html#getAlphabet()">getAlphabet()</a></span> - Method in interface org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SymbolTokenization.html" title="interface in org.biojava.bio.seq.io">SymbolTokenization</a></dt>
<dd>
<div class="block">The alphabet to which this tokenization applies.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/WordTokenization.html#getAlphabet()">getAlphabet()</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/WordTokenization.html" title="class in org.biojava.bio.seq.io">WordTokenization</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/NewSimpleAssembly.html#getAlphabet()">getAlphabet()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/NewSimpleAssembly.html" title="class in org.biojava.bio.seq">NewSimpleAssembly</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/ProteinTools.html#getAlphabet()">getAlphabet()</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/ProteinTools.html" title="class in org.biojava.bio.seq">ProteinTools</a></dt>
<dd>
<div class="block">Gets the protein alphabet</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/SimpleAssembly.html#getAlphabet()">getAlphabet()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/SimpleAssembly.html" title="class in org.biojava.bio.seq">SimpleAssembly</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AlphabetIndex.html#getAlphabet()">getAlphabet()</a></span> - Method in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AlphabetIndex.html" title="interface in org.biojava.bio.symbol">AlphabetIndex</a></dt>
<dd>
<div class="block">Retrieve the alphabet that this indexes.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/ChunkedSymbolList.html#getAlphabet()">getAlphabet()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/ChunkedSymbolList.html" title="class in org.biojava.bio.symbol">ChunkedSymbolList</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/DNAAmbPack.html#getAlphabet()">getAlphabet()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/DNAAmbPack.html" title="class in org.biojava.bio.symbol">DNAAmbPack</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/DNANoAmbPack.html#getAlphabet()">getAlphabet()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/DNANoAmbPack.html" title="class in org.biojava.bio.symbol">DNANoAmbPack</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/DummySymbolList.html#getAlphabet()">getAlphabet()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/DummySymbolList.html" title="class in org.biojava.bio.symbol">DummySymbolList</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/PackedSymbolList.html#getAlphabet()">getAlphabet()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/PackedSymbolList.html" title="class in org.biojava.bio.symbol">PackedSymbolList</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/Packing.html#getAlphabet()">getAlphabet()</a></span> - Method in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/Packing.html" title="interface in org.biojava.bio.symbol">Packing</a></dt>
<dd>
<div class="block">The FiniteAlphabet this packing is for.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/RelabeledAlignment.html#getAlphabet()">getAlphabet()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/RelabeledAlignment.html" title="class in org.biojava.bio.symbol">RelabeledAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleAlignment.html#getAlphabet()">getAlphabet()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleAlignment.html" title="class in org.biojava.bio.symbol">SimpleAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleGappedSymbolList.html#getAlphabet()">getAlphabet()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleGappedSymbolList.html" title="class in org.biojava.bio.symbol">SimpleGappedSymbolList</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleSymbolList.html#getAlphabet()">getAlphabet()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleSymbolList.html" title="class in org.biojava.bio.symbol">SimpleSymbolList</a></dt>
<dd>
<div class="block">Get the alphabet of this SymbolList.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleSymbolPropertyTable.html#getAlphabet()">getAlphabet()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleSymbolPropertyTable.html" title="class in org.biojava.bio.symbol">SimpleSymbolPropertyTable</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SoftMaskedAlphabet.CaseSensitiveTokenization.html#getAlphabet()">getAlphabet()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SoftMaskedAlphabet.CaseSensitiveTokenization.html" title="class in org.biojava.bio.symbol">SoftMaskedAlphabet.CaseSensitiveTokenization</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SuffixTree.html#getAlphabet()">getAlphabet()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SuffixTree.html" title="class in org.biojava.bio.symbol">SuffixTree</a></dt>
<dd>
<div class="block">Return the Alphabet containing all Symbols which might be found in
this SuffixTree.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SymbolList.html#getAlphabet()">getAlphabet()</a></span> - Method in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SymbolList.html" title="interface in org.biojava.bio.symbol">SymbolList</a></dt>
<dd>
<div class="block">The alphabet that this SymbolList is over.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SymbolPropertyTable.html#getAlphabet()">getAlphabet()</a></span> - Method in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SymbolPropertyTable.html" title="interface in org.biojava.bio.symbol">SymbolPropertyTable</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/regex/Pattern.html#getAlphabet()">getAlphabet()</a></span> - Method in class org.biojava.utils.regex.<a href="./org/biojava/utils/regex/Pattern.html" title="class in org.biojava.utils.regex">Pattern</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/InfinitelyAmbiguousSymbolList.html#getAlphabet()">getAlphabet()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/InfinitelyAmbiguousSymbolList.html" title="class in org.biojavax.bio.seq">InfinitelyAmbiguousSymbolList</a></dt>
<dd>
<div class="block">The alphabet that this SymbolList is over.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/ThinRichSequence.html#getAlphabet()">getAlphabet()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/ThinRichSequence.html" title="class in org.biojavax.bio.seq">ThinRichSequence</a></dt>
<dd>
<div class="block">The alphabet that this SymbolList is over.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AlphabetManager.html#getAlphabetIndex(org.biojava.bio.symbol.FiniteAlphabet)">getAlphabetIndex(FiniteAlphabet)</a></span> - Static method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AlphabetManager.html" title="class in org.biojava.bio.symbol">AlphabetManager</a></dt>
<dd>
<div class="block">Get an indexer for a specified alphabet.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AlphabetManager.html#getAlphabetIndex(org.biojava.bio.symbol.Symbol[])">getAlphabetIndex(Symbol[])</a></span> - Static method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AlphabetManager.html" title="class in org.biojava.bio.symbol">AlphabetManager</a></dt>
<dd>
<div class="block">Get an indexer for an array of symbols.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/ThinRichSequence.html#getAlphabetName()">getAlphabetName()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/ThinRichSequence.html" title="class in org.biojavax.bio.seq">ThinRichSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/Alphabet.html#getAlphabets()">getAlphabets()</a></span> - Method in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/Alphabet.html" title="interface in org.biojava.bio.symbol">Alphabet</a></dt>
<dd>
<div class="block">Return an ordered List of the alphabets which make up a
compound alphabet.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/DoubleAlphabet.html#getAlphabets()">getAlphabets()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/DoubleAlphabet.html" title="class in org.biojava.bio.symbol">DoubleAlphabet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/DoubleAlphabet.SubDoubleAlphabet.html#getAlphabets()">getAlphabets()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/DoubleAlphabet.SubDoubleAlphabet.html" title="class in org.biojava.bio.symbol">DoubleAlphabet.SubDoubleAlphabet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/IntegerAlphabet.html#getAlphabets()">getAlphabets()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/IntegerAlphabet.html" title="class in org.biojava.bio.symbol">IntegerAlphabet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/IntegerAlphabet.SubIntegerAlphabet.html#getAlphabets()">getAlphabets()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/IntegerAlphabet.SubIntegerAlphabet.html" title="class in org.biojava.bio.symbol">IntegerAlphabet.SubIntegerAlphabet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleAlphabet.html#getAlphabets()">getAlphabets()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleAlphabet.html" title="class in org.biojava.bio.symbol">SimpleAlphabet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SingletonAlphabet.html#getAlphabets()">getAlphabets()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SingletonAlphabet.html" title="class in org.biojava.bio.symbol">SingletonAlphabet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SoftMaskedAlphabet.html#getAlphabets()">getAlphabets()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SoftMaskedAlphabet.html" title="class in org.biojava.bio.symbol">SoftMaskedAlphabet</a></dt>
<dd>
<div class="block">Gets the components of the <code>Alphabet</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/AlphaCTools.html#getAlphaCarbonAngleAlphabet()">getAlphaCarbonAngleAlphabet()</a></span> - Static method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/AlphaCTools.html" title="class in org.biojava.bio.structure">AlphaCTools</a></dt>
<dd>
<div class="block">Returns a reference to the Alphabet that contains Symbols that represent PHI,
PSI angles.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/SVMRegressionModel.html#getAlphaStar(int)">getAlphaStar(int)</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/SVMRegressionModel.html" title="class in org.biojava.stats.svm">SVMRegressionModel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/AlternativeAlignment.html#getAltAligNumber()">getAltAligNumber()</a></span> - Method in class org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/AlternativeAlignment.html" title="class in org.biojava.bio.structure.align.pairwise">AlternativeAlignment</a></dt>
<dd>
<div class="block">returns the sequential number of this alternative alignment</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/JMatrixPanel.html#getAlternativeAligs()">getAlternativeAligs()</a></span> - Method in class org.biojava.bio.structure.gui.<a href="./org/biojava/bio/structure/gui/JMatrixPanel.html" title="class in org.biojava.bio.structure.gui">JMatrixPanel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/ScaleableMatrixPanel.html#getAlternativeAligs()">getAlternativeAligs()</a></span> - Method in class org.biojava.bio.structure.gui.<a href="./org/biojava/bio/structure/gui/ScaleableMatrixPanel.html" title="class in org.biojava.bio.structure.gui">ScaleableMatrixPanel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/Agave2AgaveAnnotFilter.html#getAltIds(org.biojava.bio.Annotation)">getAltIds(Annotation)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/Agave2AgaveAnnotFilter.html" title="class in org.biojava.bio.seq.io.agave">Agave2AgaveAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEAnnotFilter.html#getAltIds(org.biojava.bio.Annotation)">getAltIds(Annotation)</a></span> - Method in interface org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEAnnotFilter.html" title="interface in org.biojava.bio.seq.io.agave">AGAVEAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/SimpleAnnotFilter.html#getAltIds(org.biojava.bio.Annotation)">getAltIds(Annotation)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/SimpleAnnotFilter.html" title="class in org.biojava.bio.seq.io.agave">SimpleAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Atom.html#getAltLoc()">getAltLoc()</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Atom.html" title="interface in org.biojava.bio.structure">Atom</a></dt>
<dd>
<div class="block">get set alternate Location.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/AtomImpl.html#getAltLoc()">getAltLoc()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/AtomImpl.html" title="class in org.biojava.bio.structure">AtomImpl</a></dt>
<dd>
<div class="block">get alternate Location.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AbstractAlphabet.html#getAmbiguity(java.util.Set)">getAmbiguity(Set)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AbstractAlphabet.html" title="class in org.biojava.bio.symbol">AbstractAlphabet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/Alphabet.html#getAmbiguity(java.util.Set)">getAmbiguity(Set)</a></span> - Method in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/Alphabet.html" title="interface in org.biojava.bio.symbol">Alphabet</a></dt>
<dd>
<div class="block">
Get a symbol that represents the set of symbols in syms.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/DoubleAlphabet.html#getAmbiguity(java.util.Set)">getAmbiguity(Set)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/DoubleAlphabet.html" title="class in org.biojava.bio.symbol">DoubleAlphabet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/DoubleAlphabet.SubDoubleAlphabet.html#getAmbiguity(java.util.Set)">getAmbiguity(Set)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/DoubleAlphabet.SubDoubleAlphabet.html" title="class in org.biojava.bio.symbol">DoubleAlphabet.SubDoubleAlphabet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/IntegerAlphabet.html#getAmbiguity(java.util.Set)">getAmbiguity(Set)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/IntegerAlphabet.html" title="class in org.biojava.bio.symbol">IntegerAlphabet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SoftMaskedAlphabet.html#getAmbiguity(java.util.Set)">getAmbiguity(Set)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SoftMaskedAlphabet.html" title="class in org.biojava.bio.symbol">SoftMaskedAlphabet</a></dt>
<dd>
<div class="block">This is not supported.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AbstractAlphabet.html#getAmbiguityImpl(java.util.Set)">getAmbiguityImpl(Set)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AbstractAlphabet.html" title="class in org.biojava.bio.symbol">AbstractAlphabet</a></dt>
<dd>
<div class="block">Backend for getAmbiguity, called when it is actually necessarly to create a new symbol.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/StandardAminoAcid.html#getAminoAcid(java.lang.String)">getAminoAcid(String)</a></span> - Static method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/StandardAminoAcid.html" title="class in org.biojava.bio.structure">StandardAminoAcid</a></dt>
<dd>
<div class="block">get a standard amino acid.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/chem/ChemCompTools.html#getAminoOneLetter(java.lang.String)">getAminoOneLetter(String)</a></span> - Static method in class org.biojava.bio.structure.io.mmcif.chem.<a href="./org/biojava/bio/structure/io/mmcif/chem/ChemCompTools.html" title="class in org.biojava.bio.structure.io.mmcif.chem">ChemCompTools</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/chem/ChemCompTools.html#getAminoThreeLetter(java.lang.Character)">getAminoThreeLetter(Character)</a></span> - Static method in class org.biojava.bio.structure.io.mmcif.chem.<a href="./org/biojava/bio/structure/io/mmcif/chem/ChemCompTools.html" title="class in org.biojava.bio.structure.io.mmcif.chem">ChemCompTools</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/AminoAcid.html#getAminoType()">getAminoType()</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/AminoAcid.html" title="interface in org.biojava.bio.structure">AminoAcid</a></dt>
<dd>
<div class="block">returns the name of the AA, in single letter code.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/AminoAcidImpl.html#getAminoType()">getAminoType()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/AminoAcidImpl.html" title="class in org.biojava.bio.structure">AminoAcidImpl</a></dt>
<dd>
<div class="block">returns the name of the AA, in single letter code.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/CircularRendererContext.html#getAngle(int)">getAngle(int)</a></span> - Method in interface org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/CircularRendererContext.html" title="interface in org.biojava.bio.gui.sequence">CircularRendererContext</a></dt>
<dd>
<div class="block">Return the angle for an index into a sequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SubCircularRendererContext.html#getAngle(int)">getAngle(int)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SubCircularRendererContext.html" title="class in org.biojava.bio.gui.sequence">SubCircularRendererContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/StrucAligParameters.html#getAngleDiff()">getAngleDiff()</a></span> - Method in class org.biojava.bio.structure.align.<a href="./org/biojava/bio/structure/align/StrucAligParameters.html" title="class in org.biojava.bio.structure.align">StrucAligParameters</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#getAniso_B()">getAniso_B()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/SimilarityPairBuilder.html#getAnnotatedQuerySeq(java.lang.String)">getAnnotatedQuerySeq(String)</a></span> - Method in class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/SimilarityPairBuilder.html" title="class in org.biojava.bio.program.ssbind">SimilarityPairBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/SimilarityPairBuilder.html#getAnnotatedSubjectSeq(java.lang.String)">getAnnotatedSubjectSeq(String)</a></span> - Method in class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/SimilarityPairBuilder.html" title="class in org.biojava.bio.program.ssbind">SimilarityPairBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/ReferenceServer.html#getAnnotaters()">getAnnotaters()</a></span> - Method in class org.biojava.bio.program.das.<a href="./org/biojava/bio/program/das/ReferenceServer.html" title="class in org.biojava.bio.program.das">ReferenceServer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/Annotatable.html#getAnnotation()">getAnnotation()</a></span> - Method in interface org.biojava.bio.<a href="./org/biojava/bio/Annotatable.html" title="interface in org.biojava.bio">Annotatable</a></dt>
<dd>
<div class="block">Should return the associated annotation object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/SimpleEmissionState.html#getAnnotation()">getAnnotation()</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/SimpleEmissionState.html" title="class in org.biojava.bio.dp">SimpleEmissionState</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/molbio/RestrictionEnzymeManager.html#getAnnotation(org.biojava.bio.molbio.RestrictionEnzyme)">getAnnotation(RestrictionEnzyme)</a></span> - Static method in class org.biojava.bio.molbio.<a href="./org/biojava/bio/molbio/RestrictionEnzymeManager.html" title="class in org.biojava.bio.molbio">RestrictionEnzymeManager</a></dt>
<dd>
<div class="block"><code>getAnnotation</code> returns an immutable, static
annotation describing the enzyme.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/DASSequence.html#getAnnotation()">getAnnotation()</a></span> - Method in class org.biojava.bio.program.das.<a href="./org/biojava/bio/program/das/DASSequence.html" title="class in org.biojava.bio.program.das">DASSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff3/GFF3Record.Impl.html#getAnnotation()">getAnnotation()</a></span> - Method in class org.biojava.bio.program.gff3.<a href="./org/biojava/bio/program/gff3/GFF3Record.Impl.html" title="class in org.biojava.bio.program.gff3">GFF3Record.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SequenceDBSearchHit.html#getAnnotation()">getAnnotation()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SequenceDBSearchHit.html" title="class in org.biojava.bio.search">SequenceDBSearchHit</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block"><code>getAnnotation</code> returns the Annotation associated
with this hit.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SequenceDBSearchResult.html#getAnnotation()">getAnnotation()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SequenceDBSearchResult.html" title="class in org.biojava.bio.search">SequenceDBSearchResult</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block"><code>getAnnotation</code> returns the Annotation associated
with this hit.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SequenceDBSearchSubHit.html#getAnnotation()">getAnnotation()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SequenceDBSearchSubHit.html" title="class in org.biojava.bio.search">SequenceDBSearchSubHit</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SimpleSeqSimilaritySearchHit.html#getAnnotation()">getAnnotation()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SimpleSeqSimilaritySearchHit.html" title="class in org.biojava.bio.search">SimpleSeqSimilaritySearchHit</a></dt>
<dd>
<div class="block"><code>getAnnotation</code> returns the Annotation associated
with this hit.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SimpleSeqSimilaritySearchResult.html#getAnnotation()">getAnnotation()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SimpleSeqSimilaritySearchResult.html" title="class in org.biojava.bio.search">SimpleSeqSimilaritySearchResult</a></dt>
<dd>
<div class="block"><code>getAnnotation</code> returns the Annotation associated
with this hit.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SimpleSeqSimilaritySearchSubHit.html#getAnnotation()">getAnnotation()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SimpleSeqSimilaritySearchSubHit.html" title="class in org.biojava.bio.search">SimpleSeqSimilaritySearchSubHit</a></dt>
<dd>
<div class="block"><code>getAnnotation</code> returns the Annotation associated
with this sub-hit.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureTypes.RepositoryImpl.html#getAnnotation()">getAnnotation()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureTypes.RepositoryImpl.html" title="class in org.biojava.bio.seq">FeatureTypes.RepositoryImpl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/DummySequence.html#getAnnotation()">getAnnotation()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/DummySequence.html" title="class in org.biojava.bio.seq.impl">DummySequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleFeature.html#getAnnotation()">getAnnotation()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleFeature.html" title="class in org.biojava.bio.seq.impl">SimpleFeature</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleGappedSequence.html#getAnnotation()">getAnnotation()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleGappedSequence.html" title="class in org.biojava.bio.seq.impl">SimpleGappedSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleSequence.html#getAnnotation()">getAnnotation()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleSequence.html" title="class in org.biojava.bio.seq.impl">SimpleSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SubSequence.html#getAnnotation()">getAnnotation()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SubSequence.html" title="class in org.biojava.bio.seq.impl">SubSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/ViewSequence.html#getAnnotation()">getAnnotation()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/ViewSequence.html" title="class in org.biojava.bio.seq.impl">ViewSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/AlternateTokenization.html#getAnnotation()">getAnnotation()</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/AlternateTokenization.html" title="class in org.biojava.bio.seq.io">AlternateTokenization</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/CharacterTokenization.html#getAnnotation()">getAnnotation()</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/CharacterTokenization.html" title="class in org.biojava.bio.seq.io">CharacterTokenization</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/WordTokenization.html#getAnnotation()">getAnnotation()</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/WordTokenization.html" title="class in org.biojava.bio.seq.io">WordTokenization</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/NewSimpleAssembly.html#getAnnotation()">getAnnotation()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/NewSimpleAssembly.html" title="class in org.biojava.bio.seq">NewSimpleAssembly</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/SimpleAssembly.html#getAnnotation()">getAnnotation()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/SimpleAssembly.html" title="class in org.biojava.bio.seq">SimpleAssembly</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Chain.html#getAnnotation()">getAnnotation()</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Chain.html" title="interface in org.biojava.bio.structure">Chain</a></dt>
<dd>
<div class="block">get/set the Annotation of a Chain.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/ChainImpl.html#getAnnotation()">getAnnotation()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/ChainImpl.html" title="class in org.biojava.bio.structure">ChainImpl</a></dt>
<dd>
<div class="block">get/set the Annotation of a Chain.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/DoubleAlphabet.DoubleRange.html#getAnnotation()">getAnnotation()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/DoubleAlphabet.DoubleRange.html" title="class in org.biojava.bio.symbol">DoubleAlphabet.DoubleRange</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/DoubleAlphabet.DoubleSymbol.html#getAnnotation()">getAnnotation()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/DoubleAlphabet.DoubleSymbol.html" title="class in org.biojava.bio.symbol">DoubleAlphabet.DoubleSymbol</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/DoubleAlphabet.html#getAnnotation()">getAnnotation()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/DoubleAlphabet.html" title="class in org.biojava.bio.symbol">DoubleAlphabet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/DoubleAlphabet.SubDoubleAlphabet.html#getAnnotation()">getAnnotation()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/DoubleAlphabet.SubDoubleAlphabet.html" title="class in org.biojava.bio.symbol">DoubleAlphabet.SubDoubleAlphabet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/FundamentalAtomicSymbol.html#getAnnotation()">getAnnotation()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/FundamentalAtomicSymbol.html" title="class in org.biojava.bio.symbol">FundamentalAtomicSymbol</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/IntegerAlphabet.html#getAnnotation()">getAnnotation()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/IntegerAlphabet.html" title="class in org.biojava.bio.symbol">IntegerAlphabet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/IntegerAlphabet.IntegerSymbol.html#getAnnotation()">getAnnotation()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/IntegerAlphabet.IntegerSymbol.html" title="class in org.biojava.bio.symbol">IntegerAlphabet.IntegerSymbol</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/IntegerAlphabet.SubIntegerAlphabet.html#getAnnotation()">getAnnotation()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/IntegerAlphabet.SubIntegerAlphabet.html" title="class in org.biojava.bio.symbol">IntegerAlphabet.SubIntegerAlphabet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleAlphabet.html#getAnnotation()">getAnnotation()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleAlphabet.html" title="class in org.biojava.bio.symbol">SimpleAlphabet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SingletonAlphabet.html#getAnnotation()">getAnnotation()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SingletonAlphabet.html" title="class in org.biojava.bio.symbol">SingletonAlphabet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SoftMaskedAlphabet.CaseSensitiveTokenization.html#getAnnotation()">getAnnotation()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SoftMaskedAlphabet.CaseSensitiveTokenization.html" title="class in org.biojava.bio.symbol">SoftMaskedAlphabet.CaseSensitiveTokenization</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SoftMaskedAlphabet.html#getAnnotation()">getAnnotation()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SoftMaskedAlphabet.html" title="class in org.biojava.bio.symbol">SoftMaskedAlphabet</a></dt>
<dd>
<div class="block">The SoftMaskedAlphabet has no annotation</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/taxa/AbstractTaxon.html#getAnnotation()">getAnnotation()</a></span> - Method in class org.biojava.bio.taxa.<a href="./org/biojava/bio/taxa/AbstractTaxon.html" title="class in org.biojava.bio.taxa">AbstractTaxon</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/IntegerOntology.IntTerm.html#getAnnotation()">getAnnotation()</a></span> - Method in class org.biojava.ontology.<a href="./org/biojava/ontology/IntegerOntology.IntTerm.html" title="class in org.biojava.ontology">IntegerOntology.IntTerm</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/OntologyTerm.Impl.html#getAnnotation()">getAnnotation()</a></span> - Method in class org.biojava.ontology.<a href="./org/biojava/ontology/OntologyTerm.Impl.html" title="class in org.biojava.ontology">OntologyTerm.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/RemoteTerm.Impl.html#getAnnotation()">getAnnotation()</a></span> - Method in class org.biojava.ontology.<a href="./org/biojava/ontology/RemoteTerm.Impl.html" title="class in org.biojava.ontology">RemoteTerm.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/Term.Impl.html#getAnnotation()">getAnnotation()</a></span> - Method in class org.biojava.ontology.<a href="./org/biojava/ontology/Term.Impl.html" title="class in org.biojava.ontology">Term.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/Triple.Impl.html#getAnnotation()">getAnnotation()</a></span> - Method in class org.biojava.ontology.<a href="./org/biojava/ontology/Triple.Impl.html" title="class in org.biojava.ontology">Triple.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/CompoundRichLocation.html#getAnnotation()">getAnnotation()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/CompoundRichLocation.html" title="class in org.biojavax.bio.seq">CompoundRichLocation</a></dt>
<dd>
<div class="block">Should return the associated annotation object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/EmptyRichLocation.html#getAnnotation()">getAnnotation()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/EmptyRichLocation.html" title="class in org.biojavax.bio.seq">EmptyRichLocation</a></dt>
<dd>
<div class="block">Should return the associated annotation object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichFeature.html#getAnnotation()">getAnnotation()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichFeature.html" title="class in org.biojavax.bio.seq">SimpleRichFeature</a></dt>
<dd>
<div class="block">Should return the associated annotation object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichLocation.html#getAnnotation()">getAnnotation()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichLocation.html" title="class in org.biojavax.bio.seq">SimpleRichLocation</a></dt>
<dd>
<div class="block">Should return the associated annotation object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/SimpleBioEntry.html#getAnnotation()">getAnnotation()</a></span> - Method in class org.biojavax.bio.<a href="./org/biojavax/bio/SimpleBioEntry.html" title="class in org.biojavax.bio">SimpleBioEntry</a></dt>
<dd>
<div class="block">Should return the associated annotation object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ontology/SimpleComparableTerm.html#getAnnotation()">getAnnotation()</a></span> - Method in class org.biojavax.ontology.<a href="./org/biojavax/ontology/SimpleComparableTerm.html" title="class in org.biojavax.ontology">SimpleComparableTerm</a></dt>
<dd>
<div class="block">Should return the associated annotation object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ontology/SimpleComparableTriple.html#getAnnotation()">getAnnotation()</a></span> - Method in class org.biojavax.ontology.<a href="./org/biojavax/ontology/SimpleComparableTriple.html" title="class in org.biojavax.ontology">SimpleComparableTriple</a></dt>
<dd>
<div class="block">Should return the associated annotation object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleCrossRef.html#getAnnotation()">getAnnotation()</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleCrossRef.html" title="class in org.biojavax">SimpleCrossRef</a></dt>
<dd>
<div class="block">Should return the associated annotation object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/MergeAnnotation.html#getAnnotations()">getAnnotations()</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/MergeAnnotation.html" title="class in org.biojava.bio">MergeAnnotation</a></dt>
<dd>
<div class="block">Gets an unmodifiable view of the list of Annotations that are part of the
MergeAnnotation.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/PropertyConstraint.ByAnnotationType.html#getAnnotationType()">getAnnotationType()</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/PropertyConstraint.ByAnnotationType.html" title="class in org.biojava.bio">PropertyConstraint.ByAnnotationType</a></dt>
<dd>
<div class="block">Get the AnnotationType used as a constraint.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/filterxml/XMLAnnotationTypeHandler.html#getAnnotationType()">getAnnotationType()</a></span> - Method in class org.biojava.bio.seq.io.filterxml.<a href="./org/biojava/bio/seq/io/filterxml/XMLAnnotationTypeHandler.html" title="class in org.biojava.bio.seq.io.filterxml">XMLAnnotationTypeHandler</a></dt>
<dd>
<div class="block">Return the AnnotationType built by this handler</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFEntrySet.html#getAnnotator()">getAnnotator()</a></span> - Method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFEntrySet.html" title="class in org.biojava.bio.program.gff">GFFEntrySet</a></dt>
<dd>
<div class="block">Get an annotator that can add GFF features to a
<span class="type">Sequence</span> using the features in this
<span class="type">GFFEntrySet</span>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFEntrySet.html#getAnnotator(boolean)">getAnnotator(boolean)</a></span> - Method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFEntrySet.html" title="class in org.biojava.bio.program.gff">GFFEntrySet</a></dt>
<dd>
<div class="block">Get an annotator that can add GFF features to a
<span class="type">Sequence</span> using the features in this
<span class="type">GFFEntrySet</span>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/ProteaseManager.html#getArg_C()">getArg_C()</a></span> - Static method in class org.biojava.bio.proteomics.<a href="./org/biojava/bio/proteomics/ProteaseManager.html" title="class in org.biojava.bio.proteomics">ProteaseManager</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/jama/Matrix.html#getArray()">getArray()</a></span> - Method in class org.biojava.bio.structure.jama.<a href="./org/biojava/bio/structure/jama/Matrix.html" title="class in org.biojava.bio.structure.jama">Matrix</a></dt>
<dd>
<div class="block">Access the internal two-dimensional array.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/jama/Matrix.html#getArrayCopy()">getArrayCopy()</a></span> - Method in class org.biojava.bio.structure.jama.<a href="./org/biojava/bio/structure/jama/Matrix.html" title="class in org.biojava.bio.structure.jama">Matrix</a></dt>
<dd>
<div class="block">Copy the internal two-dimensional array.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/ArrowedFeatureRenderer.html#getArrowHeadSize()">getArrowHeadSize()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/ArrowedFeatureRenderer.html" title="class in org.biojava.bio.gui.sequence">ArrowedFeatureRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/ArrowedFeatureRenderer.html#getArrowScoop()">getArrowScoop()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/ArrowedFeatureRenderer.html" title="class in org.biojava.bio.gui.sequence">ArrowedFeatureRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/BasicFeatureRenderer.html#getArrowScoop()">getArrowScoop()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/BasicFeatureRenderer.html" title="class in org.biojava.bio.gui.sequence">BasicFeatureRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/ArrowedFeatureRenderer.html#getArrowSize()">getArrowSize()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/ArrowedFeatureRenderer.html" title="class in org.biojava.bio.gui.sequence">ArrowedFeatureRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/BasicFeatureRenderer.html#getArrowSize()">getArrowSize()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/BasicFeatureRenderer.html" title="class in org.biojava.bio.gui.sequence">BasicFeatureRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/aaindex/AAindex.html#getArticleAuthors()">getArticleAuthors()</a></span> - Method in class org.biojava.bio.proteomics.aaindex.<a href="./org/biojava/bio/proteomics/aaindex/AAindex.html" title="class in org.biojava.bio.proteomics.aaindex">AAindex</a></dt>
<dd>
<div class="block">Gets the names of the authors which first published an article about the
AAindex entry.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/aaindex/AAindex.html#getArticleTitle()">getArticleTitle()</a></span> - Method in class org.biojava.bio.proteomics.aaindex.<a href="./org/biojava/bio/proteomics/aaindex/AAindex.html" title="class in org.biojava.bio.proteomics.aaindex">AAindex</a></dt>
<dd>
<div class="block">Gets the title of the article which describes the AAindex entry.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/ProteaseManager.html#getAsp_N()">getAsp_N()</a></span> - Static method in class org.biojava.bio.proteomics.<a href="./org/biojava/bio/proteomics/ProteaseManager.html" title="class in org.biojava.bio.proteomics">ProteaseManager</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/PdbxNonPolyScheme.html#getAsym_id()">getAsym_id()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/PdbxNonPolyScheme.html" title="class in org.biojava.bio.structure.io.mmcif.model">PdbxNonPolyScheme</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/PdbxPolySeqScheme.html#getAsym_id()">getAsym_id()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/PdbxPolySeqScheme.html" title="class in org.biojava.bio.structure.io.mmcif.model">PdbxPolySeqScheme</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Compound.html#getAtcc()">getAtcc()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure">Compound</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Group.html#getAtom(java.lang.String)">getAtom(String)</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Group.html" title="interface in org.biojava.bio.structure">Group</a></dt>
<dd>
<div class="block">Get an atom.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Group.html#getAtom(int)">getAtom(int)</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Group.html" title="interface in org.biojava.bio.structure">Group</a></dt>
<dd>
<div class="block">Get at atom by position.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/HetatomImpl.html#getAtom(java.lang.String)">getAtom(String)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/HetatomImpl.html" title="class in org.biojava.bio.structure">HetatomImpl</a></dt>
<dd>
<div class="block">get an atom throws StructureException if atom not found.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/HetatomImpl.html#getAtom(int)">getAtom(int)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/HetatomImpl.html" title="class in org.biojava.bio.structure">HetatomImpl</a></dt>
<dd>
<div class="block">return an atom by its position in the internal List.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/StructureTools.html#getAtomArray(org.biojava.bio.structure.Structure, java.lang.String[])">getAtomArray(Structure, String[])</a></span> - Static method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/StructureTools.html" title="class in org.biojava.bio.structure">StructureTools</a></dt>
<dd>
<div class="block">Returns an array of the requested Atoms from the Structure object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/StructureTools.html#getAtomCAArray(org.biojava.bio.structure.Structure)">getAtomCAArray(Structure)</a></span> - Static method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/StructureTools.html" title="class in org.biojava.bio.structure">StructureTools</a></dt>
<dd>
<div class="block">Returns an Atom array of the CA atoms.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Chain.html#getAtomGroup(int)">getAtomGroup(int)</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Chain.html" title="interface in org.biojava.bio.structure">Chain</a></dt>
<dd>
<div class="block">return the Group at position X.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/ChainImpl.html#getAtomGroup(int)">getAtomGroup(int)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/ChainImpl.html" title="class in org.biojava.bio.structure">ChainImpl</a></dt>
<dd>
<div class="block">return the group at position .</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Chain.html#getAtomGroups()">getAtomGroups()</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Chain.html" title="interface in org.biojava.bio.structure">Chain</a></dt>
<dd>
<div class="block">Return all groups that have been specified in the ATOM section of this chain .</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Chain.html#getAtomGroups(java.lang.String)">getAtomGroups(String)</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Chain.html" title="interface in org.biojava.bio.structure">Chain</a></dt>
<dd>
<div class="block">Return a List of all groups of a special type (e.g.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/ChainImpl.html#getAtomGroups(java.lang.String)">getAtomGroups(String)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/ChainImpl.html" title="class in org.biojava.bio.structure">ChainImpl</a></dt>
<dd>
<div class="block">Get the Groups of a certain type, that are listed int the ATOM records of the PDB file.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/ChainImpl.html#getAtomGroups()">getAtomGroups()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/ChainImpl.html" title="class in org.biojava.bio.structure">ChainImpl</a></dt>
<dd>
<div class="block">Return all groups that have been specified in the ATOM section of this chain .</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Chain.html#getAtomLength()">getAtomLength()</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Chain.html" title="interface in org.biojava.bio.structure">Chain</a></dt>
<dd>
<div class="block">Return the number of Groups in the ATOM records of the chain.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/ChainImpl.html#getAtomLength()">getAtomLength()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/ChainImpl.html" title="class in org.biojava.bio.structure">ChainImpl</a></dt>
<dd>
<div class="block">Return the number of Groups in the ATOM records of the chain.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Group.html#getAtoms()">getAtoms()</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Group.html" title="interface in org.biojava.bio.structure">Group</a></dt>
<dd>
<div class="block">Get list of atoms.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/HetatomImpl.html#getAtoms()">getAtoms()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/HetatomImpl.html" title="class in org.biojava.bio.structure">HetatomImpl</a></dt>
<dd>
<div class="block">get all atoms of this group .</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Chain.html#getAtomSequence()">getAtomSequence()</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Chain.html" title="interface in org.biojava.bio.structure">Chain</a></dt>
<dd>
<div class="block">Return the sequence of amino acids as it has been provided in the ATOM records.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/ChainImpl.html#getAtomSequence()">getAtomSequence()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/ChainImpl.html" title="class in org.biojava.bio.structure">ChainImpl</a></dt>
<dd>
<div class="block">Return the sequence of amino acids as it has been provided in the ATOM records.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/naming/ObdaContext.html#getAttributes(javax.naming.Name)">getAttributes(Name)</a></span> - Method in class org.biojava.naming.<a href="./org/biojava/naming/ObdaContext.html" title="class in org.biojava.naming">ObdaContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/naming/ObdaContext.html#getAttributes(javax.naming.Name, java.lang.String[])">getAttributes(Name, String[])</a></span> - Method in class org.biojava.naming.<a href="./org/biojava/naming/ObdaContext.html" title="class in org.biojava.naming">ObdaContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/naming/ObdaContext.html#getAttributes(java.lang.String)">getAttributes(String)</a></span> - Method in class org.biojava.naming.<a href="./org/biojava/naming/ObdaContext.html" title="class in org.biojava.naming">ObdaContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/naming/ObdaContext.html#getAttributes(java.lang.String, java.lang.String[])">getAttributes(String, String[])</a></span> - Method in class org.biojava.naming.<a href="./org/biojava/naming/ObdaContext.html" title="class in org.biojava.naming">ObdaContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html#getAuth_asym_id()">getAuth_asym_id()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html" title="class in org.biojava.bio.structure.io.mmcif.model">AtomSite</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html#getAuth_atom_id()">getAuth_atom_id()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html" title="class in org.biojava.bio.structure.io.mmcif.model">AtomSite</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html#getAuth_comp_id()">getAuth_comp_id()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html" title="class in org.biojava.bio.structure.io.mmcif.model">AtomSite</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/PdbxNonPolyScheme.html#getAuth_mon_id()">getAuth_mon_id()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/PdbxNonPolyScheme.html" title="class in org.biojava.bio.structure.io.mmcif.model">PdbxNonPolyScheme</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/PdbxPolySeqScheme.html#getAuth_mon_id()">getAuth_mon_id()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/PdbxPolySeqScheme.html" title="class in org.biojava.bio.structure.io.mmcif.model">PdbxPolySeqScheme</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html#getAuth_seq_id()">getAuth_seq_id()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html" title="class in org.biojava.bio.structure.io.mmcif.model">AtomSite</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/PdbxNonPolyScheme.html#getAuth_seq_num()">getAuth_seq_num()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/PdbxNonPolyScheme.html" title="class in org.biojava.bio.structure.io.mmcif.model">PdbxNonPolyScheme</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/PdbxPolySeqScheme.html#getAuth_seq_num()">getAuth_seq_num()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/PdbxPolySeqScheme.html" title="class in org.biojava.bio.structure.io.mmcif.model">PdbxPolySeqScheme</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/Namespace.html#getAuthority()">getAuthority()</a></span> - Method in interface org.biojavax.<a href="./org/biojavax/Namespace.html" title="interface in org.biojavax">Namespace</a></dt>
<dd>
<div class="block">This method will return the authority that governs the namespace.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleNamespace.html#getAuthority()">getAuthority()</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleNamespace.html" title="class in org.biojavax">SimpleNamespace</a></dt>
<dd>
<div class="block">This method will return the authority that governs the namespace.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/lsid/LifeScienceIdentifier.html#getAuthorityId()">getAuthorityId()</a></span> - Method in class org.biojava.utils.lsid.<a href="./org/biojava/utils/lsid/LifeScienceIdentifier.html" title="class in org.biojava.utils.lsid">LifeScienceIdentifier</a></dt>
<dd>
<div class="block">Return the authority id for this identifier.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/JournalArticle.html#getAuthorList()">getAuthorList()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/JournalArticle.html" title="class in org.biojava.bio.structure">JournalArticle</a></dt>
<dd>
<div class="block">Get the list of Authors of the JournalArticle</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/DocRef.html#getAuthorList()">getAuthorList()</a></span> - Method in interface org.biojavax.<a href="./org/biojavax/DocRef.html" title="interface in org.biojavax">DocRef</a></dt>
<dd>
<div class="block">Returns the authors of the document reference as a set of DocRefAuthor
implementation instances.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleDocRef.html#getAuthorList()">getAuthorList()</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleDocRef.html" title="class in org.biojavax">SimpleDocRef</a></dt>
<dd>
<div class="block">Returns the authors of the document reference as a set of DocRefAuthor
implementation instances.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/DocRef.html#getAuthors()">getAuthors()</a></span> - Method in interface org.biojavax.<a href="./org/biojavax/DocRef.html" title="interface in org.biojavax">DocRef</a></dt>
<dd>
<div class="block">Returns the authors of the document reference.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleDocRef.html#getAuthors()">getAuthors()</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleDocRef.html" title="class in org.biojavax">SimpleDocRef</a></dt>
<dd>
<div class="block">Returns the authors of the document reference.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/automata/FiniteAutomaton.html#getAutomaton()">getAutomaton()</a></span> - Method in class org.biojava.utils.automata.<a href="./org/biojava/utils/automata/FiniteAutomaton.html" title="class in org.biojava.utils.automata">FiniteAutomaton</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/automata/NfaBuilder.html#getAutomaton()">getAutomaton()</a></span> - Method in interface org.biojava.utils.automata.<a href="./org/biojava/utils/automata/NfaBuilder.html" title="interface in org.biojava.utils.automata">NfaBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/automata/NfaSubModel.html#getAutomaton()">getAutomaton()</a></span> - Method in class org.biojava.utils.automata.<a href="./org/biojava/utils/automata/NfaSubModel.html" title="class in org.biojava.utils.automata">NfaSubModel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/StructureTools.html#getB()">getB()</a></span> - Method in class org.biojava.bio.proteomics.<a href="./org/biojava/bio/proteomics/StructureTools.html" title="class in org.biojava.bio.proteomics">StructureTools</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ListTools.Doublet.html#getB()">getB()</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/ListTools.Doublet.html" title="class in org.biojava.utils">ListTools.Doublet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ListTools.Triplet.html#getB()">getB()</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/ListTools.Triplet.html" title="class in org.biojava.utils">ListTools.Triplet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#getB_iso_max()">getB_iso_max()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#getB_iso_mean()">getB_iso_mean()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#getB_iso_min()">getB_iso_min()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html#getB_iso_or_equiv()">getB_iso_or_equiv()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html" title="class in org.biojava.bio.structure.io.mmcif.model">AtomSite</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html#getB_iso_or_equiv_esd()">getB_iso_or_equiv_esd()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html" title="class in org.biojava.bio.structure.io.mmcif.model">AtomSite</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/StructureTools.html#getBackboneAtomArray(org.biojava.bio.structure.Structure)">getBackboneAtomArray(Structure)</a></span> - Static method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/StructureTools.html" title="class in org.biojava.bio.structure">StructureTools</a></dt>
<dd>
<div class="block">Returns an Atom array of the MainChain atoms.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/DP.html#getBackwardTransitions()">getBackwardTransitions()</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/DP.html" title="class in org.biojava.bio.dp">DP</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/DP.html#getBackwardTransitionScores(org.biojava.bio.dp.ScoreType)">getBackwardTransitionScores(ScoreType)</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/DP.html" title="class in org.biojava.bio.dp">DP</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/AbstractChromatogram.html#getBaseCalls()">getBaseCalls()</a></span> - Method in class org.biojava.bio.chromatogram.<a href="./org/biojava/bio/chromatogram/AbstractChromatogram.html" title="class in org.biojava.bio.chromatogram">AbstractChromatogram</a></dt>
<dd>
<div class="block">Return the total number of base calls.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/Chromatogram.html#getBaseCalls()">getBaseCalls()</a></span> - Method in interface org.biojava.bio.chromatogram.<a href="./org/biojava/bio/chromatogram/Chromatogram.html" title="interface in org.biojava.bio.chromatogram">Chromatogram</a></dt>
<dd>
<div class="block">Returns an alignment that describes the base calls for this chromatogram.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/abi/ABITrace.html#getBasecalls()">getBasecalls()</a></span> - Method in class org.biojava.bio.program.abi.<a href="./org/biojava/bio/program/abi/ABITrace.html" title="class in org.biojava.bio.program.abi">ABITrace</a></dt>
<dd>
<div class="block">Returns an <code>int[]</code> array that represents the basecalls - each int in the
array corresponds to an x-coordinate point in the graph that is a peak (a base location).</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.html#getBaseColor(org.biojava.bio.symbol.Symbol)">getBaseColor(Symbol)</a></span> - Method in class org.biojava.bio.chromatogram.graphic.<a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.html" title="class in org.biojava.bio.chromatogram.graphic">ChromatogramGraphic</a></dt>
<dd>
<div class="block">Returns the color that will be used to draw the trace for the
given DNA symbol.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.html#getBaseFillColor(org.biojava.bio.symbol.Symbol)">getBaseFillColor(Symbol)</a></span> - Method in class org.biojava.bio.chromatogram.graphic.<a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.html" title="class in org.biojava.bio.chromatogram.graphic">ChromatogramGraphic</a></dt>
<dd>
<div class="block">Returns the color that will be used to fill in the callboxes for
calls with the given symbol.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/SimpleEmissionState.html#getBases()">getBases()</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/SimpleEmissionState.html" title="class in org.biojava.bio.dp">SimpleEmissionState</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/DoubleAlphabet.DoubleSymbol.html#getBases()">getBases()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/DoubleAlphabet.DoubleSymbol.html" title="class in org.biojava.bio.symbol">DoubleAlphabet.DoubleSymbol</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/IntegerAlphabet.IntegerSymbol.html#getBases()">getBases()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/IntegerAlphabet.IntegerSymbol.html" title="class in org.biojava.bio.symbol">IntegerAlphabet.IntegerSymbol</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/FetchURL.html#getbaseURL()">getbaseURL()</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/FetchURL.html" title="class in org.biojava.bio.seq.db">FetchURL</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/AbstractBeadRenderer.html#getBeadDepth()">getBeadDepth()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/AbstractBeadRenderer.html" title="class in org.biojava.bio.gui.sequence">AbstractBeadRenderer</a></dt>
<dd>
<div class="block"><code>getBeadDepth</code> returns the depth of a single bead
produced by this renderer.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/BeadFeatureRenderer.html#getBeadDepth()">getBeadDepth()</a></span> - Method in interface org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/BeadFeatureRenderer.html" title="interface in org.biojava.bio.gui.sequence">BeadFeatureRenderer</a></dt>
<dd>
<div class="block"><code>getBeadDepth</code> returns the depth of a single bead
produced by the renderer.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/RectangularImapRenderer.html#getBeadDepth()">getBeadDepth()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/RectangularImapRenderer.html" title="class in org.biojava.bio.gui.sequence">RectangularImapRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/AbstractBeadRenderer.html#getBeadDisplacement()">getBeadDisplacement()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/AbstractBeadRenderer.html" title="class in org.biojava.bio.gui.sequence">AbstractBeadRenderer</a></dt>
<dd>
<div class="block"><code>getBeadDisplacement</code> returns the displacement of
beads from the centre line of the renderer.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/BeadFeatureRenderer.html#getBeadDisplacement()">getBeadDisplacement()</a></span> - Method in interface org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/BeadFeatureRenderer.html" title="interface in org.biojava.bio.gui.sequence">BeadFeatureRenderer</a></dt>
<dd>
<div class="block"><code>getBeadDisplacement</code> returns the displacement of
beads from the centre line of the renderer.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/RectangularImapRenderer.html#getBeadDisplacement()">getBeadDisplacement()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/RectangularImapRenderer.html" title="class in org.biojava.bio.gui.sequence">RectangularImapRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/AbstractBeadRenderer.html#getBeadFill()">getBeadFill()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/AbstractBeadRenderer.html" title="class in org.biojava.bio.gui.sequence">AbstractBeadRenderer</a></dt>
<dd>
<div class="block"><code>getBeadFill</code> returns the bead fill paint.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/AbstractBeadRenderer.html#getBeadOutline()">getBeadOutline()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/AbstractBeadRenderer.html" title="class in org.biojava.bio.gui.sequence">AbstractBeadRenderer</a></dt>
<dd>
<div class="block"><code>getBeadOutline</code> returns the bead outline paint.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/AbstractBeadRenderer.html#getBeadStroke()">getBeadStroke()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/AbstractBeadRenderer.html" title="class in org.biojava.bio.gui.sequence">AbstractBeadRenderer</a></dt>
<dd>
<div class="block"><code>getBeadStroke</code> returns the bead outline stroke.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BibRefQuery.html#getBibRefAsXML(org.biojava.bibliography.BibRef)">getBibRefAsXML(BibRef)</a></span> - Method in interface org.biojava.bibliography.<a href="./org/biojava/bibliography/BibRefQuery.html" title="interface in org.biojava.bibliography">BibRefQuery</a></dt>
<dd>
<div class="block">
A convenient utility method converting a given citation to its
XML representation.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BibRefQuery.html#getBibRefCount()">getBibRefCount()</a></span> - Method in interface org.biojava.bibliography.<a href="./org/biojava/bibliography/BibRefQuery.html" title="interface in org.biojava.bibliography">BibRefQuery</a></dt>
<dd>
<div class="block">
It returns the number of citations in the current collection.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BibRefQuery.html#getBibRefs()">getBibRefs()</a></span> - Method in interface org.biojava.bibliography.<a href="./org/biojava/bibliography/BibRefQuery.html" title="interface in org.biojava.bibliography">BibRefQuery</a></dt>
<dd>
<div class="block">
It returns an enumeration of all citations from the current collection.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BibRefQuery.html#getBibRefs(java.lang.String[])">getBibRefs(String[])</a></span> - Method in interface org.biojava.bibliography.<a href="./org/biojava/bibliography/BibRefQuery.html" title="interface in org.biojava.bibliography">BibRefQuery</a></dt>
<dd>
<div class="block">
It returns an enumeration of all citations from the current collection,
perhaps with a limited number of attributes.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BibRefQuery.html#getBibRefsAsXML()">getBibRefsAsXML()</a></span> - Method in interface org.biojava.bibliography.<a href="./org/biojava/bibliography/BibRefQuery.html" title="interface in org.biojava.bibliography">BibRefQuery</a></dt>
<dd>
<div class="block">
It returns an enumeration of all citations from the current collection.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ga/util/GATools.html#getBinaryAlphabet()">getBinaryAlphabet()</a></span> - Static method in class org.biojavax.ga.util.<a href="./org/biojavax/ga/util/GATools.html" title="class in org.biojavax.ga.util">GATools</a></dt>
<dd>
<div class="block">Gets a Reference to the FlyWeight GA_Binary <code>Alphabet</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/AbstractRichSequenceDB.html#getBioEntry(java.lang.String)">getBioEntry(String)</a></span> - Method in class org.biojavax.bio.db.<a href="./org/biojavax/bio/db/AbstractRichSequenceDB.html" title="class in org.biojavax.bio.db">AbstractRichSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/BioEntryDBLite.html#getBioEntry(java.lang.String)">getBioEntry(String)</a></span> - Method in interface org.biojavax.bio.db.<a href="./org/biojavax/bio/db/BioEntryDBLite.html" title="interface in org.biojavax.bio.db">BioEntryDBLite</a></dt>
<dd>
<div class="block">Retrieve a single BioEntry by its id.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLBioEntryDB.html#getBioEntry(java.lang.String)">getBioEntry(String)</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLBioEntryDB.html" title="class in org.biojavax.bio.db.biosql">BioSQLBioEntryDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/HashBioEntryDB.html#getBioEntry(java.lang.String)">getBioEntry(String)</a></span> - Method in class org.biojavax.bio.db.<a href="./org/biojavax/bio/db/HashBioEntryDB.html" title="class in org.biojavax.bio.db">HashBioEntryDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/AbstractBioEntryDB.html#getBioEntryIterator()">getBioEntryIterator()</a></span> - Method in class org.biojavax.bio.db.<a href="./org/biojavax/bio/db/AbstractBioEntryDB.html" title="class in org.biojavax.bio.db">AbstractBioEntryDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/AbstractRichSequenceDB.html#getBioEntryIterator()">getBioEntryIterator()</a></span> - Method in class org.biojavax.bio.db.<a href="./org/biojavax/bio/db/AbstractRichSequenceDB.html" title="class in org.biojavax.bio.db">AbstractRichSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/BioEntryDB.html#getBioEntryIterator()">getBioEntryIterator()</a></span> - Method in interface org.biojavax.bio.db.<a href="./org/biojavax/bio/db/BioEntryDB.html" title="interface in org.biojavax.bio.db">BioEntryDB</a></dt>
<dd>
<div class="block">Returns a BioEntryIterator over all BioEntrys in the database.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/AbstractRichSequenceDB.html#getBioEntrys(java.util.Set)">getBioEntrys(Set)</a></span> - Method in class org.biojavax.bio.db.<a href="./org/biojavax/bio/db/AbstractRichSequenceDB.html" title="class in org.biojavax.bio.db">AbstractRichSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/AbstractRichSequenceDB.html#getBioEntrys(java.util.Set, org.biojavax.bio.db.BioEntryDB)">getBioEntrys(Set, BioEntryDB)</a></span> - Method in class org.biojavax.bio.db.<a href="./org/biojavax/bio/db/AbstractRichSequenceDB.html" title="class in org.biojavax.bio.db">AbstractRichSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/BioEntryDBLite.html#getBioEntrys(java.util.Set)">getBioEntrys(Set)</a></span> - Method in interface org.biojavax.bio.db.<a href="./org/biojavax/bio/db/BioEntryDBLite.html" title="interface in org.biojavax.bio.db">BioEntryDBLite</a></dt>
<dd>
<div class="block">Retrieve multiple BioEntry by their ids.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/BioEntryDBLite.html#getBioEntrys(java.util.Set, org.biojavax.bio.db.BioEntryDB)">getBioEntrys(Set, BioEntryDB)</a></span> - Method in interface org.biojavax.bio.db.<a href="./org/biojavax/bio/db/BioEntryDBLite.html" title="interface in org.biojavax.bio.db">BioEntryDBLite</a></dt>
<dd>
<div class="block">Retrieve multiple BioEntry into a specific sequence database.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLBioEntryDB.html#getBioEntrys(java.util.Set)">getBioEntrys(Set)</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLBioEntryDB.html" title="class in org.biojavax.bio.db.biosql">BioSQLBioEntryDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLBioEntryDB.html#getBioEntrys(java.util.Set, org.biojavax.bio.db.BioEntryDB)">getBioEntrys(Set, BioEntryDB)</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLBioEntryDB.html" title="class in org.biojavax.bio.db.biosql">BioSQLBioEntryDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/HashBioEntryDB.html#getBioEntrys(java.util.Set)">getBioEntrys(Set)</a></span> - Method in class org.biojavax.bio.db.<a href="./org/biojavax/bio/db/HashBioEntryDB.html" title="class in org.biojavax.bio.db">HashBioEntryDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/HashBioEntryDB.html#getBioEntrys(java.util.Set, org.biojavax.bio.db.BioEntryDB)">getBioEntrys(Set, BioEntryDB)</a></span> - Method in class org.biojavax.bio.db.<a href="./org/biojavax/bio/db/HashBioEntryDB.html" title="class in org.biojavax.bio.db">HashBioEntryDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/StructRef.html#getBiol_id()">getBiol_id()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/StructRef.html" title="class in org.biojava.bio.structure.io.mmcif.model">StructRef</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Compound.html#getBiologicalUnit()">getBiologicalUnit()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure">Compound</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/biosql/DBHelper.html#getBioSequenceStyle()">getBioSequenceStyle()</a></span> - Method in class org.biojava.bio.seq.db.biosql.<a href="./org/biojava/bio/seq/db/biosql/DBHelper.html" title="class in org.biojava.bio.seq.db.biosql">DBHelper</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Returns the an object indicating the style of biosequence storage
that this database should employ.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/biosql/OracleDBHelper.html#getBioSequenceStyle()">getBioSequenceStyle()</a></span> - Method in class org.biojava.bio.seq.db.biosql.<a href="./org/biojava/bio/seq/db/biosql/OracleDBHelper.html" title="class in org.biojava.bio.seq.db.biosql">OracleDBHelper</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Chain.html#getBJSequence()">getBJSequence()</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Chain.html" title="interface in org.biojava.bio.structure">Chain</a></dt>
<dd>
<div class="block">Convert the SEQRES groups of a Chain to a Biojava Sequence object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/ChainImpl.html#getBJSequence()">getBJSequence()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/ChainImpl.html" title="class in org.biojava.bio.structure">ChainImpl</a></dt>
<dd>
<div class="block">Convert the SEQRES groups of a Chain to a Biojava Sequence object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/dasalignment/Alignment.html#getBlockAnnotationType()">getBlockAnnotationType()</a></span> - Static method in class org.biojava.bio.program.das.dasalignment.<a href="./org/biojava/bio/program/das/dasalignment/Alignment.html" title="class in org.biojava.bio.program.das.dasalignment">Alignment</a></dt>
<dd>
<div class="block">define the alignment Block Annotation Type.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SixFrameZiggyRenderer.html#getBlockDepth()">getBlockDepth()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SixFrameZiggyRenderer.html" title="class in org.biojava.bio.gui.sequence">SixFrameZiggyRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/ZiggyFeatureRenderer.html#getBlockDepth()">getBlockDepth()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/ZiggyFeatureRenderer.html" title="class in org.biojava.bio.gui.sequence">ZiggyFeatureRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/DistributionLogo.html#getBlockPainter()">getBlockPainter()</a></span> - Method in class org.biojava.bio.gui.<a href="./org/biojava/bio/gui/DistributionLogo.html" title="class in org.biojava.bio.gui">DistributionLogo</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/LogoContext.html#getBlockPainter()">getBlockPainter()</a></span> - Method in interface org.biojava.bio.gui.<a href="./org/biojava/bio/gui/LogoContext.html" title="interface in org.biojava.bio.gui">LogoContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/dasalignment/Alignment.html#getBlocks()">getBlocks()</a></span> - Method in class org.biojava.bio.program.das.dasalignment.<a href="./org/biojava/bio/program/das/dasalignment/Alignment.html" title="class in org.biojava.bio.program.das.dasalignment">Alignment</a></dt>
<dd>
<div class="block">get all Annotations of type "Block".</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SixFrameRenderer.html#getBlockWidth()">getBlockWidth()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SixFrameRenderer.html" title="class in org.biojava.bio.gui.sequence">SixFrameRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/Aggregator.html#getBoundaryFinder()">getBoundaryFinder()</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/Aggregator.html" title="class in org.biojava.bio.program.tagvalue">Aggregator</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/MultiTagger.html#getBoundaryFinder()">getBoundaryFinder()</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/MultiTagger.html" title="class in org.biojava.bio.program.tagvalue">MultiTagger</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/glyph/ArrowGlyph.html#getBounds()">getBounds()</a></span> - Method in class org.biojava.bio.gui.glyph.<a href="./org/biojava/bio/gui/glyph/ArrowGlyph.html" title="class in org.biojava.bio.gui.glyph">ArrowGlyph</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/glyph/Glyph.html#getBounds()">getBounds()</a></span> - Method in interface org.biojava.bio.gui.glyph.<a href="./org/biojava/bio/gui/glyph/Glyph.html" title="interface in org.biojava.bio.gui.glyph">Glyph</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/glyph/HelixGlyph.html#getBounds()">getBounds()</a></span> - Method in class org.biojava.bio.gui.glyph.<a href="./org/biojava/bio/gui/glyph/HelixGlyph.html" title="class in org.biojava.bio.gui.glyph">HelixGlyph</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/glyph/RectangleGlyph.html#getBounds()">getBounds()</a></span> - Method in class org.biojava.bio.gui.glyph.<a href="./org/biojava/bio/gui/glyph/RectangleGlyph.html" title="class in org.biojava.bio.gui.glyph">RectangleGlyph</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/glyph/TurnGlyph.html#getBounds()">getBounds()</a></span> - Method in class org.biojava.bio.gui.glyph.<a href="./org/biojava/bio/gui/glyph/TurnGlyph.html" title="class in org.biojava.bio.gui.glyph">TurnGlyph</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/glyph/TwoHeadedArrowGlyph.html#getBounds()">getBounds()</a></span> - Method in class org.biojava.bio.gui.glyph.<a href="./org/biojava/bio/gui/glyph/TwoHeadedArrowGlyph.html" title="class in org.biojava.bio.gui.glyph">TwoHeadedArrowGlyph</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/LogoContext.html#getBounds()">getBounds()</a></span> - Method in interface org.biojava.bio.gui.<a href="./org/biojava/bio/gui/LogoContext.html" title="interface in org.biojava.bio.gui">LogoContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOTools.html#getBuilderFactory(int)">getBuilderFactory(int)</a></span> - Static method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOTools.html" title="class in org.biojava.bio.seq.io">SeqIOTools</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block"><code>getBuilderFactory</code> accepts a value which represents
a sequence format and returns the relevant
<code>SequenceBuilderFactory</code> object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/molbio/DNAComposition.html#getC()">getC()</a></span> - Method in class org.biojava.bio.molbio.<a href="./org/biojava/bio/molbio/DNAComposition.html" title="class in org.biojava.bio.molbio">DNAComposition</a></dt>
<dd>
<div class="block">Get the relative compositon of 'C'.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/StructureTools.html#getC()">getC()</a></span> - Method in class org.biojava.bio.proteomics.<a href="./org/biojava/bio/proteomics/StructureTools.html" title="class in org.biojava.bio.proteomics">StructureTools</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/AminoAcid.html#getC()">getC()</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/AminoAcid.html" title="interface in org.biojava.bio.structure">AminoAcid</a></dt>
<dd>
<div class="block">get C atom.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/AminoAcidImpl.html#getC()">getC()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/AminoAcidImpl.html" title="class in org.biojava.bio.structure">AminoAcidImpl</a></dt>
<dd>
<div class="block">get C atom.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/SMOTrainer.html#getC()">getC()</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/SMOTrainer.html" title="class in org.biojava.stats.svm">SMOTrainer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ListTools.Triplet.html#getC()">getC()</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/ListTools.Triplet.html" title="class in org.biojava.utils">ListTools.Triplet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/AminoAcid.html#getCA()">getCA()</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/AminoAcid.html" title="interface in org.biojava.bio.structure">AminoAcid</a></dt>
<dd>
<div class="block">get CA atom.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/AminoAcidImpl.html#getCA()">getCA()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/AminoAcidImpl.html" title="class in org.biojava.bio.structure">AminoAcidImpl</a></dt>
<dd>
<div class="block">get CA atom.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/server/SimpleStructureServer.html#getCacheSize()">getCacheSize()</a></span> - Method in class org.biojava.bio.structure.server.<a href="./org/biojava/bio/structure/server/SimpleStructureServer.html" title="class in org.biojava.bio.structure.server">SimpleStructureServer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/server/StructureServer.html#getCacheSize()">getCacheSize()</a></span> - Method in interface org.biojava.bio.structure.server.<a href="./org/biojava/bio/structure/server/StructureServer.html" title="interface in org.biojava.bio.structure.server">StructureServer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.html#getCallboxBounds(int)">getCallboxBounds(int)</a></span> - Method in class org.biojava.bio.chromatogram.graphic.<a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.html" title="class in org.biojava.bio.chromatogram.graphic">ChromatogramGraphic</a></dt>
<dd>
<div class="block">Returns the screen-coordinate bounds of the callbox for a given call.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.html#getCallboxBounds(int, boolean)">getCallboxBounds(int, boolean)</a></span> - Method in class org.biojava.bio.chromatogram.graphic.<a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.html" title="class in org.biojava.bio.chromatogram.graphic">ChromatogramGraphic</a></dt>
<dd>
<div class="block">Returns the bounds of the callbox for a given call.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.html#getCallboxCount()">getCallboxCount()</a></span> - Method in class org.biojava.bio.chromatogram.graphic.<a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.html" title="class in org.biojava.bio.chromatogram.graphic">ChromatogramGraphic</a></dt>
<dd>
<div class="block">Returns the number of callboxes, regenerating them if necessary.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.html#getCallContaining(java.awt.geom.Point2D, boolean)">getCallContaining(Point2D, boolean)</a></span> - Method in class org.biojava.bio.chromatogram.graphic.<a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.html" title="class in org.biojava.bio.chromatogram.graphic">ChromatogramGraphic</a></dt>
<dd>
<div class="block">Returns the <b>0-based</b> index of the call containing a given
point.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.html#getCallContaining(java.awt.geom.Point2D)">getCallContaining(Point2D)</a></span> - Method in class org.biojava.bio.chromatogram.graphic.<a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.html" title="class in org.biojava.bio.chromatogram.graphic">ChromatogramGraphic</a></dt>
<dd>
<div class="block">Synonym for <a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.html#getCallContaining(java.awt.geom.Point2D, boolean)"><code>ChromatogramGraphic.getCallContaining(Point2D, boolean)</code></a> with
<code>pointOnScreen</code>=true.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.html#getCallContaining(float, boolean)">getCallContaining(float, boolean)</a></span> - Method in class org.biojava.bio.chromatogram.graphic.<a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.html" title="class in org.biojava.bio.chromatogram.graphic">ChromatogramGraphic</a></dt>
<dd>
<div class="block">Same as <a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.html#getCallContaining(java.awt.geom.Point2D, boolean)"><code>ChromatogramGraphic.getCallContaining(Point2D, boolean)</code></a>, except that
only the x-coordinate of the point is specified.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.html#getCallContaining(float)">getCallContaining(float)</a></span> - Method in class org.biojava.bio.chromatogram.graphic.<a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.html" title="class in org.biojava.bio.chromatogram.graphic">ChromatogramGraphic</a></dt>
<dd>
<div class="block">Synonym for <a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.html#getCallContaining(float, boolean)"><code>ChromatogramGraphic.getCallContaining(float, boolean)</code></a> with
<code>pointOnScreen</code>=true.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/CAConverter.html#getCAOnly(java.util.List)">getCAOnly(List<Chain>)</a></span> - Static method in class org.biojava.bio.structure.io.<a href="./org/biojava/bio/structure/io/CAConverter.html" title="class in org.biojava.bio.structure.io">CAConverter</a></dt>
<dd>
<div class="block">Convert a List of chain objects to another List of chains, containing C-alpha atoms only.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/CAConverter.html#getCAOnly(org.biojava.bio.structure.Chain)">getCAOnly(Chain)</a></span> - Static method in class org.biojava.bio.structure.io.<a href="./org/biojava/bio/structure/io/CAConverter.html" title="class in org.biojava.bio.structure.io">CAConverter</a></dt>
<dd>
<div class="block">Convert a Chain to a new Chain containing C-alpha atoms only.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/CollectionConstraint.AllValuesIn.html#getCardinalityConstraint()">getCardinalityConstraint()</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/CollectionConstraint.AllValuesIn.html" title="class in org.biojava.bio">CollectionConstraint.AllValuesIn</a></dt>
<dd>
<div class="block">Get the cardinality constraint used to validate the number of property
values.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/CollectionConstraint.Contains.html#getCardinalityConstraint()">getCardinalityConstraint()</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/CollectionConstraint.Contains.html" title="class in org.biojava.bio">CollectionConstraint.Contains</a></dt>
<dd>
<div class="block">Get the cardinality constraint used to validate the number of property
values.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html#getCartn_x()">getCartn_x()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html" title="class in org.biojava.bio.structure.io.mmcif.model">AtomSite</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html#getCartn_x_esd()">getCartn_x_esd()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html" title="class in org.biojava.bio.structure.io.mmcif.model">AtomSite</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html#getCartn_y()">getCartn_y()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html" title="class in org.biojava.bio.structure.io.mmcif.model">AtomSite</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html#getCartn_y_esd()">getCartn_y_esd()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html" title="class in org.biojava.bio.structure.io.mmcif.model">AtomSite</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html#getCartn_z()">getCartn_z()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html" title="class in org.biojava.bio.structure.io.mmcif.model">AtomSite</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html#getCartn_z_esd()">getCartn_z_esd()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html" title="class in org.biojava.bio.structure.io.mmcif.model">AtomSite</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/Synonym.html#getCategory()">getCategory()</a></span> - Method in class org.biojava.ontology.<a href="./org/biojava/ontology/Synonym.html" title="class in org.biojava.ontology">Synonym</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/AminoAcid.html#getCB()">getCB()</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/AminoAcid.html" title="interface in org.biojava.bio.structure">AminoAcid</a></dt>
<dd>
<div class="block">get CB atom.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/AminoAcidImpl.html#getCB()">getCB()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/AminoAcidImpl.html" title="class in org.biojava.bio.structure">AminoAcidImpl</a></dt>
<dd>
<div class="block">get CB atom.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/DPMatrix.html#getCell(int[])">getCell(int[])</a></span> - Method in interface org.biojava.bio.dp.<a href="./org/biojava/bio/dp/DPMatrix.html" title="interface in org.biojava.bio.dp">DPMatrix</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/onehead/SingleDPMatrix.html#getCell(int[])">getCell(int[])</a></span> - Method in class org.biojava.bio.dp.onehead.<a href="./org/biojava/bio/dp/onehead/SingleDPMatrix.html" title="class in org.biojava.bio.dp.onehead">SingleDPMatrix</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/twohead/PairDPMatrix.html#getCell(int[])">getCell(int[])</a></span> - Method in class org.biojava.bio.dp.twohead.<a href="./org/biojava/bio/dp/twohead/PairDPMatrix.html" title="class in org.biojava.bio.dp.twohead">PairDPMatrix</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Compound.html#getCell()">getCell()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure">Compound</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Compound.html#getCellLine()">getCellLine()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure">Compound</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Compound.html#getCellularLocation()">getCellularLocation()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure">Compound</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/helper/AlignTools.html#getCenter(org.biojava.bio.structure.Atom[], int, int)">getCenter(Atom[], int, int)</a></span> - Static method in class org.biojava.bio.structure.align.helper.<a href="./org/biojava/bio/structure/align/helper/AlignTools.html" title="class in org.biojava.bio.structure.align.helper">AlignTools</a></dt>
<dd>
<div class="block">get the centroid for the set of atoms starting fromposition pos, length fragmentLenght</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/FragmentPair.html#getCenter1()">getCenter1()</a></span> - Method in class org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/FragmentPair.html" title="class in org.biojava.bio.structure.align.pairwise">FragmentPair</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/FragmentPair.html#getCenter2()">getCenter2()</a></span> - Method in class org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/FragmentPair.html" title="class in org.biojava.bio.structure.align.pairwise">FragmentPair</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Calc.html#getCenterVector(org.biojava.bio.structure.Atom[])">getCenterVector(Atom[])</a></span> - Static method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Calc.html" title="class in org.biojava.bio.structure">Calc</a></dt>
<dd>
<div class="block">Returns the Vector that needs to be applied to shift a set of atoms
to the Centroid.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Calc.html#getCentroid(org.biojava.bio.structure.Atom[])">getCentroid(Atom[])</a></span> - Static method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Calc.html" title="class in org.biojava.bio.structure">Calc</a></dt>
<dd>
<div class="block">Returns the center of mass of the set of atoms.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/util/SequenceScalePanel.html#getChain()">getChain()</a></span> - Method in class org.biojava.bio.structure.gui.util.<a href="./org/biojava/bio/structure/gui/util/SequenceScalePanel.html" title="class in org.biojava.bio.structure.gui.util">SequenceScalePanel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Structure.html#getChain(int)">getChain(int)</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Structure.html" title="interface in org.biojava.bio.structure">Structure</a></dt>
<dd>
<div class="block">retrieve a chain by it's position within the Structure .</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Structure.html#getChain(int, int)">getChain(int, int)</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Structure.html" title="interface in org.biojava.bio.structure">Structure</a></dt>
<dd>
<div class="block">retrieve a chain by it's position within the Structure and model number.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/StructureImpl.html#getChain(int)">getChain(int)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/StructureImpl.html" title="class in org.biojava.bio.structure">StructureImpl</a></dt>
<dd>
<div class="block">retrieve a chain by it's position within the Structure.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/StructureImpl.html#getChain(int, int)">getChain(int, int)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/StructureImpl.html" title="class in org.biojava.bio.structure">StructureImpl</a></dt>
<dd>
<div class="block">retrieve a chain by it's position within the Structure and model number.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Structure.html#getChainByPDB(java.lang.String)">getChainByPDB(String)</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Structure.html" title="interface in org.biojava.bio.structure">Structure</a></dt>
<dd>
<div class="block">request a chain by it's PDB code
by default takes only the first model</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Structure.html#getChainByPDB(java.lang.String, int)">getChainByPDB(String, int)</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Structure.html" title="interface in org.biojava.bio.structure">Structure</a></dt>
<dd>
<div class="block">request a chain by it's PDB code
by default takes only the first model</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/StructureImpl.html#getChainByPDB(java.lang.String, int)">getChainByPDB(String, int)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/StructureImpl.html" title="class in org.biojava.bio.structure">StructureImpl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/StructureImpl.html#getChainByPDB(java.lang.String)">getChainByPDB(String)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/StructureImpl.html" title="class in org.biojava.bio.structure">StructureImpl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ChangeEvent.html#getChainedEvent()">getChainedEvent()</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/ChangeEvent.html" title="class in org.biojava.utils">ChangeEvent</a></dt>
<dd>
<div class="block">Return the event which caused this to be fired, or <code>null</code>
if this change was not caused by another event.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Compound.html#getChainId()">getChainId()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure">Compound</a></dt>
<dd>
<div class="block">Returns the chain id value.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/DBRef.html#getChainId()">getChainId()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/DBRef.html" title="class in org.biojava.bio.structure">DBRef</a></dt>
<dd>
<div class="block">The chain ID of the corresponding chain.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/SSBond.html#getChainID1()">getChainID1()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/SSBond.html" title="class in org.biojava.bio.structure">SSBond</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/SSBond.html#getChainID2()">getChainID2()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/SSBond.html" title="class in org.biojava.bio.structure">SSBond</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/server/FlatFileInstallation.html#getChainInfoFile()">getChainInfoFile()</a></span> - Method in class org.biojava.bio.structure.server.<a href="./org/biojava/bio/structure/server/FlatFileInstallation.html" title="class in org.biojava.bio.structure.server">FlatFileInstallation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Compound.html#getChains()">getChains()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure">Compound</a></dt>
<dd>
<div class="block">get the chains that are part of this Compound</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Structure.html#getChains()">getChains()</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Structure.html" title="interface in org.biojava.bio.structure">Structure</a></dt>
<dd>
<div class="block">retrieve all chains - if it is a NMR structure will return the chains of the first model.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Structure.html#getChains(int)">getChains(int)</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Structure.html" title="interface in org.biojava.bio.structure">Structure</a></dt>
<dd>
<div class="block">retrieve all chains of a model.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/StructureImpl.html#getChains(int)">getChains(int)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/StructureImpl.html" title="class in org.biojava.bio.structure">StructureImpl</a></dt>
<dd>
<div class="block">retrieve all chains of a model.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/StructureImpl.html#getChains()">getChains()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/StructureImpl.html" title="class in org.biojava.bio.structure">StructureImpl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ChangeEvent.html#getChange()">getChange()</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/ChangeEvent.html" title="class in org.biojava.utils">ChangeEvent</a></dt>
<dd>
<div class="block">Return an object which is to be the new value of some property,
or is to be added to a collection.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/ChangeVetoException.html#getChangeEvent()">getChangeEvent()</a></span> - Method in exception org.biojava.utils.<a href="./org/biojava/utils/ChangeVetoException.html" title="class in org.biojava.utils">ChangeVetoException</a></dt>
<dd>
<div class="block">Return the ChangeEvent which is being vetoed.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/AnnotationChanger.html#getChanger()">getChanger()</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/AnnotationChanger.html" title="class in org.biojava.bio">AnnotationChanger</a></dt>
<dd>
<div class="block"><code>getMapper</code> returns the <code>ValueChanger</code> being
used to remap the <code>Annotation</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/ChangeTable.html#getChanger(java.lang.Object)">getChanger(Object)</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/ChangeTable.html" title="class in org.biojava.bio.program.tagvalue">ChangeTable</a></dt>
<dd>
<div class="block">Get the Changer currently registered to handle a tag.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/AbstractDistribution.html#getChangeSupport(org.biojava.utils.ChangeType)">getChangeSupport(ChangeType)</a></span> - Method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/AbstractDistribution.html" title="class in org.biojava.bio.dist">AbstractDistribution</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/AbstractOrderNDistribution.html#getChangeSupport(org.biojava.utils.ChangeType)">getChangeSupport(ChangeType)</a></span> - Method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/AbstractOrderNDistribution.html" title="class in org.biojava.bio.dist">AbstractOrderNDistribution</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/TranslatedDistribution.html#getChangeSupport(org.biojava.utils.ChangeType)">getChangeSupport(ChangeType)</a></span> - Method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/TranslatedDistribution.html" title="class in org.biojava.bio.dist">TranslatedDistribution</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/SimpleEmissionState.html#getChangeSupport(org.biojava.utils.ChangeType)">getChangeSupport(ChangeType)</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/SimpleEmissionState.html" title="class in org.biojava.bio.dp">SimpleEmissionState</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/SimpleMarkovModel.html#getChangeSupport(org.biojava.utils.ChangeType)">getChangeSupport(ChangeType)</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/SimpleMarkovModel.html" title="class in org.biojava.bio.dp">SimpleMarkovModel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/BumpedRenderer.html#getChangeSupport(org.biojava.utils.ChangeType)">getChangeSupport(ChangeType)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/BumpedRenderer.html" title="class in org.biojava.bio.gui.sequence">BumpedRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/FeatureBlockSequenceRenderer.html#getChangeSupport(org.biojava.utils.ChangeType)">getChangeSupport(ChangeType)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/FeatureBlockSequenceRenderer.html" title="class in org.biojava.bio.gui.sequence">FeatureBlockSequenceRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/FilteringRenderer.html#getChangeSupport(org.biojava.utils.ChangeType)">getChangeSupport(ChangeType)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/FilteringRenderer.html" title="class in org.biojava.bio.gui.sequence">FilteringRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/MultiLineRenderer.html#getChangeSupport(org.biojava.utils.ChangeType)">getChangeSupport(ChangeType)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/MultiLineRenderer.html" title="class in org.biojava.bio.gui.sequence">MultiLineRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/OverlayRendererWrapper.html#getChangeSupport(org.biojava.utils.ChangeType)">getChangeSupport(ChangeType)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/OverlayRendererWrapper.html" title="class in org.biojava.bio.gui.sequence">OverlayRendererWrapper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PaddingRenderer.html#getChangeSupport(org.biojava.utils.ChangeType)">getChangeSupport(ChangeType)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PaddingRenderer.html" title="class in org.biojava.bio.gui.sequence">PaddingRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PairwiseFilteringRenderer.html#getChangeSupport(org.biojava.utils.ChangeType)">getChangeSupport(ChangeType)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PairwiseFilteringRenderer.html" title="class in org.biojava.bio.gui.sequence">PairwiseFilteringRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PairwiseOverlayRenderer.html#getChangeSupport(org.biojava.utils.ChangeType)">getChangeSupport(ChangeType)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PairwiseOverlayRenderer.html" title="class in org.biojava.bio.gui.sequence">PairwiseOverlayRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PairwiseSequencePanel.html#getChangeSupport(org.biojava.utils.ChangeType)">getChangeSupport(ChangeType)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PairwiseSequencePanel.html" title="class in org.biojava.bio.gui.sequence">PairwiseSequencePanel</a></dt>
<dd>
<div class="block"><code>getChangeSupport</code> lazily instantiates a helper for
change listeners.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePanel.html#getChangeSupport(org.biojava.utils.ChangeType)">getChangeSupport(ChangeType)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePanel.html" title="class in org.biojava.bio.gui.sequence">SequencePanel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePoster.html#getChangeSupport(org.biojava.utils.ChangeType)">getChangeSupport(ChangeType)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePoster.html" title="class in org.biojava.bio.gui.sequence">SequencePoster</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequenceRendererWrapper.html#getChangeSupport(org.biojava.utils.ChangeType)">getChangeSupport(ChangeType)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequenceRendererWrapper.html" title="class in org.biojava.bio.gui.sequence">SequenceRendererWrapper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/TranslatedSequencePanel.html#getChangeSupport(org.biojava.utils.ChangeType)">getChangeSupport(ChangeType)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/TranslatedSequencePanel.html" title="class in org.biojava.bio.gui.sequence">TranslatedSequencePanel</a></dt>
<dd>
<div class="block"><code>getChangeSupport</code> lazily instantiates a helper for
change listeners.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/MergeAnnotation.html#getChangeSupport(org.biojava.utils.ChangeType)">getChangeSupport(ChangeType)</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/MergeAnnotation.html" title="class in org.biojava.bio">MergeAnnotation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/OverlayAnnotation.html#getChangeSupport(org.biojava.utils.ChangeType)">getChangeSupport(ChangeType)</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/OverlayAnnotation.html" title="class in org.biojava.bio">OverlayAnnotation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/DASSequence.html#getChangeSupport(org.biojava.utils.ChangeType)">getChangeSupport(ChangeType)</a></span> - Method in class org.biojava.bio.program.das.<a href="./org/biojava/bio/program/das/DASSequence.html" title="class in org.biojava.bio.program.das">DASSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/ReferenceServer.html#getChangeSupport(org.biojava.utils.ChangeType)">getChangeSupport(ChangeType)</a></span> - Method in class org.biojava.bio.program.das.<a href="./org/biojava/bio/program/das/ReferenceServer.html" title="class in org.biojava.bio.program.das">ReferenceServer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SequenceDBSearchHit.html#getChangeSupport(org.biojava.utils.ChangeType)">getChangeSupport(ChangeType)</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SequenceDBSearchHit.html" title="class in org.biojava.bio.search">SequenceDBSearchHit</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SequenceDBSearchResult.html#getChangeSupport(org.biojava.utils.ChangeType)">getChangeSupport(ChangeType)</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SequenceDBSearchResult.html" title="class in org.biojava.bio.search">SequenceDBSearchResult</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SequenceDBSearchSubHit.html#getChangeSupport(org.biojava.utils.ChangeType)">getChangeSupport(ChangeType)</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SequenceDBSearchSubHit.html" title="class in org.biojava.bio.search">SequenceDBSearchSubHit</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SimpleSeqSimilaritySearchHit.html#getChangeSupport(org.biojava.utils.ChangeType)">getChangeSupport(ChangeType)</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SimpleSeqSimilaritySearchHit.html" title="class in org.biojava.bio.search">SimpleSeqSimilaritySearchHit</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SimpleSeqSimilaritySearchResult.html#getChangeSupport(org.biojava.utils.ChangeType)">getChangeSupport(ChangeType)</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SimpleSeqSimilaritySearchResult.html" title="class in org.biojava.bio.search">SimpleSeqSimilaritySearchResult</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SimpleSeqSimilaritySearchSubHit.html#getChangeSupport(org.biojava.utils.ChangeType)">getChangeSupport(ChangeType)</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SimpleSeqSimilaritySearchSubHit.html" title="class in org.biojava.bio.search">SimpleSeqSimilaritySearchSubHit</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/SequenceDBWrapper.html#getChangeSupport(org.biojava.utils.ChangeType)">getChangeSupport(ChangeType)</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/SequenceDBWrapper.html" title="class in org.biojava.bio.seq.db">SequenceDBWrapper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/distributed/DistributedSequenceDB.html#getChangeSupport()">getChangeSupport()</a></span> - Method in class org.biojava.bio.seq.distributed.<a href="./org/biojava/bio/seq/distributed/DistributedSequenceDB.html" title="class in org.biojava.bio.seq.distributed">DistributedSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureTypes.RepositoryImpl.html#getChangeSupport(org.biojava.utils.ChangeType)">getChangeSupport(ChangeType)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureTypes.RepositoryImpl.html" title="class in org.biojava.bio.seq">FeatureTypes.RepositoryImpl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/LazyFilterFeatureHolder.html#getChangeSupport()">getChangeSupport()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/LazyFilterFeatureHolder.html" title="class in org.biojava.bio.seq.impl">LazyFilterFeatureHolder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleFeature.html#getChangeSupport(org.biojava.utils.ChangeType)">getChangeSupport(ChangeType)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleFeature.html" title="class in org.biojava.bio.seq.impl">SimpleFeature</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleSequence.html#getChangeSupport(org.biojava.utils.ChangeType)">getChangeSupport(ChangeType)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleSequence.html" title="class in org.biojava.bio.seq.impl">SimpleSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/LazyFeatureHolder.html#getChangeSupport(org.biojava.utils.ChangeType)">getChangeSupport(ChangeType)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/LazyFeatureHolder.html" title="class in org.biojava.bio.seq">LazyFeatureHolder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/NewSimpleAssembly.html#getChangeSupport(org.biojava.utils.ChangeType)">getChangeSupport(ChangeType)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/NewSimpleAssembly.html" title="class in org.biojava.bio.seq">NewSimpleAssembly</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/SimpleAssembly.html#getChangeSupport(org.biojava.utils.ChangeType)">getChangeSupport(ChangeType)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/SimpleAssembly.html" title="class in org.biojava.bio.seq">SimpleAssembly</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AbstractSymbol.html#getChangeSupport(org.biojava.utils.ChangeType)">getChangeSupport(ChangeType)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AbstractSymbol.html" title="class in org.biojava.bio.symbol">AbstractSymbol</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleAlphabet.html#getChangeSupport(org.biojava.utils.ChangeType)">getChangeSupport(ChangeType)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleAlphabet.html" title="class in org.biojava.bio.symbol">SimpleAlphabet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/taxa/AbstractTaxon.html#getChangeSupport(org.biojava.utils.ChangeType)">getChangeSupport(ChangeType)</a></span> - Method in class org.biojava.bio.taxa.<a href="./org/biojava/bio/taxa/AbstractTaxon.html" title="class in org.biojava.bio.taxa">AbstractTaxon</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/AbstractTerm.html#getChangeSupport(org.biojava.utils.ChangeType)">getChangeSupport(ChangeType)</a></span> - Method in class org.biojava.ontology.<a href="./org/biojava/ontology/AbstractTerm.html" title="class in org.biojava.ontology">AbstractTerm</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/OntologyTerm.Impl.html#getChangeSupport(org.biojava.utils.ChangeType)">getChangeSupport(ChangeType)</a></span> - Method in class org.biojava.ontology.<a href="./org/biojava/ontology/OntologyTerm.Impl.html" title="class in org.biojava.ontology">OntologyTerm.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/AbstractChangeable.html#getChangeSupport(org.biojava.utils.ChangeType)">getChangeSupport(ChangeType)</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/AbstractChangeable.html" title="class in org.biojava.utils">AbstractChangeable</a></dt>
<dd>
<div class="block">Called to retrieve the ChangeSupport for this object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/ValueChanger.html#getChangeTable()">getChangeTable()</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/ValueChanger.html" title="class in org.biojava.bio.program.tagvalue">ValueChanger</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ChangeType.html#getChangeTypes(java.lang.Class)">getChangeTypes(Class)</a></span> - Static method in class org.biojava.utils.<a href="./org/biojava/utils/ChangeType.html" title="class in org.biojava.utils">ChangeType</a></dt>
<dd>
<div class="block">Get all ChangeType objects defined within a class.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/io/LargeBuffer.html#getChar(long)">getChar(long)</a></span> - Method in class org.biojava.utils.io.<a href="./org/biojava/utils/io/LargeBuffer.html" title="class in org.biojava.utils.io">LargeBuffer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/io/LargeBuffer.html#getChar()">getChar()</a></span> - Method in class org.biojava.utils.io.<a href="./org/biojava/utils/io/LargeBuffer.html" title="class in org.biojava.utils.io">LargeBuffer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/RepeatedCharSequence.html#getCharacter()">getCharacter()</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/RepeatedCharSequence.html" title="class in org.biojava.utils">RepeatedCharSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ParserException.html#getCharacterOffset()">getCharacterOffset()</a></span> - Method in exception org.biojava.utils.<a href="./org/biojava/utils/ParserException.html" title="class in org.biojava.utils">ParserException</a></dt>
<dd>
<div class="block">Get the character offset in the line where an error was detected.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.Not.html#getChild()">getChild()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.Not.html" title="class in org.biojava.bio.seq">FeatureFilter.Not</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SuffixTree.html#getChild(org.biojava.bio.symbol.SuffixTree.SuffixNode, org.biojava.bio.symbol.Symbol)">getChild(SuffixTree.SuffixNode, Symbol)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SuffixTree.html" title="class in org.biojava.bio.symbol">SuffixTree</a></dt>
<dd>
<div class="block">Get a child of a SuffixTree.SuffixNode, constructing a new
one if need be.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SuffixTree.html#getChild(org.biojava.bio.symbol.SuffixTree.SuffixNode, int)">getChild(SuffixTree.SuffixNode, int)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SuffixTree.html" title="class in org.biojava.bio.symbol">SuffixTree</a></dt>
<dd>
<div class="block">Get the n'th child of a node.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.Not.html#getChild()">getChild()</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.Not.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.Not</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/CollectionConstraint.And.html#getChild1()">getChild1()</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/CollectionConstraint.And.html" title="class in org.biojava.bio">CollectionConstraint.And</a></dt>
<dd>
<div class="block">Get the first child CollectionConstraint.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/CollectionConstraint.Or.html#getChild1()">getChild1()</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/CollectionConstraint.Or.html" title="class in org.biojava.bio">CollectionConstraint.Or</a></dt>
<dd>
<div class="block">Get the first child CollectionConstraint.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/PropertyConstraint.And.html#getChild1()">getChild1()</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/PropertyConstraint.And.html" title="class in org.biojava.bio">PropertyConstraint.And</a></dt>
<dd>
<div class="block">Get the first child PropertyConstraint.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/PropertyConstraint.Or.html#getChild1()">getChild1()</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/PropertyConstraint.Or.html" title="class in org.biojava.bio">PropertyConstraint.Or</a></dt>
<dd>
<div class="block">Get the first child PropertyConstraint.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.And.html#getChild1()">getChild1()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.And.html" title="class in org.biojava.bio.seq">FeatureFilter.And</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.Or.html#getChild1()">getChild1()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.Or.html" title="class in org.biojava.bio.seq">FeatureFilter.Or</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.And.html#getChild1()">getChild1()</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.And.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.And</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.Or.html#getChild1()">getChild1()</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.Or.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.Or</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/CollectionConstraint.And.html#getChild2()">getChild2()</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/CollectionConstraint.And.html" title="class in org.biojava.bio">CollectionConstraint.And</a></dt>
<dd>
<div class="block">Get the seccond child CollectionConstraint.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/CollectionConstraint.Or.html#getChild2()">getChild2()</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/CollectionConstraint.Or.html" title="class in org.biojava.bio">CollectionConstraint.Or</a></dt>
<dd>
<div class="block">Get the seccond child CollectionConstraint.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/PropertyConstraint.And.html#getChild2()">getChild2()</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/PropertyConstraint.And.html" title="class in org.biojava.bio">PropertyConstraint.And</a></dt>
<dd>
<div class="block">Get the seccond child PropertyConstraint.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/PropertyConstraint.Or.html#getChild2()">getChild2()</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/PropertyConstraint.Or.html" title="class in org.biojava.bio">PropertyConstraint.Or</a></dt>
<dd>
<div class="block">Get the seccond child PropertyConstraint.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.And.html#getChild2()">getChild2()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.And.html" title="class in org.biojava.bio.seq">FeatureFilter.And</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.Or.html#getChild2()">getChild2()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.Or.html" title="class in org.biojava.bio.seq">FeatureFilter.Or</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.And.html#getChild2()">getChild2()</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.And.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.And</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.Or.html#getChild2()">getChild2()</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.Or.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.Or</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/taxa/SimpleTaxon.html#getChildren()">getChildren()</a></span> - Method in class org.biojava.bio.taxa.<a href="./org/biojava/bio/taxa/SimpleTaxon.html" title="class in org.biojava.bio.taxa">SimpleTaxon</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/taxa/Taxon.html#getChildren()">getChildren()</a></span> - Method in interface org.biojava.bio.taxa.<a href="./org/biojava/bio/taxa/Taxon.html" title="interface in org.biojava.bio.taxa">Taxon</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">The children of this Taxon.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/taxa/WeakTaxon.html#getChildren()">getChildren()</a></span> - Method in class org.biojava.bio.taxa.<a href="./org/biojava/bio/taxa/WeakTaxon.html" title="class in org.biojava.bio.taxa">WeakTaxon</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/biosql/TaxonSQL.html#getChildrenOf(java.sql.Connection, java.lang.String)">getChildrenOf(Connection, String)</a></span> - Static method in class org.biojava.bio.seq.db.biosql.<a href="./org/biojava/bio/seq/db/biosql/TaxonSQL.html" title="class in org.biojava.bio.seq.db.biosql">TaxonSQL</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Returns all children of the specified taxon.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/biosql/TaxonSQL.html#getChildrenOf(java.sql.Connection, org.biojava.bio.taxa.Taxon)">getChildrenOf(Connection, Taxon)</a></span> - Static method in class org.biojava.bio.seq.db.biosql.<a href="./org/biojava/bio/seq/db/biosql/TaxonSQL.html" title="class in org.biojava.bio.seq.db.biosql">TaxonSQL</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Returns the children as a <code>Stack</code> of this given taxon.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/taxa/WeakTaxon.html#getChildrenRaw()">getChildrenRaw()</a></span> - Method in class org.biojava.bio.taxa.<a href="./org/biojava/bio/taxa/WeakTaxon.html" title="class in org.biojava.bio.taxa">WeakTaxon</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.html#getChromatogram()">getChromatogram()</a></span> - Method in class org.biojava.bio.chromatogram.graphic.<a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.html" title="class in org.biojava.bio.chromatogram.graphic">ChromatogramGraphic</a></dt>
<dd>
<div class="block">Accessor for the in-use chromatogram.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/Agave2AgaveAnnotFilter.html#getChromNum(org.biojava.bio.Annotation)">getChromNum(Annotation)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/Agave2AgaveAnnotFilter.html" title="class in org.biojava.bio.seq.io.agave">Agave2AgaveAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEAnnotFilter.html#getChromNum(org.biojava.bio.Annotation)">getChromNum(Annotation)</a></span> - Method in interface org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEAnnotFilter.html" title="interface in org.biojava.bio.seq.io.agave">AGAVEAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/SimpleAnnotFilter.html#getChromNum(org.biojava.bio.Annotation)">getChromNum(Annotation)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/SimpleAnnotFilter.html" title="class in org.biojava.bio.seq.io.agave">SimpleAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/Agave2AgaveAnnotFilter.html#getChromosome(org.biojava.bio.Annotation)">getChromosome(Annotation)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/Agave2AgaveAnnotFilter.html" title="class in org.biojava.bio.seq.io.agave">Agave2AgaveAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEAnnotFilter.html#getChromosome(org.biojava.bio.Annotation)">getChromosome(Annotation)</a></span> - Method in interface org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEAnnotFilter.html" title="interface in org.biojava.bio.seq.io.agave">AGAVEAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEMapLocation.html#getChromosome()">getChromosome()</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEMapLocation.html" title="class in org.biojava.bio.seq.io.agave">AGAVEMapLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/SimpleAnnotFilter.html#getChromosome(org.biojava.bio.Annotation)">getChromosome(Annotation)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/SimpleAnnotFilter.html" title="class in org.biojava.bio.seq.io.agave">SimpleAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/functions/GACross.html#getChromosomes()">getChromosomes()</a></span> - Method in interface org.biojavax.ga.functions.<a href="./org/biojavax/ga/functions/GACross.html" title="interface in org.biojavax.ga.functions">GACross</a></dt>
<dd>
<div class="block">Gets the chromosomes after the cross</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ga/functions/GACrossResult.html#getChromosomes()">getChromosomes()</a></span> - Method in interface org.biojavax.ga.functions.<a href="./org/biojavax/ga/functions/GACrossResult.html" title="interface in org.biojavax.ga.functions">GACrossResult</a></dt>
<dd>
<div class="block">Gets the chromosomes after the cross</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ga/functions/SimpleGACrossResult.html#getChromosomes()">getChromosomes()</a></span> - Method in class org.biojavax.ga.functions.<a href="./org/biojavax/ga/functions/SimpleGACrossResult.html" title="class in org.biojavax.ga.functions">SimpleGACrossResult</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/impl/AbstractOrganism.html#getChromosomes()">getChromosomes()</a></span> - Method in class org.biojavax.ga.impl.<a href="./org/biojavax/ga/impl/AbstractOrganism.html" title="class in org.biojavax.ga.impl">AbstractOrganism</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/Organism.html#getChromosomes()">getChromosomes()</a></span> - Method in interface org.biojavax.ga.<a href="./org/biojavax/ga/Organism.html" title="interface in org.biojavax.ga">Organism</a></dt>
<dd>
<div class="block">Gets the organisms 'chromosome' sequences</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/ProteaseManager.html#getChymotrypsin()">getChymotrypsin()</a></span> - Static method in class org.biojava.bio.proteomics.<a href="./org/biojava/bio/proteomics/ProteaseManager.html" title="class in org.biojava.bio.proteomics">ProteaseManager</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.html#getCircular()">getCircular()</a></span> - Method in interface org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.html" title="interface in org.biojavax.bio.seq">RichSequence</a></dt>
<dd>
<div class="block">Is the sequence circular? Circularity has implications for work with
locations and any coordinate work eg symbolAt(int i).</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/ThinRichSequence.html#getCircular()">getCircular()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/ThinRichSequence.html" title="class in org.biojavax.bio.seq">ThinRichSequence</a></dt>
<dd>
<div class="block">Is the sequence circular? Circularity has implications for work with
locations and any coordinate work eg symbolAt(int i).</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/EmptyRichLocation.html#getCircularLength()">getCircularLength()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/EmptyRichLocation.html" title="class in org.biojavax.bio.seq">EmptyRichLocation</a></dt>
<dd>
<div class="block">Retrieves the circular length of this location.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/MultiSourceCompoundRichLocation.html#getCircularLength()">getCircularLength()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/MultiSourceCompoundRichLocation.html" title="class in org.biojavax.bio.seq">MultiSourceCompoundRichLocation</a></dt>
<dd>
<div class="block">Retrieves the circular length of this location.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichLocation.html#getCircularLength()">getCircularLength()</a></span> - Method in interface org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichLocation.html" title="interface in org.biojavax.bio.seq">RichLocation</a></dt>
<dd>
<div class="block">Retrieves the circular length of this location.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichLocation.html#getCircularLength()">getCircularLength()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichLocation.html" title="class in org.biojavax.bio.seq">SimpleRichLocation</a></dt>
<dd>
<div class="block">Retrieves the circular length of this location.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/PDBHeader.html#getClassification()">getClassification()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/PDBHeader.html" title="class in org.biojava.bio.structure">PDBHeader</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/Agave2AgaveAnnotFilter.html#getClassifyId(org.biojava.bio.Annotation)">getClassifyId(Annotation)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/Agave2AgaveAnnotFilter.html" title="class in org.biojava.bio.seq.io.agave">Agave2AgaveAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEAnnotFilter.html#getClassifyId(org.biojava.bio.Annotation)">getClassifyId(Annotation)</a></span> - Method in interface org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEAnnotFilter.html" title="interface in org.biojava.bio.seq.io.agave">AGAVEAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/SimpleAnnotFilter.html#getClassifyId(org.biojava.bio.Annotation)">getClassifyId(Annotation)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/SimpleAnnotFilter.html" title="class in org.biojava.bio.seq.io.agave">SimpleAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/Agave2AgaveAnnotFilter.html#getClassifySystem(org.biojava.bio.Annotation)">getClassifySystem(Annotation)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/Agave2AgaveAnnotFilter.html" title="class in org.biojava.bio.seq.io.agave">Agave2AgaveAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEAnnotFilter.html#getClassifySystem(org.biojava.bio.Annotation)">getClassifySystem(Annotation)</a></span> - Method in interface org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEAnnotFilter.html" title="interface in org.biojava.bio.seq.io.agave">AGAVEAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/SimpleAnnotFilter.html#getClassifySystem(org.biojava.bio.Annotation)">getClassifySystem(Annotation)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/SimpleAnnotFilter.html" title="class in org.biojava.bio.seq.io.agave">SimpleAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/Agave2AgaveAnnotFilter.html#getClassifyType(org.biojava.bio.Annotation)">getClassifyType(Annotation)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/Agave2AgaveAnnotFilter.html" title="class in org.biojava.bio.seq.io.agave">Agave2AgaveAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEAnnotFilter.html#getClassifyType(org.biojava.bio.Annotation)">getClassifyType(Annotation)</a></span> - Method in interface org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEAnnotFilter.html" title="interface in org.biojava.bio.seq.io.agave">AGAVEAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/SimpleAnnotFilter.html#getClassifyType(org.biojava.bio.Annotation)">getClassifyType(Annotation)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/SimpleAnnotFilter.html" title="class in org.biojava.bio.seq.io.agave">SimpleAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ClassTools.html#getClassLoader(java.lang.Object)">getClassLoader(Object)</a></span> - Static method in class org.biojava.utils.<a href="./org/biojava/utils/ClassTools.html" title="class in org.biojava.utils">ClassTools</a></dt>
<dd>
<div class="block">Get the classloader which loaded the class of <code>obj</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/ClassTools.html#getClassLoader(java.lang.Class)">getClassLoader(Class)</a></span> - Static method in class org.biojava.utils.<a href="./org/biojava/utils/ClassTools.html" title="class in org.biojava.utils">ClassTools</a></dt>
<dd>
<div class="block">Get the classloader which loaded <code>clazz</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/EcNumber.html#getClassNumber(int)">getClassNumber(int)</a></span> - Method in interface org.biojava.bio.<a href="./org/biojava/bio/EcNumber.html" title="interface in org.biojava.bio">EcNumber</a></dt>
<dd>
<div class="block">Get the class number associated with the particular level of the ec number.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/EcNumber.Impl.html#getClassNumber(int)">getClassNumber(int)</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/EcNumber.Impl.html" title="class in org.biojava.bio">EcNumber.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/Protease.html#getCleaveageResidues()">getCleaveageResidues()</a></span> - Method in class org.biojava.bio.proteomics.<a href="./org/biojava/bio/proteomics/Protease.html" title="class in org.biojava.bio.proteomics">Protease</a></dt>
<dd>
<div class="block">The list of residues that the protease will cleave at.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/Agave2AgaveAnnotFilter.html#getCloneId(org.biojava.bio.Annotation)">getCloneId(Annotation)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/Agave2AgaveAnnotFilter.html" title="class in org.biojava.bio.seq.io.agave">Agave2AgaveAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEAnnotFilter.html#getCloneId(org.biojava.bio.Annotation)">getCloneId(Annotation)</a></span> - Method in interface org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEAnnotFilter.html" title="interface in org.biojava.bio.seq.io.agave">AGAVEAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/SimpleAnnotFilter.html#getCloneId(org.biojava.bio.Annotation)">getCloneId(Annotation)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/SimpleAnnotFilter.html" title="class in org.biojava.bio.seq.io.agave">SimpleAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/Agave2AgaveAnnotFilter.html#getCloneLibrary(org.biojava.bio.Annotation)">getCloneLibrary(Annotation)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/Agave2AgaveAnnotFilter.html" title="class in org.biojava.bio.seq.io.agave">Agave2AgaveAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEAnnotFilter.html#getCloneLibrary(org.biojava.bio.Annotation)">getCloneLibrary(Annotation)</a></span> - Method in interface org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEAnnotFilter.html" title="interface in org.biojava.bio.seq.io.agave">AGAVEAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/SimpleAnnotFilter.html#getCloneLibrary(org.biojava.bio.Annotation)">getCloneLibrary(Annotation)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/SimpleAnnotFilter.html" title="class in org.biojava.bio.seq.io.agave">SimpleAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/unigene/UnigeneDB.html#getCluster(java.lang.String)">getCluster(String)</a></span> - Method in interface org.biojava.bio.program.unigene.<a href="./org/biojava/bio/program/unigene/UnigeneDB.html" title="interface in org.biojava.bio.program.unigene">UnigeneDB</a></dt>
<dd>
<div class="block">Fetch a cluster by its cluster id.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/AlternativeAlignment.html#getCluster()">getCluster()</a></span> - Method in class org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/AlternativeAlignment.html" title="class in org.biojava.bio.structure.align.pairwise">AlternativeAlignment</a></dt>
<dd>
<div class="block">get the number of the cluster this alignment belongs to</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/FragmentPair.html#getCluster()">getCluster()</a></span> - Method in class org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/FragmentPair.html" title="class in org.biojava.bio.structure.align.pairwise">FragmentPair</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/ProteaseManager.html#getCNBr()">getCNBr()</a></span> - Static method in class org.biojava.bio.proteomics.<a href="./org/biojava/bio/proteomics/ProteaseManager.html" title="class in org.biojava.bio.proteomics">ProteaseManager</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/DNATools.html#getCodonAlphabet()">getCodonAlphabet()</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/DNATools.html" title="class in org.biojava.bio.seq">DNATools</a></dt>
<dd>
<div class="block">Gets the (DNA x DNA x DNA) Alphabet</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/RNATools.html#getCodonAlphabet()">getCodonAlphabet()</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/RNATools.html" title="class in org.biojava.bio.seq">RNATools</a></dt>
<dd>
<div class="block">Gets the (RNA x RNA x RNA) Alphabet</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/CodonPrefFilter.ByName.html#getCodonPref()">getCodonPref()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/CodonPrefFilter.ByName.html" title="class in org.biojava.bio.symbol">CodonPrefFilter.ByName</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/CodonPrefTools.html#getCodonPreference(java.lang.String)">getCodonPreference(String)</a></span> - Static method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/CodonPrefTools.html" title="class in org.biojava.bio.symbol">CodonPrefTools</a></dt>
<dd>
<div class="block">get the specified codon preference.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/CodonPrefFilter.AcceptAll.html#getCodonPrefs()">getCodonPrefs()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/CodonPrefFilter.AcceptAll.html" title="class in org.biojava.bio.symbol">CodonPrefFilter.AcceptAll</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/helper/IndexPair.html#getCol()">getCol()</a></span> - Method in class org.biojava.bio.structure.align.helper.<a href="./org/biojava/bio/structure/align/helper/IndexPair.html" title="class in org.biojava.bio.structure.align.helper">IndexPair</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/FeatureBlockSequenceRenderer.html#getCollapsing()">getCollapsing()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/FeatureBlockSequenceRenderer.html" title="class in org.biojava.bio.gui.sequence">FeatureBlockSequenceRenderer</a></dt>
<dd>
<div class="block">Returns <code>true</code> if this class collapses to zero depth when there are
no visible features.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/filterxml/XMLAnnotationTypeHandler.CollectionConstraintHandler.html#getCollectionConstraint()">getCollectionConstraint()</a></span> - Method in interface org.biojava.bio.seq.io.filterxml.<a href="./org/biojava/bio/seq/io/filterxml/XMLAnnotationTypeHandler.CollectionConstraintHandler.html" title="interface in org.biojava.bio.seq.io.filterxml">XMLAnnotationTypeHandler.CollectionConstraintHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BibRefQuery.html#getCollectionId()">getCollectionId()</a></span> - Method in interface org.biojava.bibliography.<a href="./org/biojava/bibliography/BibRefQuery.html" title="interface in org.biojava.bibliography">BibRefQuery</a></dt>
<dd>
<div class="block">
It returns an identification of the current query collection.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/blast2html/AbstractAlignmentStyler.html#getColourClass(java.lang.String)">getColourClass(String)</a></span> - Method in class org.biojava.bio.program.blast2html.<a href="./org/biojava/bio/program/blast2html/AbstractAlignmentStyler.html" title="class in org.biojava.bio.program.blast2html">AbstractAlignmentStyler</a></dt>
<dd>
<div class="block">Returns the colour class for the specified colour (in hex).</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/Alignable.html#getCols()">getCols()</a></span> - Method in interface org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/Alignable.html" title="interface in org.biojava.bio.structure.align.pairwise">Alignable</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/StrCompAlignment.html#getCols()">getCols()</a></span> - Method in class org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/StrCompAlignment.html" title="class in org.biojava.bio.structure.align.pairwise">StrCompAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/SimpleWeightMatrix.html#getColumn(int)">getColumn(int)</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/SimpleWeightMatrix.html" title="class in org.biojava.bio.dp">SimpleWeightMatrix</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/WeightMatrix.html#getColumn(int)">getColumn(int)</a></span> - Method in interface org.biojava.bio.dp.<a href="./org/biojava/bio/dp/WeightMatrix.html" title="interface in org.biojava.bio.dp">WeightMatrix</a></dt>
<dd>
<div class="block">Retrieve a column as an EmissionState.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/jama/Matrix.html#getColumnDimension()">getColumnDimension()</a></span> - Method in class org.biojava.bio.structure.jama.<a href="./org/biojava/bio/structure/jama/Matrix.html" title="class in org.biojava.bio.structure.jama">Matrix</a></dt>
<dd>
<div class="block">Get column dimension.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/jama/Matrix.html#getColumnPackedCopy()">getColumnPackedCopy()</a></span> - Method in class org.biojava.bio.structure.jama.<a href="./org/biojava/bio/structure/jama/Matrix.html" title="class in org.biojava.bio.structure.jama">Matrix</a></dt>
<dd>
<div class="block">Make a one-dimensional column packed copy of the internal array.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/process/ExternalProcess.html#getCommands()">getCommands()</a></span> - Method in class org.biojava.utils.process.<a href="./org/biojava/utils/process/ExternalProcess.html" title="class in org.biojava.utils.process">ExternalProcess</a></dt>
<dd>
<div class="block">Gets the command line including the path or name of the external program
and its command line arguments.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/AnnotationType.html#getComment()">getComment()</a></span> - Method in interface org.biojava.bio.<a href="./org/biojava/bio/AnnotationType.html" title="interface in org.biojava.bio">AnnotationType</a></dt>
<dd>
<div class="block">Get the comment for the whole AnnotationType.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/AnnotationType.html#getComment(java.lang.Object)">getComment(Object)</a></span> - Method in interface org.biojava.bio.<a href="./org/biojava/bio/AnnotationType.html" title="interface in org.biojava.bio">AnnotationType</a></dt>
<dd>
<div class="block">Get the comment for a particular property.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/AnnotationType.Impl.html#getComment()">getComment()</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/AnnotationType.Impl.html" title="class in org.biojava.bio">AnnotationType.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/AnnotationType.Impl.html#getComment(java.lang.Object)">getComment(Object)</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/AnnotationType.Impl.html" title="class in org.biojava.bio">AnnotationType.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFRecord.html#getComment()">getComment()</a></span> - Method in interface org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFRecord.html" title="interface in org.biojava.bio.program.gff">GFFRecord</a></dt>
<dd>
<div class="block">The feature comment.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/SimpleGFFRecord.html#getComment()">getComment()</a></span> - Method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/SimpleGFFRecord.html" title="class in org.biojava.bio.program.gff">SimpleGFFRecord</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/aaindex/AAindex.html#getComment()">getComment()</a></span> - Method in class org.biojava.bio.proteomics.aaindex.<a href="./org/biojava/bio/proteomics/aaindex/AAindex.html" title="class in org.biojava.bio.proteomics.aaindex">AAindex</a></dt>
<dd>
<div class="block">Gets the user comment for the AAindex entry.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/tools/SVM_Light.LabelledVector.html#getComment()">getComment()</a></span> - Method in class org.biojava.stats.svm.tools.<a href="./org/biojava/stats/svm/tools/SVM_Light.LabelledVector.html" title="class in org.biojava.stats.svm.tools">SVM_Light.LabelledVector</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtCommentParser.Event.html#getComment()">getComment()</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtCommentParser.Event.html" title="class in org.biojavax.bio.seq.io">UniProtCommentParser.Event</a></dt>
<dd>
<div class="block">Getter for property comment.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/Comment.html#getComment()">getComment()</a></span> - Method in interface org.biojavax.<a href="./org/biojavax/Comment.html" title="interface in org.biojavax">Comment</a></dt>
<dd>
<div class="block">Returns the comment part of this comment.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleComment.html#getComment()">getComment()</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleComment.html" title="class in org.biojavax">SimpleComment</a></dt>
<dd>
<div class="block">Returns the comment part of this comment.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/scf/SCF.html#getComments()">getComments()</a></span> - Method in class org.biojava.bio.program.scf.<a href="./org/biojava/bio/program/scf/SCF.html" title="class in org.biojava.bio.program.scf">SCF</a></dt>
<dd>
<div class="block">Returns the comments fields as a <code>Properties</code> mapping.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/BioEntry.html#getComments()">getComments()</a></span> - Method in interface org.biojavax.bio.<a href="./org/biojavax/bio/BioEntry.html" title="interface in org.biojavax.bio">BioEntry</a></dt>
<dd>
<div class="block">Returns a set of all comments associated with this bioentry.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/SimpleBioEntry.html#getComments()">getComments()</a></span> - Method in class org.biojavax.bio.<a href="./org/biojavax/bio/SimpleBioEntry.html" title="class in org.biojavax.bio">SimpleBioEntry</a></dt>
<dd>
<div class="block">Returns a set of all comments associated with this bioentry.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html#getCommentType()">getCommentType()</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html" title="class in org.biojavax.bio.seq.io">UniProtCommentParser</a></dt>
<dd>
<div class="block">Getter for property commentType.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/taxa/AbstractTaxon.html#getCommonName()">getCommonName()</a></span> - Method in class org.biojava.bio.taxa.<a href="./org/biojava/bio/taxa/AbstractTaxon.html" title="class in org.biojava.bio.taxa">AbstractTaxon</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/taxa/Taxon.html#getCommonName()">getCommonName()</a></span> - Method in interface org.biojava.bio.taxa.<a href="./org/biojava/bio/taxa/Taxon.html" title="interface in org.biojava.bio.taxa">Taxon</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">The common name of the Taxon.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/PdbxEntityNonPoly.html#getComp_id()">getComp_id()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/PdbxEntityNonPoly.html" title="class in org.biojava.bio.structure.io.mmcif.model">PdbxEntityNonPoly</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/FileAsList.html#getComparator()">getComparator()</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/FileAsList.html" title="class in org.biojava.utils">FileAsList</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/MergeLocation.html#getComponentList(boolean)">getComponentList(boolean)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/MergeLocation.html" title="class in org.biojava.bio.symbol">MergeLocation</a></dt>
<dd>
<div class="block">Gets the component locations that make up this one</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/ComponentFeature.html#getComponentLocation()">getComponentLocation()</a></span> - Method in interface org.biojava.bio.seq.<a href="./org/biojava/bio/seq/ComponentFeature.html" title="interface in org.biojava.bio.seq">ComponentFeature</a></dt>
<dd>
<div class="block">Return a location which identifies a portion of the component
sequence which is to be included in the assembly.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/AssembledSymbolList.html#getComponentLocationSet()">getComponentLocationSet()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/AssembledSymbolList.html" title="class in org.biojava.bio.seq.impl">AssembledSymbolList</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/NewAssembledSymbolList.html#getComponentLocationSet()">getComponentLocationSet()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/NewAssembledSymbolList.html" title="class in org.biojava.bio.seq.impl">NewAssembledSymbolList</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ByComponentName.html#getComponentName()">getComponentName()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ByComponentName.html" title="class in org.biojava.bio.seq">FeatureFilter.ByComponentName</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/ComponentFeature.html#getComponentSequence()">getComponentSequence()</a></span> - Method in interface org.biojava.bio.seq.<a href="./org/biojava/bio/seq/ComponentFeature.html" title="interface in org.biojava.bio.seq">ComponentFeature</a></dt>
<dd>
<div class="block">Get the sequence object which provides a component of this
feature's parent sequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/ComponentFeature.html#getComponentSequenceName()">getComponentSequenceName()</a></span> - Method in interface org.biojava.bio.seq.<a href="./org/biojava/bio/seq/ComponentFeature.html" title="interface in org.biojava.bio.seq">ComponentFeature</a></dt>
<dd>
<div class="block">Get the name of the component sequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Structure.html#getCompoundById(java.lang.String)">getCompoundById(String)</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Structure.html" title="interface in org.biojava.bio.structure">Structure</a></dt>
<dd>
<div class="block">request a particular compound by its id</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/StructureImpl.html#getCompoundById(java.lang.String)">getCompoundById(String)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/StructureImpl.html" title="class in org.biojava.bio.structure">StructureImpl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Structure.html#getCompounds()">getCompounds()</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Structure.html" title="interface in org.biojava.bio.structure">Structure</a></dt>
<dd>
<div class="block">get all the Compounds that are defined in the PDB Header</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/StructureImpl.html#getCompounds()">getCompounds()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/StructureImpl.html" title="class in org.biojava.bio.structure">StructureImpl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/AbstractOrderNDistribution.html#getConditionedAlphabet()">getConditionedAlphabet()</a></span> - Method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/AbstractOrderNDistribution.html" title="class in org.biojava.bio.dist">AbstractOrderNDistribution</a></dt>
<dd>
<div class="block">Get the conditioned alphabet.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/OrderNDistribution.html#getConditionedAlphabet()">getConditionedAlphabet()</a></span> - Method in interface org.biojava.bio.dist.<a href="./org/biojava/bio/dist/OrderNDistribution.html" title="interface in org.biojava.bio.dist">OrderNDistribution</a></dt>
<dd>
<div class="block">Get the conditioned alphabet.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/AbstractOrderNDistribution.html#getConditioningAlphabet()">getConditioningAlphabet()</a></span> - Method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/AbstractOrderNDistribution.html" title="class in org.biojava.bio.dist">AbstractOrderNDistribution</a></dt>
<dd>
<div class="block">Get the conditioning alphabet of this distribution.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/OrderNDistribution.html#getConditioningAlphabet()">getConditioningAlphabet()</a></span> - Method in interface org.biojava.bio.dist.<a href="./org/biojava/bio/dist/OrderNDistribution.html" title="interface in org.biojava.bio.dist">OrderNDistribution</a></dt>
<dd>
<div class="block">Get the conditioning alphabet of this distribution.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/Agave2AgaveAnnotFilter.html#getConfidence(org.biojava.bio.Annotation)">getConfidence(Annotation)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/Agave2AgaveAnnotFilter.html" title="class in org.biojava.bio.seq.io.agave">Agave2AgaveAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEAnnotFilter.html#getConfidence(org.biojava.bio.Annotation)">getConfidence(Annotation)</a></span> - Method in interface org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEAnnotFilter.html" title="interface in org.biojava.bio.seq.io.agave">AGAVEAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/SimpleAnnotFilter.html#getConfidence(org.biojava.bio.Annotation)">getConfidence(Annotation)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/SimpleAnnotFilter.html" title="class in org.biojava.bio.seq.io.agave">SimpleAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/directory/RegistryConfiguration.Composite.html#getConfigLocator()">getConfigLocator()</a></span> - Method in class org.biojava.directory.<a href="./org/biojava/directory/RegistryConfiguration.Composite.html" title="class in org.biojava.directory">RegistryConfiguration.Composite</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/directory/RegistryConfiguration.html#getConfigLocator()">getConfigLocator()</a></span> - Method in interface org.biojava.directory.<a href="./org/biojava/directory/RegistryConfiguration.html" title="interface in org.biojava.directory">RegistryConfiguration</a></dt>
<dd>
<div class="block"><code>getConfigLocator</code> returns a locator for the
configuration.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/directory/RegistryConfiguration.Impl.html#getConfigLocator()">getConfigLocator()</a></span> - Method in class org.biojava.directory.<a href="./org/biojava/directory/RegistryConfiguration.Impl.html" title="class in org.biojava.directory">RegistryConfiguration.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/directory/RegistryConfiguration.Composite.html#getConfiguration()">getConfiguration()</a></span> - Method in class org.biojava.directory.<a href="./org/biojava/directory/RegistryConfiguration.Composite.html" title="class in org.biojava.directory">RegistryConfiguration.Composite</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/directory/RegistryConfiguration.html#getConfiguration()">getConfiguration()</a></span> - Method in interface org.biojava.directory.<a href="./org/biojava/directory/RegistryConfiguration.html" title="interface in org.biojava.directory">RegistryConfiguration</a></dt>
<dd>
<div class="block"><code>getConfiguration</code> returns a mapping of registry
database names to collections of tag-value pairs.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/directory/RegistryConfiguration.Impl.html#getConfiguration()">getConfiguration()</a></span> - Method in class org.biojava.directory.<a href="./org/biojava/directory/RegistryConfiguration.Impl.html" title="class in org.biojava.directory">RegistryConfiguration.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Structure.html#getConnections()">getConnections()</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Structure.html" title="interface in org.biojava.bio.structure">Structure</a></dt>
<dd>
<div class="block">Returns the connections value.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/StructureImpl.html#getConnections()">getConnections()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/StructureImpl.html" title="class in org.biojava.bio.structure">StructureImpl</a></dt>
<dd>
<div class="block">Returns the connections value.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/PolynomialKernel.html#getConstant()">getConstant()</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/PolynomialKernel.html" title="class in org.biojava.stats.svm">PolynomialKernel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/SigmoidKernel.html#getConstant()">getConstant()</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/SigmoidKernel.html" title="class in org.biojava.stats.svm">SigmoidKernel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/AnnotationType.html#getConstraint(java.lang.Object)">getConstraint(Object)</a></span> - Method in interface org.biojava.bio.<a href="./org/biojava/bio/AnnotationType.html" title="interface in org.biojava.bio">AnnotationType</a></dt>
<dd>
<div class="block">Retrieve the constraint that will be applied to all
properties with a given key.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/AnnotationType.Impl.html#getConstraint(java.lang.Object)">getConstraint(Object)</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/AnnotationType.Impl.html" title="class in org.biojava.bio">AnnotationType.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/FragmentPair.html#getContacts()">getContacts()</a></span> - Method in class org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/FragmentPair.html" title="class in org.biojava.bio.structure.align.pairwise">FragmentPair</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichFeatureRelationship.html#getContainsTerm()">getContainsTerm()</a></span> - Static method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichFeatureRelationship.html" title="class in org.biojavax.bio.seq">SimpleRichFeatureRelationship</a></dt>
<dd>
<div class="block">Gets the default CONTAINS term used for defining the relationship between features.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/sax/blastxml/BlastXMLParserFacade.html#getContentHandler()">getContentHandler()</a></span> - Method in class org.biojava.bio.program.sax.blastxml.<a href="./org/biojava/bio/program/sax/blastxml/BlastXMLParserFacade.html" title="class in org.biojava.bio.program.sax.blastxml">BlastXMLParserFacade</a></dt>
<dd>
<div class="block">correct this later</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/FilteringRenderer.html#getContext(org.biojava.bio.gui.sequence.SequenceRenderContext)">getContext(SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/FilteringRenderer.html" title="class in org.biojava.bio.gui.sequence">FilteringRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/projection/ProjectedFeatureHolder.html#getContext()">getContext()</a></span> - Method in class org.biojava.bio.seq.projection.<a href="./org/biojava/bio/seq/projection/ProjectedFeatureHolder.html" title="class in org.biojava.bio.seq.projection">ProjectedFeatureHolder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/TrainingEvent.html#getContext()">getContext()</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/TrainingEvent.html" title="class in org.biojava.stats.svm">TrainingEvent</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/helper/AligMatEl.html#getContig()">getContig()</a></span> - Method in class org.biojava.bio.structure.align.helper.<a href="./org/biojava/bio/structure/align/helper/AligMatEl.html" title="class in org.biojava.bio.structure.align.helper">AligMatEl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/LineSplitParser.html#getContinueOnEmptyTag()">getContinueOnEmptyTag()</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/LineSplitParser.html" title="class in org.biojava.bio.program.tagvalue">LineSplitParser</a></dt>
<dd>
<div class="block">See if empty tags are treated as a continuation of previous tags or as a
new tag with the value of the empty string.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/RegexParser.html#getContinueOnEmptyTag()">getContinueOnEmptyTag()</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/RegexParser.html" title="class in org.biojava.bio.program.tagvalue">RegexParser</a></dt>
<dd>
<div class="block">Report whether empty tags will be treated as continuations of the last non
-empty tag.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/ImageMap.HotSpot.html#getCoordinates()">getCoordinates()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/ImageMap.HotSpot.html" title="class in org.biojava.bio.gui.sequence">ImageMap.HotSpot</a></dt>
<dd>
<div class="block"><code>getCoordinates</code> returns the hotspot coordinates.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Atom.html#getCoords()">getCoords()</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Atom.html" title="interface in org.biojava.bio.structure">Atom</a></dt>
<dd>
<div class="block">get the coordinates.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/AtomImpl.html#getCoords()">getCoords()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/AtomImpl.html" title="class in org.biojava.bio.structure">AtomImpl</a></dt>
<dd>
<div class="block">get the coordinates as a double[3] array .</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.Terms.html#getCopyrightTerm()">getCopyrightTerm()</a></span> - Static method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.Terms.html" title="class in org.biojavax.bio.seq">RichSequence.Terms</a></dt>
<dd>
<div class="block">Getter for the copyright term</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/OntoTools.html#getCoreOntology()">getCoreOntology()</a></span> - Static method in class org.biojava.ontology.<a href="./org/biojava/ontology/OntoTools.html" title="class in org.biojava.ontology">OntoTools</a></dt>
<dd>
<div class="block">Get the Ontology that defines our core "central dogma".</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#getCorrelation_coeff_Fo_to_Fc()">getCorrelation_coeff_Fo_to_Fc()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#getCorrelation_coeff_Fo_to_Fc_free()">getCorrelation_coeff_Fo_to_Fc_free()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/Count.html#getCount(org.biojava.bio.symbol.AtomicSymbol)">getCount(AtomicSymbol)</a></span> - Method in interface org.biojava.bio.dist.<a href="./org/biojava/bio/dist/Count.html" title="interface in org.biojava.bio.dist">Count</a></dt>
<dd>
<div class="block">Return the counts for a given Symbol.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/DistributionTrainer.html#getCount(org.biojava.bio.dist.DistributionTrainerContext, org.biojava.bio.symbol.AtomicSymbol)">getCount(DistributionTrainerContext, AtomicSymbol)</a></span> - Method in interface org.biojava.bio.dist.<a href="./org/biojava/bio/dist/DistributionTrainer.html" title="interface in org.biojava.bio.dist">DistributionTrainer</a></dt>
<dd>
<div class="block">
Get the current count for this state.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/DistributionTrainerContext.html#getCount(org.biojava.bio.dist.Distribution, org.biojava.bio.symbol.Symbol)">getCount(Distribution, Symbol)</a></span> - Method in interface org.biojava.bio.dist.<a href="./org/biojava/bio/dist/DistributionTrainerContext.html" title="interface in org.biojava.bio.dist">DistributionTrainerContext</a></dt>
<dd>
<div class="block">Return the number of counts of a particular symbol which will be used
to train the specified distribution.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/IgnoreCountsTrainer.html#getCount(org.biojava.bio.dist.DistributionTrainerContext, org.biojava.bio.symbol.AtomicSymbol)">getCount(DistributionTrainerContext, AtomicSymbol)</a></span> - Method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/IgnoreCountsTrainer.html" title="class in org.biojava.bio.dist">IgnoreCountsTrainer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/IndexedCount.html#getCount(org.biojava.bio.symbol.AtomicSymbol)">getCount(AtomicSymbol)</a></span> - Method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/IndexedCount.html" title="class in org.biojava.bio.dist">IndexedCount</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/SimpleDistribution.Trainer.html#getCount(org.biojava.bio.dist.DistributionTrainerContext, org.biojava.bio.symbol.AtomicSymbol)">getCount(DistributionTrainerContext, AtomicSymbol)</a></span> - Method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/SimpleDistribution.Trainer.html" title="class in org.biojava.bio.dist">SimpleDistribution.Trainer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/SimpleDistributionTrainer.html#getCount(org.biojava.bio.dist.DistributionTrainerContext, org.biojava.bio.symbol.AtomicSymbol)">getCount(DistributionTrainerContext, AtomicSymbol)</a></span> - Method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/SimpleDistributionTrainer.html" title="class in org.biojava.bio.dist">SimpleDistributionTrainer</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/SimpleDistributionTrainerContext.html#getCount(org.biojava.bio.dist.Distribution, org.biojava.bio.symbol.Symbol)">getCount(Distribution, Symbol)</a></span> - Method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/SimpleDistributionTrainerContext.html" title="class in org.biojava.bio.dist">SimpleDistributionTrainerContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/candy/CandyVocabulary.html#getCount()">getCount()</a></span> - Method in interface org.biojava.utils.candy.<a href="./org/biojava/utils/candy/CandyVocabulary.html" title="interface in org.biojava.utils.candy">CandyVocabulary</a></dt>
<dd>
<div class="block">It returns a number of entries contained in this vocabulary.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/FragmentPair.html#getCovered()">getCovered()</a></span> - Method in class org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/FragmentPair.html" title="class in org.biojava.bio.structure.align.pairwise">FragmentPair</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/DocRef.html#getCRC()">getCRC()</a></span> - Method in interface org.biojavax.<a href="./org/biojavax/DocRef.html" title="interface in org.biojavax">DocRef</a></dt>
<dd>
<div class="block">Returns a CRC64 checksum of this document reference, allowing for easy
comparisons with other document references.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleDocRef.html#getCRC()">getCRC()</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleDocRef.html" title="class in org.biojavax">SimpleDocRef</a></dt>
<dd>
<div class="block">Returns a CRC64 checksum of this document reference, allowing for easy
comparisons with other document references.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/StrucAligParameters.html#getCreate_co()">getCreate_co()</a></span> - Method in class org.biojava.bio.structure.align.<a href="./org/biojava/bio/structure/align/StrucAligParameters.html" title="class in org.biojava.bio.structure.align">StrucAligParameters</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/Agave2AgaveAnnotFilter.html#getCreateDate(org.biojava.bio.Annotation)">getCreateDate(Annotation)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/Agave2AgaveAnnotFilter.html" title="class in org.biojava.bio.seq.io.agave">Agave2AgaveAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEAnnotFilter.html#getCreateDate(org.biojava.bio.Annotation)">getCreateDate(Annotation)</a></span> - Method in interface org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEAnnotFilter.html" title="interface in org.biojava.bio.seq.io.agave">AGAVEAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/SimpleAnnotFilter.html#getCreateDate(org.biojava.bio.Annotation)">getCreateDate(Annotation)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/SimpleAnnotFilter.html" title="class in org.biojava.bio.seq.io.agave">SimpleAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleGappedSequence.html#getCreateOnUnderlyingSequence()">getCreateOnUnderlyingSequence()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleGappedSequence.html" title="class in org.biojava.bio.seq.impl">SimpleGappedSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/GeneticAlgorithm.html#getCrossOverFunction()">getCrossOverFunction()</a></span> - Method in interface org.biojavax.ga.<a href="./org/biojavax/ga/GeneticAlgorithm.html" title="interface in org.biojavax.ga">GeneticAlgorithm</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/impl/AbstractGeneticAlgorithm.html#getCrossOverFunction()">getCrossOverFunction()</a></span> - Method in class org.biojavax.ga.impl.<a href="./org/biojavax/ga/impl/AbstractGeneticAlgorithm.html" title="class in org.biojavax.ga.impl">AbstractGeneticAlgorithm</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/functions/GACross.html#getCrossOverPositions()">getCrossOverPositions()</a></span> - Method in interface org.biojavax.ga.functions.<a href="./org/biojavax/ga/functions/GACross.html" title="interface in org.biojavax.ga.functions">GACross</a></dt>
<dd>
<div class="block">Returns the collection of cross over locations from the last cross</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ga/functions/GACrossResult.html#getCrossOverPositions()">getCrossOverPositions()</a></span> - Method in interface org.biojavax.ga.functions.<a href="./org/biojavax/ga/functions/GACrossResult.html" title="interface in org.biojavax.ga.functions">GACrossResult</a></dt>
<dd>
<div class="block">Returns the collection of cross over locations from the last cross</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ga/functions/SimpleGACrossResult.html#getCrossOverPositions()">getCrossOverPositions()</a></span> - Method in class org.biojavax.ga.functions.<a href="./org/biojavax/ga/functions/SimpleGACrossResult.html" title="class in org.biojavax.ga.functions">SimpleGACrossResult</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/functions/AbstractCrossOverFunction.html#getCrossOverProbs()">getCrossOverProbs()</a></span> - Method in class org.biojavax.ga.functions.<a href="./org/biojavax/ga/functions/AbstractCrossOverFunction.html" title="class in org.biojavax.ga.functions">AbstractCrossOverFunction</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/functions/CrossOverFunction.html#getCrossOverProbs()">getCrossOverProbs()</a></span> - Method in interface org.biojavax.ga.functions.<a href="./org/biojavax/ga/functions/CrossOverFunction.html" title="interface in org.biojavax.ga.functions">CrossOverFunction</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/functions/CrossOverFunction.NoCross.html#getCrossOverProbs()">getCrossOverProbs()</a></span> - Method in class org.biojavax.ga.functions.<a href="./org/biojavax/ga/functions/CrossOverFunction.NoCross.html" title="class in org.biojavax.ga.functions">CrossOverFunction.NoCross</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AlphabetManager.html#getCrossProductAlphabet(java.util.List)">getCrossProductAlphabet(List)</a></span> - Static method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AlphabetManager.html" title="class in org.biojava.bio.symbol">AlphabetManager</a></dt>
<dd>
<div class="block">
Retrieve a CrossProductAlphabet instance over the alphabets in aList.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AlphabetManager.html#getCrossProductAlphabet(java.util.List, java.lang.String)">getCrossProductAlphabet(List, String)</a></span> - Static method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AlphabetManager.html" title="class in org.biojava.bio.symbol">AlphabetManager</a></dt>
<dd>
<div class="block">Attempts to create a cross product alphabet and register it under a name.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AlphabetManager.html#getCrossProductAlphabet(java.util.List, org.biojava.bio.symbol.Alphabet)">getCrossProductAlphabet(List, Alphabet)</a></span> - Static method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AlphabetManager.html" title="class in org.biojava.bio.symbol">AlphabetManager</a></dt>
<dd>
<div class="block">
Retrieve a CrossProductAlphabet instance over the alphabets in aList.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/EmptyRichLocation.html#getCrossRef()">getCrossRef()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/EmptyRichLocation.html" title="class in org.biojavax.bio.seq">EmptyRichLocation</a></dt>
<dd>
<div class="block">Retrieves the crossref associated with this location.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/MultiSourceCompoundRichLocation.html#getCrossRef()">getCrossRef()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/MultiSourceCompoundRichLocation.html" title="class in org.biojavax.bio.seq">MultiSourceCompoundRichLocation</a></dt>
<dd>
<div class="block">Retrieves the crossref associated with this location.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichLocation.html#getCrossRef()">getCrossRef()</a></span> - Method in interface org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichLocation.html" title="interface in org.biojavax.bio.seq">RichLocation</a></dt>
<dd>
<div class="block">Retrieves the crossref associated with this location.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichLocation.html#getCrossRef()">getCrossRef()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichLocation.html" title="class in org.biojavax.bio.seq">SimpleRichLocation</a></dt>
<dd>
<div class="block">Retrieves the crossref associated with this location.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/DocRef.html#getCrossref()">getCrossref()</a></span> - Method in interface org.biojavax.<a href="./org/biojavax/DocRef.html" title="interface in org.biojavax">DocRef</a></dt>
<dd>
<div class="block">The document reference may refer to an object in another database.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/RankedCrossRef.html#getCrossRef()">getCrossRef()</a></span> - Method in interface org.biojavax.<a href="./org/biojavax/RankedCrossRef.html" title="interface in org.biojavax">RankedCrossRef</a></dt>
<dd>
<div class="block">Return the cross reference associated with this object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleDocRef.html#getCrossref()">getCrossref()</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleDocRef.html" title="class in org.biojavax">SimpleDocRef</a></dt>
<dd>
<div class="block">The document reference may refer to an object in another database.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleRankedCrossRef.html#getCrossRef()">getCrossRef()</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleRankedCrossRef.html" title="class in org.biojavax">SimpleRankedCrossRef</a></dt>
<dd>
<div class="block">Return the cross reference associated with this object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ga/impl/SimpleGeneticAlgorithm.html#getCrossResults()">getCrossResults()</a></span> - Method in class org.biojavax.ga.impl.<a href="./org/biojavax/ga/impl/SimpleGeneticAlgorithm.html" title="class in org.biojavax.ga.impl">SimpleGeneticAlgorithm</a></dt>
<dd>
<div class="block">Get a List containing details of all the cross over events during the run.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Exptl.html#getCrystals_number()">getCrystals_number()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Exptl.html" title="class in org.biojava.bio.structure.io.mmcif.model">Exptl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/AtomIterator.html#getCurrentChain()">getCurrentChain()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/AtomIterator.html" title="class in org.biojava.bio.structure">AtomIterator</a></dt>
<dd>
<div class="block">Get the chain that contains the current atom.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/GroupIterator.html#getCurrentChain()">getCurrentChain()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/GroupIterator.html" title="class in org.biojava.bio.structure">GroupIterator</a></dt>
<dd>
<div class="block">Get the current Chain.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/TrainingContext.html#getCurrentCycle()">getCurrentCycle()</a></span> - Method in interface org.biojava.stats.svm.<a href="./org/biojava/stats/svm/TrainingContext.html" title="interface in org.biojava.stats.svm">TrainingContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/DebuggingRichSeqIOListener.html#getCurrentFeature()">getCurrentFeature()</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/DebuggingRichSeqIOListener.html" title="class in org.biojavax.bio.seq.io">DebuggingRichSeqIOListener</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/RichSeqIOAdapter.html#getCurrentFeature()">getCurrentFeature()</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/RichSeqIOAdapter.html" title="class in org.biojavax.bio.seq.io">RichSeqIOAdapter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/RichSeqIOListener.html#getCurrentFeature()">getCurrentFeature()</a></span> - Method in interface org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/RichSeqIOListener.html" title="interface in org.biojavax.bio.seq.io">RichSeqIOListener</a></dt>
<dd>
<div class="block">Gets the feature currently being created.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/SimpleRichSequenceBuilder.html#getCurrentFeature()">getCurrentFeature()</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/SimpleRichSequenceBuilder.html" title="class in org.biojavax.bio.seq.io">SimpleRichSequenceBuilder</a></dt>
<dd>
<div class="block">Gets the feature currently being created.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/AtomIterator.html#getCurrentModel()">getCurrentModel()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/AtomIterator.html" title="class in org.biojava.bio.structure">AtomIterator</a></dt>
<dd>
<div class="block">Get the model number of the model containing the current atom.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/GroupIterator.html#getCurrentModel()">getCurrentModel()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/GroupIterator.html" title="class in org.biojava.bio.structure">GroupIterator</a></dt>
<dd>
<div class="block">Get the model number of the current model.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/AbstractTrainer.html#getCurrentScore()">getCurrentScore()</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/AbstractTrainer.html" title="class in org.biojava.bio.dp">AbstractTrainer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/TrainingAlgorithm.html#getCurrentScore()">getCurrentScore()</a></span> - Method in interface org.biojava.bio.dp.<a href="./org/biojava/bio/dp/TrainingAlgorithm.html" title="interface in org.biojava.bio.dp">TrainingAlgorithm</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/functions/SelectionFunction.Threshold.html#getCutoff()">getCutoff()</a></span> - Method in class org.biojavax.ga.functions.<a href="./org/biojavax/ga/functions/SelectionFunction.Threshold.html" title="class in org.biojavax.ga.functions">SelectionFunction.Threshold</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/molbio/RestrictionEnzyme.html#getCutType()">getCutType()</a></span> - Method in class org.biojava.bio.molbio.<a href="./org/biojava/bio/molbio/RestrictionEnzyme.html" title="class in org.biojava.bio.molbio">RestrictionEnzyme</a></dt>
<dd>
<div class="block"><code>getCutType</code> returns the type of cut produced by the
enzyme.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/AbstractTrainer.html#getCycle()">getCycle()</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/AbstractTrainer.html" title="class in org.biojava.bio.dp">AbstractTrainer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/TrainingAlgorithm.html#getCycle()">getCycle()</a></span> - Method in interface org.biojava.bio.dp.<a href="./org/biojava/bio/dp/TrainingAlgorithm.html" title="interface in org.biojava.bio.dp">TrainingAlgorithm</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/jama/EigenvalueDecomposition.html#getD()">getD()</a></span> - Method in class org.biojava.bio.structure.jama.<a href="./org/biojava/bio/structure/jama/EigenvalueDecomposition.html" title="class in org.biojava.bio.structure.jama">EigenvalueDecomposition</a></dt>
<dd>
<div class="block">Return the block diagonal eigenvalue matrix</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/abi/ABIFParser.html#getDataAccess()">getDataAccess()</a></span> - Method in class org.biojava.bio.program.abi.<a href="./org/biojava/bio/program/abi/ABIFParser.html" title="class in org.biojava.bio.program.abi">ABIFParser</a></dt>
<dd>
<div class="block">Returns the accessor for the raw data being parsed by this parser.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/NCBISequenceDB.html#getDataBase()">getDataBase()</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/NCBISequenceDB.html" title="class in org.biojava.bio.seq.db">NCBISequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/DBRef.html#getDatabase()">getDatabase()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/DBRef.html" title="class in org.biojava.bio.structure">DBRef</a></dt>
<dd>
<div class="block">The database of the db-ref.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/directory/Registry.html#getDatabase(java.lang.String)">getDatabase(String)</a></span> - Method in class org.biojava.directory.<a href="./org/biojava/directory/Registry.html" title="class in org.biojava.directory">Registry</a></dt>
<dd>
<div class="block"><code>getDatabase</code> retrieves a database instance known by
a name <code>String</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html#getDatabaseName()">getDatabaseName()</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html" title="class in org.biojavax.bio.seq.io">UniProtCommentParser</a></dt>
<dd>
<div class="block">Getter for property databaseName.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/blast2html/DefaultURLGeneratorFactory.html#getDatabaseURLGenerators()">getDatabaseURLGenerators()</a></span> - Method in class org.biojava.bio.program.blast2html.<a href="./org/biojava/bio/program/blast2html/DefaultURLGeneratorFactory.html" title="class in org.biojava.bio.program.blast2html">DefaultURLGeneratorFactory</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/blast2html/URLGeneratorFactory.html#getDatabaseURLGenerators()">getDatabaseURLGenerators()</a></span> - Method in interface org.biojava.bio.program.blast2html.<a href="./org/biojava/bio/program/blast2html/URLGeneratorFactory.html" title="interface in org.biojava.bio.program.blast2html">URLGeneratorFactory</a></dt>
<dd>
<div class="block">Returns a list of 0, 1 or more <code>DatabaseURLGenerator</code>
The first is used to link from the id in the summary table, all are
used as a list of links in the detail section.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLFormat.Terms.html#getDataClassTerm()">getDataClassTerm()</a></span> - Static method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLFormat.Terms.html" title="class in org.biojavax.bio.seq.io">EMBLFormat.Terms</a></dt>
<dd>
<div class="block">Getter for the Ensembl-specific 'dataClass' term</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.Terms.html#getDataClassTerm()">getDataClassTerm()</a></span> - Static method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.Terms.html" title="class in org.biojavax.bio.seq.io">EMBLxmlFormat.Terms</a></dt>
<dd>
<div class="block">Getter for the Ensembl-specific 'dataClass' term</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.Terms.html#getDataClassTerm()">getDataClassTerm()</a></span> - Static method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.Terms.html" title="class in org.biojavax.bio.seq">RichSequence.Terms</a></dt>
<dd>
<div class="block">Getter for the DataClass term</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/abi/ABIFParser.html#getDataRecord(java.lang.String, int)">getDataRecord(String, int)</a></span> - Method in class org.biojava.bio.program.abi.<a href="./org/biojava/bio/program/abi/ABIFParser.html" title="class in org.biojava.bio.program.abi">ABIFParser</a></dt>
<dd>
<div class="block">Get the entry from the file TOC with the given name and tag number.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/JDBCPooledDataSource.html#getDataSource(java.lang.String, java.lang.String, java.lang.String, java.lang.String)">getDataSource(String, String, String, String)</a></span> - Static method in class org.biojava.utils.<a href="./org/biojava/utils/JDBCPooledDataSource.html" title="class in org.biojava.utils">JDBCPooledDataSource</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/distributed/DistributedSequenceDB.html#getDataSources()">getDataSources()</a></span> - Method in class org.biojava.bio.seq.distributed.<a href="./org/biojava/bio/seq/distributed/DistributedSequenceDB.html" title="class in org.biojava.bio.seq.distributed">DistributedSequenceDB</a></dt>
<dd>
<div class="block">Get the current set of all currently registered data sources.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssaha/CompactedDataStoreFactory.html#getDataStore(java.io.File)">getDataStore(File)</a></span> - Method in class org.biojava.bio.program.ssaha.<a href="./org/biojava/bio/program/ssaha/CompactedDataStoreFactory.html" title="class in org.biojava.bio.program.ssaha">CompactedDataStoreFactory</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssaha/DataStoreFactory.html#getDataStore(java.io.File)">getDataStore(File)</a></span> - Method in interface org.biojava.bio.program.ssaha.<a href="./org/biojava/bio/program/ssaha/DataStoreFactory.html" title="interface in org.biojava.bio.program.ssaha">DataStoreFactory</a></dt>
<dd>
<div class="block">Get a pre-built data store associated with a file.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssaha/MappedDataStoreFactory.html#getDataStore(java.io.File)">getDataStore(File)</a></span> - Method in class org.biojava.bio.program.ssaha.<a href="./org/biojava/bio/program/ssaha/MappedDataStoreFactory.html" title="class in org.biojava.bio.program.ssaha">MappedDataStoreFactory</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssaha/NIODataStoreFactory.html#getDataStore(java.io.File)">getDataStore(File)</a></span> - Method in class org.biojava.bio.program.ssaha.<a href="./org/biojava/bio/program/ssaha/NIODataStoreFactory.html" title="class in org.biojava.bio.program.ssaha">NIODataStoreFactory</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEProperty.html#getDataType()">getDataType()</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEProperty.html" title="class in org.biojava.bio.seq.io.agave">AGAVEProperty</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/DatabasePDBrev.html#getDate()">getDate()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/DatabasePDBrev.html" title="class in org.biojava.bio.structure.io.mmcif.model">DatabasePDBrev</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/DatabasePDBrev.html#getDate_original()">getDate_original()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/DatabasePDBrev.html" title="class in org.biojava.bio.structure.io.mmcif.model">DatabasePDBrev</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.Terms.html#getDateAnnotatedTerm()">getDateAnnotatedTerm()</a></span> - Static method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.Terms.html" title="class in org.biojavax.bio.seq">RichSequence.Terms</a></dt>
<dd>
<div class="block">Getter for the date annotated term</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.Terms.html#getDateCreatedTerm()">getDateCreatedTerm()</a></span> - Static method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.Terms.html" title="class in org.biojavax.bio.seq">RichSequence.Terms</a></dt>
<dd>
<div class="block">Getter for the date created term</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.Terms.html#getDateUpdatedTerm()">getDateUpdatedTerm()</a></span> - Static method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.Terms.html" title="class in org.biojavax.bio.seq">RichSequence.Terms</a></dt>
<dd>
<div class="block">Getter for the date updated term</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/ReferenceServer.html#getDB()">getDB()</a></span> - Method in class org.biojava.bio.program.das.<a href="./org/biojava/bio/program/das/ReferenceServer.html" title="class in org.biojava.bio.program.das">ReferenceServer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/HomologeneBuilder.html#getDB()">getDB()</a></span> - Method in interface org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/HomologeneBuilder.html" title="interface in org.biojava.bio.program.homologene">HomologeneBuilder</a></dt>
<dd>
<div class="block">retrieve the DB that has just been built</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/SimpleHomologeneBuilder.html#getDB()">getDB()</a></span> - Method in class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/SimpleHomologeneBuilder.html" title="class in org.biojava.bio.program.homologene">SimpleHomologeneBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/FetchURL.html#getDB()">getDB()</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/FetchURL.html" title="class in org.biojava.bio.seq.db">FetchURL</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/StructRefSeq.html#getDb_align_beg()">getDb_align_beg()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/StructRefSeq.html" title="class in org.biojava.bio.structure.io.mmcif.model">StructRefSeq</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/StructRefSeq.html#getDb_align_end()">getDb_align_end()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/StructRefSeq.html" title="class in org.biojava.bio.structure.io.mmcif.model">StructRefSeq</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/StructRef.html#getDb_code()">getDb_code()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/StructRef.html" title="class in org.biojava.bio.structure.io.mmcif.model">StructRef</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/StructRef.html#getDb_name()">getDb_name()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/StructRef.html" title="class in org.biojava.bio.structure.io.mmcif.model">StructRef</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/DBRef.html#getDbAccession()">getDbAccession()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/DBRef.html" title="class in org.biojava.bio.structure">DBRef</a></dt>
<dd>
<div class="block">Sequence database accession code.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEDbId.html#getDbCode()">getDbCode()</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEDbId.html" title="class in org.biojava.bio.seq.io.agave">AGAVEDbId</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/biosql/DBHelper.html#getDBHelper(java.sql.Connection)">getDBHelper(Connection)</a></span> - Static method in class org.biojava.bio.seq.db.biosql.<a href="./org/biojava/bio/seq/db/biosql/DBHelper.html" title="class in org.biojava.bio.seq.db.biosql">DBHelper</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Returns a DBHelper implementation suitable for a particular
database.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/Agave2AgaveAnnotFilter.html#getDbId(org.biojava.bio.Annotation)">getDbId(Annotation)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/Agave2AgaveAnnotFilter.html" title="class in org.biojava.bio.seq.io.agave">Agave2AgaveAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEAnnotFilter.html#getDbId(org.biojava.bio.Annotation)">getDbId(Annotation)</a></span> - Method in interface org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEAnnotFilter.html" title="interface in org.biojava.bio.seq.io.agave">AGAVEAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEMatchRegion.html#getDbId()">getDbId()</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEMatchRegion.html" title="class in org.biojava.bio.seq.io.agave">AGAVEMatchRegion</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEQueryRegion.html#getDbId()">getDbId()</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEQueryRegion.html" title="class in org.biojava.bio.seq.io.agave">AGAVEQueryRegion</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEXref.html#getDbId()">getDbId()</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEXref.html" title="class in org.biojava.bio.seq.io.agave">AGAVEXref</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/Embl2AgaveAnnotFilter.html#getDbId(org.biojava.bio.Annotation)">getDbId(Annotation)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/Embl2AgaveAnnotFilter.html" title="class in org.biojava.bio.seq.io.agave">Embl2AgaveAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/SimpleAnnotFilter.html#getDbId(org.biojava.bio.Annotation)">getDbId(Annotation)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/SimpleAnnotFilter.html" title="class in org.biojava.bio.seq.io.agave">SimpleAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/DBRef.html#getDbIdCode()">getDbIdCode()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/DBRef.html" title="class in org.biojava.bio.structure">DBRef</a></dt>
<dd>
<div class="block">Sequence database identification code.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEMapPosition.html#getDbIds()">getDbIds()</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEMapPosition.html" title="class in org.biojava.bio.seq.io.agave">AGAVEMapPosition</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEXrefs.html#getDbIds()">getDbIds()</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEXrefs.html" title="class in org.biojava.bio.seq.io.agave">AGAVEXrefs</a></dt>
<dd>
<div class="block">return a set of DbId</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/CrossRef.html#getDbname()">getDbname()</a></span> - Method in interface org.biojavax.<a href="./org/biojavax/CrossRef.html" title="interface in org.biojavax">CrossRef</a></dt>
<dd>
<div class="block">Returns the name of the database the cross reference refers to.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleCrossRef.html#getDbname()">getDbname()</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleCrossRef.html" title="class in org.biojavax">SimpleCrossRef</a></dt>
<dd>
<div class="block">Returns the name of the database the cross reference refers to.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Structure.html#getDBRefs()">getDBRefs()</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Structure.html" title="interface in org.biojava.bio.structure">Structure</a></dt>
<dd>
<div class="block">get the list of database references</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/StructureImpl.html#getDBRefs()">getDBRefs()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/StructureImpl.html" title="class in org.biojava.bio.structure">StructureImpl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/StrucAligParameters.html#getDBSearchParameters()">getDBSearchParameters()</a></span> - Static method in class org.biojava.bio.structure.align.<a href="./org/biojava/bio/structure/align/StrucAligParameters.html" title="class in org.biojava.bio.structure.align">StrucAligParameters</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/DBRef.html#getDbSeqBegin()">getDbSeqBegin()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/DBRef.html" title="class in org.biojava.bio.structure">DBRef</a></dt>
<dd>
<div class="block">Initial sequence number of the
database seqment.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/DBRef.html#getDbSeqEnd()">getDbSeqEnd()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/DBRef.html" title="class in org.biojava.bio.structure">DBRef</a></dt>
<dd>
<div class="block">Ending sequence position of the database segment.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/biosql/TaxonSQL.html#getDBTaxon(java.sql.Connection, int)">getDBTaxon(Connection, int)</a></span> - Static method in class org.biojava.bio.seq.db.biosql.<a href="./org/biojava/bio/seq/db/biosql/TaxonSQL.html" title="class in org.biojava.bio.seq.db.biosql">TaxonSQL</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Attempts to get a Taxon object corresponding to the specified
taxon_id (i.e.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game/GAMEDbxrefPropHandler.DbXrefElement.html#getDbXrefId()">getDbXrefId()</a></span> - Method in class org.biojava.bio.seq.io.game.<a href="./org/biojava/bio/seq/io/game/GAMEDbxrefPropHandler.DbXrefElement.html" title="class in org.biojava.bio.seq.io.game">GAMEDbxrefPropHandler.DbXrefElement</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/obo/OboFileParser.html#getDbxrefList(java.lang.String, int, int)">getDbxrefList(String, int, int)</a></span> - Method in class org.biojava.ontology.obo.<a href="./org/biojava/ontology/obo/OboFileParser.html" title="class in org.biojava.ontology.obo">OboFileParser</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AbstractLocation.html#getDecorator(java.lang.Class)">getDecorator(Class)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AbstractLocation.html" title="class in org.biojava.bio.symbol">AbstractLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AbstractLocationDecorator.html#getDecorator(java.lang.Class)">getDecorator(Class)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AbstractLocationDecorator.html" title="class in org.biojava.bio.symbol">AbstractLocationDecorator</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/Location.html#getDecorator(java.lang.Class)">getDecorator(Class)</a></span> - Method in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/Location.html" title="interface in org.biojava.bio.symbol">Location</a></dt>
<dd>
<div class="block">Checks the decorator chain for an instance of <class>decoratorClass</class>
and return it if found.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/CompoundRichLocation.html#getDecorator(java.lang.Class)">getDecorator(Class)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/CompoundRichLocation.html" title="class in org.biojavax.bio.seq">CompoundRichLocation</a></dt>
<dd>
<div class="block">Checks the decorator chain for an instance of <class>decoratorClass</class>
and return it if found.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/EmptyRichLocation.html#getDecorator(java.lang.Class)">getDecorator(Class)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/EmptyRichLocation.html" title="class in org.biojavax.bio.seq">EmptyRichLocation</a></dt>
<dd>
<div class="block">Checks the decorator chain for an instance of <class>decoratorClass</class>
and return it if found.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichLocation.html#getDecorator(java.lang.Class)">getDecorator(Class)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichLocation.html" title="class in org.biojavax.bio.seq">SimpleRichLocation</a></dt>
<dd>
<div class="block">Checks the decorator chain for an instance of <class>decoratorClass</class>
and return it if found.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/ValueChanger.html#getDefaultChanger()">getDefaultChanger()</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/ValueChanger.html" title="class in org.biojava.bio.program.tagvalue">ValueChanger</a></dt>
<dd>
<div class="block">Get the changer that will be applied to values of tags with no specific
handler registered.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/AnnotationType.html#getDefaultConstraint()">getDefaultConstraint()</a></span> - Method in interface org.biojava.bio.<a href="./org/biojava/bio/AnnotationType.html" title="interface in org.biojava.bio">AnnotationType</a></dt>
<dd>
<div class="block">Get the CollectionConstraint that will be applied to all properties without
an explicit binding.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/AnnotationType.Impl.html#getDefaultConstraint()">getDefaultConstraint()</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/AnnotationType.Impl.html" title="class in org.biojava.bio">AnnotationType.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/RichObjectFactory.html#getDefaultCrossReferenceResolver()">getDefaultCrossReferenceResolver()</a></span> - Static method in class org.biojavax.<a href="./org/biojavax/RichObjectFactory.html" title="class in org.biojavax">RichObjectFactory</a></dt>
<dd>
<div class="block">Returns the default cross ref resolver object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/OntoTools.html#getDefaultFactory()">getDefaultFactory()</a></span> - Static method in class org.biojava.ontology.<a href="./org/biojava/ontology/OntoTools.html" title="class in org.biojava.ontology">OntoTools</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/phred/PhredFormat.html#getDefaultFormat()">getDefaultFormat()</a></span> - Method in class org.biojava.bio.program.phred.<a href="./org/biojava/bio/program/phred/PhredFormat.html" title="class in org.biojava.bio.program.phred">PhredFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span> </div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/EmblLikeFormat.html#getDefaultFormat()">getDefaultFormat()</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/EmblLikeFormat.html" title="class in org.biojava.bio.seq.io">EmblLikeFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span> </div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/FastaFormat.html#getDefaultFormat()">getDefaultFormat()</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/FastaFormat.html" title="class in org.biojava.bio.seq.io">FastaFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span> </div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/GAMEFormat.html#getDefaultFormat()">getDefaultFormat()</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/GAMEFormat.html" title="class in org.biojava.bio.seq.io">GAMEFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span> </div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/GenbankFormat.html#getDefaultFormat()">getDefaultFormat()</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/GenbankFormat.html" title="class in org.biojava.bio.seq.io">GenbankFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span> </div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/GenbankXmlFormat.html#getDefaultFormat()">getDefaultFormat()</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/GenbankXmlFormat.html" title="class in org.biojava.bio.seq.io">GenbankXmlFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/GenpeptFormat.html#getDefaultFormat()">getDefaultFormat()</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/GenpeptFormat.html" title="class in org.biojava.bio.seq.io">GenpeptFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SequenceFormat.html#getDefaultFormat()">getDefaultFormat()</a></span> - Method in interface org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SequenceFormat.html" title="interface in org.biojava.bio.seq.io">SequenceFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>new implementations should only write a single
format.</i></div>
</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLFormat.html#getDefaultFormat()">getDefaultFormat()</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLFormat.html" title="class in org.biojavax.bio.seq.io">EMBLFormat</a></dt>
<dd>
<div class="block"><code>getDefaultFormat</code> returns the String identifier for
the default sub-format written by a <code>SequenceFormat</code>
implementation.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html#getDefaultFormat()">getDefaultFormat()</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html" title="class in org.biojavax.bio.seq.io">EMBLxmlFormat</a></dt>
<dd>
<div class="block"><code>getDefaultFormat</code> returns the String identifier for
the default sub-format written by a <code>SequenceFormat</code>
implementation.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/FastaFormat.html#getDefaultFormat()">getDefaultFormat()</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/FastaFormat.html" title="class in org.biojavax.bio.seq.io">FastaFormat</a></dt>
<dd>
<div class="block"><code>getDefaultFormat</code> returns the String identifier for
the default sub-format written by a <code>SequenceFormat</code>
implementation.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/GenbankFormat.html#getDefaultFormat()">getDefaultFormat()</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/GenbankFormat.html" title="class in org.biojavax.bio.seq.io">GenbankFormat</a></dt>
<dd>
<div class="block"><code>getDefaultFormat</code> returns the String identifier for
the default sub-format written by a <code>SequenceFormat</code>
implementation.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/INSDseqFormat.html#getDefaultFormat()">getDefaultFormat()</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/INSDseqFormat.html" title="class in org.biojavax.bio.seq.io">INSDseqFormat</a></dt>
<dd>
<div class="block"><code>getDefaultFormat</code> returns the String identifier for
the default sub-format written by a <code>SequenceFormat</code>
implementation.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtFormat.html#getDefaultFormat()">getDefaultFormat()</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtFormat.html" title="class in org.biojavax.bio.seq.io">UniProtFormat</a></dt>
<dd>
<div class="block"><code>getDefaultFormat</code> returns the String identifier for
the default sub-format written by a <code>SequenceFormat</code>
implementation.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#getDefaultFormat()">getDefaultFormat()</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd>
<div class="block"><code>getDefaultFormat</code> returns the String identifier for
the default sub-format written by a <code>SequenceFormat</code>
implementation.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/RichObjectFactory.html#getDefaultNamespace()">getDefaultNamespace()</a></span> - Static method in class org.biojavax.<a href="./org/biojavax/RichObjectFactory.html" title="class in org.biojavax">RichObjectFactory</a></dt>
<dd>
<div class="block">Returns the default namespace object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/RichObjectFactory.html#getDefaultOntology()">getDefaultOntology()</a></span> - Static method in class org.biojavax.<a href="./org/biojavax/RichObjectFactory.html" title="class in org.biojavax">RichObjectFactory</a></dt>
<dd>
<div class="block">Returns the default ontology object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PeptideDigestRenderer.html#getDefaultPaint()">getDefaultPaint()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PeptideDigestRenderer.html" title="class in org.biojava.bio.gui.sequence">PeptideDigestRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/StrucAligParameters.html#getDefaultParameters()">getDefaultParameters()</a></span> - Static method in class org.biojava.bio.structure.align.<a href="./org/biojava/bio/structure/align/StrucAligParameters.html" title="class in org.biojava.bio.structure.align">StrucAligParameters</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/RichObjectFactory.html#getDefaultPositionResolver()">getDefaultPositionResolver()</a></span> - Static method in class org.biojavax.<a href="./org/biojavax/RichObjectFactory.html" title="class in org.biojavax">RichObjectFactory</a></dt>
<dd>
<div class="block">Returns the default position resolver object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/RichObjectFactory.html#getDefaultRichSequenceHandler()">getDefaultRichSequenceHandler()</a></span> - Static method in class org.biojavax.<a href="./org/biojavax/RichObjectFactory.html" title="class in org.biojavax">RichObjectFactory</a></dt>
<dd>
<div class="block">Returns the default sequence resolver object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/ValueChanger.html#getDefaultSplitter()">getDefaultSplitter()</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/ValueChanger.html" title="class in org.biojava.bio.program.tagvalue">ValueChanger</a></dt>
<dd>
<div class="block">Get the splitter that will be applied to values of tags with no specific
handler registered.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/AbstractWrapper.html#getDelegate()">getDelegate()</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/AbstractWrapper.html" title="class in org.biojava.bio.program.tagvalue">AbstractWrapper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/SimpleTagValueWrapper.html#getDelegate()">getDelegate()</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/SimpleTagValueWrapper.html" title="class in org.biojava.bio.program.tagvalue">SimpleTagValueWrapper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/StateMachine.html#getDelegate()">getDelegate()</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/StateMachine.html" title="class in org.biojava.bio.program.tagvalue">StateMachine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/TagValueWrapper.html#getDelegate()">getDelegate()</a></span> - Method in interface org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/TagValueWrapper.html" title="interface in org.biojava.bio.program.tagvalue">TagValueWrapper</a></dt>
<dd>
<div class="block">get listener to which all calls will be delegated</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOFilter.html#getDelegate()">getDelegate()</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOFilter.html" title="class in org.biojava.bio.seq.io">SeqIOFilter</a></dt>
<dd>
<div class="block">Retrieve the delegate that is wrapped.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SequenceBuilderFilter.html#getDelegate()">getDelegate()</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SequenceBuilderFilter.html" title="class in org.biojava.bio.seq.io">SequenceBuilderFilter</a></dt>
<dd>
<div class="block">Retrieve the delegate that is wrapped.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SoftMaskedAlphabet.html#getDelegate()">getDelegate()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SoftMaskedAlphabet.html" title="class in org.biojava.bio.symbol">SoftMaskedAlphabet</a></dt>
<dd>
<div class="block">The compound alpha that holds the symbols used by this wrapper</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/TagDelegator.html#getDelegateParser()">getDelegateParser()</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/TagDelegator.html" title="class in org.biojava.bio.program.tagvalue">TagDelegator</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/NeedlemanWunsch.html#getDelete()">getDelete()</a></span> - Method in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/NeedlemanWunsch.html" title="class in org.biojava.bio.alignment">NeedlemanWunsch</a></dt>
<dd>
<div class="block">Returns the current expenses of a single delete operation.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/ProfileHMM.html#getDelete(int)">getDelete(int)</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/ProfileHMM.html" title="class in org.biojava.bio.dp">ProfileHMM</a></dt>
<dd>
<div class="block">Retrieves the delete state for column indx.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/biosql/DBHelper.html#getDeleteStyle()">getDeleteStyle()</a></span> - Method in class org.biojava.bio.seq.db.biosql.<a href="./org/biojava/bio/seq/db/biosql/DBHelper.html" title="class in org.biojava.bio.seq.db.biosql">DBHelper</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Returns the an object indicating the style of deletion that
this database should employ.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/biosql/MySQLDBHelper.html#getDeleteStyle()">getDeleteStyle()</a></span> - Method in class org.biojava.bio.seq.db.biosql.<a href="./org/biojava/bio/seq/db/biosql/MySQLDBHelper.html" title="class in org.biojava.bio.seq.db.biosql">MySQLDBHelper</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/biosql/PostgreSQLDBHelper.html#getDeleteStyle()">getDeleteStyle()</a></span> - Method in class org.biojava.bio.seq.db.biosql.<a href="./org/biojava/bio/seq/db/biosql/PostgreSQLDBHelper.html" title="class in org.biojava.bio.seq.db.biosql">PostgreSQLDBHelper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/biosql/UnknownDBHelper.html#getDeleteStyle()">getDeleteStyle()</a></span> - Method in class org.biojava.bio.seq.db.biosql.<a href="./org/biojava/bio/seq/db/biosql/UnknownDBHelper.html" title="class in org.biojava.bio.seq.db.biosql">UnknownDBHelper</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/StrucAligParameters.html#getDensityCutoff()">getDensityCutoff()</a></span> - Method in class org.biojava.bio.structure.align.<a href="./org/biojava/bio/structure/align/StrucAligParameters.html" title="class in org.biojava.bio.structure.align">StrucAligParameters</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/PDBHeader.html#getDepDate()">getDepDate()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/PDBHeader.html" title="class in org.biojava.bio.structure">PDBHeader</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/twohead/AbstractMatrixPairDPCursor.html#getDepth()">getDepth()</a></span> - Method in class org.biojava.bio.dp.twohead.<a href="./org/biojava/bio/dp/twohead/AbstractMatrixPairDPCursor.html" title="class in org.biojava.bio.dp.twohead">AbstractMatrixPairDPCursor</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/twohead/LightPairDPCursor.html#getDepth()">getDepth()</a></span> - Method in class org.biojava.bio.dp.twohead.<a href="./org/biojava/bio/dp/twohead/LightPairDPCursor.html" title="class in org.biojava.bio.dp.twohead">LightPairDPCursor</a></dt>
<dd>
<div class="block">Gets the Depth attribute of the LightPairDPCursor object</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/twohead/PairDPCursor.html#getDepth()">getDepth()</a></span> - Method in interface org.biojava.bio.dp.twohead.<a href="./org/biojava/bio/dp/twohead/PairDPCursor.html" title="interface in org.biojava.bio.dp.twohead">PairDPCursor</a></dt>
<dd>
<div class="block">retrieve the depth of this cursor</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/AbiTraceRenderer.html#getDepth(org.biojava.bio.gui.sequence.SequenceRenderContext)">getDepth(SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/AbiTraceRenderer.html" title="class in org.biojava.bio.gui.sequence">AbiTraceRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/AbstractBeadRenderer.html#getDepth(org.biojava.bio.gui.sequence.SequenceRenderContext)">getDepth(SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/AbstractBeadRenderer.html" title="class in org.biojava.bio.gui.sequence">AbstractBeadRenderer</a></dt>
<dd>
<div class="block"><code>getDepth</code> calculates the depth required by this
renderer to display its beads.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/AlignmentRenderer.html#getDepth(org.biojava.bio.gui.sequence.SequenceRenderContext)">getDepth(SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/AlignmentRenderer.html" title="class in org.biojava.bio.gui.sequence">AlignmentRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/ArrowedFeatureRenderer.html#getDepth(org.biojava.bio.gui.sequence.SequenceRenderContext)">getDepth(SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/ArrowedFeatureRenderer.html" title="class in org.biojava.bio.gui.sequence">ArrowedFeatureRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/BasicFeatureRenderer.html#getDepth(org.biojava.bio.gui.sequence.SequenceRenderContext)">getDepth(SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/BasicFeatureRenderer.html" title="class in org.biojava.bio.gui.sequence">BasicFeatureRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/BasicImapRenderer.html#getDepth(org.biojava.bio.gui.sequence.SequenceRenderContext)">getDepth(SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/BasicImapRenderer.html" title="class in org.biojava.bio.gui.sequence">BasicImapRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/BumpedRenderer.html#getDepth(org.biojava.bio.gui.sequence.SequenceRenderContext)">getDepth(SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/BumpedRenderer.html" title="class in org.biojava.bio.gui.sequence">BumpedRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/CircularFeatureFilteringRenderer.html#getDepth(org.biojava.bio.gui.sequence.CircularRendererContext)">getDepth(CircularRendererContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/CircularFeatureFilteringRenderer.html" title="class in org.biojava.bio.gui.sequence">CircularFeatureFilteringRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/CircularFeatureRenderer.html#getDepth(org.biojava.bio.gui.sequence.CircularRendererContext)">getDepth(CircularRendererContext)</a></span> - Method in interface org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/CircularFeatureRenderer.html" title="interface in org.biojava.bio.gui.sequence">CircularFeatureRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/CircularFeaturesRenderer.html#getDepth(org.biojava.bio.gui.sequence.CircularRendererContext)">getDepth(CircularRendererContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/CircularFeaturesRenderer.html" title="class in org.biojava.bio.gui.sequence">CircularFeaturesRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/CircularMLR.html#getDepth(org.biojava.bio.gui.sequence.CircularRendererContext)">getDepth(CircularRendererContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/CircularMLR.html" title="class in org.biojava.bio.gui.sequence">CircularMLR</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/CircularPaddedRenderer.html#getDepth(org.biojava.bio.gui.sequence.CircularRendererContext)">getDepth(CircularRendererContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/CircularPaddedRenderer.html" title="class in org.biojava.bio.gui.sequence">CircularPaddedRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/CircularRenderer.html#getDepth(org.biojava.bio.gui.sequence.CircularRendererContext)">getDepth(CircularRendererContext)</a></span> - Method in interface org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/CircularRenderer.html" title="interface in org.biojava.bio.gui.sequence">CircularRenderer</a></dt>
<dd>
<div class="block">Get the depth needed for this renderer.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/EllipticalBeadRenderer.html#getDepth(org.biojava.bio.gui.sequence.SequenceRenderContext)">getDepth(SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/EllipticalBeadRenderer.html" title="class in org.biojava.bio.gui.sequence">EllipticalBeadRenderer</a></dt>
<dd>
<div class="block"><code>getDepth</code> calculates the depth required by this
renderer to display its beads.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/FeatureBlockSequenceRenderer.html#getDepth(org.biojava.bio.gui.sequence.SequenceRenderContext)">getDepth(SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/FeatureBlockSequenceRenderer.html" title="class in org.biojava.bio.gui.sequence">FeatureBlockSequenceRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/FeatureLabelRenderer.html#getDepth(org.biojava.bio.gui.sequence.SequenceRenderContext)">getDepth(SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/FeatureLabelRenderer.html" title="class in org.biojava.bio.gui.sequence">FeatureLabelRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/FeatureRenderer.html#getDepth(org.biojava.bio.gui.sequence.SequenceRenderContext)">getDepth(SequenceRenderContext)</a></span> - Method in interface org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/FeatureRenderer.html" title="interface in org.biojava.bio.gui.sequence">FeatureRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/FilteringRenderer.html#getDepth(org.biojava.bio.gui.sequence.SequenceRenderContext)">getDepth(SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/FilteringRenderer.html" title="class in org.biojava.bio.gui.sequence">FilteringRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/GappedRenderer.html#getDepth(org.biojava.bio.gui.sequence.SequenceRenderContext)">getDepth(SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/GappedRenderer.html" title="class in org.biojava.bio.gui.sequence">GappedRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/GlyphFeatureRenderer.html#getDepth(org.biojava.bio.gui.sequence.SequenceRenderContext)">getDepth(SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/GlyphFeatureRenderer.html" title="class in org.biojava.bio.gui.sequence">GlyphFeatureRenderer</a></dt>
<dd>
<div class="block">Returns the depth property of this class.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/LabelledSequenceRenderer.html#getDepth(org.biojava.bio.gui.sequence.SequenceRenderContext)">getDepth(SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/LabelledSequenceRenderer.html" title="class in org.biojava.bio.gui.sequence">LabelledSequenceRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/LayeredRenderer.html#getDepth(java.util.List, java.util.List)">getDepth(List, List)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/LayeredRenderer.html" title="class in org.biojava.bio.gui.sequence">LayeredRenderer</a></dt>
<dd>
<div class="block"><code>getDepth</code> returns the total depth of a list of
<code>SequenceRenderer</code>s.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/LineInfo.html#getDepth(org.biojava.bio.gui.sequence.SequenceRenderer)">getDepth(SequenceRenderer)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/LineInfo.html" title="class in org.biojava.bio.gui.sequence">LineInfo</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/MultiLineRenderer.html#getDepth(org.biojava.bio.gui.sequence.SequenceRenderContext)">getDepth(SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/MultiLineRenderer.html" title="class in org.biojava.bio.gui.sequence">MultiLineRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/OffsetRulerRenderer.html#getDepth(org.biojava.bio.gui.sequence.SequenceRenderContext)">getDepth(SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/OffsetRulerRenderer.html" title="class in org.biojava.bio.gui.sequence">OffsetRulerRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/OverlayRendererWrapper.html#getDepth(org.biojava.bio.gui.sequence.SequenceRenderContext)">getDepth(SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/OverlayRendererWrapper.html" title="class in org.biojava.bio.gui.sequence">OverlayRendererWrapper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PaddingRenderer.html#getDepth(org.biojava.bio.gui.sequence.SequenceRenderContext)">getDepth(SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PaddingRenderer.html" title="class in org.biojava.bio.gui.sequence">PaddingRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/RectangularBeadRenderer.html#getDepth(org.biojava.bio.gui.sequence.SequenceRenderContext)">getDepth(SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/RectangularBeadRenderer.html" title="class in org.biojava.bio.gui.sequence">RectangularBeadRenderer</a></dt>
<dd>
<div class="block"><code>getDepth</code> calculates the depth required by this
renderer to display its beads.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/RectangularImapRenderer.html#getDepth(org.biojava.bio.gui.sequence.SequenceRenderContext)">getDepth(SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/RectangularImapRenderer.html" title="class in org.biojava.bio.gui.sequence">RectangularImapRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/RoundRectangularBeadRenderer.html#getDepth(org.biojava.bio.gui.sequence.SequenceRenderContext)">getDepth(SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/RoundRectangularBeadRenderer.html" title="class in org.biojava.bio.gui.sequence">RoundRectangularBeadRenderer</a></dt>
<dd>
<div class="block"><code>getDepth</code> calculates the depth required by this
renderer to display its beads.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/RulerRenderer.html#getDepth(org.biojava.bio.gui.sequence.SequenceRenderContext)">getDepth(SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/RulerRenderer.html" title="class in org.biojava.bio.gui.sequence">RulerRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequenceRenderer.html#getDepth(org.biojava.bio.gui.sequence.SequenceRenderContext)">getDepth(SequenceRenderContext)</a></span> - Method in interface org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequenceRenderer.html" title="interface in org.biojava.bio.gui.sequence">SequenceRenderer</a></dt>
<dd>
<div class="block">Retrieve the depth of this renderer when rendering src.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequenceRendererWrapper.html#getDepth(org.biojava.bio.gui.sequence.SequenceRenderContext)">getDepth(SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequenceRendererWrapper.html" title="class in org.biojava.bio.gui.sequence">SequenceRendererWrapper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SixFrameRenderer.html#getDepth(org.biojava.bio.gui.sequence.SequenceRenderContext)">getDepth(SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SixFrameRenderer.html" title="class in org.biojava.bio.gui.sequence">SixFrameRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SixFrameZiggyRenderer.html#getDepth(org.biojava.bio.gui.sequence.SequenceRenderContext)">getDepth(SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SixFrameZiggyRenderer.html" title="class in org.biojava.bio.gui.sequence">SixFrameZiggyRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/StackedFeatureRenderer.html#getDepth(org.biojava.bio.gui.sequence.SequenceRenderContext)">getDepth(SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/StackedFeatureRenderer.html" title="class in org.biojava.bio.gui.sequence">StackedFeatureRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/StopRenderer.html#getDepth(org.biojava.bio.gui.sequence.SequenceRenderContext)">getDepth(SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/StopRenderer.html" title="class in org.biojava.bio.gui.sequence">StopRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SymbolSequenceRenderer.html#getDepth(org.biojava.bio.gui.sequence.SequenceRenderContext)">getDepth(SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SymbolSequenceRenderer.html" title="class in org.biojava.bio.gui.sequence">SymbolSequenceRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/TickFeatureRenderer.html#getDepth()">getDepth()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/TickFeatureRenderer.html" title="class in org.biojava.bio.gui.sequence">TickFeatureRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/TickFeatureRenderer.html#getDepth(org.biojava.bio.gui.sequence.SequenceRenderContext)">getDepth(SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/TickFeatureRenderer.html" title="class in org.biojava.bio.gui.sequence">TickFeatureRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/ZiggyFeatureRenderer.html#getDepth(org.biojava.bio.gui.sequence.SequenceRenderContext)">getDepth(SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/ZiggyFeatureRenderer.html" title="class in org.biojava.bio.gui.sequence">ZiggyFeatureRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/ZiggyImapRenderer.html#getDepth(org.biojava.bio.gui.sequence.SequenceRenderContext)">getDepth(SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/ZiggyImapRenderer.html" title="class in org.biojava.bio.gui.sequence">ZiggyImapRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/tools/SuffixTreeKernel.html#getDepthScaler()">getDepthScaler()</a></span> - Method in class org.biojava.stats.svm.tools.<a href="./org/biojava/stats/svm/tools/SuffixTreeKernel.html" title="class in org.biojava.stats.svm.tools">SuffixTreeKernel</a></dt>
<dd>
<div class="block">Retrieve the current <span class="type">DepthScaler</span>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/SubstitutionMatrix.html#getDescription()">getDescription()</a></span> - Method in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/SubstitutionMatrix.html" title="class in org.biojava.bio.alignment">SubstitutionMatrix</a></dt>
<dd>
<div class="block">This gives you the description of this matrix if there is one.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/DataSource.html#getDescription()">getDescription()</a></span> - Method in class org.biojava.bio.program.das.<a href="./org/biojava/bio/program/das/DataSource.html" title="class in org.biojava.bio.program.das">DataSource</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/fastq/Fastq.html#getDescription()">getDescription()</a></span> - Method in class org.biojava.bio.program.fastq.<a href="./org/biojava/bio/program/fastq/Fastq.html" title="class in org.biojava.bio.program.fastq">Fastq</a></dt>
<dd>
<div class="block">Return the description of this FASTQ formatted sequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/fastq/FastqBuilder.html#getDescription()">getDescription()</a></span> - Method in class org.biojava.bio.program.fastq.<a href="./org/biojava/bio/program/fastq/FastqBuilder.html" title="class in org.biojava.bio.program.fastq">FastqBuilder</a></dt>
<dd>
<div class="block">Return the description for this FASTQ formatted sequence builder.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/fastq/FastqVariant.html#getDescription()">getDescription()</a></span> - Method in enum org.biojava.bio.program.fastq.<a href="./org/biojava/bio/program/fastq/FastqVariant.html" title="enum in org.biojava.bio.program.fastq">FastqVariant</a></dt>
<dd>
<div class="block">Return the description of this FASTQ sequence format variant.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/SimilarityType.PlaceHolder.html#getDescription()">getDescription()</a></span> - Method in class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/SimilarityType.PlaceHolder.html" title="class in org.biojava.bio.program.homologene">SimilarityType.PlaceHolder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/Taxon.html#getDescription()">getDescription()</a></span> - Method in interface org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/Taxon.html" title="interface in org.biojava.bio.program.homologene">Taxon</a></dt>
<dd>
<div class="block">returns the name of the Taxon</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/Taxon.TaxonStub.html#getDescription()">getDescription()</a></span> - Method in class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/Taxon.TaxonStub.html" title="class in org.biojava.bio.program.homologene">Taxon.TaxonStub</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/aaindex/AAindex.html#getDescription()">getDescription()</a></span> - Method in class org.biojava.bio.proteomics.aaindex.<a href="./org/biojava/bio/proteomics/aaindex/AAindex.html" title="class in org.biojava.bio.proteomics.aaindex">AAindex</a></dt>
<dd>
<div class="block">Gets the description for the AAindex entry.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/Agave2AgaveAnnotFilter.html#getDescription(org.biojava.bio.Annotation)">getDescription(Annotation)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/Agave2AgaveAnnotFilter.html" title="class in org.biojava.bio.seq.io.agave">Agave2AgaveAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEAnnotFilter.html#getDescription(org.biojava.bio.Annotation)">getDescription(Annotation)</a></span> - Method in interface org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEAnnotFilter.html" title="interface in org.biojava.bio.seq.io.agave">AGAVEAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/Embl2AgaveAnnotFilter.html#getDescription(org.biojava.bio.Annotation)">getDescription(Annotation)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/Embl2AgaveAnnotFilter.html" title="class in org.biojava.bio.seq.io.agave">Embl2AgaveAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/SimpleAnnotFilter.html#getDescription(org.biojava.bio.Annotation)">getDescription(Annotation)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/SimpleAnnotFilter.html" title="class in org.biojava.bio.seq.io.agave">SimpleAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/PDBHeader.html#getDescription()">getDescription()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/PDBHeader.html" title="class in org.biojava.bio.structure">PDBHeader</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleGeneticCodeTable.html#getDescription()">getDescription()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleGeneticCodeTable.html" title="class in org.biojava.bio.symbol">SimpleGeneticCodeTable</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/IntegerOntology.html#getDescription()">getDescription()</a></span> - Method in class org.biojava.ontology.<a href="./org/biojava/ontology/IntegerOntology.html" title="class in org.biojava.ontology">IntegerOntology</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/IntegerOntology.IntTerm.html#getDescription()">getDescription()</a></span> - Method in class org.biojava.ontology.<a href="./org/biojava/ontology/IntegerOntology.IntTerm.html" title="class in org.biojava.ontology">IntegerOntology.IntTerm</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/Ontology.html#getDescription()">getDescription()</a></span> - Method in interface org.biojava.ontology.<a href="./org/biojava/ontology/Ontology.html" title="interface in org.biojava.ontology">Ontology</a></dt>
<dd>
<div class="block">Return a human-readable description of this ontology, or the empty
string if none is available</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/Ontology.Impl.html#getDescription()">getDescription()</a></span> - Method in class org.biojava.ontology.<a href="./org/biojava/ontology/Ontology.Impl.html" title="class in org.biojava.ontology">Ontology.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/OntologyTerm.Impl.html#getDescription()">getDescription()</a></span> - Method in class org.biojava.ontology.<a href="./org/biojava/ontology/OntologyTerm.Impl.html" title="class in org.biojava.ontology">OntologyTerm.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/RemoteTerm.Impl.html#getDescription()">getDescription()</a></span> - Method in class org.biojava.ontology.<a href="./org/biojava/ontology/RemoteTerm.Impl.html" title="class in org.biojava.ontology">RemoteTerm.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/Term.html#getDescription()">getDescription()</a></span> - Method in interface org.biojava.ontology.<a href="./org/biojava/ontology/Term.html" title="interface in org.biojava.ontology">Term</a></dt>
<dd>
<div class="block">Return a human-readable description of this term, or the empty string if
none is available.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/Term.Impl.html#getDescription()">getDescription()</a></span> - Method in class org.biojava.ontology.<a href="./org/biojava/ontology/Term.Impl.html" title="class in org.biojava.ontology">Term.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/Triple.Impl.html#getDescription()">getDescription()</a></span> - Method in class org.biojava.ontology.<a href="./org/biojava/ontology/Triple.Impl.html" title="class in org.biojava.ontology">Triple.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/candy/CandyVocabulary.html#getDescription()">getDescription()</a></span> - Method in interface org.biojava.utils.candy.<a href="./org/biojava/utils/candy/CandyVocabulary.html" title="interface in org.biojava.utils.candy">CandyVocabulary</a></dt>
<dd>
<div class="block">It returns a description of this vocabulary.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/BioEntry.html#getDescription()">getDescription()</a></span> - Method in interface org.biojavax.bio.<a href="./org/biojavax/bio/BioEntry.html" title="interface in org.biojavax.bio">BioEntry</a></dt>
<dd>
<div class="block">Returns a description of this sequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/SimpleBioEntry.html#getDescription()">getDescription()</a></span> - Method in class org.biojavax.bio.<a href="./org/biojavax/bio/SimpleBioEntry.html" title="class in org.biojavax.bio">SimpleBioEntry</a></dt>
<dd>
<div class="block">Returns a description of this sequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/Namespace.html#getDescription()">getDescription()</a></span> - Method in interface org.biojavax.<a href="./org/biojavax/Namespace.html" title="interface in org.biojavax">Namespace</a></dt>
<dd>
<div class="block">Returns a description of this namespace.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ontology/ComparableOntology.html#getDescription()">getDescription()</a></span> - Method in interface org.biojavax.ontology.<a href="./org/biojavax/ontology/ComparableOntology.html" title="interface in org.biojavax.ontology">ComparableOntology</a></dt>
<dd>
<div class="block">Return a human-readable description of this ontology.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ontology/SimpleComparableOntology.html#getDescription()">getDescription()</a></span> - Method in class org.biojavax.ontology.<a href="./org/biojavax/ontology/SimpleComparableOntology.html" title="class in org.biojavax.ontology">SimpleComparableOntology</a></dt>
<dd>
<div class="block">Return a human-readable description of this ontology.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ontology/SimpleComparableTerm.html#getDescription()">getDescription()</a></span> - Method in class org.biojavax.ontology.<a href="./org/biojavax/ontology/SimpleComparableTerm.html" title="class in org.biojavax.ontology">SimpleComparableTerm</a></dt>
<dd>
<div class="block">Return a human-readable description of this term, or the empty string if
none is available.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ontology/SimpleComparableTriple.html#getDescription()">getDescription()</a></span> - Method in class org.biojavax.ontology.<a href="./org/biojavax/ontology/SimpleComparableTriple.html" title="class in org.biojavax.ontology">SimpleComparableTriple</a></dt>
<dd>
<div class="block">Return a human-readable description of this term, or the empty string if
none is available.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleNamespace.html#getDescription()">getDescription()</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleNamespace.html" title="class in org.biojavax">SimpleNamespace</a></dt>
<dd>
<div class="block">Returns a description of this namespace.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ontology/ComparableTriple.html#getDescriptors()">getDescriptors()</a></span> - Method in interface org.biojavax.ontology.<a href="./org/biojavax/ontology/ComparableTriple.html" title="interface in org.biojavax.ontology">ComparableTriple</a></dt>
<dd>
<div class="block">Returns all descriptors.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ontology/SimpleComparableTriple.html#getDescriptors()">getDescriptors()</a></span> - Method in class org.biojavax.ontology.<a href="./org/biojavax/ontology/SimpleComparableTriple.html" title="class in org.biojavax.ontology">SimpleComparableTriple</a></dt>
<dd>
<div class="block">Returns all descriptors.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Compound.html#getDetails()">getDetails()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure">Compound</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Entity.html#getDetails()">getDetails()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Entity.html" title="class in org.biojava.bio.structure.io.mmcif.model">Entity</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Exptl.html#getDetails()">getDetails()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Exptl.html" title="class in org.biojava.bio.structure.io.mmcif.model">Exptl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#getDetails()">getDetails()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/StructAsym.html#getDetails()">getDetails()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/StructAsym.html" title="class in org.biojava.bio.structure.io.mmcif.model">StructAsym</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/StructRefSeq.html#getDetails()">getDetails()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/StructRefSeq.html" title="class in org.biojava.bio.structure.io.mmcif.model">StructRefSeq</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/xff/XFFFeatureSetHandler.html#getDetailsHandler()">getDetailsHandler()</a></span> - Method in class org.biojava.bio.program.xff.<a href="./org/biojava/bio/program/xff/XFFFeatureSetHandler.html" title="class in org.biojava.bio.program.xff">XFFFeatureSetHandler</a></dt>
<dd>
<div class="block">Return a handler for the XFF <code>details</code> element.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/automata/DfaBuilder.html#getDFA()">getDFA()</a></span> - Method in class org.biojava.utils.automata.<a href="./org/biojava/utils/automata/DfaBuilder.html" title="class in org.biojava.utils.automata">DfaBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/helper/AlignTools.html#getDiagonalAtK(org.biojava.bio.structure.Atom[], int)">getDiagonalAtK(Atom[], int)</a></span> - Static method in class org.biojava.bio.structure.align.helper.<a href="./org/biojava/bio/structure/align/helper/AlignTools.html" title="class in org.biojava.bio.structure.align.helper">AlignTools</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/StrucAligParameters.html#getDiagonalDistance()">getDiagonalDistance()</a></span> - Method in class org.biojava.bio.structure.align.<a href="./org/biojava/bio/structure/align/StrucAligParameters.html" title="class in org.biojava.bio.structure.align">StrucAligParameters</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/StrucAligParameters.html#getDiagonalDistance2()">getDiagonalDistance2()</a></span> - Method in class org.biojava.bio.structure.align.<a href="./org/biojava/bio/structure/align/StrucAligParameters.html" title="class in org.biojava.bio.structure.align">StrucAligParameters</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/ChemCompConsumer.html#getDictionary()">getDictionary()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/ChemCompConsumer.html" title="class in org.biojava.bio.structure.io.mmcif">ChemCompConsumer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/SparseVector.html#getDimAtIndex(int)">getDimAtIndex(int)</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/SparseVector.html" title="class in org.biojava.stats.svm">SparseVector</a></dt>
<dd>
<div class="block">Retrieve the dimension at a specific index.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/EllipticalBeadRenderer.html#getDimensionRatio()">getDimensionRatio()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/EllipticalBeadRenderer.html" title="class in org.biojava.bio.gui.sequence">EllipticalBeadRenderer</a></dt>
<dd>
<div class="block"><code>getDimensionRatio</code> returns the maximum ratio of
long dimension to short dimension of the bead.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/CodonPrefTools.html#getDinucleotideAlphabet()">getDinucleotideAlphabet()</a></span> - Static method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/CodonPrefTools.html" title="class in org.biojava.bio.symbol">CodonPrefTools</a></dt>
<dd>
<div class="block">returns an RNA dinucleotide alphabet.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/HeadlessRenderContext.html#getDirection()">getDirection()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/HeadlessRenderContext.html" title="class in org.biojava.bio.gui.sequence">HeadlessRenderContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PairwiseSequencePanel.html#getDirection()">getDirection()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PairwiseSequencePanel.html" title="class in org.biojava.bio.gui.sequence">PairwiseSequencePanel</a></dt>
<dd>
<div class="block"><code>getDirection</code> returns the direction in which this
context expects the sequence to be rendered - HORIZONTAL or
VERTICAL.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePanel.html#getDirection()">getDirection()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePanel.html" title="class in org.biojava.bio.gui.sequence">SequencePanel</a></dt>
<dd>
<div class="block">Retrieve the current rendering direction.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePanelWrapper.html#getDirection()">getDirection()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePanelWrapper.html" title="class in org.biojava.bio.gui.sequence">SequencePanelWrapper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePoster.html#getDirection()">getDirection()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePoster.html" title="class in org.biojava.bio.gui.sequence">SequencePoster</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Retrieve the current rendering direction.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequenceRenderContext.html#getDirection()">getDirection()</a></span> - Method in interface org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequenceRenderContext.html" title="interface in org.biojava.bio.gui.sequence">SequenceRenderContext</a></dt>
<dd>
<div class="block">Gets the direction in which this context expects sequences to be rendered
- HORIZONTAL or VERTICAL.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SubPairwiseRenderContext.html#getDirection()">getDirection()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SubPairwiseRenderContext.html" title="class in org.biojava.bio.gui.sequence">SubPairwiseRenderContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SubSequenceRenderContext.html#getDirection()">getDirection()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SubSequenceRenderContext.html" title="class in org.biojava.bio.gui.sequence">SubSequenceRenderContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/TranslatedSequencePanel.html#getDirection()">getDirection()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/TranslatedSequencePanel.html" title="class in org.biojava.bio.gui.sequence">TranslatedSequencePanel</a></dt>
<dd>
<div class="block"><code>getDirection</code> returns the direction in which this
context expects sequences to be rendered - HORIZONTAL or
VERTICAL.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/taxa/NCBITaxon.html#getDisplayName()">getDisplayName()</a></span> - Method in interface org.biojavax.bio.taxa.<a href="./org/biojavax/bio/taxa/NCBITaxon.html" title="interface in org.biojavax.bio.taxa">NCBITaxon</a></dt>
<dd>
<div class="block">Returns the name of this taxon entry in the form:
scientific (common)
or if there is no common name:
scientific</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/taxa/SimpleNCBITaxon.html#getDisplayName()">getDisplayName()</a></span> - Method in class org.biojavax.bio.taxa.<a href="./org/biojavax/bio/taxa/SimpleNCBITaxon.html" title="class in org.biojavax.bio.taxa">SimpleNCBITaxon</a></dt>
<dd>
<div class="block">Returns the name of this taxon entry in the form:
scientific (common)
or if there is no common name:
scientific
or if there are no scientific names at all, the empty string.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Calc.html#getDistance(org.biojava.bio.structure.Atom, org.biojava.bio.structure.Atom)">getDistance(Atom, Atom)</a></span> - Static method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Calc.html" title="class in org.biojava.bio.structure">Calc</a></dt>
<dd>
<div class="block">calculate distance between two atoms.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/AbstractPeptideDigestRenderer.html#getDistanceBetweenFeatures()">getDistanceBetweenFeatures()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/AbstractPeptideDigestRenderer.html" title="class in org.biojava.bio.gui.sequence">AbstractPeptideDigestRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/helper/AlignTools.html#getDistanceMatrix(org.biojava.bio.structure.Atom[], org.biojava.bio.structure.Atom[])">getDistanceMatrix(Atom[], Atom[])</a></span> - Static method in class org.biojava.bio.structure.align.helper.<a href="./org/biojava/bio/structure/align/helper/AlignTools.html" title="class in org.biojava.bio.structure.align.helper">AlignTools</a></dt>
<dd>
<div class="block">matrix of all distances between two sets of 3d coords"</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/AlternativeAlignment.html#getDistanceMatrix(org.biojava.bio.structure.Atom[], org.biojava.bio.structure.Atom[])">getDistanceMatrix(Atom[], Atom[])</a></span> - Static method in class org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/AlternativeAlignment.html" title="class in org.biojava.bio.structure.align.pairwise">AlternativeAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/AlternativeAlignment.html#getDistanceMatrix()">getDistanceMatrix()</a></span> - Method in class org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/AlternativeAlignment.html" title="class in org.biojava.bio.structure.align.pairwise">AlternativeAlignment</a></dt>
<dd>
<div class="block">The distance matrix this alignment is based on</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/DataSource.html#getDistDataSource()">getDistDataSource()</a></span> - Method in class org.biojava.bio.program.das.<a href="./org/biojava/bio/program/das/DataSource.html" title="class in org.biojava.bio.program.das">DataSource</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/ReferenceServer.html#getDistDataSource()">getDistDataSource()</a></span> - Method in class org.biojava.bio.program.das.<a href="./org/biojava/bio/program/das/ReferenceServer.html" title="class in org.biojava.bio.program.das">ReferenceServer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/StructurePairAligner.html#getDistMat()">getDistMat()</a></span> - Method in class org.biojava.bio.structure.align.<a href="./org/biojava/bio/structure/align/StructurePairAligner.html" title="class in org.biojava.bio.structure.align">StructurePairAligner</a></dt>
<dd>
<div class="block">return the difference of distance matrix between the two structures</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/OrderNDistribution.html#getDistribution(org.biojava.bio.symbol.Symbol)">getDistribution(Symbol)</a></span> - Method in interface org.biojava.bio.dist.<a href="./org/biojava/bio/dist/OrderNDistribution.html" title="interface in org.biojava.bio.dist">OrderNDistribution</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/EmissionState.html#getDistribution()">getDistribution()</a></span> - Method in interface org.biojava.bio.dp.<a href="./org/biojava/bio/dp/EmissionState.html" title="interface in org.biojava.bio.dp">EmissionState</a></dt>
<dd>
<div class="block">
Get the Distribution associated with this state.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/SimpleEmissionState.html#getDistribution()">getDistribution()</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/SimpleEmissionState.html" title="class in org.biojava.bio.dp">SimpleEmissionState</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/DistributionLogo.html#getDistribution()">getDistribution()</a></span> - Method in class org.biojava.bio.gui.<a href="./org/biojava/bio/gui/DistributionLogo.html" title="class in org.biojava.bio.gui">DistributionLogo</a></dt>
<dd>
<div class="block">Retrieve the currently rendered dist.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/LogoContext.html#getDistribution()">getDistribution()</a></span> - Method in interface org.biojava.bio.gui.<a href="./org/biojava/bio/gui/LogoContext.html" title="interface in org.biojava.bio.gui">LogoContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/molbio/Composition.html#getDistribution()">getDistribution()</a></span> - Method in class org.biojava.bio.molbio.<a href="./org/biojava/bio/molbio/Composition.html" title="class in org.biojava.bio.molbio">Composition</a></dt>
<dd>
<div class="block">Returns the distribution backing this class.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/BioEntry.html#getDivision()">getDivision()</a></span> - Method in interface org.biojavax.bio.<a href="./org/biojavax/bio/BioEntry.html" title="interface in org.biojavax.bio">BioEntry</a></dt>
<dd>
<div class="block">Returns the division of this bioentry.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/SimpleBioEntry.html#getDivision()">getDivision()</a></span> - Method in class org.biojavax.bio.<a href="./org/biojavax/bio/SimpleBioEntry.html" title="class in org.biojavax.bio">SimpleBioEntry</a></dt>
<dd>
<div class="block">Returns the division of this bioentry.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/phred/PhredSequence.html#getDNA()">getDNA()</a></span> - Method in class org.biojava.bio.program.phred.<a href="./org/biojava/bio/program/phred/PhredSequence.html" title="class in org.biojava.bio.program.phred">PhredSequence</a></dt>
<dd>
<div class="block">Extracts the DNA part of the PhredAlpahbet SymbolList and returns it as a SymbolList</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/DNATools.html#getDNA()">getDNA()</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/DNATools.html" title="class in org.biojava.bio.seq">DNATools</a></dt>
<dd>
<div class="block">Return the DNA alphabet.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/phred/PhredSequence.html#getDNAAt(int)">getDNAAt(int)</a></span> - Method in class org.biojava.bio.program.phred.<a href="./org/biojava/bio/program/phred/PhredSequence.html" title="class in org.biojava.bio.program.phred">PhredSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/DNATools.html#getDNADistribution(double)">getDNADistribution(double)</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/DNATools.html" title="class in org.biojava.bio.seq">DNATools</a></dt>
<dd>
<div class="block">return a SimpleDistribution of specified GC content.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/chem/ChemCompTools.html#getDNAOneLetter(java.lang.String)">getDNAOneLetter(String)</a></span> - Static method in class org.biojava.bio.structure.io.mmcif.chem.<a href="./org/biojava/bio/structure/io/mmcif/chem/ChemCompTools.html" title="class in org.biojava.bio.structure.io.mmcif.chem">ChemCompTools</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.IOTools.html#getDNAParser()">getDNAParser()</a></span> - Static method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.IOTools.html" title="class in org.biojavax.bio.seq">RichSequence.IOTools</a></dt>
<dd>
<div class="block">Creates a DNA symbol tokenizer.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/ChromatogramTools.html#getDNASequence(org.biojava.bio.chromatogram.Chromatogram)">getDNASequence(Chromatogram)</a></span> - Static method in class org.biojava.bio.chromatogram.<a href="./org/biojava/bio/chromatogram/ChromatogramTools.html" title="class in org.biojava.bio.chromatogram">ChromatogramTools</a></dt>
<dd>
<div class="block">Get the called DNA sequence from a chromatogram.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/chem/ChemCompTools.html#getDNATwoLetter(java.lang.Character)">getDNATwoLetter(Character)</a></span> - Static method in class org.biojava.bio.structure.io.mmcif.chem.<a href="./org/biojava/bio/structure/io/mmcif/chem/ChemCompTools.html" title="class in org.biojava.bio.structure.io.mmcif.chem">ChemCompTools</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/DNATools.html#getDNAxDNA()">getDNAxDNA()</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/DNATools.html" title="class in org.biojava.bio.seq">DNATools</a></dt>
<dd>
<div class="block">Gets the (DNA x DNA) Alphabet</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/DNATools.html#getDNAxDNADistribution(double, double)">getDNAxDNADistribution(double, double)</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/DNATools.html" title="class in org.biojava.bio.seq">DNATools</a></dt>
<dd>
<div class="block">return a (DNA x DNA) cross-product Distribution with specified
DNA contents in each component Alphabet.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/RankedDocRef.html#getDocumentReference()">getDocumentReference()</a></span> - Method in interface org.biojavax.<a href="./org/biojavax/RankedDocRef.html" title="interface in org.biojavax">RankedDocRef</a></dt>
<dd>
<div class="block">Represents a reference to a document.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleRankedDocRef.html#getDocumentReference()">getDocumentReference()</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleRankedDocRef.html" title="class in org.biojavax">SimpleRankedDocRef</a></dt>
<dd>
<div class="block">Represents a reference to a document.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/JournalArticle.html#getDoi()">getDoi()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/JournalArticle.html" title="class in org.biojava.bio.structure">JournalArticle</a></dt>
<dd>
<div class="block">Get the value of DOI field.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/DP.html#getDotStatesIndex()">getDotStatesIndex()</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/DP.html" title="class in org.biojava.bio.dp">DP</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/io/LargeBuffer.html#getDouble(long)">getDouble(long)</a></span> - Method in class org.biojava.utils.io.<a href="./org/biojava/utils/io/LargeBuffer.html" title="class in org.biojava.utils.io">LargeBuffer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/io/LargeBuffer.html#getDouble()">getDouble()</a></span> - Method in class org.biojava.utils.io.<a href="./org/biojava/utils/io/LargeBuffer.html" title="class in org.biojava.utils.io">LargeBuffer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/jama/LUDecomposition.html#getDoublePivot()">getDoublePivot()</a></span> - Method in class org.biojava.bio.structure.jama.<a href="./org/biojava/bio/structure/jama/LUDecomposition.html" title="class in org.biojava.bio.structure.jama">LUDecomposition</a></dt>
<dd>
<div class="block">Return pivot permutation vector as a one-dimensional double array</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleSymbolPropertyTable.html#getDoubleValue(org.biojava.bio.symbol.Symbol)">getDoubleValue(Symbol)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleSymbolPropertyTable.html" title="class in org.biojava.bio.symbol">SimpleSymbolPropertyTable</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SymbolPropertyTable.html#getDoubleValue(org.biojava.bio.symbol.Symbol)">getDoubleValue(Symbol)</a></span> - Method in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SymbolPropertyTable.html" title="interface in org.biojava.bio.symbol">SymbolPropertyTable</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/molbio/RestrictionEnzyme.html#getDownstreamCut()">getDownstreamCut()</a></span> - Method in class org.biojava.bio.molbio.<a href="./org/biojava/bio/molbio/RestrictionEnzyme.html" title="class in org.biojava.bio.molbio">RestrictionEnzyme</a></dt>
<dd>
<div class="block"><code>getDownstreamCut</code> returns the cut site within or
downstream of the recognition site.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/molbio/RestrictionEnzyme.html#getDownstreamEndType()">getDownstreamEndType()</a></span> - Method in class org.biojava.bio.molbio.<a href="./org/biojava/bio/molbio/RestrictionEnzyme.html" title="class in org.biojava.bio.molbio">RestrictionEnzyme</a></dt>
<dd>
<div class="block"><code>getDownstreamEndType</code> returns the double-stranded
end type produced by the primary (intra-site or downstream)
cut.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/AbstractTrainer.html#getDP()">getDP()</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/AbstractTrainer.html" title="class in org.biojava.bio.dp">AbstractTrainer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/TrainingAlgorithm.html#getDP()">getDP()</a></span> - Method in interface org.biojava.bio.dp.<a href="./org/biojava/bio/dp/TrainingAlgorithm.html" title="interface in org.biojava.bio.dp">TrainingAlgorithm</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/sax/blastxml/BlastXMLParserFacade.html#getDTDHandler()">getDTDHandler()</a></span> - Method in class org.biojava.bio.program.sax.blastxml.<a href="./org/biojava/bio/program/sax/blastxml/BlastXMLParserFacade.html" title="class in org.biojava.bio.program.sax.blastxml">BlastXMLParserFacade</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/StructureTools.html#getE()">getE()</a></span> - Method in class org.biojava.bio.proteomics.<a href="./org/biojava/bio/proteomics/StructureTools.html" title="class in org.biojava.bio.proteomics">StructureTools</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/Agave2AgaveAnnotFilter.html#getEcNumber(org.biojava.bio.Annotation)">getEcNumber(Annotation)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/Agave2AgaveAnnotFilter.html" title="class in org.biojava.bio.seq.io.agave">Agave2AgaveAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEAnnotFilter.html#getEcNumber(org.biojava.bio.Annotation)">getEcNumber(Annotation)</a></span> - Method in interface org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEAnnotFilter.html" title="interface in org.biojava.bio.seq.io.agave">AGAVEAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/SimpleAnnotFilter.html#getEcNumber(org.biojava.bio.Annotation)">getEcNumber(Annotation)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/SimpleAnnotFilter.html" title="class in org.biojava.bio.seq.io.agave">SimpleAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Compound.html#getEcNums()">getEcNums()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure">Compound</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/UkkonenSuffixTree.html#getEdgeLabel(org.biojava.bio.symbol.UkkonenSuffixTree.SuffixNode)">getEdgeLabel(UkkonenSuffixTree.SuffixNode)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/UkkonenSuffixTree.html" title="class in org.biojava.bio.symbol">UkkonenSuffixTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/UkkonenSuffixTree.html#getEdgeLength(org.biojava.bio.symbol.UkkonenSuffixTree.SuffixNode)">getEdgeLength(UkkonenSuffixTree.SuffixNode)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/UkkonenSuffixTree.html" title="class in org.biojava.bio.symbol">UkkonenSuffixTree</a></dt>
<dd>
<div class="block">Tree navigation methods</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/NeedlemanWunsch.html#getEditDistance()">getEditDistance()</a></span> - Method in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/NeedlemanWunsch.html" title="class in org.biojava.bio.alignment">NeedlemanWunsch</a></dt>
<dd>
<div class="block">This gives the edit distance according to the given parameters of this
certain object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/JournalArticle.html#getEditorList()">getEditorList()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/JournalArticle.html" title="class in org.biojava.bio.structure">JournalArticle</a></dt>
<dd>
<div class="block">Get the list of editors of the JournalArticle</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/Agave2AgaveAnnotFilter.html#getElementId(org.biojava.bio.Annotation)">getElementId(Annotation)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/Agave2AgaveAnnotFilter.html" title="class in org.biojava.bio.seq.io.agave">Agave2AgaveAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEAnnotFilter.html#getElementId(org.biojava.bio.Annotation)">getElementId(Annotation)</a></span> - Method in interface org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEAnnotFilter.html" title="interface in org.biojava.bio.seq.io.agave">AGAVEAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEMatchRegion.html#getElementId()">getElementId()</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEMatchRegion.html" title="class in org.biojava.bio.seq.io.agave">AGAVEMatchRegion</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/SimpleAnnotFilter.html#getElementId(org.biojava.bio.Annotation)">getElementId(Annotation)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/SimpleAnnotFilter.html" title="class in org.biojava.bio.seq.io.agave">SimpleAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/Agave2AgaveAnnotFilter.html#getElementIds(org.biojava.bio.Annotation)">getElementIds(Annotation)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/Agave2AgaveAnnotFilter.html" title="class in org.biojava.bio.seq.io.agave">Agave2AgaveAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEAnnotFilter.html#getElementIds(org.biojava.bio.Annotation)">getElementIds(Annotation)</a></span> - Method in interface org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEAnnotFilter.html" title="interface in org.biojava.bio.seq.io.agave">AGAVEAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVERelatedAnnot.html#getElementIds()">getElementIds()</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVERelatedAnnot.html" title="class in org.biojava.bio.seq.io.agave">AGAVERelatedAnnot</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/SimpleAnnotFilter.html#getElementIds(org.biojava.bio.Annotation)">getElementIds(Annotation)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/SimpleAnnotFilter.html" title="class in org.biojava.bio.seq.io.agave">SimpleAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/RichSequenceFormat.BasicFormat.html#getElideComments()">getElideComments()</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/RichSequenceFormat.BasicFormat.html" title="class in org.biojavax.bio.seq.io">RichSequenceFormat.BasicFormat</a></dt>
<dd>
<div class="block">Is the format going to emit events when comments data or remarks from
bibliographic references are read?</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/RichSequenceFormat.html#getElideComments()">getElideComments()</a></span> - Method in interface org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/RichSequenceFormat.html" title="interface in org.biojavax.bio.seq.io">RichSequenceFormat</a></dt>
<dd>
<div class="block">Is the format going to emit events when comments data or remarks from
bibliographic references are read?</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/RichSequenceFormat.BasicFormat.html#getElideFeatures()">getElideFeatures()</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/RichSequenceFormat.BasicFormat.html" title="class in org.biojavax.bio.seq.io">RichSequenceFormat.BasicFormat</a></dt>
<dd>
<div class="block">Is the format going to emit events when feature data is read?</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/RichSequenceFormat.html#getElideFeatures()">getElideFeatures()</a></span> - Method in interface org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/RichSequenceFormat.html" title="interface in org.biojavax.bio.seq.io">RichSequenceFormat</a></dt>
<dd>
<div class="block">Is the format going to emit events when feature data is read?</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/RichSequenceFormat.BasicFormat.html#getElideReferences()">getElideReferences()</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/RichSequenceFormat.BasicFormat.html" title="class in org.biojavax.bio.seq.io">RichSequenceFormat.BasicFormat</a></dt>
<dd>
<div class="block">Is the format going to emit events when bibliographic reference data is read?</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/RichSequenceFormat.html#getElideReferences()">getElideReferences()</a></span> - Method in interface org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/RichSequenceFormat.html" title="interface in org.biojavax.bio.seq.io">RichSequenceFormat</a></dt>
<dd>
<div class="block">Is the format going to emit events when bibliographic reference data is read?</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/EmblLikeFormat.html#getElideSymbols()">getElideSymbols()</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/EmblLikeFormat.html" title="class in org.biojava.bio.seq.io">EmblLikeFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Return a flag indicating if symbol data will be skipped
when parsing streams.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/GenbankFormat.html#getElideSymbols()">getElideSymbols()</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/GenbankFormat.html" title="class in org.biojava.bio.seq.io">GenbankFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/RichSequenceFormat.BasicFormat.html#getElideSymbols()">getElideSymbols()</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/RichSequenceFormat.BasicFormat.html" title="class in org.biojavax.bio.seq.io">RichSequenceFormat.BasicFormat</a></dt>
<dd>
<div class="block">Is the format going to emit events when sequence data is read?</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/RichSequenceFormat.html#getElideSymbols()">getElideSymbols()</a></span> - Method in interface org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/RichSequenceFormat.html" title="interface in org.biojavax.bio.seq.io">RichSequenceFormat</a></dt>
<dd>
<div class="block">Is the format going to emit events when sequence data is read?</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOTools.html#getEmblBuilderFactory()">getEmblBuilderFactory()</a></span> - Static method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOTools.html" title="class in org.biojava.bio.seq.io">SeqIOTools</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Get a default SequenceBuilderFactory for handling EMBL
files.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLFormat.Terms.html#getEMBLTerm()">getEMBLTerm()</a></span> - Static method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLFormat.Terms.html" title="class in org.biojavax.bio.seq.io">EMBLFormat.Terms</a></dt>
<dd>
<div class="block">Getter for the EMBL term</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.Terms.html#getEMBLxmlTerm()">getEMBLxmlTerm()</a></span> - Static method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.Terms.html" title="class in org.biojavax.bio.seq.io">EMBLxmlFormat.Terms</a></dt>
<dd>
<div class="block">Getter for the EMBLxml term</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/onehead/SingleDP.html#getEmission(org.biojava.bio.symbol.Symbol, org.biojava.bio.dp.ScoreType)">getEmission(Symbol, ScoreType)</a></span> - Method in class org.biojava.bio.dp.onehead.<a href="./org/biojava/bio/dp/onehead/SingleDP.html" title="class in org.biojava.bio.dp.onehead">SingleDP</a></dt>
<dd>
<div class="block">This method is public for the benefit of training algorithms,
and in the future we should look at a better way of exposing
the emissions cache.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/twohead/EmissionCache.html#getEmissions(java.util.List)">getEmissions(List)</a></span> - Method in class org.biojava.bio.dp.twohead.<a href="./org/biojava/bio/dp/twohead/EmissionCache.html" title="class in org.biojava.bio.dp.twohead">EmissionCache</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/twohead/EmissionCache.html#getEmissions(java.util.List, boolean)">getEmissions(List, boolean)</a></span> - Method in class org.biojava.bio.dp.twohead.<a href="./org/biojava/bio/dp/twohead/EmissionCache.html" title="class in org.biojava.bio.dp.twohead">EmissionCache</a></dt>
<dd>
<div class="block">Retrieve the emission scores from the cache for every EmissionState
for the specified symbols.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFRecord.html#getEnd()">getEnd()</a></span> - Method in interface org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFRecord.html" title="interface in org.biojava.bio.program.gff">GFFRecord</a></dt>
<dd>
<div class="block">The end of this feature within the source sequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/SimpleGFFRecord.html#getEnd()">getEnd()</a></span> - Method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/SimpleGFFRecord.html" title="class in org.biojava.bio.program.gff">SimpleGFFRecord</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff3/GFF3Record.html#getEnd()">getEnd()</a></span> - Method in interface org.biojava.bio.program.gff3.<a href="./org/biojava/bio/program/gff3/GFF3Record.html" title="interface in org.biojava.bio.program.gff3">GFF3Record</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff3/GFF3Record.Impl.html#getEnd()">getEnd()</a></span> - Method in class org.biojava.bio.program.gff3.<a href="./org/biojava/bio/program/gff3/GFF3Record.Impl.html" title="class in org.biojava.bio.program.gff3">GFF3Record.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SubSequence.html#getEnd()">getEnd()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SubSequence.html" title="class in org.biojava.bio.seq.impl">SubSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEMatchRegion.html#getEnd()">getEnd()</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEMatchRegion.html" title="class in org.biojava.bio.seq.io.agave">AGAVEMatchRegion</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEQueryRegion.html#getEnd()">getEnd()</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEQueryRegion.html" title="class in org.biojava.bio.seq.io.agave">AGAVEQueryRegion</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/automata/FiniteAutomaton.html#getEnd()">getEnd()</a></span> - Method in class org.biojava.utils.automata.<a href="./org/biojava/utils/automata/FiniteAutomaton.html" title="class in org.biojava.utils.automata">FiniteAutomaton</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/automata/NfaBuilder.html#getEnd()">getEnd()</a></span> - Method in interface org.biojava.utils.automata.<a href="./org/biojava/utils/automata/NfaBuilder.html" title="interface in org.biojava.utils.automata">NfaBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/automata/NfaSubModel.html#getEnd()">getEnd()</a></span> - Method in class org.biojava.utils.automata.<a href="./org/biojava/utils/automata/NfaSubModel.html" title="class in org.biojava.utils.automata">NfaSubModel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/Position.html#getEnd()">getEnd()</a></span> - Method in interface org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/Position.html" title="interface in org.biojavax.bio.seq">Position</a></dt>
<dd>
<div class="block">Returns the end of the range of bases this base could lie in.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimplePosition.html#getEnd()">getEnd()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimplePosition.html" title="class in org.biojavax.bio.seq">SimplePosition</a></dt>
<dd>
<div class="block">Returns the end of the range of bases this base could lie in.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/RankedDocRef.html#getEnd()">getEnd()</a></span> - Method in interface org.biojavax.<a href="./org/biojavax/RankedDocRef.html" title="interface in org.biojavax">RankedDocRef</a></dt>
<dd>
<div class="block">The end position in the sequence that this reference is referred to from.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleRankedDocRef.html#getEnd()">getEnd()</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleRankedDocRef.html" title="class in org.biojavax">SimpleRankedDocRef</a></dt>
<dd>
<div class="block">The end position in the sequence that this reference is referred to from.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/LineSplitParser.html#getEndOfRecord()">getEndOfRecord()</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/LineSplitParser.html" title="class in org.biojava.bio.program.tagvalue">LineSplitParser</a></dt>
<dd>
<div class="block">Get the current string indicating that a record has ended.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/RegexParser.html#getEndOfRecord()">getEndOfRecord()</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/RegexParser.html" title="class in org.biojava.bio.program.tagvalue">RegexParser</a></dt>
<dd>
<div class="block">Get the explicit end-of-record string.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Compound.html#getEngineered()">getEngineered()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure">Compound</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/EntityPolySeq.html#getEntity_id()">getEntity_id()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/EntityPolySeq.html" title="class in org.biojava.bio.structure.io.mmcif.model">EntityPolySeq</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/PdbxEntityNonPoly.html#getEntity_id()">getEntity_id()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/PdbxEntityNonPoly.html" title="class in org.biojava.bio.structure.io.mmcif.model">PdbxEntityNonPoly</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/PdbxNonPolyScheme.html#getEntity_id()">getEntity_id()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/PdbxNonPolyScheme.html" title="class in org.biojava.bio.structure.io.mmcif.model">PdbxNonPolyScheme</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/PdbxPolySeqScheme.html#getEntity_id()">getEntity_id()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/PdbxPolySeqScheme.html" title="class in org.biojava.bio.structure.io.mmcif.model">PdbxPolySeqScheme</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/StructAsym.html#getEntity_id()">getEntity_id()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/StructAsym.html" title="class in org.biojava.bio.structure.io.mmcif.model">StructAsym</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/StructRef.html#getEntity_id()">getEntity_id()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/StructRef.html" title="class in org.biojava.bio.structure.io.mmcif.model">StructRef</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/sax/blastxml/BlastXMLParserFacade.html#getEntityResolver()">getEntityResolver()</a></span> - Method in class org.biojava.bio.program.sax.blastxml.<a href="./org/biojava/bio/program/sax/blastxml/BlastXMLParserFacade.html" title="class in org.biojava.bio.program.sax.blastxml">BlastXMLParserFacade</a></dt>
<dd>
<div class="block">This class has an EntityResolver that
resolves the public ID specifying the
NCBI DTDs to resource files within the
BioJava libraries.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Exptl.html#getEntry_id()">getEntry_id()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Exptl.html" title="class in org.biojava.bio.structure.io.mmcif.model">Exptl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#getEntry_id()">getEntry_id()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Struct.html#getEntry_id()">getEntry_id()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Struct.html" title="class in org.biojava.bio.structure.io.mmcif.model">Struct</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/StructKeywords.html#getEntry_id()">getEntry_id()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/StructKeywords.html" title="class in org.biojava.bio.structure.io.mmcif.model">StructKeywords</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/candy/CandyVocabulary.html#getEntryByName(java.lang.String)">getEntryByName(String)</a></span> - Method in interface org.biojava.utils.candy.<a href="./org/biojava/utils/candy/CandyVocabulary.html" title="interface in org.biojava.utils.candy">CandyVocabulary</a></dt>
<dd>
<div class="block">It returns a selected vocabulary entry.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/naming/ObdaContext.html#getEnvironment()">getEnvironment()</a></span> - Method in class org.biojava.naming.<a href="./org/biojava/naming/ObdaContext.html" title="class in org.biojava.naming">ObdaContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/process/ExternalProcess.html#getEnvironmentProperties()">getEnvironmentProperties()</a></span> - Method in class org.biojava.utils.process.<a href="./org/biojava/utils/process/ExternalProcess.html" title="class in org.biojava.utils.process">ExternalProcess</a></dt>
<dd>
<div class="block">Gets environment variables for the external process.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/molbio/RestrictionEnzymeManager.html#getEnzyme(java.lang.String)">getEnzyme(String)</a></span> - Static method in class org.biojava.bio.molbio.<a href="./org/biojava/bio/molbio/RestrictionEnzymeManager.html" title="class in org.biojava.bio.molbio">RestrictionEnzymeManager</a></dt>
<dd>
<div class="block"><code>getEnzyme</code> returns an enzyme by name.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/molbio/RestrictionSite.html#getEnzyme()">getEnzyme()</a></span> - Method in interface org.biojava.bio.molbio.<a href="./org/biojava/bio/molbio/RestrictionSite.html" title="interface in org.biojava.bio.molbio">RestrictionSite</a></dt>
<dd>
<div class="block"><code>getEnzyme</code> returns the enzyme which cuts at this
site.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleRestrictionSite.html#getEnzyme()">getEnzyme()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleRestrictionSite.html" title="class in org.biojava.bio.seq.impl">SimpleRestrictionSite</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/SMOTrainer.html#getEpsilon()">getEpsilon()</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/SMOTrainer.html" title="class in org.biojava.stats.svm">SMOTrainer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/AlternativeAlignment.html#getEqr()">getEqr()</a></span> - Method in class org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/AlternativeAlignment.html" title="class in org.biojava.bio.structure.align.pairwise">AlternativeAlignment</a></dt>
<dd>
<div class="block">returns the number of euqivalent residues in this alignment</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/util/AlignedPosition.html#getEquivalent()">getEquivalent()</a></span> - Method in class org.biojava.bio.structure.gui.util.<a href="./org/biojava/bio/structure/gui/util/AlignedPosition.html" title="class in org.biojava.bio.structure.gui.util">AlignedPosition</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFParser.html#getErrorHandler()">getErrorHandler()</a></span> - Method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFParser.html" title="class in org.biojava.bio.program.gff">GFFParser</a></dt>
<dd>
<div class="block">Find the error handler used by this parser.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff3/GFF3Parser.html#getErrorHandler()">getErrorHandler()</a></span> - Method in class org.biojava.bio.program.gff3.<a href="./org/biojava/bio/program/gff3/GFF3Parser.html" title="class in org.biojava.bio.program.gff3">GFF3Parser</a></dt>
<dd>
<div class="block">Find the error handler used by this parser.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/sax/blastxml/BlastXMLParserFacade.html#getErrorHandler()">getErrorHandler()</a></span> - Method in class org.biojava.bio.program.sax.blastxml.<a href="./org/biojava/bio/program/sax/blastxml/BlastXMLParserFacade.html" title="class in org.biojava.bio.program.sax.blastxml">BlastXMLParserFacade</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/process/ExternalProcess.html#getErrorHandler()">getErrorHandler()</a></span> - Method in class org.biojava.utils.process.<a href="./org/biojava/utils/process/ExternalProcess.html" title="class in org.biojava.utils.process">ExternalProcess</a></dt>
<dd>
<div class="block">Gets the output error handler which is responsible for the standard error
output of the external process.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/ExecRunner.html#getErrString()">getErrString()</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/ExecRunner.html" title="class in org.biojava.utils">ExecRunner</a></dt>
<dd>
<div class="block">Returns the error string if exec(String) was invoked.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/StrucAligParameters.html#getEvalCutoff()">getEvalCutoff()</a></span> - Method in class org.biojava.bio.structure.align.<a href="./org/biojava/bio/structure/align/StrucAligParameters.html" title="class in org.biojava.bio.structure.align">StrucAligParameters</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SeqSimilaritySearchHit.html#getEValue()">getEValue()</a></span> - Method in interface org.biojava.bio.search.<a href="./org/biojava/bio/search/SeqSimilaritySearchHit.html" title="interface in org.biojava.bio.search">SeqSimilaritySearchHit</a></dt>
<dd>
<div class="block">Return the overall E-value of this hit.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SeqSimilaritySearchSubHit.html#getEValue()">getEValue()</a></span> - Method in interface org.biojava.bio.search.<a href="./org/biojava/bio/search/SeqSimilaritySearchSubHit.html" title="interface in org.biojava.bio.search">SeqSimilaritySearchSubHit</a></dt>
<dd>
<div class="block">Return the E-value of this sub-hit.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SequenceDBSearchHit.html#getEValue()">getEValue()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SequenceDBSearchHit.html" title="class in org.biojava.bio.search">SequenceDBSearchHit</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SequenceDBSearchSubHit.html#getEValue()">getEValue()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SequenceDBSearchSubHit.html" title="class in org.biojava.bio.search">SequenceDBSearchSubHit</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SimpleSeqSimilaritySearchHit.html#getEValue()">getEValue()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SimpleSeqSimilaritySearchHit.html" title="class in org.biojava.bio.search">SimpleSeqSimilaritySearchHit</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SimpleSeqSimilaritySearchSubHit.html#getEValue()">getEValue()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SimpleSeqSimilaritySearchSubHit.html" title="class in org.biojava.bio.search">SimpleSeqSimilaritySearchSubHit</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ChangeListener.ChangeEventRecorder.html#getEvent()">getEvent()</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/ChangeListener.ChangeEventRecorder.html" title="class in org.biojava.utils">ChangeListener.ChangeEventRecorder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html#getEvents()">getEvents()</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html" title="class in org.biojavax.bio.seq.io">UniProtCommentParser</a></dt>
<dd>
<div class="block">Getter for property events.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.Terms.html#getEvidenceAttrTerm()">getEvidenceAttrTerm()</a></span> - Static method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.Terms.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat.Terms</a></dt>
<dd>
<div class="block">Getter for the evidence attr term</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.Terms.html#getEvidenceCategoryTerm()">getEvidenceCategoryTerm()</a></span> - Static method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.Terms.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat.Terms</a></dt>
<dd>
<div class="block">Getter for the evidence category term</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.Terms.html#getEvidenceDateTerm()">getEvidenceDateTerm()</a></span> - Static method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.Terms.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat.Terms</a></dt>
<dd>
<div class="block">Getter for the evidence date term</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.Terms.html#getEvidenceTypeTerm()">getEvidenceTypeTerm()</a></span> - Static method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.Terms.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat.Terms</a></dt>
<dd>
<div class="block">Getter for the evidence type term</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/Agave2AgaveAnnotFilter.html#getExonIds(org.biojava.bio.Annotation)">getExonIds(Annotation)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/Agave2AgaveAnnotFilter.html" title="class in org.biojava.bio.seq.io.agave">Agave2AgaveAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEAnnotFilter.html#getExonIds(org.biojava.bio.Annotation)">getExonIds(Annotation)</a></span> - Method in interface org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEAnnotFilter.html" title="interface in org.biojava.bio.seq.io.agave">AGAVEAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/SimpleAnnotFilter.html#getExonIds(org.biojava.bio.Annotation)">getExonIds(Annotation)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/SimpleAnnotFilter.html" title="class in org.biojava.bio.seq.io.agave">SimpleAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Compound.html#getExpressionSystem()">getExpressionSystem()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure">Compound</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Compound.html#getExpressionSystemAtccNumber()">getExpressionSystemAtccNumber()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure">Compound</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Compound.html#getExpressionSystemCell()">getExpressionSystemCell()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure">Compound</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Compound.html#getExpressionSystemCellLine()">getExpressionSystemCellLine()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure">Compound</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Compound.html#getExpressionSystemCellularLocation()">getExpressionSystemCellularLocation()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure">Compound</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Compound.html#getExpressionSystemGene()">getExpressionSystemGene()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure">Compound</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Compound.html#getExpressionSystemOrgan()">getExpressionSystemOrgan()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure">Compound</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Compound.html#getExpressionSystemOrganelle()">getExpressionSystemOrganelle()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure">Compound</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Compound.html#getExpressionSystemOtherDetails()">getExpressionSystemOtherDetails()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure">Compound</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Compound.html#getExpressionSystemPlasmid()">getExpressionSystemPlasmid()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure">Compound</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Compound.html#getExpressionSystemStrain()">getExpressionSystemStrain()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure">Compound</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Compound.html#getExpressionSystemTaxId()">getExpressionSystemTaxId()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure">Compound</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Compound.html#getExpressionSystemTissue()">getExpressionSystemTissue()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure">Compound</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Compound.html#getExpressionSystemVariant()">getExpressionSystemVariant()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure">Compound</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Compound.html#getExpressionSystemVector()">getExpressionSystemVector()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure">Compound</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Compound.html#getExpressionSystemVectorType()">getExpressionSystemVectorType()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure">Compound</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/DocRefAuthor.html#getExtendedName()">getExtendedName()</a></span> - Method in interface org.biojavax.<a href="./org/biojavax/DocRefAuthor.html" title="interface in org.biojavax">DocRefAuthor</a></dt>
<dd>
<div class="block">Returns the extended version of the authors name.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleDocRefAuthor.html#getExtendedName()">getExtendedName()</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleDocRefAuthor.html" title="class in org.biojavax">SimpleDocRefAuthor</a></dt>
<dd>
<div class="block">Returns the extended version of the authors name.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/automata/ArrayStateMachineToolkit.html#getFactory(java.lang.String, org.biojava.utils.automata.FiniteAutomaton)">getFactory(String, FiniteAutomaton)</a></span> - Method in class org.biojava.utils.automata.<a href="./org/biojava/utils/automata/ArrayStateMachineToolkit.html" title="class in org.biojava.utils.automata">ArrayStateMachineToolkit</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/ncbi/GenbankRichSequenceDB.html#getFactory()">getFactory()</a></span> - Method in class org.biojavax.bio.db.ncbi.<a href="./org/biojavax/bio/db/ncbi/GenbankRichSequenceDB.html" title="class in org.biojavax.bio.db.ncbi">GenbankRichSequenceDB</a></dt>
<dd>
<div class="block">Getter for property factory.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/ncbi/GenpeptRichSequenceDB.html#getFactory()">getFactory()</a></span> - Method in class org.biojavax.bio.db.ncbi.<a href="./org/biojavax/bio/db/ncbi/GenpeptRichSequenceDB.html" title="class in org.biojavax.bio.db.ncbi">GenpeptRichSequenceDB</a></dt>
<dd>
<div class="block">Getter for property factory.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOTools.html#getFastaBuilderFactory()">getFastaBuilderFactory()</a></span> - Static method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOTools.html" title="class in org.biojava.bio.seq.io">SeqIOTools</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Get a default SequenceBuilderFactory for handling FASTA
files.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFRecord.html#getFeature()">getFeature()</a></span> - Method in interface org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFRecord.html" title="interface in org.biojava.bio.program.gff">GFFRecord</a></dt>
<dd>
<div class="block">The feature type filed.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFRecordFilter.FeatureFilter.html#getFeature()">getFeature()</a></span> - Method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFRecordFilter.FeatureFilter.html" title="class in org.biojava.bio.program.gff">GFFRecordFilter.FeatureFilter</a></dt>
<dd>
<div class="block">Retrieve the current feature.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/SimpleGFFRecord.html#getFeature()">getFeature()</a></span> - Method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/SimpleGFFRecord.html" title="class in org.biojava.bio.program.gff">SimpleGFFRecord</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/sax/blastxml/BlastXMLParserFacade.html#getFeature(java.lang.String)">getFeature(String)</a></span> - Method in class org.biojava.bio.program.sax.blastxml.<a href="./org/biojava/bio/program/sax/blastxml/BlastXMLParserFacade.html" title="class in org.biojava.bio.program.sax.blastxml">BlastXMLParserFacade</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ByFeature.html#getFeature()">getFeature()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ByFeature.html" title="class in org.biojava.bio.seq">FeatureFilter.ByFeature</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/EmptyRichLocation.html#getFeature()">getFeature()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/EmptyRichLocation.html" title="class in org.biojavax.bio.seq">EmptyRichLocation</a></dt>
<dd>
<div class="block">Retrieves the feature this location is associated with.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichLocation.html#getFeature()">getFeature()</a></span> - Method in interface org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichLocation.html" title="interface in org.biojavax.bio.seq">RichLocation</a></dt>
<dd>
<div class="block">Retrieves the feature this location is associated with.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichLocation.html#getFeature()">getFeature()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichLocation.html" title="class in org.biojavax.bio.seq">SimpleRichLocation</a></dt>
<dd>
<div class="block">Retrieves the feature this location is associated with.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.Terms.html#getFeatureDescTerm()">getFeatureDescTerm()</a></span> - Static method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.Terms.html" title="class in org.biojavax.bio.seq">RichSequence.Terms</a></dt>
<dd>
<div class="block">Getter for the FeatureDesc term</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/GlyphFeatureRenderer.html#getFeatureFilter(int)">getFeatureFilter(int)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/GlyphFeatureRenderer.html" title="class in org.biojava.bio.gui.sequence">GlyphFeatureRenderer</a></dt>
<dd>
<div class="block">Returns the ith <a href="./org/biojava/bio/seq/FeatureFilter.html" title="interface in org.biojava.bio.seq"><code>FeatureFilter</code></a> in this renderer.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/SequencesAsGFF.html#getFeatureFilter()">getFeatureFilter()</a></span> - Method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/SequencesAsGFF.html" title="class in org.biojava.bio.program.gff">SequencesAsGFF</a></dt>
<dd>
<div class="block">Return the current <span class="type">FeatureFilter</span>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/filterxml/XMLFilterHandler.FilterHandler.html#getFeatureFilter()">getFeatureFilter()</a></span> - Method in interface org.biojava.bio.seq.io.filterxml.<a href="./org/biojava/bio/seq/io/filterxml/XMLFilterHandler.FilterHandler.html" title="interface in org.biojava.bio.seq.io.filterxml">XMLFilterHandler.FilterHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/RevCompSequence.html#getFeatureFromOriginal(org.biojava.bio.seq.Feature)">getFeatureFromOriginal(Feature)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/RevCompSequence.html" title="class in org.biojava.bio.seq.impl">RevCompSequence</a></dt>
<dd>
<div class="block">getFeatureFromOriginal() Since you can not create a feature on a projectedFeature at this time, I am
including this method so that you can get the corresponding feature from the original sequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/FeatureSource.html#getFeatureHolder()">getFeatureHolder()</a></span> - Method in interface org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/FeatureSource.html" title="interface in org.biojava.bio.gui.sequence">FeatureSource</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleFeature.html#getFeatureHolder()">getFeatureHolder()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleFeature.html" title="class in org.biojava.bio.seq.impl">SimpleFeature</a></dt>
<dd>
<div class="block">A utility function to retrieve the feature holder delegate, creating it if
necessary.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleSequence.html#getFeatureHolder()">getFeatureHolder()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleSequence.html" title="class in org.biojava.bio.seq.impl">SimpleSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/xff/BasicXFFHelper.html#getFeatureID(org.biojava.bio.seq.Feature)">getFeatureID(Feature)</a></span> - Method in class org.biojava.bio.program.xff.<a href="./org/biojava/bio/program/xff/BasicXFFHelper.html" title="class in org.biojava.bio.program.xff">BasicXFFHelper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/xff/XFFHelper.html#getFeatureID(org.biojava.bio.seq.Feature)">getFeatureID(Feature)</a></span> - Method in interface org.biojava.bio.program.xff.<a href="./org/biojava/bio/program/xff/XFFHelper.html" title="interface in org.biojava.bio.program.xff">XFFHelper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/xff/XFFFeatureSetHandler.html#getFeatureListener()">getFeatureListener()</a></span> - Method in class org.biojava.bio.program.xff.<a href="./org/biojava/bio/program/xff/XFFFeatureSetHandler.html" title="class in org.biojava.bio.program.xff">XFFFeatureSetHandler</a></dt>
<dd>
<div class="block">Return the object which receives startFeature/endFeature notifications.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/StAXFeatureHandler.html#getFeatureListener()">getFeatureListener()</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/StAXFeatureHandler.html" title="class in org.biojava.bio.seq.io.agave">StAXFeatureHandler</a></dt>
<dd>
<div class="block">Return current feature listener</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game/StAXFeatureHandler.html#getFeatureListener()">getFeatureListener()</a></span> - Method in class org.biojava.bio.seq.io.game.<a href="./org/biojava/bio/seq/io/game/StAXFeatureHandler.html" title="class in org.biojava.bio.seq.io.game">StAXFeatureHandler</a></dt>
<dd>
<div class="block">Return current feature listener</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.Terms.html#getFeatureOriginalTerm()">getFeatureOriginalTerm()</a></span> - Static method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.Terms.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat.Terms</a></dt>
<dd>
<div class="block">Getter for the feature original term</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleSequenceFactory.html#getFeatureRealizer()">getFeatureRealizer()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleSequenceFactory.html" title="class in org.biojava.bio.seq.impl">SimpleSequenceFactory</a></dt>
<dd>
<div class="block">Returns the FeatureRealizer set by "setFeatureRealizer".</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.Terms.html#getFeatureRefTerm()">getFeatureRefTerm()</a></span> - Static method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.Terms.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat.Terms</a></dt>
<dd>
<div class="block">Getter for the feature ref term</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichFeatureRelationshipHolder.html#getFeatureRelationshipSet()">getFeatureRelationshipSet()</a></span> - Method in interface org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichFeatureRelationshipHolder.html" title="interface in org.biojavax.bio.seq">RichFeatureRelationshipHolder</a></dt>
<dd>
<div class="block">Returns the set of relationships held in this feature holder.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichFeature.html#getFeatureRelationshipSet()">getFeatureRelationshipSet()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichFeature.html" title="class in org.biojavax.bio.seq">SimpleRichFeature</a></dt>
<dd>
<div class="block">Returns the set of relationships held in this feature holder.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/FeatureBlockSequenceRenderer.html#getFeatureRenderer()">getFeatureRenderer()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/FeatureBlockSequenceRenderer.html" title="class in org.biojava.bio.gui.sequence">FeatureBlockSequenceRenderer</a></dt>
<dd>
<div class="block"><code>getFeatureRenderer</code> returns the currently active
renderer.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/CircularRendererContext.html#getFeatures()">getFeatures()</a></span> - Method in interface org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/CircularRendererContext.html" title="interface in org.biojava.bio.gui.sequence">CircularRendererContext</a></dt>
<dd>
<div class="block">The features to render.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/HeadlessRenderContext.html#getFeatures()">getFeatures()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/HeadlessRenderContext.html" title="class in org.biojava.bio.gui.sequence">HeadlessRenderContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PairwiseSequencePanel.html#getFeatures()">getFeatures()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PairwiseSequencePanel.html" title="class in org.biojava.bio.gui.sequence">PairwiseSequencePanel</a></dt>
<dd>
<div class="block"><code>getFeatures</code> returns all of the
<code>Feature</code>s belonging to the currently rendered
<code>Sequence</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePanel.html#getFeatures()">getFeatures()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePanel.html" title="class in org.biojava.bio.gui.sequence">SequencePanel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePoster.html#getFeatures()">getFeatures()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePoster.html" title="class in org.biojava.bio.gui.sequence">SequencePoster</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequenceRenderContext.html#getFeatures()">getFeatures()</a></span> - Method in interface org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequenceRenderContext.html" title="interface in org.biojava.bio.gui.sequence">SequenceRenderContext</a></dt>
<dd>
<div class="block">The features to render.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SubCircularRendererContext.html#getFeatures()">getFeatures()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SubCircularRendererContext.html" title="class in org.biojava.bio.gui.sequence">SubCircularRendererContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SubPairwiseRenderContext.html#getFeatures()">getFeatures()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SubPairwiseRenderContext.html" title="class in org.biojava.bio.gui.sequence">SubPairwiseRenderContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SubSequenceRenderContext.html#getFeatures()">getFeatures()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SubSequenceRenderContext.html" title="class in org.biojava.bio.gui.sequence">SubSequenceRenderContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/TranslatedSequencePanel.html#getFeatures()">getFeatures()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/TranslatedSequencePanel.html" title="class in org.biojava.bio.gui.sequence">TranslatedSequencePanel</a></dt>
<dd>
<div class="block"><code>getFeatures</code> returns all of the
<code>Feature</code>s belonging to the currently rendered
<code>Sequence</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/distributed/DistDataSource.html#getFeatures(org.biojava.bio.seq.FeatureFilter)">getFeatures(FeatureFilter)</a></span> - Method in interface org.biojava.bio.seq.distributed.<a href="./org/biojava/bio/seq/distributed/DistDataSource.html" title="interface in org.biojava.bio.seq.distributed">DistDataSource</a></dt>
<dd>
<div class="block">Get all features matching a FeatureFilter provided by this DistDataSource.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/distributed/DistDataSource.html#getFeatures(java.lang.String, org.biojava.bio.seq.FeatureFilter, boolean)">getFeatures(String, FeatureFilter, boolean)</a></span> - Method in interface org.biojava.bio.seq.distributed.<a href="./org/biojava/bio/seq/distributed/DistDataSource.html" title="interface in org.biojava.bio.seq.distributed">DistDataSource</a></dt>
<dd>
<div class="block">Get all features matching a FeatureFilter on a Sequence with an ID and recurse flats.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/distributed/GFFDataSource.html#getFeatures(org.biojava.bio.seq.FeatureFilter)">getFeatures(FeatureFilter)</a></span> - Method in class org.biojava.bio.seq.distributed.<a href="./org/biojava/bio/seq/distributed/GFFDataSource.html" title="class in org.biojava.bio.seq.distributed">GFFDataSource</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/distributed/GFFDataSource.html#getFeatures(java.lang.String, org.biojava.bio.seq.FeatureFilter, boolean)">getFeatures(String, FeatureFilter, boolean)</a></span> - Method in class org.biojava.bio.seq.distributed.<a href="./org/biojava/bio/seq/distributed/GFFDataSource.html" title="class in org.biojava.bio.seq.distributed">GFFDataSource</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/distributed/SequenceDBDataSource.html#getFeatures(org.biojava.bio.seq.FeatureFilter)">getFeatures(FeatureFilter)</a></span> - Method in class org.biojava.bio.seq.distributed.<a href="./org/biojava/bio/seq/distributed/SequenceDBDataSource.html" title="class in org.biojava.bio.seq.distributed">SequenceDBDataSource</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/distributed/SequenceDBDataSource.html#getFeatures(java.lang.String, org.biojava.bio.seq.FeatureFilter, boolean)">getFeatures(String, FeatureFilter, boolean)</a></span> - Method in class org.biojava.bio.seq.distributed.<a href="./org/biojava/bio/seq/distributed/SequenceDBDataSource.html" title="class in org.biojava.bio.seq.distributed">SequenceDBDataSource</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/homol/Homology.html#getFeatures()">getFeatures()</a></span> - Method in interface org.biojava.bio.seq.homol.<a href="./org/biojava/bio/seq/homol/Homology.html" title="interface in org.biojava.bio.seq.homol">Homology</a></dt>
<dd>
<div class="block">Retrieve the set of features that mark homologous regions.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/homol/SimpleHomology.html#getFeatures()">getFeatures()</a></span> - Method in class org.biojava.bio.seq.homol.<a href="./org/biojava/bio/seq/homol/SimpleHomology.html" title="class in org.biojava.bio.seq.homol">SimpleHomology</a></dt>
<dd>
<div class="block"><code>getFeatures</code> returns the constituent
<code>HomologyFeature</code>s which are also used as the keys
in the alignment.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SubSequence.html#getFeatures()">getFeatures()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SubSequence.html" title="class in org.biojava.bio.seq.impl">SubSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/SimpleFeatureHolder.html#getFeatures()">getFeatures()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/SimpleFeatureHolder.html" title="class in org.biojava.bio.seq">SimpleFeatureHolder</a></dt>
<dd>
<div class="block">Returns the list of features in this featureholder.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.html#getFeatureSet()">getFeatureSet()</a></span> - Method in interface org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.html" title="interface in org.biojavax.bio.seq">RichSequence</a></dt>
<dd>
<div class="block">The features for this sequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/ThinRichSequence.html#getFeatureSet()">getFeatureSet()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/ThinRichSequence.html" title="class in org.biojavax.bio.seq">ThinRichSequence</a></dt>
<dd>
<div class="block">The features for this sequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/AbstractPeptideDigestRenderer.html#getFeatureSource()">getFeatureSource()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/AbstractPeptideDigestRenderer.html" title="class in org.biojava.bio.gui.sequence">AbstractPeptideDigestRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.Terms.html#getFeatureStatusTerm()">getFeatureStatusTerm()</a></span> - Static method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.Terms.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat.Terms</a></dt>
<dd>
<div class="block">Getter for the feature status term</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/xff/FeatureHandler.html#getFeatureTemplate()">getFeatureTemplate()</a></span> - Method in class org.biojava.bio.program.xff.<a href="./org/biojava/bio/program/xff/FeatureHandler.html" title="class in org.biojava.bio.program.xff">FeatureHandler</a></dt>
<dd>
<div class="block">Get the template for the feature being constructed.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/Agave2AgaveAnnotFilter.html#getFeatureType(org.biojava.bio.Annotation)">getFeatureType(Annotation)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/Agave2AgaveAnnotFilter.html" title="class in org.biojava.bio.seq.io.agave">Agave2AgaveAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEAnnotFilter.html#getFeatureType(org.biojava.bio.Annotation)">getFeatureType(Annotation)</a></span> - Method in interface org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEAnnotFilter.html" title="interface in org.biojava.bio.seq.io.agave">AGAVEAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/SimpleAnnotFilter.html#getFeatureType(org.biojava.bio.Annotation)">getFeatureType(Annotation)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/SimpleAnnotFilter.html" title="class in org.biojava.bio.seq.io.agave">SimpleAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.Terms.html#getFeatureVariationTerm()">getFeatureVariationTerm()</a></span> - Static method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.Terms.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat.Terms</a></dt>
<dd>
<div class="block">Getter for the feature variation term</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/ChangeType.html#getField()">getField()</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/ChangeType.html" title="class in org.biojava.utils">ChangeType</a></dt>
<dd>
<div class="block">Return a Field object where this change type is declared.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/indexdb/Record.html#getFile()">getFile()</a></span> - Method in interface org.biojava.bio.program.indexdb.<a href="./org/biojava/bio/program/indexdb/Record.html" title="interface in org.biojava.bio.program.indexdb">Record</a></dt>
<dd>
<div class="block"><code>getFile</code> returns the random access file in which
the record belongs.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/indexdb/Record.Impl.html#getFile()">getFile()</a></span> - Method in class org.biojava.bio.program.indexdb.<a href="./org/biojava/bio/program/indexdb/Record.Impl.html" title="class in org.biojava.bio.program.indexdb">Record.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/emblcd/EmblCDROMRandomAccess.html#getFile()">getFile()</a></span> - Method in class org.biojava.bio.seq.db.emblcd.<a href="./org/biojava/bio/seq/db/emblcd/EmblCDROMRandomAccess.html" title="class in org.biojava.bio.seq.db.emblcd">EmblCDROMRandomAccess</a></dt>
<dd>
<div class="block"><code>getFile</code> returns the <code>File</code> wrapped.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/Index.html#getFile()">getFile()</a></span> - Method in interface org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/Index.html" title="interface in org.biojava.bio.seq.db">Index</a></dt>
<dd>
<div class="block">The file to retrieve from.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/SimpleIndex.html#getFile()">getFile()</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/SimpleIndex.html" title="class in org.biojava.bio.seq.db">SimpleIndex</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/io/RAF.html#getFile()">getFile()</a></span> - Method in class org.biojava.utils.io.<a href="./org/biojava/utils/io/RAF.html" title="class in org.biojava.utils.io">RAF</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/TabIndexStore.html#getFileIndex(java.io.File)">getFileIndex(File)</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/TabIndexStore.html" title="class in org.biojava.bio.seq.db">TabIndexStore</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/server/FlatFileInstallation.html#getFilePath()">getFilePath()</a></span> - Method in class org.biojava.bio.structure.server.<a href="./org/biojava/bio/structure/server/FlatFileInstallation.html" title="class in org.biojava.bio.structure.server">FlatFileInstallation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/io/CountedBufferedReader.html#getFilePointer()">getFilePointer()</a></span> - Method in class org.biojava.utils.io.<a href="./org/biojava/utils/io/CountedBufferedReader.html" title="class in org.biojava.utils.io">CountedBufferedReader</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/io/RandomAccessReader.html#getFilePointer()">getFilePointer()</a></span> - Method in class org.biojava.utils.io.<a href="./org/biojava/utils/io/RandomAccessReader.html" title="class in org.biojava.utils.io">RandomAccessReader</a></dt>
<dd>
<div class="block"><code>getFilePointer</code> returns the effective position of
the pointer in the underlying <code>RandomAccessFile</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/BioIndex.html#getFiles()">getFiles()</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/BioIndex.html" title="class in org.biojava.bio.seq.db">BioIndex</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/EmblCDROMIndexStore.html#getFiles()">getFiles()</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/EmblCDROMIndexStore.html" title="class in org.biojava.bio.seq.db">EmblCDROMIndexStore</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/IndexStore.html#getFiles()">getFiles()</a></span> - Method in interface org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/IndexStore.html" title="interface in org.biojava.bio.seq.db">IndexStore</a></dt>
<dd>
<div class="block">Retrieve the Set of files that are currently indexed.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/TabIndexStore.html#getFiles()">getFiles()</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/TabIndexStore.html" title="class in org.biojava.bio.seq.db">TabIndexStore</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/ArrowedFeatureRenderer.html#getFill()">getFill()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/ArrowedFeatureRenderer.html" title="class in org.biojava.bio.gui.sequence">ArrowedFeatureRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/BasicFeatureRenderer.html#getFill()">getFill()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/BasicFeatureRenderer.html" title="class in org.biojava.bio.gui.sequence">BasicFeatureRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SixFrameRenderer.html#getFill()">getFill()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SixFrameRenderer.html" title="class in org.biojava.bio.gui.sequence">SixFrameRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SixFrameZiggyRenderer.html#getFill()">getFill()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SixFrameZiggyRenderer.html" title="class in org.biojava.bio.gui.sequence">SixFrameZiggyRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/TickFeatureRenderer.html#getFill()">getFill()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/TickFeatureRenderer.html" title="class in org.biojava.bio.gui.sequence">TickFeatureRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/ZiggyFeatureRenderer.html#getFill()">getFill()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/ZiggyFeatureRenderer.html" title="class in org.biojava.bio.gui.sequence">ZiggyFeatureRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/LabelledSequenceRenderer.html#getFillColor()">getFillColor()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/LabelledSequenceRenderer.html" title="class in org.biojava.bio.gui.sequence">LabelledSequenceRenderer</a></dt>
<dd>
<div class="block">Get the background color of the label area.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/glyph/ArrowGlyph.html#getFillPaint()">getFillPaint()</a></span> - Method in class org.biojava.bio.gui.glyph.<a href="./org/biojava/bio/gui/glyph/ArrowGlyph.html" title="class in org.biojava.bio.gui.glyph">ArrowGlyph</a></dt>
<dd>
<div class="block">Returns the paint properties of this glyph.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/AbstractPeptideDigestRenderer.html#getFilter()">getFilter()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/AbstractPeptideDigestRenderer.html" title="class in org.biojava.bio.gui.sequence">AbstractPeptideDigestRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/FilteringRenderer.html#getFilter()">getFilter()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/FilteringRenderer.html" title="class in org.biojava.bio.gui.sequence">FilteringRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PairwiseFilteringRenderer.html#getFilter()">getFilter()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PairwiseFilteringRenderer.html" title="class in org.biojava.bio.gui.sequence">PairwiseFilteringRenderer</a></dt>
<dd>
<div class="block"><code>getFilter</code> returns the current filter.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFRecordFilter.NotFilter.html#getFilter()">getFilter()</a></span> - Method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFRecordFilter.NotFilter.html" title="class in org.biojava.bio.program.gff">GFFRecordFilter.NotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ByAncestor.html#getFilter()">getFilter()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ByAncestor.html" title="class in org.biojava.bio.seq">FeatureFilter.ByAncestor</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ByChild.html#getFilter()">getFilter()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ByChild.html" title="class in org.biojava.bio.seq">FeatureFilter.ByChild</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ByDescendant.html#getFilter()">getFilter()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ByDescendant.html" title="class in org.biojava.bio.seq">FeatureFilter.ByDescendant</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ByParent.html#getFilter()">getFilter()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ByParent.html" title="class in org.biojava.bio.seq">FeatureFilter.ByParent</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.OnlyChildren.html#getFilter()">getFilter()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.OnlyChildren.html" title="class in org.biojava.bio.seq">FeatureFilter.OnlyChildren</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.OnlyDescendants.html#getFilter()">getFilter()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.OnlyDescendants.html" title="class in org.biojava.bio.seq">FeatureFilter.OnlyDescendants</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/candy/CandyFinder.html#getFinderName()">getFinderName()</a></span> - Method in interface org.biojava.utils.candy.<a href="./org/biojava/utils/candy/CandyFinder.html" title="interface in org.biojava.utils.candy">CandyFinder</a></dt>
<dd>
<div class="block">It returns a name of this vocabulary finder.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtCommentParser.Interaction.html#getFirstIntActID()">getFirstIntActID()</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtCommentParser.Interaction.html" title="class in org.biojavax.bio.seq.io">UniProtCommentParser.Interaction</a></dt>
<dd>
<div class="block">Getter for property firstIntActID.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/OrthoPair.html#getFirstOrthologue()">getFirstOrthologue()</a></span> - Method in interface org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/OrthoPair.html" title="interface in org.biojava.bio.program.homologene">OrthoPair</a></dt>
<dd>
<div class="block">gets the first orthologue in the orthology
relationship.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/SimpleOrthoPair.html#getFirstOrthologue()">getFirstOrthologue()</a></span> - Method in class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/SimpleOrthoPair.html" title="class in org.biojava.bio.program.homologene">SimpleOrthoPair</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/impl/AbstractOrganism.html#getFitness()">getFitness()</a></span> - Method in class org.biojavax.ga.impl.<a href="./org/biojavax/ga/impl/AbstractOrganism.html" title="class in org.biojavax.ga.impl">AbstractOrganism</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/Organism.html#getFitness()">getFitness()</a></span> - Method in interface org.biojavax.ga.<a href="./org/biojavax/ga/Organism.html" title="interface in org.biojavax.ga">Organism</a></dt>
<dd>
<div class="block">Returns the current fitness of this organism.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ga/functions/SelectionFunction.SelectAll.html#getFitnessFunction()">getFitnessFunction()</a></span> - Method in class org.biojavax.ga.functions.<a href="./org/biojavax/ga/functions/SelectionFunction.SelectAll.html" title="class in org.biojavax.ga.functions">SelectionFunction.SelectAll</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/GeneticAlgorithm.html#getFitnessFunction()">getFitnessFunction()</a></span> - Method in interface org.biojavax.ga.<a href="./org/biojavax/ga/GeneticAlgorithm.html" title="interface in org.biojavax.ga">GeneticAlgorithm</a></dt>
<dd>
<div class="block">Returns the fitness function, i.e.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ga/impl/AbstractGeneticAlgorithm.html#getFitnessFunction()">getFitnessFunction()</a></span> - Method in class org.biojavax.ga.impl.<a href="./org/biojavax/ga/impl/AbstractGeneticAlgorithm.html" title="class in org.biojavax.ga.impl">AbstractGeneticAlgorithm</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/io/LargeBuffer.html#getFloat(long)">getFloat(long)</a></span> - Method in class org.biojava.utils.io.<a href="./org/biojava/utils/io/LargeBuffer.html" title="class in org.biojava.utils.io">LargeBuffer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/io/LargeBuffer.html#getFloat()">getFloat()</a></span> - Method in class org.biojava.utils.io.<a href="./org/biojava/utils/io/LargeBuffer.html" title="class in org.biojava.utils.io">LargeBuffer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.html#getFloatOption(org.biojava.bio.chromatogram.graphic.ChromatogramGraphic.Option)">getFloatOption(ChromatogramGraphic.Option)</a></span> - Method in class org.biojava.bio.chromatogram.graphic.<a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.html" title="class in org.biojava.bio.chromatogram.graphic">ChromatogramGraphic</a></dt>
<dd>
<div class="block">Helper method for converting a <code>Number</code>-valued
option into a <code>float</code> primitive.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/HeadlessRenderContext.html#getFont()">getFont()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/HeadlessRenderContext.html" title="class in org.biojava.bio.gui.sequence">HeadlessRenderContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequenceRenderContext.html#getFont()">getFont()</a></span> - Method in interface org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequenceRenderContext.html" title="interface in org.biojava.bio.gui.sequence">SequenceRenderContext</a></dt>
<dd>
<div class="block">Gets the Font attribute of the SequenceRenderContext object</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SubPairwiseRenderContext.html#getFont()">getFont()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SubPairwiseRenderContext.html" title="class in org.biojava.bio.gui.sequence">SubPairwiseRenderContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SubSequenceRenderContext.html#getFont()">getFont()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SubSequenceRenderContext.html" title="class in org.biojava.bio.gui.sequence">SubSequenceRenderContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/formats/FormatTools.html#getFormat(java.lang.String)">getFormat(String)</a></span> - Static method in class org.biojava.bio.program.formats.<a href="./org/biojava/bio/program/formats/FormatTools.html" title="class in org.biojava.bio.program.formats">FormatTools</a></dt>
<dd>
<div class="block">Attempt to find aformat for a format identifer string.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/BioIndex.html#getFormat()">getFormat()</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/BioIndex.html" title="class in org.biojava.bio.seq.db">BioIndex</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/EmblCDROMIndexStore.html#getFormat()">getFormat()</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/EmblCDROMIndexStore.html" title="class in org.biojava.bio.seq.db">EmblCDROMIndexStore</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/IndexStore.html#getFormat()">getFormat()</a></span> - Method in interface org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/IndexStore.html" title="interface in org.biojava.bio.seq.db">IndexStore</a></dt>
<dd>
<div class="block">Retrieve the format of the index file.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/TabIndexStore.html#getFormat()">getFormat()</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/TabIndexStore.html" title="class in org.biojava.bio.seq.db">TabIndexStore</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html#getFormula()">getFormula()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html" title="class in org.biojava.bio.structure.io.mmcif.model">ChemComp</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html#getFormula_weight()">getFormula_weight()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html" title="class in org.biojava.bio.structure.io.mmcif.model">ChemComp</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Entity.html#getFormula_weight()">getFormula_weight()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Entity.html" title="class in org.biojava.bio.structure.io.mmcif.model">Entity</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/Unchangeable.html#getForwarders(org.biojava.utils.ChangeType)">getForwarders(ChangeType)</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/Unchangeable.html" title="class in org.biojava.utils">Unchangeable</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/molbio/RestrictionEnzyme.html#getForwardRegex()">getForwardRegex()</a></span> - Method in class org.biojava.bio.molbio.<a href="./org/biojava/bio/molbio/RestrictionEnzyme.html" title="class in org.biojava.bio.molbio">RestrictionEnzyme</a></dt>
<dd>
<div class="block"><code>getForwardRegex</code> returns a regular expression which
matches the forward strand of the recognition site.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/DP.html#getForwardTransitions()">getForwardTransitions()</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/DP.html" title="class in org.biojava.bio.dp">DP</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/DP.html#getForwardTransitionScores(org.biojava.bio.dp.ScoreType)">getForwardTransitionScores(ScoreType)</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/DP.html" title="class in org.biojava.bio.dp">DP</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/StrucAligParameters.html#getFragCompat()">getFragCompat()</a></span> - Method in class org.biojava.bio.structure.align.<a href="./org/biojava/bio/structure/align/StrucAligParameters.html" title="class in org.biojava.bio.structure.align">StrucAligParameters</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/helper/AlignTools.html#getFragment(org.biojava.bio.structure.Atom[], int, int)">getFragment(Atom[], int, int)</a></span> - Static method in class org.biojava.bio.structure.align.helper.<a href="./org/biojava/bio/structure/align/helper/AlignTools.html" title="class in org.biojava.bio.structure.align.helper">AlignTools</a></dt>
<dd>
<div class="block">get a continue subset of Atoms based by the starting position and the length</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Compound.html#getFragment()">getFragment()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure">Compound</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/helper/AlignTools.html#getFragmentFromIdxList(org.biojava.bio.structure.Atom[], int[])">getFragmentFromIdxList(Atom[], int[])</a></span> - Static method in class org.biojava.bio.structure.align.helper.<a href="./org/biojava/bio/structure/align/helper/AlignTools.html" title="class in org.biojava.bio.structure.align.helper">AlignTools</a></dt>
<dd>
<div class="block">get a subset of Atoms based by their positions</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/StrucAligParameters.html#getFragmentLength()">getFragmentLength()</a></span> - Method in class org.biojava.bio.structure.align.<a href="./org/biojava/bio/structure/align/StrucAligParameters.html" title="class in org.biojava.bio.structure.align">StrucAligParameters</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/StrucAligParameters.html#getFragmentMiniDistance()">getFragmentMiniDistance()</a></span> - Method in class org.biojava.bio.structure.align.<a href="./org/biojava/bio/structure/align/StrucAligParameters.html" title="class in org.biojava.bio.structure.align">StrucAligParameters</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/helper/AlignTools.html#getFragmentNoClone(org.biojava.bio.structure.Atom[], int, int)">getFragmentNoClone(Atom[], int, int)</a></span> - Static method in class org.biojava.bio.structure.align.helper.<a href="./org/biojava/bio/structure/align/helper/AlignTools.html" title="class in org.biojava.bio.structure.align.helper">AlignTools</a></dt>
<dd>
<div class="block">get a continue subset of Atoms based by the starting position and the length
does not clone the original atoms.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/StructurePairAligner.html#getFragmentPairs()">getFragmentPairs()</a></span> - Method in class org.biojava.bio.structure.align.<a href="./org/biojava/bio/structure/align/StructurePairAligner.html" title="class in org.biojava.bio.structure.align">StructurePairAligner</a></dt>
<dd>
<div class="block">get the results of step 1 - the FragmentPairs used for seeding the alignment</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/JMatrixPanel.html#getFragmentPairs()">getFragmentPairs()</a></span> - Method in class org.biojava.bio.structure.gui.<a href="./org/biojava/bio/structure/gui/JMatrixPanel.html" title="class in org.biojava.bio.structure.gui">JMatrixPanel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/ScaleableMatrixPanel.html#getFragmentPairs()">getFragmentPairs()</a></span> - Method in class org.biojava.bio.structure.gui.<a href="./org/biojava/bio/structure/gui/ScaleableMatrixPanel.html" title="class in org.biojava.bio.structure.gui">ScaleableMatrixPanel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFRecord.html#getFrame()">getFrame()</a></span> - Method in interface org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFRecord.html" title="interface in org.biojava.bio.program.gff">GFFRecord</a></dt>
<dd>
<div class="block">The frame of the feature.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFRecordFilter.FrameFilter.html#getFrame()">getFrame()</a></span> - Method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFRecordFilter.FrameFilter.html" title="class in org.biojava.bio.program.gff">GFFRecordFilter.FrameFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/SimpleGFFRecord.html#getFrame()">getFrame()</a></span> - Method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/SimpleGFFRecord.html" title="class in org.biojava.bio.program.gff">SimpleGFFRecord</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.FrameFilter.html#getFrame()">getFrame()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.FrameFilter.html" title="class in org.biojava.bio.seq">FeatureFilter.FrameFilter</a></dt>
<dd>
<div class="block">Retrieve the reading frame this filter matches.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/Frame.html#getFrame()">getFrame()</a></span> - Method in interface org.biojava.bio.seq.<a href="./org/biojava/bio/seq/Frame.html" title="interface in org.biojava.bio.seq">Frame</a></dt>
<dd>
<div class="block">A method to get the frame information of the implementing object</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FramedFeature.ReadingFrame.html#getFrame()">getFrame()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FramedFeature.ReadingFrame.html" title="class in org.biojava.bio.seq">FramedFeature.ReadingFrame</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleFramedFeature.html#getFrame()">getFrame()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleFramedFeature.html" title="class in org.biojava.bio.seq.impl">SimpleFramedFeature</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/CodonPref.html#getFrequency()">getFrequency()</a></span> - Method in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/CodonPref.html" title="interface in org.biojava.bio.symbol">CodonPref</a></dt>
<dd>
<div class="block">returns a Distribution giving the
frequency of codons (sums to one over the
totality of codons).</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleCodonPref.html#getFrequency()">getFrequency()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleCodonPref.html" title="class in org.biojava.bio.symbol">SimpleCodonPref</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/CodonPref.html#getFrequencyForSynonyms(org.biojava.bio.symbol.Symbol)">getFrequencyForSynonyms(Symbol)</a></span> - Method in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/CodonPref.html" title="interface in org.biojava.bio.symbol">CodonPref</a></dt>
<dd>
<div class="block">returns a Distribution giving the
frequency of synonymous codons.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleCodonPref.html#getFrequencyForSynonyms(org.biojava.bio.symbol.Symbol)">getFrequencyForSynonyms(Symbol)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleCodonPref.html" title="class in org.biojava.bio.symbol">SimpleCodonPref</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/WobbleDistribution.html#getFrequencyOfNonWobbleBases()">getFrequencyOfNonWobbleBases()</a></span> - Method in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/WobbleDistribution.html" title="interface in org.biojava.bio.symbol">WobbleDistribution</a></dt>
<dd>
<div class="block">returns the frequency with which
synonymous codons start with a
specified pair of bases.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/IllegalTransitionException.html#getFrom()">getFrom()</a></span> - Method in exception org.biojava.bio.dp.<a href="./org/biojava/bio/dp/IllegalTransitionException.html" title="class in org.biojava.bio.dp">IllegalTransitionException</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.Terms.html#getFTIdTerm()">getFTIdTerm()</a></span> - Static method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.Terms.html" title="class in org.biojavax.bio.seq">RichSequence.Terms</a></dt>
<dd>
<div class="block">Getter for the FTId term</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/SeqRes2AtomAligner.html#getFullAtomSequence(java.util.List)">getFullAtomSequence(List<Group>)</a></span> - Method in class org.biojava.bio.structure.io.<a href="./org/biojava/bio/structure/io/SeqRes2AtomAligner.html" title="class in org.biojava.bio.structure.io">SeqRes2AtomAligner</a></dt>
<dd>
<div class="block">returns the full sequence of the Atom records of a chain
with X instead of HETATMSs.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Atom.html#getFullName()">getFullName()</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Atom.html" title="interface in org.biojava.bio.structure">Atom</a></dt>
<dd>
<div class="block">get full name of atom e.g.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/AtomImpl.html#getFullName()">getFullName()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/AtomImpl.html" title="class in org.biojava.bio.structure">AtomImpl</a></dt>
<dd>
<div class="block">get full name of atom e.g.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/Position.html#getFuzzyEnd()">getFuzzyEnd()</a></span> - Method in interface org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/Position.html" title="interface in org.biojavax.bio.seq">Position</a></dt>
<dd>
<div class="block">Returns true if the position has a fuzzy end.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimplePosition.html#getFuzzyEnd()">getFuzzyEnd()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimplePosition.html" title="class in org.biojavax.bio.seq">SimplePosition</a></dt>
<dd>
<div class="block">Returns true if the position has a fuzzy end.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/Position.html#getFuzzyStart()">getFuzzyStart()</a></span> - Method in interface org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/Position.html" title="interface in org.biojavax.bio.seq">Position</a></dt>
<dd>
<div class="block">Returns true if the position has a fuzzy start.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimplePosition.html#getFuzzyStart()">getFuzzyStart()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimplePosition.html" title="class in org.biojavax.bio.seq">SimplePosition</a></dt>
<dd>
<div class="block">Returns true if the position has a fuzzy start.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/molbio/DNAComposition.html#getG()">getG()</a></span> - Method in class org.biojava.bio.molbio.<a href="./org/biojava/bio/molbio/DNAComposition.html" title="class in org.biojava.bio.molbio">DNAComposition</a></dt>
<dd>
<div class="block">Get the relative compositon of 'G'.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/StructureTools.html#getG()">getG()</a></span> - Method in class org.biojava.bio.proteomics.<a href="./org/biojava/bio/proteomics/StructureTools.html" title="class in org.biojava.bio.proteomics">StructureTools</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/NeedlemanWunsch.html#getGapExt()">getGapExt()</a></span> - Method in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/NeedlemanWunsch.html" title="class in org.biojava.bio.alignment">NeedlemanWunsch</a></dt>
<dd>
<div class="block">Returns the current expenses of any extension of a gap operation.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/Alignable.html#getGapExtCol()">getGapExtCol()</a></span> - Method in interface org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/Alignable.html" title="interface in org.biojava.bio.structure.align.pairwise">Alignable</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/StrCompAlignment.html#getGapExtCol()">getGapExtCol()</a></span> - Method in class org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/StrCompAlignment.html" title="class in org.biojava.bio.structure.align.pairwise">StrCompAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/StrucAligParameters.html#getGapExtension()">getGapExtension()</a></span> - Method in class org.biojava.bio.structure.align.<a href="./org/biojava/bio/structure/align/StrucAligParameters.html" title="class in org.biojava.bio.structure.align">StrucAligParameters</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/Alignable.html#getGapExtRow()">getGapExtRow()</a></span> - Method in interface org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/Alignable.html" title="interface in org.biojava.bio.structure.align.pairwise">Alignable</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/StrCompAlignment.html#getGapExtRow()">getGapExtRow()</a></span> - Method in class org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/StrCompAlignment.html" title="class in org.biojava.bio.structure.align.pairwise">StrCompAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/StrucAligParameters.html#getGapOpen()">getGapOpen()</a></span> - Method in class org.biojava.bio.structure.align.<a href="./org/biojava/bio/structure/align/StrucAligParameters.html" title="class in org.biojava.bio.structure.align">StrucAligParameters</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/Alignable.html#getGapOpenCol()">getGapOpenCol()</a></span> - Method in interface org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/Alignable.html" title="interface in org.biojava.bio.structure.align.pairwise">Alignable</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/StrCompAlignment.html#getGapOpenCol()">getGapOpenCol()</a></span> - Method in class org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/StrCompAlignment.html" title="class in org.biojava.bio.structure.align.pairwise">StrCompAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/Alignable.html#getGapOpenRow()">getGapOpenRow()</a></span> - Method in interface org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/Alignable.html" title="interface in org.biojava.bio.structure.align.pairwise">Alignable</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/StrCompAlignment.html#getGapOpenRow()">getGapOpenRow()</a></span> - Method in class org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/StrCompAlignment.html" title="class in org.biojava.bio.structure.align.pairwise">StrCompAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/AlternativeAlignment.html#getGaps()">getGaps()</a></span> - Method in class org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/AlternativeAlignment.html" title="class in org.biojava.bio.structure.align.pairwise">AlternativeAlignment</a></dt>
<dd>
<div class="block">return the number of gaps in this alignment</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AbstractAlphabet.html#getGapSymbol()">getGapSymbol()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AbstractAlphabet.html" title="class in org.biojava.bio.symbol">AbstractAlphabet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/Alphabet.html#getGapSymbol()">getGapSymbol()</a></span> - Method in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/Alphabet.html" title="interface in org.biojava.bio.symbol">Alphabet</a></dt>
<dd>
<div class="block">
Get the 'gap' ambiguity symbol that is most appropriate for this alphabet.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AlphabetManager.html#getGapSymbol()">getGapSymbol()</a></span> - Static method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AlphabetManager.html" title="class in org.biojava.bio.symbol">AlphabetManager</a></dt>
<dd>
<div class="block">
Get the special `gap' Symbol.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AlphabetManager.html#getGapSymbol(java.util.List)">getGapSymbol(List)</a></span> - Static method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AlphabetManager.html" title="class in org.biojava.bio.symbol">AlphabetManager</a></dt>
<dd>
<div class="block">
Get the gap symbol appropriate to this list of alphabets.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/DoubleAlphabet.html#getGapSymbol()">getGapSymbol()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/DoubleAlphabet.html" title="class in org.biojava.bio.symbol">DoubleAlphabet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/DoubleAlphabet.SubDoubleAlphabet.html#getGapSymbol()">getGapSymbol()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/DoubleAlphabet.SubDoubleAlphabet.html" title="class in org.biojava.bio.symbol">DoubleAlphabet.SubDoubleAlphabet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/IntegerAlphabet.html#getGapSymbol()">getGapSymbol()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/IntegerAlphabet.html" title="class in org.biojava.bio.symbol">IntegerAlphabet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SoftMaskedAlphabet.html#getGapSymbol()">getGapSymbol()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SoftMaskedAlphabet.html" title="class in org.biojava.bio.symbol">SoftMaskedAlphabet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOTools.html#getGenbankBuilderFactory()">getGenbankBuilderFactory()</a></span> - Static method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOTools.html" title="class in org.biojava.bio.seq.io">SeqIOTools</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Get a default SequenceBuilderFactory for handling GenBank
files.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/GenbankFormat.Terms.html#getGenBankTerm()">getGenBankTerm()</a></span> - Static method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/GenbankFormat.Terms.html" title="class in org.biojavax.bio.seq.io">GenbankFormat.Terms</a></dt>
<dd>
<div class="block">Getter for the Genbank term</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Compound.html#getGene()">getGene()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure">Compound</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.Terms.html#getGeneNameTerm()">getGeneNameTerm()</a></span> - Static method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.Terms.html" title="class in org.biojavax.bio.seq">RichSequence.Terms</a></dt>
<dd>
<div class="block">Getter for the GeneName term</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/SequencesAsGFF.html#getGenerateSequenceHeader()">getGenerateSequenceHeader()</a></span> - Method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/SequencesAsGFF.html" title="class in org.biojava.bio.program.gff">SequencesAsGFF</a></dt>
<dd>
<div class="block">Discover if per-sequence header lines will be generated.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ga/GeneticAlgorithm.html#getGeneration()">getGeneration()</a></span> - Method in interface org.biojavax.ga.<a href="./org/biojavax/ga/GeneticAlgorithm.html" title="interface in org.biojavax.ga">GeneticAlgorithm</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/impl/SimpleGeneticAlgorithm.html#getGeneration()">getGeneration()</a></span> - Method in class org.biojavax.ga.impl.<a href="./org/biojavax/ga/impl/SimpleGeneticAlgorithm.html" title="class in org.biojavax.ga.impl">SimpleGeneticAlgorithm</a></dt>
<dd>
<div class="block">The current generation</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.Terms.html#getGeneSynonymTerm()">getGeneSynonymTerm()</a></span> - Static method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.Terms.html" title="class in org.biojavax.bio.seq">RichSequence.Terms</a></dt>
<dd>
<div class="block">Getter for the GeneSynonym term</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/RNATools.html#getGeneticCode(java.lang.String)">getGeneticCode(String)</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/RNATools.html" title="class in org.biojava.bio.seq">RNATools</a></dt>
<dd>
<div class="block">Retrieve a TranslationTable by name.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/RNATools.html#getGeneticCode(int)">getGeneticCode(int)</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/RNATools.html" title="class in org.biojava.bio.seq">RNATools</a></dt>
<dd>
<div class="block">Retrieve a TranslationTable by number.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/CodonPref.html#getGeneticCode()">getGeneticCode()</a></span> - Method in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/CodonPref.html" title="interface in org.biojava.bio.symbol">CodonPref</a></dt>
<dd>
<div class="block">the genetic code that this codon
preference is based on.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleCodonPref.html#getGeneticCode()">getGeneticCode()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleCodonPref.html" title="class in org.biojava.bio.symbol">SimpleCodonPref</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/taxa/NCBITaxon.html#getGeneticCode()">getGeneticCode()</a></span> - Method in interface org.biojavax.bio.taxa.<a href="./org/biojavax/bio/taxa/NCBITaxon.html" title="interface in org.biojavax.bio.taxa">NCBITaxon</a></dt>
<dd>
<div class="block">Returns the genetic code of this taxon, which may be null if not known.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/taxa/SimpleNCBITaxon.html#getGeneticCode()">getGeneticCode()</a></span> - Method in class org.biojavax.bio.taxa.<a href="./org/biojavax/bio/taxa/SimpleNCBITaxon.html" title="class in org.biojavax.bio.taxa">SimpleNCBITaxon</a></dt>
<dd>
<div class="block">Returns the genetic code of this taxon, which may be null if not known.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/CodonPref.html#getGeneticCodeName()">getGeneticCodeName()</a></span> - Method in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/CodonPref.html" title="interface in org.biojava.bio.symbol">CodonPref</a></dt>
<dd>
<div class="block">get the name of the genetic code</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleCodonPref.html#getGeneticCodeName()">getGeneticCodeName()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleCodonPref.html" title="class in org.biojava.bio.symbol">SimpleCodonPref</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/RNATools.html#getGeneticCodeNames()">getGeneticCodeNames()</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/RNATools.html" title="class in org.biojava.bio.seq">RNATools</a></dt>
<dd>
<div class="block">Retrieve a Set containing the name of each genetic code.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLFormat.Terms.html#getGenomicTerm()">getGenomicTerm()</a></span> - Static method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLFormat.Terms.html" title="class in org.biojavax.bio.seq.io">EMBLFormat.Terms</a></dt>
<dd>
<div class="block">Getter for the Ensembl-specific 'genomic' term</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOTools.html#getGenpeptBuilderFactory()">getGenpeptBuilderFactory()</a></span> - Static method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOTools.html" title="class in org.biojava.bio.seq.io">SeqIOTools</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Get a default SequenceBuilderFactory for handling Genpept
files.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/ProteaseManager.html#getGlu_C_bicarbonate()">getGlu_C_bicarbonate()</a></span> - Static method in class org.biojava.bio.proteomics.<a href="./org/biojava/bio/proteomics/ProteaseManager.html" title="class in org.biojava.bio.proteomics">ProteaseManager</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/ProteaseManager.html#getGlu_C_phosphate()">getGlu_C_phosphate()</a></span> - Static method in class org.biojava.bio.proteomics.<a href="./org/biojava/bio/proteomics/ProteaseManager.html" title="class in org.biojava.bio.proteomics">ProteaseManager</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/GlyphFeatureRenderer.html#getGlyphForFilter(org.biojava.bio.seq.FeatureFilter)">getGlyphForFilter(FeatureFilter)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/GlyphFeatureRenderer.html" title="class in org.biojava.bio.gui.sequence">GlyphFeatureRenderer</a></dt>
<dd>
<div class="block">Returns the <a href="./org/biojava/bio/gui/glyph/Glyph.html" title="interface in org.biojava.bio.gui.glyph"><code>Glyph</code></a> object which is assigned to the given feature
filter.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/LogoContext.html#getGraphics()">getGraphics()</a></span> - Method in interface org.biojava.bio.gui.<a href="./org/biojava/bio/gui/LogoContext.html" title="interface in org.biojava.bio.gui">LogoContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Chain.html#getGroup(int)">getGroup(int)</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Chain.html" title="interface in org.biojava.bio.structure">Chain</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>use getAtomGroup or getSeqResGroup instead</i></div>
</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/ChainImpl.html#getGroup(int)">getGroup(int)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/ChainImpl.html" title="class in org.biojava.bio.structure">ChainImpl</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>use getAtomGroup or getSeqResGroup instead</i></div>
</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html#getGroup_PDB()">getGroup_PDB()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html" title="class in org.biojava.bio.structure.io.mmcif.model">AtomSite</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFRecord.html#getGroupAttributes()">getGroupAttributes()</a></span> - Method in interface org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFRecord.html" title="interface in org.biojava.bio.program.gff">GFFRecord</a></dt>
<dd>
<div class="block">A <span class="type">Map</span> containing the group / attribute information.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/SimpleGFFRecord.html#getGroupAttributes()">getGroupAttributes()</a></span> - Method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/SimpleGFFRecord.html" title="class in org.biojava.bio.program.gff">SimpleGFFRecord</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Chain.html#getGroupByPDB(java.lang.String)">getGroupByPDB(String)</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Chain.html" title="interface in org.biojava.bio.structure">Chain</a></dt>
<dd>
<div class="block">get a group by its PDB residue numbering.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/ChainImpl.html#getGroupByPDB(java.lang.String)">getGroupByPDB(String)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/ChainImpl.html" title="class in org.biojava.bio.structure">ChainImpl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/Agave2AgaveAnnotFilter.html#getGroupOrder(org.biojava.bio.Annotation)">getGroupOrder(Annotation)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/Agave2AgaveAnnotFilter.html" title="class in org.biojava.bio.seq.io.agave">Agave2AgaveAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEAnnotFilter.html#getGroupOrder(org.biojava.bio.Annotation)">getGroupOrder(Annotation)</a></span> - Method in interface org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEAnnotFilter.html" title="interface in org.biojava.bio.seq.io.agave">AGAVEAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/SimpleAnnotFilter.html#getGroupOrder(org.biojava.bio.Annotation)">getGroupOrder(Annotation)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/SimpleAnnotFilter.html" title="class in org.biojava.bio.seq.io.agave">SimpleAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Chain.html#getGroups(java.lang.String)">getGroups(String)</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Chain.html" title="interface in org.biojava.bio.structure">Chain</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>use getAtomGroups or getSeqResGroups instead</i></div>
</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Chain.html#getGroups()">getGroups()</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Chain.html" title="interface in org.biojava.bio.structure">Chain</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>use getAtomGroups or getSeqResGroups instead</i></div>
</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/ChainImpl.html#getGroups(java.lang.String)">getGroups(String)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/ChainImpl.html" title="class in org.biojava.bio.structure">ChainImpl</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>use getAtomGroups instead</i></div>
</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/ChainImpl.html#getGroups()">getGroups()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/ChainImpl.html" title="class in org.biojava.bio.structure">ChainImpl</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>use getAtomGroups instead</i></div>
</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Chain.html#getGroupsByPDB(java.lang.String, java.lang.String)">getGroupsByPDB(String, String)</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Chain.html" title="interface in org.biojava.bio.structure">Chain</a></dt>
<dd>
<div class="block">Get all groups that are located between two PDB residue numbers.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Chain.html#getGroupsByPDB(java.lang.String, java.lang.String, boolean)">getGroupsByPDB(String, String, boolean)</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Chain.html" title="interface in org.biojava.bio.structure">Chain</a></dt>
<dd>
<div class="block">Get all groups that are located between two PDB residue numbers.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/ChainImpl.html#getGroupsByPDB(java.lang.String, java.lang.String, boolean)">getGroupsByPDB(String, String, boolean)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/ChainImpl.html" title="class in org.biojava.bio.structure">ChainImpl</a></dt>
<dd>
<div class="block">Get all groups that are located between two PDB residue numbers.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/ChainImpl.html#getGroupsByPDB(java.lang.String, java.lang.String)">getGroupsByPDB(String, String)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/ChainImpl.html" title="class in org.biojava.bio.structure">ChainImpl</a></dt>
<dd>
<div class="block">Get all groups that are located between two PDB residue numbers.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/StructureTools.html#getH()">getH()</a></span> - Method in class org.biojava.bio.proteomics.<a href="./org/biojava/bio/proteomics/StructureTools.html" title="class in org.biojava.bio.proteomics">StructureTools</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/jama/QRDecomposition.html#getH()">getH()</a></span> - Method in class org.biojava.bio.structure.jama.<a href="./org/biojava/bio/structure/jama/QRDecomposition.html" title="class in org.biojava.bio.structure.jama">QRDecomposition</a></dt>
<dd>
<div class="block">Return the Householder vectors</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/StAXHandlerFactory.html#getHandler(org.biojava.bio.program.ssbind.SeqSimilarityStAXAdapter)">getHandler(SeqSimilarityStAXAdapter)</a></span> - Method in interface org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/StAXHandlerFactory.html" title="interface in org.biojava.bio.program.ssbind">StAXHandlerFactory</a></dt>
<dd>
<div class="block"><code>getHandler</code> returns an appropriate
<code>StAXContentHandler</code> implementation containing a
reference to a parent context.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/StAXHandlerFactory.html#getHandler(org.biojava.bio.seq.io.agave.StAXFeatureHandler)">getHandler(StAXFeatureHandler)</a></span> - Method in interface org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/StAXHandlerFactory.html" title="interface in org.biojava.bio.seq.io.agave">StAXHandlerFactory</a></dt>
<dd>
<div class="block">Return a suitable StAX content handler.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/filterxml/XMLFilterHandler.html#getHandler(java.lang.String, java.lang.String)">getHandler(String, String)</a></span> - Method in class org.biojava.bio.seq.io.filterxml.<a href="./org/biojava/bio/seq/io/filterxml/XMLFilterHandler.html" title="class in org.biojava.bio.seq.io.filterxml">XMLFilterHandler</a></dt>
<dd>
<div class="block">Retrieve a <code>FilterHandler</code> for the specified tag name.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game/StAXHandlerFactory.html#getHandler(org.biojava.bio.seq.io.game.StAXFeatureHandler)">getHandler(StAXFeatureHandler)</a></span> - Method in interface org.biojava.bio.seq.io.game.<a href="./org/biojava/bio/seq/io/game/StAXHandlerFactory.html" title="interface in org.biojava.bio.seq.io.game">StAXHandlerFactory</a></dt>
<dd>
<div class="block">Return a suitable StAX content handler.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game12/StAXHandlerFactory.html#getHandler(org.biojava.bio.seq.io.game12.StAXFeatureHandler)">getHandler(StAXFeatureHandler)</a></span> - Method in interface org.biojava.bio.seq.io.game12.<a href="./org/biojava/bio/seq/io/game12/StAXHandlerFactory.html" title="interface in org.biojava.bio.seq.io.game12">StAXHandlerFactory</a></dt>
<dd>
<div class="block">Return a suitable StAX content handler.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/StAXFeatureHandler.html#getHandlerStackIterator(int)">getHandlerStackIterator(int)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/StAXFeatureHandler.html" title="class in org.biojava.bio.seq.io.agave">StAXFeatureHandler</a></dt>
<dd>
<div class="block">return iterator to callbackStack</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/StAXPropertyHandler.html#getHandlerStackIterator()">getHandlerStackIterator()</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/StAXPropertyHandler.html" title="class in org.biojava.bio.seq.io.agave">StAXPropertyHandler</a></dt>
<dd>
<div class="block">get iterator for current stack starting at the position
below mine.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game/StAXFeatureHandler.html#getHandlerStackIterator(int)">getHandlerStackIterator(int)</a></span> - Method in class org.biojava.bio.seq.io.game.<a href="./org/biojava/bio/seq/io/game/StAXFeatureHandler.html" title="class in org.biojava.bio.seq.io.game">StAXFeatureHandler</a></dt>
<dd>
<div class="block">return iterator to callbackStack</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game/StAXPropertyHandler.html#getHandlerStackIterator()">getHandlerStackIterator()</a></span> - Method in class org.biojava.bio.seq.io.game.<a href="./org/biojava/bio/seq/io/game/StAXPropertyHandler.html" title="class in org.biojava.bio.seq.io.game">StAXPropertyHandler</a></dt>
<dd>
<div class="block">get iterator for current stack starting at the position
below mine.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Chain.html#getHeader()">getHeader()</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Chain.html" title="interface in org.biojava.bio.structure">Chain</a></dt>
<dd>
<div class="block">Returns the Header ( a Compound object) for this chain.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/ChainImpl.html#getHeader()">getHeader()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/ChainImpl.html" title="class in org.biojava.bio.structure">ChainImpl</a></dt>
<dd>
<div class="block">Returns the Header ( a Compound object) for this chain.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Structure.html#getHeader()">getHeader()</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Structure.html" title="interface in org.biojava.bio.structure">Structure</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>use getPDBHeader instead</i></div>
</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/StructureImpl.html#getHeader()">getHeader()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/StructureImpl.html" title="class in org.biojava.bio.structure">StructureImpl</a></dt>
<dd>
<div class="block">get Header data.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/FastaFormat.html#getHeader()">getHeader()</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/FastaFormat.html" title="class in org.biojavax.bio.seq.io">FastaFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/blast2html/HTMLRenderer.html#getHeaderDefinitions()">getHeaderDefinitions()</a></span> - Method in class org.biojava.bio.program.blast2html.<a href="./org/biojava/bio/program/blast2html/HTMLRenderer.html" title="class in org.biojava.bio.program.blast2html">HTMLRenderer</a></dt>
<dd>
<div class="block">Returns the appropriate style and javascript definitions for this
renderer.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Compound.html#getHeaderVars()">getHeaderVars()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure">Compound</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.html#getHeight()">getHeight()</a></span> - Method in class org.biojava.bio.chromatogram.graphic.<a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.html" title="class in org.biojava.bio.chromatogram.graphic">ChromatogramGraphic</a></dt>
<dd>
<div class="block">Returns the height of the whole graphic (in pixels).</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/RectangularBeadRenderer.html#getHeightScaling()">getHeightScaling()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/RectangularBeadRenderer.html" title="class in org.biojava.bio.gui.sequence">RectangularBeadRenderer</a></dt>
<dd>
<div class="block"><code>getHeightScaling</code> returns the state of the height
scaling policy.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/RectangularImapRenderer.html#getHeightScaling()">getHeightScaling()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/RectangularImapRenderer.html" title="class in org.biojava.bio.gui.sequence">RectangularImapRenderer</a></dt>
<dd>
<div class="block"><code>getHeightScaling</code> returns the state of the height
scaling policy.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/EntityPolySeq.html#getHetero()">getHetero()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/EntityPolySeq.html" title="class in org.biojava.bio.structure.io.mmcif.model">EntityPolySeq</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/PdbxPolySeqScheme.html#getHetero()">getHetero()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/PdbxPolySeqScheme.html" title="class in org.biojava.bio.structure.io.mmcif.model">PdbxPolySeqScheme</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLBioEntryDB.html#getHibernateSession()">getHibernateSession()</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLBioEntryDB.html" title="class in org.biojavax.bio.db.biosql">BioSQLBioEntryDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLRichSequenceDB.html#getHibernateSession()">getHibernateSession()</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLRichSequenceDB.html" title="class in org.biojavax.bio.db.biosql">BioSQLRichSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/BlastLikeSearchFilter.Node.html#getHitProperty(java.lang.Object)">getHitProperty(Object)</a></span> - Method in interface org.biojava.bio.search.<a href="./org/biojava/bio/search/BlastLikeSearchFilter.Node.html" title="interface in org.biojava.bio.search">BlastLikeSearchFilter.Node</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/FilteringContentHandler.html#getHitProperty(java.lang.Object)">getHitProperty(Object)</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/FilteringContentHandler.html" title="class in org.biojava.bio.search">FilteringContentHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SeqSimilaritySearchResult.html#getHits()">getHits()</a></span> - Method in interface org.biojava.bio.search.<a href="./org/biojava/bio/search/SeqSimilaritySearchResult.html" title="interface in org.biojava.bio.search">SeqSimilaritySearchResult</a></dt>
<dd>
<div class="block">Return all hits in this sequence similarity search result.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SequenceDBSearchResult.html#getHits()">getHits()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SequenceDBSearchResult.html" title="class in org.biojava.bio.search">SequenceDBSearchResult</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SimpleSeqSimilaritySearchResult.html#getHits()">getHits()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SimpleSeqSimilaritySearchResult.html" title="class in org.biojava.bio.search">SimpleSeqSimilaritySearchResult</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/Orthologue.html#getHomologeneID()">getHomologeneID()</a></span> - Method in interface org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/Orthologue.html" title="interface in org.biojava.bio.program.homologene">Orthologue</a></dt>
<dd>
<div class="block">get the Homologene ID.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/SimpleOrthologue.html#getHomologeneID()">getHomologeneID()</a></span> - Method in class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/SimpleOrthologue.html" title="class in org.biojava.bio.program.homologene">SimpleOrthologue</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/homol/HomologyFeature.html#getHomology()">getHomology()</a></span> - Method in interface org.biojava.bio.seq.homol.<a href="./org/biojava/bio/seq/homol/HomologyFeature.html" title="interface in org.biojava.bio.seq.homol">HomologyFeature</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleHomologyFeature.html#getHomology()">getHomology()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleHomologyFeature.html" title="class in org.biojava.bio.seq.impl">SimpleHomologyFeature</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.html#getHorizontalScale()">getHorizontalScale()</a></span> - Method in class org.biojava.bio.chromatogram.graphic.<a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.html" title="class in org.biojava.bio.chromatogram.graphic">ChromatogramGraphic</a></dt>
<dd>
<div class="block">Returns the in-use horizontal scale factor.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/StructureTools.html#getI()">getI()</a></span> - Method in class org.biojava.bio.proteomics.<a href="./org/biojava/bio/proteomics/StructureTools.html" title="class in org.biojava.bio.proteomics">StructureTools</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/indexdb/Record.html#getID()">getID()</a></span> - Method in interface org.biojava.bio.program.indexdb.<a href="./org/biojava/bio/program/indexdb/Record.html" title="interface in org.biojava.bio.program.indexdb">Record</a></dt>
<dd>
<div class="block"><code>getID</code> returns the primary identifier of the
record.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/indexdb/Record.Impl.html#getID()">getID()</a></span> - Method in class org.biojava.bio.program.indexdb.<a href="./org/biojava/bio/program/indexdb/Record.Impl.html" title="class in org.biojava.bio.program.indexdb">Record.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/unigene/UnigeneCluster.html#getID()">getID()</a></span> - Method in interface org.biojava.bio.program.unigene.<a href="./org/biojava/bio/program/unigene/UnigeneCluster.html" title="interface in org.biojava.bio.program.unigene">UnigeneCluster</a></dt>
<dd>
<div class="block">The public unigene ID.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/Index.html#getID()">getID()</a></span> - Method in interface org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/Index.html" title="interface in org.biojava.bio.seq.db">Index</a></dt>
<dd>
<div class="block">The ID of the sequence at this position in this file.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/SimpleIndex.html#getID()">getID()</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/SimpleIndex.html" title="class in org.biojava.bio.seq.db">SimpleIndex</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEDbId.html#getId()">getId()</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEDbId.html" title="class in org.biojava.bio.seq.io.agave">AGAVEDbId</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEIdAlias.html#getID()">getID()</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEIdAlias.html" title="class in org.biojava.bio.seq.io.agave">AGAVEIdAlias</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/AtomImpl.html#getId()">getId()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/AtomImpl.html" title="class in org.biojava.bio.structure">AtomImpl</a></dt>
<dd>
<div class="block">Get the Hibernate database ID.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Chain.html#getId()">getId()</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Chain.html" title="interface in org.biojava.bio.structure">Chain</a></dt>
<dd>
<div class="block">Get the ID used by Hibernate.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/ChainImpl.html#getId()">getId()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/ChainImpl.html" title="class in org.biojava.bio.structure">ChainImpl</a></dt>
<dd>
<div class="block">Get the ID used by Hibernate.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Compound.html#getId()">getId()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure">Compound</a></dt>
<dd>
<div class="block">get the ID used by Hibernate</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/DBRef.html#getId()">getId()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/DBRef.html" title="class in org.biojava.bio.structure">DBRef</a></dt>
<dd>
<div class="block">Get the ID used by Hibernate.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/HetatomImpl.html#getId()">getId()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/HetatomImpl.html" title="class in org.biojava.bio.structure">HetatomImpl</a></dt>
<dd>
<div class="block">the Hibernate database ID</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html#getId()">getId()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html" title="class in org.biojava.bio.structure.io.mmcif.model">AtomSite</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html#getId()">getId()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html" title="class in org.biojava.bio.structure.io.mmcif.model">ChemComp</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/DatabasePDBremark.html#getId()">getId()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/DatabasePDBremark.html" title="class in org.biojava.bio.structure.io.mmcif.model">DatabasePDBremark</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Entity.html#getId()">getId()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Entity.html" title="class in org.biojava.bio.structure.io.mmcif.model">Entity</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/StructAsym.html#getId()">getId()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/StructAsym.html" title="class in org.biojava.bio.structure.io.mmcif.model">StructAsym</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/StructRef.html#getId()">getId()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/StructRef.html" title="class in org.biojava.bio.structure.io.mmcif.model">StructRef</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/PDBHeader.html#getId()">getId()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/PDBHeader.html" title="class in org.biojava.bio.structure">PDBHeader</a></dt>
<dd>
<div class="block">Get the ID used by Hibernate.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Structure.html#getId()">getId()</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Structure.html" title="interface in org.biojava.bio.structure">Structure</a></dt>
<dd>
<div class="block">get the ID used by Hibernate</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/StructureImpl.html#getId()">getId()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/StructureImpl.html" title="class in org.biojava.bio.structure">StructureImpl</a></dt>
<dd>
<div class="block">get the ID used by Hibernate</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtCommentParser.Interaction.html#getID()">getID()</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtCommentParser.Interaction.html" title="class in org.biojavax.bio.seq.io">UniProtCommentParser.Interaction</a></dt>
<dd>
<div class="block">Getter for property ID.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimplePosition.html#getId()">getId()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimplePosition.html" title="class in org.biojavax.bio.seq">SimplePosition</a></dt>
<dd>
<div class="block">Gets the Hibernate ID.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichFeature.html#getId()">getId()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichFeature.html" title="class in org.biojavax.bio.seq">SimpleRichFeature</a></dt>
<dd>
<div class="block">Gets the Hibernate ID.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichFeatureRelationship.html#getId()">getId()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichFeatureRelationship.html" title="class in org.biojavax.bio.seq">SimpleRichFeatureRelationship</a></dt>
<dd>
<div class="block">Gets the Hibernate ID.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichLocation.html#getId()">getId()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichLocation.html" title="class in org.biojavax.bio.seq">SimpleRichLocation</a></dt>
<dd>
<div class="block">Gets the Hibernate ID.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/SimpleBioEntry.html#getId()">getId()</a></span> - Method in class org.biojavax.bio.<a href="./org/biojavax/bio/SimpleBioEntry.html" title="class in org.biojavax.bio">SimpleBioEntry</a></dt>
<dd>
<div class="block">Gets the Hibernate ID.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/SimpleBioEntryRelationship.html#getId()">getId()</a></span> - Method in class org.biojavax.bio.<a href="./org/biojavax/bio/SimpleBioEntryRelationship.html" title="class in org.biojavax.bio">SimpleBioEntryRelationship</a></dt>
<dd>
<div class="block">Gets the Hibernate ID.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/taxa/SimpleNCBITaxon.html#getId()">getId()</a></span> - Method in class org.biojavax.bio.taxa.<a href="./org/biojavax/bio/taxa/SimpleNCBITaxon.html" title="class in org.biojavax.bio.taxa">SimpleNCBITaxon</a></dt>
<dd>
<div class="block">Gets the Hibernate ID.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ontology/SimpleComparableOntology.html#getId()">getId()</a></span> - Method in class org.biojavax.ontology.<a href="./org/biojavax/ontology/SimpleComparableOntology.html" title="class in org.biojavax.ontology">SimpleComparableOntology</a></dt>
<dd>
<div class="block">Gets the Hibernate ID.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ontology/SimpleComparableTerm.html#getId()">getId()</a></span> - Method in class org.biojavax.ontology.<a href="./org/biojavax/ontology/SimpleComparableTerm.html" title="class in org.biojavax.ontology">SimpleComparableTerm</a></dt>
<dd>
<div class="block">Gets the Hibernate ID.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ontology/SimpleComparableTriple.html#getId()">getId()</a></span> - Method in class org.biojavax.ontology.<a href="./org/biojavax/ontology/SimpleComparableTriple.html" title="class in org.biojavax.ontology">SimpleComparableTriple</a></dt>
<dd>
<div class="block">Gets the Hibernate ID.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleComment.html#getId()">getId()</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleComment.html" title="class in org.biojavax">SimpleComment</a></dt>
<dd>
<div class="block">Gets the Hibernate ID.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleCrossRef.html#getId()">getId()</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleCrossRef.html" title="class in org.biojavax">SimpleCrossRef</a></dt>
<dd>
<div class="block">Gets the Hibernate ID.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleDocRef.html#getId()">getId()</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleDocRef.html" title="class in org.biojavax">SimpleDocRef</a></dt>
<dd>
<div class="block">Gets the Hibernate ID.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleNamespace.html#getId()">getId()</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleNamespace.html" title="class in org.biojavax">SimpleNamespace</a></dt>
<dd>
<div class="block">Gets the Hibernate ID.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/Agave2AgaveAnnotFilter.html#getIdAlias(org.biojava.bio.Annotation)">getIdAlias(Annotation)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/Agave2AgaveAnnotFilter.html" title="class in org.biojava.bio.seq.io.agave">Agave2AgaveAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEAnnotFilter.html#getIdAlias(org.biojava.bio.Annotation)">getIdAlias(Annotation)</a></span> - Method in interface org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEAnnotFilter.html" title="interface in org.biojava.bio.seq.io.agave">AGAVEAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/SimpleAnnotFilter.html#getIdAlias(org.biojava.bio.Annotation)">getIdAlias(Annotation)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/SimpleAnnotFilter.html" title="class in org.biojava.bio.seq.io.agave">SimpleAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/DBRef.html#getIdbnsBegin()">getIdbnsBegin()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/DBRef.html" title="class in org.biojava.bio.structure">DBRef</a></dt>
<dd>
<div class="block">Insertion code of initial residue of the segment, if PDB is the
reference.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/DBRef.html#getIdbnsEnd()">getIdbnsEnd()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/DBRef.html" title="class in org.biojava.bio.structure">DBRef</a></dt>
<dd>
<div class="block">Insertion code of the ending
residue of the segment, if PDB is
the reference.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/DBRef.html#getIdCode()">getIdCode()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/DBRef.html" title="class in org.biojava.bio.structure">DBRef</a></dt>
<dd>
<div class="block">get the idCode for this entry</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/PDBHeader.html#getIdCode()">getIdCode()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/PDBHeader.html" title="class in org.biojava.bio.structure">PDBHeader</a></dt>
<dd>
<div class="block">The PDB code for this protein structure.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/lsid/Identifiable.html#getIdentifier()">getIdentifier()</a></span> - Method in interface org.biojava.utils.lsid.<a href="./org/biojava/utils/lsid/Identifiable.html" title="interface in org.biojava.utils.lsid">Identifiable</a></dt>
<dd>
<div class="block">Return the identifier of this object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/BioEntry.html#getIdentifier()">getIdentifier()</a></span> - Method in interface org.biojavax.bio.<a href="./org/biojavax/bio/BioEntry.html" title="interface in org.biojavax.bio">BioEntry</a></dt>
<dd>
<div class="block">Returns the identifier of this bioentry.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/SimpleBioEntry.html#getIdentifier()">getIdentifier()</a></span> - Method in class org.biojavax.bio.<a href="./org/biojavax/bio/SimpleBioEntry.html" title="class in org.biojavax.bio">SimpleBioEntry</a></dt>
<dd>
<div class="block">Returns the identifier of this bioentry.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ontology/ComparableTerm.html#getIdentifier()">getIdentifier()</a></span> - Method in interface org.biojavax.ontology.<a href="./org/biojavax/ontology/ComparableTerm.html" title="interface in org.biojavax.ontology">ComparableTerm</a></dt>
<dd>
<div class="block">Returns the (optional) identifier associated with this term.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ontology/SimpleComparableTerm.html#getIdentifier()">getIdentifier()</a></span> - Method in class org.biojavax.ontology.<a href="./org/biojavax/ontology/SimpleComparableTerm.html" title="class in org.biojavax.ontology">SimpleComparableTerm</a></dt>
<dd>
<div class="block">Returns the (optional) identifier associated with this term.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/HashSequenceDB.html#getIDMaker()">getIDMaker()</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/HashSequenceDB.html" title="class in org.biojava.bio.seq.db">HashSequenceDB</a></dt>
<dd>
<div class="block">Retrieve the IDMaker associated with this database.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/HashRichSequenceDB.html#getIDMaker()">getIDMaker()</a></span> - Method in class org.biojavax.bio.db.<a href="./org/biojavax/bio/db/HashRichSequenceDB.html" title="class in org.biojavax.bio.db">HashRichSequenceDB</a></dt>
<dd>
<div class="block">Retrieve the IDMaker associated with this database.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/BioIndex.html#getIDs()">getIDs()</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/BioIndex.html" title="class in org.biojava.bio.seq.db">BioIndex</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/EmblCDROMIndexStore.html#getIDs()">getIDs()</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/EmblCDROMIndexStore.html" title="class in org.biojava.bio.seq.db">EmblCDROMIndexStore</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/IndexStore.html#getIDs()">getIDs()</a></span> - Method in interface org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/IndexStore.html" title="interface in org.biojava.bio.seq.db">IndexStore</a></dt>
<dd>
<div class="block">Retrieve the set of all current IDs.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/TabIndexStore.html#getIDs()">getIDs()</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/TabIndexStore.html" title="class in org.biojava.bio.seq.db">TabIndexStore</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/AlternativeAlignment.html#getIdx1()">getIdx1()</a></span> - Method in class org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/AlternativeAlignment.html" title="class in org.biojava.bio.structure.align.pairwise">AlternativeAlignment</a></dt>
<dd>
<div class="block">the positions of the structure equivalent positions in atom set 1</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/SequenceDisplay.html#getIdx1()">getIdx1()</a></span> - Method in class org.biojava.bio.structure.gui.<a href="./org/biojava/bio/structure/gui/SequenceDisplay.html" title="class in org.biojava.bio.structure.gui">SequenceDisplay</a></dt>
<dd>
<div class="block">get the identical position in the alignment</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/AlternativeAlignment.html#getIdx2()">getIdx2()</a></span> - Method in class org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/AlternativeAlignment.html" title="class in org.biojava.bio.structure.align.pairwise">AlternativeAlignment</a></dt>
<dd>
<div class="block">the positions of the structure equivalent atoms in atom set 2</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/SequenceDisplay.html#getIdx2()">getIdx2()</a></span> - Method in class org.biojava.bio.structure.gui.<a href="./org/biojava/bio/structure/gui/SequenceDisplay.html" title="class in org.biojava.bio.structure.gui">SequenceDisplay</a></dt>
<dd>
<div class="block">get the identical position in the alignment</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/helper/JointFragments.html#getIdxlist()">getIdxlist()</a></span> - Method in class org.biojava.bio.structure.align.helper.<a href="./org/biojava/bio/structure/align/helper/JointFragments.html" title="class in org.biojava.bio.structure.align.helper">JointFragments</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/abi/ABITrace.html#getImage(int, int)">getImage(int, int)</a></span> - Method in class org.biojava.bio.program.abi.<a href="./org/biojava/bio/program/abi/ABITrace.html" title="class in org.biojava.bio.program.abi">ABITrace</a></dt>
<dd>
<div class="block">Returns a BufferedImage that represents the entire trace.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/jama/EigenvalueDecomposition.html#getImagEigenvalues()">getImagEigenvalues()</a></span> - Method in class org.biojava.bio.structure.jama.<a href="./org/biojava/bio/structure/jama/EigenvalueDecomposition.html" title="class in org.biojava.bio.structure.jama">EigenvalueDecomposition</a></dt>
<dd>
<div class="block">Return the imaginary parts of the eigenvalues</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/BasicImapRenderer.html#getImageMap()">getImageMap()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/BasicImapRenderer.html" title="class in org.biojava.bio.gui.sequence">BasicImapRenderer</a></dt>
<dd>
<div class="block"><code>getImageMap</code> returns the current image map.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/RectangularImapRenderer.html#getImageMap()">getImageMap()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/RectangularImapRenderer.html" title="class in org.biojava.bio.gui.sequence">RectangularImapRenderer</a></dt>
<dd>
<div class="block"><code>getImageMap</code> returns the current image map.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/ZiggyImapRenderer.html#getImageMap()">getImageMap()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/ZiggyImapRenderer.html" title="class in org.biojava.bio.gui.sequence">ZiggyImapRenderer</a></dt>
<dd>
<div class="block"><code>getImageMap</code> returns the current image map.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/Services.html#getImplementationNames(java.lang.Class)">getImplementationNames(Class)</a></span> - Static method in class org.biojava.utils.<a href="./org/biojava/utils/Services.html" title="class in org.biojava.utils">Services</a></dt>
<dd>
<div class="block">Return a Set of names of implementations of the
given service interface in the classloader from
which BioJava was loaded.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/Services.html#getImplementationNames(java.lang.Class, java.lang.ClassLoader)">getImplementationNames(Class, ClassLoader)</a></span> - Static method in class org.biojava.utils.<a href="./org/biojava/utils/Services.html" title="class in org.biojava.utils">Services</a></dt>
<dd>
<div class="block">Return a List of names of implementations of the
given service interface available in a given
classloader.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/CircularRendererContext.html#getIndex(double)">getIndex(double)</a></span> - Method in interface org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/CircularRendererContext.html" title="interface in org.biojava.bio.gui.sequence">CircularRendererContext</a></dt>
<dd>
<div class="block">Calculate the position in the sequence relating to the angle.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SubCircularRendererContext.html#getIndex(double)">getIndex(double)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SubCircularRendererContext.html" title="class in org.biojava.bio.gui.sequence">SubCircularRendererContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/helper/GapArray.html#getIndex()">getIndex()</a></span> - Method in class org.biojava.bio.structure.align.helper.<a href="./org/biojava/bio/structure/align/helper/GapArray.html" title="class in org.biojava.bio.structure.align.helper">GapArray</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/IndexedSequenceDB.html#getIndexStore()">getIndexStore()</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/IndexedSequenceDB.html" title="class in org.biojava.bio.seq.db">IndexedSequenceDB</a></dt>
<dd>
<div class="block">Retrieve the IndexStore.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/naming/ObdaInitialContextFactory.html#getInitialContext(java.util.Hashtable)">getInitialContext(Hashtable)</a></span> - Method in class org.biojava.naming.<a href="./org/biojava/naming/ObdaInitialContextFactory.html" title="class in org.biojava.naming">ObdaInitialContextFactory</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/StrucAligParameters.html#getInitialK()">getInitialK()</a></span> - Method in class org.biojava.bio.structure.align.<a href="./org/biojava/bio/structure/align/StrucAligParameters.html" title="class in org.biojava.bio.structure.align">StrucAligParameters</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Author.html#getInitials()">getInitials()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Author.html" title="class in org.biojava.bio.structure">Author</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/FuzzyLocation.html#getInnerMax()">getInnerMax()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/FuzzyLocation.html" title="class in org.biojava.bio.symbol">FuzzyLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/FuzzyLocation.html#getInnerMin()">getInnerMin()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/FuzzyLocation.html" title="class in org.biojava.bio.symbol">FuzzyLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/process/OutputHandler.html#getInput()">getInput()</a></span> - Method in interface org.biojava.utils.process.<a href="./org/biojava/utils/process/OutputHandler.html" title="interface in org.biojava.utils.process">OutputHandler</a></dt>
<dd>
<div class="block">Gets the input stream.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/process/StreamPipe.html#getInput()">getInput()</a></span> - Method in class org.biojava.utils.process.<a href="./org/biojava/utils/process/StreamPipe.html" title="class in org.biojava.utils.process">StreamPipe</a></dt>
<dd>
<div class="block">Gets the input stream</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/process/WriterOutputHandler.html#getInput()">getInput()</a></span> - Method in class org.biojava.utils.process.<a href="./org/biojava/utils/process/WriterOutputHandler.html" title="class in org.biojava.utils.process">WriterOutputHandler</a></dt>
<dd>
<div class="block">Gets the input stream.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/process/ExternalProcess.html#getInputHandler()">getInputHandler()</a></span> - Method in class org.biojava.utils.process.<a href="./org/biojava/utils/process/ExternalProcess.html" title="class in org.biojava.utils.process">ExternalProcess</a></dt>
<dd>
<div class="block">Gets the input handler which is responsible for the standard input
of the external process.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/io/InputStreamProvider.html#getInputStream(java.lang.String)">getInputStream(String)</a></span> - Method in class org.biojava.utils.io.<a href="./org/biojava/utils/io/InputStreamProvider.html" title="class in org.biojava.utils.io">InputStreamProvider</a></dt>
<dd>
<div class="block">get an InputStream for this file</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/io/InputStreamProvider.html#getInputStream(java.io.File)">getInputStream(File)</a></span> - Method in class org.biojava.utils.io.<a href="./org/biojava/utils/io/InputStreamProvider.html" title="class in org.biojava.utils.io">InputStreamProvider</a></dt>
<dd>
<div class="block">get an InputStream for the file</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/SSBond.html#getInsCode1()">getInsCode1()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/SSBond.html" title="class in org.biojava.bio.structure">SSBond</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/SSBond.html#getInsCode2()">getInsCode2()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/SSBond.html" title="class in org.biojava.bio.structure">SSBond</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/INSDseqFormat.Terms.html#getINSDseqTerm()">getINSDseqTerm()</a></span> - Static method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/INSDseqFormat.Terms.html" title="class in org.biojavax.bio.seq.io">INSDseqFormat.Terms</a></dt>
<dd>
<div class="block">Getter for the INSDseq term</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/NeedlemanWunsch.html#getInsert()">getInsert()</a></span> - Method in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/NeedlemanWunsch.html" title="class in org.biojava.bio.alignment">NeedlemanWunsch</a></dt>
<dd>
<div class="block">Returns the current expenses of a single insert operation.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/ProfileHMM.html#getInsert(int)">getInsert(int)</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/ProfileHMM.html" title="class in org.biojava.bio.dp">ProfileHMM</a></dt>
<dd>
<div class="block">Retrieves the insert state at column indx.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/DBRef.html#getInsertBegin()">getInsertBegin()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/DBRef.html" title="class in org.biojava.bio.structure">DBRef</a></dt>
<dd>
<div class="block">Initial insertion code of the PDB sequence segment.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/DBRef.html#getInsertEnd()">getInsertEnd()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/DBRef.html" title="class in org.biojava.bio.structure">DBRef</a></dt>
<dd>
<div class="block">Ending insertion code of the PDB sequence segment.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/biosql/DBHelper.html#getInsertID(java.sql.Connection, java.lang.String, java.lang.String)">getInsertID(Connection, String, String)</a></span> - Method in class org.biojava.bio.seq.db.biosql.<a href="./org/biojava/bio/seq/db/biosql/DBHelper.html" title="class in org.biojava.bio.seq.db.biosql">DBHelper</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Returns the id value created during the last insert
command.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/biosql/HypersonicDBHelper.html#getInsertID(java.sql.Connection, java.lang.String, java.lang.String)">getInsertID(Connection, String, String)</a></span> - Method in class org.biojava.bio.seq.db.biosql.<a href="./org/biojava/bio/seq/db/biosql/HypersonicDBHelper.html" title="class in org.biojava.bio.seq.db.biosql">HypersonicDBHelper</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/biosql/MySQLDBHelper.html#getInsertID(java.sql.Connection, java.lang.String, java.lang.String)">getInsertID(Connection, String, String)</a></span> - Method in class org.biojava.bio.seq.db.biosql.<a href="./org/biojava/bio/seq/db/biosql/MySQLDBHelper.html" title="class in org.biojava.bio.seq.db.biosql">MySQLDBHelper</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/biosql/OracleDBHelper.html#getInsertID(java.sql.Connection, java.lang.String, java.lang.String)">getInsertID(Connection, String, String)</a></span> - Method in class org.biojava.bio.seq.db.biosql.<a href="./org/biojava/bio/seq/db/biosql/OracleDBHelper.html" title="class in org.biojava.bio.seq.db.biosql">OracleDBHelper</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/biosql/PostgreSQLDBHelper.html#getInsertID(java.sql.Connection, java.lang.String, java.lang.String)">getInsertID(Connection, String, String)</a></span> - Method in class org.biojava.bio.seq.db.biosql.<a href="./org/biojava/bio/seq/db/biosql/PostgreSQLDBHelper.html" title="class in org.biojava.bio.seq.db.biosql">PostgreSQLDBHelper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/biosql/UnknownDBHelper.html#getInsertID(java.sql.Connection, java.lang.String, java.lang.String)">getInsertID(Connection, String, String)</a></span> - Method in class org.biojava.bio.seq.db.biosql.<a href="./org/biojava/bio/seq/db/biosql/UnknownDBHelper.html" title="class in org.biojava.bio.seq.db.biosql">UnknownDBHelper</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/graphic/ChromatogramNonlinearScaler.Identity.html#getInstance()">getInstance()</a></span> - Static method in class org.biojava.bio.chromatogram.graphic.<a href="./org/biojava/bio/chromatogram/graphic/ChromatogramNonlinearScaler.Identity.html" title="class in org.biojava.bio.chromatogram.graphic">ChromatogramNonlinearScaler.Identity</a></dt>
<dd>
<div class="block">Retrieve the singleton instance of this class.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/IgnoreCountsTrainer.html#getInstance()">getInstance()</a></span> - Static method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/IgnoreCountsTrainer.html" title="class in org.biojava.bio.dist">IgnoreCountsTrainer</a></dt>
<dd>
<div class="block">Returns the global singleton instance of the IgnoreCountsTrainer.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/ProteaseManager.html#getInstance()">getInstance()</a></span> - Static method in class org.biojava.bio.proteomics.<a href="./org/biojava/bio/proteomics/ProteaseManager.html" title="class in org.biojava.bio.proteomics">ProteaseManager</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEAnnotFilterFactory.html#getInstance()">getInstance()</a></span> - Method in interface org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEAnnotFilterFactory.html" title="interface in org.biojava.bio.seq.io.agave">AGAVEAnnotFilterFactory</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/DoubleAlphabet.html#getInstance()">getInstance()</a></span> - Static method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/DoubleAlphabet.html" title="class in org.biojava.bio.symbol">DoubleAlphabet</a></dt>
<dd>
<div class="block">Retrieve the single DoubleAlphabet instance.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/IntegerAlphabet.html#getInstance()">getInstance()</a></span> - Static method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/IntegerAlphabet.html" title="class in org.biojava.bio.symbol">IntegerAlphabet</a></dt>
<dd>
<div class="block">Retrieve the single IntegerAlphabet instance.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SoftMaskedAlphabet.html#getInstance(org.biojava.bio.symbol.FiniteAlphabet)">getInstance(FiniteAlphabet)</a></span> - Static method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SoftMaskedAlphabet.html" title="class in org.biojava.bio.symbol">SoftMaskedAlphabet</a></dt>
<dd>
<div class="block">Generates a soft masked Alphabet where lowercase tokens are assumed to be
soft masked.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SoftMaskedAlphabet.html#getInstance(org.biojava.bio.symbol.FiniteAlphabet, org.biojava.bio.symbol.SoftMaskedAlphabet.MaskingDetector)">getInstance(FiniteAlphabet, SoftMaskedAlphabet.MaskingDetector)</a></span> - Static method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SoftMaskedAlphabet.html" title="class in org.biojava.bio.symbol">SoftMaskedAlphabet</a></dt>
<dd>
<div class="block">Creates a compound alphabet that is a hybrid of the alphabet that is to
be soft masked and a binary alphabet that indicates if any
<code>Symbol</code> is soft masked or not.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/taxa/EbiFormat.html#getInstance()">getInstance()</a></span> - Static method in class org.biojava.bio.taxa.<a href="./org/biojava/bio/taxa/EbiFormat.html" title="class in org.biojava.bio.taxa">EbiFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/naming/ObdaUriParser.html#getInstance()">getInstance()</a></span> - Static method in class org.biojava.naming.<a href="./org/biojava/naming/ObdaUriParser.html" title="class in org.biojava.naming">ObdaUriParser</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/walker/WalkerFactory.html#getInstance(java.lang.Class)">getInstance(Class)</a></span> - Static method in class org.biojava.utils.walker.<a href="./org/biojava/utils/walker/WalkerFactory.html" title="class in org.biojava.utils.walker">WalkerFactory</a></dt>
<dd>
<div class="block">Make a WalkerFactory that handles a Visitor for
a class of type typeClazz.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/walker/WalkerFactory.html#getInstance()">getInstance()</a></span> - Static method in class org.biojava.utils.walker.<a href="./org/biojava/utils/walker/WalkerFactory.html" title="class in org.biojava.utils.walker">WalkerFactory</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/io/LargeBuffer.html#getInt(long)">getInt(long)</a></span> - Method in class org.biojava.utils.io.<a href="./org/biojava/utils/io/LargeBuffer.html" title="class in org.biojava.utils.io">LargeBuffer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/io/LargeBuffer.html#getInt()">getInt()</a></span> - Method in class org.biojava.utils.io.<a href="./org/biojava/utils/io/LargeBuffer.html" title="class in org.biojava.utils.io">LargeBuffer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/OntoTools.html#getIntegerOntology()">getIntegerOntology()</a></span> - Static method in class org.biojava.ontology.<a href="./org/biojava/ontology/OntoTools.html" title="class in org.biojava.ontology">OntoTools</a></dt>
<dd>
<div class="block">Get the Ontology that defines integers.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html#getInteractions()">getInteractions()</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html" title="class in org.biojavax.bio.seq.io">UniProtCommentParser</a></dt>
<dd>
<div class="block">Getter for property interactions.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.html#getInternalSymbolList()">getInternalSymbolList()</a></span> - Method in interface org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.html" title="interface in org.biojavax.bio.seq">RichSequence</a></dt>
<dd>
<div class="block">A special function that returns the SymbolList that this RichSequence is
based around.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichSequence.html#getInternalSymbolList()">getInternalSymbolList()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichSequence.html" title="class in org.biojavax.bio.seq">SimpleRichSequence</a></dt>
<dd>
<div class="block">A special function that returns the SymbolList that this RichSequence is
based around.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/ThinRichSequence.html#getInternalSymbolList()">getInternalSymbolList()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/ThinRichSequence.html" title="class in org.biojavax.bio.seq">ThinRichSequence</a></dt>
<dd>
<div class="block">A special function that returns the SymbolList that this RichSequence is
based around.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/ChromatogramTools.html#getIntFromSymbolList(org.biojava.bio.symbol.SymbolList, int)">getIntFromSymbolList(SymbolList, int)</a></span> - Static method in class org.biojava.bio.chromatogram.<a href="./org/biojava/bio/chromatogram/ChromatogramTools.html" title="class in org.biojava.bio.chromatogram">ChromatogramTools</a></dt>
<dd>
<div class="block">Retrieves, unwraps, and returns an <code>int</code> from a
SymbolList containing <a href="./org/biojava/bio/symbol/IntegerAlphabet.IntegerSymbol.html" title="class in org.biojava.bio.symbol"><code>IntegerAlphabet.IntegerSymbol</code></a>s.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.html#getIntOption(org.biojava.bio.chromatogram.graphic.ChromatogramGraphic.Option)">getIntOption(ChromatogramGraphic.Option)</a></span> - Method in class org.biojava.bio.chromatogram.graphic.<a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.html" title="class in org.biojava.bio.chromatogram.graphic">ChromatogramGraphic</a></dt>
<dd>
<div class="block">Helper method for converting a <code>Number</code>-valued
option into an <code>int</code> primitive.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.html#getInvTransform()">getInvTransform()</a></span> - Method in class org.biojava.bio.chromatogram.graphic.<a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.html" title="class in org.biojava.bio.chromatogram.graphic">ChromatogramGraphic</a></dt>
<dd>
<div class="block">Returns a new AffineTransform describing the transformation from
output space to chromatogram space.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/IsoelectricPointCalc.html#getIsoelectricPoint(org.biojava.bio.symbol.SymbolList)">getIsoelectricPoint(SymbolList)</a></span> - Static method in class org.biojava.bio.proteomics.<a href="./org/biojava/bio/proteomics/IsoelectricPointCalc.html" title="class in org.biojava.bio.proteomics">IsoelectricPointCalc</a></dt>
<dd>
<div class="block">Static public method to compute the pI for a polypeptide in
denaturating and reduced conditions with both free ends.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html#getIsoforms()">getIsoforms()</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html" title="class in org.biojavax.bio.seq.io">UniProtCommentParser</a></dt>
<dd>
<div class="block">Getter for property isoforms.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtCommentParser.Isoform.html#getIsoIDs()">getIsoIDs()</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtCommentParser.Isoform.html" title="class in org.biojavax.bio.seq.io">UniProtCommentParser.Isoform</a></dt>
<dd>
<div class="block">Getter for property isoIDs.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/molbio/RestrictionEnzymeManager.html#getIsoschizomers(java.lang.String)">getIsoschizomers(String)</a></span> - Static method in class org.biojava.bio.molbio.<a href="./org/biojava/bio/molbio/RestrictionEnzymeManager.html" title="class in org.biojava.bio.molbio">RestrictionEnzymeManager</a></dt>
<dd>
<div class="block"><code>getIsoschizomers</code> returns an unmodifable set of the
isoschizomers of this enzyme.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/ItemValue.html#getItem()">getItem()</a></span> - Method in interface org.biojava.stats.svm.<a href="./org/biojava/stats/svm/ItemValue.html" title="interface in org.biojava.stats.svm">ItemValue</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/SimpleItemValue.html#getItem()">getItem()</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/SimpleItemValue.html" title="class in org.biojava.stats.svm">SimpleItemValue</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ListTools.Doublet.html#getIterator()">getIterator()</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/ListTools.Doublet.html" title="class in org.biojava.utils">ListTools.Doublet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ListTools.Triplet.html#getIterator()">getIterator()</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/ListTools.Triplet.html" title="class in org.biojava.utils">ListTools.Triplet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/Aggregator.html#getJoiner()">getJoiner()</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/Aggregator.html" title="class in org.biojava.bio.program.tagvalue">Aggregator</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/StrucAligParameters.html#getJoinRMSCutoff()">getJoinRMSCutoff()</a></span> - Method in class org.biojava.bio.structure.align.<a href="./org/biojava/bio/structure/align/StrucAligParameters.html" title="class in org.biojava.bio.structure.align">StrucAligParameters</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/biosql/DBHelper.html#getJoinStyle()">getJoinStyle()</a></span> - Method in class org.biojava.bio.seq.db.biosql.<a href="./org/biojava/bio/seq/db/biosql/DBHelper.html" title="class in org.biojava.bio.seq.db.biosql">DBHelper</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Returns the an object indicating the style of table joining that
this database should employ.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/biosql/OracleDBHelper.html#getJoinStyle()">getJoinStyle()</a></span> - Method in class org.biojava.bio.seq.db.biosql.<a href="./org/biojava/bio/seq/db/biosql/OracleDBHelper.html" title="class in org.biojava.bio.seq.db.biosql">OracleDBHelper</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/CompoundRichLocation.html#getJoinTerm()">getJoinTerm()</a></span> - Static method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/CompoundRichLocation.html" title="class in org.biojavax.bio.seq">CompoundRichLocation</a></dt>
<dd>
<div class="block">Getter for the "join" term</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Structure.html#getJournalArticle()">getJournalArticle()</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Structure.html" title="interface in org.biojava.bio.structure">Structure</a></dt>
<dd>
<div class="block">get the associated publication as defined by the JRNL records in a PDB
file.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/StructureImpl.html#getJournalArticle()">getJournalArticle()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/StructureImpl.html" title="class in org.biojava.bio.structure">StructureImpl</a></dt>
<dd>
<div class="block">get the associated publication as defined by the JRNL records in a PDB
file.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/JournalArticle.html#getJournalName()">getJournalName()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/JournalArticle.html" title="class in org.biojava.bio.structure">JournalArticle</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/aaindex/AAindex.html#getJournalReference()">getJournalReference()</a></span> - Method in class org.biojava.bio.proteomics.aaindex.<a href="./org/biojava/bio/proteomics/aaindex/AAindex.html" title="class in org.biojava.bio.proteomics.aaindex">AAindex</a></dt>
<dd>
<div class="block">Gets a reference to the journal which published the article about the
AAindex entry.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/SimpleSVMClassifierModel.html#getKernel()">getKernel()</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/SimpleSVMClassifierModel.html" title="class in org.biojava.stats.svm">SimpleSVMClassifierModel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/SVMClassifierModel.html#getKernel()">getKernel()</a></span> - Method in interface org.biojava.stats.svm.<a href="./org/biojava/stats/svm/SVMClassifierModel.html" title="interface in org.biojava.stats.svm">SVMClassifierModel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/SVMRegressionModel.html#getKernel()">getKernel()</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/SVMRegressionModel.html" title="class in org.biojava.stats.svm">SVMRegressionModel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/tools/ClassifierExample.PointClassifier.html#getKernel()">getKernel()</a></span> - Method in class org.biojava.stats.svm.tools.<a href="./org/biojava/stats/svm/tools/ClassifierExample.PointClassifier.html" title="class in org.biojava.stats.svm.tools">ClassifierExample.PointClassifier</a></dt>
<dd>
<div class="block">Retrieve the currently used kernel</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/SVMRegressionModel.html#getKernelValue(int, int)">getKernelValue(int, int)</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/SVMRegressionModel.html" title="class in org.biojava.stats.svm">SVMRegressionModel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/FeatureLabelRenderer.AnnotationLabelMaker.html#getKey()">getKey()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/FeatureLabelRenderer.AnnotationLabelMaker.html" title="class in org.biojava.bio.gui.sequence">FeatureLabelRenderer.AnnotationLabelMaker</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.AnnotationContains.html#getKey()">getKey()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.AnnotationContains.html" title="class in org.biojava.bio.seq">FeatureFilter.AnnotationContains</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ByAnnotation.html#getKey()">getKey()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ByAnnotation.html" title="class in org.biojava.bio.seq">FeatureFilter.ByAnnotation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.HasAnnotation.html#getKey()">getKey()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.HasAnnotation.html" title="class in org.biojava.bio.seq">FeatureFilter.HasAnnotation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/cache/KeyedWeakReference.html#getKey()">getKey()</a></span> - Method in class org.biojava.utils.cache.<a href="./org/biojava/utils/cache/KeyedWeakReference.html" title="class in org.biojava.utils.cache">KeyedWeakReference</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/Index2Model.html#getKeyPath(java.lang.String)">getKeyPath(String)</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/Index2Model.html" title="class in org.biojava.bio.program.tagvalue">Index2Model</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/indexdb/BioStoreFactory.html#getKeys()">getKeys()</a></span> - Method in class org.biojava.bio.program.indexdb.<a href="./org/biojava/bio/program/indexdb/BioStoreFactory.html" title="class in org.biojava.bio.program.indexdb">BioStoreFactory</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/Index2Model.html#getKeys()">getKeys()</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/Index2Model.html" title="class in org.biojava.bio.program.tagvalue">Index2Model</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/Agave2AgaveAnnotFilter.html#getKeyword(org.biojava.bio.Annotation)">getKeyword(Annotation)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/Agave2AgaveAnnotFilter.html" title="class in org.biojava.bio.seq.io.agave">Agave2AgaveAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEAnnotFilter.html#getKeyword(org.biojava.bio.Annotation)">getKeyword(Annotation)</a></span> - Method in interface org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEAnnotFilter.html" title="interface in org.biojava.bio.seq.io.agave">AGAVEAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/Embl2AgaveAnnotFilter.html#getKeyword(org.biojava.bio.Annotation)">getKeyword(Annotation)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/Embl2AgaveAnnotFilter.html" title="class in org.biojava.bio.seq.io.agave">Embl2AgaveAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/SimpleAnnotFilter.html#getKeyword(org.biojava.bio.Annotation)">getKeyword(Annotation)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/SimpleAnnotFilter.html" title="class in org.biojava.bio.seq.io.agave">SimpleAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.Terms.html#getKeywordTerm()">getKeywordTerm()</a></span> - Static method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.Terms.html" title="class in org.biojavax.bio.seq">RichSequence.Terms</a></dt>
<dd>
<div class="block">Getter for the keyword term</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html#getKineticsNote()">getKineticsNote()</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html" title="class in org.biojavax.bio.seq.io">UniProtCommentParser</a></dt>
<dd>
<div class="block">Getter for property kineticsNote.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/KnuthMorrisPrattSearch.html#getKmpNextTable()">getKmpNextTable()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/KnuthMorrisPrattSearch.html" title="class in org.biojava.bio.search">KnuthMorrisPrattSearch</a></dt>
<dd>
<div class="block">Returns the table of border lengths</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html#getKMs()">getKMs()</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html" title="class in org.biojavax.bio.seq.io">UniProtCommentParser</a></dt>
<dd>
<div class="block">Getter for property KMs.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/jama/CholeskyDecomposition.html#getL()">getL()</a></span> - Method in class org.biojava.bio.structure.jama.<a href="./org/biojava/bio/structure/jama/CholeskyDecomposition.html" title="class in org.biojava.bio.structure.jama">CholeskyDecomposition</a></dt>
<dd>
<div class="block">Return triangular factor.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/jama/LUDecomposition.html#getL()">getL()</a></span> - Method in class org.biojava.bio.structure.jama.<a href="./org/biojava/bio/structure/jama/LUDecomposition.html" title="class in org.biojava.bio.structure.jama">LUDecomposition</a></dt>
<dd>
<div class="block">Return lower triangular factor</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/AlignmentElement.html#getLabel()">getLabel()</a></span> - Method in interface org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/AlignmentElement.html" title="interface in org.biojava.bio.alignment">AlignmentElement</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/SimpleAlignmentElement.html#getLabel()">getLabel()</a></span> - Method in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/SimpleAlignmentElement.html" title="class in org.biojava.bio.alignment">SimpleAlignmentElement</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/AlignmentRenderer.html#getLabel()">getLabel()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/AlignmentRenderer.html" title="class in org.biojava.bio.gui.sequence">AlignmentRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SimpleLabelRenderer.html#getLabel()">getLabel()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SimpleLabelRenderer.html" title="class in org.biojava.bio.gui.sequence">SimpleLabelRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/StateMachine.BasicState.html#getLabel()">getLabel()</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/StateMachine.BasicState.html" title="class in org.biojava.bio.program.tagvalue">StateMachine.BasicState</a></dt>
<dd>
<div class="block">return the label of this class.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/StateMachine.State.html#getLabel()">getLabel()</a></span> - Method in interface org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/StateMachine.State.html" title="interface in org.biojava.bio.program.tagvalue">StateMachine.State</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/Agave2AgaveAnnotFilter.html#getLabel(org.biojava.bio.Annotation)">getLabel(Annotation)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/Agave2AgaveAnnotFilter.html" title="class in org.biojava.bio.seq.io.agave">Agave2AgaveAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEAnnotFilter.html#getLabel(org.biojava.bio.Annotation)">getLabel(Annotation)</a></span> - Method in interface org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEAnnotFilter.html" title="interface in org.biojava.bio.seq.io.agave">AGAVEAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/SimpleAnnotFilter.html#getLabel(org.biojava.bio.Annotation)">getLabel(Annotation)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/SimpleAnnotFilter.html" title="class in org.biojava.bio.seq.io.agave">SimpleAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/UkkonenSuffixTree.html#getLabel(org.biojava.bio.symbol.UkkonenSuffixTree.SuffixNode)">getLabel(UkkonenSuffixTree.SuffixNode)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/UkkonenSuffixTree.html" title="class in org.biojava.bio.symbol">UkkonenSuffixTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/tools/SVM_Light.LabelledVector.html#getLabel()">getLabel()</a></span> - Method in class org.biojava.stats.svm.tools.<a href="./org/biojava/stats/svm/tools/SVM_Light.LabelledVector.html" title="class in org.biojava.stats.svm.tools">SVM_Light.LabelledVector</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtCommentParser.Interaction.html#getLabel()">getLabel()</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtCommentParser.Interaction.html" title="class in org.biojavax.bio.seq.io">UniProtCommentParser.Interaction</a></dt>
<dd>
<div class="block">Getter for property label.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html#getLabel_alt_id()">getLabel_alt_id()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html" title="class in org.biojava.bio.structure.io.mmcif.model">AtomSite</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html#getLabel_asym_id()">getLabel_asym_id()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html" title="class in org.biojava.bio.structure.io.mmcif.model">AtomSite</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html#getLabel_atom_id()">getLabel_atom_id()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html" title="class in org.biojava.bio.structure.io.mmcif.model">AtomSite</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html#getLabel_comp_id()">getLabel_comp_id()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html" title="class in org.biojava.bio.structure.io.mmcif.model">AtomSite</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html#getLabel_entity_id()">getLabel_entity_id()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html" title="class in org.biojava.bio.structure.io.mmcif.model">AtomSite</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html#getLabel_seq_id()">getLabel_seq_id()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html" title="class in org.biojava.bio.structure.io.mmcif.model">AtomSite</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SimpleLabelRenderer.html#getLabelGlyph(org.biojava.bio.gui.sequence.SequenceRenderContext, java.awt.font.FontRenderContext)">getLabelGlyph(SequenceRenderContext, FontRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SimpleLabelRenderer.html" title="class in org.biojava.bio.gui.sequence">SimpleLabelRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/FeatureLabelRenderer.html#getLabelMaker()">getLabelMaker()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/FeatureLabelRenderer.html" title="class in org.biojava.bio.gui.sequence">FeatureLabelRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/AbstractULAlignment.SubULAlignment.html#getLabels()">getLabels()</a></span> - Method in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/AbstractULAlignment.SubULAlignment.html" title="class in org.biojava.bio.alignment">AbstractULAlignment.SubULAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/FlexibleAlignment.html#getLabels()">getLabels()</a></span> - Method in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/FlexibleAlignment.html" title="class in org.biojava.bio.alignment">FlexibleAlignment</a></dt>
<dd>
<div class="block">getLabels will return a list of labels in left to right order</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/SimpleStatePath.html#getLabels()">getLabels()</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/SimpleStatePath.html" title="class in org.biojava.bio.dp">SimpleStatePath</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/homol/SimilarityPairFeature.EmptyPairwiseAlignment.html#getLabels()">getLabels()</a></span> - Method in class org.biojava.bio.seq.homol.<a href="./org/biojava/bio/seq/homol/SimilarityPairFeature.EmptyPairwiseAlignment.html" title="class in org.biojava.bio.seq.homol">SimilarityPairFeature.EmptyPairwiseAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/Alignment.html#getLabels()">getLabels()</a></span> - Method in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/Alignment.html" title="interface in org.biojava.bio.symbol">Alignment</a></dt>
<dd>
<div class="block">
The list of SymbolLists in the alignment.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/RelabeledAlignment.html#getLabels()">getLabels()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/RelabeledAlignment.html" title="class in org.biojava.bio.symbol">RelabeledAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleAlignment.html#getLabels()">getLabels()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleAlignment.html" title="class in org.biojava.bio.symbol">SimpleAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/FlexibleAlignment.html#getLabelsAt(int)">getLabelsAt(int)</a></span> - Method in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/FlexibleAlignment.html" title="class in org.biojava.bio.alignment">FlexibleAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/DiagonalAddKernel.html#getLambda()">getLambda()</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/DiagonalAddKernel.html" title="class in org.biojava.stats.svm">DiagonalAddKernel</a></dt>
<dd>
<div class="block">Retrieve the scale factor.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/AnnotationBuilder.html#getLast()">getLast()</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/AnnotationBuilder.html" title="class in org.biojava.bio.program.tagvalue">AnnotationBuilder</a></dt>
<dd>
<div class="block">
Get the last complete annotation built.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/AbstractTrainer.html#getLastScore()">getLastScore()</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/AbstractTrainer.html" title="class in org.biojava.bio.dp">AbstractTrainer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/TrainingAlgorithm.html#getLastScore()">getLastScore()</a></span> - Method in interface org.biojava.bio.dp.<a href="./org/biojava/bio/dp/TrainingAlgorithm.html" title="interface in org.biojava.bio.dp">TrainingAlgorithm</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ListTools.SeriesList.html#getLeader()">getLeader()</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/ListTools.SeriesList.html" title="class in org.biojava.utils">ListTools.SeriesList</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/HeadlessRenderContext.html#getLeadingBorder()">getLeadingBorder()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/HeadlessRenderContext.html" title="class in org.biojava.bio.gui.sequence">HeadlessRenderContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PairwiseSequencePanel.html#getLeadingBorder()">getLeadingBorder()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PairwiseSequencePanel.html" title="class in org.biojava.bio.gui.sequence">PairwiseSequencePanel</a></dt>
<dd>
<div class="block"><code>getLeadingBorder</code> returns the leading border of the
primary sequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePanel.html#getLeadingBorder()">getLeadingBorder()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePanel.html" title="class in org.biojava.bio.gui.sequence">SequencePanel</a></dt>
<dd>
<div class="block">Retrieve the object that encapsulates the leading border area - the space
before sequence information is rendered.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePoster.html#getLeadingBorder()">getLeadingBorder()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePoster.html" title="class in org.biojava.bio.gui.sequence">SequencePoster</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Retrieve the object that encapsulates the leading border area - the space
before sequence information is rendered.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequenceRenderContext.html#getLeadingBorder()">getLeadingBorder()</a></span> - Method in interface org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequenceRenderContext.html" title="interface in org.biojava.bio.gui.sequence">SequenceRenderContext</a></dt>
<dd>
<div class="block">Gets the LeadingBorder attribute of the SequenceRenderContext object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SubPairwiseRenderContext.html#getLeadingBorder()">getLeadingBorder()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SubPairwiseRenderContext.html" title="class in org.biojava.bio.gui.sequence">SubPairwiseRenderContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SubSequenceRenderContext.html#getLeadingBorder()">getLeadingBorder()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SubSequenceRenderContext.html" title="class in org.biojava.bio.gui.sequence">SubSequenceRenderContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/TranslatedSequencePanel.html#getLeadingBorder()">getLeadingBorder()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/TranslatedSequencePanel.html" title="class in org.biojava.bio.gui.sequence">TranslatedSequencePanel</a></dt>
<dd>
<div class="block"><code>getLeadingBorder</code> returns the leading border.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/BumpedRenderer.html#getLeadingPixles()">getLeadingPixles()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/BumpedRenderer.html" title="class in org.biojava.bio.gui.sequence">BumpedRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/taxa/NCBITaxon.html#getLeftValue()">getLeftValue()</a></span> - Method in interface org.biojavax.bio.taxa.<a href="./org/biojavax/bio/taxa/NCBITaxon.html" title="interface in org.biojavax.bio.taxa">NCBITaxon</a></dt>
<dd>
<div class="block">Gets the left value.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/taxa/SimpleNCBITaxon.html#getLeftValue()">getLeftValue()</a></span> - Method in class org.biojavax.bio.taxa.<a href="./org/biojavax/bio/taxa/SimpleNCBITaxon.html" title="class in org.biojavax.bio.taxa">SimpleNCBITaxon</a></dt>
<dd>
<div class="block">Gets the left value.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/indexdb/Record.html#getLength()">getLength()</a></span> - Method in interface org.biojava.bio.program.indexdb.<a href="./org/biojava/bio/program/indexdb/Record.html" title="interface in org.biojava.bio.program.indexdb">Record</a></dt>
<dd>
<div class="block"><code>getLength</code> returns the length of the record in
bytes.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/indexdb/Record.Impl.html#getLength()">getLength()</a></span> - Method in class org.biojava.bio.program.indexdb.<a href="./org/biojava/bio/program/indexdb/Record.Impl.html" title="class in org.biojava.bio.program.indexdb">Record.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SeqContentPattern.html#getLength()">getLength()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SeqContentPattern.html" title="class in org.biojava.bio.search">SeqContentPattern</a></dt>
<dd>
<div class="block">Get the current length.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/Index.html#getLength()">getLength()</a></span> - Method in interface org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/Index.html" title="interface in org.biojava.bio.seq.db">Index</a></dt>
<dd>
<div class="block">The entry can be slurped out of the file by grabbing length bytes from
start.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/SimpleIndex.html#getLength()">getLength()</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/SimpleIndex.html" title="class in org.biojava.bio.seq.db">SimpleIndex</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/FragmentPair.html#getLength()">getLength()</a></span> - Method in class org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/FragmentPair.html" title="class in org.biojava.bio.structure.align.pairwise">FragmentPair</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Chain.html#getLength()">getLength()</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Chain.html" title="interface in org.biojava.bio.structure">Chain</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>please use getAtomLength or getLengthSeqRes instead</i></div>
</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/ChainImpl.html#getLength()">getLength()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/ChainImpl.html" title="class in org.biojava.bio.structure">ChainImpl</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>use getAtomLength instead</i></div>
</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/CircularLocation.html#getLength()">getLength()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/CircularLocation.html" title="class in org.biojava.bio.symbol">CircularLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/RepeatedCharSequence.html#getLength()">getLength()</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/RepeatedCharSequence.html" title="class in org.biojava.utils">RepeatedCharSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Chain.html#getLengthAminos()">getLengthAminos()</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Chain.html" title="interface in org.biojava.bio.structure">Chain</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>use getAtomGroups("amino").size() instead.</i></div>
</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/ChainImpl.html#getLengthAminos()">getLengthAminos()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/ChainImpl.html" title="class in org.biojava.bio.structure">ChainImpl</a></dt>
<dd>
<div class="block">returns the length of the AminoAcids in the ATOM records of this chain.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/StAXFeatureHandler.html#getLevel()">getLevel()</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/StAXFeatureHandler.html" title="class in org.biojava.bio.seq.io.agave">StAXFeatureHandler</a></dt>
<dd>
<div class="block">return current stack level.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game/StAXFeatureHandler.html#getLevel()">getLevel()</a></span> - Method in class org.biojava.bio.seq.io.game.<a href="./org/biojava/bio/seq/io/game/StAXFeatureHandler.html" title="class in org.biojava.bio.seq.io.game">StAXFeatureHandler</a></dt>
<dd>
<div class="block">return current stack level.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/cache/FixedSizeCache.html#getLimit()">getLimit()</a></span> - Method in class org.biojava.utils.cache.<a href="./org/biojava/utils/cache/FixedSizeCache.html" title="class in org.biojava.utils.cache">FixedSizeCache</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ParserException.html#getLine()">getLine()</a></span> - Method in exception org.biojava.utils.<a href="./org/biojava/utils/ParserException.html" title="class in org.biojava.utils">ParserException</a></dt>
<dd>
<div class="block">Get the text of the line where the exception occured.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/ParserException.html#getLineNumber()">getLineNumber()</a></span> - Method in exception org.biojava.utils.<a href="./org/biojava/utils/ParserException.html" title="class in org.biojava.utils">ParserException</a></dt>
<dd>
<div class="block">Get the line number in the stream where this exception occured.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePoster.html#getLines()">getLines()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePoster.html" title="class in org.biojava.bio.gui.sequence">SequencePoster</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Retrieve the number of lines that the sequence will be rendered over.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/phred/PhredFormat.html#getLineWidth()">getLineWidth()</a></span> - Method in class org.biojava.bio.program.phred.<a href="./org/biojava/bio/program/phred/PhredFormat.html" title="class in org.biojava.bio.program.phred">PhredFormat</a></dt>
<dd>
<div class="block">Retrive the current line width.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/FastaFormat.html#getLineWidth()">getLineWidth()</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/FastaFormat.html" title="class in org.biojava.bio.seq.io">FastaFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Retrive the current line width.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/RichSequenceFormat.BasicFormat.html#getLineWidth()">getLineWidth()</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/RichSequenceFormat.BasicFormat.html" title="class in org.biojavax.bio.seq.io">RichSequenceFormat.BasicFormat</a></dt>
<dd>
<div class="block">Retrive the current line width.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/RichSequenceFormat.html#getLineWidth()">getLineWidth()</a></span> - Method in interface org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/RichSequenceFormat.html" title="interface in org.biojavax.bio.seq.io">RichSequenceFormat</a></dt>
<dd>
<div class="block">Retrive the current line width.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/DASLink.html#getLinkURL()">getLinkURL()</a></span> - Method in class org.biojava.bio.program.das.<a href="./org/biojava/bio/program/das/DASLink.html" title="class in org.biojava.bio.program.das">DASLink</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/ParserListener.html#getListener()">getListener()</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/ParserListener.html" title="class in org.biojava.bio.program.tagvalue">ParserListener</a></dt>
<dd>
<div class="block"><code>getListener</code> returns the listener of the pair.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/StateMachine.BasicState.html#getListener()">getListener()</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/StateMachine.BasicState.html" title="class in org.biojava.bio.program.tagvalue">StateMachine.BasicState</a></dt>
<dd>
<div class="block">return the TagValueListener assigned to this State.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/StateMachine.State.html#getListener()">getListener()</a></span> - Method in interface org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/StateMachine.State.html" title="interface in org.biojava.bio.program.tagvalue">StateMachine.State</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/TagDelegator.html#getListener(java.lang.Object)">getListener(Object)</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/TagDelegator.html" title="class in org.biojava.bio.program.tagvalue">TagDelegator</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/Unchangeable.html#getListeners(org.biojava.utils.ChangeType)">getListeners(ChangeType)</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/Unchangeable.html" title="class in org.biojava.utils">Unchangeable</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/aaindex/AAindex.html#getLITDBEntryNumbers()">getLITDBEntryNumbers()</a></span> - Method in class org.biojava.bio.proteomics.aaindex.<a href="./org/biojava/bio/proteomics/aaindex/AAindex.html" title="class in org.biojava.bio.proteomics.aaindex">AAindex</a></dt>
<dd>
<div class="block">Gets the list of literature database identifiers for the AAindex entry.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/AlignmentElement.html#getLoc()">getLoc()</a></span> - Method in interface org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/AlignmentElement.html" title="interface in org.biojava.bio.alignment">AlignmentElement</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/SimpleAlignmentElement.html#getLoc()">getLoc()</a></span> - Method in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/SimpleAlignmentElement.html" title="class in org.biojava.bio.alignment">SimpleAlignmentElement</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/indexdb/BioStore.html#getLocation()">getLocation()</a></span> - Method in class org.biojava.bio.program.indexdb.<a href="./org/biojava/bio/program/indexdb/BioStore.html" title="class in org.biojava.bio.program.indexdb">BioStore</a></dt>
<dd>
<div class="block"><code>getLocation</code> returns the directory where the index
is located.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/Feature.html#getLocation()">getLocation()</a></span> - Method in interface org.biojava.bio.seq.<a href="./org/biojava/bio/seq/Feature.html" title="interface in org.biojava.bio.seq">Feature</a></dt>
<dd>
<div class="block">The location of this feature.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ContainedByLocation.html#getLocation()">getLocation()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ContainedByLocation.html" title="class in org.biojava.bio.seq">FeatureFilter.ContainedByLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.OverlapsLocation.html#getLocation()">getLocation()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.OverlapsLocation.html" title="class in org.biojava.bio.seq">FeatureFilter.OverlapsLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ShadowContainedByLocation.html#getLocation()">getLocation()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ShadowContainedByLocation.html" title="class in org.biojava.bio.seq">FeatureFilter.ShadowContainedByLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ShadowOverlapsLocation.html#getLocation()">getLocation()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ShadowOverlapsLocation.html" title="class in org.biojava.bio.seq">FeatureFilter.ShadowOverlapsLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleFeature.html#getLocation()">getLocation()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleFeature.html" title="class in org.biojava.bio.seq.impl">SimpleFeature</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/RemoteFeature.Region.html#getLocation()">getLocation()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/RemoteFeature.Region.html" title="class in org.biojava.bio.seq">RemoteFeature.Region</a></dt>
<dd>
<div class="block">Retrieve the Location of the Region.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichFeature.html#getLocation()">getLocation()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichFeature.html" title="class in org.biojavax.bio.seq">SimpleRichFeature</a></dt>
<dd>
<div class="block">The location of this feature.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/DocRef.html#getLocation()">getLocation()</a></span> - Method in interface org.biojavax.<a href="./org/biojavax/DocRef.html" title="interface in org.biojavax">DocRef</a></dt>
<dd>
<div class="block">Returns a textual description of the document reference.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/RankedDocRef.html#getLocation()">getLocation()</a></span> - Method in interface org.biojavax.<a href="./org/biojavax/RankedDocRef.html" title="interface in org.biojavax">RankedDocRef</a></dt>
<dd>
<div class="block">If this object was constructed using a location instead of two integers,
then this method will return that location.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleDocRef.html#getLocation()">getLocation()</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleDocRef.html" title="class in org.biojavax">SimpleDocRef</a></dt>
<dd>
<div class="block">Returns a textual description of the document reference.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleRankedDocRef.html#getLocation()">getLocation()</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleRankedDocRef.html" title="class in org.biojavax">SimpleRankedDocRef</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/xff/FeatureHandler.html#getLocationHandler()">getLocationHandler()</a></span> - Method in class org.biojava.bio.program.xff.<a href="./org/biojava/bio/program/xff/FeatureHandler.html" title="class in org.biojava.bio.program.xff">FeatureHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.Terms.html#getLocationSequenceTerm()">getLocationSequenceTerm()</a></span> - Static method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.Terms.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat.Terms</a></dt>
<dd>
<div class="block">Getter for the location seq term</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/ParserException.html#getLocator()">getLocator()</a></span> - Method in exception org.biojava.utils.<a href="./org/biojava/utils/ParserException.html" title="class in org.biojava.utils">ParserException</a></dt>
<dd>
<div class="block">Get a locator for the stream which caused this exception.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/Orthologue.html#getLocusID()">getLocusID()</a></span> - Method in interface org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/Orthologue.html" title="interface in org.biojava.bio.program.homologene">Orthologue</a></dt>
<dd>
<div class="block">get the locus ID associated with this orthologue.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/SimpleOrthologue.html#getLocusID()">getLocusID()</a></span> - Method in class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/SimpleOrthologue.html" title="class in org.biojava.bio.program.homologene">SimpleOrthologue</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/TextBlock.html#getLogoFont()">getLogoFont()</a></span> - Method in class org.biojava.bio.gui.<a href="./org/biojava/bio/gui/TextBlock.html" title="class in org.biojava.bio.gui">TextBlock</a></dt>
<dd>
<div class="block">Retrieve the current font.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/TextLogoPainter.html#getLogoFont()">getLogoFont()</a></span> - Method in class org.biojava.bio.gui.<a href="./org/biojava/bio/gui/TextLogoPainter.html" title="class in org.biojava.bio.gui">TextLogoPainter</a></dt>
<dd>
<div class="block">Retrieve the current font.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/DistributionLogo.html#getLogoPainter()">getLogoPainter()</a></span> - Method in class org.biojava.bio.gui.<a href="./org/biojava/bio/gui/DistributionLogo.html" title="class in org.biojava.bio.gui">DistributionLogo</a></dt>
<dd>
<div class="block">Retrieve the current logo painter.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/io/LargeBuffer.html#getLong(long)">getLong(long)</a></span> - Method in class org.biojava.utils.io.<a href="./org/biojava/utils/io/LargeBuffer.html" title="class in org.biojava.utils.io">LargeBuffer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/io/LargeBuffer.html#getLong()">getLong()</a></span> - Method in class org.biojava.utils.io.<a href="./org/biojava/utils/io/LargeBuffer.html" title="class in org.biojava.utils.io">LargeBuffer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#getLs_d_res_high()">getLs_d_res_high()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#getLs_d_res_low()">getLs_d_res_low()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#getLs_number_parameters()">getLs_number_parameters()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#getLs_number_reflns_all()">getLs_number_reflns_all()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#getLs_number_reflns_obs()">getLs_number_reflns_obs()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#getLs_number_reflns_R_free()">getLs_number_reflns_R_free()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#getLs_number_restraints()">getLs_number_restraints()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#getLs_percent_reflns_obs()">getLs_percent_reflns_obs()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#getLs_percent_reflns_R_free()">getLs_percent_reflns_R_free()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#getLs_R_factor_all()">getLs_R_factor_all()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#getLs_R_factor_obs()">getLs_R_factor_obs()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#getLs_R_factor_R_free()">getLs_R_factor_R_free()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#getLs_R_factor_R_free_error()">getLs_R_factor_R_free_error()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#getLs_R_factor_R_free_error_details()">getLs_R_factor_R_free_error_details()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#getLs_R_factor_R_work()">getLs_R_factor_R_work()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#getLs_redundancy_reflns_obs()">getLs_redundancy_reflns_obs()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#getLs_wR_factor_R_free()">getLs_wR_factor_R_free()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#getLs_wR_factor_R_work()">getLs_wR_factor_R_work()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/formats/Embl.html#getLSID()">getLSID()</a></span> - Method in class org.biojava.bio.program.formats.<a href="./org/biojava/bio/program/formats/Embl.html" title="class in org.biojava.bio.program.formats">Embl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/formats/Enzyme.html#getLSID()">getLSID()</a></span> - Method in class org.biojava.bio.program.formats.<a href="./org/biojava/bio/program/formats/Enzyme.html" title="class in org.biojava.bio.program.formats">Enzyme</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/formats/Format.html#getLSID()">getLSID()</a></span> - Method in interface org.biojava.bio.program.formats.<a href="./org/biojava/bio/program/formats/Format.html" title="interface in org.biojava.bio.program.formats">Format</a></dt>
<dd>
<div class="block">Retrieve the LSID associated with this format.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/formats/Ligand.Compound.html#getLSID()">getLSID()</a></span> - Method in class org.biojava.bio.program.formats.<a href="./org/biojava/bio/program/formats/Ligand.Compound.html" title="class in org.biojava.bio.program.formats">Ligand.Compound</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/formats/Ligand.Enzyme.html#getLSID()">getLSID()</a></span> - Method in class org.biojava.bio.program.formats.<a href="./org/biojava/bio/program/formats/Ligand.Enzyme.html" title="class in org.biojava.bio.program.formats">Ligand.Enzyme</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/formats/Ligand.Reaction.html#getLSID()">getLSID()</a></span> - Method in class org.biojava.bio.program.formats.<a href="./org/biojava/bio/program/formats/Ligand.Reaction.html" title="class in org.biojava.bio.program.formats">Ligand.Reaction</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/formats/Swissprot.html#getLSID()">getLSID()</a></span> - Method in class org.biojava.bio.program.formats.<a href="./org/biojava/bio/program/formats/Swissprot.html" title="class in org.biojava.bio.program.formats">Swissprot</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/ProteaseManager.html#getLys_C()">getLys_C()</a></span> - Static method in class org.biojava.bio.proteomics.<a href="./org/biojava/bio/proteomics/ProteaseManager.html" title="class in org.biojava.bio.proteomics">ProteaseManager</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/MagicalState.html#getMagicalState(org.biojava.bio.symbol.Alphabet, int)">getMagicalState(Alphabet, int)</a></span> - Static method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/MagicalState.html" title="class in org.biojava.bio.dp">MagicalState</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/StateMachine.html#getMagicalState()">getMagicalState()</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/StateMachine.html" title="class in org.biojava.bio.program.tagvalue">StateMachine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/molbio/RestrictionMapper.html#getMapAll()">getMapAll()</a></span> - Method in class org.biojava.bio.molbio.<a href="./org/biojava/bio/molbio/RestrictionMapper.html" title="class in org.biojava.bio.molbio">RestrictionMapper</a></dt>
<dd>
<div class="block"><code>getMapAll</code> returns whether all sites should be
marked, including those which have recognition sites within the
sequence, but cut outside it.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/Agave2AgaveAnnotFilter.html#getMapLocation(org.biojava.bio.Annotation)">getMapLocation(Annotation)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/Agave2AgaveAnnotFilter.html" title="class in org.biojava.bio.seq.io.agave">Agave2AgaveAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEAnnotFilter.html#getMapLocation(org.biojava.bio.Annotation)">getMapLocation(Annotation)</a></span> - Method in interface org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEAnnotFilter.html" title="interface in org.biojava.bio.seq.io.agave">AGAVEAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/SimpleAnnotFilter.html#getMapLocation(org.biojava.bio.Annotation)">getMapLocation(Annotation)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/SimpleAnnotFilter.html" title="class in org.biojava.bio.seq.io.agave">SimpleAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/AnnotationRenamer.html#getMapper()">getMapper()</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/AnnotationRenamer.html" title="class in org.biojava.bio">AnnotationRenamer</a></dt>
<dd>
<div class="block"><code>getMapper</code> returns the <code>TagMapper</code> being
used to remap the <code>Annotation</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/TagRenamer.html#getMapper()">getMapper()</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/TagRenamer.html" title="class in org.biojava.bio.program.tagvalue">TagRenamer</a></dt>
<dd>
<div class="block">Retrieve the mapper used to rename tags</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/Agave2AgaveAnnotFilter.html#getMapPosition(org.biojava.bio.Annotation)">getMapPosition(Annotation)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/Agave2AgaveAnnotFilter.html" title="class in org.biojava.bio.seq.io.agave">Agave2AgaveAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEAnnotFilter.html#getMapPosition(org.biojava.bio.Annotation)">getMapPosition(Annotation)</a></span> - Method in interface org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEAnnotFilter.html" title="interface in org.biojava.bio.seq.io.agave">AGAVEAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/SimpleAnnotFilter.html#getMapPosition(org.biojava.bio.Annotation)">getMapPosition(Annotation)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/SimpleAnnotFilter.html" title="class in org.biojava.bio.seq.io.agave">SimpleAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEMapLocation.html#getMapType()">getMapType()</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEMapLocation.html" title="class in org.biojava.bio.seq.io.agave">AGAVEMapLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/DataSource.html#getMapURL()">getMapURL()</a></span> - Method in class org.biojava.bio.program.das.<a href="./org/biojava/bio/program/das/DataSource.html" title="class in org.biojava.bio.program.das">DataSource</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SoftMaskedAlphabet.html#getMaskedAlphabet()">getMaskedAlphabet()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SoftMaskedAlphabet.html" title="class in org.biojava.bio.symbol">SoftMaskedAlphabet</a></dt>
<dd>
<div class="block">Gets the <CODE>Alphabet</CODE> upon which masking is being applied</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SoftMaskedAlphabet.html#getMaskingDetector()">getMaskingDetector()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SoftMaskedAlphabet.html" title="class in org.biojava.bio.symbol">SoftMaskedAlphabet</a></dt>
<dd>
<div class="block">Getter for the <code>MaskingDetector<code></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/MassCalc.html#getMass(org.biojava.bio.symbol.SymbolList, java.lang.String, boolean)">getMass(SymbolList, String, boolean)</a></span> - Static method in class org.biojava.bio.proteomics.<a href="./org/biojava/bio/proteomics/MassCalc.html" title="class in org.biojava.bio.proteomics">MassCalc</a></dt>
<dd>
<div class="block"><code>getMass</code> calculates the mass of this peptide.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/MassCalc.html#getMass(org.biojava.bio.symbol.SymbolList)">getMass(SymbolList)</a></span> - Method in class org.biojava.bio.proteomics.<a href="./org/biojava/bio/proteomics/MassCalc.html" title="class in org.biojava.bio.proteomics">MassCalc</a></dt>
<dd>
<div class="block">Get the Mass of this peptide.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/NeedlemanWunsch.html#getMatch()">getMatch()</a></span> - Method in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/NeedlemanWunsch.html" title="class in org.biojava.bio.alignment">NeedlemanWunsch</a></dt>
<dd>
<div class="block">Returns the current expenses of a single match operation.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/ProfileHMM.html#getMatch(int)">getMatch(int)</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/ProfileHMM.html" title="class in org.biojava.bio.dp">ProfileHMM</a></dt>
<dd>
<div class="block">Retrieve the match state at column indx.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/Agave2AgaveAnnotFilter.html#getMatchAlign(org.biojava.bio.Annotation)">getMatchAlign(Annotation)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/Agave2AgaveAnnotFilter.html" title="class in org.biojava.bio.seq.io.agave">Agave2AgaveAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEAnnotFilter.html#getMatchAlign(org.biojava.bio.Annotation)">getMatchAlign(Annotation)</a></span> - Method in interface org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEAnnotFilter.html" title="interface in org.biojava.bio.seq.io.agave">AGAVEAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/SimpleAnnotFilter.html#getMatchAlign(org.biojava.bio.Annotation)">getMatchAlign(Annotation)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/SimpleAnnotFilter.html" title="class in org.biojava.bio.seq.io.agave">SimpleAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/Agave2AgaveAnnotFilter.html#getMatchDesc(org.biojava.bio.Annotation)">getMatchDesc(Annotation)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/Agave2AgaveAnnotFilter.html" title="class in org.biojava.bio.seq.io.agave">Agave2AgaveAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEAnnotFilter.html#getMatchDesc(org.biojava.bio.Annotation)">getMatchDesc(Annotation)</a></span> - Method in interface org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEAnnotFilter.html" title="interface in org.biojava.bio.seq.io.agave">AGAVEAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/SimpleAnnotFilter.html#getMatchDesc(org.biojava.bio.Annotation)">getMatchDesc(Annotation)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/SimpleAnnotFilter.html" title="class in org.biojava.bio.seq.io.agave">SimpleAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/SimpleEmissionState.html#getMatches()">getMatches()</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/SimpleEmissionState.html" title="class in org.biojava.bio.dp">SimpleEmissionState</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/DoubleAlphabet.DoubleRange.html#getMatches()">getMatches()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/DoubleAlphabet.DoubleRange.html" title="class in org.biojava.bio.symbol">DoubleAlphabet.DoubleRange</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/DoubleAlphabet.DoubleSymbol.html#getMatches()">getMatches()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/DoubleAlphabet.DoubleSymbol.html" title="class in org.biojava.bio.symbol">DoubleAlphabet.DoubleSymbol</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/FundamentalAtomicSymbol.html#getMatches()">getMatches()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/FundamentalAtomicSymbol.html" title="class in org.biojava.bio.symbol">FundamentalAtomicSymbol</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/IntegerAlphabet.IntegerSymbol.html#getMatches()">getMatches()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/IntegerAlphabet.IntegerSymbol.html" title="class in org.biojava.bio.symbol">IntegerAlphabet.IntegerSymbol</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/Symbol.html#getMatches()">getMatches()</a></span> - Method in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/Symbol.html" title="interface in org.biojava.bio.symbol">Symbol</a></dt>
<dd>
<div class="block">The alphabet containing the symbols matched by this ambiguity symbol.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/Agave2AgaveAnnotFilter.html#getMatchRegion(org.biojava.bio.Annotation)">getMatchRegion(Annotation)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/Agave2AgaveAnnotFilter.html" title="class in org.biojava.bio.seq.io.agave">Agave2AgaveAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEAnnotFilter.html#getMatchRegion(org.biojava.bio.Annotation)">getMatchRegion(Annotation)</a></span> - Method in interface org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEAnnotFilter.html" title="interface in org.biojava.bio.seq.io.agave">AGAVEAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/SimpleAnnotFilter.html#getMatchRegion(org.biojava.bio.Annotation)">getMatchRegion(Annotation)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/SimpleAnnotFilter.html" title="class in org.biojava.bio.seq.io.agave">SimpleAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/dasalignment/Alignment.html#getMatrices()">getMatrices()</a></span> - Method in class org.biojava.bio.program.das.dasalignment.<a href="./org/biojava/bio/program/das/dasalignment/Alignment.html" title="class in org.biojava.bio.program.das.dasalignment">Alignment</a></dt>
<dd>
<div class="block">Returns the matrices.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/JMatrixPanel.html#getMatrix()">getMatrix()</a></span> - Method in class org.biojava.bio.structure.gui.<a href="./org/biojava/bio/structure/gui/JMatrixPanel.html" title="class in org.biojava.bio.structure.gui">JMatrixPanel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/ScaleableMatrixPanel.html#getMatrix()">getMatrix()</a></span> - Method in class org.biojava.bio.structure.gui.<a href="./org/biojava/bio/structure/gui/ScaleableMatrixPanel.html" title="class in org.biojava.bio.structure.gui">ScaleableMatrixPanel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/jama/Matrix.html#getMatrix(int, int, int, int)">getMatrix(int, int, int, int)</a></span> - Method in class org.biojava.bio.structure.jama.<a href="./org/biojava/bio/structure/jama/Matrix.html" title="class in org.biojava.bio.structure.jama">Matrix</a></dt>
<dd>
<div class="block">Get a submatrix.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/jama/Matrix.html#getMatrix(int[], int[])">getMatrix(int[], int[])</a></span> - Method in class org.biojava.bio.structure.jama.<a href="./org/biojava/bio/structure/jama/Matrix.html" title="class in org.biojava.bio.structure.jama">Matrix</a></dt>
<dd>
<div class="block">Get a submatrix.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/jama/Matrix.html#getMatrix(int, int, int[])">getMatrix(int, int, int[])</a></span> - Method in class org.biojava.bio.structure.jama.<a href="./org/biojava/bio/structure/jama/Matrix.html" title="class in org.biojava.bio.structure.jama">Matrix</a></dt>
<dd>
<div class="block">Get a submatrix.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/jama/Matrix.html#getMatrix(int[], int, int)">getMatrix(int[], int, int)</a></span> - Method in class org.biojava.bio.structure.jama.<a href="./org/biojava/bio/structure/jama/Matrix.html" title="class in org.biojava.bio.structure.jama">Matrix</a></dt>
<dd>
<div class="block">Get a submatrix.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/dasalignment/Alignment.html#getMatrixAnnotationType()">getMatrixAnnotationType()</a></span> - Static method in class org.biojava.bio.program.das.dasalignment.<a href="./org/biojava/bio/program/das/dasalignment/Alignment.html" title="class in org.biojava.bio.program.das.dasalignment">Alignment</a></dt>
<dd>
<div class="block">define the rotation matrix annotation type</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/SubstitutionMatrix.html#getMax()">getMax()</a></span> - Method in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/SubstitutionMatrix.html" title="class in org.biojava.bio.alignment">SubstitutionMatrix</a></dt>
<dd>
<div class="block">The maximum score in this matrix.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/AbstractChromatogram.html#getMax()">getMax()</a></span> - Method in class org.biojava.bio.chromatogram.<a href="./org/biojava/bio/chromatogram/AbstractChromatogram.html" title="class in org.biojava.bio.chromatogram">AbstractChromatogram</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/AbstractChromatogram.html#getMax(org.biojava.bio.symbol.AtomicSymbol)">getMax(AtomicSymbol)</a></span> - Method in class org.biojava.bio.chromatogram.<a href="./org/biojava/bio/chromatogram/AbstractChromatogram.html" title="class in org.biojava.bio.chromatogram">AbstractChromatogram</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/Chromatogram.html#getMax()">getMax()</a></span> - Method in interface org.biojava.bio.chromatogram.<a href="./org/biojava/bio/chromatogram/Chromatogram.html" title="interface in org.biojava.bio.chromatogram">Chromatogram</a></dt>
<dd>
<div class="block">Gets the max intensity from all the traces.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/Chromatogram.html#getMax(org.biojava.bio.symbol.AtomicSymbol)">getMax(AtomicSymbol)</a></span> - Method in interface org.biojava.bio.chromatogram.<a href="./org/biojava/bio/chromatogram/Chromatogram.html" title="interface in org.biojava.bio.chromatogram">Chromatogram</a></dt>
<dd>
<div class="block">Gets the max intensity on the trace for the specified nucleotide.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AbstractLocationDecorator.html#getMax()">getMax()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AbstractLocationDecorator.html" title="class in org.biojava.bio.symbol">AbstractLocationDecorator</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/CircularLocation.html#getMax()">getMax()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/CircularLocation.html" title="class in org.biojava.bio.symbol">CircularLocation</a></dt>
<dd>
<div class="block">This will give you the coordinate of the maximum point contained by this
Location.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/FuzzyLocation.html#getMax()">getMax()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/FuzzyLocation.html" title="class in org.biojava.bio.symbol">FuzzyLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/FuzzyPointLocation.html#getMax()">getMax()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/FuzzyPointLocation.html" title="class in org.biojava.bio.symbol">FuzzyPointLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/Location.html#getMax()">getMax()</a></span> - Method in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/Location.html" title="interface in org.biojava.bio.symbol">Location</a></dt>
<dd>
<div class="block">The maximum position contained.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/PointLocation.html#getMax()">getMax()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/PointLocation.html" title="class in org.biojava.bio.symbol">PointLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/RangeLocation.html#getMax()">getMax()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/RangeLocation.html" title="class in org.biojava.bio.symbol">RangeLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/EmptyRichLocation.html#getMax()">getMax()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/EmptyRichLocation.html" title="class in org.biojavax.bio.seq">EmptyRichLocation</a></dt>
<dd>
<div class="block">The maximum position contained.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/MultiSourceCompoundRichLocation.html#getMax()">getMax()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/MultiSourceCompoundRichLocation.html" title="class in org.biojavax.bio.seq">MultiSourceCompoundRichLocation</a></dt>
<dd>
<div class="block">The maximum position contained.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/PositionResolver.AverageResolver.html#getMax(org.biojavax.bio.seq.Position)">getMax(Position)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/PositionResolver.AverageResolver.html" title="class in org.biojavax.bio.seq">PositionResolver.AverageResolver</a></dt>
<dd>
<div class="block">Resolves the maximum possible base for this position.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/PositionResolver.html#getMax(org.biojavax.bio.seq.Position)">getMax(Position)</a></span> - Method in interface org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/PositionResolver.html" title="interface in org.biojavax.bio.seq">PositionResolver</a></dt>
<dd>
<div class="block">Resolves the maximum possible base for this position.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/PositionResolver.MaximalResolver.html#getMax(org.biojavax.bio.seq.Position)">getMax(Position)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/PositionResolver.MaximalResolver.html" title="class in org.biojavax.bio.seq">PositionResolver.MaximalResolver</a></dt>
<dd>
<div class="block">Resolves the maximum possible base for this position.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/PositionResolver.MinimalResolver.html#getMax(org.biojavax.bio.seq.Position)">getMax(Position)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/PositionResolver.MinimalResolver.html" title="class in org.biojavax.bio.seq">PositionResolver.MinimalResolver</a></dt>
<dd>
<div class="block">Resolves the maximum possible base for this position.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichLocation.html#getMax()">getMax()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichLocation.html" title="class in org.biojavax.bio.seq">SimpleRichLocation</a></dt>
<dd>
<div class="block">The maximum position contained.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SeqContentPattern.html#getMaxCounts(org.biojava.bio.symbol.AtomicSymbol)">getMaxCounts(AtomicSymbol)</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SeqContentPattern.html" title="class in org.biojava.bio.search">SeqContentPattern</a></dt>
<dd>
<div class="block">Get the maximum counts required for a symbol.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ga/functions/AbstractCrossOverFunction.html#getMaxCrossOvers()">getMaxCrossOvers()</a></span> - Method in class org.biojavax.ga.functions.<a href="./org/biojavax/ga/functions/AbstractCrossOverFunction.html" title="class in org.biojavax.ga.functions">AbstractCrossOverFunction</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/functions/CrossOverFunction.html#getMaxCrossOvers()">getMaxCrossOvers()</a></span> - Method in interface org.biojavax.ga.functions.<a href="./org/biojavax/ga/functions/CrossOverFunction.html" title="interface in org.biojavax.ga.functions">CrossOverFunction</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/functions/CrossOverFunction.NoCross.html#getMaxCrossOvers()">getMaxCrossOvers()</a></span> - Method in class org.biojavax.ga.functions.<a href="./org/biojavax/ga/functions/CrossOverFunction.NoCross.html" title="class in org.biojavax.ga.functions">CrossOverFunction.NoCross</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/GAStoppingCriteria.MaximumGeneration.html#getMaxGenerations()">getMaxGenerations()</a></span> - Method in class org.biojavax.ga.<a href="./org/biojavax/ga/GAStoppingCriteria.MaximumGeneration.html" title="class in org.biojavax.ga">GAStoppingCriteria.MaximumGeneration</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/StrucAligParameters.html#getMaxIter()">getMaxIter()</a></span> - Method in class org.biojava.bio.structure.align.<a href="./org/biojava/bio/structure/align/StrucAligParameters.html" title="class in org.biojava.bio.structure.align">StrucAligParameters</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/EmptyRichLocation.html#getMaxPosition()">getMaxPosition()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/EmptyRichLocation.html" title="class in org.biojavax.bio.seq">EmptyRichLocation</a></dt>
<dd>
<div class="block">Retrieves the end position of this location.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/MultiSourceCompoundRichLocation.html#getMaxPosition()">getMaxPosition()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/MultiSourceCompoundRichLocation.html" title="class in org.biojavax.bio.seq">MultiSourceCompoundRichLocation</a></dt>
<dd>
<div class="block">Retrieves the end position of this location.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichLocation.html#getMaxPosition()">getMaxPosition()</a></span> - Method in interface org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichLocation.html" title="interface in org.biojavax.bio.seq">RichLocation</a></dt>
<dd>
<div class="block">Retrieves the end position of this location.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichLocation.html#getMaxPosition()">getMaxPosition()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichLocation.html" title="class in org.biojavax.bio.seq">SimpleRichLocation</a></dt>
<dd>
<div class="block">Retrieves the end position of this location.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/StrucAligParameters.html#getMaxrefine()">getMaxrefine()</a></span> - Method in class org.biojava.bio.structure.align.<a href="./org/biojava/bio/structure/align/StrucAligParameters.html" title="class in org.biojava.bio.structure.align">StrucAligParameters</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ExecRunner.html#getMaxRunTimeExceeded()">getMaxRunTimeExceeded()</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/ExecRunner.html" title="class in org.biojava.utils">ExecRunner</a></dt>
<dd>
<div class="block">Returns whether the maximum runtime was exceeded or not.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/ExecRunner.html#getMaxRunTimeSecs()">getMaxRunTimeSecs()</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/ExecRunner.html" title="class in org.biojava.utils">ExecRunner</a></dt>
<dd>
<div class="block">Returns the maximum run time in seconds for this object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ByPairwiseScore.html#getMaxScore()">getMaxScore()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ByPairwiseScore.html" title="class in org.biojava.bio.seq">FeatureFilter.ByPairwiseScore</a></dt>
<dd>
<div class="block"><code>getMaxScore</code> returns the maximum score
accepted.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/cache/FixedSizeMap.html#getMaxSize()">getMaxSize()</a></span> - Method in class org.biojava.utils.cache.<a href="./org/biojava/utils/cache/FixedSizeMap.html" title="class in org.biojava.utils.cache">FixedSizeMap</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/DoubleAlphabet.DoubleRange.html#getMaxValue()">getMaxValue()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/DoubleAlphabet.DoubleRange.html" title="class in org.biojava.bio.symbol">DoubleAlphabet.DoubleRange</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/xff/XFFFeatureSetHandler.html#getMergeAnnotation()">getMergeAnnotation()</a></span> - Method in class org.biojava.bio.program.xff.<a href="./org/biojava/bio/program/xff/XFFFeatureSetHandler.html" title="class in org.biojava.bio.program.xff">XFFFeatureSetHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/annodb/MergingAnnotationDB.html#getMerged()">getMerged()</a></span> - Method in class org.biojava.bio.annodb.<a href="./org/biojava/bio/annodb/MergingAnnotationDB.html" title="class in org.biojava.bio.annodb">MergingAnnotationDB</a></dt>
<dd>
<div class="block">Return a list of merged DBs.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/LineSplitParser.html#getMergeSameTag()">getMergeSameTag()</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/LineSplitParser.html" title="class in org.biojava.bio.program.tagvalue">LineSplitParser</a></dt>
<dd>
<div class="block">See if tags are being merged.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/RegexParser.html#getMergeSameTag()">getMergeSameTag()</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/RegexParser.html" title="class in org.biojava.bio.program.tagvalue">RegexParser</a></dt>
<dd>
<div class="block">Report whether empty tags will be treated as continuations of the last non
-empty tag.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/ParseErrorEvent.html#getMessage()">getMessage()</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/ParseErrorEvent.html" title="class in org.biojava.utils">ParseErrorEvent</a></dt>
<dd>
<div class="block">Find the message about this event</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/indexdb/BioStore.html#getMetaData()">getMetaData()</a></span> - Method in class org.biojava.bio.program.indexdb.<a href="./org/biojava/bio/program/indexdb/BioStore.html" title="class in org.biojava.bio.program.indexdb">BioStore</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/indexdb/IndexStore.html#getMetaData()">getMetaData()</a></span> - Method in interface org.biojava.bio.program.indexdb.<a href="./org/biojava/bio/program/indexdb/IndexStore.html" title="interface in org.biojava.bio.program.indexdb">IndexStore</a></dt>
<dd>
<div class="block"><code>getMetaData</code> returns a data structure which
represents an OBDA "config.dat" flatfile indexing configuration
file.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/annodb/IndexedAnnotationDB.StaticMethodRPFactory.html#getMethod()">getMethod()</a></span> - Method in class org.biojava.bio.annodb.<a href="./org/biojava/bio/annodb/IndexedAnnotationDB.StaticMethodRPFactory.html" title="class in org.biojava.bio.annodb">IndexedAnnotationDB.StaticMethodRPFactory</a></dt>
<dd>
<div class="block">Get the Method used.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Exptl.html#getMethod()">getMethod()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Exptl.html" title="class in org.biojava.bio.structure.io.mmcif.model">Exptl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/PDBHeader.html#getMethod()">getMethod()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/PDBHeader.html" title="class in org.biojava.bio.structure">PDBHeader</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Exptl.html#getMethod_details()">getMethod_details()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Exptl.html" title="class in org.biojava.bio.structure.io.mmcif.model">Exptl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/SubstitutionMatrix.html#getMin()">getMin()</a></span> - Method in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/SubstitutionMatrix.html" title="class in org.biojava.bio.alignment">SubstitutionMatrix</a></dt>
<dd>
<div class="block">The minimum score of this matrix.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AbstractLocationDecorator.html#getMin()">getMin()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AbstractLocationDecorator.html" title="class in org.biojava.bio.symbol">AbstractLocationDecorator</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/CircularLocation.html#getMin()">getMin()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/CircularLocation.html" title="class in org.biojava.bio.symbol">CircularLocation</a></dt>
<dd>
<div class="block">This will give you the coordinate of the minimum point contained by this
Location.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/FuzzyLocation.html#getMin()">getMin()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/FuzzyLocation.html" title="class in org.biojava.bio.symbol">FuzzyLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/FuzzyPointLocation.html#getMin()">getMin()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/FuzzyPointLocation.html" title="class in org.biojava.bio.symbol">FuzzyPointLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/Location.html#getMin()">getMin()</a></span> - Method in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/Location.html" title="interface in org.biojava.bio.symbol">Location</a></dt>
<dd>
<div class="block">The minimum position contained.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/PointLocation.html#getMin()">getMin()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/PointLocation.html" title="class in org.biojava.bio.symbol">PointLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/RangeLocation.html#getMin()">getMin()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/RangeLocation.html" title="class in org.biojava.bio.symbol">RangeLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/EmptyRichLocation.html#getMin()">getMin()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/EmptyRichLocation.html" title="class in org.biojavax.bio.seq">EmptyRichLocation</a></dt>
<dd>
<div class="block">The minimum position contained.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/MultiSourceCompoundRichLocation.html#getMin()">getMin()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/MultiSourceCompoundRichLocation.html" title="class in org.biojavax.bio.seq">MultiSourceCompoundRichLocation</a></dt>
<dd>
<div class="block">The minimum position contained.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/PositionResolver.AverageResolver.html#getMin(org.biojavax.bio.seq.Position)">getMin(Position)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/PositionResolver.AverageResolver.html" title="class in org.biojavax.bio.seq">PositionResolver.AverageResolver</a></dt>
<dd>
<div class="block">Resolves the minimum possible base for this position.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/PositionResolver.html#getMin(org.biojavax.bio.seq.Position)">getMin(Position)</a></span> - Method in interface org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/PositionResolver.html" title="interface in org.biojavax.bio.seq">PositionResolver</a></dt>
<dd>
<div class="block">Resolves the minimum possible base for this position.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/PositionResolver.MaximalResolver.html#getMin(org.biojavax.bio.seq.Position)">getMin(Position)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/PositionResolver.MaximalResolver.html" title="class in org.biojavax.bio.seq">PositionResolver.MaximalResolver</a></dt>
<dd>
<div class="block">Resolves the minimum possible base for this position.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/PositionResolver.MinimalResolver.html#getMin(org.biojavax.bio.seq.Position)">getMin(Position)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/PositionResolver.MinimalResolver.html" title="class in org.biojavax.bio.seq">PositionResolver.MinimalResolver</a></dt>
<dd>
<div class="block">Resolves the minimum possible base for this position.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichLocation.html#getMin()">getMin()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichLocation.html" title="class in org.biojavax.bio.seq">SimpleRichLocation</a></dt>
<dd>
<div class="block">The minimum position contained.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SeqContentPattern.html#getMinCounts(org.biojava.bio.symbol.AtomicSymbol)">getMinCounts(AtomicSymbol)</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SeqContentPattern.html" title="class in org.biojava.bio.search">SeqContentPattern</a></dt>
<dd>
<div class="block">Get the minimum counts required for a symbol.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/OrthoPairSet.html#getMinIdentity()">getMinIdentity()</a></span> - Method in interface org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/OrthoPairSet.html" title="interface in org.biojava.bio.program.homologene">OrthoPairSet</a></dt>
<dd>
<div class="block">get the lowest level of identity observed
in this Group</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/SimpleOrthoPairSet.html#getMinIdentity()">getMinIdentity()</a></span> - Method in class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/SimpleOrthoPairSet.html" title="class in org.biojava.bio.program.homologene">SimpleOrthoPairSet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/AbiTraceRenderer.html#getMinimumLeader(org.biojava.bio.gui.sequence.SequenceRenderContext)">getMinimumLeader(SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/AbiTraceRenderer.html" title="class in org.biojava.bio.gui.sequence">AbiTraceRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/AlignmentRenderer.html#getMinimumLeader(org.biojava.bio.gui.sequence.SequenceRenderContext)">getMinimumLeader(SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/AlignmentRenderer.html" title="class in org.biojava.bio.gui.sequence">AlignmentRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/BumpedRenderer.html#getMinimumLeader(org.biojava.bio.gui.sequence.SequenceRenderContext)">getMinimumLeader(SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/BumpedRenderer.html" title="class in org.biojava.bio.gui.sequence">BumpedRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/FeatureBlockSequenceRenderer.html#getMinimumLeader(org.biojava.bio.gui.sequence.SequenceRenderContext)">getMinimumLeader(SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/FeatureBlockSequenceRenderer.html" title="class in org.biojava.bio.gui.sequence">FeatureBlockSequenceRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/FeatureLabelRenderer.html#getMinimumLeader(org.biojava.bio.gui.sequence.SequenceRenderContext)">getMinimumLeader(SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/FeatureLabelRenderer.html" title="class in org.biojava.bio.gui.sequence">FeatureLabelRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/FilteringRenderer.html#getMinimumLeader(org.biojava.bio.gui.sequence.SequenceRenderContext)">getMinimumLeader(SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/FilteringRenderer.html" title="class in org.biojava.bio.gui.sequence">FilteringRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/GappedRenderer.html#getMinimumLeader(org.biojava.bio.gui.sequence.SequenceRenderContext)">getMinimumLeader(SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/GappedRenderer.html" title="class in org.biojava.bio.gui.sequence">GappedRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/LabelledSequenceRenderer.html#getMinimumLeader(org.biojava.bio.gui.sequence.SequenceRenderContext)">getMinimumLeader(SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/LabelledSequenceRenderer.html" title="class in org.biojava.bio.gui.sequence">LabelledSequenceRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/LayeredRenderer.html#getMinimumLeader(java.util.List, java.util.List)">getMinimumLeader(List, List)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/LayeredRenderer.html" title="class in org.biojava.bio.gui.sequence">LayeredRenderer</a></dt>
<dd>
<div class="block"><code>getMinimumLeader</code> returns the maximum value of
getMinimumLeader() for a list of <code>SequenceRenderer</code>s.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/MultiLineRenderer.html#getMinimumLeader(org.biojava.bio.gui.sequence.SequenceRenderContext)">getMinimumLeader(SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/MultiLineRenderer.html" title="class in org.biojava.bio.gui.sequence">MultiLineRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/OffsetRulerRenderer.html#getMinimumLeader(org.biojava.bio.gui.sequence.SequenceRenderContext)">getMinimumLeader(SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/OffsetRulerRenderer.html" title="class in org.biojava.bio.gui.sequence">OffsetRulerRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/OverlayRendererWrapper.html#getMinimumLeader(org.biojava.bio.gui.sequence.SequenceRenderContext)">getMinimumLeader(SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/OverlayRendererWrapper.html" title="class in org.biojava.bio.gui.sequence">OverlayRendererWrapper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PaddingRenderer.html#getMinimumLeader(org.biojava.bio.gui.sequence.SequenceRenderContext)">getMinimumLeader(SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PaddingRenderer.html" title="class in org.biojava.bio.gui.sequence">PaddingRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/RulerRenderer.html#getMinimumLeader(org.biojava.bio.gui.sequence.SequenceRenderContext)">getMinimumLeader(SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/RulerRenderer.html" title="class in org.biojava.bio.gui.sequence">RulerRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequenceRenderer.html#getMinimumLeader(org.biojava.bio.gui.sequence.SequenceRenderContext)">getMinimumLeader(SequenceRenderContext)</a></span> - Method in interface org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequenceRenderer.html" title="interface in org.biojava.bio.gui.sequence">SequenceRenderer</a></dt>
<dd>
<div class="block">Retrieve the minimum leading distance for this renderer when rendering src.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequenceRendererWrapper.html#getMinimumLeader(org.biojava.bio.gui.sequence.SequenceRenderContext)">getMinimumLeader(SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequenceRendererWrapper.html" title="class in org.biojava.bio.gui.sequence">SequenceRendererWrapper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SixFrameRenderer.html#getMinimumLeader(org.biojava.bio.gui.sequence.SequenceRenderContext)">getMinimumLeader(SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SixFrameRenderer.html" title="class in org.biojava.bio.gui.sequence">SixFrameRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/StopRenderer.html#getMinimumLeader(org.biojava.bio.gui.sequence.SequenceRenderContext)">getMinimumLeader(SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/StopRenderer.html" title="class in org.biojava.bio.gui.sequence">StopRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SymbolSequenceRenderer.html#getMinimumLeader(org.biojava.bio.gui.sequence.SequenceRenderContext)">getMinimumLeader(SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SymbolSequenceRenderer.html" title="class in org.biojava.bio.gui.sequence">SymbolSequenceRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/AbiTraceRenderer.html#getMinimumTrailer(org.biojava.bio.gui.sequence.SequenceRenderContext)">getMinimumTrailer(SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/AbiTraceRenderer.html" title="class in org.biojava.bio.gui.sequence">AbiTraceRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/AlignmentRenderer.html#getMinimumTrailer(org.biojava.bio.gui.sequence.SequenceRenderContext)">getMinimumTrailer(SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/AlignmentRenderer.html" title="class in org.biojava.bio.gui.sequence">AlignmentRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/BumpedRenderer.html#getMinimumTrailer(org.biojava.bio.gui.sequence.SequenceRenderContext)">getMinimumTrailer(SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/BumpedRenderer.html" title="class in org.biojava.bio.gui.sequence">BumpedRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/FeatureBlockSequenceRenderer.html#getMinimumTrailer(org.biojava.bio.gui.sequence.SequenceRenderContext)">getMinimumTrailer(SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/FeatureBlockSequenceRenderer.html" title="class in org.biojava.bio.gui.sequence">FeatureBlockSequenceRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/FeatureLabelRenderer.html#getMinimumTrailer(org.biojava.bio.gui.sequence.SequenceRenderContext)">getMinimumTrailer(SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/FeatureLabelRenderer.html" title="class in org.biojava.bio.gui.sequence">FeatureLabelRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/FilteringRenderer.html#getMinimumTrailer(org.biojava.bio.gui.sequence.SequenceRenderContext)">getMinimumTrailer(SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/FilteringRenderer.html" title="class in org.biojava.bio.gui.sequence">FilteringRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/GappedRenderer.html#getMinimumTrailer(org.biojava.bio.gui.sequence.SequenceRenderContext)">getMinimumTrailer(SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/GappedRenderer.html" title="class in org.biojava.bio.gui.sequence">GappedRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/LabelledSequenceRenderer.html#getMinimumTrailer(org.biojava.bio.gui.sequence.SequenceRenderContext)">getMinimumTrailer(SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/LabelledSequenceRenderer.html" title="class in org.biojava.bio.gui.sequence">LabelledSequenceRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/LayeredRenderer.html#getMinimumTrailer(java.util.List, java.util.List)">getMinimumTrailer(List, List)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/LayeredRenderer.html" title="class in org.biojava.bio.gui.sequence">LayeredRenderer</a></dt>
<dd>
<div class="block"><code>getMinimumTrailer</code> returns the maximum value of
getMinimumTrailer() for a list of <code>SequenceRenderer</code>s.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/MultiLineRenderer.html#getMinimumTrailer(org.biojava.bio.gui.sequence.SequenceRenderContext)">getMinimumTrailer(SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/MultiLineRenderer.html" title="class in org.biojava.bio.gui.sequence">MultiLineRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/OffsetRulerRenderer.html#getMinimumTrailer(org.biojava.bio.gui.sequence.SequenceRenderContext)">getMinimumTrailer(SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/OffsetRulerRenderer.html" title="class in org.biojava.bio.gui.sequence">OffsetRulerRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/OverlayRendererWrapper.html#getMinimumTrailer(org.biojava.bio.gui.sequence.SequenceRenderContext)">getMinimumTrailer(SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/OverlayRendererWrapper.html" title="class in org.biojava.bio.gui.sequence">OverlayRendererWrapper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PaddingRenderer.html#getMinimumTrailer(org.biojava.bio.gui.sequence.SequenceRenderContext)">getMinimumTrailer(SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PaddingRenderer.html" title="class in org.biojava.bio.gui.sequence">PaddingRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/RulerRenderer.html#getMinimumTrailer(org.biojava.bio.gui.sequence.SequenceRenderContext)">getMinimumTrailer(SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/RulerRenderer.html" title="class in org.biojava.bio.gui.sequence">RulerRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequenceRenderer.html#getMinimumTrailer(org.biojava.bio.gui.sequence.SequenceRenderContext)">getMinimumTrailer(SequenceRenderContext)</a></span> - Method in interface org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequenceRenderer.html" title="interface in org.biojava.bio.gui.sequence">SequenceRenderer</a></dt>
<dd>
<div class="block">Retrieve the minimum trailing distance for this renderer when rendering src.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequenceRendererWrapper.html#getMinimumTrailer(org.biojava.bio.gui.sequence.SequenceRenderContext)">getMinimumTrailer(SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequenceRendererWrapper.html" title="class in org.biojava.bio.gui.sequence">SequenceRendererWrapper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SixFrameRenderer.html#getMinimumTrailer(org.biojava.bio.gui.sequence.SequenceRenderContext)">getMinimumTrailer(SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SixFrameRenderer.html" title="class in org.biojava.bio.gui.sequence">SixFrameRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/StopRenderer.html#getMinimumTrailer(org.biojava.bio.gui.sequence.SequenceRenderContext)">getMinimumTrailer(SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/StopRenderer.html" title="class in org.biojava.bio.gui.sequence">StopRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SymbolSequenceRenderer.html#getMinimumTrailer(org.biojava.bio.gui.sequence.SequenceRenderContext)">getMinimumTrailer(SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SymbolSequenceRenderer.html" title="class in org.biojava.bio.gui.sequence">SymbolSequenceRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/LabelRenderer.html#getMinimumWidth(org.biojava.bio.gui.sequence.SequenceRenderContext)">getMinimumWidth(SequenceRenderContext)</a></span> - Method in interface org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/LabelRenderer.html" title="interface in org.biojava.bio.gui.sequence">LabelRenderer</a></dt>
<dd>
<div class="block">Retrieve the minimum space required to render the label.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/LabelRenderer.RenderNothing.html#getMinimumWidth(org.biojava.bio.gui.sequence.SequenceRenderContext)">getMinimumWidth(SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/LabelRenderer.RenderNothing.html" title="class in org.biojava.bio.gui.sequence">LabelRenderer.RenderNothing</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SimpleLabelRenderer.html#getMinimumWidth(org.biojava.bio.gui.sequence.SequenceRenderContext)">getMinimumWidth(SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SimpleLabelRenderer.html" title="class in org.biojava.bio.gui.sequence">SimpleLabelRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/EmptyRichLocation.html#getMinPosition()">getMinPosition()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/EmptyRichLocation.html" title="class in org.biojavax.bio.seq">EmptyRichLocation</a></dt>
<dd>
<div class="block">Retrieves the start position of this location.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/MultiSourceCompoundRichLocation.html#getMinPosition()">getMinPosition()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/MultiSourceCompoundRichLocation.html" title="class in org.biojavax.bio.seq">MultiSourceCompoundRichLocation</a></dt>
<dd>
<div class="block">Retrieves the start position of this location.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichLocation.html#getMinPosition()">getMinPosition()</a></span> - Method in interface org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichLocation.html" title="interface in org.biojavax.bio.seq">RichLocation</a></dt>
<dd>
<div class="block">Retrieves the start position of this location.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichLocation.html#getMinPosition()">getMinPosition()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichLocation.html" title="class in org.biojavax.bio.seq">SimpleRichLocation</a></dt>
<dd>
<div class="block">Retrieves the start position of this location.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ByPairwiseScore.html#getMinScore()">getMinScore()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ByPairwiseScore.html" title="class in org.biojava.bio.seq">FeatureFilter.ByPairwiseScore</a></dt>
<dd>
<div class="block"><code>getMinScore</code> returns the minimum score
accepted.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/DoubleAlphabet.DoubleRange.html#getMinValue()">getMinValue()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/DoubleAlphabet.DoubleRange.html" title="class in org.biojava.bio.symbol">DoubleAlphabet.DoubleRange</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/MaxMismatchPattern.html#getMismatches()">getMismatches()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/MaxMismatchPattern.html" title="class in org.biojava.bio.search">MaxMismatchPattern</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/taxa/NCBITaxon.html#getMitoGeneticCode()">getMitoGeneticCode()</a></span> - Method in interface org.biojavax.bio.taxa.<a href="./org/biojavax/bio/taxa/NCBITaxon.html" title="interface in org.biojavax.bio.taxa">NCBITaxon</a></dt>
<dd>
<div class="block">Returns the mitochondrial genetic code of this taxon, which may be null
if not known.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/taxa/SimpleNCBITaxon.html#getMitoGeneticCode()">getMitoGeneticCode()</a></span> - Method in class org.biojavax.bio.taxa.<a href="./org/biojavax/bio/taxa/SimpleNCBITaxon.html" title="class in org.biojavax.bio.taxa">SimpleNCBITaxon</a></dt>
<dd>
<div class="block">Getter for property mitoGeneticCode.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/DatabasePDBrev.html#getMod_type()">getMod_type()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/DatabasePDBrev.html" title="class in org.biojava.bio.structure.io.mmcif.model">DatabasePDBrev</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/PDBHeader.html#getModDate()">getModDate()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/PDBHeader.html" title="class in org.biojava.bio.structure">PDBHeader</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/DP.html#getModel()">getModel()</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/DP.html" title="class in org.biojava.bio.dp">DP</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/ModelInState.html#getModel()">getModel()</a></span> - Method in interface org.biojava.bio.dp.<a href="./org/biojava/bio/dp/ModelInState.html" title="interface in org.biojava.bio.dp">ModelInState</a></dt>
<dd>
<div class="block">The model that is inside this state.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/SimpleModelInState.html#getModel()">getModel()</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/SimpleModelInState.html" title="class in org.biojava.bio.dp">SimpleModelInState</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/hmmer/HmmerProfileParser.html#getModel()">getModel()</a></span> - Method in class org.biojava.bio.program.hmmer.<a href="./org/biojava/bio/program/hmmer/HmmerProfileParser.html" title="class in org.biojava.bio.program.hmmer">HmmerProfileParser</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Structure.html#getModel(int)">getModel(int)</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Structure.html" title="interface in org.biojava.bio.structure">Structure</a></dt>
<dd>
<div class="block">retrieve all Chains belonging to a model .</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/StructureImpl.html#getModel(int)">getModel(int)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/StructureImpl.html" title="class in org.biojava.bio.structure">StructureImpl</a></dt>
<dd>
<div class="block">retrieve all Chains belonging to a model .</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/MergingSet.html#getModifiable()">getModifiable()</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/MergingSet.html" title="class in org.biojava.utils">MergingSet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/MassCalc.html#getMolecularWeight(org.biojava.bio.symbol.SymbolList)">getMolecularWeight(SymbolList)</a></span> - Static method in class org.biojava.bio.proteomics.<a href="./org/biojava/bio/proteomics/MassCalc.html" title="class in org.biojava.bio.proteomics">MassCalc</a></dt>
<dd>
<div class="block">Calculate the molecular weight of a protein, making estimates whenever it is
possible like averaging mass values for ambiguity symbols or counting
zero when gaps are encountered.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html#getMolecularWeight()">getMolecularWeight()</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html" title="class in org.biojavax.bio.seq.io">UniProtCommentParser</a></dt>
<dd>
<div class="block">Getter for property molecularWeight.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Compound.html#getMolId()">getMolId()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure">Compound</a></dt>
<dd>
<div class="block">Returns the mol id value.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Compound.html#getMolName()">getMolName()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure">Compound</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/Agave2AgaveAnnotFilter.html#getMolType(org.biojava.bio.Annotation)">getMolType(Annotation)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/Agave2AgaveAnnotFilter.html" title="class in org.biojava.bio.seq.io.agave">Agave2AgaveAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEAnnotFilter.html#getMolType(org.biojava.bio.Annotation)">getMolType(Annotation)</a></span> - Method in interface org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEAnnotFilter.html" title="interface in org.biojava.bio.seq.io.agave">AGAVEAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/Embl2AgaveAnnotFilter.html#getMolType(org.biojava.bio.Annotation)">getMolType(Annotation)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/Embl2AgaveAnnotFilter.html" title="class in org.biojava.bio.seq.io.agave">Embl2AgaveAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/SimpleAnnotFilter.html#getMolType(org.biojava.bio.Annotation)">getMolType(Annotation)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/SimpleAnnotFilter.html" title="class in org.biojava.bio.seq.io.agave">SimpleAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.Terms.html#getMolTypeTerm()">getMolTypeTerm()</a></span> - Static method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.Terms.html" title="class in org.biojavax.bio.seq">RichSequence.Terms</a></dt>
<dd>
<div class="block">getter for the MolType term</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html#getMolWeightError()">getMolWeightError()</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html" title="class in org.biojavax.bio.seq.io">UniProtCommentParser</a></dt>
<dd>
<div class="block">Getter for property molWeightError.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html#getMolWeightMethod()">getMolWeightMethod()</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html" title="class in org.biojavax.bio.seq.io">UniProtCommentParser</a></dt>
<dd>
<div class="block">Getter for property molWeightMethod.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html#getMolWeightRangeEnd()">getMolWeightRangeEnd()</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html" title="class in org.biojavax.bio.seq.io">UniProtCommentParser</a></dt>
<dd>
<div class="block">Getter for property molWeightRangeEnd.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html#getMolWeightRangeStart()">getMolWeightRangeStart()</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html" title="class in org.biojavax.bio.seq.io">UniProtCommentParser</a></dt>
<dd>
<div class="block">Getter for property molWeightRangeStart.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/EntityPolySeq.html#getMon_id()">getMon_id()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/EntityPolySeq.html" title="class in org.biojava.bio.structure.io.mmcif.model">EntityPolySeq</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/PdbxNonPolyScheme.html#getMon_id()">getMon_id()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/PdbxNonPolyScheme.html" title="class in org.biojava.bio.structure.io.mmcif.model">PdbxNonPolyScheme</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/PdbxPolySeqScheme.html#getMon_id()">getMon_id()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/PdbxPolySeqScheme.html" title="class in org.biojava.bio.structure.io.mmcif.model">PdbxPolySeqScheme</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html#getMon_nstd_flag()">getMon_nstd_flag()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html" title="class in org.biojava.bio.structure.io.mmcif.model">ChemComp</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html#getMon_nstd_parent_comp_id()">getMon_nstd_parent_comp_id()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html" title="class in org.biojava.bio.structure.io.mmcif.model">ChemComp</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/sax/FastaSearchSAXParser.html#getMoreSearches()">getMoreSearches()</a></span> - Method in class org.biojava.bio.program.sax.<a href="./org/biojava/bio/program/sax/FastaSearchSAXParser.html" title="class in org.biojava.bio.program.sax">FastaSearchSAXParser</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/BlastLikeHomologyBuilder.html#getMoreSearches()">getMoreSearches()</a></span> - Method in class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/BlastLikeHomologyBuilder.html" title="class in org.biojava.bio.program.ssbind">BlastLikeHomologyBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/BlastLikeSearchBuilder.html#getMoreSearches()">getMoreSearches()</a></span> - Method in class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/BlastLikeSearchBuilder.html" title="class in org.biojava.bio.program.ssbind">BlastLikeSearchBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/SimilarityPairBuilder.html#getMoreSearches()">getMoreSearches()</a></span> - Method in class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/SimilarityPairBuilder.html" title="class in org.biojava.bio.program.ssbind">SimilarityPairBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SearchContentAdapter.html#getMoreSearches()">getMoreSearches()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SearchContentAdapter.html" title="class in org.biojava.bio.search">SearchContentAdapter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SearchContentFilter.html#getMoreSearches()">getMoreSearches()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SearchContentFilter.html" title="class in org.biojava.bio.search">SearchContentFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SearchContentHandler.html#getMoreSearches()">getMoreSearches()</a></span> - Method in interface org.biojava.bio.search.<a href="./org/biojava/bio/search/SearchContentHandler.html" title="interface in org.biojava.bio.search">SearchContentHandler</a></dt>
<dd>
<div class="block"><code>getMoreSearches</code> returns the state of the
<code>SearchContentHandler</code> with respect to further
searches from its data source.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SearchContentHandlerDebugger.html#getMoreSearches()">getMoreSearches()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SearchContentHandlerDebugger.html" title="class in org.biojava.bio.search">SearchContentHandlerDebugger</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/Meme.html#getMotifs()">getMotifs()</a></span> - Method in class org.biojava.bio.program.<a href="./org/biojava/bio/program/Meme.html" title="class in org.biojava.bio.program">Meme</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequenceViewerEvent.html#getMouseEvent()">getMouseEvent()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequenceViewerEvent.html" title="class in org.biojava.bio.gui.sequence">SequenceViewerEvent</a></dt>
<dd>
<div class="block">Get the mouse event that caused this.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/PolynomialKernel.html#getMultiplier()">getMultiplier()</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/PolynomialKernel.html" title="class in org.biojava.stats.svm">PolynomialKernel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/SigmoidKernel.html#getMultiplier()">getMultiplier()</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/SigmoidKernel.html" title="class in org.biojava.stats.svm">SigmoidKernel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Compound.html#getMutation()">getMutation()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure">Compound</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/GeneticAlgorithm.html#getMutationFunction()">getMutationFunction()</a></span> - Method in interface org.biojavax.ga.<a href="./org/biojavax/ga/GeneticAlgorithm.html" title="interface in org.biojavax.ga">GeneticAlgorithm</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/impl/AbstractGeneticAlgorithm.html#getMutationFunction()">getMutationFunction()</a></span> - Method in class org.biojavax.ga.impl.<a href="./org/biojavax/ga/impl/AbstractGeneticAlgorithm.html" title="class in org.biojavax.ga.impl">AbstractGeneticAlgorithm</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/functions/AbstractMutationFunction.html#getMutationProbs()">getMutationProbs()</a></span> - Method in class org.biojavax.ga.functions.<a href="./org/biojavax/ga/functions/AbstractMutationFunction.html" title="class in org.biojavax.ga.functions">AbstractMutationFunction</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/functions/MutationFunction.html#getMutationProbs()">getMutationProbs()</a></span> - Method in interface org.biojavax.ga.functions.<a href="./org/biojavax/ga/functions/MutationFunction.html" title="interface in org.biojavax.ga.functions">MutationFunction</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/functions/MutationFunction.NoMutation.html#getMutationProbs()">getMutationProbs()</a></span> - Method in class org.biojavax.ga.functions.<a href="./org/biojavax/ga/functions/MutationFunction.NoMutation.html" title="class in org.biojavax.ga.functions">MutationFunction.NoMutation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/functions/AbstractMutationFunction.html#getMutationSpectrum()">getMutationSpectrum()</a></span> - Method in class org.biojavax.ga.functions.<a href="./org/biojavax/ga/functions/AbstractMutationFunction.html" title="class in org.biojavax.ga.functions">AbstractMutationFunction</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/functions/MutationFunction.html#getMutationSpectrum()">getMutationSpectrum()</a></span> - Method in interface org.biojavax.ga.functions.<a href="./org/biojavax/ga/functions/MutationFunction.html" title="interface in org.biojavax.ga.functions">MutationFunction</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/functions/MutationFunction.NoMutation.html#getMutationSpectrum()">getMutationSpectrum()</a></span> - Method in class org.biojavax.ga.functions.<a href="./org/biojavax/ga/functions/MutationFunction.NoMutation.html" title="class in org.biojavax.ga.functions">MutationFunction.NoMutation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/naming/ObdaContext.html#getMyComponents(javax.naming.Name)">getMyComponents(Name)</a></span> - Method in class org.biojava.naming.<a href="./org/biojava/naming/ObdaContext.html" title="class in org.biojava.naming">ObdaContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/AminoAcid.html#getN()">getN()</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/AminoAcid.html" title="interface in org.biojava.bio.structure">AminoAcid</a></dt>
<dd>
<div class="block">get N atom.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/AminoAcidImpl.html#getN()">getN()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/AminoAcidImpl.html" title="class in org.biojava.bio.structure">AminoAcidImpl</a></dt>
<dd>
<div class="block">get N atom.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/SubstitutionMatrix.html#getName()">getName()</a></span> - Method in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/SubstitutionMatrix.html" title="class in org.biojava.bio.alignment">SubstitutionMatrix</a></dt>
<dd>
<div class="block">Every substitution matrix has a name like "BLOSUM30" or "PAM160".</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/annodb/AnnotationDB.html#getName()">getName()</a></span> - Method in interface org.biojava.bio.annodb.<a href="./org/biojava/bio/annodb/AnnotationDB.html" title="interface in org.biojava.bio.annodb">AnnotationDB</a></dt>
<dd>
<div class="block">The name of this AnnotationDB.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/annodb/IndexedAnnotationDB.html#getName()">getName()</a></span> - Method in class org.biojava.bio.annodb.<a href="./org/biojava/bio/annodb/IndexedAnnotationDB.html" title="class in org.biojava.bio.annodb">IndexedAnnotationDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/annodb/LazyFilteredAnnotationDB.html#getName()">getName()</a></span> - Method in class org.biojava.bio.annodb.<a href="./org/biojava/bio/annodb/LazyFilteredAnnotationDB.html" title="class in org.biojava.bio.annodb">LazyFilteredAnnotationDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/annodb/LazySearchedAnnotationDB.html#getName()">getName()</a></span> - Method in class org.biojava.bio.annodb.<a href="./org/biojava/bio/annodb/LazySearchedAnnotationDB.html" title="class in org.biojava.bio.annodb">LazySearchedAnnotationDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/annodb/MergingAnnotationDB.html#getName()">getName()</a></span> - Method in class org.biojava.bio.annodb.<a href="./org/biojava/bio/annodb/MergingAnnotationDB.html" title="class in org.biojava.bio.annodb">MergingAnnotationDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/annodb/SimpleAnnotationDB.html#getName()">getName()</a></span> - Method in class org.biojava.bio.annodb.<a href="./org/biojava/bio/annodb/SimpleAnnotationDB.html" title="class in org.biojava.bio.annodb">SimpleAnnotationDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/SimpleEmissionState.html#getName()">getName()</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/SimpleEmissionState.html" title="class in org.biojava.bio.dp">SimpleEmissionState</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/molbio/RestrictionEnzyme.html#getName()">getName()</a></span> - Method in class org.biojava.bio.molbio.<a href="./org/biojava/bio/molbio/RestrictionEnzyme.html" title="class in org.biojava.bio.molbio">RestrictionEnzyme</a></dt>
<dd>
<div class="block"><code>getName</code> returns the enzyme name.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/DASSequence.html#getName()">getName()</a></span> - Method in class org.biojava.bio.program.das.<a href="./org/biojava/bio/program/das/DASSequence.html" title="class in org.biojava.bio.program.das">DASSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/DASSequenceDB.html#getName()">getName()</a></span> - Method in class org.biojava.bio.program.das.<a href="./org/biojava/bio/program/das/DASSequenceDB.html" title="class in org.biojava.bio.program.das">DASSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/DASSequenceDBProvider.html#getName()">getName()</a></span> - Method in class org.biojava.bio.program.das.<a href="./org/biojava/bio/program/das/DASSequenceDBProvider.html" title="class in org.biojava.bio.program.das">DASSequenceDBProvider</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/DataSource.html#getName()">getName()</a></span> - Method in class org.biojava.bio.program.das.<a href="./org/biojava/bio/program/das/DataSource.html" title="class in org.biojava.bio.program.das">DataSource</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/OrthoPairSet.html#getName()">getName()</a></span> - Method in interface org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/OrthoPairSet.html" title="interface in org.biojava.bio.program.homologene">OrthoPairSet</a></dt>
<dd>
<div class="block">retrieves name of this group.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/SimpleOrthoPairSet.html#getName()">getName()</a></span> - Method in class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/SimpleOrthoPairSet.html" title="class in org.biojava.bio.program.homologene">SimpleOrthoPairSet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/indexdb/BioStore.html#getName()">getName()</a></span> - Method in class org.biojava.bio.program.indexdb.<a href="./org/biojava/bio/program/indexdb/BioStore.html" title="class in org.biojava.bio.program.indexdb">BioStore</a></dt>
<dd>
<div class="block">The name of this store or null if the name has not been set.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/Protease.html#getName()">getName()</a></span> - Method in class org.biojava.bio.proteomics.<a href="./org/biojava/bio/proteomics/Protease.html" title="class in org.biojava.bio.proteomics">Protease</a></dt>
<dd>
<div class="block">Gets the name of this Protease</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/AnnotatedSequenceDB.html#getName()">getName()</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/AnnotatedSequenceDB.html" title="class in org.biojava.bio.seq.db">AnnotatedSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/biofetch/BioFetchSequenceDB.html#getName()">getName()</a></span> - Method in class org.biojava.bio.seq.db.biofetch.<a href="./org/biojava/bio/seq/db/biofetch/BioFetchSequenceDB.html" title="class in org.biojava.bio.seq.db.biofetch">BioFetchSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/biofetch/BioFetchSequenceDBProvider.html#getName()">getName()</a></span> - Method in class org.biojava.bio.seq.db.biofetch.<a href="./org/biojava/bio/seq/db/biofetch/BioFetchSequenceDBProvider.html" title="class in org.biojava.bio.seq.db.biofetch">BioFetchSequenceDBProvider</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/BioIndex.html#getName()">getName()</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/BioIndex.html" title="class in org.biojava.bio.seq.db">BioIndex</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/biosql/BioSQLSequenceDB.html#getName()">getName()</a></span> - Method in class org.biojava.bio.seq.db.biosql.<a href="./org/biojava/bio/seq/db/biosql/BioSQLSequenceDB.html" title="class in org.biojava.bio.seq.db.biosql">BioSQLSequenceDB</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/biosql/BioSQLSequenceDBProvider.html#getName()">getName()</a></span> - Method in class org.biojava.bio.seq.db.biosql.<a href="./org/biojava/bio/seq/db/biosql/BioSQLSequenceDBProvider.html" title="class in org.biojava.bio.seq.db.biosql">BioSQLSequenceDBProvider</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/CachingSequenceDB.html#getName()">getName()</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/CachingSequenceDB.html" title="class in org.biojava.bio.seq.db">CachingSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/DummySequenceDB.html#getName()">getName()</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/DummySequenceDB.html" title="class in org.biojava.bio.seq.db">DummySequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/EmblCDROMIndexStore.html#getName()">getName()</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/EmblCDROMIndexStore.html" title="class in org.biojava.bio.seq.db">EmblCDROMIndexStore</a></dt>
<dd>
<div class="block"><code>getName</code> returns the database name as defined
within the EMBL CD-ROM index.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/flat/FlatSequenceDB.html#getName()">getName()</a></span> - Method in class org.biojava.bio.seq.db.flat.<a href="./org/biojava/bio/seq/db/flat/FlatSequenceDB.html" title="class in org.biojava.bio.seq.db.flat">FlatSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/flat/FlatSequenceDBProvider.html#getName()">getName()</a></span> - Method in class org.biojava.bio.seq.db.flat.<a href="./org/biojava/bio/seq/db/flat/FlatSequenceDBProvider.html" title="class in org.biojava.bio.seq.db.flat">FlatSequenceDBProvider</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/GenbankSequenceDB.html#getName()">getName()</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/GenbankSequenceDB.html" title="class in org.biojava.bio.seq.db">GenbankSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/GenpeptSequenceDB.html#getName()">getName()</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/GenpeptSequenceDB.html" title="class in org.biojava.bio.seq.db">GenpeptSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/HashSequenceDB.html#getName()">getName()</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/HashSequenceDB.html" title="class in org.biojava.bio.seq.db">HashSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/IndexedSequenceDB.html#getName()">getName()</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/IndexedSequenceDB.html" title="class in org.biojava.bio.seq.db">IndexedSequenceDB</a></dt>
<dd>
<div class="block">Get the name of this sequence database.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/IndexStore.html#getName()">getName()</a></span> - Method in interface org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/IndexStore.html" title="interface in org.biojava.bio.seq.db">IndexStore</a></dt>
<dd>
<div class="block">Retrieve the name of this store.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/NCBISequenceDB.html#getName()">getName()</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/NCBISequenceDB.html" title="class in org.biojava.bio.seq.db">NCBISequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/SequenceDBLite.html#getName()">getName()</a></span> - Method in interface org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/SequenceDBLite.html" title="interface in org.biojava.bio.seq.db">SequenceDBLite</a></dt>
<dd>
<div class="block">Get the name of this sequence database.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/SubSequenceDB.html#getName()">getName()</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/SubSequenceDB.html" title="class in org.biojava.bio.seq.db">SubSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/SwissprotSequenceDB.html#getName()">getName()</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/SwissprotSequenceDB.html" title="class in org.biojava.bio.seq.db">SwissprotSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/TabIndexStore.html#getName()">getName()</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/TabIndexStore.html" title="class in org.biojava.bio.seq.db">TabIndexStore</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/ViewingSequenceDB.html#getName()">getName()</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/ViewingSequenceDB.html" title="class in org.biojava.bio.seq.db">ViewingSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/distributed/DistributedSequenceDB.html#getName()">getName()</a></span> - Method in class org.biojava.bio.seq.distributed.<a href="./org/biojava/bio/seq/distributed/DistributedSequenceDB.html" title="class in org.biojava.bio.seq.distributed">DistributedSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureTypes.Repository.html#getName()">getName()</a></span> - Method in interface org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureTypes.Repository.html" title="interface in org.biojava.bio.seq">FeatureTypes.Repository</a></dt>
<dd>
<div class="block">The name of this repository.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureTypes.RepositoryImpl.html#getName()">getName()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureTypes.RepositoryImpl.html" title="class in org.biojava.bio.seq">FeatureTypes.RepositoryImpl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureTypes.Type.html#getName()">getName()</a></span> - Method in interface org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureTypes.Type.html" title="interface in org.biojava.bio.seq">FeatureTypes.Type</a></dt>
<dd>
<div class="block">Get the name of this type.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/DummySequence.html#getName()">getName()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/DummySequence.html" title="class in org.biojava.bio.seq.impl">DummySequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleGappedSequence.html#getName()">getName()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleGappedSequence.html" title="class in org.biojava.bio.seq.impl">SimpleGappedSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleSequence.html#getName()">getName()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleSequence.html" title="class in org.biojava.bio.seq.impl">SimpleSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SubSequence.html#getName()">getName()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SubSequence.html" title="class in org.biojava.bio.seq.impl">SubSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/ViewSequence.html#getName()">getName()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/ViewSequence.html" title="class in org.biojava.bio.seq.impl">ViewSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/NewSimpleAssembly.html#getName()">getName()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/NewSimpleAssembly.html" title="class in org.biojava.bio.seq">NewSimpleAssembly</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/Sequence.html#getName()">getName()</a></span> - Method in interface org.biojava.bio.seq.<a href="./org/biojava/bio/seq/Sequence.html" title="interface in org.biojava.bio.seq">Sequence</a></dt>
<dd>
<div class="block">The name of this sequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/SimpleAssembly.html#getName()">getName()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/SimpleAssembly.html" title="class in org.biojava.bio.seq">SimpleAssembly</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Atom.html#getName()">getName()</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Atom.html" title="interface in org.biojava.bio.structure">Atom</a></dt>
<dd>
<div class="block">get trimmed version of atom name, e.g.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/AtomImpl.html#getName()">getName()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/AtomImpl.html" title="class in org.biojava.bio.structure">AtomImpl</a></dt>
<dd>
<div class="block">Gets this object's name.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Chain.html#getName()">getName()</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Chain.html" title="interface in org.biojava.bio.structure">Chain</a></dt>
<dd>
<div class="block">get and set the name of this chain (Chain id in PDB file ).</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/ChainImpl.html#getName()">getName()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/ChainImpl.html" title="class in org.biojava.bio.structure">ChainImpl</a></dt>
<dd>
<div class="block">get and set the name of this chain (Chain id in PDB file ).</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html#getName()">getName()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html" title="class in org.biojava.bio.structure.io.mmcif.model">ChemComp</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/PdbxEntityNonPoly.html#getName()">getName()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/PdbxEntityNonPoly.html" title="class in org.biojava.bio.structure.io.mmcif.model">PdbxEntityNonPoly</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Structure.html#getName()">getName()</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Structure.html" title="interface in org.biojava.bio.structure">Structure</a></dt>
<dd>
<div class="block">get biological name of Structure.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/StructureImpl.html#getName()">getName()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/StructureImpl.html" title="class in org.biojava.bio.structure">StructureImpl</a></dt>
<dd>
<div class="block">get biological name of Structure.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/Alphabet.html#getName()">getName()</a></span> - Method in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/Alphabet.html" title="interface in org.biojava.bio.symbol">Alphabet</a></dt>
<dd>
<div class="block">Get the name of the alphabet.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/CodonPref.html#getName()">getName()</a></span> - Method in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/CodonPref.html" title="interface in org.biojava.bio.symbol">CodonPref</a></dt>
<dd>
<div class="block">get name of object</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/DoubleAlphabet.DoubleRange.html#getName()">getName()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/DoubleAlphabet.DoubleRange.html" title="class in org.biojava.bio.symbol">DoubleAlphabet.DoubleRange</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/DoubleAlphabet.DoubleSymbol.html#getName()">getName()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/DoubleAlphabet.DoubleSymbol.html" title="class in org.biojava.bio.symbol">DoubleAlphabet.DoubleSymbol</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/DoubleAlphabet.html#getName()">getName()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/DoubleAlphabet.html" title="class in org.biojava.bio.symbol">DoubleAlphabet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/DoubleAlphabet.SubDoubleAlphabet.html#getName()">getName()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/DoubleAlphabet.SubDoubleAlphabet.html" title="class in org.biojava.bio.symbol">DoubleAlphabet.SubDoubleAlphabet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/FundamentalAtomicSymbol.html#getName()">getName()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/FundamentalAtomicSymbol.html" title="class in org.biojava.bio.symbol">FundamentalAtomicSymbol</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/IntegerAlphabet.html#getName()">getName()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/IntegerAlphabet.html" title="class in org.biojava.bio.symbol">IntegerAlphabet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/IntegerAlphabet.IntegerSymbol.html#getName()">getName()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/IntegerAlphabet.IntegerSymbol.html" title="class in org.biojava.bio.symbol">IntegerAlphabet.IntegerSymbol</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/IntegerAlphabet.SubIntegerAlphabet.html#getName()">getName()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/IntegerAlphabet.SubIntegerAlphabet.html" title="class in org.biojava.bio.symbol">IntegerAlphabet.SubIntegerAlphabet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleAlphabet.html#getName()">getName()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleAlphabet.html" title="class in org.biojava.bio.symbol">SimpleAlphabet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleCodonPref.html#getName()">getName()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleCodonPref.html" title="class in org.biojava.bio.symbol">SimpleCodonPref</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleSymbolPropertyTable.html#getName()">getName()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleSymbolPropertyTable.html" title="class in org.biojava.bio.symbol">SimpleSymbolPropertyTable</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SingletonAlphabet.html#getName()">getName()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SingletonAlphabet.html" title="class in org.biojava.bio.symbol">SingletonAlphabet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SoftMaskedAlphabet.html#getName()">getName()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SoftMaskedAlphabet.html" title="class in org.biojava.bio.symbol">SoftMaskedAlphabet</a></dt>
<dd>
<div class="block">The name of the Alphabet</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/Symbol.html#getName()">getName()</a></span> - Method in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/Symbol.html" title="interface in org.biojava.bio.symbol">Symbol</a></dt>
<dd>
<div class="block">The long name for the symbol.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SymbolPropertyTable.html#getName()">getName()</a></span> - Method in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SymbolPropertyTable.html" title="interface in org.biojava.bio.symbol">SymbolPropertyTable</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/taxa/SimpleTaxonFactory.html#getName()">getName()</a></span> - Method in class org.biojava.bio.taxa.<a href="./org/biojava/bio/taxa/SimpleTaxonFactory.html" title="class in org.biojava.bio.taxa">SimpleTaxonFactory</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/taxa/TaxonFactory.html#getName()">getName()</a></span> - Method in interface org.biojava.bio.taxa.<a href="./org/biojava/bio/taxa/TaxonFactory.html" title="interface in org.biojava.bio.taxa">TaxonFactory</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Name for this TaxonFactory.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/taxa/WeakTaxonFactory.html#getName()">getName()</a></span> - Method in class org.biojava.bio.taxa.<a href="./org/biojava/bio/taxa/WeakTaxonFactory.html" title="class in org.biojava.bio.taxa">WeakTaxonFactory</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/directory/SequenceDBProvider.html#getName()">getName()</a></span> - Method in interface org.biojava.directory.<a href="./org/biojava/directory/SequenceDBProvider.html" title="interface in org.biojava.directory">SequenceDBProvider</a></dt>
<dd>
<div class="block">The name of this provider.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/IntegerOntology.html#getName()">getName()</a></span> - Method in class org.biojava.ontology.<a href="./org/biojava/ontology/IntegerOntology.html" title="class in org.biojava.ontology">IntegerOntology</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/IntegerOntology.IntTerm.html#getName()">getName()</a></span> - Method in class org.biojava.ontology.<a href="./org/biojava/ontology/IntegerOntology.IntTerm.html" title="class in org.biojava.ontology">IntegerOntology.IntTerm</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/Ontology.html#getName()">getName()</a></span> - Method in interface org.biojava.ontology.<a href="./org/biojava/ontology/Ontology.html" title="interface in org.biojava.ontology">Ontology</a></dt>
<dd>
<div class="block">Return the name of this ontology</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/Ontology.Impl.html#getName()">getName()</a></span> - Method in class org.biojava.ontology.<a href="./org/biojava/ontology/Ontology.Impl.html" title="class in org.biojava.ontology">Ontology.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/OntologyTerm.Impl.html#getName()">getName()</a></span> - Method in class org.biojava.ontology.<a href="./org/biojava/ontology/OntologyTerm.Impl.html" title="class in org.biojava.ontology">OntologyTerm.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/RemoteTerm.Impl.html#getName()">getName()</a></span> - Method in class org.biojava.ontology.<a href="./org/biojava/ontology/RemoteTerm.Impl.html" title="class in org.biojava.ontology">RemoteTerm.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/Synonym.html#getName()">getName()</a></span> - Method in class org.biojava.ontology.<a href="./org/biojava/ontology/Synonym.html" title="class in org.biojava.ontology">Synonym</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/Term.html#getName()">getName()</a></span> - Method in interface org.biojava.ontology.<a href="./org/biojava/ontology/Term.html" title="interface in org.biojava.ontology">Term</a></dt>
<dd>
<div class="block">Return the name of this term.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/Term.Impl.html#getName()">getName()</a></span> - Method in class org.biojava.ontology.<a href="./org/biojava/ontology/Term.Impl.html" title="class in org.biojava.ontology">Term.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/Triple.Impl.html#getName()">getName()</a></span> - Method in class org.biojava.ontology.<a href="./org/biojava/ontology/Triple.Impl.html" title="class in org.biojava.ontology">Triple.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/candy/CandyVocabulary.html#getName()">getName()</a></span> - Method in interface org.biojava.utils.candy.<a href="./org/biojava/utils/candy/CandyVocabulary.html" title="interface in org.biojava.utils.candy">CandyVocabulary</a></dt>
<dd>
<div class="block">It returns a name of this vocabulary.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/ChangeType.html#getName()">getName()</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/ChangeType.html" title="class in org.biojava.utils">ChangeType</a></dt>
<dd>
<div class="block">Return the name of this change.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/regex/Pattern.html#getName()">getName()</a></span> - Method in class org.biojava.utils.regex.<a href="./org/biojava/utils/regex/Pattern.html" title="class in org.biojava.utils.regex">Pattern</a></dt>
<dd>
<div class="block">return the String label associated with this pattern.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/BioEntry.html#getName()">getName()</a></span> - Method in interface org.biojavax.bio.<a href="./org/biojavax/bio/BioEntry.html" title="interface in org.biojavax.bio">BioEntry</a></dt>
<dd>
<div class="block">Returns the name of this bioentry.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/BioEntryDBLite.html#getName()">getName()</a></span> - Method in interface org.biojavax.bio.db.<a href="./org/biojavax/bio/db/BioEntryDBLite.html" title="interface in org.biojavax.bio.db">BioEntryDBLite</a></dt>
<dd>
<div class="block">Get the name of this sequence database.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLBioEntryDB.html#getName()">getName()</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLBioEntryDB.html" title="class in org.biojavax.bio.db.biosql">BioSQLBioEntryDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByName.html#getName()">getName()</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByName.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.ByName</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLRichSequenceDB.html#getName()">getName()</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLRichSequenceDB.html" title="class in org.biojavax.bio.db.biosql">BioSQLRichSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/HashBioEntryDB.html#getName()">getName()</a></span> - Method in class org.biojavax.bio.db.<a href="./org/biojavax/bio/db/HashBioEntryDB.html" title="class in org.biojavax.bio.db">HashBioEntryDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/HashRichSequenceDB.html#getName()">getName()</a></span> - Method in class org.biojavax.bio.db.<a href="./org/biojavax/bio/db/HashRichSequenceDB.html" title="class in org.biojavax.bio.db">HashRichSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/ncbi/GenbankRichSequenceDB.html#getName()">getName()</a></span> - Method in class org.biojavax.bio.db.ncbi.<a href="./org/biojavax/bio/db/ncbi/GenbankRichSequenceDB.html" title="class in org.biojavax.bio.db.ncbi">GenbankRichSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/ncbi/GenpeptRichSequenceDB.html#getName()">getName()</a></span> - Method in class org.biojavax.bio.db.ncbi.<a href="./org/biojavax/bio/db/ncbi/GenpeptRichSequenceDB.html" title="class in org.biojavax.bio.db.ncbi">GenpeptRichSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichFeature.html#getName()">getName()</a></span> - Method in interface org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichFeature.html" title="interface in org.biojavax.bio.seq">RichFeature</a></dt>
<dd>
<div class="block">Returns the name of this feature.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichLocation.Strand.html#getName()">getName()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichLocation.Strand.html" title="class in org.biojavax.bio.seq">RichLocation.Strand</a></dt>
<dd>
<div class="block">Returns the string symbol of this strand.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichFeature.html#getName()">getName()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichFeature.html" title="class in org.biojavax.bio.seq">SimpleRichFeature</a></dt>
<dd>
<div class="block">Returns the name of this feature.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/SimpleBioEntry.html#getName()">getName()</a></span> - Method in class org.biojavax.bio.<a href="./org/biojavax/bio/SimpleBioEntry.html" title="class in org.biojavax.bio">SimpleBioEntry</a></dt>
<dd>
<div class="block">Returns the name of this bioentry.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/taxa/SimpleNCBITaxonName.html#getName()">getName()</a></span> - Method in class org.biojavax.bio.taxa.<a href="./org/biojavax/bio/taxa/SimpleNCBITaxonName.html" title="class in org.biojavax.bio.taxa">SimpleNCBITaxonName</a></dt>
<dd>
<div class="block">Returns this name.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/DocRefAuthor.html#getName()">getName()</a></span> - Method in interface org.biojavax.<a href="./org/biojavax/DocRefAuthor.html" title="interface in org.biojavax">DocRefAuthor</a></dt>
<dd>
<div class="block">Returns a textual description of the authors name.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ga/impl/AbstractOrganism.html#getName()">getName()</a></span> - Method in class org.biojavax.ga.impl.<a href="./org/biojavax/ga/impl/AbstractOrganism.html" title="class in org.biojavax.ga.impl">AbstractOrganism</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/impl/AbstractPopulation.html#getName()">getName()</a></span> - Method in class org.biojavax.ga.impl.<a href="./org/biojavax/ga/impl/AbstractPopulation.html" title="class in org.biojavax.ga.impl">AbstractPopulation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/Organism.html#getName()">getName()</a></span> - Method in interface org.biojavax.ga.<a href="./org/biojavax/ga/Organism.html" title="interface in org.biojavax.ga">Organism</a></dt>
<dd>
<div class="block">Gets the organisms name</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ga/Population.html#getName()">getName()</a></span> - Method in interface org.biojavax.ga.<a href="./org/biojavax/ga/Population.html" title="interface in org.biojavax.ga">Population</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/Namespace.html#getName()">getName()</a></span> - Method in interface org.biojavax.<a href="./org/biojavax/Namespace.html" title="interface in org.biojavax">Namespace</a></dt>
<dd>
<div class="block">The name of the namespace is immutable and must be set by the constructor
of the instantiating class.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ontology/SimpleComparableOntology.html#getName()">getName()</a></span> - Method in class org.biojavax.ontology.<a href="./org/biojavax/ontology/SimpleComparableOntology.html" title="class in org.biojavax.ontology">SimpleComparableOntology</a></dt>
<dd>
<div class="block">Return the name of this ontology</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ontology/SimpleComparableTerm.html#getName()">getName()</a></span> - Method in class org.biojavax.ontology.<a href="./org/biojavax/ontology/SimpleComparableTerm.html" title="class in org.biojavax.ontology">SimpleComparableTerm</a></dt>
<dd>
<div class="block">Return the name of this term.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ontology/SimpleComparableTriple.html#getName()">getName()</a></span> - Method in class org.biojavax.ontology.<a href="./org/biojavax/ontology/SimpleComparableTriple.html" title="class in org.biojavax.ontology">SimpleComparableTriple</a></dt>
<dd>
<div class="block">Return the name of this term.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleDocRefAuthor.html#getName()">getName()</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleDocRefAuthor.html" title="class in org.biojavax">SimpleDocRefAuthor</a></dt>
<dd>
<div class="block">Returns a textual description of the authors name.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleNamespace.html#getName()">getName()</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleNamespace.html" title="class in org.biojavax">SimpleNamespace</a></dt>
<dd>
<div class="block">The name of the namespace is immutable and must be set by the constructor
of the instantiating class.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/taxa/SimpleNCBITaxonName.html#getNameClass()">getNameClass()</a></span> - Method in class org.biojavax.bio.taxa.<a href="./org/biojavax/bio/taxa/SimpleNCBITaxonName.html" title="class in org.biojavax.bio.taxa">SimpleNCBITaxonName</a></dt>
<dd>
<div class="block">Returns the class of this name.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/taxa/NCBITaxon.html#getNameClasses()">getNameClasses()</a></span> - Method in interface org.biojavax.bio.taxa.<a href="./org/biojavax/bio/taxa/NCBITaxon.html" title="interface in org.biojavax.bio.taxa">NCBITaxon</a></dt>
<dd>
<div class="block">Returns all the name classes available for a taxon.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/taxa/SimpleNCBITaxon.html#getNameClasses()">getNameClasses()</a></span> - Method in class org.biojavax.bio.taxa.<a href="./org/biojavax/bio/taxa/SimpleNCBITaxon.html" title="class in org.biojavax.bio.taxa">SimpleNCBITaxon</a></dt>
<dd>
<div class="block">Returns all the name classes available for a taxon.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtCommentParser.Event.html#getNamedIsoforms()">getNamedIsoforms()</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtCommentParser.Event.html" title="class in org.biojavax.bio.seq.io">UniProtCommentParser.Event</a></dt>
<dd>
<div class="block">Getter for property namedIsoforms.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/taxa/NCBITaxon.html#getNameHierarchy()">getNameHierarchy()</a></span> - Method in interface org.biojavax.bio.taxa.<a href="./org/biojavax/bio/taxa/NCBITaxon.html" title="interface in org.biojavax.bio.taxa">NCBITaxon</a></dt>
<dd>
<div class="block">Returns the taxonomy hierarchy of this taxon entry in the form:
least specific; more specific; ...; most specific.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/taxa/SimpleNCBITaxon.html#getNameHierarchy()">getNameHierarchy()</a></span> - Method in class org.biojavax.bio.taxa.<a href="./org/biojavax/bio/taxa/SimpleNCBITaxon.html" title="class in org.biojavax.bio.taxa">SimpleNCBITaxon</a></dt>
<dd>
<div class="block">Returns the taxonomy hierarchy of this taxon entry in the form:
most specific; less specific; ...; least specific.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/naming/ObdaContext.html#getNameInNamespace()">getNameInNamespace()</a></span> - Method in class org.biojava.naming.<a href="./org/biojava/naming/ObdaContext.html" title="class in org.biojava.naming">ObdaContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/naming/ObdaContext.html#getNameParser(javax.naming.Name)">getNameParser(Name)</a></span> - Method in class org.biojava.naming.<a href="./org/biojava/naming/ObdaContext.html" title="class in org.biojava.naming">ObdaContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/naming/ObdaContext.html#getNameParser(java.lang.String)">getNameParser(String)</a></span> - Method in class org.biojava.naming.<a href="./org/biojava/naming/ObdaContext.html" title="class in org.biojava.naming">ObdaContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/ProteaseManager.html#getNames()">getNames()</a></span> - Static method in class org.biojava.bio.proteomics.<a href="./org/biojava/bio/proteomics/ProteaseManager.html" title="class in org.biojava.bio.proteomics">ProteaseManager</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtCommentParser.Isoform.html#getNames()">getNames()</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtCommentParser.Isoform.html" title="class in org.biojavax.bio.seq.io">UniProtCommentParser.Isoform</a></dt>
<dd>
<div class="block">Getter for property names.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/taxa/NCBITaxon.html#getNames(java.lang.String)">getNames(String)</a></span> - Method in interface org.biojavax.bio.taxa.<a href="./org/biojavax/bio/taxa/NCBITaxon.html" title="interface in org.biojavax.bio.taxa">NCBITaxon</a></dt>
<dd>
<div class="block">Returns all the names available for a taxon in a given class.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/taxa/SimpleNCBITaxon.html#getNames(java.lang.String)">getNames(String)</a></span> - Method in class org.biojavax.bio.taxa.<a href="./org/biojavax/bio/taxa/SimpleNCBITaxon.html" title="class in org.biojavax.bio.taxa">SimpleNCBITaxon</a></dt>
<dd>
<div class="block">Returns all the names available for a taxon in a given class.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/taxa/SimpleNCBITaxon.html#getNameSet()">getNameSet()</a></span> - Method in class org.biojavax.bio.taxa.<a href="./org/biojavax/bio/taxa/SimpleNCBITaxon.html" title="class in org.biojavax.bio.taxa">SimpleNCBITaxon</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/taxa/SimpleNCBITaxon.html#getNamesMap()">getNamesMap()</a></span> - Method in class org.biojavax.bio.taxa.<a href="./org/biojavax/bio/taxa/SimpleNCBITaxon.html" title="class in org.biojavax.bio.taxa">SimpleNCBITaxon</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/BioEntry.html#getNamespace()">getNamespace()</a></span> - Method in interface org.biojavax.bio.<a href="./org/biojavax/bio/BioEntry.html" title="interface in org.biojavax.bio">BioEntry</a></dt>
<dd>
<div class="block">Returns the namespace of this bioentry.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/ncbi/GenbankRichSequenceDB.html#getNamespace()">getNamespace()</a></span> - Method in class org.biojavax.bio.db.ncbi.<a href="./org/biojavax/bio/db/ncbi/GenbankRichSequenceDB.html" title="class in org.biojavax.bio.db.ncbi">GenbankRichSequenceDB</a></dt>
<dd>
<div class="block">Getter for property namespace.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/ncbi/GenpeptRichSequenceDB.html#getNamespace()">getNamespace()</a></span> - Method in class org.biojavax.bio.db.ncbi.<a href="./org/biojavax/bio/db/ncbi/GenpeptRichSequenceDB.html" title="class in org.biojavax.bio.db.ncbi">GenpeptRichSequenceDB</a></dt>
<dd>
<div class="block">Getter for property namespace.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/SimpleBioEntry.html#getNamespace()">getNamespace()</a></span> - Method in class org.biojavax.bio.<a href="./org/biojavax/bio/SimpleBioEntry.html" title="class in org.biojavax.bio">SimpleBioEntry</a></dt>
<dd>
<div class="block">Returns the namespace of this bioentry.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/lsid/LifeScienceIdentifier.html#getNamespaceId()">getNamespaceId()</a></span> - Method in class org.biojava.utils.lsid.<a href="./org/biojava/utils/lsid/LifeScienceIdentifier.html" title="class in org.biojava.utils.lsid">LifeScienceIdentifier</a></dt>
<dd>
<div class="block">Return the namespace id for this identifier
within the authority.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/NameTokenization.html#getNameToSymbol()">getNameToSymbol()</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/NameTokenization.html" title="class in org.biojava.bio.seq.io">NameTokenization</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/taxa/NCBITaxon.html#getNCBITaxID()">getNCBITaxID()</a></span> - Method in interface org.biojavax.bio.taxa.<a href="./org/biojavax/bio/taxa/NCBITaxon.html" title="interface in org.biojavax.bio.taxa">NCBITaxon</a></dt>
<dd>
<div class="block">Gets the NCBI taxon ID.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/taxa/SimpleNCBITaxon.html#getNCBITaxID()">getNCBITaxID()</a></span> - Method in class org.biojavax.bio.taxa.<a href="./org/biojavax/bio/taxa/SimpleNCBITaxon.html" title="class in org.biojavax.bio.taxa">SimpleNCBITaxon</a></dt>
<dd>
<div class="block">Gets the NCBI taxon ID.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/molbio/RestrictionEnzymeManager.html#getNCutters(int)">getNCutters(int)</a></span> - Static method in class org.biojava.bio.molbio.<a href="./org/biojava/bio/molbio/RestrictionEnzymeManager.html" title="class in org.biojava.bio.molbio">RestrictionEnzymeManager</a></dt>
<dd>
<div class="block"><code>getNCutters</code> returns an unmodifable set of all
enzymes with a cut site of size n.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/PdbxNonPolyScheme.html#getNdb_seq_num()">getNdb_seq_num()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/PdbxNonPolyScheme.html" title="class in org.biojava.bio.structure.io.mmcif.model">PdbxNonPolyScheme</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/PdbxPolySeqScheme.html#getNdb_seq_num()">getNdb_seq_num()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/PdbxPolySeqScheme.html" title="class in org.biojava.bio.structure.io.mmcif.model">PdbxPolySeqScheme</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/tools/ClassifierExample.PointClassifier.html#getNegShape()">getNegShape()</a></span> - Method in class org.biojava.stats.svm.tools.<a href="./org/biojava/stats/svm/tools/ClassifierExample.PointClassifier.html" title="class in org.biojava.stats.svm.tools">ClassifierExample.PointClassifier</a></dt>
<dd>
<div class="block">Retrieve the shape used to represent negative points.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/NestedKernel.html#getNestedKernel()">getNestedKernel()</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/NestedKernel.html" title="class in org.biojava.stats.svm">NestedKernel</a></dt>
<dd>
<div class="block">Retrieve the currently nested <span class="type">SVMKernel</span>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/obo/OboFileParser.html#getNestedValue(org.biojava.ontology.obo.NestedValue, java.lang.String, int)">getNestedValue(NestedValue, String, int)</a></span> - Method in class org.biojava.ontology.obo.<a href="./org/biojava/ontology/obo/OboFileParser.html" title="class in org.biojava.ontology.obo">OboFileParser</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/PropertyChanger.html#getNewTag(java.lang.Object)">getNewTag(Object)</a></span> - Method in interface org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/PropertyChanger.html" title="interface in org.biojava.bio.program.tagvalue">PropertyChanger</a></dt>
<dd>
<div class="block">
<code>getNewTag</code> returns the tag which substitutes the
specified value.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/TagMapper.html#getNewTag(java.lang.Object)">getNewTag(Object)</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/TagMapper.html" title="class in org.biojava.bio.program.tagvalue">TagMapper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/taxa/NCBITaxon.html#getNodeRank()">getNodeRank()</a></span> - Method in interface org.biojavax.bio.taxa.<a href="./org/biojavax/bio/taxa/NCBITaxon.html" title="interface in org.biojavax.bio.taxa">NCBITaxon</a></dt>
<dd>
<div class="block">Gets the node rank of this taxon.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/taxa/SimpleNCBITaxon.html#getNodeRank()">getNodeRank()</a></span> - Method in class org.biojavax.bio.taxa.<a href="./org/biojavax/bio/taxa/SimpleNCBITaxon.html" title="class in org.biojavax.bio.taxa">SimpleNCBITaxon</a></dt>
<dd>
<div class="block">Gets the node rank of this taxon.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/automata/FiniteAutomaton.html#getNodes()">getNodes()</a></span> - Method in class org.biojava.utils.automata.<a href="./org/biojava/utils/automata/FiniteAutomaton.html" title="class in org.biojava.utils.automata">FiniteAutomaton</a></dt>
<dd>
<div class="block">get all Nodes within this instance.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/automata/NfaBuilder.html#getNodes()">getNodes()</a></span> - Method in interface org.biojava.utils.automata.<a href="./org/biojava/utils/automata/NfaBuilder.html" title="interface in org.biojava.utils.automata">NfaBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/automata/NfaSubModel.html#getNodes()">getNodes()</a></span> - Method in class org.biojava.utils.automata.<a href="./org/biojava/utils/automata/NfaSubModel.html" title="class in org.biojava.utils.automata">NfaSubModel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/WobbleDistribution.html#getNonWobbleBases()">getNonWobbleBases()</a></span> - Method in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/WobbleDistribution.html" title="interface in org.biojava.bio.symbol">WobbleDistribution</a></dt>
<dd>
<div class="block">returns Set containing the nonWobbleBases that
occur in codons that encode this residue</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/SparseVector.NormalizingKernel.html#getNormalizingVector()">getNormalizingVector()</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/SparseVector.NormalizingKernel.html" title="class in org.biojava.stats.svm">SparseVector.NormalizingKernel</a></dt>
<dd>
<div class="block">Retrive the current normalizing vector.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/Protease.html#getNotCleaveResidues()">getNotCleaveResidues()</a></span> - Method in class org.biojava.bio.proteomics.<a href="./org/biojava/bio/proteomics/Protease.html" title="class in org.biojava.bio.proteomics">Protease</a></dt>
<dd>
<div class="block">The list of residues that will prevent cleavage if they follow the cleavage
residue.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/Agave2AgaveAnnotFilter.html#getNote(org.biojava.bio.Annotation)">getNote(Annotation)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/Agave2AgaveAnnotFilter.html" title="class in org.biojava.bio.seq.io.agave">Agave2AgaveAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEAnnotFilter.html#getNote(org.biojava.bio.Annotation)">getNote(Annotation)</a></span> - Method in interface org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEAnnotFilter.html" title="interface in org.biojava.bio.seq.io.agave">AGAVEAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/Embl2AgaveAnnotFilter.html#getNote(org.biojava.bio.Annotation)">getNote(Annotation)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/Embl2AgaveAnnotFilter.html" title="class in org.biojava.bio.seq.io.agave">Embl2AgaveAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/SimpleAnnotFilter.html#getNote(org.biojava.bio.Annotation)">getNote(Annotation)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/SimpleAnnotFilter.html" title="class in org.biojava.bio.seq.io.agave">SimpleAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByNote.html#getNote()">getNote()</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByNote.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.ByNote</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html#getNote()">getNote()</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html" title="class in org.biojavax.bio.seq.io">UniProtCommentParser</a></dt>
<dd>
<div class="block">Getter for property note.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtCommentParser.Isoform.html#getNote()">getNote()</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtCommentParser.Isoform.html" title="class in org.biojavax.bio.seq.io">UniProtCommentParser.Isoform</a></dt>
<dd>
<div class="block">Getter for property note.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtCommentParser.SeqCaution.html#getNote()">getNote()</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtCommentParser.SeqCaution.html" title="class in org.biojavax.bio.seq.io">UniProtCommentParser.SeqCaution</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/EmptyRichAnnotation.html#getNote(org.biojavax.Note)">getNote(Note)</a></span> - Method in class org.biojavax.<a href="./org/biojavax/EmptyRichAnnotation.html" title="class in org.biojavax">EmptyRichAnnotation</a></dt>
<dd>
<div class="block">Uses the term and rank to lookup a note in this annotation.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/RichAnnotation.html#getNote(org.biojavax.Note)">getNote(Note)</a></span> - Method in interface org.biojavax.<a href="./org/biojavax/RichAnnotation.html" title="interface in org.biojavax">RichAnnotation</a></dt>
<dd>
<div class="block">Uses the term and rank to lookup a note in this annotation.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleRichAnnotation.html#getNote(org.biojavax.Note)">getNote(Note)</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleRichAnnotation.html" title="class in org.biojavax">SimpleRichAnnotation</a></dt>
<dd>
<div class="block">Uses the term and rank to lookup a note in this annotation.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/CompoundRichLocation.html#getNoteSet()">getNoteSet()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/CompoundRichLocation.html" title="class in org.biojavax.bio.seq">CompoundRichLocation</a></dt>
<dd>
<div class="block">Returns the set of notes associated with this object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/EmptyRichLocation.html#getNoteSet()">getNoteSet()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/EmptyRichLocation.html" title="class in org.biojavax.bio.seq">EmptyRichLocation</a></dt>
<dd>
<div class="block">Returns the set of notes associated with this object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichFeature.html#getNoteSet()">getNoteSet()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichFeature.html" title="class in org.biojavax.bio.seq">SimpleRichFeature</a></dt>
<dd>
<div class="block">Returns the set of notes associated with this object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichLocation.html#getNoteSet()">getNoteSet()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichLocation.html" title="class in org.biojavax.bio.seq">SimpleRichLocation</a></dt>
<dd>
<div class="block">Returns the set of notes associated with this object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/SimpleBioEntry.html#getNoteSet()">getNoteSet()</a></span> - Method in class org.biojavax.bio.<a href="./org/biojavax/bio/SimpleBioEntry.html" title="class in org.biojavax.bio">SimpleBioEntry</a></dt>
<dd>
<div class="block">Returns the set of notes associated with this object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/EmptyRichAnnotation.html#getNoteSet()">getNoteSet()</a></span> - Method in class org.biojavax.<a href="./org/biojavax/EmptyRichAnnotation.html" title="class in org.biojavax">EmptyRichAnnotation</a></dt>
<dd>
<div class="block">Returns an immutable set of all notes in this annotation.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/RichAnnotatable.html#getNoteSet()">getNoteSet()</a></span> - Method in interface org.biojavax.<a href="./org/biojavax/RichAnnotatable.html" title="interface in org.biojavax">RichAnnotatable</a></dt>
<dd>
<div class="block">Returns the set of notes associated with this object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/RichAnnotation.html#getNoteSet()">getNoteSet()</a></span> - Method in interface org.biojavax.<a href="./org/biojavax/RichAnnotation.html" title="interface in org.biojavax">RichAnnotation</a></dt>
<dd>
<div class="block">Returns an immutable set of all notes in this annotation.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleCrossRef.html#getNoteSet()">getNoteSet()</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleCrossRef.html" title="class in org.biojavax">SimpleCrossRef</a></dt>
<dd>
<div class="block">Returns the set of notes associated with this object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleRichAnnotation.html#getNoteSet()">getNoteSet()</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleRichAnnotation.html" title="class in org.biojavax">SimpleRichAnnotation</a></dt>
<dd>
<div class="block">Returns an immutable set of all notes in this annotation.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/StructureTools.html#getNrAtoms(org.biojava.bio.structure.Structure)">getNrAtoms(Structure)</a></span> - Static method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/StructureTools.html" title="class in org.biojava.bio.structure">StructureTools</a></dt>
<dd>
<div class="block">Count how many number of Atoms are contained within a Structure object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/server/SimpleStructureServer.html#getNrCPUs()">getNrCPUs()</a></span> - Method in class org.biojava.bio.structure.server.<a href="./org/biojava/bio/structure/server/SimpleStructureServer.html" title="class in org.biojava.bio.structure.server">SimpleStructureServer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/StructureTools.html#getNrGroups(org.biojava.bio.structure.Structure)">getNrGroups(Structure)</a></span> - Static method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/StructureTools.html" title="class in org.biojava.bio.structure">StructureTools</a></dt>
<dd>
<div class="block">Count how many groups are contained within a structure object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/NucleotideTools.html#getNucleotide()">getNucleotide()</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/NucleotideTools.html" title="class in org.biojava.bio.seq">NucleotideTools</a></dt>
<dd>
<div class="block">Return the Nucleotide alphabet.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.IOTools.html#getNucleotideParser()">getNucleotideParser()</a></span> - Static method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.IOTools.html" title="class in org.biojavax.bio.seq">RichSequence.IOTools</a></dt>
<dd>
<div class="block">Creates a nucleotide symbol tokenizer.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/AbstractOrderNDistribution.html#getNullModel()">getNullModel()</a></span> - Method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/AbstractOrderNDistribution.html" title="class in org.biojava.bio.dist">AbstractOrderNDistribution</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/Distribution.html#getNullModel()">getNullModel()</a></span> - Method in interface org.biojava.bio.dist.<a href="./org/biojava/bio/dist/Distribution.html" title="interface in org.biojava.bio.dist">Distribution</a></dt>
<dd>
<div class="block">Retrieve the null model Distribution that this Distribution recognizes.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/GapDistribution.html#getNullModel()">getNullModel()</a></span> - Method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/GapDistribution.html" title="class in org.biojava.bio.dist">GapDistribution</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/PairDistribution.html#getNullModel(org.biojava.bio.dist.Distribution, org.biojava.bio.dist.Distribution)">getNullModel(Distribution, Distribution)</a></span> - Static method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/PairDistribution.html" title="class in org.biojava.bio.dist">PairDistribution</a></dt>
<dd>
<div class="block">Get a uniform null model over a PairDistribution over [first,second].</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/PairDistribution.html#getNullModel()">getNullModel()</a></span> - Method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/PairDistribution.html" title="class in org.biojava.bio.dist">PairDistribution</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/SimpleDistribution.html#getNullModel()">getNullModel()</a></span> - Method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/SimpleDistribution.html" title="class in org.biojava.bio.dist">SimpleDistribution</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/TranslatedDistribution.html#getNullModel()">getNullModel()</a></span> - Method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/TranslatedDistribution.html" title="class in org.biojava.bio.dist">TranslatedDistribution</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/UniformDistribution.html#getNullModel()">getNullModel()</a></span> - Method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/UniformDistribution.html" title="class in org.biojava.bio.dist">UniformDistribution</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/DistributionTrainerContext.html#getNullModelWeight()">getNullModelWeight()</a></span> - Method in interface org.biojava.bio.dist.<a href="./org/biojava/bio/dist/DistributionTrainerContext.html" title="interface in org.biojava.bio.dist">DistributionTrainerContext</a></dt>
<dd>
<div class="block">Return the number of pseudocounts added to the distribution when training.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/SimpleDistributionTrainerContext.html#getNullModelWeight()">getNullModelWeight()</a></span> - Method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/SimpleDistributionTrainerContext.html" title="class in org.biojava.bio.dist">SimpleDistributionTrainerContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/DatabasePDBrev.html#getNum()">getNum()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/DatabasePDBrev.html" title="class in org.biojava.bio.structure.io.mmcif.model">DatabasePDBrev</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/EntityPolySeq.html#getNum()">getNum()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/EntityPolySeq.html" title="class in org.biojava.bio.structure.io.mmcif.model">EntityPolySeq</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SuffixTree.SuffixNode.html#getNumber()">getNumber()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SuffixTree.SuffixNode.html" title="class in org.biojava.bio.symbol">SuffixTree.SuffixNode</a></dt>
<dd>
<div class="block">Return a number (usually, but not always, a motif count)
associated with this node of the tree.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtCommentParser.Interaction.html#getNumberExperiments()">getNumberExperiments()</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtCommentParser.Interaction.html" title="class in org.biojavax.bio.seq.io">UniProtCommentParser.Interaction</a></dt>
<dd>
<div class="block">Getter for property numberExperiments.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/candy/CandyFinder.html#getNumCount()">getNumCount()</a></span> - Method in interface org.biojava.utils.candy.<a href="./org/biojava/utils/candy/CandyFinder.html" title="interface in org.biojava.utils.candy">CandyFinder</a></dt>
<dd>
<div class="block">It returns the number of available vocabularies.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Compound.html#getNumRes()">getNumRes()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure">Compound</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/AminoAcid.html#getO()">getO()</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/AminoAcid.html" title="interface in org.biojava.bio.structure">AminoAcid</a></dt>
<dd>
<div class="block">get O atom.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/AminoAcidImpl.html#getO()">getO()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/AminoAcidImpl.html" title="class in org.biojava.bio.structure">AminoAcidImpl</a></dt>
<dd>
<div class="block">get O atom.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/Triple.html#getObject()">getObject()</a></span> - Method in interface org.biojava.ontology.<a href="./org/biojava/ontology/Triple.html" title="interface in org.biojava.ontology">Triple</a></dt>
<dd>
<div class="block">Return the object term of this triple.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/Triple.Impl.html#getObject()">getObject()</a></span> - Method in class org.biojava.ontology.<a href="./org/biojava/ontology/Triple.Impl.html" title="class in org.biojava.ontology">Triple.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/BioEntryRelationship.html#getObject()">getObject()</a></span> - Method in interface org.biojavax.bio.<a href="./org/biojavax/bio/BioEntryRelationship.html" title="interface in org.biojavax.bio">BioEntryRelationship</a></dt>
<dd>
<div class="block">Returns the object of this relationship (ie.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichFeatureRelationship.html#getObject()">getObject()</a></span> - Method in interface org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichFeatureRelationship.html" title="interface in org.biojavax.bio.seq">RichFeatureRelationship</a></dt>
<dd>
<div class="block">Returns the object of this relationship (ie.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichFeatureRelationship.html#getObject()">getObject()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichFeatureRelationship.html" title="class in org.biojavax.bio.seq">SimpleRichFeatureRelationship</a></dt>
<dd>
<div class="block">Returns the object of this relationship (ie.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/SimpleBioEntryRelationship.html#getObject()">getObject()</a></span> - Method in class org.biojavax.bio.<a href="./org/biojavax/bio/SimpleBioEntryRelationship.html" title="class in org.biojavax.bio">SimpleBioEntryRelationship</a></dt>
<dd>
<div class="block">Returns the object of this relationship (ie.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ontology/SimpleComparableTriple.html#getObject()">getObject()</a></span> - Method in class org.biojavax.ontology.<a href="./org/biojavax/ontology/SimpleComparableTriple.html" title="class in org.biojavax.ontology">SimpleComparableTriple</a></dt>
<dd>
<div class="block">Return the object term of this triple.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/RichObjectFactory.html#getObject(java.lang.Class, java.lang.Object[])">getObject(Class, Object[])</a></span> - Static method in class org.biojavax.<a href="./org/biojavax/RichObjectFactory.html" title="class in org.biojavax">RichObjectFactory</a></dt>
<dd>
<div class="block">Delegates to a RichObjectBuilder to construct/retrieve the object, and returns it.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/dasalignment/Alignment.html#getObjectAnnotationType()">getObjectAnnotationType()</a></span> - Static method in class org.biojava.bio.program.das.dasalignment.<a href="./org/biojava/bio/program/das/dasalignment/Alignment.html" title="class in org.biojava.bio.program.das.dasalignment">Alignment</a></dt>
<dd>
<div class="block">define the alignment object Annotation Type.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/lsid/LifeScienceIdentifier.html#getObjectId()">getObjectId()</a></span> - Method in class org.biojava.utils.lsid.<a href="./org/biojava/utils/lsid/LifeScienceIdentifier.html" title="class in org.biojava.utils.lsid">LifeScienceIdentifier</a></dt>
<dd>
<div class="block">Return the object id of this identifier.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/dasalignment/Alignment.html#getObjects()">getObjects()</a></span> - Method in class org.biojava.bio.program.das.dasalignment.<a href="./org/biojava/bio/program/das/dasalignment/Alignment.html" title="class in org.biojava.bio.program.das.dasalignment">Alignment</a></dt>
<dd>
<div class="block">Returns the Annotation of all objects in this Alignment.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/obo/OboFileParser.html#getOboFileEventListener()">getOboFileEventListener()</a></span> - Method in class org.biojava.ontology.obo.<a href="./org/biojava/ontology/obo/OboFileParser.html" title="class in org.biojava.ontology.obo">OboFileParser</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ontology/ComparableTerm.html#getObsolete()">getObsolete()</a></span> - Method in interface org.biojavax.ontology.<a href="./org/biojavax/ontology/ComparableTerm.html" title="interface in org.biojavax.ontology">ComparableTerm</a></dt>
<dd>
<div class="block">Checks to see if this term is obsolete.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ontology/SimpleComparableTerm.html#getObsolete()">getObsolete()</a></span> - Method in class org.biojavax.ontology.<a href="./org/biojavax/ontology/SimpleComparableTerm.html" title="class in org.biojavax.ontology">SimpleComparableTerm</a></dt>
<dd>
<div class="block">Checks to see if this term is obsolete.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Atom.html#getOccupancy()">getOccupancy()</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Atom.html" title="interface in org.biojava.bio.structure">Atom</a></dt>
<dd>
<div class="block">get occupancy.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/AtomImpl.html#getOccupancy()">getOccupancy()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/AtomImpl.html" title="class in org.biojava.bio.structure">AtomImpl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html#getOccupancy()">getOccupancy()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html" title="class in org.biojava.bio.structure.io.mmcif.model">AtomSite</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html#getOccupancy_esd()">getOccupancy_esd()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html" title="class in org.biojava.bio.structure.io.mmcif.model">AtomSite</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#getOccupancy_max()">getOccupancy_max()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#getOccupancy_min()">getOccupancy_min()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/CircularRendererContext.html#getOffset()">getOffset()</a></span> - Method in interface org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/CircularRendererContext.html" title="interface in org.biojava.bio.gui.sequence">CircularRendererContext</a></dt>
<dd>
<div class="block">Get the angle through which the origin of the sequence is rotated through.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/CircularRendererPanel.html#getOffset()">getOffset()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/CircularRendererPanel.html" title="class in org.biojava.bio.gui.sequence">CircularRendererPanel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SubCircularRendererContext.html#getOffset()">getOffset()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SubCircularRendererContext.html" title="class in org.biojava.bio.gui.sequence">SubCircularRendererContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/indexdb/Record.html#getOffset()">getOffset()</a></span> - Method in interface org.biojava.bio.program.indexdb.<a href="./org/biojava/bio/program/indexdb/Record.html" title="interface in org.biojava.bio.program.indexdb">Record</a></dt>
<dd>
<div class="block"><code>getOffset</code> returns the byte offset in the file at
which the record begins.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/indexdb/Record.Impl.html#getOffset()">getOffset()</a></span> - Method in class org.biojava.bio.program.indexdb.<a href="./org/biojava/bio/program/indexdb/Record.Impl.html" title="class in org.biojava.bio.program.indexdb">Record.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/xff/FeatureHandler.html#getOldIDHandler()">getOldIDHandler()</a></span> - Method in class org.biojava.bio.program.xff.<a href="./org/biojava/bio/program/xff/FeatureHandler.html" title="class in org.biojava.bio.program.xff">FeatureHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html#getOne_letter_code()">getOne_letter_code()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html" title="class in org.biojava.bio.structure.io.mmcif.model">ChemComp</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/chem/ChemCompTools.html#getOneLetterCode(org.biojava.bio.structure.io.mmcif.model.ChemComp, org.biojava.bio.structure.io.mmcif.ChemicalComponentDictionary)">getOneLetterCode(ChemComp, ChemicalComponentDictionary)</a></span> - Static method in class org.biojava.bio.structure.io.mmcif.chem.<a href="./org/biojava/bio/structure/io/mmcif/chem/ChemCompTools.html" title="class in org.biojava.bio.structure.io.mmcif.chem">ChemCompTools</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/biosql/BioSQLSequenceDB.html#getOntology(java.lang.String)">getOntology(String)</a></span> - Method in class org.biojava.bio.seq.db.biosql.<a href="./org/biojava/bio/seq/db/biosql/BioSQLSequenceDB.html" title="class in org.biojava.bio.seq.db.biosql">BioSQLSequenceDB</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/IntegerOntology.IntTerm.html#getOntology()">getOntology()</a></span> - Method in class org.biojava.ontology.<a href="./org/biojava/ontology/IntegerOntology.IntTerm.html" title="class in org.biojava.ontology">IntegerOntology.IntTerm</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/OntologyTerm.html#getOntology()">getOntology()</a></span> - Method in interface org.biojava.ontology.<a href="./org/biojava/ontology/OntologyTerm.html" title="interface in org.biojava.ontology">OntologyTerm</a></dt>
<dd>
<div class="block">Get the remote ontology referenced by this term</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/OntologyTerm.Impl.html#getOntology()">getOntology()</a></span> - Method in class org.biojava.ontology.<a href="./org/biojava/ontology/OntologyTerm.Impl.html" title="class in org.biojava.ontology">OntologyTerm.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/RemoteTerm.Impl.html#getOntology()">getOntology()</a></span> - Method in class org.biojava.ontology.<a href="./org/biojava/ontology/RemoteTerm.Impl.html" title="class in org.biojava.ontology">RemoteTerm.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/Term.html#getOntology()">getOntology()</a></span> - Method in interface org.biojava.ontology.<a href="./org/biojava/ontology/Term.html" title="interface in org.biojava.ontology">Term</a></dt>
<dd>
<div class="block">Return the ontology in which this term exists.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/Term.Impl.html#getOntology()">getOntology()</a></span> - Method in class org.biojava.ontology.<a href="./org/biojava/ontology/Term.Impl.html" title="class in org.biojava.ontology">Term.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/Triple.Impl.html#getOntology()">getOntology()</a></span> - Method in class org.biojava.ontology.<a href="./org/biojava/ontology/Triple.Impl.html" title="class in org.biojava.ontology">Triple.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ontology/SimpleComparableTerm.html#getOntology()">getOntology()</a></span> - Method in class org.biojavax.ontology.<a href="./org/biojavax/ontology/SimpleComparableTerm.html" title="class in org.biojavax.ontology">SimpleComparableTerm</a></dt>
<dd>
<div class="block">Return the ontology in which this term exists.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ontology/SimpleComparableTriple.html#getOntology()">getOntology()</a></span> - Method in class org.biojavax.ontology.<a href="./org/biojavax/ontology/SimpleComparableTriple.html" title="class in org.biojavax.ontology">SimpleComparableTriple</a></dt>
<dd>
<div class="block">Return the ontology in which this term exists.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/IntegerOntology.html#getOps()">getOps()</a></span> - Method in class org.biojava.ontology.<a href="./org/biojava/ontology/IntegerOntology.html" title="class in org.biojava.ontology">IntegerOntology</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/Ontology.html#getOps()">getOps()</a></span> - Method in interface org.biojava.ontology.<a href="./org/biojava/ontology/Ontology.html" title="interface in org.biojava.ontology">Ontology</a></dt>
<dd>
<div class="block">Return the associated OntologyOps.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/Ontology.Impl.html#getOps()">getOps()</a></span> - Method in class org.biojava.ontology.<a href="./org/biojava/ontology/Ontology.Impl.html" title="class in org.biojava.ontology">Ontology.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ontology/SimpleComparableOntology.html#getOps()">getOps()</a></span> - Method in class org.biojavax.ontology.<a href="./org/biojavax/ontology/SimpleComparableOntology.html" title="class in org.biojavax.ontology">SimpleComparableOntology</a></dt>
<dd>
<div class="block">Return the associated OntologyOps.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.html#getOption(org.biojava.bio.chromatogram.graphic.ChromatogramGraphic.Option)">getOption(ChromatogramGraphic.Option)</a></span> - Method in class org.biojava.bio.chromatogram.graphic.<a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.html" title="class in org.biojava.bio.chromatogram.graphic">ChromatogramGraphic</a></dt>
<dd>
<div class="block">Returns the current value for the specified option.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ontology/ComparableOntology.html#getOrCreateTerm(java.lang.String)">getOrCreateTerm(String)</a></span> - Method in interface org.biojavax.ontology.<a href="./org/biojavax/ontology/ComparableOntology.html" title="interface in org.biojavax.ontology">ComparableOntology</a></dt>
<dd>
<div class="block">Looks for a term with the given name and returns it.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ontology/SimpleComparableOntology.html#getOrCreateTerm(java.lang.String)">getOrCreateTerm(String)</a></span> - Method in class org.biojavax.ontology.<a href="./org/biojavax/ontology/SimpleComparableOntology.html" title="class in org.biojavax.ontology">SimpleComparableOntology</a></dt>
<dd>
<div class="block">Looks for a term with the given name and returns it.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ontology/ComparableOntology.html#getOrCreateTriple(org.biojava.ontology.Term, org.biojava.ontology.Term, org.biojava.ontology.Term)">getOrCreateTriple(Term, Term, Term)</a></span> - Method in interface org.biojavax.ontology.<a href="./org/biojavax/ontology/ComparableOntology.html" title="interface in org.biojavax.ontology">ComparableOntology</a></dt>
<dd>
<div class="block">Looks for a triple with the given subject object and predicate and returns it.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ontology/SimpleComparableOntology.html#getOrCreateTriple(org.biojava.ontology.Term, org.biojava.ontology.Term, org.biojava.ontology.Term)">getOrCreateTriple(Term, Term, Term)</a></span> - Method in class org.biojavax.ontology.<a href="./org/biojavax/ontology/SimpleComparableOntology.html" title="class in org.biojavax.ontology">SimpleComparableOntology</a></dt>
<dd>
<div class="block">Looks for a triple with the given subject object and predicate and returns it.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/PolynomialKernel.html#getOrder()">getOrder()</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/PolynomialKernel.html" title="class in org.biojava.stats.svm">PolynomialKernel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.Terms.html#getOrderedLocusNameTerm()">getOrderedLocusNameTerm()</a></span> - Static method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.Terms.html" title="class in org.biojavax.bio.seq">RichSequence.Terms</a></dt>
<dd>
<div class="block">Getter for the OrderedLocusName term</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/CompoundRichLocation.html#getOrderTerm()">getOrderTerm()</a></span> - Static method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/CompoundRichLocation.html" title="class in org.biojavax.bio.seq">CompoundRichLocation</a></dt>
<dd>
<div class="block">Getter for the "order" term</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.Terms.html#getORFNameTerm()">getORFNameTerm()</a></span> - Static method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.Terms.html" title="class in org.biojavax.bio.seq">RichSequence.Terms</a></dt>
<dd>
<div class="block">Getter for the ORFName term</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Compound.html#getOrgan()">getOrgan()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure">Compound</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Compound.html#getOrganelle()">getOrganelle()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure">Compound</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.Terms.html#getOrganelleTerm()">getOrganelleTerm()</a></span> - Static method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.Terms.html" title="class in org.biojavax.bio.seq">RichSequence.Terms</a></dt>
<dd>
<div class="block">Getter for the Organelle term</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/Agave2AgaveAnnotFilter.html#getOrganism(org.biojava.bio.Annotation)">getOrganism(Annotation)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/Agave2AgaveAnnotFilter.html" title="class in org.biojava.bio.seq.io.agave">Agave2AgaveAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEAnnotFilter.html#getOrganism(org.biojava.bio.Annotation)">getOrganism(Annotation)</a></span> - Method in interface org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEAnnotFilter.html" title="interface in org.biojava.bio.seq.io.agave">AGAVEAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/Embl2AgaveAnnotFilter.html#getOrganism(org.biojava.bio.Annotation)">getOrganism(Annotation)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/Embl2AgaveAnnotFilter.html" title="class in org.biojava.bio.seq.io.agave">Embl2AgaveAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/SimpleAnnotFilter.html#getOrganism(org.biojava.bio.Annotation)">getOrganism(Annotation)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/SimpleAnnotFilter.html" title="class in org.biojava.bio.seq.io.agave">SimpleAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/impl/SimplePopulation.html#getOrganismByName(java.lang.String)">getOrganismByName(String)</a></span> - Method in class org.biojavax.ga.impl.<a href="./org/biojavax/ga/impl/SimplePopulation.html" title="class in org.biojavax.ga.impl">SimplePopulation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/Population.html#getOrganismByName(java.lang.String)">getOrganismByName(String)</a></span> - Method in interface org.biojavax.ga.<a href="./org/biojavax/ga/Population.html" title="interface in org.biojavax.ga">Population</a></dt>
<dd>
<div class="block">Gets the specified organism</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Compound.html#getOrganismCommon()">getOrganismCommon()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure">Compound</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/impl/SimplePopulation.html#getOrganisms()">getOrganisms()</a></span> - Method in class org.biojavax.ga.impl.<a href="./org/biojavax/ga/impl/SimplePopulation.html" title="class in org.biojavax.ga.impl">SimplePopulation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/Population.html#getOrganisms()">getOrganisms()</a></span> - Method in interface org.biojavax.ga.<a href="./org/biojavax/ga/Population.html" title="interface in org.biojavax.ga">Population</a></dt>
<dd>
<div class="block">Gets the Set of Organisms</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Compound.html#getOrganismScientific()">getOrganismScientific()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure">Compound</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Compound.html#getOrganismTaxId()">getOrganismTaxId()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure">Compound</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEMapLocation.html#getOrientation()">getOrientation()</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEMapLocation.html" title="class in org.biojava.bio.seq.io.agave">AGAVEMapLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ontology/ComparableOntology.html#getOrImportTerm(org.biojava.ontology.Term)">getOrImportTerm(Term)</a></span> - Method in interface org.biojavax.ontology.<a href="./org/biojavax/ontology/ComparableOntology.html" title="interface in org.biojavax.ontology">ComparableOntology</a></dt>
<dd>
<div class="block">Looks for a term with the same name as the given term and returns it.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ontology/SimpleComparableOntology.html#getOrImportTerm(org.biojava.ontology.Term)">getOrImportTerm(Term)</a></span> - Method in class org.biojavax.ontology.<a href="./org/biojavax/ontology/SimpleComparableOntology.html" title="class in org.biojavax.ontology">SimpleComparableOntology</a></dt>
<dd>
<div class="block">Looks for a term with the same name as the given term and returns it.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/HomologeneDB.html#getOrthologue(java.lang.String)">getOrthologue(String)</a></span> - Method in interface org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/HomologeneDB.html" title="interface in org.biojava.bio.program.homologene">HomologeneDB</a></dt>
<dd>
<div class="block">Returns an orthologue of specified ID.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/OrthologueSet.html#getOrthologue(java.lang.String)">getOrthologue(String)</a></span> - Method in interface org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/OrthologueSet.html" title="interface in org.biojava.bio.program.homologene">OrthologueSet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/SimpleHomologeneDB.html#getOrthologue(java.lang.String)">getOrthologue(String)</a></span> - Method in class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/SimpleHomologeneDB.html" title="class in org.biojava.bio.program.homologene">SimpleHomologeneDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/SimpleOrthologueSet.html#getOrthologue(java.lang.String)">getOrthologue(String)</a></span> - Method in class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/SimpleOrthologueSet.html" title="class in org.biojava.bio.program.homologene">SimpleOrthologueSet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/HomologeneDB.html#getOrthoPairSets()">getOrthoPairSets()</a></span> - Method in interface org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/HomologeneDB.html" title="interface in org.biojava.bio.program.homologene">HomologeneDB</a></dt>
<dd>
<div class="block">Get the HomologeneGroups in this database.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/SimpleHomologeneDB.html#getOrthoPairSets()">getOrthoPairSets()</a></span> - Method in class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/SimpleHomologeneDB.html" title="class in org.biojava.bio.program.homologene">SimpleHomologeneDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/Agave2AgaveAnnotFilter.html#getOS(org.biojava.bio.Annotation)">getOS(Annotation)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/Agave2AgaveAnnotFilter.html" title="class in org.biojava.bio.seq.io.agave">Agave2AgaveAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEAnnotFilter.html#getOS(org.biojava.bio.Annotation)">getOS(Annotation)</a></span> - Method in interface org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEAnnotFilter.html" title="interface in org.biojava.bio.seq.io.agave">AGAVEAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/Embl2AgaveAnnotFilter.html#getOS(org.biojava.bio.Annotation)">getOS(Annotation)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/Embl2AgaveAnnotFilter.html" title="class in org.biojava.bio.seq.io.agave">Embl2AgaveAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/SimpleAnnotFilter.html#getOS(org.biojava.bio.Annotation)">getOS(Annotation)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/SimpleAnnotFilter.html" title="class in org.biojava.bio.seq.io.agave">SimpleAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/INSDseqFormat.Terms.html#getOtherSeqIdTerm()">getOtherSeqIdTerm()</a></span> - Static method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/INSDseqFormat.Terms.html" title="class in org.biojavax.bio.seq.io">INSDseqFormat.Terms</a></dt>
<dd>
<div class="block">Getter for the INSDseq term</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/FuzzyLocation.html#getOuterMax()">getOuterMax()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/FuzzyLocation.html" title="class in org.biojava.bio.symbol">FuzzyLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/FuzzyLocation.html#getOuterMin()">getOuterMin()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/FuzzyLocation.html" title="class in org.biojava.bio.symbol">FuzzyLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/glyph/ArrowGlyph.html#getOuterPaint()">getOuterPaint()</a></span> - Method in class org.biojava.bio.gui.glyph.<a href="./org/biojava/bio/gui/glyph/ArrowGlyph.html" title="class in org.biojava.bio.gui.glyph">ArrowGlyph</a></dt>
<dd>
<div class="block">Returns the paint properties of the outer line of this glyph.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/ArrowedFeatureRenderer.html#getOutline()">getOutline()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/ArrowedFeatureRenderer.html" title="class in org.biojava.bio.gui.sequence">ArrowedFeatureRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/BasicFeatureRenderer.html#getOutline()">getOutline()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/BasicFeatureRenderer.html" title="class in org.biojava.bio.gui.sequence">BasicFeatureRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/CrosshairRenderer.html#getOutline()">getOutline()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/CrosshairRenderer.html" title="class in org.biojava.bio.gui.sequence">CrosshairRenderer</a></dt>
<dd>
<div class="block"><code>getOutline</code> returns the colour used to draw the
lines.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PairwiseDiagonalRenderer.html#getOutline()">getOutline()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PairwiseDiagonalRenderer.html" title="class in org.biojava.bio.gui.sequence">PairwiseDiagonalRenderer</a></dt>
<dd>
<div class="block"><code>getOutline</code> returns the colour used to draw the
lines.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SixFrameRenderer.html#getOutline()">getOutline()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SixFrameRenderer.html" title="class in org.biojava.bio.gui.sequence">SixFrameRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SixFrameZiggyRenderer.html#getOutline()">getOutline()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SixFrameZiggyRenderer.html" title="class in org.biojava.bio.gui.sequence">SixFrameZiggyRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/TickFeatureRenderer.html#getOutline()">getOutline()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/TickFeatureRenderer.html" title="class in org.biojava.bio.gui.sequence">TickFeatureRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/ZiggyFeatureRenderer.html#getOutline()">getOutline()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/ZiggyFeatureRenderer.html" title="class in org.biojava.bio.gui.sequence">ZiggyFeatureRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/process/InputHandler.html#getOutput()">getOutput()</a></span> - Method in interface org.biojava.utils.process.<a href="./org/biojava/utils/process/InputHandler.html" title="interface in org.biojava.utils.process">InputHandler</a></dt>
<dd>
<div class="block">Gets the output stream.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/process/ReaderInputHandler.html#getOutput()">getOutput()</a></span> - Method in class org.biojava.utils.process.<a href="./org/biojava/utils/process/ReaderInputHandler.html" title="class in org.biojava.utils.process">ReaderInputHandler</a></dt>
<dd>
<div class="block">Gets the output stream.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/process/StreamPipe.html#getOutput()">getOutput()</a></span> - Method in class org.biojava.utils.process.<a href="./org/biojava/utils/process/StreamPipe.html" title="class in org.biojava.utils.process">StreamPipe</a></dt>
<dd>
<div class="block">Gets the output stream.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/process/ExternalProcess.html#getOutputHandler()">getOutputHandler()</a></span> - Method in class org.biojava.utils.process.<a href="./org/biojava/utils/process/ExternalProcess.html" title="class in org.biojava.utils.process">ExternalProcess</a></dt>
<dd>
<div class="block">Gets the output handler which is responsible for the standard output
of the external process.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/ExecRunner.html#getOutString()">getOutString()</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/ExecRunner.html" title="class in org.biojava.utils">ExecRunner</a></dt>
<dd>
<div class="block">Returns the output string if exec(String) was invoked.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#getOverall_FOM_free_R_set()">getOverall_FOM_free_R_set()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#getOverall_FOM_work_R_set()">getOverall_FOM_work_R_set()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#getOverall_SU_B()">getOverall_SU_B()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#getOverall_SU_ML()">getOverall_SU_ML()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#getOverall_SU_R_Cruickshank_DPI()">getOverall_SU_R_Cruickshank_DPI()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#getOverall_SU_R_free()">getOverall_SU_R_free()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/OverlayAnnotation.html#getOverlay()">getOverlay()</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/OverlayAnnotation.html" title="class in org.biojava.bio">OverlayAnnotation</a></dt>
<dd>
<div class="block">Get the map used for the overlay.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/OverlayMap.html#getOverlayMap()">getOverlayMap()</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/OverlayMap.html" title="class in org.biojava.utils">OverlayMap</a></dt>
<dd>
<div class="block">Return the object containing the overlay mappings.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/PackingFactory.html#getPacking(org.biojava.bio.symbol.FiniteAlphabet, boolean)">getPacking(FiniteAlphabet, boolean)</a></span> - Static method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/PackingFactory.html" title="class in org.biojava.bio.symbol">PackingFactory</a></dt>
<dd>
<div class="block">Get the default packing for an alphabet.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PaddingRenderer.html#getPadding()">getPadding()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PaddingRenderer.html" title="class in org.biojava.bio.gui.sequence">PaddingRenderer</a></dt>
<dd>
<div class="block">Retrieve the current padding.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/glyph/RectangleGlyph.html#getPaint()">getPaint()</a></span> - Method in class org.biojava.bio.gui.glyph.<a href="./org/biojava/bio/gui/glyph/RectangleGlyph.html" title="class in org.biojava.bio.gui.glyph">RectangleGlyph</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/glyph/TurnGlyph.html#getPaint()">getPaint()</a></span> - Method in class org.biojava.bio.gui.glyph.<a href="./org/biojava/bio/gui/glyph/TurnGlyph.html" title="class in org.biojava.bio.gui.glyph">TurnGlyph</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/util/CoordManager.html#getPanelPos(int)">getPanelPos(int)</a></span> - Method in class org.biojava.bio.structure.gui.util.<a href="./org/biojava/bio/structure/gui/util/CoordManager.html" title="class in org.biojava.bio.structure.gui.util">CoordManager</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/StructurePairAligner.html#getParams()">getParams()</a></span> - Method in class org.biojava.bio.structure.align.<a href="./org/biojava/bio/structure/align/StructurePairAligner.html" title="class in org.biojava.bio.structure.align">StructurePairAligner</a></dt>
<dd>
<div class="block">get the parameters.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/AnnotatedSequenceDB.html#getParent()">getParent()</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/AnnotatedSequenceDB.html" title="class in org.biojava.bio.seq.db">AnnotatedSequenceDB</a></dt>
<dd>
<div class="block">Get the original sequenceDB from this annotated sequenceDB.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/SequenceDBWrapper.html#getParent()">getParent()</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/SequenceDBWrapper.html" title="class in org.biojava.bio.seq.db">SequenceDBWrapper</a></dt>
<dd>
<div class="block">Return the parent SequenceDB.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/Feature.html#getParent()">getParent()</a></span> - Method in interface org.biojava.bio.seq.<a href="./org/biojava/bio/seq/Feature.html" title="interface in org.biojava.bio.seq">Feature</a></dt>
<dd>
<div class="block">Return the <code>FeatureHolder</code> to which this feature has been
attached.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleFeature.html#getParent()">getParent()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleFeature.html" title="class in org.biojava.bio.seq.impl">SimpleFeature</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/projection/ProjectedFeature.html#getParent()">getParent()</a></span> - Method in class org.biojava.bio.seq.projection.<a href="./org/biojava/bio/seq/projection/ProjectedFeature.html" title="class in org.biojava.bio.seq.projection">ProjectedFeature</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/projection/ProjectionContext.html#getParent(org.biojava.bio.seq.Feature)">getParent(Feature)</a></span> - Method in interface org.biojava.bio.seq.projection.<a href="./org/biojava/bio/seq/projection/ProjectionContext.html" title="interface in org.biojava.bio.seq.projection">ProjectionContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/projection/ReparentContext.html#getParent()">getParent()</a></span> - Method in class org.biojava.bio.seq.projection.<a href="./org/biojava/bio/seq/projection/ReparentContext.html" title="class in org.biojava.bio.seq.projection">ReparentContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/projection/ReparentContext.html#getParent(org.biojava.bio.seq.Feature)">getParent(Feature)</a></span> - Method in class org.biojava.bio.seq.projection.<a href="./org/biojava/bio/seq/projection/ReparentContext.html" title="class in org.biojava.bio.seq.projection">ReparentContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Atom.html#getParent()">getParent()</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Atom.html" title="interface in org.biojava.bio.structure">Atom</a></dt>
<dd>
<div class="block">Returns the parent Group of the Atom.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/AtomImpl.html#getParent()">getParent()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/AtomImpl.html" title="class in org.biojava.bio.structure">AtomImpl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Chain.html#getParent()">getParent()</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Chain.html" title="interface in org.biojava.bio.structure">Chain</a></dt>
<dd>
<div class="block">Returns the parent Structure of this chain.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/ChainImpl.html#getParent()">getParent()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/ChainImpl.html" title="class in org.biojava.bio.structure">ChainImpl</a></dt>
<dd>
<div class="block">Returns the parent Structure of this chain.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/DBRef.html#getParent()">getParent()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/DBRef.html" title="class in org.biojava.bio.structure">DBRef</a></dt>
<dd>
<div class="block">Get the structure object that this DBRef relates to.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Group.html#getParent()">getParent()</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Group.html" title="interface in org.biojava.bio.structure">Group</a></dt>
<dd>
<div class="block">Returns the parent Chain of the Group.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/HetatomImpl.html#getParent()">getParent()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/HetatomImpl.html" title="class in org.biojava.bio.structure">HetatomImpl</a></dt>
<dd>
<div class="block">Returns the parent Chain of the Group</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/ChemicalComponentDictionary.html#getParent(org.biojava.bio.structure.io.mmcif.model.ChemComp)">getParent(ChemComp)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/ChemicalComponentDictionary.html" title="class in org.biojava.bio.structure.io.mmcif">ChemicalComponentDictionary</a></dt>
<dd>
<div class="block">Get the parent of a component.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/taxa/SimpleTaxon.html#getParent()">getParent()</a></span> - Method in class org.biojava.bio.taxa.<a href="./org/biojava/bio/taxa/SimpleTaxon.html" title="class in org.biojava.bio.taxa">SimpleTaxon</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/taxa/Taxon.html#getParent()">getParent()</a></span> - Method in interface org.biojava.bio.taxa.<a href="./org/biojava/bio/taxa/Taxon.html" title="interface in org.biojava.bio.taxa">Taxon</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">The parent of this Taxon.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/taxa/WeakTaxon.html#getParent()">getParent()</a></span> - Method in class org.biojava.bio.taxa.<a href="./org/biojava/bio/taxa/WeakTaxon.html" title="class in org.biojava.bio.taxa">WeakTaxon</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichFeature.html#getParent()">getParent()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichFeature.html" title="class in org.biojavax.bio.seq">SimpleRichFeature</a></dt>
<dd>
<div class="block">Return the <code>FeatureHolder</code> to which this feature has been
attached.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/DASSequence.html#getParentDB()">getParentDB()</a></span> - Method in class org.biojava.bio.program.das.<a href="./org/biojava/bio/program/das/DASSequence.html" title="class in org.biojava.bio.program.das">DASSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/OverlayMap.html#getParentMap()">getParentMap()</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/OverlayMap.html" title="class in org.biojava.utils">OverlayMap</a></dt>
<dd>
<div class="block">Return the object containing the fallback mappings.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/taxa/NCBITaxon.html#getParentNCBITaxID()">getParentNCBITaxID()</a></span> - Method in interface org.biojavax.bio.taxa.<a href="./org/biojavax/bio/taxa/NCBITaxon.html" title="interface in org.biojavax.bio.taxa">NCBITaxon</a></dt>
<dd>
<div class="block">Returns the parent NCBI taxon ID, if known.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/taxa/SimpleNCBITaxon.html#getParentNCBITaxID()">getParentNCBITaxID()</a></span> - Method in class org.biojavax.bio.taxa.<a href="./org/biojavax/bio/taxa/SimpleNCBITaxon.html" title="class in org.biojavax.bio.taxa">SimpleNCBITaxon</a></dt>
<dd>
<div class="block">Returns the parent NCBI taxon ID, if known.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureTypes.Type.html#getParents()">getParents()</a></span> - Method in interface org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureTypes.Type.html" title="interface in org.biojava.bio.seq">FeatureTypes.Type</a></dt>
<dd>
<div class="block">Get a set of URIs for parent types.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/ParserListener.html#getParser()">getParser()</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/ParserListener.html" title="class in org.biojava.bio.program.tagvalue">ParserListener</a></dt>
<dd>
<div class="block"><code>getParser</code> returns the parser of the pair.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/TagDelegator.html#getParser(java.lang.Object)">getParser(Object)</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/TagDelegator.html" title="class in org.biojava.bio.program.tagvalue">TagDelegator</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/annodb/IndexedAnnotationDB.ParserListenerFactory.html#getParserListener(org.biojava.bio.program.tagvalue.TagValueListener)">getParserListener(TagValueListener)</a></span> - Method in interface org.biojava.bio.annodb.<a href="./org/biojava/bio/annodb/IndexedAnnotationDB.ParserListenerFactory.html" title="interface in org.biojava.bio.annodb">IndexedAnnotationDB.ParserListenerFactory</a></dt>
<dd>
<div class="block">Get the ParserListener for a TagValueListener.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/annodb/IndexedAnnotationDB.StaticMethodRPFactory.html#getParserListener(org.biojava.bio.program.tagvalue.TagValueListener)">getParserListener(TagValueListener)</a></span> - Method in class org.biojava.bio.annodb.<a href="./org/biojava/bio/annodb/IndexedAnnotationDB.StaticMethodRPFactory.html" title="class in org.biojava.bio.annodb">IndexedAnnotationDB.StaticMethodRPFactory</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/formats/Embl.html#getParserListener(org.biojava.bio.program.tagvalue.TagValueListener)">getParserListener(TagValueListener)</a></span> - Method in class org.biojava.bio.program.formats.<a href="./org/biojava/bio/program/formats/Embl.html" title="class in org.biojava.bio.program.formats">Embl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/formats/Enzyme.html#getParserListener(org.biojava.bio.program.tagvalue.TagValueListener)">getParserListener(TagValueListener)</a></span> - Method in class org.biojava.bio.program.formats.<a href="./org/biojava/bio/program/formats/Enzyme.html" title="class in org.biojava.bio.program.formats">Enzyme</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/formats/Format.html#getParserListener(org.biojava.bio.program.tagvalue.TagValueListener)">getParserListener(TagValueListener)</a></span> - Method in interface org.biojava.bio.program.formats.<a href="./org/biojava/bio/program/formats/Format.html" title="interface in org.biojava.bio.program.formats">Format</a></dt>
<dd>
<div class="block">Retrieve a ParserListener pair for the format that will pass all events
on to a listener.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/formats/Ligand.Compound.html#getParserListener(org.biojava.bio.program.tagvalue.TagValueListener)">getParserListener(TagValueListener)</a></span> - Method in class org.biojava.bio.program.formats.<a href="./org/biojava/bio/program/formats/Ligand.Compound.html" title="class in org.biojava.bio.program.formats">Ligand.Compound</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/formats/Ligand.Enzyme.html#getParserListener(org.biojava.bio.program.tagvalue.TagValueListener)">getParserListener(TagValueListener)</a></span> - Method in class org.biojava.bio.program.formats.<a href="./org/biojava/bio/program/formats/Ligand.Enzyme.html" title="class in org.biojava.bio.program.formats">Ligand.Enzyme</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/formats/Ligand.Reaction.html#getParserListener(org.biojava.bio.program.tagvalue.TagValueListener)">getParserListener(TagValueListener)</a></span> - Method in class org.biojava.bio.program.formats.<a href="./org/biojava/bio/program/formats/Ligand.Reaction.html" title="class in org.biojava.bio.program.formats">Ligand.Reaction</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/formats/Swissprot.html#getParserListener(org.biojava.bio.program.tagvalue.TagValueListener)">getParserListener(TagValueListener)</a></span> - Method in class org.biojava.bio.program.formats.<a href="./org/biojava/bio/program/formats/Swissprot.html" title="class in org.biojava.bio.program.formats">Swissprot</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/annodb/IndexedAnnotationDB.html#getParserListenerFactory()">getParserListenerFactory()</a></span> - Method in class org.biojava.bio.annodb.<a href="./org/biojava/bio/annodb/IndexedAnnotationDB.html" title="class in org.biojava.bio.annodb">IndexedAnnotationDB</a></dt>
<dd>
<div class="block">Get the ParserListenerFactory used by this IndexedAnnotationDB.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/xff/XFFPartHandlerFactory.html#getPartHandler(org.biojava.bio.program.xff.XFFFeatureSetHandler)">getPartHandler(XFFFeatureSetHandler)</a></span> - Method in interface org.biojava.bio.program.xff.<a href="./org/biojava/bio/program/xff/XFFPartHandlerFactory.html" title="interface in org.biojava.bio.program.xff">XFFPartHandlerFactory</a></dt>
<dd>
<div class="block">Return a suitable StAX content handler.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequenceViewerEvent.html#getPath()">getPath()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequenceViewerEvent.html" title="class in org.biojava.bio.gui.sequence">SequenceViewerEvent</a></dt>
<dd>
<div class="block">Get the list of SequenceRenderer instances that were passed through to
produce this event</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/Alignable.html#getPath()">getPath()</a></span> - Method in interface org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/Alignable.html" title="interface in org.biojava.bio.structure.align.pairwise">Alignable</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/StrCompAlignment.html#getPath()">getPath()</a></span> - Method in class org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/StrCompAlignment.html" title="class in org.biojava.bio.structure.align.pairwise">StrCompAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/MMCIFFileReader.html#getPath()">getPath()</a></span> - Method in class org.biojava.bio.structure.io.<a href="./org/biojava/bio/structure/io/MMCIFFileReader.html" title="class in org.biojava.bio.structure.io">MMCIFFileReader</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/PDBFileReader.html#getPath()">getPath()</a></span> - Method in class org.biojava.bio.structure.io.<a href="./org/biojava/bio/structure/io/PDBFileReader.html" title="class in org.biojava.bio.structure.io">PDBFileReader</a></dt>
<dd>
<div class="block">Returns the path value.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/StructureIOFile.html#getPath()">getPath()</a></span> - Method in interface org.biojava.bio.structure.io.<a href="./org/biojava/bio/structure/io/StructureIOFile.html" title="interface in org.biojava.bio.structure.io">StructureIOFile</a></dt>
<dd>
<div class="block">get the directory path to the files</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/UkkonenSuffixTree.html#getPathEnd(org.biojava.bio.symbol.UkkonenSuffixTree.SuffixNode)">getPathEnd(UkkonenSuffixTree.SuffixNode)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/UkkonenSuffixTree.html" title="class in org.biojava.bio.symbol">UkkonenSuffixTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/UkkonenSuffixTree.html#getPathLength(org.biojava.bio.symbol.UkkonenSuffixTree.SuffixNode)">getPathLength(UkkonenSuffixTree.SuffixNode)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/UkkonenSuffixTree.html" title="class in org.biojava.bio.symbol">UkkonenSuffixTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/EmblCDROMIndexStore.html#getPathPrefix()">getPathPrefix()</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/EmblCDROMIndexStore.html" title="class in org.biojava.bio.seq.db">EmblCDROMIndexStore</a></dt>
<dd>
<div class="block"><code>getPathPrefix</code> returns the abstract path currently
being appended to the raw sequence database filenames extracted
from the binary index.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/Alignable.html#getPathSize()">getPathSize()</a></span> - Method in interface org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/Alignable.html" title="interface in org.biojava.bio.structure.align.pairwise">Alignable</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/StrCompAlignment.html#getPathSize()">getPathSize()</a></span> - Method in class org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/StrCompAlignment.html" title="class in org.biojava.bio.structure.align.pairwise">StrCompAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/RegexParser.html#getPattern()">getPattern()</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/RegexParser.html" title="class in org.biojava.bio.program.tagvalue">RegexParser</a></dt>
<dd>
<div class="block">Get the Pattern currently used to split lines.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/KnuthMorrisPrattSearch.html#getPattern()">getPattern()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/KnuthMorrisPrattSearch.html" title="class in org.biojava.bio.search">KnuthMorrisPrattSearch</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/MaxMismatchPattern.html#getPattern()">getPattern()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/MaxMismatchPattern.html" title="class in org.biojava.bio.search">MaxMismatchPattern</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/molbio/RestrictionEnzymeManager.html#getPatterns(org.biojava.bio.molbio.RestrictionEnzyme)">getPatterns(RestrictionEnzyme)</a></span> - Static method in class org.biojava.bio.molbio.<a href="./org/biojava/bio/molbio/RestrictionEnzymeManager.html" title="class in org.biojava.bio.molbio">RestrictionEnzymeManager</a></dt>
<dd>
<div class="block"><code>getPatterns</code> returns two <code>Pattern</code>
objects for an enzyme, one matches the forward strand and one
the reverse.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/PdbxNonPolyScheme.html#getPdb_ins_code()">getPdb_ins_code()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/PdbxNonPolyScheme.html" title="class in org.biojava.bio.structure.io.mmcif.model">PdbxNonPolyScheme</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/PdbxPolySeqScheme.html#getPdb_ins_code()">getPdb_ins_code()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/PdbxPolySeqScheme.html" title="class in org.biojava.bio.structure.io.mmcif.model">PdbxPolySeqScheme</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/PdbxNonPolyScheme.html#getPdb_mon_id()">getPdb_mon_id()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/PdbxNonPolyScheme.html" title="class in org.biojava.bio.structure.io.mmcif.model">PdbxNonPolyScheme</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/PdbxPolySeqScheme.html#getPdb_mon_id()">getPdb_mon_id()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/PdbxPolySeqScheme.html" title="class in org.biojava.bio.structure.io.mmcif.model">PdbxPolySeqScheme</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/PdbxNonPolyScheme.html#getPdb_seq_num()">getPdb_seq_num()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/PdbxNonPolyScheme.html" title="class in org.biojava.bio.structure.io.mmcif.model">PdbxNonPolyScheme</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/PdbxPolySeqScheme.html#getPdb_seq_num()">getPdb_seq_num()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/PdbxPolySeqScheme.html" title="class in org.biojava.bio.structure.io.mmcif.model">PdbxPolySeqScheme</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/PdbxNonPolyScheme.html#getPdb_strand_id()">getPdb_strand_id()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/PdbxNonPolyScheme.html" title="class in org.biojava.bio.structure.io.mmcif.model">PdbxNonPolyScheme</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/PdbxPolySeqScheme.html#getPdb_strand_id()">getPdb_strand_id()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/PdbxPolySeqScheme.html" title="class in org.biojava.bio.structure.io.mmcif.model">PdbxPolySeqScheme</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Group.html#getPDBCode()">getPDBCode()</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Group.html" title="interface in org.biojava.bio.structure">Group</a></dt>
<dd>
<div class="block">Return the PDBcode (residue number + insertion code ) of this group.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/HetatomImpl.html#getPDBCode()">getPDBCode()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/HetatomImpl.html" title="class in org.biojava.bio.structure">HetatomImpl</a></dt>
<dd>
<div class="block">Returns the PDBCode.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/server/StructureEvent.html#getPDBCode()">getPDBCode()</a></span> - Method in interface org.biojava.bio.structure.server.<a href="./org/biojava/bio/structure/server/StructureEvent.html" title="interface in org.biojava.bio.structure.server">StructureEvent</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/server/StructureEventImpl.html#getPDBCode()">getPDBCode()</a></span> - Method in class org.biojava.bio.structure.server.<a href="./org/biojava/bio/structure/server/StructureEventImpl.html" title="class in org.biojava.bio.structure.server">StructureEventImpl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Structure.html#getPDBCode()">getPDBCode()</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Structure.html" title="interface in org.biojava.bio.structure">Structure</a></dt>
<dd>
<div class="block">get PDB code of structure.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/StructureImpl.html#getPDBCode()">getPDBCode()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/StructureImpl.html" title="class in org.biojava.bio.structure">StructureImpl</a></dt>
<dd>
<div class="block">get PDB code of structure .</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/server/FlatFileInstallation.html#getPDBHeader(java.lang.String)">getPDBHeader(String)</a></span> - Method in class org.biojava.bio.structure.server.<a href="./org/biojava/bio/structure/server/FlatFileInstallation.html" title="class in org.biojava.bio.structure.server">FlatFileInstallation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/server/MMCIFFileInstallation.html#getPDBHeader(java.lang.String)">getPDBHeader(String)</a></span> - Method in class org.biojava.bio.structure.server.<a href="./org/biojava/bio/structure/server/MMCIFFileInstallation.html" title="class in org.biojava.bio.structure.server">MMCIFFileInstallation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/server/PDBInstallation.html#getPDBHeader(java.lang.String)">getPDBHeader(String)</a></span> - Method in interface org.biojava.bio.structure.server.<a href="./org/biojava/bio/structure/server/PDBInstallation.html" title="interface in org.biojava.bio.structure.server">PDBInstallation</a></dt>
<dd>
<div class="block">get the PDB header for a single protein structure</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Structure.html#getPDBHeader()">getPDBHeader()</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Structure.html" title="interface in org.biojava.bio.structure">Structure</a></dt>
<dd>
<div class="block">return the header information for this PDB file</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/StructureImpl.html#getPDBHeader()">getPDBHeader()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/StructureImpl.html" title="class in org.biojava.bio.structure">StructureImpl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/server/FlatFileInstallation.html#getPDBInfoFile()">getPDBInfoFile()</a></span> - Method in class org.biojava.bio.structure.server.<a href="./org/biojava/bio/structure/server/FlatFileInstallation.html" title="class in org.biojava.bio.structure.server">FlatFileInstallation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/server/SimpleStructureServer.html#getPDBInstallation()">getPDBInstallation()</a></span> - Method in class org.biojava.bio.structure.server.<a href="./org/biojava/bio/structure/server/SimpleStructureServer.html" title="class in org.biojava.bio.structure.server">SimpleStructureServer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/server/StructureServer.html#getPDBInstallation()">getPDBInstallation()</a></span> - Method in interface org.biojava.bio.structure.server.<a href="./org/biojava/bio/structure/server/StructureServer.html" title="interface in org.biojava.bio.structure.server">StructureServer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Atom.html#getPDBline()">getPDBline()</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Atom.html" title="interface in org.biojava.bio.structure">Atom</a></dt>
<dd>
<div class="block">store the whole line.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/AtomImpl.html#getPDBline()">getPDBline()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/AtomImpl.html" title="class in org.biojava.bio.structure">AtomImpl</a></dt>
<dd>
<div class="block">get the whole line .</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Group.html#getPDBName()">getPDBName()</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Group.html" title="interface in org.biojava.bio.structure">Group</a></dt>
<dd>
<div class="block">Get the PDB 3 character name for this group.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/HetatomImpl.html#getPDBName()">getPDBName()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/HetatomImpl.html" title="class in org.biojava.bio.structure">HetatomImpl</a></dt>
<dd>
<div class="block">Returns the PDBName.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/AlternativeAlignment.html#getPDBresnum1()">getPDBresnum1()</a></span> - Method in class org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/AlternativeAlignment.html" title="class in org.biojava.bio.structure.align.pairwise">AlternativeAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/AlternativeAlignment.html#getPDBresnum2()">getPDBresnum2()</a></span> - Method in class org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/AlternativeAlignment.html" title="class in org.biojava.bio.structure.align.pairwise">AlternativeAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Atom.html#getPDBserial()">getPDBserial()</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Atom.html" title="interface in org.biojava.bio.structure">Atom</a></dt>
<dd>
<div class="block">get PDB atom number.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/AtomImpl.html#getPDBserial()">getPDBserial()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/AtomImpl.html" title="class in org.biojava.bio.structure">AtomImpl</a></dt>
<dd>
<div class="block">get PDB atom number.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/StructRef.html#getPdbx_align_begin()">getPdbx_align_begin()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/StructRef.html" title="class in org.biojava.bio.structure.io.mmcif.model">StructRef</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html#getPdbx_ambiguous_flag()">getPdbx_ambiguous_flag()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html" title="class in org.biojava.bio.structure.io.mmcif.model">ChemComp</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/StructRefSeq.html#getPdbx_auth_seq_align_beg()">getPdbx_auth_seq_align_beg()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/StructRefSeq.html" title="class in org.biojava.bio.structure.io.mmcif.model">StructRefSeq</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/StructRefSeq.html#getPdbx_auth_seq_align_end()">getPdbx_auth_seq_align_end()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/StructRefSeq.html" title="class in org.biojava.bio.structure.io.mmcif.model">StructRefSeq</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/StructAsym.html#getPdbx_blank_PDB_chainid_flag()">getPdbx_blank_PDB_chainid_flag()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/StructAsym.html" title="class in org.biojava.bio.structure.io.mmcif.model">StructAsym</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#getPdbx_data_cutoff_high_absF()">getPdbx_data_cutoff_high_absF()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#getPdbx_data_cutoff_high_rms_absF()">getPdbx_data_cutoff_high_rms_absF()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#getPdbx_data_cutoff_low_absF()">getPdbx_data_cutoff_low_absF()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/StructRef.html#getPdbx_db_accession()">getPdbx_db_accession()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/StructRef.html" title="class in org.biojava.bio.structure.io.mmcif.model">StructRef</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/StructRefSeq.html#getPdbx_db_accession()">getPdbx_db_accession()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/StructRefSeq.html" title="class in org.biojava.bio.structure.io.mmcif.model">StructRefSeq</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/StructRefSeq.html#getPdbx_db_align_beg_ins_code()">getPdbx_db_align_beg_ins_code()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/StructRefSeq.html" title="class in org.biojava.bio.structure.io.mmcif.model">StructRefSeq</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/StructRefSeq.html#getPdbx_db_align_end_ins_code()">getPdbx_db_align_end_ins_code()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/StructRefSeq.html" title="class in org.biojava.bio.structure.io.mmcif.model">StructRefSeq</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Entity.html#getPdbx_description()">getPdbx_description()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Entity.html" title="class in org.biojava.bio.structure.io.mmcif.model">Entity</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Struct.html#getPdbx_descriptor()">getPdbx_descriptor()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Struct.html" title="class in org.biojava.bio.structure.io.mmcif.model">Struct</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Entity.html#getPdbx_ec()">getPdbx_ec()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Entity.html" title="class in org.biojava.bio.structure.io.mmcif.model">Entity</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html#getPdbx_formal_charge()">getPdbx_formal_charge()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html" title="class in org.biojava.bio.structure.io.mmcif.model">AtomSite</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html#getPdbx_formal_charge()">getPdbx_formal_charge()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html" title="class in org.biojava.bio.structure.io.mmcif.model">ChemComp</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Entity.html#getPdbx_fragment()">getPdbx_fragment()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Entity.html" title="class in org.biojava.bio.structure.io.mmcif.model">Entity</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html#getPdbx_ideal_coordinates_details()">getPdbx_ideal_coordinates_details()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html" title="class in org.biojava.bio.structure.io.mmcif.model">ChemComp</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html#getPdbx_ideal_coordinates_missing_flag()">getPdbx_ideal_coordinates_missing_flag()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html" title="class in org.biojava.bio.structure.io.mmcif.model">ChemComp</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html#getPdbx_initial_date()">getPdbx_initial_date()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html" title="class in org.biojava.bio.structure.io.mmcif.model">ChemComp</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#getPdbx_isotropic_thermal_model()">getPdbx_isotropic_thermal_model()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/StructKeywords.html#getPdbx_keywords()">getPdbx_keywords()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/StructKeywords.html" title="class in org.biojava.bio.structure.io.mmcif.model">StructKeywords</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#getPdbx_ls_cross_valid_method()">getPdbx_ls_cross_valid_method()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#getPdbx_ls_sigma_F()">getPdbx_ls_sigma_F()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#getPdbx_ls_sigma_I()">getPdbx_ls_sigma_I()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#getPdbx_method_to_determine_struct()">getPdbx_method_to_determine_struct()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html#getPdbx_model_coordinates_db_code()">getPdbx_model_coordinates_db_code()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html" title="class in org.biojava.bio.structure.io.mmcif.model">ChemComp</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html#getPdbx_model_coordinates_details()">getPdbx_model_coordinates_details()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html" title="class in org.biojava.bio.structure.io.mmcif.model">ChemComp</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html#getPdbx_model_coordinates_missing_flag()">getPdbx_model_coordinates_missing_flag()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html" title="class in org.biojava.bio.structure.io.mmcif.model">ChemComp</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Struct.html#getPdbx_model_details()">getPdbx_model_details()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Struct.html" title="class in org.biojava.bio.structure.io.mmcif.model">Struct</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Struct.html#getPdbx_model_type_details()">getPdbx_model_type_details()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Struct.html" title="class in org.biojava.bio.structure.io.mmcif.model">Struct</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/StructAsym.html#getPdbx_modified()">getPdbx_modified()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/StructAsym.html" title="class in org.biojava.bio.structure.io.mmcif.model">StructAsym</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html#getPdbx_modified_date()">getPdbx_modified_date()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html" title="class in org.biojava.bio.structure.io.mmcif.model">ChemComp</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Entity.html#getPdbx_mutation()">getPdbx_mutation()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Entity.html" title="class in org.biojava.bio.structure.io.mmcif.model">Entity</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Entity.html#getPdbx_number_of_molecules()">getPdbx_number_of_molecules()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Entity.html" title="class in org.biojava.bio.structure.io.mmcif.model">Entity</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#getPdbx_overall_ESU_R()">getPdbx_overall_ESU_R()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#getPdbx_overall_ESU_R_Free()">getPdbx_overall_ESU_R_Free()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#getPdbx_overall_phase_error()">getPdbx_overall_phase_error()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/StructRefSeq.html#getPdbx_PDB_id_code()">getPdbx_PDB_id_code()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/StructRefSeq.html" title="class in org.biojava.bio.structure.io.mmcif.model">StructRefSeq</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html#getPdbx_PDB_ins_code()">getPdbx_PDB_ins_code()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html" title="class in org.biojava.bio.structure.io.mmcif.model">AtomSite</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html#getPdbx_PDB_model_num()">getPdbx_PDB_model_num()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html" title="class in org.biojava.bio.structure.io.mmcif.model">AtomSite</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html#getPdbx_processing_site()">getPdbx_processing_site()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html" title="class in org.biojava.bio.structure.io.mmcif.model">ChemComp</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#getPdbx_R_Free_selection_details()">getPdbx_R_Free_selection_details()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#getPdbx_refine_id()">getPdbx_refine_id()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html#getPdbx_release_status()">getPdbx_release_status()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html" title="class in org.biojava.bio.structure.io.mmcif.model">ChemComp</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html#getPdbx_replaced_by()">getPdbx_replaced_by()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html" title="class in org.biojava.bio.structure.io.mmcif.model">ChemComp</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html#getPdbx_replaces()">getPdbx_replaces()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html" title="class in org.biojava.bio.structure.io.mmcif.model">ChemComp</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/StructRefSeq.html#getPdbx_seq_align_beg_ins_code()">getPdbx_seq_align_beg_ins_code()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/StructRefSeq.html" title="class in org.biojava.bio.structure.io.mmcif.model">StructRefSeq</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/StructRefSeq.html#getPdbx_seq_align_end_ins_code()">getPdbx_seq_align_end_ins_code()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/StructRefSeq.html" title="class in org.biojava.bio.structure.io.mmcif.model">StructRefSeq</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/StructRef.html#getPdbx_seq_one_letter_code()">getPdbx_seq_one_letter_code()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/StructRef.html" title="class in org.biojava.bio.structure.io.mmcif.model">StructRef</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#getPdbx_solvent_ion_probe_radii()">getPdbx_solvent_ion_probe_radii()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#getPdbx_solvent_shrinkage_radii()">getPdbx_solvent_shrinkage_radii()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#getPdbx_solvent_vdw_probe_radii()">getPdbx_solvent_vdw_probe_radii()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#getPdbx_starting_model()">getPdbx_starting_model()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#getPdbx_stereochem_target_val_spec_case()">getPdbx_stereochem_target_val_spec_case()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#getPdbx_stereochemistry_target_values()">getPdbx_stereochemistry_target_values()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/StructRefSeq.html#getPdbx_strand_id()">getPdbx_strand_id()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/StructRefSeq.html" title="class in org.biojava.bio.structure.io.mmcif.model">StructRefSeq</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html#getPdbx_subcomponent_list()">getPdbx_subcomponent_list()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html" title="class in org.biojava.bio.structure.io.mmcif.model">ChemComp</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html#getPdbx_synonyms()">getPdbx_synonyms()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html" title="class in org.biojava.bio.structure.io.mmcif.model">ChemComp</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html#getPdbx_type()">getPdbx_type()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html" title="class in org.biojava.bio.structure.io.mmcif.model">ChemComp</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/OrthoPair.html#getPercentIdentity()">getPercentIdentity()</a></span> - Method in interface org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/OrthoPair.html" title="interface in org.biojava.bio.program.homologene">OrthoPair</a></dt>
<dd>
<div class="block">get percentage identity.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/SimpleOrthoPair.html#getPercentIdentity()">getPercentIdentity()</a></span> - Method in class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/SimpleOrthoPair.html" title="class in org.biojava.bio.program.homologene">SimpleOrthoPair</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/AlternativeAlignment.html#getPercId()">getPercId()</a></span> - Method in class org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/AlternativeAlignment.html" title="class in org.biojava.bio.structure.align.pairwise">AlternativeAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/StrucAligParameters.html#getPermutationSize()">getPermutationSize()</a></span> - Method in class org.biojava.bio.structure.align.<a href="./org/biojava/bio/structure/align/StrucAligParameters.html" title="class in org.biojava.bio.structure.align">StrucAligParameters</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff3/GFF3Record.html#getPhase()">getPhase()</a></span> - Method in interface org.biojava.bio.program.gff3.<a href="./org/biojava/bio/program/gff3/GFF3Record.html" title="interface in org.biojava.bio.program.gff3">GFF3Record</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff3/GFF3Record.Impl.html#getPhase()">getPhase()</a></span> - Method in class org.biojava.bio.program.gff3.<a href="./org/biojava/bio/program/gff3/GFF3Record.Impl.html" title="class in org.biojava.bio.program.gff3">GFF3Record.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html#getPHDependence()">getPHDependence()</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html" title="class in org.biojavax.bio.seq.io">UniProtCommentParser</a></dt>
<dd>
<div class="block">Getter for property PHDependence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Calc.html#getPhi(org.biojava.bio.structure.AminoAcid, org.biojava.bio.structure.AminoAcid)">getPhi(AminoAcid, AminoAcid)</a></span> - Static method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Calc.html" title="class in org.biojava.bio.structure">Calc</a></dt>
<dd>
<div class="block">phi angle.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/AlphaCTools.html#getPhiAngle(org.biojava.bio.symbol.Symbol)">getPhiAngle(Symbol)</a></span> - Static method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/AlphaCTools.html" title="class in org.biojava.bio.structure">AlphaCTools</a></dt>
<dd>
<div class="block">extracts the Phi angle from a <code>Symbol</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/AlphaCTools.html#getPhiPsiSymbol(double, double)">getPhiPsiSymbol(double, double)</a></span> - Static method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/AlphaCTools.html" title="class in org.biojava.bio.structure">AlphaCTools</a></dt>
<dd>
<div class="block">Makes a Phi - Psi Symbol from the ALPHA CARBON ANGLES alphabet.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/phred/PhredTools.html#getPhredAlphabet()">getPhredAlphabet()</a></span> - Static method in class org.biojava.bio.program.phred.<a href="./org/biojava/bio/program/phred/PhredTools.html" title="class in org.biojava.bio.program.phred">PhredTools</a></dt>
<dd>
<div class="block">Retrieves the PHRED alphabet from the AlphabetManager.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/phred/PhredTools.html#getPhredSymbol(org.biojava.bio.symbol.Symbol, org.biojava.bio.symbol.Symbol)">getPhredSymbol(Symbol, Symbol)</a></span> - Static method in class org.biojava.bio.program.phred.<a href="./org/biojava/bio/program/phred/PhredTools.html" title="class in org.biojava.bio.program.phred">PhredTools</a></dt>
<dd>
<div class="block">Creates a symbol from the PHRED alphabet by combining a Symbol from the
DNA alphabet and a Symbol from the IntegerAlphabet (or one of its subsets).</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/IsoelectricPointCalc.html#getPI(org.biojava.bio.symbol.SymbolList, boolean, boolean)">getPI(SymbolList, boolean, boolean)</a></span> - Method in class org.biojava.bio.proteomics.<a href="./org/biojava/bio/proteomics/IsoelectricPointCalc.html" title="class in org.biojava.bio.proteomics">IsoelectricPointCalc</a></dt>
<dd>
<div class="block">Computes isoelectric point of specified peptide.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/jama/LUDecomposition.html#getPivot()">getPivot()</a></span> - Method in class org.biojava.bio.structure.jama.<a href="./org/biojava/bio/structure/jama/LUDecomposition.html" title="class in org.biojava.bio.structure.jama">LUDecomposition</a></dt>
<dd>
<div class="block">Return pivot permutation vector</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.Terms.html#getPlasmidTerm()">getPlasmidTerm()</a></span> - Static method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.Terms.html" title="class in org.biojavax.bio.seq">RichSequence.Terms</a></dt>
<dd>
<div class="block">Getter for the Plasmid term</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/JournalArticle.html#getPmid()">getPmid()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/JournalArticle.html" title="class in org.biojava.bio.structure">JournalArticle</a></dt>
<dd>
<div class="block">Get the value of PMID field.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html#getPolymerType()">getPolymerType()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html" title="class in org.biojava.bio.structure.io.mmcif.model">ChemComp</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/GeneticAlgorithm.html#getPopulation()">getPopulation()</a></span> - Method in interface org.biojavax.ga.<a href="./org/biojavax/ga/GeneticAlgorithm.html" title="interface in org.biojavax.ga">GeneticAlgorithm</a></dt>
<dd>
<div class="block">The registered <code>Population</code></div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ga/impl/AbstractGeneticAlgorithm.html#getPopulation()">getPopulation()</a></span> - Method in class org.biojavax.ga.impl.<a href="./org/biojavax/ga/impl/AbstractGeneticAlgorithm.html" title="class in org.biojavax.ga.impl">AbstractGeneticAlgorithm</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequenceViewerEvent.html#getPos()">getPos()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequenceViewerEvent.html" title="class in org.biojava.bio.gui.sequence">SequenceViewerEvent</a></dt>
<dd>
<div class="block">Get the offset within the sequence - the symbol index.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEMapPosition.html#getPos()">getPos()</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEMapPosition.html" title="class in org.biojava.bio.seq.io.agave">AGAVEMapPosition</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/util/AlignedPosition.html#getPos(int)">getPos(int)</a></span> - Method in class org.biojava.bio.structure.gui.util.<a href="./org/biojava/bio/structure/gui/util/AlignedPosition.html" title="class in org.biojava.bio.structure.gui.util">AlignedPosition</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/FragmentPair.html#getPos1()">getPos1()</a></span> - Method in class org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/FragmentPair.html" title="class in org.biojava.bio.structure.align.pairwise">FragmentPair</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/util/AlignedPosition.html#getPos1()">getPos1()</a></span> - Method in class org.biojava.bio.structure.gui.util.<a href="./org/biojava/bio/structure/gui/util/AlignedPosition.html" title="class in org.biojava.bio.structure.gui.util">AlignedPosition</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/FragmentPair.html#getPos2()">getPos2()</a></span> - Method in class org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/FragmentPair.html" title="class in org.biojava.bio.structure.align.pairwise">FragmentPair</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/util/AlignedPosition.html#getPos2()">getPos2()</a></span> - Method in class org.biojava.bio.structure.gui.util.<a href="./org/biojava/bio/structure/gui/util/AlignedPosition.html" title="class in org.biojava.bio.structure.gui.util">AlignedPosition</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/molbio/RestrictionSite.html#getPosition()">getPosition()</a></span> - Method in interface org.biojava.bio.molbio.<a href="./org/biojava/bio/molbio/RestrictionSite.html" title="interface in org.biojava.bio.molbio">RestrictionSite</a></dt>
<dd>
<div class="block"><code>getPosition</code> returns the common, forward strand cut
site.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleRestrictionSite.html#getPosition()">getPosition()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleRestrictionSite.html" title="class in org.biojava.bio.seq.impl">SimpleRestrictionSite</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEMapLocation.html#getPosition1()">getPosition1()</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEMapLocation.html" title="class in org.biojava.bio.seq.io.agave">AGAVEMapLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEMapLocation.html#getPosition2()">getPosition2()</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEMapLocation.html" title="class in org.biojava.bio.seq.io.agave">AGAVEMapLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtCommentParser.SeqCaution.html#getPositions()">getPositions()</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtCommentParser.SeqCaution.html" title="class in org.biojavax.bio.seq.io">UniProtCommentParser.SeqCaution</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/tools/ClassifierExample.PointClassifier.html#getPosShape()">getPosShape()</a></span> - Method in class org.biojava.stats.svm.tools.<a href="./org/biojava/stats/svm/tools/ClassifierExample.PointClassifier.html" title="class in org.biojava.stats.svm.tools">ClassifierExample.PointClassifier</a></dt>
<dd>
<div class="block">Retrieve the shape used to represent positive points.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/Triple.html#getPredicate()">getPredicate()</a></span> - Method in interface org.biojava.ontology.<a href="./org/biojava/ontology/Triple.html" title="interface in org.biojava.ontology">Triple</a></dt>
<dd>
<div class="block">Return a Term which defines the type of relationship between the subject and object terms.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/Triple.Impl.html#getPredicate()">getPredicate()</a></span> - Method in class org.biojava.ontology.<a href="./org/biojava/ontology/Triple.Impl.html" title="class in org.biojava.ontology">Triple.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ontology/SimpleComparableTriple.html#getPredicate()">getPredicate()</a></span> - Method in class org.biojavax.ontology.<a href="./org/biojavax/ontology/SimpleComparableTriple.html" title="class in org.biojavax.ontology">SimpleComparableTriple</a></dt>
<dd>
<div class="block">Return a Term which defines the type of relationship between the subject and object terms.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/ChangeEvent.html#getPrevious()">getPrevious()</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/ChangeEvent.html" title="class in org.biojava.utils">ChangeEvent</a></dt>
<dd>
<div class="block">Return the old value of a property being changed.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/indexdb/BioStoreFactory.html#getPrimaryKey()">getPrimaryKey()</a></span> - Method in class org.biojava.bio.program.indexdb.<a href="./org/biojava/bio/program/indexdb/BioStoreFactory.html" title="class in org.biojava.bio.program.indexdb">BioStoreFactory</a></dt>
<dd>
<div class="block"><code>getPrimaryKey</code> returns the primary identifier
namespace.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/Index2Model.html#getPrimaryKeyName()">getPrimaryKeyName()</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/Index2Model.html" title="class in org.biojava.bio.program.tagvalue">Index2Model</a></dt>
<dd>
<div class="block">Retrieve the tag currently used as primary key.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/Indexer.html#getPrimaryKeyName()">getPrimaryKeyName()</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/Indexer.html" title="class in org.biojava.bio.program.tagvalue">Indexer</a></dt>
<dd>
<div class="block">Retrieve the tag currently used as primary key.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/EmblFileFormer.html#getPrintStream()">getPrintStream()</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/EmblFileFormer.html" title="class in org.biojava.bio.seq.io">EmblFileFormer</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/GenbankFileFormer.html#getPrintStream()">getPrintStream()</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/GenbankFileFormer.html" title="class in org.biojava.bio.seq.io">GenbankFileFormer</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqFileFormer.html#getPrintStream()">getPrintStream()</a></span> - Method in interface org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqFileFormer.html" title="interface in org.biojava.bio.seq.io">SeqFileFormer</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block"><code>getPrintStream</code> returns the
<code>PrintStream</code> to which an instance will write the
formatted data.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SwissprotFileFormer.html#getPrintStream()">getPrintStream()</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SwissprotFileFormer.html" title="class in org.biojava.bio.seq.io">SwissprotFileFormer</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block"><code>getPrintStream</code> returns the
<code>PrintStream</code> to which an instance of SwissprotFileFormer
will write the formatted data.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/RichSequenceFormat.BasicFormat.html#getPrintStream()">getPrintStream()</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/RichSequenceFormat.BasicFormat.html" title="class in org.biojavax.bio.seq.io">RichSequenceFormat.BasicFormat</a></dt>
<dd>
<div class="block">Gets the print stream currently being written to.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/RichSequenceFormat.html#getPrintStream()">getPrintStream()</a></span> - Method in interface org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/RichSequenceFormat.html" title="interface in org.biojavax.bio.seq.io">RichSequenceFormat</a></dt>
<dd>
<div class="block">Gets the print stream currently being written to.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/scf/SCF.html#getProbabilityAlphabet()">getProbabilityAlphabet()</a></span> - Static method in class org.biojava.bio.program.scf.<a href="./org/biojava/bio/program/scf/SCF.html" title="class in org.biojava.bio.program.scf">SCF</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.Terms.html#getProjectAccessionTerm()">getProjectAccessionTerm()</a></span> - Static method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.Terms.html" title="class in org.biojavax.bio.seq.io">EMBLxmlFormat.Terms</a></dt>
<dd>
<div class="block">Getter for the ProjectAccession term</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/projection/ProjectedFeature.html#getProjectedFeatures()">getProjectedFeatures()</a></span> - Method in class org.biojava.bio.seq.projection.<a href="./org/biojava/bio/seq/projection/ProjectedFeature.html" title="class in org.biojava.bio.seq.projection">ProjectedFeature</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/projection/ProjectedFeature.html#getProjectionContext()">getProjectionContext()</a></span> - Method in class org.biojava.bio.seq.projection.<a href="./org/biojava/bio/seq/projection/ProjectedFeature.html" title="class in org.biojava.bio.seq.projection">ProjectedFeature</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/projection/Projection.html#getProjectionContext()">getProjectionContext()</a></span> - Method in interface org.biojava.bio.seq.projection.<a href="./org/biojava/bio/seq/projection/Projection.html" title="interface in org.biojava.bio.seq.projection">Projection</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEProperty.html#getPropClass()">getPropClass()</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEProperty.html" title="class in org.biojava.bio.seq.io.agave">AGAVEProperty</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/AbstractAnnotation.html#getProperties()">getProperties()</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/AbstractAnnotation.html" title="class in org.biojava.bio">AbstractAnnotation</a></dt>
<dd>
<div class="block">Implement this to return the Map delegate.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/AnnotationChanger.html#getProperties()">getProperties()</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/AnnotationChanger.html" title="class in org.biojava.bio">AnnotationChanger</a></dt>
<dd>
<div class="block"><code>getProperties</code> returns the mapped contents of the
underlying <code>Annotation</code> as a <code>Map</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/AnnotationRenamer.html#getProperties()">getProperties()</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/AnnotationRenamer.html" title="class in org.biojava.bio">AnnotationRenamer</a></dt>
<dd>
<div class="block"><code>getProperties</code> returns the mapped contents of the
underlying <code>Annotation</code> as a <code>Map</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/AnnotationType.html#getProperties()">getProperties()</a></span> - Method in interface org.biojava.bio.<a href="./org/biojava/bio/AnnotationType.html" title="interface in org.biojava.bio">AnnotationType</a></dt>
<dd>
<div class="block">Retrieve the set of properties for which constraints have been explicity specified.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/AnnotationType.Impl.html#getProperties()">getProperties()</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/AnnotationType.Impl.html" title="class in org.biojava.bio">AnnotationType.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/BeanAsAnnotation.html#getProperties()">getProperties()</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/BeanAsAnnotation.html" title="class in org.biojava.bio">BeanAsAnnotation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/ReferenceAnnotation.html#getProperties()">getProperties()</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/ReferenceAnnotation.html" title="class in org.biojava.bio.seq.io">ReferenceAnnotation</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/SimpleAnnotation.html#getProperties()">getProperties()</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/SimpleAnnotation.html" title="class in org.biojava.bio">SimpleAnnotation</a></dt>
<dd>
<div class="block">Get the property value pairs in this annotation</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/SmallAnnotation.html#getProperties()">getProperties()</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/SmallAnnotation.html" title="class in org.biojava.bio">SmallAnnotation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Group.html#getProperties()">getProperties()</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Group.html" title="interface in org.biojava.bio.structure">Group</a></dt>
<dd>
<div class="block">return properties.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/HetatomImpl.html#getProperties()">getProperties()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/HetatomImpl.html" title="class in org.biojava.bio.structure">HetatomImpl</a></dt>
<dd>
<div class="block">return properties.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/EmptyRichAnnotation.html#getProperties(java.lang.Object)">getProperties(Object)</a></span> - Method in class org.biojavax.<a href="./org/biojavax/EmptyRichAnnotation.html" title="class in org.biojavax">EmptyRichAnnotation</a></dt>
<dd>
<div class="block">Find all the <code>Note</code>s with any rank that match the key.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/RichAnnotation.html#getProperties(java.lang.Object)">getProperties(Object)</a></span> - Method in interface org.biojavax.<a href="./org/biojavax/RichAnnotation.html" title="interface in org.biojavax">RichAnnotation</a></dt>
<dd>
<div class="block">Find all the <code>Note</code>s with any rank that match the key.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleRichAnnotation.html#getProperties(java.lang.Object)">getProperties(Object)</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleRichAnnotation.html" title="class in org.biojavax">SimpleRichAnnotation</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span> </div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/AbstractAnnotation.html#getProperty(java.lang.Object)">getProperty(Object)</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/AbstractAnnotation.html" title="class in org.biojava.bio">AbstractAnnotation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/Annotation.html#getProperty(java.lang.Object)">getProperty(Object)</a></span> - Method in interface org.biojava.bio.<a href="./org/biojava/bio/Annotation.html" title="interface in org.biojava.bio">Annotation</a></dt>
<dd>
<div class="block">
Retrieve the value of a property by key.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/AnnotationType.Abstract.html#getProperty(org.biojava.bio.Annotation, java.lang.Object)">getProperty(Annotation, Object)</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/AnnotationType.Abstract.html" title="class in org.biojava.bio">AnnotationType.Abstract</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/AnnotationType.html#getProperty(org.biojava.bio.Annotation, java.lang.Object)">getProperty(Annotation, Object)</a></span> - Method in interface org.biojava.bio.<a href="./org/biojava/bio/AnnotationType.html" title="interface in org.biojava.bio">AnnotationType</a></dt>
<dd>
<div class="block">Get the Collection of values associated with an Annotation bundle
according to the type we believe it to be.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/MergeAnnotation.html#getProperty(java.lang.Object)">getProperty(Object)</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/MergeAnnotation.html" title="class in org.biojava.bio">MergeAnnotation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/OverlayAnnotation.html#getProperty(java.lang.Object)">getProperty(Object)</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/OverlayAnnotation.html" title="class in org.biojava.bio">OverlayAnnotation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/sax/blastxml/BlastXMLParserFacade.html#getProperty(java.lang.String)">getProperty(String)</a></span> - Method in class org.biojava.bio.program.sax.blastxml.<a href="./org/biojava/bio/program/sax/blastxml/BlastXMLParserFacade.html" title="class in org.biojava.bio.program.sax.blastxml">BlastXMLParserFacade</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/Agave2AgaveAnnotFilter.html#getProperty(org.biojava.bio.Annotation, java.lang.String)">getProperty(Annotation, String)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/Agave2AgaveAnnotFilter.html" title="class in org.biojava.bio.seq.io.agave">Agave2AgaveAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEAnnotFilter.html#getProperty(org.biojava.bio.Annotation, java.lang.String)">getProperty(Annotation, String)</a></span> - Method in interface org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEAnnotFilter.html" title="interface in org.biojava.bio.seq.io.agave">AGAVEAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/SimpleAnnotFilter.html#getProperty(org.biojava.bio.Annotation, java.lang.String)">getProperty(Annotation, String)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/SimpleAnnotFilter.html" title="class in org.biojava.bio.seq.io.agave">SimpleAnnotFilter</a></dt>
<dd>
<div class="block">ThomasD made this a bit safer...</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/UtilHelper.html#getProperty(org.biojava.bio.Annotation, java.lang.String)">getProperty(Annotation, String)</a></span> - Static method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/UtilHelper.html" title="class in org.biojava.bio.seq.io.agave">UtilHelper</a></dt>
<dd>
<div class="block">inhibit the getProperty(key) of Annotation from throw exception when
key does not exist.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Group.html#getProperty(java.lang.String)">getProperty(String)</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Group.html" title="interface in org.biojava.bio.structure">Group</a></dt>
<dd>
<div class="block">get a single property .</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/HetatomImpl.html#getProperty(java.lang.String)">getProperty(String)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/HetatomImpl.html" title="class in org.biojava.bio.structure">HetatomImpl</a></dt>
<dd>
<div class="block">get a single property .</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/EmptyRichAnnotation.html#getProperty(java.lang.Object)">getProperty(Object)</a></span> - Method in class org.biojavax.<a href="./org/biojavax/EmptyRichAnnotation.html" title="class in org.biojavax">EmptyRichAnnotation</a></dt>
<dd>
<div class="block">
Retrieve the value of a property by key.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleRichAnnotation.html#getProperty(java.lang.Object)">getProperty(Object)</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleRichAnnotation.html" title="class in org.biojavax">SimpleRichAnnotation</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span> </div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/TypedProperties.html#getPropertyAsBoolean(java.lang.String)">getPropertyAsBoolean(String)</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/TypedProperties.html" title="class in org.biojava.utils">TypedProperties</a></dt>
<dd>
<div class="block">Searches for the property with the specified key in this property list.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/TypedProperties.html#getPropertyAsDouble(java.lang.String)">getPropertyAsDouble(String)</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/TypedProperties.html" title="class in org.biojava.utils">TypedProperties</a></dt>
<dd>
<div class="block">Searches for the property with the specified key in this property list.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/TypedProperties.html#getPropertyAsInteger(java.lang.String)">getPropertyAsInteger(String)</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/TypedProperties.html" title="class in org.biojava.utils">TypedProperties</a></dt>
<dd>
<div class="block">Searches for the property with the specified key in this property list.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/TypedProperties.html#getPropertyAsLong(java.lang.String)">getPropertyAsLong(String)</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/TypedProperties.html" title="class in org.biojava.utils">TypedProperties</a></dt>
<dd>
<div class="block">Searches for the property with the specified key in this property list.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/TypedProperties.html#getPropertyAsStringList(java.lang.String, java.lang.String)">getPropertyAsStringList(String, String)</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/TypedProperties.html" title="class in org.biojava.utils">TypedProperties</a></dt>
<dd>
<div class="block">Searches for the property with the specified key in this property list.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/TypedProperties.html#getPropertyAsStringList(java.lang.String)">getPropertyAsStringList(String)</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/TypedProperties.html" title="class in org.biojava.utils">TypedProperties</a></dt>
<dd>
<div class="block">just like getPropertyAsStringList(String key, String delims) but uses ',' (comma), ';' (semicolon) and '\t' (tab)
as the possible delimiters.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/PropertyConstraint.ByClass.html#getPropertyClass()">getPropertyClass()</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/PropertyConstraint.ByClass.html" title="class in org.biojava.bio">PropertyConstraint.ByClass</a></dt>
<dd>
<div class="block">Get the Class used as the constraint.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/CollectionConstraint.AllValuesIn.html#getPropertyConstraint()">getPropertyConstraint()</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/CollectionConstraint.AllValuesIn.html" title="class in org.biojava.bio">CollectionConstraint.AllValuesIn</a></dt>
<dd>
<div class="block">Get the PropertyConstraint used to validate each property value.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/CollectionConstraint.Contains.html#getPropertyConstraint()">getPropertyConstraint()</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/CollectionConstraint.Contains.html" title="class in org.biojava.bio">CollectionConstraint.Contains</a></dt>
<dd>
<div class="block">Get the PropertyConstraint used to validate each property value.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/filterxml/XMLAnnotationTypeHandler.PropertyConstraintHandler.html#getPropertyConstraint()">getPropertyConstraint()</a></span> - Method in interface org.biojava.bio.seq.io.filterxml.<a href="./org/biojava/bio/seq/io/filterxml/XMLAnnotationTypeHandler.PropertyConstraintHandler.html" title="interface in org.biojava.bio.seq.io.filterxml">XMLAnnotationTypeHandler.PropertyConstraintHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVERelatedAnnot.html#getProps()">getProps()</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVERelatedAnnot.html" title="class in org.biojava.bio.seq.io.agave">AGAVERelatedAnnot</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEProperty.html#getPropType()">getPropType()</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEProperty.html" title="class in org.biojava.bio.seq.io.agave">AGAVEProperty</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/Protease.html#getProteaseByName(java.lang.String)">getProteaseByName(String)</a></span> - Static method in class org.biojava.bio.proteomics.<a href="./org/biojava/bio/proteomics/Protease.html" title="class in org.biojava.bio.proteomics">Protease</a></dt>
<dd>
<div class="block">Retrieves a reference to the named Protease.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/ProteaseManager.html#getProteaseByName(java.lang.String)">getProteaseByName(String)</a></span> - Static method in class org.biojava.bio.proteomics.<a href="./org/biojava/bio/proteomics/ProteaseManager.html" title="class in org.biojava.bio.proteomics">ProteaseManager</a></dt>
<dd>
<div class="block">Gets a Protease instance by name.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/Protease.html#getProteaseList()">getProteaseList()</a></span> - Static method in class org.biojava.bio.proteomics.<a href="./org/biojava/bio/proteomics/Protease.html" title="class in org.biojava.bio.proteomics">Protease</a></dt>
<dd>
<div class="block">Get the list of Protease names defined in the ProteaseManager
(Internally calls ProteaseManager.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtFormat.Terms.html#getProteinExistsTerm()">getProteinExistsTerm()</a></span> - Static method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtFormat.Terms.html" title="class in org.biojavax.bio.seq.io">UniProtFormat.Terms</a></dt>
<dd>
<div class="block">Getter for the protein exists term</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.Terms.html#getProteinExistsTerm()">getProteinExistsTerm()</a></span> - Static method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.Terms.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat.Terms</a></dt>
<dd>
<div class="block">Getter for the protein exists term</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.IOTools.html#getProteinParser()">getProteinParser()</a></span> - Static method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.IOTools.html" title="class in org.biojavax.bio.seq">RichSequence.IOTools</a></dt>
<dd>
<div class="block">Creates a protein symbol tokenizer.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.Terms.html#getProteinTypeTerm()">getProteinTypeTerm()</a></span> - Static method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.Terms.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat.Terms</a></dt>
<dd>
<div class="block">Getter for the protein type term</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Calc.html#getPsi(org.biojava.bio.structure.AminoAcid, org.biojava.bio.structure.AminoAcid)">getPsi(AminoAcid, AminoAcid)</a></span> - Static method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Calc.html" title="class in org.biojava.bio.structure">Calc</a></dt>
<dd>
<div class="block">psi angle.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/AlphaCTools.html#getPsiAngle(org.biojava.bio.symbol.Symbol)">getPsiAngle(Symbol)</a></span> - Static method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/AlphaCTools.html" title="class in org.biojava.bio.structure">AlphaCTools</a></dt>
<dd>
<div class="block">extracts the Psi angle from a <code>Symbol</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/JournalArticle.html#getPublicationDate()">getPublicationDate()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/JournalArticle.html" title="class in org.biojava.bio.structure">JournalArticle</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/JournalArticle.html#getPublisher()">getPublisher()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/JournalArticle.html" title="class in org.biojava.bio.structure">JournalArticle</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SeqSimilaritySearchHit.html#getPValue()">getPValue()</a></span> - Method in interface org.biojava.bio.search.<a href="./org/biojava/bio/search/SeqSimilaritySearchHit.html" title="interface in org.biojava.bio.search">SeqSimilaritySearchHit</a></dt>
<dd>
<div class="block">Return the overall P-value of this hit.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SeqSimilaritySearchSubHit.html#getPValue()">getPValue()</a></span> - Method in interface org.biojava.bio.search.<a href="./org/biojava/bio/search/SeqSimilaritySearchSubHit.html" title="interface in org.biojava.bio.search">SeqSimilaritySearchSubHit</a></dt>
<dd>
<div class="block">Return the P-value of this sub-hit.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SequenceDBSearchHit.html#getPValue()">getPValue()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SequenceDBSearchHit.html" title="class in org.biojava.bio.search">SequenceDBSearchHit</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SequenceDBSearchSubHit.html#getPValue()">getPValue()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SequenceDBSearchSubHit.html" title="class in org.biojava.bio.search">SequenceDBSearchSubHit</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SimpleSeqSimilaritySearchHit.html#getPValue()">getPValue()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SimpleSeqSimilaritySearchHit.html" title="class in org.biojava.bio.search">SimpleSeqSimilaritySearchHit</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SimpleSeqSimilaritySearchSubHit.html#getPValue()">getPValue()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SimpleSeqSimilaritySearchSubHit.html" title="class in org.biojava.bio.search">SimpleSeqSimilaritySearchSubHit</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/jama/QRDecomposition.html#getQ()">getQ()</a></span> - Method in class org.biojava.bio.structure.jama.<a href="./org/biojava/bio/structure/jama/QRDecomposition.html" title="class in org.biojava.bio.structure.jama">QRDecomposition</a></dt>
<dd>
<div class="block">Generate and return the (economy-sized) orthogonal factor</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/fastq/Fastq.html#getQuality()">getQuality()</a></span> - Method in class org.biojava.bio.program.fastq.<a href="./org/biojava/bio/program/fastq/Fastq.html" title="class in org.biojava.bio.program.fastq">Fastq</a></dt>
<dd>
<div class="block">Return the quality scores for this FASTQ formatted sequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/phred/PhredSequence.html#getQuality()">getQuality()</a></span> - Method in class org.biojava.bio.program.phred.<a href="./org/biojava/bio/program/phred/PhredSequence.html" title="class in org.biojava.bio.program.phred">PhredSequence</a></dt>
<dd>
<div class="block">Extracts the quality part if the Phred Alphabet and returns it as a SymbolList
over the Integer SubAlphabet from 0..99.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/phred/Qualitative.html#getQuality()">getQuality()</a></span> - Method in interface org.biojava.bio.program.phred.<a href="./org/biojava/bio/program/phred/Qualitative.html" title="interface in org.biojava.bio.program.phred">Qualitative</a></dt>
<dd>
<div class="block">Retreives the list of quality symbols from the underlying object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/phred/PhredSequence.html#getQualityAt(int)">getQualityAt(int)</a></span> - Method in class org.biojava.bio.program.phred.<a href="./org/biojava/bio/program/phred/PhredSequence.html" title="class in org.biojava.bio.program.phred">PhredSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/phred/Qualitative.html#getQualityAt(int)">getQualityAt(int)</a></span> - Method in interface org.biojava.bio.program.phred.<a href="./org/biojava/bio/program/phred/Qualitative.html" title="interface in org.biojava.bio.program.phred">Qualitative</a></dt>
<dd>
<div class="block">Retreives the quality symbol for the specified index.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/dasalignment/DASAlignmentClient.html#getQuery()">getQuery()</a></span> - Method in class org.biojava.bio.program.das.dasalignment.<a href="./org/biojava/bio/program/das/dasalignment/DASAlignmentClient.html" title="class in org.biojava.bio.program.das.dasalignment">DASAlignmentClient</a></dt>
<dd>
<div class="block">Returns the query.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SeqSimilaritySearchHit.html#getQueryEnd()">getQueryEnd()</a></span> - Method in interface org.biojava.bio.search.<a href="./org/biojava/bio/search/SeqSimilaritySearchHit.html" title="interface in org.biojava.bio.search">SeqSimilaritySearchHit</a></dt>
<dd>
<div class="block">Return the end position of the last sub-hit in the query
sequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SeqSimilaritySearchSubHit.html#getQueryEnd()">getQueryEnd()</a></span> - Method in interface org.biojava.bio.search.<a href="./org/biojava/bio/search/SeqSimilaritySearchSubHit.html" title="interface in org.biojava.bio.search">SeqSimilaritySearchSubHit</a></dt>
<dd>
<div class="block">Return the end position of the sub-hit in the query sequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SequenceDBSearchHit.html#getQueryEnd()">getQueryEnd()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SequenceDBSearchHit.html" title="class in org.biojava.bio.search">SequenceDBSearchHit</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SequenceDBSearchSubHit.html#getQueryEnd()">getQueryEnd()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SequenceDBSearchSubHit.html" title="class in org.biojava.bio.search">SequenceDBSearchSubHit</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SimpleSeqSimilaritySearchHit.html#getQueryEnd()">getQueryEnd()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SimpleSeqSimilaritySearchHit.html" title="class in org.biojava.bio.search">SimpleSeqSimilaritySearchHit</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SimpleSeqSimilaritySearchSubHit.html#getQueryEnd()">getQueryEnd()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SimpleSeqSimilaritySearchSubHit.html" title="class in org.biojava.bio.search">SimpleSeqSimilaritySearchSubHit</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/Agave2AgaveAnnotFilter.html#getQueryRegion(org.biojava.bio.Annotation)">getQueryRegion(Annotation)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/Agave2AgaveAnnotFilter.html" title="class in org.biojava.bio.seq.io.agave">Agave2AgaveAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEAnnotFilter.html#getQueryRegion(org.biojava.bio.Annotation)">getQueryRegion(Annotation)</a></span> - Method in interface org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEAnnotFilter.html" title="interface in org.biojava.bio.seq.io.agave">AGAVEAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/SimpleAnnotFilter.html#getQueryRegion(org.biojava.bio.Annotation)">getQueryRegion(Annotation)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/SimpleAnnotFilter.html" title="class in org.biojava.bio.seq.io.agave">SimpleAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/ViewSequenceFactory.html#getQuerySeqHolder()">getQuerySeqHolder()</a></span> - Method in class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/ViewSequenceFactory.html" title="class in org.biojava.bio.program.ssbind">ViewSequenceFactory</a></dt>
<dd>
<div class="block"><code>getQuerySeqHolder</code> returns the database of query
sequences used to retrieve sequences for creation of the
various result objects.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SeqSimilaritySearchResult.html#getQuerySequence()">getQuerySequence()</a></span> - Method in interface org.biojava.bio.search.<a href="./org/biojava/bio/search/SeqSimilaritySearchResult.html" title="interface in org.biojava.bio.search">SeqSimilaritySearchResult</a></dt>
<dd>
<div class="block">Returns the query sequence which was used to perform the search.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SequenceDBSearchResult.html#getQuerySequence()">getQuerySequence()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SequenceDBSearchResult.html" title="class in org.biojava.bio.search">SequenceDBSearchResult</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SimpleSeqSimilaritySearchResult.html#getQuerySequence()">getQuerySequence()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SimpleSeqSimilaritySearchResult.html" title="class in org.biojava.bio.search">SimpleSeqSimilaritySearchResult</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SeqSimilaritySearchHit.html#getQueryStart()">getQueryStart()</a></span> - Method in interface org.biojava.bio.search.<a href="./org/biojava/bio/search/SeqSimilaritySearchHit.html" title="interface in org.biojava.bio.search">SeqSimilaritySearchHit</a></dt>
<dd>
<div class="block">Return the start position of the first sub-hit in the query
sequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SeqSimilaritySearchSubHit.html#getQueryStart()">getQueryStart()</a></span> - Method in interface org.biojava.bio.search.<a href="./org/biojava/bio/search/SeqSimilaritySearchSubHit.html" title="interface in org.biojava.bio.search">SeqSimilaritySearchSubHit</a></dt>
<dd>
<div class="block">Return the start position of the sub-hit in the query sequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SequenceDBSearchHit.html#getQueryStart()">getQueryStart()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SequenceDBSearchHit.html" title="class in org.biojava.bio.search">SequenceDBSearchHit</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SequenceDBSearchSubHit.html#getQueryStart()">getQueryStart()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SequenceDBSearchSubHit.html" title="class in org.biojava.bio.search">SequenceDBSearchSubHit</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SimpleSeqSimilaritySearchHit.html#getQueryStart()">getQueryStart()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SimpleSeqSimilaritySearchHit.html" title="class in org.biojava.bio.search">SimpleSeqSimilaritySearchHit</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SimpleSeqSimilaritySearchSubHit.html#getQueryStart()">getQueryStart()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SimpleSeqSimilaritySearchSubHit.html" title="class in org.biojava.bio.search">SimpleSeqSimilaritySearchSubHit</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SeqSimilaritySearchHit.html#getQueryStrand()">getQueryStrand()</a></span> - Method in interface org.biojava.bio.search.<a href="./org/biojava/bio/search/SeqSimilaritySearchHit.html" title="interface in org.biojava.bio.search">SeqSimilaritySearchHit</a></dt>
<dd>
<div class="block">Return the strand of the hit with respect to the query
sequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SeqSimilaritySearchSubHit.html#getQueryStrand()">getQueryStrand()</a></span> - Method in interface org.biojava.bio.search.<a href="./org/biojava/bio/search/SeqSimilaritySearchSubHit.html" title="interface in org.biojava.bio.search">SeqSimilaritySearchSubHit</a></dt>
<dd>
<div class="block">Return the strand of the sub-hit with respect to the query
sequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SequenceDBSearchHit.html#getQueryStrand()">getQueryStrand()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SequenceDBSearchHit.html" title="class in org.biojava.bio.search">SequenceDBSearchHit</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SequenceDBSearchSubHit.html#getQueryStrand()">getQueryStrand()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SequenceDBSearchSubHit.html" title="class in org.biojava.bio.search">SequenceDBSearchSubHit</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SimpleSeqSimilaritySearchHit.html#getQueryStrand()">getQueryStrand()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SimpleSeqSimilaritySearchHit.html" title="class in org.biojava.bio.search">SimpleSeqSimilaritySearchHit</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SimpleSeqSimilaritySearchSubHit.html#getQueryStrand()">getQueryStrand()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SimpleSeqSimilaritySearchSubHit.html" title="class in org.biojava.bio.search">SimpleSeqSimilaritySearchSubHit</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/jama/QRDecomposition.html#getR()">getR()</a></span> - Method in class org.biojava.bio.structure.jama.<a href="./org/biojava/bio/structure/jama/QRDecomposition.html" title="class in org.biojava.bio.structure.jama">QRDecomposition</a></dt>
<dd>
<div class="block">Return the upper triangular factor</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/CircularRendererContext.html#getRadius()">getRadius()</a></span> - Method in interface org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/CircularRendererContext.html" title="interface in org.biojava.bio.gui.sequence">CircularRendererContext</a></dt>
<dd>
<div class="block">Get the current radius at which data should be rendered.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/CircularRendererPanel.html#getRadius()">getRadius()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/CircularRendererPanel.html" title="class in org.biojava.bio.gui.sequence">CircularRendererPanel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SubCircularRendererContext.html#getRadius()">getRadius()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SubCircularRendererContext.html" title="class in org.biojava.bio.gui.sequence">SubCircularRendererContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/HeadlessRenderContext.html#getRange()">getRange()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/HeadlessRenderContext.html" title="class in org.biojava.bio.gui.sequence">HeadlessRenderContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PairwiseSequencePanel.html#getRange()">getRange()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PairwiseSequencePanel.html" title="class in org.biojava.bio.gui.sequence">PairwiseSequencePanel</a></dt>
<dd>
<div class="block"><code>getRange</code> returns a <code>RangeLocation</code>
representing the region of the sequence currently being
rendered.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePanel.html#getRange()">getRange()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePanel.html" title="class in org.biojava.bio.gui.sequence">SequencePanel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePanelWrapper.html#getRange()">getRange()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePanelWrapper.html" title="class in org.biojava.bio.gui.sequence">SequencePanelWrapper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePoster.html#getRange()">getRange()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePoster.html" title="class in org.biojava.bio.gui.sequence">SequencePoster</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequenceRenderContext.html#getRange()">getRange()</a></span> - Method in interface org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequenceRenderContext.html" title="interface in org.biojava.bio.gui.sequence">SequenceRenderContext</a></dt>
<dd>
<div class="block">The range of the SymbolList to render.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SubPairwiseRenderContext.html#getRange()">getRange()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SubPairwiseRenderContext.html" title="class in org.biojava.bio.gui.sequence">SubPairwiseRenderContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SubSequenceRenderContext.html#getRange()">getRange()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SubSequenceRenderContext.html" title="class in org.biojava.bio.gui.sequence">SubSequenceRenderContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/TranslatedSequencePanel.html#getRange()">getRange()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/TranslatedSequencePanel.html" title="class in org.biojava.bio.gui.sequence">TranslatedSequencePanel</a></dt>
<dd>
<div class="block"><code>getRange</code> returns a <code>RangeLocation</code>
representing the region of the sequence currently being
rendered.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/tracklayout/SimpleTrackLayout.html#getRanges()">getRanges()</a></span> - Method in class org.biojava.bio.gui.sequence.tracklayout.<a href="./org/biojava/bio/gui/sequence/tracklayout/SimpleTrackLayout.html" title="class in org.biojava.bio.gui.sequence.tracklayout">SimpleTrackLayout</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/tracklayout/TrackLayout.html#getRanges()">getRanges()</a></span> - Method in interface org.biojava.bio.gui.sequence.tracklayout.<a href="./org/biojava/bio/gui/sequence/tracklayout/TrackLayout.html" title="interface in org.biojava.bio.gui.sequence.tracklayout">TrackLayout</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/tracklayout/UserDefinedTrackLayout.html#getRanges()">getRanges()</a></span> - Method in class org.biojava.bio.gui.sequence.tracklayout.<a href="./org/biojava/bio/gui/sequence/tracklayout/UserDefinedTrackLayout.html" title="class in org.biojava.bio.gui.sequence.tracklayout">UserDefinedTrackLayout</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/BioEntryRelationship.html#getRank()">getRank()</a></span> - Method in interface org.biojavax.bio.<a href="./org/biojavax/bio/BioEntryRelationship.html" title="interface in org.biojavax.bio">BioEntryRelationship</a></dt>
<dd>
<div class="block">Returns the rank of this relationship.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByRank.html#getRank()">getRank()</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByRank.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.ByRank</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/EmptyRichLocation.html#getRank()">getRank()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/EmptyRichLocation.html" title="class in org.biojavax.bio.seq">EmptyRichLocation</a></dt>
<dd>
<div class="block">Retrieves the rank associated with this location.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichFeature.html#getRank()">getRank()</a></span> - Method in interface org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichFeature.html" title="interface in org.biojavax.bio.seq">RichFeature</a></dt>
<dd>
<div class="block">Returns the rank of this feature.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichFeatureRelationship.html#getRank()">getRank()</a></span> - Method in interface org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichFeatureRelationship.html" title="interface in org.biojavax.bio.seq">RichFeatureRelationship</a></dt>
<dd>
<div class="block">Gets the rank of this relationship.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichLocation.html#getRank()">getRank()</a></span> - Method in interface org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichLocation.html" title="interface in org.biojavax.bio.seq">RichLocation</a></dt>
<dd>
<div class="block">Retrieves the rank associated with this location.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichFeature.html#getRank()">getRank()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichFeature.html" title="class in org.biojavax.bio.seq">SimpleRichFeature</a></dt>
<dd>
<div class="block">Returns the rank of this feature.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichFeatureRelationship.html#getRank()">getRank()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichFeatureRelationship.html" title="class in org.biojavax.bio.seq">SimpleRichFeatureRelationship</a></dt>
<dd>
<div class="block">Gets the rank of this relationship.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichLocation.html#getRank()">getRank()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichLocation.html" title="class in org.biojavax.bio.seq">SimpleRichLocation</a></dt>
<dd>
<div class="block">Retrieves the rank associated with this location.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/SimpleBioEntryRelationship.html#getRank()">getRank()</a></span> - Method in class org.biojavax.bio.<a href="./org/biojavax/bio/SimpleBioEntryRelationship.html" title="class in org.biojavax.bio">SimpleBioEntryRelationship</a></dt>
<dd>
<div class="block">Returns the rank of this relationship.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/Comment.html#getRank()">getRank()</a></span> - Method in interface org.biojavax.<a href="./org/biojavax/Comment.html" title="interface in org.biojavax">Comment</a></dt>
<dd>
<div class="block">Returns the rank of this comment.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/Note.html#getRank()">getRank()</a></span> - Method in interface org.biojavax.<a href="./org/biojavax/Note.html" title="interface in org.biojavax">Note</a></dt>
<dd>
<div class="block">Gets the rank that defines this note.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/RankedCrossRef.html#getRank()">getRank()</a></span> - Method in interface org.biojavax.<a href="./org/biojavax/RankedCrossRef.html" title="interface in org.biojavax">RankedCrossRef</a></dt>
<dd>
<div class="block">Return the rank associated with the cross reference.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/RankedDocRef.html#getRank()">getRank()</a></span> - Method in interface org.biojavax.<a href="./org/biojavax/RankedDocRef.html" title="interface in org.biojavax">RankedDocRef</a></dt>
<dd>
<div class="block">The rank of this reference.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleComment.html#getRank()">getRank()</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleComment.html" title="class in org.biojavax">SimpleComment</a></dt>
<dd>
<div class="block">Returns the rank of this comment.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleNote.html#getRank()">getRank()</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleNote.html" title="class in org.biojavax">SimpleNote</a></dt>
<dd>
<div class="block">Gets the rank that defines this note.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleRankedCrossRef.html#getRank()">getRank()</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleRankedCrossRef.html" title="class in org.biojavax">SimpleRankedCrossRef</a></dt>
<dd>
<div class="block">Return the rank associated with the cross reference.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleRankedDocRef.html#getRank()">getRank()</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleRankedDocRef.html" title="class in org.biojavax">SimpleRankedDocRef</a></dt>
<dd>
<div class="block">The rank of this reference.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichFeature.html#getRankedCrossRefs()">getRankedCrossRefs()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichFeature.html" title="class in org.biojavax.bio.seq">SimpleRichFeature</a></dt>
<dd>
<div class="block">Returns the set of all ranked cross references associated with an object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/SimpleBioEntry.html#getRankedCrossRefs()">getRankedCrossRefs()</a></span> - Method in class org.biojavax.bio.<a href="./org/biojavax/bio/SimpleBioEntry.html" title="class in org.biojavax.bio">SimpleBioEntry</a></dt>
<dd>
<div class="block">Returns the set of all ranked cross references associated with an object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ontology/SimpleComparableTerm.html#getRankedCrossRefs()">getRankedCrossRefs()</a></span> - Method in class org.biojavax.ontology.<a href="./org/biojavax/ontology/SimpleComparableTerm.html" title="class in org.biojavax.ontology">SimpleComparableTerm</a></dt>
<dd>
<div class="block">Returns the set of all ranked cross references associated with an object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/RankedCrossRefable.html#getRankedCrossRefs()">getRankedCrossRefs()</a></span> - Method in interface org.biojavax.<a href="./org/biojavax/RankedCrossRefable.html" title="interface in org.biojavax">RankedCrossRefable</a></dt>
<dd>
<div class="block">Returns the set of all ranked cross references associated with an object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/BioEntry.html#getRankedDocRefs()">getRankedDocRefs()</a></span> - Method in interface org.biojavax.bio.<a href="./org/biojavax/bio/BioEntry.html" title="interface in org.biojavax.bio">BioEntry</a></dt>
<dd>
<div class="block">Returns a set of all bioentrydocrefs associated with this bioentry.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/SimpleBioEntry.html#getRankedDocRefs()">getRankedDocRefs()</a></span> - Method in class org.biojavax.bio.<a href="./org/biojavax/bio/SimpleBioEntry.html" title="class in org.biojavax.bio">SimpleBioEntry</a></dt>
<dd>
<div class="block">Returns a set of all bioentrydocrefs associated with this bioentry.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/Indexer.html#getReader()">getReader()</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/Indexer.html" title="class in org.biojava.bio.program.tagvalue">Indexer</a></dt>
<dd>
<div class="block">Retrieve the reader that can be safely used to index this file.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/Indexer2.html#getReader()">getReader()</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/Indexer2.html" title="class in org.biojava.bio.program.tagvalue">Indexer2</a></dt>
<dd>
<div class="block">Retrieve the reader that can be safely used to index this file.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/process/ReaderWriterPipe.html#getReader()">getReader()</a></span> - Method in class org.biojava.utils.process.<a href="./org/biojava/utils/process/ReaderWriterPipe.html" title="class in org.biojava.utils.process">ReaderWriterPipe</a></dt>
<dd>
<div class="block">Gets the reader.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FramedFeature.html#getReadingFrame()">getReadingFrame()</a></span> - Method in interface org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FramedFeature.html" title="interface in org.biojava.bio.seq">FramedFeature</a></dt>
<dd>
<div class="block">return the reading frame of the feature.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleFramedFeature.html#getReadingFrame()">getReadingFrame()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleFramedFeature.html" title="class in org.biojava.bio.seq.impl">SimpleFramedFeature</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/jama/EigenvalueDecomposition.html#getRealEigenvalues()">getRealEigenvalues()</a></span> - Method in class org.biojava.bio.structure.jama.<a href="./org/biojava/bio/structure/jama/EigenvalueDecomposition.html" title="class in org.biojava.bio.structure.jama">EigenvalueDecomposition</a></dt>
<dd>
<div class="block">Return the real parts of the eigenvalues</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/biosql/TaxonSQL.html#getRealScientificName(org.biojava.bio.taxa.Taxon)">getRealScientificName(Taxon)</a></span> - Static method in class org.biojava.bio.seq.db.biosql.<a href="./org/biojava/bio/seq/db/biosql/TaxonSQL.html" title="class in org.biojava.bio.seq.db.biosql">TaxonSQL</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">This returns the true scientific name of a given taxon, if there is one.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/molbio/RestrictionEnzymeManager.html#getRecognitionSequence(java.lang.String)">getRecognitionSequence(String)</a></span> - Static method in class org.biojava.bio.molbio.<a href="./org/biojava/bio/molbio/RestrictionEnzymeManager.html" title="class in org.biojava.bio.molbio">RestrictionEnzymeManager</a></dt>
<dd>
<div class="block"><code>getRecognitionSequence</code> returns a string that describes
the recognition site of this enzyme.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/molbio/RestrictionEnzyme.html#getRecognitionSite()">getRecognitionSite()</a></span> - Method in class org.biojava.bio.molbio.<a href="./org/biojava/bio/molbio/RestrictionEnzyme.html" title="class in org.biojava.bio.molbio">RestrictionEnzyme</a></dt>
<dd>
<div class="block"><code>getRecognitionSite</code> returns the forward strand of
the recognition site.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/emblcd/EmblCDROMRandomAccess.html#getRecordKey(java.lang.Object[])">getRecordKey(Object[])</a></span> - Method in class org.biojava.bio.seq.db.emblcd.<a href="./org/biojava/bio/seq/db/emblcd/EmblCDROMRandomAccess.html" title="class in org.biojava.bio.seq.db.emblcd">EmblCDROMRandomAccess</a></dt>
<dd>
<div class="block"><code>getRecordKey</code> returns the field from the record on
which the records were sorted in the index.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/emblcd/EntryNamRandomAccess.html#getRecordKey(java.lang.Object[])">getRecordKey(Object[])</a></span> - Method in class org.biojava.bio.seq.db.emblcd.<a href="./org/biojava/bio/seq/db/emblcd/EntryNamRandomAccess.html" title="class in org.biojava.bio.seq.db.emblcd">EntryNamRandomAccess</a></dt>
<dd>
<div class="block"><code>getRecordKey</code> returns the field from the record on
which the records were sorted in the index.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/indexdb/BioStore.html#getRecordList()">getRecordList()</a></span> - Method in class org.biojava.bio.program.indexdb.<a href="./org/biojava/bio/program/indexdb/BioStore.html" title="class in org.biojava.bio.program.indexdb">BioStore</a></dt>
<dd>
<div class="block"><code>getRecordList</code> returns all the <code>Record</code>s
in the index.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/AminoAcid.html#getRecordType()">getRecordType()</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/AminoAcid.html" title="interface in org.biojava.bio.structure">AminoAcid</a></dt>
<dd>
<div class="block">Allows to distinguish between amino acids that are provided
as ATOM records and a SEQRES records.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/AminoAcidImpl.html#getRecordType()">getRecordType()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/AminoAcidImpl.html" title="class in org.biojava.bio.structure">AminoAcidImpl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/FilteringRenderer.html#getRecurse()">getRecurse()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/FilteringRenderer.html" title="class in org.biojava.bio.gui.sequence">FilteringRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PairwiseFilteringRenderer.html#getRecurse()">getRecurse()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PairwiseFilteringRenderer.html" title="class in org.biojava.bio.gui.sequence">PairwiseFilteringRenderer</a></dt>
<dd>
<div class="block"><code>getRecurse</code> returns the recursion flag of the
filter.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/SequencesAsGFF.html#getRecurse()">getRecurse()</a></span> - Method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/SequencesAsGFF.html" title="class in org.biojava.bio.program.gff">SequencesAsGFF</a></dt>
<dd>
<div class="block">Return whether features will be filtered recursively or not.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/DelegationManager.html#getRecursive()">getRecursive()</a></span> - Method in interface org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/DelegationManager.html" title="interface in org.biojava.bio.seq.io.agave">DelegationManager</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html#getRedoxPotential()">getRedoxPotential()</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html" title="class in org.biojavax.bio.seq.io">UniProtCommentParser</a></dt>
<dd>
<div class="block">Getter for property redoxPotential.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/OrthoPair.html#getRef()">getRef()</a></span> - Method in interface org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/OrthoPair.html" title="interface in org.biojava.bio.program.homologene">OrthoPair</a></dt>
<dd>
<div class="block">get reference to evidence for
orthology.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/SimpleOrthoPair.html#getRef()">getRef()</a></span> - Method in class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/SimpleOrthoPair.html" title="class in org.biojava.bio.program.homologene">SimpleOrthoPair</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/JournalArticle.html#getRef()">getRef()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/JournalArticle.html" title="class in org.biojava.bio.structure">JournalArticle</a></dt>
<dd>
<div class="block">Get the value of REF field.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/StructRefSeq.html#getRef_id()">getRef_id()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/StructRefSeq.html" title="class in org.biojava.bio.structure.io.mmcif.model">StructRefSeq</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Compound.html#getRefChainId()">getRefChainId()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure">Compound</a></dt>
<dd>
<div class="block">Returns the ref chain id value.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/DAS.html#getReferenceServers()">getReferenceServers()</a></span> - Method in class org.biojava.bio.program.das.<a href="./org/biojava/bio/program/das/DAS.html" title="class in org.biojava.bio.program.das">DAS</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/JournalArticle.html#getRefn()">getRefn()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/JournalArticle.html" title="class in org.biojava.bio.structure">JournalArticle</a></dt>
<dd>
<div class="block">Get the value of REFN field.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleRemoteFeature.html#getRegions()">getRegions()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleRemoteFeature.html" title="class in org.biojava.bio.seq.impl">SimpleRemoteFeature</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/RemoteFeature.html#getRegions()">getRegions()</a></span> - Method in interface org.biojava.bio.seq.<a href="./org/biojava/bio/seq/RemoteFeature.html" title="interface in org.biojava.bio.seq">RemoteFeature</a></dt>
<dd>
<div class="block">Retrieve the list of Regions that locate this feature both localy and
remotely.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/directory/Registry.html#getRegistryConfiguration()">getRegistryConfiguration()</a></span> - Method in class org.biojava.directory.<a href="./org/biojava/directory/Registry.html" title="class in org.biojava.directory">Registry</a></dt>
<dd>
<div class="block"><code>getRegistryConfiguration</code> returns the configuration
of the registry.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/directory/SystemRegistry.html#getRegistryPath()">getRegistryPath()</a></span> - Static method in class org.biojava.directory.<a href="./org/biojava/directory/SystemRegistry.html" title="class in org.biojava.directory">SystemRegistry</a></dt>
<dd>
<div class="block">Get the list of places that will be searched for registry
files.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVERelatedAnnot.html#getRel()">getRel()</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVERelatedAnnot.html" title="class in org.biojava.bio.seq.io.agave">AGAVERelatedAnnot</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEXref.html#getRel()">getRel()</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEXref.html" title="class in org.biojava.bio.seq.io.agave">AGAVEXref</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.Terms.html#getRelAnnotatedTerm()">getRelAnnotatedTerm()</a></span> - Static method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.Terms.html" title="class in org.biojavax.bio.seq">RichSequence.Terms</a></dt>
<dd>
<div class="block">Getter for the release annotated term</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/Agave2AgaveAnnotFilter.html#getRelatedAnnot(org.biojava.bio.Annotation)">getRelatedAnnot(Annotation)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/Agave2AgaveAnnotFilter.html" title="class in org.biojava.bio.seq.io.agave">Agave2AgaveAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEAnnotFilter.html#getRelatedAnnot(org.biojava.bio.Annotation)">getRelatedAnnot(Annotation)</a></span> - Method in interface org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEAnnotFilter.html" title="interface in org.biojava.bio.seq.io.agave">AGAVEAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/SimpleAnnotFilter.html#getRelatedAnnot(org.biojava.bio.Annotation)">getRelatedAnnot(Annotation)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/SimpleAnnotFilter.html" title="class in org.biojava.bio.seq.io.agave">SimpleAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/BioEntry.html#getRelationships()">getRelationships()</a></span> - Method in interface org.biojavax.bio.<a href="./org/biojavax/bio/BioEntry.html" title="interface in org.biojavax.bio">BioEntry</a></dt>
<dd>
<div class="block">Returns a set of all relationships associated with this bioentry.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/SimpleBioEntry.html#getRelationships()">getRelationships()</a></span> - Method in class org.biojavax.bio.<a href="./org/biojavax/bio/SimpleBioEntry.html" title="class in org.biojavax.bio">SimpleBioEntry</a></dt>
<dd>
<div class="block">Returns a set of all relationships associated with this bioentry.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.Terms.html#getRelCreatedTerm()">getRelCreatedTerm()</a></span> - Static method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.Terms.html" title="class in org.biojavax.bio.seq">RichSequence.Terms</a></dt>
<dd>
<div class="block">Getter for the release created term</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLFormat.Terms.html#getRelUpdatedRecordVersionTerm()">getRelUpdatedRecordVersionTerm()</a></span> - Static method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLFormat.Terms.html" title="class in org.biojavax.bio.seq.io">EMBLFormat.Terms</a></dt>
<dd>
<div class="block">Getter for the RelUpdatedRecordVersion term</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.Terms.html#getRelUpdatedTerm()">getRelUpdatedTerm()</a></span> - Static method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.Terms.html" title="class in org.biojavax.bio.seq">RichSequence.Terms</a></dt>
<dd>
<div class="block">Getter for the release updated term</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/DocRef.html#getRemark()">getRemark()</a></span> - Method in interface org.biojavax.<a href="./org/biojavax/DocRef.html" title="interface in org.biojavax">DocRef</a></dt>
<dd>
<div class="block">If remarks have been made about this document reference, this method
will return them.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleDocRef.html#getRemark()">getRemark()</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleDocRef.html" title="class in org.biojavax">SimpleDocRef</a></dt>
<dd>
<div class="block">If remarks have been made about this document reference, this method
will return them.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLCrossReferenceResolver.html#getRemoteBioEntry(org.biojavax.CrossRef)">getRemoteBioEntry(CrossRef)</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLCrossReferenceResolver.html" title="class in org.biojavax.bio.db.biosql">BioSQLCrossReferenceResolver</a></dt>
<dd>
<div class="block">Given the <code>CrossRef</code> return the corresponding
<code>BioEntry</code></div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/CrossReferenceResolver.html#getRemoteBioEntry(org.biojavax.CrossRef)">getRemoteBioEntry(CrossRef)</a></span> - Method in interface org.biojavax.<a href="./org/biojavax/CrossReferenceResolver.html" title="interface in org.biojavax">CrossReferenceResolver</a></dt>
<dd>
<div class="block">Given the <code>CrossRef</code> return the corresponding
<code>BioEntry</code></div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/DummyCrossReferenceResolver.html#getRemoteBioEntry(org.biojavax.CrossRef)">getRemoteBioEntry(CrossRef)</a></span> - Method in class org.biojavax.<a href="./org/biojavax/DummyCrossReferenceResolver.html" title="class in org.biojavax">DummyCrossReferenceResolver</a></dt>
<dd>
<div class="block">Given the <code>CrossRef</code> return the corresponding
<code>BioEntry</code></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleRemoteFeature.html#getRemoteFeature()">getRemoteFeature()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleRemoteFeature.html" title="class in org.biojava.bio.seq.impl">SimpleRemoteFeature</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/RemoteFeature.html#getRemoteFeature()">getRemoteFeature()</a></span> - Method in interface org.biojava.bio.seq.<a href="./org/biojava/bio/seq/RemoteFeature.html" title="interface in org.biojava.bio.seq">RemoteFeature</a></dt>
<dd>
<div class="block">Retrieve the Feature on some assembly Sequence that can represent this
RemoteFeature properly.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLCrossReferenceResolver.html#getRemoteSymbolList(org.biojavax.CrossRef, org.biojava.bio.symbol.Alphabet)">getRemoteSymbolList(CrossRef, Alphabet)</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLCrossReferenceResolver.html" title="class in org.biojavax.bio.db.biosql">BioSQLCrossReferenceResolver</a></dt>
<dd>
<div class="block">Given a cross reference, return the corresponding symbol list.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/CrossReferenceResolver.html#getRemoteSymbolList(org.biojavax.CrossRef, org.biojava.bio.symbol.Alphabet)">getRemoteSymbolList(CrossRef, Alphabet)</a></span> - Method in interface org.biojavax.<a href="./org/biojavax/CrossReferenceResolver.html" title="interface in org.biojavax">CrossReferenceResolver</a></dt>
<dd>
<div class="block">Given a cross reference, return the corresponding symbol list.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/DummyCrossReferenceResolver.html#getRemoteSymbolList(org.biojavax.CrossRef, org.biojava.bio.symbol.Alphabet)">getRemoteSymbolList(CrossRef, Alphabet)</a></span> - Method in class org.biojavax.<a href="./org/biojavax/DummyCrossReferenceResolver.html" title="class in org.biojavax">DummyCrossReferenceResolver</a></dt>
<dd>
<div class="block">Given a cross reference, return the corresponding symbol list.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/RemoteTerm.html#getRemoteTerm()">getRemoteTerm()</a></span> - Method in interface org.biojava.ontology.<a href="./org/biojava/ontology/RemoteTerm.html" title="interface in org.biojava.ontology">RemoteTerm</a></dt>
<dd>
<div class="block">Return the imported term</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/RemoteTerm.Impl.html#getRemoteTerm()">getRemoteTerm()</a></span> - Method in class org.biojava.ontology.<a href="./org/biojava/ontology/RemoteTerm.Impl.html" title="class in org.biojava.ontology">RemoteTerm.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/OntologyOps.html#getRemoteTerms()">getRemoteTerms()</a></span> - Method in interface org.biojava.ontology.<a href="./org/biojava/ontology/OntologyOps.html" title="interface in org.biojava.ontology">OntologyOps</a></dt>
<dd>
<div class="block">Get the set of all remote terms.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.html#getRenderedWidth()">getRenderedWidth()</a></span> - Method in class org.biojava.bio.chromatogram.graphic.<a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.html" title="class in org.biojava.bio.chromatogram.graphic">ChromatogramGraphic</a></dt>
<dd>
<div class="block">Returns the width of the graphic as it will be rendered.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.html#getRenderedWidth(float)">getRenderedWidth(float)</a></span> - Method in class org.biojava.bio.chromatogram.graphic.<a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.html" title="class in org.biojava.bio.chromatogram.graphic">ChromatogramGraphic</a></dt>
<dd>
<div class="block">Returns the width of the graphic as it would be rendered with
the specified horizontal scale.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/CircularFeaturesRenderer.html#getRenderer()">getRenderer()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/CircularFeaturesRenderer.html" title="class in org.biojava.bio.gui.sequence">CircularFeaturesRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/CircularRendererPanel.html#getRenderer()">getRenderer()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/CircularRendererPanel.html" title="class in org.biojava.bio.gui.sequence">CircularRendererPanel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/OverlayRendererWrapper.html#getRenderer()">getRenderer()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/OverlayRendererWrapper.html" title="class in org.biojava.bio.gui.sequence">OverlayRendererWrapper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PairwiseFilteringRenderer.html#getRenderer()">getRenderer()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PairwiseFilteringRenderer.html" title="class in org.biojava.bio.gui.sequence">PairwiseFilteringRenderer</a></dt>
<dd>
<div class="block"><code>getRenderer</code> return the current renderer.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PairwiseSequencePanel.html#getRenderer()">getRenderer()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PairwiseSequencePanel.html" title="class in org.biojava.bio.gui.sequence">PairwiseSequencePanel</a></dt>
<dd>
<div class="block"><code>getRenderer</code> returns the current
<code>PairwiseSequenceRenderer</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePanelWrapper.html#getRenderer()">getRenderer()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePanelWrapper.html" title="class in org.biojava.bio.gui.sequence">SequencePanelWrapper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequenceRendererWrapper.html#getRenderer()">getRenderer()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequenceRendererWrapper.html" title="class in org.biojava.bio.gui.sequence">SequenceRendererWrapper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/TranslatedSequencePanel.html#getRenderer()">getRenderer()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/TranslatedSequencePanel.html" title="class in org.biojava.bio.gui.sequence">TranslatedSequencePanel</a></dt>
<dd>
<div class="block"><code>getRenderer</code> returns the current
<code>SequenceRenderer</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/DistributionLogo.html#getRenderingHints()">getRenderingHints()</a></span> - Method in class org.biojava.bio.gui.<a href="./org/biojava/bio/gui/DistributionLogo.html" title="class in org.biojava.bio.gui">DistributionLogo</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PairwiseSequencePanel.html#getRenderingHints()">getRenderingHints()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PairwiseSequencePanel.html" title="class in org.biojava.bio.gui.sequence">PairwiseSequencePanel</a></dt>
<dd>
<div class="block"><code>getRenderingHints</code> returns the
<code>RenderingHints</code> currently being used by the
<code>Graphics2D</code> instances of delegate renderers.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePanel.html#getRenderingHints()">getRenderingHints()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePanel.html" title="class in org.biojava.bio.gui.sequence">SequencePanel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePanelWrapper.html#getRenderingHints()">getRenderingHints()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePanelWrapper.html" title="class in org.biojava.bio.gui.sequence">SequencePanelWrapper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePoster.html#getRenderingHints()">getRenderingHints()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePoster.html" title="class in org.biojava.bio.gui.sequence">SequencePoster</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/TranslatedSequencePanel.html#getRenderingHints()">getRenderingHints()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/TranslatedSequencePanel.html" title="class in org.biojava.bio.gui.sequence">TranslatedSequencePanel</a></dt>
<dd>
<div class="block"><code>getRenderingHints</code> returns the
<code>RenderingHints</code> currently being used by the
<code>Graphics2D</code> instances of delegate renderers.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/NeedlemanWunsch.html#getReplace()">getReplace()</a></span> - Method in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/NeedlemanWunsch.html" title="class in org.biojava.bio.alignment">NeedlemanWunsch</a></dt>
<dd>
<div class="block">Returns the current expenses of a single replace operation.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/ChemicalComponentDictionary.html#getReplaced(org.biojava.bio.structure.io.mmcif.model.ChemComp)">getReplaced(ChemComp)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/ChemicalComponentDictionary.html" title="class in org.biojava.bio.structure.io.mmcif">ChemicalComponentDictionary</a></dt>
<dd>
<div class="block">if ChemComp is replacing another one, get the old version
otherwise return the same ChemComp again.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/ChemicalComponentDictionary.html#getReplaced(java.lang.String)">getReplaced(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/ChemicalComponentDictionary.html" title="class in org.biojava.bio.structure.io.mmcif">ChemicalComponentDictionary</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/ChemicalComponentDictionary.html#getReplacer(org.biojava.bio.structure.io.mmcif.model.ChemComp)">getReplacer(ChemComp)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/ChemicalComponentDictionary.html" title="class in org.biojava.bio.structure.io.mmcif">ChemicalComponentDictionary</a></dt>
<dd>
<div class="block">if ChemComp is replaced by another one, get the newer version
otherwise return the same ChemComp again.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/ChemicalComponentDictionary.html#getReplacer(java.lang.String)">getReplacer(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/ChemicalComponentDictionary.html" title="class in org.biojava.bio.structure.io.mmcif">ChemicalComponentDictionary</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/DatabasePDBrev.html#getReplaces()">getReplaces()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/DatabasePDBrev.html" title="class in org.biojava.bio.structure.io.mmcif.model">DatabasePDBrev</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureTypes.html#getRepository(java.lang.String)">getRepository(String)</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureTypes.html" title="class in org.biojava.bio.seq">FeatureTypes</a></dt>
<dd>
<div class="block">Fetch a repository by name.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureTypes.html#getRepositoryNames()">getRepositoryNames()</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureTypes.html" title="class in org.biojava.bio.seq">FeatureTypes</a></dt>
<dd>
<div class="block">Find the names of all known repositories.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/WobbleDistribution.html#getResidue()">getResidue()</a></span> - Method in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/WobbleDistribution.html" title="interface in org.biojava.bio.symbol">WobbleDistribution</a></dt>
<dd>
<div class="block">returns the residue encoded by this WobbleDistribution</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html#getResidueType()">getResidueType()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html" title="class in org.biojava.bio.structure.io.mmcif.model">ChemComp</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/chem/ResidueType.html#getResidueTypeFromString(java.lang.String)">getResidueTypeFromString(String)</a></span> - Static method in enum org.biojava.bio.structure.io.mmcif.chem.<a href="./org/biojava/bio/structure/io/mmcif/chem/ResidueType.html" title="enum in org.biojava.bio.structure.io.mmcif.chem">ResidueType</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Compound.html#getResNames()">getResNames()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure">Compound</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/SSBond.html#getResnum1()">getResnum1()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/SSBond.html" title="class in org.biojava.bio.structure">SSBond</a></dt>
<dd>
<div class="block">get residue number for first CYS.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/SSBond.html#getResnum2()">getResnum2()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/SSBond.html" title="class in org.biojava.bio.structure">SSBond</a></dt>
<dd>
<div class="block">get residue number for second CYS.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/PDBHeader.html#getResolution()">getResolution()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/PDBHeader.html" title="class in org.biojava.bio.structure">PDBHeader</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleRemoteFeature.html#getResolver()">getResolver()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleRemoteFeature.html" title="class in org.biojava.bio.seq.impl">SimpleRemoteFeature</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/RemoteFeature.html#getResolver()">getResolver()</a></span> - Method in interface org.biojava.bio.seq.<a href="./org/biojava/bio/seq/RemoteFeature.html" title="interface in org.biojava.bio.seq">RemoteFeature</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/FuzzyLocation.html#getResolver()">getResolver()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/FuzzyLocation.html" title="class in org.biojava.bio.symbol">FuzzyLocation</a></dt>
<dd>
<div class="block">Retrieve the Location that this decorates.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/FuzzyPointLocation.html#getResolver()">getResolver()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/FuzzyPointLocation.html" title="class in org.biojava.bio.symbol">FuzzyPointLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/Agave2AgaveAnnotFilter.html#getResultType(org.biojava.bio.Annotation)">getResultType(Annotation)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/Agave2AgaveAnnotFilter.html" title="class in org.biojava.bio.seq.io.agave">Agave2AgaveAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEAnnotFilter.html#getResultType(org.biojava.bio.Annotation)">getResultType(Annotation)</a></span> - Method in interface org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEAnnotFilter.html" title="interface in org.biojava.bio.seq.io.agave">AGAVEAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/SimpleAnnotFilter.html#getResultType(org.biojava.bio.Annotation)">getResultType(Annotation)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/SimpleAnnotFilter.html" title="class in org.biojava.bio.seq.io.agave">SimpleAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ProcessTimeoutException.html#getReturnCode()">getReturnCode()</a></span> - Method in exception org.biojava.utils.<a href="./org/biojava/utils/ProcessTimeoutException.html" title="class in org.biojava.utils">ProcessTimeoutException</a></dt>
<dd>
<div class="block">Get the return code from the dying child process.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/FetchURL.html#getReturnFormat()">getReturnFormat()</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/FetchURL.html" title="class in org.biojava.bio.seq.db">FetchURL</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/molbio/RestrictionEnzyme.html#getReverseRegex()">getReverseRegex()</a></span> - Method in class org.biojava.bio.molbio.<a href="./org/biojava/bio/molbio/RestrictionEnzyme.html" title="class in org.biojava.bio.molbio">RestrictionEnzyme</a></dt>
<dd>
<div class="block"><code>getReverseRegex</code> returns a regular expression which
matches the reverse strand of the recognition site.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SubSequence.SubProjectedFeatureContext.html#getReverter()">getReverter()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SubSequence.SubProjectedFeatureContext.html" title="class in org.biojava.bio.seq.impl">SubSequence.SubProjectedFeatureContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/projection/ReparentContext.html#getReverter()">getReverter()</a></span> - Method in class org.biojava.bio.seq.projection.<a href="./org/biojava/bio/seq/projection/ReparentContext.html" title="class in org.biojava.bio.seq.projection">ReparentContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/projection/TranslateFlipContext.html#getReverter()">getReverter()</a></span> - Method in class org.biojava.bio.seq.projection.<a href="./org/biojava/bio/seq/projection/TranslateFlipContext.html" title="class in org.biojava.bio.seq.projection">TranslateFlipContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/lsid/LifeScienceIdentifier.html#getRevisionId()">getRevisionId()</a></span> - Method in class org.biojava.utils.lsid.<a href="./org/biojava/utils/lsid/LifeScienceIdentifier.html" title="class in org.biojava.utils.lsid">LifeScienceIdentifier</a></dt>
<dd>
<div class="block">Return the revision id of this identifier.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/CompoundRichLocation.html#getRichAnnotation()">getRichAnnotation()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/CompoundRichLocation.html" title="class in org.biojavax.bio.seq">CompoundRichLocation</a></dt>
<dd>
<div class="block">Return the associated annotation object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/EmptyRichLocation.html#getRichAnnotation()">getRichAnnotation()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/EmptyRichLocation.html" title="class in org.biojavax.bio.seq">EmptyRichLocation</a></dt>
<dd>
<div class="block">Return the associated annotation object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichFeature.html#getRichAnnotation()">getRichAnnotation()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichFeature.html" title="class in org.biojavax.bio.seq">SimpleRichFeature</a></dt>
<dd>
<div class="block">Return the associated annotation object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichLocation.html#getRichAnnotation()">getRichAnnotation()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichLocation.html" title="class in org.biojavax.bio.seq">SimpleRichLocation</a></dt>
<dd>
<div class="block">Return the associated annotation object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/SimpleBioEntry.html#getRichAnnotation()">getRichAnnotation()</a></span> - Method in class org.biojavax.bio.<a href="./org/biojavax/bio/SimpleBioEntry.html" title="class in org.biojavax.bio">SimpleBioEntry</a></dt>
<dd>
<div class="block">Return the associated annotation object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/RichAnnotatable.html#getRichAnnotation()">getRichAnnotation()</a></span> - Method in interface org.biojavax.<a href="./org/biojavax/RichAnnotatable.html" title="interface in org.biojavax">RichAnnotatable</a></dt>
<dd>
<div class="block">Return the associated annotation object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleCrossRef.html#getRichAnnotation()">getRichAnnotation()</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleCrossRef.html" title="class in org.biojavax">SimpleCrossRef</a></dt>
<dd>
<div class="block">Return the associated annotation object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ContainedByRichLocation.html#getRichLocation()">getRichLocation()</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ContainedByRichLocation.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.ContainedByRichLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.OverlapsRichLocation.html#getRichLocation()">getRichLocation()</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.OverlapsRichLocation.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.OverlapsRichLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLRichSequenceDB.html#getRichSequence(java.lang.String)">getRichSequence(String)</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLRichSequenceDB.html" title="class in org.biojavax.bio.db.biosql">BioSQLRichSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/HashRichSequenceDB.html#getRichSequence(java.lang.String)">getRichSequence(String)</a></span> - Method in class org.biojavax.bio.db.<a href="./org/biojavax/bio/db/HashRichSequenceDB.html" title="class in org.biojavax.bio.db">HashRichSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/ncbi/GenbankRichSequenceDB.html#getRichSequence(java.lang.String)">getRichSequence(String)</a></span> - Method in class org.biojavax.bio.db.ncbi.<a href="./org/biojavax/bio/db/ncbi/GenbankRichSequenceDB.html" title="class in org.biojavax.bio.db.ncbi">GenbankRichSequenceDB</a></dt>
<dd>
<div class="block">Given the appropriate Genbank ID, return the matching RichSequence object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/ncbi/GenbankRichSequenceDB.html#getRichSequence(java.lang.String, org.biojavax.Namespace)">getRichSequence(String, Namespace)</a></span> - Method in class org.biojavax.bio.db.ncbi.<a href="./org/biojavax/bio/db/ncbi/GenbankRichSequenceDB.html" title="class in org.biojavax.bio.db.ncbi">GenbankRichSequenceDB</a></dt>
<dd>
<div class="block">Given the appropriate Genbank ID, return the matching RichSequence object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/ncbi/GenpeptRichSequenceDB.html#getRichSequence(java.lang.String)">getRichSequence(String)</a></span> - Method in class org.biojavax.bio.db.ncbi.<a href="./org/biojavax/bio/db/ncbi/GenpeptRichSequenceDB.html" title="class in org.biojavax.bio.db.ncbi">GenpeptRichSequenceDB</a></dt>
<dd>
<div class="block">Given the appropriate Genbank ID, return the matching RichSequence object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/ncbi/GenpeptRichSequenceDB.html#getRichSequence(java.lang.String, org.biojavax.Namespace)">getRichSequence(String, Namespace)</a></span> - Method in class org.biojavax.bio.db.ncbi.<a href="./org/biojavax/bio/db/ncbi/GenpeptRichSequenceDB.html" title="class in org.biojavax.bio.db.ncbi">GenpeptRichSequenceDB</a></dt>
<dd>
<div class="block">Given the appropriate Genbank ID, return the matching RichSequence object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/RichSequenceDBLite.html#getRichSequence(java.lang.String)">getRichSequence(String)</a></span> - Method in interface org.biojavax.bio.db.<a href="./org/biojavax/bio/db/RichSequenceDBLite.html" title="interface in org.biojavax.bio.db">RichSequenceDBLite</a></dt>
<dd>
<div class="block">Retrieve a single RichSequence by its id.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/AbstractRichSequenceDB.html#getRichSequenceIterator()">getRichSequenceIterator()</a></span> - Method in class org.biojavax.bio.db.<a href="./org/biojavax/bio/db/AbstractRichSequenceDB.html" title="class in org.biojavax.bio.db">AbstractRichSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/RichSequenceDB.html#getRichSequenceIterator()">getRichSequenceIterator()</a></span> - Method in interface org.biojavax.bio.db.<a href="./org/biojavax/bio/db/RichSequenceDB.html" title="interface in org.biojavax.bio.db">RichSequenceDB</a></dt>
<dd>
<div class="block">Returns a RichSequenceIterator over all sequences in the database.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLRichSequenceDB.html#getRichSequences(java.util.Set)">getRichSequences(Set)</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLRichSequenceDB.html" title="class in org.biojavax.bio.db.biosql">BioSQLRichSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLRichSequenceDB.html#getRichSequences(java.util.Set, org.biojavax.bio.db.RichSequenceDB)">getRichSequences(Set, RichSequenceDB)</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLRichSequenceDB.html" title="class in org.biojavax.bio.db.biosql">BioSQLRichSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/HashRichSequenceDB.html#getRichSequences(java.util.Set)">getRichSequences(Set)</a></span> - Method in class org.biojavax.bio.db.<a href="./org/biojavax/bio/db/HashRichSequenceDB.html" title="class in org.biojavax.bio.db">HashRichSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/HashRichSequenceDB.html#getRichSequences(java.util.Set, org.biojavax.bio.db.RichSequenceDB)">getRichSequences(Set, RichSequenceDB)</a></span> - Method in class org.biojavax.bio.db.<a href="./org/biojavax/bio/db/HashRichSequenceDB.html" title="class in org.biojavax.bio.db">HashRichSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/ncbi/GenbankRichSequenceDB.html#getRichSequences(java.util.Set)">getRichSequences(Set)</a></span> - Method in class org.biojavax.bio.db.ncbi.<a href="./org/biojavax/bio/db/ncbi/GenbankRichSequenceDB.html" title="class in org.biojavax.bio.db.ncbi">GenbankRichSequenceDB</a></dt>
<dd>
<div class="block">Retrieve rich sequences from a Genbank</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/ncbi/GenbankRichSequenceDB.html#getRichSequences(java.util.Set, org.biojavax.bio.db.RichSequenceDB)">getRichSequences(Set, RichSequenceDB)</a></span> - Method in class org.biojavax.bio.db.ncbi.<a href="./org/biojavax/bio/db/ncbi/GenbankRichSequenceDB.html" title="class in org.biojavax.bio.db.ncbi">GenbankRichSequenceDB</a></dt>
<dd>
<div class="block">Retrieve rich sequences from a Genbank</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/ncbi/GenpeptRichSequenceDB.html#getRichSequences(java.util.Set)">getRichSequences(Set)</a></span> - Method in class org.biojavax.bio.db.ncbi.<a href="./org/biojavax/bio/db/ncbi/GenpeptRichSequenceDB.html" title="class in org.biojavax.bio.db.ncbi">GenpeptRichSequenceDB</a></dt>
<dd>
<div class="block">Retrieve rich sequences from a Genbank</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/ncbi/GenpeptRichSequenceDB.html#getRichSequences(java.util.Set, org.biojavax.bio.db.RichSequenceDB)">getRichSequences(Set, RichSequenceDB)</a></span> - Method in class org.biojavax.bio.db.ncbi.<a href="./org/biojavax/bio/db/ncbi/GenpeptRichSequenceDB.html" title="class in org.biojavax.bio.db.ncbi">GenpeptRichSequenceDB</a></dt>
<dd>
<div class="block">Retrieve rich sequences from a Genbank</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/RichSequenceDBLite.html#getRichSequences(java.util.Set)">getRichSequences(Set)</a></span> - Method in interface org.biojavax.bio.db.<a href="./org/biojavax/bio/db/RichSequenceDBLite.html" title="interface in org.biojavax.bio.db">RichSequenceDBLite</a></dt>
<dd>
<div class="block">Retrieve multiple RichSequence by its id.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/RichSequenceDBLite.html#getRichSequences(java.util.Set, org.biojavax.bio.db.RichSequenceDB)">getRichSequences(Set, RichSequenceDB)</a></span> - Method in interface org.biojavax.bio.db.<a href="./org/biojavax/bio/db/RichSequenceDBLite.html" title="interface in org.biojavax.bio.db">RichSequenceDBLite</a></dt>
<dd>
<div class="block">Retrieve multiple RichSequence into a specific sequence database.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/taxa/NCBITaxon.html#getRightValue()">getRightValue()</a></span> - Method in interface org.biojavax.bio.taxa.<a href="./org/biojavax/bio/taxa/NCBITaxon.html" title="interface in org.biojavax.bio.taxa">NCBITaxon</a></dt>
<dd>
<div class="block">Gets the right value.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/taxa/SimpleNCBITaxon.html#getRightValue()">getRightValue()</a></span> - Method in class org.biojavax.bio.taxa.<a href="./org/biojavax/bio/taxa/SimpleNCBITaxon.html" title="class in org.biojavax.bio.taxa">SimpleNCBITaxon</a></dt>
<dd>
<div class="block">Gets the right value.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/helper/JointFragments.html#getRms()">getRms()</a></span> - Method in class org.biojava.bio.structure.align.helper.<a href="./org/biojava/bio/structure/align/helper/JointFragments.html" title="class in org.biojava.bio.structure.align.helper">JointFragments</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/FragmentJoiner.html#getRMS(org.biojava.bio.structure.Atom[], org.biojava.bio.structure.Atom[], org.biojava.bio.structure.align.helper.JointFragments)">getRMS(Atom[], Atom[], JointFragments)</a></span> - Static method in class org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/FragmentJoiner.html" title="class in org.biojava.bio.structure.align.pairwise">FragmentJoiner</a></dt>
<dd>
<div class="block">get the RMS of the JointFragments pair frag</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/FragmentPair.html#getRms()">getRms()</a></span> - Method in class org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/FragmentPair.html" title="class in org.biojava.bio.structure.align.pairwise">FragmentPair</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/SVDSuperimposer.html#getRMS(org.biojava.bio.structure.Atom[], org.biojava.bio.structure.Atom[])">getRMS(Atom[], Atom[])</a></span> - Static method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/SVDSuperimposer.html" title="class in org.biojava.bio.structure">SVDSuperimposer</a></dt>
<dd>
<div class="block">Calculate the RMS (root mean square) deviation of two sets of atoms.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/AlternativeAlignment.html#getRmsd()">getRmsd()</a></span> - Method in class org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/AlternativeAlignment.html" title="class in org.biojava.bio.structure.align.pairwise">AlternativeAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/RNATools.html#getRNA()">getRNA()</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/RNATools.html" title="class in org.biojava.bio.seq">RNATools</a></dt>
<dd>
<div class="block">Return the RNA alphabet.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.IOTools.html#getRNAParser()">getRNAParser()</a></span> - Static method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.IOTools.html" title="class in org.biojavax.bio.seq">RichSequence.IOTools</a></dt>
<dd>
<div class="block">Creates a RNA symbol tokenizer.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/DASLink.html#getRole()">getRole()</a></span> - Method in class org.biojava.bio.program.das.<a href="./org/biojava/bio/program/das/DASLink.html" title="class in org.biojava.bio.program.das">DASLink</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SuffixTree.html#getRoot()">getRoot()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SuffixTree.html" title="class in org.biojava.bio.symbol">SuffixTree</a></dt>
<dd>
<div class="block">Return the node object which is the root of this suffix tree.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/UkkonenSuffixTree.html#getRoot()">getRoot()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/UkkonenSuffixTree.html" title="class in org.biojava.bio.symbol">UkkonenSuffixTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/taxa/SimpleTaxonFactory.html#getRoot()">getRoot()</a></span> - Method in class org.biojava.bio.taxa.<a href="./org/biojava/bio/taxa/SimpleTaxonFactory.html" title="class in org.biojava.bio.taxa">SimpleTaxonFactory</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/taxa/TaxonFactory.html#getRoot()">getRoot()</a></span> - Method in interface org.biojava.bio.taxa.<a href="./org/biojava/bio/taxa/TaxonFactory.html" title="interface in org.biojava.bio.taxa">TaxonFactory</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Retrieve the root upon which all rooted Taxon that this
factory knows about are rooted.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/taxa/WeakTaxonFactory.html#getRoot()">getRoot()</a></span> - Method in class org.biojava.bio.taxa.<a href="./org/biojava/bio/taxa/WeakTaxonFactory.html" title="class in org.biojava.bio.taxa">WeakTaxonFactory</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/FragmentPair.html#getRot()">getRot()</a></span> - Method in class org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/FragmentPair.html" title="class in org.biojava.bio.structure.align.pairwise">FragmentPair</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/SVDSuperimposer.html#getRotation()">getRotation()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/SVDSuperimposer.html" title="class in org.biojava.bio.structure">SVDSuperimposer</a></dt>
<dd>
<div class="block">Get the Rotation matrix that is required to superimpose the two atom sets.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/AlternativeAlignment.html#getRotationMatrix()">getRotationMatrix()</a></span> - Method in class org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/AlternativeAlignment.html" title="class in org.biojava.bio.structure.align.pairwise">AlternativeAlignment</a></dt>
<dd>
<div class="block">returns the rotation matrix that needs to be applied to structure 2 to rotate on structure 1</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/helper/IndexPair.html#getRow()">getRow()</a></span> - Method in class org.biojava.bio.structure.align.helper.<a href="./org/biojava/bio/structure/align/helper/IndexPair.html" title="class in org.biojava.bio.structure.align.helper">IndexPair</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/jama/Matrix.html#getRowDimension()">getRowDimension()</a></span> - Method in class org.biojava.bio.structure.jama.<a href="./org/biojava/bio/structure/jama/Matrix.html" title="class in org.biojava.bio.structure.jama">Matrix</a></dt>
<dd>
<div class="block">Get row dimension.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/jama/Matrix.html#getRowPackedCopy()">getRowPackedCopy()</a></span> - Method in class org.biojava.bio.structure.jama.<a href="./org/biojava/bio/structure/jama/Matrix.html" title="class in org.biojava.bio.structure.jama">Matrix</a></dt>
<dd>
<div class="block">Make a one-dimensional row packed copy of the internal array.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/Alignable.html#getRows()">getRows()</a></span> - Method in interface org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/Alignable.html" title="interface in org.biojava.bio.structure.align.pairwise">Alignable</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/StrCompAlignment.html#getRows()">getRows()</a></span> - Method in class org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/StrCompAlignment.html" title="class in org.biojava.bio.structure.align.pairwise">StrCompAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/StructureTools.html#getS()">getS()</a></span> - Method in class org.biojava.bio.proteomics.<a href="./org/biojava/bio/proteomics/StructureTools.html" title="class in org.biojava.bio.proteomics">StructureTools</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/jama/SingularValueDecomposition.html#getS()">getS()</a></span> - Method in class org.biojava.bio.structure.jama.<a href="./org/biojava/bio/structure/jama/SingularValueDecomposition.html" title="class in org.biojava.bio.structure.jama">SingularValueDecomposition</a></dt>
<dd>
<div class="block">Return the diagonal matrix of singular values</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/JMatrixPanel.html#getSaturation()">getSaturation()</a></span> - Method in class org.biojava.bio.structure.gui.<a href="./org/biojava/bio/structure/gui/JMatrixPanel.html" title="class in org.biojava.bio.structure.gui">JMatrixPanel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/BioIndex.html#getSBFactory()">getSBFactory()</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/BioIndex.html" title="class in org.biojava.bio.seq.db">BioIndex</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/EmblCDROMIndexStore.html#getSBFactory()">getSBFactory()</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/EmblCDROMIndexStore.html" title="class in org.biojava.bio.seq.db">EmblCDROMIndexStore</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/IndexStore.html#getSBFactory()">getSBFactory()</a></span> - Method in interface org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/IndexStore.html" title="interface in org.biojava.bio.seq.db">IndexStore</a></dt>
<dd>
<div class="block">Retrieve the SequenceBuilderFactory used to build Sequence instances.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/TabIndexStore.html#getSBFactory()">getSBFactory()</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/TabIndexStore.html" title="class in org.biojava.bio.seq.db">TabIndexStore</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/HeadlessRenderContext.html#getScale()">getScale()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/HeadlessRenderContext.html" title="class in org.biojava.bio.gui.sequence">HeadlessRenderContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PairwiseSequencePanel.html#getScale()">getScale()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PairwiseSequencePanel.html" title="class in org.biojava.bio.gui.sequence">PairwiseSequencePanel</a></dt>
<dd>
<div class="block"><code>getScale</code> returns the scale in pixels per
<code>Symbol</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePanel.html#getScale()">getScale()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePanel.html" title="class in org.biojava.bio.gui.sequence">SequencePanel</a></dt>
<dd>
<div class="block">Retrieve the current scale.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePanelWrapper.html#getScale()">getScale()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePanelWrapper.html" title="class in org.biojava.bio.gui.sequence">SequencePanelWrapper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePoster.html#getScale()">getScale()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePoster.html" title="class in org.biojava.bio.gui.sequence">SequencePoster</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Retrieve the current scale.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequenceRenderContext.html#getScale()">getScale()</a></span> - Method in interface org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequenceRenderContext.html" title="interface in org.biojava.bio.gui.sequence">SequenceRenderContext</a></dt>
<dd>
<div class="block">Gets the scale as pixels per Symbol</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SubPairwiseRenderContext.html#getScale()">getScale()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SubPairwiseRenderContext.html" title="class in org.biojava.bio.gui.sequence">SubPairwiseRenderContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SubSequenceRenderContext.html#getScale()">getScale()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SubSequenceRenderContext.html" title="class in org.biojava.bio.gui.sequence">SubSequenceRenderContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/TranslatedSequencePanel.html#getScale()">getScale()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/TranslatedSequencePanel.html" title="class in org.biojava.bio.gui.sequence">TranslatedSequencePanel</a></dt>
<dd>
<div class="block"><code>getScale</code> returns the scale in pixels per
<code>Symbol</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/JMatrixPanel.html#getScale()">getScale()</a></span> - Method in class org.biojava.bio.structure.gui.<a href="./org/biojava/bio/structure/gui/JMatrixPanel.html" title="class in org.biojava.bio.structure.gui">JMatrixPanel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/SequenceDisplay.html#getScale()">getScale()</a></span> - Method in class org.biojava.bio.structure.gui.<a href="./org/biojava/bio/structure/gui/SequenceDisplay.html" title="class in org.biojava.bio.structure.gui">SequenceDisplay</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/util/SequenceScalePanel.html#getScale()">getScale()</a></span> - Method in class org.biojava.bio.structure.gui.util.<a href="./org/biojava/bio/structure/gui/util/SequenceScalePanel.html" title="class in org.biojava.bio.structure.gui.util">SequenceScalePanel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/tools/SuffixTreeKernel.DepthScaler.html#getScale(int)">getScale(int)</a></span> - Method in interface org.biojava.stats.svm.tools.<a href="./org/biojava/stats/svm/tools/SuffixTreeKernel.DepthScaler.html" title="interface in org.biojava.stats.svm.tools">SuffixTreeKernel.DepthScaler</a></dt>
<dd>
<div class="block">Retrieve the scaling factor at a given depth</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/tools/SuffixTreeKernel.MultipleScalar.html#getScale(int)">getScale(int)</a></span> - Method in class org.biojava.stats.svm.tools.<a href="./org/biojava/stats/svm/tools/SuffixTreeKernel.MultipleScalar.html" title="class in org.biojava.stats.svm.tools">SuffixTreeKernel.MultipleScalar</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/tools/SuffixTreeKernel.NullModelScaler.html#getScale(int)">getScale(int)</a></span> - Method in class org.biojava.stats.svm.tools.<a href="./org/biojava/stats/svm/tools/SuffixTreeKernel.NullModelScaler.html" title="class in org.biojava.stats.svm.tools">SuffixTreeKernel.NullModelScaler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/tools/SuffixTreeKernel.SelectionScalar.html#getScale(int)">getScale(int)</a></span> - Method in class org.biojava.stats.svm.tools.<a href="./org/biojava/stats/svm/tools/SuffixTreeKernel.SelectionScalar.html" title="class in org.biojava.stats.svm.tools">SuffixTreeKernel.SelectionScalar</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/tools/SuffixTreeKernel.UniformScaler.html#getScale(int)">getScale(int)</a></span> - Method in class org.biojava.stats.svm.tools.<a href="./org/biojava/stats/svm/tools/SuffixTreeKernel.UniformScaler.html" title="class in org.biojava.stats.svm.tools">SuffixTreeKernel.UniformScaler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/JMatrixPanel.html#getScalevalue()">getScalevalue()</a></span> - Method in class org.biojava.bio.structure.gui.<a href="./org/biojava/bio/structure/gui/JMatrixPanel.html" title="class in org.biojava.bio.structure.gui">JMatrixPanel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/annodb/AnnotationDB.html#getSchema()">getSchema()</a></span> - Method in interface org.biojava.bio.annodb.<a href="./org/biojava/bio/annodb/AnnotationDB.html" title="interface in org.biojava.bio.annodb">AnnotationDB</a></dt>
<dd>
<div class="block">
Get an AnnotationType that accepts all Annotation instances in this DB.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/annodb/IndexedAnnotationDB.html#getSchema()">getSchema()</a></span> - Method in class org.biojava.bio.annodb.<a href="./org/biojava/bio/annodb/IndexedAnnotationDB.html" title="class in org.biojava.bio.annodb">IndexedAnnotationDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/annodb/LazyFilteredAnnotationDB.html#getSchema()">getSchema()</a></span> - Method in class org.biojava.bio.annodb.<a href="./org/biojava/bio/annodb/LazyFilteredAnnotationDB.html" title="class in org.biojava.bio.annodb">LazyFilteredAnnotationDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/annodb/LazySearchedAnnotationDB.html#getSchema()">getSchema()</a></span> - Method in class org.biojava.bio.annodb.<a href="./org/biojava/bio/annodb/LazySearchedAnnotationDB.html" title="class in org.biojava.bio.annodb">LazySearchedAnnotationDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/annodb/MergingAnnotationDB.html#getSchema()">getSchema()</a></span> - Method in class org.biojava.bio.annodb.<a href="./org/biojava/bio/annodb/MergingAnnotationDB.html" title="class in org.biojava.bio.annodb">MergingAnnotationDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/annodb/SimpleAnnotationDB.html#getSchema()">getSchema()</a></span> - Method in class org.biojava.bio.annodb.<a href="./org/biojava/bio/annodb/SimpleAnnotationDB.html" title="class in org.biojava.bio.annodb">SimpleAnnotationDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/DASSequence.html#getSchema()">getSchema()</a></span> - Method in class org.biojava.bio.program.das.<a href="./org/biojava/bio/program/das/DASSequence.html" title="class in org.biojava.bio.program.das">DASSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureHolder.EmptyFeatureHolder.html#getSchema()">getSchema()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureHolder.EmptyFeatureHolder.html" title="class in org.biojava.bio.seq">FeatureHolder.EmptyFeatureHolder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureHolder.html#getSchema()">getSchema()</a></span> - Method in interface org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureHolder.html" title="interface in org.biojava.bio.seq">FeatureHolder</a></dt>
<dd>
<div class="block">Return a schema-filter for this <code>FeatureHolder</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureTypes.Type.html#getSchema()">getSchema()</a></span> - Method in interface org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureTypes.Type.html" title="interface in org.biojava.bio.seq">FeatureTypes.Type</a></dt>
<dd>
<div class="block">Get the schema for this type.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/DummySequence.html#getSchema()">getSchema()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/DummySequence.html" title="class in org.biojava.bio.seq.impl">DummySequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/LazyFilterFeatureHolder.html#getSchema()">getSchema()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/LazyFilterFeatureHolder.html" title="class in org.biojava.bio.seq.impl">LazyFilterFeatureHolder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleFeature.html#getSchema()">getSchema()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleFeature.html" title="class in org.biojava.bio.seq.impl">SimpleFeature</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleGappedSequence.html#getSchema()">getSchema()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleGappedSequence.html" title="class in org.biojava.bio.seq.impl">SimpleGappedSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleSequence.html#getSchema()">getSchema()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleSequence.html" title="class in org.biojava.bio.seq.impl">SimpleSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SubSequence.html#getSchema()">getSchema()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SubSequence.html" title="class in org.biojava.bio.seq.impl">SubSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/ViewSequence.html#getSchema()">getSchema()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/ViewSequence.html" title="class in org.biojava.bio.seq.impl">ViewSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/LazyFeatureHolder.html#getSchema()">getSchema()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/LazyFeatureHolder.html" title="class in org.biojava.bio.seq">LazyFeatureHolder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/MergeFeatureHolder.html#getSchema()">getSchema()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/MergeFeatureHolder.html" title="class in org.biojava.bio.seq">MergeFeatureHolder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/NewSimpleAssembly.html#getSchema()">getSchema()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/NewSimpleAssembly.html" title="class in org.biojava.bio.seq">NewSimpleAssembly</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/projection/ProjectedFeatureHolder.html#getSchema()">getSchema()</a></span> - Method in class org.biojava.bio.seq.projection.<a href="./org/biojava/bio/seq/projection/ProjectedFeatureHolder.html" title="class in org.biojava.bio.seq.projection">ProjectedFeatureHolder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/projection/ReparentContext.html#getSchema(org.biojava.bio.seq.Feature)">getSchema(Feature)</a></span> - Method in class org.biojava.bio.seq.projection.<a href="./org/biojava/bio/seq/projection/ReparentContext.html" title="class in org.biojava.bio.seq.projection">ReparentContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/SimpleAssembly.html#getSchema()">getSchema()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/SimpleAssembly.html" title="class in org.biojava.bio.seq">SimpleAssembly</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/SimpleFeatureHolder.html#getSchema()">getSchema()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/SimpleFeatureHolder.html" title="class in org.biojava.bio.seq">SimpleFeatureHolder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/naming/ObdaContext.html#getSchema(javax.naming.Name)">getSchema(Name)</a></span> - Method in class org.biojava.naming.<a href="./org/biojava/naming/ObdaContext.html" title="class in org.biojava.naming">ObdaContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/naming/ObdaContext.html#getSchema(java.lang.String)">getSchema(String)</a></span> - Method in class org.biojava.naming.<a href="./org/biojava/naming/ObdaContext.html" title="class in org.biojava.naming">ObdaContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichFeature.html#getSchema()">getSchema()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichFeature.html" title="class in org.biojavax.bio.seq">SimpleRichFeature</a></dt>
<dd>
<div class="block">Return a schema-filter for this <code>FeatureHolder</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/ThinRichSequence.html#getSchema()">getSchema()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/ThinRichSequence.html" title="class in org.biojavax.bio.seq">ThinRichSequence</a></dt>
<dd>
<div class="block">Return a schema-filter for this <code>FeatureHolder</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/naming/ObdaContext.html#getSchemaClassDefinition(javax.naming.Name)">getSchemaClassDefinition(Name)</a></span> - Method in class org.biojava.naming.<a href="./org/biojava/naming/ObdaContext.html" title="class in org.biojava.naming">ObdaContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/naming/ObdaContext.html#getSchemaClassDefinition(java.lang.String)">getSchemaClassDefinition(String)</a></span> - Method in class org.biojava.naming.<a href="./org/biojava/naming/ObdaContext.html" title="class in org.biojava.naming">ObdaContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/taxa/AbstractTaxon.html#getScientificName()">getScientificName()</a></span> - Method in class org.biojava.bio.taxa.<a href="./org/biojava/bio/taxa/AbstractTaxon.html" title="class in org.biojava.bio.taxa">AbstractTaxon</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/taxa/Taxon.html#getScientificName()">getScientificName()</a></span> - Method in interface org.biojava.bio.taxa.<a href="./org/biojava/bio/taxa/Taxon.html" title="interface in org.biojava.bio.taxa">Taxon</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">The scientific name of this taxon.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/Synonym.html#getScope()">getScope()</a></span> - Method in class org.biojava.ontology.<a href="./org/biojava/ontology/Synonym.html" title="class in org.biojava.ontology">Synonym</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/DPMatrix.html#getScore()">getScore()</a></span> - Method in interface org.biojava.bio.dp.<a href="./org/biojava/bio/dp/DPMatrix.html" title="interface in org.biojava.bio.dp">DPMatrix</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/onehead/SingleDPMatrix.html#getScore()">getScore()</a></span> - Method in class org.biojava.bio.dp.onehead.<a href="./org/biojava/bio/dp/onehead/SingleDPMatrix.html" title="class in org.biojava.bio.dp.onehead">SingleDPMatrix</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/SimpleStatePath.html#getScore()">getScore()</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/SimpleStatePath.html" title="class in org.biojava.bio.dp">SimpleStatePath</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/StatePath.html#getScore()">getScore()</a></span> - Method in interface org.biojava.bio.dp.<a href="./org/biojava/bio/dp/StatePath.html" title="interface in org.biojava.bio.dp">StatePath</a></dt>
<dd>
<div class="block">Return the overall score for this state-path and it's emissions.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/twohead/PairDPMatrix.html#getScore()">getScore()</a></span> - Method in class org.biojava.bio.dp.twohead.<a href="./org/biojava/bio/dp/twohead/PairDPMatrix.html" title="class in org.biojava.bio.dp.twohead">PairDPMatrix</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFRecord.html#getScore()">getScore()</a></span> - Method in interface org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFRecord.html" title="interface in org.biojava.bio.program.gff">GFFRecord</a></dt>
<dd>
<div class="block">The score of the feature.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/SimpleGFFRecord.html#getScore()">getScore()</a></span> - Method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/SimpleGFFRecord.html" title="class in org.biojava.bio.program.gff">SimpleGFFRecord</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff3/GFF3Record.html#getScore()">getScore()</a></span> - Method in interface org.biojava.bio.program.gff3.<a href="./org/biojava/bio/program/gff3/GFF3Record.html" title="interface in org.biojava.bio.program.gff3">GFF3Record</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff3/GFF3Record.Impl.html#getScore()">getScore()</a></span> - Method in class org.biojava.bio.program.gff3.<a href="./org/biojava/bio/program/gff3/GFF3Record.Impl.html" title="class in org.biojava.bio.program.gff3">GFF3Record.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SeqSimilaritySearchHit.html#getScore()">getScore()</a></span> - Method in interface org.biojava.bio.search.<a href="./org/biojava/bio/search/SeqSimilaritySearchHit.html" title="interface in org.biojava.bio.search">SeqSimilaritySearchHit</a></dt>
<dd>
<div class="block">Return the overall score of this hit in the units defined by the
search algorithm.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SeqSimilaritySearchSubHit.html#getScore()">getScore()</a></span> - Method in interface org.biojava.bio.search.<a href="./org/biojava/bio/search/SeqSimilaritySearchSubHit.html" title="interface in org.biojava.bio.search">SeqSimilaritySearchSubHit</a></dt>
<dd>
<div class="block">Return the score of this sub-hit in the units defined by the
search algorithm.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SequenceDBSearchHit.html#getScore()">getScore()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SequenceDBSearchHit.html" title="class in org.biojava.bio.search">SequenceDBSearchHit</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SequenceDBSearchSubHit.html#getScore()">getScore()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SequenceDBSearchSubHit.html" title="class in org.biojava.bio.search">SequenceDBSearchSubHit</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SimpleSeqSimilaritySearchHit.html#getScore()">getScore()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SimpleSeqSimilaritySearchHit.html" title="class in org.biojava.bio.search">SimpleSeqSimilaritySearchHit</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SimpleSeqSimilaritySearchSubHit.html#getScore()">getScore()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SimpleSeqSimilaritySearchSubHit.html" title="class in org.biojava.bio.search">SimpleSeqSimilaritySearchSubHit</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/homol/SimilarityPairFeature.html#getScore()">getScore()</a></span> - Method in interface org.biojava.bio.seq.homol.<a href="./org/biojava/bio/seq/homol/SimilarityPairFeature.html" title="interface in org.biojava.bio.seq.homol">SimilarityPairFeature</a></dt>
<dd>
<div class="block"><code>getScore</code> returns the alignment score.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleSimilarityPairFeature.html#getScore()">getScore()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleSimilarityPairFeature.html" title="class in org.biojava.bio.seq.impl">SimpleSimilarityPairFeature</a></dt>
<dd>
<div class="block"><code>getScore</code> returns the alignment score.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVERelatedAnnot.html#getScore()">getScore()</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVERelatedAnnot.html" title="class in org.biojava.bio.seq.io.agave">AGAVERelatedAnnot</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/Alignable.html#getScore()">getScore()</a></span> - Method in interface org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/Alignable.html" title="interface in org.biojava.bio.structure.align.pairwise">Alignable</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/AlternativeAlignment.html#getScore()">getScore()</a></span> - Method in class org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/AlternativeAlignment.html" title="class in org.biojava.bio.structure.align.pairwise">AlternativeAlignment</a></dt>
<dd>
<div class="block">the alignment score</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/StrCompAlignment.html#getScore()">getScore()</a></span> - Method in class org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/StrCompAlignment.html" title="class in org.biojava.bio.structure.align.pairwise">StrCompAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/dasalignment/Alignment.html#getScoreAnnotationType()">getScoreAnnotationType()</a></span> - Static method in class org.biojava.bio.program.das.dasalignment.<a href="./org/biojava/bio/program/das/dasalignment/Alignment.html" title="class in org.biojava.bio.program.das.dasalignment">Alignment</a></dt>
<dd>
<div class="block">define the alignment Score Annotation Type.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/dasalignment/Alignment.html#getScores()">getScores()</a></span> - Method in class org.biojava.bio.program.das.dasalignment.<a href="./org/biojava/bio/program/das/dasalignment/Alignment.html" title="class in org.biojava.bio.program.das.dasalignment">Alignment</a></dt>
<dd>
<div class="block">get all "Score" Annotations.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SeqSimilaritySearcher.html#getSearchableDBs()">getSearchableDBs()</a></span> - Method in interface org.biojava.bio.search.<a href="./org/biojava/bio/search/SeqSimilaritySearcher.html" title="interface in org.biojava.bio.search">SeqSimilaritySearcher</a></dt>
<dd>
<div class="block">Return a set of all databases that can be searched with this
sequence similarity searcher.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/SeqSimilarityAdapter.html#getSearchContentHandler()">getSearchContentHandler()</a></span> - Method in class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/SeqSimilarityAdapter.html" title="class in org.biojava.bio.program.ssbind">SeqSimilarityAdapter</a></dt>
<dd>
<div class="block"><code>getSearchContentHandler</code> gets the handler which
will recieve the method calls generated by the adapter.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/SeqSimilarityStAXAdapter.html#getSearchContentHandler()">getSearchContentHandler()</a></span> - Method in class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/SeqSimilarityStAXAdapter.html" title="class in org.biojava.bio.program.ssbind">SeqSimilarityStAXAdapter</a></dt>
<dd>
<div class="block"><code>getSearchContentHandler</code> gets the handler which
will receive the method calls generated by the adapter.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SeqSimilaritySearchResult.html#getSearchParameters()">getSearchParameters()</a></span> - Method in interface org.biojava.bio.search.<a href="./org/biojava/bio/search/SeqSimilaritySearchResult.html" title="interface in org.biojava.bio.search">SeqSimilaritySearchResult</a></dt>
<dd>
<div class="block">Returns the search parameters used in the search that produced
this search result.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SequenceDBSearchResult.html#getSearchParameters()">getSearchParameters()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SequenceDBSearchResult.html" title="class in org.biojava.bio.search">SequenceDBSearchResult</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SimpleSeqSimilaritySearchResult.html#getSearchParameters()">getSearchParameters()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SimpleSeqSimilaritySearchResult.html" title="class in org.biojava.bio.search">SimpleSeqSimilaritySearchResult</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/BlastLikeSearchFilter.Node.html#getSearchProperty(java.lang.Object)">getSearchProperty(Object)</a></span> - Method in interface org.biojava.bio.search.<a href="./org/biojava/bio/search/BlastLikeSearchFilter.Node.html" title="interface in org.biojava.bio.search">BlastLikeSearchFilter.Node</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/FilteringContentHandler.html#getSearchProperty(java.lang.Object)">getSearchProperty(Object)</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/FilteringContentHandler.html" title="class in org.biojava.bio.search">FilteringContentHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PairwiseRenderContext.html#getSecondaryDirection()">getSecondaryDirection()</a></span> - Method in interface org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PairwiseRenderContext.html" title="interface in org.biojava.bio.gui.sequence">PairwiseRenderContext</a></dt>
<dd>
<div class="block"><code>getSecondaryDirection</code> returns the direction in
which the secondary sequence is rendered.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PairwiseSequencePanel.html#getSecondaryDirection()">getSecondaryDirection()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PairwiseSequencePanel.html" title="class in org.biojava.bio.gui.sequence">PairwiseSequencePanel</a></dt>
<dd>
<div class="block"><code>getSecondaryDirection</code> returns the direction in
which this context expects the secondary sequence to be
rendered - HORIZONTAL or VERTICAL.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SubPairwiseRenderContext.html#getSecondaryDirection()">getSecondaryDirection()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SubPairwiseRenderContext.html" title="class in org.biojava.bio.gui.sequence">SubPairwiseRenderContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PairwiseRenderContext.html#getSecondaryFeatures()">getSecondaryFeatures()</a></span> - Method in interface org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PairwiseRenderContext.html" title="interface in org.biojava.bio.gui.sequence">PairwiseRenderContext</a></dt>
<dd>
<div class="block"><code>getSecondaryFeatures</code> returns the features on the
secondary sequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PairwiseSequencePanel.html#getSecondaryFeatures()">getSecondaryFeatures()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PairwiseSequencePanel.html" title="class in org.biojava.bio.gui.sequence">PairwiseSequencePanel</a></dt>
<dd>
<div class="block"><code>getSecondaryFeatures</code> returns all of the
<code>Feature</code>s belonging to the currently rendered
secondary <code>Sequence</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SubPairwiseRenderContext.html#getSecondaryFeatures()">getSecondaryFeatures()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SubPairwiseRenderContext.html" title="class in org.biojava.bio.gui.sequence">SubPairwiseRenderContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PairwiseRenderContext.html#getSecondaryRange()">getSecondaryRange()</a></span> - Method in interface org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PairwiseRenderContext.html" title="interface in org.biojava.bio.gui.sequence">PairwiseRenderContext</a></dt>
<dd>
<div class="block"><code>getSecondaryRange</code> returns the range of the
secondary sequence currently rendered.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PairwiseSequencePanel.html#getSecondaryRange()">getSecondaryRange()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PairwiseSequencePanel.html" title="class in org.biojava.bio.gui.sequence">PairwiseSequencePanel</a></dt>
<dd>
<div class="block"><code>getSecondaryRange</code> returns a
<code>RangeLocation</code> representing the region of the
secondary sequence currently being rendered.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SubPairwiseRenderContext.html#getSecondaryRange()">getSecondaryRange()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SubPairwiseRenderContext.html" title="class in org.biojava.bio.gui.sequence">SubPairwiseRenderContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PairwiseSequencePanel.html#getSecondarySequence()">getSecondarySequence()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PairwiseSequencePanel.html" title="class in org.biojava.bio.gui.sequence">PairwiseSequencePanel</a></dt>
<dd>
<div class="block"><code>getSecondarySequence</code> returns the entire secondary
<code>Sequence</code> currently being rendered.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PairwiseRenderContext.html#getSecondarySymbols()">getSecondarySymbols()</a></span> - Method in interface org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PairwiseRenderContext.html" title="interface in org.biojava.bio.gui.sequence">PairwiseRenderContext</a></dt>
<dd>
<div class="block"><code>getSecondarySymbols</code> returns the symbols of the
secondary sequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PairwiseSequencePanel.html#getSecondarySymbols()">getSecondarySymbols()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PairwiseSequencePanel.html" title="class in org.biojava.bio.gui.sequence">PairwiseSequencePanel</a></dt>
<dd>
<div class="block"><code>getSecondarySymbols</code> returns all of the
<code>Symbol</code>s belonging to the currently rendered
secondary <code>Sequence</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SubPairwiseRenderContext.html#getSecondarySymbols()">getSecondarySymbols()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SubPairwiseRenderContext.html" title="class in org.biojava.bio.gui.sequence">SubPairwiseRenderContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PairwiseSequencePanel.html#getSecondarySymbolTranslation()">getSecondarySymbolTranslation()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PairwiseSequencePanel.html" title="class in org.biojava.bio.gui.sequence">PairwiseSequencePanel</a></dt>
<dd>
<div class="block"><code>getSecondarySymbolTranslation</code> returns the current
translation in <code>Symbol</code>s which will be applied when
rendering.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtCommentParser.Interaction.html#getSecondIntActID()">getSecondIntActID()</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtCommentParser.Interaction.html" title="class in org.biojavax.bio.seq.io">UniProtCommentParser.Interaction</a></dt>
<dd>
<div class="block">Getter for property secondIntActID.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/OrthoPair.html#getSecondOrthologue()">getSecondOrthologue()</a></span> - Method in interface org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/OrthoPair.html" title="interface in org.biojava.bio.program.homologene">OrthoPair</a></dt>
<dd>
<div class="block">gets the first orthologue in the orthology
relationship.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/SimpleOrthoPair.html#getSecondOrthologue()">getSecondOrthologue()</a></span> - Method in class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/SimpleOrthoPair.html" title="class in org.biojava.bio.program.homologene">SimpleOrthoPair</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Compound.html#getSecretion()">getSecretion()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure">Compound</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/AminoAcid.html#getSecStruc()">getSecStruc()</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/AminoAcid.html" title="interface in org.biojava.bio.structure">AminoAcid</a></dt>
<dd>
<div class="block">get secondary structure data .</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/AminoAcidImpl.html#getSecStruc()">getSecStruc()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/AminoAcidImpl.html" title="class in org.biojava.bio.structure">AminoAcidImpl</a></dt>
<dd>
<div class="block">get secondary structure data .</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/StrucAligParameters.html#getSeedFragmentLength()">getSeedFragmentLength()</a></span> - Method in class org.biojava.bio.structure.align.<a href="./org/biojava/bio/structure/align/StrucAligParameters.html" title="class in org.biojava.bio.structure.align">StrucAligParameters</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/StrucAligParameters.html#getSeedRmsdCutoff()">getSeedRmsdCutoff()</a></span> - Method in class org.biojava.bio.structure.align.<a href="./org/biojava/bio/structure/align/StrucAligParameters.html" title="class in org.biojava.bio.structure.align">StrucAligParameters</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/dasalignment/Alignment.html#getSegmentAnnotationType()">getSegmentAnnotationType()</a></span> - Static method in class org.biojava.bio.program.das.dasalignment.<a href="./org/biojava/bio/program/das/dasalignment/Alignment.html" title="class in org.biojava.bio.program.das.dasalignment">Alignment</a></dt>
<dd>
<div class="block">define the alignment Segment Annotation Type.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/JMatrixPanel.html#getSelectedAlignmentPos()">getSelectedAlignmentPos()</a></span> - Method in class org.biojava.bio.structure.gui.<a href="./org/biojava/bio/structure/gui/JMatrixPanel.html" title="class in org.biojava.bio.structure.gui">JMatrixPanel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/GeneticAlgorithm.html#getSelectionFunction()">getSelectionFunction()</a></span> - Method in interface org.biojavax.ga.<a href="./org/biojavax/ga/GeneticAlgorithm.html" title="interface in org.biojavax.ga">GeneticAlgorithm</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/impl/AbstractGeneticAlgorithm.html#getSelectionFunction()">getSelectionFunction()</a></span> - Method in class org.biojavax.ga.impl.<a href="./org/biojavax/ga/impl/AbstractGeneticAlgorithm.html" title="class in org.biojavax.ga.impl">AbstractGeneticAlgorithm</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/StructRefSeq.html#getSeq_align_beg()">getSeq_align_beg()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/StructRefSeq.html" title="class in org.biojava.bio.structure.io.mmcif.model">StructRefSeq</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/StructRefSeq.html#getSeq_align_end()">getSeq_align_end()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/StructRefSeq.html" title="class in org.biojava.bio.structure.io.mmcif.model">StructRefSeq</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/PdbxNonPolyScheme.html#getSeq_id()">getSeq_id()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/PdbxNonPolyScheme.html" title="class in org.biojava.bio.structure.io.mmcif.model">PdbxNonPolyScheme</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/PdbxPolySeqScheme.html#getSeq_id()">getSeq_id()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/PdbxPolySeqScheme.html" title="class in org.biojava.bio.structure.io.mmcif.model">PdbxPolySeqScheme</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/DBRef.html#getSeqBegin()">getSeqBegin()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/DBRef.html" title="class in org.biojava.bio.structure">DBRef</a></dt>
<dd>
<div class="block">Initial sequence number of the PDB sequence segment.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html#getSeqCautions()">getSeqCautions()</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html" title="class in org.biojavax.bio.seq.io">UniProtCommentParser</a></dt>
<dd>
<div class="block">Getter for property seqCautions.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleRemoteFeature.DBResolver.html#getSeqDB()">getSeqDB()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleRemoteFeature.DBResolver.html" title="class in org.biojava.bio.seq.impl">SimpleRemoteFeature.DBResolver</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/homol/HomologyDB.html#getSeqDBs()">getSeqDBs()</a></span> - Method in interface org.biojava.bio.seq.homol.<a href="./org/biojava/bio/seq/homol/HomologyDB.html" title="interface in org.biojava.bio.seq.homol">HomologyDB</a></dt>
<dd>
<div class="block">Retrieve the SeqDBs that have been searched against each other.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/DBRef.html#getSeqEnd()">getSeqEnd()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/DBRef.html" title="class in org.biojava.bio.structure">DBRef</a></dt>
<dd>
<div class="block">Ending sequence number of the PDB sequence segment.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/RemoteFeature.Region.html#getSeqID()">getSeqID()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/RemoteFeature.Region.html" title="class in org.biojava.bio.seq">RemoteFeature.Region</a></dt>
<dd>
<div class="block">Return the remote Sequence ID if this Region is on another Sequence
(isRemote will return true), null otherwise.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/Meme.html#getSeqIDs()">getSeqIDs()</a></span> - Method in class org.biojava.bio.program.<a href="./org/biojava/bio/program/Meme.html" title="class in org.biojava.bio.program">Meme</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOEventEmitter.html#getSeqIOEvents(org.biojava.bio.seq.Sequence, org.biojava.bio.seq.io.SeqIOListener)">getSeqIOEvents(Sequence, SeqIOListener)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOEventEmitter.html" title="class in org.biojava.bio.seq.io">SeqIOEventEmitter</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block"><code>getSeqIOEvents</code> scans a <code>Sequence</code>
object and sends events describing its data to the
<code>SeqIOListener</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFRecord.html#getSeqName()">getSeqName()</a></span> - Method in interface org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFRecord.html" title="interface in org.biojava.bio.program.gff">GFFRecord</a></dt>
<dd>
<div class="block">The sequence name field.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFRecordFilter.SequenceFilter.html#getSeqName()">getSeqName()</a></span> - Method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFRecordFilter.SequenceFilter.html" title="class in org.biojava.bio.program.gff">GFFRecordFilter.SequenceFilter</a></dt>
<dd>
<div class="block">Retrieve the current sequence name.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/SimpleGFFRecord.html#getSeqName()">getSeqName()</a></span> - Method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/SimpleGFFRecord.html" title="class in org.biojava.bio.program.gff">SimpleGFFRecord</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/util/CoordManager.html#getSeqPos(int)">getSeqPos(int)</a></span> - Method in class org.biojava.bio.structure.gui.util.<a href="./org/biojava/bio/structure/gui/util/CoordManager.html" title="class in org.biojava.bio.structure.gui.util">CoordManager</a></dt>
<dd>
<div class="block">start counting at 0...</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Chain.html#getSeqResGroup(int)">getSeqResGroup(int)</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Chain.html" title="interface in org.biojava.bio.structure">Chain</a></dt>
<dd>
<div class="block">return the Group at position X.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/ChainImpl.html#getSeqResGroup(int)">getSeqResGroup(int)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/ChainImpl.html" title="class in org.biojava.bio.structure">ChainImpl</a></dt>
<dd>
<div class="block">return the Group at position X.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Chain.html#getSeqResGroups(java.lang.String)">getSeqResGroups(String)</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Chain.html" title="interface in org.biojava.bio.structure">Chain</a></dt>
<dd>
<div class="block">Return a List of all groups of a special type (e.g.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Chain.html#getSeqResGroups()">getSeqResGroups()</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Chain.html" title="interface in org.biojava.bio.structure">Chain</a></dt>
<dd>
<div class="block">Return all groups of this chain.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/ChainImpl.html#getSeqResGroups(java.lang.String)">getSeqResGroups(String)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/ChainImpl.html" title="class in org.biojava.bio.structure">ChainImpl</a></dt>
<dd>
<div class="block">Return a List of all groups of a special type (e.g.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/ChainImpl.html#getSeqResGroups()">getSeqResGroups()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/ChainImpl.html" title="class in org.biojava.bio.structure">ChainImpl</a></dt>
<dd>
<div class="block">Return all groups of this chain.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Chain.html#getSeqResLength()">getSeqResLength()</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Chain.html" title="interface in org.biojava.bio.structure">Chain</a></dt>
<dd>
<div class="block">Returns the number of groups in the SEQRES records of the chain.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/ChainImpl.html#getSeqResLength()">getSeqResLength()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/ChainImpl.html" title="class in org.biojava.bio.structure">ChainImpl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Chain.html#getSeqResSequence()">getSeqResSequence()</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Chain.html" title="interface in org.biojava.bio.structure">Chain</a></dt>
<dd>
<div class="block">Get the sequence for all amino acids as it is specified in the SEQRES residues.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/ChainImpl.html#getSeqResSequence()">getSeqResSequence()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/ChainImpl.html" title="class in org.biojava.bio.structure">ChainImpl</a></dt>
<dd>
<div class="block">Get the sequence for all amino acids as it is specified in the SEQRES residues.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/CircularRendererPanel.html#getSequence()">getSequence()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/CircularRendererPanel.html" title="class in org.biojava.bio.gui.sequence">CircularRendererPanel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PairwiseSequencePanel.html#getSequence()">getSequence()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PairwiseSequencePanel.html" title="class in org.biojava.bio.gui.sequence">PairwiseSequencePanel</a></dt>
<dd>
<div class="block"><code>getSequence</code> returns the entire
<code>Sequence</code> currently being rendered.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePanel.html#getSequence()">getSequence()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePanel.html" title="class in org.biojava.bio.gui.sequence">SequencePanel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePanelWrapper.html#getSequence()">getSequence()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePanelWrapper.html" title="class in org.biojava.bio.gui.sequence">SequencePanelWrapper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePoster.html#getSequence()">getSequence()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePoster.html" title="class in org.biojava.bio.gui.sequence">SequencePoster</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/TranslatedSequencePanel.html#getSequence()">getSequence()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/TranslatedSequencePanel.html" title="class in org.biojava.bio.gui.sequence">TranslatedSequencePanel</a></dt>
<dd>
<div class="block"><code>getSequence</code> returns the entire
<code>Sequence</code> currently being rendered.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/abi/ABITrace.html#getSequence()">getSequence()</a></span> - Method in class org.biojava.bio.program.abi.<a href="./org/biojava/bio/program/abi/ABITrace.html" title="class in org.biojava.bio.program.abi">ABITrace</a></dt>
<dd>
<div class="block">Returns the original programatically determined (unedited) sequence as a <code>SymbolList</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/DASSequenceDB.html#getSequence(java.lang.String)">getSequence(String)</a></span> - Method in class org.biojava.bio.program.das.<a href="./org/biojava/bio/program/das/DASSequenceDB.html" title="class in org.biojava.bio.program.das">DASSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/fastq/Fastq.html#getSequence()">getSequence()</a></span> - Method in class org.biojava.bio.program.fastq.<a href="./org/biojava/bio/program/fastq/Fastq.html" title="class in org.biojava.bio.program.fastq">Fastq</a></dt>
<dd>
<div class="block">Return the sequence for this FASTQ formatted sequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/Digest.html#getSequence()">getSequence()</a></span> - Method in class org.biojava.bio.proteomics.<a href="./org/biojava/bio/proteomics/Digest.html" title="class in org.biojava.bio.proteomics">Digest</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/AnnotatedSequenceDB.html#getSequence(java.lang.String)">getSequence(String)</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/AnnotatedSequenceDB.html" title="class in org.biojava.bio.seq.db">AnnotatedSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/biofetch/BioFetchSequenceDB.html#getSequence(java.lang.String)">getSequence(String)</a></span> - Method in class org.biojava.bio.seq.db.biofetch.<a href="./org/biojava/bio/seq/db/biofetch/BioFetchSequenceDB.html" title="class in org.biojava.bio.seq.db.biofetch">BioFetchSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/biosql/BioSQLSequenceDB.html#getSequence(java.lang.String)">getSequence(String)</a></span> - Method in class org.biojava.bio.seq.db.biosql.<a href="./org/biojava/bio/seq/db/biosql/BioSQLSequenceDB.html" title="class in org.biojava.bio.seq.db.biosql">BioSQLSequenceDB</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/biosql/BioSQLSequenceDB.html#getSequence(int)">getSequence(int)</a></span> - Method in class org.biojava.bio.seq.db.biosql.<a href="./org/biojava/bio/seq/db/biosql/BioSQLSequenceDB.html" title="class in org.biojava.bio.seq.db.biosql">BioSQLSequenceDB</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/CachingSequenceDB.html#getSequence(java.lang.String)">getSequence(String)</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/CachingSequenceDB.html" title="class in org.biojava.bio.seq.db">CachingSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/DummySequenceDB.html#getSequence(java.lang.String)">getSequence(String)</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/DummySequenceDB.html" title="class in org.biojava.bio.seq.db">DummySequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/flat/FlatSequenceDB.html#getSequence(java.lang.String)">getSequence(String)</a></span> - Method in class org.biojava.bio.seq.db.flat.<a href="./org/biojava/bio/seq/db/flat/FlatSequenceDB.html" title="class in org.biojava.bio.seq.db.flat">FlatSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/GenbankSequenceDB.html#getSequence(java.lang.String)">getSequence(String)</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/GenbankSequenceDB.html" title="class in org.biojava.bio.seq.db">GenbankSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/GenpeptSequenceDB.html#getSequence(java.lang.String)">getSequence(String)</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/GenpeptSequenceDB.html" title="class in org.biojava.bio.seq.db">GenpeptSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/HashSequenceDB.html#getSequence(java.lang.String)">getSequence(String)</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/HashSequenceDB.html" title="class in org.biojava.bio.seq.db">HashSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/IndexedSequenceDB.html#getSequence(java.lang.String)">getSequence(String)</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/IndexedSequenceDB.html" title="class in org.biojava.bio.seq.db">IndexedSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/SequenceDBLite.html#getSequence(java.lang.String)">getSequence(String)</a></span> - Method in interface org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/SequenceDBLite.html" title="interface in org.biojava.bio.seq.db">SequenceDBLite</a></dt>
<dd>
<div class="block">Retrieve a single sequence by its id.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/SubSequenceDB.html#getSequence(java.lang.String)">getSequence(String)</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/SubSequenceDB.html" title="class in org.biojava.bio.seq.db">SubSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/SwissprotSequenceDB.html#getSequence(java.lang.String)">getSequence(String)</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/SwissprotSequenceDB.html" title="class in org.biojava.bio.seq.db">SwissprotSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/ViewingSequenceDB.html#getSequence(java.lang.String)">getSequence(String)</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/ViewingSequenceDB.html" title="class in org.biojava.bio.seq.db">ViewingSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/WebSequenceDB.html#getSequence(java.lang.String)">getSequence(String)</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/WebSequenceDB.html" title="class in org.biojava.bio.seq.db">WebSequenceDB</a></dt>
<dd>
<div class="block">Gets a sequence using its unique ID (eg for GenBank this would be the GI number)</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/distributed/DistDataSource.html#getSequence(java.lang.String)">getSequence(String)</a></span> - Method in interface org.biojava.bio.seq.distributed.<a href="./org/biojava/bio/seq/distributed/DistDataSource.html" title="interface in org.biojava.bio.seq.distributed">DistDataSource</a></dt>
<dd>
<div class="block">Get a Sequence object for an ID.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/distributed/DistributedSequenceDB.html#getSequence(java.lang.String)">getSequence(String)</a></span> - Method in class org.biojava.bio.seq.distributed.<a href="./org/biojava/bio/seq/distributed/DistributedSequenceDB.html" title="class in org.biojava.bio.seq.distributed">DistributedSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/distributed/GFFDataSource.html#getSequence(java.lang.String)">getSequence(String)</a></span> - Method in class org.biojava.bio.seq.distributed.<a href="./org/biojava/bio/seq/distributed/GFFDataSource.html" title="class in org.biojava.bio.seq.distributed">GFFDataSource</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/distributed/SequenceDBDataSource.html#getSequence(java.lang.String)">getSequence(String)</a></span> - Method in class org.biojava.bio.seq.distributed.<a href="./org/biojava/bio/seq/distributed/SequenceDBDataSource.html" title="class in org.biojava.bio.seq.distributed">SequenceDBDataSource</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/Feature.html#getSequence()">getSequence()</a></span> - Method in interface org.biojava.bio.seq.<a href="./org/biojava/bio/seq/Feature.html" title="interface in org.biojava.bio.seq">Feature</a></dt>
<dd>
<div class="block">Return the <code>Sequence</code> object to which this feature
is (ultimately) attached.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleFeature.html#getSequence()">getSequence()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleFeature.html" title="class in org.biojava.bio.seq.impl">SimpleFeature</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SubSequence.html#getSequence()">getSequence()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SubSequence.html" title="class in org.biojava.bio.seq.impl">SubSequence</a></dt>
<dd>
<div class="block">Return the parent sequence of which this is a partial view</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/projection/ProjectedFeature.html#getSequence()">getSequence()</a></span> - Method in class org.biojava.bio.seq.projection.<a href="./org/biojava/bio/seq/projection/ProjectedFeature.html" title="class in org.biojava.bio.seq.projection">ProjectedFeature</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/projection/ProjectionContext.html#getSequence(org.biojava.bio.seq.Feature)">getSequence(Feature)</a></span> - Method in interface org.biojava.bio.seq.projection.<a href="./org/biojava/bio/seq/projection/ProjectionContext.html" title="interface in org.biojava.bio.seq.projection">ProjectionContext</a></dt>
<dd>
<div class="block">Get the sequence for a feature.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/projection/ReparentContext.html#getSequence(org.biojava.bio.seq.Feature)">getSequence(Feature)</a></span> - Method in class org.biojava.bio.seq.projection.<a href="./org/biojava/bio/seq/projection/ReparentContext.html" title="class in org.biojava.bio.seq.projection">ReparentContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Chain.html#getSequence()">getSequence()</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Chain.html" title="interface in org.biojava.bio.structure">Chain</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>use getAtomSequence instead</i></div>
</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/ChainImpl.html#getSequence()">getSequence()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/ChainImpl.html" title="class in org.biojava.bio.structure">ChainImpl</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>use getAtomSequence instead</i></div>
</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/AbstractRichSequenceDB.html#getSequence(java.lang.String)">getSequence(String)</a></span> - Method in class org.biojavax.bio.db.<a href="./org/biojavax/bio/db/AbstractRichSequenceDB.html" title="class in org.biojavax.bio.db">AbstractRichSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtCommentParser.SeqCaution.html#getSequence()">getSequence()</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtCommentParser.SeqCaution.html" title="class in org.biojavax.bio.seq.io">UniProtCommentParser.SeqCaution</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichFeature.html#getSequence()">getSequence()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichFeature.html" title="class in org.biojavax.bio.seq">SimpleRichFeature</a></dt>
<dd>
<div class="block">Return the <code>Sequence</code> object to which this feature
is (ultimately) attached.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/DASSequenceDBProvider.html#getSequenceDB(java.util.Map)">getSequenceDB(Map)</a></span> - Method in class org.biojava.bio.program.das.<a href="./org/biojava/bio/program/das/DASSequenceDBProvider.html" title="class in org.biojava.bio.program.das">DASSequenceDBProvider</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SeqSimilaritySearchResult.html#getSequenceDB()">getSequenceDB()</a></span> - Method in interface org.biojava.bio.search.<a href="./org/biojava/bio/search/SeqSimilaritySearchResult.html" title="interface in org.biojava.bio.search">SeqSimilaritySearchResult</a></dt>
<dd>
<div class="block">Returns the sequence database against which the search was
performed.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SequenceDBSearchResult.html#getSequenceDB()">getSequenceDB()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SequenceDBSearchResult.html" title="class in org.biojava.bio.search">SequenceDBSearchResult</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SimpleSeqSimilaritySearchResult.html#getSequenceDB()">getSequenceDB()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SimpleSeqSimilaritySearchResult.html" title="class in org.biojava.bio.search">SimpleSeqSimilaritySearchResult</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/biofetch/BioFetchSequenceDBProvider.html#getSequenceDB(java.util.Map)">getSequenceDB(Map)</a></span> - Method in class org.biojava.bio.seq.db.biofetch.<a href="./org/biojava/bio/seq/db/biofetch/BioFetchSequenceDBProvider.html" title="class in org.biojava.bio.seq.db.biofetch">BioFetchSequenceDBProvider</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/biosql/BioSQLSequenceDBProvider.html#getSequenceDB(java.util.Map)">getSequenceDB(Map)</a></span> - Method in class org.biojava.bio.seq.db.biosql.<a href="./org/biojava/bio/seq/db/biosql/BioSQLSequenceDBProvider.html" title="class in org.biojava.bio.seq.db.biosql">BioSQLSequenceDBProvider</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/DummySequenceDBInstallation.html#getSequenceDB(java.lang.String)">getSequenceDB(String)</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/DummySequenceDBInstallation.html" title="class in org.biojava.bio.seq.db">DummySequenceDBInstallation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/flat/FlatSequenceDBProvider.html#getSequenceDB(java.util.Map)">getSequenceDB(Map)</a></span> - Method in class org.biojava.bio.seq.db.flat.<a href="./org/biojava/bio/seq/db/flat/FlatSequenceDBProvider.html" title="class in org.biojava.bio.seq.db.flat">FlatSequenceDBProvider</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/SequenceDBInstallation.html#getSequenceDB(java.lang.String)">getSequenceDB(String)</a></span> - Method in interface org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/SequenceDBInstallation.html" title="interface in org.biojava.bio.seq.db">SequenceDBInstallation</a></dt>
<dd>
<div class="block">
Return the SequenceDB for the given identifier.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/SimpleSequenceDBInstallation.html#getSequenceDB(java.lang.String)">getSequenceDB(String)</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/SimpleSequenceDBInstallation.html" title="class in org.biojava.bio.seq.db">SimpleSequenceDBInstallation</a></dt>
<dd>
<div class="block">If the given identifier is known to this sequence db installation
because it has been used in a call to addSequenceDB(), then this
method returns the SequenceDB associated with this
identifier.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/directory/SequenceDBProvider.html#getSequenceDB(java.util.Map)">getSequenceDB(Map)</a></span> - Method in interface org.biojava.directory.<a href="./org/biojava/directory/SequenceDBProvider.html" title="interface in org.biojava.directory">SequenceDBProvider</a></dt>
<dd>
<div class="block">Get a sequence database.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/DummySequenceDBInstallation.html#getSequenceDBs()">getSequenceDBs()</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/DummySequenceDBInstallation.html" title="class in org.biojava.bio.seq.db">DummySequenceDBInstallation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/SequenceDBInstallation.html#getSequenceDBs()">getSequenceDBs()</a></span> - Method in interface org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/SequenceDBInstallation.html" title="interface in org.biojava.bio.seq.db">SequenceDBInstallation</a></dt>
<dd>
<div class="block">Return all sequence dbs available in this sequence db
installation.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/SimpleSequenceDBInstallation.html#getSequenceDBs()">getSequenceDBs()</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/SimpleSequenceDBInstallation.html" title="class in org.biojava.bio.seq.db">SimpleSequenceDBInstallation</a></dt>
<dd>
<div class="block">Return a newly created set of the SequenceDB objects that were
already created through method addSequenceDB().</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/indexdb/BioStoreFactory.html#getSequenceFormat()">getSequenceFormat()</a></span> - Method in class org.biojava.bio.program.indexdb.<a href="./org/biojava/bio/program/indexdb/BioStoreFactory.html" title="class in org.biojava.bio.program.indexdb">BioStoreFactory</a></dt>
<dd>
<div class="block"><code>getSequenceFormat</code> returns the current sequence
format name.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/GenbankSequenceDB.html#getSequenceFormat()">getSequenceFormat()</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/GenbankSequenceDB.html" title="class in org.biojava.bio.seq.db">GenbankSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/GenpeptSequenceDB.html#getSequenceFormat()">getSequenceFormat()</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/GenpeptSequenceDB.html" title="class in org.biojava.bio.seq.db">GenpeptSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/NCBISequenceDB.html#getSequenceFormat()">getSequenceFormat()</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/NCBISequenceDB.html" title="class in org.biojava.bio.seq.db">NCBISequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/SwissprotSequenceDB.html#getSequenceFormat()">getSequenceFormat()</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/SwissprotSequenceDB.html" title="class in org.biojava.bio.seq.db">SwissprotSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/WebSequenceDB.html#getSequenceFormat()">getSequenceFormat()</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/WebSequenceDB.html" title="class in org.biojava.bio.seq.db">WebSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOTools.html#getSequenceFormat(int)">getSequenceFormat(int)</a></span> - Static method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOTools.html" title="class in org.biojava.bio.seq.io">SeqIOTools</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block"><code>getSequenceFormat</code> accepts a value which represents
a sequence format and returns the relevant
<code>SequenceFormat</code> object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff3/GFF3Record.html#getSequenceID()">getSequenceID()</a></span> - Method in interface org.biojava.bio.program.gff3.<a href="./org/biojava/bio/program/gff3/GFF3Record.html" title="interface in org.biojava.bio.program.gff3">GFF3Record</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff3/GFF3Record.Impl.html#getSequenceID()">getSequenceID()</a></span> - Method in class org.biojava.bio.program.gff3.<a href="./org/biojava/bio/program/gff3/GFF3Record.Impl.html" title="class in org.biojava.bio.program.gff3">GFF3Record.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEAnnotFilter.html#getSequenceId(org.biojava.bio.Annotation)">getSequenceId(Annotation)</a></span> - Method in interface org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEAnnotFilter.html" title="interface in org.biojava.bio.seq.io.agave">AGAVEAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/SimpleAnnotFilter.html#getSequenceId(org.biojava.bio.Annotation)">getSequenceId(Annotation)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/SimpleAnnotFilter.html" title="class in org.biojava.bio.seq.io.agave">SimpleAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/AbstractChromatogram.html#getSequenceLength()">getSequenceLength()</a></span> - Method in class org.biojava.bio.chromatogram.<a href="./org/biojava/bio/chromatogram/AbstractChromatogram.html" title="class in org.biojava.bio.chromatogram">AbstractChromatogram</a></dt>
<dd>
<div class="block">Return the sequence length.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/Chromatogram.html#getSequenceLength()">getSequenceLength()</a></span> - Method in interface org.biojava.bio.chromatogram.<a href="./org/biojava/bio/chromatogram/Chromatogram.html" title="interface in org.biojava.bio.chromatogram">Chromatogram</a></dt>
<dd>
<div class="block">Returns the number of bases called by whatever base-calling software
analyzed the chromatogram as loaded.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/abi/ABITrace.html#getSequenceLength()">getSequenceLength()</a></span> - Method in class org.biojava.bio.program.abi.<a href="./org/biojava/bio/program/abi/ABITrace.html" title="class in org.biojava.bio.program.abi">ABITrace</a></dt>
<dd>
<div class="block">Returns the length of the sequence (number of bases) in this trace.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game12/GAMESeqHandler.html#getSequenceLength()">getSequenceLength()</a></span> - Method in class org.biojava.bio.seq.io.game12.<a href="./org/biojava/bio/seq/io/game12/GAMESeqHandler.html" title="class in org.biojava.bio.seq.io.game12">GAMESeqHandler</a></dt>
<dd>
<div class="block">Gets the sequenceLength attribute of the GAMESeqHandler object</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichSequence.html#getSequenceLength()">getSequenceLength()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichSequence.html" title="class in org.biojavax.bio.seq">SimpleRichSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/ThinRichSequence.html#getSequenceLength()">getSequenceLength()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/ThinRichSequence.html" title="class in org.biojavax.bio.seq">ThinRichSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.BySequenceName.html#getSequenceName()">getSequenceName()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.BySequenceName.html" title="class in org.biojava.bio.seq">FeatureFilter.BySequenceName</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.BySequenceName.html#getSequenceName()">getSequenceName()</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.BySequenceName.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.BySequenceName</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/OffsetRulerRenderer.html#getSequenceOffset()">getSequenceOffset()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/OffsetRulerRenderer.html" title="class in org.biojava.bio.gui.sequence">OffsetRulerRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtCommentParser.Isoform.html#getSequenceRef()">getSequenceRef()</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtCommentParser.Isoform.html" title="class in org.biojavax.bio.seq.io">UniProtCommentParser.Isoform</a></dt>
<dd>
<div class="block">Getter for property sequenceRef.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/GenbankSequenceDB.html#getSequences(java.util.Set)">getSequences(Set)</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/GenbankSequenceDB.html" title="class in org.biojava.bio.seq.db">GenbankSequenceDB</a></dt>
<dd>
<div class="block">Retrieve sequences from a Genbank</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/GenbankSequenceDB.html#getSequences(java.util.Set, org.biojava.bio.seq.db.SequenceDB)">getSequences(Set, SequenceDB)</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/GenbankSequenceDB.html" title="class in org.biojava.bio.seq.db">GenbankSequenceDB</a></dt>
<dd>
<div class="block">Retrieve sequences from a Genbank</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEChromosomeHandler.html#getSequences()">getSequences()</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEChromosomeHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEChromosomeHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEHandler.html#getSequences()">getSequences()</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEHandler</a></dt>
<dd>
<div class="block">get all the top level sequences
bio_sequence --> SimpleSequence
contig --> SimpleAssembly
--> SimpleSequence( if only one sequence )
chromosome -> SimpleAssembly
-> SimpleSequence( if only one sequence)</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtCommentParser.Isoform.html#getSequenceType()">getSequenceType()</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtCommentParser.Isoform.html" title="class in org.biojavax.bio.seq.io">UniProtCommentParser.Isoform</a></dt>
<dd>
<div class="block">Getter for property sequenceType.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.html#getSeqVersion()">getSeqVersion()</a></span> - Method in interface org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.html" title="interface in org.biojavax.bio.seq">RichSequence</a></dt>
<dd>
<div class="block">The version of the associated symbol list.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/ThinRichSequence.html#getSeqVersion()">getSeqVersion()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/ThinRichSequence.html" title="class in org.biojavax.bio.seq">ThinRichSequence</a></dt>
<dd>
<div class="block">The version of the associated symbol list.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/SSBond.html#getSerNum()">getSerNum()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/SSBond.html" title="class in org.biojava.bio.structure">SSBond</a></dt>
<dd>
<div class="block">set serial number of this SSBOND in PDB file</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/dasalignment/DASAlignmentCall.html#getServerurl()">getServerurl()</a></span> - Method in class org.biojava.bio.program.das.dasalignment.<a href="./org/biojava/bio/program/das/dasalignment/DASAlignmentCall.html" title="class in org.biojava.bio.program.das.dasalignment">DASAlignmentCall</a></dt>
<dd>
<div class="block">get url of alignment service.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/dasstructure/DASStructureCall.html#getServerurl()">getServerurl()</a></span> - Method in class org.biojava.bio.program.das.dasstructure.<a href="./org/biojava/bio/program/das/dasstructure/DASStructureCall.html" title="class in org.biojava.bio.program.das.dasstructure">DASStructureCall</a></dt>
<dd>
<div class="block">get url of structure service.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/glyph/GlyphUtils.html#getShape(java.util.List, java.util.List)">getShape(List, List)</a></span> - Static method in class org.biojava.bio.gui.glyph.<a href="./org/biojava/bio/gui/glyph/GlyphUtils.html" title="class in org.biojava.bio.gui.glyph">GlyphUtils</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/glyph/GlyphUtils.html#getShape(java.util.List)">getShape(List)</a></span> - Static method in class org.biojava.bio.gui.glyph.<a href="./org/biojava/bio/gui/glyph/GlyphUtils.html" title="class in org.biojava.bio.gui.glyph">GlyphUtils</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/glyph/GlyphUtils.html#getShape(int[], int[])">getShape(int[], int[])</a></span> - Static method in class org.biojava.bio.gui.glyph.<a href="./org/biojava/bio/gui/glyph/GlyphUtils.html" title="class in org.biojava.bio.gui.glyph">GlyphUtils</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/SequencesAsGFF.html#getShatter()">getShatter()</a></span> - Method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/SequencesAsGFF.html" title="class in org.biojava.bio.program.gff">SequencesAsGFF</a></dt>
<dd>
<div class="block">Determine if features with non-contiguous locations will be broken into
multiple GFF records.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/AlternativeAlignment.html#getShift()">getShift()</a></span> - Method in class org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/AlternativeAlignment.html" title="class in org.biojava.bio.structure.align.pairwise">AlternativeAlignment</a></dt>
<dd>
<div class="block">returns the shift vector that has to be applied on structure to to shift on structure one</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/io/LargeBuffer.html#getShort(long)">getShort(long)</a></span> - Method in class org.biojava.utils.io.<a href="./org/biojava/utils/io/LargeBuffer.html" title="class in org.biojava.utils.io">LargeBuffer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/io/LargeBuffer.html#getShort()">getShort()</a></span> - Method in class org.biojava.utils.io.<a href="./org/biojava/utils/io/LargeBuffer.html" title="class in org.biojava.utils.io">LargeBuffer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/homol/SimilarityPairFeature.html#getSibling()">getSibling()</a></span> - Method in interface org.biojava.bio.seq.homol.<a href="./org/biojava/bio/seq/homol/SimilarityPairFeature.html" title="interface in org.biojava.bio.seq.homol">SimilarityPairFeature</a></dt>
<dd>
<div class="block"><code>getSibling</code> returns the sibling
<code>Feature</code>, query for subject and vice versa.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleSimilarityPairFeature.html#getSibling()">getSibling()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleSimilarityPairFeature.html" title="class in org.biojava.bio.seq.impl">SimpleSimilarityPairFeature</a></dt>
<dd>
<div class="block"><code>getSibling</code> returns the sibling feature of the
pair.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/AbstractChromatogram.html#getSignificantBits()">getSignificantBits()</a></span> - Method in class org.biojava.bio.chromatogram.<a href="./org/biojava/bio/chromatogram/AbstractChromatogram.html" title="class in org.biojava.bio.chromatogram">AbstractChromatogram</a></dt>
<dd>
<div class="block">Return the number of significant bits.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/Chromatogram.html#getSignificantBits()">getSignificantBits()</a></span> - Method in interface org.biojava.bio.chromatogram.<a href="./org/biojava/bio/chromatogram/Chromatogram.html" title="interface in org.biojava.bio.chromatogram">Chromatogram</a></dt>
<dd>
<div class="block">Returns the number of bits of the traces which are significant.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/OrthoPair.html#getSimilarity()">getSimilarity()</a></span> - Method in interface org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/OrthoPair.html" title="interface in org.biojava.bio.program.homologene">OrthoPair</a></dt>
<dd>
<div class="block">gets the second orthologue in the
orthology relationship.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/SimpleOrthoPair.html#getSimilarity()">getSimilarity()</a></span> - Method in class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/SimpleOrthoPair.html" title="class in org.biojava.bio.program.homologene">SimpleOrthoPair</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/jama/SingularValueDecomposition.html#getSingularValues()">getSingularValues()</a></span> - Method in class org.biojava.bio.structure.jama.<a href="./org/biojava/bio/structure/jama/SingularValueDecomposition.html" title="class in org.biojava.bio.structure.jama">SingularValueDecomposition</a></dt>
<dd>
<div class="block">Return the one-dimensional array of singular values</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePanel.Border.html#getSize()">getSize()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePanel.Border.html" title="class in org.biojava.bio.gui.sequence">SequencePanel.Border</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePoster.Border.html#getSize()">getSize()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePoster.Border.html" title="class in org.biojava.bio.gui.sequence">SequencePoster.Border</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequenceRenderContext.Border.html#getSize()">getSize()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequenceRenderContext.Border.html" title="class in org.biojava.bio.gui.sequence">SequenceRenderContext.Border</a></dt>
<dd>
<div class="block">Gets the current size of the border in pixels.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/process/ExternalProcess.html#getSleepTime()">getSleepTime()</a></span> - Method in class org.biojava.utils.process.<a href="./org/biojava/utils/process/ExternalProcess.html" title="class in org.biojava.utils.process">ExternalProcess</a></dt>
<dd>
<div class="block">Gets the number of milliseconds the <a href="./org/biojava/utils/process/ExternalProcess.html#execute(java.util.Properties)">ExternalProcess.execute(Properties)</a>
method should pauses after the external process is terminated.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#getSolvent_model_details()">getSolvent_model_details()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#getSolvent_model_param_bsol()">getSolvent_model_param_bsol()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#getSolvent_model_param_ksol()">getSolvent_model_param_ksol()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFRecord.html#getSource()">getSource()</a></span> - Method in interface org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFRecord.html" title="interface in org.biojava.bio.program.gff">GFFRecord</a></dt>
<dd>
<div class="block">The source, or creator of this feature.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFRecordFilter.SourceFilter.html#getSource()">getSource()</a></span> - Method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFRecordFilter.SourceFilter.html" title="class in org.biojava.bio.program.gff">GFFRecordFilter.SourceFilter</a></dt>
<dd>
<div class="block">Retrieve the current source.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/SimpleGFFRecord.html#getSource()">getSource()</a></span> - Method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/SimpleGFFRecord.html" title="class in org.biojava.bio.program.gff">SimpleGFFRecord</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff3/GFF3Record.html#getSource()">getSource()</a></span> - Method in interface org.biojava.bio.program.gff3.<a href="./org/biojava/bio/program/gff3/GFF3Record.html" title="interface in org.biojava.bio.program.gff3">GFF3Record</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff3/GFF3Record.Impl.html#getSource()">getSource()</a></span> - Method in class org.biojava.bio.program.gff3.<a href="./org/biojava/bio/program/gff3/GFF3Record.Impl.html" title="class in org.biojava.bio.program.gff3">GFF3Record.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/Feature.html#getSource()">getSource()</a></span> - Method in interface org.biojava.bio.seq.<a href="./org/biojava/bio/seq/Feature.html" title="interface in org.biojava.bio.seq">Feature</a></dt>
<dd>
<div class="block">The source of the feature.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.BySource.html#getSource()">getSource()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.BySource.html" title="class in org.biojava.bio.seq">FeatureFilter.BySource</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleFeature.html#getSource()">getSource()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleFeature.html" title="class in org.biojava.bio.seq.impl">SimpleFeature</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEMapLocation.html#getSource()">getSource()</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEMapLocation.html" title="class in org.biojava.bio.seq.io.agave">AGAVEMapLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ChangeForwarder.html#getSource()">getSource()</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/ChangeForwarder.html" title="class in org.biojava.utils">ChangeForwarder</a></dt>
<dd>
<div class="block">Retrieve the 'source' object for <code>ChangeEvent</code>s fired by this forwarder.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichFeature.html#getSource()">getSource()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichFeature.html" title="class in org.biojavax.bio.seq">SimpleRichFeature</a></dt>
<dd>
<div class="block">The source of the feature.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AbstractManyToOneTranslationTable.html#getSourceAlphabet()">getSourceAlphabet()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AbstractManyToOneTranslationTable.html" title="class in org.biojava.bio.symbol">AbstractManyToOneTranslationTable</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AbstractReversibleTranslationTable.html#getSourceAlphabet()">getSourceAlphabet()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AbstractReversibleTranslationTable.html" title="class in org.biojava.bio.symbol">AbstractReversibleTranslationTable</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleManyToOneTranslationTable.html#getSourceAlphabet()">getSourceAlphabet()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleManyToOneTranslationTable.html" title="class in org.biojava.bio.symbol">SimpleManyToOneTranslationTable</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleReversibleTranslationTable.html#getSourceAlphabet()">getSourceAlphabet()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleReversibleTranslationTable.html" title="class in org.biojava.bio.symbol">SimpleReversibleTranslationTable</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleTranslationTable.html#getSourceAlphabet()">getSourceAlphabet()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleTranslationTable.html" title="class in org.biojava.bio.symbol">SimpleTranslationTable</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/TranslationTable.html#getSourceAlphabet()">getSourceAlphabet()</a></span> - Method in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/TranslationTable.html" title="interface in org.biojava.bio.symbol">TranslationTable</a></dt>
<dd>
<div class="block">The alphabet of Symbols that can be translated.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/xff/FeatureHandler.html#getSourceHandler()">getSourceHandler()</a></span> - Method in class org.biojava.bio.program.xff.<a href="./org/biojava/bio/program/xff/FeatureHandler.html" title="class in org.biojava.bio.program.xff">FeatureHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/GappedSymbolList.html#getSourceSymbolList()">getSourceSymbolList()</a></span> - Method in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/GappedSymbolList.html" title="interface in org.biojava.bio.symbol">GappedSymbolList</a></dt>
<dd>
<div class="block">Return the underlying (ungapped) SymbolList.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleGappedSymbolList.html#getSourceSymbolList()">getSourceSymbolList()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleGappedSymbolList.html" title="class in org.biojava.bio.symbol">SimpleGappedSymbolList</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/Feature.html#getSourceTerm()">getSourceTerm()</a></span> - Method in interface org.biojava.bio.seq.<a href="./org/biojava/bio/seq/Feature.html" title="interface in org.biojava.bio.seq">Feature</a></dt>
<dd>
<div class="block">An ontology term defining the source of this feature.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleFeature.html#getSourceTerm()">getSourceTerm()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleFeature.html" title="class in org.biojava.bio.seq.impl">SimpleFeature</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.BySourceTerm.html#getSourceTerm()">getSourceTerm()</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.BySourceTerm.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.BySourceTerm</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichFeature.html#getSourceTerm()">getSourceTerm()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichFeature.html" title="class in org.biojavax.bio.seq">SimpleRichFeature</a></dt>
<dd>
<div class="block">An ontology term defining the source of this feature.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.BySourceTermName.html#getSourceTermName()">getSourceTermName()</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.BySourceTermName.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.BySourceTermName</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePoster.html#getSpacer()">getSpacer()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePoster.html" title="class in org.biojava.bio.gui.sequence">SequencePoster</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Retrieve the current spacer value</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/unigene/UnigeneTools.html#getSpeciesForShortName(java.lang.String)">getSpeciesForShortName(String)</a></span> - Static method in class org.biojava.bio.program.unigene.<a href="./org/biojava/bio/program/unigene/UnigeneTools.html" title="class in org.biojava.bio.program.unigene">UnigeneTools</a></dt>
<dd>
<div class="block">Converts short species names (like Hs) to long species names (like Homo
Sapiens).</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.Terms.html#getSpeciesTerm()">getSpeciesTerm()</a></span> - Static method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.Terms.html" title="class in org.biojavax.bio.seq">RichSequence.Terms</a></dt>
<dd>
<div class="block">Getter for the Species term</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/LineSplitParser.html#getSplitOffset()">getSplitOffset()</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/LineSplitParser.html" title="class in org.biojava.bio.program.tagvalue">LineSplitParser</a></dt>
<dd>
<div class="block">Get the current offset at which lines are split.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/ChangeTable.html#getSplitter(java.lang.Object)">getSplitter(Object)</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/ChangeTable.html" title="class in org.biojava.bio.program.tagvalue">ChangeTable</a></dt>
<dd>
<div class="block">Get the Splitter currently registered to handle a tag.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Entity.html#getSrc_method()">getSrc_method()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Entity.html" title="class in org.biojava.bio.structure.io.mmcif.model">Entity</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Structure.html#getSSBonds()">getSSBonds()</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Structure.html" title="interface in org.biojava.bio.structure">Structure</a></dt>
<dd>
<div class="block">get the list of SSBonds as they have been defined in the PDB files</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/StructureImpl.html#getSSBonds()">getSSBonds()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/StructureImpl.html" title="class in org.biojava.bio.structure">StructureImpl</a></dt>
<dd>
<div class="block">get the list of SSBonds as they have been defined in the PDB files</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/SimpleSymbolStyle.html#getStandardFillPaints(org.biojava.bio.symbol.Alphabet)">getStandardFillPaints(Alphabet)</a></span> - Static method in class org.biojava.bio.gui.<a href="./org/biojava/bio/gui/SimpleSymbolStyle.html" title="class in org.biojava.bio.gui">SimpleSymbolStyle</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/SimpleSymbolStyle.html#getStandardOutlinePaints(org.biojava.bio.symbol.Alphabet)">getStandardOutlinePaints(Alphabet)</a></span> - Static method in class org.biojava.bio.gui.<a href="./org/biojava/bio/gui/SimpleSymbolStyle.html" title="class in org.biojava.bio.gui">SimpleSymbolStyle</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFRecord.html#getStart()">getStart()</a></span> - Method in interface org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFRecord.html" title="interface in org.biojava.bio.program.gff">GFFRecord</a></dt>
<dd>
<div class="block">The start of this feature within the source sequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/SimpleGFFRecord.html#getStart()">getStart()</a></span> - Method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/SimpleGFFRecord.html" title="class in org.biojava.bio.program.gff">SimpleGFFRecord</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff3/GFF3Record.html#getStart()">getStart()</a></span> - Method in interface org.biojava.bio.program.gff3.<a href="./org/biojava/bio/program/gff3/GFF3Record.html" title="interface in org.biojava.bio.program.gff3">GFF3Record</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff3/GFF3Record.Impl.html#getStart()">getStart()</a></span> - Method in class org.biojava.bio.program.gff3.<a href="./org/biojava/bio/program/gff3/GFF3Record.Impl.html" title="class in org.biojava.bio.program.gff3">GFF3Record.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/Index.html#getStart()">getStart()</a></span> - Method in interface org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/Index.html" title="interface in org.biojava.bio.seq.db">Index</a></dt>
<dd>
<div class="block">Skipping this number of bytes through the file should put the file pointer
to the first byte of the sequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/SimpleIndex.html#getStart()">getStart()</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/SimpleIndex.html" title="class in org.biojava.bio.seq.db">SimpleIndex</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SubSequence.html#getStart()">getStart()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SubSequence.html" title="class in org.biojava.bio.seq.impl">SubSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEMatchRegion.html#getStart()">getStart()</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEMatchRegion.html" title="class in org.biojava.bio.seq.io.agave">AGAVEMatchRegion</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEQueryRegion.html#getStart()">getStart()</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEQueryRegion.html" title="class in org.biojava.bio.seq.io.agave">AGAVEQueryRegion</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/automata/FiniteAutomaton.html#getStart()">getStart()</a></span> - Method in class org.biojava.utils.automata.<a href="./org/biojava/utils/automata/FiniteAutomaton.html" title="class in org.biojava.utils.automata">FiniteAutomaton</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/automata/NfaBuilder.html#getStart()">getStart()</a></span> - Method in interface org.biojava.utils.automata.<a href="./org/biojava/utils/automata/NfaBuilder.html" title="interface in org.biojava.utils.automata">NfaBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/automata/NfaSubModel.html#getStart()">getStart()</a></span> - Method in class org.biojava.utils.automata.<a href="./org/biojava/utils/automata/NfaSubModel.html" title="class in org.biojava.utils.automata">NfaSubModel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/automata/StateMachineInstance.html#getStart()">getStart()</a></span> - Method in interface org.biojava.utils.automata.<a href="./org/biojava/utils/automata/StateMachineInstance.html" title="interface in org.biojava.utils.automata">StateMachineInstance</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/Position.html#getStart()">getStart()</a></span> - Method in interface org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/Position.html" title="interface in org.biojavax.bio.seq">Position</a></dt>
<dd>
<div class="block">Returns the beginning of the range of bases this base could lie in.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimplePosition.html#getStart()">getStart()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimplePosition.html" title="class in org.biojavax.bio.seq">SimplePosition</a></dt>
<dd>
<div class="block">Returns the beginning of the range of bases this base could lie in.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/RankedDocRef.html#getStart()">getStart()</a></span> - Method in interface org.biojavax.<a href="./org/biojavax/RankedDocRef.html" title="interface in org.biojavax">RankedDocRef</a></dt>
<dd>
<div class="block">The start position in the sequence that this reference is referred to from.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleRankedDocRef.html#getStart()">getStart()</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleRankedDocRef.html" title="class in org.biojavax">SimpleRankedDocRef</a></dt>
<dd>
<div class="block">The start position in the sequence that this reference is referred to from.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/JournalArticle.html#getStartPage()">getStartPage()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/JournalArticle.html" title="class in org.biojava.bio.structure">JournalArticle</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/StateMachine.html#getState(java.lang.String)">getState(String)</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/StateMachine.html" title="class in org.biojava.bio.program.tagvalue">StateMachine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/DP.html#getStates()">getStates()</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/DP.html" title="class in org.biojava.bio.dp">DP</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/DatabasePDBrev.html#getStatus()">getStatus()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/DatabasePDBrev.html" title="class in org.biojava.bio.structure.io.mmcif.model">DatabasePDBrev</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.Terms.html#getStatusDateTerm()">getStatusDateTerm()</a></span> - Static method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.Terms.html" title="class in org.biojavax.bio.seq.io">EMBLxmlFormat.Terms</a></dt>
<dd>
<div class="block">Getter for the StatusDate term</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.Terms.html#getStatusTerm()">getStatusTerm()</a></span> - Static method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.Terms.html" title="class in org.biojavax.bio.seq.io">EMBLxmlFormat.Terms</a></dt>
<dd>
<div class="block">Getter for the Status term</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/filterxml/XMLFilterHandler.html#getStAXContentHandler()">getStAXContentHandler()</a></span> - Method in class org.biojava.bio.seq.io.filterxml.<a href="./org/biojava/bio/seq/io/filterxml/XMLFilterHandler.html" title="class in org.biojava.bio.seq.io.filterxml">XMLFilterHandler</a></dt>
<dd>
<div class="block">Return a StAXContentHandler which can deal with any FilterXML construct known to this class.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/indexdb/BioStoreFactory.html#getStoreLocation()">getStoreLocation()</a></span> - Method in class org.biojava.bio.program.indexdb.<a href="./org/biojava/bio/program/indexdb/BioStoreFactory.html" title="class in org.biojava.bio.program.indexdb">BioStoreFactory</a></dt>
<dd>
<div class="block"><code>getStoreLocation</code> returns the directory of the bew
index.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/indexdb/BioStoreFactory.html#getStoreName()">getStoreName()</a></span> - Method in class org.biojava.bio.program.indexdb.<a href="./org/biojava/bio/program/indexdb/BioStoreFactory.html" title="class in org.biojava.bio.program.indexdb">BioStoreFactory</a></dt>
<dd>
<div class="block"><code>getStoreName</code> returns the name to be given to the
new index.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Compound.html#getStrain()">getStrain()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure">Compound</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.Terms.html#getStrainTerm()">getStrainTerm()</a></span> - Static method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.Terms.html" title="class in org.biojavax.bio.seq">RichSequence.Terms</a></dt>
<dd>
<div class="block">Getter for the Strain term</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFRecord.html#getStrand()">getStrand()</a></span> - Method in interface org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFRecord.html" title="interface in org.biojava.bio.program.gff">GFFRecord</a></dt>
<dd>
<div class="block">The strand of the feature.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFRecordFilter.StrandFilter.html#getStrand()">getStrand()</a></span> - Method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFRecordFilter.StrandFilter.html" title="class in org.biojava.bio.program.gff">GFFRecordFilter.StrandFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/SimpleGFFRecord.html#getStrand()">getStrand()</a></span> - Method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/SimpleGFFRecord.html" title="class in org.biojava.bio.program.gff">SimpleGFFRecord</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff3/GFF3Record.html#getStrand()">getStrand()</a></span> - Method in interface org.biojava.bio.program.gff3.<a href="./org/biojava/bio/program/gff3/GFF3Record.html" title="interface in org.biojava.bio.program.gff3">GFF3Record</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff3/GFF3Record.Impl.html#getStrand()">getStrand()</a></span> - Method in class org.biojava.bio.program.gff3.<a href="./org/biojava/bio/program/gff3/GFF3Record.Impl.html" title="class in org.biojava.bio.program.gff3">GFF3Record.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.StrandFilter.html#getStrand()">getStrand()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.StrandFilter.html" title="class in org.biojava.bio.seq">FeatureFilter.StrandFilter</a></dt>
<dd>
<div class="block">Retrieve the strand this matches.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FramedFeature.html#getStrand()">getStrand()</a></span> - Method in interface org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FramedFeature.html" title="interface in org.biojava.bio.seq">FramedFeature</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleStrandedFeature.html#getStrand()">getStrand()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleStrandedFeature.html" title="class in org.biojava.bio.seq.impl">SimpleStrandedFeature</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/StrandedFeature.html#getStrand()">getStrand()</a></span> - Method in interface org.biojava.bio.seq.<a href="./org/biojava/bio/seq/StrandedFeature.html" title="interface in org.biojava.bio.seq">StrandedFeature</a></dt>
<dd>
<div class="block">Retrieve the strand that this feature lies upon.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByStrand.html#getStrand()">getStrand()</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByStrand.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.ByStrand</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/EmptyRichLocation.html#getStrand()">getStrand()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/EmptyRichLocation.html" title="class in org.biojavax.bio.seq">EmptyRichLocation</a></dt>
<dd>
<div class="block">Retrieves the strand associated with this location.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/MultiSourceCompoundRichLocation.html#getStrand()">getStrand()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/MultiSourceCompoundRichLocation.html" title="class in org.biojavax.bio.seq">MultiSourceCompoundRichLocation</a></dt>
<dd>
<div class="block">Retrieves the strand associated with this location.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichLocation.html#getStrand()">getStrand()</a></span> - Method in interface org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichLocation.html" title="interface in org.biojavax.bio.seq">RichLocation</a></dt>
<dd>
<div class="block">Retrieves the strand associated with this location.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichFeature.html#getStrand()">getStrand()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichFeature.html" title="class in org.biojavax.bio.seq">SimpleRichFeature</a></dt>
<dd>
<div class="block">Retrieve the strand that this feature lies upon.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichLocation.html#getStrand()">getStrand()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichLocation.html" title="class in org.biojavax.bio.seq">SimpleRichLocation</a></dt>
<dd>
<div class="block">Retrieves the strand associated with this location.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/xff/StrandedFeatureHandler.html#getStrandedFeatureTemplate()">getStrandedFeatureTemplate()</a></span> - Method in class org.biojava.bio.program.xff.<a href="./org/biojava/bio/program/xff/StrandedFeatureHandler.html" title="class in org.biojava.bio.program.xff">StrandedFeatureHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.Terms.html#getStrandedTerm()">getStrandedTerm()</a></span> - Static method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.Terms.html" title="class in org.biojavax.bio.seq">RichSequence.Terms</a></dt>
<dd>
<div class="block">Getter for the Strand term; legal values are "single", "double", and
"mixed".</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichSequence.html#getStringSequence()">getStringSequence()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichSequence.html" title="class in org.biojavax.bio.seq">SimpleRichSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/dasstructure/DASStructureCall.html#getStructure(java.lang.String)">getStructure(String)</a></span> - Method in class org.biojava.bio.program.das.dasstructure.<a href="./org/biojava/bio/program/das/dasstructure/DASStructureCall.html" title="class in org.biojava.bio.program.das.dasstructure">DASStructureCall</a></dt>
<dd>
<div class="block">connect to a DAS structure service and retreive 3D data.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/StructureTools.html#getStructure()">getStructure()</a></span> - Method in class org.biojava.bio.proteomics.<a href="./org/biojava/bio/proteomics/StructureTools.html" title="class in org.biojava.bio.proteomics">StructureTools</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/SimpleMMcifConsumer.html#getStructure()">getStructure()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/SimpleMMcifConsumer.html" title="class in org.biojava.bio.structure.io.mmcif">SimpleMMcifConsumer</a></dt>
<dd>
<div class="block">This method will return the parsed protein structure, once the parsing has been finished</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/MMCIFFileReader.html#getStructure(java.lang.String)">getStructure(String)</a></span> - Method in class org.biojava.bio.structure.io.<a href="./org/biojava/bio/structure/io/MMCIFFileReader.html" title="class in org.biojava.bio.structure.io">MMCIFFileReader</a></dt>
<dd>
<div class="block">Opens filename, parses it and returns
a Structure object .</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/MMCIFFileReader.html#getStructure(java.io.File)">getStructure(File)</a></span> - Method in class org.biojava.bio.structure.io.<a href="./org/biojava/bio/structure/io/MMCIFFileReader.html" title="class in org.biojava.bio.structure.io">MMCIFFileReader</a></dt>
<dd>
<div class="block">Opens filename, parses it and returns a Structure object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/PDBFileReader.html#getStructure(java.lang.String)">getStructure(String)</a></span> - Method in class org.biojava.bio.structure.io.<a href="./org/biojava/bio/structure/io/PDBFileReader.html" title="class in org.biojava.bio.structure.io">PDBFileReader</a></dt>
<dd>
<div class="block">opens filename, parses it and returns
aStructure object .</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/PDBFileReader.html#getStructure(java.io.File)">getStructure(File)</a></span> - Method in class org.biojava.bio.structure.io.<a href="./org/biojava/bio/structure/io/PDBFileReader.html" title="class in org.biojava.bio.structure.io">PDBFileReader</a></dt>
<dd>
<div class="block">opens filename, parses it and returns a Structure object</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/StructureIOFile.html#getStructure(java.lang.String)">getStructure(String)</a></span> - Method in interface org.biojava.bio.structure.io.<a href="./org/biojava/bio/structure/io/StructureIOFile.html" title="interface in org.biojava.bio.structure.io">StructureIOFile</a></dt>
<dd>
<div class="block">open filename and returns
a Structure object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/StructureIOFile.html#getStructure(java.io.File)">getStructure(File)</a></span> - Method in interface org.biojava.bio.structure.io.<a href="./org/biojava/bio/structure/io/StructureIOFile.html" title="interface in org.biojava.bio.structure.io">StructureIOFile</a></dt>
<dd>
<div class="block">read file from File and returns
a Structure object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/server/FlatFileInstallation.html#getStructure(java.lang.String)">getStructure(String)</a></span> - Method in class org.biojava.bio.structure.server.<a href="./org/biojava/bio/structure/server/FlatFileInstallation.html" title="class in org.biojava.bio.structure.server">FlatFileInstallation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/server/MMCIFFileInstallation.html#getStructure(java.lang.String)">getStructure(String)</a></span> - Method in class org.biojava.bio.structure.server.<a href="./org/biojava/bio/structure/server/MMCIFFileInstallation.html" title="class in org.biojava.bio.structure.server">MMCIFFileInstallation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/server/PDBInstallation.html#getStructure(java.lang.String)">getStructure(String)</a></span> - Method in interface org.biojava.bio.structure.server.<a href="./org/biojava/bio/structure/server/PDBInstallation.html" title="interface in org.biojava.bio.structure.server">PDBInstallation</a></dt>
<dd>
<div class="block">request a structure by its PDB identifier</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/server/StructureEvent.html#getStructure()">getStructure()</a></span> - Method in interface org.biojava.bio.structure.server.<a href="./org/biojava/bio/structure/server/StructureEvent.html" title="interface in org.biojava.bio.structure.server">StructureEvent</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/server/StructureEventImpl.html#getStructure()">getStructure()</a></span> - Method in class org.biojava.bio.structure.server.<a href="./org/biojava/bio/structure/server/StructureEventImpl.html" title="class in org.biojava.bio.structure.server">StructureEventImpl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/util/PDBDirPanel.html#getStructure1()">getStructure1()</a></span> - Method in class org.biojava.bio.structure.gui.util.<a href="./org/biojava/bio/structure/gui/util/PDBDirPanel.html" title="class in org.biojava.bio.structure.gui.util">PDBDirPanel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/util/PDBServerPanel.html#getStructure1()">getStructure1()</a></span> - Method in class org.biojava.bio.structure.gui.util.<a href="./org/biojava/bio/structure/gui/util/PDBServerPanel.html" title="class in org.biojava.bio.structure.gui.util">PDBServerPanel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/util/PDBUploadPanel.html#getStructure1()">getStructure1()</a></span> - Method in class org.biojava.bio.structure.gui.util.<a href="./org/biojava/bio/structure/gui/util/PDBUploadPanel.html" title="class in org.biojava.bio.structure.gui.util">PDBUploadPanel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/util/StructurePairSelector.html#getStructure1()">getStructure1()</a></span> - Method in interface org.biojava.bio.structure.gui.util.<a href="./org/biojava/bio/structure/gui/util/StructurePairSelector.html" title="interface in org.biojava.bio.structure.gui.util">StructurePairSelector</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/util/PDBDirPanel.html#getStructure2()">getStructure2()</a></span> - Method in class org.biojava.bio.structure.gui.util.<a href="./org/biojava/bio/structure/gui/util/PDBDirPanel.html" title="class in org.biojava.bio.structure.gui.util">PDBDirPanel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/util/PDBServerPanel.html#getStructure2()">getStructure2()</a></span> - Method in class org.biojava.bio.structure.gui.util.<a href="./org/biojava/bio/structure/gui/util/PDBServerPanel.html" title="class in org.biojava.bio.structure.gui.util">PDBServerPanel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/util/PDBUploadPanel.html#getStructure2()">getStructure2()</a></span> - Method in class org.biojava.bio.structure.gui.util.<a href="./org/biojava/bio/structure/gui/util/PDBUploadPanel.html" title="class in org.biojava.bio.structure.gui.util">PDBUploadPanel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/util/StructurePairSelector.html#getStructure2()">getStructure2()</a></span> - Method in interface org.biojava.bio.structure.gui.util.<a href="./org/biojava/bio/structure/gui/util/StructurePairSelector.html" title="interface in org.biojava.bio.structure.gui.util">StructurePairSelector</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/DASStructureClient.html#getStructureById(java.lang.String)">getStructureById(String)</a></span> - Method in class org.biojava.bio.structure.io.<a href="./org/biojava/bio/structure/io/DASStructureClient.html" title="class in org.biojava.bio.structure.io">DASStructureClient</a></dt>
<dd>
<div class="block">if pdb code is set (setId):
connect to a DAS-structure service and retreive data.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/MMCIFFileReader.html#getStructureById(java.lang.String)">getStructureById(String)</a></span> - Method in class org.biojava.bio.structure.io.<a href="./org/biojava/bio/structure/io/MMCIFFileReader.html" title="class in org.biojava.bio.structure.io">MMCIFFileReader</a></dt>
<dd>
<div class="block">Get a structure by PDB code.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/PDBFileReader.html#getStructureById(java.lang.String)">getStructureById(String)</a></span> - Method in class org.biojava.bio.structure.io.<a href="./org/biojava/bio/structure/io/PDBFileReader.html" title="class in org.biojava.bio.structure.io">PDBFileReader</a></dt>
<dd>
<div class="block">load a structure from local file system and return a PDBStructure object</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/PDBMSDReader.html#getStructureById(java.lang.String)">getStructureById(String)</a></span> - Method in class org.biojava.bio.structure.io.<a href="./org/biojava/bio/structure/io/PDBMSDReader.html" title="class in org.biojava.bio.structure.io">PDBMSDReader</a></dt>
<dd>
<div class="block">Get a structure by providing a PDB code.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/PDBSRSReader.html#getStructureById(java.lang.String)">getStructureById(String)</a></span> - Method in class org.biojava.bio.structure.io.<a href="./org/biojava/bio/structure/io/PDBSRSReader.html" title="class in org.biojava.bio.structure.io">PDBSRSReader</a></dt>
<dd>
<div class="block">load a structure from from SRS installation using wgetz
returns null if no structure found</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/StructureIO.html#getStructureById(java.lang.String)">getStructureById(String)</a></span> - Method in interface org.biojava.bio.structure.io.<a href="./org/biojava/bio/structure/io/StructureIO.html" title="interface in org.biojava.bio.structure.io">StructureIO</a></dt>
<dd>
<div class="block">Get a structure by providing a PDB code.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/server/StructureFetcherRunnable.html#getStructureListeners()">getStructureListeners()</a></span> - Method in class org.biojava.bio.structure.server.<a href="./org/biojava/bio/structure/server/StructureFetcherRunnable.html" title="class in org.biojava.bio.structure.server">StructureFetcherRunnable</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/SequenceDisplay.html#getStructurePairAligner()">getStructurePairAligner()</a></span> - Method in class org.biojava.bio.structure.gui.<a href="./org/biojava/bio/structure/gui/SequenceDisplay.html" title="class in org.biojava.bio.structure.gui">SequenceDisplay</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/DistributionLogo.html#getStyle()">getStyle()</a></span> - Method in class org.biojava.bio.gui.<a href="./org/biojava/bio/gui/DistributionLogo.html" title="class in org.biojava.bio.gui">DistributionLogo</a></dt>
<dd>
<div class="block">Retrieve the current style.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/LogoContext.html#getStyle()">getStyle()</a></span> - Method in interface org.biojava.bio.gui.<a href="./org/biojava/bio/gui/LogoContext.html" title="interface in org.biojava.bio.gui">LogoContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/blast2html/AbstractAlignmentStyler.html#getStyle(java.lang.String, java.lang.String, java.lang.String[])">getStyle(String, String, String[])</a></span> - Method in class org.biojava.bio.program.blast2html.<a href="./org/biojava/bio/program/blast2html/AbstractAlignmentStyler.html" title="class in org.biojava.bio.program.blast2html">AbstractAlignmentStyler</a></dt>
<dd>
<div class="block">
Return the styles for the two aligned characters.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/blast2html/SimpleAlignmentStyler.html#getStyle(java.lang.String, java.lang.String, java.lang.String[])">getStyle(String, String, String[])</a></span> - Method in class org.biojava.bio.program.blast2html.<a href="./org/biojava/bio/program/blast2html/SimpleAlignmentStyler.html" title="class in org.biojava.bio.program.blast2html">SimpleAlignmentStyler</a></dt>
<dd>
<div class="block">Returns the styles for the two aligned characters in the form
of predefined font classes.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/DoubleAlphabet.html#getSubAlphabet(double, double)">getSubAlphabet(double, double)</a></span> - Static method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/DoubleAlphabet.html" title="class in org.biojava.bio.symbol">DoubleAlphabet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/IntegerAlphabet.html#getSubAlphabet(int, int)">getSubAlphabet(int, int)</a></span> - Static method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/IntegerAlphabet.html" title="class in org.biojava.bio.symbol">IntegerAlphabet</a></dt>
<dd>
<div class="block">Construct a finite contiguous subset of the <code>IntegerAlphabet</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PairwiseFilteringRenderer.html#getSubContext(org.biojava.bio.gui.sequence.PairwiseRenderContext)">getSubContext(PairwiseRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PairwiseFilteringRenderer.html" title="class in org.biojava.bio.gui.sequence">PairwiseFilteringRenderer</a></dt>
<dd>
<div class="block"><code>getSubContext</code> creates a new context which has
<code>FeatureHolder</code>s filtered using the current filter.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/BlastLikeSearchFilter.Node.html#getSubHitProperty(java.lang.Object)">getSubHitProperty(Object)</a></span> - Method in interface org.biojava.bio.search.<a href="./org/biojava/bio/search/BlastLikeSearchFilter.Node.html" title="interface in org.biojava.bio.search">BlastLikeSearchFilter.Node</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/FilteringContentHandler.html#getSubHitProperty(java.lang.Object)">getSubHitProperty(Object)</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/FilteringContentHandler.html" title="class in org.biojava.bio.search">FilteringContentHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SeqSimilaritySearchHit.html#getSubHits()">getSubHits()</a></span> - Method in interface org.biojava.bio.search.<a href="./org/biojava/bio/search/SeqSimilaritySearchHit.html" title="interface in org.biojava.bio.search">SeqSimilaritySearchHit</a></dt>
<dd>
<div class="block">Return all sub-hits for this sequence similarity search
hit.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SequenceDBSearchHit.html#getSubHits()">getSubHits()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SequenceDBSearchHit.html" title="class in org.biojava.bio.search">SequenceDBSearchHit</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SimpleSeqSimilaritySearchHit.html#getSubHits()">getSubHits()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SimpleSeqSimilaritySearchHit.html" title="class in org.biojava.bio.search">SimpleSeqSimilaritySearchHit</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/Triple.html#getSubject()">getSubject()</a></span> - Method in interface org.biojava.ontology.<a href="./org/biojava/ontology/Triple.html" title="interface in org.biojava.ontology">Triple</a></dt>
<dd>
<div class="block">Return the subject term of this triple</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/Triple.Impl.html#getSubject()">getSubject()</a></span> - Method in class org.biojava.ontology.<a href="./org/biojava/ontology/Triple.Impl.html" title="class in org.biojava.ontology">Triple.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/BioEntryRelationship.html#getSubject()">getSubject()</a></span> - Method in interface org.biojavax.bio.<a href="./org/biojavax/bio/BioEntryRelationship.html" title="interface in org.biojavax.bio">BioEntryRelationship</a></dt>
<dd>
<div class="block">Returns the subject of this relationship (ie.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichFeatureRelationship.html#getSubject()">getSubject()</a></span> - Method in interface org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichFeatureRelationship.html" title="interface in org.biojavax.bio.seq">RichFeatureRelationship</a></dt>
<dd>
<div class="block">Gets the feature that this relationship refers to.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichFeatureRelationship.html#getSubject()">getSubject()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichFeatureRelationship.html" title="class in org.biojavax.bio.seq">SimpleRichFeatureRelationship</a></dt>
<dd>
<div class="block">Gets the feature that this relationship refers to.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/SimpleBioEntryRelationship.html#getSubject()">getSubject()</a></span> - Method in class org.biojavax.bio.<a href="./org/biojavax/bio/SimpleBioEntryRelationship.html" title="class in org.biojavax.bio">SimpleBioEntryRelationship</a></dt>
<dd>
<div class="block">Returns the subject of this relationship (ie.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ontology/SimpleComparableTriple.html#getSubject()">getSubject()</a></span> - Method in class org.biojavax.ontology.<a href="./org/biojavax/ontology/SimpleComparableTriple.html" title="class in org.biojavax.ontology">SimpleComparableTriple</a></dt>
<dd>
<div class="block">Return the subject term of this triple</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/ViewSequenceFactory.html#getSubjectDBInstallation()">getSubjectDBInstallation()</a></span> - Method in class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/ViewSequenceFactory.html" title="class in org.biojava.bio.program.ssbind">ViewSequenceFactory</a></dt>
<dd>
<div class="block"><code>getSubjectDBInstallation</code> returns the installation
in which all the databases searched may be
found.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SeqSimilaritySearchHit.html#getSubjectEnd()">getSubjectEnd()</a></span> - Method in interface org.biojava.bio.search.<a href="./org/biojava/bio/search/SeqSimilaritySearchHit.html" title="interface in org.biojava.bio.search">SeqSimilaritySearchHit</a></dt>
<dd>
<div class="block">Return the end position of the last sub-hit in the subject
sequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SeqSimilaritySearchSubHit.html#getSubjectEnd()">getSubjectEnd()</a></span> - Method in interface org.biojava.bio.search.<a href="./org/biojava/bio/search/SeqSimilaritySearchSubHit.html" title="interface in org.biojava.bio.search">SeqSimilaritySearchSubHit</a></dt>
<dd>
<div class="block">Return the start position of the sub-hit in the subject
sequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SequenceDBSearchHit.html#getSubjectEnd()">getSubjectEnd()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SequenceDBSearchHit.html" title="class in org.biojava.bio.search">SequenceDBSearchHit</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SequenceDBSearchSubHit.html#getSubjectEnd()">getSubjectEnd()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SequenceDBSearchSubHit.html" title="class in org.biojava.bio.search">SequenceDBSearchSubHit</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SimpleSeqSimilaritySearchHit.html#getSubjectEnd()">getSubjectEnd()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SimpleSeqSimilaritySearchHit.html" title="class in org.biojava.bio.search">SimpleSeqSimilaritySearchHit</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SimpleSeqSimilaritySearchSubHit.html#getSubjectEnd()">getSubjectEnd()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SimpleSeqSimilaritySearchSubHit.html" title="class in org.biojava.bio.search">SimpleSeqSimilaritySearchSubHit</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SeqSimilaritySearchHit.html#getSubjectID()">getSubjectID()</a></span> - Method in interface org.biojava.bio.search.<a href="./org/biojava/bio/search/SeqSimilaritySearchHit.html" title="interface in org.biojava.bio.search">SeqSimilaritySearchHit</a></dt>
<dd>
<div class="block">The sequence identifier of this hit within the sequence
database against which the search was performed.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SequenceDBSearchHit.html#getSubjectID()">getSubjectID()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SequenceDBSearchHit.html" title="class in org.biojava.bio.search">SequenceDBSearchHit</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SimpleSeqSimilaritySearchHit.html#getSubjectID()">getSubjectID()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SimpleSeqSimilaritySearchHit.html" title="class in org.biojava.bio.search">SimpleSeqSimilaritySearchHit</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SeqSimilaritySearchHit.html#getSubjectStart()">getSubjectStart()</a></span> - Method in interface org.biojava.bio.search.<a href="./org/biojava/bio/search/SeqSimilaritySearchHit.html" title="interface in org.biojava.bio.search">SeqSimilaritySearchHit</a></dt>
<dd>
<div class="block">Return the start position of the first sub-hit in the subject
sequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SeqSimilaritySearchSubHit.html#getSubjectStart()">getSubjectStart()</a></span> - Method in interface org.biojava.bio.search.<a href="./org/biojava/bio/search/SeqSimilaritySearchSubHit.html" title="interface in org.biojava.bio.search">SeqSimilaritySearchSubHit</a></dt>
<dd>
<div class="block">Return the start position of the sub-hit in the subject
sequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SequenceDBSearchHit.html#getSubjectStart()">getSubjectStart()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SequenceDBSearchHit.html" title="class in org.biojava.bio.search">SequenceDBSearchHit</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SequenceDBSearchSubHit.html#getSubjectStart()">getSubjectStart()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SequenceDBSearchSubHit.html" title="class in org.biojava.bio.search">SequenceDBSearchSubHit</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SimpleSeqSimilaritySearchHit.html#getSubjectStart()">getSubjectStart()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SimpleSeqSimilaritySearchHit.html" title="class in org.biojava.bio.search">SimpleSeqSimilaritySearchHit</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SimpleSeqSimilaritySearchSubHit.html#getSubjectStart()">getSubjectStart()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SimpleSeqSimilaritySearchSubHit.html" title="class in org.biojava.bio.search">SimpleSeqSimilaritySearchSubHit</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SeqSimilaritySearchHit.html#getSubjectStrand()">getSubjectStrand()</a></span> - Method in interface org.biojava.bio.search.<a href="./org/biojava/bio/search/SeqSimilaritySearchHit.html" title="interface in org.biojava.bio.search">SeqSimilaritySearchHit</a></dt>
<dd>
<div class="block">Return the strand of the sub-hit with respect to the subject
sequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SeqSimilaritySearchSubHit.html#getSubjectStrand()">getSubjectStrand()</a></span> - Method in interface org.biojava.bio.search.<a href="./org/biojava/bio/search/SeqSimilaritySearchSubHit.html" title="interface in org.biojava.bio.search">SeqSimilaritySearchSubHit</a></dt>
<dd>
<div class="block">Return the strand of the sub-hit with respect to the subject
sequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SequenceDBSearchHit.html#getSubjectStrand()">getSubjectStrand()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SequenceDBSearchHit.html" title="class in org.biojava.bio.search">SequenceDBSearchHit</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SequenceDBSearchSubHit.html#getSubjectStrand()">getSubjectStrand()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SequenceDBSearchSubHit.html" title="class in org.biojava.bio.search">SequenceDBSearchSubHit</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SimpleSeqSimilaritySearchHit.html#getSubjectStrand()">getSubjectStrand()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SimpleSeqSimilaritySearchHit.html" title="class in org.biojava.bio.search">SimpleSeqSimilaritySearchHit</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SimpleSeqSimilaritySearchSubHit.html#getSubjectStrand()">getSubjectStrand()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SimpleSeqSimilaritySearchSubHit.html" title="class in org.biojava.bio.search">SimpleSeqSimilaritySearchSubHit</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.Terms.html#getSubmitterAccessionTerm()">getSubmitterAccessionTerm()</a></span> - Static method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.Terms.html" title="class in org.biojavax.bio.seq.io">EMBLxmlFormat.Terms</a></dt>
<dd>
<div class="block">Getter for the SubmitterAccession term</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.Terms.html#getSubmitterVersionTerm()">getSubmitterVersionTerm()</a></span> - Static method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.Terms.html" title="class in org.biojavax.bio.seq.io">EMBLxmlFormat.Terms</a></dt>
<dd>
<div class="block">Getter for the SubmitterVersion term</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.Terms.html#getSubmitterWgsVersionTerm()">getSubmitterWgsVersionTerm()</a></span> - Static method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.Terms.html" title="class in org.biojavax.bio.seq.io">EMBLxmlFormat.Terms</a></dt>
<dd>
<div class="block">Getter for the SubmitterWgsVersion term</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEMapLocation.html#getSubSeqStart()">getSubSeqStart()</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEMapLocation.html" title="class in org.biojava.bio.seq.io.agave">AGAVEMapLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/SubstitutionMatrix.html#getSubstitutionMatrix(java.io.BufferedReader)">getSubstitutionMatrix(BufferedReader)</a></span> - Static method in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/SubstitutionMatrix.html" title="class in org.biojava.bio.alignment">SubstitutionMatrix</a></dt>
<dd>
<div class="block">This constructor can be used to guess the alphabet of this substitution
matrix.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/SeqRes2AtomAligner.html#getSubstitutionMatrix(org.biojava.bio.symbol.FiniteAlphabet)">getSubstitutionMatrix(FiniteAlphabet)</a></span> - Static method in class org.biojava.bio.structure.io.<a href="./org/biojava/bio/structure/io/SeqRes2AtomAligner.html" title="class in org.biojava.bio.structure.io">SeqRes2AtomAligner</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/molbio/RestrictionEnzymeManager.html#getSuppliers(org.biojava.bio.molbio.RestrictionEnzyme)">getSuppliers(RestrictionEnzyme)</a></span> - Static method in class org.biojava.bio.molbio.<a href="./org/biojava/bio/molbio/RestrictionEnzymeManager.html" title="class in org.biojava.bio.molbio">RestrictionEnzymeManager</a></dt>
<dd>
<div class="block"><code>getSuppliers</code> returns a string describing the suppliers
of this enzyme according to REBASE encoding for commercial sources
or an empty String if the enzyme is not commecially available.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BibRefSupport.html#getSupportedCriteria()">getSupportedCriteria()</a></span> - Method in interface org.biojava.bibliography.<a href="./org/biojava/bibliography/BibRefSupport.html" title="interface in org.biojava.bibliography">BibRefSupport</a></dt>
<dd>
<div class="block">
It returns all supported searching and sorting criteria for the
whole bibliographic repository.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BibRefSupport.html#getSupportedCriteria(java.lang.String)">getSupportedCriteria(String)</a></span> - Method in interface org.biojava.bibliography.<a href="./org/biojava/bibliography/BibRefSupport.html" title="interface in org.biojava.bibliography">BibRefSupport</a></dt>
<dd>
<div class="block">
It returns all supported searching and sorting criteria in the given
repository subset.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BibRefSupport.html#getSupportedValues(java.lang.String, java.lang.String)">getSupportedValues(String, String)</a></span> - Method in interface org.biojava.bibliography.<a href="./org/biojava/bibliography/BibRefSupport.html" title="interface in org.biojava.bibliography">BibRefSupport</a></dt>
<dd>
<div class="block">
It returns a controlled vocabulary containing all possible
values of the attribute given in <tt>attrName</tt> in the
context given in <tt>resourceType</tt>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Author.html#getSurname()">getSurname()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Author.html" title="class in org.biojava.bio.structure">Author</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOTools.html#getSwissprotBuilderFactory()">getSwissprotBuilderFactory()</a></span> - Static method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOTools.html" title="class in org.biojava.bio.seq.io">SeqIOTools</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Get a default SequenceBuilderFactory for handling Swissprot
files.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Chain.html#getSwissprotId()">getSwissprotId()</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Chain.html" title="interface in org.biojava.bio.structure">Chain</a></dt>
<dd>
<div class="block">Get the Swissprot id of this chain.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/ChainImpl.html#getSwissprotId()">getSwissprotId()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/ChainImpl.html" title="class in org.biojava.bio.structure">ChainImpl</a></dt>
<dd>
<div class="block">get the Swissprot id of this chains .</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AbstractAlphabet.html#getSymbol(java.util.List)">getSymbol(List)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AbstractAlphabet.html" title="class in org.biojava.bio.symbol">AbstractAlphabet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/Alphabet.html#getSymbol(java.util.List)">getSymbol(List)</a></span> - Method in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/Alphabet.html" title="interface in org.biojava.bio.symbol">Alphabet</a></dt>
<dd>
<div class="block">
Get a symbol from the Alphabet which corresponds
to the specified ordered list of symbols.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/DoubleAlphabet.html#getSymbol(double)">getSymbol(double)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/DoubleAlphabet.html" title="class in org.biojava.bio.symbol">DoubleAlphabet</a></dt>
<dd>
<div class="block">Retrieve the Symbol for a double.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/DoubleAlphabet.html#getSymbol(double, double)">getSymbol(double, double)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/DoubleAlphabet.html" title="class in org.biojava.bio.symbol">DoubleAlphabet</a></dt>
<dd>
<div class="block">Retrieve the symbol for a range of doubles.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/DoubleAlphabet.html#getSymbol(java.util.List)">getSymbol(List)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/DoubleAlphabet.html" title="class in org.biojava.bio.symbol">DoubleAlphabet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/DoubleAlphabet.SubDoubleAlphabet.html#getSymbol(java.util.List)">getSymbol(List)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/DoubleAlphabet.SubDoubleAlphabet.html" title="class in org.biojava.bio.symbol">DoubleAlphabet.SubDoubleAlphabet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/DoubleAlphabet.SubDoubleAlphabet.html#getSymbol(double)">getSymbol(double)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/DoubleAlphabet.SubDoubleAlphabet.html" title="class in org.biojava.bio.symbol">DoubleAlphabet.SubDoubleAlphabet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/IllegalSymbolException.html#getSymbol()">getSymbol()</a></span> - Method in exception org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/IllegalSymbolException.html" title="class in org.biojava.bio.symbol">IllegalSymbolException</a></dt>
<dd>
<div class="block">Retrieve the symbol that caused this exception, or null.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/IntegerAlphabet.html#getSymbol(int)">getSymbol(int)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/IntegerAlphabet.html" title="class in org.biojava.bio.symbol">IntegerAlphabet</a></dt>
<dd>
<div class="block">Retrieve the Symbol for an int.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/IntegerAlphabet.html#getSymbol(java.util.List)">getSymbol(List)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/IntegerAlphabet.html" title="class in org.biojava.bio.symbol">IntegerAlphabet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/IntegerAlphabet.SubIntegerAlphabet.html#getSymbol(int)">getSymbol(int)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/IntegerAlphabet.SubIntegerAlphabet.html" title="class in org.biojava.bio.symbol">IntegerAlphabet.SubIntegerAlphabet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SoftMaskedAlphabet.html#getSymbol(java.util.List)">getSymbol(List)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SoftMaskedAlphabet.html" title="class in org.biojava.bio.symbol">SoftMaskedAlphabet</a></dt>
<dd>
<div class="block">Gets the compound symbol composed of the <code>Symbols</code> in the List.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleSymbolList.html#getSymbolArray()">getSymbolArray()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleSymbolList.html" title="class in org.biojava.bio.symbol">SimpleSymbolList</a></dt>
<dd>
<div class="block">Return the Java Symbol[] array that backs this object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AbstractAlphabet.html#getSymbolImpl(java.util.List)">getSymbolImpl(List)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AbstractAlphabet.html" title="class in org.biojava.bio.symbol">AbstractAlphabet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/IntegerAlphabet.SubIntegerAlphabet.html#getSymbolImpl(java.util.List)">getSymbolImpl(List)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/IntegerAlphabet.SubIntegerAlphabet.html" title="class in org.biojava.bio.symbol">IntegerAlphabet.SubIntegerAlphabet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleAlphabet.html#getSymbolImpl(java.util.List)">getSymbolImpl(List)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleAlphabet.html" title="class in org.biojava.bio.symbol">SimpleAlphabet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SingletonAlphabet.html#getSymbolImpl(java.util.List)">getSymbolImpl(List)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SingletonAlphabet.html" title="class in org.biojava.bio.symbol">SingletonAlphabet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/AlignmentElement.html#getSymbolList()">getSymbolList()</a></span> - Method in interface org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/AlignmentElement.html" title="interface in org.biojava.bio.alignment">AlignmentElement</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/SimpleAlignmentElement.html#getSymbolList()">getSymbolList()</a></span> - Method in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/SimpleAlignmentElement.html" title="class in org.biojava.bio.alignment">SimpleAlignmentElement</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/BioIndex.html#getSymbolParser()">getSymbolParser()</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/BioIndex.html" title="class in org.biojava.bio.seq.db">BioIndex</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/EmblCDROMIndexStore.html#getSymbolParser()">getSymbolParser()</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/EmblCDROMIndexStore.html" title="class in org.biojava.bio.seq.db">EmblCDROMIndexStore</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/IndexStore.html#getSymbolParser()">getSymbolParser()</a></span> - Method in interface org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/IndexStore.html" title="interface in org.biojava.bio.seq.db">IndexStore</a></dt>
<dd>
<div class="block">Retrieve the symbol parser used to turn the sequence characters
into Symobl objects.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/TabIndexStore.html#getSymbolParser()">getSymbolParser()</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/TabIndexStore.html" title="class in org.biojava.bio.seq.db">TabIndexStore</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/ProteinTools.html#getSymbolPropertyTable(java.lang.String)">getSymbolPropertyTable(String)</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/ProteinTools.html" title="class in org.biojava.bio.seq">ProteinTools</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/SimpleEmissionState.html#getSymbols()">getSymbols()</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/SimpleEmissionState.html" title="class in org.biojava.bio.dp">SimpleEmissionState</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/CircularRendererContext.html#getSymbols()">getSymbols()</a></span> - Method in interface org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/CircularRendererContext.html" title="interface in org.biojava.bio.gui.sequence">CircularRendererContext</a></dt>
<dd>
<div class="block">The SymbolList that is currently rendered by this context.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/HeadlessRenderContext.html#getSymbols()">getSymbols()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/HeadlessRenderContext.html" title="class in org.biojava.bio.gui.sequence">HeadlessRenderContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PairwiseSequencePanel.html#getSymbols()">getSymbols()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PairwiseSequencePanel.html" title="class in org.biojava.bio.gui.sequence">PairwiseSequencePanel</a></dt>
<dd>
<div class="block"><code>getSymbols</code> returns all of the <code>Symbol</code>s
belonging to the currently rendered <code>Sequence</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePanel.html#getSymbols()">getSymbols()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePanel.html" title="class in org.biojava.bio.gui.sequence">SequencePanel</a></dt>
<dd>
<div class="block">Retrieve the currently rendered SymbolList</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePoster.html#getSymbols()">getSymbols()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePoster.html" title="class in org.biojava.bio.gui.sequence">SequencePoster</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Retrieve the currently rendered SymbolList</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequenceRenderContext.html#getSymbols()">getSymbols()</a></span> - Method in interface org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequenceRenderContext.html" title="interface in org.biojava.bio.gui.sequence">SequenceRenderContext</a></dt>
<dd>
<div class="block">The SymbolList that is currently rendered by this SequenceRenderContext.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SubCircularRendererContext.html#getSymbols()">getSymbols()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SubCircularRendererContext.html" title="class in org.biojava.bio.gui.sequence">SubCircularRendererContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SubPairwiseRenderContext.html#getSymbols()">getSymbols()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SubPairwiseRenderContext.html" title="class in org.biojava.bio.gui.sequence">SubPairwiseRenderContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SubSequenceRenderContext.html#getSymbols()">getSymbols()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SubSequenceRenderContext.html" title="class in org.biojava.bio.gui.sequence">SubSequenceRenderContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/TranslatedSequencePanel.html#getSymbols()">getSymbols()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/TranslatedSequencePanel.html" title="class in org.biojava.bio.gui.sequence">TranslatedSequencePanel</a></dt>
<dd>
<div class="block"><code>getSymbols</code> returns all of the <code>Symbol</code>s
belonging to the currently rendered <code>Sequence</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/DASSequence.html#getSymbols()">getSymbols()</a></span> - Method in class org.biojava.bio.program.das.<a href="./org/biojava/bio/program/das/DASSequence.html" title="class in org.biojava.bio.program.das">DASSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/Feature.html#getSymbols()">getSymbols()</a></span> - Method in interface org.biojava.bio.seq.<a href="./org/biojava/bio/seq/Feature.html" title="interface in org.biojava.bio.seq">Feature</a></dt>
<dd>
<div class="block">Return a list of symbols that are contained in this feature.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleFeature.html#getSymbols()">getSymbols()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleFeature.html" title="class in org.biojava.bio.seq.impl">SimpleFeature</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleStrandedFeature.html#getSymbols()">getSymbols()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleStrandedFeature.html" title="class in org.biojava.bio.seq.impl">SimpleStrandedFeature</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/projection/ProjectedFeature.html#getSymbols()">getSymbols()</a></span> - Method in class org.biojava.bio.seq.projection.<a href="./org/biojava/bio/seq/projection/ProjectedFeature.html" title="class in org.biojava.bio.seq.projection">ProjectedFeature</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/StrandedFeature.html#getSymbols()">getSymbols()</a></span> - Method in interface org.biojava.bio.seq.<a href="./org/biojava/bio/seq/StrandedFeature.html" title="interface in org.biojava.bio.seq">StrandedFeature</a></dt>
<dd>
<div class="block">Return a list of symbols that are contained in this feature.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/BasisSymbol.html#getSymbols()">getSymbols()</a></span> - Method in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/BasisSymbol.html" title="interface in org.biojava.bio.symbol">BasisSymbol</a></dt>
<dd>
<div class="block">
The list of symbols that this symbol is composed from.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/DoubleAlphabet.DoubleRange.html#getSymbols()">getSymbols()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/DoubleAlphabet.DoubleRange.html" title="class in org.biojava.bio.symbol">DoubleAlphabet.DoubleRange</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/DoubleAlphabet.DoubleSymbol.html#getSymbols()">getSymbols()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/DoubleAlphabet.DoubleSymbol.html" title="class in org.biojava.bio.symbol">DoubleAlphabet.DoubleSymbol</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/FundamentalAtomicSymbol.html#getSymbols()">getSymbols()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/FundamentalAtomicSymbol.html" title="class in org.biojava.bio.symbol">FundamentalAtomicSymbol</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/IntegerAlphabet.IntegerSymbol.html#getSymbols()">getSymbols()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/IntegerAlphabet.IntegerSymbol.html" title="class in org.biojava.bio.symbol">IntegerAlphabet.IntegerSymbol</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichFeature.html#getSymbols()">getSymbols()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichFeature.html" title="class in org.biojavax.bio.seq">SimpleRichFeature</a></dt>
<dd>
<div class="block">Return a list of symbols that are contained in this feature.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PairwiseSequencePanel.html#getSymbolTranslation()">getSymbolTranslation()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PairwiseSequencePanel.html" title="class in org.biojava.bio.gui.sequence">PairwiseSequencePanel</a></dt>
<dd>
<div class="block"><code>getSymbolTranslation</code> returns the current
translation in <code>Symbol</code>s which will be applied when
rendering.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/TranslatedSequencePanel.html#getSymbolTranslation()">getSymbolTranslation()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/TranslatedSequencePanel.html" title="class in org.biojava.bio.gui.sequence">TranslatedSequencePanel</a></dt>
<dd>
<div class="block"><code>getSymbolTranslation</code> returns the current
translation in <code>Symbol</code>s which will be applied when
rendering.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/PackedSymbolList.html#getSyms()">getSyms()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/PackedSymbolList.html" title="class in org.biojava.bio.symbol">PackedSymbolList</a></dt>
<dd>
<div class="block">
Return the long array within which the symbols are bit-packed.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Compound.html#getSynonyms()">getSynonyms()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure">Compound</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/IntegerOntology.IntTerm.html#getSynonyms()">getSynonyms()</a></span> - Method in class org.biojava.ontology.<a href="./org/biojava/ontology/IntegerOntology.IntTerm.html" title="class in org.biojava.ontology">IntegerOntology.IntTerm</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/OntologyTerm.Impl.html#getSynonyms()">getSynonyms()</a></span> - Method in class org.biojava.ontology.<a href="./org/biojava/ontology/OntologyTerm.Impl.html" title="class in org.biojava.ontology">OntologyTerm.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/RemoteTerm.Impl.html#getSynonyms()">getSynonyms()</a></span> - Method in class org.biojava.ontology.<a href="./org/biojava/ontology/RemoteTerm.Impl.html" title="class in org.biojava.ontology">RemoteTerm.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/Term.html#getSynonyms()">getSynonyms()</a></span> - Method in interface org.biojava.ontology.<a href="./org/biojava/ontology/Term.html" title="interface in org.biojava.ontology">Term</a></dt>
<dd>
<div class="block">Return the synonyms for this term.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/Term.Impl.html#getSynonyms()">getSynonyms()</a></span> - Method in class org.biojava.ontology.<a href="./org/biojava/ontology/Term.Impl.html" title="class in org.biojava.ontology">Term.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/Triple.Impl.html#getSynonyms()">getSynonyms()</a></span> - Method in class org.biojava.ontology.<a href="./org/biojava/ontology/Triple.Impl.html" title="class in org.biojava.ontology">Triple.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ontology/SimpleComparableTerm.html#getSynonyms()">getSynonyms()</a></span> - Method in class org.biojavax.ontology.<a href="./org/biojavax/ontology/SimpleComparableTerm.html" title="class in org.biojavax.ontology">SimpleComparableTerm</a></dt>
<dd>
<div class="block">Return the synonyms for this term.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ontology/SimpleComparableTriple.html#getSynonyms()">getSynonyms()</a></span> - Method in class org.biojavax.ontology.<a href="./org/biojavax/ontology/SimpleComparableTriple.html" title="class in org.biojavax.ontology">SimpleComparableTriple</a></dt>
<dd>
<div class="block">Return the synonyms for this term.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Compound.html#getSynthetic()">getSynthetic()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure">Compound</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/molbio/DNAComposition.html#getT()">getT()</a></span> - Method in class org.biojava.bio.molbio.<a href="./org/biojava/bio/molbio/DNAComposition.html" title="class in org.biojava.bio.molbio">DNAComposition</a></dt>
<dd>
<div class="block">Get the relative compositon of 'T'.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/StructureTools.html#getT()">getT()</a></span> - Method in class org.biojava.bio.proteomics.<a href="./org/biojava/bio/proteomics/StructureTools.html" title="class in org.biojava.bio.proteomics">StructureTools</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/TranslatedDistribution.html#getTable()">getTable()</a></span> - Method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/TranslatedDistribution.html" title="class in org.biojava.bio.dist">TranslatedDistribution</a></dt>
<dd>
<div class="block">Retrieve the translation table encapsulating the map from this emission
spectrum to the underlying one.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleGeneticCodeTable.html#getTableNumber()">getTableNumber()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleGeneticCodeTable.html" title="class in org.biojava.bio.symbol">SimpleGeneticCodeTable</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/TagValue.html#getTag()">getTag()</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/TagValue.html" title="class in org.biojava.bio.program.tagvalue">TagValue</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/RegexParser.html#getTagGroup()">getTagGroup()</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/RegexParser.html" title="class in org.biojava.bio.program.tagvalue">RegexParser</a></dt>
<dd>
<div class="block">Get the group number that matches the tag.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/TagDelegator.html#getTags()">getTags()</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/TagDelegator.html" title="class in org.biojava.bio.program.tagvalue">TagDelegator</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/TagDropper.html#getTags()">getTags()</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/TagDropper.html" title="class in org.biojava.bio.program.tagvalue">TagDropper</a></dt>
<dd>
<div class="block">Get the complete set of tags that are currently recognized.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/ProteinTools.html#getTAlphabet()">getTAlphabet()</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/ProteinTools.html" title="class in org.biojava.bio.seq">ProteinTools</a></dt>
<dd>
<div class="block">Gets the protein alphabet including the translation termination symbols</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequenceViewerEvent.html#getTarget()">getTarget()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequenceViewerEvent.html" title="class in org.biojava.bio.gui.sequence">SequenceViewerEvent</a></dt>
<dd>
<div class="block">Get the Object that was the target of the mouse gesture or null if the
mouse is not gesturing over any recognizable rendered object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/SimpleSVMTarget.html#getTarget(java.lang.Object)">getTarget(Object)</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/SimpleSVMTarget.html" title="class in org.biojava.stats.svm">SimpleSVMTarget</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/SVMTarget.html#getTarget(java.lang.Object)">getTarget(Object)</a></span> - Method in interface org.biojava.stats.svm.<a href="./org/biojava/stats/svm/SVMTarget.html" title="interface in org.biojava.stats.svm">SVMTarget</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AbstractManyToOneTranslationTable.html#getTargetAlphabet()">getTargetAlphabet()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AbstractManyToOneTranslationTable.html" title="class in org.biojava.bio.symbol">AbstractManyToOneTranslationTable</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AbstractReversibleTranslationTable.html#getTargetAlphabet()">getTargetAlphabet()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AbstractReversibleTranslationTable.html" title="class in org.biojava.bio.symbol">AbstractReversibleTranslationTable</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleManyToOneTranslationTable.html#getTargetAlphabet()">getTargetAlphabet()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleManyToOneTranslationTable.html" title="class in org.biojava.bio.symbol">SimpleManyToOneTranslationTable</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleReversibleTranslationTable.html#getTargetAlphabet()">getTargetAlphabet()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleReversibleTranslationTable.html" title="class in org.biojava.bio.symbol">SimpleReversibleTranslationTable</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleTranslationTable.html#getTargetAlphabet()">getTargetAlphabet()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleTranslationTable.html" title="class in org.biojava.bio.symbol">SimpleTranslationTable</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/TranslationTable.html#getTargetAlphabet()">getTargetAlphabet()</a></span> - Method in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/TranslationTable.html" title="interface in org.biojava.bio.symbol">TranslationTable</a></dt>
<dd>
<div class="block">The alphabet of Symbols that will be produced.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/OntologyTerm.Impl.html#getTargetOntology()">getTargetOntology()</a></span> - Method in class org.biojava.ontology.<a href="./org/biojava/ontology/OntologyTerm.Impl.html" title="class in org.biojava.ontology">OntologyTerm.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/OrthoPairSet.html#getTaxa()">getTaxa()</a></span> - Method in interface org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/OrthoPairSet.html" title="interface in org.biojava.bio.program.homologene">OrthoPairSet</a></dt>
<dd>
<div class="block">get the taxa represented in this group</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/SimpleOrthoPairSet.html#getTaxa()">getTaxa()</a></span> - Method in class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/SimpleOrthoPairSet.html" title="class in org.biojava.bio.program.homologene">SimpleOrthoPairSet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/HomologeneTools.html#getTaxon(int)">getTaxon(int)</a></span> - Static method in class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/HomologeneTools.html" title="class in org.biojava.bio.program.homologene">HomologeneTools</a></dt>
<dd>
<div class="block">get the Taxon corresponding to this Taxon ID</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/Orthologue.html#getTaxon()">getTaxon()</a></span> - Method in interface org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/Orthologue.html" title="interface in org.biojava.bio.program.homologene">Orthologue</a></dt>
<dd>
<div class="block">return the Taxon associated with this orthologue</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/SimpleOrthologue.html#getTaxon()">getTaxon()</a></span> - Method in class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/SimpleOrthologue.html" title="class in org.biojava.bio.program.homologene">SimpleOrthologue</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/biosql/TaxonSQL.html#getTaxon(java.sql.Connection, int)">getTaxon(Connection, int)</a></span> - Static method in class org.biojava.bio.seq.db.biosql.<a href="./org/biojava/bio/seq/db/biosql/TaxonSQL.html" title="class in org.biojava.bio.seq.db.biosql">TaxonSQL</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Attempts to get a Taxon object corresponding to the specified
NCBI taxon ID.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/biosql/TaxonSQL.html#getTaxon(java.sql.Connection, java.lang.String)">getTaxon(Connection, String)</a></span> - Static method in class org.biojava.bio.seq.db.biosql.<a href="./org/biojava/bio/seq/db/biosql/TaxonSQL.html" title="class in org.biojava.bio.seq.db.biosql">TaxonSQL</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Attempts to get a Taxon object corresponding to the specified
name.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/BioEntry.html#getTaxon()">getTaxon()</a></span> - Method in interface org.biojavax.bio.<a href="./org/biojavax/bio/BioEntry.html" title="interface in org.biojavax.bio">BioEntry</a></dt>
<dd>
<div class="block">Gets the taxon associated with this bioentry.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/SimpleBioEntry.html#getTaxon()">getTaxon()</a></span> - Method in class org.biojavax.bio.<a href="./org/biojavax/bio/SimpleBioEntry.html" title="class in org.biojavax.bio">SimpleBioEntry</a></dt>
<dd>
<div class="block">Gets the taxon associated with this bioentry.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/Orthologue.html#getTaxonID()">getTaxonID()</a></span> - Method in interface org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/Orthologue.html" title="interface in org.biojava.bio.program.homologene">Orthologue</a></dt>
<dd>
<div class="block">a convenience method to return the TaxonID for thsi orhtologue.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/SimpleOrthologue.html#getTaxonID()">getTaxonID()</a></span> - Method in class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/SimpleOrthologue.html" title="class in org.biojava.bio.program.homologene">SimpleOrthologue</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/Taxon.html#getTaxonID()">getTaxonID()</a></span> - Method in interface org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/Taxon.html" title="interface in org.biojava.bio.program.homologene">Taxon</a></dt>
<dd>
<div class="block">returns the taxon ID</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/Taxon.TaxonStub.html#getTaxonID()">getTaxonID()</a></span> - Method in class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/Taxon.TaxonStub.html" title="class in org.biojava.bio.program.homologene">Taxon.TaxonStub</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/Agave2AgaveAnnotFilter.html#getTaxonId(org.biojava.bio.Annotation)">getTaxonId(Annotation)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/Agave2AgaveAnnotFilter.html" title="class in org.biojava.bio.seq.io.agave">Agave2AgaveAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEAnnotFilter.html#getTaxonId(org.biojava.bio.Annotation)">getTaxonId(Annotation)</a></span> - Method in interface org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEAnnotFilter.html" title="interface in org.biojava.bio.seq.io.agave">AGAVEAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/SimpleAnnotFilter.html#getTaxonId(org.biojava.bio.Annotation)">getTaxonId(Annotation)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/SimpleAnnotFilter.html" title="class in org.biojava.bio.seq.io.agave">SimpleAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/PDBHeader.html#getTechnique()">getTechnique()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/PDBHeader.html" title="class in org.biojava.bio.structure">PDBHeader</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/obo/OboFileParser.html#getTempBuffer()">getTempBuffer()</a></span> - Method in class org.biojava.ontology.obo.<a href="./org/biojava/ontology/obo/OboFileParser.html" title="class in org.biojava.ontology.obo">OboFileParser</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html#getTemperatureDependence()">getTemperatureDependence()</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html" title="class in org.biojavax.bio.seq.io">UniProtCommentParser</a></dt>
<dd>
<div class="block">Getter for property temperatureDependence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Atom.html#getTempFactor()">getTempFactor()</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Atom.html" title="interface in org.biojava.bio.structure">Atom</a></dt>
<dd>
<div class="block">get set temp factor.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/AtomImpl.html#getTempFactor()">getTempFactor()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/AtomImpl.html" title="class in org.biojava.bio.structure">AtomImpl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/IntegerOntology.html#getTerm(java.lang.String)">getTerm(String)</a></span> - Method in class org.biojava.ontology.<a href="./org/biojava/ontology/IntegerOntology.html" title="class in org.biojava.ontology">IntegerOntology</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/Ontology.html#getTerm(java.lang.String)">getTerm(String)</a></span> - Method in interface org.biojava.ontology.<a href="./org/biojava/ontology/Ontology.html" title="interface in org.biojava.ontology">Ontology</a></dt>
<dd>
<div class="block">Fetch the term with the specified name.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/Ontology.Impl.html#getTerm(java.lang.String)">getTerm(String)</a></span> - Method in class org.biojava.ontology.<a href="./org/biojava/ontology/Ontology.Impl.html" title="class in org.biojava.ontology">Ontology.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/BioEntryRelationship.html#getTerm()">getTerm()</a></span> - Method in interface org.biojavax.bio.<a href="./org/biojavax/bio/BioEntryRelationship.html" title="interface in org.biojavax.bio">BioEntryRelationship</a></dt>
<dd>
<div class="block">Returns the term describing the relationship.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByNoteTermOnly.html#getTerm()">getTerm()</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByNoteTermOnly.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.ByNoteTermOnly</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/EmptyRichLocation.html#getTerm()">getTerm()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/EmptyRichLocation.html" title="class in org.biojavax.bio.seq">EmptyRichLocation</a></dt>
<dd>
<div class="block">Retrieves the term associated with this location.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichFeatureRelationship.html#getTerm()">getTerm()</a></span> - Method in interface org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichFeatureRelationship.html" title="interface in org.biojavax.bio.seq">RichFeatureRelationship</a></dt>
<dd>
<div class="block">Gets the term that describes this relationship.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichLocation.html#getTerm()">getTerm()</a></span> - Method in interface org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichLocation.html" title="interface in org.biojavax.bio.seq">RichLocation</a></dt>
<dd>
<div class="block">Retrieves the term associated with this location.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichFeatureRelationship.html#getTerm()">getTerm()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichFeatureRelationship.html" title="class in org.biojavax.bio.seq">SimpleRichFeatureRelationship</a></dt>
<dd>
<div class="block">Gets the term that describes this relationship.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichLocation.html#getTerm()">getTerm()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichLocation.html" title="class in org.biojavax.bio.seq">SimpleRichLocation</a></dt>
<dd>
<div class="block">Retrieves the term associated with this location.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/SimpleBioEntryRelationship.html#getTerm()">getTerm()</a></span> - Method in class org.biojavax.bio.<a href="./org/biojavax/bio/SimpleBioEntryRelationship.html" title="class in org.biojavax.bio">SimpleBioEntryRelationship</a></dt>
<dd>
<div class="block">Returns the term describing the relationship.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/Note.html#getTerm()">getTerm()</a></span> - Method in interface org.biojavax.<a href="./org/biojavax/Note.html" title="interface in org.biojavax">Note</a></dt>
<dd>
<div class="block">Gets the term that defines this note.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ontology/SimpleComparableOntology.html#getTerm(java.lang.String)">getTerm(String)</a></span> - Method in class org.biojavax.ontology.<a href="./org/biojavax/ontology/SimpleComparableOntology.html" title="class in org.biojavax.ontology">SimpleComparableOntology</a></dt>
<dd>
<div class="block">Fetch the term with the specified name.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleNote.html#getTerm()">getTerm()</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleNote.html" title="class in org.biojavax">SimpleNote</a></dt>
<dd>
<div class="block">Gets the term that defines this note.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/MassCalc.html#getTermMass()">getTermMass()</a></span> - Method in class org.biojava.bio.proteomics.<a href="./org/biojava/bio/proteomics/MassCalc.html" title="class in org.biojava.bio.proteomics">MassCalc</a></dt>
<dd>
<div class="block"><code>getTermMass</code> returns the terminal mass being used
by the instance methods.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/IntegerOntology.html#getTerms()">getTerms()</a></span> - Method in class org.biojava.ontology.<a href="./org/biojava/ontology/IntegerOntology.html" title="class in org.biojava.ontology">IntegerOntology</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/Ontology.html#getTerms()">getTerms()</a></span> - Method in interface org.biojava.ontology.<a href="./org/biojava/ontology/Ontology.html" title="interface in org.biojava.ontology">Ontology</a></dt>
<dd>
<div class="block">Return all the terms in this ontology</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/Ontology.Impl.html#getTerms()">getTerms()</a></span> - Method in class org.biojava.ontology.<a href="./org/biojava/ontology/Ontology.Impl.html" title="class in org.biojava.ontology">Ontology.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ontology/SimpleComparableOntology.html#getTerms()">getTerms()</a></span> - Method in class org.biojavax.ontology.<a href="./org/biojavax/ontology/SimpleComparableOntology.html" title="class in org.biojavax.ontology">SimpleComparableOntology</a></dt>
<dd>
<div class="block">Return all the terms in this ontology</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ontology/ComparableOntology.html#getTermSet()">getTermSet()</a></span> - Method in interface org.biojavax.ontology.<a href="./org/biojavax/ontology/ComparableOntology.html" title="interface in org.biojavax.ontology">ComparableOntology</a></dt>
<dd>
<div class="block">Returns the set of terms in this ontology.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ontology/SimpleComparableOntology.html#getTermSet()">getTermSet()</a></span> - Method in class org.biojavax.ontology.<a href="./org/biojavax/ontology/SimpleComparableOntology.html" title="class in org.biojavax.ontology">SimpleComparableOntology</a></dt>
<dd>
<div class="block">Returns the set of terms in this ontology.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ByClass.html#getTestClass()">getTestClass()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ByClass.html" title="class in org.biojava.bio.seq">FeatureFilter.ByClass</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/DatabasePDBremark.html#getText()">getText()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/DatabasePDBremark.html" title="class in org.biojava.bio.structure.io.mmcif.model">DatabasePDBremark</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/StructKeywords.html#getText()">getText()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/StructKeywords.html" title="class in org.biojava.bio.structure.io.mmcif.model">StructKeywords</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html#getText()">getText()</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html" title="class in org.biojavax.bio.seq.io">UniProtCommentParser</a></dt>
<dd>
<div class="block">Getter for property text.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/LabelledSequenceRenderer.html#getTextColor()">getTextColor()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/LabelledSequenceRenderer.html" title="class in org.biojava.bio.gui.sequence">LabelledSequenceRenderer</a></dt>
<dd>
<div class="block">Get the color of the label text</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/DAS.html#getThreadFetches()">getThreadFetches()</a></span> - Static method in class org.biojava.bio.program.das.<a href="./org/biojava/bio/program/das/DAS.html" title="class in org.biojava.bio.program.das">DAS</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html#getThree_letter_code()">getThree_letter_code()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html" title="class in org.biojava.bio.structure.io.mmcif.model">ChemComp</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/SimpleSVMClassifierModel.html#getThreshold()">getThreshold()</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/SimpleSVMClassifierModel.html" title="class in org.biojava.stats.svm">SimpleSVMClassifierModel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/SVMClassifierModel.html#getThreshold()">getThreshold()</a></span> - Method in interface org.biojava.stats.svm.<a href="./org/biojava/stats/svm/SVMClassifierModel.html" title="interface in org.biojava.stats.svm">SVMClassifierModel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/SVMRegressionModel.html#getThreshold()">getThreshold()</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/SVMRegressionModel.html" title="class in org.biojava.stats.svm">SVMRegressionModel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/OffsetRulerRenderer.html#getTickDirection()">getTickDirection()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/OffsetRulerRenderer.html" title="class in org.biojava.bio.gui.sequence">OffsetRulerRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/dasstructure/DASStructureCall.html#getTimeStamp()">getTimeStamp()</a></span> - Method in class org.biojava.bio.program.das.dasstructure.<a href="./org/biojava/bio/program/das/dasstructure/DASStructureCall.html" title="class in org.biojava.bio.program.das.dasstructure">DASStructureCall</a></dt>
<dd>
<div class="block">Returns a time stamp .</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/PDBFileParser.html#getTimeStamp()">getTimeStamp()</a></span> - Method in class org.biojava.bio.structure.io.<a href="./org/biojava/bio/structure/io/PDBFileParser.html" title="class in org.biojava.bio.structure.io">PDBFileParser</a></dt>
<dd>
<div class="block">Returns a time stamp.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Compound.html#getTissue()">getTissue()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure">Compound</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.Terms.html#getTissueTerm()">getTissueTerm()</a></span> - Static method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.Terms.html" title="class in org.biojavax.bio.seq">RichSequence.Terms</a></dt>
<dd>
<div class="block">Getter for the Tissue term</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/Orthologue.html#getTitle()">getTitle()</a></span> - Method in interface org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/Orthologue.html" title="interface in org.biojava.bio.program.homologene">Orthologue</a></dt>
<dd>
<div class="block">return the title used by Genbank for this protein</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/SimpleOrthologue.html#getTitle()">getTitle()</a></span> - Method in class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/SimpleOrthologue.html" title="class in org.biojava.bio.program.homologene">SimpleOrthologue</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/unigene/UnigeneCluster.html#getTitle()">getTitle()</a></span> - Method in interface org.biojava.bio.program.unigene.<a href="./org/biojava/bio/program/unigene/UnigeneCluster.html" title="interface in org.biojava.bio.program.unigene">UnigeneCluster</a></dt>
<dd>
<div class="block">The cluster title.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Compound.html#getTitle()">getTitle()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure">Compound</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Struct.html#getTitle()">getTitle()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Struct.html" title="class in org.biojava.bio.structure.io.mmcif.model">Struct</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/JournalArticle.html#getTitle()">getTitle()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/JournalArticle.html" title="class in org.biojava.bio.structure">JournalArticle</a></dt>
<dd>
<div class="block">Get the value of title</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/PDBHeader.html#getTitle()">getTitle()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/PDBHeader.html" title="class in org.biojava.bio.structure">PDBHeader</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/DocRef.html#getTitle()">getTitle()</a></span> - Method in interface org.biojavax.<a href="./org/biojavax/DocRef.html" title="interface in org.biojavax">DocRef</a></dt>
<dd>
<div class="block">Returns the title of the document reference.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleDocRef.html#getTitle()">getTitle()</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleDocRef.html" title="class in org.biojavax">SimpleDocRef</a></dt>
<dd>
<div class="block">Returns the title of the document reference.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/IllegalTransitionException.html#getTo()">getTo()</a></span> - Method in exception org.biojava.bio.dp.<a href="./org/biojava/bio/dp/IllegalTransitionException.html" title="class in org.biojava.bio.dp">IllegalTransitionException</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/SimpleEmissionState.html#getToken()">getToken()</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/SimpleEmissionState.html" title="class in org.biojava.bio.dp">SimpleEmissionState</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/StrandedFeature.Strand.html#getToken()">getToken()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/StrandedFeature.Strand.html" title="class in org.biojava.bio.seq">StrandedFeature.Strand</a></dt>
<dd>
<div class="block">Returns the token for strandedness.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AbstractAlphabet.html#getTokenization(java.lang.String)">getTokenization(String)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AbstractAlphabet.html" title="class in org.biojava.bio.symbol">AbstractAlphabet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/Alphabet.html#getTokenization(java.lang.String)">getTokenization(String)</a></span> - Method in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/Alphabet.html" title="interface in org.biojava.bio.symbol">Alphabet</a></dt>
<dd>
<div class="block">
Get a SymbolTokenization by name.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/DoubleAlphabet.html#getTokenization(java.lang.String)">getTokenization(String)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/DoubleAlphabet.html" title="class in org.biojava.bio.symbol">DoubleAlphabet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/DoubleAlphabet.SubDoubleAlphabet.html#getTokenization(java.lang.String)">getTokenization(String)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/DoubleAlphabet.SubDoubleAlphabet.html" title="class in org.biojava.bio.symbol">DoubleAlphabet.SubDoubleAlphabet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/IntegerAlphabet.html#getTokenization(java.lang.String)">getTokenization(String)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/IntegerAlphabet.html" title="class in org.biojava.bio.symbol">IntegerAlphabet</a></dt>
<dd>
<div class="block">Creates a new parser (Mark Schreiber 3 May 2001).</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/IntegerAlphabet.SubIntegerAlphabet.html#getTokenization(java.lang.String)">getTokenization(String)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/IntegerAlphabet.SubIntegerAlphabet.html" title="class in org.biojava.bio.symbol">IntegerAlphabet.SubIntegerAlphabet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SingletonAlphabet.html#getTokenization(java.lang.String)">getTokenization(String)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SingletonAlphabet.html" title="class in org.biojava.bio.symbol">SingletonAlphabet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SoftMaskedAlphabet.html#getTokenization(java.lang.String)">getTokenization(String)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SoftMaskedAlphabet.html" title="class in org.biojava.bio.symbol">SoftMaskedAlphabet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/CharacterTokenization.html#getTokenTable()">getTokenTable()</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/CharacterTokenization.html" title="class in org.biojava.bio.seq.io">CharacterTokenization</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/AlternateTokenization.html#getTokenType()">getTokenType()</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/AlternateTokenization.html" title="class in org.biojava.bio.seq.io">AlternateTokenization</a></dt>
<dd>
<div class="block">Tokens have fixed size.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/CharacterTokenization.html#getTokenType()">getTokenType()</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/CharacterTokenization.html" title="class in org.biojava.bio.seq.io">CharacterTokenization</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SymbolTokenization.html#getTokenType()">getTokenType()</a></span> - Method in interface org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SymbolTokenization.html" title="interface in org.biojava.bio.seq.io">SymbolTokenization</a></dt>
<dd>
<div class="block">Determine the style of tokenization represented by this object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/WordTokenization.html#getTokenType()">getTokenType()</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/WordTokenization.html" title="class in org.biojava.bio.seq.io">WordTokenization</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SoftMaskedAlphabet.CaseSensitiveTokenization.html#getTokenType()">getTokenType()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SoftMaskedAlphabet.CaseSensitiveTokenization.html" title="class in org.biojava.bio.symbol">SoftMaskedAlphabet.CaseSensitiveTokenization</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/LineInfo.html#getTotalDepth()">getTotalDepth()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/LineInfo.html" title="class in org.biojava.bio.gui.sequence">LineInfo</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/util/WeightedSet.html#getTotalWeight()">getTotalWeight()</a></span> - Method in class org.biojavax.ga.util.<a href="./org/biojavax/ga/util/WeightedSet.html" title="class in org.biojavax.ga.util">WeightedSet</a></dt>
<dd>
<div class="block">The total weight that has been added to this Set.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/AbstractChromatogram.html#getTrace(org.biojava.bio.symbol.AtomicSymbol)">getTrace(AtomicSymbol)</a></span> - Method in class org.biojava.bio.chromatogram.<a href="./org/biojava/bio/chromatogram/AbstractChromatogram.html" title="class in org.biojava.bio.chromatogram">AbstractChromatogram</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/Chromatogram.html#getTrace(org.biojava.bio.symbol.AtomicSymbol)">getTrace(AtomicSymbol)</a></span> - Method in interface org.biojava.bio.chromatogram.<a href="./org/biojava/bio/chromatogram/Chromatogram.html" title="interface in org.biojava.bio.chromatogram">Chromatogram</a></dt>
<dd>
<div class="block">Returns an array containing the intensities of the sampled waveform
representing the chromatogram trace for base <code>nucleotide</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/AbiTraceRenderer.html#getTrace()">getTrace()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/AbiTraceRenderer.html" title="class in org.biojava.bio.gui.sequence">AbiTraceRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/abi/ABITrace.html#getTrace(org.biojava.bio.symbol.AtomicSymbol)">getTrace(AtomicSymbol)</a></span> - Method in class org.biojava.bio.program.abi.<a href="./org/biojava/bio/program/abi/ABITrace.html" title="class in org.biojava.bio.program.abi">ABITrace</a></dt>
<dd>
<div class="block">Returns one of the four traces - all of the y-coordinate values,
each of which correspond to a single x-coordinate relative to the
position in the array, so that if element 4 in the array is 972, then
x is 4 and y is 972 for that point.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/AbstractChromatogram.html#getTraceLength()">getTraceLength()</a></span> - Method in class org.biojava.bio.chromatogram.<a href="./org/biojava/bio/chromatogram/AbstractChromatogram.html" title="class in org.biojava.bio.chromatogram">AbstractChromatogram</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/Chromatogram.html#getTraceLength()">getTraceLength()</a></span> - Method in interface org.biojava.bio.chromatogram.<a href="./org/biojava/bio/chromatogram/Chromatogram.html" title="interface in org.biojava.bio.chromatogram">Chromatogram</a></dt>
<dd>
<div class="block">Returns the length of the trace of the Chromatogram.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/abi/ABITrace.html#getTraceLength()">getTraceLength()</a></span> - Method in class org.biojava.bio.program.abi.<a href="./org/biojava/bio/program/abi/ABITrace.html" title="class in org.biojava.bio.program.abi">ABITrace</a></dt>
<dd>
<div class="block">Returns the length of the trace (number of x-coordinate points in the graph).</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/ChromatogramTools.html#getTraceOffset(org.biojava.bio.chromatogram.Chromatogram, int)">getTraceOffset(Chromatogram, int)</a></span> - Static method in class org.biojava.bio.chromatogram.<a href="./org/biojava/bio/chromatogram/ChromatogramTools.html" title="class in org.biojava.bio.chromatogram">ChromatogramTools</a></dt>
<dd>
<div class="block">Get a specific value from the trace offset sequence in the given
chromatogram and extract its <code>int</code> value.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/ChromatogramTools.html#getTraceOffsetArray(org.biojava.bio.chromatogram.Chromatogram)">getTraceOffsetArray(Chromatogram)</a></span> - Static method in class org.biojava.bio.chromatogram.<a href="./org/biojava/bio/chromatogram/ChromatogramTools.html" title="class in org.biojava.bio.chromatogram">ChromatogramTools</a></dt>
<dd>
<div class="block">Converts the peak offsets list of the given chromatogram
into a new <code>int</code> array.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/ChromatogramTools.html#getTraceOffsets(org.biojava.bio.chromatogram.Chromatogram)">getTraceOffsets(Chromatogram)</a></span> - Static method in class org.biojava.bio.chromatogram.<a href="./org/biojava/bio/chromatogram/ChromatogramTools.html" title="class in org.biojava.bio.chromatogram">ChromatogramTools</a></dt>
<dd>
<div class="block">Get the peak offsets for the called bases of a chromatogram.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePanelWrapper.html#getTrackLayout()">getTrackLayout()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePanelWrapper.html" title="class in org.biojava.bio.gui.sequence">SequencePanelWrapper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ListTools.SeriesList.html#getTrailer()">getTrailer()</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/ListTools.SeriesList.html" title="class in org.biojava.utils">ListTools.SeriesList</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/HeadlessRenderContext.html#getTrailingBorder()">getTrailingBorder()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/HeadlessRenderContext.html" title="class in org.biojava.bio.gui.sequence">HeadlessRenderContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PairwiseSequencePanel.html#getTrailingBorder()">getTrailingBorder()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PairwiseSequencePanel.html" title="class in org.biojava.bio.gui.sequence">PairwiseSequencePanel</a></dt>
<dd>
<div class="block"><code>getTrailingBorder</code> returns the trailing border of
the primary sequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePanel.html#getTrailingBorder()">getTrailingBorder()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePanel.html" title="class in org.biojava.bio.gui.sequence">SequencePanel</a></dt>
<dd>
<div class="block">Retrieve the object that encapsulates the trailing border area - the space
after sequence information is rendered.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePoster.html#getTrailingBorder()">getTrailingBorder()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePoster.html" title="class in org.biojava.bio.gui.sequence">SequencePoster</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Retrieve the object that encapsulates the trailing border area - the space
after sequence information is rendered.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequenceRenderContext.html#getTrailingBorder()">getTrailingBorder()</a></span> - Method in interface org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequenceRenderContext.html" title="interface in org.biojava.bio.gui.sequence">SequenceRenderContext</a></dt>
<dd>
<div class="block">Gets the TrailingBorder attribute of the SequenceRenderContext object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SubPairwiseRenderContext.html#getTrailingBorder()">getTrailingBorder()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SubPairwiseRenderContext.html" title="class in org.biojava.bio.gui.sequence">SubPairwiseRenderContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SubSequenceRenderContext.html#getTrailingBorder()">getTrailingBorder()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SubSequenceRenderContext.html" title="class in org.biojava.bio.gui.sequence">SubSequenceRenderContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/TranslatedSequencePanel.html#getTrailingBorder()">getTrailingBorder()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/TranslatedSequencePanel.html" title="class in org.biojava.bio.gui.sequence">TranslatedSequencePanel</a></dt>
<dd>
<div class="block"><code>getTrailingBorder</code> returns the trailing border.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/BumpedRenderer.html#getTrailingPixles()">getTrailingPixles()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/BumpedRenderer.html" title="class in org.biojava.bio.gui.sequence">BumpedRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/DistributionTrainerContext.html#getTrainer(org.biojava.bio.dist.Distribution)">getTrainer(Distribution)</a></span> - Method in interface org.biojava.bio.dist.<a href="./org/biojava/bio/dist/DistributionTrainerContext.html" title="interface in org.biojava.bio.dist">DistributionTrainerContext</a></dt>
<dd>
<div class="block">Return the Distribution trainer object from the current context.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/SimpleDistributionTrainerContext.html#getTrainer(org.biojava.bio.dist.Distribution)">getTrainer(Distribution)</a></span> - Method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/SimpleDistributionTrainerContext.html" title="class in org.biojava.bio.dist">SimpleDistributionTrainerContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/FragmentPair.html#getTrans()">getTrans()</a></span> - Method in class org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/FragmentPair.html" title="class in org.biojava.bio.structure.align.pairwise">FragmentPair</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.html#getTransform()">getTransform()</a></span> - Method in class org.biojava.bio.chromatogram.graphic.<a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.html" title="class in org.biojava.bio.chromatogram.graphic">ChromatogramGraphic</a></dt>
<dd>
<div class="block">Returns a new AffineTransform describing the transformation
from chromatogram coordinates to output coordinates.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.html#getTransformAndConcat(java.awt.geom.AffineTransform)">getTransformAndConcat(AffineTransform)</a></span> - Method in class org.biojava.bio.chromatogram.graphic.<a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.html" title="class in org.biojava.bio.chromatogram.graphic">ChromatogramGraphic</a></dt>
<dd>
<div class="block">Concatenates the chromatogram-to-output transform to the
provided given AffineTransform.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SubSequence.SubProjectedFeatureContext.html#getTransformer()">getTransformer()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SubSequence.SubProjectedFeatureContext.html" title="class in org.biojava.bio.seq.impl">SubSequence.SubProjectedFeatureContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/projection/ReparentContext.html#getTransformer()">getTransformer()</a></span> - Method in class org.biojava.bio.seq.projection.<a href="./org/biojava/bio/seq/projection/ReparentContext.html" title="class in org.biojava.bio.seq.projection">ReparentContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/projection/TranslateFlipContext.html#getTransformer()">getTransformer()</a></span> - Method in class org.biojava.bio.seq.projection.<a href="./org/biojava/bio/seq/projection/TranslateFlipContext.html" title="class in org.biojava.bio.seq.projection">TranslateFlipContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/automata/FiniteAutomaton.html#getTransitions()">getTransitions()</a></span> - Method in class org.biojava.utils.automata.<a href="./org/biojava/utils/automata/FiniteAutomaton.html" title="class in org.biojava.utils.automata">FiniteAutomaton</a></dt>
<dd>
<div class="block">retrieve Set of all transitions in instance.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/automata/NfaBuilder.html#getTransitions()">getTransitions()</a></span> - Method in interface org.biojava.utils.automata.<a href="./org/biojava/utils/automata/NfaBuilder.html" title="interface in org.biojava.utils.automata">NfaBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/automata/NfaSubModel.html#getTransitions()">getTransitions()</a></span> - Method in class org.biojava.utils.automata.<a href="./org/biojava/utils/automata/NfaSubModel.html" title="class in org.biojava.utils.automata">NfaSubModel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/StateMachine.BasicState.html#getTransitionTable()">getTransitionTable()</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/StateMachine.BasicState.html" title="class in org.biojava.bio.program.tagvalue">StateMachine.BasicState</a></dt>
<dd>
<div class="block">retrieve the TransitionTable for this State.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/projection/TranslateFlipContext.html#getTranslation()">getTranslation()</a></span> - Method in class org.biojava.bio.seq.projection.<a href="./org/biojava/bio/seq/projection/TranslateFlipContext.html" title="class in org.biojava.bio.seq.projection">TranslateFlipContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/SVDSuperimposer.html#getTranslation()">getTranslation()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/SVDSuperimposer.html" title="class in org.biojava.bio.structure">SVDSuperimposer</a></dt>
<dd>
<div class="block">Get the shift vector.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.Terms.html#getTransposonTerm()">getTransposonTerm()</a></span> - Static method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.Terms.html" title="class in org.biojavax.bio.seq">RichSequence.Terms</a></dt>
<dd>
<div class="block">Getter for the Transposon term</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/LineSplitParser.html#getTrimTag()">getTrimTag()</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/LineSplitParser.html" title="class in org.biojava.bio.program.tagvalue">LineSplitParser</a></dt>
<dd>
<div class="block">See if tag trimming is enabled.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/RegexParser.html#getTrimTag()">getTrimTag()</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/RegexParser.html" title="class in org.biojava.bio.program.tagvalue">RegexParser</a></dt>
<dd>
<div class="block">See if trimming of tags is enabled.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/LineSplitParser.html#getTrimValue()">getTrimValue()</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/LineSplitParser.html" title="class in org.biojava.bio.program.tagvalue">LineSplitParser</a></dt>
<dd>
<div class="block">See if value trimming is enabled.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/RegexParser.html#getTrimValue()">getTrimValue()</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/RegexParser.html" title="class in org.biojava.bio.program.tagvalue">RegexParser</a></dt>
<dd>
<div class="block">See if trimming of values is enabled.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/IntegerOntology.html#getTriples(org.biojava.ontology.Term, org.biojava.ontology.Term, org.biojava.ontology.Term)">getTriples(Term, Term, Term)</a></span> - Method in class org.biojava.ontology.<a href="./org/biojava/ontology/IntegerOntology.html" title="class in org.biojava.ontology">IntegerOntology</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/Ontology.html#getTriples(org.biojava.ontology.Term, org.biojava.ontology.Term, org.biojava.ontology.Term)">getTriples(Term, Term, Term)</a></span> - Method in interface org.biojava.ontology.<a href="./org/biojava/ontology/Ontology.html" title="interface in org.biojava.ontology">Ontology</a></dt>
<dd>
<div class="block">Return all triples from this ontology which match the supplied
pattern.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/Ontology.Impl.html#getTriples(org.biojava.ontology.Term, org.biojava.ontology.Term, org.biojava.ontology.Term)">getTriples(Term, Term, Term)</a></span> - Method in class org.biojava.ontology.<a href="./org/biojava/ontology/Ontology.Impl.html" title="class in org.biojava.ontology">Ontology.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ontology/SimpleComparableOntology.html#getTriples(org.biojava.ontology.Term, org.biojava.ontology.Term, org.biojava.ontology.Term)">getTriples(Term, Term, Term)</a></span> - Method in class org.biojavax.ontology.<a href="./org/biojavax/ontology/SimpleComparableOntology.html" title="class in org.biojavax.ontology">SimpleComparableOntology</a></dt>
<dd>
<div class="block">Return all triples from this ontology which match the supplied
pattern.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ontology/ComparableOntology.html#getTripleSet()">getTripleSet()</a></span> - Method in interface org.biojavax.ontology.<a href="./org/biojavax/ontology/ComparableOntology.html" title="interface in org.biojavax.ontology">ComparableOntology</a></dt>
<dd>
<div class="block">Returns the set of triples in this ontology.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ontology/SimpleComparableOntology.html#getTripleSet()">getTripleSet()</a></span> - Method in class org.biojavax.ontology.<a href="./org/biojavax/ontology/SimpleComparableOntology.html" title="class in org.biojavax.ontology">SimpleComparableOntology</a></dt>
<dd>
<div class="block">Returns the set of triples in this ontology.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/ProteaseManager.html#getTrypsin()">getTrypsin()</a></span> - Static method in class org.biojava.bio.proteomics.<a href="./org/biojava/bio/proteomics/ProteaseManager.html" title="class in org.biojava.bio.proteomics">ProteaseManager</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/ImageMap.HotSpot.html#getType()">getType()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/ImageMap.HotSpot.html" title="class in org.biojava.bio.gui.sequence">ImageMap.HotSpot</a></dt>
<dd>
<div class="block"><code>getType</code> returns the type of hotspot.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/formats/Embl.html#getType()">getType()</a></span> - Method in class org.biojava.bio.program.formats.<a href="./org/biojava/bio/program/formats/Embl.html" title="class in org.biojava.bio.program.formats">Embl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/formats/Enzyme.html#getType()">getType()</a></span> - Method in class org.biojava.bio.program.formats.<a href="./org/biojava/bio/program/formats/Enzyme.html" title="class in org.biojava.bio.program.formats">Enzyme</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/formats/Format.html#getType()">getType()</a></span> - Method in interface org.biojava.bio.program.formats.<a href="./org/biojava/bio/program/formats/Format.html" title="interface in org.biojava.bio.program.formats">Format</a></dt>
<dd>
<div class="block">Get the AnnotationType that constrains the events that will be fired.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/formats/Ligand.Compound.html#getType()">getType()</a></span> - Method in class org.biojava.bio.program.formats.<a href="./org/biojava/bio/program/formats/Ligand.Compound.html" title="class in org.biojava.bio.program.formats">Ligand.Compound</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/formats/Ligand.Enzyme.html#getType()">getType()</a></span> - Method in class org.biojava.bio.program.formats.<a href="./org/biojava/bio/program/formats/Ligand.Enzyme.html" title="class in org.biojava.bio.program.formats">Ligand.Enzyme</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/formats/Ligand.Reaction.html#getType()">getType()</a></span> - Method in class org.biojava.bio.program.formats.<a href="./org/biojava/bio/program/formats/Ligand.Reaction.html" title="class in org.biojava.bio.program.formats">Ligand.Reaction</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/formats/Swissprot.html#getType()">getType()</a></span> - Method in class org.biojava.bio.program.formats.<a href="./org/biojava/bio/program/formats/Swissprot.html" title="class in org.biojava.bio.program.formats">Swissprot</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff3/GFF3Record.html#getType()">getType()</a></span> - Method in interface org.biojava.bio.program.gff3.<a href="./org/biojava/bio/program/gff3/GFF3Record.html" title="interface in org.biojava.bio.program.gff3">GFF3Record</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff3/GFF3Record.Impl.html#getType()">getType()</a></span> - Method in class org.biojava.bio.program.gff3.<a href="./org/biojava/bio/program/gff3/GFF3Record.Impl.html" title="class in org.biojava.bio.program.gff3">GFF3Record.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/Feature.html#getType()">getType()</a></span> - Method in interface org.biojava.bio.seq.<a href="./org/biojava/bio/seq/Feature.html" title="interface in org.biojava.bio.seq">Feature</a></dt>
<dd>
<div class="block">The type of the feature.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ByAnnotationType.html#getType()">getType()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ByAnnotationType.html" title="class in org.biojava.bio.seq">FeatureFilter.ByAnnotationType</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ByType.html#getType()">getType()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ByType.html" title="class in org.biojava.bio.seq">FeatureFilter.ByType</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureTypes.html#getType(java.lang.String)">getType(String)</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureTypes.html" title="class in org.biojava.bio.seq">FeatureTypes</a></dt>
<dd>
<div class="block">Get a Type by URI.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureTypes.Repository.html#getType(java.lang.String)">getType(String)</a></span> - Method in interface org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureTypes.Repository.html" title="interface in org.biojava.bio.seq">FeatureTypes.Repository</a></dt>
<dd>
<div class="block">Find the type for a name.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureTypes.RepositoryImpl.html#getType(java.lang.String)">getType(String)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureTypes.RepositoryImpl.html" title="class in org.biojava.bio.seq">FeatureTypes.RepositoryImpl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleFeature.html#getType()">getType()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleFeature.html" title="class in org.biojava.bio.seq.impl">SimpleFeature</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEIdAlias.html#getType()">getType()</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEIdAlias.html" title="class in org.biojava.bio.seq.io.agave">AGAVEIdAlias</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/AminoAcidImpl.html#getType()">getType()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/AminoAcidImpl.html" title="class in org.biojava.bio.structure">AminoAcidImpl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Group.html#getType()">getType()</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Group.html" title="interface in org.biojava.bio.structure">Group</a></dt>
<dd>
<div class="block">get Type of group, e.g.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/HetatomImpl.html#getType()">getType()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/HetatomImpl.html" title="class in org.biojava.bio.structure">HetatomImpl</a></dt>
<dd>
<div class="block">Returns the type value.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html#getType()">getType()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html" title="class in org.biojava.bio.structure.io.mmcif.model">ChemComp</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Entity.html#getType()">getType()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Entity.html" title="class in org.biojava.bio.structure.io.mmcif.model">Entity</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/NucleotideImpl.html#getType()">getType()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/NucleotideImpl.html" title="class in org.biojava.bio.structure">NucleotideImpl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ChangeEvent.html#getType()">getType()</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/ChangeEvent.html" title="class in org.biojava.utils">ChangeEvent</a></dt>
<dd>
<div class="block">Find the type of this event.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/ChangeForwarder.Retyper.html#getType()">getType()</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/ChangeForwarder.Retyper.html" title="class in org.biojava.utils">ChangeForwarder.Retyper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtCommentParser.Event.html#getType()">getType()</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtCommentParser.Event.html" title="class in org.biojavax.bio.seq.io">UniProtCommentParser.Event</a></dt>
<dd>
<div class="block">Getter for property type.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtCommentParser.SeqCaution.html#getType()">getType()</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtCommentParser.SeqCaution.html" title="class in org.biojavax.bio.seq.io">UniProtCommentParser.SeqCaution</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/Position.html#getType()">getType()</a></span> - Method in interface org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/Position.html" title="interface in org.biojavax.bio.seq">Position</a></dt>
<dd>
<div class="block">Returns the type of this position if it is not a point/single position.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimplePosition.html#getType()">getType()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimplePosition.html" title="class in org.biojavax.bio.seq">SimplePosition</a></dt>
<dd>
<div class="block">Returns the type of this position if it is not a point/single position.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichFeature.html#getType()">getType()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichFeature.html" title="class in org.biojavax.bio.seq">SimpleRichFeature</a></dt>
<dd>
<div class="block">The type of the feature.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html#getType_symbol()">getType_symbol()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html" title="class in org.biojava.bio.structure.io.mmcif.model">AtomSite</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/walker/WalkerFactory.html#getTypeClass()">getTypeClass()</a></span> - Method in class org.biojava.utils.walker.<a href="./org/biojava/utils/walker/WalkerFactory.html" title="class in org.biojava.utils.walker">WalkerFactory</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/xff/FeatureHandler.html#getTypeHandler()">getTypeHandler()</a></span> - Method in class org.biojava.bio.program.xff.<a href="./org/biojava/bio/program/xff/FeatureHandler.html" title="class in org.biojava.bio.program.xff">FeatureHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/DAS.html#getTypes(java.net.URL)">getTypes(URL)</a></span> - Static method in class org.biojava.bio.program.das.<a href="./org/biojava/bio/program/das/DAS.html" title="class in org.biojava.bio.program.das">DAS</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureTypes.Repository.html#getTypes()">getTypes()</a></span> - Method in interface org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureTypes.Repository.html" title="interface in org.biojava.bio.seq">FeatureTypes.Repository</a></dt>
<dd>
<div class="block">Get a set of all type names defined in this repository.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureTypes.RepositoryImpl.html#getTypes()">getTypes()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureTypes.RepositoryImpl.html" title="class in org.biojava.bio.seq">FeatureTypes.RepositoryImpl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/Feature.html#getTypeTerm()">getTypeTerm()</a></span> - Method in interface org.biojava.bio.seq.<a href="./org/biojava/bio/seq/Feature.html" title="interface in org.biojava.bio.seq">Feature</a></dt>
<dd>
<div class="block">An ontology term defining the type of feature.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleFeature.html#getTypeTerm()">getTypeTerm()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleFeature.html" title="class in org.biojava.bio.seq.impl">SimpleFeature</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByTypeTerm.html#getTypeTerm()">getTypeTerm()</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByTypeTerm.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.ByTypeTerm</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichFeature.html#getTypeTerm()">getTypeTerm()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichFeature.html" title="class in org.biojavax.bio.seq">SimpleRichFeature</a></dt>
<dd>
<div class="block">An ontology term defining the type of feature.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByTypeTermName.html#getTypeTermName()">getTypeTermName()</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByTypeTermName.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.ByTypeTermName</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/jama/LUDecomposition.html#getU()">getU()</a></span> - Method in class org.biojava.bio.structure.jama.<a href="./org/biojava/bio/structure/jama/LUDecomposition.html" title="class in org.biojava.bio.structure.jama">LUDecomposition</a></dt>
<dd>
<div class="block">Return upper triangular factor</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/jama/SingularValueDecomposition.html#getU()">getU()</a></span> - Method in class org.biojava.bio.structure.jama.<a href="./org/biojava/bio/structure/jama/SingularValueDecomposition.html" title="class in org.biojava.bio.structure.jama">SingularValueDecomposition</a></dt>
<dd>
<div class="block">Return the left singular vectors</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/GappedSymbolList.html#getUngappedLocation()">getUngappedLocation()</a></span> - Method in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/GappedSymbolList.html" title="interface in org.biojava.bio.symbol">GappedSymbolList</a></dt>
<dd>
<div class="block">Get a Location that contains exactly those positions that are not gaps.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleGappedSymbolList.html#getUngappedLocation()">getUngappedLocation()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleGappedSymbolList.html" title="class in org.biojava.bio.symbol">SimpleGappedSymbolList</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtFormat.Terms.html#getUniProtDBNameTerm()">getUniProtDBNameTerm()</a></span> - Static method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtFormat.Terms.html" title="class in org.biojavax.bio.seq.io">UniProtFormat.Terms</a></dt>
<dd>
<div class="block">Getter for the UniProt combined database term</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.Terms.html#getUniprotKWOnto()">getUniprotKWOnto()</a></span> - Static method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.Terms.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat.Terms</a></dt>
<dd>
<div class="block">Getter for the private uniprot ontology.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtFormat.Terms.html#getUniProtTerm()">getUniProtTerm()</a></span> - Static method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtFormat.Terms.html" title="class in org.biojavax.bio.seq.io">UniProtFormat.Terms</a></dt>
<dd>
<div class="block">Getter for the UniProt term</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.Terms.html#getUniProtXMLTerm()">getUniProtXMLTerm()</a></span> - Static method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.Terms.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat.Terms</a></dt>
<dd>
<div class="block">Getter for the UniProtXML term</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/unigene/UnigeneCluster.html#getUnique()">getUnique()</a></span> - Method in interface org.biojava.bio.program.unigene.<a href="./org/biojava/bio/program/unigene/UnigeneCluster.html" title="interface in org.biojava.bio.program.unigene">UnigeneCluster</a></dt>
<dd>
<div class="block">The unique sequence that is used as a representative for this cluster.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEMapLocation.html#getUnits()">getUnits()</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEMapLocation.html" title="class in org.biojava.bio.seq.io.agave">AGAVEMapLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/FragmentPair.html#getUnitv()">getUnitv()</a></span> - Method in class org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/FragmentPair.html" title="class in org.biojava.bio.structure.align.pairwise">FragmentPair</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/projection/ProjectionContext.html#getUnprojectedFeatures()">getUnprojectedFeatures()</a></span> - Method in interface org.biojava.bio.seq.projection.<a href="./org/biojava/bio/seq/projection/ProjectionContext.html" title="interface in org.biojava.bio.seq.projection">ProjectionContext</a></dt>
<dd>
<div class="block">Get the features before projection.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/projection/ReparentContext.html#getUnprojectedFeatures()">getUnprojectedFeatures()</a></span> - Method in class org.biojava.bio.seq.projection.<a href="./org/biojava/bio/seq/projection/ReparentContext.html" title="class in org.biojava.bio.seq.projection">ReparentContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/Agave2AgaveAnnotFilter.html#getUpdateDate(org.biojava.bio.Annotation)">getUpdateDate(Annotation)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/Agave2AgaveAnnotFilter.html" title="class in org.biojava.bio.seq.io.agave">Agave2AgaveAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEAnnotFilter.html#getUpdateDate(org.biojava.bio.Annotation)">getUpdateDate(Annotation)</a></span> - Method in interface org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEAnnotFilter.html" title="interface in org.biojava.bio.seq.io.agave">AGAVEAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/SimpleAnnotFilter.html#getUpdateDate(org.biojava.bio.Annotation)">getUpdateDate(Annotation)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/SimpleAnnotFilter.html" title="class in org.biojava.bio.seq.io.agave">SimpleAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/molbio/RestrictionEnzyme.html#getUpstreamCut()">getUpstreamCut()</a></span> - Method in class org.biojava.bio.molbio.<a href="./org/biojava/bio/molbio/RestrictionEnzyme.html" title="class in org.biojava.bio.molbio">RestrictionEnzyme</a></dt>
<dd>
<div class="block"><code>getUpstreamCut</code> returns the cut site upstream of
the recognition site.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/molbio/RestrictionEnzyme.html#getUpstreamEndType()">getUpstreamEndType()</a></span> - Method in class org.biojava.bio.molbio.<a href="./org/biojava/bio/molbio/RestrictionEnzyme.html" title="class in org.biojava.bio.molbio">RestrictionEnzyme</a></dt>
<dd>
<div class="block"><code>getUpstreamEndType</code> returns the double-stranded end
type produced by the secondary (upstream) cut.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureTypes.Type.html#getURI()">getURI()</a></span> - Method in interface org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureTypes.Type.html" title="interface in org.biojava.bio.seq">FeatureTypes.Type</a></dt>
<dd>
<div class="block">Get the URI for this type.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html#getUri()">getUri()</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html" title="class in org.biojavax.bio.seq.io">UniProtCommentParser</a></dt>
<dd>
<div class="block">Getter for property uri.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/Namespace.html#getURI()">getURI()</a></span> - Method in interface org.biojavax.<a href="./org/biojavax/Namespace.html" title="interface in org.biojavax">Namespace</a></dt>
<dd>
<div class="block">If the namespace has a URI, this will return it.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleNamespace.html#getURI()">getURI()</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleNamespace.html" title="class in org.biojavax">SimpleNamespace</a></dt>
<dd>
<div class="block">If the namespace has a URI, this will return it.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/ImageMap.HotSpot.html#getURL()">getURL()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/ImageMap.HotSpot.html" title="class in org.biojava.bio.gui.sequence">ImageMap.HotSpot</a></dt>
<dd>
<div class="block"><code>getURL</code> returns the hotspot URL.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/DASSequenceDB.html#getURL()">getURL()</a></span> - Method in class org.biojava.bio.program.das.<a href="./org/biojava/bio/program/das/DASSequenceDB.html" title="class in org.biojava.bio.program.das">DASSequenceDB</a></dt>
<dd>
<div class="block">Return the URL of the reference server for this database.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/DataSource.html#getURL()">getURL()</a></span> - Method in class org.biojava.bio.program.das.<a href="./org/biojava/bio/program/das/DataSource.html" title="class in org.biojava.bio.program.das">DataSource</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/DASSequence.html#getURN()">getURN()</a></span> - Method in class org.biojava.bio.program.das.<a href="./org/biojava/bio/program/das/DASSequence.html" title="class in org.biojava.bio.program.das">DASSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/DummySequence.html#getURN()">getURN()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/DummySequence.html" title="class in org.biojava.bio.seq.impl">DummySequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleGappedSequence.html#getURN()">getURN()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleGappedSequence.html" title="class in org.biojava.bio.seq.impl">SimpleGappedSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleSequence.html#getURN()">getURN()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleSequence.html" title="class in org.biojava.bio.seq.impl">SimpleSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SubSequence.html#getURN()">getURN()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SubSequence.html" title="class in org.biojava.bio.seq.impl">SubSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/ViewSequence.html#getURN()">getURN()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/ViewSequence.html" title="class in org.biojava.bio.seq.impl">ViewSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/NewSimpleAssembly.html#getURN()">getURN()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/NewSimpleAssembly.html" title="class in org.biojava.bio.seq">NewSimpleAssembly</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/Sequence.html#getURN()">getURN()</a></span> - Method in interface org.biojava.bio.seq.<a href="./org/biojava/bio/seq/Sequence.html" title="interface in org.biojava.bio.seq">Sequence</a></dt>
<dd>
<div class="block">A <a href="http://www.rfc-editor.org/rfc/rfc2396.txt">Uniform
Resource Identifier</a> (URI) which identifies the sequence
represented by this object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/SimpleAssembly.html#getURN()">getURN()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/SimpleAssembly.html" title="class in org.biojava.bio.seq">SimpleAssembly</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/ThinRichSequence.html#getURN()">getURN()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/ThinRichSequence.html" title="class in org.biojavax.bio.seq">ThinRichSequence</a></dt>
<dd>
<div class="block">A <a href="http://www.rfc-editor.org/rfc/rfc2396.txt">Uniform
Resource Identifier</a> (URI) which identifies the sequence
represented by this object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/FragmentPair.html#getUsed()">getUsed()</a></span> - Method in class org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/FragmentPair.html" title="class in org.biojava.bio.structure.align.pairwise">FragmentPair</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/StrucAligParameters.html#getUsedAtomNames()">getUsedAtomNames()</a></span> - Method in class org.biojava.bio.structure.align.<a href="./org/biojava/bio/structure/align/StrucAligParameters.html" title="class in org.biojava.bio.structure.align">StrucAligParameters</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/ImageMap.HotSpot.html#getUserObject()">getUserObject()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/ImageMap.HotSpot.html" title="class in org.biojava.bio.gui.sequence">ImageMap.HotSpot</a></dt>
<dd>
<div class="block"><code>getUserObject</code> returns the current user object
(or null).</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/jama/EigenvalueDecomposition.html#getV()">getV()</a></span> - Method in class org.biojava.bio.structure.jama.<a href="./org/biojava/bio/structure/jama/EigenvalueDecomposition.html" title="class in org.biojava.bio.structure.jama">EigenvalueDecomposition</a></dt>
<dd>
<div class="block">Return the eigenvector matrix</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/jama/SingularValueDecomposition.html#getV()">getV()</a></span> - Method in class org.biojava.bio.structure.jama.<a href="./org/biojava/bio/structure/jama/SingularValueDecomposition.html" title="class in org.biojava.bio.structure.jama">SingularValueDecomposition</a></dt>
<dd>
<div class="block">Return the right singular vectors</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/TagValue.html#getValue()">getValue()</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/TagValue.html" title="class in org.biojava.bio.program.tagvalue">TagValue</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/PropertyConstraint.ExactValue.html#getValue()">getValue()</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/PropertyConstraint.ExactValue.html" title="class in org.biojava.bio">PropertyConstraint.ExactValue</a></dt>
<dd>
<div class="block">Get the value that all properties must match.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.AnnotationContains.html#getValue()">getValue()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.AnnotationContains.html" title="class in org.biojava.bio.seq">FeatureFilter.AnnotationContains</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ByAnnotation.html#getValue()">getValue()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ByAnnotation.html" title="class in org.biojava.bio.seq">FeatureFilter.ByAnnotation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEProperty.html#getValue()">getValue()</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEProperty.html" title="class in org.biojava.bio.seq.io.agave">AGAVEProperty</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/StrandedFeature.Strand.html#getValue()">getValue()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/StrandedFeature.Strand.html" title="class in org.biojava.bio.seq">StrandedFeature.Strand</a></dt>
<dd>
<div class="block">Returns the integer label for strandedness.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/helper/AligMatEl.html#getValue()">getValue()</a></span> - Method in class org.biojava.bio.structure.align.helper.<a href="./org/biojava/bio/structure/align/helper/AligMatEl.html" title="class in org.biojava.bio.structure.align.helper">AligMatEl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/helper/GapArray.html#getValue()">getValue()</a></span> - Method in class org.biojava.bio.structure.align.helper.<a href="./org/biojava/bio/structure/align/helper/GapArray.html" title="class in org.biojava.bio.structure.align.helper">GapArray</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/ItemValue.html#getValue()">getValue()</a></span> - Method in interface org.biojava.stats.svm.<a href="./org/biojava/stats/svm/ItemValue.html" title="interface in org.biojava.stats.svm">ItemValue</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/SimpleItemValue.html#getValue()">getValue()</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/SimpleItemValue.html" title="class in org.biojava.stats.svm">SimpleItemValue</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/walker/Walker.html#getValue()">getValue()</a></span> - Method in interface org.biojava.utils.walker.<a href="./org/biojava/utils/walker/Walker.html" title="interface in org.biojava.utils.walker">Walker</a></dt>
<dd>
<div class="block">If the visitor has a return value, then the result of applying the visitor
to the tree can be obtained using this method, otherwise the result will
be null.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/Note.html#getValue()">getValue()</a></span> - Method in interface org.biojavax.<a href="./org/biojavax/Note.html" title="interface in org.biojavax">Note</a></dt>
<dd>
<div class="block">Gets the value that defines this note.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleNote.html#getValue()">getValue()</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleNote.html" title="class in org.biojavax">SimpleNote</a></dt>
<dd>
<div class="block">Gets the value that defines this note.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/utils/CRC64Checksum.html#getValue()">getValue()</a></span> - Method in class org.biojavax.utils.<a href="./org/biojavax/utils/CRC64Checksum.html" title="class in org.biojavax.utils">CRC64Checksum</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/SubstitutionMatrix.html#getValueAt(org.biojava.bio.symbol.Symbol, org.biojava.bio.symbol.Symbol)">getValueAt(Symbol, Symbol)</a></span> - Method in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/SubstitutionMatrix.html" title="class in org.biojava.bio.alignment">SubstitutionMatrix</a></dt>
<dd>
<div class="block">There are some substitution matrices containing more columns than lines.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/SparseVector.html#getValueAtIndex(int)">getValueAtIndex(int)</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/SparseVector.html" title="class in org.biojava.stats.svm">SparseVector</a></dt>
<dd>
<div class="block">Retrieve the value at a specific index.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/RegexParser.html#getValueGroup()">getValueGroup()</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/RegexParser.html" title="class in org.biojava.bio.program.tagvalue">RegexParser</a></dt>
<dd>
<div class="block">Get the group number that matches the value.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/PropertyConstraint.Enumeration.html#getValues()">getValues()</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/PropertyConstraint.Enumeration.html" title="class in org.biojava.bio">PropertyConstraint.Enumeration</a></dt>
<dd>
<div class="block"><code>getValues</code> returns the set of values which
constrain the property.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/MassCalc.html#getVariableMasses(org.biojava.bio.symbol.SymbolList)">getVariableMasses(SymbolList)</a></span> - Method in class org.biojava.bio.proteomics.<a href="./org/biojava/bio/proteomics/MassCalc.html" title="class in org.biojava.bio.proteomics">MassCalc</a></dt>
<dd>
<div class="block">Get all masses including the variable mass.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/fastq/Fastq.html#getVariant()">getVariant()</a></span> - Method in class org.biojava.bio.program.fastq.<a href="./org/biojava/bio/program/fastq/Fastq.html" title="class in org.biojava.bio.program.fastq">Fastq</a></dt>
<dd>
<div class="block">Return the FASTQ sequence format variant for this FASTQ formatted sequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/fastq/IlluminaFastqReader.html#getVariant()">getVariant()</a></span> - Method in class org.biojava.bio.program.fastq.<a href="./org/biojava/bio/program/fastq/IlluminaFastqReader.html" title="class in org.biojava.bio.program.fastq">IlluminaFastqReader</a></dt>
<dd>
<div class="block">Return the FASTQ sequence format variant for this reader.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/fastq/SangerFastqReader.html#getVariant()">getVariant()</a></span> - Method in class org.biojava.bio.program.fastq.<a href="./org/biojava/bio/program/fastq/SangerFastqReader.html" title="class in org.biojava.bio.program.fastq">SangerFastqReader</a></dt>
<dd>
<div class="block">Return the FASTQ sequence format variant for this reader.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/fastq/SolexaFastqReader.html#getVariant()">getVariant()</a></span> - Method in class org.biojava.bio.program.fastq.<a href="./org/biojava/bio/program/fastq/SolexaFastqReader.html" title="class in org.biojava.bio.program.fastq">SolexaFastqReader</a></dt>
<dd>
<div class="block">Return the FASTQ sequence format variant for this reader.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Compound.html#getVariant()">getVariant()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure">Compound</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/SVMRegressionModel.html#getVector(int)">getVector(int)</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/SVMRegressionModel.html" title="class in org.biojava.stats.svm">SVMRegressionModel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/tools/SVM_Light.LabelledVector.html#getVector()">getVector()</a></span> - Method in class org.biojava.stats.svm.tools.<a href="./org/biojava/stats/svm/tools/SVM_Light.LabelledVector.html" title="class in org.biojava.stats.svm.tools">SVM_Light.LabelledVector</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/dasalignment/Alignment.html#getVectorAnnotationType()">getVectorAnnotationType()</a></span> - Static method in class org.biojava.bio.program.das.dasalignment.<a href="./org/biojava/bio/program/das/dasalignment/Alignment.html" title="class in org.biojava.bio.program.das.dasalignment">Alignment</a></dt>
<dd>
<div class="block">define the shift vector annotation type</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/GenbankFileFormer.html#getVectorNTISupport()">getVectorNTISupport()</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/GenbankFileFormer.html" title="class in org.biojava.bio.seq.io">GenbankFileFormer</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Is VectorNTI compatable output being produced?</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/dasalignment/Alignment.html#getVectors()">getVectors()</a></span> - Method in class org.biojava.bio.program.das.dasalignment.<a href="./org/biojava/bio/program/das/dasalignment/Alignment.html" title="class in org.biojava.bio.program.das.dasalignment">Alignment</a></dt>
<dd>
<div class="block">Returns the shift vectors.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/Agave2AgaveAnnotFilter.html#getVersion(org.biojava.bio.Annotation)">getVersion(Annotation)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/Agave2AgaveAnnotFilter.html" title="class in org.biojava.bio.seq.io.agave">Agave2AgaveAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEAnnotFilter.html#getVersion(org.biojava.bio.Annotation)">getVersion(Annotation)</a></span> - Method in interface org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEAnnotFilter.html" title="interface in org.biojava.bio.seq.io.agave">AGAVEAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEDbId.html#getVersion()">getVersion()</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEDbId.html" title="class in org.biojava.bio.seq.io.agave">AGAVEDbId</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/Embl2AgaveAnnotFilter.html#getVersion(org.biojava.bio.Annotation)">getVersion(Annotation)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/Embl2AgaveAnnotFilter.html" title="class in org.biojava.bio.seq.io.agave">Embl2AgaveAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/SimpleAnnotFilter.html#getVersion(org.biojava.bio.Annotation)">getVersion(Annotation)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/SimpleAnnotFilter.html" title="class in org.biojava.bio.seq.io.agave">SimpleAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/candy/CandyVocabulary.html#getVersion()">getVersion()</a></span> - Method in interface org.biojava.utils.candy.<a href="./org/biojava/utils/candy/CandyVocabulary.html" title="interface in org.biojava.utils.candy">CandyVocabulary</a></dt>
<dd>
<div class="block">It returns a vesrion of this vocabulary.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/BioEntry.html#getVersion()">getVersion()</a></span> - Method in interface org.biojavax.bio.<a href="./org/biojavax/bio/BioEntry.html" title="interface in org.biojavax.bio">BioEntry</a></dt>
<dd>
<div class="block">Gets the version of this bioentry.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/SimpleBioEntry.html#getVersion()">getVersion()</a></span> - Method in class org.biojavax.bio.<a href="./org/biojavax/bio/SimpleBioEntry.html" title="class in org.biojavax.bio">SimpleBioEntry</a></dt>
<dd>
<div class="block">Gets the version of this bioentry.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/CrossRef.html#getVersion()">getVersion()</a></span> - Method in interface org.biojavax.<a href="./org/biojavax/CrossRef.html" title="interface in org.biojavax">CrossRef</a></dt>
<dd>
<div class="block">Returns the version of the object that the crossref refers to.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleCrossRef.html#getVersion()">getVersion()</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleCrossRef.html" title="class in org.biojavax">SimpleCrossRef</a></dt>
<dd>
<div class="block">Returns the version of the object that the crossref refers to.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLFormat.Terms.html#getVersionLineTerm()">getVersionLineTerm()</a></span> - Static method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLFormat.Terms.html" title="class in org.biojavax.bio.seq.io">EMBLFormat.Terms</a></dt>
<dd>
<div class="block">Getter for the Ensembl-specific 'versionLine' term</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.html#getVerticalScale()">getVerticalScale()</a></span> - Method in class org.biojava.bio.chromatogram.graphic.<a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.html" title="class in org.biojava.bio.chromatogram.graphic">ChromatogramGraphic</a></dt>
<dd>
<div class="block">Returns the in use vertical scale factor.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/projection/ProjectedFeature.html#getViewedFeature()">getViewedFeature()</a></span> - Method in class org.biojava.bio.seq.projection.<a href="./org/biojava/bio/seq/projection/ProjectedFeature.html" title="class in org.biojava.bio.seq.projection">ProjectedFeature</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/projection/Projection.html#getViewedFeature()">getViewedFeature()</a></span> - Method in interface org.biojava.bio.seq.projection.<a href="./org/biojava/bio/seq/projection/Projection.html" title="interface in org.biojava.bio.seq.projection">Projection</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/GUITools.html#getVisibleRange(org.biojava.bio.gui.sequence.SequenceRenderContext, java.awt.Graphics2D)">getVisibleRange(SequenceRenderContext, Graphics2D)</a></span> - Static method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/GUITools.html" title="class in org.biojava.bio.gui.sequence">GUITools</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePoster.html#getVisibleRange()">getVisibleRange()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePoster.html" title="class in org.biojava.bio.gui.sequence">SequencePoster</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PairwiseSequencePanel.html#getVisibleSecondarySymbolCount()">getVisibleSecondarySymbolCount()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PairwiseSequencePanel.html" title="class in org.biojava.bio.gui.sequence">PairwiseSequencePanel</a></dt>
<dd>
<div class="block"><code>getVisibleSecondarySymbolCount</code> returns the
<strong>maximum</strong> number of secondary
<code>Symbol</code>s which can be rendered in the visible area
(excluding all borders) of the
<code>PairwiseSequencePanel</code> at the current scale.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PairwiseSequencePanel.html#getVisibleSymbolCount()">getVisibleSymbolCount()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PairwiseSequencePanel.html" title="class in org.biojava.bio.gui.sequence">PairwiseSequencePanel</a></dt>
<dd>
<div class="block"><code>getVisibleSymbolCount</code> returns the
<strong>maximum</strong> number of <code>Symbol</code>s which
can be rendered in the visible area (excluding all borders) of
the <code>PairwiseSequencePanel</code> at the current
scale.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/TranslatedSequencePanel.html#getVisibleSymbolCount()">getVisibleSymbolCount()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/TranslatedSequencePanel.html" title="class in org.biojava.bio.gui.sequence">TranslatedSequencePanel</a></dt>
<dd>
<div class="block"><code>getVisibleSymbolCount</code> returns the
<strong>maximum</strong> number of <code>Symbol</code>s which
can be rendered in the visible area (excluding all borders) of
the <code>TranslatedSequencePanel</code> at the current
scale.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html#getVMaxes()">getVMaxes()</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html" title="class in org.biojavax.bio.seq.io">UniProtCommentParser</a></dt>
<dd>
<div class="block">Getter for property VMaxes.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/candy/CandyFinder.html#getVocabularyByName(java.lang.String)">getVocabularyByName(String)</a></span> - Method in interface org.biojava.utils.candy.<a href="./org/biojava/utils/candy/CandyFinder.html" title="interface in org.biojava.utils.candy">CandyFinder</a></dt>
<dd>
<div class="block">It returns a selected vocabulary.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BibRefSupport.html#getVocabularyFinder()">getVocabularyFinder()</a></span> - Method in interface org.biojava.bibliography.<a href="./org/biojava/bibliography/BibRefSupport.html" title="interface in org.biojava.bibliography">BibRefSupport</a></dt>
<dd>
<div class="block">
It returns an object representing a central place where all
controlled vocabularies can be received from and shared by all
users.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/JournalArticle.html#getVolume()">getVolume()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/JournalArticle.html" title="class in org.biojava.bio.structure">JournalArticle</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/walker/WalkerFactory.html#getWalker(org.biojava.utils.walker.Visitor)">getWalker(Visitor)</a></span> - Method in class org.biojava.utils.walker.<a href="./org/biojava/utils/walker/WalkerFactory.html" title="class in org.biojava.utils.walker">WalkerFactory</a></dt>
<dd>
<div class="block">Get a Walker that is customosed to a particular visitor.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/AbstractDistribution.html#getWeight(org.biojava.bio.symbol.Symbol)">getWeight(Symbol)</a></span> - Method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/AbstractDistribution.html" title="class in org.biojava.bio.dist">AbstractDistribution</a></dt>
<dd>
<div class="block">Retrieve the weight for this distribution.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/Distribution.html#getWeight(org.biojava.bio.symbol.Symbol)">getWeight(Symbol)</a></span> - Method in interface org.biojava.bio.dist.<a href="./org/biojava/bio/dist/Distribution.html" title="interface in org.biojava.bio.dist">Distribution</a></dt>
<dd>
<div class="block">
Return the probability that Symbol s is emitted by this spectrum.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/GapDistribution.html#getWeight(org.biojava.bio.symbol.Symbol)">getWeight(Symbol)</a></span> - Method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/GapDistribution.html" title="class in org.biojava.bio.dist">GapDistribution</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/PairDistribution.html#getWeight(org.biojava.bio.symbol.Symbol)">getWeight(Symbol)</a></span> - Method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/PairDistribution.html" title="class in org.biojava.bio.dist">PairDistribution</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/TranslatedDistribution.html#getWeight(org.biojava.bio.symbol.Symbol)">getWeight(Symbol)</a></span> - Method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/TranslatedDistribution.html" title="class in org.biojava.bio.dist">TranslatedDistribution</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/util/WeightedSet.html#getWeight(java.lang.Object)">getWeight(Object)</a></span> - Method in class org.biojavax.ga.util.<a href="./org/biojavax/ga/util/WeightedSet.html" title="class in org.biojavax.ga.util">WeightedSet</a></dt>
<dd>
<div class="block">Determines the normalized weight for <code>o</code></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/AbstractDistribution.html#getWeightImpl(org.biojava.bio.symbol.AtomicSymbol)">getWeightImpl(AtomicSymbol)</a></span> - Method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/AbstractDistribution.html" title="class in org.biojava.bio.dist">AbstractDistribution</a></dt>
<dd>
<div class="block">Override this method to implement getting the weight for an atomic
symbol.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/AbstractOrderNDistribution.html#getWeightImpl(org.biojava.bio.symbol.AtomicSymbol)">getWeightImpl(AtomicSymbol)</a></span> - Method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/AbstractOrderNDistribution.html" title="class in org.biojava.bio.dist">AbstractOrderNDistribution</a></dt>
<dd>
<div class="block">Get a weight from one of the sub-distributions, conditioned
on the first part of the symbol.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/SimpleDistribution.html#getWeightImpl(org.biojava.bio.symbol.AtomicSymbol)">getWeightImpl(AtomicSymbol)</a></span> - Method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/SimpleDistribution.html" title="class in org.biojava.bio.dist">SimpleDistribution</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/UniformDistribution.html#getWeightImpl(org.biojava.bio.symbol.AtomicSymbol)">getWeightImpl(AtomicSymbol)</a></span> - Method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/UniformDistribution.html" title="class in org.biojava.bio.dist">UniformDistribution</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/WeightMatrixAnnotator.html#getWeightMatrixID()">getWeightMatrixID()</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/WeightMatrixAnnotator.html" title="class in org.biojava.bio.dp">WeightMatrixAnnotator</a></dt>
<dd>
<div class="block">Get the value of the weight matrix id.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/SimpleDistribution.html#getWeights()">getWeights()</a></span> - Method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/SimpleDistribution.html" title="class in org.biojava.bio.dist">SimpleDistribution</a></dt>
<dd>
<div class="block">Get the underlying array that stores the weights.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/MarkovModel.html#getWeights(org.biojava.bio.dp.State)">getWeights(State)</a></span> - Method in interface org.biojava.bio.dp.<a href="./org/biojava/bio/dp/MarkovModel.html" title="interface in org.biojava.bio.dp">MarkovModel</a></dt>
<dd>
<div class="block">Get a probability Distribution over the transition from 'source'.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/SimpleMarkovModel.html#getWeights(org.biojava.bio.dp.State)">getWeights(State)</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/SimpleMarkovModel.html" title="class in org.biojava.bio.dp">SimpleMarkovModel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/WMAsMM.html#getWeights(org.biojava.bio.dp.State)">getWeights(State)</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/WMAsMM.html" title="class in org.biojava.bio.dp">WMAsMM</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.html#getWidth()">getWidth()</a></span> - Method in class org.biojava.bio.chromatogram.graphic.<a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.html" title="class in org.biojava.bio.chromatogram.graphic">ChromatogramGraphic</a></dt>
<dd>
<div class="block">Returns the width of the whole graphic (in pixels).</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/AlternateTokenization.html#getWidth()">getWidth()</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/AlternateTokenization.html" title="class in org.biojava.bio.seq.io">AlternateTokenization</a></dt>
<dd>
<div class="block">Get the width of the tokens.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/RadialBaseKernel.html#getWidth()">getWidth()</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/RadialBaseKernel.html" title="class in org.biojava.stats.svm">RadialBaseKernel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/CodonPref.html#getWobbleDistributionForSynonyms(org.biojava.bio.symbol.Symbol)">getWobbleDistributionForSynonyms(Symbol)</a></span> - Method in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/CodonPref.html" title="interface in org.biojava.bio.symbol">CodonPref</a></dt>
<dd>
<div class="block">returns a WobbleDistribution for
a specified residue.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleCodonPref.html#getWobbleDistributionForSynonyms(org.biojava.bio.symbol.Symbol)">getWobbleDistributionForSynonyms(Symbol)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleCodonPref.html" title="class in org.biojava.bio.symbol">SimpleCodonPref</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/WobbleDistribution.html#getWobbleFrequency(org.biojava.bio.symbol.Symbol)">getWobbleFrequency(Symbol)</a></span> - Method in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/WobbleDistribution.html" title="interface in org.biojava.bio.symbol">WobbleDistribution</a></dt>
<dd>
<div class="block">returns the frequency of a specific
wobble base in a set of synonymous
codons that start with the same two
bases.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/process/ExternalProcess.html#getWorkingDirectory()">getWorkingDirectory()</a></span> - Method in class org.biojava.utils.process.<a href="./org/biojava/utils/process/ExternalProcess.html" title="class in org.biojava.utils.process">ExternalProcess</a></dt>
<dd>
<div class="block">Gets the working directory for the external process.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePanelWrapper.html#getWrap()">getWrap()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePanelWrapper.html" title="class in org.biojava.bio.gui.sequence">SequencePanelWrapper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/tracklayout/SimpleTrackLayout.html#getWrap()">getWrap()</a></span> - Method in class org.biojava.bio.gui.sequence.tracklayout.<a href="./org/biojava/bio/gui/sequence/tracklayout/SimpleTrackLayout.html" title="class in org.biojava.bio.gui.sequence.tracklayout">SimpleTrackLayout</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/tracklayout/TrackLayout.html#getWrap()">getWrap()</a></span> - Method in interface org.biojava.bio.gui.sequence.tracklayout.<a href="./org/biojava/bio/gui/sequence/tracklayout/TrackLayout.html" title="interface in org.biojava.bio.gui.sequence.tracklayout">TrackLayout</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/tracklayout/UserDefinedTrackLayout.html#getWrap()">getWrap()</a></span> - Method in class org.biojava.bio.gui.sequence.tracklayout.<a href="./org/biojava/bio/gui/sequence/tracklayout/UserDefinedTrackLayout.html" title="class in org.biojava.bio.gui.sequence.tracklayout">UserDefinedTrackLayout</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/tracklayout/SimpleTrackLayout.html#getWrapIncrement()">getWrapIncrement()</a></span> - Method in class org.biojava.bio.gui.sequence.tracklayout.<a href="./org/biojava/bio/gui/sequence/tracklayout/SimpleTrackLayout.html" title="class in org.biojava.bio.gui.sequence.tracklayout">SimpleTrackLayout</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/tracklayout/TrackLayout.html#getWrapIncrement()">getWrapIncrement()</a></span> - Method in interface org.biojava.bio.gui.sequence.tracklayout.<a href="./org/biojava/bio/gui/sequence/tracklayout/TrackLayout.html" title="interface in org.biojava.bio.gui.sequence.tracklayout">TrackLayout</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/tracklayout/UserDefinedTrackLayout.html#getWrapIncrement()">getWrapIncrement()</a></span> - Method in class org.biojava.bio.gui.sequence.tracklayout.<a href="./org/biojava/bio/gui/sequence/tracklayout/UserDefinedTrackLayout.html" title="class in org.biojava.bio.gui.sequence.tracklayout">UserDefinedTrackLayout</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/AnnotationChanger.html#getWrapped()">getWrapped()</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/AnnotationChanger.html" title="class in org.biojava.bio">AnnotationChanger</a></dt>
<dd>
<div class="block"><code>getWrapped</code> returns the <code>Annotation</code>
being remapped.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/AnnotationRenamer.html#getWrapped()">getWrapped()</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/AnnotationRenamer.html" title="class in org.biojava.bio">AnnotationRenamer</a></dt>
<dd>
<div class="block"><code>getWrapped</code> returns the <code>Annotation</code>
being remapped.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AbstractLocationDecorator.html#getWrapped()">getWrapped()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AbstractLocationDecorator.html" title="class in org.biojava.bio.symbol">AbstractLocationDecorator</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/SigmoidKernel.html#getWrappedKernel()">getWrappedKernel()</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/SigmoidKernel.html" title="class in org.biojava.stats.svm">SigmoidKernel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/process/ReaderWriterPipe.html#getWriter()">getWriter()</a></span> - Method in class org.biojava.utils.process.<a href="./org/biojava/utils/process/ReaderWriterPipe.html" title="class in org.biojava.utils.process">ReaderWriterPipe</a></dt>
<dd>
<div class="block">Gets the writer.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Atom.html#getX()">getX()</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Atom.html" title="interface in org.biojava.bio.structure">Atom</a></dt>
<dd>
<div class="block">Get coordinate X.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/AtomImpl.html#getX()">getX()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/AtomImpl.html" title="class in org.biojava.bio.structure">AtomImpl</a></dt>
<dd>
<div class="block">Get the X coordinate.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/xff/FeatureHandler.html#getXFFEnvironment()">getXFFEnvironment()</a></span> - Method in class org.biojava.bio.program.xff.<a href="./org/biojava/bio/program/xff/FeatureHandler.html" title="class in org.biojava.bio.program.xff">FeatureHandler</a></dt>
<dd>
<div class="block">Return the XFF processing environment passed in when this handler was
created.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game/GAMEDbxrefPropHandler.DbXrefElement.html#getXrefDb()">getXrefDb()</a></span> - Method in class org.biojava.bio.seq.io.game.<a href="./org/biojava/bio/seq/io/game/GAMEDbxrefPropHandler.DbXrefElement.html" title="class in org.biojava.bio.seq.io.game">GAMEDbxrefPropHandler.DbXrefElement</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEXref.html#getXrefProps()">getXrefProps()</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEXref.html" title="class in org.biojava.bio.seq.io.agave">AGAVEXref</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/Agave2AgaveAnnotFilter.html#getXrefs(org.biojava.bio.Annotation)">getXrefs(Annotation)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/Agave2AgaveAnnotFilter.html" title="class in org.biojava.bio.seq.io.agave">Agave2AgaveAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEAnnotFilter.html#getXrefs(org.biojava.bio.Annotation)">getXrefs(Annotation)</a></span> - Method in interface org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEAnnotFilter.html" title="interface in org.biojava.bio.seq.io.agave">AGAVEAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEXrefs.html#getXrefs()">getXrefs()</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEXrefs.html" title="class in org.biojava.bio.seq.io.agave">AGAVEXrefs</a></dt>
<dd>
<div class="block">return a set of AGAVEXref</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/SimpleAnnotFilter.html#getXrefs(org.biojava.bio.Annotation)">getXrefs(Annotation)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/SimpleAnnotFilter.html" title="class in org.biojava.bio.seq.io.agave">SimpleAnnotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Calc.html#getXYZEuler(org.biojava.bio.structure.jama.Matrix)">getXYZEuler(Matrix)</a></span> - Static method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Calc.html" title="class in org.biojava.bio.structure">Calc</a></dt>
<dd>
<div class="block">Convert a rotation Matrix to Euler angles.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Atom.html#getY()">getY()</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Atom.html" title="interface in org.biojava.bio.structure">Atom</a></dt>
<dd>
<div class="block">Get coordinate Y.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/AtomImpl.html#getY()">getY()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/AtomImpl.html" title="class in org.biojava.bio.structure">AtomImpl</a></dt>
<dd>
<div class="block">Get the Y coordinate.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Atom.html#getZ()">getZ()</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Atom.html" title="interface in org.biojava.bio.structure">Atom</a></dt>
<dd>
<div class="block">Get coordinate Z.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/AtomImpl.html#getZ()">getZ()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/AtomImpl.html" title="class in org.biojava.bio.structure">AtomImpl</a></dt>
<dd>
<div class="block">Get the Z coordinate.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Calc.html#getZYZEuler(org.biojava.bio.structure.jama.Matrix)">getZYZEuler(Matrix)</a></span> - Static method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Calc.html" title="class in org.biojava.bio.structure">Calc</a></dt>
<dd>
<div class="block">Gget euler angles for a matrix given in ZYZ convention.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOConstants.html#GFF">GFF</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOConstants.html" title="class in org.biojava.bio.seq.io">SeqIOConstants</a></dt>
<dd>
<div class="block"><code>GFF</code> indicates that the sequence format is GFF.</div>
</dd>
<dt><a href="./org/biojava/bio/program/gff3/GFF3DocumentHandler.html" title="interface in org.biojava.bio.program.gff3"><span class="strong">GFF3DocumentHandler</span></a> - Interface in <a href="./org/biojava/bio/program/gff3/package-summary.html">org.biojava.bio.program.gff3</a></dt>
<dd>
<div class="block">The interface for things that listen to GFF event streams.</div>
</dd>
<dt><a href="./org/biojava/bio/program/gff3/GFF3Parser.html" title="class in org.biojava.bio.program.gff3"><span class="strong">GFF3Parser</span></a> - Class in <a href="./org/biojava/bio/program/gff3/package-summary.html">org.biojava.bio.program.gff3</a></dt>
<dd>
<div class="block">Parse a stream of GFF text into a stream of records and comments.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff3/GFF3Parser.html#GFF3Parser()">GFF3Parser()</a></span> - Constructor for class org.biojava.bio.program.gff3.<a href="./org/biojava/bio/program/gff3/GFF3Parser.html" title="class in org.biojava.bio.program.gff3">GFF3Parser</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/gff3/GFF3Record.html" title="interface in org.biojava.bio.program.gff3"><span class="strong">GFF3Record</span></a> - Interface in <a href="./org/biojava/bio/program/gff3/package-summary.html">org.biojava.bio.program.gff3</a></dt>
<dd>
<div class="block">A record in a GFF3 formatted file.</div>
</dd>
<dt><a href="./org/biojava/bio/program/gff3/GFF3Record.Impl.html" title="class in org.biojava.bio.program.gff3"><span class="strong">GFF3Record.Impl</span></a> - Class in <a href="./org/biojava/bio/program/gff3/package-summary.html">org.biojava.bio.program.gff3</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff3/GFF3Record.Impl.html#GFF3Record.Impl()">GFF3Record.Impl()</a></span> - Constructor for class org.biojava.bio.program.gff3.<a href="./org/biojava/bio/program/gff3/GFF3Record.Impl.html" title="class in org.biojava.bio.program.gff3">GFF3Record.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff3/GFF3Record.Impl.html#GFF3Record.Impl(org.biojava.bio.program.gff3.GFF3Record)">GFF3Record.Impl(GFF3Record)</a></span> - Constructor for class org.biojava.bio.program.gff3.<a href="./org/biojava/bio/program/gff3/GFF3Record.Impl.html" title="class in org.biojava.bio.program.gff3">GFF3Record.Impl</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/distributed/GFFDataSource.html" title="class in org.biojava.bio.seq.distributed"><span class="strong">GFFDataSource</span></a> - Class in <a href="./org/biojava/bio/seq/distributed/package-summary.html">org.biojava.bio.seq.distributed</a></dt>
<dd>
<div class="block">Use a GFFEntrySet as a DataSource for adding annotation to sequences.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/distributed/GFFDataSource.html#GFFDataSource(org.biojava.bio.program.gff.GFFEntrySet)">GFFDataSource(GFFEntrySet)</a></span> - Constructor for class org.biojava.bio.seq.distributed.<a href="./org/biojava/bio/seq/distributed/GFFDataSource.html" title="class in org.biojava.bio.seq.distributed">GFFDataSource</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/gff/GFFDocumentHandler.html" title="interface in org.biojava.bio.program.gff"><span class="strong">GFFDocumentHandler</span></a> - Interface in <a href="./org/biojava/bio/program/gff/package-summary.html">org.biojava.bio.program.gff</a></dt>
<dd>
<div class="block">The interface for things that listen to GFF event streams.</div>
</dd>
<dt><a href="./org/biojava/bio/program/gff/GFFEntrySet.html" title="class in org.biojava.bio.program.gff"><span class="strong">GFFEntrySet</span></a> - Class in <a href="./org/biojava/bio/program/gff/package-summary.html">org.biojava.bio.program.gff</a></dt>
<dd>
<div class="block">A set of entries and comments as a representation of a GFF file.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFEntrySet.html#GFFEntrySet()">GFFEntrySet()</a></span> - Constructor for class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFEntrySet.html" title="class in org.biojava.bio.program.gff">GFFEntrySet</a></dt>
<dd>
<div class="block">Make an empty <span class="type">GFFEntrySet</span>.</div>
</dd>
<dt><a href="./org/biojava/bio/program/gff/GFFErrorHandler.html" title="interface in org.biojava.bio.program.gff"><span class="strong">GFFErrorHandler</span></a> - Interface in <a href="./org/biojava/bio/program/gff/package-summary.html">org.biojava.bio.program.gff</a></dt>
<dd>
<div class="block">Interface which captures any errors which occur when parsing
a GFF stream.</div>
</dd>
<dt><a href="./org/biojava/bio/program/gff/GFFErrorHandler.AbortErrorHandler.html" title="class in org.biojava.bio.program.gff"><span class="strong">GFFErrorHandler.AbortErrorHandler</span></a> - Class in <a href="./org/biojava/bio/program/gff/package-summary.html">org.biojava.bio.program.gff</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFErrorHandler.AbortErrorHandler.html#GFFErrorHandler.AbortErrorHandler()">GFFErrorHandler.AbortErrorHandler()</a></span> - Constructor for class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFErrorHandler.AbortErrorHandler.html" title="class in org.biojava.bio.program.gff">GFFErrorHandler.AbortErrorHandler</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/gff/GFFErrorHandler.SkipRecordErrorHandler.html" title="class in org.biojava.bio.program.gff"><span class="strong">GFFErrorHandler.SkipRecordErrorHandler</span></a> - Class in <a href="./org/biojava/bio/program/gff/package-summary.html">org.biojava.bio.program.gff</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFErrorHandler.SkipRecordErrorHandler.html#GFFErrorHandler.SkipRecordErrorHandler()">GFFErrorHandler.SkipRecordErrorHandler()</a></span> - Constructor for class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFErrorHandler.SkipRecordErrorHandler.html" title="class in org.biojava.bio.program.gff">GFFErrorHandler.SkipRecordErrorHandler</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/gff/GFFFilterer.html" title="class in org.biojava.bio.program.gff"><span class="strong">GFFFilterer</span></a> - Class in <a href="./org/biojava/bio/program/gff/package-summary.html">org.biojava.bio.program.gff</a></dt>
<dd>
<div class="block">An object that filters a stream of GFF, forwarding some
<span class="type">GFFRecord</span>s to a
listening <span class="type">GFFDocumentHandler</span>, and dropping others.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFFilterer.html#GFFFilterer(org.biojava.bio.program.gff.GFFDocumentHandler, org.biojava.bio.program.gff.GFFRecordFilter)">GFFFilterer(GFFDocumentHandler, GFFRecordFilter)</a></span> - Constructor for class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFFilterer.html" title="class in org.biojava.bio.program.gff">GFFFilterer</a></dt>
<dd>
<div class="block">Create a new <span class="type">GFFFilterer</span> that will forward
to <span class="arg">handler</span> everything that
<span class="arg">filter</span> accepts.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFTools.html#gffFromSeqDB(org.biojava.bio.seq.db.SequenceDB)">gffFromSeqDB(SequenceDB)</a></span> - Static method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFTools.html" title="class in org.biojava.bio.program.gff">GFFTools</a></dt>
<dd>
<div class="block">Creates a GFFEntrySet containing one entry for each feature on each
sequence of a SequenceDB.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFTools.html#gffFromSequence(org.biojava.bio.seq.Sequence)">gffFromSequence(Sequence)</a></span> - Static method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFTools.html" title="class in org.biojava.bio.program.gff">GFFTools</a></dt>
<dd>
<div class="block">Creates a GFFEntrySet containing one entry for each feature on a sequence.</div>
</dd>
<dt><a href="./org/biojava/bio/program/gff/GFFParser.html" title="class in org.biojava.bio.program.gff"><span class="strong">GFFParser</span></a> - Class in <a href="./org/biojava/bio/program/gff/package-summary.html">org.biojava.bio.program.gff</a></dt>
<dd>
<div class="block">Parse a stream of GFF text into a stream of records and comments.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFParser.html#GFFParser()">GFFParser()</a></span> - Constructor for class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFParser.html" title="class in org.biojava.bio.program.gff">GFFParser</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/gff/GFFRecord.html" title="interface in org.biojava.bio.program.gff"><span class="strong">GFFRecord</span></a> - Interface in <a href="./org/biojava/bio/program/gff/package-summary.html">org.biojava.bio.program.gff</a></dt>
<dd>
<div class="block">A single GFF record.</div>
</dd>
<dt><a href="./org/biojava/bio/program/gff/GFFRecordFilter.html" title="interface in org.biojava.bio.program.gff"><span class="strong">GFFRecordFilter</span></a> - Interface in <a href="./org/biojava/bio/program/gff/package-summary.html">org.biojava.bio.program.gff</a></dt>
<dd>
<div class="block">A filter that will accept or reject a <span class="type">GFFEntry</span>.</div>
</dd>
<dt><a href="./org/biojava/bio/program/gff/GFFRecordFilter.AcceptAll.html" title="class in org.biojava.bio.program.gff"><span class="strong">GFFRecordFilter.AcceptAll</span></a> - Class in <a href="./org/biojava/bio/program/gff/package-summary.html">org.biojava.bio.program.gff</a></dt>
<dd>
<div class="block">Implementation of <span class="type">GFFRecordFilter</span> that accepts everything.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFRecordFilter.AcceptAll.html#GFFRecordFilter.AcceptAll()">GFFRecordFilter.AcceptAll()</a></span> - Constructor for class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFRecordFilter.AcceptAll.html" title="class in org.biojava.bio.program.gff">GFFRecordFilter.AcceptAll</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/gff/GFFRecordFilter.FeatureFilter.html" title="class in org.biojava.bio.program.gff"><span class="strong">GFFRecordFilter.FeatureFilter</span></a> - Class in <a href="./org/biojava/bio/program/gff/package-summary.html">org.biojava.bio.program.gff</a></dt>
<dd>
<div class="block">Implementation of <span class="type">GFFRecordFilter</span> that accepts
records based upon the feature field.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFRecordFilter.FeatureFilter.html#GFFRecordFilter.FeatureFilter()">GFFRecordFilter.FeatureFilter()</a></span> - Constructor for class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFRecordFilter.FeatureFilter.html" title="class in org.biojava.bio.program.gff">GFFRecordFilter.FeatureFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFRecordFilter.FeatureFilter.html#GFFRecordFilter.FeatureFilter(java.lang.String)">GFFRecordFilter.FeatureFilter(String)</a></span> - Constructor for class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFRecordFilter.FeatureFilter.html" title="class in org.biojava.bio.program.gff">GFFRecordFilter.FeatureFilter</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/gff/GFFRecordFilter.FrameFilter.html" title="class in org.biojava.bio.program.gff"><span class="strong">GFFRecordFilter.FrameFilter</span></a> - Class in <a href="./org/biojava/bio/program/gff/package-summary.html">org.biojava.bio.program.gff</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFRecordFilter.FrameFilter.html#GFFRecordFilter.FrameFilter()">GFFRecordFilter.FrameFilter()</a></span> - Constructor for class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFRecordFilter.FrameFilter.html" title="class in org.biojava.bio.program.gff">GFFRecordFilter.FrameFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFRecordFilter.FrameFilter.html#GFFRecordFilter.FrameFilter(int)">GFFRecordFilter.FrameFilter(int)</a></span> - Constructor for class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFRecordFilter.FrameFilter.html" title="class in org.biojava.bio.program.gff">GFFRecordFilter.FrameFilter</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/gff/GFFRecordFilter.NotFilter.html" title="class in org.biojava.bio.program.gff"><span class="strong">GFFRecordFilter.NotFilter</span></a> - Class in <a href="./org/biojava/bio/program/gff/package-summary.html">org.biojava.bio.program.gff</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFRecordFilter.NotFilter.html#GFFRecordFilter.NotFilter()">GFFRecordFilter.NotFilter()</a></span> - Constructor for class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFRecordFilter.NotFilter.html" title="class in org.biojava.bio.program.gff">GFFRecordFilter.NotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFRecordFilter.NotFilter.html#GFFRecordFilter.NotFilter(org.biojava.bio.program.gff.GFFRecordFilter)">GFFRecordFilter.NotFilter(GFFRecordFilter)</a></span> - Constructor for class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFRecordFilter.NotFilter.html" title="class in org.biojava.bio.program.gff">GFFRecordFilter.NotFilter</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/gff/GFFRecordFilter.SequenceFilter.html" title="class in org.biojava.bio.program.gff"><span class="strong">GFFRecordFilter.SequenceFilter</span></a> - Class in <a href="./org/biojava/bio/program/gff/package-summary.html">org.biojava.bio.program.gff</a></dt>
<dd>
<div class="block">Implementation of <span class="type">GFFRecordFilter</span> that accepts
records based upon the sequence name.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFRecordFilter.SequenceFilter.html#GFFRecordFilter.SequenceFilter()">GFFRecordFilter.SequenceFilter()</a></span> - Constructor for class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFRecordFilter.SequenceFilter.html" title="class in org.biojava.bio.program.gff">GFFRecordFilter.SequenceFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFRecordFilter.SequenceFilter.html#GFFRecordFilter.SequenceFilter(java.lang.String)">GFFRecordFilter.SequenceFilter(String)</a></span> - Constructor for class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFRecordFilter.SequenceFilter.html" title="class in org.biojava.bio.program.gff">GFFRecordFilter.SequenceFilter</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/gff/GFFRecordFilter.SourceFilter.html" title="class in org.biojava.bio.program.gff"><span class="strong">GFFRecordFilter.SourceFilter</span></a> - Class in <a href="./org/biojava/bio/program/gff/package-summary.html">org.biojava.bio.program.gff</a></dt>
<dd>
<div class="block">Implementation of <span class="type">GFFRecordFilter</span> that accepts
records based upon the source field.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFRecordFilter.SourceFilter.html#GFFRecordFilter.SourceFilter()">GFFRecordFilter.SourceFilter()</a></span> - Constructor for class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFRecordFilter.SourceFilter.html" title="class in org.biojava.bio.program.gff">GFFRecordFilter.SourceFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFRecordFilter.SourceFilter.html#GFFRecordFilter.SourceFilter(java.lang.String)">GFFRecordFilter.SourceFilter(String)</a></span> - Constructor for class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFRecordFilter.SourceFilter.html" title="class in org.biojava.bio.program.gff">GFFRecordFilter.SourceFilter</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/gff/GFFRecordFilter.StrandFilter.html" title="class in org.biojava.bio.program.gff"><span class="strong">GFFRecordFilter.StrandFilter</span></a> - Class in <a href="./org/biojava/bio/program/gff/package-summary.html">org.biojava.bio.program.gff</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFRecordFilter.StrandFilter.html#GFFRecordFilter.StrandFilter()">GFFRecordFilter.StrandFilter()</a></span> - Constructor for class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFRecordFilter.StrandFilter.html" title="class in org.biojava.bio.program.gff">GFFRecordFilter.StrandFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFRecordFilter.StrandFilter.html#GFFRecordFilter.StrandFilter(org.biojava.bio.seq.StrandedFeature.Strand)">GFFRecordFilter.StrandFilter(StrandedFeature.Strand)</a></span> - Constructor for class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFRecordFilter.StrandFilter.html" title="class in org.biojava.bio.program.gff">GFFRecordFilter.StrandFilter</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/gff/GFFTools.html" title="class in org.biojava.bio.program.gff"><span class="strong">GFFTools</span></a> - Class in <a href="./org/biojava/bio/program/gff/package-summary.html">org.biojava.bio.program.gff</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFTools.html#GFFTools()">GFFTools()</a></span> - Constructor for class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFTools.html" title="class in org.biojava.bio.program.gff">GFFTools</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/gff/GFFWriter.html" title="class in org.biojava.bio.program.gff"><span class="strong">GFFWriter</span></a> - Class in <a href="./org/biojava/bio/program/gff/package-summary.html">org.biojava.bio.program.gff</a></dt>
<dd>
<div class="block">Listens to a stream of GFF events and writes the lines to a
<span class="type">PrintWriter</span>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFWriter.html#GFFWriter(java.io.PrintWriter)">GFFWriter(PrintWriter)</a></span> - Constructor for class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFWriter.html" title="class in org.biojava.bio.program.gff">GFFWriter</a></dt>
<dd>
<div class="block">Create a new <span class="type">GFFWriter</span> that will write to
<span class="arg">out</span>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/GenbankFormat.html#GI_TAG">GI_TAG</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/GenbankFormat.html" title="class in org.biojava.bio.seq.io">GenbankFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/GlyphFeatureRenderer.html#gList">gList</a></span> - Variable in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/GlyphFeatureRenderer.html" title="class in org.biojava.bio.gui.sequence">GlyphFeatureRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/ProteinTools.html#gln()">gln()</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/ProteinTools.html" title="class in org.biojava.bio.seq">ProteinTools</a></dt>
<dd>
<div class="block">Returns the <code>AtomicSymbol</code> for the amino acid
Glutamine (Q)</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/taxa/SimpleTaxonFactory.html#GLOBAL">GLOBAL</a></span> - Static variable in class org.biojava.bio.taxa.<a href="./org/biojava/bio/taxa/SimpleTaxonFactory.html" title="class in org.biojava.bio.taxa">SimpleTaxonFactory</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">The TaxonFactory that the biojava system should use for storing
the taxonomy used by swissprot and embl as in-memory objects.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/taxa/WeakTaxonFactory.html#GLOBAL">GLOBAL</a></span> - Static variable in class org.biojava.bio.taxa.<a href="./org/biojava/bio/taxa/WeakTaxonFactory.html" title="class in org.biojava.bio.taxa">WeakTaxonFactory</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">The TaxonFactory that the biojava system should use for storing
the taxonomy used by swissprot and embl as in-memory objects.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/ProteinTools.html#glu()">glu()</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/ProteinTools.html" title="class in org.biojava.bio.seq">ProteinTools</a></dt>
<dd>
<div class="block">Returns the <code>AtomicSymbol</code> for the amino acid
Glutamic Acid (E)</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/Protease.html#GLU_C_BICARB">GLU_C_BICARB</a></span> - Static variable in class org.biojava.bio.proteomics.<a href="./org/biojava/bio/proteomics/Protease.html" title="class in org.biojava.bio.proteomics">Protease</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/ProteaseManager.html#GLU_C_BICARB">GLU_C_BICARB</a></span> - Static variable in class org.biojava.bio.proteomics.<a href="./org/biojava/bio/proteomics/ProteaseManager.html" title="class in org.biojava.bio.proteomics">ProteaseManager</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/Protease.html#GLU_C_PHOS">GLU_C_PHOS</a></span> - Static variable in class org.biojava.bio.proteomics.<a href="./org/biojava/bio/proteomics/Protease.html" title="class in org.biojava.bio.proteomics">Protease</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/ProteaseManager.html#GLU_C_PHOS">GLU_C_PHOS</a></span> - Static variable in class org.biojava.bio.proteomics.<a href="./org/biojava/bio/proteomics/ProteaseManager.html" title="class in org.biojava.bio.proteomics">ProteaseManager</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/ProteinTools.html#gly()">gly()</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/ProteinTools.html" title="class in org.biojava.bio.seq">ProteinTools</a></dt>
<dd>
<div class="block">Returns the <code>AtomicSymbol</code> for the amino acid
Glycine (G)</div>
</dd>
<dt><a href="./org/biojava/bio/gui/glyph/Glyph.html" title="interface in org.biojava.bio.gui.glyph"><span class="strong">Glyph</span></a> - Interface in <a href="./org/biojava/bio/gui/glyph/package-summary.html">org.biojava.bio.gui.glyph</a></dt>
<dd>
<div class="block">The Glyph interface for painting a shape within bounds</div>
</dd>
<dt><a href="./org/biojava/bio/gui/sequence/GlyphFeatureRenderer.html" title="class in org.biojava.bio.gui.sequence"><span class="strong">GlyphFeatureRenderer</span></a> - Class in <a href="./org/biojava/bio/gui/sequence/package-summary.html">org.biojava.bio.gui.sequence</a></dt>
<dd>
<div class="block">A FeatureRenderer that renders a particular Glyph for Features accepted by a
particular FeatureFilter</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/GlyphFeatureRenderer.html#GlyphFeatureRenderer()">GlyphFeatureRenderer()</a></span> - Constructor for class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/GlyphFeatureRenderer.html" title="class in org.biojava.bio.gui.sequence">GlyphFeatureRenderer</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/gui/glyph/GlyphUtils.html" title="class in org.biojava.bio.gui.glyph"><span class="strong">GlyphUtils</span></a> - Class in <a href="./org/biojava/bio/gui/glyph/package-summary.html">org.biojava.bio.gui.glyph</a></dt>
<dd>
<div class="block">Utils class used by Glyph implementors.</div>
</dd>
<dt><a href="./org/biojava/ontology/io/GOParser.html" title="class in org.biojava.ontology.io"><span class="strong">GOParser</span></a> - Class in <a href="./org/biojava/ontology/io/package-summary.html">org.biojava.ontology.io</a></dt>
<dd>
<div class="block">Simple parser for the Gene Ontology (GO) flatfile format.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/io/GOParser.html#GOParser()">GOParser()</a></span> - Constructor for class org.biojava.ontology.io.<a href="./org/biojava/ontology/io/GOParser.html" title="class in org.biojava.ontology.io">GOParser</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/structure/align/pairwise/Gotoh.html" title="class in org.biojava.bio.structure.align.pairwise"><span class="strong">Gotoh</span></a> - Class in <a href="./org/biojava/bio/structure/align/pairwise/package-summary.html">org.biojava.bio.structure.align.pairwise</a></dt>
<dd>
<div class="block">a class to perform Gotoh algorithm</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/Gotoh.html#Gotoh(org.biojava.bio.structure.align.pairwise.Alignable)">Gotoh(Alignable)</a></span> - Constructor for class org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/Gotoh.html" title="class in org.biojava.bio.structure.align.pairwise">Gotoh</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PairwiseRenderContext.html#graphicsToSecondarySequence(double)">graphicsToSecondarySequence(double)</a></span> - Method in interface org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PairwiseRenderContext.html" title="interface in org.biojava.bio.gui.sequence">PairwiseRenderContext</a></dt>
<dd>
<div class="block"><code>graphicsToSecondarySequence</code> converts a graphical
position to a sequence coordinate on the secondary sequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PairwiseRenderContext.html#graphicsToSecondarySequence(java.awt.Point)">graphicsToSecondarySequence(Point)</a></span> - Method in interface org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PairwiseRenderContext.html" title="interface in org.biojava.bio.gui.sequence">PairwiseRenderContext</a></dt>
<dd>
<div class="block"><code>graphicsToSecondarySequence</code> converts a graphical
position to a secondary sequence index.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PairwiseSequencePanel.html#graphicsToSecondarySequence(double)">graphicsToSecondarySequence(double)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PairwiseSequencePanel.html" title="class in org.biojava.bio.gui.sequence">PairwiseSequencePanel</a></dt>
<dd>
<div class="block"><code>graphicsToSecondarySequence</code> converts a graphical
position to a secondary sequence index.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PairwiseSequencePanel.html#graphicsToSecondarySequence(java.awt.Point)">graphicsToSecondarySequence(Point)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PairwiseSequencePanel.html" title="class in org.biojava.bio.gui.sequence">PairwiseSequencePanel</a></dt>
<dd>
<div class="block"><code>graphicsToSecondarySequence</code> converts a graphical
position to a secondary sequence index.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SubPairwiseRenderContext.html#graphicsToSecondarySequence(double)">graphicsToSecondarySequence(double)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SubPairwiseRenderContext.html" title="class in org.biojava.bio.gui.sequence">SubPairwiseRenderContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SubPairwiseRenderContext.html#graphicsToSecondarySequence(java.awt.Point)">graphicsToSecondarySequence(Point)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SubPairwiseRenderContext.html" title="class in org.biojava.bio.gui.sequence">SubPairwiseRenderContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/HeadlessRenderContext.html#graphicsToSequence(java.awt.geom.Point2D)">graphicsToSequence(Point2D)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/HeadlessRenderContext.html" title="class in org.biojava.bio.gui.sequence">HeadlessRenderContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/HeadlessRenderContext.html#graphicsToSequence(double)">graphicsToSequence(double)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/HeadlessRenderContext.html" title="class in org.biojava.bio.gui.sequence">HeadlessRenderContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PairwiseSequencePanel.html#graphicsToSequence(double)">graphicsToSequence(double)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PairwiseSequencePanel.html" title="class in org.biojava.bio.gui.sequence">PairwiseSequencePanel</a></dt>
<dd>
<div class="block"><code>graphicsToSequence</code> converts a graphical position
to a sequence index.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PairwiseSequencePanel.html#graphicsToSequence(java.awt.geom.Point2D)">graphicsToSequence(Point2D)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PairwiseSequencePanel.html" title="class in org.biojava.bio.gui.sequence">PairwiseSequencePanel</a></dt>
<dd>
<div class="block"><code>graphicsToSequence</code> converts a graphical position
to a sequence index.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePanel.html#graphicsToSequence(double)">graphicsToSequence(double)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePanel.html" title="class in org.biojava.bio.gui.sequence">SequencePanel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePanel.html#graphicsToSequence(java.awt.geom.Point2D)">graphicsToSequence(Point2D)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePanel.html" title="class in org.biojava.bio.gui.sequence">SequencePanel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePoster.html#graphicsToSequence(double)">graphicsToSequence(double)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePoster.html" title="class in org.biojava.bio.gui.sequence">SequencePoster</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePoster.html#graphicsToSequence(java.awt.geom.Point2D)">graphicsToSequence(Point2D)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePoster.html" title="class in org.biojava.bio.gui.sequence">SequencePoster</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequenceRenderContext.html#graphicsToSequence(double)">graphicsToSequence(double)</a></span> - Method in interface org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequenceRenderContext.html" title="interface in org.biojava.bio.gui.sequence">SequenceRenderContext</a></dt>
<dd>
<div class="block">Converts a graphical position into a sequence coordinate.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequenceRenderContext.html#graphicsToSequence(java.awt.geom.Point2D)">graphicsToSequence(Point2D)</a></span> - Method in interface org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequenceRenderContext.html" title="interface in org.biojava.bio.gui.sequence">SequenceRenderContext</a></dt>
<dd>
<div class="block">Converts a graphical position into a sequence coordinate.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SubPairwiseRenderContext.html#graphicsToSequence(double)">graphicsToSequence(double)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SubPairwiseRenderContext.html" title="class in org.biojava.bio.gui.sequence">SubPairwiseRenderContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SubPairwiseRenderContext.html#graphicsToSequence(java.awt.geom.Point2D)">graphicsToSequence(Point2D)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SubPairwiseRenderContext.html" title="class in org.biojava.bio.gui.sequence">SubPairwiseRenderContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SubSequenceRenderContext.html#graphicsToSequence(double)">graphicsToSequence(double)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SubSequenceRenderContext.html" title="class in org.biojava.bio.gui.sequence">SubSequenceRenderContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SubSequenceRenderContext.html#graphicsToSequence(java.awt.geom.Point2D)">graphicsToSequence(Point2D)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SubSequenceRenderContext.html" title="class in org.biojava.bio.gui.sequence">SubSequenceRenderContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/TranslatedSequencePanel.html#graphicsToSequence(double)">graphicsToSequence(double)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/TranslatedSequencePanel.html" title="class in org.biojava.bio.gui.sequence">TranslatedSequencePanel</a></dt>
<dd>
<div class="block"><code>graphicsToSequence</code> converts a graphical position
to a sequence index.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/TranslatedSequencePanel.html#graphicsToSequence(java.awt.geom.Point2D)">graphicsToSequence(Point2D)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/TranslatedSequencePanel.html" title="class in org.biojava.bio.gui.sequence">TranslatedSequencePanel</a></dt>
<dd>
<div class="block"><code>graphicsToSequence</code> converts a graphical position
to a sequence index.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/FlexibleAlignment.html#greater(int, int)">greater(int, int)</a></span> - Method in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/FlexibleAlignment.html" title="class in org.biojava.bio.alignment">FlexibleAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/BioMatcher.html#group()">group()</a></span> - Method in interface org.biojava.bio.search.<a href="./org/biojava/bio/search/BioMatcher.html" title="interface in org.biojava.bio.search">BioMatcher</a></dt>
<dd>
<div class="block">Get the matching region as a SymbolList.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/MaxMismatchMatcher.html#group()">group()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/MaxMismatchMatcher.html" title="class in org.biojava.bio.search">MaxMismatchMatcher</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/structure/Group.html" title="interface in org.biojava.bio.structure"><span class="strong">Group</span></a> - Interface in <a href="./org/biojava/bio/structure/package-summary.html">org.biojava.bio.structure</a></dt>
<dd>
<div class="block">This is the data structure for a single Group of atoms.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/regex/Matcher.html#group()">group()</a></span> - Method in class org.biojava.utils.regex.<a href="./org/biojava/utils/regex/Matcher.html" title="class in org.biojava.utils.regex">Matcher</a></dt>
<dd>
<div class="block">Returns the input subsequence matched by the previous match.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/regex/Matcher.html#group(int)">group(int)</a></span> - Method in class org.biojava.utils.regex.<a href="./org/biojava/utils/regex/Matcher.html" title="class in org.biojava.utils.regex">Matcher</a></dt>
<dd>
<div class="block">Returns the input subsequence captured by the given group during the previous match operation.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/regex/Matcher.html#groupCount()">groupCount()</a></span> - Method in class org.biojava.utils.regex.<a href="./org/biojava/utils/regex/Matcher.html" title="class in org.biojava.utils.regex">Matcher</a></dt>
<dd>
<div class="block">Returns the number of capturing groups in this matcher's pattern.</div>
</dd>
<dt><a href="./org/biojava/bio/structure/GroupIterator.html" title="class in org.biojava.bio.structure"><span class="strong">GroupIterator</span></a> - Class in <a href="./org/biojava/bio/structure/package-summary.html">org.biojava.bio.structure</a></dt>
<dd>
<div class="block">An iterator over all groups of a structure.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/GroupIterator.html#GroupIterator(org.biojava.bio.structure.Structure)">GroupIterator(Structure)</a></span> - Constructor for class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/GroupIterator.html" title="class in org.biojava.bio.structure">GroupIterator</a></dt>
<dd>
<div class="block">Constructs a GroupIterator object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/SimpleOrthoPairCollection.html#groups">groups</a></span> - Variable in class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/SimpleOrthoPairCollection.html" title="class in org.biojava.bio.program.homologene">SimpleOrthoPairCollection</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/structure/GroupType.html" title="class in org.biojava.bio.structure"><span class="strong">GroupType</span></a> - Class in <a href="./org/biojava/bio/structure/package-summary.html">org.biojava.bio.structure</a></dt>
<dd>
<div class="block">contains only the static declaration of which types of Groups are available</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/GroupType.html#GroupType()">GroupType()</a></span> - Constructor for class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/GroupType.html" title="class in org.biojava.bio.structure">GroupType</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ChangeSupport.html#growIfNecessary()">growIfNecessary()</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/ChangeSupport.html" title="class in org.biojava.utils">ChangeSupport</a></dt>
<dd>
<div class="block">Grows the internal resources if by adding one more listener they would be
full.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOTools.html#guessFileType(java.io.File)">guessFileType(File)</a></span> - Static method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOTools.html" title="class in org.biojava.bio.seq.io">SeqIOTools</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>because there is no standard file naming convention
and guessing by file name is inherantly error prone and bad.</i></div>
</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/BioIndex.html#guessRecLen(java.io.RandomAccessFile)">guessRecLen(RandomAccessFile)</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/BioIndex.html" title="class in org.biojava.bio.seq.db">BioIndex</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLFormat.html#guessSymbolTokenization(java.io.File)">guessSymbolTokenization(File)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLFormat.html" title="class in org.biojavax.bio.seq.io">EMBLFormat</a></dt>
<dd>
<div class="block">On the assumption that the file is readable by this format (not checked),
attempt to guess which symbol tokenization we should use to read it.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLFormat.html#guessSymbolTokenization(java.io.BufferedInputStream)">guessSymbolTokenization(BufferedInputStream)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLFormat.html" title="class in org.biojavax.bio.seq.io">EMBLFormat</a></dt>
<dd>
<div class="block">On the assumption that the stream is readable by this format (not checked),
attempt to guess which symbol tokenization we should use to read it.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html#guessSymbolTokenization(java.io.File)">guessSymbolTokenization(File)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html" title="class in org.biojavax.bio.seq.io">EMBLxmlFormat</a></dt>
<dd>
<div class="block">On the assumption that the file is readable by this format (not checked),
attempt to guess which symbol tokenization we should use to read it.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html#guessSymbolTokenization(java.io.BufferedInputStream)">guessSymbolTokenization(BufferedInputStream)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html" title="class in org.biojavax.bio.seq.io">EMBLxmlFormat</a></dt>
<dd>
<div class="block">On the assumption that the stream is readable by this format (not checked),
attempt to guess which symbol tokenization we should use to read it.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/FastaFormat.html#guessSymbolTokenization(java.io.File)">guessSymbolTokenization(File)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/FastaFormat.html" title="class in org.biojavax.bio.seq.io">FastaFormat</a></dt>
<dd>
<div class="block">On the assumption that the file is readable by this format (not checked),
attempt to guess which symbol tokenization we should use to read it.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/FastaFormat.html#guessSymbolTokenization(java.io.BufferedInputStream)">guessSymbolTokenization(BufferedInputStream)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/FastaFormat.html" title="class in org.biojavax.bio.seq.io">FastaFormat</a></dt>
<dd>
<div class="block">On the assumption that the stream is readable by this format (not checked),
attempt to guess which symbol tokenization we should use to read it.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/GenbankFormat.html#guessSymbolTokenization(java.io.File)">guessSymbolTokenization(File)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/GenbankFormat.html" title="class in org.biojavax.bio.seq.io">GenbankFormat</a></dt>
<dd>
<div class="block">On the assumption that the file is readable by this format (not checked),
attempt to guess which symbol tokenization we should use to read it.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/GenbankFormat.html#guessSymbolTokenization(java.io.BufferedInputStream)">guessSymbolTokenization(BufferedInputStream)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/GenbankFormat.html" title="class in org.biojavax.bio.seq.io">GenbankFormat</a></dt>
<dd>
<div class="block">On the assumption that the stream is readable by this format (not checked),
attempt to guess which symbol tokenization we should use to read it.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/INSDseqFormat.html#guessSymbolTokenization(java.io.File)">guessSymbolTokenization(File)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/INSDseqFormat.html" title="class in org.biojavax.bio.seq.io">INSDseqFormat</a></dt>
<dd>
<div class="block">On the assumption that the file is readable by this format (not checked),
attempt to guess which symbol tokenization we should use to read it.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/INSDseqFormat.html#guessSymbolTokenization(java.io.BufferedInputStream)">guessSymbolTokenization(BufferedInputStream)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/INSDseqFormat.html" title="class in org.biojavax.bio.seq.io">INSDseqFormat</a></dt>
<dd>
<div class="block">On the assumption that the stream is readable by this format (not checked),
attempt to guess which symbol tokenization we should use to read it.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/RichSequenceFormat.BasicFormat.html#guessSymbolTokenization(java.io.File)">guessSymbolTokenization(File)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/RichSequenceFormat.BasicFormat.html" title="class in org.biojavax.bio.seq.io">RichSequenceFormat.BasicFormat</a></dt>
<dd>
<div class="block">On the assumption that the file is readable by this format (not checked),
attempt to guess which symbol tokenization we should use to read it.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/RichSequenceFormat.html#guessSymbolTokenization(java.io.File)">guessSymbolTokenization(File)</a></span> - Method in interface org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/RichSequenceFormat.html" title="interface in org.biojavax.bio.seq.io">RichSequenceFormat</a></dt>
<dd>
<div class="block">On the assumption that the file is readable by this format (not checked),
attempt to guess which symbol tokenization we should use to read it.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/RichSequenceFormat.html#guessSymbolTokenization(java.io.BufferedInputStream)">guessSymbolTokenization(BufferedInputStream)</a></span> - Method in interface org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/RichSequenceFormat.html" title="interface in org.biojavax.bio.seq.io">RichSequenceFormat</a></dt>
<dd>
<div class="block">On the assumption that the stream is readable by this format (not checked),
attempt to guess which symbol tokenization we should use to read it.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtFormat.html#guessSymbolTokenization(java.io.File)">guessSymbolTokenization(File)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtFormat.html" title="class in org.biojavax.bio.seq.io">UniProtFormat</a></dt>
<dd>
<div class="block">On the assumption that the file is readable by this format (not checked),
attempt to guess which symbol tokenization we should use to read it.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtFormat.html#guessSymbolTokenization(java.io.BufferedInputStream)">guessSymbolTokenization(BufferedInputStream)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtFormat.html" title="class in org.biojavax.bio.seq.io">UniProtFormat</a></dt>
<dd>
<div class="block">On the assumption that the stream is readable by this format (not checked),
attempt to guess which symbol tokenization we should use to read it.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#guessSymbolTokenization(java.io.File)">guessSymbolTokenization(File)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd>
<div class="block">On the assumption that the file is readable by this format (not checked),
attempt to guess which symbol tokenization we should use to read it.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#guessSymbolTokenization(java.io.BufferedInputStream)">guessSymbolTokenization(BufferedInputStream)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd>
<div class="block">On the assumption that the stream is readable by this format (not checked),
attempt to guess which symbol tokenization we should use to read it.</div>
</dd>
<dt><a href="./org/biojava/bio/gui/sequence/GUITools.html" title="class in org.biojava.bio.gui.sequence"><span class="strong">GUITools</span></a> - Class in <a href="./org/biojava/bio/gui/sequence/package-summary.html">org.biojava.bio.gui.sequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/io/InputStreamProvider.html#GZIP_MAGIC">GZIP_MAGIC</a></span> - Static variable in class org.biojava.utils.io.<a href="./org/biojava/utils/io/InputStreamProvider.html" title="class in org.biojava.utils.io">InputStreamProvider</a></dt>
<dd>
<div class="block">The magic number found at the start of a GZIP stream.</div>
</dd>
</dl>
<a name="_H_">
<!-- -->
</a>
<h2 class="title">H</h2>
<dl>
<dt><span class="strong"><a href="./org/biojava/bio/seq/DNATools.html#h()">h()</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/DNATools.html" title="class in org.biojava.bio.seq">DNATools</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/NucleotideTools.html#h()">h()</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/NucleotideTools.html" title="class in org.biojava.bio.seq">NucleotideTools</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/ProteinTools.html#h()">h()</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/ProteinTools.html" title="class in org.biojava.bio.seq">ProteinTools</a></dt>
<dd>
<div class="block">Returns the <code>AtomicSymbol</code> for the amino acid
Histidine</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/Taxon.html#H_SAPIENS">H_SAPIENS</a></span> - Static variable in interface org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/Taxon.html" title="interface in org.biojava.bio.program.homologene">Taxon</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/Taxon.html#H_VULGARE">H_VULGARE</a></span> - Static variable in interface org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/Taxon.html" title="interface in org.biojava.bio.program.homologene">Taxon</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/HitStAXHandler.html#handleEndElement(java.lang.String, java.lang.String, java.lang.String)">handleEndElement(String, String, String)</a></span> - Method in class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/HitStAXHandler.html" title="class in org.biojava.bio.program.ssbind">HitStAXHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/HSPStAXHandler.html#handleEndElement(java.lang.String, java.lang.String, java.lang.String)">handleEndElement(String, String, String)</a></span> - Method in class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/HSPStAXHandler.html" title="class in org.biojava.bio.program.ssbind">HSPStAXHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/SeqSimilarityStAXHandler.html#handleEndElement(java.lang.String, java.lang.String, java.lang.String)">handleEndElement(String, String, String)</a></span> - Method in class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/SeqSimilarityStAXHandler.html" title="class in org.biojava.bio.program.ssbind">SeqSimilarityStAXHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/DNAAmbPack.html#handlesAmbiguity()">handlesAmbiguity()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/DNAAmbPack.html" title="class in org.biojava.bio.symbol">DNAAmbPack</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/DNANoAmbPack.html#handlesAmbiguity()">handlesAmbiguity()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/DNANoAmbPack.html" title="class in org.biojava.bio.symbol">DNANoAmbPack</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/Packing.html#handlesAmbiguity()">handlesAmbiguity()</a></span> - Method in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/Packing.html" title="interface in org.biojava.bio.symbol">Packing</a></dt>
<dd>
<div class="block">
Flag to state if ambiguities are stored.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/HitStAXHandler.html#handleStartElement(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes)">handleStartElement(String, String, String, Attributes)</a></span> - Method in class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/HitStAXHandler.html" title="class in org.biojava.bio.program.ssbind">HitStAXHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/HSPStAXHandler.html#handleStartElement(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes)">handleStartElement(String, String, String, Attributes)</a></span> - Method in class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/HSPStAXHandler.html" title="class in org.biojava.bio.program.ssbind">HSPStAXHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/HSPSummaryStAXHandler.html#handleStartElement(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes)">handleStartElement(String, String, String, Attributes)</a></span> - Method in class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/HSPSummaryStAXHandler.html" title="class in org.biojava.bio.program.ssbind">HSPSummaryStAXHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/SeqSimilarityStAXHandler.html#handleStartElement(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes)">handleStartElement(String, String, String, Attributes)</a></span> - Method in class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/SeqSimilarityStAXHandler.html" title="class in org.biojava.bio.program.ssbind">SeqSimilarityStAXHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Group.html#has3D()">has3D()</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Group.html" title="interface in org.biojava.bio.structure">Group</a></dt>
<dd>
<div class="block">returns true or false, depending if this group has 3D coordinates or not.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/HetatomImpl.html#has3D()">has3D()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/HetatomImpl.html" title="class in org.biojava.bio.structure">HetatomImpl</a></dt>
<dd>
<div class="block">returns true or false, depending if this group has 3D coordinates or not.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Group.html#hasAminoAtoms()">hasAminoAtoms()</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Group.html" title="interface in org.biojava.bio.structure">Group</a></dt>
<dd>
<div class="block">calculate if a groups has all atoms required for an amino acid.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/HetatomImpl.html#hasAminoAtoms()">hasAminoAtoms()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/HetatomImpl.html" title="class in org.biojava.bio.structure">HetatomImpl</a></dt>
<dd>
<div class="block">calculate if a groups has all atoms required for an amino acid
this allows to include chemically modified amino acids that
are labeled hetatoms into some computations ...</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FilterUtils.html#hasAnnotation(java.lang.Object)">hasAnnotation(Object)</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FilterUtils.html" title="class in org.biojava.bio.seq">FilterUtils</a></dt>
<dd>
<div class="block">Match features where the property <code>key</code> has been defined as having
some value, regardless of the exact value.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Group.html#hasAtom(java.lang.String)">hasAtom(String)</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Group.html" title="interface in org.biojava.bio.structure">Group</a></dt>
<dd>
<div class="block">Teturns flag whether a particular atom is existing within this group .</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/HetatomImpl.html#hasAtom(java.lang.String)">hasAtom(String)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/HetatomImpl.html" title="class in org.biojava.bio.structure">HetatomImpl</a></dt>
<dd>
<div class="block">test is an Atom with name is existing.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/FuzzyLocation.html#hasBoundedMax()">hasBoundedMax()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/FuzzyLocation.html" title="class in org.biojava.bio.symbol">FuzzyLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/FuzzyPointLocation.html#hasBoundedMax()">hasBoundedMax()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/FuzzyPointLocation.html" title="class in org.biojava.bio.symbol">FuzzyPointLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/FuzzyLocation.html#hasBoundedMin()">hasBoundedMin()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/FuzzyLocation.html" title="class in org.biojava.bio.symbol">FuzzyLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/FuzzyPointLocation.html#hasBoundedMin()">hasBoundedMin()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/FuzzyPointLocation.html" title="class in org.biojava.bio.symbol">FuzzyPointLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Structure.html#hasChain(java.lang.String)">hasChain(String)</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Structure.html" title="interface in org.biojava.bio.structure">Structure</a></dt>
<dd>
<div class="block">check if a chain with the id chainId is contained in this structure.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/StructureImpl.html#hasChain(java.lang.String)">hasChain(String)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/StructureImpl.html" title="class in org.biojava.bio.structure">StructureImpl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePanel.html#hasChangeListeners()">hasChangeListeners()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePanel.html" title="class in org.biojava.bio.gui.sequence">SequencePanel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePoster.html#hasChangeListeners()">hasChangeListeners()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePoster.html" title="class in org.biojava.bio.gui.sequence">SequencePoster</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/distributed/DistributedSequenceDB.html#hasChangeSupport()">hasChangeSupport()</a></span> - Method in class org.biojava.bio.seq.distributed.<a href="./org/biojava/bio/seq/distributed/DistributedSequenceDB.html" title="class in org.biojava.bio.seq.distributed">DistributedSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SuffixTree.SuffixNode.html#hasChild(int)">hasChild(int)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SuffixTree.SuffixNode.html" title="class in org.biojava.bio.symbol">SuffixTree.SuffixNode</a></dt>
<dd>
<div class="block">Determine if this node has a child corresponding to a given
index number.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/UkkonenSuffixTree.SuffixNode.html#hasChild(java.lang.Character)">hasChild(Character)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/UkkonenSuffixTree.SuffixNode.html" title="class in org.biojava.bio.symbol">UkkonenSuffixTree.SuffixNode</a></dt>
<dd>
<div class="block">Determine if this node has a child corresponding to a given character</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/distributed/DistDataSource.html#hasFeatures(java.lang.String)">hasFeatures(String)</a></span> - Method in interface org.biojava.bio.seq.distributed.<a href="./org/biojava/bio/seq/distributed/DistDataSource.html" title="interface in org.biojava.bio.seq.distributed">DistDataSource</a></dt>
<dd>
<div class="block">Find out if this DistDataSource can provide features on a sequence with a particular ID.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/distributed/GFFDataSource.html#hasFeatures(java.lang.String)">hasFeatures(String)</a></span> - Method in class org.biojava.bio.seq.distributed.<a href="./org/biojava/bio/seq/distributed/GFFDataSource.html" title="class in org.biojava.bio.seq.distributed">GFFDataSource</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/distributed/SequenceDBDataSource.html#hasFeatures(java.lang.String)">hasFeatures(String)</a></span> - Method in class org.biojava.bio.seq.distributed.<a href="./org/biojava/bio/seq/distributed/SequenceDBDataSource.html" title="class in org.biojava.bio.seq.distributed">SequenceDBDataSource</a></dt>
<dd> </dd>
<dt><a href="./org/biojavax/bio/db/HashBioEntryDB.html" title="class in org.biojavax.bio.db"><span class="strong">HashBioEntryDB</span></a> - Class in <a href="./org/biojavax/bio/db/package-summary.html">org.biojavax.bio.db</a></dt>
<dd>
<div class="block">An implementation of RichSequenceDB that uses an underlying HashMap to store the
RichSequence objects.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/HashBioEntryDB.html#HashBioEntryDB()">HashBioEntryDB()</a></span> - Constructor for class org.biojavax.bio.db.<a href="./org/biojavax/bio/db/HashBioEntryDB.html" title="class in org.biojavax.bio.db">HashBioEntryDB</a></dt>
<dd>
<div class="block">Generate a HashRichSequenceDB object that will use byName to generate ids for
sequences and have a null name.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/HashBioEntryDB.html#HashBioEntryDB(java.lang.String)">HashBioEntryDB(String)</a></span> - Constructor for class org.biojavax.bio.db.<a href="./org/biojavax/bio/db/HashBioEntryDB.html" title="class in org.biojavax.bio.db">HashBioEntryDB</a></dt>
<dd>
<div class="block">Generate a HashRichSequenceDB object that will use byName to generate ids and
will have the requested name.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/AbstractAnnotation.html#hashCode()">hashCode()</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/AbstractAnnotation.html" title="class in org.biojava.bio">AbstractAnnotation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/CollectionConstraint.AllValuesIn.html#hashCode()">hashCode()</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/CollectionConstraint.AllValuesIn.html" title="class in org.biojava.bio">CollectionConstraint.AllValuesIn</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/CollectionConstraint.Contains.html#hashCode()">hashCode()</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/CollectionConstraint.Contains.html" title="class in org.biojava.bio">CollectionConstraint.Contains</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/AbstractDistribution.html#hashCode()">hashCode()</a></span> - Method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/AbstractDistribution.html" title="class in org.biojava.bio.dist">AbstractDistribution</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/SimpleWeightMatrix.html#hashCode()">hashCode()</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/SimpleWeightMatrix.html" title="class in org.biojava.bio.dp">SimpleWeightMatrix</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/TrainerTransition.html#hashCode()">hashCode()</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/TrainerTransition.html" title="class in org.biojava.bio.dp">TrainerTransition</a></dt>
<dd>
<div class="block">The hash code is model.hashCode() ^ from.hashCode() ^ to.hashCode()</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/Transition.html#hashCode()">hashCode()</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/Transition.html" title="class in org.biojava.bio.dp">Transition</a></dt>
<dd>
<div class="block">The hash code is from.hashCode() ^ to.hashCode()</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/EcNumber.Impl.html#hashCode()">hashCode()</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/EcNumber.Impl.html" title="class in org.biojava.bio">EcNumber.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePanel.html#hashCode()">hashCode()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePanel.html" title="class in org.biojava.bio.gui.sequence">SequencePanel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/molbio/RestrictionEnzyme.html#hashCode()">hashCode()</a></span> - Method in class org.biojava.bio.molbio.<a href="./org/biojava/bio/molbio/RestrictionEnzyme.html" title="class in org.biojava.bio.molbio">RestrictionEnzyme</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/DataSource.html#hashCode()">hashCode()</a></span> - Method in class org.biojava.bio.program.das.<a href="./org/biojava/bio/program/das/DataSource.html" title="class in org.biojava.bio.program.das">DataSource</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/Taxon.TaxonStub.html#hashCode()">hashCode()</a></span> - Method in class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/Taxon.TaxonStub.html" title="class in org.biojava.bio.program.homologene">Taxon.TaxonStub</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SequenceDBSearchHit.html#hashCode()">hashCode()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SequenceDBSearchHit.html" title="class in org.biojava.bio.search">SequenceDBSearchHit</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SequenceDBSearchResult.html#hashCode()">hashCode()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SequenceDBSearchResult.html" title="class in org.biojava.bio.search">SequenceDBSearchResult</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SequenceDBSearchSubHit.html#hashCode()">hashCode()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SequenceDBSearchSubHit.html" title="class in org.biojava.bio.search">SequenceDBSearchSubHit</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SimpleSeqSimilaritySearchHit.html#hashCode()">hashCode()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SimpleSeqSimilaritySearchHit.html" title="class in org.biojava.bio.search">SimpleSeqSimilaritySearchHit</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SimpleSeqSimilaritySearchResult.html#hashCode()">hashCode()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SimpleSeqSimilaritySearchResult.html" title="class in org.biojava.bio.search">SimpleSeqSimilaritySearchResult</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SimpleSeqSimilaritySearchSubHit.html#hashCode()">hashCode()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SimpleSeqSimilaritySearchSubHit.html" title="class in org.biojava.bio.search">SimpleSeqSimilaritySearchSubHit</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/SimpleSequenceDBInstallation.html#hashCode()">hashCode()</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/SimpleSequenceDBInstallation.html" title="class in org.biojava.bio.seq.db">SimpleSequenceDBInstallation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/Feature.Template.html#hashCode()">hashCode()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/Feature.Template.html" title="class in org.biojava.bio.seq">Feature.Template</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.And.html#hashCode()">hashCode()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.And.html" title="class in org.biojava.bio.seq">FeatureFilter.And</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ByAncestor.html#hashCode()">hashCode()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ByAncestor.html" title="class in org.biojava.bio.seq">FeatureFilter.ByAncestor</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ByAnnotationType.html#hashCode()">hashCode()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ByAnnotationType.html" title="class in org.biojava.bio.seq">FeatureFilter.ByAnnotationType</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ByChild.html#hashCode()">hashCode()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ByChild.html" title="class in org.biojava.bio.seq">FeatureFilter.ByChild</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ByClass.html#hashCode()">hashCode()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ByClass.html" title="class in org.biojava.bio.seq">FeatureFilter.ByClass</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ByComponentName.html#hashCode()">hashCode()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ByComponentName.html" title="class in org.biojava.bio.seq">FeatureFilter.ByComponentName</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ByDescendant.html#hashCode()">hashCode()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ByDescendant.html" title="class in org.biojava.bio.seq">FeatureFilter.ByDescendant</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ByFeature.html#hashCode()">hashCode()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ByFeature.html" title="class in org.biojava.bio.seq">FeatureFilter.ByFeature</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ByPairwiseScore.html#hashCode()">hashCode()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ByPairwiseScore.html" title="class in org.biojava.bio.seq">FeatureFilter.ByPairwiseScore</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ByParent.html#hashCode()">hashCode()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ByParent.html" title="class in org.biojava.bio.seq">FeatureFilter.ByParent</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.BySequenceName.html#hashCode()">hashCode()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.BySequenceName.html" title="class in org.biojava.bio.seq">FeatureFilter.BySequenceName</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.BySource.html#hashCode()">hashCode()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.BySource.html" title="class in org.biojava.bio.seq">FeatureFilter.BySource</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ByType.html#hashCode()">hashCode()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ByType.html" title="class in org.biojava.bio.seq">FeatureFilter.ByType</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ContainedByLocation.html#hashCode()">hashCode()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ContainedByLocation.html" title="class in org.biojava.bio.seq">FeatureFilter.ContainedByLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.FrameFilter.html#hashCode()">hashCode()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.FrameFilter.html" title="class in org.biojava.bio.seq">FeatureFilter.FrameFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.Not.html#hashCode()">hashCode()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.Not.html" title="class in org.biojava.bio.seq">FeatureFilter.Not</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.OnlyChildren.html#hashCode()">hashCode()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.OnlyChildren.html" title="class in org.biojava.bio.seq">FeatureFilter.OnlyChildren</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.OnlyDescendants.html#hashCode()">hashCode()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.OnlyDescendants.html" title="class in org.biojava.bio.seq">FeatureFilter.OnlyDescendants</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.Or.html#hashCode()">hashCode()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.Or.html" title="class in org.biojava.bio.seq">FeatureFilter.Or</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.OverlapsLocation.html#hashCode()">hashCode()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.OverlapsLocation.html" title="class in org.biojava.bio.seq">FeatureFilter.OverlapsLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ShadowContainedByLocation.html#hashCode()">hashCode()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ShadowContainedByLocation.html" title="class in org.biojava.bio.seq">FeatureFilter.ShadowContainedByLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ShadowOverlapsLocation.html#hashCode()">hashCode()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ShadowOverlapsLocation.html" title="class in org.biojava.bio.seq">FeatureFilter.ShadowOverlapsLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.StrandFilter.html#hashCode()">hashCode()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.StrandFilter.html" title="class in org.biojava.bio.seq">FeatureFilter.StrandFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleFeature.html#hashCode()">hashCode()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleFeature.html" title="class in org.biojava.bio.seq.impl">SimpleFeature</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/projection/ProjectedFeature.html#hashCode()">hashCode()</a></span> - Method in class org.biojava.bio.seq.projection.<a href="./org/biojava/bio/seq/projection/ProjectedFeature.html" title="class in org.biojava.bio.seq.projection">ProjectedFeature</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Author.html#hashCode()">hashCode()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Author.html" title="class in org.biojava.bio.structure">Author</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AbstractLocation.html#hashCode()">hashCode()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AbstractLocation.html" title="class in org.biojava.bio.symbol">AbstractLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AbstractSymbolList.html#hashCode()">hashCode()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AbstractSymbolList.html" title="class in org.biojava.bio.symbol">AbstractSymbolList</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/FuzzyPointLocation.html#hashCode()">hashCode()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/FuzzyPointLocation.html" title="class in org.biojava.bio.symbol">FuzzyPointLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/IntegerAlphabet.IntegerSymbol.html#hashCode()">hashCode()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/IntegerAlphabet.IntegerSymbol.html" title="class in org.biojava.bio.symbol">IntegerAlphabet.IntegerSymbol</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/taxa/AbstractTaxon.html#hashCode()">hashCode()</a></span> - Method in class org.biojava.bio.taxa.<a href="./org/biojava/bio/taxa/AbstractTaxon.html" title="class in org.biojava.bio.taxa">AbstractTaxon</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/taxa/Taxon.html#hashCode()">hashCode()</a></span> - Method in interface org.biojava.bio.taxa.<a href="./org/biojava/bio/taxa/Taxon.html" title="interface in org.biojava.bio.taxa">Taxon</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">The hash-code of a Taxon is equal to the hash-code of it's
scientific name.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/Term.Impl.html#hashCode()">hashCode()</a></span> - Method in class org.biojava.ontology.<a href="./org/biojava/ontology/Term.Impl.html" title="class in org.biojava.ontology">Term.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/Triple.html#hashCode()">hashCode()</a></span> - Method in interface org.biojava.ontology.<a href="./org/biojava/ontology/Triple.html" title="interface in org.biojava.ontology">Triple</a></dt>
<dd>
<div class="block">The hashcode for a Triple.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/Triple.Impl.html#hashCode()">hashCode()</a></span> - Method in class org.biojava.ontology.<a href="./org/biojava/ontology/Triple.Impl.html" title="class in org.biojava.ontology">Triple.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ListTools.Doublet.html#hashCode()">hashCode()</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/ListTools.Doublet.html" title="class in org.biojava.utils">ListTools.Doublet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ListTools.Triplet.html#hashCode()">hashCode()</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/ListTools.Triplet.html" title="class in org.biojava.utils">ListTools.Triplet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/lsid/LifeScienceIdentifier.html#hashCode()">hashCode()</a></span> - Method in class org.biojava.utils.lsid.<a href="./org/biojava/utils/lsid/LifeScienceIdentifier.html" title="class in org.biojava.utils.lsid">LifeScienceIdentifier</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ObjectUtil.html#hashCode(int, boolean)">hashCode(int, boolean)</a></span> - Static method in class org.biojava.utils.<a href="./org/biojava/utils/ObjectUtil.html" title="class in org.biojava.utils">ObjectUtil</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ObjectUtil.html#hashCode(int, int)">hashCode(int, int)</a></span> - Static method in class org.biojava.utils.<a href="./org/biojava/utils/ObjectUtil.html" title="class in org.biojava.utils">ObjectUtil</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ObjectUtil.html#hashCode(int, long)">hashCode(int, long)</a></span> - Static method in class org.biojava.utils.<a href="./org/biojava/utils/ObjectUtil.html" title="class in org.biojava.utils">ObjectUtil</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ObjectUtil.html#hashCode(int, float)">hashCode(int, float)</a></span> - Static method in class org.biojava.utils.<a href="./org/biojava/utils/ObjectUtil.html" title="class in org.biojava.utils">ObjectUtil</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ObjectUtil.html#hashCode(int, double)">hashCode(int, double)</a></span> - Static method in class org.biojava.utils.<a href="./org/biojava/utils/ObjectUtil.html" title="class in org.biojava.utils">ObjectUtil</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ObjectUtil.html#hashCode(int, boolean[])">hashCode(int, boolean[])</a></span> - Static method in class org.biojava.utils.<a href="./org/biojava/utils/ObjectUtil.html" title="class in org.biojava.utils">ObjectUtil</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ObjectUtil.html#hashCode(int, int[])">hashCode(int, int[])</a></span> - Static method in class org.biojava.utils.<a href="./org/biojava/utils/ObjectUtil.html" title="class in org.biojava.utils">ObjectUtil</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ObjectUtil.html#hashCode(int, long[])">hashCode(int, long[])</a></span> - Static method in class org.biojava.utils.<a href="./org/biojava/utils/ObjectUtil.html" title="class in org.biojava.utils">ObjectUtil</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ObjectUtil.html#hashCode(int, float[])">hashCode(int, float[])</a></span> - Static method in class org.biojava.utils.<a href="./org/biojava/utils/ObjectUtil.html" title="class in org.biojava.utils">ObjectUtil</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ObjectUtil.html#hashCode(int, double[])">hashCode(int, double[])</a></span> - Static method in class org.biojava.utils.<a href="./org/biojava/utils/ObjectUtil.html" title="class in org.biojava.utils">ObjectUtil</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ObjectUtil.html#hashCode(int, java.lang.Object[])">hashCode(int, Object[])</a></span> - Static method in class org.biojava.utils.<a href="./org/biojava/utils/ObjectUtil.html" title="class in org.biojava.utils">ObjectUtil</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ObjectUtil.html#hashCode(int, java.lang.Object)">hashCode(int, Object)</a></span> - Static method in class org.biojava.utils.<a href="./org/biojava/utils/ObjectUtil.html" title="class in org.biojava.utils">ObjectUtil</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/TypedProperties.html#hashCode()">hashCode()</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/TypedProperties.html" title="class in org.biojava.utils">TypedProperties</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLAcceptAllFilter.html#hashCode()">hashCode()</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLAcceptAllFilter.html" title="class in org.biojavax.bio.db.biosql">BioSQLAcceptAllFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLAcceptNoneFilter.html#hashCode()">hashCode()</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLAcceptNoneFilter.html" title="class in org.biojavax.bio.db.biosql">BioSQLAcceptNoneFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.And.html#hashCode()">hashCode()</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.And.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.And</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByName.html#hashCode()">hashCode()</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByName.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.ByName</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByNote.html#hashCode()">hashCode()</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByNote.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.ByNote</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByNoteTermOnly.html#hashCode()">hashCode()</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByNoteTermOnly.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.ByNoteTermOnly</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByRank.html#hashCode()">hashCode()</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByRank.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.ByRank</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.BySequenceName.html#hashCode()">hashCode()</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.BySequenceName.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.BySequenceName</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.BySourceTerm.html#hashCode()">hashCode()</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.BySourceTerm.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.BySourceTerm</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.BySourceTermName.html#hashCode()">hashCode()</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.BySourceTermName.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.BySourceTermName</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByStrand.html#hashCode()">hashCode()</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByStrand.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.ByStrand</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByTypeTerm.html#hashCode()">hashCode()</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByTypeTerm.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.ByTypeTerm</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByTypeTermName.html#hashCode()">hashCode()</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByTypeTermName.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.ByTypeTermName</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ContainedByRichLocation.html#hashCode()">hashCode()</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ContainedByRichLocation.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.ContainedByRichLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.Not.html#hashCode()">hashCode()</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.Not.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.Not</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.Or.html#hashCode()">hashCode()</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.Or.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.Or</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.OverlapsRichLocation.html#hashCode()">hashCode()</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.OverlapsRichLocation.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.OverlapsRichLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/CompoundRichLocation.html#hashCode()">hashCode()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/CompoundRichLocation.html" title="class in org.biojavax.bio.seq">CompoundRichLocation</a></dt>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/EmptyRichLocation.html#hashCode()">hashCode()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/EmptyRichLocation.html" title="class in org.biojavax.bio.seq">EmptyRichLocation</a></dt>
<dd>
<div class="block">
ALWAYS RETURNS 17</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichLocation.Strand.html#hashCode()">hashCode()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichLocation.Strand.html" title="class in org.biojavax.bio.seq">RichLocation.Strand</a></dt>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichFeature.html#hashCode()">hashCode()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichFeature.html" title="class in org.biojavax.bio.seq">SimpleRichFeature</a></dt>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichFeatureRelationship.html#hashCode()">hashCode()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichFeatureRelationship.html" title="class in org.biojavax.bio.seq">SimpleRichFeatureRelationship</a></dt>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichLocation.html#hashCode()">hashCode()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichLocation.html" title="class in org.biojavax.bio.seq">SimpleRichLocation</a></dt>
<dt><span class="strong"><a href="./org/biojavax/bio/SimpleBioEntry.html#hashCode()">hashCode()</a></span> - Method in class org.biojavax.bio.<a href="./org/biojavax/bio/SimpleBioEntry.html" title="class in org.biojavax.bio">SimpleBioEntry</a></dt>
<dt><span class="strong"><a href="./org/biojavax/bio/SimpleBioEntryRelationship.html#hashCode()">hashCode()</a></span> - Method in class org.biojavax.bio.<a href="./org/biojavax/bio/SimpleBioEntryRelationship.html" title="class in org.biojavax.bio">SimpleBioEntryRelationship</a></dt>
<dt><span class="strong"><a href="./org/biojavax/bio/taxa/SimpleNCBITaxon.html#hashCode()">hashCode()</a></span> - Method in class org.biojavax.bio.taxa.<a href="./org/biojavax/bio/taxa/SimpleNCBITaxon.html" title="class in org.biojavax.bio.taxa">SimpleNCBITaxon</a></dt>
<dt><span class="strong"><a href="./org/biojavax/bio/taxa/SimpleNCBITaxonName.html#hashCode()">hashCode()</a></span> - Method in class org.biojavax.bio.taxa.<a href="./org/biojavax/bio/taxa/SimpleNCBITaxonName.html" title="class in org.biojavax.bio.taxa">SimpleNCBITaxonName</a></dt>
<dt><span class="strong"><a href="./org/biojavax/EmptyRichAnnotation.html#hashCode()">hashCode()</a></span> - Method in class org.biojavax.<a href="./org/biojavax/EmptyRichAnnotation.html" title="class in org.biojavax">EmptyRichAnnotation</a></dt>
<dt><span class="strong"><a href="./org/biojavax/ontology/SimpleComparableOntology.html#hashCode()">hashCode()</a></span> - Method in class org.biojavax.ontology.<a href="./org/biojavax/ontology/SimpleComparableOntology.html" title="class in org.biojavax.ontology">SimpleComparableOntology</a></dt>
<dt><span class="strong"><a href="./org/biojavax/ontology/SimpleComparableTerm.html#hashCode()">hashCode()</a></span> - Method in class org.biojavax.ontology.<a href="./org/biojavax/ontology/SimpleComparableTerm.html" title="class in org.biojavax.ontology">SimpleComparableTerm</a></dt>
<dt><span class="strong"><a href="./org/biojavax/ontology/SimpleComparableTriple.html#hashCode()">hashCode()</a></span> - Method in class org.biojavax.ontology.<a href="./org/biojavax/ontology/SimpleComparableTriple.html" title="class in org.biojavax.ontology">SimpleComparableTriple</a></dt>
<dd>
<div class="block">The hashcode for a Triple.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleComment.html#hashCode()">hashCode()</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleComment.html" title="class in org.biojavax">SimpleComment</a></dt>
<dt><span class="strong"><a href="./org/biojavax/SimpleCrossRef.html#hashCode()">hashCode()</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleCrossRef.html" title="class in org.biojavax">SimpleCrossRef</a></dt>
<dt><span class="strong"><a href="./org/biojavax/SimpleDocRef.html#hashCode()">hashCode()</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleDocRef.html" title="class in org.biojavax">SimpleDocRef</a></dt>
<dt><span class="strong"><a href="./org/biojavax/SimpleDocRefAuthor.html#hashCode()">hashCode()</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleDocRefAuthor.html" title="class in org.biojavax">SimpleDocRefAuthor</a></dt>
<dt><span class="strong"><a href="./org/biojavax/SimpleNamespace.html#hashCode()">hashCode()</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleNamespace.html" title="class in org.biojavax">SimpleNamespace</a></dt>
<dt><span class="strong"><a href="./org/biojavax/SimpleNote.html#hashCode()">hashCode()</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleNote.html" title="class in org.biojavax">SimpleNote</a></dt>
<dt><span class="strong"><a href="./org/biojavax/SimpleRankedCrossRef.html#hashCode()">hashCode()</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleRankedCrossRef.html" title="class in org.biojavax">SimpleRankedCrossRef</a></dt>
<dt><span class="strong"><a href="./org/biojavax/SimpleRankedDocRef.html#hashCode()">hashCode()</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleRankedDocRef.html" title="class in org.biojavax">SimpleRankedDocRef</a></dt>
<dt><a href="./org/biojavax/bio/seq/io/HashedFastaIterator.html" title="class in org.biojavax.bio.seq.io"><span class="strong">HashedFastaIterator</span></a> - Class in <a href="./org/biojavax/bio/seq/io/package-summary.html">org.biojavax.bio.seq.io</a></dt>
<dd>
<div class="block">Iterates over a Fasta file that is kept in memory for optimized access.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/HashedFastaIterator.html#HashedFastaIterator(java.io.BufferedInputStream, org.biojava.bio.symbol.Alphabet, org.biojavax.Namespace)">HashedFastaIterator(BufferedInputStream, Alphabet, Namespace)</a></span> - Constructor for class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/HashedFastaIterator.html" title="class in org.biojavax.bio.seq.io">HashedFastaIterator</a></dt>
<dd> </dd>
<dt><a href="./org/biojavax/bio/db/HashRichSequenceDB.html" title="class in org.biojavax.bio.db"><span class="strong">HashRichSequenceDB</span></a> - Class in <a href="./org/biojavax/bio/db/package-summary.html">org.biojavax.bio.db</a></dt>
<dd>
<div class="block">An implementation of RichSequenceDB that uses an underlying HashMap to store the
RichSequence objects.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/HashRichSequenceDB.html#HashRichSequenceDB()">HashRichSequenceDB()</a></span> - Constructor for class org.biojavax.bio.db.<a href="./org/biojavax/bio/db/HashRichSequenceDB.html" title="class in org.biojavax.bio.db">HashRichSequenceDB</a></dt>
<dd>
<div class="block">Generate a HashRichSequenceDB object that will use byName to generate ids for
sequences and have a null name.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/HashRichSequenceDB.html#HashRichSequenceDB(org.biojava.bio.seq.db.IDMaker)">HashRichSequenceDB(IDMaker)</a></span> - Constructor for class org.biojavax.bio.db.<a href="./org/biojavax/bio/db/HashRichSequenceDB.html" title="class in org.biojavax.bio.db">HashRichSequenceDB</a></dt>
<dd>
<div class="block">Generate a HashRichSequenceDB object that will use idMaker to generate ids for
sequences and have a null name.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/HashRichSequenceDB.html#HashRichSequenceDB(java.lang.String)">HashRichSequenceDB(String)</a></span> - Constructor for class org.biojavax.bio.db.<a href="./org/biojavax/bio/db/HashRichSequenceDB.html" title="class in org.biojavax.bio.db">HashRichSequenceDB</a></dt>
<dd>
<div class="block">Generate a HashRichSequenceDB object that will use byName to generate ids and
will have the requested name.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/HashRichSequenceDB.html#HashRichSequenceDB(org.biojava.bio.seq.db.IDMaker, java.lang.String)">HashRichSequenceDB(IDMaker, String)</a></span> - Constructor for class org.biojavax.bio.db.<a href="./org/biojavax/bio/db/HashRichSequenceDB.html" title="class in org.biojavax.bio.db">HashRichSequenceDB</a></dt>
<dd>
<div class="block">Generate a HashRichSequenceDB object that will use idMaker to generate ids for
sequences and have the requested name.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/db/HashSequenceDB.html" title="class in org.biojava.bio.seq.db"><span class="strong">HashSequenceDB</span></a> - Class in <a href="./org/biojava/bio/seq/db/package-summary.html">org.biojava.bio.seq.db</a></dt>
<dd>
<div class="block">An implementation of SequenceDB that uses an underlying HashMap to store the
sequence objects.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/HashSequenceDB.html#HashSequenceDB()">HashSequenceDB()</a></span> - Constructor for class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/HashSequenceDB.html" title="class in org.biojava.bio.seq.db">HashSequenceDB</a></dt>
<dd>
<div class="block">Generate a HashSequenceDB object that will use byName to generate ids for
sequences and have a null name.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/HashSequenceDB.html#HashSequenceDB(org.biojava.bio.seq.db.IDMaker)">HashSequenceDB(IDMaker)</a></span> - Constructor for class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/HashSequenceDB.html" title="class in org.biojava.bio.seq.db">HashSequenceDB</a></dt>
<dd>
<div class="block">Generate a HashSequenceDB object that will use idMaker to generate ids for
sequences and have a null name.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/HashSequenceDB.html#HashSequenceDB(java.lang.String)">HashSequenceDB(String)</a></span> - Constructor for class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/HashSequenceDB.html" title="class in org.biojava.bio.seq.db">HashSequenceDB</a></dt>
<dd>
<div class="block">Generate a HashSequenceDB object that will use byName to generate ids and
will have the requested name.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/HashSequenceDB.html#HashSequenceDB(org.biojava.bio.seq.db.IDMaker, java.lang.String)">HashSequenceDB(IDMaker, String)</a></span> - Constructor for class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/HashSequenceDB.html" title="class in org.biojava.bio.seq.db">HashSequenceDB</a></dt>
<dd>
<div class="block">Generate a HashSequenceDB object that will use idMaker to generate ids for
sequences and have the requested name.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Structure.html#hasJournalArticle()">hasJournalArticle()</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Structure.html" title="interface in org.biojava.bio.structure">Structure</a></dt>
<dd>
<div class="block">return whether or not the entry has an associated journal article
or publication.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/StructureImpl.html#hasJournalArticle()">hasJournalArticle()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/StructureImpl.html" title="class in org.biojava.bio.structure">StructureImpl</a></dt>
<dd>
<div class="block">Return whether or not the entry has an associated journal article
or publication.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/BumpedRenderer.html#hasListeners()">hasListeners()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/BumpedRenderer.html" title="class in org.biojava.bio.gui.sequence">BumpedRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/FilteringRenderer.html#hasListeners()">hasListeners()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/FilteringRenderer.html" title="class in org.biojava.bio.gui.sequence">FilteringRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PaddingRenderer.html#hasListeners()">hasListeners()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PaddingRenderer.html" title="class in org.biojava.bio.gui.sequence">PaddingRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PairwiseSequencePanel.html#hasListeners()">hasListeners()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PairwiseSequencePanel.html" title="class in org.biojava.bio.gui.sequence">PairwiseSequencePanel</a></dt>
<dd>
<div class="block"><code>hasListeners</code> returns true if there are active
listeners for BioJava events.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePanel.html#hasListeners()">hasListeners()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePanel.html" title="class in org.biojava.bio.gui.sequence">SequencePanel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/TranslatedSequencePanel.html#hasListeners()">hasListeners()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/TranslatedSequencePanel.html" title="class in org.biojava.bio.gui.sequence">TranslatedSequencePanel</a></dt>
<dd>
<div class="block"><code>hasListeners</code> returns true if there are active
listeners for BioJava events.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/StackedLogoPainter.html#hasListeners(java.lang.String)">hasListeners(String)</a></span> - Method in class org.biojava.bio.gui.<a href="./org/biojava/bio/gui/StackedLogoPainter.html" title="class in org.biojava.bio.gui">StackedLogoPainter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/TextLogoPainter.html#hasListeners(java.lang.String)">hasListeners(String)</a></span> - Method in class org.biojava.bio.gui.<a href="./org/biojava/bio/gui/TextLogoPainter.html" title="class in org.biojava.bio.gui">TextLogoPainter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/ReferenceServer.html#hasListeners()">hasListeners()</a></span> - Method in class org.biojava.bio.program.das.<a href="./org/biojava/bio/program/das/ReferenceServer.html" title="class in org.biojava.bio.program.das">ReferenceServer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/LazyFilterFeatureHolder.html#hasListeners()">hasListeners()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/LazyFilterFeatureHolder.html" title="class in org.biojava.bio.seq.impl">LazyFilterFeatureHolder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/AbstractChangeable.html#hasListeners()">hasListeners()</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/AbstractChangeable.html" title="class in org.biojava.utils">AbstractChangeable</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>use hasListeners(ChangeType) if at all possible</i></div>
</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/AbstractChangeable.html#hasListeners(org.biojava.utils.ChangeType)">hasListeners(ChangeType)</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/AbstractChangeable.html" title="class in org.biojava.utils">AbstractChangeable</a></dt>
<dd>
<div class="block">Discover if we have listeners registered for a particular change type.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/ChangeSupport.html#hasListeners()">hasListeners()</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/ChangeSupport.html" title="class in org.biojava.utils">ChangeSupport</a></dt>
<dd>
<div class="block">Return true if we have any listeners registered at all.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/ChangeSupport.html#hasListeners(org.biojava.utils.ChangeType)">hasListeners(ChangeType)</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/ChangeSupport.html" title="class in org.biojava.utils">ChangeSupport</a></dt>
<dd>
<div class="block">Return true if we have listeners registered for a particular change type.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SymbolReader.html#hasMoreSymbols()">hasMoreSymbols()</a></span> - Method in interface org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SymbolReader.html" title="interface in org.biojava.bio.seq.io">SymbolReader</a></dt>
<dd>
<div class="block">Determine if there are more symbols left to read in this stream.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/DP.ReverseIterator.html#hasNext()">hasNext()</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/DP.ReverseIterator.html" title="class in org.biojava.bio.dp">DP.ReverseIterator</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/twohead/BackMatrixPairDPCursor.html#hasNext()">hasNext()</a></span> - Method in class org.biojava.bio.dp.twohead.<a href="./org/biojava/bio/dp/twohead/BackMatrixPairDPCursor.html" title="class in org.biojava.bio.dp.twohead">BackMatrixPairDPCursor</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/twohead/LightPairDPCursor.html#hasNext()">hasNext()</a></span> - Method in class org.biojava.bio.dp.twohead.<a href="./org/biojava/bio/dp/twohead/LightPairDPCursor.html" title="class in org.biojava.bio.dp.twohead">LightPairDPCursor</a></dt>
<dd>
<div class="block">Are there further Cells to be computed?</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/twohead/MatrixPairDPCursor.html#hasNext()">hasNext()</a></span> - Method in class org.biojava.bio.dp.twohead.<a href="./org/biojava/bio/dp/twohead/MatrixPairDPCursor.html" title="class in org.biojava.bio.dp.twohead">MatrixPairDPCursor</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/twohead/PairDPCursor.html#hasNext()">hasNext()</a></span> - Method in interface org.biojava.bio.dp.twohead.<a href="./org/biojava/bio/dp/twohead/PairDPCursor.html" title="interface in org.biojava.bio.dp.twohead">PairDPCursor</a></dt>
<dd>
<div class="block">test wether the cursor can be advanced further</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/OrthologueSet.Iterator.html#hasNext()">hasNext()</a></span> - Method in interface org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/OrthologueSet.Iterator.html" title="interface in org.biojava.bio.program.homologene">OrthologueSet.Iterator</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/OrthoPairCollection.Iterator.html#hasNext()">hasNext()</a></span> - Method in interface org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/OrthoPairCollection.Iterator.html" title="interface in org.biojava.bio.program.homologene">OrthoPairCollection.Iterator</a></dt>
<dd>
<div class="block">are more OrthoPairSets available?</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/OrthoPairSet.Iterator.html#hasNext()">hasNext()</a></span> - Method in interface org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/OrthoPairSet.Iterator.html" title="interface in org.biojava.bio.program.homologene">OrthoPairSet.Iterator</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/SimpleOrthologueSet.Iterator.html#hasNext()">hasNext()</a></span> - Method in class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/SimpleOrthologueSet.Iterator.html" title="class in org.biojava.bio.program.homologene">SimpleOrthologueSet.Iterator</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/SimpleOrthoPairCollection.Iterator.html#hasNext()">hasNext()</a></span> - Method in class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/SimpleOrthoPairCollection.Iterator.html" title="class in org.biojava.bio.program.homologene">SimpleOrthoPairCollection.Iterator</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/SimpleOrthoPairSet.Iterator.html#hasNext()">hasNext()</a></span> - Method in class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/SimpleOrthoPairSet.Iterator.html" title="class in org.biojava.bio.program.homologene">SimpleOrthoPairSet.Iterator</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssaha/SequenceStreamer.FileStreamer.html#hasNext()">hasNext()</a></span> - Method in class org.biojava.bio.program.ssaha.<a href="./org/biojava/bio/program/ssaha/SequenceStreamer.FileStreamer.html" title="class in org.biojava.bio.program.ssaha">SequenceStreamer.FileStreamer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssaha/SequenceStreamer.html#hasNext()">hasNext()</a></span> - Method in interface org.biojava.bio.program.ssaha.<a href="./org/biojava/bio/program/ssaha/SequenceStreamer.html" title="interface in org.biojava.bio.program.ssaha">SequenceStreamer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssaha/SequenceStreamer.SequenceDBStreamer.html#hasNext()">hasNext()</a></span> - Method in class org.biojava.bio.program.ssaha.<a href="./org/biojava/bio/program/ssaha/SequenceStreamer.SequenceDBStreamer.html" title="class in org.biojava.bio.program.ssaha">SequenceStreamer.SequenceDBStreamer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/aaindex/AAindexStreamReader.html#hasNext()">hasNext()</a></span> - Method in class org.biojava.bio.proteomics.aaindex.<a href="./org/biojava/bio/proteomics/aaindex/AAindexStreamReader.html" title="class in org.biojava.bio.proteomics.aaindex">AAindexStreamReader</a></dt>
<dd>
<div class="block">Checks if there is a further
<a href="./org/biojava/bio/symbol/SymbolPropertyTable.html" title="interface in org.biojava.bio.symbol"><code>SymbolPropertyTable</code></a> object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/aaindex/SymbolPropertyTableIterator.html#hasNext()">hasNext()</a></span> - Method in interface org.biojava.bio.proteomics.aaindex.<a href="./org/biojava/bio/proteomics/aaindex/SymbolPropertyTableIterator.html" title="interface in org.biojava.bio.proteomics.aaindex">SymbolPropertyTableIterator</a></dt>
<dd>
<div class="block">Checks if there is a further
<a href="./org/biojava/bio/symbol/SymbolPropertyTable.html" title="interface in org.biojava.bio.symbol"><code>SymbolPropertyTable</code></a> object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/StreamReader.html#hasNext()">hasNext()</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/StreamReader.html" title="class in org.biojava.bio.seq.io">StreamReader</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/SequenceIterator.html#hasNext()">hasNext()</a></span> - Method in interface org.biojava.bio.seq.<a href="./org/biojava/bio/seq/SequenceIterator.html" title="interface in org.biojava.bio.seq">SequenceIterator</a></dt>
<dd>
<div class="block">Returns whether there are more sequences to iterate over.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/AtomIterator.html#hasNext()">hasNext()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/AtomIterator.html" title="class in org.biojava.bio.structure">AtomIterator</a></dt>
<dd>
<div class="block">Is there a next atom ?</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/GroupIterator.html#hasNext()">hasNext()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/GroupIterator.html" title="class in org.biojava.bio.structure">GroupIterator</a></dt>
<dd>
<div class="block">is there a group after the current one in the structure?</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/server/FlatFileInstallation.html#hasNext()">hasNext()</a></span> - Method in class org.biojava.bio.structure.server.<a href="./org/biojava/bio/structure/server/FlatFileInstallation.html" title="class in org.biojava.bio.structure.server">FlatFileInstallation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/server/MMCIFFileInstallation.html#hasNext()">hasNext()</a></span> - Method in class org.biojava.bio.structure.server.<a href="./org/biojava/bio/structure/server/MMCIFFileInstallation.html" title="class in org.biojava.bio.structure.server">MMCIFFileInstallation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/server/PDBInstallation.html#hasNext()">hasNext()</a></span> - Method in interface org.biojava.bio.structure.server.<a href="./org/biojava/bio/structure/server/PDBInstallation.html" title="interface in org.biojava.bio.structure.server">PDBInstallation</a></dt>
<dd>
<div class="block">return if the iteration over all structures will return another structure</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/Alignment.SymbolListIterator.html#hasNext()">hasNext()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/Alignment.SymbolListIterator.html" title="class in org.biojava.bio.symbol">Alignment.SymbolListIterator</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/MergingIterator.html#hasNext()">hasNext()</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/MergingIterator.html" title="class in org.biojava.utils">MergingIterator</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/BioEntryIterator.html#hasNext()">hasNext()</a></span> - Method in interface org.biojavax.bio.<a href="./org/biojavax/bio/BioEntryIterator.html" title="interface in org.biojavax.bio">BioEntryIterator</a></dt>
<dd>
<div class="block">Returns whether there are more sequences to iterate over.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/HashedFastaIterator.html#hasNext()">hasNext()</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/HashedFastaIterator.html" title="class in org.biojavax.bio.seq.io">HashedFastaIterator</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/RichStreamReader.html#hasNext()">hasNext()</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/RichStreamReader.html" title="class in org.biojavax.bio.seq.io">RichStreamReader</a></dt>
<dd>
<div class="block">Returns whether there are more sequences to iterate over.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.IOTools.SingleRichSeqIterator.html#hasNext()">hasNext()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.IOTools.SingleRichSeqIterator.html" title="class in org.biojavax.bio.seq">RichSequence.IOTools.SingleRichSeqIterator</a></dt>
<dd>
<div class="block">Returns whether there are more sequences to iterate over.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/server/SimpleStructureServer.html#hasNextStructure()">hasNextStructure()</a></span> - Method in class org.biojava.bio.structure.server.<a href="./org/biojava/bio/structure/server/SimpleStructureServer.html" title="class in org.biojava.bio.structure.server">SimpleStructureServer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/server/StructureServer.html#hasNextStructure()">hasNextStructure()</a></span> - Method in interface org.biojava.bio.structure.server.<a href="./org/biojava/bio/structure/server/StructureServer.html" title="interface in org.biojava.bio.structure.server">StructureServer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/abi/ABIFParser.TaggedDataRecord.html#hasOffsetData">hasOffsetData</a></span> - Variable in class org.biojava.bio.program.abi.<a href="./org/biojava/bio/program/abi/ABIFParser.TaggedDataRecord.html" title="class in org.biojava.bio.program.abi">ABIFParser.TaggedDataRecord</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html#hasParent()">hasParent()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html" title="class in org.biojava.bio.structure.io.mmcif.model">ChemComp</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/distributed/DistDataSource.html#hasSequence(java.lang.String)">hasSequence(String)</a></span> - Method in interface org.biojava.bio.seq.distributed.<a href="./org/biojava/bio/seq/distributed/DistDataSource.html" title="interface in org.biojava.bio.seq.distributed">DistDataSource</a></dt>
<dd>
<div class="block">Find out if this DistDataSource provides the sequence information for a sequence ID.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/distributed/GFFDataSource.html#hasSequence(java.lang.String)">hasSequence(String)</a></span> - Method in class org.biojava.bio.seq.distributed.<a href="./org/biojava/bio/seq/distributed/GFFDataSource.html" title="class in org.biojava.bio.seq.distributed">GFFDataSource</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/distributed/SequenceDBDataSource.html#hasSequence(java.lang.String)">hasSequence(String)</a></span> - Method in class org.biojava.bio.seq.distributed.<a href="./org/biojava/bio/seq/distributed/SequenceDBDataSource.html" title="class in org.biojava.bio.seq.distributed">SequenceDBDataSource</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/SimpleDistribution.html#hasWeights()">hasWeights()</a></span> - Method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/SimpleDistribution.html" title="class in org.biojava.bio.dist">SimpleDistribution</a></dt>
<dd>
<div class="block">Indicate whether the weights array has been allocated yet.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/MassCalc.html#Havg">Havg</a></span> - Static variable in class org.biojava.bio.proteomics.<a href="./org/biojava/bio/proteomics/MassCalc.html" title="class in org.biojava.bio.proteomics">MassCalc</a></dt>
<dd>
<div class="block">Constant value of Hydrogen average mass</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/HeaderStAXHandler.html#HEADER_HANDLER_FACTORY">HEADER_HANDLER_FACTORY</a></span> - Static variable in class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/HeaderStAXHandler.html" title="class in org.biojava.bio.program.ssbind">HeaderStAXHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLFormat.html#headerLine">headerLine</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLFormat.html" title="class in org.biojavax.bio.seq.io">EMBLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/GenbankFormat.html#headerLine">headerLine</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/GenbankFormat.html" title="class in org.biojavax.bio.seq.io">GenbankFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtFormat.html#headerLine">headerLine</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtFormat.html" title="class in org.biojavax.bio.seq.io">UniProtFormat</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/ssbind/HeaderStAXHandler.html" title="class in org.biojava.bio.program.ssbind"><span class="strong">HeaderStAXHandler</span></a> - Class in <a href="./org/biojava/bio/program/ssbind/package-summary.html">org.biojava.bio.program.ssbind</a></dt>
<dd>
<div class="block"><code>HeaderStAXHandler</code> handles the Header element of
BioJava BlastLike XML.</div>
</dd>
<dt><a href="./org/biojava/bio/gui/sequence/HeadlessRenderContext.html" title="class in org.biojava.bio.gui.sequence"><span class="strong">HeadlessRenderContext</span></a> - Class in <a href="./org/biojava/bio/gui/sequence/package-summary.html">org.biojava.bio.gui.sequence</a></dt>
<dd>
<div class="block">
A stand-alone SequenceRenderContext to make it easy to render to an image.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/HeadlessRenderContext.html#HeadlessRenderContext(org.biojava.bio.seq.Sequence, org.biojava.bio.symbol.RangeLocation, int)">HeadlessRenderContext(Sequence, RangeLocation, int)</a></span> - Constructor for class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/HeadlessRenderContext.html" title="class in org.biojava.bio.gui.sequence">HeadlessRenderContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/MarkovModel.html#heads()">heads()</a></span> - Method in interface org.biojava.bio.dp.<a href="./org/biojava/bio/dp/MarkovModel.html" title="interface in org.biojava.bio.dp">MarkovModel</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>use <code>advance().length</code></i></div>
</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/SimpleMarkovModel.html#heads()">heads()</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/SimpleMarkovModel.html" title="class in org.biojava.bio.dp">SimpleMarkovModel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/WMAsMM.html#heads()">heads()</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/WMAsMM.html" title="class in org.biojava.bio.dp">WMAsMM</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.Option.html#HEIGHT_IS_AUTHORITATIVE">HEIGHT_IS_AUTHORITATIVE</a></span> - Static variable in class org.biojava.bio.chromatogram.graphic.<a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.Option.html" title="class in org.biojava.bio.chromatogram.graphic">ChromatogramGraphic.Option</a></dt>
<dd>
<div class="block">Option indicating whether height or vertical scale is
the authoritative measure.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/RectangularBeadRenderer.html#HEIGHTSCALING">HEIGHTSCALING</a></span> - Static variable in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/RectangularBeadRenderer.html" title="class in org.biojava.bio.gui.sequence">RectangularBeadRenderer</a></dt>
<dd>
<div class="block">Constant <code>HEIGHTSCALING</code> indicating a change to the
feature height scaling policy.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/PDBFileParser.html#HELIX">HELIX</a></span> - Static variable in class org.biojava.bio.structure.io.<a href="./org/biojava/bio/structure/io/PDBFileParser.html" title="class in org.biojava.bio.structure.io">PDBFileParser</a></dt>
<dd>
<div class="block">Helix secondary structure assignment.</div>
</dd>
<dt><a href="./org/biojava/bio/gui/glyph/HelixGlyph.html" title="class in org.biojava.bio.gui.glyph"><span class="strong">HelixGlyph</span></a> - Class in <a href="./org/biojava/bio/gui/glyph/package-summary.html">org.biojava.bio.gui.glyph</a></dt>
<dd>
<div class="block">A Glyph that paints a Helix within the bounds</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/glyph/HelixGlyph.html#HelixGlyph()">HelixGlyph()</a></span> - Constructor for class org.biojava.bio.gui.glyph.<a href="./org/biojava/bio/gui/glyph/HelixGlyph.html" title="class in org.biojava.bio.gui.glyph">HelixGlyph</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/glyph/HelixGlyph.html#HelixGlyph(java.awt.geom.Rectangle2D.Float)">HelixGlyph(Rectangle2D.Float)</a></span> - Constructor for class org.biojava.bio.gui.glyph.<a href="./org/biojava/bio/gui/glyph/HelixGlyph.html" title="class in org.biojava.bio.gui.glyph">HelixGlyph</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/GroupType.html#HETATM">HETATM</a></span> - Static variable in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/GroupType.html" title="class in org.biojava.bio.structure">GroupType</a></dt>
<dd>
<div class="block">the type for hetero groups</div>
</dd>
<dt><a href="./org/biojava/bio/structure/HetatomImpl.html" title="class in org.biojava.bio.structure"><span class="strong">HetatomImpl</span></a> - Class in <a href="./org/biojava/bio/structure/package-summary.html">org.biojava.bio.structure</a></dt>
<dd>
<div class="block">Generic Implementation of a Group interface.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/HetatomImpl.html#HetatomImpl()">HetatomImpl()</a></span> - Constructor for class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/HetatomImpl.html" title="class in org.biojava.bio.structure">HetatomImpl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/taxa/NCBITaxon.html#HIDDEN">HIDDEN</a></span> - Static variable in interface org.biojavax.bio.taxa.<a href="./org/biojavax/bio/taxa/NCBITaxon.html" title="interface in org.biojavax.bio.taxa">NCBITaxon</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/ProteinTools.html#his()">his()</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/ProteinTools.html" title="class in org.biojava.bio.seq">ProteinTools</a></dt>
<dd>
<div class="block">Returns the <code>AtomicSymbol</code> for the amino acid
Histidine (H)</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssaha/HitMerger.html#hit(int, int, int, int)">hit(int, int, int, int)</a></span> - Method in class org.biojava.bio.program.ssaha.<a href="./org/biojava/bio/program/ssaha/HitMerger.html" title="class in org.biojava.bio.program.ssaha">HitMerger</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssaha/SearchListener.Echo.html#hit(int, int, int, int)">hit(int, int, int, int)</a></span> - Method in class org.biojava.bio.program.ssaha.<a href="./org/biojava/bio/program/ssaha/SearchListener.Echo.html" title="class in org.biojava.bio.program.ssaha">SearchListener.Echo</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssaha/SearchListener.FilterByLength.html#hit(int, int, int, int)">hit(int, int, int, int)</a></span> - Method in class org.biojava.bio.program.ssaha.<a href="./org/biojava/bio/program/ssaha/SearchListener.FilterByLength.html" title="class in org.biojava.bio.program.ssaha">SearchListener.FilterByLength</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssaha/SearchListener.html#hit(int, int, int, int)">hit(int, int, int, int)</a></span> - Method in interface org.biojava.bio.program.ssaha.<a href="./org/biojava/bio/program/ssaha/SearchListener.html" title="interface in org.biojava.bio.program.ssaha">SearchListener</a></dt>
<dd>
<div class="block">There has been a hit between the query sequence and a database
sequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssaha/SearchListener.Tee.html#hit(int, int, int, int)">hit(int, int, int, int)</a></span> - Method in class org.biojava.bio.program.ssaha.<a href="./org/biojava/bio/program/ssaha/SearchListener.Tee.html" title="class in org.biojava.bio.program.ssaha">SearchListener.Tee</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssaha/SearchListener.Wrapper.html#hit(int, int, int, int)">hit(int, int, int, int)</a></span> - Method in class org.biojava.bio.program.ssaha.<a href="./org/biojava/bio/program/ssaha/SearchListener.Wrapper.html" title="class in org.biojava.bio.program.ssaha">SearchListener.Wrapper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/HitStAXHandler.html#HIT_HANDLER_FACTORY">HIT_HANDLER_FACTORY</a></span> - Static variable in class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/HitStAXHandler.html" title="class in org.biojava.bio.program.ssbind">HitStAXHandler</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/ssaha/HitMerger.html" title="class in org.biojava.bio.program.ssaha"><span class="strong">HitMerger</span></a> - Class in <a href="./org/biojava/bio/program/ssaha/package-summary.html">org.biojava.bio.program.ssaha</a></dt>
<dd>
<div class="block">A listener that merges overlapping hits and culls all hits under a given
length.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssaha/HitMerger.html#HitMerger(org.biojava.bio.program.ssaha.SearchListener, int)">HitMerger(SearchListener, int)</a></span> - Constructor for class org.biojava.bio.program.ssaha.<a href="./org/biojava/bio/program/ssaha/HitMerger.html" title="class in org.biojava.bio.program.ssaha">HitMerger</a></dt>
<dd>
<div class="block">Build a new HitMerger that will pass events on to a delegate.</div>
</dd>
<dt><a href="./org/biojava/bio/program/ssbind/HitStAXHandler.html" title="class in org.biojava.bio.program.ssbind"><span class="strong">HitStAXHandler</span></a> - Class in <a href="./org/biojava/bio/program/ssbind/package-summary.html">org.biojava.bio.program.ssbind</a></dt>
<dd>
<div class="block"><code>AlignmentStAXHandler</code> handles the Hit element of
BioJava BlastLike XML.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/hmmer/FullHmmerProfileHMM.html#hmm()">hmm()</a></span> - Method in class org.biojava.bio.program.hmmer.<a href="./org/biojava/bio/program/hmmer/FullHmmerProfileHMM.html" title="class in org.biojava.bio.program.hmmer">FullHmmerProfileHMM</a></dt>
<dd>
<div class="block">Gets the inner HmmerProfileHMM state</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/hmmer/HmmerProfileParser.html#hmm">hmm</a></span> - Variable in class org.biojava.bio.program.hmmer.<a href="./org/biojava/bio/program/hmmer/HmmerProfileParser.html" title="class in org.biojava.bio.program.hmmer">HmmerProfileParser</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/hmmer/HmmerProfileHMM.html" title="class in org.biojava.bio.program.hmmer"><span class="strong">HmmerProfileHMM</span></a> - Class in <a href="./org/biojava/bio/program/hmmer/package-summary.html">org.biojava.bio.program.hmmer</a></dt>
<dd>
<div class="block">This is a class for representing HMMER generated Profile HMM.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/hmmer/HmmerProfileHMM.html#HmmerProfileHMM(org.biojava.bio.symbol.Alphabet, int, org.biojava.bio.dist.DistributionFactory, org.biojava.bio.dist.DistributionFactory, java.lang.String)">HmmerProfileHMM(Alphabet, int, DistributionFactory, DistributionFactory, String)</a></span> - Constructor for class org.biojava.bio.program.hmmer.<a href="./org/biojava/bio/program/hmmer/HmmerProfileHMM.html" title="class in org.biojava.bio.program.hmmer">HmmerProfileHMM</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/hmmer/HmmerProfileParser.html" title="class in org.biojava.bio.program.hmmer"><span class="strong">HmmerProfileParser</span></a> - Class in <a href="./org/biojava/bio/program/hmmer/package-summary.html">org.biojava.bio.program.hmmer</a></dt>
<dd>
<div class="block">A class for parsing in Hmmer markov models from HMM_ls files generated by HMMER training
note that this class is still currently experimental.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/hmmer/HmmerProfileParser.html#HmmerProfileParser(java.lang.String)">HmmerProfileParser(String)</a></span> - Constructor for class org.biojava.bio.program.hmmer.<a href="./org/biojava/bio/program/hmmer/HmmerProfileParser.html" title="class in org.biojava.bio.program.hmmer">HmmerProfileParser</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/dp/HMMTrainer.html" title="interface in org.biojava.bio.dp"><span class="strong">HMMTrainer</span></a> - Interface in <a href="./org/biojava/bio/dp/package-summary.html">org.biojava.bio.dp</a></dt>
<dd>
<div class="block">interface implemented by objects that train HMMs.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/MassCalc.html#Hmono">Hmono</a></span> - Static variable in class org.biojava.bio.proteomics.<a href="./org/biojava/bio/proteomics/MassCalc.html" title="class in org.biojava.bio.proteomics">MassCalc</a></dt>
<dd>
<div class="block">Constant value of Hydrogen monoisotopic mass</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/HomologeneBuilder.html#HOMOID">HOMOID</a></span> - Static variable in interface org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/HomologeneBuilder.html" title="interface in org.biojava.bio.program.homologene">HomologeneBuilder</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/homologene/HomologeneBuilder.html" title="interface in org.biojava.bio.program.homologene"><span class="strong">HomologeneBuilder</span></a> - Interface in <a href="./org/biojava/bio/program/homologene/package-summary.html">org.biojava.bio.program.homologene</a></dt>
<dd>
<div class="block">an interface for Homologene dataset Builders</div>
</dd>
<dt><a href="./org/biojava/bio/program/homologene/HomologeneDB.html" title="interface in org.biojava.bio.program.homologene"><span class="strong">HomologeneDB</span></a> - Interface in <a href="./org/biojava/bio/program/homologene/package-summary.html">org.biojava.bio.program.homologene</a></dt>
<dd>
<div class="block">Homologene is a NCBI dataset that curates sets
of orthologues from the reference model organisms.</div>
</dd>
<dt><a href="./org/biojava/bio/program/homologene/HomologeneTools.html" title="class in org.biojava.bio.program.homologene"><span class="strong">HomologeneTools</span></a> - Class in <a href="./org/biojava/bio/program/homologene/package-summary.html">org.biojava.bio.program.homologene</a></dt>
<dd>
<div class="block">Homologene is a NCBI dataset that curates sets
of orthologues from the reference model ogranisms.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/HomologeneTools.html#HomologeneTools()">HomologeneTools()</a></span> - Constructor for class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/HomologeneTools.html" title="class in org.biojava.bio.program.homologene">HomologeneTools</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/homol/Homology.html" title="interface in org.biojava.bio.seq.homol"><span class="strong">Homology</span></a> - Interface in <a href="./org/biojava/bio/seq/homol/package-summary.html">org.biojava.bio.seq.homol</a></dt>
<dd>
<div class="block">
Signifies that two or more features are homologous.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/homol/HomologyFeature.Template.html#homology">homology</a></span> - Variable in class org.biojava.bio.seq.homol.<a href="./org/biojava/bio/seq/homol/HomologyFeature.Template.html" title="class in org.biojava.bio.seq.homol">HomologyFeature.Template</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/BlastLikeHomologyBuilder.html#HOMOLOGY_FEATURE_TYPE">HOMOLOGY_FEATURE_TYPE</a></span> - Static variable in class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/BlastLikeHomologyBuilder.html" title="class in org.biojava.bio.program.ssbind">BlastLikeHomologyBuilder</a></dt>
<dd>
<div class="block"><code>HOMOLOGY_FEATURE_TYPE</code> is the type String used by
<code>BlastLikeHomologyBuilder</code> when creating
<code>HomologyFeature</code>s.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/homol/HomologyDB.html" title="interface in org.biojava.bio.seq.homol"><span class="strong">HomologyDB</span></a> - Interface in <a href="./org/biojava/bio/seq/homol/package-summary.html">org.biojava.bio.seq.homol</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/homol/HomologyFeature.html" title="interface in org.biojava.bio.seq.homol"><span class="strong">HomologyFeature</span></a> - Interface in <a href="./org/biojava/bio/seq/homol/package-summary.html">org.biojava.bio.seq.homol</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/homol/HomologyFeature.Template.html" title="class in org.biojava.bio.seq.homol"><span class="strong">HomologyFeature.Template</span></a> - Class in <a href="./org/biojava/bio/seq/homol/package-summary.html">org.biojava.bio.seq.homol</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/homol/HomologyFeature.Template.html#HomologyFeature.Template()">HomologyFeature.Template()</a></span> - Constructor for class org.biojava.bio.seq.homol.<a href="./org/biojava/bio/seq/homol/HomologyFeature.Template.html" title="class in org.biojava.bio.seq.homol">HomologyFeature.Template</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.Option.html#HORIZONTAL_NONLINEAR_SCALER">HORIZONTAL_NONLINEAR_SCALER</a></span> - Static variable in class org.biojava.bio.chromatogram.graphic.<a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.Option.html" title="class in org.biojava.bio.chromatogram.graphic">ChromatogramGraphic.Option</a></dt>
<dd>
<div class="block">Option specifying the non-linear scaling function to apply, as
embodied in a <a href="./org/biojava/bio/chromatogram/graphic/ChromatogramNonlinearScaler.html" title="interface in org.biojava.bio.chromatogram.graphic"><code>ChromatogramNonlinearScaler</code></a> object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/ImageMap.ClientSide.html#hotSpots()">hotSpots()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/ImageMap.ClientSide.html" title="class in org.biojava.bio.gui.sequence">ImageMap.ClientSide</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/ImageMap.html#hotSpots()">hotSpots()</a></span> - Method in interface org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/ImageMap.html" title="interface in org.biojava.bio.gui.sequence">ImageMap</a></dt>
<dd>
<div class="block"><code>hotSpots</code> iterates over the hotspots in the map</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/ImageMap.ServerSide.html#hotSpots()">hotSpots()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/ImageMap.ServerSide.html" title="class in org.biojava.bio.gui.sequence">ImageMap.ServerSide</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/FastaFormat.html#hp">hp</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/FastaFormat.html" title="class in org.biojavax.bio.seq.io">FastaFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/HSPStAXHandler.html#HSP_HANDLER_FACTORY">HSP_HANDLER_FACTORY</a></span> - Static variable in class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/HSPStAXHandler.html" title="class in org.biojava.bio.program.ssbind">HSPStAXHandler</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/ssbind/HSPStAXHandler.html" title="class in org.biojava.bio.program.ssbind"><span class="strong">HSPStAXHandler</span></a> - Class in <a href="./org/biojava/bio/program/ssbind/package-summary.html">org.biojava.bio.program.ssbind</a></dt>
<dd>
<div class="block"><code>HSPStAXHandler</code> handles the HSP element of BioJava
BlastLike XML.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/HSPSummaryStAXHandler.html#HSPSUMMARY_HANDLER_FACTORY">HSPSUMMARY_HANDLER_FACTORY</a></span> - Static variable in class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/HSPSummaryStAXHandler.html" title="class in org.biojava.bio.program.ssbind">HSPSummaryStAXHandler</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/ssbind/HSPSummaryStAXHandler.html" title="class in org.biojava.bio.program.ssbind"><span class="strong">HSPSummaryStAXHandler</span></a> - Class in <a href="./org/biojava/bio/program/ssbind/package-summary.html">org.biojava.bio.program.ssbind</a></dt>
<dd>
<div class="block"><code>HSPSummaryStAXHandler</code> handles the HSPSummary element
of BioJava BlastLike XML.</div>
</dd>
<dt><a href="./org/biojava/bio/program/blast2html/HTMLRenderer.html" title="class in org.biojava.bio.program.blast2html"><span class="strong">HTMLRenderer</span></a> - Class in <a href="./org/biojava/bio/program/blast2html/package-summary.html">org.biojava.bio.program.blast2html</a></dt>
<dd>
<div class="block">Renders HTML version of blast-like output.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/blast2html/HTMLRenderer.html#HTMLRenderer(java.io.PrintWriter, java.lang.String, int, org.biojava.bio.program.blast2html.URLGeneratorFactory, org.biojava.bio.program.blast2html.AlignmentMarker, java.util.Properties)">HTMLRenderer(PrintWriter, String, int, URLGeneratorFactory, AlignmentMarker, Properties)</a></span> - Constructor for class org.biojava.bio.program.blast2html.<a href="./org/biojava/bio/program/blast2html/HTMLRenderer.html" title="class in org.biojava.bio.program.blast2html">HTMLRenderer</a></dt>
<dd>
<div class="block">Creates an HTMLRenderer, that outputs the HTML to the specified
PrintWriter.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SymbolPropertyTable.html#HYDROPATHICITY">HYDROPATHICITY</a></span> - Static variable in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SymbolPropertyTable.html" title="interface in org.biojava.bio.symbol">SymbolPropertyTable</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/db/biosql/HypersonicDBHelper.html" title="class in org.biojava.bio.seq.db.biosql"><span class="strong">HypersonicDBHelper</span></a> - Class in <a href="./org/biojava/bio/seq/db/biosql/package-summary.html">org.biojava.bio.seq.db.biosql</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>Use hibernate and org.biojavax.bio.db.*</i></div>
</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/biosql/HypersonicDBHelper.html#HypersonicDBHelper()">HypersonicDBHelper()</a></span> - Constructor for class org.biojava.bio.seq.db.biosql.<a href="./org/biojava/bio/seq/db/biosql/HypersonicDBHelper.html" title="class in org.biojava.bio.seq.db.biosql">HypersonicDBHelper</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/jama/Maths.html#hypot(double, double)">hypot(double, double)</a></span> - Static method in class org.biojava.bio.structure.jama.<a href="./org/biojava/bio/structure/jama/Maths.html" title="class in org.biojava.bio.structure.jama">Maths</a></dt>
<dd>
<div class="block">sqrt(a^2 + b^2) without under/overflow.</div>
</dd>
</dl>
<a name="_I_">
<!-- -->
</a>
<h2 class="title">I</h2>
<dl>
<dt><span class="strong"><a href="./org/biojava/bio/seq/ProteinTools.html#i()">i()</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/ProteinTools.html" title="class in org.biojava.bio.seq">ProteinTools</a></dt>
<dd>
<div class="block">Returns the <code>AtomicSymbol</code> for the amino acid
Isoleucine</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#ID_ATTR">ID_ATTR</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/obo/OboFileHandler.html#ID_KEY">ID_KEY</a></span> - Static variable in class org.biojava.ontology.obo.<a href="./org/biojava/ontology/obo/OboFileHandler.html" title="class in org.biojava.ontology.obo">OboFileHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/EmblLikeFormat.html#ID_TAG">ID_TAG</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/EmblLikeFormat.html" title="class in org.biojava.bio.seq.io">EmblLikeFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#ID_TAG">ID_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/utils/lsid/Identifiable.html" title="interface in org.biojava.utils.lsid"><span class="strong">Identifiable</span></a> - Interface in <a href="./org/biojava/utils/lsid/package-summary.html">org.biojava.utils.lsid</a></dt>
<dd>
<div class="block">Marks an implementor as having a LifeScienceIdentifier.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BibRef.html#identifier">identifier</a></span> - Variable in class org.biojava.bibliography.<a href="./org/biojava/bibliography/BibRef.html" title="class in org.biojava.bibliography">BibRef</a></dt>
<dd>
<div class="block">It is an unambiguous reference to this citation "within the world".</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/BioEntry.html#IDENTIFIER">IDENTIFIER</a></span> - Static variable in interface org.biojavax.bio.<a href="./org/biojavax/bio/BioEntry.html" title="interface in org.biojavax.bio">BioEntry</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ontology/ComparableTerm.html#IDENTIFIER">IDENTIFIER</a></span> - Static variable in interface org.biojavax.ontology.<a href="./org/biojavax/ontology/ComparableTerm.html" title="interface in org.biojavax.ontology">ComparableTerm</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOTools.html#identifyFormat(java.lang.String, java.lang.String)">identifyFormat(String, String)</a></span> - Static method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOTools.html" title="class in org.biojava.bio.seq.io">SeqIOTools</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block"><code>identifyFormat</code> performs a case-insensitive mapping
of a pair of common sequence format name (such as 'embl',
'genbank' or 'fasta') and alphabet name (such as 'dna', 'rna',
'protein', 'aa') to an integer.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/jama/Matrix.html#identity(int, int)">identity(int, int)</a></span> - Static method in class org.biojava.bio.structure.jama.<a href="./org/biojava/bio/structure/jama/Matrix.html" title="class in org.biojava.bio.structure.jama">Matrix</a></dt>
<dd>
<div class="block">Generate identity matrix</div>
</dd>
<dt><a href="./org/biojava/bio/seq/db/IDMaker.html" title="interface in org.biojava.bio.seq.db"><span class="strong">IDMaker</span></a> - Interface in <a href="./org/biojava/bio/seq/db/package-summary.html">org.biojava.bio.seq.db</a></dt>
<dd>
<div class="block">Interface for objects that define how to make an ID for a sequence.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/db/IDMaker.ByName.html" title="class in org.biojava.bio.seq.db"><span class="strong">IDMaker.ByName</span></a> - Class in <a href="./org/biojava/bio/seq/db/package-summary.html">org.biojava.bio.seq.db</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/IDMaker.ByName.html#IDMaker.ByName()">IDMaker.ByName()</a></span> - Constructor for class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/IDMaker.ByName.html" title="class in org.biojava.bio.seq.db">IDMaker.ByName</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/db/IDMaker.ByURN.html" title="class in org.biojava.bio.seq.db"><span class="strong">IDMaker.ByURN</span></a> - Class in <a href="./org/biojava/bio/seq/db/package-summary.html">org.biojava.bio.seq.db</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/IDMaker.ByURN.html#IDMaker.ByURN()">IDMaker.ByURN()</a></span> - Constructor for class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/IDMaker.ByURN.html" title="class in org.biojava.bio.seq.db">IDMaker.ByURN</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/DASSequenceDB.html#ids()">ids()</a></span> - Method in class org.biojava.bio.program.das.<a href="./org/biojava/bio/program/das/DASSequenceDB.html" title="class in org.biojava.bio.program.das">DASSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/AnnotatedSequenceDB.html#ids()">ids()</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/AnnotatedSequenceDB.html" title="class in org.biojava.bio.seq.db">AnnotatedSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/biosql/BioSQLSequenceDB.html#ids()">ids()</a></span> - Method in class org.biojava.bio.seq.db.biosql.<a href="./org/biojava/bio/seq/db/biosql/BioSQLSequenceDB.html" title="class in org.biojava.bio.seq.db.biosql">BioSQLSequenceDB</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/CachingSequenceDB.html#ids()">ids()</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/CachingSequenceDB.html" title="class in org.biojava.bio.seq.db">CachingSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/DummySequenceDB.html#ids()">ids()</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/DummySequenceDB.html" title="class in org.biojava.bio.seq.db">DummySequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/HashSequenceDB.html#ids()">ids()</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/HashSequenceDB.html" title="class in org.biojava.bio.seq.db">HashSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/IndexedSequenceDB.html#ids()">ids()</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/IndexedSequenceDB.html" title="class in org.biojava.bio.seq.db">IndexedSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/SequenceDB.html#ids()">ids()</a></span> - Method in interface org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/SequenceDB.html" title="interface in org.biojava.bio.seq.db">SequenceDB</a></dt>
<dd>
<div class="block">Get an immutable set of all of the IDs in the database.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/SubSequenceDB.html#ids()">ids()</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/SubSequenceDB.html" title="class in org.biojava.bio.seq.db">SubSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/ViewingSequenceDB.html#ids()">ids()</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/ViewingSequenceDB.html" title="class in org.biojava.bio.seq.db">ViewingSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/distributed/DistDataSource.html#ids(boolean)">ids(boolean)</a></span> - Method in interface org.biojava.bio.seq.distributed.<a href="./org/biojava/bio/seq/distributed/DistDataSource.html" title="interface in org.biojava.bio.seq.distributed">DistDataSource</a></dt>
<dd>
<div class="block">Get the complete set of sequence IDs provided by this DistDataSource.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/distributed/DistributedSequenceDB.html#ids()">ids()</a></span> - Method in class org.biojava.bio.seq.distributed.<a href="./org/biojava/bio/seq/distributed/DistributedSequenceDB.html" title="class in org.biojava.bio.seq.distributed">DistributedSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/distributed/GFFDataSource.html#ids(boolean)">ids(boolean)</a></span> - Method in class org.biojava.bio.seq.distributed.<a href="./org/biojava/bio/seq/distributed/GFFDataSource.html" title="class in org.biojava.bio.seq.distributed">GFFDataSource</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/distributed/SequenceDBDataSource.html#ids(boolean)">ids(boolean)</a></span> - Method in class org.biojava.bio.seq.distributed.<a href="./org/biojava/bio/seq/distributed/SequenceDBDataSource.html" title="class in org.biojava.bio.seq.distributed">SequenceDBDataSource</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/BioEntryDB.html#ids()">ids()</a></span> - Method in interface org.biojavax.bio.db.<a href="./org/biojavax/bio/db/BioEntryDB.html" title="interface in org.biojavax.bio.db">BioEntryDB</a></dt>
<dd>
<div class="block">Get an immutable set of all of the IDs in the database.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLBioEntryDB.html#ids()">ids()</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLBioEntryDB.html" title="class in org.biojavax.bio.db.biosql">BioSQLBioEntryDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLRichSequenceDB.html#ids()">ids()</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLRichSequenceDB.html" title="class in org.biojavax.bio.db.biosql">BioSQLRichSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/HashBioEntryDB.html#ids()">ids()</a></span> - Method in class org.biojavax.bio.db.<a href="./org/biojavax/bio/db/HashBioEntryDB.html" title="class in org.biojavax.bio.db">HashBioEntryDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/HashRichSequenceDB.html#ids()">ids()</a></span> - Method in class org.biojavax.bio.db.<a href="./org/biojavax/bio/db/HashRichSequenceDB.html" title="class in org.biojavax.bio.db">HashRichSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/ncbi/GenbankRichSequenceDB.html#ids()">ids()</a></span> - Method in class org.biojavax.bio.db.ncbi.<a href="./org/biojavax/bio/db/ncbi/GenbankRichSequenceDB.html" title="class in org.biojavax.bio.db.ncbi">GenbankRichSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/ncbi/GenpeptRichSequenceDB.html#ids()">ids()</a></span> - Method in class org.biojavax.bio.db.ncbi.<a href="./org/biojavax/bio/db/ncbi/GenpeptRichSequenceDB.html" title="class in org.biojavax.bio.db.ncbi">GenpeptRichSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/util/SequenceScalePanel.html#IDX_COLOR">IDX_COLOR</a></span> - Static variable in class org.biojava.bio.structure.gui.util.<a href="./org/biojava/bio/structure/gui/util/SequenceScalePanel.html" title="class in org.biojava.bio.structure.gui.util">SequenceScalePanel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOConstants.html#IG">IG</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOConstants.html" title="class in org.biojava.bio.seq.io">SeqIOConstants</a></dt>
<dd>
<div class="block"><code>IG</code> indicates that the sequence format is IG.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/SeqSimilarityAdapter.html#ignorableWhitespace(char[], int, int)">ignorableWhitespace(char[], int, int)</a></span> - Method in class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/SeqSimilarityAdapter.html" title="class in org.biojava.bio.program.ssbind">SeqSimilarityAdapter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/SAX2StAXAdaptor.html#ignorableWhitespace(char[], int, int)">ignorableWhitespace(char[], int, int)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/SAX2StAXAdaptor.html" title="class in org.biojava.bio.seq.io.agave">SAX2StAXAdaptor</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/StAXContentHandler.html#ignorableWhitespace(char[], int, int)">ignorableWhitespace(char[], int, int)</a></span> - Method in interface org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/StAXContentHandler.html" title="interface in org.biojava.bio.seq.io.agave">StAXContentHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/StAXContentHandlerBase.html#ignorableWhitespace(char[], int, int)">ignorableWhitespace(char[], int, int)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/StAXContentHandlerBase.html" title="class in org.biojava.bio.seq.io.agave">StAXContentHandlerBase</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/stax/SAX2StAXAdaptor.html#ignorableWhitespace(char[], int, int)">ignorableWhitespace(char[], int, int)</a></span> - Method in class org.biojava.utils.stax.<a href="./org/biojava/utils/stax/SAX2StAXAdaptor.html" title="class in org.biojava.utils.stax">SAX2StAXAdaptor</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/stax/StAXContentHandler.html#ignorableWhitespace(char[], int, int)">ignorableWhitespace(char[], int, int)</a></span> - Method in interface org.biojava.utils.stax.<a href="./org/biojava/utils/stax/StAXContentHandler.html" title="interface in org.biojava.utils.stax">StAXContentHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/stax/StAXContentHandlerBase.html#ignorableWhitespace(char[], int, int)">ignorableWhitespace(char[], int, int)</a></span> - Method in class org.biojava.utils.stax.<a href="./org/biojava/utils/stax/StAXContentHandlerBase.html" title="class in org.biojava.utils.stax">StAXContentHandlerBase</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/dist/IgnoreCountsTrainer.html" title="class in org.biojava.bio.dist"><span class="strong">IgnoreCountsTrainer</span></a> - Class in <a href="./org/biojava/bio/dist/package-summary.html">org.biojava.bio.dist</a></dt>
<dd>
<div class="block">A distribution trainer that just ignores all counts.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/IgnoreCountsTrainer.html#IgnoreCountsTrainer()">IgnoreCountsTrainer()</a></span> - Constructor for class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/IgnoreCountsTrainer.html" title="class in org.biojava.bio.dist">IgnoreCountsTrainer</a></dt>
<dd>
<div class="block">Constructor intended for sub-classes.</div>
</dd>
<dt><a href="./org/biojava/bio/program/gff/IgnoreRecordException.html" title="class in org.biojava.bio.program.gff"><span class="strong">IgnoreRecordException</span></a> - Exception in <a href="./org/biojava/bio/program/gff/package-summary.html">org.biojava.bio.program.gff</a></dt>
<dd>
<div class="block">Ignore this record in the stream.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/IgnoreRecordException.html#IgnoreRecordException()">IgnoreRecordException()</a></span> - Constructor for exception org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/IgnoreRecordException.html" title="class in org.biojava.bio.program.gff">IgnoreRecordException</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/ProteinTools.html#ile()">ile()</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/ProteinTools.html" title="class in org.biojava.bio.seq">ProteinTools</a></dt>
<dd>
<div class="block">Returns the <code>AtomicSymbol</code> for the amino acid
Isoleucine (I)</div>
</dd>
<dt><a href="./org/biojava/bio/alignment/IllegalAlignmentEditException.html" title="class in org.biojava.bio.alignment"><span class="strong">IllegalAlignmentEditException</span></a> - Exception in <a href="./org/biojava/bio/alignment/package-summary.html">org.biojava.bio.alignment</a></dt>
<dd>
<div class="block">
The usual reason for throwing an IllegalAlignmentEditException is that you are
trying to shift a group of bases in such a way that it would require deleting bases.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/IllegalAlignmentEditException.html#IllegalAlignmentEditException()">IllegalAlignmentEditException()</a></span> - Constructor for exception org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/IllegalAlignmentEditException.html" title="class in org.biojava.bio.alignment">IllegalAlignmentEditException</a></dt>
<dd>
<div class="block">Just make the exception.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/IllegalAlignmentEditException.html#IllegalAlignmentEditException(java.lang.String)">IllegalAlignmentEditException(String)</a></span> - Constructor for exception org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/IllegalAlignmentEditException.html" title="class in org.biojava.bio.alignment">IllegalAlignmentEditException</a></dt>
<dd>
<div class="block">Make the exception with a message.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/IllegalAlignmentEditException.html#IllegalAlignmentEditException(java.lang.Throwable)">IllegalAlignmentEditException(Throwable)</a></span> - Constructor for exception org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/IllegalAlignmentEditException.html" title="class in org.biojava.bio.alignment">IllegalAlignmentEditException</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/IllegalAlignmentEditException.html#IllegalAlignmentEditException(java.lang.Throwable, java.lang.String)">IllegalAlignmentEditException(Throwable, String)</a></span> - Constructor for exception org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/IllegalAlignmentEditException.html" title="class in org.biojava.bio.alignment">IllegalAlignmentEditException</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/symbol/IllegalAlphabetException.html" title="class in org.biojava.bio.symbol"><span class="strong">IllegalAlphabetException</span></a> - Exception in <a href="./org/biojava/bio/symbol/package-summary.html">org.biojava.bio.symbol</a></dt>
<dd>
<div class="block">
The exception to indicate that an invalid alphabet has been used.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/IllegalAlphabetException.html#IllegalAlphabetException()">IllegalAlphabetException()</a></span> - Constructor for exception org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/IllegalAlphabetException.html" title="class in org.biojava.bio.symbol">IllegalAlphabetException</a></dt>
<dd>
<div class="block">Just make the exception.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/IllegalAlphabetException.html#IllegalAlphabetException(java.lang.String)">IllegalAlphabetException(String)</a></span> - Constructor for exception org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/IllegalAlphabetException.html" title="class in org.biojava.bio.symbol">IllegalAlphabetException</a></dt>
<dd>
<div class="block">Make the exception with a message.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/IllegalAlphabetException.html#IllegalAlphabetException(java.lang.Throwable)">IllegalAlphabetException(Throwable)</a></span> - Constructor for exception org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/IllegalAlphabetException.html" title="class in org.biojava.bio.symbol">IllegalAlphabetException</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/IllegalAlphabetException.html#IllegalAlphabetException(java.lang.Throwable, java.lang.String)">IllegalAlphabetException(Throwable, String)</a></span> - Constructor for exception org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/IllegalAlphabetException.html" title="class in org.biojava.bio.symbol">IllegalAlphabetException</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/db/IllegalIDException.html" title="class in org.biojava.bio.seq.db"><span class="strong">IllegalIDException</span></a> - Exception in <a href="./org/biojava/bio/seq/db/package-summary.html">org.biojava.bio.seq.db</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/IllegalIDException.html#IllegalIDException()">IllegalIDException()</a></span> - Constructor for exception org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/IllegalIDException.html" title="class in org.biojava.bio.seq.db">IllegalIDException</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/IllegalIDException.html#IllegalIDException(java.lang.Throwable)">IllegalIDException(Throwable)</a></span> - Constructor for exception org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/IllegalIDException.html" title="class in org.biojava.bio.seq.db">IllegalIDException</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/IllegalIDException.html#IllegalIDException(java.lang.String)">IllegalIDException(String)</a></span> - Constructor for exception org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/IllegalIDException.html" title="class in org.biojava.bio.seq.db">IllegalIDException</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/IllegalIDException.html#IllegalIDException(java.lang.Throwable, java.lang.String)">IllegalIDException(Throwable, String)</a></span> - Constructor for exception org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/IllegalIDException.html" title="class in org.biojava.bio.seq.db">IllegalIDException</a></dt>
<dd> </dd>
<dt><a href="./org/biojavax/ga/exception/IllegalOrganismException.html" title="class in org.biojavax.ga.exception"><span class="strong">IllegalOrganismException</span></a> - Exception in <a href="./org/biojavax/ga/exception/package-summary.html">org.biojavax.ga.exception</a></dt>
<dd>
<div class="block">Indicates an invalid organism</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ga/exception/IllegalOrganismException.html#IllegalOrganismException()">IllegalOrganismException()</a></span> - Constructor for exception org.biojavax.ga.exception.<a href="./org/biojavax/ga/exception/IllegalOrganismException.html" title="class in org.biojavax.ga.exception">IllegalOrganismException</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/exception/IllegalOrganismException.html#IllegalOrganismException(java.lang.String)">IllegalOrganismException(String)</a></span> - Constructor for exception org.biojavax.ga.exception.<a href="./org/biojavax/ga/exception/IllegalOrganismException.html" title="class in org.biojavax.ga.exception">IllegalOrganismException</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/symbol/IllegalSymbolException.html" title="class in org.biojava.bio.symbol"><span class="strong">IllegalSymbolException</span></a> - Exception in <a href="./org/biojava/bio/symbol/package-summary.html">org.biojava.bio.symbol</a></dt>
<dd>
<div class="block">The exception to indicate that a symbol is not valid within a context.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/IllegalSymbolException.html#IllegalSymbolException(java.lang.String)">IllegalSymbolException(String)</a></span> - Constructor for exception org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/IllegalSymbolException.html" title="class in org.biojava.bio.symbol">IllegalSymbolException</a></dt>
<dd>
<div class="block">Make the exception with a message.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/IllegalSymbolException.html#IllegalSymbolException(org.biojava.bio.symbol.Symbol, java.lang.String)">IllegalSymbolException(Symbol, String)</a></span> - Constructor for exception org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/IllegalSymbolException.html" title="class in org.biojava.bio.symbol">IllegalSymbolException</a></dt>
<dd>
<div class="block">Make the exception with a message and a symbol.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/IllegalSymbolException.html#IllegalSymbolException(java.lang.Throwable, java.lang.String)">IllegalSymbolException(Throwable, String)</a></span> - Constructor for exception org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/IllegalSymbolException.html" title="class in org.biojava.bio.symbol">IllegalSymbolException</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/IllegalSymbolException.html#IllegalSymbolException(java.lang.Throwable, org.biojava.bio.symbol.Symbol, java.lang.String)">IllegalSymbolException(Throwable, Symbol, String)</a></span> - Constructor for exception org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/IllegalSymbolException.html" title="class in org.biojava.bio.symbol">IllegalSymbolException</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/dp/IllegalTransitionException.html" title="class in org.biojava.bio.dp"><span class="strong">IllegalTransitionException</span></a> - Exception in <a href="./org/biojava/bio/dp/package-summary.html">org.biojava.bio.dp</a></dt>
<dd>
<div class="block">This exception indicates that there is no transition between two states.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/IllegalTransitionException.html#IllegalTransitionException(org.biojava.bio.dp.State, org.biojava.bio.dp.State, java.lang.String)">IllegalTransitionException(State, State, String)</a></span> - Constructor for exception org.biojava.bio.dp.<a href="./org/biojava/bio/dp/IllegalTransitionException.html" title="class in org.biojava.bio.dp">IllegalTransitionException</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/IllegalTransitionException.html#IllegalTransitionException(org.biojava.bio.dp.State, org.biojava.bio.dp.State)">IllegalTransitionException(State, State)</a></span> - Constructor for exception org.biojava.bio.dp.<a href="./org/biojava/bio/dp/IllegalTransitionException.html" title="class in org.biojava.bio.dp">IllegalTransitionException</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/IllegalTransitionException.html#IllegalTransitionException()">IllegalTransitionException()</a></span> - Constructor for exception org.biojava.bio.dp.<a href="./org/biojava/bio/dp/IllegalTransitionException.html" title="class in org.biojava.bio.dp">IllegalTransitionException</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/fastq/IlluminaFastqReader.html" title="class in org.biojava.bio.program.fastq"><span class="strong">IlluminaFastqReader</span></a> - Class in <a href="./org/biojava/bio/program/fastq/package-summary.html">org.biojava.bio.program.fastq</a></dt>
<dd>
<div class="block">Reader for <a href="./org/biojava/bio/program/fastq/FastqVariant.html#FASTQ_ILLUMINA"><code>FastqVariant.FASTQ_ILLUMINA</code></a> formatted sequences.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/fastq/IlluminaFastqReader.html#IlluminaFastqReader()">IlluminaFastqReader()</a></span> - Constructor for class org.biojava.bio.program.fastq.<a href="./org/biojava/bio/program/fastq/IlluminaFastqReader.html" title="class in org.biojava.bio.program.fastq">IlluminaFastqReader</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/fastq/IlluminaFastqWriter.html" title="class in org.biojava.bio.program.fastq"><span class="strong">IlluminaFastqWriter</span></a> - Class in <a href="./org/biojava/bio/program/fastq/package-summary.html">org.biojava.bio.program.fastq</a></dt>
<dd>
<div class="block">Writer for <a href="./org/biojava/bio/program/fastq/FastqVariant.html#FASTQ_ILLUMINA"><code>FastqVariant.FASTQ_ILLUMINA</code></a> formatted sequences.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/fastq/IlluminaFastqWriter.html#IlluminaFastqWriter()">IlluminaFastqWriter()</a></span> - Constructor for class org.biojava.bio.program.fastq.<a href="./org/biojava/bio/program/fastq/IlluminaFastqWriter.html" title="class in org.biojava.bio.program.fastq">IlluminaFastqWriter</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/gui/sequence/ImageMap.html" title="interface in org.biojava.bio.gui.sequence"><span class="strong">ImageMap</span></a> - Interface in <a href="./org/biojava/bio/gui/sequence/package-summary.html">org.biojava.bio.gui.sequence</a></dt>
<dd>
<div class="block"><code>ImageMap</code> represents a collection of image map
hotspots.</div>
</dd>
<dt><a href="./org/biojava/bio/gui/sequence/ImageMap.ClientSide.html" title="class in org.biojava.bio.gui.sequence"><span class="strong">ImageMap.ClientSide</span></a> - Class in <a href="./org/biojava/bio/gui/sequence/package-summary.html">org.biojava.bio.gui.sequence</a></dt>
<dd>
<div class="block"><code>ClientSide</code> represents a client-side style image
map.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/ImageMap.ClientSide.html#ImageMap.ClientSide(java.lang.String)">ImageMap.ClientSide(String)</a></span> - Constructor for class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/ImageMap.ClientSide.html" title="class in org.biojava.bio.gui.sequence">ImageMap.ClientSide</a></dt>
<dd>
<div class="block">Creates a new <code>ClientSide</code> image map.</div>
</dd>
<dt><a href="./org/biojava/bio/gui/sequence/ImageMap.HotSpot.html" title="class in org.biojava.bio.gui.sequence"><span class="strong">ImageMap.HotSpot</span></a> - Class in <a href="./org/biojava/bio/gui/sequence/package-summary.html">org.biojava.bio.gui.sequence</a></dt>
<dd>
<div class="block"><code>HotSpot</code>s represent an image map hotspot.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/ImageMap.HotSpot.html#ImageMap.HotSpot(java.lang.String, java.net.URL, java.lang.Integer[])">ImageMap.HotSpot(String, URL, Integer[])</a></span> - Constructor for class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/ImageMap.HotSpot.html" title="class in org.biojava.bio.gui.sequence">ImageMap.HotSpot</a></dt>
<dd>
<div class="block">Creates a new <code>HotSpot</code> with a null user object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/ImageMap.HotSpot.html#ImageMap.HotSpot(java.lang.String, java.net.URL, java.lang.Integer[], java.lang.Object)">ImageMap.HotSpot(String, URL, Integer[], Object)</a></span> - Constructor for class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/ImageMap.HotSpot.html" title="class in org.biojava.bio.gui.sequence">ImageMap.HotSpot</a></dt>
<dd>
<div class="block">Creates a new <code>HotSpot</code>.</div>
</dd>
<dt><a href="./org/biojava/bio/gui/sequence/ImageMap.ServerSide.html" title="class in org.biojava.bio.gui.sequence"><span class="strong">ImageMap.ServerSide</span></a> - Class in <a href="./org/biojava/bio/gui/sequence/package-summary.html">org.biojava.bio.gui.sequence</a></dt>
<dd>
<div class="block"><code>ServerSide</code> represents a server-side style image
map.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/ImageMap.ServerSide.html#ImageMap.ServerSide()">ImageMap.ServerSide()</a></span> - Constructor for class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/ImageMap.ServerSide.html" title="class in org.biojava.bio.gui.sequence">ImageMap.ServerSide</a></dt>
<dd>
<div class="block">Creates a new <code>ServerSide</code> image map.</div>
</dd>
<dt><a href="./org/biojava/bio/gui/sequence/ImageMapRenderer.html" title="interface in org.biojava.bio.gui.sequence"><span class="strong">ImageMapRenderer</span></a> - Interface in <a href="./org/biojava/bio/gui/sequence/package-summary.html">org.biojava.bio.gui.sequence</a></dt>
<dd>
<div class="block"><code>ImageMapRenderer</code>s create strings representing
<code>Feature</code>s suitable for use in HTML image
maps.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/taxa/SimpleTaxonFactory.html#importTaxon(org.biojava.bio.taxa.Taxon)">importTaxon(Taxon)</a></span> - Method in class org.biojava.bio.taxa.<a href="./org/biojava/bio/taxa/SimpleTaxonFactory.html" title="class in org.biojava.bio.taxa">SimpleTaxonFactory</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/taxa/TaxonFactory.html#importTaxon(org.biojava.bio.taxa.Taxon)">importTaxon(Taxon)</a></span> - Method in interface org.biojava.bio.taxa.<a href="./org/biojava/bio/taxa/TaxonFactory.html" title="interface in org.biojava.bio.taxa">TaxonFactory</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Import a Taxon and all its children into the implementation
provided by this factory.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/taxa/WeakTaxonFactory.html#importTaxon(org.biojava.bio.taxa.Taxon)">importTaxon(Taxon)</a></span> - Method in class org.biojava.bio.taxa.<a href="./org/biojava/bio/taxa/WeakTaxonFactory.html" title="class in org.biojava.bio.taxa">WeakTaxonFactory</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/IntegerOntology.html#importTerm(org.biojava.ontology.Term, java.lang.String)">importTerm(Term, String)</a></span> - Method in class org.biojava.ontology.<a href="./org/biojava/ontology/IntegerOntology.html" title="class in org.biojava.ontology">IntegerOntology</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/Ontology.Impl.html#importTerm(org.biojava.ontology.Term, java.lang.String)">importTerm(Term, String)</a></span> - Method in class org.biojava.ontology.<a href="./org/biojava/ontology/Ontology.Impl.html" title="class in org.biojava.ontology">Ontology.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/Ontology.html#importTerm(org.biojava.ontology.Term, java.lang.String)">importTerm(Term, String)</a></span> - Method in interface org.biojava.ontology.<a href="./org/biojava/ontology/Ontology.html" title="interface in org.biojava.ontology">Ontology</a></dt>
<dd>
<div class="block">Create a view of a term from another ontology.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ontology/SimpleComparableOntology.html#importTerm(org.biojava.ontology.Term, java.lang.String)">importTerm(Term, String)</a></span> - Method in class org.biojavax.ontology.<a href="./org/biojavax/ontology/SimpleComparableOntology.html" title="class in org.biojavax.ontology">SimpleComparableOntology</a></dt>
<dd>
<div class="block">Create a view of a term from another ontology.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/io/CachingInputStream.html#in">in</a></span> - Variable in class org.biojava.utils.io.<a href="./org/biojava/utils/io/CachingInputStream.html" title="class in org.biojava.utils.io">CachingInputStream</a></dt>
<dd>
<div class="block">The underlying input stream whose data we're caching</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/Position.html#IN_RANGE">IN_RANGE</a></span> - Static variable in interface org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/Position.html" title="interface in org.biojavax.bio.seq">Position</a></dt>
<dd>
<div class="block">A symbol representing a position that occupies a single base somewhere
in a range, eg.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SuffixTree.html#incCounts(int, int)">incCounts(int, int)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SuffixTree.html" title="class in org.biojava.bio.symbol">SuffixTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.Terms.html#INCLUDES_PREFIX">INCLUDES_PREFIX</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.Terms.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat.Terms</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/Count.html#increaseCount(org.biojava.bio.symbol.AtomicSymbol, double)">increaseCount(AtomicSymbol, double)</a></span> - Method in interface org.biojava.bio.dist.<a href="./org/biojava/bio/dist/Count.html" title="interface in org.biojava.bio.dist">Count</a></dt>
<dd>
<div class="block">Set the probability or odds that Symbol s is emitted by this state.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/IndexedCount.html#increaseCount(org.biojava.bio.symbol.AtomicSymbol, double)">increaseCount(AtomicSymbol, double)</a></span> - Method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/IndexedCount.html" title="class in org.biojava.bio.dist">IndexedCount</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/xml/BaseXMLWriter.html#indent()">indent()</a></span> - Method in class org.biojava.bio.program.xml.<a href="./org/biojava/bio/program/xml/BaseXMLWriter.html" title="class in org.biojava.bio.program.xml">BaseXMLWriter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AgaveWriter.html#INDENT">INDENT</a></span> - Static variable in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AgaveWriter.html" title="class in org.biojava.bio.seq.io.agave">AgaveWriter</a></dt>
<dd>
<div class="block">use a two space indent</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AgaveWriter.Indent.html#indent()">indent()</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AgaveWriter.Indent.html" title="class in org.biojava.bio.seq.io.agave">AgaveWriter.Indent</a></dt>
<dd>
<div class="block">Add a level of indentation</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/TriState.html#INDETERMINATE">INDETERMINATE</a></span> - Static variable in class org.biojava.utils.<a href="./org/biojava/utils/TriState.html" title="class in org.biojava.utils">TriState</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/WMAsMM.html#index(org.biojava.bio.dp.State)">index(State)</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/WMAsMM.html" title="class in org.biojava.bio.dp">WMAsMM</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/db/Index.html" title="interface in org.biojava.bio.seq.db"><span class="strong">Index</span></a> - Interface in <a href="./org/biojava/bio/seq/db/package-summary.html">org.biojava.bio.seq.db</a></dt>
<dd>
<div class="block">This defines an index entry for an individual sequence within a set of
indexed files.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/DNATools.html#index(org.biojava.bio.symbol.Symbol)">index(Symbol)</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/DNATools.html" title="class in org.biojava.bio.seq">DNATools</a></dt>
<dd>
<div class="block">Return an integer index for a symbol - compatible with
<code>forIndex</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/NucleotideTools.html#index(org.biojava.bio.symbol.Symbol)">index(Symbol)</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/NucleotideTools.html" title="class in org.biojava.bio.seq">NucleotideTools</a></dt>
<dd>
<div class="block">Return an integer index for a symbol - compatible with
<code>forIndex</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/RNATools.html#index(org.biojava.bio.symbol.Symbol)">index(Symbol)</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/RNATools.html" title="class in org.biojava.bio.seq">RNATools</a></dt>
<dd>
<div class="block">Return an integer index for a symbol - compatible with forIndex.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/helper/GapArray.html#index">index</a></span> - Variable in class org.biojava.bio.structure.align.helper.<a href="./org/biojava/bio/structure/align/helper/GapArray.html" title="class in org.biojava.bio.structure.align.helper">GapArray</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AlphabetIndex.html#INDEX">INDEX</a></span> - Static variable in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AlphabetIndex.html" title="interface in org.biojava.bio.symbol">AlphabetIndex</a></dt>
<dd>
<div class="block">
Indicates that the index is changing, probably due to the underlying
alphabet changing.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/obo/OboFileParser.SOPair.html#index">index</a></span> - Variable in class org.biojava.ontology.obo.<a href="./org/biojava/ontology/obo/OboFileParser.SOPair.html" title="class in org.biojava.ontology.obo">OboFileParser.SOPair</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/tagvalue/Index2Model.html" title="class in org.biojava.bio.program.tagvalue"><span class="strong">Index2Model</span></a> - Class in <a href="./org/biojava/bio/program/tagvalue/package-summary.html">org.biojava.bio.program.tagvalue</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/Index2Model.html#Index2Model()">Index2Model()</a></span> - Constructor for class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/Index2Model.html" title="class in org.biojava.bio.program.tagvalue">Index2Model</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/annodb/IndexedAnnotationDB.html" title="class in org.biojava.bio.annodb"><span class="strong">IndexedAnnotationDB</span></a> - Class in <a href="./org/biojava/bio/annodb/package-summary.html">org.biojava.bio.annodb</a></dt>
<dd>
<div class="block">A database of Annotation instances backed by an indexed file set.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/annodb/IndexedAnnotationDB.html#IndexedAnnotationDB(java.lang.String, java.io.File, org.biojava.bio.program.tagvalue.Index2Model, java.util.List, int, org.biojava.bio.AnnotationType, org.biojava.bio.annodb.IndexedAnnotationDB.ParserListenerFactory)">IndexedAnnotationDB(String, File, Index2Model, List, int, AnnotationType, IndexedAnnotationDB.ParserListenerFactory)</a></span> - Constructor for class org.biojava.bio.annodb.<a href="./org/biojava/bio/annodb/IndexedAnnotationDB.html" title="class in org.biojava.bio.annodb">IndexedAnnotationDB</a></dt>
<dd>
<div class="block">Create a new IndexedAnnotationDB.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/annodb/IndexedAnnotationDB.html#IndexedAnnotationDB(org.biojava.bio.program.indexdb.BioStore)">IndexedAnnotationDB(BioStore)</a></span> - Constructor for class org.biojava.bio.annodb.<a href="./org/biojava/bio/annodb/IndexedAnnotationDB.html" title="class in org.biojava.bio.annodb">IndexedAnnotationDB</a></dt>
<dd>
<div class="block">Initialise the db from a store.</div>
</dd>
<dt><a href="./org/biojava/bio/annodb/IndexedAnnotationDB.ParserListenerFactory.html" title="interface in org.biojava.bio.annodb"><span class="strong">IndexedAnnotationDB.ParserListenerFactory</span></a> - Interface in <a href="./org/biojava/bio/annodb/package-summary.html">org.biojava.bio.annodb</a></dt>
<dd>
<div class="block">A factory for retrieving parsers and listeners.</div>
</dd>
<dt><a href="./org/biojava/bio/annodb/IndexedAnnotationDB.StaticMethodRPFactory.html" title="class in org.biojava.bio.annodb"><span class="strong">IndexedAnnotationDB.StaticMethodRPFactory</span></a> - Class in <a href="./org/biojava/bio/annodb/package-summary.html">org.biojava.bio.annodb</a></dt>
<dd>
<div class="block">An implementation of ParserListenerFactory that uses a static method.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/annodb/IndexedAnnotationDB.StaticMethodRPFactory.html#IndexedAnnotationDB.StaticMethodRPFactory(java.lang.reflect.Method)">IndexedAnnotationDB.StaticMethodRPFactory(Method)</a></span> - Constructor for class org.biojava.bio.annodb.<a href="./org/biojava/bio/annodb/IndexedAnnotationDB.StaticMethodRPFactory.html" title="class in org.biojava.bio.annodb">IndexedAnnotationDB.StaticMethodRPFactory</a></dt>
<dd>
<div class="block">Create a new StaticMethodRPFactory for a method.</div>
</dd>
<dt><a href="./org/biojava/utils/IndexedChangeHub.html" title="class in org.biojava.utils"><span class="strong">IndexedChangeHub</span></a> - Class in <a href="./org/biojava/utils/package-summary.html">org.biojava.utils</a></dt>
<dd>
<div class="block">implements Changeable support with a ChangeHub that
stores ChangeListener by key.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/IndexedChangeHub.html#IndexedChangeHub()">IndexedChangeHub()</a></span> - Constructor for class org.biojava.utils.<a href="./org/biojava/utils/IndexedChangeHub.html" title="class in org.biojava.utils">IndexedChangeHub</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/utils/IndexedChangeHub.ListenerMemento.html" title="class in org.biojava.utils"><span class="strong">IndexedChangeHub.ListenerMemento</span></a> - Class in <a href="./org/biojava/utils/package-summary.html">org.biojava.utils</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/IndexedChangeHub.ListenerMemento.html#IndexedChangeHub.ListenerMemento(org.biojava.utils.ChangeType, java.lang.ref.Reference)">IndexedChangeHub.ListenerMemento(ChangeType, Reference)</a></span> - Constructor for class org.biojava.utils.<a href="./org/biojava/utils/IndexedChangeHub.ListenerMemento.html" title="class in org.biojava.utils">IndexedChangeHub.ListenerMemento</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/dist/IndexedCount.html" title="class in org.biojava.bio.dist"><span class="strong">IndexedCount</span></a> - Class in <a href="./org/biojava/bio/dist/package-summary.html">org.biojava.bio.dist</a></dt>
<dd>
<div class="block">An encapsulation of a count over the Symbols within a FiniteAlphabet using
an AlphabetIndex object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/IndexedCount.html#IndexedCount(org.biojava.bio.symbol.FiniteAlphabet)">IndexedCount(FiniteAlphabet)</a></span> - Constructor for class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/IndexedCount.html" title="class in org.biojava.bio.dist">IndexedCount</a></dt>
<dd>
<div class="block">Get a new IdexedCount for an alphabet using the default indexer.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/IndexedCount.html#IndexedCount(org.biojava.bio.symbol.AlphabetIndex)">IndexedCount(AlphabetIndex)</a></span> - Constructor for class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/IndexedCount.html" title="class in org.biojava.bio.dist">IndexedCount</a></dt>
<dd>
<div class="block">Get a new InexedCount for an alphabet indexer.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/db/IndexedSequenceDB.html" title="class in org.biojava.bio.seq.db"><span class="strong">IndexedSequenceDB</span></a> - Class in <a href="./org/biojava/bio/seq/db/package-summary.html">org.biojava.bio.seq.db</a></dt>
<dd>
<div class="block">
This class implements SequenceDB on top of a set of sequence files
and sequence offsets within these files.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/IndexedSequenceDB.html#IndexedSequenceDB(org.biojava.bio.seq.db.IDMaker, org.biojava.bio.seq.db.IndexStore)">IndexedSequenceDB(IDMaker, IndexStore)</a></span> - Constructor for class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/IndexedSequenceDB.html" title="class in org.biojava.bio.seq.db">IndexedSequenceDB</a></dt>
<dd>
<div class="block">Create an IndexedSequenceDB by specifying both the IDMaker and
IndexStore used.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/IndexedSequenceDB.html#IndexedSequenceDB(org.biojava.bio.seq.db.IndexStore)">IndexedSequenceDB(IndexStore)</a></span> - Constructor for class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/IndexedSequenceDB.html" title="class in org.biojava.bio.seq.db">IndexedSequenceDB</a></dt>
<dd>
<div class="block">Create an IndexedSequenceDB by specifying IndexStore used.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/indexdb/IndexTools.html#indexEmbl(java.lang.String, java.io.File, java.io.File[], int)">indexEmbl(String, File, File[], int)</a></span> - Static method in class org.biojava.bio.program.indexdb.<a href="./org/biojava/bio/program/indexdb/IndexTools.html" title="class in org.biojava.bio.program.indexdb">IndexTools</a></dt>
<dd>
<div class="block"><code>indexEmbl</code> indexes DNA, RNA or protein EMBL format
sequence files on ID as primary identifier and AC as secondary.</div>
</dd>
<dt><a href="./org/biojava/bio/program/tagvalue/Indexer.html" title="class in org.biojava.bio.program.tagvalue"><span class="strong">Indexer</span></a> - Class in <a href="./org/biojava/bio/program/tagvalue/package-summary.html">org.biojava.bio.program.tagvalue</a></dt>
<dd>
<div class="block">
Listens to tag-value events and passes on indexing events to an IndexStore.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/Indexer.html#Indexer(java.io.File, org.biojava.bio.program.indexdb.IndexStore)">Indexer(File, IndexStore)</a></span> - Constructor for class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/Indexer.html" title="class in org.biojava.bio.program.tagvalue">Indexer</a></dt>
<dd>
<div class="block">Build a new Indexer.</div>
</dd>
<dt><a href="./org/biojava/bio/program/tagvalue/Indexer2.html" title="class in org.biojava.bio.program.tagvalue"><span class="strong">Indexer2</span></a> - Class in <a href="./org/biojava/bio/program/tagvalue/package-summary.html">org.biojava.bio.program.tagvalue</a></dt>
<dd>
<div class="block">
Listens to tag-value events and passes on indexing events to an IndexStore.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/Indexer2.html#Indexer2(java.io.File, org.biojava.bio.program.indexdb.IndexStore, org.biojava.bio.program.tagvalue.Index2Model)">Indexer2(File, IndexStore, Index2Model)</a></span> - Constructor for class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/Indexer2.html" title="class in org.biojava.bio.program.tagvalue">Indexer2</a></dt>
<dd>
<div class="block">Build a new Indexer.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/indexdb/IndexTools.html#indexFasta(java.lang.String, java.io.File, java.io.File[], int)">indexFasta(String, File, File[], int)</a></span> - Static method in class org.biojava.bio.program.indexdb.<a href="./org/biojava/bio/program/indexdb/IndexTools.html" title="class in org.biojava.bio.program.indexdb">IndexTools</a></dt>
<dd>
<div class="block"><code>indexFasta</code> indexes DNA, RNA or protein Fasta
format sequence files on primary identifier.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AlphabetIndex.html#indexForSymbol(org.biojava.bio.symbol.Symbol)">indexForSymbol(Symbol)</a></span> - Method in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AlphabetIndex.html" title="interface in org.biojava.bio.symbol">AlphabetIndex</a></dt>
<dd>
<div class="block">Return the unique index for a symbol.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/indexdb/IndexTools.html#indexGenbank(java.lang.String, java.io.File, java.io.File[], int)">indexGenbank(String, File, File[], int)</a></span> - Static method in class org.biojava.bio.program.indexdb.<a href="./org/biojava/bio/program/indexdb/IndexTools.html" title="class in org.biojava.bio.program.indexdb">IndexTools</a></dt>
<dd>
<div class="block"><code>indexGenbank</code> indexes DNA, RNA or protein Genbank
format sequence files on LOCUS as primary identifier and
ACCESSION as secondary.</div>
</dd>
<dt><a href="./org/biojava/bio/structure/align/helper/IndexPair.html" title="class in org.biojava.bio.structure.align.helper"><span class="strong">IndexPair</span></a> - Class in <a href="./org/biojava/bio/structure/align/helper/package-summary.html">org.biojava.bio.structure.align.helper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/helper/IndexPair.html#IndexPair()">IndexPair()</a></span> - Constructor for class org.biojava.bio.structure.align.helper.<a href="./org/biojava/bio/structure/align/helper/IndexPair.html" title="class in org.biojava.bio.structure.align.helper">IndexPair</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/helper/IndexPair.html#IndexPair(short, short)">IndexPair(short, short)</a></span> - Constructor for class org.biojava.bio.structure.align.helper.<a href="./org/biojava/bio/structure/align/helper/IndexPair.html" title="class in org.biojava.bio.structure.align.helper">IndexPair</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/indexdb/IndexStore.html" title="interface in org.biojava.bio.program.indexdb"><span class="strong">IndexStore</span></a> - Interface in <a href="./org/biojava/bio/program/indexdb/package-summary.html">org.biojava.bio.program.indexdb</a></dt>
<dd>
<div class="block"><code>IndexStore</code> is an interface for indexing flatfiles
according to the OBDA specification.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/db/IndexStore.html" title="interface in org.biojava.bio.seq.db"><span class="strong">IndexStore</span></a> - Interface in <a href="./org/biojava/bio/seq/db/package-summary.html">org.biojava.bio.seq.db</a></dt>
<dd>
<div class="block">This defines the objects that IndexedSequenceDB uses to store all of the
database state, such as name, format, sequence builder and the actual file
offsets.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/indexdb/IndexTools.html#indexSwissprot(java.lang.String, java.io.File, java.io.File[])">indexSwissprot(String, File, File[])</a></span> - Static method in class org.biojava.bio.program.indexdb.<a href="./org/biojava/bio/program/indexdb/IndexTools.html" title="class in org.biojava.bio.program.indexdb">IndexTools</a></dt>
<dd>
<div class="block"><code>indexSwissprot</code> indexes Swissprot format protein
sequence files on ID as primary identifier.</div>
</dd>
<dt><a href="./org/biojava/bio/program/indexdb/IndexTools.html" title="class in org.biojava.bio.program.indexdb"><span class="strong">IndexTools</span></a> - Class in <a href="./org/biojava/bio/program/indexdb/package-summary.html">org.biojava.bio.program.indexdb</a></dt>
<dd>
<div class="block"><code>IndexTools</code> contains static utility methods for
creating flatfile indices according to the OBDA standard.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/FeatureTableParser.html#inFeature()">inFeature()</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/FeatureTableParser.html" title="class in org.biojava.bio.seq.io">FeatureTableParser</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><a href="./org/biojavax/bio/seq/InfinitelyAmbiguousSymbolList.html" title="class in org.biojavax.bio.seq"><span class="strong">InfinitelyAmbiguousSymbolList</span></a> - Class in <a href="./org/biojavax/bio/seq/package-summary.html">org.biojavax.bio.seq</a></dt>
<dd>
<div class="block">A symbol list that is <code>Integer.MAX_VALUE</code>long, never gives index out of
bounds and always returns ambiguity symbols for everything.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/InfinitelyAmbiguousSymbolList.html#InfinitelyAmbiguousSymbolList(org.biojava.bio.symbol.FiniteAlphabet)">InfinitelyAmbiguousSymbolList(FiniteAlphabet)</a></span> - Constructor for class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/InfinitelyAmbiguousSymbolList.html" title="class in org.biojavax.bio.seq">InfinitelyAmbiguousSymbolList</a></dt>
<dd>
<div class="block">Creates a new instance of InfinitelyAmbiguousSymbolList</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/xml/Initializable.html#init()">init()</a></span> - Method in interface org.biojava.utils.xml.<a href="./org/biojava/utils/xml/Initializable.html" title="interface in org.biojava.utils.xml">Initializable</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BibRefSupport.html#INIT_PROP_LOG">INIT_PROP_LOG</a></span> - Static variable in interface org.biojava.bibliography.<a href="./org/biojava/bibliography/BibRefSupport.html" title="interface in org.biojava.bibliography">BibRefSupport</a></dt>
<dd>
<div class="block">
A property name ("<b>log</b>").</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BibRefSupport.html#INIT_PROP_SUPPORT">INIT_PROP_SUPPORT</a></span> - Static variable in interface org.biojava.bibliography.<a href="./org/biojava/bibliography/BibRefSupport.html" title="interface in org.biojava.bibliography">BibRefSupport</a></dt>
<dd>
<div class="block">
A property name ("<b>bibrefsupport</b>").</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/server/SimpleStructureServer.html#initCache()">initCache()</a></span> - Method in class org.biojava.bio.structure.server.<a href="./org/biojava/bio/structure/server/SimpleStructureServer.html" title="class in org.biojava.bio.structure.server">SimpleStructureServer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePanelWrapper.html#initComponents()">initComponents()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePanelWrapper.html" title="class in org.biojava.bio.gui.sequence">SequencePanelWrapper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/hmmer/HmmerProfileParser.html#initialiseProfileHMM(int)">initialiseProfileHMM(int)</a></span> - Method in class org.biojava.bio.program.hmmer.<a href="./org/biojava/bio/program/hmmer/HmmerProfileParser.html" title="class in org.biojava.bio.program.hmmer">HmmerProfileParser</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/utils/xml/Initializable.html" title="interface in org.biojava.utils.xml"><span class="strong">Initializable</span></a> - Interface in <a href="./org/biojava/utils/xml/package-summary.html">org.biojava.utils.xml</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/twohead/CellCalculator.html#initialize(org.biojava.bio.dp.twohead.Cell[][])">initialize(Cell[][])</a></span> - Method in interface org.biojava.bio.dp.twohead.<a href="./org/biojava/bio/dp/twohead/CellCalculator.html" title="interface in org.biojava.bio.dp.twohead">CellCalculator</a></dt>
<dd>
<div class="block">Initialize the cell at [0][0] to the recursion initial parameters.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/TabIndexStore.html#initialize()">initialize()</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/TabIndexStore.html" title="class in org.biojava.bio.seq.db">TabIndexStore</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/FuzzyLocation.html#initializeVariables(int, int, int, int, boolean, boolean, org.biojava.bio.symbol.FuzzyLocation.RangeResolver)">initializeVariables(int, int, int, int, boolean, boolean, FuzzyLocation.RangeResolver)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/FuzzyLocation.html" title="class in org.biojava.bio.symbol">FuzzyLocation</a></dt>
<dd>
<div class="block">Refactored initialization code from the constructors.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/util/MenuCreator.html#initMenu()">initMenu()</a></span> - Static method in class org.biojava.bio.structure.gui.util.<a href="./org/biojava/bio/structure/gui/util/MenuCreator.html" title="class in org.biojava.bio.structure.gui.util">MenuCreator</a></dt>
<dd>
<div class="block">provide a JMenuBar that can be added to a JFrame</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ga/impl/AbstractGeneticAlgorithm.html#initPopulation()">initPopulation()</a></span> - Method in class org.biojavax.ga.impl.<a href="./org/biojavax/ga/impl/AbstractGeneticAlgorithm.html" title="class in org.biojavax.ga.impl">AbstractGeneticAlgorithm</a></dt>
<dd>
<div class="block">Assigns a fitness value to each organism within the population according to
the currently set fitness function.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/emblcd/EmblCDROMIndexReader.html#input">input</a></span> - Variable in class org.biojava.bio.seq.db.emblcd.<a href="./org/biojava/bio/seq/db/emblcd/EmblCDROMIndexReader.html" title="class in org.biojava.bio.seq.db.emblcd">EmblCDROMIndexReader</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/utils/process/InputHandler.html" title="interface in org.biojava.utils.process"><span class="strong">InputHandler</span></a> - Interface in <a href="./org/biojava/utils/process/package-summary.html">org.biojava.utils.process</a></dt>
<dd>
<div class="block">Interface to a threadable input handler for
an <a href="./org/biojava/utils/process/ExternalProcess.html" title="class in org.biojava.utils.process">external process</a>.</div>
</dd>
<dt><a href="./org/biojava/utils/io/InputStreamProvider.html" title="class in org.biojava.utils.io"><span class="strong">InputStreamProvider</span></a> - Class in <a href="./org/biojava/utils/io/package-summary.html">org.biojava.utils.io</a></dt>
<dd>
<div class="block">A class that provides an InputStream from a File.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/io/InputStreamProvider.html#InputStreamProvider()">InputStreamProvider()</a></span> - Constructor for class org.biojava.utils.io.<a href="./org/biojava/utils/io/InputStreamProvider.html" title="class in org.biojava.utils.io">InputStreamProvider</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/INSDseqFormat.html#INSDSEQ_FORMAT">INSDSEQ_FORMAT</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/INSDseqFormat.html" title="class in org.biojavax.bio.seq.io">INSDseqFormat</a></dt>
<dd>
<div class="block">The name of this format</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/INSDseqFormat.html#INSDSEQ_TAG">INSDSEQ_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/INSDseqFormat.html" title="class in org.biojavax.bio.seq.io">INSDseqFormat</a></dt>
<dd> </dd>
<dt><a href="./org/biojavax/bio/seq/io/INSDseqFormat.html" title="class in org.biojavax.bio.seq.io"><span class="strong">INSDseqFormat</span></a> - Class in <a href="./org/biojavax/bio/seq/io/package-summary.html">org.biojavax.bio.seq.io</a></dt>
<dd>
<div class="block">Format reader for INSDseq files.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/INSDseqFormat.html#INSDseqFormat()">INSDseqFormat()</a></span> - Constructor for class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/INSDseqFormat.html" title="class in org.biojavax.bio.seq.io">INSDseqFormat</a></dt>
<dd> </dd>
<dt><a href="./org/biojavax/bio/seq/io/INSDseqFormat.Terms.html" title="class in org.biojavax.bio.seq.io"><span class="strong">INSDseqFormat.Terms</span></a> - Class in <a href="./org/biojavax/bio/seq/io/package-summary.html">org.biojavax.bio.seq.io</a></dt>
<dd>
<div class="block">Implements some INSDseq-specific terms.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/INSDseqFormat.Terms.html#INSDseqFormat.Terms()">INSDseqFormat.Terms()</a></span> - Constructor for class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/INSDseqFormat.Terms.html" title="class in org.biojavax.bio.seq.io">INSDseqFormat.Terms</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/INSDseqFormat.html#INSDSEQS_GROUP_TAG">INSDSEQS_GROUP_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/INSDseqFormat.html" title="class in org.biojavax.bio.seq.io">INSDseqFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/LayeredRenderer.html#INSTANCE">INSTANCE</a></span> - Static variable in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/LayeredRenderer.html" title="class in org.biojava.bio.gui.sequence">LayeredRenderer</a></dt>
<dd>
<div class="block">Static <code>LayeredRenderer</code> <code>INSTANCE</code> used
by <code>MultiLineRenderer</code>s.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/GenEmblFeatureComparator.html#INSTANCE">INSTANCE</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/GenEmblFeatureComparator.html" title="class in org.biojava.bio.seq.io">GenEmblFeatureComparator</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/GenEmblPropertyComparator.html#INSTANCE">INSTANCE</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/GenEmblPropertyComparator.html" title="class in org.biojava.bio.seq.io">GenEmblPropertyComparator</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AlphabetManager.html#instance()">instance()</a></span> - Static method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AlphabetManager.html" title="class in org.biojava.bio.symbol">AlphabetManager</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>all AlphabetManager methods have become static</i></div>
</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/DoubleAlphabet.html#INSTANCE">INSTANCE</a></span> - Static variable in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/DoubleAlphabet.html" title="class in org.biojava.bio.symbol">DoubleAlphabet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/IntegerAlphabet.html#INSTANCE">INSTANCE</a></span> - Static variable in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/IntegerAlphabet.html" title="class in org.biojava.bio.symbol">IntegerAlphabet</a></dt>
<dd>
<div class="block">The singleton instance of the IntegerAlphabet class.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/directory/SystemRegistry.html#instance()">instance()</a></span> - Static method in class org.biojava.directory.<a href="./org/biojava/directory/SystemRegistry.html" title="class in org.biojava.directory">SystemRegistry</a></dt>
<dd>
<div class="block">Get the singleton Registry instance representing the system-wide
default registry.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/xml/XMLBeans.html#INSTANCE">INSTANCE</a></span> - Static variable in class org.biojava.utils.xml.<a href="./org/biojava/utils/xml/XMLBeans.html" title="class in org.biojava.utils.xml">XMLBeans</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/AnnotationType.Abstract.html#instanceOf(org.biojava.bio.Annotation)">instanceOf(Annotation)</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/AnnotationType.Abstract.html" title="class in org.biojava.bio">AnnotationType.Abstract</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/AnnotationType.html#instanceOf(org.biojava.bio.Annotation)">instanceOf(Annotation)</a></span> - Method in interface org.biojava.bio.<a href="./org/biojava/bio/AnnotationType.html" title="interface in org.biojava.bio">AnnotationType</a></dt>
<dd>
<div class="block">Validate an Annotation against this AnnotationType.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/xml/XMLBeans.html#instantiateBean(org.w3c.dom.Element)">instantiateBean(Element)</a></span> - Method in class org.biojava.utils.xml.<a href="./org/biojava/utils/xml/XMLBeans.html" title="class in org.biojava.utils.xml">XMLBeans</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/xml/XMLBeans.html#instantiateBean(org.w3c.dom.Element, java.lang.ClassLoader, java.util.Map)">instantiateBean(Element, ClassLoader, Map)</a></span> - Method in class org.biojava.utils.xml.<a href="./org/biojava/utils/xml/XMLBeans.html" title="class in org.biojava.utils.xml">XMLBeans</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/HomologeneTools.html#instantiateDB(java.net.URL, org.biojava.bio.program.homologene.HomologeneBuilder)">instantiateDB(URL, HomologeneBuilder)</a></span> - Static method in class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/HomologeneTools.html" title="class in org.biojava.bio.program.homologene">HomologeneTools</a></dt>
<dd>
<div class="block">instantiate a HomologeneDB.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/TemplateUtils.html#instantiateTemplate(org.biojava.bio.seq.Feature)">instantiateTemplate(Feature)</a></span> - Static method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/TemplateUtils.html" title="class in org.biojava.bio.seq.impl">TemplateUtils</a></dt>
<dd>
<div class="block">This attempts to divine the 'best' template class for a feature and return
a new instance readly for pupulating.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOConstants.html#INTEGER">INTEGER</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOConstants.html" title="class in org.biojava.bio.seq.io">SeqIOConstants</a></dt>
<dd>
<div class="block"><code>INTEGER</code> indicates that a sequence contains integer
alphabet symbols, such as used to describe sequence quality
data.</div>
</dd>
<dt><a href="./org/biojava/bio/symbol/IntegerAlphabet.html" title="class in org.biojava.bio.symbol"><span class="strong">IntegerAlphabet</span></a> - Class in <a href="./org/biojava/bio/symbol/package-summary.html">org.biojava.bio.symbol</a></dt>
<dd>
<div class="block">
An efficient implementation of an Alphabet over the infinite set of integer
values.</div>
</dd>
<dt><a href="./org/biojava/bio/symbol/IntegerAlphabet.IntegerSymbol.html" title="class in org.biojava.bio.symbol"><span class="strong">IntegerAlphabet.IntegerSymbol</span></a> - Class in <a href="./org/biojava/bio/symbol/package-summary.html">org.biojava.bio.symbol</a></dt>
<dd>
<div class="block">A single int value.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/IntegerAlphabet.IntegerSymbol.html#IntegerAlphabet.IntegerSymbol(int)">IntegerAlphabet.IntegerSymbol(int)</a></span> - Constructor for class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/IntegerAlphabet.IntegerSymbol.html" title="class in org.biojava.bio.symbol">IntegerAlphabet.IntegerSymbol</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/symbol/IntegerAlphabet.SubIntegerAlphabet.html" title="class in org.biojava.bio.symbol"><span class="strong">IntegerAlphabet.SubIntegerAlphabet</span></a> - Class in <a href="./org/biojava/bio/symbol/package-summary.html">org.biojava.bio.symbol</a></dt>
<dd>
<div class="block">A class to represent a finite contiguous subset of the infinite IntegerAlphabet</div>
</dd>
<dt><a href="./org/biojava/ontology/IntegerOntology.html" title="class in org.biojava.ontology"><span class="strong">IntegerOntology</span></a> - Class in <a href="./org/biojava/ontology/package-summary.html">org.biojava.ontology</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/ontology/IntegerOntology.IntTerm.html" title="class in org.biojava.ontology"><span class="strong">IntegerOntology.IntTerm</span></a> - Class in <a href="./org/biojava/ontology/package-summary.html">org.biojava.ontology</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/IntegerOntology.IntTerm.html#IntegerOntology.IntTerm(int)">IntegerOntology.IntTerm(int)</a></span> - Constructor for class org.biojava.ontology.<a href="./org/biojava/ontology/IntegerOntology.IntTerm.html" title="class in org.biojava.ontology">IntegerOntology.IntTerm</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/IntegerOntology.IntTerm.html#IntegerOntology.IntTerm(int, java.lang.Object[])">IntegerOntology.IntTerm(int, Object[])</a></span> - Constructor for class org.biojava.ontology.<a href="./org/biojava/ontology/IntegerOntology.IntTerm.html" title="class in org.biojava.ontology">IntegerOntology.IntTerm</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/phred/PhredTools.html#integerSymbolFromPhred(org.biojava.bio.symbol.Symbol)">integerSymbolFromPhred(Symbol)</a></span> - Static method in class org.biojava.bio.program.phred.<a href="./org/biojava/bio/program/phred/PhredTools.html" title="class in org.biojava.bio.program.phred">PhredTools</a></dt>
<dd>
<div class="block">Retrives the IntegerSymbol component of the Phred BasisSymbol from the
PHRED alphabet.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/IntegerTokenization.html" title="class in org.biojava.bio.seq.io"><span class="strong">IntegerTokenization</span></a> - Class in <a href="./org/biojava/bio/seq/io/package-summary.html">org.biojava.bio.seq.io</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/IntegerTokenization.html#IntegerTokenization()">IntegerTokenization()</a></span> - Constructor for class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/IntegerTokenization.html" title="class in org.biojava.bio.seq.io">IntegerTokenization</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/utils/stax/IntElementHandlerBase.html" title="class in org.biojava.utils.stax"><span class="strong">IntElementHandlerBase</span></a> - Class in <a href="./org/biojava/utils/stax/package-summary.html">org.biojava.utils.stax</a></dt>
<dd>
<div class="block">StAX handler for any element which just contains a string representation of
an integer.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/stax/IntElementHandlerBase.html#IntElementHandlerBase()">IntElementHandlerBase()</a></span> - Constructor for class org.biojava.utils.stax.<a href="./org/biojava/utils/stax/IntElementHandlerBase.html" title="class in org.biojava.utils.stax">IntElementHandlerBase</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html#INTERACTION">INTERACTION</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html" title="class in org.biojavax.bio.seq.io">UniProtCommentParser</a></dt>
<dd>
<div class="block">A name for a comment type.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/SVMRegressionModel.html#internalClassify(int)">internalClassify(int)</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/SVMRegressionModel.html" title="class in org.biojava.stats.svm">SVMRegressionModel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/util/AlignmentCalc.html#interrupt()">interrupt()</a></span> - Method in class org.biojava.bio.structure.gui.util.<a href="./org/biojava/bio/structure/gui/util/AlignmentCalc.html" title="class in org.biojava.bio.structure.gui.util">AlignmentCalc</a></dt>
<dd>
<div class="block">stops what is currently happening and does not continue</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureHolderUtils.html#intersect(org.biojava.bio.seq.FeatureHolder, org.biojava.bio.seq.FeatureHolder)">intersect(FeatureHolder, FeatureHolder)</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureHolderUtils.html" title="class in org.biojava.bio.seq">FeatureHolderUtils</a></dt>
<dd>
<div class="block">Operator: Intersect FeatureHolder1 with FeatureHolder2</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/AnnotationTools.html#intersection(org.biojava.bio.AnnotationType, org.biojava.bio.AnnotationType)">intersection(AnnotationType, AnnotationType)</a></span> - Static method in class org.biojava.bio.<a href="./org/biojava/bio/AnnotationTools.html" title="class in org.biojava.bio">AnnotationTools</a></dt>
<dd>
<div class="block">Calculate an AnnotationType that matches all Annotation instances matched
by both types.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/AnnotationTools.html#intersection(org.biojava.bio.PropertyConstraint, org.biojava.bio.PropertyConstraint)">intersection(PropertyConstraint, PropertyConstraint)</a></span> - Static method in class org.biojava.bio.<a href="./org/biojava/bio/AnnotationTools.html" title="class in org.biojava.bio">AnnotationTools</a></dt>
<dd>
<div class="block">Calculate the intersection of two PropertyConstraint instances.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/AnnotationTools.html#intersection(org.biojava.bio.CollectionConstraint, org.biojava.bio.CollectionConstraint)">intersection(CollectionConstraint, CollectionConstraint)</a></span> - Static method in class org.biojava.bio.<a href="./org/biojava/bio/AnnotationTools.html" title="class in org.biojava.bio">AnnotationTools</a></dt>
<dd>
<div class="block">Return the CollectionConstraint which accept only collections accepted by
both of those specified.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AbstractLocation.html#intersection(org.biojava.bio.symbol.Location)">intersection(Location)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AbstractLocation.html" title="class in org.biojava.bio.symbol">AbstractLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AbstractLocationDecorator.html#intersection(org.biojava.bio.symbol.Location)">intersection(Location)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AbstractLocationDecorator.html" title="class in org.biojava.bio.symbol">AbstractLocationDecorator</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/CircularLocation.html#intersection(org.biojava.bio.symbol.Location)">intersection(Location)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/CircularLocation.html" title="class in org.biojava.bio.symbol">CircularLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/FuzzyPointLocation.html#intersection(org.biojava.bio.symbol.Location)">intersection(Location)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/FuzzyPointLocation.html" title="class in org.biojava.bio.symbol">FuzzyPointLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/Location.html#intersection(org.biojava.bio.symbol.Location)">intersection(Location)</a></span> - Method in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/Location.html" title="interface in org.biojava.bio.symbol">Location</a></dt>
<dd>
<div class="block">Returns a Location that contains all points common to both ranges.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/LocationTools.html#intersection(org.biojava.bio.symbol.Location, org.biojava.bio.symbol.Location)">intersection(Location, Location)</a></span> - Static method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/LocationTools.html" title="class in org.biojava.bio.symbol">LocationTools</a></dt>
<dd>
<div class="block">Return the intersection of two locations.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/CompoundRichLocation.html#intersection(org.biojava.bio.symbol.Location)">intersection(Location)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/CompoundRichLocation.html" title="class in org.biojavax.bio.seq">CompoundRichLocation</a></dt>
<dd>
<div class="block">Returns a Location that contains all points common to both ranges.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/EmptyRichLocation.html#intersection(org.biojava.bio.symbol.Location)">intersection(Location)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/EmptyRichLocation.html" title="class in org.biojavax.bio.seq">EmptyRichLocation</a></dt>
<dd>
<div class="block">Returns a Location that contains all points common to both ranges.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichLocation.html#intersection(org.biojava.bio.symbol.Location)">intersection(Location)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichLocation.html" title="class in org.biojavax.bio.seq">SimpleRichLocation</a></dt>
<dd>
<div class="block">Returns a Location that contains all points common to both ranges.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/obo/OboFileHandler.html#INTERSECTION_OF">INTERSECTION_OF</a></span> - Static variable in class org.biojava.ontology.obo.<a href="./org/biojava/ontology/obo/OboFileHandler.html" title="class in org.biojava.ontology.obo">OboFileHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/IntegerAlphabet.IntegerSymbol.html#intValue()">intValue()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/IntegerAlphabet.IntegerSymbol.html" title="class in org.biojava.bio.symbol">IntegerAlphabet.IntegerSymbol</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/IntegerOntology.IntTerm.html#intValue()">intValue()</a></span> - Method in class org.biojava.ontology.<a href="./org/biojava/ontology/IntegerOntology.IntTerm.html" title="class in org.biojava.ontology">IntegerOntology.IntTerm</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichLocation.Strand.html#intValue()">intValue()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichLocation.Strand.html" title="class in org.biojavax.bio.seq">RichLocation.Strand</a></dt>
<dd>
<div class="block">Returns the numeric value of this strand.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/blast2html/AbstractAlignmentStyler.html#iNumberOfColours">iNumberOfColours</a></span> - Variable in class org.biojava.bio.program.blast2html.<a href="./org/biojava/bio/program/blast2html/AbstractAlignmentStyler.html" title="class in org.biojava.bio.program.blast2html">AbstractAlignmentStyler</a></dt>
<dd>
<div class="block">The number of unique colours.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFErrorHandler.AbortErrorHandler.html#invalidEnd(java.lang.String)">invalidEnd(String)</a></span> - Method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFErrorHandler.AbortErrorHandler.html" title="class in org.biojava.bio.program.gff">GFFErrorHandler.AbortErrorHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFErrorHandler.html#invalidEnd(java.lang.String)">invalidEnd(String)</a></span> - Method in interface org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFErrorHandler.html" title="interface in org.biojava.bio.program.gff">GFFErrorHandler</a></dt>
<dd>
<div class="block">The `end' field of the GFF entry was not a valid value.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFErrorHandler.SkipRecordErrorHandler.html#invalidEnd(java.lang.String)">invalidEnd(String)</a></span> - Method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFErrorHandler.SkipRecordErrorHandler.html" title="class in org.biojava.bio.program.gff">GFFErrorHandler.SkipRecordErrorHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFWriter.html#invalidEnd(java.lang.String, java.lang.NumberFormatException)">invalidEnd(String, NumberFormatException)</a></span> - Method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFWriter.html" title="class in org.biojava.bio.program.gff">GFFWriter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFErrorHandler.AbortErrorHandler.html#invalidFrame(java.lang.String)">invalidFrame(String)</a></span> - Method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFErrorHandler.AbortErrorHandler.html" title="class in org.biojava.bio.program.gff">GFFErrorHandler.AbortErrorHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFErrorHandler.html#invalidFrame(java.lang.String)">invalidFrame(String)</a></span> - Method in interface org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFErrorHandler.html" title="interface in org.biojava.bio.program.gff">GFFErrorHandler</a></dt>
<dd>
<div class="block">The `frame' field of the GFF entry was not a valid value.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFErrorHandler.SkipRecordErrorHandler.html#invalidFrame(java.lang.String)">invalidFrame(String)</a></span> - Method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFErrorHandler.SkipRecordErrorHandler.html" title="class in org.biojava.bio.program.gff">GFFErrorHandler.SkipRecordErrorHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFWriter.html#invalidFrame(java.lang.String, java.lang.NumberFormatException)">invalidFrame(String, NumberFormatException)</a></span> - Method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFWriter.html" title="class in org.biojava.bio.program.gff">GFFWriter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFErrorHandler.AbortErrorHandler.html#invalidScore(java.lang.String)">invalidScore(String)</a></span> - Method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFErrorHandler.AbortErrorHandler.html" title="class in org.biojava.bio.program.gff">GFFErrorHandler.AbortErrorHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFErrorHandler.html#invalidScore(java.lang.String)">invalidScore(String)</a></span> - Method in interface org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFErrorHandler.html" title="interface in org.biojava.bio.program.gff">GFFErrorHandler</a></dt>
<dd>
<div class="block">The `score' field of the GFF entry was not a valid value.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFErrorHandler.SkipRecordErrorHandler.html#invalidScore(java.lang.String)">invalidScore(String)</a></span> - Method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFErrorHandler.SkipRecordErrorHandler.html" title="class in org.biojava.bio.program.gff">GFFErrorHandler.SkipRecordErrorHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFWriter.html#invalidScore(java.lang.String, java.lang.NumberFormatException)">invalidScore(String, NumberFormatException)</a></span> - Method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFWriter.html" title="class in org.biojava.bio.program.gff">GFFWriter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFErrorHandler.AbortErrorHandler.html#invalidStart(java.lang.String)">invalidStart(String)</a></span> - Method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFErrorHandler.AbortErrorHandler.html" title="class in org.biojava.bio.program.gff">GFFErrorHandler.AbortErrorHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFErrorHandler.html#invalidStart(java.lang.String)">invalidStart(String)</a></span> - Method in interface org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFErrorHandler.html" title="interface in org.biojava.bio.program.gff">GFFErrorHandler</a></dt>
<dd>
<div class="block">The `start' field of the GFF entry was not a valid value.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFErrorHandler.SkipRecordErrorHandler.html#invalidStart(java.lang.String)">invalidStart(String)</a></span> - Method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFErrorHandler.SkipRecordErrorHandler.html" title="class in org.biojava.bio.program.gff">GFFErrorHandler.SkipRecordErrorHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFWriter.html#invalidStart(java.lang.String, java.lang.NumberFormatException)">invalidStart(String, NumberFormatException)</a></span> - Method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFWriter.html" title="class in org.biojava.bio.program.gff">GFFWriter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFErrorHandler.AbortErrorHandler.html#invalidStrand(java.lang.String)">invalidStrand(String)</a></span> - Method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFErrorHandler.AbortErrorHandler.html" title="class in org.biojava.bio.program.gff">GFFErrorHandler.AbortErrorHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFErrorHandler.html#invalidStrand(java.lang.String)">invalidStrand(String)</a></span> - Method in interface org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFErrorHandler.html" title="interface in org.biojava.bio.program.gff">GFFErrorHandler</a></dt>
<dd>
<div class="block">The `strand' field of the GFF entry was not a valid value.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFErrorHandler.SkipRecordErrorHandler.html#invalidStrand(java.lang.String)">invalidStrand(String)</a></span> - Method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFErrorHandler.SkipRecordErrorHandler.html" title="class in org.biojava.bio.program.gff">GFFErrorHandler.SkipRecordErrorHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFWriter.html#invalidStrand(java.lang.String)">invalidStrand(String)</a></span> - Method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFWriter.html" title="class in org.biojava.bio.program.gff">GFFWriter</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/ontology/InvalidTermException.html" title="class in org.biojava.ontology"><span class="strong">InvalidTermException</span></a> - Exception in <a href="./org/biojava/ontology/package-summary.html">org.biojava.ontology</a></dt>
<dd>
<div class="block">Thrown to indicate that an ontology term is not acceptable or
appropriate in a given context</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/InvalidTermException.html#InvalidTermException()">InvalidTermException()</a></span> - Constructor for exception org.biojava.ontology.<a href="./org/biojava/ontology/InvalidTermException.html" title="class in org.biojava.ontology">InvalidTermException</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/InvalidTermException.html#InvalidTermException(java.lang.String)">InvalidTermException(String)</a></span> - Constructor for exception org.biojava.ontology.<a href="./org/biojava/ontology/InvalidTermException.html" title="class in org.biojava.ontology">InvalidTermException</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/InvalidTermException.html#InvalidTermException(java.lang.Throwable)">InvalidTermException(Throwable)</a></span> - Constructor for exception org.biojava.ontology.<a href="./org/biojava/ontology/InvalidTermException.html" title="class in org.biojava.ontology">InvalidTermException</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/InvalidTermException.html#InvalidTermException(java.lang.String, java.lang.Throwable)">InvalidTermException(String, Throwable)</a></span> - Constructor for exception org.biojava.ontology.<a href="./org/biojava/ontology/InvalidTermException.html" title="class in org.biojava.ontology">InvalidTermException</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/jama/Matrix.html#inverse()">inverse()</a></span> - Method in class org.biojava.bio.structure.jama.<a href="./org/biojava/bio/structure/jama/Matrix.html" title="class in org.biojava.bio.structure.jama">Matrix</a></dt>
<dd>
<div class="block">Matrix inverse or pseudoinverse</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/TranslationTable.html#INVERT_MITO">INVERT_MITO</a></span> - Static variable in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/TranslationTable.html" title="interface in org.biojava.bio.symbol">TranslationTable</a></dt>
<dd>
<div class="block">Translation table name for the invertebrate mitochondrial
genetic code.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/GenbankSequenceDB.html#IOExceptionFound">IOExceptionFound</a></span> - Variable in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/GenbankSequenceDB.html" title="class in org.biojava.bio.seq.db">GenbankSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/obo/OboFileHandler.html#IS_A">IS_A</a></span> - Static variable in class org.biojava.ontology.obo.<a href="./org/biojava/ontology/obo/OboFileHandler.html" title="class in org.biojava.ontology.obo">OboFileHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/OntoTools.html#IS_A">IS_A</a></span> - Static variable in class org.biojava.ontology.<a href="./org/biojava/ontology/OntoTools.html" title="class in org.biojava.ontology">OntoTools</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/obo/OboFileHandler.html#IS_OBSOLETE">IS_OBSOLETE</a></span> - Static variable in class org.biojava.ontology.obo.<a href="./org/biojava/ontology/obo/OboFileHandler.html" title="class in org.biojava.ontology.obo">OboFileHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PairwiseSequencePanel.html#isActive()">isActive()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PairwiseSequencePanel.html" title="class in org.biojava.bio.gui.sequence">PairwiseSequencePanel</a></dt>
<dd>
<div class="block"><code>isActive</code> returns true if both the
<code>Sequence</code>s to be rendered and the
<code>PairwiseHomologyRenderer</code> are not null.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePanel.html#isActive()">isActive()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePanel.html" title="class in org.biojava.bio.gui.sequence">SequencePanel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePanelWrapper.html#isActive()">isActive()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePanelWrapper.html" title="class in org.biojava.bio.gui.sequence">SequencePanelWrapper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePoster.html#isActive()">isActive()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePoster.html" title="class in org.biojava.bio.gui.sequence">SequencePoster</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/TranslatedSequencePanel.html#isActive()">isActive()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/TranslatedSequencePanel.html" title="class in org.biojava.bio.gui.sequence">TranslatedSequencePanel</a></dt>
<dd>
<div class="block"><code>isActive</code> returns true if both the
<code>Sequence</code> to be rendered and the
<code>SequenceRenderer</code> are not null.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/SimpleMMcifConsumer.html#isAlignSeqRes()">isAlignSeqRes()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/SimpleMMcifConsumer.html" title="class in org.biojava.bio.structure.io.mmcif">SimpleMMcifConsumer</a></dt>
<dd>
<div class="block">Flag if the SEQRES amino acids should be aligned with the ATOM amino acids.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/PDBFileParser.html#isAlignSeqRes()">isAlignSeqRes()</a></span> - Method in class org.biojava.bio.structure.io.<a href="./org/biojava/bio/structure/io/PDBFileParser.html" title="class in org.biojava.bio.structure.io">PDBFileParser</a></dt>
<dd>
<div class="block">Flag if the SEQRES amino acids should be aligned with the ATOM amino acids.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/PDBFileReader.html#isAlignSeqRes()">isAlignSeqRes()</a></span> - Method in class org.biojava.bio.structure.io.<a href="./org/biojava/bio/structure/io/PDBFileReader.html" title="class in org.biojava.bio.structure.io">PDBFileReader</a></dt>
<dd>
<div class="block">get the flag if the SEQRES and ATOM amino acids are going to be aligned</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/MMCIFFileReader.html#isAutoFetch()">isAutoFetch()</a></span> - Method in class org.biojava.bio.structure.io.<a href="./org/biojava/bio/structure/io/MMCIFFileReader.html" title="class in org.biojava.bio.structure.io">MMCIFFileReader</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/PDBFileReader.html#isAutoFetch()">isAutoFetch()</a></span> - Method in class org.biojava.bio.structure.io.<a href="./org/biojava/bio/structure/io/PDBFileReader.html" title="class in org.biojava.bio.structure.io">PDBFileReader</a></dt>
<dd>
<div class="block">should the parser to fetch missing PDB files from the EBI FTP server automatically?
default is false</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/StructureIOFile.html#isAutoFetch()">isAutoFetch()</a></span> - Method in interface org.biojava.bio.structure.io.<a href="./org/biojava/bio/structure/io/StructureIOFile.html" title="interface in org.biojava.bio.structure.io">StructureIOFile</a></dt>
<dd>
<div class="block">Fetch files automatically from FTP server.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/server/MMCIFFileInstallation.html#isAutoFetch()">isAutoFetch()</a></span> - Method in class org.biojava.bio.structure.server.<a href="./org/biojava/bio/structure/server/MMCIFFileInstallation.html" title="class in org.biojava.bio.structure.server">MMCIFFileInstallation</a></dt>
<dd>
<div class="block">should the parser to fetch missing mmCif files from the RCSB FTP server automatically?
default is false</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BiblioBook.html#isbn">isbn</a></span> - Variable in class org.biojava.bibliography.<a href="./org/biojava/bibliography/BiblioBook.html" title="class in org.biojava.bibliography">BiblioBook</a></dt>
<dd>
<div class="block">ISBN number.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/BoundaryFinder.html#isBoundaryEnd(java.lang.Object)">isBoundaryEnd(Object)</a></span> - Method in interface org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/BoundaryFinder.html" title="interface in org.biojava.bio.program.tagvalue">BoundaryFinder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/BoundaryFinder.html#isBoundaryStart(java.lang.Object)">isBoundaryStart(Object)</a></span> - Method in interface org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/BoundaryFinder.html" title="interface in org.biojava.bio.program.tagvalue">BoundaryFinder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/candy/CandyVocabulary.html#isCaseSensitive()">isCaseSensitive()</a></span> - Method in interface org.biojava.utils.candy.<a href="./org/biojava/utils/candy/CandyVocabulary.html" title="interface in org.biojava.utils.candy">CandyVocabulary</a></dt>
<dd>
<div class="block">It returns <tt>true</tt> if the vocabulary entries should
be considered as case-sensitive.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/blast2html/ColourCommand.html#isColoured(java.lang.String, java.lang.String)">isColoured(String, String)</a></span> - Method in interface org.biojava.bio.program.blast2html.<a href="./org/biojava/bio/program/blast2html/ColourCommand.html" title="interface in org.biojava.bio.program.blast2html">ColourCommand</a></dt>
<dd>
<div class="block">Returns true if the alignment pair should be coloured
else false.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/ComponentFeature.html#isComponentResolvable()">isComponentResolvable()</a></span> - Method in interface org.biojava.bio.seq.<a href="./org/biojava/bio/seq/ComponentFeature.html" title="interface in org.biojava.bio.seq">ComponentFeature</a></dt>
<dd>
<div class="block">Determine if the sequence references by this ComponentFeature
is available in this context.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Calc.html#isConnected(org.biojava.bio.structure.AminoAcid, org.biojava.bio.structure.AminoAcid)">isConnected(AminoAcid, AminoAcid)</a></span> - Static method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Calc.html" title="class in org.biojava.bio.structure">Calc</a></dt>
<dd>
<div class="block">test if two amino acids are connected, i.e.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/DocRefAuthor.html#isConsortium()">isConsortium()</a></span> - Method in interface org.biojavax.<a href="./org/biojavax/DocRefAuthor.html" title="interface in org.biojavax">DocRefAuthor</a></dt>
<dd>
<div class="block">Is this author actually a consortium?</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleDocRefAuthor.html#isConsortium()">isConsortium()</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleDocRefAuthor.html" title="class in org.biojavax">SimpleDocRefAuthor</a></dt>
<dd>
<div class="block">Is this author actually a consortium?</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AbstractLocationDecorator.html#isContiguous()">isContiguous()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AbstractLocationDecorator.html" title="class in org.biojava.bio.symbol">AbstractLocationDecorator</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AbstractRangeLocation.html#isContiguous()">isContiguous()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AbstractRangeLocation.html" title="class in org.biojava.bio.symbol">AbstractRangeLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/CircularLocation.html#isContiguous()">isContiguous()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/CircularLocation.html" title="class in org.biojava.bio.symbol">CircularLocation</a></dt>
<dd>
<div class="block">Delegates to the wrapped location.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/FuzzyPointLocation.html#isContiguous()">isContiguous()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/FuzzyPointLocation.html" title="class in org.biojava.bio.symbol">FuzzyPointLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/Location.html#isContiguous()">isContiguous()</a></span> - Method in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/Location.html" title="interface in org.biojava.bio.symbol">Location</a></dt>
<dd>
<div class="block">Determine if a Location is contiguous.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/CompoundRichLocation.html#isContiguous()">isContiguous()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/CompoundRichLocation.html" title="class in org.biojavax.bio.seq">CompoundRichLocation</a></dt>
<dd>
<div class="block">Determine if a Location is contiguous.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/EmptyRichLocation.html#isContiguous()">isContiguous()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/EmptyRichLocation.html" title="class in org.biojavax.bio.seq">EmptyRichLocation</a></dt>
<dd>
<div class="block">Determine if a Location is contiguous.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichLocation.html#isContiguous()">isContiguous()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichLocation.html" title="class in org.biojavax.bio.seq">SimpleRichLocation</a></dt>
<dd>
<div class="block">Determine if a Location is contiguous.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/StructurePairAligner.html#isDebug()">isDebug()</a></span> - Method in class org.biojava.bio.structure.align.<a href="./org/biojava/bio/structure/align/StructurePairAligner.html" title="class in org.biojava.bio.structure.align">StructurePairAligner</a></dt>
<dd>
<div class="block">check if debug mode is set on</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/SeqRes2AtomAligner.html#isDEBUG()">isDEBUG()</a></span> - Method in class org.biojava.bio.structure.io.<a href="./org/biojava/bio/structure/io/SeqRes2AtomAligner.html" title="class in org.biojava.bio.structure.io">SeqRes2AtomAligner</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ByAncestor.html#isDisjoint(org.biojava.bio.seq.FeatureFilter)">isDisjoint(FeatureFilter)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ByAncestor.html" title="class in org.biojava.bio.seq">FeatureFilter.ByAncestor</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ByAnnotationType.html#isDisjoint(org.biojava.bio.seq.FeatureFilter)">isDisjoint(FeatureFilter)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ByAnnotationType.html" title="class in org.biojava.bio.seq">FeatureFilter.ByAnnotationType</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ByChild.html#isDisjoint(org.biojava.bio.seq.FeatureFilter)">isDisjoint(FeatureFilter)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ByChild.html" title="class in org.biojava.bio.seq">FeatureFilter.ByChild</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ByClass.html#isDisjoint(org.biojava.bio.seq.FeatureFilter)">isDisjoint(FeatureFilter)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ByClass.html" title="class in org.biojava.bio.seq">FeatureFilter.ByClass</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ByComponentName.html#isDisjoint(org.biojava.bio.seq.FeatureFilter)">isDisjoint(FeatureFilter)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ByComponentName.html" title="class in org.biojava.bio.seq">FeatureFilter.ByComponentName</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ByDescendant.html#isDisjoint(org.biojava.bio.seq.FeatureFilter)">isDisjoint(FeatureFilter)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ByDescendant.html" title="class in org.biojava.bio.seq">FeatureFilter.ByDescendant</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ByFeature.html#isDisjoint(org.biojava.bio.seq.FeatureFilter)">isDisjoint(FeatureFilter)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ByFeature.html" title="class in org.biojava.bio.seq">FeatureFilter.ByFeature</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ByPairwiseScore.html#isDisjoint(org.biojava.bio.seq.FeatureFilter)">isDisjoint(FeatureFilter)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ByPairwiseScore.html" title="class in org.biojava.bio.seq">FeatureFilter.ByPairwiseScore</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ByParent.html#isDisjoint(org.biojava.bio.seq.FeatureFilter)">isDisjoint(FeatureFilter)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ByParent.html" title="class in org.biojava.bio.seq">FeatureFilter.ByParent</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.BySequenceName.html#isDisjoint(org.biojava.bio.seq.FeatureFilter)">isDisjoint(FeatureFilter)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.BySequenceName.html" title="class in org.biojava.bio.seq">FeatureFilter.BySequenceName</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.BySource.html#isDisjoint(org.biojava.bio.seq.FeatureFilter)">isDisjoint(FeatureFilter)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.BySource.html" title="class in org.biojava.bio.seq">FeatureFilter.BySource</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ByType.html#isDisjoint(org.biojava.bio.seq.FeatureFilter)">isDisjoint(FeatureFilter)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ByType.html" title="class in org.biojava.bio.seq">FeatureFilter.ByType</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ContainedByLocation.html#isDisjoint(org.biojava.bio.seq.FeatureFilter)">isDisjoint(FeatureFilter)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ContainedByLocation.html" title="class in org.biojava.bio.seq">FeatureFilter.ContainedByLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.FrameFilter.html#isDisjoint(org.biojava.bio.seq.FeatureFilter)">isDisjoint(FeatureFilter)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.FrameFilter.html" title="class in org.biojava.bio.seq">FeatureFilter.FrameFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.OnlyChildren.html#isDisjoint(org.biojava.bio.seq.FeatureFilter)">isDisjoint(FeatureFilter)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.OnlyChildren.html" title="class in org.biojava.bio.seq">FeatureFilter.OnlyChildren</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.OnlyDescendants.html#isDisjoint(org.biojava.bio.seq.FeatureFilter)">isDisjoint(FeatureFilter)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.OnlyDescendants.html" title="class in org.biojava.bio.seq">FeatureFilter.OnlyDescendants</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.OverlapsLocation.html#isDisjoint(org.biojava.bio.seq.FeatureFilter)">isDisjoint(FeatureFilter)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.OverlapsLocation.html" title="class in org.biojava.bio.seq">FeatureFilter.OverlapsLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ShadowContainedByLocation.html#isDisjoint(org.biojava.bio.seq.FeatureFilter)">isDisjoint(FeatureFilter)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ShadowContainedByLocation.html" title="class in org.biojava.bio.seq">FeatureFilter.ShadowContainedByLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ShadowOverlapsLocation.html#isDisjoint(org.biojava.bio.seq.FeatureFilter)">isDisjoint(FeatureFilter)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ShadowOverlapsLocation.html" title="class in org.biojava.bio.seq">FeatureFilter.ShadowOverlapsLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.StrandFilter.html#isDisjoint(org.biojava.bio.seq.FeatureFilter)">isDisjoint(FeatureFilter)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.StrandFilter.html" title="class in org.biojava.bio.seq">FeatureFilter.StrandFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/OptimizableFilter.html#isDisjoint(org.biojava.bio.seq.FeatureFilter)">isDisjoint(FeatureFilter)</a></span> - Method in interface org.biojava.bio.seq.<a href="./org/biojava/bio/seq/OptimizableFilter.html" title="interface in org.biojava.bio.seq">OptimizableFilter</a></dt>
<dd>
<div class="block">Returns true if this filter is disjoint from filt - that is, there is no
Feature that is accepted by both filters.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/StrucAligParameters.html#isDoAngleCheck()">isDoAngleCheck()</a></span> - Method in class org.biojava.bio.structure.align.<a href="./org/biojava/bio/structure/align/StrucAligParameters.html" title="class in org.biojava.bio.structure.align">StrucAligParameters</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/StrucAligParameters.html#isDoDensityCheck()">isDoDensityCheck()</a></span> - Method in class org.biojava.bio.structure.align.<a href="./org/biojava/bio/structure/align/StrucAligParameters.html" title="class in org.biojava.bio.structure.align">StrucAligParameters</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/StrucAligParameters.html#isDoDistanceCheck()">isDoDistanceCheck()</a></span> - Method in class org.biojava.bio.structure.align.<a href="./org/biojava/bio/structure/align/StrucAligParameters.html" title="class in org.biojava.bio.structure.align">StrucAligParameters</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/StrucAligParameters.html#isDoRMSCheck()">isDoRMSCheck()</a></span> - Method in class org.biojava.bio.structure.align.<a href="./org/biojava/bio/structure/align/StrucAligParameters.html" title="class in org.biojava.bio.structure.align">StrucAligParameters</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/DocRefAuthor.html#isEditor()">isEditor()</a></span> - Method in interface org.biojavax.<a href="./org/biojavax/DocRefAuthor.html" title="interface in org.biojavax">DocRefAuthor</a></dt>
<dd>
<div class="block">Is this author actually an editor?</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleDocRefAuthor.html#isEditor()">isEditor()</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleDocRefAuthor.html" title="class in org.biojavax">SimpleDocRefAuthor</a></dt>
<dd>
<div class="block">Is this author actually an editor?</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/AbstractOrthoPairCollection.html#isEmpty()">isEmpty()</a></span> - Method in class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/AbstractOrthoPairCollection.html" title="class in org.biojava.bio.program.homologene">AbstractOrthoPairCollection</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/OrthoPairCollection.html#isEmpty()">isEmpty()</a></span> - Method in interface org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/OrthoPairCollection.html" title="interface in org.biojava.bio.program.homologene">OrthoPairCollection</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/SimpleOrthoPairCollection.html#isEmpty()">isEmpty()</a></span> - Method in class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/SimpleOrthoPairCollection.html" title="class in org.biojava.bio.program.homologene">SimpleOrthoPairCollection</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/util/WeightedSet.html#isEmpty()">isEmpty()</a></span> - Method in class org.biojavax.ga.util.<a href="./org/biojavax/ga/util/WeightedSet.html" title="class in org.biojavax.ga.util">WeightedSet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/Protease.html#isEndoProtease()">isEndoProtease()</a></span> - Method in class org.biojava.bio.proteomics.<a href="./org/biojava/bio/proteomics/Protease.html" title="class in org.biojava.bio.proteomics">Protease</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/obo/OboFileParser.html#isEscapeStarter(char)">isEscapeStarter(char)</a></span> - Static method in class org.biojava.ontology.obo.<a href="./org/biojava/ontology/obo/OboFileParser.html" title="class in org.biojava.ontology.obo">OboFileParser</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/jama/QRDecomposition.html#isFullRank()">isFullRank()</a></span> - Method in class org.biojava.bio.structure.jama.<a href="./org/biojava/bio/structure/jama/QRDecomposition.html" title="class in org.biojava.bio.structure.jama">QRDecomposition</a></dt>
<dd>
<div class="block">Is the matrix full rank?</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ga/impl/AbstractOrganism.html#isHaploid()">isHaploid()</a></span> - Method in class org.biojavax.ga.impl.<a href="./org/biojavax/ga/impl/AbstractOrganism.html" title="class in org.biojavax.ga.impl">AbstractOrganism</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/impl/SimpleOrganism.html#isHaploid()">isHaploid()</a></span> - Method in class org.biojavax.ga.impl.<a href="./org/biojavax/ga/impl/SimpleOrganism.html" title="class in org.biojavax.ga.impl">SimpleOrganism</a></dt>
<dd>
<div class="block">Simple Organisms are Halpoid</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ga/Organism.html#isHaploid()">isHaploid()</a></span> - Method in interface org.biojavax.ga.<a href="./org/biojavax/ga/Organism.html" title="interface in org.biojavax.ga">Organism</a></dt>
<dd>
<div class="block">Is the organism Haploid?</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/fastq/FastqVariant.html#isIllumina()">isIllumina()</a></span> - Method in enum org.biojava.bio.program.fastq.<a href="./org/biojava/bio/program/fastq/FastqVariant.html" title="enum in org.biojava.bio.program.fastq">FastqVariant</a></dt>
<dd>
<div class="block">Return true if this FASTQ sequence format variant is <a href="./org/biojava/bio/program/fastq/FastqVariant.html#FASTQ_ILLUMINA"><code>FastqVariant.FASTQ_ILLUMINA</code></a>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/StrucAligParameters.html#isJoinPlo()">isJoinPlo()</a></span> - Method in class org.biojava.bio.structure.align.<a href="./org/biojava/bio/structure/align/StrucAligParameters.html" title="class in org.biojava.bio.structure.align">StrucAligParameters</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SoftMaskedAlphabet.html#isMasked(org.biojava.bio.symbol.BasisSymbol)">isMasked(BasisSymbol)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SoftMaskedAlphabet.html" title="class in org.biojava.bio.symbol">SoftMaskedAlphabet</a></dt>
<dd>
<div class="block">Determines if a <code>Symbol</code> is masked.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SoftMaskedAlphabet.MaskingDetector.DefaultMaskingDetector.html#isMasked(java.lang.String)">isMasked(String)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SoftMaskedAlphabet.MaskingDetector.DefaultMaskingDetector.html" title="class in org.biojava.bio.symbol">SoftMaskedAlphabet.MaskingDetector.DefaultMaskingDetector</a></dt>
<dd>
<div class="block">Default Behaivour is that if the whole token is lower case it is
masked.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SoftMaskedAlphabet.MaskingDetector.html#isMasked(java.lang.String)">isMasked(String)</a></span> - Method in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SoftMaskedAlphabet.MaskingDetector.html" title="interface in org.biojava.bio.symbol">SoftMaskedAlphabet.MaskingDetector</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ChangeType.html#isMatchingType(org.biojava.utils.ChangeType)">isMatchingType(ChangeType)</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/ChangeType.html" title="class in org.biojava.utils">ChangeType</a></dt>
<dd>
<div class="block">Return <code>true</code> iff <code>ct</code> is equal to this type
or any of it's supertypes (including ChangeType.UNKNOWN).</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/FuzzyLocation.html#isMaxFuzzy()">isMaxFuzzy()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/FuzzyLocation.html" title="class in org.biojava.bio.symbol">FuzzyLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/FuzzyLocation.html#isMinFuzzy()">isMinFuzzy()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/FuzzyLocation.html" title="class in org.biojava.bio.symbol">FuzzyLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichLocation.Tools.html#isMultiSource(java.util.Collection)">isMultiSource(Collection<Location>)</a></span> - Static method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichLocation.Tools.html" title="class in org.biojavax.bio.seq">RichLocation.Tools</a></dt>
<dd>
<div class="block">Returns false if all the locations in the set are from the same
strand of the same sequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/IndexedChangeHub.html#isMyChangeEvent(org.biojava.utils.ChangeEvent, org.biojava.utils.IndexedChangeHub.ListenerMemento)">isMyChangeEvent(ChangeEvent, IndexedChangeHub.ListenerMemento)</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/IndexedChangeHub.html" title="class in org.biojava.utils">IndexedChangeHub</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/TagValue.html#isNewTag()">isNewTag()</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/TagValue.html" title="class in org.biojava.bio.program.tagvalue">TagValue</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Structure.html#isNmr()">isNmr()</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Structure.html" title="interface in org.biojava.bio.structure">Structure</a></dt>
<dd>
<div class="block">test if this structure is an nmr structure.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/StructureImpl.html#isNmr()">isNmr()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/StructureImpl.html" title="class in org.biojava.bio.structure">StructureImpl</a></dt>
<dd>
<div class="block">is this structure an nmr structure ?</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/jama/LUDecomposition.html#isNonsingular()">isNonsingular()</a></span> - Method in class org.biojava.bio.structure.jama.<a href="./org/biojava/bio/structure/jama/LUDecomposition.html" title="class in org.biojava.bio.structure.jama">LUDecomposition</a></dt>
<dd>
<div class="block">Is the matrix nonsingular?</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/StructureTools.html#isNucleotide(java.lang.String)">isNucleotide(String)</a></span> - Static method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/StructureTools.html" title="class in org.biojava.bio.structure">StructureTools</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/proteomics/IsoelectricPointCalc.html" title="class in org.biojava.bio.proteomics"><span class="strong">IsoelectricPointCalc</span></a> - Class in <a href="./org/biojava/bio/proteomics/package-summary.html">org.biojava.bio.proteomics</a></dt>
<dd>
<div class="block">Class that computes isoelectric point for denaturated proteins.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/IsoelectricPointCalc.html#IsoelectricPointCalc()">IsoelectricPointCalc()</a></span> - Constructor for class org.biojava.bio.proteomics.<a href="./org/biojava/bio/proteomics/IsoelectricPointCalc.html" title="class in org.biojava.bio.proteomics">IsoelectricPointCalc</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/proteomics/IsoelectricPointCalc.ChargeCalculator.html" title="class in org.biojava.bio.proteomics"><span class="strong">IsoelectricPointCalc.ChargeCalculator</span></a> - Class in <a href="./org/biojava/bio/proteomics/package-summary.html">org.biojava.bio.proteomics</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/projection/TranslateFlipContext.html#isOppositeStrand()">isOppositeStrand()</a></span> - Method in class org.biojava.bio.seq.projection.<a href="./org/biojava/bio/seq/projection/TranslateFlipContext.html" title="class in org.biojava.bio.seq.projection">TranslateFlipContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtCommentParser.Interaction.html#isOrganismsDiffer()">isOrganismsDiffer()</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtCommentParser.Interaction.html" title="class in org.biojavax.bio.seq.io">UniProtCommentParser.Interaction</a></dt>
<dd>
<div class="block">Getter for property organismsDiffer.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/molbio/RestrictionEnzyme.html#isPalindromic()">isPalindromic()</a></span> - Method in class org.biojava.bio.molbio.<a href="./org/biojava/bio/molbio/RestrictionEnzyme.html" title="class in org.biojava.bio.molbio">RestrictionEnzyme</a></dt>
<dd>
<div class="block"><code>isPalindromic</code> returns true if the recognition site
is palindromic.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html#isParseable(org.biojavax.Comment)">isParseable(Comment)</a></span> - Static method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html" title="class in org.biojavax.bio.seq.io">UniProtCommentParser</a></dt>
<dd>
<div class="block">Returns true if the comment may be parseable (starts with -!-).</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html#isParseable(java.lang.String)">isParseable(String)</a></span> - Static method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html" title="class in org.biojavax.bio.seq.io">UniProtCommentParser</a></dt>
<dd>
<div class="block">Returns true if the comment may be parseable (starts with -!-).</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/SimpleMMcifConsumer.html#isParseCAOnly()">isParseCAOnly()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/SimpleMMcifConsumer.html" title="class in org.biojava.bio.structure.io.mmcif">SimpleMMcifConsumer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/PDBFileParser.html#isParseCAOnly()">isParseCAOnly()</a></span> - Method in class org.biojava.bio.structure.io.<a href="./org/biojava/bio/structure/io/PDBFileParser.html" title="class in org.biojava.bio.structure.io">PDBFileParser</a></dt>
<dd>
<div class="block">the flag if only the C-alpha atoms of the structure should be parsed.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/PDBFileReader.html#isParseCAOnly()">isParseCAOnly()</a></span> - Method in class org.biojava.bio.structure.io.<a href="./org/biojava/bio/structure/io/PDBFileReader.html" title="class in org.biojava.bio.structure.io">PDBFileReader</a></dt>
<dd>
<div class="block">return the flag if only the CA atoms should be parsed</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/PDBFileParser.html#isParseSecStruc()">isParseSecStruc()</a></span> - Method in class org.biojava.bio.structure.io.<a href="./org/biojava/bio/structure/io/PDBFileParser.html" title="class in org.biojava.bio.structure.io">PDBFileParser</a></dt>
<dd>
<div class="block">is secondary structure assignment being parsed from the file?
default is null</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/PDBFileReader.html#isParseSecStruc()">isParseSecStruc()</a></span> - Method in class org.biojava.bio.structure.io.<a href="./org/biojava/bio/structure/io/PDBFileReader.html" title="class in org.biojava.bio.structure.io">PDBFileReader</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ByAncestor.html#isProperSubset(org.biojava.bio.seq.FeatureFilter)">isProperSubset(FeatureFilter)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ByAncestor.html" title="class in org.biojava.bio.seq">FeatureFilter.ByAncestor</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ByAnnotationType.html#isProperSubset(org.biojava.bio.seq.FeatureFilter)">isProperSubset(FeatureFilter)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ByAnnotationType.html" title="class in org.biojava.bio.seq">FeatureFilter.ByAnnotationType</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ByChild.html#isProperSubset(org.biojava.bio.seq.FeatureFilter)">isProperSubset(FeatureFilter)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ByChild.html" title="class in org.biojava.bio.seq">FeatureFilter.ByChild</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ByClass.html#isProperSubset(org.biojava.bio.seq.FeatureFilter)">isProperSubset(FeatureFilter)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ByClass.html" title="class in org.biojava.bio.seq">FeatureFilter.ByClass</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ByComponentName.html#isProperSubset(org.biojava.bio.seq.FeatureFilter)">isProperSubset(FeatureFilter)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ByComponentName.html" title="class in org.biojava.bio.seq">FeatureFilter.ByComponentName</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ByDescendant.html#isProperSubset(org.biojava.bio.seq.FeatureFilter)">isProperSubset(FeatureFilter)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ByDescendant.html" title="class in org.biojava.bio.seq">FeatureFilter.ByDescendant</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ByFeature.html#isProperSubset(org.biojava.bio.seq.FeatureFilter)">isProperSubset(FeatureFilter)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ByFeature.html" title="class in org.biojava.bio.seq">FeatureFilter.ByFeature</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ByPairwiseScore.html#isProperSubset(org.biojava.bio.seq.FeatureFilter)">isProperSubset(FeatureFilter)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ByPairwiseScore.html" title="class in org.biojava.bio.seq">FeatureFilter.ByPairwiseScore</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ByParent.html#isProperSubset(org.biojava.bio.seq.FeatureFilter)">isProperSubset(FeatureFilter)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ByParent.html" title="class in org.biojava.bio.seq">FeatureFilter.ByParent</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.BySequenceName.html#isProperSubset(org.biojava.bio.seq.FeatureFilter)">isProperSubset(FeatureFilter)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.BySequenceName.html" title="class in org.biojava.bio.seq">FeatureFilter.BySequenceName</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.BySource.html#isProperSubset(org.biojava.bio.seq.FeatureFilter)">isProperSubset(FeatureFilter)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.BySource.html" title="class in org.biojava.bio.seq">FeatureFilter.BySource</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ByType.html#isProperSubset(org.biojava.bio.seq.FeatureFilter)">isProperSubset(FeatureFilter)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ByType.html" title="class in org.biojava.bio.seq">FeatureFilter.ByType</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ContainedByLocation.html#isProperSubset(org.biojava.bio.seq.FeatureFilter)">isProperSubset(FeatureFilter)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ContainedByLocation.html" title="class in org.biojava.bio.seq">FeatureFilter.ContainedByLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.FrameFilter.html#isProperSubset(org.biojava.bio.seq.FeatureFilter)">isProperSubset(FeatureFilter)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.FrameFilter.html" title="class in org.biojava.bio.seq">FeatureFilter.FrameFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.OnlyChildren.html#isProperSubset(org.biojava.bio.seq.FeatureFilter)">isProperSubset(FeatureFilter)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.OnlyChildren.html" title="class in org.biojava.bio.seq">FeatureFilter.OnlyChildren</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.OnlyDescendants.html#isProperSubset(org.biojava.bio.seq.FeatureFilter)">isProperSubset(FeatureFilter)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.OnlyDescendants.html" title="class in org.biojava.bio.seq">FeatureFilter.OnlyDescendants</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.OverlapsLocation.html#isProperSubset(org.biojava.bio.seq.FeatureFilter)">isProperSubset(FeatureFilter)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.OverlapsLocation.html" title="class in org.biojava.bio.seq">FeatureFilter.OverlapsLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ShadowContainedByLocation.html#isProperSubset(org.biojava.bio.seq.FeatureFilter)">isProperSubset(FeatureFilter)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ShadowContainedByLocation.html" title="class in org.biojava.bio.seq">FeatureFilter.ShadowContainedByLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ShadowOverlapsLocation.html#isProperSubset(org.biojava.bio.seq.FeatureFilter)">isProperSubset(FeatureFilter)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ShadowOverlapsLocation.html" title="class in org.biojava.bio.seq">FeatureFilter.ShadowOverlapsLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.StrandFilter.html#isProperSubset(org.biojava.bio.seq.FeatureFilter)">isProperSubset(FeatureFilter)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.StrandFilter.html" title="class in org.biojava.bio.seq">FeatureFilter.StrandFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/OptimizableFilter.html#isProperSubset(org.biojava.bio.seq.FeatureFilter)">isProperSubset(FeatureFilter)</a></span> - Method in interface org.biojava.bio.seq.<a href="./org/biojava/bio/seq/OptimizableFilter.html" title="interface in org.biojava.bio.seq">OptimizableFilter</a></dt>
<dd>
<div class="block">Returns true if this filter is a proper subset of sup - that is, for every
feature that matches this, it also matches sup.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/JournalArticle.html#isPublished()">isPublished()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/JournalArticle.html" title="class in org.biojava.bio.structure">JournalArticle</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/obo/OboFileParser.html#isQuote(char)">isQuote(char)</a></span> - Static method in class org.biojava.ontology.obo.<a href="./org/biojava/ontology/obo/OboFileParser.html" title="class in org.biojava.ontology.obo">OboFileParser</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BibRefQuery.html#isReady()">isReady()</a></span> - Method in interface org.biojava.bibliography.<a href="./org/biojava/bibliography/BibRefQuery.html" title="interface in org.biojava.bibliography">BibRefQuery</a></dt>
<dd>
<div class="block">It checks if the repository is available.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BibRefSupport.html#isReady()">isReady()</a></span> - Method in interface org.biojava.bibliography.<a href="./org/biojava/bibliography/BibRefSupport.html" title="interface in org.biojava.bibliography">BibRefSupport</a></dt>
<dd>
<div class="block">It checks if a utility object is available.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/candy/CandyFinder.html#isReady()">isReady()</a></span> - Method in interface org.biojava.utils.candy.<a href="./org/biojava/utils/candy/CandyFinder.html" title="interface in org.biojava.utils.candy">CandyFinder</a></dt>
<dd>
<div class="block">It checks if a vocabulary finder object is available.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/RemoteFeature.Region.html#isRemote()">isRemote()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/RemoteFeature.Region.html" title="class in org.biojava.bio.seq">RemoteFeature.Region</a></dt>
<dd>
<div class="block">Return whether this Region is remote or local.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/ChemicalComponentDictionary.html#isReplaced(org.biojava.bio.structure.io.mmcif.model.ChemComp)">isReplaced(ChemComp)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/ChemicalComponentDictionary.html" title="class in org.biojava.bio.structure.io.mmcif">ChemicalComponentDictionary</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/ChemicalComponentDictionary.html#isReplaced(java.lang.String)">isReplaced(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/ChemicalComponentDictionary.html" title="class in org.biojava.bio.structure.io.mmcif">ChemicalComponentDictionary</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/ChemicalComponentDictionary.html#isReplacer(org.biojava.bio.structure.io.mmcif.model.ChemComp)">isReplacer(ChemComp)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/ChemicalComponentDictionary.html" title="class in org.biojava.bio.structure.io.mmcif">ChemicalComponentDictionary</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/ChemicalComponentDictionary.html#isReplacer(java.lang.String)">isReplacer(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/ChemicalComponentDictionary.html" title="class in org.biojava.bio.structure.io.mmcif">ChemicalComponentDictionary</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/CodonPrefFilter.AcceptAll.html#isRequired(java.lang.String)">isRequired(String)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/CodonPrefFilter.AcceptAll.html" title="class in org.biojava.bio.symbol">CodonPrefFilter.AcceptAll</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/CodonPrefFilter.ByName.html#isRequired(java.lang.String)">isRequired(String)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/CodonPrefFilter.ByName.html" title="class in org.biojava.bio.symbol">CodonPrefFilter.ByName</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/CodonPrefFilter.EverythingToXML.html#isRequired(java.lang.String)">isRequired(String)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/CodonPrefFilter.EverythingToXML.html" title="class in org.biojava.bio.symbol">CodonPrefFilter.EverythingToXML</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/CodonPrefFilter.html#isRequired(java.lang.String)">isRequired(String)</a></span> - Method in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/CodonPrefFilter.html" title="interface in org.biojava.bio.symbol">CodonPrefFilter</a></dt>
<dd>
<div class="block">indicates if the current CodonPref is to be accepted</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleGappedSymbolList.Block.html#isSane()">isSane()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleGappedSymbolList.Block.html" title="class in org.biojava.bio.symbol">SimpleGappedSymbolList.Block</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleGappedSymbolList.html#isSane()">isSane()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleGappedSymbolList.html" title="class in org.biojava.bio.symbol">SimpleGappedSymbolList</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/fastq/FastqVariant.html#isSanger()">isSanger()</a></span> - Method in enum org.biojava.bio.program.fastq.<a href="./org/biojava/bio/program/fastq/FastqVariant.html" title="enum in org.biojava.bio.program.fastq">FastqVariant</a></dt>
<dd>
<div class="block">Return true if this FASTQ sequence format variant is <a href="./org/biojava/bio/program/fastq/FastqVariant.html#FASTQ_SANGER"><code>FastqVariant.FASTQ_SANGER</code></a>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/DistributionLogo.html#isScaleByInformation()">isScaleByInformation()</a></span> - Method in class org.biojava.bio.gui.<a href="./org/biojava/bio/gui/DistributionLogo.html" title="class in org.biojava.bio.gui">DistributionLogo</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/FastaHeader.html#isShowAccession()">isShowAccession()</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/FastaHeader.html" title="class in org.biojavax.bio.seq.io">FastaHeader</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/FastaHeader.html#isShowDescription()">isShowDescription()</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/FastaHeader.html" title="class in org.biojavax.bio.seq.io">FastaHeader</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/FastaHeader.html#isShowIdentifier()">isShowIdentifier()</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/FastaHeader.html" title="class in org.biojavax.bio.seq.io">FastaHeader</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/FastaHeader.html#isShowName()">isShowName()</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/FastaHeader.html" title="class in org.biojavax.bio.seq.io">FastaHeader</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/FastaHeader.html#isShowNamespace()">isShowNamespace()</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/FastaHeader.html" title="class in org.biojavax.bio.seq.io">FastaHeader</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/FastaHeader.html#isShowVersion()">isShowVersion()</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/FastaHeader.html" title="class in org.biojavax.bio.seq.io">FastaHeader</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BiblioJournal.html#issn">issn</a></span> - Variable in class org.biojava.bibliography.<a href="./org/biojava/bibliography/BiblioJournal.html" title="class in org.biojava.bibliography">BiblioJournal</a></dt>
<dd>
<div class="block">
A standard number for journals.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/fastq/FastqVariant.html#isSolexa()">isSolexa()</a></span> - Method in enum org.biojava.bio.program.fastq.<a href="./org/biojava/bio/program/fastq/FastqVariant.html" title="enum in org.biojava.bio.program.fastq">FastqVariant</a></dt>
<dd>
<div class="block">Return true if this FASTQ sequence format variant is <a href="./org/biojava/bio/program/fastq/FastqVariant.html#FASTQ_SOLEXA"><code>FastqVariant.FASTQ_SOLEXA</code></a>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/jama/CholeskyDecomposition.html#isSPD()">isSPD()</a></span> - Method in class org.biojava.bio.structure.jama.<a href="./org/biojava/bio/structure/jama/CholeskyDecomposition.html" title="class in org.biojava.bio.structure.jama">CholeskyDecomposition</a></dt>
<dd>
<div class="block">Is the matrix symmetric and positive definite?</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html#isStandard()">isStandard()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html" title="class in org.biojava.bio.structure.io.mmcif.model">ChemComp</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/chem/ChemCompTools.html#isStandardChemComp(org.biojava.bio.structure.io.mmcif.model.ChemComp)">isStandardChemComp(ChemComp)</a></span> - Static method in class org.biojava.bio.structure.io.mmcif.chem.<a href="./org/biojava/bio/structure/io/mmcif/chem/ChemCompTools.html" title="class in org.biojava.bio.structure.io.mmcif.chem">ChemCompTools</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/filterxml/XMLAnnotationTypeWriter.html#isStrict()">isStrict()</a></span> - Method in class org.biojava.bio.seq.io.filterxml.<a href="./org/biojava/bio/seq/io/filterxml/XMLAnnotationTypeWriter.html" title="class in org.biojava.bio.seq.io.filterxml">XMLAnnotationTypeWriter</a></dt>
<dd>
<div class="block">Determine if this writer is in strict mode.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/filterxml/XMLFilterWriter.html#isStrict()">isStrict()</a></span> - Method in class org.biojava.bio.seq.io.filterxml.<a href="./org/biojava/bio/seq/io/filterxml/XMLFilterWriter.html" title="class in org.biojava.bio.seq.io.filterxml">XMLFilterWriter</a></dt>
<dd>
<div class="block">Determine if this writer is in strict mode.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureTypes.html#isSubTypeOf(org.biojava.bio.seq.FeatureTypes.Type, org.biojava.bio.seq.FeatureTypes.Type)">isSubTypeOf(FeatureTypes.Type, FeatureTypes.Type)</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureTypes.html" title="class in org.biojava.bio.seq">FeatureTypes</a></dt>
<dd>
<div class="block">Work out if one type is a sub-type of another.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BiblioJournalArticle.html#issue">issue</a></span> - Variable in class org.biojava.bibliography.<a href="./org/biojava/bibliography/BiblioJournalArticle.html" title="class in org.biojava.bibliography">BiblioJournalArticle</a></dt>
<dd>
<div class="block">The issue of the journal.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BiblioJournalArticle.html#issueSupplement">issueSupplement</a></span> - Variable in class org.biojava.bibliography.<a href="./org/biojava/bibliography/BiblioJournalArticle.html" title="class in org.biojava.bibliography">BiblioJournalArticle</a></dt>
<dd>
<div class="block">Suplement.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/taxa/NCBITaxon.html#isTaxonHidden()">isTaxonHidden()</a></span> - Method in interface org.biojavax.bio.taxa.<a href="./org/biojavax/bio/taxa/NCBITaxon.html" title="interface in org.biojavax.bio.taxa">NCBITaxon</a></dt>
<dd>
<div class="block">used in getNameHierarchy() to determine whether this taxonomy level is displayed</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/taxa/SimpleNCBITaxon.html#isTaxonHidden()">isTaxonHidden()</a></span> - Method in class org.biojavax.bio.taxa.<a href="./org/biojavax/bio/taxa/SimpleNCBITaxon.html" title="class in org.biojavax.bio.taxa">SimpleNCBITaxon</a></dt>
<dd>
<div class="block">Returns the taxonomy hierarchy of this taxon entry in the form:
most specific; less specific; ...; least specific.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SuffixTree.SuffixNode.html#isTerminal()">isTerminal()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SuffixTree.SuffixNode.html" title="class in org.biojava.bio.symbol">SuffixTree.SuffixNode</a></dt>
<dd>
<div class="block">Determine is this node is terminal (has no children).</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/UkkonenSuffixTree.SuffixNode.html#isTerminal()">isTerminal()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/UkkonenSuffixTree.SuffixNode.html" title="class in org.biojava.bio.symbol">UkkonenSuffixTree.SuffixNode</a></dt>
<dd>
<div class="block">Determine is this node is terminal (has no children).</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/StoppingCriteria.html#isTrainingComplete(org.biojava.bio.dp.TrainingAlgorithm)">isTrainingComplete(TrainingAlgorithm)</a></span> - Method in interface org.biojava.bio.dp.<a href="./org/biojava/bio/dp/StoppingCriteria.html" title="interface in org.biojava.bio.dp">StoppingCriteria</a></dt>
<dd>
<div class="block">Decide if the training has completed.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PairwiseSequencePanel.html#isUnchanging(org.biojava.utils.ChangeType)">isUnchanging(ChangeType)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PairwiseSequencePanel.html" title="class in org.biojava.bio.gui.sequence">PairwiseSequencePanel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePanel.html#isUnchanging(org.biojava.utils.ChangeType)">isUnchanging(ChangeType)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePanel.html" title="class in org.biojava.bio.gui.sequence">SequencePanel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePoster.html#isUnchanging(org.biojava.utils.ChangeType)">isUnchanging(ChangeType)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePoster.html" title="class in org.biojava.bio.gui.sequence">SequencePoster</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/TranslatedSequencePanel.html#isUnchanging(org.biojava.utils.ChangeType)">isUnchanging(ChangeType)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/TranslatedSequencePanel.html" title="class in org.biojava.bio.gui.sequence">TranslatedSequencePanel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/ReferenceServer.html#isUnchanging(org.biojava.utils.ChangeType)">isUnchanging(ChangeType)</a></span> - Method in class org.biojava.bio.program.das.<a href="./org/biojava/bio/program/das/ReferenceServer.html" title="class in org.biojava.bio.program.das">ReferenceServer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/LazyFilterFeatureHolder.html#isUnchanging(org.biojava.utils.ChangeType)">isUnchanging(ChangeType)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/LazyFilterFeatureHolder.html" title="class in org.biojava.bio.seq.impl">LazyFilterFeatureHolder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SubSequence.html#isUnchanging(org.biojava.utils.ChangeType)">isUnchanging(ChangeType)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SubSequence.html" title="class in org.biojava.bio.seq.impl">SubSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/projection/ProjectedFeature.html#isUnchanging(org.biojava.utils.ChangeType)">isUnchanging(ChangeType)</a></span> - Method in class org.biojava.bio.seq.projection.<a href="./org/biojava/bio/seq/projection/ProjectedFeature.html" title="class in org.biojava.bio.seq.projection">ProjectedFeature</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/AbstractChangeable.html#isUnchanging(org.biojava.utils.ChangeType)">isUnchanging(ChangeType)</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/AbstractChangeable.html" title="class in org.biojava.utils">AbstractChangeable</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/Changeable.html#isUnchanging(org.biojava.utils.ChangeType)">isUnchanging(ChangeType)</a></span> - Method in interface org.biojava.utils.<a href="./org/biojava/utils/Changeable.html" title="interface in org.biojava.utils">Changeable</a></dt>
<dd>
<div class="block">
A particular ChangeType can never be raised by this Changeable.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/ChangeSupport.html#isUnchanging(org.biojava.utils.ChangeType)">isUnchanging(ChangeType)</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/ChangeSupport.html" title="class in org.biojava.utils">ChangeSupport</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/Unchangeable.html#isUnchanging(org.biojava.utils.ChangeType)">isUnchanging(ChangeType)</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/Unchangeable.html" title="class in org.biojava.utils">Unchangeable</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/InfinitelyAmbiguousSymbolList.html#isUnchanging(org.biojava.utils.ChangeType)">isUnchanging(ChangeType)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/InfinitelyAmbiguousSymbolList.html" title="class in org.biojavax.bio.seq">InfinitelyAmbiguousSymbolList</a></dt>
<dd>
<div class="block">
A particular ChangeType can never be raised by this Changeable.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ga/functions/CrossOverFunction.NoCross.html#isUnchanging(org.biojava.utils.ChangeType)">isUnchanging(ChangeType)</a></span> - Method in class org.biojavax.ga.functions.<a href="./org/biojavax/ga/functions/CrossOverFunction.NoCross.html" title="class in org.biojavax.ga.functions">CrossOverFunction.NoCross</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/functions/MutationFunction.NoMutation.html#isUnchanging(org.biojava.utils.ChangeType)">isUnchanging(ChangeType)</a></span> - Method in class org.biojavax.ga.functions.<a href="./org/biojavax/ga/functions/MutationFunction.NoMutation.html" title="class in org.biojavax.ga.functions">MutationFunction.NoMutation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/SimpleSVMClassifierModel.html#itemAlphas()">itemAlphas()</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/SimpleSVMClassifierModel.html" title="class in org.biojava.stats.svm">SimpleSVMClassifierModel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/SVMClassifierModel.html#itemAlphas()">itemAlphas()</a></span> - Method in interface org.biojava.stats.svm.<a href="./org/biojava/stats/svm/SVMClassifierModel.html" title="interface in org.biojava.stats.svm">SVMClassifierModel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/SimpleSVMClassifierModel.html#items()">items()</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/SimpleSVMClassifierModel.html" title="class in org.biojava.stats.svm">SimpleSVMClassifierModel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/SimpleSVMTarget.html#items()">items()</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/SimpleSVMTarget.html" title="class in org.biojava.stats.svm">SimpleSVMTarget</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/SVMClassifierModel.html#items()">items()</a></span> - Method in interface org.biojava.stats.svm.<a href="./org/biojava/stats/svm/SVMClassifierModel.html" title="interface in org.biojava.stats.svm">SVMClassifierModel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/SVMTarget.html#items()">items()</a></span> - Method in interface org.biojava.stats.svm.<a href="./org/biojava/stats/svm/SVMTarget.html" title="interface in org.biojava.stats.svm">SVMTarget</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/SimpleSVMTarget.html#itemTargets()">itemTargets()</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/SimpleSVMTarget.html" title="class in org.biojava.stats.svm">SimpleSVMTarget</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/SVMTarget.html#itemTargets()">itemTargets()</a></span> - Method in interface org.biojava.stats.svm.<a href="./org/biojava/stats/svm/SVMTarget.html" title="interface in org.biojava.stats.svm">SVMTarget</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/stats/svm/ItemValue.html" title="interface in org.biojava.stats.svm"><span class="strong">ItemValue</span></a> - Interface in <a href="./org/biojava/stats/svm/package-summary.html">org.biojava.stats.svm</a></dt>
<dd>
<div class="block">A simple Object-double tuple.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/annodb/AnnotationDB.html#iterator()">iterator()</a></span> - Method in interface org.biojava.bio.annodb.<a href="./org/biojava/bio/annodb/AnnotationDB.html" title="interface in org.biojava.bio.annodb">AnnotationDB</a></dt>
<dd>
<div class="block">Loop over each Annotation in this db.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/annodb/IndexedAnnotationDB.html#iterator()">iterator()</a></span> - Method in class org.biojava.bio.annodb.<a href="./org/biojava/bio/annodb/IndexedAnnotationDB.html" title="class in org.biojava.bio.annodb">IndexedAnnotationDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/annodb/LazyFilteredAnnotationDB.html#iterator()">iterator()</a></span> - Method in class org.biojava.bio.annodb.<a href="./org/biojava/bio/annodb/LazyFilteredAnnotationDB.html" title="class in org.biojava.bio.annodb">LazyFilteredAnnotationDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/annodb/LazySearchedAnnotationDB.html#iterator()">iterator()</a></span> - Method in class org.biojava.bio.annodb.<a href="./org/biojava/bio/annodb/LazySearchedAnnotationDB.html" title="class in org.biojava.bio.annodb">LazySearchedAnnotationDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/annodb/MergingAnnotationDB.html#iterator()">iterator()</a></span> - Method in class org.biojava.bio.annodb.<a href="./org/biojava/bio/annodb/MergingAnnotationDB.html" title="class in org.biojava.bio.annodb">MergingAnnotationDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/annodb/SimpleAnnotationDB.html#iterator()">iterator()</a></span> - Method in class org.biojava.bio.annodb.<a href="./org/biojava/bio/annodb/SimpleAnnotationDB.html" title="class in org.biojava.bio.annodb">SimpleAnnotationDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/SimpleStatePath.html#iterator()">iterator()</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/SimpleStatePath.html" title="class in org.biojava.bio.dp">SimpleStatePath</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/DASSequence.html#iterator()">iterator()</a></span> - Method in class org.biojava.bio.program.das.<a href="./org/biojava/bio/program/das/DASSequence.html" title="class in org.biojava.bio.program.das">DASSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/AbstractOrthoPairCollection.html#iterator()">iterator()</a></span> - Method in class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/AbstractOrthoPairCollection.html" title="class in org.biojava.bio.program.homologene">AbstractOrthoPairCollection</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/OrthologueSet.html#iterator()">iterator()</a></span> - Method in interface org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/OrthologueSet.html" title="interface in org.biojava.bio.program.homologene">OrthologueSet</a></dt>
<dd>
<div class="block">Return an iterator to the contents of the set.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/OrthoPairCollection.html#iterator()">iterator()</a></span> - Method in interface org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/OrthoPairCollection.html" title="interface in org.biojava.bio.program.homologene">OrthoPairCollection</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/OrthoPairSet.html#iterator()">iterator()</a></span> - Method in interface org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/OrthoPairSet.html" title="interface in org.biojava.bio.program.homologene">OrthoPairSet</a></dt>
<dd>
<div class="block">returns an iterator to the members of this set</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/SimpleOrthologueSet.html#iterator()">iterator()</a></span> - Method in class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/SimpleOrthologueSet.html" title="class in org.biojava.bio.program.homologene">SimpleOrthologueSet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/SimpleOrthoPairCollection.html#iterator()">iterator()</a></span> - Method in class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/SimpleOrthoPairCollection.html" title="class in org.biojava.bio.program.homologene">SimpleOrthoPairCollection</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/SimpleOrthoPairSet.html#iterator()">iterator()</a></span> - Method in class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/SimpleOrthoPairSet.html" title="class in org.biojava.bio.program.homologene">SimpleOrthoPairSet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/homol/SimilarityPairFeature.EmptyPairwiseAlignment.html#iterator()">iterator()</a></span> - Method in class org.biojava.bio.seq.homol.<a href="./org/biojava/bio/seq/homol/SimilarityPairFeature.EmptyPairwiseAlignment.html" title="class in org.biojava.bio.seq.homol">SimilarityPairFeature.EmptyPairwiseAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/DummySequence.html#iterator()">iterator()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/DummySequence.html" title="class in org.biojava.bio.seq.impl">DummySequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleSequence.html#iterator()">iterator()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleSequence.html" title="class in org.biojava.bio.seq.impl">SimpleSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SubSequence.html#iterator()">iterator()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SubSequence.html" title="class in org.biojava.bio.seq.impl">SubSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/ViewSequence.html#iterator()">iterator()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/ViewSequence.html" title="class in org.biojava.bio.seq.impl">ViewSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/NewSimpleAssembly.html#iterator()">iterator()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/NewSimpleAssembly.html" title="class in org.biojava.bio.seq">NewSimpleAssembly</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/SimpleAssembly.html#iterator()">iterator()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/SimpleAssembly.html" title="class in org.biojava.bio.seq">SimpleAssembly</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Group.html#iterator()">iterator()</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Group.html" title="interface in org.biojava.bio.structure">Group</a></dt>
<dd>
<div class="block">get an Atom Iterator.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/HetatomImpl.html#iterator()">iterator()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/HetatomImpl.html" title="class in org.biojava.bio.structure">HetatomImpl</a></dt>
<dd>
<div class="block">return an AtomIterator.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AbstractSymbolList.html#iterator()">iterator()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AbstractSymbolList.html" title="class in org.biojava.bio.symbol">AbstractSymbolList</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/FiniteAlphabet.html#iterator()">iterator()</a></span> - Method in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/FiniteAlphabet.html" title="interface in org.biojava.bio.symbol">FiniteAlphabet</a></dt>
<dd>
<div class="block">Retrieve an Iterator over the AtomicSymbols in this FiniteAlphabet.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/IntegerAlphabet.SubIntegerAlphabet.html#iterator()">iterator()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/IntegerAlphabet.SubIntegerAlphabet.html" title="class in org.biojava.bio.symbol">IntegerAlphabet.SubIntegerAlphabet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/RelabeledAlignment.html#iterator()">iterator()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/RelabeledAlignment.html" title="class in org.biojava.bio.symbol">RelabeledAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleAlphabet.html#iterator()">iterator()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleAlphabet.html" title="class in org.biojava.bio.symbol">SimpleAlphabet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SingletonAlphabet.html#iterator()">iterator()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SingletonAlphabet.html" title="class in org.biojava.bio.symbol">SingletonAlphabet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SoftMaskedAlphabet.html#iterator()">iterator()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SoftMaskedAlphabet.html" title="class in org.biojava.bio.symbol">SoftMaskedAlphabet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SymbolList.html#iterator()">iterator()</a></span> - Method in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SymbolList.html" title="interface in org.biojava.bio.symbol">SymbolList</a></dt>
<dd>
<div class="block">An Iterator over all Symbols in this SymbolList.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/FileAsList.html#iterator()">iterator()</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/FileAsList.html" title="class in org.biojava.utils">FileAsList</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/MergingSet.html#iterator()">iterator()</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/MergingSet.html" title="class in org.biojava.utils">MergingSet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/SmallSet.html#iterator()">iterator()</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/SmallSet.html" title="class in org.biojava.utils">SmallSet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLRichSequenceHandler.html#iterator(org.biojavax.bio.seq.RichSequence)">iterator(RichSequence)</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLRichSequenceHandler.html" title="class in org.biojavax.bio.db.biosql">BioSQLRichSequenceHandler</a></dt>
<dd>
<div class="block">An Iterator over all Symbols in this SymbolList.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/DummyRichSequenceHandler.html#iterator(org.biojavax.bio.seq.RichSequence)">iterator(RichSequence)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/DummyRichSequenceHandler.html" title="class in org.biojavax.bio.seq">DummyRichSequenceHandler</a></dt>
<dd>
<div class="block">An Iterator over all Symbols in this SymbolList.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/InfinitelyAmbiguousSymbolList.html#iterator()">iterator()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/InfinitelyAmbiguousSymbolList.html" title="class in org.biojavax.bio.seq">InfinitelyAmbiguousSymbolList</a></dt>
<dd>
<div class="block">An Iterator over all Symbols in this SymbolList.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequenceHandler.html#iterator(org.biojavax.bio.seq.RichSequence)">iterator(RichSequence)</a></span> - Method in interface org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequenceHandler.html" title="interface in org.biojavax.bio.seq">RichSequenceHandler</a></dt>
<dd>
<div class="block">An Iterator over all Symbols in this SymbolList.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/ThinRichSequence.html#iterator()">iterator()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/ThinRichSequence.html" title="class in org.biojavax.bio.seq">ThinRichSequence</a></dt>
<dd>
<div class="block">An Iterator over all Symbols in this SymbolList.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ga/util/WeightedSet.html#iterator()">iterator()</a></span> - Method in class org.biojavax.ga.util.<a href="./org/biojavax/ga/util/WeightedSet.html" title="class in org.biojavax.ga.util">WeightedSet</a></dt>
<dd>
<div class="block">Returns an unmodifiable iterator over the keys of the set.</div>
</dd>
</dl>
<a name="_J_">
<!-- -->
</a>
<h2 class="title">J</h2>
<dl>
<dt><a href="./org/biojava/utils/JDBCConnectionPool.html" title="class in org.biojava.utils"><span class="strong">JDBCConnectionPool</span></a> - Class in <a href="./org/biojava/utils/package-summary.html">org.biojava.utils</a></dt>
<dd>
<div class="block">Really simple connection pool for JDBC databases.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/JDBCConnectionPool.html#JDBCConnectionPool(java.lang.String, java.lang.String, java.lang.String)">JDBCConnectionPool(String, String, String)</a></span> - Constructor for class org.biojava.utils.<a href="./org/biojava/utils/JDBCConnectionPool.html" title="class in org.biojava.utils">JDBCConnectionPool</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/JDBCConnectionPool.html#JDBCConnectionPool(java.lang.String)">JDBCConnectionPool(String)</a></span> - Constructor for class org.biojava.utils.<a href="./org/biojava/utils/JDBCConnectionPool.html" title="class in org.biojava.utils">JDBCConnectionPool</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/utils/JDBCPooledDataSource.html" title="class in org.biojava.utils"><span class="strong">JDBCPooledDataSource</span></a> - Class in <a href="./org/biojava/utils/package-summary.html">org.biojava.utils</a></dt>
<dd>
<div class="block">Returns a DataSource that implements connection pooling
Uses Jakarta Commons DBCP and Pool packages.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/JDBCPooledDataSource.html#JDBCPooledDataSource()">JDBCPooledDataSource()</a></span> - Constructor for class org.biojava.utils.<a href="./org/biojava/utils/JDBCPooledDataSource.html" title="class in org.biojava.utils">JDBCPooledDataSource</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/structure/gui/JMatrixPanel.html" title="class in org.biojava.bio.structure.gui"><span class="strong">JMatrixPanel</span></a> - Class in <a href="./org/biojava/bio/structure/gui/package-summary.html">org.biojava.bio.structure.gui</a></dt>
<dd>
<div class="block">a JPanel that can display a difference of distance matrix and paths that have been
taken for the alignment</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/JMatrixPanel.html#JMatrixPanel()">JMatrixPanel()</a></span> - Constructor for class org.biojava.bio.structure.gui.<a href="./org/biojava/bio/structure/gui/JMatrixPanel.html" title="class in org.biojava.bio.structure.gui">JMatrixPanel</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/structure/gui/events/JmolAlignedPositionListener.html" title="class in org.biojava.bio.structure.gui.events"><span class="strong">JmolAlignedPositionListener</span></a> - Class in <a href="./org/biojava/bio/structure/gui/events/package-summary.html">org.biojava.bio.structure.gui.events</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/events/JmolAlignedPositionListener.html#JmolAlignedPositionListener(org.biojava.bio.structure.gui.BiojavaJmol, org.biojava.bio.structure.align.StructurePairAligner)">JmolAlignedPositionListener(BiojavaJmol, StructurePairAligner)</a></span> - Constructor for class org.biojava.bio.structure.gui.events.<a href="./org/biojava/bio/structure/gui/events/JmolAlignedPositionListener.html" title="class in org.biojava.bio.structure.gui.events">JmolAlignedPositionListener</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/BiojavaJmol.html#jmolInClassPath()">jmolInClassPath()</a></span> - Static method in class org.biojava.bio.structure.gui.<a href="./org/biojava/bio/structure/gui/BiojavaJmol.html" title="class in org.biojava.bio.structure.gui">BiojavaJmol</a></dt>
<dd>
<div class="block">returns true if Jmol can be found in the classpath, otherwise false.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/biosql/DBHelper.html#JOIN_GENERIC">JOIN_GENERIC</a></span> - Static variable in class org.biojava.bio.seq.db.biosql.<a href="./org/biojava/bio/seq/db/biosql/DBHelper.html" title="class in org.biojava.bio.seq.db.biosql">DBHelper</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/biosql/DBHelper.html#JOIN_ORACLE8">JOIN_ORACLE8</a></span> - Static variable in class org.biojava.bio.seq.db.biosql.<a href="./org/biojava/bio/seq/db/biosql/DBHelper.html" title="class in org.biojava.bio.seq.db.biosql">DBHelper</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/process/ExternalProcess.html#joinCommands(java.lang.Object[])">joinCommands(Object[])</a></span> - Static method in class org.biojava.utils.process.<a href="./org/biojava/utils/process/ExternalProcess.html" title="class in org.biojava.utils.process">ExternalProcess</a></dt>
<dd>
<div class="block">Joins a command list to a single command string.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/DistributionTools.html#jointDistOverAlignment(org.biojava.bio.symbol.Alignment, boolean, double, int[])">jointDistOverAlignment(Alignment, boolean, double, int[])</a></span> - Static method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/DistributionTools.html" title="class in org.biojava.bio.dist">DistributionTools</a></dt>
<dd>
<div class="block">Creates a joint distribution.</div>
</dd>
<dt><a href="./org/biojava/bio/structure/align/helper/JointFragments.html" title="class in org.biojava.bio.structure.align.helper"><span class="strong">JointFragments</span></a> - Class in <a href="./org/biojava/bio/structure/align/helper/package-summary.html">org.biojava.bio.structure.align.helper</a></dt>
<dd>
<div class="block">A utility class that defines which set of atoms are considered
to be on equivalent positions.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/helper/JointFragments.html#JointFragments()">JointFragments()</a></span> - Constructor for class org.biojava.bio.structure.align.helper.<a href="./org/biojava/bio/structure/align/helper/JointFragments.html" title="class in org.biojava.bio.structure.align.helper">JointFragments</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BibRefSupport.html#JOURNAL_ABBREV">JOURNAL_ABBREV</a></span> - Static variable in interface org.biojava.bibliography.<a href="./org/biojava/bibliography/BibRefSupport.html" title="interface in org.biojava.bibliography">BibRefSupport</a></dt>
<dd>
<div class="block">A vocabulary name.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/EmblLikeFormat.html#JOURNAL_TAG">JOURNAL_TAG</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/EmblLikeFormat.html" title="class in org.biojava.bio.seq.io">EmblLikeFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/GenbankFormat.html#JOURNAL_TAG">JOURNAL_TAG</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/GenbankFormat.html" title="class in org.biojava.bio.seq.io">GenbankFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/GenbankFormat.html#JOURNAL_TAG">JOURNAL_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/GenbankFormat.html" title="class in org.biojavax.bio.seq.io">GenbankFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/INSDseqFormat.html#JOURNAL_TAG">JOURNAL_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/INSDseqFormat.html" title="class in org.biojavax.bio.seq.io">INSDseqFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BibRefSupport.html#JOURNAL_TITLES">JOURNAL_TITLES</a></span> - Static variable in interface org.biojava.bibliography.<a href="./org/biojava/bibliography/BibRefSupport.html" title="interface in org.biojava.bibliography">BibRefSupport</a></dt>
<dd>
<div class="block">A vocabulary name.</div>
</dd>
<dt><a href="./org/biojava/bio/structure/JournalArticle.html" title="class in org.biojava.bio.structure"><span class="strong">JournalArticle</span></a> - Class in <a href="./org/biojava/bio/structure/package-summary.html">org.biojava.bio.structure</a></dt>
<dd>
<div class="block">PDB-specific</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/JournalArticle.html#JournalArticle()">JournalArticle()</a></span> - Constructor for class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/JournalArticle.html" title="class in org.biojava.bio.structure">JournalArticle</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/hmmer/FullHmmerProfileHMM.html#jState()">jState()</a></span> - Method in class org.biojava.bio.program.hmmer.<a href="./org/biojava/bio/program/hmmer/FullHmmerProfileHMM.html" title="class in org.biojava.bio.program.hmmer">FullHmmerProfileHMM</a></dt>
<dd>
<div class="block">Gets the J loop state</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/phylo/MultipleHitCorrection.html#JukesCantor(java.lang.String, java.lang.String)">JukesCantor(String, String)</a></span> - Static method in class org.biojavax.bio.phylo.<a href="./org/biojavax/bio/phylo/MultipleHitCorrection.html" title="class in org.biojavax.bio.phylo">MultipleHitCorrection</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/UkkonenSuffixTree.html#jumpTo(org.biojava.bio.symbol.UkkonenSuffixTree.SuffixNode, java.lang.CharSequence, int, int)">jumpTo(UkkonenSuffixTree.SuffixNode, CharSequence, int, int)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/UkkonenSuffixTree.html" title="class in org.biojava.bio.symbol">UkkonenSuffixTree</a></dt>
<dd>
<div class="block">Just like walkTo, but faster when used during tree construction, as it
assumes that a mismatch can only occurs with the last character of the
target string.</div>
</dd>
</dl>
<a name="_K_">
<!-- -->
</a>
<h2 class="title">K</h2>
<dl>
<dt><span class="strong"><a href="./org/biojava/bio/seq/DNATools.html#k()">k()</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/DNATools.html" title="class in org.biojava.bio.seq">DNATools</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/NucleotideTools.html#k()">k()</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/NucleotideTools.html" title="class in org.biojava.bio.seq">NucleotideTools</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/ProteinTools.html#k()">k()</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/ProteinTools.html" title="class in org.biojava.bio.seq">ProteinTools</a></dt>
<dd>
<div class="block">Returns the <code>AtomicSymbol</code> for the amino acid
Lysine</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/SparseVector.html#kernel">kernel</a></span> - Static variable in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/SparseVector.html" title="class in org.biojava.stats.svm">SparseVector</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#KEY_ATTR">KEY_ATTR</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/BlastLikeSearchFilter.html#KEY_QUERY_ID">KEY_QUERY_ID</a></span> - Static variable in interface org.biojava.bio.search.<a href="./org/biojava/bio/search/BlastLikeSearchFilter.html" title="interface in org.biojava.bio.search">BlastLikeSearchFilter</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/utils/cache/KeyedWeakReference.html" title="class in org.biojava.utils.cache"><span class="strong">KeyedWeakReference</span></a> - Class in <a href="./org/biojava/utils/cache/package-summary.html">org.biojava.utils.cache</a></dt>
<dd>
<div class="block">Subclass of WeakReference which includes and extra field (the key)
which can be used to help cleanup once this reference has been
enqueued.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/cache/KeyedWeakReference.html#KeyedWeakReference(java.lang.Object, java.lang.Object)">KeyedWeakReference(Object, Object)</a></span> - Constructor for class org.biojava.utils.cache.<a href="./org/biojava/utils/cache/KeyedWeakReference.html" title="class in org.biojava.utils.cache">KeyedWeakReference</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/cache/KeyedWeakReference.html#KeyedWeakReference(java.lang.Object, java.lang.Object, java.lang.ref.ReferenceQueue)">KeyedWeakReference(Object, Object, ReferenceQueue)</a></span> - Constructor for class org.biojava.utils.cache.<a href="./org/biojava/utils/cache/KeyedWeakReference.html" title="class in org.biojava.utils.cache">KeyedWeakReference</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/RasmolCommandListener.html#keyReleased(java.awt.event.KeyEvent)">keyReleased(KeyEvent)</a></span> - Method in class org.biojava.bio.structure.gui.<a href="./org/biojava/bio/structure/gui/RasmolCommandListener.html" title="class in org.biojava.bio.structure.gui">RasmolCommandListener</a></dt>
<dd>
<div class="block">takes care of the cursor up/down keys.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/AbstractAnnotation.html#keys()">keys()</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/AbstractAnnotation.html" title="class in org.biojava.bio">AbstractAnnotation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/Annotation.html#keys()">keys()</a></span> - Method in interface org.biojava.bio.<a href="./org/biojava/bio/Annotation.html" title="interface in org.biojava.bio">Annotation</a></dt>
<dd>
<div class="block">Get a set of key objects.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/MergeAnnotation.html#keys()">keys()</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/MergeAnnotation.html" title="class in org.biojava.bio">MergeAnnotation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/OverlayAnnotation.html#keys()">keys()</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/OverlayAnnotation.html" title="class in org.biojava.bio">OverlayAnnotation</a></dt>
<dd>
<div class="block">Return a <code>Set</code> containing all key objects
visible in this annotation.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/indexdb/BioStoreFactory.html#KEYS">KEYS</a></span> - Static variable in class org.biojava.bio.program.indexdb.<a href="./org/biojava/bio/program/indexdb/BioStoreFactory.html" title="class in org.biojava.bio.program.indexdb">BioStoreFactory</a></dt>
<dd>
<div class="block"><code>KEYS</code> is the key used to identify the secondary
namespaces in the OBDA config.dat files.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/EmptyRichAnnotation.html#keys()">keys()</a></span> - Method in class org.biojavax.<a href="./org/biojavax/EmptyRichAnnotation.html" title="class in org.biojavax">EmptyRichAnnotation</a></dt>
<dd>
<div class="block">Get a set of key objects.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleRichAnnotation.html#keys()">keys()</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleRichAnnotation.html" title="class in org.biojavax">SimpleRichAnnotation</a></dt>
<dd>
<div class="block">Get a set of key objects.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/OverlayMap.html#keySet()">keySet()</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/OverlayMap.html" title="class in org.biojava.utils">OverlayMap</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/SmallMap.html#keySet()">keySet()</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/SmallMap.html" title="class in org.biojava.utils">SmallMap</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html#KEYWORD_TAG">KEYWORD_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html" title="class in org.biojavax.bio.seq.io">EMBLxmlFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/INSDseqFormat.html#KEYWORD_TAG">KEYWORD_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/INSDseqFormat.html" title="class in org.biojavax.bio.seq.io">INSDseqFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#KEYWORD_TAG">KEYWORD_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BiblioSubject.html#keywords">keywords</a></span> - Variable in class org.biojava.bibliography.<a href="./org/biojava/bibliography/BiblioSubject.html" title="class in org.biojava.bibliography">BiblioSubject</a></dt>
<dd>
<div class="block">The keywords are usually (but not limited to) one word long.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/INSDseqFormat.html#KEYWORDS_GROUP_TAG">KEYWORDS_GROUP_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/INSDseqFormat.html" title="class in org.biojavax.bio.seq.io">INSDseqFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/EmblLikeFormat.html#KEYWORDS_TAG">KEYWORDS_TAG</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/EmblLikeFormat.html" title="class in org.biojava.bio.seq.io">EmblLikeFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/GenbankFormat.html#KEYWORDS_TAG">KEYWORDS_TAG</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/GenbankFormat.html" title="class in org.biojava.bio.seq.io">GenbankFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLFormat.html#KEYWORDS_TAG">KEYWORDS_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLFormat.html" title="class in org.biojavax.bio.seq.io">EMBLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/GenbankFormat.html#KEYWORDS_TAG">KEYWORDS_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/GenbankFormat.html" title="class in org.biojavax.bio.seq.io">GenbankFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtFormat.html#KEYWORDS_TAG">KEYWORDS_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtFormat.html" title="class in org.biojavax.bio.seq.io">UniProtFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/phylo/MultipleHitCorrection.html#KimuraTwoParameter(java.lang.String, java.lang.String)">KimuraTwoParameter(String, String)</a></span> - Static method in class org.biojavax.bio.phylo.<a href="./org/biojavax/bio/phylo/MultipleHitCorrection.html" title="class in org.biojavax.bio.phylo">MultipleHitCorrection</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/DistributionTools.html#KLDistance(org.biojava.bio.dist.Distribution, org.biojava.bio.dist.Distribution, double)">KLDistance(Distribution, Distribution, double)</a></span> - Static method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/DistributionTools.html" title="class in org.biojava.bio.dist">DistributionTools</a></dt>
<dd>
<div class="block">A method to calculate the Kullback-Liebler Distance (relative entropy).</div>
</dd>
<dt><a href="./org/biojava/bio/search/KnuthMorrisPrattSearch.html" title="class in org.biojava.bio.search"><span class="strong">KnuthMorrisPrattSearch</span></a> - Class in <a href="./org/biojava/bio/search/package-summary.html">org.biojava.bio.search</a></dt>
<dd>
<div class="block">An object to find exact subsequences within a sequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/KnuthMorrisPrattSearch.html#KnuthMorrisPrattSearch(org.biojava.bio.symbol.SymbolList)">KnuthMorrisPrattSearch(SymbolList)</a></span> - Constructor for class org.biojava.bio.search.<a href="./org/biojava/bio/search/KnuthMorrisPrattSearch.html" title="class in org.biojava.bio.search">KnuthMorrisPrattSearch</a></dt>
<dd>
<div class="block">Constructs a KMP matcher to find exact occurances of
<code>pattern</code> in <code>text</code> using the
Knuth-Morris-Pratt algorithm.</div>
</dd>
</dl>
<a name="_L_">
<!-- -->
</a>
<h2 class="title">L</h2>
<dl>
<dt><span class="strong"><a href="./org/biojava/bio/seq/ProteinTools.html#l()">l()</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/ProteinTools.html" title="class in org.biojava.bio.seq">ProteinTools</a></dt>
<dd>
<div class="block">Returns the <code>AtomicSymbol</code> for the amino acid
Leucine</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/Taxon.html#L_ESCULENTUM">L_ESCULENTUM</a></span> - Static variable in interface org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/Taxon.html" title="interface in org.biojava.bio.program.homologene">Taxon</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/SimpleAlignmentElement.html#label">label</a></span> - Variable in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/SimpleAlignmentElement.html" title="class in org.biojava.bio.alignment">SimpleAlignmentElement</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/AlignmentRenderer.html#LABEL">LABEL</a></span> - Static variable in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/AlignmentRenderer.html" title="class in org.biojava.bio.gui.sequence">AlignmentRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SimpleLabelRenderer.html#LABEL">LABEL</a></span> - Static variable in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SimpleLabelRenderer.html" title="class in org.biojava.bio.gui.sequence">SimpleLabelRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/FeatureLabelRenderer.html#LABEL_MAKER">LABEL_MAKER</a></span> - Static variable in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/FeatureLabelRenderer.html" title="class in org.biojava.bio.gui.sequence">FeatureLabelRenderer</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/gui/sequence/LabelledSequenceRenderer.html" title="class in org.biojava.bio.gui.sequence"><span class="strong">LabelledSequenceRenderer</span></a> - Class in <a href="./org/biojava/bio/gui/sequence/package-summary.html">org.biojava.bio.gui.sequence</a></dt>
<dd>
<div class="block">Renderer which draws a track of sequence with a textual label.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/LabelledSequenceRenderer.html#LabelledSequenceRenderer()">LabelledSequenceRenderer()</a></span> - Constructor for class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/LabelledSequenceRenderer.html" title="class in org.biojava.bio.gui.sequence">LabelledSequenceRenderer</a></dt>
<dd>
<div class="block">Creates new LabelledSequenceRenderer with default width and depth;</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/LabelledSequenceRenderer.html#LabelledSequenceRenderer(java.lang.String, org.biojava.bio.gui.sequence.SequenceRenderer)">LabelledSequenceRenderer(String, SequenceRenderer)</a></span> - Constructor for class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/LabelledSequenceRenderer.html" title="class in org.biojava.bio.gui.sequence">LabelledSequenceRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/LabelledSequenceRenderer.html#LabelledSequenceRenderer(double, double)">LabelledSequenceRenderer(double, double)</a></span> - Constructor for class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/LabelledSequenceRenderer.html" title="class in org.biojava.bio.gui.sequence">LabelledSequenceRenderer</a></dt>
<dd>
<div class="block">Creates new LabelledSequenceRenderer with the specified width and depth.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/FlexibleAlignment.html#labelOrder">labelOrder</a></span> - Variable in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/FlexibleAlignment.html" title="class in org.biojava.bio.alignment">FlexibleAlignment</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/gui/sequence/LabelRenderer.html" title="interface in org.biojava.bio.gui.sequence"><span class="strong">LabelRenderer</span></a> - Interface in <a href="./org/biojava/bio/gui/sequence/package-summary.html">org.biojava.bio.gui.sequence</a></dt>
<dd>
<div class="block">The interface for things that can render labels for a line of information
about a sequence.</div>
</dd>
<dt><a href="./org/biojava/bio/gui/sequence/LabelRenderer.RenderNothing.html" title="class in org.biojava.bio.gui.sequence"><span class="strong">LabelRenderer.RenderNothing</span></a> - Class in <a href="./org/biojava/bio/gui/sequence/package-summary.html">org.biojava.bio.gui.sequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/LabelRenderer.RenderNothing.html#LabelRenderer.RenderNothing()">LabelRenderer.RenderNothing()</a></span> - Constructor for class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/LabelRenderer.RenderNothing.html" title="class in org.biojava.bio.gui.sequence">LabelRenderer.RenderNothing</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/AbstractULAlignment.html#labelsAt(int)">labelsAt(int)</a></span> - Method in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/AbstractULAlignment.html" title="class in org.biojava.bio.alignment">AbstractULAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/AbstractULAlignment.SubULAlignment.html#labelsAt(int)">labelsAt(int)</a></span> - Method in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/AbstractULAlignment.SubULAlignment.html" title="class in org.biojava.bio.alignment">AbstractULAlignment.SubULAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/UnequalLengthAlignment.html#labelsAt(int)">labelsAt(int)</a></span> - Method in interface org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/UnequalLengthAlignment.html" title="interface in org.biojava.bio.alignment">UnequalLengthAlignment</a></dt>
<dd>
<div class="block">Returns a list labels, of all seqs that cover that column</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/AbstractULAlignment.html#labelsInRange(org.biojava.bio.symbol.Location)">labelsInRange(Location)</a></span> - Method in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/AbstractULAlignment.html" title="class in org.biojava.bio.alignment">AbstractULAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/AbstractULAlignment.SubULAlignment.html#labelsInRange(org.biojava.bio.symbol.Location)">labelsInRange(Location)</a></span> - Method in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/AbstractULAlignment.SubULAlignment.html" title="class in org.biojava.bio.alignment">AbstractULAlignment.SubULAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/UnequalLengthAlignment.html#labelsInRange(org.biojava.bio.symbol.Location)">labelsInRange(Location)</a></span> - Method in interface org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/UnequalLengthAlignment.html" title="interface in org.biojava.bio.alignment">UnequalLengthAlignment</a></dt>
<dd>
<div class="block">Returns list of all the labels that intersect that range</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/AbstractPeptideDigestRenderer.html#LANE">LANE</a></span> - Static variable in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/AbstractPeptideDigestRenderer.html" title="class in org.biojava.bio.gui.sequence">AbstractPeptideDigestRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BiblioDescription.html#language">language</a></span> - Variable in class org.biojava.bibliography.<a href="./org/biojava/bibliography/BiblioDescription.html" title="class in org.biojava.bibliography">BiblioDescription</a></dt>
<dd>
<div class="block">
It defines a language used for <a href="./org/biojava/bibliography/BiblioDescription.html#theAbstract"><code>BiblioDescription.theAbstract</code></a> and <a href="./org/biojava/bibliography/BiblioDescription.html#tableOfContents"><code>BiblioDescription.tableOfContents</code></a>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BibRef.html#language">language</a></span> - Variable in class org.biojava.bibliography.<a href="./org/biojava/bibliography/BibRef.html" title="class in org.biojava.bibliography">BibRef</a></dt>
<dd>
<div class="block">
It defines a language of the intellectual contents of the cited resource.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BibRefSupport.html#LANGUAGES">LANGUAGES</a></span> - Static variable in interface org.biojava.bibliography.<a href="./org/biojava/bibliography/BibRefSupport.html" title="interface in org.biojava.bibliography">BibRefSupport</a></dt>
<dd>
<div class="block">A vocabulary name.</div>
</dd>
<dt><a href="./org/biojava/utils/io/LargeBuffer.html" title="class in org.biojava.utils.io"><span class="strong">LargeBuffer</span></a> - Class in <a href="./org/biojava/utils/io/package-summary.html">org.biojava.utils.io</a></dt>
<dd>
<div class="block">Wrapper arround MappedByteBuffers to allow long-indexed access to files
larger than 2 gigs.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/io/LargeBuffer.html#LargeBuffer(java.nio.channels.FileChannel, java.nio.channels.FileChannel.MapMode, long, long)">LargeBuffer(FileChannel, FileChannel.MapMode, long, long)</a></span> - Constructor for class org.biojava.utils.io.<a href="./org/biojava/utils/io/LargeBuffer.html" title="class in org.biojava.utils.io">LargeBuffer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/onehead/DPCursor.html#lastCol()">lastCol()</a></span> - Method in interface org.biojava.bio.dp.onehead.<a href="./org/biojava/bio/dp/onehead/DPCursor.html" title="interface in org.biojava.bio.dp.onehead">DPCursor</a></dt>
<dd>
<div class="block">The previous column.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/onehead/SmallCursor.html#lastCol()">lastCol()</a></span> - Method in class org.biojava.bio.dp.onehead.<a href="./org/biojava/bio/dp/onehead/SmallCursor.html" title="class in org.biojava.bio.dp.onehead">SmallCursor</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BiblioEntryStatus.html#lastModifiedDate">lastModifiedDate</a></span> - Variable in class org.biojava.bibliography.<a href="./org/biojava/bibliography/BiblioEntryStatus.html" title="class in org.biojava.bibliography">BiblioEntryStatus</a></dt>
<dd>
<div class="block">
It defines when the citation record was added or last modified.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/GappedSymbolList.html#lastNonGap()">lastNonGap()</a></span> - Method in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/GappedSymbolList.html" title="interface in org.biojava.bio.symbol">GappedSymbolList</a></dt>
<dd>
<div class="block">Return the index of the last Symbol that is not a Gap character.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleGappedSymbolList.html#lastNonGap()">lastNonGap()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleGappedSymbolList.html" title="class in org.biojava.bio.symbol">SimpleGappedSymbolList</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BiblioArticle.html#lastPage">lastPage</a></span> - Variable in class org.biojava.bibliography.<a href="./org/biojava/bibliography/BiblioArticle.html" title="class in org.biojava.bibliography">BiblioArticle</a></dt>
<dd>
<div class="block">Last page of the article.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/onehead/DPCursor.html#lastRes()">lastRes()</a></span> - Method in interface org.biojava.bio.dp.onehead.<a href="./org/biojava/bio/dp/onehead/DPCursor.html" title="interface in org.biojava.bio.dp.onehead">DPCursor</a></dt>
<dd>
<div class="block">The previous symbol.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/BumpedRenderer.html#layer(org.biojava.bio.gui.sequence.SequenceRenderContext)">layer(SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/BumpedRenderer.html" title="class in org.biojava.bio.gui.sequence">BumpedRenderer</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/gui/sequence/LayeredRenderer.html" title="class in org.biojava.bio.gui.sequence"><span class="strong">LayeredRenderer</span></a> - Class in <a href="./org/biojava/bio/gui/sequence/package-summary.html">org.biojava.bio.gui.sequence</a></dt>
<dd>
<div class="block"><code>LayeredRenderer</code> handles the lane offsets for
<code>MultiLineRender</code>s.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/LayeredRenderer.html#LayeredRenderer()">LayeredRenderer()</a></span> - Constructor for class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/LayeredRenderer.html" title="class in org.biojava.bio.gui.sequence">LayeredRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequenceRenderContext.html#LAYOUT">LAYOUT</a></span> - Static variable in interface org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequenceRenderContext.html" title="interface in org.biojava.bio.gui.sequence">SequenceRenderContext</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/LazyFeatureHolder.html" title="class in org.biojava.bio.seq"><span class="strong">LazyFeatureHolder</span></a> - Class in <a href="./org/biojava/bio/seq/package-summary.html">org.biojava.bio.seq</a></dt>
<dd>
<div class="block">Wrapper implementation of FeatureHolder which calls a method
to create a contained FeatureHolder on demand.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/LazyFeatureHolder.html#LazyFeatureHolder()">LazyFeatureHolder()</a></span> - Constructor for class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/LazyFeatureHolder.html" title="class in org.biojava.bio.seq">LazyFeatureHolder</a></dt>
<dd>
<div class="block">Construct a LazyFeatureHolder with the schema of its contained featureholder</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/LazyFeatureHolder.html#LazyFeatureHolder(org.biojava.bio.seq.FeatureFilter)">LazyFeatureHolder(FeatureFilter)</a></span> - Constructor for class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/LazyFeatureHolder.html" title="class in org.biojava.bio.seq">LazyFeatureHolder</a></dt>
<dd>
<div class="block">Construct a LazyFeatureHolder with the specified schema</div>
</dd>
<dt><a href="./org/biojava/bio/annodb/LazyFilteredAnnotationDB.html" title="class in org.biojava.bio.annodb"><span class="strong">LazyFilteredAnnotationDB</span></a> - Class in <a href="./org/biojava/bio/annodb/package-summary.html">org.biojava.bio.annodb</a></dt>
<dd>
<div class="block">An implementation of AnnotationDB that lazily applies a filter.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/annodb/LazyFilteredAnnotationDB.html#LazyFilteredAnnotationDB(java.lang.String, org.biojava.bio.annodb.AnnotationDB, org.biojava.bio.AnnotationType)">LazyFilteredAnnotationDB(String, AnnotationDB, AnnotationType)</a></span> - Constructor for class org.biojava.bio.annodb.<a href="./org/biojava/bio/annodb/LazyFilteredAnnotationDB.html" title="class in org.biojava.bio.annodb">LazyFilteredAnnotationDB</a></dt>
<dd>
<div class="block">Create a new DB by wrapping another with a schema.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/impl/LazyFilterFeatureHolder.html" title="class in org.biojava.bio.seq.impl"><span class="strong">LazyFilterFeatureHolder</span></a> - Class in <a href="./org/biojava/bio/seq/impl/package-summary.html">org.biojava.bio.seq.impl</a></dt>
<dd>
<div class="block">FeatureHolder which lazily applies a specified filter to another FeatureHolder.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/LazyFilterFeatureHolder.html#LazyFilterFeatureHolder(org.biojava.bio.seq.FeatureHolder, org.biojava.bio.seq.FeatureFilter)">LazyFilterFeatureHolder(FeatureHolder, FeatureFilter)</a></span> - Constructor for class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/LazyFilterFeatureHolder.html" title="class in org.biojava.bio.seq.impl">LazyFilterFeatureHolder</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/annodb/LazySearchedAnnotationDB.html" title="class in org.biojava.bio.annodb"><span class="strong">LazySearchedAnnotationDB</span></a> - Class in <a href="./org/biojava/bio/annodb/package-summary.html">org.biojava.bio.annodb</a></dt>
<dd>
<div class="block">An implementation of AnnotationDB that does a JIT search on another set.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/annodb/LazySearchedAnnotationDB.html#LazySearchedAnnotationDB(java.lang.String, org.biojava.bio.annodb.AnnotationDB, org.biojava.bio.AnnotationType)">LazySearchedAnnotationDB(String, AnnotationDB, AnnotationType)</a></span> - Constructor for class org.biojava.bio.annodb.<a href="./org/biojava/bio/annodb/LazySearchedAnnotationDB.html" title="class in org.biojava.bio.annodb">LazySearchedAnnotationDB</a></dt>
<dd>
<div class="block">Create a new DB from an old one by applying a schema.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.HibernateFeatureFilter.html#le">le</a></span> - Variable in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.HibernateFeatureFilter.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.HibernateFeatureFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.html#leaf">leaf</a></span> - Static variable in interface org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.html" title="interface in org.biojava.bio.seq">FeatureFilter</a></dt>
<dd>
<div class="block">A filter which accepts features with no children</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FilterUtils.html#leaf()">leaf()</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FilterUtils.html" title="class in org.biojava.bio.seq">FilterUtils</a></dt>
<dd>
<div class="block">Return a filter which matches features with zero children.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/utils/StringTools.html#leftIndent(java.lang.String, int)">leftIndent(String, int)</a></span> - Static method in class org.biojavax.utils.<a href="./org/biojavax/utils/StringTools.html" title="class in org.biojavax.utils">StringTools</a></dt>
<dd>
<div class="block">Takes an input string and appends spaces to the left.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/AbstractULAlignment.html#leftMost()">leftMost()</a></span> - Method in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/AbstractULAlignment.html" title="class in org.biojava.bio.alignment">AbstractULAlignment</a></dt>
<dd>
<div class="block">leftMost and rightMost return labels.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/utils/StringTools.html#leftPad(java.lang.String, int)">leftPad(String, int)</a></span> - Static method in class org.biojavax.utils.<a href="./org/biojavax/utils/StringTools.html" title="class in org.biojavax.utils">StringTools</a></dt>
<dd>
<div class="block">Pads a string to be a certain width by prepending spaces.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/utils/StringTools.html#leftPad(java.lang.String, char, int)">leftPad(String, char, int)</a></span> - Static method in class org.biojavax.utils.<a href="./org/biojavax/utils/StringTools.html" title="class in org.biojavax.utils">StringTools</a></dt>
<dd>
<div class="block">Pads a string to be a certain width by prepending given symbols.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/taxa/NCBITaxon.html#LEFTVALUE">LEFTVALUE</a></span> - Static variable in interface org.biojavax.bio.taxa.<a href="./org/biojavax/bio/taxa/NCBITaxon.html" title="interface in org.biojavax.bio.taxa">NCBITaxon</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/AbstractULAlignment.SubULAlignment.html#length()">length()</a></span> - Method in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/AbstractULAlignment.SubULAlignment.html" title="class in org.biojava.bio.alignment">AbstractULAlignment.SubULAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/FlexibleAlignment.html#length()">length()</a></span> - Method in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/FlexibleAlignment.html" title="class in org.biojava.bio.alignment">FlexibleAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/onehead/DPCursor.html#length()">length()</a></span> - Method in interface org.biojava.bio.dp.onehead.<a href="./org/biojava/bio/dp/onehead/DPCursor.html" title="interface in org.biojava.bio.dp.onehead">DPCursor</a></dt>
<dd>
<div class="block">
The length of the sequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/onehead/SmallCursor.html#length()">length()</a></span> - Method in class org.biojava.bio.dp.onehead.<a href="./org/biojava/bio/dp/onehead/SmallCursor.html" title="class in org.biojava.bio.dp.onehead">SmallCursor</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/SimpleStatePath.html#length()">length()</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/SimpleStatePath.html" title="class in org.biojava.bio.dp">SimpleStatePath</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/DASSequence.html#length()">length()</a></span> - Method in class org.biojava.bio.program.das.<a href="./org/biojava/bio/program/das/DASSequence.html" title="class in org.biojava.bio.program.das">DASSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/homol/SimilarityPairFeature.EmptyPairwiseAlignment.html#length()">length()</a></span> - Method in class org.biojava.bio.seq.homol.<a href="./org/biojava/bio/seq/homol/SimilarityPairFeature.EmptyPairwiseAlignment.html" title="class in org.biojava.bio.seq.homol">SimilarityPairFeature.EmptyPairwiseAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/AssembledSymbolList.html#length()">length()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/AssembledSymbolList.html" title="class in org.biojava.bio.seq.impl">AssembledSymbolList</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/DummySequence.html#length()">length()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/DummySequence.html" title="class in org.biojava.bio.seq.impl">DummySequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/NewAssembledSymbolList.html#length()">length()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/NewAssembledSymbolList.html" title="class in org.biojava.bio.seq.impl">NewAssembledSymbolList</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleSequence.html#length()">length()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleSequence.html" title="class in org.biojava.bio.seq.impl">SimpleSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SubSequence.html#length()">length()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SubSequence.html" title="class in org.biojava.bio.seq.impl">SubSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/ViewSequence.html#length()">length()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/ViewSequence.html" title="class in org.biojava.bio.seq.impl">ViewSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SymbolListCharSequence.html#length()">length()</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SymbolListCharSequence.html" title="class in org.biojava.bio.seq.io">SymbolListCharSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/NewSimpleAssembly.html#length()">length()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/NewSimpleAssembly.html" title="class in org.biojava.bio.seq">NewSimpleAssembly</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/SimpleAssembly.html#length()">length()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/SimpleAssembly.html" title="class in org.biojava.bio.seq">SimpleAssembly</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/ChunkedSymbolList.html#length()">length()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/ChunkedSymbolList.html" title="class in org.biojava.bio.symbol">ChunkedSymbolList</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/DummySymbolList.html#length()">length()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/DummySymbolList.html" title="class in org.biojava.bio.symbol">DummySymbolList</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/Edit.html#length">length</a></span> - Variable in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/Edit.html" title="class in org.biojava.bio.symbol">Edit</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/PackedSymbolList.html#length()">length()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/PackedSymbolList.html" title="class in org.biojava.bio.symbol">PackedSymbolList</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/RelabeledAlignment.html#length()">length()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/RelabeledAlignment.html" title="class in org.biojava.bio.symbol">RelabeledAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleAlignment.html#length()">length()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleAlignment.html" title="class in org.biojava.bio.symbol">SimpleAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleGappedSymbolList.html#length()">length()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleGappedSymbolList.html" title="class in org.biojava.bio.symbol">SimpleGappedSymbolList</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleSymbolList.html#length()">length()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleSymbolList.html" title="class in org.biojava.bio.symbol">SimpleSymbolList</a></dt>
<dd>
<div class="block">Get the length of this SymbolList.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SymbolList.html#length()">length()</a></span> - Method in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SymbolList.html" title="interface in org.biojava.bio.symbol">SymbolList</a></dt>
<dd>
<div class="block">The number of symbols in this SymbolList.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/io/RandomAccessReader.html#length()">length()</a></span> - Method in class org.biojava.utils.io.<a href="./org/biojava/utils/io/RandomAccessReader.html" title="class in org.biojava.utils.io">RandomAccessReader</a></dt>
<dd>
<div class="block"><code>length</code> returns the length of the underlying
<code>RandomAccessFile</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/RepeatedCharSequence.html#length()">length()</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/RepeatedCharSequence.html" title="class in org.biojava.utils">RepeatedCharSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/InfinitelyAmbiguousSymbolList.html#length()">length()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/InfinitelyAmbiguousSymbolList.html" title="class in org.biojavax.bio.seq">InfinitelyAmbiguousSymbolList</a></dt>
<dd>
<div class="block">The number of symbols in this SymbolList.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichSequence.html#length()">length()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichSequence.html" title="class in org.biojavax.bio.seq">SimpleRichSequence</a></dt>
<dd>
<div class="block">The number of symbols in this SymbolList.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/ThinRichSequence.html#length()">length()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/ThinRichSequence.html" title="class in org.biojavax.bio.seq">ThinRichSequence</a></dt>
<dd>
<div class="block">The number of symbols in this SymbolList.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/INSDseqFormat.html#LENGTH_TAG">LENGTH_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/INSDseqFormat.html" title="class in org.biojavax.bio.seq.io">INSDseqFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/FlexibleAlignment.html#lesser(int, int)">lesser(int, int)</a></span> - Method in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/FlexibleAlignment.html" title="class in org.biojava.bio.alignment">FlexibleAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/ProteinTools.html#leu()">leu()</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/ProteinTools.html" title="class in org.biojava.bio.seq">ProteinTools</a></dt>
<dd>
<div class="block">Returns the <code>AtomicSymbol</code> for the amino acid
Leucine (L)</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/unigene/UnigeneTools.html#LIBRARY_ANNOTATION">LIBRARY_ANNOTATION</a></span> - Static variable in class org.biojava.bio.program.unigene.<a href="./org/biojava/bio/program/unigene/UnigeneTools.html" title="class in org.biojava.bio.program.unigene">UnigeneTools</a></dt>
<dd>
<div class="block">
Annotation schema for all Unigene libraries.</div>
</dd>
<dt><a href="./org/biojava/utils/lsid/LifeScienceIdentifier.html" title="class in org.biojava.utils.lsid"><span class="strong">LifeScienceIdentifier</span></a> - Class in <a href="./org/biojava/utils/lsid/package-summary.html">org.biojava.utils.lsid</a></dt>
<dd>
<div class="block">Life Science Identifier (LSID).</div>
</dd>
<dt><a href="./org/biojava/utils/lsid/LifeScienceIdentifierParseException.html" title="class in org.biojava.utils.lsid"><span class="strong">LifeScienceIdentifierParseException</span></a> - Exception in <a href="./org/biojava/utils/lsid/package-summary.html">org.biojava.utils.lsid</a></dt>
<dd>
<div class="block">Exception thrown in the event of an error in
parsing a LSID-formatted string.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/lsid/LifeScienceIdentifierParseException.html#LifeScienceIdentifierParseException()">LifeScienceIdentifierParseException()</a></span> - Constructor for exception org.biojava.utils.lsid.<a href="./org/biojava/utils/lsid/LifeScienceIdentifierParseException.html" title="class in org.biojava.utils.lsid">LifeScienceIdentifierParseException</a></dt>
<dd>
<div class="block">Construct a new parse exception with no message.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/lsid/LifeScienceIdentifierParseException.html#LifeScienceIdentifierParseException(java.lang.String)">LifeScienceIdentifierParseException(String)</a></span> - Constructor for exception org.biojava.utils.lsid.<a href="./org/biojava/utils/lsid/LifeScienceIdentifierParseException.html" title="class in org.biojava.utils.lsid">LifeScienceIdentifierParseException</a></dt>
<dd>
<div class="block">Construct a new parse exception with the
specified error message.</div>
</dd>
<dt><a href="./org/biojava/bio/program/formats/Ligand.html" title="class in org.biojava.bio.program.formats"><span class="strong">Ligand</span></a> - Class in <a href="./org/biojava/bio/program/formats/package-summary.html">org.biojava.bio.program.formats</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/formats/Ligand.Compound.html" title="class in org.biojava.bio.program.formats"><span class="strong">Ligand.Compound</span></a> - Class in <a href="./org/biojava/bio/program/formats/package-summary.html">org.biojava.bio.program.formats</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/formats/Ligand.Compound.html#Ligand.Compound()">Ligand.Compound()</a></span> - Constructor for class org.biojava.bio.program.formats.<a href="./org/biojava/bio/program/formats/Ligand.Compound.html" title="class in org.biojava.bio.program.formats">Ligand.Compound</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/formats/Ligand.Enzyme.html" title="class in org.biojava.bio.program.formats"><span class="strong">Ligand.Enzyme</span></a> - Class in <a href="./org/biojava/bio/program/formats/package-summary.html">org.biojava.bio.program.formats</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/formats/Ligand.Enzyme.html#Ligand.Enzyme()">Ligand.Enzyme()</a></span> - Constructor for class org.biojava.bio.program.formats.<a href="./org/biojava/bio/program/formats/Ligand.Enzyme.html" title="class in org.biojava.bio.program.formats">Ligand.Enzyme</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/formats/Ligand.Reaction.html" title="class in org.biojava.bio.program.formats"><span class="strong">Ligand.Reaction</span></a> - Class in <a href="./org/biojava/bio/program/formats/package-summary.html">org.biojava.bio.program.formats</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/formats/Ligand.Reaction.html#Ligand.Reaction()">Ligand.Reaction()</a></span> - Constructor for class org.biojava.bio.program.formats.<a href="./org/biojava/bio/program/formats/Ligand.Reaction.html" title="class in org.biojava.bio.program.formats">Ligand.Reaction</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/dp/twohead/LightPairDPCursor.html" title="class in org.biojava.bio.dp.twohead"><span class="strong">LightPairDPCursor</span></a> - Class in <a href="./org/biojava/bio/dp/twohead/package-summary.html">org.biojava.bio.dp.twohead</a></dt>
<dd>
<div class="block">A LIGHT implementation of PairDPCursor.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/twohead/LightPairDPCursor.html#LightPairDPCursor(org.biojava.bio.symbol.SymbolList, org.biojava.bio.symbol.SymbolList, int, int, int, org.biojava.bio.dp.twohead.EmissionCache)">LightPairDPCursor(SymbolList, SymbolList, int, int, int, EmissionCache)</a></span> - Constructor for class org.biojava.bio.dp.twohead.<a href="./org/biojava/bio/dp/twohead/LightPairDPCursor.html" title="class in org.biojava.bio.dp.twohead">LightPairDPCursor</a></dt>
<dd>
<div class="block">Constructor for the LightPairDPCursor object</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PairwiseDiagonalRenderer.html#line">line</a></span> - Variable in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PairwiseDiagonalRenderer.html" title="class in org.biojava.bio.gui.sequence">PairwiseDiagonalRenderer</a></dt>
<dd>
<div class="block"><code>line</code> is the line to be drawn for each feature.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/obo/OboFileParser.html#line">line</a></span> - Variable in class org.biojava.ontology.obo.<a href="./org/biojava/ontology/obo/OboFileParser.html" title="class in org.biojava.ontology.obo">OboFileParser</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/util/SequenceScalePanel.html#LINE_HEIGHT">LINE_HEIGHT</a></span> - Static variable in class org.biojava.bio.structure.gui.util.<a href="./org/biojava/bio/structure/gui/util/SequenceScalePanel.html" title="class in org.biojava.bio.structure.gui.util">SequenceScalePanel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html#LINEAGE_TAG">LINEAGE_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html" title="class in org.biojavax.bio.seq.io">EMBLxmlFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#LINEAGE_TAG">LINEAGE_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/stats/svm/LinearKernel.html" title="class in org.biojava.stats.svm"><span class="strong">LinearKernel</span></a> - Class in <a href="./org/biojava/stats/svm/package-summary.html">org.biojava.stats.svm</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>Just use SparseVector.kernel instead...</i></div>
</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/LinearKernel.html#LinearKernel()">LinearKernel()</a></span> - Constructor for class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/LinearKernel.html" title="class in org.biojava.stats.svm">LinearKernel</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><a href="./org/biojava/bio/gui/sequence/LineInfo.html" title="class in org.biojava.bio.gui.sequence"><span class="strong">LineInfo</span></a> - Class in <a href="./org/biojava/bio/gui/sequence/package-summary.html">org.biojava.bio.gui.sequence</a></dt>
<dd>
<div class="block">Encapsulates the rendering info for a single line of the display.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/LineInfo.html#LineInfo()">LineInfo()</a></span> - Constructor for class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/LineInfo.html" title="class in org.biojava.bio.gui.sequence">LineInfo</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFEntrySet.html#lineIterator()">lineIterator()</a></span> - Method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFEntrySet.html" title="class in org.biojava.bio.program.gff">GFFEntrySet</a></dt>
<dd>
<div class="block">Loop over all lines in the set.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/obo/OboFileParser.html#linenum">linenum</a></span> - Variable in class org.biojava.ontology.obo.<a href="./org/biojava/ontology/obo/OboFileParser.html" title="class in org.biojava.ontology.obo">OboFileParser</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/tagvalue/LineSplitParser.html" title="class in org.biojava.bio.program.tagvalue"><span class="strong">LineSplitParser</span></a> - Class in <a href="./org/biojava/bio/program/tagvalue/package-summary.html">org.biojava.bio.program.tagvalue</a></dt>
<dd>
<div class="block">
A parser that splits a line into tag/value at a given column number.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/LineSplitParser.html#LineSplitParser()">LineSplitParser()</a></span> - Constructor for class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/LineSplitParser.html" title="class in org.biojava.bio.program.tagvalue">LineSplitParser</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/LineSplitParser.html#LineSplitParser(org.biojava.bio.program.tagvalue.LineSplitParser)">LineSplitParser(LineSplitParser)</a></span> - Constructor for class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/LineSplitParser.html" title="class in org.biojava.bio.program.tagvalue">LineSplitParser</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/FastaFormat.html#lineWidth">lineWidth</a></span> - Variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/FastaFormat.html" title="class in org.biojava.bio.seq.io">FastaFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">The line width for output.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/PDBFileParser.html#linkChains2Compound(org.biojava.bio.structure.Structure)">linkChains2Compound(Structure)</a></span> - Method in class org.biojava.bio.structure.io.<a href="./org/biojava/bio/structure/io/PDBFileParser.html" title="class in org.biojava.bio.structure.io">PDBFileParser</a></dt>
<dd>
<div class="block">After the parsing of a PDB file the <a href="./org/biojava/bio/structure/Chain.html" title="interface in org.biojava.bio.structure"><code>Chain</code></a> and <a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure"><code>Compound</code></a>
objects need to be linked to each other.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/naming/ObdaContext.html#list(javax.naming.Name)">list(Name)</a></span> - Method in class org.biojava.naming.<a href="./org/biojava/naming/ObdaContext.html" title="class in org.biojava.naming">ObdaContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/naming/ObdaContext.html#list(java.lang.String)">list(String)</a></span> - Method in class org.biojava.naming.<a href="./org/biojava/naming/ObdaContext.html" title="class in org.biojava.naming">ObdaContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/naming/ObdaContext.html#listBindings(javax.naming.Name)">listBindings(Name)</a></span> - Method in class org.biojava.naming.<a href="./org/biojava/naming/ObdaContext.html" title="class in org.biojava.naming">ObdaContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/naming/ObdaContext.html#listBindings(java.lang.String)">listBindings(String)</a></span> - Method in class org.biojava.naming.<a href="./org/biojava/naming/ObdaContext.html" title="class in org.biojava.naming">ObdaContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/IndexedChangeHub.ListenerMemento.html#listener">listener</a></span> - Variable in class org.biojava.utils.<a href="./org/biojava/utils/IndexedChangeHub.ListenerMemento.html" title="class in org.biojava.utils">IndexedChangeHub.ListenerMemento</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/AbstractULAlignment.SubULAlignment.html#listIntersection(java.util.List, java.util.List)">listIntersection(List, List)</a></span> - Method in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/AbstractULAlignment.SubULAlignment.html" title="class in org.biojava.bio.alignment">AbstractULAlignment.SubULAlignment</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/stats/svm/ListSumKernel.html" title="class in org.biojava.stats.svm"><span class="strong">ListSumKernel</span></a> - Class in <a href="./org/biojava/stats/svm/package-summary.html">org.biojava.stats.svm</a></dt>
<dd>
<div class="block">This kernel computes the sum of the dot products between items of two lists
at corresponding indexes.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/ListSumKernel.html#ListSumKernel()">ListSumKernel()</a></span> - Constructor for class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/ListSumKernel.html" title="class in org.biojava.stats.svm">ListSumKernel</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/utils/ListTools.html" title="class in org.biojava.utils"><span class="strong">ListTools</span></a> - Class in <a href="./org/biojava/utils/package-summary.html">org.biojava.utils</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ListTools.html#ListTools()">ListTools()</a></span> - Constructor for class org.biojava.utils.<a href="./org/biojava/utils/ListTools.html" title="class in org.biojava.utils">ListTools</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/utils/ListTools.Doublet.html" title="class in org.biojava.utils"><span class="strong">ListTools.Doublet</span></a> - Class in <a href="./org/biojava/utils/package-summary.html">org.biojava.utils</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ListTools.Doublet.html#ListTools.Doublet()">ListTools.Doublet()</a></span> - Constructor for class org.biojava.utils.<a href="./org/biojava/utils/ListTools.Doublet.html" title="class in org.biojava.utils">ListTools.Doublet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ListTools.Doublet.html#ListTools.Doublet(java.lang.Object, java.lang.Object)">ListTools.Doublet(Object, Object)</a></span> - Constructor for class org.biojava.utils.<a href="./org/biojava/utils/ListTools.Doublet.html" title="class in org.biojava.utils">ListTools.Doublet</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/utils/ListTools.Mapper.html" title="interface in org.biojava.utils"><span class="strong">ListTools.Mapper</span></a> - Interface in <a href="./org/biojava/utils/package-summary.html">org.biojava.utils</a></dt>
<dd>
<div class="block">Maps one object to another.</div>
</dd>
<dt><a href="./org/biojava/utils/ListTools.SeriesList.html" title="class in org.biojava.utils"><span class="strong">ListTools.SeriesList</span></a> - Class in <a href="./org/biojava/utils/package-summary.html">org.biojava.utils</a></dt>
<dd>
<div class="block">A list that represents a series of values.</div>
</dd>
<dt><a href="./org/biojava/utils/ListTools.Triplet.html" title="class in org.biojava.utils"><span class="strong">ListTools.Triplet</span></a> - Class in <a href="./org/biojava/utils/package-summary.html">org.biojava.utils</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ListTools.Triplet.html#ListTools.Triplet()">ListTools.Triplet()</a></span> - Constructor for class org.biojava.utils.<a href="./org/biojava/utils/ListTools.Triplet.html" title="class in org.biojava.utils">ListTools.Triplet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ListTools.Triplet.html#ListTools.Triplet(java.lang.Object, java.lang.Object, java.lang.Object)">ListTools.Triplet(Object, Object, Object)</a></span> - Constructor for class org.biojava.utils.<a href="./org/biojava/utils/ListTools.Triplet.html" title="class in org.biojava.utils">ListTools.Triplet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/abi/ABIFChromatogram.html#load(java.io.File)">load(File)</a></span> - Method in class org.biojava.bio.program.abi.<a href="./org/biojava/bio/program/abi/ABIFChromatogram.html" title="class in org.biojava.bio.program.abi">ABIFChromatogram</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/abi/ABIFChromatogram.html#load(java.io.InputStream)">load(InputStream)</a></span> - Method in class org.biojava.bio.program.abi.<a href="./org/biojava/bio/program/abi/ABIFChromatogram.html" title="class in org.biojava.bio.program.abi">ABIFChromatogram</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/scf/SCF.html#load(java.io.File)">load(File)</a></span> - Method in class org.biojava.bio.program.scf.<a href="./org/biojava/bio/program/scf/SCF.html" title="class in org.biojava.bio.program.scf">SCF</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/scf/SCF.html#load(java.io.InputStream, long)">load(InputStream, long)</a></span> - Method in class org.biojava.bio.program.scf.<a href="./org/biojava/bio/program/scf/SCF.html" title="class in org.biojava.bio.program.scf">SCF</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/TypedProperties.html#load(java.lang.String)">load(String)</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/TypedProperties.html" title="class in org.biojava.utils">TypedProperties</a></dt>
<dd>
<div class="block">Reads a property list (key and element pairs) from the file with the given file name.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/TypedProperties.html#load(java.lang.Class, java.lang.String)">load(Class, String)</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/TypedProperties.html" title="class in org.biojava.utils">TypedProperties</a></dt>
<dd>
<div class="block">Reads a property list (key and element pairs) from the given
file which is interpreted as a resource of the given class.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AlphabetManager.html#loadAlphabets(org.xml.sax.InputSource)">loadAlphabets(InputSource)</a></span> - Static method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AlphabetManager.html" title="class in org.biojava.bio.symbol">AlphabetManager</a></dt>
<dd>
<div class="block">Load additional Alphabets, defined in XML format, into the AlphabetManager's registry.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/molbio/RestrictionEnzymeManager.html#loadEnzymeFile(java.io.InputStream, boolean)">loadEnzymeFile(InputStream, boolean)</a></span> - Static method in class org.biojava.bio.molbio.<a href="./org/biojava/bio/molbio/RestrictionEnzymeManager.html" title="class in org.biojava.bio.molbio">RestrictionEnzymeManager</a></dt>
<dd>
<div class="block"><code>loadEnzymeFile</code> loads a new REBASE file (or any file using
REBASE format #31).</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/unigene/FlatFileUnigeneFactory.html#loadUnigene(java.net.URL)">loadUnigene(URL)</a></span> - Method in class org.biojava.bio.program.unigene.<a href="./org/biojava/bio/program/unigene/FlatFileUnigeneFactory.html" title="class in org.biojava.bio.program.unigene">FlatFileUnigeneFactory</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/unigene/SQLUnigeneFactory.html#loadUnigene(java.net.URL)">loadUnigene(URL)</a></span> - Method in class org.biojava.bio.program.unigene.<a href="./org/biojava/bio/program/unigene/SQLUnigeneFactory.html" title="class in org.biojava.bio.program.unigene">SQLUnigeneFactory</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/unigene/UnigeneFactory.html#loadUnigene(java.net.URL)">loadUnigene(URL)</a></span> - Method in interface org.biojava.bio.program.unigene.<a href="./org/biojava/bio/program/unigene/UnigeneFactory.html" title="interface in org.biojava.bio.program.unigene">UnigeneFactory</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/unigene/UnigeneTools.html#loadUnigene(java.net.URL)">loadUnigene(URL)</a></span> - Static method in class org.biojava.bio.program.unigene.<a href="./org/biojava/bio/program/unigene/UnigeneTools.html" title="class in org.biojava.bio.program.unigene">UnigeneTools</a></dt>
<dd>
<div class="block">Load a UnigeneDB instance referred to by a URL.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/SimpleAlignmentElement.html#loc">loc</a></span> - Variable in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/SimpleAlignmentElement.html" title="class in org.biojava.bio.alignment">SimpleAlignmentElement</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html#LOC_ELEMENT_ACC_ATTR">LOC_ELEMENT_ACC_ATTR</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html" title="class in org.biojavax.bio.seq.io">EMBLxmlFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html#LOC_ELEMENT_COMPL_ATTR">LOC_ELEMENT_COMPL_ATTR</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html" title="class in org.biojavax.bio.seq.io">EMBLxmlFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html#LOC_ELEMENT_TYPE_ATTR">LOC_ELEMENT_TYPE_ATTR</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html" title="class in org.biojavax.bio.seq.io">EMBLxmlFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html#LOC_ELEMENT_VER_ATTR">LOC_ELEMENT_VER_ATTR</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html" title="class in org.biojavax.bio.seq.io">EMBLxmlFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.Terms.html#LOC_FUZZY_END_KEY">LOC_FUZZY_END_KEY</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.Terms.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat.Terms</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.Terms.html#LOC_FUZZY_START_KEY">LOC_FUZZY_START_KEY</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.Terms.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat.Terms</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/EditableAlignment.html#LOCATION">LOCATION</a></span> - Static variable in interface org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/EditableAlignment.html" title="interface in org.biojava.bio.alignment">EditableAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/Feature.html#LOCATION">LOCATION</a></span> - Static variable in interface org.biojava.bio.seq.<a href="./org/biojava/bio/seq/Feature.html" title="interface in org.biojava.bio.seq">Feature</a></dt>
<dd>
<div class="block">The location of this feature is being altered.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/Feature.Template.html#location">location</a></span> - Variable in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/Feature.Template.html" title="class in org.biojava.bio.seq">Feature.Template</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/symbol/Location.html" title="interface in org.biojava.bio.symbol"><span class="strong">Location</span></a> - Interface in <a href="./org/biojava/bio/symbol/package-summary.html">org.biojava.bio.symbol</a></dt>
<dd>
<div class="block">A set of integers, often used to represent positions on biological sequences.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichFeature.html#LOCATION">LOCATION</a></span> - Static variable in interface org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichFeature.html" title="interface in org.biojavax.bio.seq">RichFeature</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/RankedDocRef.html#LOCATION">LOCATION</a></span> - Static variable in interface org.biojavax.<a href="./org/biojavax/RankedDocRef.html" title="interface in org.biojavax">RankedDocRef</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#LOCATION_BEGIN_TAG">LOCATION_BEGIN_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html#LOCATION_COMPL_ATTR">LOCATION_COMPL_ATTR</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html" title="class in org.biojavax.bio.seq.io">EMBLxmlFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html#LOCATION_ELEMENT_TAG">LOCATION_ELEMENT_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html" title="class in org.biojavax.bio.seq.io">EMBLxmlFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#LOCATION_END_TAG">LOCATION_END_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#LOCATION_POSITION_ATTR">LOCATION_POSITION_ATTR</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#LOCATION_POSITION_TAG">LOCATION_POSITION_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#LOCATION_SEQ_ATTR">LOCATION_SEQ_ATTR</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html#LOCATION_TAG">LOCATION_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html" title="class in org.biojavax.bio.seq.io">EMBLxmlFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtFormat.html#LOCATION_TAG">LOCATION_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtFormat.html" title="class in org.biojavax.bio.seq.io">UniProtFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#LOCATION_TAG">LOCATION_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html#LOCATION_TYPE_ATTR">LOCATION_TYPE_ATTR</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html" title="class in org.biojavax.bio.seq.io">EMBLxmlFormat</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/xff/LocationHandlerBase.html" title="class in org.biojava.bio.program.xff"><span class="strong">LocationHandlerBase</span></a> - Class in <a href="./org/biojava/bio/program/xff/package-summary.html">org.biojava.bio.program.xff</a></dt>
<dd>
<div class="block">Handler to the XFF location type.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/xff/LocationHandlerBase.html#LocationHandlerBase()">LocationHandlerBase()</a></span> - Constructor for class org.biojava.bio.program.xff.<a href="./org/biojava/bio/program/xff/LocationHandlerBase.html" title="class in org.biojava.bio.program.xff">LocationHandlerBase</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleGappedSymbolList.html#locationToGapped(org.biojava.bio.symbol.Location)">locationToGapped(Location)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleGappedSymbolList.html" title="class in org.biojava.bio.symbol">SimpleGappedSymbolList</a></dt>
<dd>
<div class="block">Translate a Location onto the gapped view, splitting blocks if necessary</div>
</dd>
<dt><a href="./org/biojava/bio/symbol/LocationTools.html" title="class in org.biojava.bio.symbol"><span class="strong">LocationTools</span></a> - Class in <a href="./org/biojava/bio/symbol/package-summary.html">org.biojava.bio.symbol</a></dt>
<dd>
<div class="block">Tools class containing a number of operators for working with <code>Location</code> objects.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLFormat.html#LOCATOR_TAG">LOCATOR_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLFormat.html" title="class in org.biojavax.bio.seq.io">EMBLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html#LOCATOR_TAG">LOCATOR_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html" title="class in org.biojavax.bio.seq.io">EMBLxmlFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#LOCATOR_TAG">LOCATOR_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/AbstractULAlignment.SubULAlignment.html#locInAlignment(java.lang.Object)">locInAlignment(Object)</a></span> - Method in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/AbstractULAlignment.SubULAlignment.html" title="class in org.biojava.bio.alignment">AbstractULAlignment.SubULAlignment</a></dt>
<dd>
<div class="block">The location of an individual SymbolList relative to overall Alignment</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/FlexibleAlignment.html#locInAlignment(java.lang.Object)">locInAlignment(Object)</a></span> - Method in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/FlexibleAlignment.html" title="class in org.biojava.bio.alignment">FlexibleAlignment</a></dt>
<dd>
<div class="block">The location of an individual SymbolList relative to overall Alignment</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/UnequalLengthAlignment.html#locInAlignment(java.lang.Object)">locInAlignment(Object)</a></span> - Method in interface org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/UnequalLengthAlignment.html" title="interface in org.biojava.bio.alignment">UnequalLengthAlignment</a></dt>
<dd>
<div class="block">The location of an individual SymbolList relative to overall Alignment</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/FlexibleAlignment.html#locInSeq(java.lang.Object, org.biojava.bio.symbol.Location)">locInSeq(Object, Location)</a></span> - Method in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/FlexibleAlignment.html" title="class in org.biojava.bio.alignment">FlexibleAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/automata/PatternBlitz.html#lock()">lock()</a></span> - Method in class org.biojava.utils.automata.<a href="./org/biojava/utils/automata/PatternBlitz.html" title="class in org.biojava.utils.automata">PatternBlitz</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/DP.html#lockModel()">lockModel()</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/DP.html" title="class in org.biojava.bio.dp">DP</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/GenbankFormat.html#LOCUS_TAG">LOCUS_TAG</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/GenbankFormat.html" title="class in org.biojava.bio.seq.io">GenbankFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLFormat.html#LOCUS_TAG">LOCUS_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLFormat.html" title="class in org.biojavax.bio.seq.io">EMBLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/GenbankFormat.html#LOCUS_TAG">LOCUS_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/GenbankFormat.html" title="class in org.biojavax.bio.seq.io">GenbankFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/INSDseqFormat.html#LOCUS_TAG">LOCUS_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/INSDseqFormat.html" title="class in org.biojavax.bio.seq.io">INSDseqFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtFormat.html#LOCUS_TAG">LOCUS_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtFormat.html" title="class in org.biojavax.bio.seq.io">UniProtFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/HomologeneBuilder.html#LOCUSID">LOCUSID</a></span> - Static variable in interface org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/HomologeneBuilder.html" title="interface in org.biojava.bio.program.homologene">HomologeneBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/hmmer/HmmerProfileHMM.html#log2(double)">log2(double)</a></span> - Static method in class org.biojava.bio.program.hmmer.<a href="./org/biojava/bio/program/hmmer/HmmerProfileHMM.html" title="class in org.biojava.bio.program.hmmer">HmmerProfileHMM</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/hmmer/ProfileEmissionState.html#log2(double)">log2(double)</a></span> - Static method in class org.biojava.bio.program.hmmer.<a href="./org/biojava/bio/program/hmmer/ProfileEmissionState.html" title="class in org.biojava.bio.program.hmmer">ProfileEmissionState</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ChangeListener.html#LOG_TO_OUT">LOG_TO_OUT</a></span> - Static variable in interface org.biojava.utils.<a href="./org/biojava/utils/ChangeListener.html" title="interface in org.biojava.utils">ChangeListener</a></dt>
<dd>
<div class="block">Convenience implementation that echoes all events to out.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/AlternativeAlignment.html#logger">logger</a></span> - Static variable in class org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/AlternativeAlignment.html" title="class in org.biojava.bio.structure.align.pairwise">AlternativeAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/FragmentJoiner.html#logger">logger</a></span> - Static variable in class org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/FragmentJoiner.html" title="class in org.biojava.bio.structure.align.pairwise">FragmentJoiner</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/AlignmentGui.html#logger">logger</a></span> - Static variable in class org.biojava.bio.structure.gui.<a href="./org/biojava/bio/structure/gui/AlignmentGui.html" title="class in org.biojava.bio.structure.gui">AlignmentGui</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/util/AlignmentCalc.html#logger">logger</a></span> - Static variable in class org.biojava.bio.structure.gui.util.<a href="./org/biojava/bio/structure/gui/util/AlignmentCalc.html" title="class in org.biojava.bio.structure.gui.util">AlignmentCalc</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/util/AlternativeAlignmentFrame.html#logger">logger</a></span> - Static variable in class org.biojava.bio.structure.gui.util.<a href="./org/biojava/bio/structure/gui/util/AlternativeAlignmentFrame.html" title="class in org.biojava.bio.structure.gui.util">AlternativeAlignmentFrame</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/util/PDBDirPanel.html#logger">logger</a></span> - Static variable in class org.biojava.bio.structure.gui.util.<a href="./org/biojava/bio/structure/gui/util/PDBDirPanel.html" title="class in org.biojava.bio.structure.gui.util">PDBDirPanel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/util/PDBServerPanel.html#logger">logger</a></span> - Static variable in class org.biojava.bio.structure.gui.util.<a href="./org/biojava/bio/structure/gui/util/PDBServerPanel.html" title="class in org.biojava.bio.structure.gui.util">PDBServerPanel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/util/PDBUploadPanel.html#logger">logger</a></span> - Static variable in class org.biojava.bio.structure.gui.util.<a href="./org/biojava/bio/structure/gui/util/PDBUploadPanel.html" title="class in org.biojava.bio.structure.gui.util">PDBUploadPanel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/SimpleMMcifConsumer.html#logger">logger</a></span> - Static variable in class org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/SimpleMMcifConsumer.html" title="class in org.biojava.bio.structure.io.mmcif">SimpleMMcifConsumer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/SimpleMMcifParser.html#logger">logger</a></span> - Static variable in class org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/SimpleMMcifParser.html" title="class in org.biojava.bio.structure.io.mmcif">SimpleMMcifParser</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/server/FlatFileInstallation.html#logger">logger</a></span> - Static variable in class org.biojava.bio.structure.server.<a href="./org/biojava/bio/structure/server/FlatFileInstallation.html" title="class in org.biojava.bio.structure.server">FlatFileInstallation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/server/MMCIFFileInstallation.html#logger">logger</a></span> - Static variable in class org.biojava.bio.structure.server.<a href="./org/biojava/bio/structure/server/MMCIFFileInstallation.html" title="class in org.biojava.bio.structure.server">MMCIFFileInstallation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/server/PrepareMMcifIndexFile.html#logger">logger</a></span> - Static variable in class org.biojava.bio.structure.server.<a href="./org/biojava/bio/structure/server/PrepareMMcifIndexFile.html" title="class in org.biojava.bio.structure.server">PrepareMMcifIndexFile</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/server/SimpleStructureServer.html#logger">logger</a></span> - Static variable in class org.biojava.bio.structure.server.<a href="./org/biojava/bio/structure/server/SimpleStructureServer.html" title="class in org.biojava.bio.structure.server">SimpleStructureServer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/StructureTools.html#logger">logger</a></span> - Static variable in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/StructureTools.html" title="class in org.biojava.bio.structure">StructureTools</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/gui/LogoContext.html" title="interface in org.biojava.bio.gui"><span class="strong">LogoContext</span></a> - Interface in <a href="./org/biojava/bio/gui/package-summary.html">org.biojava.bio.gui</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/gui/LogoPainter.html" title="interface in org.biojava.bio.gui"><span class="strong">LogoPainter</span></a> - Interface in <a href="./org/biojava/bio/gui/package-summary.html">org.biojava.bio.gui</a></dt>
<dd>
<div class="block">The interface for something that will draw the sequence logo for a state.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/server/PrepareIndexFile.html#logPDBInfoFile(java.io.PrintWriter, java.io.PrintWriter, org.biojava.bio.structure.io.StructureIOFile, java.io.File[])">logPDBInfoFile(PrintWriter, PrintWriter, StructureIOFile, File[])</a></span> - Method in class org.biojava.bio.structure.server.<a href="./org/biojava/bio/structure/server/PrepareIndexFile.html" title="class in org.biojava.bio.structure.server">PrepareIndexFile</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/hmmer/ProfileEmissionState.html#logProb(org.biojava.bio.symbol.Symbol)">logProb(Symbol)</a></span> - Method in class org.biojava.bio.program.hmmer.<a href="./org/biojava/bio/program/hmmer/ProfileEmissionState.html" title="class in org.biojava.bio.program.hmmer">ProfileEmissionState</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/utils/stax/LongElementHandlerBase.html" title="class in org.biojava.utils.stax"><span class="strong">LongElementHandlerBase</span></a> - Class in <a href="./org/biojava/utils/stax/package-summary.html">org.biojava.utils.stax</a></dt>
<dd>
<div class="block">StAX handler for any element which just contains a string representation of
a long.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/stax/LongElementHandlerBase.html#LongElementHandlerBase()">LongElementHandlerBase()</a></span> - Constructor for class org.biojava.utils.stax.<a href="./org/biojava/utils/stax/LongElementHandlerBase.html" title="class in org.biojava.utils.stax">LongElementHandlerBase</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/regex/Matcher.html#lookingAt()">lookingAt()</a></span> - Method in class org.biojava.utils.regex.<a href="./org/biojava/utils/regex/Matcher.html" title="class in org.biojava.utils.regex">Matcher</a></dt>
<dd>
<div class="block">Attempts to match the input SymbolList, starting at the beginning, against the pattern.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.Option.html#lookup(java.lang.String)">lookup(String)</a></span> - Static method in class org.biojava.bio.chromatogram.graphic.<a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.Option.html" title="class in org.biojava.bio.chromatogram.graphic">ChromatogramGraphic.Option</a></dt>
<dd>
<div class="block">Looks up an <code>Option</code> instance based on its
string description.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/naming/ObdaContext.html#lookup(javax.naming.Name)">lookup(Name)</a></span> - Method in class org.biojava.naming.<a href="./org/biojava/naming/ObdaContext.html" title="class in org.biojava.naming">ObdaContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/naming/ObdaContext.html#lookup(java.lang.String)">lookup(String)</a></span> - Method in class org.biojava.naming.<a href="./org/biojava/naming/ObdaContext.html" title="class in org.biojava.naming">ObdaContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/naming/ObdaContext.html#lookupLink(javax.naming.Name)">lookupLink(Name)</a></span> - Method in class org.biojava.naming.<a href="./org/biojava/naming/ObdaContext.html" title="class in org.biojava.naming">ObdaContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/naming/ObdaContext.html#lookupLink(java.lang.String)">lookupLink(String)</a></span> - Method in class org.biojava.naming.<a href="./org/biojava/naming/ObdaContext.html" title="class in org.biojava.naming">ObdaContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/SimpleMMcifParser.html#LOOP_END">LOOP_END</a></span> - Static variable in class org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/SimpleMMcifParser.html" title="class in org.biojava.bio.structure.io.mmcif">SimpleMMcifParser</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/SimpleMMcifParser.html#LOOP_START">LOOP_START</a></span> - Static variable in class org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/SimpleMMcifParser.html" title="class in org.biojava.bio.structure.io.mmcif">SimpleMMcifParser</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/fastq/FastqVariant.html#lowercaseName()">lowercaseName()</a></span> - Method in enum org.biojava.bio.program.fastq.<a href="./org/biojava/bio/program/fastq/FastqVariant.html" title="enum in org.biojava.bio.program.fastq">FastqVariant</a></dt>
<dd>
<div class="block">Return the name of this FASTQ sequence format variant in <code>lowercase-with-dashes</code> style.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLFormat.html#lp">lp</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLFormat.html" title="class in org.biojavax.bio.seq.io">EMBLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/GenbankFormat.html#lp">lp</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/GenbankFormat.html" title="class in org.biojavax.bio.seq.io">GenbankFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtFormat.html#lp_ipi">lp_ipi</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtFormat.html" title="class in org.biojavax.bio.seq.io">UniProtFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtFormat.html#lp_uniprot">lp_uniprot</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtFormat.html" title="class in org.biojavax.bio.seq.io">UniProtFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLFormat.html#lpPre87">lpPre87</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLFormat.html" title="class in org.biojavax.bio.seq.io">EMBLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOConstants.html#LSID_EMBL_AA">LSID_EMBL_AA</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOConstants.html" title="class in org.biojava.bio.seq.io">SeqIOConstants</a></dt>
<dd>
<div class="block"><code>LSID_EMBL_AA</code> sequence format LSID for EMBL AA.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOConstants.html#LSID_EMBL_DNA">LSID_EMBL_DNA</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOConstants.html" title="class in org.biojava.bio.seq.io">SeqIOConstants</a></dt>
<dd>
<div class="block"><code>LSID_EMBL_DNA</code> sequence format LSID for EMBL DNA.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOConstants.html#LSID_EMBL_RNA">LSID_EMBL_RNA</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOConstants.html" title="class in org.biojava.bio.seq.io">SeqIOConstants</a></dt>
<dd>
<div class="block"><code>LSID_EMBL_RNA</code> sequence format LSID for EMBL RNA.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOConstants.html#LSID_FASTA_AA">LSID_FASTA_AA</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOConstants.html" title="class in org.biojava.bio.seq.io">SeqIOConstants</a></dt>
<dd>
<div class="block"><code>LSID_FASTA_AA</code> sequence format LSID for Fasta AA.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOConstants.html#LSID_FASTA_DNA">LSID_FASTA_DNA</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOConstants.html" title="class in org.biojava.bio.seq.io">SeqIOConstants</a></dt>
<dd>
<div class="block"><code>LSID_FASTA_DNA</code> sequence format LSID for Fasta DNA.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOConstants.html#LSID_FASTA_RNA">LSID_FASTA_RNA</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOConstants.html" title="class in org.biojava.bio.seq.io">SeqIOConstants</a></dt>
<dd>
<div class="block"><code>LSID_FASTA_RNA</code> sequence format LSID for Fasta RNA.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOConstants.html#LSID_GENBANK_AA">LSID_GENBANK_AA</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOConstants.html" title="class in org.biojava.bio.seq.io">SeqIOConstants</a></dt>
<dd>
<div class="block"><code>LSID_GENBANK_AA</code> sequence format LSID for Genbank
AA.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOConstants.html#LSID_GENBANK_DNA">LSID_GENBANK_DNA</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOConstants.html" title="class in org.biojava.bio.seq.io">SeqIOConstants</a></dt>
<dd>
<div class="block"><code>LSID_GENBANK_DNA</code> sequence format LSID for Genbank
DNA.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOConstants.html#LSID_GENBANK_RNA">LSID_GENBANK_RNA</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOConstants.html" title="class in org.biojava.bio.seq.io">SeqIOConstants</a></dt>
<dd>
<div class="block"><code>LSID_GENBANK_RNA</code> sequence format LSID for Genbank
RNA.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOConstants.html#LSID_SWISSPROT">LSID_SWISSPROT</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOConstants.html" title="class in org.biojava.bio.seq.io">SeqIOConstants</a></dt>
<dd>
<div class="block"><code>LSID_SWISSPROT</code> sequence format LSID for Swissprot.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/jama/Matrix.html#lu()">lu()</a></span> - Method in class org.biojava.bio.structure.jama.<a href="./org/biojava/bio/structure/jama/Matrix.html" title="class in org.biojava.bio.structure.jama">Matrix</a></dt>
<dd>
<div class="block">LU Decomposition</div>
</dd>
<dt><a href="./org/biojava/bio/structure/jama/LUDecomposition.html" title="class in org.biojava.bio.structure.jama"><span class="strong">LUDecomposition</span></a> - Class in <a href="./org/biojava/bio/structure/jama/package-summary.html">org.biojava.bio.structure.jama</a></dt>
<dd>
<div class="block">LU Decomposition.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/jama/LUDecomposition.html#LUDecomposition(org.biojava.bio.structure.jama.Matrix)">LUDecomposition(Matrix)</a></span> - Constructor for class org.biojava.bio.structure.jama.<a href="./org/biojava/bio/structure/jama/LUDecomposition.html" title="class in org.biojava.bio.structure.jama">LUDecomposition</a></dt>
<dd>
<div class="block">LU Decomposition provides a data structure to access L, U and piv.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/ProteinTools.html#lys()">lys()</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/ProteinTools.html" title="class in org.biojava.bio.seq">ProteinTools</a></dt>
<dd>
<div class="block">Returns the <code>AtomicSymbol</code> for the amino acid
Lysine (K)</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/Protease.html#LYS_C">LYS_C</a></span> - Static variable in class org.biojava.bio.proteomics.<a href="./org/biojava/bio/proteomics/Protease.html" title="class in org.biojava.bio.proteomics">Protease</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/ProteaseManager.html#LYS_C">LYS_C</a></span> - Static variable in class org.biojava.bio.proteomics.<a href="./org/biojava/bio/proteomics/ProteaseManager.html" title="class in org.biojava.bio.proteomics">ProteaseManager</a></dt>
<dd> </dd>
</dl>
<a name="_M_">
<!-- -->
</a>
<h2 class="title">M</h2>
<dl>
<dt><span class="strong"><a href="./org/biojava/bio/seq/DNATools.html#m()">m()</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/DNATools.html" title="class in org.biojava.bio.seq">DNATools</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/NucleotideTools.html#m()">m()</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/NucleotideTools.html" title="class in org.biojava.bio.seq">NucleotideTools</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/ProteinTools.html#m()">m()</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/ProteinTools.html" title="class in org.biojava.bio.seq">ProteinTools</a></dt>
<dd>
<div class="block">Returns the <code>AtomicSymbol</code> for the amino acid
Methionine</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/Taxon.html#M_MUSCULUS">M_MUSCULUS</a></span> - Static variable in interface org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/Taxon.html" title="interface in org.biojava.bio.program.homologene">Taxon</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/Taxon.html#M_TRUNCULATA">M_TRUNCULATA</a></span> - Static variable in interface org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/Taxon.html" title="interface in org.biojava.bio.program.homologene">Taxon</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/StateMachine.html#MAGICAL_STATE">MAGICAL_STATE</a></span> - Static variable in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/StateMachine.html" title="class in org.biojava.bio.program.tagvalue">StateMachine</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/dp/MagicalState.html" title="class in org.biojava.bio.dp"><span class="strong">MagicalState</span></a> - Class in <a href="./org/biojava/bio/dp/package-summary.html">org.biojava.bio.dp</a></dt>
<dd>
<div class="block">Start/end state for HMMs.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/MarkovModel.html#magicalState()">magicalState()</a></span> - Method in interface org.biojava.bio.dp.<a href="./org/biojava/bio/dp/MarkovModel.html" title="interface in org.biojava.bio.dp">MarkovModel</a></dt>
<dd>
<div class="block">The MagicalState for this model.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/SimpleMarkovModel.html#magicalState()">magicalState()</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/SimpleMarkovModel.html" title="class in org.biojava.bio.dp">SimpleMarkovModel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/WMAsMM.html#magicalState()">magicalState()</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/WMAsMM.html" title="class in org.biojava.bio.dp">WMAsMM</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/KnuthMorrisPrattSearch.html#main(java.lang.String[])">main(String[])</a></span> - Static method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/KnuthMorrisPrattSearch.html" title="class in org.biojava.bio.search">KnuthMorrisPrattSearch</a></dt>
<dd>
<div class="block">Demo and Test method</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/SimpleSequenceDBInstallation.html#main(java.lang.String[])">main(String[])</a></span> - Static method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/SimpleSequenceDBInstallation.html" title="class in org.biojava.bio.seq.db">SimpleSequenceDBInstallation</a></dt>
<dd>
<div class="block">Test this class</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/MSFAlignmentFormat.html#main(java.lang.String[])">main(String[])</a></span> - Static method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/MSFAlignmentFormat.html" title="class in org.biojava.bio.seq.io">MSFAlignmentFormat</a></dt>
<dd>
<div class="block">used to quick test the code</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/StructurePairAligner.html#main(java.lang.String[])">main(String[])</a></span> - Static method in class org.biojava.bio.structure.align.<a href="./org/biojava/bio/structure/align/StructurePairAligner.html" title="class in org.biojava.bio.structure.align">StructurePairAligner</a></dt>
<dd>
<div class="block">example usage of this class</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/AlignmentGui.html#main(java.lang.String[])">main(String[])</a></span> - Static method in class org.biojava.bio.structure.gui.<a href="./org/biojava/bio/structure/gui/AlignmentGui.html" title="class in org.biojava.bio.structure.gui">AlignmentGui</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/BiojavaJmol.html#main(java.lang.String[])">main(String[])</a></span> - Static method in class org.biojava.bio.structure.gui.<a href="./org/biojava/bio/structure/gui/BiojavaJmol.html" title="class in org.biojava.bio.structure.gui">BiojavaJmol</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/ScaleableMatrixPanel.html#main(java.lang.String[])">main(String[])</a></span> - Static method in class org.biojava.bio.structure.gui.<a href="./org/biojava/bio/structure/gui/ScaleableMatrixPanel.html" title="class in org.biojava.bio.structure.gui">ScaleableMatrixPanel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/SequenceDisplay.html#main(java.lang.String[])">main(String[])</a></span> - Static method in class org.biojava.bio.structure.gui.<a href="./org/biojava/bio/structure/gui/SequenceDisplay.html" title="class in org.biojava.bio.structure.gui">SequenceDisplay</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/SimpleMMcifParser.html#main(java.lang.String[])">main(String[])</a></span> - Static method in class org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/SimpleMMcifParser.html" title="class in org.biojava.bio.structure.io.mmcif">SimpleMMcifParser</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/MMCIFFileReader.html#main(java.lang.String[])">main(String[])</a></span> - Static method in class org.biojava.bio.structure.io.<a href="./org/biojava/bio/structure/io/MMCIFFileReader.html" title="class in org.biojava.bio.structure.io">MMCIFFileReader</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/PDBFileReader.html#main(java.lang.String[])">main(String[])</a></span> - Static method in class org.biojava.bio.structure.io.<a href="./org/biojava/bio/structure/io/PDBFileReader.html" title="class in org.biojava.bio.structure.io">PDBFileReader</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/server/DemoStructureServer.html#main(java.lang.String[])">main(String[])</a></span> - Static method in class org.biojava.bio.structure.server.<a href="./org/biojava/bio/structure/server/DemoStructureServer.html" title="class in org.biojava.bio.structure.server">DemoStructureServer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/server/PrepareIndexFile.html#main(java.lang.String[])">main(String[])</a></span> - Static method in class org.biojava.bio.structure.server.<a href="./org/biojava/bio/structure/server/PrepareIndexFile.html" title="class in org.biojava.bio.structure.server">PrepareIndexFile</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/server/PrepareMMcifIndexFile.html#main(java.lang.String[])">main(String[])</a></span> - Static method in class org.biojava.bio.structure.server.<a href="./org/biojava/bio/structure/server/PrepareMMcifIndexFile.html" title="class in org.biojava.bio.structure.server">PrepareMMcifIndexFile</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/tools/ClassifierExample.html#main(java.lang.String[])">main(String[])</a></span> - Static method in class org.biojava.stats.svm.tools.<a href="./org/biojava/stats/svm/tools/ClassifierExample.html" title="class in org.biojava.stats.svm.tools">ClassifierExample</a></dt>
<dd>
<div class="block">Entry point for the application.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/tools/Classify.html#main(java.lang.String[])">main(String[])</a></span> - Static method in class org.biojava.stats.svm.tools.<a href="./org/biojava/stats/svm/tools/Classify.html" title="class in org.biojava.stats.svm.tools">Classify</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/tools/Train.html#main(java.lang.String[])">main(String[])</a></span> - Static method in class org.biojava.stats.svm.tools.<a href="./org/biojava/stats/svm/tools/Train.html" title="class in org.biojava.stats.svm.tools">Train</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/tools/TrainRegression.html#main(java.lang.String[])">main(String[])</a></span> - Static method in class org.biojava.stats.svm.tools.<a href="./org/biojava/stats/svm/tools/TrainRegression.html" title="class in org.biojava.stats.svm.tools">TrainRegression</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ExecRunner.html#main(java.lang.String[])">main(String[])</a></span> - Static method in class org.biojava.utils.<a href="./org/biojava/utils/ExecRunner.html" title="class in org.biojava.utils">ExecRunner</a></dt>
<dd>
<div class="block">This is for unit testing of the class.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/io/UncompressInputStream.html#main(java.lang.String[])">main(String[])</a></span> - Static method in class org.biojava.utils.io.<a href="./org/biojava/utils/io/UncompressInputStream.html" title="class in org.biojava.utils.io">UncompressInputStream</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/JDBCPooledDataSource.html#main(java.lang.String[])">main(String[])</a></span> - Static method in class org.biojava.utils.<a href="./org/biojava/utils/JDBCPooledDataSource.html" title="class in org.biojava.utils">JDBCPooledDataSource</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/process/ExternalProcess.html#main(java.lang.String[])">main(String[])</a></span> - Static method in class org.biojava.utils.process.<a href="./org/biojava/utils/process/ExternalProcess.html" title="class in org.biojava.utils.process">ExternalProcess</a></dt>
<dd>
<div class="block">Runs an external program from the command line.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/xml/AppBeanRunner.html#main(java.lang.String[])">main(String[])</a></span> - Static method in class org.biojava.utils.xml.<a href="./org/biojava/utils/xml/AppBeanRunner.html" title="class in org.biojava.utils.xml">AppBeanRunner</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/twohead/CellCalculatorFactoryMaker.html#make(org.biojava.bio.dp.DP)">make(DP)</a></span> - Method in interface org.biojava.bio.dp.twohead.<a href="./org/biojava/bio/dp/twohead/CellCalculatorFactoryMaker.html" title="interface in org.biojava.bio.dp.twohead">CellCalculatorFactoryMaker</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/twohead/DPCompiler.html#make(org.biojava.bio.dp.DP)">make(DP)</a></span> - Method in class org.biojava.bio.dp.twohead.<a href="./org/biojava/bio/dp/twohead/DPCompiler.html" title="class in org.biojava.bio.dp.twohead">DPCompiler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/twohead/DPInterpreter.Maker.html#make(org.biojava.bio.dp.DP)">make(DP)</a></span> - Method in class org.biojava.bio.dp.twohead.<a href="./org/biojava/bio/dp/twohead/DPInterpreter.Maker.html" title="class in org.biojava.bio.dp.twohead">DPInterpreter.Maker</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/ChunkedSymbolListFactory.html#make(org.biojava.bio.seq.io.SymbolReader)">make(SymbolReader)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/ChunkedSymbolListFactory.html" title="class in org.biojava.bio.seq.io">ChunkedSymbolListFactory</a></dt>
<dd>
<div class="block">Method to create a Sequence with a SymbolReader.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/AnnotationFactory.html#makeAnnotation(java.util.Map)">makeAnnotation(Map)</a></span> - Static method in class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/AnnotationFactory.html" title="class in org.biojava.bio.program.ssbind">AnnotationFactory</a></dt>
<dd>
<div class="block"><code>makeAnnotation</code> creates the annotation.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/GenbankSequenceDB.html#makeBatchRequest(java.net.URL, java.util.Set)">makeBatchRequest(URL, Set)</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/GenbankSequenceDB.html" title="class in org.biojava.bio.seq.db">GenbankSequenceDB</a></dt>
<dd>
<div class="block">Create the Http Post Request to fetch (in batch mode) a list of sequence
with Genbank.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/ncbi/GenbankRichSequenceDB.html#makeBatchRequest(java.net.URL, java.util.Set)">makeBatchRequest(URL, Set)</a></span> - Method in class org.biojavax.bio.db.ncbi.<a href="./org/biojavax/bio/db/ncbi/GenbankRichSequenceDB.html" title="class in org.biojavax.bio.db.ncbi">GenbankRichSequenceDB</a></dt>
<dd>
<div class="block">Create the Http Post Request to fetch (in batch mode) a list of sequence
with Genbank.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/ncbi/GenpeptRichSequenceDB.html#makeBatchRequest(java.net.URL, java.util.Set)">makeBatchRequest(URL, Set)</a></span> - Method in class org.biojavax.bio.db.ncbi.<a href="./org/biojavax/bio/db/ncbi/GenpeptRichSequenceDB.html" title="class in org.biojavax.bio.db.ncbi">GenpeptRichSequenceDB</a></dt>
<dd>
<div class="block">Create the Http Post Request to fetch (in batch mode) a list of sequence
with Genbank.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/LocationTools.html#makeCircularLocation(int, int, int)">makeCircularLocation(int, int, int)</a></span> - Static method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/LocationTools.html" title="class in org.biojava.bio.symbol">LocationTools</a></dt>
<dd>
<div class="block">A simple method to generate a RangeLocation wrapped
in a CircularLocation.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/indexdb/BioStoreFactory.html#makeConfigFile(java.io.File)">makeConfigFile(File)</a></span> - Static method in class org.biojava.bio.program.indexdb.<a href="./org/biojava/bio/program/indexdb/BioStoreFactory.html" title="class in org.biojava.bio.program.indexdb">BioStoreFactory</a></dt>
<dd>
<div class="block"><code>makeConfigFile</code> returns a file which represents an
OBDA "config.dat" in the specified index directory.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/GappedRenderer.html#makeContext(org.biojava.bio.gui.sequence.SequenceRenderContext, org.biojava.bio.symbol.RangeLocation)">makeContext(SequenceRenderContext, RangeLocation)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/GappedRenderer.html" title="class in org.biojava.bio.gui.sequence">GappedRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichFeature.Tools.html#makeEmptyFeature()">makeEmptyFeature()</a></span> - Static method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichFeature.Tools.html" title="class in org.biojavax.bio.seq">RichFeature.Tools</a></dt>
<dd>
<div class="block">A way to make a dummy feature</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/regex/PatternFactory.html#makeFactory(org.biojava.bio.symbol.FiniteAlphabet)">makeFactory(FiniteAlphabet)</a></span> - Static method in class org.biojava.utils.regex.<a href="./org/biojava/utils/regex/PatternFactory.html" title="class in org.biojava.utils.regex">PatternFactory</a></dt>
<dd>
<div class="block">Returns a factory for Patterns in the specified Alphabet.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/filterxml/XMLAnnotationTypeHandler.CollectionConstraintHandlerFactory.html#makeHandler(java.lang.String, java.lang.String)">makeHandler(String, String)</a></span> - Method in interface org.biojava.bio.seq.io.filterxml.<a href="./org/biojava/bio/seq/io/filterxml/XMLAnnotationTypeHandler.CollectionConstraintHandlerFactory.html" title="interface in org.biojava.bio.seq.io.filterxml">XMLAnnotationTypeHandler.CollectionConstraintHandlerFactory</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/filterxml/XMLAnnotationTypeHandler.PropertyConstraintHandlerFactory.html#makeHandler(java.lang.String, java.lang.String)">makeHandler(String, String)</a></span> - Method in interface org.biojava.bio.seq.io.filterxml.<a href="./org/biojava/bio/seq/io/filterxml/XMLAnnotationTypeHandler.PropertyConstraintHandlerFactory.html" title="interface in org.biojava.bio.seq.io.filterxml">XMLAnnotationTypeHandler.PropertyConstraintHandlerFactory</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/filterxml/XMLFilterHandler.FilterHandlerFactory.html#makeHandler(java.lang.String, java.lang.String, org.biojava.bio.seq.io.filterxml.XMLFilterHandler)">makeHandler(String, String, XMLFilterHandler)</a></span> - Method in interface org.biojava.bio.seq.io.filterxml.<a href="./org/biojava/bio/seq/io/filterxml/XMLFilterHandler.FilterHandlerFactory.html" title="interface in org.biojava.bio.seq.io.filterxml">XMLFilterHandler.FilterHandlerFactory</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/FeatureLabelRenderer.AnnotationLabelMaker.html#makeLabel(org.biojava.bio.seq.Feature)">makeLabel(Feature)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/FeatureLabelRenderer.AnnotationLabelMaker.html" title="class in org.biojava.bio.gui.sequence">FeatureLabelRenderer.AnnotationLabelMaker</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/FeatureLabelRenderer.LabelMaker.html#makeLabel(org.biojava.bio.seq.Feature)">makeLabel(Feature)</a></span> - Method in interface org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/FeatureLabelRenderer.LabelMaker.html" title="interface in org.biojava.bio.gui.sequence">FeatureLabelRenderer.LabelMaker</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/FeatureLabelRenderer.SourceLabelMaker.html#makeLabel(org.biojava.bio.seq.Feature)">makeLabel(Feature)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/FeatureLabelRenderer.SourceLabelMaker.html" title="class in org.biojava.bio.gui.sequence">FeatureLabelRenderer.SourceLabelMaker</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/FeatureLabelRenderer.TypeLabelMaker.html#makeLabel(org.biojava.bio.seq.Feature)">makeLabel(Feature)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/FeatureLabelRenderer.TypeLabelMaker.html" title="class in org.biojava.bio.gui.sequence">FeatureLabelRenderer.TypeLabelMaker</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/LocationTools.html#makeLocation(int, int)">makeLocation(int, int)</a></span> - Static method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/LocationTools.html" title="class in org.biojava.bio.symbol">LocationTools</a></dt>
<dd>
<div class="block">Return a contiguous Location from min to max.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/twohead/DPCompiler.html#makeName(java.lang.String, org.biojava.bio.dp.MarkovModel)">makeName(String, MarkovModel)</a></span> - Static method in class org.biojava.bio.dp.twohead.<a href="./org/biojava/bio/dp/twohead/DPCompiler.html" title="class in org.biojava.bio.dp.twohead">DPCompiler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/hmmer/HmmerProfileHMM.html#makeNewInsertState(java.lang.String, org.biojava.bio.Annotation, int[], org.biojava.bio.dist.Distribution)">makeNewInsertState(String, Annotation, int[], Distribution)</a></span> - Method in class org.biojava.bio.program.hmmer.<a href="./org/biojava/bio/program/hmmer/HmmerProfileHMM.html" title="class in org.biojava.bio.program.hmmer">HmmerProfileHMM</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/hmmer/HmmerProfileHMM.html#makeNewMatchState(java.lang.String, org.biojava.bio.Annotation, int[], org.biojava.bio.dist.Distribution)">makeNewMatchState(String, Annotation, int[], Distribution)</a></span> - Method in class org.biojava.bio.program.hmmer.<a href="./org/biojava/bio/program/hmmer/HmmerProfileHMM.html" title="class in org.biojava.bio.program.hmmer">HmmerProfileHMM</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/indexdb/BioStoreFactory.html#makePrimaryKeyFile(java.io.File, java.lang.String)">makePrimaryKeyFile(File, String)</a></span> - Static method in class org.biojava.bio.program.indexdb.<a href="./org/biojava/bio/program/indexdb/BioStoreFactory.html" title="class in org.biojava.bio.program.indexdb">BioStoreFactory</a></dt>
<dd>
<div class="block"><code>makePrimaryKeyFile</code> returns a file which represents
an OBDA "key_<primary namespace>.key" primary key file on the
specified index directory.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/projection/ProjectedFeatureHolder.html#makeProjectionSet(org.biojava.bio.seq.FeatureHolder)">makeProjectionSet(FeatureHolder)</a></span> - Method in class org.biojava.bio.seq.projection.<a href="./org/biojava/bio/seq/projection/ProjectedFeatureHolder.html" title="class in org.biojava.bio.seq.projection">ProjectedFeatureHolder</a></dt>
<dd>
<div class="block">Called internally to construct a lightweight projected view of a set of
features</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/ViewSequenceFactory.html#makeQueryViewSequence(java.lang.String)">makeQueryViewSequence(String)</a></span> - Method in class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/ViewSequenceFactory.html" title="class in org.biojava.bio.program.ssbind">ViewSequenceFactory</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/cache/Cache.html#makeReference(java.lang.Object)">makeReference(Object)</a></span> - Method in interface org.biojava.utils.cache.<a href="./org/biojava/utils/cache/Cache.html" title="interface in org.biojava.utils.cache">Cache</a></dt>
<dd>
<div class="block">Construct a temporary reference to an object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/cache/FixedSizeCache.html#makeReference(java.lang.Object)">makeReference(Object)</a></span> - Method in class org.biojava.utils.cache.<a href="./org/biojava/utils/cache/FixedSizeCache.html" title="class in org.biojava.utils.cache">FixedSizeCache</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/cache/SoftReferenceCache.html#makeReference(java.lang.Object)">makeReference(Object)</a></span> - Method in class org.biojava.utils.cache.<a href="./org/biojava/utils/cache/SoftReferenceCache.html" title="class in org.biojava.utils.cache">SoftReferenceCache</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/RichSequenceBuilder.html#makeRichSequence()">makeRichSequence()</a></span> - Method in interface org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/RichSequenceBuilder.html" title="interface in org.biojavax.bio.seq.io">RichSequenceBuilder</a></dt>
<dd>
<div class="block">Build a RichSequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/SimpleRichSequenceBuilder.html#makeRichSequence()">makeRichSequence()</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/SimpleRichSequenceBuilder.html" title="class in org.biojavax.bio.seq.io">SimpleRichSequenceBuilder</a></dt>
<dd>
<div class="block">Build a RichSequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/BlastLikeSearchBuilder.html#makeSearchResult()">makeSearchResult()</a></span> - Method in class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/BlastLikeSearchBuilder.html" title="class in org.biojava.bio.program.ssbind">BlastLikeSearchBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SearchBuilder.html#makeSearchResult()">makeSearchResult()</a></span> - Method in interface org.biojava.bio.search.<a href="./org/biojava/bio/search/SearchBuilder.html" title="interface in org.biojava.bio.search">SearchBuilder</a></dt>
<dd>
<div class="block">The <code>makeSearchResult</code> method returns a
<code>SeqSimilaritySearchResult</code> instance created from
accumulated data.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/indexdb/BioStoreFactory.html#makeSecondaryFile(java.io.File, java.lang.String)">makeSecondaryFile(File, String)</a></span> - Static method in class org.biojava.bio.program.indexdb.<a href="./org/biojava/bio/program/indexdb/BioStoreFactory.html" title="class in org.biojava.bio.program.indexdb">BioStoreFactory</a></dt>
<dd>
<div class="block"><code>makeSecondaryFile</code> returns a file which represents
an OBDA "id_<secondary namespace>.index" secondary key file on
the specified.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SequenceBuilder.html#makeSequence()">makeSequence()</a></span> - Method in interface org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SequenceBuilder.html" title="interface in org.biojava.bio.seq.io">SequenceBuilder</a></dt>
<dd>
<div class="block">Return the Sequence object which has been constructed
by this builder.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SequenceBuilderBase.html#makeSequence()">makeSequence()</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SequenceBuilderBase.html" title="class in org.biojava.bio.seq.io">SequenceBuilderBase</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SequenceBuilderFilter.html#makeSequence()">makeSequence()</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SequenceBuilderFilter.html" title="class in org.biojava.bio.seq.io">SequenceBuilderFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SequenceDBSequenceBuilder.html#makeSequence()">makeSequence()</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SequenceDBSequenceBuilder.html" title="class in org.biojava.bio.seq.io">SequenceDBSequenceBuilder</a></dt>
<dd>
<div class="block">create the sequence</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SimpleAssemblyBuilder.html#makeSequence()">makeSequence()</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SimpleAssemblyBuilder.html" title="class in org.biojava.bio.seq.io">SimpleAssemblyBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SimpleSequenceBuilder.html#makeSequence()">makeSequence()</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SimpleSequenceBuilder.html" title="class in org.biojava.bio.seq.io">SimpleSequenceBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SmartSequenceBuilder.html#makeSequence()">makeSequence()</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SmartSequenceBuilder.html" title="class in org.biojava.bio.seq.io">SmartSequenceBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/RichSequenceBuilder.html#makeSequence()">makeSequence()</a></span> - Method in interface org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/RichSequenceBuilder.html" title="interface in org.biojavax.bio.seq.io">RichSequenceBuilder</a></dt>
<dd>
<div class="block">Return the Sequence object which has been constructed
by this builder.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/SimpleRichSequenceBuilder.html#makeSequence()">makeSequence()</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/SimpleRichSequenceBuilder.html" title="class in org.biojavax.bio.seq.io">SimpleRichSequenceBuilder</a></dt>
<dd>
<div class="block">Return the Sequence object which has been constructed
by this builder.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/EmblProcessor.Factory.html#makeSequenceBuilder()">makeSequenceBuilder()</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/EmblProcessor.Factory.html" title="class in org.biojava.bio.seq.io">EmblProcessor.Factory</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/FastaDescriptionLineParser.Factory.html#makeSequenceBuilder()">makeSequenceBuilder()</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/FastaDescriptionLineParser.Factory.html" title="class in org.biojava.bio.seq.io">FastaDescriptionLineParser.Factory</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/GenbankProcessor.Factory.html#makeSequenceBuilder()">makeSequenceBuilder()</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/GenbankProcessor.Factory.html" title="class in org.biojava.bio.seq.io">GenbankProcessor.Factory</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/GenbankProcessor.Factory.html#makeSequenceBuilder(java.lang.String)">makeSequenceBuilder(String)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/GenbankProcessor.Factory.html" title="class in org.biojava.bio.seq.io">GenbankProcessor.Factory</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/OrganismParser.Factory.html#makeSequenceBuilder()">makeSequenceBuilder()</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/OrganismParser.Factory.html" title="class in org.biojava.bio.seq.io">OrganismParser.Factory</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/ProteinRefSeqProcessor.Factory.html#makeSequenceBuilder()">makeSequenceBuilder()</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/ProteinRefSeqProcessor.Factory.html" title="class in org.biojava.bio.seq.io">ProteinRefSeqProcessor.Factory</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SequenceBuilderFactory.html#makeSequenceBuilder()">makeSequenceBuilder()</a></span> - Method in interface org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SequenceBuilderFactory.html" title="interface in org.biojava.bio.seq.io">SequenceBuilderFactory</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SwissprotProcessor.Factory.html#makeSequenceBuilder()">makeSequenceBuilder()</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SwissprotProcessor.Factory.html" title="class in org.biojava.bio.seq.io">SwissprotProcessor.Factory</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SwissprotProcessor.Factory.html#makeSequenceBuilder(java.lang.String)">makeSequenceBuilder(String)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SwissprotProcessor.Factory.html" title="class in org.biojava.bio.seq.io">SwissprotProcessor.Factory</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/SimpleRichSequenceBuilderFactory.html#makeSequenceBuilder()">makeSequenceBuilder()</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/SimpleRichSequenceBuilderFactory.html" title="class in org.biojavax.bio.seq.io">SimpleRichSequenceBuilderFactory</a></dt>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/ViewSequenceFactory.html#makeSubjectViewSequence(java.lang.String)">makeSubjectViewSequence(String)</a></span> - Method in class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/ViewSequenceFactory.html" title="class in org.biojava.bio.program.ssbind">ViewSequenceFactory</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/ChunkedSymbolListFactory.html#makeSymbolList()">makeSymbolList()</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/ChunkedSymbolListFactory.html" title="class in org.biojava.bio.seq.io">ChunkedSymbolListFactory</a></dt>
<dd>
<div class="block">Converts accumulated Symbols to a SymbolList</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/PackedSymbolListFactory.html#makeSymbolList(org.biojava.bio.symbol.Symbol[], int, org.biojava.bio.symbol.Alphabet)">makeSymbolList(Symbol[], int, Alphabet)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/PackedSymbolListFactory.html" title="class in org.biojava.bio.symbol">PackedSymbolListFactory</a></dt>
<dd>
<div class="block">Makes a packed SymbolList out of a list of Symbols.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleSymbolListFactory.html#makeSymbolList(org.biojava.bio.symbol.Symbol[], int, org.biojava.bio.symbol.Alphabet)">makeSymbolList(Symbol[], int, Alphabet)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleSymbolListFactory.html" title="class in org.biojava.bio.symbol">SimpleSymbolListFactory</a></dt>
<dd>
<div class="block">Create a factory for SimpleSymbolLists.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SymbolListFactory.html#makeSymbolList(org.biojava.bio.symbol.Symbol[], int, org.biojava.bio.symbol.Alphabet)">makeSymbolList(Symbol[], int, Alphabet)</a></span> - Method in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SymbolListFactory.html" title="interface in org.biojava.bio.symbol">SymbolListFactory</a></dt>
<dd>
<div class="block">makes a SymbolList containing size Symbols from a Symbol array.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/Feature.html#makeTemplate()">makeTemplate()</a></span> - Method in interface org.biojava.bio.seq.<a href="./org/biojava/bio/seq/Feature.html" title="interface in org.biojava.bio.seq">Feature</a></dt>
<dd>
<div class="block">Create a new Template that could be used to generate a feature identical
to this one.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleFeature.html#makeTemplate()">makeTemplate()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleFeature.html" title="class in org.biojava.bio.seq.impl">SimpleFeature</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleFramedFeature.html#makeTemplate()">makeTemplate()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleFramedFeature.html" title="class in org.biojava.bio.seq.impl">SimpleFramedFeature</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleHomologyFeature.html#makeTemplate()">makeTemplate()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleHomologyFeature.html" title="class in org.biojava.bio.seq.impl">SimpleHomologyFeature</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleRemoteFeature.html#makeTemplate()">makeTemplate()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleRemoteFeature.html" title="class in org.biojava.bio.seq.impl">SimpleRemoteFeature</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleSimilarityPairFeature.html#makeTemplate()">makeTemplate()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleSimilarityPairFeature.html" title="class in org.biojava.bio.seq.impl">SimpleSimilarityPairFeature</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleStrandedFeature.html#makeTemplate()">makeTemplate()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleStrandedFeature.html" title="class in org.biojava.bio.seq.impl">SimpleStrandedFeature</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/TemplateUtils.html#makeTemplate(org.biojava.bio.seq.Feature)">makeTemplate(Feature)</a></span> - Static method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/TemplateUtils.html" title="class in org.biojava.bio.seq.impl">TemplateUtils</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/projection/ProjectedFeature.html#makeTemplate()">makeTemplate()</a></span> - Method in class org.biojava.bio.seq.projection.<a href="./org/biojava/bio/seq/projection/ProjectedFeature.html" title="class in org.biojava.bio.seq.projection">ProjectedFeature</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichFeature.html#makeTemplate()">makeTemplate()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichFeature.html" title="class in org.biojavax.bio.seq">SimpleRichFeature</a></dt>
<dd>
<div class="block">Create a new Template that could be used to generate a feature identical
to this one.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/CodonPrefTools.html#MAN_NUCLEAR">MAN_NUCLEAR</a></span> - Static variable in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/CodonPrefTools.html" title="class in org.biojava.bio.symbol">CodonPrefTools</a></dt>
<dd>
<div class="block">Homo sapiens codon preferences</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AgaveWriter.html#mAnnotFilter">mAnnotFilter</a></span> - Variable in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AgaveWriter.html" title="class in org.biojava.bio.seq.io.agave">AgaveWriter</a></dt>
<dd>
<div class="block">The AnnotationMap to use for getting
AGAVE XML attributes from a Sequence Annotation.</div>
</dd>
<dt><a href="./org/biojava/bio/symbol/ManyToOneTranslationTable.html" title="interface in org.biojava.bio.symbol"><span class="strong">ManyToOneTranslationTable</span></a> - Interface in <a href="./org/biojava/bio/symbol/package-summary.html">org.biojava.bio.symbol</a></dt>
<dd>
<div class="block">A translation table that will handle the many-to-one mappings
that you see, for example, with genetic codes.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/RelabeledAlignment.html#map(java.util.Set)">map(Set)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/RelabeledAlignment.html" title="class in org.biojava.bio.symbol">RelabeledAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/RelabeledAlignment.html#map(java.lang.Object)">map(Object)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/RelabeledAlignment.html" title="class in org.biojava.bio.symbol">RelabeledAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ListTools.Mapper.html#map(java.lang.Object)">map(Object)</a></span> - Method in interface org.biojava.utils.<a href="./org/biojava/utils/ListTools.Mapper.html" title="interface in org.biojava.utils">ListTools.Mapper</a></dt>
<dd>
<div class="block">Map the object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/ListTools.html#mapList(java.util.List, org.biojava.utils.ListTools.Mapper)">mapList(List, ListTools.Mapper)</a></span> - Static method in class org.biojava.utils.<a href="./org/biojava/utils/ListTools.html" title="class in org.biojava.utils">ListTools</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleGappedSequence.GappedContext.html#mapLocation(org.biojava.bio.symbol.Location)">mapLocation(Location)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleGappedSequence.GappedContext.html" title="class in org.biojava.bio.seq.impl">SimpleGappedSequence.GappedContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ListTools.html#mapMap(java.util.Map, org.biojava.utils.ListTools.Mapper, org.biojava.utils.ListTools.Mapper)">mapMap(Map, ListTools.Mapper, ListTools.Mapper)</a></span> - Static method in class org.biojava.utils.<a href="./org/biojava/utils/ListTools.html" title="class in org.biojava.utils">ListTools</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/ssaha/MappedDataStoreFactory.html" title="class in org.biojava.bio.program.ssaha"><span class="strong">MappedDataStoreFactory</span></a> - Class in <a href="./org/biojava/bio/program/ssaha/package-summary.html">org.biojava.bio.program.ssaha</a></dt>
<dd>
<div class="block">
Builder for a data store that is backed by a java.nio.MappedByteBuffer.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssaha/MappedDataStoreFactory.html#MappedDataStoreFactory()">MappedDataStoreFactory()</a></span> - Constructor for class org.biojava.bio.program.ssaha.<a href="./org/biojava/bio/program/ssaha/MappedDataStoreFactory.html" title="class in org.biojava.bio.program.ssaha">MappedDataStoreFactory</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ListTools.html#mapSet(java.util.Set, org.biojava.utils.ListTools.Mapper)">mapSet(Set, ListTools.Mapper)</a></span> - Static method in class org.biojava.utils.<a href="./org/biojava/utils/ListTools.html" title="class in org.biojava.utils">ListTools</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/io/CountedBufferedReader.html#mark(int)">mark(int)</a></span> - Method in class org.biojava.utils.io.<a href="./org/biojava/utils/io/CountedBufferedReader.html" title="class in org.biojava.utils.io">CountedBufferedReader</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/dp/MarkovModel.html" title="interface in org.biojava.bio.dp"><span class="strong">MarkovModel</span></a> - Interface in <a href="./org/biojava/bio/dp/package-summary.html">org.biojava.bio.dp</a></dt>
<dd>
<div class="block">A markov model.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/io/CountedBufferedReader.html#markSupported()">markSupported()</a></span> - Method in class org.biojava.utils.io.<a href="./org/biojava/utils/io/CountedBufferedReader.html" title="class in org.biojava.utils.io">CountedBufferedReader</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/io/UncompressInputStream.html#markSupported()">markSupported()</a></span> - Method in class org.biojava.utils.io.<a href="./org/biojava/utils/io/UncompressInputStream.html" title="class in org.biojava.utils.io">UncompressInputStream</a></dt>
<dd>
<div class="block">This stream does not support mark/reset on the stream.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SoftMaskedAlphabet.MaskingDetector.DefaultMaskingDetector.html#mask(java.lang.String)">mask(String)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SoftMaskedAlphabet.MaskingDetector.DefaultMaskingDetector.html" title="class in org.biojava.bio.symbol">SoftMaskedAlphabet.MaskingDetector.DefaultMaskingDetector</a></dt>
<dd>
<div class="block">Masks a token by making it lowercase</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SoftMaskedAlphabet.MaskingDetector.html#mask(java.lang.String)">mask(String)</a></span> - Method in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SoftMaskedAlphabet.MaskingDetector.html" title="interface in org.biojava.bio.symbol">SoftMaskedAlphabet.MaskingDetector</a></dt>
<dd>
<div class="block">Present the token for a <code>Symbol</code> as it would appear if masked</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/SequenceTools.html#maskSequence(org.biojava.bio.seq.Sequence, org.biojava.bio.symbol.RangeLocation)">maskSequence(Sequence, RangeLocation)</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/SequenceTools.html" title="class in org.biojava.bio.seq">SequenceTools</a></dt>
<dd>
<div class="block">Mask of a sequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html#MASS_SPECTROMETRY">MASS_SPECTROMETRY</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html" title="class in org.biojavax.bio.seq.io">UniProtCommentParser</a></dt>
<dd>
<div class="block">A name for a comment type.</div>
</dd>
<dt><a href="./org/biojava/bio/proteomics/MassCalc.html" title="class in org.biojava.bio.proteomics"><span class="strong">MassCalc</span></a> - Class in <a href="./org/biojava/bio/proteomics/package-summary.html">org.biojava.bio.proteomics</a></dt>
<dd>
<div class="block"><code>MassCalc</code> calculates the mass of peptides which for our
purposes are <code>SymbolList</code>s which contain
<code>Symbol</code>sfrom the protein <code>Alphabet</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/MassCalc.html#MassCalc(java.lang.String, boolean)">MassCalc(String, boolean)</a></span> - Constructor for class org.biojava.bio.proteomics.<a href="./org/biojava/bio/proteomics/MassCalc.html" title="class in org.biojava.bio.proteomics">MassCalc</a></dt>
<dd>
<div class="block">Creates a new <code>MassCalc</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/BioPattern.html#matcher(org.biojava.bio.symbol.SymbolList)">matcher(SymbolList)</a></span> - Method in interface org.biojava.bio.search.<a href="./org/biojava/bio/search/BioPattern.html" title="interface in org.biojava.bio.search">BioPattern</a></dt>
<dd>
<div class="block">Get a matcher that will use these parameters to search a SymbolList.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/MaxMismatchPattern.html#matcher(org.biojava.bio.symbol.SymbolList)">matcher(SymbolList)</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/MaxMismatchPattern.html" title="class in org.biojava.bio.search">MaxMismatchPattern</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SeqContentPattern.html#matcher(org.biojava.bio.symbol.SymbolList)">matcher(SymbolList)</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SeqContentPattern.html" title="class in org.biojava.bio.search">SeqContentPattern</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/utils/regex/Matcher.html" title="class in org.biojava.utils.regex"><span class="strong">Matcher</span></a> - Class in <a href="./org/biojava/utils/regex/package-summary.html">org.biojava.utils.regex</a></dt>
<dd>
<div class="block">This class is analogous to java.util.Matcher except that it works
on SymbolLists instead of Strings.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/regex/Pattern.html#matcher(org.biojava.bio.symbol.SymbolList)">matcher(SymbolList)</a></span> - Method in class org.biojava.utils.regex.<a href="./org/biojava/utils/regex/Pattern.html" title="class in org.biojava.utils.regex">Pattern</a></dt>
<dd>
<div class="block">Creates a matcher that will match the given input against this pattern.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/regex/Matcher.html#matches()">matches()</a></span> - Method in class org.biojava.utils.regex.<a href="./org/biojava/utils/regex/Matcher.html" title="class in org.biojava.utils.regex">Matcher</a></dt>
<dd>
<div class="block">Attempts to match the entire input sequence against the pattern.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/ChangeType.html#matchingTypes()">matchingTypes()</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/ChangeType.html" title="class in org.biojava.utils">ChangeType</a></dt>
<dd>
<div class="block">Return an iterator which contains this type, and all supertypes.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/BaumWelchTrainer.html#mathExp(double)">mathExp(double)</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/BaumWelchTrainer.html" title="class in org.biojava.bio.dp">BaumWelchTrainer</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/structure/jama/Maths.html" title="class in org.biojava.bio.structure.jama"><span class="strong">Maths</span></a> - Class in <a href="./org/biojava/bio/structure/jama/package-summary.html">org.biojava.bio.structure.jama</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/jama/Maths.html#Maths()">Maths()</a></span> - Constructor for class org.biojava.bio.structure.jama.<a href="./org/biojava/bio/structure/jama/Maths.html" title="class in org.biojava.bio.structure.jama">Maths</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/SubstitutionMatrix.html#matrix">matrix</a></span> - Variable in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/SubstitutionMatrix.html" title="class in org.biojava.bio.alignment">SubstitutionMatrix</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/structure/jama/Matrix.html" title="class in org.biojava.bio.structure.jama"><span class="strong">Matrix</span></a> - Class in <a href="./org/biojava/bio/structure/jama/package-summary.html">org.biojava.bio.structure.jama</a></dt>
<dd>
<div class="block">Jama = Java Matrix class.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/jama/Matrix.html#Matrix(int, int)">Matrix(int, int)</a></span> - Constructor for class org.biojava.bio.structure.jama.<a href="./org/biojava/bio/structure/jama/Matrix.html" title="class in org.biojava.bio.structure.jama">Matrix</a></dt>
<dd>
<div class="block">Construct an m-by-n matrix of zeros.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/jama/Matrix.html#Matrix(int, int, double)">Matrix(int, int, double)</a></span> - Constructor for class org.biojava.bio.structure.jama.<a href="./org/biojava/bio/structure/jama/Matrix.html" title="class in org.biojava.bio.structure.jama">Matrix</a></dt>
<dd>
<div class="block">Construct an m-by-n constant matrix.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/jama/Matrix.html#Matrix(double[][])">Matrix(double[][])</a></span> - Constructor for class org.biojava.bio.structure.jama.<a href="./org/biojava/bio/structure/jama/Matrix.html" title="class in org.biojava.bio.structure.jama">Matrix</a></dt>
<dd>
<div class="block">Construct a matrix from a 2-D array.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/jama/Matrix.html#Matrix(double[][], int, int)">Matrix(double[][], int, int)</a></span> - Constructor for class org.biojava.bio.structure.jama.<a href="./org/biojava/bio/structure/jama/Matrix.html" title="class in org.biojava.bio.structure.jama">Matrix</a></dt>
<dd>
<div class="block">Construct a matrix quickly without checking arguments.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/jama/Matrix.html#Matrix(double[], int)">Matrix(double[], int)</a></span> - Constructor for class org.biojava.bio.structure.jama.<a href="./org/biojava/bio/structure/jama/Matrix.html" title="class in org.biojava.bio.structure.jama">Matrix</a></dt>
<dd>
<div class="block">Construct a matrix from a one-dimensional packed array</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Calc.html#matrixFromEuler(double, double, double)">matrixFromEuler(double, double, double)</a></span> - Static method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Calc.html" title="class in org.biojava.bio.structure">Calc</a></dt>
<dd>
<div class="block">This conversion uses NASA standard aeroplane conventions as described on page:
http://www.euclideanspace.com/maths/geometry/rotations/euler/index.htm
Coordinate System: right hand
Positive angle: right hand
Order of euler angles: heading first, then attitude, then bank.</div>
</dd>
<dt><a href="./org/biojava/bio/dp/twohead/MatrixPairDPCursor.html" title="class in org.biojava.bio.dp.twohead"><span class="strong">MatrixPairDPCursor</span></a> - Class in <a href="./org/biojava/bio/dp/twohead/package-summary.html">org.biojava.bio.dp.twohead</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/twohead/MatrixPairDPCursor.html#MatrixPairDPCursor(org.biojava.bio.symbol.SymbolList, org.biojava.bio.symbol.SymbolList, int, int, org.biojava.bio.dp.twohead.PairDPMatrix, org.biojava.bio.dp.twohead.EmissionCache)">MatrixPairDPCursor(SymbolList, SymbolList, int, int, PairDPMatrix, EmissionCache)</a></span> - Constructor for class org.biojava.bio.dp.twohead.<a href="./org/biojava/bio/dp/twohead/MatrixPairDPCursor.html" title="class in org.biojava.bio.dp.twohead">MatrixPairDPCursor</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/SubstitutionMatrix.html#max">max</a></span> - Variable in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/SubstitutionMatrix.html" title="class in org.biojava.bio.alignment">SubstitutionMatrix</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AbstractSymbolList.EditScreener.html#max">max</a></span> - Variable in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AbstractSymbolList.EditScreener.html" title="class in org.biojava.bio.symbol">AbstractSymbolList.EditScreener</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/AlphaCTools.html#MAX_ANGLE">MAX_ANGLE</a></span> - Static variable in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/AlphaCTools.html" title="class in org.biojava.bio.structure">AlphaCTools</a></dt>
<dd>
<div class="block">MAX_ANGLE .</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/PDBFileParser.html#MAX_ATOMS">MAX_ATOMS</a></span> - Static variable in class org.biojava.bio.structure.io.<a href="./org/biojava/bio/structure/io/PDBFileParser.html" title="class in org.biojava.bio.structure.io">PDBFileParser</a></dt>
<dd>
<div class="block">the maximum number of atoms we will add to a structure
this protects from memory overflows in the few really big protein structures.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ga/functions/CrossOverFunction.html#MAX_CROSSES">MAX_CROSSES</a></span> - Static variable in interface org.biojavax.ga.functions.<a href="./org/biojavax/ga/functions/CrossOverFunction.html" title="interface in org.biojavax.ga.functions">CrossOverFunction</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/SequenceDisplay.html#MAX_SCALE">MAX_SCALE</a></span> - Static variable in class org.biojava.bio.structure.gui.<a href="./org/biojava/bio/structure/gui/SequenceDisplay.html" title="class in org.biojava.bio.structure.gui">SequenceDisplay</a></dt>
<dd>
<div class="block">the maximum value that the scale can get</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/SparseVector.html#maxIndex()">maxIndex()</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/SparseVector.html" title="class in org.biojava.stats.svm">SparseVector</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SuffixTree.html#maxLength()">maxLength()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SuffixTree.html" title="class in org.biojava.bio.symbol">SuffixTree</a></dt>
<dd>
<div class="block">Return the length of the longest motif represented in this
SuffixTree</div>
</dd>
<dt><a href="./org/biojava/bio/search/MaxMismatchMatcher.html" title="class in org.biojava.bio.search"><span class="strong">MaxMismatchMatcher</span></a> - Class in <a href="./org/biojava/bio/search/package-summary.html">org.biojava.bio.search</a></dt>
<dd>
<div class="block">A BioMatcher class returned by MaxMismatchPattern.matcher() that implements
searching of a SymbolList.</div>
</dd>
<dt><a href="./org/biojava/bio/search/MaxMismatchPattern.html" title="class in org.biojava.bio.search"><span class="strong">MaxMismatchPattern</span></a> - Class in <a href="./org/biojava/bio/search/package-summary.html">org.biojava.bio.search</a></dt>
<dd>
<div class="block">This class permits searching a SymbolList with another SymbolList while
permitting a specified number of mismatches.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/MaxMismatchPattern.html#MaxMismatchPattern()">MaxMismatchPattern()</a></span> - Constructor for class org.biojava.bio.search.<a href="./org/biojava/bio/search/MaxMismatchPattern.html" title="class in org.biojava.bio.search">MaxMismatchPattern</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/MaxMismatchPattern.html#MaxMismatchPattern(org.biojava.bio.symbol.SymbolList, int)">MaxMismatchPattern(SymbolList, int)</a></span> - Constructor for class org.biojava.bio.search.<a href="./org/biojava/bio/search/MaxMismatchPattern.html" title="class in org.biojava.bio.search">MaxMismatchPattern</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.Terms.html#MEDLINE_KEY">MEDLINE_KEY</a></span> - Static variable in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.Terms.html" title="class in org.biojavax.bio.seq">RichSequence.Terms</a></dt>
<dd>
<div class="block">Holds a reference to the key that must be used to store Medline
references.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/GenbankFormat.html#MEDLINE_TAG">MEDLINE_TAG</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/GenbankFormat.html" title="class in org.biojava.bio.seq.io">GenbankFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/GenbankFormat.html#MEDLINE_TAG">MEDLINE_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/GenbankFormat.html" title="class in org.biojavax.bio.seq.io">GenbankFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/CompoundRichLocation.html#members">members</a></span> - Variable in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/CompoundRichLocation.html" title="class in org.biojavax.bio.seq">CompoundRichLocation</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/Meme.html" title="class in org.biojava.bio.program"><span class="strong">Meme</span></a> - Class in <a href="./org/biojava/bio/program/package-summary.html">org.biojava.bio.program</a></dt>
<dd>
<div class="block">The results of a meme run.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/Meme.html#Meme(java.io.InputStream, org.biojava.bio.seq.io.SymbolTokenization)">Meme(InputStream, SymbolTokenization)</a></span> - Constructor for class org.biojava.bio.program.<a href="./org/biojava/bio/program/Meme.html" title="class in org.biojava.bio.program">Meme</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/structure/gui/util/MenuCreator.html" title="class in org.biojava.bio.structure.gui.util"><span class="strong">MenuCreator</span></a> - Class in <a href="./org/biojava/bio/structure/gui/util/package-summary.html">org.biojava.bio.structure.gui.util</a></dt>
<dd>
<div class="block">Create the menu for BiojavaJmol</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/util/MenuCreator.html#MenuCreator()">MenuCreator()</a></span> - Constructor for class org.biojava.bio.structure.gui.util.<a href="./org/biojava/bio/structure/gui/util/MenuCreator.html" title="class in org.biojava.bio.structure.gui.util">MenuCreator</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/MergingSet.html#merge(java.util.Set, java.util.Set)">merge(Set, Set)</a></span> - Static method in class org.biojava.utils.<a href="./org/biojava/utils/MergingSet.html" title="class in org.biojava.utils">MergingSet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichLocation.Tools.html#merge(java.util.Collection)">merge(Collection<Location>)</a></span> - Static method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichLocation.Tools.html" title="class in org.biojavax.bio.seq">RichLocation.Tools</a></dt>
<dd>
<div class="block">Takes a set of locations and tries to merge all pairs where the union
operation results in a simple rich location, not a compound one.</div>
</dd>
<dt><a href="./org/biojava/bio/MergeAnnotation.html" title="class in org.biojava.bio"><span class="strong">MergeAnnotation</span></a> - Class in <a href="./org/biojava/bio/package-summary.html">org.biojava.bio</a></dt>
<dd>
<div class="block">Merged view onto a list of underlying Annotation objects.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/MergeAnnotation.html#MergeAnnotation()">MergeAnnotation()</a></span> - Constructor for class org.biojava.bio.<a href="./org/biojava/bio/MergeAnnotation.html" title="class in org.biojava.bio">MergeAnnotation</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/MergeAnnotation.PropertyForwarder.html" title="class in org.biojava.bio"><span class="strong">MergeAnnotation.PropertyForwarder</span></a> - Class in <a href="./org/biojava/bio/package-summary.html">org.biojava.bio</a></dt>
<dd>
<div class="block">Listener used to forward changes for any of the underlying annotations to
listeners on this annotation.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/MergeAnnotation.PropertyForwarder.html#MergeAnnotation.PropertyForwarder(java.lang.Object, org.biojava.utils.ChangeSupport)">MergeAnnotation.PropertyForwarder(Object, ChangeSupport)</a></span> - Constructor for class org.biojava.bio.<a href="./org/biojava/bio/MergeAnnotation.PropertyForwarder.html" title="class in org.biojava.bio">MergeAnnotation.PropertyForwarder</a></dt>
<dd>
<div class="block">Create a new forwarder on behalf of a source using the change support.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/MergeFeatureHolder.html" title="class in org.biojava.bio.seq"><span class="strong">MergeFeatureHolder</span></a> - Class in <a href="./org/biojava/bio/seq/package-summary.html">org.biojava.bio.seq</a></dt>
<dd>
<div class="block">FeatureHolder which exposes all the features in a set
of sub-FeatureHolders.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/MergeFeatureHolder.html#MergeFeatureHolder()">MergeFeatureHolder()</a></span> - Constructor for class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/MergeFeatureHolder.html" title="class in org.biojava.bio.seq">MergeFeatureHolder</a></dt>
<dd>
<div class="block">Create a new, empty, MergeFeatureHolder.</div>
</dd>
<dt><a href="./org/biojava/bio/symbol/MergeLocation.html" title="class in org.biojava.bio.symbol"><span class="strong">MergeLocation</span></a> - Class in <a href="./org/biojava/bio/symbol/package-summary.html">org.biojava.bio.symbol</a></dt>
<dd>
<div class="block">Produced by LocationTools as a result of union operations.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/MergeLocation.html#mergeLocations(java.util.List)">mergeLocations(List)</a></span> - Static method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/MergeLocation.html" title="class in org.biojava.bio.symbol">MergeLocation</a></dt>
<dd>
<div class="block">Static Factory method for getting an instance of a <code>MergeLocation</code></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/MergeLocation.html#mergeLocations(org.biojava.bio.symbol.Location, org.biojava.bio.symbol.Location)">mergeLocations(Location, Location)</a></span> - Static method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/MergeLocation.html" title="class in org.biojava.bio.symbol">MergeLocation</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/annodb/MergingAnnotationDB.html" title="class in org.biojava.bio.annodb"><span class="strong">MergingAnnotationDB</span></a> - Class in <a href="./org/biojava/bio/annodb/package-summary.html">org.biojava.bio.annodb</a></dt>
<dd>
<div class="block">An AnnotationDB that provides a merged view of a list of underlying DBs.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/annodb/MergingAnnotationDB.html#MergingAnnotationDB(java.lang.String)">MergingAnnotationDB(String)</a></span> - Constructor for class org.biojava.bio.annodb.<a href="./org/biojava/bio/annodb/MergingAnnotationDB.html" title="class in org.biojava.bio.annodb">MergingAnnotationDB</a></dt>
<dd>
<div class="block">Create a new MergingAnnotationDB with a name and no DBs to merge.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/annodb/MergingAnnotationDB.html#MergingAnnotationDB(java.lang.String, java.util.List)">MergingAnnotationDB(String, List)</a></span> - Constructor for class org.biojava.bio.annodb.<a href="./org/biojava/bio/annodb/MergingAnnotationDB.html" title="class in org.biojava.bio.annodb">MergingAnnotationDB</a></dt>
<dd>
<div class="block">Create a new MergingAnnotationDB with a name and a list of DBs to merge.</div>
</dd>
<dt><a href="./org/biojava/utils/MergingIterator.html" title="class in org.biojava.utils"><span class="strong">MergingIterator</span></a> - Class in <a href="./org/biojava/utils/package-summary.html">org.biojava.utils</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/MergingIterator.html#MergingIterator(java.util.Iterator)">MergingIterator(Iterator)</a></span> - Constructor for class org.biojava.utils.<a href="./org/biojava/utils/MergingIterator.html" title="class in org.biojava.utils">MergingIterator</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/utils/MergingSet.html" title="class in org.biojava.utils"><span class="strong">MergingSet</span></a> - Class in <a href="./org/biojava/utils/package-summary.html">org.biojava.utils</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/MergingSet.html#MergingSet()">MergingSet()</a></span> - Constructor for class org.biojava.utils.<a href="./org/biojava/utils/MergingSet.html" title="class in org.biojava.utils">MergingSet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/MergingSet.html#MergingSet(java.util.Set)">MergingSet(Set)</a></span> - Constructor for class org.biojava.utils.<a href="./org/biojava/utils/MergingSet.html" title="class in org.biojava.utils">MergingSet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/ProteinTools.html#met()">met()</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/ProteinTools.html" title="class in org.biojava.bio.seq">ProteinTools</a></dt>
<dd>
<div class="block">Returns the <code>AtomicSymbol</code> for the amino acid
Methionine (M)</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/indexdb/BioStoreFactory.html#META_DATA_TYPE">META_DATA_TYPE</a></span> - Static variable in class org.biojava.bio.program.indexdb.<a href="./org/biojava/bio/program/indexdb/BioStoreFactory.html" title="class in org.biojava.bio.program.indexdb">BioStoreFactory</a></dt>
<dd>
<div class="block">AnnotationType that all meta-data files should fit.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AgaveWriter.html#mFilter">mFilter</a></span> - Variable in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AgaveWriter.html" title="class in org.biojava.bio.seq.io.agave">AgaveWriter</a></dt>
<dd>
<div class="block">writes PCDATA replacing XML characters with escape entities</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BiblioPerson.html#midInitials">midInitials</a></span> - Variable in class org.biojava.bibliography.<a href="./org/biojava/bibliography/BiblioPerson.html" title="class in org.biojava.bibliography">BiblioPerson</a></dt>
<dd>
<div class="block">Any middle innitials.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/NeedlemanWunsch.html#min(int, int, int)">min(int, int, int)</a></span> - Static method in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/NeedlemanWunsch.html" title="class in org.biojava.bio.alignment">NeedlemanWunsch</a></dt>
<dd>
<div class="block">This just computes the minimum of three integer values.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/SubstitutionMatrix.html#min">min</a></span> - Variable in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/SubstitutionMatrix.html" title="class in org.biojava.bio.alignment">SubstitutionMatrix</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AbstractSymbolList.EditScreener.html#min">min</a></span> - Variable in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AbstractSymbolList.EditScreener.html" title="class in org.biojava.bio.symbol">AbstractSymbolList.EditScreener</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/AlphaCTools.html#MIN_ANGLE">MIN_ANGLE</a></span> - Static variable in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/AlphaCTools.html" title="class in org.biojava.bio.structure">AlphaCTools</a></dt>
<dd>
<div class="block">MIN_ANGLE .</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AgaveWriter.Indent.html#mIndent">mIndent</a></span> - Variable in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AgaveWriter.Indent.html" title="class in org.biojava.bio.seq.io.agave">AgaveWriter.Indent</a></dt>
<dd>
<div class="block">Base indent</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AgaveWriter.html#mIndent">mIndent</a></span> - Variable in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AgaveWriter.html" title="class in org.biojava.bio.seq.io.agave">AgaveWriter</a></dt>
<dd>
<div class="block">indent</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/util/SequenceScalePanel.html#MINIMUM_HEIGHT">MINIMUM_HEIGHT</a></span> - Static variable in class org.biojava.bio.structure.gui.util.<a href="./org/biojava/bio/structure/gui/util/SequenceScalePanel.html" title="class in org.biojava.bio.structure.gui.util">SequenceScalePanel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/jama/Matrix.html#minus(org.biojava.bio.structure.jama.Matrix)">minus(Matrix)</a></span> - Method in class org.biojava.bio.structure.jama.<a href="./org/biojava/bio/structure/jama/Matrix.html" title="class in org.biojava.bio.structure.jama">Matrix</a></dt>
<dd>
<div class="block">C = A - B</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/jama/Matrix.html#minusEquals(org.biojava.bio.structure.jama.Matrix)">minusEquals(Matrix)</a></span> - Method in class org.biojava.bio.structure.jama.<a href="./org/biojava/bio/structure/jama/Matrix.html" title="class in org.biojava.bio.structure.jama">Matrix</a></dt>
<dd>
<div class="block">A = A - B</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/MaxMismatchMatcher.html#mismatchCount()">mismatchCount()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/MaxMismatchMatcher.html" title="class in org.biojava.bio.search">MaxMismatchMatcher</a></dt>
<dd>
<div class="block">Returns number of mismatches</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/taxa/NCBITaxon.html#MITOGENETICCODE">MITOGENETICCODE</a></span> - Static variable in interface org.biojavax.bio.taxa.<a href="./org/biojavax/bio/taxa/NCBITaxon.html" title="interface in org.biojavax.bio.taxa">NCBITaxon</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/FastaFormat.html#mListeners">mListeners</a></span> - Variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/FastaFormat.html" title="class in org.biojava.bio.seq.io">FastaFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><a href="./org/biojava/bio/structure/io/mmcif/MMcifConsumer.html" title="interface in org.biojava.bio.structure.io.mmcif"><span class="strong">MMcifConsumer</span></a> - Interface in <a href="./org/biojava/bio/structure/io/mmcif/package-summary.html">org.biojava.bio.structure.io.mmcif</a></dt>
<dd>
<div class="block">An interface for the events triggered by a MMcifParser.</div>
</dd>
<dt><a href="./org/biojava/bio/structure/server/MMCIFFileInstallation.html" title="class in org.biojava.bio.structure.server"><span class="strong">MMCIFFileInstallation</span></a> - Class in <a href="./org/biojava/bio/structure/server/package-summary.html">org.biojava.bio.structure.server</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/server/MMCIFFileInstallation.html#MMCIFFileInstallation(java.io.File)">MMCIFFileInstallation(File)</a></span> - Constructor for class org.biojava.bio.structure.server.<a href="./org/biojava/bio/structure/server/MMCIFFileInstallation.html" title="class in org.biojava.bio.structure.server">MMCIFFileInstallation</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/structure/io/MMCIFFileReader.html" title="class in org.biojava.bio.structure.io"><span class="strong">MMCIFFileReader</span></a> - Class in <a href="./org/biojava/bio/structure/io/package-summary.html">org.biojava.bio.structure.io</a></dt>
<dd>
<div class="block">How to parse an mmCif file:</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/MMCIFFileReader.html#MMCIFFileReader()">MMCIFFileReader()</a></span> - Constructor for class org.biojava.bio.structure.io.<a href="./org/biojava/bio/structure/io/MMCIFFileReader.html" title="class in org.biojava.bio.structure.io">MMCIFFileReader</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/structure/io/mmcif/MMcifParser.html" title="interface in org.biojava.bio.structure.io.mmcif"><span class="strong">MMcifParser</span></a> - Interface in <a href="./org/biojava/bio/structure/io/mmcif/package-summary.html">org.biojava.bio.structure.io.mmcif</a></dt>
<dd>
<div class="block">Interface that needs to be implemented by an MMcifParser</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/DPMatrix.html#model()">model()</a></span> - Method in interface org.biojava.bio.dp.<a href="./org/biojava/bio/dp/DPMatrix.html" title="interface in org.biojava.bio.dp">DPMatrix</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/onehead/SingleDPMatrix.html#model">model</a></span> - Variable in class org.biojava.bio.dp.onehead.<a href="./org/biojava/bio/dp/onehead/SingleDPMatrix.html" title="class in org.biojava.bio.dp.onehead">SingleDPMatrix</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/onehead/SingleDPMatrix.html#model()">model()</a></span> - Method in class org.biojava.bio.dp.onehead.<a href="./org/biojava/bio/dp/onehead/SingleDPMatrix.html" title="class in org.biojava.bio.dp.onehead">SingleDPMatrix</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/twohead/PairDPMatrix.html#model()">model()</a></span> - Method in class org.biojava.bio.dp.twohead.<a href="./org/biojava/bio/dp/twohead/PairDPMatrix.html" title="class in org.biojava.bio.dp.twohead">PairDPMatrix</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/dp/ModelInState.html" title="interface in org.biojava.bio.dp"><span class="strong">ModelInState</span></a> - Interface in <a href="./org/biojava/bio/dp/package-summary.html">org.biojava.bio.dp</a></dt>
<dd>
<div class="block">A state that contains an entire sub-model.</div>
</dd>
<dt><a href="./org/biojava/bio/dp/ModelTrainer.html" title="interface in org.biojava.bio.dp"><span class="strong">ModelTrainer</span></a> - Interface in <a href="./org/biojava/bio/dp/package-summary.html">org.biojava.bio.dp</a></dt>
<dd>
<div class="block">Encapsulates the training of an entire model.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/MergingSet.html#modifiableMerge()">modifiableMerge()</a></span> - Static method in class org.biojava.utils.<a href="./org/biojava/utils/MergingSet.html" title="class in org.biojava.utils">MergingSet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/MergingSet.html#modifiableMerge(java.util.Set)">modifiableMerge(Set)</a></span> - Static method in class org.biojava.utils.<a href="./org/biojava/utils/MergingSet.html" title="class in org.biojava.utils">MergingSet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/server/DemoStructureServer.html#modifiedStructure(org.biojava.bio.structure.server.StructureEvent)">modifiedStructure(StructureEvent)</a></span> - Method in class org.biojava.bio.structure.server.<a href="./org/biojava/bio/structure/server/DemoStructureServer.html" title="class in org.biojava.bio.structure.server">DemoStructureServer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/server/SimpleStructureServer.html#modifiedStructure(org.biojava.bio.structure.server.StructureEvent)">modifiedStructure(StructureEvent)</a></span> - Method in class org.biojava.bio.structure.server.<a href="./org/biojava/bio/structure/server/SimpleStructureServer.html" title="class in org.biojava.bio.structure.server">SimpleStructureServer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/server/StructureListener.html#modifiedStructure(org.biojava.bio.structure.server.StructureEvent)">modifiedStructure(StructureEvent)</a></span> - Method in interface org.biojava.bio.structure.server.<a href="./org/biojava/bio/structure/server/StructureListener.html" title="interface in org.biojava.bio.structure.server">StructureListener</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/OrthologueSet.html#MODIFY">MODIFY</a></span> - Static variable in interface org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/OrthologueSet.html" title="interface in org.biojava.bio.program.homologene">OrthologueSet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/OrthoPairSet.html#MODIFY">MODIFY</a></span> - Static variable in interface org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/OrthoPairSet.html" title="interface in org.biojava.bio.program.homologene">OrthoPairSet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/naming/ObdaContext.html#modifyAttributes(javax.naming.Name, int, javax.naming.directory.Attributes)">modifyAttributes(Name, int, Attributes)</a></span> - Method in class org.biojava.naming.<a href="./org/biojava/naming/ObdaContext.html" title="class in org.biojava.naming">ObdaContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/naming/ObdaContext.html#modifyAttributes(javax.naming.Name, javax.naming.directory.ModificationItem[])">modifyAttributes(Name, ModificationItem[])</a></span> - Method in class org.biojava.naming.<a href="./org/biojava/naming/ObdaContext.html" title="class in org.biojava.naming">ObdaContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/naming/ObdaContext.html#modifyAttributes(java.lang.String, int, javax.naming.directory.Attributes)">modifyAttributes(String, int, Attributes)</a></span> - Method in class org.biojava.naming.<a href="./org/biojava/naming/ObdaContext.html" title="class in org.biojava.naming">ObdaContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/naming/ObdaContext.html#modifyAttributes(java.lang.String, javax.naming.directory.ModificationItem[])">modifyAttributes(String, ModificationItem[])</a></span> - Method in class org.biojava.naming.<a href="./org/biojava/naming/ObdaContext.html" title="class in org.biojava.naming">ObdaContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichLocation.Tools.html#modulateCircularIndex(int, int)">modulateCircularIndex(int, int)</a></span> - Static method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichLocation.Tools.html" title="class in org.biojavax.bio.seq">RichLocation.Tools</a></dt>
<dd>
<div class="block">Takes a point on a circular location and moves it left until it falls
at the earliest possible point that represents the same base.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichLocation.Tools.html#modulateCircularLocation(int, int, int)">modulateCircularLocation(int, int, int)</a></span> - Static method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichLocation.Tools.html" title="class in org.biojavax.bio.seq">RichLocation.Tools</a></dt>
<dd>
<div class="block">Takes a start and end position on a circular location of given
length, and shifts them left along the sequence until they sit at the
earliest possible point where they still would represent the same
sequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichLocation.Tools.html#modulateCircularLocationPair(org.biojava.bio.symbol.Location, org.biojava.bio.symbol.Location, int)">modulateCircularLocationPair(Location, Location, int)</a></span> - Static method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichLocation.Tools.html" title="class in org.biojavax.bio.seq">RichLocation.Tools</a></dt>
<dd>
<div class="block">Takes two circular locations of given length, and shifts them left
along the sequence until they sit at the earliest possible point
where they still would represent the same sequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/TranslationTable.html#MOLD_MITO">MOLD_MITO</a></span> - Static variable in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/TranslationTable.html" title="interface in org.biojava.bio.symbol">TranslationTable</a></dt>
<dd>
<div class="block">Translation table name for the mold mitochondrial genetic code.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/INSDseqFormat.html#MOLTYPE_TAG">MOLTYPE_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/INSDseqFormat.html" title="class in org.biojavax.bio.seq.io">INSDseqFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SymbolPropertyTable.html#MONO_MASS">MONO_MASS</a></span> - Static variable in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SymbolPropertyTable.html" title="interface in org.biojava.bio.symbol">SymbolPropertyTable</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/symbol/MotifTools.html" title="class in org.biojava.bio.symbol"><span class="strong">MotifTools</span></a> - Class in <a href="./org/biojava/bio/symbol/package-summary.html">org.biojava.bio.symbol</a></dt>
<dd>
<div class="block"><code>MotifTools</code> contains utility methods for sequence
motifs.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/MotifTools.html#MotifTools()">MotifTools()</a></span> - Constructor for class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/MotifTools.html" title="class in org.biojava.bio.symbol">MotifTools</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/CodonPrefTools.html#MOUSE_NUCLEAR">MOUSE_NUCLEAR</a></span> - Static variable in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/CodonPrefTools.html" title="class in org.biojava.bio.symbol">CodonPrefTools</a></dt>
<dd>
<div class="block">Mus musculus codon preferences</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequenceViewerListener.html#mouseClicked(org.biojava.bio.gui.sequence.SequenceViewerEvent)">mouseClicked(SequenceViewerEvent)</a></span> - Method in interface org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequenceViewerListener.html" title="interface in org.biojava.bio.gui.sequence">SequenceViewerListener</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/RasmolCommandListener.html#mouseClicked(java.awt.event.MouseEvent)">mouseClicked(MouseEvent)</a></span> - Method in class org.biojava.bio.structure.gui.<a href="./org/biojava/bio/structure/gui/RasmolCommandListener.html" title="class in org.biojava.bio.structure.gui">RasmolCommandListener</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/util/SequenceMouseListener.html#mouseClicked(java.awt.event.MouseEvent)">mouseClicked(MouseEvent)</a></span> - Method in class org.biojava.bio.structure.gui.util.<a href="./org/biojava/bio/structure/gui/util/SequenceMouseListener.html" title="class in org.biojava.bio.structure.gui.util">SequenceMouseListener</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequenceViewerMotionListener.html#mouseDragged(org.biojava.bio.gui.sequence.SequenceViewerEvent)">mouseDragged(SequenceViewerEvent)</a></span> - Method in interface org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequenceViewerMotionListener.html" title="interface in org.biojava.bio.gui.sequence">SequenceViewerMotionListener</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/util/SequenceMouseListener.html#mouseDragged(java.awt.event.MouseEvent)">mouseDragged(MouseEvent)</a></span> - Method in class org.biojava.bio.structure.gui.util.<a href="./org/biojava/bio/structure/gui/util/SequenceMouseListener.html" title="class in org.biojava.bio.structure.gui.util">SequenceMouseListener</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/RasmolCommandListener.html#mouseEntered(java.awt.event.MouseEvent)">mouseEntered(MouseEvent)</a></span> - Method in class org.biojava.bio.structure.gui.<a href="./org/biojava/bio/structure/gui/RasmolCommandListener.html" title="class in org.biojava.bio.structure.gui">RasmolCommandListener</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/util/SequenceMouseListener.html#mouseEntered(java.awt.event.MouseEvent)">mouseEntered(MouseEvent)</a></span> - Method in class org.biojava.bio.structure.gui.util.<a href="./org/biojava/bio/structure/gui/util/SequenceMouseListener.html" title="class in org.biojava.bio.structure.gui.util">SequenceMouseListener</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/RasmolCommandListener.html#mouseExited(java.awt.event.MouseEvent)">mouseExited(MouseEvent)</a></span> - Method in class org.biojava.bio.structure.gui.<a href="./org/biojava/bio/structure/gui/RasmolCommandListener.html" title="class in org.biojava.bio.structure.gui">RasmolCommandListener</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/util/SequenceMouseListener.html#mouseExited(java.awt.event.MouseEvent)">mouseExited(MouseEvent)</a></span> - Method in class org.biojava.bio.structure.gui.util.<a href="./org/biojava/bio/structure/gui/util/SequenceMouseListener.html" title="class in org.biojava.bio.structure.gui.util">SequenceMouseListener</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequenceViewerMotionListener.html#mouseMoved(org.biojava.bio.gui.sequence.SequenceViewerEvent)">mouseMoved(SequenceViewerEvent)</a></span> - Method in interface org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequenceViewerMotionListener.html" title="interface in org.biojava.bio.gui.sequence">SequenceViewerMotionListener</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/util/SequenceMouseListener.html#mouseMoved(java.awt.event.MouseEvent)">mouseMoved(MouseEvent)</a></span> - Method in class org.biojava.bio.structure.gui.util.<a href="./org/biojava/bio/structure/gui/util/SequenceMouseListener.html" title="class in org.biojava.bio.structure.gui.util">SequenceMouseListener</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/events/AlignmentPositionListener.html#mouseOverPosition(org.biojava.bio.structure.gui.util.AlignedPosition)">mouseOverPosition(AlignedPosition)</a></span> - Method in interface org.biojava.bio.structure.gui.events.<a href="./org/biojava/bio/structure/gui/events/AlignmentPositionListener.html" title="interface in org.biojava.bio.structure.gui.events">AlignmentPositionListener</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/events/JmolAlignedPositionListener.html#mouseOverPosition(org.biojava.bio.structure.gui.util.AlignedPosition)">mouseOverPosition(AlignedPosition)</a></span> - Method in class org.biojava.bio.structure.gui.events.<a href="./org/biojava/bio/structure/gui/events/JmolAlignedPositionListener.html" title="class in org.biojava.bio.structure.gui.events">JmolAlignedPositionListener</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequenceViewerListener.html#mousePressed(org.biojava.bio.gui.sequence.SequenceViewerEvent)">mousePressed(SequenceViewerEvent)</a></span> - Method in interface org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequenceViewerListener.html" title="interface in org.biojava.bio.gui.sequence">SequenceViewerListener</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/RasmolCommandListener.html#mousePressed(java.awt.event.MouseEvent)">mousePressed(MouseEvent)</a></span> - Method in class org.biojava.bio.structure.gui.<a href="./org/biojava/bio/structure/gui/RasmolCommandListener.html" title="class in org.biojava.bio.structure.gui">RasmolCommandListener</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/util/SequenceMouseListener.html#mousePressed(java.awt.event.MouseEvent)">mousePressed(MouseEvent)</a></span> - Method in class org.biojava.bio.structure.gui.util.<a href="./org/biojava/bio/structure/gui/util/SequenceMouseListener.html" title="class in org.biojava.bio.structure.gui.util">SequenceMouseListener</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequenceViewerListener.html#mouseReleased(org.biojava.bio.gui.sequence.SequenceViewerEvent)">mouseReleased(SequenceViewerEvent)</a></span> - Method in interface org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequenceViewerListener.html" title="interface in org.biojava.bio.gui.sequence">SequenceViewerListener</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/RasmolCommandListener.html#mouseReleased(java.awt.event.MouseEvent)">mouseReleased(MouseEvent)</a></span> - Method in class org.biojava.bio.structure.gui.<a href="./org/biojava/bio/structure/gui/RasmolCommandListener.html" title="class in org.biojava.bio.structure.gui">RasmolCommandListener</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/util/SequenceMouseListener.html#mouseReleased(java.awt.event.MouseEvent)">mouseReleased(MouseEvent)</a></span> - Method in class org.biojava.bio.structure.gui.util.<a href="./org/biojava/bio/structure/gui/util/SequenceMouseListener.html" title="class in org.biojava.bio.structure.gui.util">SequenceMouseListener</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AgaveWriter.html#mOut">mOut</a></span> - Variable in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AgaveWriter.html" title="class in org.biojava.bio.seq.io.agave">AgaveWriter</a></dt>
<dd>
<div class="block">Write to XML document</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/AlignIOConstants.html#MSF">MSF</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/AlignIOConstants.html" title="class in org.biojava.bio.seq.io">AlignIOConstants</a></dt>
<dd>
<div class="block"><code>MSF</code> indicates that the alignment format is MSF.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/AlignIOConstants.html#MSF_AA">MSF_AA</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/AlignIOConstants.html" title="class in org.biojava.bio.seq.io">AlignIOConstants</a></dt>
<dd>
<div class="block"><code>MSF_AA</code> premade MSF | AA;</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/AlignIOConstants.html#MSF_DNA">MSF_DNA</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/AlignIOConstants.html" title="class in org.biojava.bio.seq.io">AlignIOConstants</a></dt>
<dd>
<div class="block"><code>MSF_DNA</code> premade MSF | DNA;</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/AlignIOConstants.html#MSF_RNA">MSF_RNA</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/AlignIOConstants.html" title="class in org.biojava.bio.seq.io">AlignIOConstants</a></dt>
<dd>
<div class="block"><code>MSF_DNA</code> premade MSF | RNA;</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/MSFAlignmentFormat.html" title="class in org.biojava.bio.seq.io"><span class="strong">MSFAlignmentFormat</span></a> - Class in <a href="./org/biojava/bio/seq/io/package-summary.html">org.biojava.bio.seq.io</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/MSFAlignmentFormat.html#MSFAlignmentFormat()">MSFAlignmentFormat()</a></span> - Constructor for class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/MSFAlignmentFormat.html" title="class in org.biojava.bio.seq.io">MSFAlignmentFormat</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/gui/sequence/MultiLineRenderer.html" title="class in org.biojava.bio.gui.sequence"><span class="strong">MultiLineRenderer</span></a> - Class in <a href="./org/biojava/bio/gui/sequence/package-summary.html">org.biojava.bio.gui.sequence</a></dt>
<dd>
<div class="block"><code>MultiLineRenderer</code> is a <code>SequenceRenderer</code>
which collects a number of other <code>SequenceRenderer</code>s
each of which render their own view of a <code>Sequence</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/MultiLineRenderer.html#MultiLineRenderer()">MultiLineRenderer()</a></span> - Constructor for class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/MultiLineRenderer.html" title="class in org.biojava.bio.gui.sequence">MultiLineRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/HomologeneBuilder.html#MULTIPLE">MULTIPLE</a></span> - Static variable in interface org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/HomologeneBuilder.html" title="interface in org.biojava.bio.program.homologene">HomologeneBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/SimilarityType.html#MULTIPLE">MULTIPLE</a></span> - Static variable in interface org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/SimilarityType.html" title="interface in org.biojava.bio.program.homologene">SimilarityType</a></dt>
<dd> </dd>
<dt><a href="./org/biojavax/bio/phylo/MultipleHitCorrection.html" title="class in org.biojavax.bio.phylo"><span class="strong">MultipleHitCorrection</span></a> - Class in <a href="./org/biojavax/bio/phylo/package-summary.html">org.biojavax.bio.phylo</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/phylo/MultipleHitCorrection.html#MultipleHitCorrection()">MultipleHitCorrection()</a></span> - Constructor for class org.biojavax.bio.phylo.<a href="./org/biojavax/bio/phylo/MultipleHitCorrection.html" title="class in org.biojavax.bio.phylo">MultipleHitCorrection</a></dt>
<dd> </dd>
<dt><a href="./org/biojavax/bio/seq/MultiSourceCompoundRichLocation.html" title="class in org.biojavax.bio.seq"><span class="strong">MultiSourceCompoundRichLocation</span></a> - Class in <a href="./org/biojavax/bio/seq/package-summary.html">org.biojavax.bio.seq</a></dt>
<dd>
<div class="block">An implementation of RichLocation which possibly covers multiple locations,
on different strands, different circular lengths, or different sequences.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/MultiSourceCompoundRichLocation.html#MultiSourceCompoundRichLocation(java.util.Collection)">MultiSourceCompoundRichLocation(Collection)</a></span> - Constructor for class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/MultiSourceCompoundRichLocation.html" title="class in org.biojavax.bio.seq">MultiSourceCompoundRichLocation</a></dt>
<dd>
<div class="block">Constructs a MultiSourceCompoundRichLocation from the given set of members, with
the default term of "join".</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/MultiSourceCompoundRichLocation.html#MultiSourceCompoundRichLocation(org.biojavax.ontology.ComparableTerm, java.util.Collection)">MultiSourceCompoundRichLocation(ComparableTerm, Collection)</a></span> - Constructor for class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/MultiSourceCompoundRichLocation.html" title="class in org.biojavax.bio.seq">MultiSourceCompoundRichLocation</a></dt>
<dd>
<div class="block">Constructs a MultiSourceCompoundRichLocation from the given set of members.</div>
</dd>
<dt><a href="./org/biojava/bio/program/tagvalue/MultiTagger.html" title="class in org.biojava.bio.program.tagvalue"><span class="strong">MultiTagger</span></a> - Class in <a href="./org/biojava/bio/program/tagvalue/package-summary.html">org.biojava.bio.program.tagvalue</a></dt>
<dd>
<div class="block">Partician multiple values for a tag into their own tag groups.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/MultiTagger.html#MultiTagger(org.biojava.bio.program.tagvalue.TagValueListener, org.biojava.bio.program.tagvalue.BoundaryFinder)">MultiTagger(TagValueListener, BoundaryFinder)</a></span> - Constructor for class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/MultiTagger.html" title="class in org.biojava.bio.program.tagvalue">MultiTagger</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Mutator.html#mutate(org.biojava.bio.structure.Structure, java.lang.String, java.lang.String, java.lang.String)">mutate(Structure, String, String, String)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Mutator.html" title="class in org.biojava.bio.structure">Mutator</a></dt>
<dd>
<div class="block">creates a new structure which is identical with the original one.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ga/functions/MutationFunction.html#mutate(org.biojava.bio.symbol.SymbolList)">mutate(SymbolList)</a></span> - Method in interface org.biojavax.ga.functions.<a href="./org/biojavax/ga/functions/MutationFunction.html" title="interface in org.biojavax.ga.functions">MutationFunction</a></dt>
<dd>
<div class="block">Produces a new SymbolList by mutation.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ga/functions/MutationFunction.NoMutation.html#mutate(org.biojava.bio.symbol.SymbolList)">mutate(SymbolList)</a></span> - Method in class org.biojavax.ga.functions.<a href="./org/biojavax/ga/functions/MutationFunction.NoMutation.html" title="class in org.biojavax.ga.functions">MutationFunction.NoMutation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/functions/SimpleMutationFunction.html#mutate(org.biojava.bio.symbol.SymbolList)">mutate(SymbolList)</a></span> - Method in class org.biojavax.ga.functions.<a href="./org/biojavax/ga/functions/SimpleMutationFunction.html" title="class in org.biojavax.ga.functions">SimpleMutationFunction</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/functions/SwapMutationFunction.html#mutate(org.biojava.bio.symbol.SymbolList)">mutate(SymbolList)</a></span> - Method in class org.biojavax.ga.functions.<a href="./org/biojavax/ga/functions/SwapMutationFunction.html" title="class in org.biojavax.ga.functions">SwapMutationFunction</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Mutator.html#mutateResidue(org.biojava.bio.structure.AminoAcid, java.lang.String)">mutateResidue(AminoAcid, String)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Mutator.html" title="class in org.biojava.bio.structure">Mutator</a></dt>
<dd>
<div class="block">create a new residue which is of the new type.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ga/GeneticAlgorithm.html#MUTATION_FUNCTION">MUTATION_FUNCTION</a></span> - Static variable in interface org.biojavax.ga.<a href="./org/biojavax/ga/GeneticAlgorithm.html" title="interface in org.biojavax.ga">GeneticAlgorithm</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/functions/MutationFunction.html#MUTATION_PROBS">MUTATION_PROBS</a></span> - Static variable in interface org.biojavax.ga.functions.<a href="./org/biojavax/ga/functions/MutationFunction.html" title="interface in org.biojavax.ga.functions">MutationFunction</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/functions/MutationFunction.html#MUTATION_SPECTRUM">MUTATION_SPECTRUM</a></span> - Static variable in interface org.biojavax.ga.functions.<a href="./org/biojavax/ga/functions/MutationFunction.html" title="interface in org.biojavax.ga.functions">MutationFunction</a></dt>
<dd> </dd>
<dt><a href="./org/biojavax/ga/functions/MutationFunction.html" title="interface in org.biojavax.ga.functions"><span class="strong">MutationFunction</span></a> - Interface in <a href="./org/biojavax/ga/functions/package-summary.html">org.biojavax.ga.functions</a></dt>
<dd>
<div class="block">A class that mutates a <code>SymbolList</code></div>
</dd>
<dt><a href="./org/biojavax/ga/functions/MutationFunction.NoMutation.html" title="class in org.biojavax.ga.functions"><span class="strong">MutationFunction.NoMutation</span></a> - Class in <a href="./org/biojavax/ga/functions/package-summary.html">org.biojavax.ga.functions</a></dt>
<dd>
<div class="block"> Place Holder class that doesn't mutate its SymbolLists</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ga/functions/MutationFunction.NoMutation.html#MutationFunction.NoMutation()">MutationFunction.NoMutation()</a></span> - Constructor for class org.biojavax.ga.functions.<a href="./org/biojavax/ga/functions/MutationFunction.NoMutation.html" title="class in org.biojavax.ga.functions">MutationFunction.NoMutation</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/structure/Mutator.html" title="class in org.biojava.bio.structure"><span class="strong">Mutator</span></a> - Class in <a href="./org/biojava/bio/structure/package-summary.html">org.biojava.bio.structure</a></dt>
<dd>
<div class="block">A class that can change one amino acid to another.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Mutator.html#Mutator()">Mutator()</a></span> - Constructor for class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Mutator.html" title="class in org.biojava.bio.structure">Mutator</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BiblioCriterion.html#mutuallyExclusiveWith">mutuallyExclusiveWith</a></span> - Variable in class org.biojava.bibliography.<a href="./org/biojava/bibliography/BiblioCriterion.html" title="class in org.biojava.bibliography">BiblioCriterion</a></dt>
<dd>
<div class="block">
A list of other criteria names that this criterion is mutually exclusive with.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AgaveWriter.html#mWriteDocType">mWriteDocType</a></span> - Variable in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AgaveWriter.html" title="class in org.biojava.bio.seq.io.agave">AgaveWriter</a></dt>
<dd>
<div class="block">write DOCTYPE if true</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/StAXFeatureHandler.html#myLocalName">myLocalName</a></span> - Variable in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/StAXFeatureHandler.html" title="class in org.biojava.bio.seq.io.agave">StAXFeatureHandler</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/db/biosql/MySQLDBHelper.html" title="class in org.biojava.bio.seq.db.biosql"><span class="strong">MySQLDBHelper</span></a> - Class in <a href="./org/biojava/bio/seq/db/biosql/package-summary.html">org.biojava.bio.seq.db.biosql</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>Use hibernate and org.biojavax.bio.db.*</i></div>
</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/biosql/MySQLDBHelper.html#MySQLDBHelper(java.sql.Connection)">MySQLDBHelper(Connection)</a></span> - Constructor for class org.biojava.bio.seq.db.biosql.<a href="./org/biojava/bio/seq/db/biosql/MySQLDBHelper.html" title="class in org.biojava.bio.seq.db.biosql">MySQLDBHelper</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
</dl>
<a name="_N_">
<!-- -->
</a>
<h2 class="title">N</h2>
<dl>
<dt><span class="strong"><a href="./org/biojava/bio/seq/DNATools.html#n()">n()</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/DNATools.html" title="class in org.biojava.bio.seq">DNATools</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/NucleotideTools.html#n()">n()</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/NucleotideTools.html" title="class in org.biojava.bio.seq">NucleotideTools</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/ProteinTools.html#n()">n()</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/ProteinTools.html" title="class in org.biojava.bio.seq">ProteinTools</a></dt>
<dd>
<div class="block">Returns the <code>AtomicSymbol</code> for the amino acid
Asparagine</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/RNATools.html#n()">n()</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/RNATools.html" title="class in org.biojava.bio.seq">RNATools</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BiblioCriterion.html#name">name</a></span> - Variable in class org.biojava.bibliography.<a href="./org/biojava/bibliography/BiblioCriterion.html" title="class in org.biojava.bibliography">BiblioCriterion</a></dt>
<dd>
<div class="block">
Each Criterion is identified by its name.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BiblioJournal.html#name">name</a></span> - Variable in class org.biojava.bibliography.<a href="./org/biojava/bibliography/BiblioJournal.html" title="class in org.biojava.bibliography">BiblioJournal</a></dt>
<dd>
<div class="block">A journal title.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BiblioOrganisation.html#name">name</a></span> - Variable in class org.biojava.bibliography.<a href="./org/biojava/bibliography/BiblioOrganisation.html" title="class in org.biojava.bibliography">BiblioOrganisation</a></dt>
<dd>
<div class="block">The name of the organisation.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BiblioService.html#name">name</a></span> - Variable in class org.biojava.bibliography.<a href="./org/biojava/bibliography/BiblioService.html" title="class in org.biojava.bibliography">BiblioService</a></dt>
<dd>
<div class="block">The name of a bibliographic service.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/SubstitutionMatrix.html#name">name</a></span> - Variable in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/SubstitutionMatrix.html" title="class in org.biojava.bio.alignment">SubstitutionMatrix</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/molbio/RestrictionEnzyme.html#name">name</a></span> - Variable in class org.biojava.bio.molbio.<a href="./org/biojava/bio/molbio/RestrictionEnzyme.html" title="class in org.biojava.bio.molbio">RestrictionEnzyme</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SequenceBuilderBase.html#name">name</a></span> - Variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SequenceBuilderBase.html" title="class in org.biojava.bio.seq.io">SequenceBuilderBase</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/obo/OboFileHandler.html#NAME">NAME</a></span> - Static variable in class org.biojava.ontology.obo.<a href="./org/biojava/ontology/obo/OboFileHandler.html" title="class in org.biojava.ontology.obo">OboFileHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichFeature.html#NAME">NAME</a></span> - Static variable in interface org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichFeature.html" title="interface in org.biojavax.bio.seq">RichFeature</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/Organism.html#NAME">NAME</a></span> - Static variable in interface org.biojavax.ga.<a href="./org/biojavax/ga/Organism.html" title="interface in org.biojavax.ga">Organism</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/Population.html#NAME">NAME</a></span> - Static variable in interface org.biojavax.ga.<a href="./org/biojavax/ga/Population.html" title="interface in org.biojavax.ga">Population</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/Namespace.html#NAME">NAME</a></span> - Static variable in interface org.biojavax.<a href="./org/biojavax/Namespace.html" title="interface in org.biojavax">Namespace</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#NAME_ATTR">NAME_ATTR</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#NAME_TAG">NAME_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/aaindex/SimpleSymbolPropertyTableDB.html#names()">names()</a></span> - Method in class org.biojava.bio.proteomics.aaindex.<a href="./org/biojava/bio/proteomics/aaindex/SimpleSymbolPropertyTableDB.html" title="class in org.biojava.bio.proteomics.aaindex">SimpleSymbolPropertyTableDB</a></dt>
<dd>
<div class="block">Returns the set of unique table names.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/aaindex/SymbolPropertyTableDB.html#names()">names()</a></span> - Method in interface org.biojava.bio.proteomics.aaindex.<a href="./org/biojava/bio/proteomics/aaindex/SymbolPropertyTableDB.html" title="interface in org.biojava.bio.proteomics.aaindex">SymbolPropertyTableDB</a></dt>
<dd>
<div class="block">Returns the set of unique table names.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/taxa/NCBITaxon.html#NAMES">NAMES</a></span> - Static variable in interface org.biojavax.bio.taxa.<a href="./org/biojavax/bio/taxa/NCBITaxon.html" title="interface in org.biojavax.bio.taxa">NCBITaxon</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/taxa/SimpleNCBITaxon.html#names">names</a></span> - Variable in class org.biojavax.bio.taxa.<a href="./org/biojavax/bio/taxa/SimpleNCBITaxon.html" title="class in org.biojavax.bio.taxa">SimpleNCBITaxon</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game/GAMEFeatureSetHandler.html#NameSetStringValue(java.lang.String)">NameSetStringValue(String)</a></span> - Method in class org.biojava.bio.seq.io.game.<a href="./org/biojava/bio/seq/io/game/GAMEFeatureSetHandler.html" title="class in org.biojava.bio.seq.io.game">GAMEFeatureSetHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game/GAMEGenePropHandler.html#NameSetStringValue(java.lang.String)">NameSetStringValue(String)</a></span> - Method in class org.biojava.bio.seq.io.game.<a href="./org/biojava/bio/seq/io/game/GAMEGenePropHandler.html" title="class in org.biojava.bio.seq.io.game">GAMEGenePropHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game/GAMENameCallbackItf.html#NameSetStringValue(java.lang.String)">NameSetStringValue(String)</a></span> - Method in interface org.biojava.bio.seq.io.game.<a href="./org/biojava/bio/seq/io/game/GAMENameCallbackItf.html" title="interface in org.biojava.bio.seq.io.game">GAMENameCallbackItf</a></dt>
<dd>
<div class="block">Callback implemented by nesting class to allow
nested class to pass string to nesting class for
handling.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game/GAMESeqPropHandler.html#NameSetStringValue(java.lang.String)">NameSetStringValue(String)</a></span> - Method in class org.biojava.bio.seq.io.game.<a href="./org/biojava/bio/seq/io/game/GAMESeqPropHandler.html" title="class in org.biojava.bio.seq.io.game">GAMESeqPropHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/SeqSimilarityStAXAdapter.html#NAMESPACE">NAMESPACE</a></span> - Static variable in class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/SeqSimilarityStAXAdapter.html" title="class in org.biojava.bio.program.ssbind">SeqSimilarityStAXAdapter</a></dt>
<dd> </dd>
<dt><a href="./org/biojavax/Namespace.html" title="interface in org.biojavax"><span class="strong">Namespace</span></a> - Interface in <a href="./org/biojavax/package-summary.html">org.biojavax</a></dt>
<dd>
<div class="block">The namespace of an entry in a database schema.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/NameTokenization.html" title="class in org.biojava.bio.seq.io"><span class="strong">NameTokenization</span></a> - Class in <a href="./org/biojava/bio/seq/io/package-summary.html">org.biojava.bio.seq.io</a></dt>
<dd>
<div class="block">Simple implementation of SymbolTokenization which uses the `name'
field of the symbols.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/NameTokenization.html#NameTokenization(org.biojava.bio.symbol.FiniteAlphabet, boolean)">NameTokenization(FiniteAlphabet, boolean)</a></span> - Constructor for class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/NameTokenization.html" title="class in org.biojava.bio.seq.io">NameTokenization</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/NameTokenization.html#NameTokenization(org.biojava.bio.symbol.FiniteAlphabet)">NameTokenization(FiniteAlphabet)</a></span> - Constructor for class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/NameTokenization.html" title="class in org.biojava.bio.seq.io">NameTokenization</a></dt>
<dd>
<div class="block">Construct a new NameTokenization, defaulting to case-insensitive.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/obo/OboFileHandler.html#NARROW_SYNONYM">NARROW_SYNONYM</a></span> - Static variable in class org.biojava.ontology.obo.<a href="./org/biojava/ontology/obo/OboFileHandler.html" title="class in org.biojava.ontology.obo">OboFileHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/Synonym.html#NARROW_SYNONYM">NARROW_SYNONYM</a></span> - Static variable in class org.biojava.ontology.<a href="./org/biojava/ontology/Synonym.html" title="class in org.biojava.ontology">Synonym</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFRecord.html#NATURAL_ORDER">NATURAL_ORDER</a></span> - Static variable in interface org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFRecord.html" title="interface in org.biojava.bio.program.gff">GFFRecord</a></dt>
<dd>
<div class="block">Comparator which defines a useful sort order for GFF records.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/Location.html#naturalOrder">naturalOrder</a></span> - Static variable in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/Location.html" title="interface in org.biojava.bio.symbol">Location</a></dt>
<dd>
<div class="block">Comparator which orders Locations naturally.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/MassCalc.html#Navg">Navg</a></span> - Static variable in class org.biojava.bio.proteomics.<a href="./org/biojava/bio/proteomics/MassCalc.html" title="class in org.biojava.bio.proteomics">MassCalc</a></dt>
<dd>
<div class="block">Constant value of Nitrogen average mass</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOConstants.html#NBRF">NBRF</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOConstants.html" title="class in org.biojava.bio.seq.io">SeqIOConstants</a></dt>
<dd>
<div class="block"><code>NBRF</code> indicates that the sequence format is NBRF.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.Terms.html#NCBI_TAXON_KEY">NCBI_TAXON_KEY</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.Terms.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat.Terms</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/blast2html/NcbiDatabaseURLGenerator.html" title="class in org.biojava.bio.program.blast2html"><span class="strong">NcbiDatabaseURLGenerator</span></a> - Class in <a href="./org/biojava/bio/program/blast2html/package-summary.html">org.biojava.bio.program.blast2html</a></dt>
<dd>
<div class="block">Simple URL generator for Entrez at the NCBI.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/blast2html/NcbiDatabaseURLGenerator.html#NcbiDatabaseURLGenerator()">NcbiDatabaseURLGenerator()</a></span> - Constructor for class org.biojava.bio.program.blast2html.<a href="./org/biojava/bio/program/blast2html/NcbiDatabaseURLGenerator.html" title="class in org.biojava.bio.program.blast2html">NcbiDatabaseURLGenerator</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/biosql/TaxonSQL.html#NCBIids(java.sql.Connection)">NCBIids(Connection)</a></span> - Static method in class org.biojava.bio.seq.db.biosql.<a href="./org/biojava/bio/seq/db/biosql/TaxonSQL.html" title="class in org.biojava.bio.seq.db.biosql">TaxonSQL</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Returns a <code>Set</code> of all NCBI-Taxon-IDs which are currently stored in
the database.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/db/NCBISequenceDB.html" title="class in org.biojava.bio.seq.db"><span class="strong">NCBISequenceDB</span></a> - Class in <a href="./org/biojava/bio/seq/db/package-summary.html">org.biojava.bio.seq.db</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/NCBISequenceDB.html#NCBISequenceDB()">NCBISequenceDB()</a></span> - Constructor for class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/NCBISequenceDB.html" title="class in org.biojava.bio.seq.db">NCBISequenceDB</a></dt>
<dd>
<div class="block">Default constructor, querys the Genbank nucleotide database on "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi"
and retrieves sequences in FastaFormat.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/NCBISequenceDB.html#NCBISequenceDB(java.lang.String, org.biojava.bio.seq.io.SequenceFormat)">NCBISequenceDB(String, SequenceFormat)</a></span> - Constructor for class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/NCBISequenceDB.html" title="class in org.biojava.bio.seq.db">NCBISequenceDB</a></dt>
<dd>
<div class="block">Parameterized constructor</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/NCBISequenceDB.html#NCBISequenceDB(java.lang.String, java.lang.String, java.lang.String, org.biojava.bio.seq.io.SequenceFormat)">NCBISequenceDB(String, String, String, SequenceFormat)</a></span> - Constructor for class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/NCBISequenceDB.html" title="class in org.biojava.bio.seq.db">NCBISequenceDB</a></dt>
<dd>
<div class="block">Parameterized constructor</div>
</dd>
<dt><a href="./org/biojavax/bio/taxa/NCBITaxon.html" title="interface in org.biojavax.bio.taxa"><span class="strong">NCBITaxon</span></a> - Interface in <a href="./org/biojavax/bio/taxa/package-summary.html">org.biojavax.bio.taxa</a></dt>
<dd>
<div class="block">Represents an NCBI Taxon entry, a combination of the taxon and taxon_name
tables in BioSQL.</div>
</dd>
<dt><a href="./org/biojavax/bio/taxa/io/NCBITaxonomyLoader.html" title="interface in org.biojavax.bio.taxa.io"><span class="strong">NCBITaxonomyLoader</span></a> - Interface in <a href="./org/biojavax/bio/taxa/io/package-summary.html">org.biojavax.bio.taxa.io</a></dt>
<dd>
<div class="block">Implementors are able to load taxonomy files and generate sets of NCBITaxon objects
that represent them.</div>
</dd>
<dt><a href="./org/biojava/bio/alignment/NeedlemanWunsch.html" title="class in org.biojava.bio.alignment"><span class="strong">NeedlemanWunsch</span></a> - Class in <a href="./org/biojava/bio/alignment/package-summary.html">org.biojava.bio.alignment</a></dt>
<dd>
<div class="block">Needleman and Wunsch defined the problem of global sequence alignments, from
the first till the last symbol of a sequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/NeedlemanWunsch.html#NeedlemanWunsch(short, short, short, short, short, org.biojava.bio.alignment.SubstitutionMatrix)">NeedlemanWunsch(short, short, short, short, short, SubstitutionMatrix)</a></span> - Constructor for class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/NeedlemanWunsch.html" title="class in org.biojava.bio.alignment">NeedlemanWunsch</a></dt>
<dd>
<div class="block">Constructs a new Object with the given parameters based on the
Needleman-Wunsch algorithm The alphabet of sequences to be aligned will be
taken from the given substitution matrix.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/StrandedFeature.html#NEGATIVE">NEGATIVE</a></span> - Static variable in interface org.biojava.bio.seq.<a href="./org/biojava/bio/seq/StrandedFeature.html" title="interface in org.biojava.bio.seq">StrandedFeature</a></dt>
<dd>
<div class="block">Flag to indicate that a feature is on the negative strand.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichLocation.Strand.html#NEGATIVE_STRAND">NEGATIVE_STRAND</a></span> - Static variable in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichLocation.Strand.html" title="class in org.biojavax.bio.seq">RichLocation.Strand</a></dt>
<dd>
<div class="block">The negative strand is represented by the symbol '-' and has the
number -1.</div>
</dd>
<dt><a href="./org/biojava/stats/svm/NestedKernel.html" title="class in org.biojava.stats.svm"><span class="strong">NestedKernel</span></a> - Class in <a href="./org/biojava/stats/svm/package-summary.html">org.biojava.stats.svm</a></dt>
<dd>
<div class="block">Encapsulates a kernel that wraps another kernel up.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/NestedKernel.html#NestedKernel()">NestedKernel()</a></span> - Constructor for class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/NestedKernel.html" title="class in org.biojava.stats.svm">NestedKernel</a></dt>
<dd>
<div class="block">Create a new <span class="type">NestedKernel</span>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/NestedKernel.html#NestedKernel(org.biojava.stats.svm.SVMKernel)">NestedKernel(SVMKernel)</a></span> - Constructor for class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/NestedKernel.html" title="class in org.biojava.stats.svm">NestedKernel</a></dt>
<dd>
<div class="block">Create a new <span class="type">NestedKernel</span> that wraps
<span class="arg">k</span>.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/impl/NewAssembledSymbolList.html" title="class in org.biojava.bio.seq.impl"><span class="strong">NewAssembledSymbolList</span></a> - Class in <a href="./org/biojava/bio/seq/impl/package-summary.html">org.biojava.bio.seq.impl</a></dt>
<dd>
<div class="block">Support class for applications which need to patch together sections
of sequence into a single SymbolList.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/NewAssembledSymbolList.html#NewAssembledSymbolList()">NewAssembledSymbolList()</a></span> - Constructor for class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/NewAssembledSymbolList.html" title="class in org.biojava.bio.seq.impl">NewAssembledSymbolList</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/ChemCompConsumer.html#newAtomSite(org.biojava.bio.structure.io.mmcif.model.AtomSite)">newAtomSite(AtomSite)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/ChemCompConsumer.html" title="class in org.biojava.bio.structure.io.mmcif">ChemCompConsumer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/MMcifConsumer.html#newAtomSite(org.biojava.bio.structure.io.mmcif.model.AtomSite)">newAtomSite(AtomSite)</a></span> - Method in interface org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/MMcifConsumer.html" title="interface in org.biojava.bio.structure.io.mmcif">MMcifConsumer</a></dt>
<dd>
<div class="block">A new AtomSite record has been read.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/SimpleMMcifConsumer.html#newAtomSite(org.biojava.bio.structure.io.mmcif.model.AtomSite)">newAtomSite(AtomSite)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/SimpleMMcifConsumer.html" title="class in org.biojava.bio.structure.io.mmcif">SimpleMMcifConsumer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/ChemCompConsumer.html#newChemComp(org.biojava.bio.structure.io.mmcif.model.ChemComp)">newChemComp(ChemComp)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/ChemCompConsumer.html" title="class in org.biojava.bio.structure.io.mmcif">ChemCompConsumer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/MMcifConsumer.html#newChemComp(org.biojava.bio.structure.io.mmcif.model.ChemComp)">newChemComp(ChemComp)</a></span> - Method in interface org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/MMcifConsumer.html" title="interface in org.biojava.bio.structure.io.mmcif">MMcifConsumer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/SimpleMMcifConsumer.html#newChemComp(org.biojava.bio.structure.io.mmcif.model.ChemComp)">newChemComp(ChemComp)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/SimpleMMcifConsumer.html" title="class in org.biojava.bio.structure.io.mmcif">SimpleMMcifConsumer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/ChemCompConsumer.html#newDatabasePDBremark(org.biojava.bio.structure.io.mmcif.model.DatabasePDBremark)">newDatabasePDBremark(DatabasePDBremark)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/ChemCompConsumer.html" title="class in org.biojava.bio.structure.io.mmcif">ChemCompConsumer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/MMcifConsumer.html#newDatabasePDBremark(org.biojava.bio.structure.io.mmcif.model.DatabasePDBremark)">newDatabasePDBremark(DatabasePDBremark)</a></span> - Method in interface org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/MMcifConsumer.html" title="interface in org.biojava.bio.structure.io.mmcif">MMcifConsumer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/SimpleMMcifConsumer.html#newDatabasePDBremark(org.biojava.bio.structure.io.mmcif.model.DatabasePDBremark)">newDatabasePDBremark(DatabasePDBremark)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/SimpleMMcifConsumer.html" title="class in org.biojava.bio.structure.io.mmcif">SimpleMMcifConsumer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/ChemCompConsumer.html#newDatabasePDBrev(org.biojava.bio.structure.io.mmcif.model.DatabasePDBrev)">newDatabasePDBrev(DatabasePDBrev)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/ChemCompConsumer.html" title="class in org.biojava.bio.structure.io.mmcif">ChemCompConsumer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/MMcifConsumer.html#newDatabasePDBrev(org.biojava.bio.structure.io.mmcif.model.DatabasePDBrev)">newDatabasePDBrev(DatabasePDBrev)</a></span> - Method in interface org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/MMcifConsumer.html" title="interface in org.biojava.bio.structure.io.mmcif">MMcifConsumer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/SimpleMMcifConsumer.html#newDatabasePDBrev(org.biojava.bio.structure.io.mmcif.model.DatabasePDBrev)">newDatabasePDBrev(DatabasePDBrev)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/SimpleMMcifConsumer.html" title="class in org.biojava.bio.structure.io.mmcif">SimpleMMcifConsumer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/ChemCompConsumer.html#newEntity(org.biojava.bio.structure.io.mmcif.model.Entity)">newEntity(Entity)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/ChemCompConsumer.html" title="class in org.biojava.bio.structure.io.mmcif">ChemCompConsumer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/MMcifConsumer.html#newEntity(org.biojava.bio.structure.io.mmcif.model.Entity)">newEntity(Entity)</a></span> - Method in interface org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/MMcifConsumer.html" title="interface in org.biojava.bio.structure.io.mmcif">MMcifConsumer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/SimpleMMcifConsumer.html#newEntity(org.biojava.bio.structure.io.mmcif.model.Entity)">newEntity(Entity)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/SimpleMMcifConsumer.html" title="class in org.biojava.bio.structure.io.mmcif">SimpleMMcifConsumer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/ChemCompConsumer.html#newEntityPolySeq(org.biojava.bio.structure.io.mmcif.model.EntityPolySeq)">newEntityPolySeq(EntityPolySeq)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/ChemCompConsumer.html" title="class in org.biojava.bio.structure.io.mmcif">ChemCompConsumer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/MMcifConsumer.html#newEntityPolySeq(org.biojava.bio.structure.io.mmcif.model.EntityPolySeq)">newEntityPolySeq(EntityPolySeq)</a></span> - Method in interface org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/MMcifConsumer.html" title="interface in org.biojava.bio.structure.io.mmcif">MMcifConsumer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/SimpleMMcifConsumer.html#newEntityPolySeq(org.biojava.bio.structure.io.mmcif.model.EntityPolySeq)">newEntityPolySeq(EntityPolySeq)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/SimpleMMcifConsumer.html" title="class in org.biojava.bio.structure.io.mmcif">SimpleMMcifConsumer</a></dt>
<dd>
<div class="block">The EntityPolySeq object provide the amino acid sequence objects for the Entities.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/ChemCompConsumer.html#newExptl(org.biojava.bio.structure.io.mmcif.model.Exptl)">newExptl(Exptl)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/ChemCompConsumer.html" title="class in org.biojava.bio.structure.io.mmcif">ChemCompConsumer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/MMcifConsumer.html#newExptl(org.biojava.bio.structure.io.mmcif.model.Exptl)">newExptl(Exptl)</a></span> - Method in interface org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/MMcifConsumer.html" title="interface in org.biojava.bio.structure.io.mmcif">MMcifConsumer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/SimpleMMcifConsumer.html#newExptl(org.biojava.bio.structure.io.mmcif.model.Exptl)">newExptl(Exptl)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/SimpleMMcifConsumer.html" title="class in org.biojava.bio.structure.io.mmcif">SimpleMMcifConsumer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/ChemCompConsumer.html#newGenericData(java.lang.String, java.util.List, java.util.List)">newGenericData(String, List<String>, List<String>)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/ChemCompConsumer.html" title="class in org.biojava.bio.structure.io.mmcif">ChemCompConsumer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/MMcifConsumer.html#newGenericData(java.lang.String, java.util.List, java.util.List)">newGenericData(String, List<String>, List<String>)</a></span> - Method in interface org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/MMcifConsumer.html" title="interface in org.biojava.bio.structure.io.mmcif">MMcifConsumer</a></dt>
<dd>
<div class="block">This method is called if no particular handler for the provided cif category
has been implemented so far.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/SimpleMMcifConsumer.html#newGenericData(java.lang.String, java.util.List, java.util.List)">newGenericData(String, List<String>, List<String>)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/SimpleMMcifConsumer.html" title="class in org.biojava.bio.structure.io.mmcif">SimpleMMcifConsumer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/projection/ProjectionEngine.Instantiator.html#newInstance(java.lang.reflect.Constructor, java.lang.Object[])">newInstance(Constructor, Object[])</a></span> - Method in interface org.biojava.bio.seq.projection.<a href="./org/biojava/bio/seq/projection/ProjectionEngine.Instantiator.html" title="interface in org.biojava.bio.seq.projection">ProjectionEngine.Instantiator</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AbstractLocation.html#newInstance(org.biojava.bio.symbol.Location)">newInstance(Location)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AbstractLocation.html" title="class in org.biojava.bio.symbol">AbstractLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AbstractLocationDecorator.html#newInstance(org.biojava.bio.symbol.Location)">newInstance(Location)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AbstractLocationDecorator.html" title="class in org.biojava.bio.symbol">AbstractLocationDecorator</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/Location.html#newInstance(org.biojava.bio.symbol.Location)">newInstance(Location)</a></span> - Method in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/Location.html" title="interface in org.biojava.bio.symbol">Location</a></dt>
<dd>
<div class="block">Create a new instance of Location with all of the same decorators as this
instance but with the data stored in <code>loc</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/CompoundRichLocation.html#newInstance(org.biojava.bio.symbol.Location)">newInstance(Location)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/CompoundRichLocation.html" title="class in org.biojavax.bio.seq">CompoundRichLocation</a></dt>
<dd>
<div class="block">Create a new instance of Location with all of the same decorators as this
instance but with the data stored in <code>loc</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/EmptyRichLocation.html#newInstance(org.biojava.bio.symbol.Location)">newInstance(Location)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/EmptyRichLocation.html" title="class in org.biojavax.bio.seq">EmptyRichLocation</a></dt>
<dd>
<div class="block">Create a new instance of Location with all of the same decorators as this
instance but with the data stored in <code>loc</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichLocation.html#newInstance(org.biojava.bio.symbol.Location)">newInstance(Location)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichLocation.html" title="class in org.biojavax.bio.seq">SimpleRichLocation</a></dt>
<dd>
<div class="block">Create a new instance of Location with all of the same decorators as this
instance but with the data stored in <code>loc</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/obo/OboFileEventListener.html#newKey(java.lang.String, java.lang.String)">newKey(String, String)</a></span> - Method in interface org.biojava.ontology.obo.<a href="./org/biojava/ontology/obo/OboFileEventListener.html" title="interface in org.biojava.ontology.obo">OboFileEventListener</a></dt>
<dd>
<div class="block">found a new key in the file</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/obo/OboFileHandler.html#newKey(java.lang.String, java.lang.String)">newKey(String, String)</a></span> - Method in class org.biojava.ontology.obo.<a href="./org/biojava/ontology/obo/OboFileHandler.html" title="class in org.biojava.ontology.obo">OboFileHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/PDBHeader.html#newline">newline</a></span> - Static variable in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/PDBHeader.html" title="class in org.biojava.bio.structure">PDBHeader</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/ParseException.html#newMessage(java.lang.Class, java.lang.String, java.lang.String, java.lang.String, java.lang.String)">newMessage(Class, String, String, String, String)</a></span> - Static method in exception org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/ParseException.html" title="class in org.biojava.bio.seq.io">ParseException</a></dt>
<dd>
<div class="block">Make a new error message.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/obo/OboFileEventListener.html#newOboFileHeader()">newOboFileHeader()</a></span> - Method in interface org.biojava.ontology.obo.<a href="./org/biojava/ontology/obo/OboFileEventListener.html" title="interface in org.biojava.ontology.obo">OboFileEventListener</a></dt>
<dd>
<div class="block">parsed a new OBO file header</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/obo/OboFileHandler.html#newOboFileHeader()">newOboFileHeader()</a></span> - Method in class org.biojava.ontology.obo.<a href="./org/biojava/ontology/obo/OboFileHandler.html" title="class in org.biojava.ontology.obo">OboFileHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/ChemCompConsumer.html#newPdbxEntityNonPoly(org.biojava.bio.structure.io.mmcif.model.PdbxEntityNonPoly)">newPdbxEntityNonPoly(PdbxEntityNonPoly)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/ChemCompConsumer.html" title="class in org.biojava.bio.structure.io.mmcif">ChemCompConsumer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/MMcifConsumer.html#newPdbxEntityNonPoly(org.biojava.bio.structure.io.mmcif.model.PdbxEntityNonPoly)">newPdbxEntityNonPoly(PdbxEntityNonPoly)</a></span> - Method in interface org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/MMcifConsumer.html" title="interface in org.biojava.bio.structure.io.mmcif">MMcifConsumer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/SimpleMMcifConsumer.html#newPdbxEntityNonPoly(org.biojava.bio.structure.io.mmcif.model.PdbxEntityNonPoly)">newPdbxEntityNonPoly(PdbxEntityNonPoly)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/SimpleMMcifConsumer.html" title="class in org.biojava.bio.structure.io.mmcif">SimpleMMcifConsumer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/ChemCompConsumer.html#newPdbxNonPolyScheme(org.biojava.bio.structure.io.mmcif.model.PdbxNonPolyScheme)">newPdbxNonPolyScheme(PdbxNonPolyScheme)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/ChemCompConsumer.html" title="class in org.biojava.bio.structure.io.mmcif">ChemCompConsumer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/MMcifConsumer.html#newPdbxNonPolyScheme(org.biojava.bio.structure.io.mmcif.model.PdbxNonPolyScheme)">newPdbxNonPolyScheme(PdbxNonPolyScheme)</a></span> - Method in interface org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/MMcifConsumer.html" title="interface in org.biojava.bio.structure.io.mmcif">MMcifConsumer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/SimpleMMcifConsumer.html#newPdbxNonPolyScheme(org.biojava.bio.structure.io.mmcif.model.PdbxNonPolyScheme)">newPdbxNonPolyScheme(PdbxNonPolyScheme)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/SimpleMMcifConsumer.html" title="class in org.biojava.bio.structure.io.mmcif">SimpleMMcifConsumer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/ChemCompConsumer.html#newPdbxPolySeqScheme(org.biojava.bio.structure.io.mmcif.model.PdbxPolySeqScheme)">newPdbxPolySeqScheme(PdbxPolySeqScheme)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/ChemCompConsumer.html" title="class in org.biojava.bio.structure.io.mmcif">ChemCompConsumer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/MMcifConsumer.html#newPdbxPolySeqScheme(org.biojava.bio.structure.io.mmcif.model.PdbxPolySeqScheme)">newPdbxPolySeqScheme(PdbxPolySeqScheme)</a></span> - Method in interface org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/MMcifConsumer.html" title="interface in org.biojava.bio.structure.io.mmcif">MMcifConsumer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/SimpleMMcifConsumer.html#newPdbxPolySeqScheme(org.biojava.bio.structure.io.mmcif.model.PdbxPolySeqScheme)">newPdbxPolySeqScheme(PdbxPolySeqScheme)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/SimpleMMcifConsumer.html" title="class in org.biojava.bio.structure.io.mmcif">SimpleMMcifConsumer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/ChemCompConsumer.html#newRefine(org.biojava.bio.structure.io.mmcif.model.Refine)">newRefine(Refine)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/ChemCompConsumer.html" title="class in org.biojava.bio.structure.io.mmcif">ChemCompConsumer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/MMcifConsumer.html#newRefine(org.biojava.bio.structure.io.mmcif.model.Refine)">newRefine(Refine)</a></span> - Method in interface org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/MMcifConsumer.html" title="interface in org.biojava.bio.structure.io.mmcif">MMcifConsumer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/SimpleMMcifConsumer.html#newRefine(org.biojava.bio.structure.io.mmcif.model.Refine)">newRefine(Refine)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/SimpleMMcifConsumer.html" title="class in org.biojava.bio.structure.io.mmcif">SimpleMMcifConsumer</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/NewSimpleAssembly.html" title="class in org.biojava.bio.seq"><span class="strong">NewSimpleAssembly</span></a> - Class in <a href="./org/biojava/bio/seq/package-summary.html">org.biojava.bio.seq</a></dt>
<dd>
<div class="block">A Sequence which is assembled from other sequences contained
in a set of ComponentFeature objects.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/NewSimpleAssembly.html#NewSimpleAssembly(int, java.lang.String, java.lang.String)">NewSimpleAssembly(int, String, String)</a></span> - Constructor for class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/NewSimpleAssembly.html" title="class in org.biojava.bio.seq">NewSimpleAssembly</a></dt>
<dd>
<div class="block">Construct a new SimpleAssembly using the DNA alphabet.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/NewSimpleAssembly.html#NewSimpleAssembly(java.lang.String, java.lang.String)">NewSimpleAssembly(String, String)</a></span> - Constructor for class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/NewSimpleAssembly.html" title="class in org.biojava.bio.seq">NewSimpleAssembly</a></dt>
<dd>
<div class="block">Construct a new NewSimpleAssembly using the DNA alphabet.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/obo/OboFileEventListener.html#newStanza(java.lang.String)">newStanza(String)</a></span> - Method in interface org.biojava.ontology.obo.<a href="./org/biojava/ontology/obo/OboFileEventListener.html" title="interface in org.biojava.ontology.obo">OboFileEventListener</a></dt>
<dd>
<div class="block">parsed a new stanza in the file</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/obo/OboFileHandler.html#newStanza(java.lang.String)">newStanza(String)</a></span> - Method in class org.biojava.ontology.obo.<a href="./org/biojava/ontology/obo/OboFileHandler.html" title="class in org.biojava.ontology.obo">OboFileHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/ChemCompConsumer.html#newStructAsym(org.biojava.bio.structure.io.mmcif.model.StructAsym)">newStructAsym(StructAsym)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/ChemCompConsumer.html" title="class in org.biojava.bio.structure.io.mmcif">ChemCompConsumer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/MMcifConsumer.html#newStructAsym(org.biojava.bio.structure.io.mmcif.model.StructAsym)">newStructAsym(StructAsym)</a></span> - Method in interface org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/MMcifConsumer.html" title="interface in org.biojava.bio.structure.io.mmcif">MMcifConsumer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/SimpleMMcifConsumer.html#newStructAsym(org.biojava.bio.structure.io.mmcif.model.StructAsym)">newStructAsym(StructAsym)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/SimpleMMcifConsumer.html" title="class in org.biojava.bio.structure.io.mmcif">SimpleMMcifConsumer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/ChemCompConsumer.html#newStructKeywords(org.biojava.bio.structure.io.mmcif.model.StructKeywords)">newStructKeywords(StructKeywords)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/ChemCompConsumer.html" title="class in org.biojava.bio.structure.io.mmcif">ChemCompConsumer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/MMcifConsumer.html#newStructKeywords(org.biojava.bio.structure.io.mmcif.model.StructKeywords)">newStructKeywords(StructKeywords)</a></span> - Method in interface org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/MMcifConsumer.html" title="interface in org.biojava.bio.structure.io.mmcif">MMcifConsumer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/SimpleMMcifConsumer.html#newStructKeywords(org.biojava.bio.structure.io.mmcif.model.StructKeywords)">newStructKeywords(StructKeywords)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/SimpleMMcifConsumer.html" title="class in org.biojava.bio.structure.io.mmcif">SimpleMMcifConsumer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/ChemCompConsumer.html#newStructRef(org.biojava.bio.structure.io.mmcif.model.StructRef)">newStructRef(StructRef)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/ChemCompConsumer.html" title="class in org.biojava.bio.structure.io.mmcif">ChemCompConsumer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/MMcifConsumer.html#newStructRef(org.biojava.bio.structure.io.mmcif.model.StructRef)">newStructRef(StructRef)</a></span> - Method in interface org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/MMcifConsumer.html" title="interface in org.biojava.bio.structure.io.mmcif">MMcifConsumer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/SimpleMMcifConsumer.html#newStructRef(org.biojava.bio.structure.io.mmcif.model.StructRef)">newStructRef(StructRef)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/SimpleMMcifConsumer.html" title="class in org.biojava.bio.structure.io.mmcif">SimpleMMcifConsumer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/ChemCompConsumer.html#newStructRefSeq(org.biojava.bio.structure.io.mmcif.model.StructRefSeq)">newStructRefSeq(StructRefSeq)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/ChemCompConsumer.html" title="class in org.biojava.bio.structure.io.mmcif">ChemCompConsumer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/MMcifConsumer.html#newStructRefSeq(org.biojava.bio.structure.io.mmcif.model.StructRefSeq)">newStructRefSeq(StructRefSeq)</a></span> - Method in interface org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/MMcifConsumer.html" title="interface in org.biojava.bio.structure.io.mmcif">MMcifConsumer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/SimpleMMcifConsumer.html#newStructRefSeq(org.biojava.bio.structure.io.mmcif.model.StructRefSeq)">newStructRefSeq(StructRefSeq)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/SimpleMMcifConsumer.html" title="class in org.biojava.bio.structure.io.mmcif">SimpleMMcifConsumer</a></dt>
<dd>
<div class="block">create a DBRef record from the StrucRefSeq record:</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/server/DemoStructureServer.html#newStructure(org.biojava.bio.structure.server.StructureEvent)">newStructure(StructureEvent)</a></span> - Method in class org.biojava.bio.structure.server.<a href="./org/biojava/bio/structure/server/DemoStructureServer.html" title="class in org.biojava.bio.structure.server">DemoStructureServer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/server/SimpleStructureServer.html#newStructure(org.biojava.bio.structure.server.StructureEvent)">newStructure(StructureEvent)</a></span> - Method in class org.biojava.bio.structure.server.<a href="./org/biojava/bio/structure/server/SimpleStructureServer.html" title="class in org.biojava.bio.structure.server">SimpleStructureServer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/server/StructureListener.html#newStructure(org.biojava.bio.structure.server.StructureEvent)">newStructure(StructureEvent)</a></span> - Method in interface org.biojava.bio.structure.server.<a href="./org/biojava/bio/structure/server/StructureListener.html" title="interface in org.biojava.bio.structure.server">StructureListener</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/obo/OboFileEventListener.html#newSynonym(org.biojava.ontology.Synonym)">newSynonym(Synonym)</a></span> - Method in interface org.biojava.ontology.obo.<a href="./org/biojava/ontology/obo/OboFileEventListener.html" title="interface in org.biojava.ontology.obo">OboFileEventListener</a></dt>
<dd>
<div class="block">a new synonym has been found</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/obo/OboFileHandler.html#newSynonym(org.biojava.ontology.Synonym)">newSynonym(Synonym)</a></span> - Method in class org.biojava.ontology.obo.<a href="./org/biojava/ontology/obo/OboFileHandler.html" title="class in org.biojava.ontology.obo">OboFileHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/DP.ReverseIterator.html#next()">next()</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/DP.ReverseIterator.html" title="class in org.biojava.bio.dp">DP.ReverseIterator</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/twohead/BackMatrixPairDPCursor.html#next(org.biojava.bio.dp.twohead.Cell[][])">next(Cell[][])</a></span> - Method in class org.biojava.bio.dp.twohead.<a href="./org/biojava/bio/dp/twohead/BackMatrixPairDPCursor.html" title="class in org.biojava.bio.dp.twohead">BackMatrixPairDPCursor</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/twohead/LightPairDPCursor.html#next(org.biojava.bio.dp.twohead.Cell[][])">next(Cell[][])</a></span> - Method in class org.biojava.bio.dp.twohead.<a href="./org/biojava/bio/dp/twohead/LightPairDPCursor.html" title="class in org.biojava.bio.dp.twohead">LightPairDPCursor</a></dt>
<dd>
<div class="block">Description of the Method</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/twohead/MatrixPairDPCursor.html#next(org.biojava.bio.dp.twohead.Cell[][])">next(Cell[][])</a></span> - Method in class org.biojava.bio.dp.twohead.<a href="./org/biojava/bio/dp/twohead/MatrixPairDPCursor.html" title="class in org.biojava.bio.dp.twohead">MatrixPairDPCursor</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/twohead/PairDPCursor.html#next(org.biojava.bio.dp.twohead.Cell[][])">next(Cell[][])</a></span> - Method in interface org.biojava.bio.dp.twohead.<a href="./org/biojava/bio/dp/twohead/PairDPCursor.html" title="interface in org.biojava.bio.dp.twohead">PairDPCursor</a></dt>
<dd>
<div class="block">retrieve the next block of cells</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/AtomIterator.html#next()">next()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/AtomIterator.html" title="class in org.biojava.bio.structure">AtomIterator</a></dt>
<dd>
<div class="block">Return next atom.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/GroupIterator.html#next()">next()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/GroupIterator.html" title="class in org.biojava.bio.structure">GroupIterator</a></dt>
<dd>
<div class="block">get next Group.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/server/FlatFileInstallation.html#next()">next()</a></span> - Method in class org.biojava.bio.structure.server.<a href="./org/biojava/bio/structure/server/FlatFileInstallation.html" title="class in org.biojava.bio.structure.server">FlatFileInstallation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/server/MMCIFFileInstallation.html#next()">next()</a></span> - Method in class org.biojava.bio.structure.server.<a href="./org/biojava/bio/structure/server/MMCIFFileInstallation.html" title="class in org.biojava.bio.structure.server">MMCIFFileInstallation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/server/PDBInstallation.html#next()">next()</a></span> - Method in interface org.biojava.bio.structure.server.<a href="./org/biojava/bio/structure/server/PDBInstallation.html" title="interface in org.biojava.bio.structure.server">PDBInstallation</a></dt>
<dd>
<div class="block">iterate over all structures in this Installation that pass the provided filters and
return the next one in the list.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/Alignment.SymbolListIterator.html#next()">next()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/Alignment.SymbolListIterator.html" title="class in org.biojava.bio.symbol">Alignment.SymbolListIterator</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/MergingIterator.html#next()">next()</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/MergingIterator.html" title="class in org.biojava.utils">MergingIterator</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/BioEntryIterator.html#nextBioEntry()">nextBioEntry()</a></span> - Method in interface org.biojavax.bio.<a href="./org/biojavax/bio/BioEntryIterator.html" title="interface in org.biojavax.bio">BioEntryIterator</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/HashedFastaIterator.html#nextBioEntry()">nextBioEntry()</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/HashedFastaIterator.html" title="class in org.biojavax.bio.seq.io">HashedFastaIterator</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/RichStreamReader.html#nextBioEntry()">nextBioEntry()</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/RichStreamReader.html" title="class in org.biojavax.bio.seq.io">RichStreamReader</a></dt>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.IOTools.SingleRichSeqIterator.html#nextBioEntry()">nextBioEntry()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.IOTools.SingleRichSeqIterator.html" title="class in org.biojavax.bio.seq">RichSequence.IOTools.SingleRichSeqIterator</a></dt>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/OrthologueSet.Iterator.html#nextOrthologue()">nextOrthologue()</a></span> - Method in interface org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/OrthologueSet.Iterator.html" title="interface in org.biojava.bio.program.homologene">OrthologueSet.Iterator</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/SimpleOrthologueSet.Iterator.html#nextOrthologue()">nextOrthologue()</a></span> - Method in class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/SimpleOrthologueSet.Iterator.html" title="class in org.biojava.bio.program.homologene">SimpleOrthologueSet.Iterator</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/OrthoPairSet.Iterator.html#nextOrthoPair()">nextOrthoPair()</a></span> - Method in interface org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/OrthoPairSet.Iterator.html" title="interface in org.biojava.bio.program.homologene">OrthoPairSet.Iterator</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/SimpleOrthoPairSet.Iterator.html#nextOrthoPair()">nextOrthoPair()</a></span> - Method in class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/SimpleOrthoPairSet.Iterator.html" title="class in org.biojava.bio.program.homologene">SimpleOrthoPairSet.Iterator</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/SimpleThreadPool.html#nextRequest()">nextRequest()</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/SimpleThreadPool.html" title="class in org.biojava.utils">SimpleThreadPool</a></dt>
<dd>
<div class="block"><code>nextRequest</code> gets the next <code>Runnable</code>
from the queue.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/HashedFastaIterator.html#nextRichSequence()">nextRichSequence()</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/HashedFastaIterator.html" title="class in org.biojavax.bio.seq.io">HashedFastaIterator</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/RichStreamReader.html#nextRichSequence()">nextRichSequence()</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/RichStreamReader.html" title="class in org.biojavax.bio.seq.io">RichStreamReader</a></dt>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.IOTools.SingleRichSeqIterator.html#nextRichSequence()">nextRichSequence()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.IOTools.SingleRichSeqIterator.html" title="class in org.biojavax.bio.seq">RichSequence.IOTools.SingleRichSeqIterator</a></dt>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequenceIterator.html#nextRichSequence()">nextRichSequence()</a></span> - Method in interface org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequenceIterator.html" title="interface in org.biojavax.bio.seq">RichSequenceIterator</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/StreamReader.html#nextSequence()">nextSequence()</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/StreamReader.html" title="class in org.biojava.bio.seq.io">StreamReader</a></dt>
<dd>
<div class="block">Pull the next sequence out of the stream.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/SequenceIterator.html#nextSequence()">nextSequence()</a></span> - Method in interface org.biojava.bio.seq.<a href="./org/biojava/bio/seq/SequenceIterator.html" title="interface in org.biojava.bio.seq">SequenceIterator</a></dt>
<dd>
<div class="block">Returns the next sequence in the iterator.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/HashedFastaIterator.html#nextSequence()">nextSequence()</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/HashedFastaIterator.html" title="class in org.biojavax.bio.seq.io">HashedFastaIterator</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/RichStreamReader.html#nextSequence()">nextSequence()</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/RichStreamReader.html" title="class in org.biojavax.bio.seq.io">RichStreamReader</a></dt>
<dd>
<div class="block">Returns the next sequence in the iterator.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.IOTools.SingleRichSeqIterator.html#nextSequence()">nextSequence()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.IOTools.SingleRichSeqIterator.html" title="class in org.biojavax.bio.seq">RichSequence.IOTools.SingleRichSeqIterator</a></dt>
<dd>
<div class="block">Returns the next sequence in the iterator.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/OrthoPairCollection.Iterator.html#nextSet()">nextSet()</a></span> - Method in interface org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/OrthoPairCollection.Iterator.html" title="interface in org.biojava.bio.program.homologene">OrthoPairCollection.Iterator</a></dt>
<dd>
<div class="block">returns the next OrthoPairSet</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/SimpleOrthoPairCollection.Iterator.html#nextSet()">nextSet()</a></span> - Method in class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/SimpleOrthoPairCollection.Iterator.html" title="class in org.biojava.bio.program.homologene">SimpleOrthoPairCollection.Iterator</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/aaindex/AAindexStreamReader.html#nextTable()">nextTable()</a></span> - Method in class org.biojava.bio.proteomics.aaindex.<a href="./org/biojava/bio/proteomics/aaindex/AAindexStreamReader.html" title="class in org.biojava.bio.proteomics.aaindex">AAindexStreamReader</a></dt>
<dd>
<div class="block">Returns the next <a href="./org/biojava/bio/symbol/SymbolPropertyTable.html" title="interface in org.biojava.bio.symbol"><code>SymbolPropertyTable</code></a>
object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/aaindex/SymbolPropertyTableIterator.html#nextTable()">nextTable()</a></span> - Method in interface org.biojava.bio.proteomics.aaindex.<a href="./org/biojava/bio/proteomics/aaindex/SymbolPropertyTableIterator.html" title="interface in org.biojava.bio.proteomics.aaindex">SymbolPropertyTableIterator</a></dt>
<dd>
<div class="block">Returns the next <a href="./org/biojava/bio/symbol/SymbolPropertyTable.html" title="interface in org.biojava.bio.symbol"><code>SymbolPropertyTable</code></a>
object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/PackingFactory.html#nextWord(org.biojava.bio.symbol.SymbolList, int, int, int, org.biojava.bio.symbol.Packing)">nextWord(SymbolList, int, int, int, Packing)</a></span> - Static method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/PackingFactory.html" title="class in org.biojava.bio.symbol">PackingFactory</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/utils/automata/Nfa.html" title="class in org.biojava.utils.automata"><span class="strong">Nfa</span></a> - Class in <a href="./org/biojava/utils/automata/package-summary.html">org.biojava.utils.automata</a></dt>
<dd>
<div class="block">Class for modelling non-deterministic finite automata.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/automata/Nfa.html#Nfa(java.lang.String, org.biojava.bio.symbol.FiniteAlphabet)">Nfa(String, FiniteAlphabet)</a></span> - Constructor for class org.biojava.utils.automata.<a href="./org/biojava/utils/automata/Nfa.html" title="class in org.biojava.utils.automata">Nfa</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/utils/automata/NfaBuilder.html" title="interface in org.biojava.utils.automata"><span class="strong">NfaBuilder</span></a> - Interface in <a href="./org/biojava/utils/automata/package-summary.html">org.biojava.utils.automata</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/utils/automata/NfaSubModel.html" title="class in org.biojava.utils.automata"><span class="strong">NfaSubModel</span></a> - Class in <a href="./org/biojava/utils/automata/package-summary.html">org.biojava.utils.automata</a></dt>
<dd>
<div class="block">This class caches a reference to all objects that
it directs its delegate to make.</div>
</dd>
<dt><a href="./org/biojava/bio/program/ssaha/NIODataStoreFactory.html" title="class in org.biojava.bio.program.ssaha"><span class="strong">NIODataStoreFactory</span></a> - Class in <a href="./org/biojava/bio/program/ssaha/package-summary.html">org.biojava.bio.program.ssaha</a></dt>
<dd>
<div class="block">
Builder for a datastore that has no practical file size limit.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssaha/NIODataStoreFactory.html#NIODataStoreFactory()">NIODataStoreFactory()</a></span> - Constructor for class org.biojava.bio.program.ssaha.<a href="./org/biojava/bio/program/ssaha/NIODataStoreFactory.html" title="class in org.biojava.bio.program.ssaha">NIODataStoreFactory</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/xml/BaseXMLWriter.html#nl()">nl()</a></span> - Method in class org.biojava.bio.program.xml.<a href="./org/biojava/bio/program/xml/BaseXMLWriter.html" title="class in org.biojava.bio.program.xml">BaseXMLWriter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/MassCalc.html#Nmono">Nmono</a></span> - Static variable in class org.biojava.bio.proteomics.<a href="./org/biojava/bio/proteomics/MassCalc.html" title="class in org.biojava.bio.proteomics">MassCalc</a></dt>
<dd>
<div class="block">Constant value of Nitrogen monoisotopic mass</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ga/functions/CrossOverFunction.html#NO_CROSS">NO_CROSS</a></span> - Static variable in interface org.biojavax.ga.functions.<a href="./org/biojavax/ga/functions/CrossOverFunction.html" title="interface in org.biojavax.ga.functions">CrossOverFunction</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFRecord.html#NO_FRAME">NO_FRAME</a></span> - Static variable in interface org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFRecord.html" title="interface in org.biojava.bio.program.gff">GFFRecord</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>Use GFFTools.NO_FRAME instead</i></div>
</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFTools.html#NO_FRAME">NO_FRAME</a></span> - Static variable in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFTools.html" title="class in org.biojava.bio.program.gff">GFFTools</a></dt>
<dd>
<div class="block">Flag to indicate that there is no frame info.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ga/functions/MutationFunction.html#NO_MUTATION">NO_MUTATION</a></span> - Static variable in interface org.biojavax.ga.functions.<a href="./org/biojavax/ga/functions/MutationFunction.html" title="interface in org.biojavax.ga.functions">MutationFunction</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFRecord.html#NO_SCORE">NO_SCORE</a></span> - Static variable in interface org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFRecord.html" title="interface in org.biojava.bio.program.gff">GFFRecord</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>Use GFFTools.NO_SCORE instead</i></div>
</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFTools.html#NO_SCORE">NO_SCORE</a></span> - Static variable in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFTools.html" title="class in org.biojava.bio.program.gff">GFFTools</a></dt>
<dd>
<div class="block">Flag to indicate that there is no score info.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/taxa/NCBITaxon.html#NODERANK">NODERANK</a></span> - Static variable in interface org.biojavax.bio.taxa.<a href="./org/biojavax/bio/taxa/NCBITaxon.html" title="interface in org.biojavax.bio.taxa">NCBITaxon</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/automata/FiniteAutomaton.html#nodes">nodes</a></span> - Variable in class org.biojava.utils.automata.<a href="./org/biojava/utils/automata/FiniteAutomaton.html" title="class in org.biojava.utils.automata">FiniteAutomaton</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/AnnotationType.html#NONE">NONE</a></span> - Static variable in interface org.biojava.bio.<a href="./org/biojava/bio/AnnotationType.html" title="interface in org.biojava.bio">AnnotationType</a></dt>
<dd>
<div class="block">The type that accepts no annotations at all and is the subtype of all
other annotations.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/CardinalityConstraint.html#NONE">NONE</a></span> - Static variable in class org.biojava.bio.<a href="./org/biojava/bio/CardinalityConstraint.html" title="class in org.biojava.bio">CardinalityConstraint</a></dt>
<dd>
<div class="block">This cardinality contains no intengers, not even zero.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/CollectionConstraint.html#NONE">NONE</a></span> - Static variable in interface org.biojava.bio.<a href="./org/biojava/bio/CollectionConstraint.html" title="interface in org.biojava.bio">CollectionConstraint</a></dt>
<dd>
<div class="block"><code>NONE</code> is a constraint which accepts no value for a property
under any condition.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/PropertyConstraint.html#NONE">NONE</a></span> - Static variable in interface org.biojava.bio.<a href="./org/biojava/bio/PropertyConstraint.html" title="interface in org.biojava.bio">PropertyConstraint</a></dt>
<dd>
<div class="block"><code>NONE</code> is a constraint which accepts no value for a property
under any condition.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.html#none">none</a></span> - Static variable in interface org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.html" title="interface in org.biojava.bio.seq">FeatureFilter</a></dt>
<dd>
<div class="block">No features are selected by this filter.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FilterUtils.html#none()">none()</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FilterUtils.html" title="class in org.biojava.bio.seq">FilterUtils</a></dt>
<dd>
<div class="block">Return a filter which matches no features.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/OntoTools.html#NONE">NONE</a></span> - Static variable in class org.biojava.ontology.<a href="./org/biojava/ontology/OntoTools.html" title="class in org.biojava.ontology">OntoTools</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.html#none">none</a></span> - Static variable in interface org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.html" title="interface in org.biojavax.bio.db.biosql">BioSQLFeatureFilter</a></dt>
<dd>
<div class="block">No features are selected by this filter.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/ListTools.html#nonRemoveIterator(java.util.Iterator)">nonRemoveIterator(Iterator)</a></span> - Static method in class org.biojava.utils.<a href="./org/biojava/utils/ListTools.html" title="class in org.biojava.utils">ListTools</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/jama/Matrix.html#norm1()">norm1()</a></span> - Method in class org.biojava.bio.structure.jama.<a href="./org/biojava/bio/structure/jama/Matrix.html" title="class in org.biojava.bio.structure.jama">Matrix</a></dt>
<dd>
<div class="block">One norm</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/jama/Matrix.html#norm2()">norm2()</a></span> - Method in class org.biojava.bio.structure.jama.<a href="./org/biojava/bio/structure/jama/Matrix.html" title="class in org.biojava.bio.structure.jama">Matrix</a></dt>
<dd>
<div class="block">Two norm</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/jama/SingularValueDecomposition.html#norm2()">norm2()</a></span> - Method in class org.biojava.bio.structure.jama.<a href="./org/biojava/bio/structure/jama/SingularValueDecomposition.html" title="class in org.biojava.bio.structure.jama">SingularValueDecomposition</a></dt>
<dd>
<div class="block">Two norm</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/SubstitutionMatrix.html#normalizeMatrix()">normalizeMatrix()</a></span> - Method in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/SubstitutionMatrix.html" title="class in org.biojava.bio.alignment">SubstitutionMatrix</a></dt>
<dd>
<div class="block">With this method you can get a “normalized”
<code>SubstitutionMatrix</code> object; however, since this
implementation uses an short matrix, the normalized matrix will be scaled
by ten.</div>
</dd>
<dt><a href="./org/biojava/stats/svm/NormalizingKernel.html" title="class in org.biojava.stats.svm"><span class="strong">NormalizingKernel</span></a> - Class in <a href="./org/biojava/stats/svm/package-summary.html">org.biojava.stats.svm</a></dt>
<dd>
<div class="block">Performs a normalization on the results of a nested kernel.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/NormalizingKernel.html#NormalizingKernel()">NormalizingKernel()</a></span> - Constructor for class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/NormalizingKernel.html" title="class in org.biojava.stats.svm">NormalizingKernel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/NormalizingKernel.html#NormalizingKernel(org.biojava.stats.svm.SVMKernel)">NormalizingKernel(SVMKernel)</a></span> - Constructor for class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/NormalizingKernel.html" title="class in org.biojava.stats.svm">NormalizingKernel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/SparseVector.html#normalLengthVector(org.biojava.stats.svm.SparseVector, double)">normalLengthVector(SparseVector, double)</a></span> - Static method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/SparseVector.html" title="class in org.biojava.stats.svm">SparseVector</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/jama/Matrix.html#normF()">normF()</a></span> - Method in class org.biojava.bio.structure.jama.<a href="./org/biojava/bio/structure/jama/Matrix.html" title="class in org.biojava.bio.structure.jama">Matrix</a></dt>
<dd>
<div class="block">Frobenius norm</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/jama/Matrix.html#normInf()">normInf()</a></span> - Method in class org.biojava.bio.structure.jama.<a href="./org/biojava/bio/structure/jama/Matrix.html" title="class in org.biojava.bio.structure.jama">Matrix</a></dt>
<dd>
<div class="block">Infinity norm</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureHolderUtils.html#not(org.biojava.bio.seq.FeatureHolder, org.biojava.bio.seq.FeatureHolder)">not(FeatureHolder, FeatureHolder)</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureHolderUtils.html" title="class in org.biojava.bio.seq">FeatureHolderUtils</a></dt>
<dd>
<div class="block">Operator: FeatureHolder 1 NOT FeatureHolder2</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/filter/FilterTransformer.html#not(org.biojava.bio.seq.FeatureFilter.Not, org.biojava.bio.seq.FeatureFilter)">not(FeatureFilter.Not, FeatureFilter)</a></span> - Method in class org.biojava.bio.seq.filter.<a href="./org/biojava/bio/seq/filter/FilterTransformer.html" title="class in org.biojava.bio.seq.filter">FilterTransformer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FilterUtils.html#not(org.biojava.bio.seq.FeatureFilter)">not(FeatureFilter)</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FilterUtils.html" title="class in org.biojava.bio.seq">FilterUtils</a></dt>
<dd>
<div class="block">Construct a new filter which is the negation of <code>filter</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.HibernateFeatureFilter.html#not">not</a></span> - Variable in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.HibernateFeatureFilter.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.HibernateFeatureFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/util/AlignedPosition.html#NOT_ALIGNED">NOT_ALIGNED</a></span> - Static variable in class org.biojava.bio.structure.gui.util.<a href="./org/biojava/bio/structure/gui/util/AlignedPosition.html" title="class in org.biojava.bio.structure.gui.util">AlignedPosition</a></dt>
<dd>
<div class="block">they can be shown in the same column (for a compact display)
, but they are not structurally equivalent</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichLocation.html#NOTE">NOTE</a></span> - Static variable in interface org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichLocation.html" title="interface in org.biojavax.bio.seq">RichLocation</a></dt>
<dd> </dd>
<dt><a href="./org/biojavax/Note.html" title="interface in org.biojavax"><span class="strong">Note</span></a> - Interface in <a href="./org/biojavax/package-summary.html">org.biojavax</a></dt>
<dd>
<div class="block">Note is a generic class intended to hold a term describing the note,
a value to associate with that term, and a rank.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#NOTE_TAG">NOTE_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/AlignmentGui.html#notifyCalcFinished()">notifyCalcFinished()</a></span> - Method in class org.biojava.bio.structure.gui.<a href="./org/biojava/bio/structure/gui/AlignmentGui.html" title="class in org.biojava.bio.structure.gui">AlignmentGui</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/StateMachine.ExitNotification.html#notifyExit()">notifyExit()</a></span> - Method in interface org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/StateMachine.ExitNotification.html" title="interface in org.biojava.bio.program.tagvalue">StateMachine.ExitNotification</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/automata/PatternListener.html#notifyHit(java.lang.String, int, int, boolean)">notifyHit(String, int, int, boolean)</a></span> - Method in interface org.biojava.utils.automata.<a href="./org/biojava/utils/automata/PatternListener.html" title="interface in org.biojava.utils.automata">PatternListener</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/StateMachine.Transition.html#notifyOnExit">notifyOnExit</a></span> - Variable in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/StateMachine.Transition.html" title="class in org.biojava.bio.program.tagvalue">StateMachine.Transition</a></dt>
<dd>
<div class="block">should the State listener be notified
that this transition is leaving the state.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/phred/PhredFormat.html#notifyParseErrorEvent(org.biojava.utils.ParseErrorEvent)">notifyParseErrorEvent(ParseErrorEvent)</a></span> - Method in class org.biojava.bio.program.phred.<a href="./org/biojava/bio/program/phred/PhredFormat.html" title="class in org.biojava.bio.program.phred">PhredFormat</a></dt>
<dd>
<div class="block">Passes the event on to all the listeners registered for ParseErrorEvents.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/EmblLikeFormat.html#notifyParseErrorEvent(org.biojava.utils.ParseErrorEvent)">notifyParseErrorEvent(ParseErrorEvent)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/EmblLikeFormat.html" title="class in org.biojava.bio.seq.io">EmblLikeFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Passes the event on to all the listeners registered for ParseErrorEvents.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/EmblProcessor.html#notifyParseErrorEvent(org.biojava.utils.ParseErrorEvent)">notifyParseErrorEvent(ParseErrorEvent)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/EmblProcessor.html" title="class in org.biojava.bio.seq.io">EmblProcessor</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Passes the event on to all the listeners registered for ParseErrorEvents.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/FastaFormat.html#notifyParseErrorEvent(org.biojava.utils.ParseErrorEvent)">notifyParseErrorEvent(ParseErrorEvent)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/FastaFormat.html" title="class in org.biojava.bio.seq.io">FastaFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Passes the event on to all the listeners registered for ParseErrorEvents.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/GenbankFormat.html#notifyParseErrorEvent(org.biojava.utils.ParseErrorEvent)">notifyParseErrorEvent(ParseErrorEvent)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/GenbankFormat.html" title="class in org.biojava.bio.seq.io">GenbankFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Passes the event on to all the listeners registered for ParseErrorEvents.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/GenbankProcessor.html#notifyParseErrorEvent(org.biojava.utils.ParseErrorEvent)">notifyParseErrorEvent(ParseErrorEvent)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/GenbankProcessor.html" title="class in org.biojava.bio.seq.io">GenbankProcessor</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Passes the event on to all the listeners registered for ParseErrorEvents.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SwissprotProcessor.html#notifyParseErrorEvent(org.biojava.utils.ParseErrorEvent)">notifyParseErrorEvent(ParseErrorEvent)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SwissprotProcessor.html" title="class in org.biojava.bio.seq.io">SwissprotProcessor</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Passes the event on to all the listeners registered for ParseErrorEvents.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Structure.html#nrModels()">nrModels()</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Structure.html" title="interface in org.biojava.bio.structure">Structure</a></dt>
<dd>
<div class="block">return number of models .</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/StructureImpl.html#nrModels()">nrModels()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/StructureImpl.html" title="class in org.biojava.bio.structure">StructureImpl</a></dt>
<dd>
<div class="block">return number of models.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/hmmer/FullHmmerProfileHMM.html#nState()">nState()</a></span> - Method in class org.biojava.bio.program.hmmer.<a href="./org/biojava/bio/program/hmmer/FullHmmerProfileHMM.html" title="class in org.biojava.bio.program.hmmer">FullHmmerProfileHMM</a></dt>
<dd>
<div class="block">Gets the n loop state</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/GroupType.html#NUCLEOTIDE">NUCLEOTIDE</a></span> - Static variable in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/GroupType.html" title="class in org.biojava.bio.structure">GroupType</a></dt>
<dd>
<div class="block">the type for nucelotide groups</div>
</dd>
<dt><a href="./org/biojava/bio/structure/NucleotideImpl.html" title="class in org.biojava.bio.structure"><span class="strong">NucleotideImpl</span></a> - Class in <a href="./org/biojava/bio/structure/package-summary.html">org.biojava.bio.structure</a></dt>
<dd>
<div class="block">A nucleotide group is almost the same as a Hetatm group.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/NucleotideImpl.html#NucleotideImpl()">NucleotideImpl()</a></span> - Constructor for class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/NucleotideImpl.html" title="class in org.biojava.bio.structure">NucleotideImpl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/NucleotideTools.html#nucleotideToken(org.biojava.bio.symbol.Symbol)">nucleotideToken(Symbol)</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/NucleotideTools.html" title="class in org.biojava.bio.seq">NucleotideTools</a></dt>
<dd>
<div class="block">Get a single-character token for a Nucleotide symbol</div>
</dd>
<dt><a href="./org/biojava/bio/seq/NucleotideTools.html" title="class in org.biojava.bio.seq"><span class="strong">NucleotideTools</span></a> - Class in <a href="./org/biojava/bio/seq/package-summary.html">org.biojava.bio.seq</a></dt>
<dd>
<div class="block">Useful functionality for processing nucleotide sequences.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/ListTools.html#NULL_MAPPER">NULL_MAPPER</a></span> - Static variable in class org.biojava.utils.<a href="./org/biojava/utils/ListTools.html" title="class in org.biojava.utils">ListTools</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/Distribution.html#NULL_MODEL">NULL_MODEL</a></span> - Static variable in interface org.biojava.bio.dist.<a href="./org/biojava/bio/dist/Distribution.html" title="interface in org.biojava.bio.dist">Distribution</a></dt>
<dd>
<div class="block">
Whenever the null model distribution changes the values that would be
returned by getWeight, either by being edited or by being replaced, a
ChangeEvent with this object as the type should be thrown.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/ScoreType.html#NULL_MODEL">NULL_MODEL</a></span> - Static variable in interface org.biojava.bio.dp.<a href="./org/biojava/bio/dp/ScoreType.html" title="interface in org.biojava.bio.dp">ScoreType</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/AbstractDistribution.html#nullModelForwarder">nullModelForwarder</a></span> - Variable in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/AbstractDistribution.html" title="class in org.biojava.bio.dist">AbstractDistribution</a></dt>
<dd>
<div class="block">Forwarder for modifications to the null model.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/abi/ABIFParser.TaggedDataRecord.html#numberOfElements">numberOfElements</a></span> - Variable in class org.biojava.bio.program.abi.<a href="./org/biojava/bio/program/abi/ABIFParser.TaggedDataRecord.html" title="class in org.biojava.bio.program.abi">ABIFParser.TaggedDataRecord</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/xml/FastXMLWriter.html#numericalEntity(char)">numericalEntity(char)</a></span> - Method in class org.biojava.utils.xml.<a href="./org/biojava/utils/xml/FastXMLWriter.html" title="class in org.biojava.utils.xml">FastXMLWriter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/xml/PrettyXMLWriter.html#numericalEntity(char)">numericalEntity(char)</a></span> - Method in class org.biojava.utils.xml.<a href="./org/biojava/utils/xml/PrettyXMLWriter.html" title="class in org.biojava.utils.xml">PrettyXMLWriter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/twohead/AbstractMatrixPairDPCursor.html#numStates">numStates</a></span> - Variable in class org.biojava.bio.dp.twohead.<a href="./org/biojava/bio/dp/twohead/AbstractMatrixPairDPCursor.html" title="class in org.biojava.bio.dp.twohead">AbstractMatrixPairDPCursor</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/twohead/LightPairDPCursor.html#numStates">numStates</a></span> - Variable in class org.biojava.bio.dp.twohead.<a href="./org/biojava/bio/dp/twohead/LightPairDPCursor.html" title="class in org.biojava.bio.dp.twohead">LightPairDPCursor</a></dt>
<dd>
<div class="block">Description of the Field</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/aaindex/SimpleSymbolPropertyTableDB.html#numTables()">numTables()</a></span> - Method in class org.biojava.bio.proteomics.aaindex.<a href="./org/biojava/bio/proteomics/aaindex/SimpleSymbolPropertyTableDB.html" title="class in org.biojava.bio.proteomics.aaindex">SimpleSymbolPropertyTableDB</a></dt>
<dd>
<div class="block">Returns the number of symbol property tables in the database.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/aaindex/SymbolPropertyTableDB.html#numTables()">numTables()</a></span> - Method in interface org.biojava.bio.proteomics.aaindex.<a href="./org/biojava/bio/proteomics/aaindex/SymbolPropertyTableDB.html" title="interface in org.biojava.bio.proteomics.aaindex">SymbolPropertyTableDB</a></dt>
<dd>
<div class="block">Returns the number of symbol property tables in the database.</div>
</dd>
</dl>
<a name="_O_">
<!-- -->
</a>
<h2 class="title">O</h2>
<dl>
<dt><span class="strong"><a href="./org/biojava/bio/seq/ProteinTools.html#o()">o()</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/ProteinTools.html" title="class in org.biojava.bio.seq">ProteinTools</a></dt>
<dd>
<div class="block">Returns the <code>AtomicSymbol</code> for the amino acid
Pyrrolysine</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/Taxon.html#O_SATIVA">O_SATIVA</a></span> - Static variable in interface org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/Taxon.html" title="interface in org.biojava.bio.program.homologene">Taxon</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/MassCalc.html#Oavg">Oavg</a></span> - Static variable in class org.biojava.bio.proteomics.<a href="./org/biojava/bio/proteomics/MassCalc.html" title="class in org.biojava.bio.proteomics">MassCalc</a></dt>
<dd>
<div class="block">Constant value of Oxygen average mass</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/directory/SystemRegistry.html#OBDA_SEARCH_ENV">OBDA_SEARCH_ENV</a></span> - Static variable in class org.biojava.directory.<a href="./org/biojava/directory/SystemRegistry.html" title="class in org.biojava.directory">SystemRegistry</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/naming/ObdaContext.html" title="class in org.biojava.naming"><span class="strong">ObdaContext</span></a> - Class in <a href="./org/biojava/naming/package-summary.html">org.biojava.naming</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/naming/ObdaInitialContextFactory.html" title="class in org.biojava.naming"><span class="strong">ObdaInitialContextFactory</span></a> - Class in <a href="./org/biojava/naming/package-summary.html">org.biojava.naming</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/naming/ObdaInitialContextFactory.html#ObdaInitialContextFactory()">ObdaInitialContextFactory()</a></span> - Constructor for class org.biojava.naming.<a href="./org/biojava/naming/ObdaInitialContextFactory.html" title="class in org.biojava.naming">ObdaInitialContextFactory</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/directory/OBDARegistryParser.html" title="class in org.biojava.directory"><span class="strong">OBDARegistryParser</span></a> - Class in <a href="./org/biojava/directory/package-summary.html">org.biojava.directory</a></dt>
<dd>
<div class="block">This class encapsulates all the parsing of the OBDA registry
configuration file.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/directory/OBDARegistryParser.html#OBDARegistryParser()">OBDARegistryParser()</a></span> - Constructor for class org.biojava.directory.<a href="./org/biojava/directory/OBDARegistryParser.html" title="class in org.biojava.directory">OBDARegistryParser</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/naming/ObdaUriParser.html" title="class in org.biojava.naming"><span class="strong">ObdaUriParser</span></a> - Class in <a href="./org/biojava/naming/package-summary.html">org.biojava.naming</a></dt>
<dd>
<div class="block">Singleton class for parsers that understand OBDA URIs.</div>
</dd>
<dt><a href="./org/biojava/utils/ObjectUtil.html" title="class in org.biojava.utils"><span class="strong">ObjectUtil</span></a> - Class in <a href="./org/biojava/utils/package-summary.html">org.biojava.utils</a></dt>
<dd>
<div class="block">utility methods for implementing the equals() and hashCode() methods of Objects.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/ObjectUtil.html#ObjectUtil()">ObjectUtil()</a></span> - Constructor for class org.biojava.utils.<a href="./org/biojava/utils/ObjectUtil.html" title="class in org.biojava.utils">ObjectUtil</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/ontology/obo/OboFileEventListener.html" title="interface in org.biojava.ontology.obo"><span class="strong">OboFileEventListener</span></a> - Interface in <a href="./org/biojava/ontology/obo/package-summary.html">org.biojava.ontology.obo</a></dt>
<dd>
<div class="block">an interface for events that occur during parsing of .obo files</div>
</dd>
<dt><a href="./org/biojava/ontology/obo/OboFileHandler.html" title="class in org.biojava.ontology.obo"><span class="strong">OboFileHandler</span></a> - Class in <a href="./org/biojava/ontology/obo/package-summary.html">org.biojava.ontology.obo</a></dt>
<dd>
<div class="block">A file handler for .obo files</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/obo/OboFileHandler.html#OboFileHandler(org.biojava.ontology.Ontology)">OboFileHandler(Ontology)</a></span> - Constructor for class org.biojava.ontology.obo.<a href="./org/biojava/ontology/obo/OboFileHandler.html" title="class in org.biojava.ontology.obo">OboFileHandler</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/ontology/obo/OboFileParser.html" title="class in org.biojava.ontology.obo"><span class="strong">OboFileParser</span></a> - Class in <a href="./org/biojava/ontology/obo/package-summary.html">org.biojava.ontology.obo</a></dt>
<dd>
<div class="block">A class to parse the content of an OBO file.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/obo/OboFileParser.html#OboFileParser()">OboFileParser()</a></span> - Constructor for class org.biojava.ontology.obo.<a href="./org/biojava/ontology/obo/OboFileParser.html" title="class in org.biojava.ontology.obo">OboFileParser</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/ontology/obo/OboFileParser.SOPair.html" title="class in org.biojava.ontology.obo"><span class="strong">OboFileParser.SOPair</span></a> - Class in <a href="./org/biojava/ontology/obo/package-summary.html">org.biojava.ontology.obo</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/obo/OboFileParser.SOPair.html#OboFileParser.SOPair(java.lang.String, int)">OboFileParser.SOPair(String, int)</a></span> - Constructor for class org.biojava.ontology.obo.<a href="./org/biojava/ontology/obo/OboFileParser.SOPair.html" title="class in org.biojava.ontology.obo">OboFileParser.SOPair</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/obo/OboFileParser.SOPair.html#OboFileParser.SOPair(java.lang.String, int, int)">OboFileParser.SOPair(String, int, int)</a></span> - Constructor for class org.biojava.ontology.obo.<a href="./org/biojava/ontology/obo/OboFileParser.SOPair.html" title="class in org.biojava.ontology.obo">OboFileParser.SOPair</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/ontology/io/OboParser.html" title="class in org.biojava.ontology.io"><span class="strong">OboParser</span></a> - Class in <a href="./org/biojava/ontology/io/package-summary.html">org.biojava.ontology.io</a></dt>
<dd>
<div class="block">Parses an OBO file.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/io/OboParser.html#OboParser()">OboParser()</a></span> - Constructor for class org.biojava.ontology.io.<a href="./org/biojava/ontology/io/OboParser.html" title="class in org.biojava.ontology.io">OboParser</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ontology/ComparableTerm.html#OBSOLETE">OBSOLETE</a></span> - Static variable in interface org.biojavax.ontology.<a href="./org/biojavax/ontology/ComparableTerm.html" title="interface in org.biojavax.ontology">ComparableTerm</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/server/DemoStructureServer.html#obsoleteStructure(org.biojava.bio.structure.server.StructureEvent)">obsoleteStructure(StructureEvent)</a></span> - Method in class org.biojava.bio.structure.server.<a href="./org/biojava/bio/structure/server/DemoStructureServer.html" title="class in org.biojava.bio.structure.server">DemoStructureServer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/server/SimpleStructureServer.html#obsoleteStructure(org.biojava.bio.structure.server.StructureEvent)">obsoleteStructure(StructureEvent)</a></span> - Method in class org.biojava.bio.structure.server.<a href="./org/biojava/bio/structure/server/SimpleStructureServer.html" title="class in org.biojava.bio.structure.server">SimpleStructureServer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/server/StructureListener.html#obsoleteStructure(org.biojava.bio.structure.server.StructureEvent)">obsoleteStructure(StructureEvent)</a></span> - Method in interface org.biojava.bio.structure.server.<a href="./org/biojava/bio/structure/server/StructureListener.html" title="interface in org.biojava.bio.structure.server">StructureListener</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/blast2html/AbstractAlignmentStyler.html#oColourClassMap">oColourClassMap</a></span> - Variable in class org.biojava.bio.program.blast2html.<a href="./org/biojava/bio/program/blast2html/AbstractAlignmentStyler.html" title="class in org.biojava.bio.program.blast2html">AbstractAlignmentStyler</a></dt>
<dd>
<div class="block">
Stores mapping from a Colour to a FONT Class.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/blast2html/AbstractAlignmentStyler.html#oColourMap">oColourMap</a></span> - Variable in class org.biojava.bio.program.blast2html.<a href="./org/biojava/bio/program/blast2html/AbstractAlignmentStyler.html" title="class in org.biojava.bio.program.blast2html">AbstractAlignmentStyler</a></dt>
<dd>
<div class="block">
Map between Char and the Colour class.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/blast2html/AbstractAlignmentStyler.html#oColourSet">oColourSet</a></span> - Variable in class org.biojava.bio.program.blast2html.<a href="./org/biojava/bio/program/blast2html/AbstractAlignmentStyler.html" title="class in org.biojava.bio.program.blast2html">AbstractAlignmentStyler</a></dt>
<dd>
<div class="block">Store the unique colours for markup.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/ScoreType.html#ODDS">ODDS</a></span> - Static variable in interface org.biojava.bio.dp.<a href="./org/biojava/bio/dp/ScoreType.html" title="interface in org.biojava.bio.dp">ScoreType</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/OffsetRulerRenderer.html#OFFSET">OFFSET</a></span> - Static variable in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/OffsetRulerRenderer.html" title="class in org.biojava.bio.gui.sequence">OffsetRulerRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/abi/ABIFParser.TaggedDataRecord.html#offsetData">offsetData</a></span> - Variable in class org.biojava.bio.program.abi.<a href="./org/biojava/bio/program/abi/ABIFParser.TaggedDataRecord.html" title="class in org.biojava.bio.program.abi">ABIFParser.TaggedDataRecord</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/gui/sequence/OffsetRulerRenderer.html" title="class in org.biojava.bio.gui.sequence"><span class="strong">OffsetRulerRenderer</span></a> - Class in <a href="./org/biojava/bio/gui/sequence/package-summary.html">org.biojava.bio.gui.sequence</a></dt>
<dd>
<div class="block">OffsetRulerRenderer can render the ruler starting from an arbitrary offset from the sequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/OffsetRulerRenderer.html#OffsetRulerRenderer()">OffsetRulerRenderer()</a></span> - Constructor for class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/OffsetRulerRenderer.html" title="class in org.biojava.bio.gui.sequence">OffsetRulerRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/OffsetRulerRenderer.html#OffsetRulerRenderer(int, int)">OffsetRulerRenderer(int, int)</a></span> - Constructor for class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/OffsetRulerRenderer.html" title="class in org.biojava.bio.gui.sequence">OffsetRulerRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/Chromatogram.html#OFFSETS">OFFSETS</a></span> - Static variable in interface org.biojava.bio.chromatogram.<a href="./org/biojava/bio/chromatogram/Chromatogram.html" title="interface in org.biojava.bio.chromatogram">Chromatogram</a></dt>
<dd>
<div class="block">The sequence label for the trace offsets of the called bases.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/MassCalc.html#Omono">Omono</a></span> - Static variable in class org.biojava.bio.proteomics.<a href="./org/biojava/bio/proteomics/MassCalc.html" title="class in org.biojava.bio.proteomics">MassCalc</a></dt>
<dd>
<div class="block">Constant value of Oxygen monoisotopic mass</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/CardinalityConstraint.html#ONE">ONE</a></span> - Static variable in class org.biojava.bio.<a href="./org/biojava/bio/CardinalityConstraint.html" title="class in org.biojava.bio">CardinalityConstraint</a></dt>
<dd>
<div class="block">The property should have exactly one value.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ga/util/GATools.html#one()">one()</a></span> - Static method in class org.biojavax.ga.util.<a href="./org/biojavax/ga/util/GATools.html" title="class in org.biojavax.ga.util">GATools</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/CardinalityConstraint.html#ONE_OR_MORE">ONE_OR_MORE</a></span> - Static variable in class org.biojava.bio.<a href="./org/biojava/bio/CardinalityConstraint.html" title="class in org.biojava.bio">CardinalityConstraint</a></dt>
<dd>
<div class="block">The property should have one or more values.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/filter/FilterTransformer.html#onlyChildren(org.biojava.bio.seq.FeatureFilter.OnlyChildren, org.biojava.bio.seq.FeatureFilter)">onlyChildren(FeatureFilter.OnlyChildren, FeatureFilter)</a></span> - Method in class org.biojava.bio.seq.filter.<a href="./org/biojava/bio/seq/filter/FilterTransformer.html" title="class in org.biojava.bio.seq.filter">FilterTransformer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FilterUtils.html#onlyChildren(org.biojava.bio.seq.FeatureFilter)">onlyChildren(FeatureFilter)</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FilterUtils.html" title="class in org.biojava.bio.seq">FilterUtils</a></dt>
<dd>
<div class="block">Construct a filter which matches features whose children all match the
specified filter.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/filter/FilterTransformer.html#onlyDescendants(org.biojava.bio.seq.FeatureFilter.OnlyDescendants, org.biojava.bio.seq.FeatureFilter)">onlyDescendants(FeatureFilter.OnlyDescendants, FeatureFilter)</a></span> - Method in class org.biojava.bio.seq.filter.<a href="./org/biojava/bio/seq/filter/FilterTransformer.html" title="class in org.biojava.bio.seq.filter">FilterTransformer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FilterUtils.html#onlyDescendants(org.biojava.bio.seq.FeatureFilter)">onlyDescendants(FeatureFilter)</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FilterUtils.html" title="class in org.biojava.bio.seq">FilterUtils</a></dt>
<dd>
<div class="block">Construct a filter which matches features whose decendants all match the
specified filter.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/obo/OboFileHandler.html#ONTOLOGY">ONTOLOGY</a></span> - Static variable in class org.biojava.ontology.obo.<a href="./org/biojava/ontology/obo/OboFileHandler.html" title="class in org.biojava.ontology.obo">OboFileHandler</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/ontology/Ontology.html" title="interface in org.biojava.ontology"><span class="strong">Ontology</span></a> - Interface in <a href="./org/biojava/ontology/package-summary.html">org.biojava.ontology</a></dt>
<dd>
<div class="block">An ontology.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/Term.html#ONTOLOGY">ONTOLOGY</a></span> - Static variable in interface org.biojava.ontology.<a href="./org/biojava/ontology/Term.html" title="interface in org.biojava.ontology">Term</a></dt>
<dd>
<div class="block">ChangeType which indicates that this term's ontology has been
altered</div>
</dd>
<dt><a href="./org/biojava/ontology/Ontology.Impl.html" title="class in org.biojava.ontology"><span class="strong">Ontology.Impl</span></a> - Class in <a href="./org/biojava/ontology/package-summary.html">org.biojava.ontology</a></dt>
<dd>
<div class="block">A basic in-memory implementation of an ontology</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/Ontology.Impl.html#Ontology.Impl(java.lang.String, java.lang.String)">Ontology.Impl(String, String)</a></span> - Constructor for class org.biojava.ontology.<a href="./org/biojava/ontology/Ontology.Impl.html" title="class in org.biojava.ontology">Ontology.Impl</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/ontology/OntologyException.html" title="class in org.biojava.ontology"><span class="strong">OntologyException</span></a> - Exception in <a href="./org/biojava/ontology/package-summary.html">org.biojava.ontology</a></dt>
<dd>
<div class="block">Thrown to indicate an error in an Ontology object</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/OntologyException.html#OntologyException()">OntologyException()</a></span> - Constructor for exception org.biojava.ontology.<a href="./org/biojava/ontology/OntologyException.html" title="class in org.biojava.ontology">OntologyException</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/OntologyException.html#OntologyException(java.lang.String)">OntologyException(String)</a></span> - Constructor for exception org.biojava.ontology.<a href="./org/biojava/ontology/OntologyException.html" title="class in org.biojava.ontology">OntologyException</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/OntologyException.html#OntologyException(java.lang.Throwable)">OntologyException(Throwable)</a></span> - Constructor for exception org.biojava.ontology.<a href="./org/biojava/ontology/OntologyException.html" title="class in org.biojava.ontology">OntologyException</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/OntologyException.html#OntologyException(java.lang.String, java.lang.Throwable)">OntologyException(String, Throwable)</a></span> - Constructor for exception org.biojava.ontology.<a href="./org/biojava/ontology/OntologyException.html" title="class in org.biojava.ontology">OntologyException</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/ontology/OntologyFactory.html" title="interface in org.biojava.ontology"><span class="strong">OntologyFactory</span></a> - Interface in <a href="./org/biojava/ontology/package-summary.html">org.biojava.ontology</a></dt>
<dd>
<div class="block">A factory for Ontology instances.</div>
</dd>
<dt><a href="./org/biojava/ontology/OntologyOps.html" title="interface in org.biojava.ontology"><span class="strong">OntologyOps</span></a> - Interface in <a href="./org/biojava/ontology/package-summary.html">org.biojava.ontology</a></dt>
<dd>
<div class="block">This is an interface for optimizing ontology operators.</div>
</dd>
<dt><a href="./org/biojava/ontology/OntologyTerm.html" title="interface in org.biojava.ontology"><span class="strong">OntologyTerm</span></a> - Interface in <a href="./org/biojava/ontology/package-summary.html">org.biojava.ontology</a></dt>
<dd>
<div class="block">A term in an ontology which identifies another ontology.</div>
</dd>
<dt><a href="./org/biojava/ontology/OntologyTerm.Impl.html" title="class in org.biojava.ontology"><span class="strong">OntologyTerm.Impl</span></a> - Class in <a href="./org/biojava/ontology/package-summary.html">org.biojava.ontology</a></dt>
<dd>
<div class="block">Simple in-memory implementation of a remote ontology term.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/OntologyTerm.Impl.html#OntologyTerm.Impl(org.biojava.ontology.Ontology, org.biojava.ontology.Ontology)">OntologyTerm.Impl(Ontology, Ontology)</a></span> - Constructor for class org.biojava.ontology.<a href="./org/biojava/ontology/OntologyTerm.Impl.html" title="class in org.biojava.ontology">OntologyTerm.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/OntologyTerm.Impl.html#OntologyTerm.Impl(org.biojava.ontology.Ontology, org.biojava.ontology.Ontology, java.lang.Object[])">OntologyTerm.Impl(Ontology, Ontology, Object[])</a></span> - Constructor for class org.biojava.ontology.<a href="./org/biojava/ontology/OntologyTerm.Impl.html" title="class in org.biojava.ontology">OntologyTerm.Impl</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/ontology/OntoTools.html" title="class in org.biojava.ontology"><span class="strong">OntoTools</span></a> - Class in <a href="./org/biojava/ontology/package-summary.html">org.biojava.ontology</a></dt>
<dd>
<div class="block">Tools for manipulating ontologies.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/TabIndexStore.html#open(java.io.File)">open(File)</a></span> - Static method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/TabIndexStore.html" title="class in org.biojava.bio.seq.db">TabIndexStore</a></dt>
<dd>
<div class="block">Open an existing index store.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/xml/FastXMLWriter.html#openTag(java.lang.String)">openTag(String)</a></span> - Method in class org.biojava.utils.xml.<a href="./org/biojava/utils/xml/FastXMLWriter.html" title="class in org.biojava.utils.xml">FastXMLWriter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/xml/PrettyXMLWriter.html#openTag(java.lang.String, java.lang.String)">openTag(String, String)</a></span> - Method in class org.biojava.utils.xml.<a href="./org/biojava/utils/xml/PrettyXMLWriter.html" title="class in org.biojava.utils.xml">PrettyXMLWriter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/xml/PrettyXMLWriter.html#openTag(java.lang.String)">openTag(String)</a></span> - Method in class org.biojava.utils.xml.<a href="./org/biojava/utils/xml/PrettyXMLWriter.html" title="class in org.biojava.utils.xml">PrettyXMLWriter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/xml/XMLWriter.html#openTag(java.lang.String, java.lang.String)">openTag(String, String)</a></span> - Method in interface org.biojava.utils.xml.<a href="./org/biojava/utils/xml/XMLWriter.html" title="interface in org.biojava.utils.xml">XMLWriter</a></dt>
<dd>
<div class="block">Open a new namespace-qualified XML tag.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/xml/XMLWriter.html#openTag(java.lang.String)">openTag(String)</a></span> - Method in interface org.biojava.utils.xml.<a href="./org/biojava/utils/xml/XMLWriter.html" title="interface in org.biojava.utils.xml">XMLWriter</a></dt>
<dd>
<div class="block">Open a new unqualified XML tag.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/OptimizableFilter.html" title="interface in org.biojava.bio.seq"><span class="strong">OptimizableFilter</span></a> - Interface in <a href="./org/biojava/bio/seq/package-summary.html">org.biojava.bio.seq</a></dt>
<dd>
<div class="block">The interface for filters that can potentialy optimize themselves, and
compare themselves with other filters.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FilterUtils.html#optimize(org.biojava.bio.seq.FeatureFilter)">optimize(FeatureFilter)</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FilterUtils.html" title="class in org.biojava.bio.seq">FilterUtils</a></dt>
<dd>
<div class="block">Attempts to reduce a FeatureFilter to an equivalent FeatureFilter with
fewer terms.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.html#optionIsTrue(org.biojava.bio.chromatogram.graphic.ChromatogramGraphic.Option)">optionIsTrue(ChromatogramGraphic.Option)</a></span> - Method in class org.biojava.bio.chromatogram.graphic.<a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.html" title="class in org.biojava.bio.chromatogram.graphic">ChromatogramGraphic</a></dt>
<dd>
<div class="block">Helper method for converting a <code>Boolean</code>-valued
option into a <code>boolean</code> primitive.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.html#options">options</a></span> - Variable in class org.biojava.bio.chromatogram.graphic.<a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.html" title="class in org.biojava.bio.chromatogram.graphic">ChromatogramGraphic</a></dt>
<dd>
<div class="block">The map containing the <a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.Option.html" title="class in org.biojava.bio.chromatogram.graphic"><code>ChromatogramGraphic.Option</code></a>s and values for this instance.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/filter/FilterTransformer.html#or(org.biojava.bio.seq.FeatureFilter.Or, org.biojava.bio.seq.FeatureFilter, org.biojava.bio.seq.FeatureFilter)">or(FeatureFilter.Or, FeatureFilter, FeatureFilter)</a></span> - Method in class org.biojava.bio.seq.filter.<a href="./org/biojava/bio/seq/filter/FilterTransformer.html" title="class in org.biojava.bio.seq.filter">FilterTransformer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FilterUtils.html#or(org.biojava.bio.seq.FeatureFilter, org.biojava.bio.seq.FeatureFilter)">or(FeatureFilter, FeatureFilter)</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FilterUtils.html" title="class in org.biojava.bio.seq">FilterUtils</a></dt>
<dd>
<div class="block">Construct a new filter which matches the union of two filters.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FilterUtils.html#or(org.biojava.bio.seq.FeatureFilter[])">or(FeatureFilter[])</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FilterUtils.html" title="class in org.biojava.bio.seq">FilterUtils</a></dt>
<dd>
<div class="block">Construct a new filter which matches the intersection of two filters.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.HibernateFeatureFilter.html#or">or</a></span> - Variable in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.HibernateFeatureFilter.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.HibernateFeatureFilter</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/db/biosql/OracleDBHelper.html" title="class in org.biojava.bio.seq.db.biosql"><span class="strong">OracleDBHelper</span></a> - Class in <a href="./org/biojava/bio/seq/db/biosql/package-summary.html">org.biojava.bio.seq.db.biosql</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>Use hibernate and org.biojavax.bio.db.*</i></div>
</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/biosql/OracleDBHelper.html#OracleDBHelper(java.sql.Connection)">OracleDBHelper(Connection)</a></span> - Constructor for class org.biojava.bio.seq.db.biosql.<a href="./org/biojava/bio/seq/db/biosql/OracleDBHelper.html" title="class in org.biojava.bio.seq.db.biosql">OracleDBHelper</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><a href="./org/biojavax/ga/functions/OrderCrossover.html" title="class in org.biojavax.ga.functions"><span class="strong">OrderCrossover</span></a> - Class in <a href="./org/biojavax/ga/functions/package-summary.html">org.biojavax.ga.functions</a></dt>
<dd>
<div class="block">This does a 2-point-crossover on two chromosomes keeping the Symbols in each
chromosome constant.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ga/functions/OrderCrossover.html#OrderCrossover()">OrderCrossover()</a></span> - Constructor for class org.biojavax.ga.functions.<a href="./org/biojavax/ga/functions/OrderCrossover.html" title="class in org.biojavax.ga.functions">OrderCrossover</a></dt>
<dd>
<div class="block">Sets the maximal number of crossover points to two and the crossover
probability to 0.5 and initializes this object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/AbstractULAlignment.html#orderedLables(java.util.Comparator)">orderedLables(Comparator)</a></span> - Method in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/AbstractULAlignment.html" title="class in org.biojava.bio.alignment">AbstractULAlignment</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/dist/OrderNDistribution.html" title="interface in org.biojava.bio.dist"><span class="strong">OrderNDistribution</span></a> - Interface in <a href="./org/biojava/bio/dist/package-summary.html">org.biojava.bio.dist</a></dt>
<dd>
<div class="block">Provides an N'th order distribution.</div>
</dd>
<dt><a href="./org/biojava/bio/dist/OrderNDistributionFactory.html" title="class in org.biojava.bio.dist"><span class="strong">OrderNDistributionFactory</span></a> - Class in <a href="./org/biojava/bio/dist/package-summary.html">org.biojava.bio.dist</a></dt>
<dd>
<div class="block">Default factory for Order-N distributions.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/OrderNDistributionFactory.html#OrderNDistributionFactory(org.biojava.bio.dist.DistributionFactory)">OrderNDistributionFactory(DistributionFactory)</a></span> - Constructor for class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/OrderNDistributionFactory.html" title="class in org.biojava.bio.dist">OrderNDistributionFactory</a></dt>
<dd>
<div class="block">Construct a new OrderNDistributionFactory with a specified factory
for conditioned distributions.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SymbolListViews.html#orderNSymbolList(org.biojava.bio.symbol.SymbolList, int)">orderNSymbolList(SymbolList, int)</a></span> - Static method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SymbolListViews.html" title="class in org.biojava.bio.symbol">SymbolListViews</a></dt>
<dd>
<div class="block">An n-th order view of another SymbolList.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.Terms.html#ORDLOCNAME_KEY">ORDLOCNAME_KEY</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.Terms.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat.Terms</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.Terms.html#ORFNAME_KEY">ORFNAME_KEY</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.Terms.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat.Terms</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bibliography/package-summary.html">org.biojava.bibliography</a> - package org.biojava.bibliography</dt>
<dd>
<div class="block">The data structures and interfaces included in this package define an
interoperable framework for bibliographic searches.</div>
</dd>
<dt><a href="./org/biojava/bio/package-summary.html">org.biojava.bio</a> - package org.biojava.bio</dt>
<dd>
<div class="block">The core classes that will be used throughout the bio packages.</div>
</dd>
<dt><a href="./org/biojava/bio/alignment/package-summary.html">org.biojava.bio.alignment</a> - package org.biojava.bio.alignment</dt>
<dd>
<div class="block">
Classes to generate and describe sequence alignments.</div>
</dd>
<dt><a href="./org/biojava/bio/annodb/package-summary.html">org.biojava.bio.annodb</a> - package org.biojava.bio.annodb</dt>
<dd>
<div class="block">
Databases of generic structured data (annotation) objects.</div>
</dd>
<dt><a href="./org/biojava/bio/chromatogram/package-summary.html">org.biojava.bio.chromatogram</a> - package org.biojava.bio.chromatogram</dt>
<dd>
<div class="block">
Interfaces and classes for chromatogram data, as produced by DNA sequencing equipment.</div>
</dd>
<dt><a href="./org/biojava/bio/chromatogram/graphic/package-summary.html">org.biojava.bio.chromatogram.graphic</a> - package org.biojava.bio.chromatogram.graphic</dt>
<dd>
<div class="block">
Tools for displaying chromatograms.</div>
</dd>
<dt><a href="./org/biojava/bio/dist/package-summary.html">org.biojava.bio.dist</a> - package org.biojava.bio.dist</dt>
<dd>
<div class="block">
Probability distributions over Alphabets.</div>
</dd>
<dt><a href="./org/biojava/bio/dp/package-summary.html">org.biojava.bio.dp</a> - package org.biojava.bio.dp</dt>
<dd>
<div class="block">HMM and Dynamic Programming Algorithms.</div>
</dd>
<dt><a href="./org/biojava/bio/dp/onehead/package-summary.html">org.biojava.bio.dp.onehead</a> - package org.biojava.bio.dp.onehead</dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/dp/twohead/package-summary.html">org.biojava.bio.dp.twohead</a> - package org.biojava.bio.dp.twohead</dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/gui/package-summary.html">org.biojava.bio.gui</a> - package org.biojava.bio.gui</dt>
<dd>
<div class="block">Graphical interfaces for biojava objects.</div>
</dd>
<dt><a href="./org/biojava/bio/gui/glyph/package-summary.html">org.biojava.bio.gui.glyph</a> - package org.biojava.bio.gui.glyph</dt>
<dd>
<div class="block">Glyphs implementations that draw shapes into SequenceRenderers</div>
</dd>
<dt><a href="./org/biojava/bio/gui/sequence/package-summary.html">org.biojava.bio.gui.sequence</a> - package org.biojava.bio.gui.sequence</dt>
<dd>
<div class="block">
Graphical displays of biological sequences and associated annotations.</div>
</dd>
<dt><a href="./org/biojava/bio/gui/sequence/tracklayout/package-summary.html">org.biojava.bio.gui.sequence.tracklayout</a> - package org.biojava.bio.gui.sequence.tracklayout</dt>
<dd>
<div class="block">Classes for the handling of the layout of a WrappedSequencePanel.</div>
</dd>
<dt><a href="./org/biojava/bio/molbio/package-summary.html">org.biojava.bio.molbio</a> - package org.biojava.bio.molbio</dt>
<dd>
<div class="block">The classes and interfaces in this package cover common molecular
biological techniques such as restriction digests and PCR.</div>
</dd>
<dt><a href="./org/biojava/bio/program/package-summary.html">org.biojava.bio.program</a> - package org.biojava.bio.program</dt>
<dd>
<div class="block">
Java wrappers for interacting with external bioinformatics tools.</div>
</dd>
<dt><a href="./org/biojava/bio/program/abi/package-summary.html">org.biojava.bio.program.abi</a> - package org.biojava.bio.program.abi</dt>
<dd>
<div class="block">ABI Trace Handling.</div>
</dd>
<dt><a href="./org/biojava/bio/program/blast2html/package-summary.html">org.biojava.bio.program.blast2html</a> - package org.biojava.bio.program.blast2html</dt>
<dd>
<div class="block">Code for generating HTML reports from blast output</div>
</dd>
<dt><a href="./org/biojava/bio/program/das/package-summary.html">org.biojava.bio.program.das</a> - package org.biojava.bio.program.das</dt>
<dd>
<div class="block">Development client for the Distributed Annotation System.</div>
</dd>
<dt><a href="./org/biojava/bio/program/das/dasalignment/package-summary.html">org.biojava.bio.program.das.dasalignment</a> - package org.biojava.bio.program.das.dasalignment</dt>
<dd>
<div class="block">
request alignments via DAS</div>
</dd>
<dt><a href="./org/biojava/bio/program/das/dasstructure/package-summary.html">org.biojava.bio.program.das.dasstructure</a> - package org.biojava.bio.program.das.dasstructure</dt>
<dd>
<div class="block">
request a protein structure via DAS</div>
</dd>
<dt><a href="./org/biojava/bio/program/fastq/package-summary.html">org.biojava.bio.program.fastq</a> - package org.biojava.bio.program.fastq</dt>
<dd>
<div class="block">FASTQ and variants sequence format IO.</div>
</dd>
<dt><a href="./org/biojava/bio/program/formats/package-summary.html">org.biojava.bio.program.formats</a> - package org.biojava.bio.program.formats</dt>
<dd>
<div class="block">
Experimental parsers using the tagvalue framework.</div>
</dd>
<dt><a href="./org/biojava/bio/program/gff/package-summary.html">org.biojava.bio.program.gff</a> - package org.biojava.bio.program.gff</dt>
<dd>
<div class="block">GFF manipulation.</div>
</dd>
<dt><a href="./org/biojava/bio/program/gff3/package-summary.html">org.biojava.bio.program.gff3</a> - package org.biojava.bio.program.gff3</dt>
<dd>
<div class="block">
Support for reading and writing GFF3.</div>
</dd>
<dt><a href="./org/biojava/bio/program/hmmer/package-summary.html">org.biojava.bio.program.hmmer</a> - package org.biojava.bio.program.hmmer</dt>
<dd>
<div class="block">
Tools for working with profile Hidden Markov Models from the HMMer package.</div>
</dd>
<dt><a href="./org/biojava/bio/program/homologene/package-summary.html">org.biojava.bio.program.homologene</a> - package org.biojava.bio.program.homologene</dt>
<dd>
<div class="block">
Support classes for Homologene data.</div>
</dd>
<dt><a href="./org/biojava/bio/program/indexdb/package-summary.html">org.biojava.bio.program.indexdb</a> - package org.biojava.bio.program.indexdb</dt>
<dd>
<div class="block">A flat-file ascii index of ascii flat files as per the OBDA specification.</div>
</dd>
<dt><a href="./org/biojava/bio/program/phred/package-summary.html">org.biojava.bio.program.phred</a> - package org.biojava.bio.program.phred</dt>
<dd>
<div class="block">Parser for Phred output</div>
</dd>
<dt><a href="./org/biojava/bio/program/sax/package-summary.html">org.biojava.bio.program.sax</a> - package org.biojava.bio.program.sax</dt>
<dd>
<div class="block">Parsers which offer XML representations of the output from common
bioinformatics tools.</div>
</dd>
<dt><a href="./org/biojava/bio/program/sax/blastxml/package-summary.html">org.biojava.bio.program.sax.blastxml</a> - package org.biojava.bio.program.sax.blastxml</dt>
<dd>
<div class="block">
Parsers for the XML output from NCBI blast.</div>
</dd>
<dt><a href="./org/biojava/bio/program/scf/package-summary.html">org.biojava.bio.program.scf</a> - package org.biojava.bio.program.scf</dt>
<dd>
<div class="block">
Support for the SCF chromatogram format.</div>
</dd>
<dt><a href="./org/biojava/bio/program/ssaha/package-summary.html">org.biojava.bio.program.ssaha</a> - package org.biojava.bio.program.ssaha</dt>
<dd>
<div class="block">SSAHA sequence searching API.</div>
</dd>
<dt><a href="./org/biojava/bio/program/ssbind/package-summary.html">org.biojava.bio.program.ssbind</a> - package org.biojava.bio.program.ssbind</dt>
<dd>
<div class="block">
Creation of objects from SAX events using the BioJava BlastLikeDataSetCollection DTD.</div>
</dd>
<dt><a href="./org/biojava/bio/program/tagvalue/package-summary.html">org.biojava.bio.program.tagvalue</a> - package org.biojava.bio.program.tagvalue</dt>
<dd>
<div class="block"> Process files as streams of records, each with tags with values.</div>
</dd>
<dt><a href="./org/biojava/bio/program/unigene/package-summary.html">org.biojava.bio.program.unigene</a> - package org.biojava.bio.program.unigene</dt>
<dd>
<div class="block">Objects for representing Unigene clusters.</div>
</dd>
<dt><a href="./org/biojava/bio/program/xff/package-summary.html">org.biojava.bio.program.xff</a> - package org.biojava.bio.program.xff</dt>
<dd>
<div class="block">Event-driven parsing system for the Extensible Feature Format (XFF).</div>
</dd>
<dt><a href="./org/biojava/bio/program/xml/package-summary.html">org.biojava.bio.program.xml</a> - package org.biojava.bio.program.xml</dt>
<dd>
<div class="block">Utility classes for the <code>org.biojava.bio.program.sax</code>
package.</div>
</dd>
<dt><a href="./org/biojava/bio/proteomics/package-summary.html">org.biojava.bio.proteomics</a> - package org.biojava.bio.proteomics</dt>
<dd>
<div class="block">Utilities to aid in performing various physical analysis of proteins.</div>
</dd>
<dt><a href="./org/biojava/bio/proteomics/aaindex/package-summary.html">org.biojava.bio.proteomics.aaindex</a> - package org.biojava.bio.proteomics.aaindex</dt>
<dd>
<div class="block">Classes and interfaces to load Amino Acid Index database files.</div>
</dd>
<dt><a href="./org/biojava/bio/search/package-summary.html">org.biojava.bio.search</a> - package org.biojava.bio.search</dt>
<dd>
<div class="block">
Interfaces and classes for representing sequence similarity search results.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/package-summary.html">org.biojava.bio.seq</a> - package org.biojava.bio.seq</dt>
<dd>
<div class="block">Classes and interfaces for defining biological sequences and informatics
objects.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/db/package-summary.html">org.biojava.bio.seq.db</a> - package org.biojava.bio.seq.db</dt>
<dd>
<div class="block">
Collections of biological sequence data.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/db/biofetch/package-summary.html">org.biojava.bio.seq.db.biofetch</a> - package org.biojava.bio.seq.db.biofetch</dt>
<dd>
<div class="block">Client for the OBDA BioFetch protocol.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/db/biosql/package-summary.html">org.biojava.bio.seq.db.biosql</a> - package org.biojava.bio.seq.db.biosql</dt>
<dd>
<div class="block">General purpose Sequence storage in a relational database.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/db/emblcd/package-summary.html">org.biojava.bio.seq.db.emblcd</a> - package org.biojava.bio.seq.db.emblcd</dt>
<dd>
<div class="block">
Readers for the EMBL CD-ROM format binary index files used by EMBOSS and Staden packages.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/db/flat/package-summary.html">org.biojava.bio.seq.db.flat</a> - package org.biojava.bio.seq.db.flat</dt>
<dd>
<div class="block">
Support for OBDA flatfile databases.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/distributed/package-summary.html">org.biojava.bio.seq.distributed</a> - package org.biojava.bio.seq.distributed</dt>
<dd>
<div class="block">Sequences and SequenceDBs which are composed from data taken
from a number of data sources.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/filter/package-summary.html">org.biojava.bio.seq.filter</a> - package org.biojava.bio.seq.filter</dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/homol/package-summary.html">org.biojava.bio.seq.homol</a> - package org.biojava.bio.seq.homol</dt>
<dd>
<div class="block">The classes and interfaces for defining sequence similarity and
honology.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/impl/package-summary.html">org.biojava.bio.seq.impl</a> - package org.biojava.bio.seq.impl</dt>
<dd>
<div class="block">Standard in-memory implementations of <code>Sequence</code> and
<code>Feature</code>.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/package-summary.html">org.biojava.bio.seq.io</a> - package org.biojava.bio.seq.io</dt>
<dd>
<div class="block">Classes and interfaces for processing and producing flat-file representations
of sequences.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/agave/package-summary.html">org.biojava.bio.seq.io.agave</a> - package org.biojava.bio.seq.io.agave</dt>
<dd>
<div class="block">Classes for converting between AGAVE XML and BioJava objects.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/filterxml/package-summary.html">org.biojava.bio.seq.io.filterxml</a> - package org.biojava.bio.seq.io.filterxml</dt>
<dd>
<div class="block">Tools for reading and writing an XML representation of BioJava's FeatureFilter language.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/game/package-summary.html">org.biojava.bio.seq.io.game</a> - package org.biojava.bio.seq.io.game</dt>
<dd>
<div class="block">Event-driven parsing system for the Gene Annotation Markup Elements (GAME).</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/game12/package-summary.html">org.biojava.bio.seq.io.game12</a> - package org.biojava.bio.seq.io.game12</dt>
<dd>
<div class="block">
Event-driven parsing system for the Gene Annotation Markup Elements (GAME).</div>
</dd>
<dt><a href="./org/biojava/bio/seq/projection/package-summary.html">org.biojava.bio.seq.projection</a> - package org.biojava.bio.seq.projection</dt>
<dd>
<div class="block">Code for projecting Feature objects and systematically altering their
properties.</div>
</dd>
<dt><a href="./org/biojava/bio/structure/package-summary.html">org.biojava.bio.structure</a> - package org.biojava.bio.structure</dt>
<dd>
<div class="block">
Interfaces and classes for protein structure (PDB).</div>
</dd>
<dt><a href="./org/biojava/bio/structure/align/package-summary.html">org.biojava.bio.structure.align</a> - package org.biojava.bio.structure.align</dt>
<dd>
<div class="block">Classes for the super-imposition of structures.</div>
</dd>
<dt><a href="./org/biojava/bio/structure/align/helper/package-summary.html">org.biojava.bio.structure.align.helper</a> - package org.biojava.bio.structure.align.helper</dt>
<dd>
<div class="block">Helper classes for structural alignment.</div>
</dd>
<dt><a href="./org/biojava/bio/structure/align/pairwise/package-summary.html">org.biojava.bio.structure.align.pairwise</a> - package org.biojava.bio.structure.align.pairwise</dt>
<dd>
<div class="block">Classes for the pairwise alignment of structures.</div>
</dd>
<dt><a href="./org/biojava/bio/structure/gui/package-summary.html">org.biojava.bio.structure.gui</a> - package org.biojava.bio.structure.gui</dt>
<dd>
<div class="block">
A few convenience classes to view protein structures with Jmol (if it is on the classpath),
to calculate a protein structure alignment and to investigate the internals of the protein structure alignment algorithm.</div>
</dd>
<dt><a href="./org/biojava/bio/structure/gui/events/package-summary.html">org.biojava.bio.structure.gui.events</a> - package org.biojava.bio.structure.gui.events</dt>
<dd>
<div class="block">
Some event classes for the protein structure GUIs.</div>
</dd>
<dt><a href="./org/biojava/bio/structure/gui/util/package-summary.html">org.biojava.bio.structure.gui.util</a> - package org.biojava.bio.structure.gui.util</dt>
<dd>
<div class="block">
Some utility classes for the protein structure GUIs.</div>
</dd>
<dt><a href="./org/biojava/bio/structure/io/package-summary.html">org.biojava.bio.structure.io</a> - package org.biojava.bio.structure.io</dt>
<dd>
<div class="block">Input and Output of Structures</div>
</dd>
<dt><a href="./org/biojava/bio/structure/io/mmcif/package-summary.html">org.biojava.bio.structure.io.mmcif</a> - package org.biojava.bio.structure.io.mmcif</dt>
<dd>
<div class="block">Input and Output of mmcif files</div>
</dd>
<dt><a href="./org/biojava/bio/structure/io/mmcif/chem/package-summary.html">org.biojava.bio.structure.io.mmcif.chem</a> - package org.biojava.bio.structure.io.mmcif.chem</dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/structure/io/mmcif/model/package-summary.html">org.biojava.bio.structure.io.mmcif.model</a> - package org.biojava.bio.structure.io.mmcif.model</dt>
<dd>
<div class="block">Datamodel objects used for processing mmcif files.</div>
</dd>
<dt><a href="./org/biojava/bio/structure/jama/package-summary.html">org.biojava.bio.structure.jama</a> - package org.biojava.bio.structure.jama</dt>
<dd>
<div class="block">Matrix package for from <a href="http://math.nist.gov/javanumerics/jama/">JAMA</a></div>
</dd>
<dt><a href="./org/biojava/bio/structure/server/package-summary.html">org.biojava.bio.structure.server</a> - package org.biojava.bio.structure.server</dt>
<dd>
<div class="block">
classes for easier management of PDB installations</div>
</dd>
<dt><a href="./org/biojava/bio/symbol/package-summary.html">org.biojava.bio.symbol</a> - package org.biojava.bio.symbol</dt>
<dd>
<div class="block">Representation of the Symbols that make up a sequence, and locations within
them.</div>
</dd>
<dt><a href="./org/biojava/bio/taxa/package-summary.html">org.biojava.bio.taxa</a> - package org.biojava.bio.taxa</dt>
<dd>
<div class="block">Taxonomy object for representing species information.</div>
</dd>
<dt><a href="./org/biojava/directory/package-summary.html">org.biojava.directory</a> - package org.biojava.directory</dt>
<dd>
<div class="block">Open Bio Sequence Database Access (OBDA) registry support.</div>
</dd>
<dt><a href="./org/biojava/naming/package-summary.html">org.biojava.naming</a> - package org.biojava.naming</dt>
<dd> </dd>
<dt><a href="./org/biojava/ontology/package-summary.html">org.biojava.ontology</a> - package org.biojava.ontology</dt>
<dd>
<div class="block">
A general-purpose API for ontologies.</div>
</dd>
<dt><a href="./org/biojava/ontology/io/package-summary.html">org.biojava.ontology.io</a> - package org.biojava.ontology.io</dt>
<dd>
<div class="block">
Tools for loading and saving ontologies.</div>
</dd>
<dt><a href="./org/biojava/ontology/obo/package-summary.html">org.biojava.ontology.obo</a> - package org.biojava.ontology.obo</dt>
<dd> </dd>
<dt><a href="./org/biojava/stats/svm/package-summary.html">org.biojava.stats.svm</a> - package org.biojava.stats.svm</dt>
<dd>
<div class="block">
Support Vector Machine classification and regression.</div>
</dd>
<dt><a href="./org/biojava/stats/svm/tools/package-summary.html">org.biojava.stats.svm.tools</a> - package org.biojava.stats.svm.tools</dt>
<dd>
<div class="block">Tools for use of the SVM package.</div>
</dd>
<dt><a href="./org/biojava/utils/package-summary.html">org.biojava.utils</a> - package org.biojava.utils</dt>
<dd>
<div class="block">
Miscellaneous utility classes used by other BioJava components.</div>
</dd>
<dt><a href="./org/biojava/utils/automata/package-summary.html">org.biojava.utils.automata</a> - package org.biojava.utils.automata</dt>
<dd> </dd>
<dt><a href="./org/biojava/utils/cache/package-summary.html">org.biojava.utils.cache</a> - package org.biojava.utils.cache</dt>
<dd>
<div class="block">A simple cache system with pluggable caching behaviours.</div>
</dd>
<dt><a href="./org/biojava/utils/candy/package-summary.html">org.biojava.utils.candy</a> - package org.biojava.utils.candy</dt>
<dd>
<div class="block">The data structures and interfaces included in this package define an
interoperable framework for simple controlled vocabularies.</div>
</dd>
<dt><a href="./org/biojava/utils/io/package-summary.html">org.biojava.utils.io</a> - package org.biojava.utils.io</dt>
<dd>
<div class="block">I/O utility classes.</div>
</dd>
<dt><a href="./org/biojava/utils/lsid/package-summary.html">org.biojava.utils.lsid</a> - package org.biojava.utils.lsid</dt>
<dd>
<div class="block">Life Science Identifier (LSID) package.</div>
</dd>
<dt><a href="./org/biojava/utils/math/package-summary.html">org.biojava.utils.math</a> - package org.biojava.utils.math</dt>
<dd>
<div class="block">
Mathematical utility classes.</div>
</dd>
<dt><a href="./org/biojava/utils/net/package-summary.html">org.biojava.utils.net</a> - package org.biojava.utils.net</dt>
<dd>
<div class="block">
Network programming utility classes.</div>
</dd>
<dt><a href="./org/biojava/utils/process/package-summary.html">org.biojava.utils.process</a> - package org.biojava.utils.process</dt>
<dd>
<div class="block">Classes and interfaces to execute external processes and to handle its input and output streams in multiple threads.</div>
</dd>
<dt><a href="./org/biojava/utils/regex/package-summary.html">org.biojava.utils.regex</a> - package org.biojava.utils.regex</dt>
<dd>
<div class="block">This package is used to perform regular expression searches of
SymbolLists defined in arbitrary Alphabets.</div>
</dd>
<dt><a href="./org/biojava/utils/stax/package-summary.html">org.biojava.utils.stax</a> - package org.biojava.utils.stax</dt>
<dd>
<div class="block">The Stack API for XML (StAX).</div>
</dd>
<dt><a href="./org/biojava/utils/walker/package-summary.html">org.biojava.utils.walker</a> - package org.biojava.utils.walker</dt>
<dd> </dd>
<dt><a href="./org/biojava/utils/xml/package-summary.html">org.biojava.utils.xml</a> - package org.biojava.utils.xml</dt>
<dd>
<div class="block">
Utility classes for handling and generating XML documents.</div>
</dd>
<dt><a href="./org/biojavax/package-summary.html">org.biojavax</a> - package org.biojavax</dt>
<dd>
<div class="block">The Biojava extensions packages, classes that extend the core biojava
functionality</div>
</dd>
<dt><a href="./org/biojavax/bio/package-summary.html">org.biojavax.bio</a> - package org.biojavax.bio</dt>
<dd>
<div class="block">Classes to represent biological entities and their relationships.</div>
</dd>
<dt><a href="./org/biojavax/bio/db/package-summary.html">org.biojavax.bio.db</a> - package org.biojavax.bio.db</dt>
<dd>
<div class="block">Interactions between biojavax objects and a DB.</div>
</dd>
<dt><a href="./org/biojavax/bio/db/biosql/package-summary.html">org.biojavax.bio.db.biosql</a> - package org.biojavax.bio.db.biosql</dt>
<dd>
<div class="block">Interface between biojava and biosql databases</div>
</dd>
<dt><a href="./org/biojavax/bio/db/ncbi/package-summary.html">org.biojavax.bio.db.ncbi</a> - package org.biojavax.bio.db.ncbi</dt>
<dd>
<div class="block">Interfaces to NCBI data.</div>
</dd>
<dt><a href="./org/biojavax/bio/phylo/package-summary.html">org.biojavax.bio.phylo</a> - package org.biojavax.bio.phylo</dt>
<dd>
<div class="block">Classes to support phlylogeny objects.</div>
</dd>
<dt><a href="./org/biojavax/bio/phylo/io/phylip/package-summary.html">org.biojavax.bio.phylo.io.phylip</a> - package org.biojavax.bio.phylo.io.phylip</dt>
<dd>
<div class="block">Classes to support the reading and writing of PHYLIP format.</div>
</dd>
<dt><a href="./org/biojavax/bio/seq/package-summary.html">org.biojavax.bio.seq</a> - package org.biojavax.bio.seq</dt>
<dd>
<div class="block">Rich implementations of Sequences, Locations and Features.</div>
</dd>
<dt><a href="./org/biojavax/bio/seq/io/package-summary.html">org.biojavax.bio.seq.io</a> - package org.biojavax.bio.seq.io</dt>
<dd>
<div class="block">Classes to support the I/O of RichSequence and
Bioentry objects.</div>
</dd>
<dt><a href="./org/biojavax/bio/taxa/package-summary.html">org.biojavax.bio.taxa</a> - package org.biojavax.bio.taxa</dt>
<dd>
<div class="block">Objects that model the NCBI taxonomy schema as described in the BioSQL
schema.</div>
</dd>
<dt><a href="./org/biojavax/bio/taxa/io/package-summary.html">org.biojavax.bio.taxa.io</a> - package org.biojavax.bio.taxa.io</dt>
<dd> </dd>
<dt><a href="./org/biojavax/ga/package-summary.html">org.biojavax.ga</a> - package org.biojavax.ga</dt>
<dd>
<div class="block">Classes to provide a genetic algorithm framework</div>
</dd>
<dt><a href="./org/biojavax/ga/exception/package-summary.html">org.biojavax.ga.exception</a> - package org.biojavax.ga.exception</dt>
<dd>
<div class="block">Exceptions related to the GA framework</div>
</dd>
<dt><a href="./org/biojavax/ga/functions/package-summary.html">org.biojavax.ga.functions</a> - package org.biojavax.ga.functions</dt>
<dd>
<div class="block">GA functions</div>
</dd>
<dt><a href="./org/biojavax/ga/impl/package-summary.html">org.biojavax.ga.impl</a> - package org.biojavax.ga.impl</dt>
<dd>
<div class="block">Default implementations and abstract classes.</div>
</dd>
<dt><a href="./org/biojavax/ga/util/package-summary.html">org.biojavax.ga.util</a> - package org.biojavax.ga.util</dt>
<dd>
<div class="block">Utility functions and helper classes</div>
</dd>
<dt><a href="./org/biojavax/ontology/package-summary.html">org.biojavax.ontology</a> - package org.biojavax.ontology</dt>
<dd>
<div class="block">Extensions to the biojava ontology model that represent BioSQL ontology.</div>
</dd>
<dt><a href="./org/biojavax/utils/package-summary.html">org.biojavax.utils</a> - package org.biojavax.utils</dt>
<dd>
<div class="block">Utility classes that are used by biojavax objects but could have wider utility
to other applications.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLFormat.html#ORGANELLE_TAG">ORGANELLE_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLFormat.html" title="class in org.biojavax.bio.seq.io">EMBLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html#ORGANELLE_TAG">ORGANELLE_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html" title="class in org.biojavax.bio.seq.io">EMBLxmlFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtFormat.html#ORGANELLE_TAG">ORGANELLE_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtFormat.html" title="class in org.biojavax.bio.seq.io">UniProtFormat</a></dt>
<dd> </dd>
<dt><a href="./org/biojavax/ga/Organism.html" title="interface in org.biojavax.ga"><span class="strong">Organism</span></a> - Interface in <a href="./org/biojavax/ga/package-summary.html">org.biojavax.ga</a></dt>
<dd>
<div class="block">A GA 'organism' contains one or more Chromosomes</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/EmblLikeFormat.html#ORGANISM_TAG">ORGANISM_TAG</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/EmblLikeFormat.html" title="class in org.biojava.bio.seq.io">EmblLikeFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/GenbankFormat.html#ORGANISM_TAG">ORGANISM_TAG</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/GenbankFormat.html" title="class in org.biojava.bio.seq.io">GenbankFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLFormat.html#ORGANISM_TAG">ORGANISM_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLFormat.html" title="class in org.biojavax.bio.seq.io">EMBLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html#ORGANISM_TAG">ORGANISM_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html" title="class in org.biojavax.bio.seq.io">EMBLxmlFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/GenbankFormat.html#ORGANISM_TAG">ORGANISM_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/GenbankFormat.html" title="class in org.biojavax.bio.seq.io">GenbankFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/INSDseqFormat.html#ORGANISM_TAG">ORGANISM_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/INSDseqFormat.html" title="class in org.biojavax.bio.seq.io">INSDseqFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtFormat.html#ORGANISM_TAG">ORGANISM_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtFormat.html" title="class in org.biojavax.bio.seq.io">UniProtFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#ORGANISM_TAG">ORGANISM_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/EmblLikeFormat.html#ORGANISM_XREF_TAG">ORGANISM_XREF_TAG</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/EmblLikeFormat.html" title="class in org.biojava.bio.seq.io">EmblLikeFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/OrganismParser.html" title="class in org.biojava.bio.seq.io"><span class="strong">OrganismParser</span></a> - Class in <a href="./org/biojava/bio/seq/io/package-summary.html">org.biojava.bio.seq.io</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>Use org.biojavax.bio.taxa framework instead</i></div>
</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/OrganismParser.html#OrganismParser(org.biojava.bio.seq.io.SequenceBuilder, org.biojava.bio.taxa.TaxonFactory, org.biojava.bio.taxa.TaxonParser, java.lang.String, java.lang.String, java.lang.String)">OrganismParser(SequenceBuilder, TaxonFactory, TaxonParser, String, String, String)</a></span> - Constructor for class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/OrganismParser.html" title="class in org.biojava.bio.seq.io">OrganismParser</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/OrganismParser.Factory.html" title="class in org.biojava.bio.seq.io"><span class="strong">OrganismParser.Factory</span></a> - Class in <a href="./org/biojava/bio/seq/io/package-summary.html">org.biojava.bio.seq.io</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Factory which wraps SequenceBuilders in an OrganismParser.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/OrganismParser.Factory.html#OrganismParser.Factory(org.biojava.bio.seq.io.SequenceBuilderFactory, org.biojava.bio.taxa.TaxonFactory, org.biojava.bio.taxa.TaxonParser, java.lang.String, java.lang.String, java.lang.String)">OrganismParser.Factory(SequenceBuilderFactory, TaxonFactory, TaxonParser, String, String, String)</a></span> - Constructor for class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/OrganismParser.Factory.html" title="class in org.biojava.bio.seq.io">OrganismParser.Factory</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ga/impl/SimplePopulation.html#organisms()">organisms()</a></span> - Method in class org.biojavax.ga.impl.<a href="./org/biojavax/ga/impl/SimplePopulation.html" title="class in org.biojavax.ga.impl">SimplePopulation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/Population.html#ORGANISMS">ORGANISMS</a></span> - Static variable in interface org.biojavax.ga.<a href="./org/biojavax/ga/Population.html" title="interface in org.biojavax.ga">Population</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/Population.html#organisms()">organisms()</a></span> - Method in interface org.biojavax.ga.<a href="./org/biojavax/ga/Population.html" title="interface in org.biojavax.ga">Population</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/RevCompSequence.html#origSeq">origSeq</a></span> - Variable in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/RevCompSequence.html" title="class in org.biojava.bio.seq.impl">RevCompSequence</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/homologene/Orthologue.html" title="interface in org.biojava.bio.program.homologene"><span class="strong">Orthologue</span></a> - Interface in <a href="./org/biojava/bio/program/homologene/package-summary.html">org.biojava.bio.program.homologene</a></dt>
<dd>
<div class="block">this entry contains data about the orthologue.</div>
</dd>
<dt><a href="./org/biojava/bio/program/homologene/OrthologueFilter.html" title="interface in org.biojava.bio.program.homologene"><span class="strong">OrthologueFilter</span></a> - Interface in <a href="./org/biojava/bio/program/homologene/package-summary.html">org.biojava.bio.program.homologene</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/homologene/OrthologueFilter.AcceptAll.html" title="class in org.biojava.bio.program.homologene"><span class="strong">OrthologueFilter.AcceptAll</span></a> - Class in <a href="./org/biojava/bio/program/homologene/package-summary.html">org.biojava.bio.program.homologene</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/OrthologueFilter.AcceptAll.html#OrthologueFilter.AcceptAll()">OrthologueFilter.AcceptAll()</a></span> - Constructor for class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/OrthologueFilter.AcceptAll.html" title="class in org.biojava.bio.program.homologene">OrthologueFilter.AcceptAll</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/homologene/OrthologueFilter.And.html" title="class in org.biojava.bio.program.homologene"><span class="strong">OrthologueFilter.And</span></a> - Class in <a href="./org/biojava/bio/program/homologene/package-summary.html">org.biojava.bio.program.homologene</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/OrthologueFilter.And.html#OrthologueFilter.And(org.biojava.bio.program.homologene.OrthologueFilter, org.biojava.bio.program.homologene.OrthologueFilter)">OrthologueFilter.And(OrthologueFilter, OrthologueFilter)</a></span> - Constructor for class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/OrthologueFilter.And.html" title="class in org.biojava.bio.program.homologene">OrthologueFilter.And</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/homologene/OrthologueFilter.ByAccession.html" title="class in org.biojava.bio.program.homologene"><span class="strong">OrthologueFilter.ByAccession</span></a> - Class in <a href="./org/biojava/bio/program/homologene/package-summary.html">org.biojava.bio.program.homologene</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/OrthologueFilter.ByAccession.html#OrthologueFilter.ByAccession(java.lang.String)">OrthologueFilter.ByAccession(String)</a></span> - Constructor for class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/OrthologueFilter.ByAccession.html" title="class in org.biojava.bio.program.homologene">OrthologueFilter.ByAccession</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/homologene/OrthologueFilter.ByHomologeneID.html" title="class in org.biojava.bio.program.homologene"><span class="strong">OrthologueFilter.ByHomologeneID</span></a> - Class in <a href="./org/biojava/bio/program/homologene/package-summary.html">org.biojava.bio.program.homologene</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/OrthologueFilter.ByHomologeneID.html#OrthologueFilter.ByHomologeneID(java.lang.String)">OrthologueFilter.ByHomologeneID(String)</a></span> - Constructor for class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/OrthologueFilter.ByHomologeneID.html" title="class in org.biojava.bio.program.homologene">OrthologueFilter.ByHomologeneID</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/homologene/OrthologueFilter.ByLocusID.html" title="class in org.biojava.bio.program.homologene"><span class="strong">OrthologueFilter.ByLocusID</span></a> - Class in <a href="./org/biojava/bio/program/homologene/package-summary.html">org.biojava.bio.program.homologene</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/OrthologueFilter.ByLocusID.html#OrthologueFilter.ByLocusID(java.lang.String)">OrthologueFilter.ByLocusID(String)</a></span> - Constructor for class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/OrthologueFilter.ByLocusID.html" title="class in org.biojava.bio.program.homologene">OrthologueFilter.ByLocusID</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/homologene/OrthologueFilter.ByTaxon.html" title="class in org.biojava.bio.program.homologene"><span class="strong">OrthologueFilter.ByTaxon</span></a> - Class in <a href="./org/biojava/bio/program/homologene/package-summary.html">org.biojava.bio.program.homologene</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/OrthologueFilter.ByTaxon.html#OrthologueFilter.ByTaxon(org.biojava.bio.program.homologene.Taxon)">OrthologueFilter.ByTaxon(Taxon)</a></span> - Constructor for class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/OrthologueFilter.ByTaxon.html" title="class in org.biojava.bio.program.homologene">OrthologueFilter.ByTaxon</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/homologene/OrthologueFilter.ByTaxonID.html" title="class in org.biojava.bio.program.homologene"><span class="strong">OrthologueFilter.ByTaxonID</span></a> - Class in <a href="./org/biojava/bio/program/homologene/package-summary.html">org.biojava.bio.program.homologene</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/OrthologueFilter.ByTaxonID.html#OrthologueFilter.ByTaxonID(int)">OrthologueFilter.ByTaxonID(int)</a></span> - Constructor for class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/OrthologueFilter.ByTaxonID.html" title="class in org.biojava.bio.program.homologene">OrthologueFilter.ByTaxonID</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/homologene/OrthologueFilter.ByTitle.html" title="class in org.biojava.bio.program.homologene"><span class="strong">OrthologueFilter.ByTitle</span></a> - Class in <a href="./org/biojava/bio/program/homologene/package-summary.html">org.biojava.bio.program.homologene</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/OrthologueFilter.ByTitle.html#OrthologueFilter.ByTitle(java.lang.String)">OrthologueFilter.ByTitle(String)</a></span> - Constructor for class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/OrthologueFilter.ByTitle.html" title="class in org.biojava.bio.program.homologene">OrthologueFilter.ByTitle</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/homologene/OrthologueFilter.Not.html" title="class in org.biojava.bio.program.homologene"><span class="strong">OrthologueFilter.Not</span></a> - Class in <a href="./org/biojava/bio/program/homologene/package-summary.html">org.biojava.bio.program.homologene</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/OrthologueFilter.Not.html#OrthologueFilter.Not(org.biojava.bio.program.homologene.OrthologueFilter)">OrthologueFilter.Not(OrthologueFilter)</a></span> - Constructor for class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/OrthologueFilter.Not.html" title="class in org.biojava.bio.program.homologene">OrthologueFilter.Not</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/homologene/OrthologueFilter.Or.html" title="class in org.biojava.bio.program.homologene"><span class="strong">OrthologueFilter.Or</span></a> - Class in <a href="./org/biojava/bio/program/homologene/package-summary.html">org.biojava.bio.program.homologene</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/OrthologueFilter.Or.html#OrthologueFilter.Or(org.biojava.bio.program.homologene.OrthologueFilter, org.biojava.bio.program.homologene.OrthologueFilter)">OrthologueFilter.Or(OrthologueFilter, OrthologueFilter)</a></span> - Constructor for class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/OrthologueFilter.Or.html" title="class in org.biojava.bio.program.homologene">OrthologueFilter.Or</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/homologene/OrthologueFilter.Xor.html" title="class in org.biojava.bio.program.homologene"><span class="strong">OrthologueFilter.Xor</span></a> - Class in <a href="./org/biojava/bio/program/homologene/package-summary.html">org.biojava.bio.program.homologene</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/OrthologueFilter.Xor.html#OrthologueFilter.Xor(org.biojava.bio.program.homologene.OrthologueFilter, org.biojava.bio.program.homologene.OrthologueFilter)">OrthologueFilter.Xor(OrthologueFilter, OrthologueFilter)</a></span> - Constructor for class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/OrthologueFilter.Xor.html" title="class in org.biojava.bio.program.homologene">OrthologueFilter.Xor</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/homologene/OrthologueSet.html" title="interface in org.biojava.bio.program.homologene"><span class="strong">OrthologueSet</span></a> - Interface in <a href="./org/biojava/bio/program/homologene/package-summary.html">org.biojava.bio.program.homologene</a></dt>
<dd>
<div class="block">Interface for classes that store and manipulate
orthologues.</div>
</dd>
<dt><a href="./org/biojava/bio/program/homologene/OrthologueSet.Iterator.html" title="interface in org.biojava.bio.program.homologene"><span class="strong">OrthologueSet.Iterator</span></a> - Interface in <a href="./org/biojava/bio/program/homologene/package-summary.html">org.biojava.bio.program.homologene</a></dt>
<dd>
<div class="block">An iterator for the contents of
an OrthologueSet.</div>
</dd>
<dt><a href="./org/biojava/bio/program/homologene/OrthoPair.html" title="interface in org.biojava.bio.program.homologene"><span class="strong">OrthoPair</span></a> - Interface in <a href="./org/biojava/bio/program/homologene/package-summary.html">org.biojava.bio.program.homologene</a></dt>
<dd>
<div class="block">Each HomologeneEntry represents a single
Homologene record that relates two
presumptive orthologues.</div>
</dd>
<dt><a href="./org/biojava/bio/program/homologene/OrthoPairCollection.html" title="interface in org.biojava.bio.program.homologene"><span class="strong">OrthoPairCollection</span></a> - Interface in <a href="./org/biojava/bio/program/homologene/package-summary.html">org.biojava.bio.program.homologene</a></dt>
<dd>
<div class="block">Interface for a Set of OrthoPairSets</div>
</dd>
<dt><a href="./org/biojava/bio/program/homologene/OrthoPairCollection.Iterator.html" title="interface in org.biojava.bio.program.homologene"><span class="strong">OrthoPairCollection.Iterator</span></a> - Interface in <a href="./org/biojava/bio/program/homologene/package-summary.html">org.biojava.bio.program.homologene</a></dt>
<dd>
<div class="block">Iterator for a OrthoPairCollection</div>
</dd>
<dt><a href="./org/biojava/bio/program/homologene/OrthoPairFilter.html" title="interface in org.biojava.bio.program.homologene"><span class="strong">OrthoPairFilter</span></a> - Interface in <a href="./org/biojava/bio/program/homologene/package-summary.html">org.biojava.bio.program.homologene</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/homologene/OrthoPairFilter.AcceptAll.html" title="class in org.biojava.bio.program.homologene"><span class="strong">OrthoPairFilter.AcceptAll</span></a> - Class in <a href="./org/biojava/bio/program/homologene/package-summary.html">org.biojava.bio.program.homologene</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/OrthoPairFilter.AcceptAll.html#OrthoPairFilter.AcceptAll()">OrthoPairFilter.AcceptAll()</a></span> - Constructor for class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/OrthoPairFilter.AcceptAll.html" title="class in org.biojava.bio.program.homologene">OrthoPairFilter.AcceptAll</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/homologene/OrthoPairFilter.And.html" title="class in org.biojava.bio.program.homologene"><span class="strong">OrthoPairFilter.And</span></a> - Class in <a href="./org/biojava/bio/program/homologene/package-summary.html">org.biojava.bio.program.homologene</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/OrthoPairFilter.And.html#OrthoPairFilter.And(org.biojava.bio.program.homologene.OrthoPairFilter, org.biojava.bio.program.homologene.OrthoPairFilter)">OrthoPairFilter.And(OrthoPairFilter, OrthoPairFilter)</a></span> - Constructor for class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/OrthoPairFilter.And.html" title="class in org.biojava.bio.program.homologene">OrthoPairFilter.And</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/homologene/OrthoPairFilter.ByMaxIdentity.html" title="class in org.biojava.bio.program.homologene"><span class="strong">OrthoPairFilter.ByMaxIdentity</span></a> - Class in <a href="./org/biojava/bio/program/homologene/package-summary.html">org.biojava.bio.program.homologene</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/OrthoPairFilter.ByMaxIdentity.html#OrthoPairFilter.ByMaxIdentity(double)">OrthoPairFilter.ByMaxIdentity(double)</a></span> - Constructor for class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/OrthoPairFilter.ByMaxIdentity.html" title="class in org.biojava.bio.program.homologene">OrthoPairFilter.ByMaxIdentity</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/homologene/OrthoPairFilter.ByMinIdentity.html" title="class in org.biojava.bio.program.homologene"><span class="strong">OrthoPairFilter.ByMinIdentity</span></a> - Class in <a href="./org/biojava/bio/program/homologene/package-summary.html">org.biojava.bio.program.homologene</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/OrthoPairFilter.ByMinIdentity.html#OrthoPairFilter.ByMinIdentity(double)">OrthoPairFilter.ByMinIdentity(double)</a></span> - Constructor for class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/OrthoPairFilter.ByMinIdentity.html" title="class in org.biojava.bio.program.homologene">OrthoPairFilter.ByMinIdentity</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/homologene/OrthoPairFilter.ByRef.html" title="class in org.biojava.bio.program.homologene"><span class="strong">OrthoPairFilter.ByRef</span></a> - Class in <a href="./org/biojava/bio/program/homologene/package-summary.html">org.biojava.bio.program.homologene</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/OrthoPairFilter.ByRef.html#OrthoPairFilter.ByRef(java.lang.String)">OrthoPairFilter.ByRef(String)</a></span> - Constructor for class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/OrthoPairFilter.ByRef.html" title="class in org.biojava.bio.program.homologene">OrthoPairFilter.ByRef</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/homologene/OrthoPairFilter.BySimilarityType.html" title="class in org.biojava.bio.program.homologene"><span class="strong">OrthoPairFilter.BySimilarityType</span></a> - Class in <a href="./org/biojava/bio/program/homologene/package-summary.html">org.biojava.bio.program.homologene</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/OrthoPairFilter.BySimilarityType.html#OrthoPairFilter.BySimilarityType(org.biojava.bio.program.homologene.SimilarityType)">OrthoPairFilter.BySimilarityType(SimilarityType)</a></span> - Constructor for class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/OrthoPairFilter.BySimilarityType.html" title="class in org.biojava.bio.program.homologene">OrthoPairFilter.BySimilarityType</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/homologene/OrthoPairFilter.Not.html" title="class in org.biojava.bio.program.homologene"><span class="strong">OrthoPairFilter.Not</span></a> - Class in <a href="./org/biojava/bio/program/homologene/package-summary.html">org.biojava.bio.program.homologene</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/OrthoPairFilter.Not.html#OrthoPairFilter.Not(org.biojava.bio.program.homologene.OrthoPairFilter)">OrthoPairFilter.Not(OrthoPairFilter)</a></span> - Constructor for class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/OrthoPairFilter.Not.html" title="class in org.biojava.bio.program.homologene">OrthoPairFilter.Not</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/homologene/OrthoPairFilter.Or.html" title="class in org.biojava.bio.program.homologene"><span class="strong">OrthoPairFilter.Or</span></a> - Class in <a href="./org/biojava/bio/program/homologene/package-summary.html">org.biojava.bio.program.homologene</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/OrthoPairFilter.Or.html#OrthoPairFilter.Or(org.biojava.bio.program.homologene.OrthoPairFilter, org.biojava.bio.program.homologene.OrthoPairFilter)">OrthoPairFilter.Or(OrthoPairFilter, OrthoPairFilter)</a></span> - Constructor for class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/OrthoPairFilter.Or.html" title="class in org.biojava.bio.program.homologene">OrthoPairFilter.Or</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/homologene/OrthoPairFilter.Xor.html" title="class in org.biojava.bio.program.homologene"><span class="strong">OrthoPairFilter.Xor</span></a> - Class in <a href="./org/biojava/bio/program/homologene/package-summary.html">org.biojava.bio.program.homologene</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/OrthoPairFilter.Xor.html#OrthoPairFilter.Xor(org.biojava.bio.program.homologene.OrthoPairFilter, org.biojava.bio.program.homologene.OrthoPairFilter)">OrthoPairFilter.Xor(OrthoPairFilter, OrthoPairFilter)</a></span> - Constructor for class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/OrthoPairFilter.Xor.html" title="class in org.biojava.bio.program.homologene">OrthoPairFilter.Xor</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/homologene/OrthoPairSet.html" title="interface in org.biojava.bio.program.homologene"><span class="strong">OrthoPairSet</span></a> - Interface in <a href="./org/biojava/bio/program/homologene/package-summary.html">org.biojava.bio.program.homologene</a></dt>
<dd>
<div class="block">represents the Homologene Group.</div>
</dd>
<dt><a href="./org/biojava/bio/program/homologene/OrthoPairSet.Iterator.html" title="interface in org.biojava.bio.program.homologene"><span class="strong">OrthoPairSet.Iterator</span></a> - Interface in <a href="./org/biojava/bio/program/homologene/package-summary.html">org.biojava.bio.program.homologene</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/homologene/OrthoPairSetFilter.html" title="interface in org.biojava.bio.program.homologene"><span class="strong">OrthoPairSetFilter</span></a> - Interface in <a href="./org/biojava/bio/program/homologene/package-summary.html">org.biojava.bio.program.homologene</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/homologene/OrthoPairSetFilter.AcceptAll.html" title="class in org.biojava.bio.program.homologene"><span class="strong">OrthoPairSetFilter.AcceptAll</span></a> - Class in <a href="./org/biojava/bio/program/homologene/package-summary.html">org.biojava.bio.program.homologene</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/OrthoPairSetFilter.AcceptAll.html#OrthoPairSetFilter.AcceptAll()">OrthoPairSetFilter.AcceptAll()</a></span> - Constructor for class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/OrthoPairSetFilter.AcceptAll.html" title="class in org.biojava.bio.program.homologene">OrthoPairSetFilter.AcceptAll</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/homologene/OrthoPairSetFilter.AllPairsInCollection.html" title="class in org.biojava.bio.program.homologene"><span class="strong">OrthoPairSetFilter.AllPairsInCollection</span></a> - Class in <a href="./org/biojava/bio/program/homologene/package-summary.html">org.biojava.bio.program.homologene</a></dt>
<dd>
<div class="block">all OrthoPairs must meet the requirement
defined by filter.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/OrthoPairSetFilter.AllPairsInCollection.html#OrthoPairSetFilter.AllPairsInCollection(org.biojava.bio.program.homologene.OrthoPairFilter)">OrthoPairSetFilter.AllPairsInCollection(OrthoPairFilter)</a></span> - Constructor for class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/OrthoPairSetFilter.AllPairsInCollection.html" title="class in org.biojava.bio.program.homologene">OrthoPairSetFilter.AllPairsInCollection</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/homologene/OrthoPairSetFilter.And.html" title="class in org.biojava.bio.program.homologene"><span class="strong">OrthoPairSetFilter.And</span></a> - Class in <a href="./org/biojava/bio/program/homologene/package-summary.html">org.biojava.bio.program.homologene</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/OrthoPairSetFilter.And.html#OrthoPairSetFilter.And(org.biojava.bio.program.homologene.OrthoPairSetFilter, org.biojava.bio.program.homologene.OrthoPairSetFilter)">OrthoPairSetFilter.And(OrthoPairSetFilter, OrthoPairSetFilter)</a></span> - Constructor for class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/OrthoPairSetFilter.And.html" title="class in org.biojava.bio.program.homologene">OrthoPairSetFilter.And</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/homologene/OrthoPairSetFilter.ByMinIdentity.html" title="class in org.biojava.bio.program.homologene"><span class="strong">OrthoPairSetFilter.ByMinIdentity</span></a> - Class in <a href="./org/biojava/bio/program/homologene/package-summary.html">org.biojava.bio.program.homologene</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/OrthoPairSetFilter.ByMinIdentity.html#OrthoPairSetFilter.ByMinIdentity(double)">OrthoPairSetFilter.ByMinIdentity(double)</a></span> - Constructor for class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/OrthoPairSetFilter.ByMinIdentity.html" title="class in org.biojava.bio.program.homologene">OrthoPairSetFilter.ByMinIdentity</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/homologene/OrthoPairSetFilter.ByTaxon.html" title="class in org.biojava.bio.program.homologene"><span class="strong">OrthoPairSetFilter.ByTaxon</span></a> - Class in <a href="./org/biojava/bio/program/homologene/package-summary.html">org.biojava.bio.program.homologene</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/OrthoPairSetFilter.ByTaxon.html#OrthoPairSetFilter.ByTaxon(org.biojava.bio.program.homologene.Taxon)">OrthoPairSetFilter.ByTaxon(Taxon)</a></span> - Constructor for class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/OrthoPairSetFilter.ByTaxon.html" title="class in org.biojava.bio.program.homologene">OrthoPairSetFilter.ByTaxon</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/homologene/OrthoPairSetFilter.Not.html" title="class in org.biojava.bio.program.homologene"><span class="strong">OrthoPairSetFilter.Not</span></a> - Class in <a href="./org/biojava/bio/program/homologene/package-summary.html">org.biojava.bio.program.homologene</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/OrthoPairSetFilter.Not.html#OrthoPairSetFilter.Not(org.biojava.bio.program.homologene.OrthoPairSetFilter)">OrthoPairSetFilter.Not(OrthoPairSetFilter)</a></span> - Constructor for class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/OrthoPairSetFilter.Not.html" title="class in org.biojava.bio.program.homologene">OrthoPairSetFilter.Not</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/homologene/OrthoPairSetFilter.Or.html" title="class in org.biojava.bio.program.homologene"><span class="strong">OrthoPairSetFilter.Or</span></a> - Class in <a href="./org/biojava/bio/program/homologene/package-summary.html">org.biojava.bio.program.homologene</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/OrthoPairSetFilter.Or.html#OrthoPairSetFilter.Or(org.biojava.bio.program.homologene.OrthoPairSetFilter, org.biojava.bio.program.homologene.OrthoPairSetFilter)">OrthoPairSetFilter.Or(OrthoPairSetFilter, OrthoPairSetFilter)</a></span> - Constructor for class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/OrthoPairSetFilter.Or.html" title="class in org.biojava.bio.program.homologene">OrthoPairSetFilter.Or</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/homologene/OrthoPairSetFilter.SomePairsInCollection.html" title="class in org.biojava.bio.program.homologene"><span class="strong">OrthoPairSetFilter.SomePairsInCollection</span></a> - Class in <a href="./org/biojava/bio/program/homologene/package-summary.html">org.biojava.bio.program.homologene</a></dt>
<dd>
<div class="block">at least one OrthoPair must meet the requirement
defined by filter.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/OrthoPairSetFilter.SomePairsInCollection.html#OrthoPairSetFilter.SomePairsInCollection(org.biojava.bio.program.homologene.OrthoPairFilter)">OrthoPairSetFilter.SomePairsInCollection(OrthoPairFilter)</a></span> - Constructor for class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/OrthoPairSetFilter.SomePairsInCollection.html" title="class in org.biojava.bio.program.homologene">OrthoPairSetFilter.SomePairsInCollection</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/homologene/OrthoPairSetFilter.Xor.html" title="class in org.biojava.bio.program.homologene"><span class="strong">OrthoPairSetFilter.Xor</span></a> - Class in <a href="./org/biojava/bio/program/homologene/package-summary.html">org.biojava.bio.program.homologene</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/OrthoPairSetFilter.Xor.html#OrthoPairSetFilter.Xor(org.biojava.bio.program.homologene.OrthoPairSetFilter, org.biojava.bio.program.homologene.OrthoPairSetFilter)">OrthoPairSetFilter.Xor(OrthoPairSetFilter, OrthoPairSetFilter)</a></span> - Constructor for class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/OrthoPairSetFilter.Xor.html" title="class in org.biojava.bio.program.homologene">OrthoPairSetFilter.Xor</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/INSDseqFormat.html#OTHER_SEQID_TAG">OTHER_SEQID_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/INSDseqFormat.html" title="class in org.biojavax.bio.seq.io">INSDseqFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/INSDseqFormat.html#OTHER_SEQIDS_GROUP_TAG">OTHER_SEQIDS_GROUP_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/INSDseqFormat.html" title="class in org.biojavax.bio.seq.io">INSDseqFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/AbstractBeadRenderer.html#OUTLINE">OUTLINE</a></span> - Static variable in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/AbstractBeadRenderer.html" title="class in org.biojava.bio.gui.sequence">AbstractBeadRenderer</a></dt>
<dd>
<div class="block">Constant <code>OUTLINE</code> indicating a change to the
outline paint of the features.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/BasicFeatureRenderer.html#OUTLINE">OUTLINE</a></span> - Static variable in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/BasicFeatureRenderer.html" title="class in org.biojava.bio.gui.sequence">BasicFeatureRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/CrosshairRenderer.html#OUTLINE">OUTLINE</a></span> - Static variable in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/CrosshairRenderer.html" title="class in org.biojava.bio.gui.sequence">CrosshairRenderer</a></dt>
<dd>
<div class="block">Constant <code>OUTLINE</code> indicating a change to the
crosshair paint.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PairwiseDiagonalRenderer.html#OUTLINE">OUTLINE</a></span> - Static variable in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PairwiseDiagonalRenderer.html" title="class in org.biojava.bio.gui.sequence">PairwiseDiagonalRenderer</a></dt>
<dd>
<div class="block">Constant <code>OUTLINE</code> indicating a change to the fill of
the features.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PairwiseDiagonalRenderer.html#outline">outline</a></span> - Variable in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PairwiseDiagonalRenderer.html" title="class in org.biojava.bio.gui.sequence">PairwiseDiagonalRenderer</a></dt>
<dd>
<div class="block"><code>outline</code> is the line colour.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/TickFeatureRenderer.html#OUTLINE">OUTLINE</a></span> - Static variable in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/TickFeatureRenderer.html" title="class in org.biojava.bio.gui.sequence">TickFeatureRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/DNAStyle.html#outlinePaint(org.biojava.bio.symbol.Symbol)">outlinePaint(Symbol)</a></span> - Method in class org.biojava.bio.gui.<a href="./org/biojava/bio/gui/DNAStyle.html" title="class in org.biojava.bio.gui">DNAStyle</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/PlainStyle.html#outlinePaint(org.biojava.bio.symbol.Symbol)">outlinePaint(Symbol)</a></span> - Method in class org.biojava.bio.gui.<a href="./org/biojava/bio/gui/PlainStyle.html" title="class in org.biojava.bio.gui">PlainStyle</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/SimpleSymbolStyle.html#outlinePaint(org.biojava.bio.symbol.Symbol)">outlinePaint(Symbol)</a></span> - Method in class org.biojava.bio.gui.<a href="./org/biojava/bio/gui/SimpleSymbolStyle.html" title="class in org.biojava.bio.gui">SimpleSymbolStyle</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/SymbolStyle.html#outlinePaint(org.biojava.bio.symbol.Symbol)">outlinePaint(Symbol)</a></span> - Method in interface org.biojava.bio.gui.<a href="./org/biojava/bio/gui/SymbolStyle.html" title="interface in org.biojava.bio.gui">SymbolStyle</a></dt>
<dd>
<div class="block">Return the outline paint for a symbol.</div>
</dd>
<dt><a href="./org/biojava/utils/process/OutputHandler.html" title="interface in org.biojava.utils.process"><span class="strong">OutputHandler</span></a> - Interface in <a href="./org/biojava/utils/process/package-summary.html">org.biojava.utils.process</a></dt>
<dd>
<div class="block">Interface to a threadable output handler for
an <a href="./org/biojava/utils/process/ExternalProcess.html" title="class in org.biojava.utils.process">external process</a>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/molbio/RestrictionEnzyme.html#OVERHANG_3PRIME">OVERHANG_3PRIME</a></span> - Static variable in class org.biojava.bio.molbio.<a href="./org/biojava/bio/molbio/RestrictionEnzyme.html" title="class in org.biojava.bio.molbio">RestrictionEnzyme</a></dt>
<dd>
<div class="block"><code>OVERHANG_3PRIME</code> the sticky end type created by
enzymes which leave a 3' overhang.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/molbio/RestrictionEnzyme.html#OVERHANG_5PRIME">OVERHANG_5PRIME</a></span> - Static variable in class org.biojava.bio.molbio.<a href="./org/biojava/bio/molbio/RestrictionEnzyme.html" title="class in org.biojava.bio.molbio">RestrictionEnzyme</a></dt>
<dd>
<div class="block"><code>OVERHANG_5PRIME</code> the sticky end type created by
enzymes which leave a 5' overhang.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AbstractLocation.html#overlaps(org.biojava.bio.symbol.Location)">overlaps(Location)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AbstractLocation.html" title="class in org.biojava.bio.symbol">AbstractLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AbstractLocationDecorator.html#overlaps(org.biojava.bio.symbol.Location)">overlaps(Location)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AbstractLocationDecorator.html" title="class in org.biojava.bio.symbol">AbstractLocationDecorator</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/CircularLocation.html#overlaps(org.biojava.bio.symbol.Location)">overlaps(Location)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/CircularLocation.html" title="class in org.biojava.bio.symbol">CircularLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/FuzzyPointLocation.html#overlaps(org.biojava.bio.symbol.Location)">overlaps(Location)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/FuzzyPointLocation.html" title="class in org.biojava.bio.symbol">FuzzyPointLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/Location.html#overlaps(org.biojava.bio.symbol.Location)">overlaps(Location)</a></span> - Method in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/Location.html" title="interface in org.biojava.bio.symbol">Location</a></dt>
<dd>
<div class="block">Checks if these two locations overlap, using this location's
concept of overlapping.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/LocationTools.html#overlaps(org.biojava.bio.symbol.Location, org.biojava.bio.symbol.Location)">overlaps(Location, Location)</a></span> - Static method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/LocationTools.html" title="class in org.biojava.bio.symbol">LocationTools</a></dt>
<dd>
<div class="block">Determines whether the locations overlap or not.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/CompoundRichLocation.html#overlaps(org.biojava.bio.symbol.Location)">overlaps(Location)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/CompoundRichLocation.html" title="class in org.biojavax.bio.seq">CompoundRichLocation</a></dt>
<dd>
<div class="block">Checks if these two locations overlap, using this location's
concept of overlapping.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/EmptyRichLocation.html#overlaps(org.biojava.bio.symbol.Location)">overlaps(Location)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/EmptyRichLocation.html" title="class in org.biojavax.bio.seq">EmptyRichLocation</a></dt>
<dd>
<div class="block">Checks if these two locations overlap, using this location's
concept of overlapping.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichLocation.html#overlaps(org.biojava.bio.symbol.Location)">overlaps(Location)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichLocation.html" title="class in org.biojavax.bio.seq">SimpleRichLocation</a></dt>
<dd>
<div class="block">Checks if these two locations overlap, using this location's
concept of overlapping.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FilterUtils.html#overlapsLocation(org.biojava.bio.symbol.Location)">overlapsLocation(Location)</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FilterUtils.html" title="class in org.biojava.bio.seq">FilterUtils</a></dt>
<dd>
<div class="block">Construct a filter which matches features with locations contained by or
overlapping the specified <code>Location</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/CircularLocation.html#overlapsOrigin()">overlapsOrigin()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/CircularLocation.html" title="class in org.biojava.bio.symbol">CircularLocation</a></dt>
<dd>
<div class="block">Does the Location overlap the origin (position 1) of the sequence?</div>
</dd>
<dt><a href="./org/biojava/bio/OverlayAnnotation.html" title="class in org.biojava.bio"><span class="strong">OverlayAnnotation</span></a> - Class in <a href="./org/biojava/bio/package-summary.html">org.biojava.bio</a></dt>
<dd>
<div class="block">Annotation implementation which allows new key-value
pairs to be layered on top of an underlying Annotation.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/OverlayAnnotation.html#OverlayAnnotation(org.biojava.bio.Annotation)">OverlayAnnotation(Annotation)</a></span> - Constructor for class org.biojava.bio.<a href="./org/biojava/bio/OverlayAnnotation.html" title="class in org.biojava.bio">OverlayAnnotation</a></dt>
<dd>
<div class="block">Construct an annotation which can overlay new key-value
pairs onto an underlying annotation.</div>
</dd>
<dt><a href="./org/biojava/bio/OverlayAnnotation.PropertyForwarder.html" title="class in org.biojava.bio"><span class="strong">OverlayAnnotation.PropertyForwarder</span></a> - Class in <a href="./org/biojava/bio/package-summary.html">org.biojava.bio</a></dt>
<dd>
<div class="block">Forwards change events from the underlying Annotation to this one.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/OverlayAnnotation.PropertyForwarder.html#OverlayAnnotation.PropertyForwarder(java.lang.Object, org.biojava.utils.ChangeSupport)">OverlayAnnotation.PropertyForwarder(Object, ChangeSupport)</a></span> - Constructor for class org.biojava.bio.<a href="./org/biojava/bio/OverlayAnnotation.PropertyForwarder.html" title="class in org.biojava.bio">OverlayAnnotation.PropertyForwarder</a></dt>
<dd>
<div class="block">Forward on behalf of source using the change support provided.</div>
</dd>
<dt><a href="./org/biojava/utils/OverlayMap.html" title="class in org.biojava.utils"><span class="strong">OverlayMap</span></a> - Class in <a href="./org/biojava/utils/package-summary.html">org.biojava.utils</a></dt>
<dd>
<div class="block">
Overlap one map onto another.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/OverlayMap.html#OverlayMap(java.util.Map, java.util.Map)">OverlayMap(Map, Map)</a></span> - Constructor for class org.biojava.utils.<a href="./org/biojava/utils/OverlayMap.html" title="class in org.biojava.utils">OverlayMap</a></dt>
<dd>
<div class="block">Build a new map with default key-value pairs.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/OverlayMap.html#OverlayMap(java.util.Map)">OverlayMap(Map)</a></span> - Constructor for class org.biojava.utils.<a href="./org/biojava/utils/OverlayMap.html" title="class in org.biojava.utils">OverlayMap</a></dt>
<dd>
<div class="block">Build a new map with default key-value pairs.</div>
</dd>
<dt><a href="./org/biojava/bio/gui/sequence/OverlayMarker.html" title="interface in org.biojava.bio.gui.sequence"><span class="strong">OverlayMarker</span></a> - Interface in <a href="./org/biojava/bio/gui/sequence/package-summary.html">org.biojava.bio.gui.sequence</a></dt>
<dd>
<div class="block">This is a dummy interface to permit identification of renderers whose
output is to be overlaid along the lines of the Marker Interface
pattern.</div>
</dd>
<dt><a href="./org/biojava/bio/gui/sequence/OverlayRendererWrapper.html" title="class in org.biojava.bio.gui.sequence"><span class="strong">OverlayRendererWrapper</span></a> - Class in <a href="./org/biojava/bio/gui/sequence/package-summary.html">org.biojava.bio.gui.sequence</a></dt>
<dd>
<div class="block">This class wraps SequenceRenderer classes to present
an Overlay Marker interface that will indicate to
LayeredRenderer that subsequent renderers should overdraw
the same space as the wrapped renderer.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/OverlayRendererWrapper.html#OverlayRendererWrapper()">OverlayRendererWrapper()</a></span> - Constructor for class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/OverlayRendererWrapper.html" title="class in org.biojava.bio.gui.sequence">OverlayRendererWrapper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/OverlayRendererWrapper.html#OverlayRendererWrapper(org.biojava.bio.gui.sequence.SequenceRenderer)">OverlayRendererWrapper(SequenceRenderer)</a></span> - Constructor for class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/OverlayRendererWrapper.html" title="class in org.biojava.bio.gui.sequence">OverlayRendererWrapper</a></dt>
<dd> </dd>
</dl>
<a name="_P_">
<!-- -->
</a>
<h2 class="title">P</h2>
<dl>
<dt><span class="strong"><a href="./org/biojava/bio/seq/ProteinTools.html#p()">p()</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/ProteinTools.html" title="class in org.biojava.bio.seq">ProteinTools</a></dt>
<dd>
<div class="block">Returns the <code>AtomicSymbol</code> for the amino acid
Proline</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/DNAAmbPack.html#pack(org.biojava.bio.symbol.Symbol)">pack(Symbol)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/DNAAmbPack.html" title="class in org.biojava.bio.symbol">DNAAmbPack</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/DNANoAmbPack.html#pack(org.biojava.bio.symbol.Symbol)">pack(Symbol)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/DNANoAmbPack.html" title="class in org.biojava.bio.symbol">DNANoAmbPack</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/Packing.html#pack(org.biojava.bio.symbol.Symbol)">pack(Symbol)</a></span> - Method in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/Packing.html" title="interface in org.biojava.bio.symbol">Packing</a></dt>
<dd>
<div class="block">
Return a byte representing the packing of a symbol.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/RichSequenceBuilderFactory.html#PACKED">PACKED</a></span> - Static variable in interface org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/RichSequenceBuilderFactory.html" title="interface in org.biojavax.bio.seq.io">RichSequenceBuilderFactory</a></dt>
<dd>
<div class="block">Accessor for a factory that produces builders that compress the
<code>SymbolList</code> of a <code>RichSequence</code>.</div>
</dd>
<dt><a href="./org/biojava/bio/symbol/PackedSymbolList.html" title="class in org.biojava.bio.symbol"><span class="strong">PackedSymbolList</span></a> - Class in <a href="./org/biojava/bio/symbol/package-summary.html">org.biojava.bio.symbol</a></dt>
<dd>
<div class="block">
A SymbolList that stores symbols as bit-patterns in an array of longs.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/PackedSymbolList.html#PackedSymbolList(org.biojava.bio.symbol.Packing, long[], int)">PackedSymbolList(Packing, long[], int)</a></span> - Constructor for class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/PackedSymbolList.html" title="class in org.biojava.bio.symbol">PackedSymbolList</a></dt>
<dd>
<div class="block">
Create a new PackedSymbolList directly from a bit pattern.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/PackedSymbolList.html#PackedSymbolList(org.biojava.bio.symbol.Packing, org.biojava.bio.symbol.SymbolList)">PackedSymbolList(Packing, SymbolList)</a></span> - Constructor for class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/PackedSymbolList.html" title="class in org.biojava.bio.symbol">PackedSymbolList</a></dt>
<dd>
<div class="block">
Create a new PackedSymbolList as a packed copy of another symbol list.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/PackedSymbolList.html#PackedSymbolList(org.biojava.bio.symbol.Packing, org.biojava.bio.symbol.Symbol[], int, org.biojava.bio.symbol.Alphabet)">PackedSymbolList(Packing, Symbol[], int, Alphabet)</a></span> - Constructor for class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/PackedSymbolList.html" title="class in org.biojava.bio.symbol">PackedSymbolList</a></dt>
<dd>
<div class="block">
Create a new PackedSymbolList from an array of Symbols.</div>
</dd>
<dt><a href="./org/biojava/bio/symbol/PackedSymbolListFactory.html" title="class in org.biojava.bio.symbol"><span class="strong">PackedSymbolListFactory</span></a> - Class in <a href="./org/biojava/bio/symbol/package-summary.html">org.biojava.bio.symbol</a></dt>
<dd>
<div class="block">This class makes PackedSymbolLists.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/PackedSymbolListFactory.html#PackedSymbolListFactory()">PackedSymbolListFactory()</a></span> - Constructor for class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/PackedSymbolListFactory.html" title="class in org.biojava.bio.symbol">PackedSymbolListFactory</a></dt>
<dd>
<div class="block">Create a factory for PackedSymbolLists.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/PackedSymbolListFactory.html#PackedSymbolListFactory(boolean)">PackedSymbolListFactory(boolean)</a></span> - Constructor for class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/PackedSymbolListFactory.html" title="class in org.biojava.bio.symbol">PackedSymbolListFactory</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>the argumentless constructor creates a SymbolListFactory
that will autoselect the packing appropriately.</i></div>
</div>
</dd>
<dt><a href="./org/biojava/bio/symbol/Packing.html" title="interface in org.biojava.bio.symbol"><span class="strong">Packing</span></a> - Interface in <a href="./org/biojava/bio/symbol/package-summary.html">org.biojava.bio.symbol</a></dt>
<dd>
<div class="block">
An encapsulation of the way symbols map to bit-patterns.</div>
</dd>
<dt><a href="./org/biojava/bio/symbol/PackingFactory.html" title="class in org.biojava.bio.symbol"><span class="strong">PackingFactory</span></a> - Class in <a href="./org/biojava/bio/symbol/package-summary.html">org.biojava.bio.symbol</a></dt>
<dd>
<div class="block">
A factory that is used to maintain associations between alphabets and
preferred bit-packings for them.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/PackingFactory.html#PackingFactory()">PackingFactory()</a></span> - Constructor for class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/PackingFactory.html" title="class in org.biojava.bio.symbol">PackingFactory</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PaddingRenderer.html#PADDING">PADDING</a></span> - Static variable in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PaddingRenderer.html" title="class in org.biojava.bio.gui.sequence">PaddingRenderer</a></dt>
<dd>
<div class="block">Event type for when the size of the padding changes.</div>
</dd>
<dt><a href="./org/biojava/bio/gui/sequence/PaddingRenderer.html" title="class in org.biojava.bio.gui.sequence"><span class="strong">PaddingRenderer</span></a> - Class in <a href="./org/biojava/bio/gui/sequence/package-summary.html">org.biojava.bio.gui.sequence</a></dt>
<dd>
<div class="block">A renderer that adds padding before and after a delegate renderer.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PaddingRenderer.html#PaddingRenderer()">PaddingRenderer()</a></span> - Constructor for class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PaddingRenderer.html" title="class in org.biojava.bio.gui.sequence">PaddingRenderer</a></dt>
<dd>
<div class="block">Build a new PaddingRenderer with zero padding.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PaddingRenderer.html#PaddingRenderer(org.biojava.bio.gui.sequence.SequenceRenderer, double)">PaddingRenderer(SequenceRenderer, double)</a></span> - Constructor for class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PaddingRenderer.html" title="class in org.biojava.bio.gui.sequence">PaddingRenderer</a></dt>
<dd>
<div class="block">Build a new PaddingRenderer that wraps <code>renderer</code> and has
padding depth <code>padding</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/AbiTraceRenderer.html#paint(java.awt.Graphics2D, org.biojava.bio.gui.sequence.SequenceRenderContext)">paint(Graphics2D, SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/AbiTraceRenderer.html" title="class in org.biojava.bio.gui.sequence">AbiTraceRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/AlignmentRenderer.html#paint(java.awt.Graphics2D, org.biojava.bio.gui.sequence.SequenceRenderContext)">paint(Graphics2D, SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/AlignmentRenderer.html" title="class in org.biojava.bio.gui.sequence">AlignmentRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/BumpedRenderer.html#paint(java.awt.Graphics2D, org.biojava.bio.gui.sequence.SequenceRenderContext)">paint(Graphics2D, SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/BumpedRenderer.html" title="class in org.biojava.bio.gui.sequence">BumpedRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/CircularFeatureFilteringRenderer.html#paint(java.awt.Graphics2D, org.biojava.bio.gui.sequence.CircularRendererContext)">paint(Graphics2D, CircularRendererContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/CircularFeatureFilteringRenderer.html" title="class in org.biojava.bio.gui.sequence">CircularFeatureFilteringRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/CircularFeaturesRenderer.html#paint(java.awt.Graphics2D, org.biojava.bio.gui.sequence.CircularRendererContext)">paint(Graphics2D, CircularRendererContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/CircularFeaturesRenderer.html" title="class in org.biojava.bio.gui.sequence">CircularFeaturesRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/CircularMLR.html#paint(java.awt.Graphics2D, org.biojava.bio.gui.sequence.CircularRendererContext)">paint(Graphics2D, CircularRendererContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/CircularMLR.html" title="class in org.biojava.bio.gui.sequence">CircularMLR</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/CircularPaddedRenderer.html#paint(java.awt.Graphics2D, org.biojava.bio.gui.sequence.CircularRendererContext)">paint(Graphics2D, CircularRendererContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/CircularPaddedRenderer.html" title="class in org.biojava.bio.gui.sequence">CircularPaddedRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/CircularRenderer.html#paint(java.awt.Graphics2D, org.biojava.bio.gui.sequence.CircularRendererContext)">paint(Graphics2D, CircularRendererContext)</a></span> - Method in interface org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/CircularRenderer.html" title="interface in org.biojava.bio.gui.sequence">CircularRenderer</a></dt>
<dd>
<div class="block">Paint this renderer.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/CrosshairRenderer.html#paint(java.awt.Graphics2D, org.biojava.bio.gui.sequence.PairwiseRenderContext)">paint(Graphics2D, PairwiseRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/CrosshairRenderer.html" title="class in org.biojava.bio.gui.sequence">CrosshairRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/FeatureBlockSequenceRenderer.html#paint(java.awt.Graphics2D, org.biojava.bio.gui.sequence.SequenceRenderContext)">paint(Graphics2D, SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/FeatureBlockSequenceRenderer.html" title="class in org.biojava.bio.gui.sequence">FeatureBlockSequenceRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/FilteringRenderer.html#paint(java.awt.Graphics2D, org.biojava.bio.gui.sequence.SequenceRenderContext)">paint(Graphics2D, SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/FilteringRenderer.html" title="class in org.biojava.bio.gui.sequence">FilteringRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/GappedRenderer.html#paint(java.awt.Graphics2D, org.biojava.bio.gui.sequence.SequenceRenderContext)">paint(Graphics2D, SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/GappedRenderer.html" title="class in org.biojava.bio.gui.sequence">GappedRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/LabelledSequenceRenderer.html#paint(java.awt.Graphics2D, org.biojava.bio.gui.sequence.SequenceRenderContext)">paint(Graphics2D, SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/LabelledSequenceRenderer.html" title="class in org.biojava.bio.gui.sequence">LabelledSequenceRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/LabelRenderer.html#paint(java.awt.Graphics2D, org.biojava.bio.gui.sequence.SequenceRenderContext, int, int, org.biojava.bio.gui.sequence.SequenceRenderContext.Border)">paint(Graphics2D, SequenceRenderContext, int, int, SequenceRenderContext.Border)</a></span> - Method in interface org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/LabelRenderer.html" title="interface in org.biojava.bio.gui.sequence">LabelRenderer</a></dt>
<dd>
<div class="block">Render a label for the information for sp to g.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/LabelRenderer.RenderNothing.html#paint(java.awt.Graphics2D, org.biojava.bio.gui.sequence.SequenceRenderContext, int, int, org.biojava.bio.gui.sequence.SequenceRenderContext.Border)">paint(Graphics2D, SequenceRenderContext, int, int, SequenceRenderContext.Border)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/LabelRenderer.RenderNothing.html" title="class in org.biojava.bio.gui.sequence">LabelRenderer.RenderNothing</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/LayeredRenderer.html#paint(java.awt.Graphics2D, java.util.List, java.util.List)">paint(Graphics2D, List, List)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/LayeredRenderer.html" title="class in org.biojava.bio.gui.sequence">LayeredRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/MultiLineRenderer.html#paint(java.awt.Graphics2D, org.biojava.bio.gui.sequence.SequenceRenderContext)">paint(Graphics2D, SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/MultiLineRenderer.html" title="class in org.biojava.bio.gui.sequence">MultiLineRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/OffsetRulerRenderer.html#paint(java.awt.Graphics2D, org.biojava.bio.gui.sequence.SequenceRenderContext)">paint(Graphics2D, SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/OffsetRulerRenderer.html" title="class in org.biojava.bio.gui.sequence">OffsetRulerRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/OverlayRendererWrapper.html#paint(java.awt.Graphics2D, org.biojava.bio.gui.sequence.SequenceRenderContext)">paint(Graphics2D, SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/OverlayRendererWrapper.html" title="class in org.biojava.bio.gui.sequence">OverlayRendererWrapper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PaddingRenderer.html#paint(java.awt.Graphics2D, org.biojava.bio.gui.sequence.SequenceRenderContext)">paint(Graphics2D, SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PaddingRenderer.html" title="class in org.biojava.bio.gui.sequence">PaddingRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PairwiseDiagonalRenderer.html#paint(java.awt.Graphics2D, org.biojava.bio.gui.sequence.PairwiseRenderContext)">paint(Graphics2D, PairwiseRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PairwiseDiagonalRenderer.html" title="class in org.biojava.bio.gui.sequence">PairwiseDiagonalRenderer</a></dt>
<dd>
<div class="block"><code>paint</code> renders the feature as a simple line.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PairwiseFilteringRenderer.html#paint(java.awt.Graphics2D, org.biojava.bio.gui.sequence.PairwiseRenderContext)">paint(Graphics2D, PairwiseRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PairwiseFilteringRenderer.html" title="class in org.biojava.bio.gui.sequence">PairwiseFilteringRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PairwiseOverlayRenderer.html#paint(java.awt.Graphics2D, org.biojava.bio.gui.sequence.PairwiseRenderContext)">paint(Graphics2D, PairwiseRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PairwiseOverlayRenderer.html" title="class in org.biojava.bio.gui.sequence">PairwiseOverlayRenderer</a></dt>
<dd>
<div class="block"><code>paint</code> applies all renderers in the order in which
they were added.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PairwiseSequenceRenderer.html#paint(java.awt.Graphics2D, org.biojava.bio.gui.sequence.PairwiseRenderContext)">paint(Graphics2D, PairwiseRenderContext)</a></span> - Method in interface org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PairwiseSequenceRenderer.html" title="interface in org.biojava.bio.gui.sequence">PairwiseSequenceRenderer</a></dt>
<dd>
<div class="block"><code>paint</code>s some or all of the information about the
sequence pair.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/RulerRenderer.html#paint(java.awt.Graphics2D, org.biojava.bio.gui.sequence.SequenceRenderContext)">paint(Graphics2D, SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/RulerRenderer.html" title="class in org.biojava.bio.gui.sequence">RulerRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePanelWrapper.html#paint(java.awt.Graphics)">paint(Graphics)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePanelWrapper.html" title="class in org.biojava.bio.gui.sequence">SequencePanelWrapper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequenceRenderer.html#paint(java.awt.Graphics2D, org.biojava.bio.gui.sequence.SequenceRenderContext)">paint(Graphics2D, SequenceRenderContext)</a></span> - Method in interface org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequenceRenderer.html" title="interface in org.biojava.bio.gui.sequence">SequenceRenderer</a></dt>
<dd>
<div class="block">Render a portion (possibly all) of the information for src to g, displaying
all of the data that would fall within seqBox.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequenceRendererWrapper.html#paint(java.awt.Graphics2D, org.biojava.bio.gui.sequence.SequenceRenderContext)">paint(Graphics2D, SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequenceRendererWrapper.html" title="class in org.biojava.bio.gui.sequence">SequenceRendererWrapper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SimpleLabelRenderer.html#paint(java.awt.Graphics2D, org.biojava.bio.gui.sequence.SequenceRenderContext, int, int, org.biojava.bio.gui.sequence.SequenceRenderContext.Border)">paint(Graphics2D, SequenceRenderContext, int, int, SequenceRenderContext.Border)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SimpleLabelRenderer.html" title="class in org.biojava.bio.gui.sequence">SimpleLabelRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SixFrameRenderer.html#paint(java.awt.Graphics2D, org.biojava.bio.gui.sequence.SequenceRenderContext)">paint(Graphics2D, SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SixFrameRenderer.html" title="class in org.biojava.bio.gui.sequence">SixFrameRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/StopRenderer.html#paint(java.awt.Graphics2D, org.biojava.bio.gui.sequence.SequenceRenderContext)">paint(Graphics2D, SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/StopRenderer.html" title="class in org.biojava.bio.gui.sequence">StopRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SymbolSequenceRenderer.html#paint(java.awt.Graphics2D, org.biojava.bio.gui.sequence.SequenceRenderContext)">paint(Graphics2D, SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SymbolSequenceRenderer.html" title="class in org.biojava.bio.gui.sequence">SymbolSequenceRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/BlockPainter.html#paintBlock(org.biojava.bio.gui.LogoContext, java.awt.geom.Rectangle2D, org.biojava.bio.symbol.AtomicSymbol)">paintBlock(LogoContext, Rectangle2D, AtomicSymbol)</a></span> - Method in interface org.biojava.bio.gui.<a href="./org/biojava/bio/gui/BlockPainter.html" title="interface in org.biojava.bio.gui">BlockPainter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/PlainBlock.html#paintBlock(org.biojava.bio.gui.LogoContext, java.awt.geom.Rectangle2D, org.biojava.bio.symbol.AtomicSymbol)">paintBlock(LogoContext, Rectangle2D, AtomicSymbol)</a></span> - Method in class org.biojava.bio.gui.<a href="./org/biojava/bio/gui/PlainBlock.html" title="class in org.biojava.bio.gui">PlainBlock</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/TextBlock.html#paintBlock(org.biojava.bio.gui.LogoContext, java.awt.geom.Rectangle2D, org.biojava.bio.symbol.AtomicSymbol)">paintBlock(LogoContext, Rectangle2D, AtomicSymbol)</a></span> - Method in class org.biojava.bio.gui.<a href="./org/biojava/bio/gui/TextBlock.html" title="class in org.biojava.bio.gui">TextBlock</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/DistributionLogo.html#paintComponent(java.awt.Graphics)">paintComponent(Graphics)</a></span> - Method in class org.biojava.bio.gui.<a href="./org/biojava/bio/gui/DistributionLogo.html" title="class in org.biojava.bio.gui">DistributionLogo</a></dt>
<dd>
<div class="block">Transforms the graphics context so that it is in bits space,
and then requests the logo painter to fill the area.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/CircularRendererPanel.html#paintComponent(java.awt.Graphics)">paintComponent(Graphics)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/CircularRendererPanel.html" title="class in org.biojava.bio.gui.sequence">CircularRendererPanel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PairwiseSequencePanel.html#paintComponent(java.awt.Graphics)">paintComponent(Graphics)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PairwiseSequencePanel.html" title="class in org.biojava.bio.gui.sequence">PairwiseSequencePanel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePanel.html#paintComponent(java.awt.Graphics)">paintComponent(Graphics)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePanel.html" title="class in org.biojava.bio.gui.sequence">SequencePanel</a></dt>
<dd>
<div class="block">Paint this component.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePanelWrapper.html#paintComponent(java.awt.Graphics)">paintComponent(Graphics)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePanelWrapper.html" title="class in org.biojava.bio.gui.sequence">SequencePanelWrapper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePoster.html#paintComponent(java.awt.Graphics)">paintComponent(Graphics)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePoster.html" title="class in org.biojava.bio.gui.sequence">SequencePoster</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Paint this component.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/TranslatedSequencePanel.html#paintComponent(java.awt.Graphics)">paintComponent(Graphics)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/TranslatedSequencePanel.html" title="class in org.biojava.bio.gui.sequence">TranslatedSequencePanel</a></dt>
<dd>
<div class="block"><code>paintComponent</code> paints this component.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/JMatrixPanel.html#paintComponent(java.awt.Graphics)">paintComponent(Graphics)</a></span> - Method in class org.biojava.bio.structure.gui.<a href="./org/biojava/bio/structure/gui/JMatrixPanel.html" title="class in org.biojava.bio.structure.gui">JMatrixPanel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/util/SequenceScalePanel.html#paintComponent(java.awt.Graphics)">paintComponent(Graphics)</a></span> - Method in class org.biojava.bio.structure.gui.util.<a href="./org/biojava/bio/structure/gui/util/SequenceScalePanel.html" title="class in org.biojava.bio.structure.gui.util">SequenceScalePanel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/tools/ClassifierExample.PointClassifier.html#paintComponent(java.awt.Graphics)">paintComponent(Graphics)</a></span> - Method in class org.biojava.stats.svm.tools.<a href="./org/biojava/stats/svm/tools/ClassifierExample.PointClassifier.html" title="class in org.biojava.stats.svm.tools">ClassifierExample.PointClassifier</a></dt>
<dd>
<div class="block">Renders this component to display the points, and if present, the
support vector machine.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/BarLogoPainter.html#paintLogo(org.biojava.bio.gui.LogoContext)">paintLogo(LogoContext)</a></span> - Method in class org.biojava.bio.gui.<a href="./org/biojava/bio/gui/BarLogoPainter.html" title="class in org.biojava.bio.gui">BarLogoPainter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/LogoPainter.html#paintLogo(org.biojava.bio.gui.LogoContext)">paintLogo(LogoContext)</a></span> - Method in interface org.biojava.bio.gui.<a href="./org/biojava/bio/gui/LogoPainter.html" title="interface in org.biojava.bio.gui">LogoPainter</a></dt>
<dd>
<div class="block">Render the state from sl onto the graphics object g.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/StackedLogoPainter.html#paintLogo(org.biojava.bio.gui.LogoContext)">paintLogo(LogoContext)</a></span> - Method in class org.biojava.bio.gui.<a href="./org/biojava/bio/gui/StackedLogoPainter.html" title="class in org.biojava.bio.gui">StackedLogoPainter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/TextLogoPainter.html#paintLogo(org.biojava.bio.gui.LogoContext)">paintLogo(LogoContext)</a></span> - Method in class org.biojava.bio.gui.<a href="./org/biojava/bio/gui/TextLogoPainter.html" title="class in org.biojava.bio.gui">TextLogoPainter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/NeedlemanWunsch.html#pairalign">pairalign</a></span> - Variable in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/NeedlemanWunsch.html" title="class in org.biojava.bio.alignment">NeedlemanWunsch</a></dt>
<dd>
<div class="block">The result of a successful alignment</div>
</dd>
<dt><a href="./org/biojava/bio/dist/PairDistribution.html" title="class in org.biojava.bio.dist"><span class="strong">PairDistribution</span></a> - Class in <a href="./org/biojava/bio/dist/package-summary.html">org.biojava.bio.dist</a></dt>
<dd>
<div class="block">Class for pairing up two independant distributions.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/PairDistribution.html#PairDistribution(org.biojava.bio.dist.Distribution, org.biojava.bio.dist.Distribution)">PairDistribution(Distribution, Distribution)</a></span> - Constructor for class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/PairDistribution.html" title="class in org.biojava.bio.dist">PairDistribution</a></dt>
<dd>
<div class="block">Create a new PairDistribution that represents the product of two other
distributions.</div>
</dd>
<dt><a href="./org/biojava/bio/dp/twohead/PairDPCursor.html" title="interface in org.biojava.bio.dp.twohead"><span class="strong">PairDPCursor</span></a> - Interface in <a href="./org/biojava/bio/dp/twohead/package-summary.html">org.biojava.bio.dp.twohead</a></dt>
<dd>
<div class="block">A cursor over a DP matrix.</div>
</dd>
<dt><a href="./org/biojava/bio/dp/twohead/PairDPMatrix.html" title="class in org.biojava.bio.dp.twohead"><span class="strong">PairDPMatrix</span></a> - Class in <a href="./org/biojava/bio/dp/twohead/package-summary.html">org.biojava.bio.dp.twohead</a></dt>
<dd>
<div class="block">Storage structure for intermediate values from a pairwise
dynamic programming run.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/twohead/PairDPMatrix.html#PairDPMatrix(org.biojava.bio.dp.DP, org.biojava.bio.symbol.SymbolList, org.biojava.bio.symbol.SymbolList)">PairDPMatrix(DP, SymbolList, SymbolList)</a></span> - Constructor for class org.biojava.bio.dp.twohead.<a href="./org/biojava/bio/dp/twohead/PairDPMatrix.html" title="class in org.biojava.bio.dp.twohead">PairDPMatrix</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/NeedlemanWunsch.html#pairwiseAlignment(org.biojava.bio.symbol.SymbolList, org.biojava.bio.symbol.SymbolList)">pairwiseAlignment(SymbolList, SymbolList)</a></span> - Method in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/NeedlemanWunsch.html" title="class in org.biojava.bio.alignment">NeedlemanWunsch</a></dt>
<dd>
<div class="block">Global pairwise sequence alignment of two BioJava-Sequence objects
according to the Needleman-Wunsch-algorithm.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/SequenceAlignment.html#pairwiseAlignment(org.biojava.bio.symbol.SymbolList, org.biojava.bio.symbol.SymbolList)">pairwiseAlignment(SymbolList, SymbolList)</a></span> - Method in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/SequenceAlignment.html" title="class in org.biojava.bio.alignment">SequenceAlignment</a></dt>
<dd>
<div class="block">Performs a pairwise sequence alignment of the two given sequences.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/SmithWaterman.html#pairwiseAlignment(org.biojava.bio.symbol.SymbolList, org.biojava.bio.symbol.SymbolList)">pairwiseAlignment(SymbolList, SymbolList)</a></span> - Method in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/SmithWaterman.html" title="class in org.biojava.bio.alignment">SmithWaterman</a></dt>
<dd>
<div class="block">Overrides the method inherited from the NeedlemanWunsch and performs only a
local alignment.</div>
</dd>
<dt><a href="./org/biojava/bio/gui/sequence/PairwiseDiagonalRenderer.html" title="class in org.biojava.bio.gui.sequence"><span class="strong">PairwiseDiagonalRenderer</span></a> - Class in <a href="./org/biojava/bio/gui/sequence/package-summary.html">org.biojava.bio.gui.sequence</a></dt>
<dd>
<div class="block"><code>PairwiseDiagonalRenderer</code> renders a region of
similarity between two sequences as a straight line.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PairwiseDiagonalRenderer.html#PairwiseDiagonalRenderer()">PairwiseDiagonalRenderer()</a></span> - Constructor for class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PairwiseDiagonalRenderer.html" title="class in org.biojava.bio.gui.sequence">PairwiseDiagonalRenderer</a></dt>
<dd>
<div class="block">Creates a new <code>PairwiseDiagonalRenderer</code> which will
draw black lines.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PairwiseDiagonalRenderer.html#PairwiseDiagonalRenderer(java.awt.Paint)">PairwiseDiagonalRenderer(Paint)</a></span> - Constructor for class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PairwiseDiagonalRenderer.html" title="class in org.biojava.bio.gui.sequence">PairwiseDiagonalRenderer</a></dt>
<dd>
<div class="block">Creates a new <code>PairwiseDiagonalRenderer</code> which will
draw lines using the specified <code>Paint</code>.</div>
</dd>
<dt><a href="./org/biojava/bio/dp/twohead/PairwiseDP.html" title="class in org.biojava.bio.dp.twohead"><span class="strong">PairwiseDP</span></a> - Class in <a href="./org/biojava/bio/dp/twohead/package-summary.html">org.biojava.bio.dp.twohead</a></dt>
<dd>
<div class="block">Algorithms for dynamic programming (alignments) between pairs
of SymbolLists.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/twohead/PairwiseDP.html#PairwiseDP(org.biojava.bio.dp.MarkovModel, org.biojava.bio.dp.twohead.CellCalculatorFactoryMaker)">PairwiseDP(MarkovModel, CellCalculatorFactoryMaker)</a></span> - Constructor for class org.biojava.bio.dp.twohead.<a href="./org/biojava/bio/dp/twohead/PairwiseDP.html" title="class in org.biojava.bio.dp.twohead">PairwiseDP</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/gui/sequence/PairwiseFilteringRenderer.html" title="class in org.biojava.bio.gui.sequence"><span class="strong">PairwiseFilteringRenderer</span></a> - Class in <a href="./org/biojava/bio/gui/sequence/package-summary.html">org.biojava.bio.gui.sequence</a></dt>
<dd>
<div class="block"><code>PairwiseFilteringRenderer</code> wraps a
<code>PairwiseSequenceRenderer</code> and filters the
<code>PairwiseRenderContext</code>s passed to it.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PairwiseFilteringRenderer.html#PairwiseFilteringRenderer(org.biojava.bio.gui.sequence.PairwiseSequenceRenderer)">PairwiseFilteringRenderer(PairwiseSequenceRenderer)</a></span> - Constructor for class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PairwiseFilteringRenderer.html" title="class in org.biojava.bio.gui.sequence">PairwiseFilteringRenderer</a></dt>
<dd>
<div class="block">Creates a new <code>PairwiseFilteringRenderer</code> which uses
a filter which accepts all features.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PairwiseFilteringRenderer.html#PairwiseFilteringRenderer(org.biojava.bio.gui.sequence.PairwiseSequenceRenderer, org.biojava.bio.seq.FeatureFilter, boolean)">PairwiseFilteringRenderer(PairwiseSequenceRenderer, FeatureFilter, boolean)</a></span> - Constructor for class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PairwiseFilteringRenderer.html" title="class in org.biojava.bio.gui.sequence">PairwiseFilteringRenderer</a></dt>
<dd>
<div class="block">Creates a new <code>PairwiseFilteringRenderer</code>.</div>
</dd>
<dt><a href="./org/biojava/bio/gui/sequence/PairwiseOverlayRenderer.html" title="class in org.biojava.bio.gui.sequence"><span class="strong">PairwiseOverlayRenderer</span></a> - Class in <a href="./org/biojava/bio/gui/sequence/package-summary.html">org.biojava.bio.gui.sequence</a></dt>
<dd>
<div class="block"><code>PairwiseOverlayRenderer</code> allows a list of other
<code>PairwiseSequenceRenderer</code>s to superimpose their
output.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PairwiseOverlayRenderer.html#PairwiseOverlayRenderer()">PairwiseOverlayRenderer()</a></span> - Constructor for class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PairwiseOverlayRenderer.html" title="class in org.biojava.bio.gui.sequence">PairwiseOverlayRenderer</a></dt>
<dd>
<div class="block">Creates a new, empty <code>PairwiseOverlayRenderer</code>.</div>
</dd>
<dt><a href="./org/biojava/bio/gui/sequence/PairwiseRenderContext.html" title="interface in org.biojava.bio.gui.sequence"><span class="strong">PairwiseRenderContext</span></a> - Interface in <a href="./org/biojava/bio/gui/sequence/package-summary.html">org.biojava.bio.gui.sequence</a></dt>
<dd>
<div class="block"><code>PairwiseRenderContext</code> encapsulates information
required for the rendering of a pair of sequences.</div>
</dd>
<dt><a href="./org/biojava/bio/gui/sequence/PairwiseSequencePanel.html" title="class in org.biojava.bio.gui.sequence"><span class="strong">PairwiseSequencePanel</span></a> - Class in <a href="./org/biojava/bio/gui/sequence/package-summary.html">org.biojava.bio.gui.sequence</a></dt>
<dd>
<div class="block">A <code>PairwiseSequencePanel</code> is a panel that displays a
pair of sequences; one sequence (the primary) may be either
left-to-right (HORIZONTAL) or from top-to-bottom (VERTICAL).</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PairwiseSequencePanel.html#PairwiseSequencePanel()">PairwiseSequencePanel()</a></span> - Constructor for class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PairwiseSequencePanel.html" title="class in org.biojava.bio.gui.sequence">PairwiseSequencePanel</a></dt>
<dd>
<div class="block">Creates a new <code>PairwiseSequencePanel</code> with the
default settings (primary sequence direction HORIZONTAL, scale
10.0 pixels per symbol, symbol translation 0, secondary symbol
translation 0, leading border 0.0, trailing border 0.0, 12
point sanserif font).</div>
</dd>
<dt><a href="./org/biojava/bio/gui/sequence/PairwiseSequenceRenderer.html" title="interface in org.biojava.bio.gui.sequence"><span class="strong">PairwiseSequenceRenderer</span></a> - Interface in <a href="./org/biojava/bio/gui/sequence/package-summary.html">org.biojava.bio.gui.sequence</a></dt>
<dd>
<div class="block"><code>PairwiseSequenceRenderer</code>s render information about the
relationship between two sequences.</div>
</dd>
<dt><a href="./org/biojava/bio/gui/sequence/PairwiseSequenceRenderer.PairwiseRendererForwarder.html" title="class in org.biojava.bio.gui.sequence"><span class="strong">PairwiseSequenceRenderer.PairwiseRendererForwarder</span></a> - Class in <a href="./org/biojava/bio/gui/sequence/package-summary.html">org.biojava.bio.gui.sequence</a></dt>
<dd>
<div class="block"><code>PairwiseRendererForwarder</code> forward events to other
renderers.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PairwiseSequenceRenderer.PairwiseRendererForwarder.html#PairwiseSequenceRenderer.PairwiseRendererForwarder(org.biojava.bio.gui.sequence.PairwiseSequenceRenderer, org.biojava.utils.ChangeSupport)">PairwiseSequenceRenderer.PairwiseRendererForwarder(PairwiseSequenceRenderer, ChangeSupport)</a></span> - Constructor for class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PairwiseSequenceRenderer.PairwiseRendererForwarder.html" title="class in org.biojava.bio.gui.sequence">PairwiseSequenceRenderer.PairwiseRendererForwarder</a></dt>
<dd>
<div class="block">Creates a new <code>PairwiseRendererForwarder</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/MarkovModel.html#PARAMETER">PARAMETER</a></span> - Static variable in interface org.biojava.bio.dp.<a href="./org/biojava/bio/dp/MarkovModel.html" title="interface in org.biojava.bio.dp">MarkovModel</a></dt>
<dd>
<div class="block">Signals that one or more parameters have altered.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/taxa/SimpleTaxon.html#parent">parent</a></span> - Variable in class org.biojava.bio.taxa.<a href="./org/biojava/bio/taxa/SimpleTaxon.html" title="class in org.biojava.bio.taxa">SimpleTaxon</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/taxa/WeakTaxon.html#parent">parent</a></span> - Variable in class org.biojava.bio.taxa.<a href="./org/biojava/bio/taxa/WeakTaxon.html" title="class in org.biojava.bio.taxa">WeakTaxon</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/automata/StateMachineInstance.html#parent()">parent()</a></span> - Method in interface org.biojava.utils.automata.<a href="./org/biojava/utils/automata/StateMachineInstance.html" title="interface in org.biojava.utils.automata">StateMachineInstance</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichFeature.html#PARENT">PARENT</a></span> - Static variable in interface org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichFeature.html" title="interface in org.biojavax.bio.seq">RichFeature</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/taxa/NCBITaxon.html#PARENT">PARENT</a></span> - Static variable in interface org.biojavax.bio.taxa.<a href="./org/biojavax/bio/taxa/NCBITaxon.html" title="interface in org.biojavax.bio.taxa">NCBITaxon</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFParser.html#parse(java.io.BufferedReader, org.biojava.bio.program.gff.GFFDocumentHandler)">parse(BufferedReader, GFFDocumentHandler)</a></span> - Method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFParser.html" title="class in org.biojava.bio.program.gff">GFFParser</a></dt>
<dd>
<div class="block">Informs <span class="arg">handler</span> of each line of
gff read from <span class="arg">bReader</span>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFParser.html#parse(java.io.BufferedReader, org.biojava.bio.program.gff.GFFDocumentHandler, java.lang.String)">parse(BufferedReader, GFFDocumentHandler, String)</a></span> - Method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFParser.html" title="class in org.biojava.bio.program.gff">GFFParser</a></dt>
<dd>
<div class="block">Informs <span class="arg">handler</span> of each line of
GFF read from <span class="arg">bReader</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff3/GFF3Parser.html#parse(java.io.BufferedReader, org.biojava.bio.program.gff3.GFF3DocumentHandler, org.biojava.ontology.Ontology)">parse(BufferedReader, GFF3DocumentHandler, Ontology)</a></span> - Method in class org.biojava.bio.program.gff3.<a href="./org/biojava/bio/program/gff3/GFF3Parser.html" title="class in org.biojava.bio.program.gff3">GFF3Parser</a></dt>
<dd>
<div class="block">Informs <span class="arg">handler</span> of each line of
gff read from <span class="arg">bReader</span>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff3/GFF3Parser.html#parse(java.io.BufferedReader, org.biojava.bio.program.gff3.GFF3DocumentHandler, org.biojava.ontology.Ontology, java.lang.String)">parse(BufferedReader, GFF3DocumentHandler, Ontology, String)</a></span> - Method in class org.biojava.bio.program.gff3.<a href="./org/biojava/bio/program/gff3/GFF3Parser.html" title="class in org.biojava.bio.program.gff3">GFF3Parser</a></dt>
<dd>
<div class="block">Informs <span class="arg">handler</span> of each line of
GFF read from <span class="arg">bReader</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/hmmer/HmmerProfileParser.html#parse(java.io.File)">parse(File)</a></span> - Static method in class org.biojava.bio.program.hmmer.<a href="./org/biojava/bio/program/hmmer/HmmerProfileParser.html" title="class in org.biojava.bio.program.hmmer">HmmerProfileParser</a></dt>
<dd>
<div class="block">Returns a profile HMM representing the core HMMER hmm</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/sax/BlastLikeSAXParser.html#parse(org.xml.sax.InputSource)">parse(InputSource)</a></span> - Method in class org.biojava.bio.program.sax.<a href="./org/biojava/bio/program/sax/BlastLikeSAXParser.html" title="class in org.biojava.bio.program.sax">BlastLikeSAXParser</a></dt>
<dd>
<div class="block"><code>parse</code> initiates the parsing operation.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/sax/blastxml/BlastXMLParserFacade.html#parse(org.xml.sax.InputSource)">parse(InputSource)</a></span> - Method in class org.biojava.bio.program.sax.blastxml.<a href="./org/biojava/bio/program/sax/blastxml/BlastXMLParserFacade.html" title="class in org.biojava.bio.program.sax.blastxml">BlastXMLParserFacade</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/sax/blastxml/BlastXMLParserFacade.html#parse(java.lang.String)">parse(String)</a></span> - Method in class org.biojava.bio.program.sax.blastxml.<a href="./org/biojava/bio/program/sax/blastxml/BlastXMLParserFacade.html" title="class in org.biojava.bio.program.sax.blastxml">BlastXMLParserFacade</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/sax/ClustalWAlignmentSAXParser.html#parse(org.xml.sax.InputSource)">parse(InputSource)</a></span> - Method in class org.biojava.bio.program.sax.<a href="./org/biojava/bio/program/sax/ClustalWAlignmentSAXParser.html" title="class in org.biojava.bio.program.sax">ClustalWAlignmentSAXParser</a></dt>
<dd>
<div class="block">Describe 'parse' method here.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/sax/FastaSearchSAXParser.html#parse(org.xml.sax.InputSource)">parse(InputSource)</a></span> - Method in class org.biojava.bio.program.sax.<a href="./org/biojava/bio/program/sax/FastaSearchSAXParser.html" title="class in org.biojava.bio.program.sax">FastaSearchSAXParser</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/sax/FastaSequenceSAXParser.html#parse(org.xml.sax.InputSource)">parse(InputSource)</a></span> - Method in class org.biojava.bio.program.sax.<a href="./org/biojava/bio/program/sax/FastaSequenceSAXParser.html" title="class in org.biojava.bio.program.sax">FastaSequenceSAXParser</a></dt>
<dd>
<div class="block">Describe 'parse' method here.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/sax/PdbSAXParser.html#parse(java.lang.String)">parse(String)</a></span> - Method in class org.biojava.bio.program.sax.<a href="./org/biojava/bio/program/sax/PdbSAXParser.html" title="class in org.biojava.bio.program.sax">PdbSAXParser</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/sax/PdbSAXParser.html#parse(org.xml.sax.InputSource)">parse(InputSource)</a></span> - Method in class org.biojava.bio.program.sax.<a href="./org/biojava/bio/program/sax/PdbSAXParser.html" title="class in org.biojava.bio.program.sax">PdbSAXParser</a></dt>
<dd>
<div class="block">Describe 'parse' method here.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/sax/SequenceAlignmentSAXParser.html#parse(org.xml.sax.InputSource)">parse(InputSource)</a></span> - Method in class org.biojava.bio.program.sax.<a href="./org/biojava/bio/program/sax/SequenceAlignmentSAXParser.html" title="class in org.biojava.bio.program.sax">SequenceAlignmentSAXParser</a></dt>
<dd>
<div class="block">Describe 'parse' method here.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/LineSplitParser.html#parse(java.lang.Object)">parse(Object)</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/LineSplitParser.html" title="class in org.biojava.bio.program.tagvalue">LineSplitParser</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/RegexParser.html#parse(java.lang.Object)">parse(Object)</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/RegexParser.html" title="class in org.biojava.bio.program.tagvalue">RegexParser</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/TagValueParser.html#parse(java.lang.Object)">parse(Object)</a></span> - Method in interface org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/TagValueParser.html" title="interface in org.biojava.bio.program.tagvalue">TagValueParser</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/MMcifParser.html#parse(java.io.BufferedReader)">parse(BufferedReader)</a></span> - Method in interface org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/MMcifParser.html" title="interface in org.biojava.bio.structure.io.mmcif">MMcifParser</a></dt>
<dd>
<div class="block">Start the actual parsing.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/MMcifParser.html#parse(java.io.InputStream)">parse(InputStream)</a></span> - Method in interface org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/MMcifParser.html" title="interface in org.biojava.bio.structure.io.mmcif">MMcifParser</a></dt>
<dd>
<div class="block">Start the actual parsing.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/SimpleMMcifParser.html#parse(java.io.InputStream)">parse(InputStream)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/SimpleMMcifParser.html" title="class in org.biojava.bio.structure.io.mmcif">SimpleMMcifParser</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/SimpleMMcifParser.html#parse(java.io.BufferedReader)">parse(BufferedReader)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/SimpleMMcifParser.html" title="class in org.biojava.bio.structure.io.mmcif">SimpleMMcifParser</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/taxa/EbiFormat.html#parse(org.biojava.bio.taxa.TaxonFactory, java.lang.String)">parse(TaxonFactory, String)</a></span> - Method in class org.biojava.bio.taxa.<a href="./org/biojava/bio/taxa/EbiFormat.html" title="class in org.biojava.bio.taxa">EbiFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/taxa/TaxonParser.html#parse(org.biojava.bio.taxa.TaxonFactory, java.lang.String)">parse(TaxonFactory, String)</a></span> - Method in interface org.biojava.bio.taxa.<a href="./org/biojava/bio/taxa/TaxonParser.html" title="interface in org.biojava.bio.taxa">TaxonParser</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Convert a stringified Taxon into a Taxon instance.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/naming/ObdaUriParser.html#parse(java.lang.String)">parse(String)</a></span> - Method in class org.biojava.naming.<a href="./org/biojava/naming/ObdaUriParser.html" title="class in org.biojava.naming">ObdaUriParser</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/io/TabDelimParser.html#parse(java.io.BufferedReader, org.biojava.ontology.OntologyFactory)">parse(BufferedReader, OntologyFactory)</a></span> - Method in class org.biojava.ontology.io.<a href="./org/biojava/ontology/io/TabDelimParser.html" title="class in org.biojava.ontology.io">TabDelimParser</a></dt>
<dd>
<div class="block">Parse an ontology from a reader.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/phylo/io/phylip/PHYLIPFileFormat.html#parse(org.biojavax.bio.phylo.io.phylip.PHYLIPFileListener, java.io.BufferedReader)">parse(PHYLIPFileListener, BufferedReader)</a></span> - Static method in class org.biojavax.bio.phylo.io.phylip.<a href="./org/biojavax/bio/phylo/io/phylip/PHYLIPFileFormat.html" title="class in org.biojavax.bio.phylo.io.phylip">PHYLIPFileFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFParser.html#parseAttribute(java.lang.String)">parseAttribute(String)</a></span> - Method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFParser.html" title="class in org.biojava.bio.program.gff">GFFParser</a></dt>
<dd>
<div class="block">Parse <span class="arg">attValList</span> into a
<span class="type">Map</span> of attributes and value lists.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff3/GFF3Parser.html#parseAttribute(java.lang.String, org.biojava.bio.Annotation, org.biojava.ontology.Ontology, org.biojava.ontology.Ontology)">parseAttribute(String, Annotation, Ontology, Ontology)</a></span> - Method in class org.biojava.bio.program.gff3.<a href="./org/biojava/bio/program/gff3/GFF3Parser.html" title="class in org.biojava.bio.program.gff3">GFF3Parser</a></dt>
<dd>
<div class="block">Parse <span class="arg">attValList</span> into a
<span class="type">Map</span> of attributes and value lists.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/DocRefAuthor.Tools.html#parseAuthorString(java.lang.String)">parseAuthorString(String)</a></span> - Static method in class org.biojavax.<a href="./org/biojavax/DocRefAuthor.Tools.html" title="class in org.biojavax">DocRefAuthor.Tools</a></dt>
<dd>
<div class="block">Takes a list of authors and returns a set of DocRefAuthor objects.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/PDBFileParser.html#parseCAOnly">parseCAOnly</a></span> - Variable in class org.biojava.bio.structure.io.<a href="./org/biojava/bio/structure/io/PDBFileParser.html" title="class in org.biojava.bio.structure.io">PDBFileParser</a></dt>
<dd>
<div class="block">Set the flag to only read in Ca atoms - this is useful for parsing large structures like 1htq.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html#parseComment(org.biojavax.Comment)">parseComment(Comment)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html" title="class in org.biojavax.bio.seq.io">UniProtCommentParser</a></dt>
<dd>
<div class="block">Parses the comment string from the given comment and populates
the internal fields appropriately.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html#parseComment(java.lang.String)">parseComment(String)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html" title="class in org.biojavax.bio.seq.io">UniProtCommentParser</a></dt>
<dd>
<div class="block">Parses the comment string from the given comment and populates
the internal fields appropriately.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/dasalignment/DASAlignmentCall.html#parseDASResponse(java.io.InputStream)">parseDASResponse(InputStream)</a></span> - Method in class org.biojava.bio.program.das.dasalignment.<a href="./org/biojava/bio/program/das/dasalignment/DASAlignmentCall.html" title="class in org.biojava.bio.program.das.dasalignment">DASAlignmentCall</a></dt>
<dd>
<div class="block">parse the Response of a DAS ALignment service and return a
biojava Alignment object.</div>
</dd>
<dt><a href="./org/biojava/utils/ParseErrorEvent.html" title="class in org.biojava.utils"><span class="strong">ParseErrorEvent</span></a> - Class in <a href="./org/biojava/utils/package-summary.html">org.biojava.utils</a></dt>
<dd>
<div class="block">Event which signals a bad line when parsing a record.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/ParseErrorEvent.html#ParseErrorEvent(java.lang.Object)">ParseErrorEvent(Object)</a></span> - Constructor for class org.biojava.utils.<a href="./org/biojava/utils/ParseErrorEvent.html" title="class in org.biojava.utils">ParseErrorEvent</a></dt>
<dd>
<div class="block">Construct a ParseErrorEvent with no other information.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/ParseErrorEvent.html#ParseErrorEvent(java.lang.Object, java.lang.String)">ParseErrorEvent(Object, String)</a></span> - Constructor for class org.biojava.utils.<a href="./org/biojava/utils/ParseErrorEvent.html" title="class in org.biojava.utils">ParseErrorEvent</a></dt>
<dd>
<div class="block">Construct a ParseErrorEvent with a message.</div>
</dd>
<dt><a href="./org/biojava/utils/ParseErrorListener.html" title="interface in org.biojava.utils"><span class="strong">ParseErrorListener</span></a> - Interface in <a href="./org/biojava/utils/package-summary.html">org.biojava.utils</a></dt>
<dd>
<div class="block">Listener for a ParseErrorEvent.</div>
</dd>
<dt><a href="./org/biojava/utils/ParseErrorSource.html" title="interface in org.biojava.utils"><span class="strong">ParseErrorSource</span></a> - Interface in <a href="./org/biojava/utils/package-summary.html">org.biojava.utils</a></dt>
<dd>
<div class="block">Source for a ParseErrorEvent.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/tools/SVM_Light.html#parseExample(java.lang.String)">parseExample(String)</a></span> - Static method in class org.biojava.stats.svm.tools.<a href="./org/biojava/stats/svm/tools/SVM_Light.html" title="class in org.biojava.stats.svm.tools">SVM_Light</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/io/ParseException.html" title="class in org.biojava.bio.seq.io"><span class="strong">ParseException</span></a> - Exception in <a href="./org/biojava/bio/seq/io/package-summary.html">org.biojava.bio.seq.io</a></dt>
<dd>
<div class="block">ParseException should be thrown to indicate that there was a problem with
parsing sequence information.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/ParseException.html#ParseException()">ParseException()</a></span> - Constructor for exception org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/ParseException.html" title="class in org.biojava.bio.seq.io">ParseException</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/ParseException.html#ParseException(java.lang.String)">ParseException(String)</a></span> - Constructor for exception org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/ParseException.html" title="class in org.biojava.bio.seq.io">ParseException</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/ParseException.html#ParseException(java.lang.Throwable)">ParseException(Throwable)</a></span> - Constructor for exception org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/ParseException.html" title="class in org.biojava.bio.seq.io">ParseException</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/ParseException.html#ParseException(java.lang.Throwable, java.lang.String)">ParseException(Throwable, String)</a></span> - Constructor for exception org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/ParseException.html" title="class in org.biojava.bio.seq.io">ParseException</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/fastq/FastqVariant.html#parseFastqVariant(java.lang.String)">parseFastqVariant(String)</a></span> - Static method in enum org.biojava.bio.program.fastq.<a href="./org/biojava/bio/program/fastq/FastqVariant.html" title="enum in org.biojava.bio.program.fastq">FastqVariant</a></dt>
<dd>
<div class="block">Return the FASTQ sequence format variant with the specified name, if any.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/phylo/io/phylip/PHYLIPFileFormat.html#parseFile(org.biojavax.bio.phylo.io.phylip.PHYLIPFileListener, java.io.File)">parseFile(PHYLIPFileListener, File)</a></span> - Static method in class org.biojavax.bio.phylo.io.phylip.<a href="./org/biojavax/bio/phylo/io/phylip/PHYLIPFileFormat.html" title="class in org.biojavax.bio.phylo.io.phylip">PHYLIPFileFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/hmmer/HmmerProfileParser.html#parseFull(java.io.File)">parseFull(File)</a></span> - Static method in class org.biojava.bio.program.hmmer.<a href="./org/biojava/bio/program/hmmer/HmmerProfileParser.html" title="class in org.biojava.bio.program.hmmer">HmmerProfileParser</a></dt>
<dd>
<div class="block">Returns the full markov model - including the core model + J,C,N loop states.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/io/GOParser.html#parseGO(java.io.BufferedReader, java.lang.String, java.lang.String, org.biojava.ontology.OntologyFactory)">parseGO(BufferedReader, String, String, OntologyFactory)</a></span> - Method in class org.biojava.ontology.io.<a href="./org/biojava/ontology/io/GOParser.html" title="class in org.biojava.ontology.io">GOParser</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/phylo/io/phylip/PHYLIPFileFormat.html#parseInputStream(org.biojavax.bio.phylo.io.phylip.PHYLIPFileListener, java.io.InputStream)">parseInputStream(PHYLIPFileListener, InputStream)</a></span> - Static method in class org.biojavax.bio.phylo.io.phylip.<a href="./org/biojavax/bio/phylo/io/phylip/PHYLIPFileFormat.html" title="class in org.biojavax.bio.phylo.io.phylip">PHYLIPFileFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/EmblLikeLocationParser.html#parseLocation(java.lang.String, org.biojava.bio.seq.Feature.Template)">parseLocation(String, Feature.Template)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/EmblLikeLocationParser.html" title="class in org.biojava.bio.seq.io">EmblLikeLocationParser</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block"><code>parseLocation</code> creates a <code>Location</code> from
the String and returns a stranded location.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/GenbankLocationParser.html#parseLocation(org.biojavax.Namespace, java.lang.String, java.lang.String)">parseLocation(Namespace, String, String)</a></span> - Static method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/GenbankLocationParser.html" title="class in org.biojavax.bio.seq.io">GenbankLocationParser</a></dt>
<dd>
<div class="block">Parses a location.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtLocationParser.html#parseLocation(java.lang.String)">parseLocation(String)</a></span> - Static method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtLocationParser.html" title="class in org.biojavax.bio.seq.io">UniProtLocationParser</a></dt>
<dd>
<div class="block">Parses a location.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/hmmer/HmmerProfileParser.html#parseModel(java.io.File)">parseModel(File)</a></span> - Method in class org.biojava.bio.program.hmmer.<a href="./org/biojava/bio/program/hmmer/HmmerProfileParser.html" title="class in org.biojava.bio.program.hmmer">HmmerProfileParser</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/io/OboParser.html#parseOBO(java.io.BufferedReader, java.lang.String, java.lang.String)">parseOBO(BufferedReader, String, String)</a></span> - Method in class org.biojava.ontology.io.<a href="./org/biojava/ontology/io/OboParser.html" title="class in org.biojava.ontology.io">OboParser</a></dt>
<dd>
<div class="block">Parse a OBO file and return its content as a BioJava Ontology object</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/obo/OboFileParser.html#parseOBO(java.io.BufferedReader)">parseOBO(BufferedReader)</a></span> - Method in class org.biojava.ontology.obo.<a href="./org/biojava/ontology/obo/OboFileParser.html" title="class in org.biojava.ontology.obo">OboFileParser</a></dt>
<dd>
<div class="block">parse an ontology file</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/PDBFileParser.html#parsePDBFile(java.io.InputStream)">parsePDBFile(InputStream)</a></span> - Method in class org.biojava.bio.structure.io.<a href="./org/biojava/bio/structure/io/PDBFileParser.html" title="class in org.biojava.bio.structure.io">PDBFileParser</a></dt>
<dd>
<div class="block">parse a PDB file and return a datastructure implementing
PDBStructure interface.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/PDBFileParser.html#parsePDBFile(java.io.BufferedReader)">parsePDBFile(BufferedReader)</a></span> - Method in class org.biojava.bio.structure.io.<a href="./org/biojava/bio/structure/io/PDBFileParser.html" title="class in org.biojava.bio.structure.io">PDBFileParser</a></dt>
<dd>
<div class="block">parse a PDB file and return a datastructure implementing
PDBStructure interface.</div>
</dd>
<dt><a href="./org/biojava/bio/program/tagvalue/Parser.html" title="class in org.biojava.bio.program.tagvalue"><span class="strong">Parser</span></a> - Class in <a href="./org/biojava/bio/program/tagvalue/package-summary.html">org.biojava.bio.program.tagvalue</a></dt>
<dd>
<div class="block">
Encapsulate the parsing of lines from a buffered reader into tag-value
events.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/Parser.html#Parser()">Parser()</a></span> - Constructor for class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/Parser.html" title="class in org.biojava.bio.program.tagvalue">Parser</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/phylo/io/phylip/PHYLIPFileFormat.html#parseReader(org.biojavax.bio.phylo.io.phylip.PHYLIPFileListener, java.io.Reader)">parseReader(PHYLIPFileListener, Reader)</a></span> - Static method in class org.biojavax.bio.phylo.io.phylip.<a href="./org/biojavax/bio/phylo/io/phylip/PHYLIPFileFormat.html" title="class in org.biojavax.bio.phylo.io.phylip">PHYLIPFileFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/FileAsList.html#parseRecord(byte[])">parseRecord(byte[])</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/FileAsList.html" title="class in org.biojava.utils">FileAsList</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/directory/OBDARegistryParser.html#parseRegistry(java.io.BufferedReader, java.lang.String)">parseRegistry(BufferedReader, String)</a></span> - Static method in class org.biojava.directory.<a href="./org/biojava/directory/OBDARegistryParser.html" title="class in org.biojava.directory">OBDARegistryParser</a></dt>
<dd>
<div class="block"><code>parseRegistry</code> parses an Open Bioinformatics Database
Access (OBDA) configuration file.</div>
</dd>
<dt><a href="./org/biojava/utils/ParserException.html" title="class in org.biojava.utils"><span class="strong">ParserException</span></a> - Exception in <a href="./org/biojava/utils/package-summary.html">org.biojava.utils</a></dt>
<dd>
<div class="block">Exception thrown when an error occurs in document parsing.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/ParserException.html#ParserException(java.lang.String)">ParserException(String)</a></span> - Constructor for exception org.biojava.utils.<a href="./org/biojava/utils/ParserException.html" title="class in org.biojava.utils">ParserException</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ParserException.html#ParserException(java.lang.String, java.lang.String)">ParserException(String, String)</a></span> - Constructor for exception org.biojava.utils.<a href="./org/biojava/utils/ParserException.html" title="class in org.biojava.utils">ParserException</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ParserException.html#ParserException(java.lang.String, java.lang.String, int)">ParserException(String, String, int)</a></span> - Constructor for exception org.biojava.utils.<a href="./org/biojava/utils/ParserException.html" title="class in org.biojava.utils">ParserException</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ParserException.html#ParserException(java.lang.String, java.lang.String, int, java.lang.String)">ParserException(String, String, int, String)</a></span> - Constructor for exception org.biojava.utils.<a href="./org/biojava/utils/ParserException.html" title="class in org.biojava.utils">ParserException</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ParserException.html#ParserException(java.lang.String, java.lang.String, int, java.lang.String, int)">ParserException(String, String, int, String, int)</a></span> - Constructor for exception org.biojava.utils.<a href="./org/biojava/utils/ParserException.html" title="class in org.biojava.utils">ParserException</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ParserException.html#ParserException(java.lang.Throwable)">ParserException(Throwable)</a></span> - Constructor for exception org.biojava.utils.<a href="./org/biojava/utils/ParserException.html" title="class in org.biojava.utils">ParserException</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ParserException.html#ParserException(java.lang.Throwable, java.lang.String)">ParserException(Throwable, String)</a></span> - Constructor for exception org.biojava.utils.<a href="./org/biojava/utils/ParserException.html" title="class in org.biojava.utils">ParserException</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>use new ParserException(detail, t)</i></div>
</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/ParserException.html#ParserException(java.lang.String, java.lang.Throwable)">ParserException(String, Throwable)</a></span> - Constructor for exception org.biojava.utils.<a href="./org/biojava/utils/ParserException.html" title="class in org.biojava.utils">ParserException</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ParserException.html#ParserException(java.lang.Throwable, java.lang.String, java.lang.String)">ParserException(Throwable, String, String)</a></span> - Constructor for exception org.biojava.utils.<a href="./org/biojava/utils/ParserException.html" title="class in org.biojava.utils">ParserException</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ParserException.html#ParserException(java.lang.Throwable, java.lang.String, java.lang.String, int)">ParserException(Throwable, String, String, int)</a></span> - Constructor for exception org.biojava.utils.<a href="./org/biojava/utils/ParserException.html" title="class in org.biojava.utils">ParserException</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ParserException.html#ParserException(java.lang.Throwable, java.lang.String, java.lang.String, int, java.lang.String)">ParserException(Throwable, String, String, int, String)</a></span> - Constructor for exception org.biojava.utils.<a href="./org/biojava/utils/ParserException.html" title="class in org.biojava.utils">ParserException</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ParserException.html#ParserException(java.lang.Throwable, java.lang.String, java.lang.String, int, java.lang.String, int)">ParserException(Throwable, String, String, int, String, int)</a></span> - Constructor for exception org.biojava.utils.<a href="./org/biojava/utils/ParserException.html" title="class in org.biojava.utils">ParserException</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/tagvalue/ParserListener.html" title="class in org.biojava.bio.program.tagvalue"><span class="strong">ParserListener</span></a> - Class in <a href="./org/biojava/bio/program/tagvalue/package-summary.html">org.biojava.bio.program.tagvalue</a></dt>
<dd>
<div class="block"><code>ParserListener</code> is an immutable pairing of a parser and
listener.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/ParserListener.html#ParserListener(org.biojava.bio.program.tagvalue.TagValueParser, org.biojava.bio.program.tagvalue.TagValueListener)">ParserListener(TagValueParser, TagValueListener)</a></span> - Constructor for class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/ParserListener.html" title="class in org.biojava.bio.program.tagvalue">ParserListener</a></dt>
<dd>
<div class="block">Creates a new <code>ParserListener</code> instance.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/Alphabet.html#PARSERS">PARSERS</a></span> - Static variable in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/Alphabet.html" title="interface in org.biojava.bio.symbol">Alphabet</a></dt>
<dd>
<div class="block">This signals that the available parsers have changed.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/StrandParser.html#parseStrand(java.lang.String)">parseStrand(String)</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/StrandParser.html" title="class in org.biojava.bio.seq">StrandParser</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/AlternateTokenization.html#parseStream(org.biojava.bio.seq.io.SeqIOListener)">parseStream(SeqIOListener)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/AlternateTokenization.html" title="class in org.biojava.bio.seq.io">AlternateTokenization</a></dt>
<dd>
<div class="block">Will throw an exception.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/CharacterTokenization.html#parseStream(org.biojava.bio.seq.io.SeqIOListener)">parseStream(SeqIOListener)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/CharacterTokenization.html" title="class in org.biojava.bio.seq.io">CharacterTokenization</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SymbolTokenization.html#parseStream(org.biojava.bio.seq.io.SeqIOListener)">parseStream(SeqIOListener)</a></span> - Method in interface org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SymbolTokenization.html" title="interface in org.biojava.bio.seq.io">SymbolTokenization</a></dt>
<dd>
<div class="block">Return an object which can parse an arbitrary character stream into
symbols.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/WordTokenization.html#parseStream(org.biojava.bio.seq.io.SeqIOListener)">parseStream(SeqIOListener)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/WordTokenization.html" title="class in org.biojava.bio.seq.io">WordTokenization</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SoftMaskedAlphabet.CaseSensitiveTokenization.html#parseStream(org.biojava.bio.seq.io.SeqIOListener)">parseStream(SeqIOListener)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SoftMaskedAlphabet.CaseSensitiveTokenization.html" title="class in org.biojava.bio.symbol">SoftMaskedAlphabet.CaseSensitiveTokenization</a></dt>
<dd>
<div class="block">The current implementation only supports character parsing.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/WordTokenization.html#parseString(java.lang.String)">parseString(String)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/WordTokenization.html" title="class in org.biojava.bio.seq.io">WordTokenization</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/AlternateTokenization.html#parseToken(java.lang.String)">parseToken(String)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/AlternateTokenization.html" title="class in org.biojava.bio.seq.io">AlternateTokenization</a></dt>
<dd>
<div class="block">Will throw an exception.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/CharacterTokenization.html#parseToken(java.lang.String)">parseToken(String)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/CharacterTokenization.html" title="class in org.biojava.bio.seq.io">CharacterTokenization</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/CrossProductTokenization.html#parseToken(java.lang.String)">parseToken(String)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/CrossProductTokenization.html" title="class in org.biojava.bio.seq.io">CrossProductTokenization</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/DoubleTokenization.html#parseToken(java.lang.String)">parseToken(String)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/DoubleTokenization.html" title="class in org.biojava.bio.seq.io">DoubleTokenization</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/IntegerTokenization.html#parseToken(java.lang.String)">parseToken(String)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/IntegerTokenization.html" title="class in org.biojava.bio.seq.io">IntegerTokenization</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/NameTokenization.html#parseToken(java.lang.String)">parseToken(String)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/NameTokenization.html" title="class in org.biojava.bio.seq.io">NameTokenization</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SubIntegerTokenization.html#parseToken(java.lang.String)">parseToken(String)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SubIntegerTokenization.html" title="class in org.biojava.bio.seq.io">SubIntegerTokenization</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SymbolTokenization.html#parseToken(java.lang.String)">parseToken(String)</a></span> - Method in interface org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SymbolTokenization.html" title="interface in org.biojava.bio.seq.io">SymbolTokenization</a></dt>
<dd>
<div class="block">Returns the symbol for a single token.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SoftMaskedAlphabet.CaseSensitiveTokenization.html#parseToken(java.lang.String)">parseToken(String)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SoftMaskedAlphabet.CaseSensitiveTokenization.html" title="class in org.biojava.bio.symbol">SoftMaskedAlphabet.CaseSensitiveTokenization</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/CharacterTokenization.html#parseTokenChar(char)">parseTokenChar(char)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/CharacterTokenization.html" title="class in org.biojava.bio.seq.io">CharacterTokenization</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/XMLDistributionReader.html#parseXML(java.io.InputStream)">parseXML(InputStream)</a></span> - Method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/XMLDistributionReader.html" title="class in org.biojava.bio.dist">XMLDistributionReader</a></dt>
<dd>
<div class="block">Reads an XML representation of a Distribution from a file.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/obo/OboFileParser.html#parseXref(java.lang.String, int, int)">parseXref(String, int, int)</a></span> - Method in class org.biojava.ontology.obo.<a href="./org/biojava/ontology/obo/OboFileParser.html" title="class in org.biojava.ontology.obo">OboFileParser</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/OntoTools.html#PART_OF">PART_OF</a></span> - Static variable in class org.biojava.ontology.<a href="./org/biojava/ontology/OntoTools.html" title="class in org.biojava.ontology">OntoTools</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/OntoTools.html#PARTIAL_ORDER">PARTIAL_ORDER</a></span> - Static variable in class org.biojava.ontology.<a href="./org/biojava/ontology/OntoTools.html" title="class in org.biojava.ontology">OntoTools</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html#PATENT_TAG">PATENT_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html" title="class in org.biojavax.bio.seq.io">EMBLxmlFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/regex/Matcher.html#pattern()">pattern()</a></span> - Method in class org.biojava.utils.regex.<a href="./org/biojava/utils/regex/Matcher.html" title="class in org.biojava.utils.regex">Matcher</a></dt>
<dd>
<div class="block">Returns the Pattern object that compiled this Matcher.</div>
</dd>
<dt><a href="./org/biojava/utils/regex/Pattern.html" title="class in org.biojava.utils.regex"><span class="strong">Pattern</span></a> - Class in <a href="./org/biojava/utils/regex/package-summary.html">org.biojava.utils.regex</a></dt>
<dd>
<div class="block">A class analogous to java.util.regex.Pattern but for SymbolLists.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/regex/Pattern.html#patternAsString()">patternAsString()</a></span> - Method in class org.biojava.utils.regex.<a href="./org/biojava/utils/regex/Pattern.html" title="class in org.biojava.utils.regex">Pattern</a></dt>
<dd>
<div class="block">returns the Pattern to be matched as a String.</div>
</dd>
<dt><a href="./org/biojava/utils/automata/PatternBlitz.html" title="class in org.biojava.utils.automata"><span class="strong">PatternBlitz</span></a> - Class in <a href="./org/biojava/utils/automata/package-summary.html">org.biojava.utils.automata</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/automata/PatternBlitz.html#PatternBlitz(org.biojava.bio.symbol.FiniteAlphabet, org.biojava.utils.automata.StateMachineToolkit)">PatternBlitz(FiniteAlphabet, StateMachineToolkit)</a></span> - Constructor for class org.biojava.utils.automata.<a href="./org/biojava/utils/automata/PatternBlitz.html" title="class in org.biojava.utils.automata">PatternBlitz</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/regex/Pattern.html#patternExpanded()">patternExpanded()</a></span> - Method in class org.biojava.utils.regex.<a href="./org/biojava/utils/regex/Pattern.html" title="class in org.biojava.utils.regex">Pattern</a></dt>
<dd>
<div class="block">returns the actual String used to construct the regex with all
ambiguities expanded.</div>
</dd>
<dt><a href="./org/biojava/utils/regex/PatternFactory.html" title="class in org.biojava.utils.regex"><span class="strong">PatternFactory</span></a> - Class in <a href="./org/biojava/utils/regex/package-summary.html">org.biojava.utils.regex</a></dt>
<dd>
<div class="block">A class that creates Patterns for regex matching on
SymbolLists of a specific Alphabet.</div>
</dd>
<dt><a href="./org/biojava/utils/automata/PatternListener.html" title="interface in org.biojava.utils.automata"><span class="strong">PatternListener</span></a> - Interface in <a href="./org/biojava/utils/automata/package-summary.html">org.biojava.utils.automata</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/utils/automata/PatternMaker.html" title="class in org.biojava.utils.automata"><span class="strong">PatternMaker</span></a> - Class in <a href="./org/biojava/utils/automata/package-summary.html">org.biojava.utils.automata</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePanel.Border.html#pcs">pcs</a></span> - Variable in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePanel.Border.html" title="class in org.biojava.bio.gui.sequence">SequencePanel.Border</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePoster.Border.html#pcs">pcs</a></span> - Variable in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePoster.Border.html" title="class in org.biojava.bio.gui.sequence">SequencePoster.Border</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOConstants.html#PDB">PDB</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOConstants.html" title="class in org.biojava.bio.seq.io">SeqIOConstants</a></dt>
<dd>
<div class="block"><code>PDB</code> indicates that the sequence format is
PDB.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/PDBFileParser.html#PDB_AUTHOR_ASSIGNMENT">PDB_AUTHOR_ASSIGNMENT</a></span> - Static variable in class org.biojava.bio.structure.io.<a href="./org/biojava/bio/structure/io/PDBFileParser.html" title="class in org.biojava.bio.structure.io">PDBFileParser</a></dt>
<dd>
<div class="block">Secondary strucuture assigned by the PDB author/</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/util/PDBDirPanel.html#PDB_DIR">PDB_DIR</a></span> - Static variable in class org.biojava.bio.structure.gui.util.<a href="./org/biojava/bio/structure/gui/util/PDBDirPanel.html" title="class in org.biojava.bio.structure.gui.util">PDBDirPanel</a></dt>
<dd>
<div class="block">the system property PDB_DIR can be used to configure the
default location for PDB files.</div>
</dd>
<dt><a href="./org/biojava/bio/structure/gui/util/PDBDirPanel.html" title="class in org.biojava.bio.structure.gui.util"><span class="strong">PDBDirPanel</span></a> - Class in <a href="./org/biojava/bio/structure/gui/util/package-summary.html">org.biojava.bio.structure.gui.util</a></dt>
<dd>
<div class="block">A class to define where a structure for the alignment is coming from</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/util/PDBDirPanel.html#PDBDirPanel()">PDBDirPanel()</a></span> - Constructor for class org.biojava.bio.structure.gui.util.<a href="./org/biojava/bio/structure/gui/util/PDBDirPanel.html" title="class in org.biojava.bio.structure.gui.util">PDBDirPanel</a></dt>
<dd>
<div class="block">load the PDB files from a local directory</div>
</dd>
<dt><a href="./org/biojava/bio/structure/io/PDBFileParser.html" title="class in org.biojava.bio.structure.io"><span class="strong">PDBFileParser</span></a> - Class in <a href="./org/biojava/bio/structure/io/package-summary.html">org.biojava.bio.structure.io</a></dt>
<dd>
<div class="block">This class implements the actual PDB file parsing.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/PDBFileParser.html#PDBFileParser()">PDBFileParser()</a></span> - Constructor for class org.biojava.bio.structure.io.<a href="./org/biojava/bio/structure/io/PDBFileParser.html" title="class in org.biojava.bio.structure.io">PDBFileParser</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/structure/io/PDBFileReader.html" title="class in org.biojava.bio.structure.io"><span class="strong">PDBFileReader</span></a> - Class in <a href="./org/biojava/bio/structure/io/package-summary.html">org.biojava.bio.structure.io</a></dt>
<dd>
<div class="block">
The wrapper class for parsing a PDB file.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/PDBFileReader.html#PDBFileReader()">PDBFileReader()</a></span> - Constructor for class org.biojava.bio.structure.io.<a href="./org/biojava/bio/structure/io/PDBFileReader.html" title="class in org.biojava.bio.structure.io">PDBFileReader</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/structure/server/PDBFilter.html" title="interface in org.biojava.bio.structure.server"><span class="strong">PDBFilter</span></a> - Interface in <a href="./org/biojava/bio/structure/server/package-summary.html">org.biojava.bio.structure.server</a></dt>
<dd>
<div class="block">defines how a filter of PDB files has to behave</div>
</dd>
<dt><a href="./org/biojava/bio/structure/PDBHeader.html" title="class in org.biojava.bio.structure"><span class="strong">PDBHeader</span></a> - Class in <a href="./org/biojava/bio/structure/package-summary.html">org.biojava.bio.structure</a></dt>
<dd>
<div class="block">A class that contains PDB Header information.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/PDBHeader.html#PDBHeader()">PDBHeader()</a></span> - Constructor for class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/PDBHeader.html" title="class in org.biojava.bio.structure">PDBHeader</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/structure/server/PDBInstallation.html" title="interface in org.biojava.bio.structure.server"><span class="strong">PDBInstallation</span></a> - Interface in <a href="./org/biojava/bio/structure/server/package-summary.html">org.biojava.bio.structure.server</a></dt>
<dd>
<div class="block">an interface that defines different access methods to PDB installations.</div>
</dd>
<dt><a href="./org/biojava/bio/structure/io/PDBMSDReader.html" title="class in org.biojava.bio.structure.io"><span class="strong">PDBMSDReader</span></a> - Class in <a href="./org/biojava/bio/structure/io/package-summary.html">org.biojava.bio.structure.io</a></dt>
<dd>
<div class="block">retreive a structure from an installation of the MSD - search
database ( http://www.ebi.ac.uk/msd/index.html ,
http://www.ebi.ac.uk/msd-srv/docs/dbdoc/ )</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/PDBMSDReader.html#PDBMSDReader()">PDBMSDReader()</a></span> - Constructor for class org.biojava.bio.structure.io.<a href="./org/biojava/bio/structure/io/PDBMSDReader.html" title="class in org.biojava.bio.structure.io">PDBMSDReader</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/structure/io/PDBParseException.html" title="class in org.biojava.bio.structure.io"><span class="strong">PDBParseException</span></a> - Exception in <a href="./org/biojava/bio/structure/io/package-summary.html">org.biojava.bio.structure.io</a></dt>
<dd>
<div class="block">An exception during the parsing of a PDB file.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/PDBParseException.html#PDBParseException(java.lang.String)">PDBParseException(String)</a></span> - Constructor for exception org.biojava.bio.structure.io.<a href="./org/biojava/bio/structure/io/PDBParseException.html" title="class in org.biojava.bio.structure.io">PDBParseException</a></dt>
<dd>
<div class="block">Constructs a PDBParseException object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/PDBParseException.html#PDBParseException(java.lang.Throwable, java.lang.String)">PDBParseException(Throwable, String)</a></span> - Constructor for exception org.biojava.bio.structure.io.<a href="./org/biojava/bio/structure/io/PDBParseException.html" title="class in org.biojava.bio.structure.io">PDBParseException</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>use new BioException(message, ex) instead</i></div>
</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/PDBParseException.html#PDBParseException(java.lang.String, java.lang.Throwable)">PDBParseException(String, Throwable)</a></span> - Constructor for exception org.biojava.bio.structure.io.<a href="./org/biojava/bio/structure/io/PDBParseException.html" title="class in org.biojava.bio.structure.io">PDBParseException</a></dt>
<dd>
<div class="block">Constructs a PDBParseException object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/PDBParseException.html#PDBParseException(java.lang.Throwable)">PDBParseException(Throwable)</a></span> - Constructor for exception org.biojava.bio.structure.io.<a href="./org/biojava/bio/structure/io/PDBParseException.html" title="class in org.biojava.bio.structure.io">PDBParseException</a></dt>
<dd>
<div class="block">Constructs a PDBParseException object.</div>
</dd>
<dt><a href="./org/biojava/bio/structure/PDBRecord.html" title="interface in org.biojava.bio.structure"><span class="strong">PDBRecord</span></a> - Interface in <a href="./org/biojava/bio/structure/package-summary.html">org.biojava.bio.structure</a></dt>
<dd>
<div class="block">An interface implemented by all classes that represent PDB records</div>
</dd>
<dt><a href="./org/biojava/bio/program/sax/PdbSAXParser.html" title="class in org.biojava.bio.program.sax"><span class="strong">PdbSAXParser</span></a> - Class in <a href="./org/biojava/bio/program/sax/package-summary.html">org.biojava.bio.program.sax</a></dt>
<dd>
<div class="block">A SAX2 parser for dealing with native PDB files.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/sax/PdbSAXParser.html#PdbSAXParser()">PdbSAXParser()</a></span> - Constructor for class org.biojava.bio.program.sax.<a href="./org/biojava/bio/program/sax/PdbSAXParser.html" title="class in org.biojava.bio.program.sax">PdbSAXParser</a></dt>
<dd>
<div class="block">Sets namespace prefix to "biojava"</div>
</dd>
<dt><a href="./org/biojava/bio/structure/gui/util/PDBServerPanel.html" title="class in org.biojava.bio.structure.gui.util"><span class="strong">PDBServerPanel</span></a> - Class in <a href="./org/biojava/bio/structure/gui/util/package-summary.html">org.biojava.bio.structure.gui.util</a></dt>
<dd>
<div class="block">A class to define where a structure for the alignment is coming from</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/util/PDBServerPanel.html#PDBServerPanel()">PDBServerPanel()</a></span> - Constructor for class org.biojava.bio.structure.gui.util.<a href="./org/biojava/bio/structure/gui/util/PDBServerPanel.html" title="class in org.biojava.bio.structure.gui.util">PDBServerPanel</a></dt>
<dd>
<div class="block">load the PDB files from a local directory</div>
</dd>
<dt><a href="./org/biojava/bio/structure/io/PDBSRSReader.html" title="class in org.biojava.bio.structure.io"><span class="strong">PDBSRSReader</span></a> - Class in <a href="./org/biojava/bio/structure/io/package-summary.html">org.biojava.bio.structure.io</a></dt>
<dd>
<div class="block">reads a PDB file from a local SRS installation using getz Actually
is the same as PDBFileReader, but instead of reading from a file stream, reads from a
buffered stream.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/PDBSRSReader.html#PDBSRSReader()">PDBSRSReader()</a></span> - Constructor for class org.biojava.bio.structure.io.<a href="./org/biojava/bio/structure/io/PDBSRSReader.html" title="class in org.biojava.bio.structure.io">PDBSRSReader</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/PdbToXMLConverter.html" title="class in org.biojava.bio.program"><span class="strong">PdbToXMLConverter</span></a> - Class in <a href="./org/biojava/bio/program/package-summary.html">org.biojava.bio.program</a></dt>
<dd>
<div class="block">
A class that converts Protein Data Bank (PDB) to
XML that will validate against the biojava:MacromolecularStructure DTD.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/PdbToXMLConverter.html#PdbToXMLConverter(java.lang.String)">PdbToXMLConverter(String)</a></span> - Constructor for class org.biojava.bio.program.<a href="./org/biojava/bio/program/PdbToXMLConverter.html" title="class in org.biojava.bio.program">PdbToXMLConverter</a></dt>
<dd>
<div class="block">Creates a new <code>BlastToXMLConverter</code> instance.</div>
</dd>
<dt><a href="./org/biojava/bio/structure/gui/util/PDBUploadPanel.html" title="class in org.biojava.bio.structure.gui.util"><span class="strong">PDBUploadPanel</span></a> - Class in <a href="./org/biojava/bio/structure/gui/util/package-summary.html">org.biojava.bio.structure.gui.util</a></dt>
<dd>
<div class="block">A JPanel to upload 2 PDB files.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/util/PDBUploadPanel.html#PDBUploadPanel()">PDBUploadPanel()</a></span> - Constructor for class org.biojava.bio.structure.gui.util.<a href="./org/biojava/bio/structure/gui/util/PDBUploadPanel.html" title="class in org.biojava.bio.structure.gui.util">PDBUploadPanel</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/structure/io/mmcif/model/PdbxEntityNonPoly.html" title="class in org.biojava.bio.structure.io.mmcif.model"><span class="strong">PdbxEntityNonPoly</span></a> - Class in <a href="./org/biojava/bio/structure/io/mmcif/model/package-summary.html">org.biojava.bio.structure.io.mmcif.model</a></dt>
<dd>
<div class="block">A bean for the Pdbx_entity_nonpoly category.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/PdbxEntityNonPoly.html#PdbxEntityNonPoly()">PdbxEntityNonPoly()</a></span> - Constructor for class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/PdbxEntityNonPoly.html" title="class in org.biojava.bio.structure.io.mmcif.model">PdbxEntityNonPoly</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/structure/io/mmcif/model/PdbxNonPolyScheme.html" title="class in org.biojava.bio.structure.io.mmcif.model"><span class="strong">PdbxNonPolyScheme</span></a> - Class in <a href="./org/biojava/bio/structure/io/mmcif/model/package-summary.html">org.biojava.bio.structure.io.mmcif.model</a></dt>
<dd>
<div class="block">A bean for the PDBX_NONPOLY_SCHEME category, which provides residue level nomenclature
mapping for non-polymer entities.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/PdbxNonPolyScheme.html#PdbxNonPolyScheme()">PdbxNonPolyScheme()</a></span> - Constructor for class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/PdbxNonPolyScheme.html" title="class in org.biojava.bio.structure.io.mmcif.model">PdbxNonPolyScheme</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/structure/io/mmcif/model/PdbxPolySeqScheme.html" title="class in org.biojava.bio.structure.io.mmcif.model"><span class="strong">PdbxPolySeqScheme</span></a> - Class in <a href="./org/biojava/bio/structure/io/mmcif/model/package-summary.html">org.biojava.bio.structure.io.mmcif.model</a></dt>
<dd>
<div class="block">A bean for the PDBX_POLY_SEQ_SCHEME category, which provides residue level nomenclature
mapping for polymer entities.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/PdbxPolySeqScheme.html#PdbxPolySeqScheme()">PdbxPolySeqScheme()</a></span> - Constructor for class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/PdbxPolySeqScheme.html" title="class in org.biojava.bio.structure.io.mmcif.model">PdbxPolySeqScheme</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/Digest.html#PEPTIDE_FEATURE_TYPE">PEPTIDE_FEATURE_TYPE</a></span> - Static variable in class org.biojava.bio.proteomics.<a href="./org/biojava/bio/proteomics/Digest.html" title="class in org.biojava.bio.proteomics">Digest</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/gui/sequence/PeptideDigestRenderer.html" title="class in org.biojava.bio.gui.sequence"><span class="strong">PeptideDigestRenderer</span></a> - Class in <a href="./org/biojava/bio/gui/sequence/package-summary.html">org.biojava.bio.gui.sequence</a></dt>
<dd>
<div class="block">A concrete AbstractPeptideDigestRenderer.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PeptideDigestRenderer.html#PeptideDigestRenderer(org.biojava.bio.gui.sequence.FeatureSource)">PeptideDigestRenderer(FeatureSource)</a></span> - Constructor for class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PeptideDigestRenderer.html" title="class in org.biojava.bio.gui.sequence">PeptideDigestRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PeptideDigestRenderer.html#PeptideDigestRenderer(org.biojava.bio.gui.sequence.FeatureSource, org.biojava.bio.seq.FeatureFilter)">PeptideDigestRenderer(FeatureSource, FeatureFilter)</a></span> - Constructor for class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PeptideDigestRenderer.html" title="class in org.biojava.bio.gui.sequence">PeptideDigestRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PeptideDigestRenderer.html#PeptideDigestRenderer(org.biojava.bio.gui.sequence.FeatureSource, org.biojava.bio.seq.FeatureFilter, int)">PeptideDigestRenderer(FeatureSource, FeatureFilter, int)</a></span> - Constructor for class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PeptideDigestRenderer.html" title="class in org.biojava.bio.gui.sequence">PeptideDigestRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/HomologeneBuilder.html#PERCENTIDENTITY">PERCENTIDENTITY</a></span> - Static variable in interface org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/HomologeneBuilder.html" title="interface in org.biojava.bio.program.homologene">HomologeneBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/functions/CrossOverFunction.NoCross.html#performCrossOver(org.biojava.bio.symbol.SymbolList, org.biojava.bio.symbol.SymbolList)">performCrossOver(SymbolList, SymbolList)</a></span> - Method in class org.biojavax.ga.functions.<a href="./org/biojavax/ga/functions/CrossOverFunction.NoCross.html" title="class in org.biojavax.ga.functions">CrossOverFunction.NoCross</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/functions/CrossOverFunction.html#performCrossOver(org.biojava.bio.symbol.SymbolList, org.biojava.bio.symbol.SymbolList)">performCrossOver(SymbolList, SymbolList)</a></span> - Method in interface org.biojavax.ga.functions.<a href="./org/biojavax/ga/functions/CrossOverFunction.html" title="interface in org.biojavax.ga.functions">CrossOverFunction</a></dt>
<dd>
<div class="block">Performs a cross between the pair of chromosomes</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ga/functions/OrderCrossover.html#performCrossOver(org.biojava.bio.symbol.SymbolList, org.biojava.bio.symbol.SymbolList)">performCrossOver(SymbolList, SymbolList)</a></span> - Method in class org.biojavax.ga.functions.<a href="./org/biojavax/ga/functions/OrderCrossover.html" title="class in org.biojavax.ga.functions">OrderCrossover</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/functions/SimpleCrossOverFunction.html#performCrossOver(org.biojava.bio.symbol.SymbolList, org.biojava.bio.symbol.SymbolList)">performCrossOver(SymbolList, SymbolList)</a></span> - Method in class org.biojavax.ga.functions.<a href="./org/biojavax/ga/functions/SimpleCrossOverFunction.html" title="class in org.biojavax.ga.functions">SimpleCrossOverFunction</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#PERSON_TAG">PERSON_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/phred/PhredTools.html#pFromQuality(double)">pFromQuality(double)</a></span> - Static method in class org.biojava.bio.program.phred.<a href="./org/biojava/bio/program/phred/PhredTools.html" title="class in org.biojava.bio.program.phred">PhredTools</a></dt>
<dd>
<div class="block">Calculates the probability of an error from the quality score via the formula
P_e = 10**(QV/-10)</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/phred/PhredTools.html#pFromQuality(int)">pFromQuality(int)</a></span> - Static method in class org.biojava.bio.program.phred.<a href="./org/biojava/bio/program/phred/PhredTools.html" title="class in org.biojava.bio.program.phred">PhredTools</a></dt>
<dd>
<div class="block">Calculates the probability of an error from the quality score via the formula
P_e = 10**(QV/-10)</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/phred/PhredTools.html#pFromQuality(org.biojava.bio.symbol.IntegerAlphabet.IntegerSymbol)">pFromQuality(IntegerAlphabet.IntegerSymbol)</a></span> - Static method in class org.biojava.bio.program.phred.<a href="./org/biojava/bio/program/phred/PhredTools.html" title="class in org.biojava.bio.program.phred">PhredTools</a></dt>
<dd>
<div class="block">Calculates the probability of an error from the quality score via the formula
P_e = 10**(QV/-10)</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/ProteinTools.html#phe()">phe()</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/ProteinTools.html" title="class in org.biojava.bio.seq">ProteinTools</a></dt>
<dd>
<div class="block">Returns the <code>AtomicSymbol</code> for the amino acid
Phenylalanine (F)</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOConstants.html#PHRED">PHRED</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOConstants.html" title="class in org.biojava.bio.seq.io">SeqIOConstants</a></dt>
<dd>
<div class="block"><code>PHRED</code> indicates that the sequence format is
PHRED.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/phred/PhredTools.html#phredAlignmentToDistArray(org.biojava.bio.symbol.Alignment)">phredAlignmentToDistArray(Alignment)</a></span> - Static method in class org.biojava.bio.program.phred.<a href="./org/biojava/bio/program/phred/PhredTools.html" title="class in org.biojava.bio.program.phred">PhredTools</a></dt>
<dd>
<div class="block">converts an Alignment of PhredSequences to a Distribution[] where each position is the average
distribution of the underlying column of the alignment.</div>
</dd>
<dt><a href="./org/biojava/bio/program/phred/PhredFormat.html" title="class in org.biojava.bio.program.phred"><span class="strong">PhredFormat</span></a> - Class in <a href="./org/biojava/bio/program/phred/package-summary.html">org.biojava.bio.program.phred</a></dt>
<dd>
<div class="block">Format object representing Phred Quality files.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/phred/PhredFormat.html#PhredFormat()">PhredFormat()</a></span> - Constructor for class org.biojava.bio.program.phred.<a href="./org/biojava/bio/program/phred/PhredFormat.html" title="class in org.biojava.bio.program.phred">PhredFormat</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/phred/PhredSequence.html" title="class in org.biojava.bio.program.phred"><span class="strong">PhredSequence</span></a> - Class in <a href="./org/biojava/bio/program/phred/package-summary.html">org.biojava.bio.program.phred</a></dt>
<dd>
<div class="block">PhredSequence is an extension of SimpleSequence that implements
Qualitative to hold Phred quality scores.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/phred/PhredSequence.html#PhredSequence(org.biojava.bio.symbol.SymbolList, java.lang.String, java.lang.String, org.biojava.bio.Annotation)">PhredSequence(SymbolList, String, String, Annotation)</a></span> - Constructor for class org.biojava.bio.program.phred.<a href="./org/biojava/bio/program/phred/PhredSequence.html" title="class in org.biojava.bio.program.phred">PhredSequence</a></dt>
<dd>
<div class="block">Constructs a new PhredSequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/phred/PhredTools.html#phredToDistArray(org.biojava.bio.program.phred.PhredSequence)">phredToDistArray(PhredSequence)</a></span> - Static method in class org.biojava.bio.program.phred.<a href="./org/biojava/bio/program/phred/PhredTools.html" title="class in org.biojava.bio.program.phred">PhredTools</a></dt>
<dd>
<div class="block">Converts a Phred sequence to an array of distributions.</div>
</dd>
<dt><a href="./org/biojava/bio/program/phred/PhredTools.html" title="class in org.biojava.bio.program.phred"><span class="strong">PhredTools</span></a> - Class in <a href="./org/biojava/bio/program/phred/package-summary.html">org.biojava.bio.program.phred</a></dt>
<dd>
<div class="block">PhredTools contains static methods for working with phred
quality data.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/phred/PhredTools.html#PhredTools()">PhredTools()</a></span> - Constructor for class org.biojava.bio.program.phred.<a href="./org/biojava/bio/program/phred/PhredTools.html" title="class in org.biojava.bio.program.phred">PhredTools</a></dt>
<dd> </dd>
<dt><a href="./org/biojavax/bio/phylo/io/phylip/PHYLIPFileBuilder.html" title="class in org.biojavax.bio.phylo.io.phylip"><span class="strong">PHYLIPFileBuilder</span></a> - Class in <a href="./org/biojavax/bio/phylo/io/phylip/package-summary.html">org.biojavax.bio.phylo.io.phylip</a></dt>
<dd>
<div class="block">Builds a PHYLIP file by listening to events.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/phylo/io/phylip/PHYLIPFileBuilder.html#PHYLIPFileBuilder()">PHYLIPFileBuilder()</a></span> - Constructor for class org.biojavax.bio.phylo.io.phylip.<a href="./org/biojavax/bio/phylo/io/phylip/PHYLIPFileBuilder.html" title="class in org.biojavax.bio.phylo.io.phylip">PHYLIPFileBuilder</a></dt>
<dd> </dd>
<dt><a href="./org/biojavax/bio/phylo/io/phylip/PHYLIPFileFormat.html" title="class in org.biojavax.bio.phylo.io.phylip"><span class="strong">PHYLIPFileFormat</span></a> - Class in <a href="./org/biojavax/bio/phylo/io/phylip/package-summary.html">org.biojavax.bio.phylo.io.phylip</a></dt>
<dd>
<div class="block">Reads PHYLIP interleaved alignment files and fires events at a PHYLIPFileListener object.</div>
</dd>
<dt><a href="./org/biojavax/bio/phylo/io/phylip/PHYLIPFileListener.html" title="interface in org.biojavax.bio.phylo.io.phylip"><span class="strong">PHYLIPFileListener</span></a> - Interface in <a href="./org/biojavax/bio/phylo/io/phylip/package-summary.html">org.biojavax.bio.phylo.io.phylip</a></dt>
<dd>
<div class="block">Listens to events fired by the PHYLIP parser.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SymbolPropertyTable.html#PK">PK</a></span> - Static variable in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SymbolPropertyTable.html" title="interface in org.biojava.bio.symbol">SymbolPropertyTable</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SymbolPropertyTable.html#PK_Cterm">PK_Cterm</a></span> - Static variable in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SymbolPropertyTable.html" title="interface in org.biojava.bio.symbol">SymbolPropertyTable</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SymbolPropertyTable.html#PK_Nterm">PK_Nterm</a></span> - Static variable in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SymbolPropertyTable.html" title="interface in org.biojava.bio.symbol">SymbolPropertyTable</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/gui/PlainBlock.html" title="class in org.biojava.bio.gui"><span class="strong">PlainBlock</span></a> - Class in <a href="./org/biojava/bio/gui/package-summary.html">org.biojava.bio.gui</a></dt>
<dd>
<div class="block">A painter that just draws a block (or bar).</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/PlainBlock.html#PlainBlock()">PlainBlock()</a></span> - Constructor for class org.biojava.bio.gui.<a href="./org/biojava/bio/gui/PlainBlock.html" title="class in org.biojava.bio.gui">PlainBlock</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/gui/PlainStyle.html" title="class in org.biojava.bio.gui"><span class="strong">PlainStyle</span></a> - Class in <a href="./org/biojava/bio/gui/package-summary.html">org.biojava.bio.gui</a></dt>
<dd>
<div class="block">A simple implementation of SymbolStyle that just uses a single paint for
outlines and a single paint for filling.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/PlainStyle.html#PlainStyle()">PlainStyle()</a></span> - Constructor for class org.biojava.bio.gui.<a href="./org/biojava/bio/gui/PlainStyle.html" title="class in org.biojava.bio.gui">PlainStyle</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/PlainStyle.html#PlainStyle(java.awt.Paint, java.awt.Paint)">PlainStyle(Paint, Paint)</a></span> - Constructor for class org.biojava.bio.gui.<a href="./org/biojava/bio/gui/PlainStyle.html" title="class in org.biojava.bio.gui">PlainStyle</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.Terms.html#PLASMID_KEY">PLASMID_KEY</a></span> - Static variable in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.Terms.html" title="class in org.biojavax.bio.seq">RichSequence.Terms</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Calc.html#plus(org.biojava.bio.structure.Structure, org.biojava.bio.structure.jama.Matrix)">plus(Structure, Matrix)</a></span> - Static method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Calc.html" title="class in org.biojava.bio.structure">Calc</a></dt>
<dd>
<div class="block">calculate structure + Matrix coodinates ...</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/jama/Matrix.html#plus(org.biojava.bio.structure.jama.Matrix)">plus(Matrix)</a></span> - Method in class org.biojava.bio.structure.jama.<a href="./org/biojava/bio/structure/jama/Matrix.html" title="class in org.biojava.bio.structure.jama">Matrix</a></dt>
<dd>
<div class="block">C = A + B</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/jama/Matrix.html#plusEquals(org.biojava.bio.structure.jama.Matrix)">plusEquals(Matrix)</a></span> - Method in class org.biojava.bio.structure.jama.<a href="./org/biojava/bio/structure/jama/Matrix.html" title="class in org.biojava.bio.structure.jama">Matrix</a></dt>
<dd>
<div class="block">A = A + B</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/CrosshairRenderer.html#point">point</a></span> - Variable in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/CrosshairRenderer.html" title="class in org.biojava.bio.gui.sequence">CrosshairRenderer</a></dt>
<dd>
<div class="block"><code>point</code> is the current location (in sequence
coordinates) of the crosshair in the X and Y sequences.</div>
</dd>
<dt><a href="./org/biojava/bio/symbol/PointLocation.html" title="class in org.biojava.bio.symbol"><span class="strong">PointLocation</span></a> - Class in <a href="./org/biojava/bio/symbol/package-summary.html">org.biojava.bio.symbol</a></dt>
<dd>
<div class="block">A location representing a single point.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/PointLocation.html#PointLocation(int)">PointLocation(int)</a></span> - Constructor for class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/PointLocation.html" title="class in org.biojava.bio.symbol">PointLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/ImageMap.html#POLY">POLY</a></span> - Static variable in interface org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/ImageMap.html" title="interface in org.biojava.bio.gui.sequence">ImageMap</a></dt>
<dd>
<div class="block"><code>POLY</code> indicates a polygonal image map hotspot.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/tools/ClassifierExample.PointClassifier.html#polyKernel">polyKernel</a></span> - Static variable in class org.biojava.stats.svm.tools.<a href="./org/biojava/stats/svm/tools/ClassifierExample.PointClassifier.html" title="class in org.biojava.stats.svm.tools">ClassifierExample.PointClassifier</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/structure/io/mmcif/chem/PolymerType.html" title="enum in org.biojava.bio.structure.io.mmcif.chem"><span class="strong">PolymerType</span></a> - Enum in <a href="./org/biojava/bio/structure/io/mmcif/chem/package-summary.html">org.biojava.bio.structure.io.mmcif.chem</a></dt>
<dd>
<div class="block">Enumerates the classification of polymers.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/chem/ResidueType.html#polymerType">polymerType</a></span> - Variable in enum org.biojava.bio.structure.io.mmcif.chem.<a href="./org/biojava/bio/structure/io/mmcif/chem/ResidueType.html" title="enum in org.biojava.bio.structure.io.mmcif.chem">ResidueType</a></dt>
<dd>
<div class="block">The associated <a href="./org/biojava/bio/structure/io/mmcif/chem/PolymerType.html" title="enum in org.biojava.bio.structure.io.mmcif.chem"><code>PolymerType</code></a></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/chem/PolymerType.html#polymerTypeFromString(java.lang.String)">polymerTypeFromString(String)</a></span> - Static method in enum org.biojava.bio.structure.io.mmcif.chem.<a href="./org/biojava/bio/structure/io/mmcif/chem/PolymerType.html" title="enum in org.biojava.bio.structure.io.mmcif.chem">PolymerType</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/stats/svm/PolynomialKernel.html" title="class in org.biojava.stats.svm"><span class="strong">PolynomialKernel</span></a> - Class in <a href="./org/biojava/stats/svm/package-summary.html">org.biojava.stats.svm</a></dt>
<dd>
<div class="block">This kernel computes all possible products of order features in feature
space.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/PolynomialKernel.html#PolynomialKernel()">PolynomialKernel()</a></span> - Constructor for class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/PolynomialKernel.html" title="class in org.biojava.stats.svm">PolynomialKernel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/PolynomialKernel.html#PolynomialKernel(org.biojava.stats.svm.SVMKernel, double, double, double)">PolynomialKernel(SVMKernel, double, double, double)</a></span> - Constructor for class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/PolynomialKernel.html" title="class in org.biojava.stats.svm">PolynomialKernel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/chem/PolymerType.html#POLYNUCLEOTIDE_ONLY">POLYNUCLEOTIDE_ONLY</a></span> - Static variable in enum org.biojava.bio.structure.io.mmcif.chem.<a href="./org/biojava/bio/structure/io/mmcif/chem/PolymerType.html" title="enum in org.biojava.bio.structure.io.mmcif.chem">PolymerType</a></dt>
<dd>
<div class="block">Convenience <tt>Set</tt> of polymer types classified as DNA.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/CodonPrefTools.html#POMBE_NUCLEAR">POMBE_NUCLEAR</a></span> - Static variable in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/CodonPrefTools.html" title="class in org.biojava.bio.symbol">CodonPrefTools</a></dt>
<dd>
<div class="block">Schizosaccharomyces pombe codon preferences</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/StAXFeatureHandler.html#pop()">pop()</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/StAXFeatureHandler.html" title="class in org.biojava.bio.seq.io.agave">StAXFeatureHandler</a></dt>
<dd>
<div class="block">pop a StAXContentHandler off the stack.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game/StAXFeatureHandler.html#pop()">pop()</a></span> - Method in class org.biojava.bio.seq.io.game.<a href="./org/biojava/bio/seq/io/game/StAXFeatureHandler.html" title="class in org.biojava.bio.seq.io.game">StAXFeatureHandler</a></dt>
<dd>
<div class="block">pop a StAXContentHandler off the stack.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/TemplateUtils.html#populate(org.biojava.bio.seq.Feature.Template, org.biojava.bio.seq.Feature)">populate(Feature.Template, Feature)</a></span> - Static method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/TemplateUtils.html" title="class in org.biojava.bio.seq.impl">TemplateUtils</a></dt>
<dd>
<div class="block">This attempts to populate the fields of a template using
the publically accessible information in a feature.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ga/GeneticAlgorithm.html#POPULATION">POPULATION</a></span> - Static variable in interface org.biojavax.ga.<a href="./org/biojavax/ga/GeneticAlgorithm.html" title="interface in org.biojavax.ga">GeneticAlgorithm</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/impl/AbstractGeneticAlgorithm.html#population">population</a></span> - Variable in class org.biojavax.ga.impl.<a href="./org/biojavax/ga/impl/AbstractGeneticAlgorithm.html" title="class in org.biojavax.ga.impl">AbstractGeneticAlgorithm</a></dt>
<dd> </dd>
<dt><a href="./org/biojavax/ga/Population.html" title="interface in org.biojavax.ga"><span class="strong">Population</span></a> - Interface in <a href="./org/biojavax/ga/package-summary.html">org.biojavax.ga</a></dt>
<dd>
<div class="block">A collection of GA organisms</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/twohead/AbstractMatrixPairDPCursor.html#pos">pos</a></span> - Variable in class org.biojava.bio.dp.twohead.<a href="./org/biojava/bio/dp/twohead/AbstractMatrixPairDPCursor.html" title="class in org.biojava.bio.dp.twohead">AbstractMatrixPairDPCursor</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/Edit.html#pos">pos</a></span> - Variable in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/Edit.html" title="class in org.biojava.bio.symbol">Edit</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/FlexibleAlignment.html#posInSeq(java.lang.Object, int)">posInSeq(Object, int)</a></span> - Method in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/FlexibleAlignment.html" title="class in org.biojava.bio.alignment">FlexibleAlignment</a></dt>
<dd>
<div class="block">get the position in the sequence corresponding to the postion within the alignment</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/io/LargeBuffer.html#position()">position()</a></span> - Method in class org.biojava.utils.io.<a href="./org/biojava/utils/io/LargeBuffer.html" title="class in org.biojava.utils.io">LargeBuffer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/io/LargeBuffer.html#position(long)">position(long)</a></span> - Method in class org.biojava.utils.io.<a href="./org/biojava/utils/io/LargeBuffer.html" title="class in org.biojava.utils.io">LargeBuffer</a></dt>
<dd> </dd>
<dt><a href="./org/biojavax/bio/seq/Position.html" title="interface in org.biojavax.bio.seq"><span class="strong">Position</span></a> - Interface in <a href="./org/biojavax/bio/seq/package-summary.html">org.biojavax.bio.seq</a></dt>
<dd>
<div class="block">Holds info about base positions.</div>
</dd>
<dt><a href="./org/biojavax/bio/seq/PositionResolver.html" title="interface in org.biojavax.bio.seq"><span class="strong">PositionResolver</span></a> - Interface in <a href="./org/biojavax/bio/seq/package-summary.html">org.biojavax.bio.seq</a></dt>
<dd>
<div class="block">Resolves a position that is fuzzy or covers a range of bases by
converting it to a single base.</div>
</dd>
<dt><a href="./org/biojavax/bio/seq/PositionResolver.AverageResolver.html" title="class in org.biojavax.bio.seq"><span class="strong">PositionResolver.AverageResolver</span></a> - Class in <a href="./org/biojavax/bio/seq/package-summary.html">org.biojavax.bio.seq</a></dt>
<dd>
<div class="block">The minimal resolver returns the base which provides the
average range, halfway between maximal and minimal.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/PositionResolver.AverageResolver.html#PositionResolver.AverageResolver()">PositionResolver.AverageResolver()</a></span> - Constructor for class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/PositionResolver.AverageResolver.html" title="class in org.biojavax.bio.seq">PositionResolver.AverageResolver</a></dt>
<dd> </dd>
<dt><a href="./org/biojavax/bio/seq/PositionResolver.MaximalResolver.html" title="class in org.biojavax.bio.seq"><span class="strong">PositionResolver.MaximalResolver</span></a> - Class in <a href="./org/biojavax/bio/seq/package-summary.html">org.biojavax.bio.seq</a></dt>
<dd>
<div class="block">The maximal resolver returns the base which provides the
largest possible range.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/PositionResolver.MaximalResolver.html#PositionResolver.MaximalResolver()">PositionResolver.MaximalResolver()</a></span> - Constructor for class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/PositionResolver.MaximalResolver.html" title="class in org.biojavax.bio.seq">PositionResolver.MaximalResolver</a></dt>
<dd> </dd>
<dt><a href="./org/biojavax/bio/seq/PositionResolver.MinimalResolver.html" title="class in org.biojavax.bio.seq"><span class="strong">PositionResolver.MinimalResolver</span></a> - Class in <a href="./org/biojavax/bio/seq/package-summary.html">org.biojavax.bio.seq</a></dt>
<dd>
<div class="block">The minimal resolver returns the base which provides the
smallest possible range.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/PositionResolver.MinimalResolver.html#PositionResolver.MinimalResolver()">PositionResolver.MinimalResolver()</a></span> - Constructor for class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/PositionResolver.MinimalResolver.html" title="class in org.biojavax.bio.seq">PositionResolver.MinimalResolver</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/events/AlignmentPositionListener.html#positionSelected(org.biojava.bio.structure.gui.util.AlignedPosition)">positionSelected(AlignedPosition)</a></span> - Method in interface org.biojava.bio.structure.gui.events.<a href="./org/biojava/bio/structure/gui/events/AlignmentPositionListener.html" title="interface in org.biojava.bio.structure.gui.events">AlignmentPositionListener</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/events/JmolAlignedPositionListener.html#positionSelected(org.biojava.bio.structure.gui.util.AlignedPosition)">positionSelected(AlignedPosition)</a></span> - Method in class org.biojava.bio.structure.gui.events.<a href="./org/biojava/bio/structure/gui/events/JmolAlignedPositionListener.html" title="class in org.biojava.bio.structure.gui.events">JmolAlignedPositionListener</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/StrandedFeature.html#POSITIVE">POSITIVE</a></span> - Static variable in interface org.biojava.bio.seq.<a href="./org/biojava/bio/seq/StrandedFeature.html" title="interface in org.biojava.bio.seq">StrandedFeature</a></dt>
<dd>
<div class="block">Flag to indicate that a feature is on the positive strand.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichLocation.Strand.html#POSITIVE_STRAND">POSITIVE_STRAND</a></span> - Static variable in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichLocation.Strand.html" title="class in org.biojavax.bio.seq">RichLocation.Strand</a></dt>
<dd>
<div class="block">The positive strand is represented by the symbol '+' and has the
number 1.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichLocation.html#posmax(org.biojavax.bio.seq.Position, org.biojavax.bio.seq.Position)">posmax(Position, Position)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichLocation.html" title="class in org.biojavax.bio.seq">SimpleRichLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichLocation.html#posmin(org.biojavax.bio.seq.Position, org.biojavax.bio.seq.Position)">posmin(Position, Position)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichLocation.html" title="class in org.biojavax.bio.seq">SimpleRichLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BiblioPerson.html#postalAddress">postalAddress</a></span> - Variable in class org.biojava.bibliography.<a href="./org/biojava/bibliography/BiblioPerson.html" title="class in org.biojava.bibliography">BiblioPerson</a></dt>
<dd>
<div class="block">Their postal address.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleSymbolList.html#postChange(org.biojava.utils.ChangeEvent)">postChange(ChangeEvent)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleSymbolList.html" title="class in org.biojava.bio.symbol">SimpleSymbolList</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ChangeAdapter.html#postChange(org.biojava.utils.ChangeEvent)">postChange(ChangeEvent)</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/ChangeAdapter.html" title="class in org.biojava.utils">ChangeAdapter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ChangeForwarder.html#postChange(org.biojava.utils.ChangeEvent)">postChange(ChangeEvent)</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/ChangeForwarder.html" title="class in org.biojava.utils">ChangeForwarder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ChangeListener.AlwaysVetoListener.html#postChange(org.biojava.utils.ChangeEvent)">postChange(ChangeEvent)</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/ChangeListener.AlwaysVetoListener.html" title="class in org.biojava.utils">ChangeListener.AlwaysVetoListener</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ChangeListener.LoggingListener.html#postChange(org.biojava.utils.ChangeEvent)">postChange(ChangeEvent)</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/ChangeListener.LoggingListener.html" title="class in org.biojava.utils">ChangeListener.LoggingListener</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ChangeListener.html#postChange(org.biojava.utils.ChangeEvent)">postChange(ChangeEvent)</a></span> - Method in interface org.biojava.utils.<a href="./org/biojava/utils/ChangeListener.html" title="interface in org.biojava.utils">ChangeListener</a></dt>
<dd>
<div class="block">
Called when a change has just taken place.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/db/biosql/PostgreSQLDBHelper.html" title="class in org.biojava.bio.seq.db.biosql"><span class="strong">PostgreSQLDBHelper</span></a> - Class in <a href="./org/biojava/bio/seq/db/biosql/package-summary.html">org.biojava.bio.seq.db.biosql</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/biosql/PostgreSQLDBHelper.html#PostgreSQLDBHelper()">PostgreSQLDBHelper()</a></span> - Constructor for class org.biojava.bio.seq.db.biosql.<a href="./org/biojava/bio/seq/db/biosql/PostgreSQLDBHelper.html" title="class in org.biojava.bio.seq.db.biosql">PostgreSQLDBHelper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleSymbolList.html#preChange(org.biojava.utils.ChangeEvent)">preChange(ChangeEvent)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleSymbolList.html" title="class in org.biojava.bio.symbol">SimpleSymbolList</a></dt>
<dd>
<div class="block">On preChange() we convert the SymolList to a non-veiw version, giving it its own copy of symbols</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/ChangeAdapter.html#preChange(org.biojava.utils.ChangeEvent)">preChange(ChangeEvent)</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/ChangeAdapter.html" title="class in org.biojava.utils">ChangeAdapter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ChangeForwarder.html#preChange(org.biojava.utils.ChangeEvent)">preChange(ChangeEvent)</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/ChangeForwarder.html" title="class in org.biojava.utils">ChangeForwarder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ChangeListener.AlwaysVetoListener.html#preChange(org.biojava.utils.ChangeEvent)">preChange(ChangeEvent)</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/ChangeListener.AlwaysVetoListener.html" title="class in org.biojava.utils">ChangeListener.AlwaysVetoListener</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ChangeListener.ChangeEventRecorder.html#preChange(org.biojava.utils.ChangeEvent)">preChange(ChangeEvent)</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/ChangeListener.ChangeEventRecorder.html" title="class in org.biojava.utils">ChangeListener.ChangeEventRecorder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ChangeListener.LoggingListener.html#preChange(org.biojava.utils.ChangeEvent)">preChange(ChangeEvent)</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/ChangeListener.LoggingListener.html" title="class in org.biojava.utils">ChangeListener.LoggingListener</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ChangeListener.html#preChange(org.biojava.utils.ChangeEvent)">preChange(ChangeEvent)</a></span> - Method in interface org.biojava.utils.<a href="./org/biojava/utils/ChangeListener.html" title="interface in org.biojava.utils">ChangeListener</a></dt>
<dd>
<div class="block">
Called before a change takes place.</div>
</dd>
<dt><a href="./org/biojava/bio/structure/server/PrepareIndexFile.html" title="class in org.biojava.bio.structure.server"><span class="strong">PrepareIndexFile</span></a> - Class in <a href="./org/biojava/bio/structure/server/package-summary.html">org.biojava.bio.structure.server</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/server/PrepareIndexFile.html#PrepareIndexFile()">PrepareIndexFile()</a></span> - Constructor for class org.biojava.bio.structure.server.<a href="./org/biojava/bio/structure/server/PrepareIndexFile.html" title="class in org.biojava.bio.structure.server">PrepareIndexFile</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/server/PrepareIndexFile.html#prepareIndexFileForInstallation(org.biojava.bio.structure.server.FlatFileInstallation)">prepareIndexFileForInstallation(FlatFileInstallation)</a></span> - Method in class org.biojava.bio.structure.server.<a href="./org/biojava/bio/structure/server/PrepareIndexFile.html" title="class in org.biojava.bio.structure.server">PrepareIndexFile</a></dt>
<dd>
<div class="block">prepare the index file for this installation</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/server/PrepareMMcifIndexFile.html#prepareIndexFileForInstallation(org.biojava.bio.structure.server.FlatFileInstallation)">prepareIndexFileForInstallation(FlatFileInstallation)</a></span> - Method in class org.biojava.bio.structure.server.<a href="./org/biojava/bio/structure/server/PrepareMMcifIndexFile.html" title="class in org.biojava.bio.structure.server">PrepareMMcifIndexFile</a></dt>
<dd>
<div class="block">prepare the index file for this installation</div>
</dd>
<dt><a href="./org/biojava/bio/structure/server/PrepareMMcifIndexFile.html" title="class in org.biojava.bio.structure.server"><span class="strong">PrepareMMcifIndexFile</span></a> - Class in <a href="./org/biojava/bio/structure/server/package-summary.html">org.biojava.bio.structure.server</a></dt>
<dd>
<div class="block">A class to index all files in a PDB installation</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/server/PrepareMMcifIndexFile.html#PrepareMMcifIndexFile()">PrepareMMcifIndexFile()</a></span> - Constructor for class org.biojava.bio.structure.server.<a href="./org/biojava/bio/structure/server/PrepareMMcifIndexFile.html" title="class in org.biojava.bio.structure.server">PrepareMMcifIndexFile</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/twohead/AbstractMatrixPairDPCursor.html#press()">press()</a></span> - Method in class org.biojava.bio.dp.twohead.<a href="./org/biojava/bio/dp/twohead/AbstractMatrixPairDPCursor.html" title="class in org.biojava.bio.dp.twohead">AbstractMatrixPairDPCursor</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/twohead/LightPairDPCursor.html#press()">press()</a></span> - Method in class org.biojava.bio.dp.twohead.<a href="./org/biojava/bio/dp/twohead/LightPairDPCursor.html" title="class in org.biojava.bio.dp.twohead">LightPairDPCursor</a></dt>
<dd>
<div class="block">Returns the minimal context of the DP matrix
necessary to compute the value of a single point
in that matrix.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/twohead/PairDPCursor.html#press()">press()</a></span> - Method in interface org.biojava.bio.dp.twohead.<a href="./org/biojava/bio/dp/twohead/PairDPCursor.html" title="interface in org.biojava.bio.dp.twohead">PairDPCursor</a></dt>
<dd>
<div class="block">press out a new correctly sized cell array</div>
</dd>
<dt><a href="./org/biojava/utils/xml/PrettyXMLWriter.html" title="class in org.biojava.utils.xml"><span class="strong">PrettyXMLWriter</span></a> - Class in <a href="./org/biojava/utils/xml/package-summary.html">org.biojava.utils.xml</a></dt>
<dd>
<div class="block">Implementation of XMLWriter which emits nicely formatted documents
to a PrintWriter.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/xml/PrettyXMLWriter.html#PrettyXMLWriter(java.io.PrintWriter)">PrettyXMLWriter(PrintWriter)</a></span> - Constructor for class org.biojava.utils.xml.<a href="./org/biojava/utils/xml/PrettyXMLWriter.html" title="class in org.biojava.utils.xml">PrettyXMLWriter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/indexdb/BioStoreFactory.html#PRIMARY_KEY_NAME">PRIMARY_KEY_NAME</a></span> - Static variable in class org.biojava.bio.program.indexdb.<a href="./org/biojava/bio/program/indexdb/BioStoreFactory.html" title="class in org.biojava.bio.program.indexdb">BioStoreFactory</a></dt>
<dd>
<div class="block"><code>PRIMARY_KEY_NAME</code> is the key used to identify the
primary namespace in the OBDA config.dat files.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/ObjectUtil.html#PRIME">PRIME</a></span> - Static variable in class org.biojava.utils.<a href="./org/biojava/utils/ObjectUtil.html" title="class in org.biojava.utils">ObjectUtil</a></dt>
<dd>
<div class="block">the current hashCode is always first multiplied with this prime before the hashCode value for a particular field is
added.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/PackingFactory.html#primeWord(org.biojava.bio.symbol.SymbolList, int, org.biojava.bio.symbol.Packing)">primeWord(SymbolList, int, Packing)</a></span> - Static method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/PackingFactory.html" title="class in org.biojava.bio.symbol">PackingFactory</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/jama/Matrix.html#print(int, int)">print(int, int)</a></span> - Method in class org.biojava.bio.structure.jama.<a href="./org/biojava/bio/structure/jama/Matrix.html" title="class in org.biojava.bio.structure.jama">Matrix</a></dt>
<dd>
<div class="block">Print the matrix to stdout.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/jama/Matrix.html#print(java.io.PrintWriter, int, int)">print(PrintWriter, int, int)</a></span> - Method in class org.biojava.bio.structure.jama.<a href="./org/biojava/bio/structure/jama/Matrix.html" title="class in org.biojava.bio.structure.jama">Matrix</a></dt>
<dd>
<div class="block">Print the matrix to the output stream.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/jama/Matrix.html#print(java.text.NumberFormat, int)">print(NumberFormat, int)</a></span> - Method in class org.biojava.bio.structure.jama.<a href="./org/biojava/bio/structure/jama/Matrix.html" title="class in org.biojava.bio.structure.jama">Matrix</a></dt>
<dd>
<div class="block">Print the matrix to stdout.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/jama/Matrix.html#print(java.io.PrintWriter, java.text.NumberFormat, int)">print(PrintWriter, NumberFormat, int)</a></span> - Method in class org.biojava.bio.structure.jama.<a href="./org/biojava/bio/structure/jama/Matrix.html" title="class in org.biojava.bio.structure.jama">Matrix</a></dt>
<dd>
<div class="block">Print the matrix to the output stream.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/xml/FastXMLWriter.html#print(java.lang.String)">print(String)</a></span> - Method in class org.biojava.utils.xml.<a href="./org/biojava/utils/xml/FastXMLWriter.html" title="class in org.biojava.utils.xml">FastXMLWriter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/xml/PrettyXMLWriter.html#print(java.lang.String)">print(String)</a></span> - Method in class org.biojava.utils.xml.<a href="./org/biojava/utils/xml/PrettyXMLWriter.html" title="class in org.biojava.utils.xml">PrettyXMLWriter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/xml/XMLWriter.html#print(java.lang.String)">print(String)</a></span> - Method in interface org.biojava.utils.xml.<a href="./org/biojava/utils/xml/XMLWriter.html" title="interface in org.biojava.utils.xml">XMLWriter</a></dt>
<dd>
<div class="block">Prints some textual content in an element.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/NeedlemanWunsch.html#printAlignment(java.lang.String)">printAlignment(String)</a></span> - Static method in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/NeedlemanWunsch.html" title="class in org.biojava.bio.alignment">NeedlemanWunsch</a></dt>
<dd>
<div class="block">prints the alignment String on the screen (standard output).</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/xml/FastXMLWriter.html#printAttributeValue(java.lang.String)">printAttributeValue(String)</a></span> - Method in class org.biojava.utils.xml.<a href="./org/biojava/utils/xml/FastXMLWriter.html" title="class in org.biojava.utils.xml">FastXMLWriter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/xml/PrettyXMLWriter.html#printAttributeValue(java.lang.String)">printAttributeValue(String)</a></span> - Method in class org.biojava.utils.xml.<a href="./org/biojava/utils/xml/PrettyXMLWriter.html" title="class in org.biojava.utils.xml">PrettyXMLWriter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/xml/FastXMLWriter.html#printChars(java.lang.String)">printChars(String)</a></span> - Method in class org.biojava.utils.xml.<a href="./org/biojava/utils/xml/FastXMLWriter.html" title="class in org.biojava.utils.xml">FastXMLWriter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/xml/PrettyXMLWriter.html#printChars(java.lang.String)">printChars(String)</a></span> - Method in class org.biojava.utils.xml.<a href="./org/biojava/utils/xml/PrettyXMLWriter.html" title="class in org.biojava.utils.xml">PrettyXMLWriter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/NeedlemanWunsch.html#printCostMatrix(int[][], char[], char[])">printCostMatrix(int[][], char[], char[])</a></span> - Static method in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/NeedlemanWunsch.html" title="class in org.biojava.bio.alignment">NeedlemanWunsch</a></dt>
<dd>
<div class="block">Prints a String representation of the CostMatrix for the given Alignment on
the screen.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/xml/FastXMLWriter.html#println(java.lang.String)">println(String)</a></span> - Method in class org.biojava.utils.xml.<a href="./org/biojava/utils/xml/FastXMLWriter.html" title="class in org.biojava.utils.xml">FastXMLWriter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/xml/PrettyXMLWriter.html#println(java.lang.String)">println(String)</a></span> - Method in class org.biojava.utils.xml.<a href="./org/biojava/utils/xml/PrettyXMLWriter.html" title="class in org.biojava.utils.xml">PrettyXMLWriter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/xml/XMLWriter.html#println(java.lang.String)">println(String)</a></span> - Method in interface org.biojava.utils.xml.<a href="./org/biojava/utils/xml/XMLWriter.html" title="interface in org.biojava.utils.xml">XMLWriter</a></dt>
<dd>
<div class="block">Prints some textual content, terminated with a newline character.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/SubstitutionMatrix.html#printMatrix()">printMatrix()</a></span> - Method in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/SubstitutionMatrix.html" title="class in org.biojava.bio.alignment">SubstitutionMatrix</a></dt>
<dd>
<div class="block">Just to perform some test.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/SVDSuperimposer.html#printMatrix(org.biojava.bio.structure.jama.Matrix)">printMatrix(Matrix)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/SVDSuperimposer.html" title="class in org.biojava.bio.structure">SVDSuperimposer</a></dt>
<dd>
<div class="block">Simple debug method to print a Matrix object on System.out.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SwissprotFileFormer.html#printOutSequenceHeaderLine(org.biojava.bio.symbol.Alphabet, org.biojava.bio.symbol.Symbol[], int, int)">printOutSequenceHeaderLine(Alphabet, Symbol[], int, int)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SwissprotFileFormer.html" title="class in org.biojava.bio.seq.io">SwissprotFileFormer</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Prints out sequence header with only length data.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/xml/FastXMLWriter.html#printRaw(java.lang.String)">printRaw(String)</a></span> - Method in class org.biojava.utils.xml.<a href="./org/biojava/utils/xml/FastXMLWriter.html" title="class in org.biojava.utils.xml">FastXMLWriter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/xml/PrettyXMLWriter.html#printRaw(java.lang.String)">printRaw(String)</a></span> - Method in class org.biojava.utils.xml.<a href="./org/biojava/utils/xml/PrettyXMLWriter.html" title="class in org.biojava.utils.xml">PrettyXMLWriter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/xml/XMLWriter.html#printRaw(java.lang.String)">printRaw(String)</a></span> - Method in interface org.biojava.utils.xml.<a href="./org/biojava/utils/xml/XMLWriter.html" title="interface in org.biojava.utils.xml">XMLWriter</a></dt>
<dd>
<div class="block">Send raw data to the stream.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/UkkonenSuffixTree.html#printTree()">printTree()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/UkkonenSuffixTree.html" title="class in org.biojava.bio.symbol">UkkonenSuffixTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/SimpleThreadPool.html#priority">priority</a></span> - Variable in class org.biojava.utils.<a href="./org/biojava/utils/SimpleThreadPool.html" title="class in org.biojava.utils">SimpleThreadPool</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/ProteinTools.html#pro()">pro()</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/ProteinTools.html" title="class in org.biojava.bio.seq">ProteinTools</a></dt>
<dd>
<div class="block">Returns the <code>AtomicSymbol</code> for the amino acid
Proline (P)</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/scf/SCF.html#PROB_NUC_A">PROB_NUC_A</a></span> - Static variable in class org.biojava.bio.program.scf.<a href="./org/biojava/bio/program/scf/SCF.html" title="class in org.biojava.bio.program.scf">SCF</a></dt>
<dd>
<div class="block">Base call alignment sequence label for the probability that call
should be A.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/scf/SCF.html#PROB_NUC_C">PROB_NUC_C</a></span> - Static variable in class org.biojava.bio.program.scf.<a href="./org/biojava/bio/program/scf/SCF.html" title="class in org.biojava.bio.program.scf">SCF</a></dt>
<dd>
<div class="block">Base call alignment sequence label for the probability that call
should be C.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/scf/SCF.html#PROB_NUC_G">PROB_NUC_G</a></span> - Static variable in class org.biojava.bio.program.scf.<a href="./org/biojava/bio/program/scf/SCF.html" title="class in org.biojava.bio.program.scf">SCF</a></dt>
<dd>
<div class="block">Base call alignment sequence label for the probability that call
should be G.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/scf/SCF.html#PROB_NUC_T">PROB_NUC_T</a></span> - Static variable in class org.biojava.bio.program.scf.<a href="./org/biojava/bio/program/scf/SCF.html" title="class in org.biojava.bio.program.scf">SCF</a></dt>
<dd>
<div class="block">Base call alignment sequence label for the probability that call
should be T.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/scf/SCF.html#PROB_OVERCALL">PROB_OVERCALL</a></span> - Static variable in class org.biojava.bio.program.scf.<a href="./org/biojava/bio/program/scf/SCF.html" title="class in org.biojava.bio.program.scf">SCF</a></dt>
<dd>
<div class="block">Base call alignment sequence label for the overcall probability.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/scf/SCF.html#PROB_SUBSTITUTION">PROB_SUBSTITUTION</a></span> - Static variable in class org.biojava.bio.program.scf.<a href="./org/biojava/bio/program/scf/SCF.html" title="class in org.biojava.bio.program.scf">SCF</a></dt>
<dd>
<div class="block">Base call alignment sequence label for the substitution
probability.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/scf/SCF.html#PROB_UNDERCALL">PROB_UNDERCALL</a></span> - Static variable in class org.biojava.bio.program.scf.<a href="./org/biojava/bio/program/scf/SCF.html" title="class in org.biojava.bio.program.scf">SCF</a></dt>
<dd>
<div class="block">Base call alignment sequence label for the undercall probability.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/ScoreType.html#PROBABILITY">PROBABILITY</a></span> - Static variable in interface org.biojava.bio.dp.<a href="./org/biojava/bio/dp/ScoreType.html" title="interface in org.biojava.bio.dp">ScoreType</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/SequencesAsGFF.html#processDB(org.biojava.bio.seq.db.SequenceDB, org.biojava.bio.program.gff.GFFDocumentHandler)">processDB(SequenceDB, GFFDocumentHandler)</a></span> - Method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/SequencesAsGFF.html" title="class in org.biojava.bio.program.gff">SequencesAsGFF</a></dt>
<dd>
<div class="block">Process all <span class="type">Sequence</span>s within a
<span class="type">SequenceDB</span>, informing
<span class="arg">handler</span> of any suitable features.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLRichSequenceDB.html#processFeatureFilter(org.biojava.bio.seq.FeatureFilter)">processFeatureFilter(FeatureFilter)</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLRichSequenceDB.html" title="class in org.biojavax.bio.db.biosql">BioSQLRichSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/FastaFormat.html#processHeader(java.lang.String, org.biojavax.bio.seq.io.RichSeqIOListener, org.biojavax.Namespace)">processHeader(String, RichSeqIOListener, Namespace)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/FastaFormat.html" title="class in org.biojavax.bio.seq.io">FastaFormat</a></dt>
<dd>
<div class="block">Parse the Header information from the Fasta Description line</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/SeqSimilarityAdapter.html#processingInstruction(java.lang.String, java.lang.String)">processingInstruction(String, String)</a></span> - Method in class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/SeqSimilarityAdapter.html" title="class in org.biojava.bio.program.ssbind">SeqSimilarityAdapter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/SAX2StAXAdaptor.html#processingInstruction(java.lang.String, java.lang.String)">processingInstruction(String, String)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/SAX2StAXAdaptor.html" title="class in org.biojava.bio.seq.io.agave">SAX2StAXAdaptor</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/StAXContentHandler.html#processingInstruction(java.lang.String, java.lang.String)">processingInstruction(String, String)</a></span> - Method in interface org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/StAXContentHandler.html" title="interface in org.biojava.bio.seq.io.agave">StAXContentHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/StAXContentHandlerBase.html#processingInstruction(java.lang.String, java.lang.String)">processingInstruction(String, String)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/StAXContentHandlerBase.html" title="class in org.biojava.bio.seq.io.agave">StAXContentHandlerBase</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/stax/SAX2StAXAdaptor.html#processingInstruction(java.lang.String, java.lang.String)">processingInstruction(String, String)</a></span> - Method in class org.biojava.utils.stax.<a href="./org/biojava/utils/stax/SAX2StAXAdaptor.html" title="class in org.biojava.utils.stax">SAX2StAXAdaptor</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/stax/StAXContentHandler.html#processingInstruction(java.lang.String, java.lang.String)">processingInstruction(String, String)</a></span> - Method in interface org.biojava.utils.stax.<a href="./org/biojava/utils/stax/StAXContentHandler.html" title="interface in org.biojava.utils.stax">StAXContentHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/stax/StAXContentHandlerBase.html#processingInstruction(java.lang.String, java.lang.String)">processingInstruction(String, String)</a></span> - Method in class org.biojava.utils.stax.<a href="./org/biojava/utils/stax/StAXContentHandlerBase.html" title="class in org.biojava.utils.stax">StAXContentHandlerBase</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/AbiTraceRenderer.html#processMouseEvent(org.biojava.bio.gui.sequence.SequenceRenderContext, java.awt.event.MouseEvent, java.util.List)">processMouseEvent(SequenceRenderContext, MouseEvent, List)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/AbiTraceRenderer.html" title="class in org.biojava.bio.gui.sequence">AbiTraceRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/AbstractBeadRenderer.html#processMouseEvent(org.biojava.bio.seq.FeatureHolder, org.biojava.bio.gui.sequence.SequenceRenderContext, java.awt.event.MouseEvent)">processMouseEvent(FeatureHolder, SequenceRenderContext, MouseEvent)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/AbstractBeadRenderer.html" title="class in org.biojava.bio.gui.sequence">AbstractBeadRenderer</a></dt>
<dd>
<div class="block"><code>processMouseEvent</code> defines the behaviour on
revieving a mouse event.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/ArrowedFeatureRenderer.html#processMouseEvent(org.biojava.bio.seq.FeatureHolder, org.biojava.bio.gui.sequence.SequenceRenderContext, java.awt.event.MouseEvent)">processMouseEvent(FeatureHolder, SequenceRenderContext, MouseEvent)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/ArrowedFeatureRenderer.html" title="class in org.biojava.bio.gui.sequence">ArrowedFeatureRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/BasicFeatureRenderer.html#processMouseEvent(org.biojava.bio.seq.FeatureHolder, org.biojava.bio.gui.sequence.SequenceRenderContext, java.awt.event.MouseEvent)">processMouseEvent(FeatureHolder, SequenceRenderContext, MouseEvent)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/BasicFeatureRenderer.html" title="class in org.biojava.bio.gui.sequence">BasicFeatureRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/BasicImapRenderer.html#processMouseEvent(org.biojava.bio.seq.FeatureHolder, org.biojava.bio.gui.sequence.SequenceRenderContext, java.awt.event.MouseEvent)">processMouseEvent(FeatureHolder, SequenceRenderContext, MouseEvent)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/BasicImapRenderer.html" title="class in org.biojava.bio.gui.sequence">BasicImapRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/BumpedRenderer.html#processMouseEvent(org.biojava.bio.gui.sequence.SequenceRenderContext, java.awt.event.MouseEvent, java.util.List)">processMouseEvent(SequenceRenderContext, MouseEvent, List)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/BumpedRenderer.html" title="class in org.biojava.bio.gui.sequence">BumpedRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/CrosshairRenderer.html#processMouseEvent(org.biojava.bio.gui.sequence.PairwiseRenderContext, java.awt.event.MouseEvent, java.util.List)">processMouseEvent(PairwiseRenderContext, MouseEvent, List)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/CrosshairRenderer.html" title="class in org.biojava.bio.gui.sequence">CrosshairRenderer</a></dt>
<dd>
<div class="block"><code>processMouseEvent</code> processes any
<code>MouseEvent</code>s directed to the renderer.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/FeatureBlockSequenceRenderer.html#processMouseEvent(org.biojava.bio.gui.sequence.SequenceRenderContext, java.awt.event.MouseEvent, java.util.List)">processMouseEvent(SequenceRenderContext, MouseEvent, List)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/FeatureBlockSequenceRenderer.html" title="class in org.biojava.bio.gui.sequence">FeatureBlockSequenceRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/FeatureLabelRenderer.html#processMouseEvent(org.biojava.bio.seq.FeatureHolder, org.biojava.bio.gui.sequence.SequenceRenderContext, java.awt.event.MouseEvent)">processMouseEvent(FeatureHolder, SequenceRenderContext, MouseEvent)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/FeatureLabelRenderer.html" title="class in org.biojava.bio.gui.sequence">FeatureLabelRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/FeatureRenderer.html#processMouseEvent(org.biojava.bio.seq.FeatureHolder, org.biojava.bio.gui.sequence.SequenceRenderContext, java.awt.event.MouseEvent)">processMouseEvent(FeatureHolder, SequenceRenderContext, MouseEvent)</a></span> - Method in interface org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/FeatureRenderer.html" title="interface in org.biojava.bio.gui.sequence">FeatureRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/FilteringRenderer.html#processMouseEvent(org.biojava.bio.gui.sequence.SequenceRenderContext, java.awt.event.MouseEvent, java.util.List)">processMouseEvent(SequenceRenderContext, MouseEvent, List)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/FilteringRenderer.html" title="class in org.biojava.bio.gui.sequence">FilteringRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/GlyphFeatureRenderer.html#processMouseEvent(org.biojava.bio.seq.FeatureHolder, org.biojava.bio.gui.sequence.SequenceRenderContext, java.awt.event.MouseEvent)">processMouseEvent(FeatureHolder, SequenceRenderContext, MouseEvent)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/GlyphFeatureRenderer.html" title="class in org.biojava.bio.gui.sequence">GlyphFeatureRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/LabelledSequenceRenderer.html#processMouseEvent(org.biojava.bio.gui.sequence.SequenceRenderContext, java.awt.event.MouseEvent, java.util.List)">processMouseEvent(SequenceRenderContext, MouseEvent, List)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/LabelledSequenceRenderer.html" title="class in org.biojava.bio.gui.sequence">LabelledSequenceRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/LayeredRenderer.html#processMouseEvent(java.util.List, java.awt.event.MouseEvent, java.util.List, java.util.List)">processMouseEvent(List, MouseEvent, List, List)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/LayeredRenderer.html" title="class in org.biojava.bio.gui.sequence">LayeredRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/MultiLineRenderer.html#processMouseEvent(org.biojava.bio.gui.sequence.SequenceRenderContext, java.awt.event.MouseEvent, java.util.List)">processMouseEvent(SequenceRenderContext, MouseEvent, List)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/MultiLineRenderer.html" title="class in org.biojava.bio.gui.sequence">MultiLineRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/OffsetRulerRenderer.html#processMouseEvent(org.biojava.bio.gui.sequence.SequenceRenderContext, java.awt.event.MouseEvent, java.util.List)">processMouseEvent(SequenceRenderContext, MouseEvent, List)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/OffsetRulerRenderer.html" title="class in org.biojava.bio.gui.sequence">OffsetRulerRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/OverlayRendererWrapper.html#processMouseEvent(org.biojava.bio.gui.sequence.SequenceRenderContext, java.awt.event.MouseEvent, java.util.List)">processMouseEvent(SequenceRenderContext, MouseEvent, List)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/OverlayRendererWrapper.html" title="class in org.biojava.bio.gui.sequence">OverlayRendererWrapper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PaddingRenderer.html#processMouseEvent(org.biojava.bio.gui.sequence.SequenceRenderContext, java.awt.event.MouseEvent, java.util.List)">processMouseEvent(SequenceRenderContext, MouseEvent, List)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PaddingRenderer.html" title="class in org.biojava.bio.gui.sequence">PaddingRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PairwiseDiagonalRenderer.html#processMouseEvent(org.biojava.bio.gui.sequence.PairwiseRenderContext, java.awt.event.MouseEvent, java.util.List)">processMouseEvent(PairwiseRenderContext, MouseEvent, List)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PairwiseDiagonalRenderer.html" title="class in org.biojava.bio.gui.sequence">PairwiseDiagonalRenderer</a></dt>
<dd>
<div class="block"><code>processMouseEvent</code> acts on a mouse gesture.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PairwiseFilteringRenderer.html#processMouseEvent(org.biojava.bio.gui.sequence.PairwiseRenderContext, java.awt.event.MouseEvent, java.util.List)">processMouseEvent(PairwiseRenderContext, MouseEvent, List)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PairwiseFilteringRenderer.html" title="class in org.biojava.bio.gui.sequence">PairwiseFilteringRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PairwiseOverlayRenderer.html#processMouseEvent(org.biojava.bio.gui.sequence.PairwiseRenderContext, java.awt.event.MouseEvent, java.util.List)">processMouseEvent(PairwiseRenderContext, MouseEvent, List)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PairwiseOverlayRenderer.html" title="class in org.biojava.bio.gui.sequence">PairwiseOverlayRenderer</a></dt>
<dd>
<div class="block"><code>processMouseEvent</code> produces a
<code>SequenceViewerEvent</code> in response to a mouse
gesture.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PairwiseSequenceRenderer.html#processMouseEvent(org.biojava.bio.gui.sequence.PairwiseRenderContext, java.awt.event.MouseEvent, java.util.List)">processMouseEvent(PairwiseRenderContext, MouseEvent, List)</a></span> - Method in interface org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PairwiseSequenceRenderer.html" title="interface in org.biojava.bio.gui.sequence">PairwiseSequenceRenderer</a></dt>
<dd>
<div class="block"><code>processMouseEvent</code> produces a
<code>SequenceViewerEvent</code> in response to a mouse
gesture.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/RectangularImapRenderer.html#processMouseEvent(org.biojava.bio.seq.FeatureHolder, org.biojava.bio.gui.sequence.SequenceRenderContext, java.awt.event.MouseEvent)">processMouseEvent(FeatureHolder, SequenceRenderContext, MouseEvent)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/RectangularImapRenderer.html" title="class in org.biojava.bio.gui.sequence">RectangularImapRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/RulerRenderer.html#processMouseEvent(org.biojava.bio.gui.sequence.SequenceRenderContext, java.awt.event.MouseEvent, java.util.List)">processMouseEvent(SequenceRenderContext, MouseEvent, List)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/RulerRenderer.html" title="class in org.biojava.bio.gui.sequence">RulerRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequenceRenderer.html#processMouseEvent(org.biojava.bio.gui.sequence.SequenceRenderContext, java.awt.event.MouseEvent, java.util.List)">processMouseEvent(SequenceRenderContext, MouseEvent, List)</a></span> - Method in interface org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequenceRenderer.html" title="interface in org.biojava.bio.gui.sequence">SequenceRenderer</a></dt>
<dd>
<div class="block">Produce a SequenceViewerEvent in response to a mouse gesture.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequenceRendererWrapper.html#processMouseEvent(org.biojava.bio.gui.sequence.SequenceRenderContext, java.awt.event.MouseEvent, java.util.List)">processMouseEvent(SequenceRenderContext, MouseEvent, List)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequenceRendererWrapper.html" title="class in org.biojava.bio.gui.sequence">SequenceRendererWrapper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SixFrameRenderer.html#processMouseEvent(org.biojava.bio.gui.sequence.SequenceRenderContext, java.awt.event.MouseEvent, java.util.List)">processMouseEvent(SequenceRenderContext, MouseEvent, List)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SixFrameRenderer.html" title="class in org.biojava.bio.gui.sequence">SixFrameRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SixFrameZiggyRenderer.html#processMouseEvent(org.biojava.bio.seq.FeatureHolder, org.biojava.bio.gui.sequence.SequenceRenderContext, java.awt.event.MouseEvent)">processMouseEvent(FeatureHolder, SequenceRenderContext, MouseEvent)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SixFrameZiggyRenderer.html" title="class in org.biojava.bio.gui.sequence">SixFrameZiggyRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/StackedFeatureRenderer.html#processMouseEvent(org.biojava.bio.seq.FeatureHolder, org.biojava.bio.gui.sequence.SequenceRenderContext, java.awt.event.MouseEvent)">processMouseEvent(FeatureHolder, SequenceRenderContext, MouseEvent)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/StackedFeatureRenderer.html" title="class in org.biojava.bio.gui.sequence">StackedFeatureRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/StopRenderer.html#processMouseEvent(org.biojava.bio.gui.sequence.SequenceRenderContext, java.awt.event.MouseEvent, java.util.List)">processMouseEvent(SequenceRenderContext, MouseEvent, List)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/StopRenderer.html" title="class in org.biojava.bio.gui.sequence">StopRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SymbolSequenceRenderer.html#processMouseEvent(org.biojava.bio.gui.sequence.SequenceRenderContext, java.awt.event.MouseEvent, java.util.List)">processMouseEvent(SequenceRenderContext, MouseEvent, List)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SymbolSequenceRenderer.html" title="class in org.biojava.bio.gui.sequence">SymbolSequenceRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/TickFeatureRenderer.html#processMouseEvent(org.biojava.bio.seq.FeatureHolder, org.biojava.bio.gui.sequence.SequenceRenderContext, java.awt.event.MouseEvent)">processMouseEvent(FeatureHolder, SequenceRenderContext, MouseEvent)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/TickFeatureRenderer.html" title="class in org.biojava.bio.gui.sequence">TickFeatureRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/ZiggyFeatureRenderer.html#processMouseEvent(org.biojava.bio.seq.FeatureHolder, org.biojava.bio.gui.sequence.SequenceRenderContext, java.awt.event.MouseEvent)">processMouseEvent(FeatureHolder, SequenceRenderContext, MouseEvent)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/ZiggyFeatureRenderer.html" title="class in org.biojava.bio.gui.sequence">ZiggyFeatureRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/ZiggyImapRenderer.html#processMouseEvent(org.biojava.bio.seq.FeatureHolder, org.biojava.bio.gui.sequence.SequenceRenderContext, java.awt.event.MouseEvent)">processMouseEvent(FeatureHolder, SequenceRenderContext, MouseEvent)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/ZiggyImapRenderer.html" title="class in org.biojava.bio.gui.sequence">ZiggyImapRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/SequencesAsGFF.html#processSequence(org.biojava.bio.seq.Sequence, org.biojava.bio.program.gff.GFFDocumentHandler)">processSequence(Sequence, GFFDocumentHandler)</a></span> - Method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/SequencesAsGFF.html" title="class in org.biojava.bio.program.gff">SequencesAsGFF</a></dt>
<dd>
<div class="block">Process an individual <span class="type">Sequence</span>, informing
<span class="arg">handler</span> of any suitable features.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/EmblLikeFormat.html#processSequenceLine(java.lang.String, org.biojava.bio.seq.io.StreamParser)">processSequenceLine(String, StreamParser)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/EmblLikeFormat.html" title="class in org.biojava.bio.seq.io">EmblLikeFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Dispatch symbol data from SQ-block line of an EMBL-like file.</div>
</dd>
<dt><a href="./org/biojava/utils/ProcessTimeoutException.html" title="class in org.biojava.utils"><span class="strong">ProcessTimeoutException</span></a> - Exception in <a href="./org/biojava/utils/package-summary.html">org.biojava.utils</a></dt>
<dd>
<div class="block">Exception which is thrown if a child process managed by <code>ProcessTools</code>
exceeds a specified time limit.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/ProcessTimeoutException.html#ProcessTimeoutException(int)">ProcessTimeoutException(int)</a></span> - Constructor for exception org.biojava.utils.<a href="./org/biojava/utils/ProcessTimeoutException.html" title="class in org.biojava.utils">ProcessTimeoutException</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ProcessTimeoutException.html#ProcessTimeoutException(int, java.lang.String)">ProcessTimeoutException(int, String)</a></span> - Constructor for exception org.biojava.utils.<a href="./org/biojava/utils/ProcessTimeoutException.html" title="class in org.biojava.utils">ProcessTimeoutException</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/utils/ProcessTools.html" title="class in org.biojava.utils"><span class="strong">ProcessTools</span></a> - Class in <a href="./org/biojava/utils/package-summary.html">org.biojava.utils</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>preferable to use org.biojava.utils.ExecRunner
or the org.biojava.utils.process package.</i></div>
</div>
</dd>
<dt><a href="./org/biojava/bio/program/hmmer/ProfileEmissionState.html" title="class in org.biojava.bio.program.hmmer"><span class="strong">ProfileEmissionState</span></a> - Class in <a href="./org/biojava/bio/program/hmmer/package-summary.html">org.biojava.bio.program.hmmer</a></dt>
<dd>
<div class="block">A state in a HMMer model.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/hmmer/ProfileEmissionState.html#ProfileEmissionState(java.lang.String, org.biojava.bio.Annotation, int[], org.biojava.bio.dist.Distribution)">ProfileEmissionState(String, Annotation, int[], Distribution)</a></span> - Constructor for class org.biojava.bio.program.hmmer.<a href="./org/biojava/bio/program/hmmer/ProfileEmissionState.html" title="class in org.biojava.bio.program.hmmer">ProfileEmissionState</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/dp/ProfileHMM.html" title="class in org.biojava.bio.dp"><span class="strong">ProfileHMM</span></a> - Class in <a href="./org/biojava/bio/dp/package-summary.html">org.biojava.bio.dp</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/ProfileHMM.html#ProfileHMM(org.biojava.bio.symbol.Alphabet, int, org.biojava.bio.dist.DistributionFactory, org.biojava.bio.dist.DistributionFactory)">ProfileHMM(Alphabet, int, DistributionFactory, DistributionFactory)</a></span> - Constructor for class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/ProfileHMM.html" title="class in org.biojava.bio.dp">ProfileHMM</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span> </div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/ProfileHMM.html#ProfileHMM(org.biojava.bio.symbol.Alphabet, int, org.biojava.bio.dist.DistributionFactory, org.biojava.bio.dist.DistributionFactory, java.lang.String)">ProfileHMM(Alphabet, int, DistributionFactory, DistributionFactory, String)</a></span> - Constructor for class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/ProfileHMM.html" title="class in org.biojava.bio.dp">ProfileHMM</a></dt>
<dd>
<div class="block">Create a new ProfileHMM.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html#PROJ_ACC_TAG">PROJ_ACC_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html" title="class in org.biojavax.bio.seq.io">EMBLxmlFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SubSequence.SubProjectedFeatureContext.html#projectChildFeatures(org.biojava.bio.seq.Feature, org.biojava.bio.seq.FeatureHolder)">projectChildFeatures(Feature, FeatureHolder)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SubSequence.SubProjectedFeatureContext.html" title="class in org.biojava.bio.seq.impl">SubSequence.SubProjectedFeatureContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/projection/ProjectionContext.html#projectChildFeatures(org.biojava.bio.seq.Feature, org.biojava.bio.seq.FeatureHolder)">projectChildFeatures(Feature, FeatureHolder)</a></span> - Method in interface org.biojava.bio.seq.projection.<a href="./org/biojava/bio/seq/projection/ProjectionContext.html" title="interface in org.biojava.bio.seq.projection">ProjectionContext</a></dt>
<dd>
<div class="block">Project all features that are children of feature so that they become
children of parent.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/projection/ReparentContext.html#projectChildFeatures(org.biojava.bio.seq.Feature, org.biojava.bio.seq.FeatureHolder)">projectChildFeatures(Feature, FeatureHolder)</a></span> - Method in class org.biojava.bio.seq.projection.<a href="./org/biojava/bio/seq/projection/ReparentContext.html" title="class in org.biojava.bio.seq.projection">ReparentContext</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/projection/ProjectedFeature.html" title="class in org.biojava.bio.seq.projection"><span class="strong">ProjectedFeature</span></a> - Class in <a href="./org/biojava/bio/seq/projection/package-summary.html">org.biojava.bio.seq.projection</a></dt>
<dd>
<div class="block">Internal class used by ProjectionEngine to wrap Feature objects.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/projection/ProjectedFeature.html#ProjectedFeature(org.biojava.bio.seq.Feature, org.biojava.bio.seq.projection.ProjectionContext)">ProjectedFeature(Feature, ProjectionContext)</a></span> - Constructor for class org.biojava.bio.seq.projection.<a href="./org/biojava/bio/seq/projection/ProjectedFeature.html" title="class in org.biojava.bio.seq.projection">ProjectedFeature</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/projection/ProjectedFeatureHolder.html" title="class in org.biojava.bio.seq.projection"><span class="strong">ProjectedFeatureHolder</span></a> - Class in <a href="./org/biojava/bio/seq/projection/package-summary.html">org.biojava.bio.seq.projection</a></dt>
<dd>
<div class="block">Helper class for projecting Feature objects into an alternative
coordinate system.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/projection/ProjectedFeatureHolder.html#ProjectedFeatureHolder(org.biojava.bio.seq.projection.ProjectionContext)">ProjectedFeatureHolder(ProjectionContext)</a></span> - Constructor for class org.biojava.bio.seq.projection.<a href="./org/biojava/bio/seq/projection/ProjectedFeatureHolder.html" title="class in org.biojava.bio.seq.projection">ProjectedFeatureHolder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SubSequence.SubProjectedFeatureContext.html#projectFeature(org.biojava.bio.seq.Feature)">projectFeature(Feature)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SubSequence.SubProjectedFeatureContext.html" title="class in org.biojava.bio.seq.impl">SubSequence.SubProjectedFeatureContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/projection/ProjectionContext.html#projectFeature(org.biojava.bio.seq.Feature)">projectFeature(Feature)</a></span> - Method in interface org.biojava.bio.seq.projection.<a href="./org/biojava/bio/seq/projection/ProjectionContext.html" title="interface in org.biojava.bio.seq.projection">ProjectionContext</a></dt>
<dd>
<div class="block">Project a single feature.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/projection/ProjectionEngine.html#projectFeature(org.biojava.bio.seq.Feature, org.biojava.bio.seq.projection.ProjectionContext)">projectFeature(Feature, ProjectionContext)</a></span> - Method in class org.biojava.bio.seq.projection.<a href="./org/biojava/bio/seq/projection/ProjectionEngine.html" title="class in org.biojava.bio.seq.projection">ProjectionEngine</a></dt>
<dd>
<div class="block">Return a projection of Feature <code>f</code> into the system
defined by a given ProjectionContext.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/projection/ReparentContext.html#projectFeature(org.biojava.bio.seq.Feature)">projectFeature(Feature)</a></span> - Method in class org.biojava.bio.seq.projection.<a href="./org/biojava/bio/seq/projection/ReparentContext.html" title="class in org.biojava.bio.seq.projection">ReparentContext</a></dt>
<dd>
<div class="block">Create a single projected feature using the rules of this <code>ProjectedFeatureHolder</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/projection/ProjectionContext.html#projectFeatures(org.biojava.bio.seq.FeatureHolder)">projectFeatures(FeatureHolder)</a></span> - Method in interface org.biojava.bio.seq.projection.<a href="./org/biojava/bio/seq/projection/ProjectionContext.html" title="interface in org.biojava.bio.seq.projection">ProjectionContext</a></dt>
<dd>
<div class="block">Project all of the features in a FeatureHolder.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/projection/ReparentContext.html#projectFeatures(org.biojava.bio.seq.FeatureHolder)">projectFeatures(FeatureHolder)</a></span> - Method in class org.biojava.bio.seq.projection.<a href="./org/biojava/bio/seq/projection/ReparentContext.html" title="class in org.biojava.bio.seq.projection">ReparentContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/projection/ProjectionContext.html#projectFilter(org.biojava.bio.seq.FeatureFilter)">projectFilter(FeatureFilter)</a></span> - Method in interface org.biojava.bio.seq.projection.<a href="./org/biojava/bio/seq/projection/ProjectionContext.html" title="interface in org.biojava.bio.seq.projection">ProjectionContext</a></dt>
<dd>
<div class="block">Transform a filter on unprojected features so that it applies to projected
features.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/projection/ReparentContext.html#projectFilter(org.biojava.bio.seq.FeatureFilter)">projectFilter(FeatureFilter)</a></span> - Method in class org.biojava.bio.seq.projection.<a href="./org/biojava/bio/seq/projection/ReparentContext.html" title="class in org.biojava.bio.seq.projection">ReparentContext</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/projection/Projection.html" title="interface in org.biojava.bio.seq.projection"><span class="strong">Projection</span></a> - Interface in <a href="./org/biojava/bio/seq/projection/package-summary.html">org.biojava.bio.seq.projection</a></dt>
<dd>
<div class="block">Interface implemented by all projected feature objects.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/projection/ProjectionContext.html" title="interface in org.biojava.bio.seq.projection"><span class="strong">ProjectionContext</span></a> - Interface in <a href="./org/biojava/bio/seq/projection/package-summary.html">org.biojava.bio.seq.projection</a></dt>
<dd>
<div class="block">Interface that defines the projection between original features and
projected features.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/projection/ProjectionEngine.html" title="class in org.biojava.bio.seq.projection"><span class="strong">ProjectionEngine</span></a> - Class in <a href="./org/biojava/bio/seq/projection/package-summary.html">org.biojava.bio.seq.projection</a></dt>
<dd>
<div class="block">Factory for proxy objects which project BioJava features
into alternate coordinate systems.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/projection/ProjectionEngine.Instantiator.html" title="interface in org.biojava.bio.seq.projection"><span class="strong">ProjectionEngine.Instantiator</span></a> - Interface in <a href="./org/biojava/bio/seq/projection/package-summary.html">org.biojava.bio.seq.projection</a></dt>
<dd>
<div class="block">Internal helper class.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/projection/ProjectionEngine.TemplateProjector.html" title="interface in org.biojava.bio.seq.projection"><span class="strong">ProjectionEngine.TemplateProjector</span></a> - Interface in <a href="./org/biojava/bio/seq/projection/package-summary.html">org.biojava.bio.seq.projection</a></dt>
<dd>
<div class="block">This is an interface for things that project feature templates.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/projection/ProjectionUtils.html" title="class in org.biojava.bio.seq.projection"><span class="strong">ProjectionUtils</span></a> - Class in <a href="./org/biojava/bio/seq/projection/package-summary.html">org.biojava.bio.seq.projection</a></dt>
<dd>
<div class="block">Some common things you want to do while projecting features.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/projection/ProjectionUtils.html#ProjectionUtils()">ProjectionUtils()</a></span> - Constructor for class org.biojava.bio.seq.projection.<a href="./org/biojava/bio/seq/projection/ProjectionUtils.html" title="class in org.biojava.bio.seq.projection">ProjectionUtils</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleGappedSequence.GappedContext.html#projectLocation(org.biojava.bio.symbol.Location)">projectLocation(Location)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleGappedSequence.GappedContext.html" title="class in org.biojava.bio.seq.impl">SimpleGappedSequence.GappedContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SubSequence.SubProjectedFeatureContext.html#projectLocation(org.biojava.bio.symbol.Location)">projectLocation(Location)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SubSequence.SubProjectedFeatureContext.html" title="class in org.biojava.bio.seq.impl">SubSequence.SubProjectedFeatureContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/projection/TranslateFlipContext.html#projectLocation(org.biojava.bio.symbol.Location)">projectLocation(Location)</a></span> - Method in class org.biojava.bio.seq.projection.<a href="./org/biojava/bio/seq/projection/TranslateFlipContext.html" title="class in org.biojava.bio.seq.projection">TranslateFlipContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/projection/TranslateFlipContext.html#projectStrand(org.biojava.bio.seq.StrandedFeature.Strand)">projectStrand(StrandedFeature.Strand)</a></span> - Method in class org.biojava.bio.seq.projection.<a href="./org/biojava/bio/seq/projection/TranslateFlipContext.html" title="class in org.biojava.bio.seq.projection">TranslateFlipContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/candy/CandyVocabulary.html#PROP_CASE_SENSITIVE">PROP_CASE_SENSITIVE</a></span> - Static variable in interface org.biojava.utils.candy.<a href="./org/biojava/utils/candy/CandyVocabulary.html" title="interface in org.biojava.utils.candy">CandyVocabulary</a></dt>
<dd>
<div class="block">A property name.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BibRefQuery.html#PROP_CRITERIONS">PROP_CRITERIONS</a></span> - Static variable in interface org.biojava.bibliography.<a href="./org/biojava/bibliography/BibRefQuery.html" title="interface in org.biojava.bibliography">BibRefQuery</a></dt>
<dd>
<div class="block">A property name specifying a list of searching and ordering criteria
names (type of the property value should be <tt>String[]</tt>).</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/candy/CandyVocabulary.html#PROP_ENTRY_COUNT">PROP_ENTRY_COUNT</a></span> - Static variable in interface org.biojava.utils.candy.<a href="./org/biojava/utils/candy/CandyVocabulary.html" title="interface in org.biojava.utils.candy">CandyVocabulary</a></dt>
<dd>
<div class="block">A property name.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BibRefQuery.html#PROP_EXCLUDED_ATTRS">PROP_EXCLUDED_ATTRS</a></span> - Static variable in interface org.biojava.bibliography.<a href="./org/biojava/bibliography/BibRefQuery.html" title="interface in org.biojava.bibliography">BibRefQuery</a></dt>
<dd>
<div class="block">
A property name specifying a list of excluded attribute names
(the type of the property value should be <tt>String[]</tt>).</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/candy/CandyVocabulary.html#PROP_VOCAB_DESC">PROP_VOCAB_DESC</a></span> - Static variable in interface org.biojava.utils.candy.<a href="./org/biojava/utils/candy/CandyVocabulary.html" title="interface in org.biojava.utils.candy">CandyVocabulary</a></dt>
<dd>
<div class="block">A property name.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/candy/CandyVocabulary.html#PROP_VOCAB_NAME">PROP_VOCAB_NAME</a></span> - Static variable in interface org.biojava.utils.candy.<a href="./org/biojava/utils/candy/CandyVocabulary.html" title="interface in org.biojava.utils.candy">CandyVocabulary</a></dt>
<dd>
<div class="block">A property name.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/candy/CandyVocabulary.html#PROP_VOCAB_VERSION">PROP_VOCAB_VERSION</a></span> - Static variable in interface org.biojava.utils.candy.<a href="./org/biojava/utils/candy/CandyVocabulary.html" title="interface in org.biojava.utils.candy">CandyVocabulary</a></dt>
<dd>
<div class="block">A property name.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/candy/CandyFinder.html#PROP_VOCABULARY">PROP_VOCABULARY</a></span> - Static variable in interface org.biojava.utils.candy.<a href="./org/biojava/utils/candy/CandyFinder.html" title="interface in org.biojava.utils.candy">CandyFinder</a></dt>
<dd>
<div class="block">
A property name.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/candy/CandyVocabulary.html#PROP_VOCABULARY">PROP_VOCABULARY</a></span> - Static variable in interface org.biojava.utils.candy.<a href="./org/biojava/utils/candy/CandyVocabulary.html" title="interface in org.biojava.utils.candy">CandyVocabulary</a></dt>
<dd>
<div class="block">A property name.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/xff/PropDetailHandler.html#PROPDETAIL_HANDLER_FACTORY">PROPDETAIL_HANDLER_FACTORY</a></span> - Static variable in class org.biojava.bio.program.xff.<a href="./org/biojava/bio/program/xff/PropDetailHandler.html" title="class in org.biojava.bio.program.xff">PropDetailHandler</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/xff/PropDetailHandler.html" title="class in org.biojava.bio.program.xff"><span class="strong">PropDetailHandler</span></a> - Class in <a href="./org/biojava/bio/program/xff/package-summary.html">org.biojava.bio.program.xff</a></dt>
<dd>
<div class="block">StAX handler for xff:prop detail elements.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/xff/PropDetailHandler.html#PropDetailHandler(org.biojava.bio.program.xff.XFFFeatureSetHandler)">PropDetailHandler(XFFFeatureSetHandler)</a></span> - Constructor for class org.biojava.bio.program.xff.<a href="./org/biojava/bio/program/xff/PropDetailHandler.html" title="class in org.biojava.bio.program.xff">PropDetailHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BiblioEntryStatus.html#properties">properties</a></span> - Variable in class org.biojava.bibliography.<a href="./org/biojava/bibliography/BiblioEntryStatus.html" title="class in org.biojava.bibliography">BiblioEntryStatus</a></dt>
<dd>
<div class="block">
The dynamic properties may be used to add features related to
the citation itself.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BiblioJournal.html#properties">properties</a></span> - Variable in class org.biojava.bibliography.<a href="./org/biojava/bibliography/BiblioJournal.html" title="class in org.biojava.bibliography">BiblioJournal</a></dt>
<dd>
<div class="block">Additional properties used when the explicit attributes
are not sufficient.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BiblioProvider.html#properties">properties</a></span> - Variable in class org.biojava.bibliography.<a href="./org/biojava/bibliography/BiblioProvider.html" title="class in org.biojava.bibliography">BiblioProvider</a></dt>
<dd>
<div class="block">Additional properties used when the explicit attributes of the
sub-classes are not sufficient.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BiblioScope.html#properties">properties</a></span> - Variable in class org.biojava.bibliography.<a href="./org/biojava/bibliography/BiblioScope.html" title="class in org.biojava.bibliography">BiblioScope</a></dt>
<dd>
<div class="block">It may contain additional properties related to the extend or
scope of the cited resource.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BibRef.html#properties">properties</a></span> - Variable in class org.biojava.bibliography.<a href="./org/biojava/bibliography/BibRef.html" title="class in org.biojava.bibliography">BibRef</a></dt>
<dd>
<div class="block">Additional attributes of this citation.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/AbstractAnnotation.html#propertiesAllocated()">propertiesAllocated()</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/AbstractAnnotation.html" title="class in org.biojava.bio">AbstractAnnotation</a></dt>
<dd>
<div class="block">A convenience method to see if we have allocated the properties
Map.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/AnnotationChanger.html#propertiesAllocated()">propertiesAllocated()</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/AnnotationChanger.html" title="class in org.biojava.bio">AnnotationChanger</a></dt>
<dd>
<div class="block"><code>propertiesAllocated</code> is a convenience method to see
if we have allocated the properties <code>Map</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/AnnotationRenamer.html#propertiesAllocated()">propertiesAllocated()</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/AnnotationRenamer.html" title="class in org.biojava.bio">AnnotationRenamer</a></dt>
<dd>
<div class="block"><code>propertiesAllocated</code> Javadoc FIXME - this overrides
a protected method and I'm not sure why (KJ).</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/BeanAsAnnotation.html#propertiesAllocated()">propertiesAllocated()</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/BeanAsAnnotation.html" title="class in org.biojava.bio">BeanAsAnnotation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/ReferenceAnnotation.html#propertiesAllocated()">propertiesAllocated()</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/ReferenceAnnotation.html" title="class in org.biojava.bio.seq.io">ReferenceAnnotation</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/SimpleAnnotation.html#propertiesAllocated()">propertiesAllocated()</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/SimpleAnnotation.html" title="class in org.biojava.bio">SimpleAnnotation</a></dt>
<dd>
<div class="block">Test to see if any properties have been allocated</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/SmallAnnotation.html#propertiesAllocated()">propertiesAllocated()</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/SmallAnnotation.html" title="class in org.biojava.bio">SmallAnnotation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/Annotation.html#PROPERTY">PROPERTY</a></span> - Static variable in interface org.biojava.bio.<a href="./org/biojava/bio/Annotation.html" title="interface in org.biojava.bio">Annotation</a></dt>
<dd>
<div class="block">This type symbolizes that one or more properties have changed.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/DASSequence.html#PROPERTY_ANNOTATIONSERVER">PROPERTY_ANNOTATIONSERVER</a></span> - Static variable in class org.biojava.bio.program.das.<a href="./org/biojava/bio/program/das/DASSequence.html" title="class in org.biojava.bio.program.das">DASSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/Feature.html#PROPERTY_DATA_KEY">PROPERTY_DATA_KEY</a></span> - Static variable in interface org.biojava.bio.seq.<a href="./org/biojava/bio/seq/Feature.html" title="interface in org.biojava.bio.seq">Feature</a></dt>
<dd>
<div class="block">This is used as a key in the <code>Annotation</code> where it
identifies internal data.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/phred/PhredFormat.html#PROPERTY_DESCRIPTIONLINE">PROPERTY_DESCRIPTIONLINE</a></span> - Static variable in class org.biojava.bio.program.phred.<a href="./org/biojava/bio/program/phred/PhredFormat.html" title="class in org.biojava.bio.program.phred">PhredFormat</a></dt>
<dd>
<div class="block">Constant string which is the property key used to notify
listeners of the description lines of Phred sequences.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/FastaFormat.html#PROPERTY_DESCRIPTIONLINE">PROPERTY_DESCRIPTIONLINE</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/FastaFormat.html" title="class in org.biojava.bio.seq.io">FastaFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Constant string which is the property key used to notify
listeners of the description lines of FASTA sequences.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/EmblProcessor.html#PROPERTY_EMBL_ACCESSIONS">PROPERTY_EMBL_ACCESSIONS</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/EmblProcessor.html" title="class in org.biojava.bio.seq.io">EmblProcessor</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/DASSequence.html#PROPERTY_FEATUREID">PROPERTY_FEATUREID</a></span> - Static variable in class org.biojava.bio.program.das.<a href="./org/biojava/bio/program/das/DASSequence.html" title="class in org.biojava.bio.program.das">DASSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/DASSequence.html#PROPERTY_FEATURELABEL">PROPERTY_FEATURELABEL</a></span> - Static variable in class org.biojava.bio.program.das.<a href="./org/biojava/bio/program/das/DASSequence.html" title="class in org.biojava.bio.program.das">DASSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/GenbankProcessor.html#PROPERTY_GENBANK_ACCESSIONS">PROPERTY_GENBANK_ACCESSIONS</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/GenbankProcessor.html" title="class in org.biojava.bio.seq.io">GenbankProcessor</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFEntrySet.html#PROPERTY_GFF_SCORE">PROPERTY_GFF_SCORE</a></span> - Static variable in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFEntrySet.html" title="class in org.biojava.bio.program.gff">GFFEntrySet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/DASSequence.html#PROPERTY_LINKS">PROPERTY_LINKS</a></span> - Static variable in class org.biojava.bio.program.das.<a href="./org/biojava/bio/program/das/DASSequence.html" title="class in org.biojava.bio.program.das">DASSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/taxa/EbiFormat.html#PROPERTY_NCBI_TAXON">PROPERTY_NCBI_TAXON</a></span> - Static variable in class org.biojava.bio.taxa.<a href="./org/biojava/bio/taxa/EbiFormat.html" title="class in org.biojava.bio.taxa">EbiFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/OrganismParser.html#PROPERTY_ORGANISM">PROPERTY_ORGANISM</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/OrganismParser.html" title="class in org.biojava.bio.seq.io">OrganismParser</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/DASSequence.html#PROPERTY_SEQUENCEVERSION">PROPERTY_SEQUENCEVERSION</a></span> - Static variable in class org.biojava.bio.program.das.<a href="./org/biojava/bio/program/das/DASSequence.html" title="class in org.biojava.bio.program.das">DASSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SwissprotProcessor.html#PROPERTY_SWISSPROT_ACCESSIONS">PROPERTY_SWISSPROT_ACCESSIONS</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SwissprotProcessor.html" title="class in org.biojava.bio.seq.io">SwissprotProcessor</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SwissprotProcessor.html#PROPERTY_SWISSPROT_COMMENT">PROPERTY_SWISSPROT_COMMENT</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SwissprotProcessor.html" title="class in org.biojava.bio.seq.io">SwissprotProcessor</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SwissprotProcessor.html#PROPERTY_SWISSPROT_FEATUREATTRIBUTE">PROPERTY_SWISSPROT_FEATUREATTRIBUTE</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SwissprotProcessor.html" title="class in org.biojava.bio.seq.io">SwissprotProcessor</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#PROPERTY_TAG">PROPERTY_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/taxa/EbiFormat.html#PROPERTY_TAXON_NAMES">PROPERTY_TAXON_NAMES</a></span> - Static variable in class org.biojava.bio.taxa.<a href="./org/biojava/bio/taxa/EbiFormat.html" title="class in org.biojava.bio.taxa">EbiFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/xff/XFFFeatureSetHandler.html#PROPERTY_XFF_ID">PROPERTY_XFF_ID</a></span> - Static variable in class org.biojava.bio.program.xff.<a href="./org/biojava/bio/program/xff/XFFFeatureSetHandler.html" title="class in org.biojava.bio.program.xff">XFFFeatureSetHandler</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/tagvalue/PropertyChanger.html" title="interface in org.biojava.bio.program.tagvalue"><span class="strong">PropertyChanger</span></a> - Interface in <a href="./org/biojava/bio/program/tagvalue/package-summary.html">org.biojava.bio.program.tagvalue</a></dt>
<dd>
<div class="block">Interface for objects that change tag names or properties systematically.</div>
</dd>
<dt><a href="./org/biojava/bio/PropertyConstraint.html" title="interface in org.biojava.bio"><span class="strong">PropertyConstraint</span></a> - Interface in <a href="./org/biojava/bio/package-summary.html">org.biojava.bio</a></dt>
<dd>
<div class="block"><code>PropertyConstraint</code>s describes a constraint applied
to the members of an annotation bundle.</div>
</dd>
<dt><a href="./org/biojava/bio/PropertyConstraint.And.html" title="class in org.biojava.bio"><span class="strong">PropertyConstraint.And</span></a> - Class in <a href="./org/biojava/bio/package-summary.html">org.biojava.bio</a></dt>
<dd>
<div class="block">A property constraint that accpepts items iff they are accepted by both
child constraints.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/PropertyConstraint.And.html#PropertyConstraint.And(org.biojava.bio.PropertyConstraint, org.biojava.bio.PropertyConstraint)">PropertyConstraint.And(PropertyConstraint, PropertyConstraint)</a></span> - Constructor for class org.biojava.bio.<a href="./org/biojava/bio/PropertyConstraint.And.html" title="class in org.biojava.bio">PropertyConstraint.And</a></dt>
<dd>
<div class="block">Create a new <code>And</code> from two child constraints.</div>
</dd>
<dt><a href="./org/biojava/bio/PropertyConstraint.ByAnnotationType.html" title="class in org.biojava.bio"><span class="strong">PropertyConstraint.ByAnnotationType</span></a> - Class in <a href="./org/biojava/bio/package-summary.html">org.biojava.bio</a></dt>
<dd>
<div class="block"><code>ByAnnotationType</code> accepts a property value if it
belongs to type defined by AnnotationType.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/PropertyConstraint.ByAnnotationType.html#PropertyConstraint.ByAnnotationType(org.biojava.bio.AnnotationType)">PropertyConstraint.ByAnnotationType(AnnotationType)</a></span> - Constructor for class org.biojava.bio.<a href="./org/biojava/bio/PropertyConstraint.ByAnnotationType.html" title="class in org.biojava.bio">PropertyConstraint.ByAnnotationType</a></dt>
<dd>
<div class="block">Create a new constraint by type.</div>
</dd>
<dt><a href="./org/biojava/bio/PropertyConstraint.ByClass.html" title="class in org.biojava.bio"><span class="strong">PropertyConstraint.ByClass</span></a> - Class in <a href="./org/biojava/bio/package-summary.html">org.biojava.bio</a></dt>
<dd>
<div class="block"><code>ByClass</code> accepts a property value if it is an
instance of a specific Java class.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/PropertyConstraint.ByClass.html#PropertyConstraint.ByClass(java.lang.Class)">PropertyConstraint.ByClass(Class)</a></span> - Constructor for class org.biojava.bio.<a href="./org/biojava/bio/PropertyConstraint.ByClass.html" title="class in org.biojava.bio">PropertyConstraint.ByClass</a></dt>
<dd>
<div class="block">Create a new ByClass instance.</div>
</dd>
<dt><a href="./org/biojava/bio/PropertyConstraint.Enumeration.html" title="class in org.biojava.bio"><span class="strong">PropertyConstraint.Enumeration</span></a> - Class in <a href="./org/biojava/bio/package-summary.html">org.biojava.bio</a></dt>
<dd>
<div class="block"><code>Enumeration</code> accepts a property if it is present
in the specified set of values.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/PropertyConstraint.Enumeration.html#PropertyConstraint.Enumeration(java.util.Set)">PropertyConstraint.Enumeration(Set)</a></span> - Constructor for class org.biojava.bio.<a href="./org/biojava/bio/PropertyConstraint.Enumeration.html" title="class in org.biojava.bio">PropertyConstraint.Enumeration</a></dt>
<dd>
<div class="block">Creates a new <code>Enumeration</code> using the members of
the specified set as a constraint.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/PropertyConstraint.Enumeration.html#PropertyConstraint.Enumeration(java.lang.Object[])">PropertyConstraint.Enumeration(Object[])</a></span> - Constructor for class org.biojava.bio.<a href="./org/biojava/bio/PropertyConstraint.Enumeration.html" title="class in org.biojava.bio">PropertyConstraint.Enumeration</a></dt>
<dd>
<div class="block">Creates a new <code>Enumeration</code> using the elements of the
specified array as a constraint.</div>
</dd>
<dt><a href="./org/biojava/bio/PropertyConstraint.ExactValue.html" title="class in org.biojava.bio"><span class="strong">PropertyConstraint.ExactValue</span></a> - Class in <a href="./org/biojava/bio/package-summary.html">org.biojava.bio</a></dt>
<dd>
<div class="block">Matches properties if they have exactly this one value.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/PropertyConstraint.ExactValue.html#PropertyConstraint.ExactValue(java.lang.Object)">PropertyConstraint.ExactValue(Object)</a></span> - Constructor for class org.biojava.bio.<a href="./org/biojava/bio/PropertyConstraint.ExactValue.html" title="class in org.biojava.bio">PropertyConstraint.ExactValue</a></dt>
<dd>
<div class="block">Get a PropertyConstraint that matches this object and all those that
are equal to it (by the Object.equals() method).</div>
</dd>
<dt><a href="./org/biojava/bio/PropertyConstraint.Or.html" title="class in org.biojava.bio"><span class="strong">PropertyConstraint.Or</span></a> - Class in <a href="./org/biojava/bio/package-summary.html">org.biojava.bio</a></dt>
<dd>
<div class="block">A property constraint that accepts items iff they are accepted by either
child constraints.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/PropertyConstraint.Or.html#PropertyConstraint.Or(org.biojava.bio.PropertyConstraint, org.biojava.bio.PropertyConstraint)">PropertyConstraint.Or(PropertyConstraint, PropertyConstraint)</a></span> - Constructor for class org.biojava.bio.<a href="./org/biojava/bio/PropertyConstraint.Or.html" title="class in org.biojava.bio">PropertyConstraint.Or</a></dt>
<dd>
<div class="block">Create a new <code>Or</code> from two child constraints.</div>
</dd>
<dt><a href="./org/biojava/bio/program/xff/PropertyWriter.html" title="class in org.biojava.bio.program.xff"><span class="strong">PropertyWriter</span></a> - Class in <a href="./org/biojava/bio/program/xff/package-summary.html">org.biojava.bio.program.xff</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/xff/PropertyWriter.html#PropertyWriter()">PropertyWriter()</a></span> - Constructor for class org.biojava.bio.program.xff.<a href="./org/biojava/bio/program/xff/PropertyWriter.html" title="class in org.biojava.bio.program.xff">PropertyWriter</a></dt>
<dd> </dd>
<dt><a href="./org/biojavax/ga/functions/ProportionalSelection.html" title="class in org.biojavax.ga.functions"><span class="strong">ProportionalSelection</span></a> - Class in <a href="./org/biojavax/ga/functions/package-summary.html">org.biojavax.ga.functions</a></dt>
<dd>
<div class="block">
A Selection function that determines the proportion of individuals in a new
population proportionally to their fitness.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ga/functions/ProportionalSelection.html#ProportionalSelection()">ProportionalSelection()</a></span> - Constructor for class org.biojavax.ga.functions.<a href="./org/biojavax/ga/functions/ProportionalSelection.html" title="class in org.biojavax.ga.functions">ProportionalSelection</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/proteomics/Protease.html" title="class in org.biojava.bio.proteomics"><span class="strong">Protease</span></a> - Class in <a href="./org/biojava/bio/proteomics/package-summary.html">org.biojava.bio.proteomics</a></dt>
<dd>
<div class="block">The protease class stores parameters needed by Digest to digest a protein sequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/Protease.html#Protease(org.biojava.bio.symbol.SymbolList, boolean, org.biojava.bio.symbol.SymbolList, java.lang.String)">Protease(SymbolList, boolean, SymbolList, String)</a></span> - Constructor for class org.biojava.bio.proteomics.<a href="./org/biojava/bio/proteomics/Protease.html" title="class in org.biojava.bio.proteomics">Protease</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/Protease.html#Protease(org.biojava.bio.symbol.SymbolList, boolean, org.biojava.bio.symbol.SymbolList)">Protease(SymbolList, boolean, SymbolList)</a></span> - Constructor for class org.biojava.bio.proteomics.<a href="./org/biojava/bio/proteomics/Protease.html" title="class in org.biojava.bio.proteomics">Protease</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>Creating a Protease with this constructor will not register it
with the ProteaseManager (use ProteaseManager.createProtease())</i></div>
</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/Protease.html#Protease(java.lang.String, boolean, java.lang.String)">Protease(String, boolean, String)</a></span> - Constructor for class org.biojava.bio.proteomics.<a href="./org/biojava/bio/proteomics/Protease.html" title="class in org.biojava.bio.proteomics">Protease</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>Creating a Protease with this constructor will not register it
with the ProteaseManager (use ProteaseManager.createProtease())</i></div>
</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/Protease.html#Protease(java.lang.String, boolean)">Protease(String, boolean)</a></span> - Constructor for class org.biojava.bio.proteomics.<a href="./org/biojava/bio/proteomics/Protease.html" title="class in org.biojava.bio.proteomics">Protease</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>Creating a Protease with this constructor will not register it
with the ProteaseManager (use ProteaseManager.createProtease())</i></div>
</div>
</dd>
<dt><a href="./org/biojava/bio/proteomics/ProteaseManager.html" title="class in org.biojava.bio.proteomics"><span class="strong">ProteaseManager</span></a> - Class in <a href="./org/biojava/bio/proteomics/package-summary.html">org.biojava.bio.proteomics</a></dt>
<dd>
<div class="block">Registry and utility methods for Proteases.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/ProteaseManager.html#ProteaseManager()">ProteaseManager()</a></span> - Constructor for class org.biojava.bio.proteomics.<a href="./org/biojava/bio/proteomics/ProteaseManager.html" title="class in org.biojava.bio.proteomics">ProteaseManager</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/FastaAlignmentFormat.html#PROTEIN">PROTEIN</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/FastaAlignmentFormat.html" title="class in org.biojava.bio.seq.io">FastaAlignmentFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/aaindex/AAindex.html#PROTEIN_ALPHABET">PROTEIN_ALPHABET</a></span> - Static variable in class org.biojava.bio.proteomics.aaindex.<a href="./org/biojava/bio/proteomics/aaindex/AAindex.html" title="class in org.biojava.bio.proteomics.aaindex">AAindex</a></dt>
<dd>
<div class="block">The alphabet of the symbol property table, that is
<a href="./org/biojava/bio/seq/ProteinTools.html#getAlphabet()">protein</a>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtFormat.html#PROTEIN_EXIST_TAG">PROTEIN_EXIST_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtFormat.html" title="class in org.biojavax.bio.seq.io">UniProtFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#PROTEIN_EXISTS_TAG">PROTEIN_EXISTS_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/chem/PolymerType.html#PROTEIN_ONLY">PROTEIN_ONLY</a></span> - Static variable in enum org.biojava.bio.structure.io.mmcif.chem.<a href="./org/biojava/bio/structure/io/mmcif/chem/PolymerType.html" title="enum in org.biojava.bio.structure.io.mmcif.chem">PolymerType</a></dt>
<dd>
<div class="block">Convenience <tt>Set</tt> of polymer types classified as protein.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#PROTEIN_TAG">PROTEIN_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#PROTEIN_TYPE_ATTR">PROTEIN_TYPE_ATTR</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/io/ProteinRefSeqFileFormer.html" title="class in org.biojava.bio.seq.io"><span class="strong">ProteinRefSeqFileFormer</span></a> - Class in <a href="./org/biojava/bio/seq/io/package-summary.html">org.biojava.bio.seq.io</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>Use org.biojavax.bio.seq.io framework instead</i></div>
</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/ProteinRefSeqFileFormer.html#ProteinRefSeqFileFormer()">ProteinRefSeqFileFormer()</a></span> - Constructor for class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/ProteinRefSeqFileFormer.html" title="class in org.biojava.bio.seq.io">ProteinRefSeqFileFormer</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/ProteinRefSeqFileFormer.html#ProteinRefSeqFileFormer(java.io.PrintStream)">ProteinRefSeqFileFormer(PrintStream)</a></span> - Constructor for class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/ProteinRefSeqFileFormer.html" title="class in org.biojava.bio.seq.io">ProteinRefSeqFileFormer</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/ProteinRefSeqProcessor.html" title="class in org.biojava.bio.seq.io"><span class="strong">ProteinRefSeqProcessor</span></a> - Class in <a href="./org/biojava/bio/seq/io/package-summary.html">org.biojava.bio.seq.io</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>Use org.biojavax.bio.seq.io framework instead</i></div>
</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/ProteinRefSeqProcessor.html#ProteinRefSeqProcessor(org.biojava.bio.seq.io.SequenceBuilder)">ProteinRefSeqProcessor(SequenceBuilder)</a></span> - Constructor for class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/ProteinRefSeqProcessor.html" title="class in org.biojava.bio.seq.io">ProteinRefSeqProcessor</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/ProteinRefSeqProcessor.Factory.html" title="class in org.biojava.bio.seq.io"><span class="strong">ProteinRefSeqProcessor.Factory</span></a> - Class in <a href="./org/biojava/bio/seq/io/package-summary.html">org.biojava.bio.seq.io</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Factory which wraps sequence builders in a ProteinRefSeqProcessor</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/ProteinRefSeqProcessor.Factory.html#ProteinRefSeqProcessor.Factory(org.biojava.bio.seq.io.SequenceBuilderFactory)">ProteinRefSeqProcessor.Factory(SequenceBuilderFactory)</a></span> - Constructor for class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/ProteinRefSeqProcessor.Factory.html" title="class in org.biojava.bio.seq.io">ProteinRefSeqProcessor.Factory</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><a href="./org/biojava/bio/seq/ProteinTools.html" title="class in org.biojava.bio.seq"><span class="strong">ProteinTools</span></a> - Class in <a href="./org/biojava/bio/seq/package-summary.html">org.biojava.bio.seq</a></dt>
<dd>
<div class="block">The central port-of-call for all information and functionality specific to
SymbolLists over the protein alphabet.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BibRefSupport.html#PROVIDER_ORGANISATION">PROVIDER_ORGANISATION</a></span> - Static variable in interface org.biojava.bibliography.<a href="./org/biojava/bibliography/BibRefSupport.html" title="interface in org.biojava.bibliography">BibRefSupport</a></dt>
<dd>
<div class="block">A name of a provider type.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BibRefSupport.html#PROVIDER_PERSON">PROVIDER_PERSON</a></span> - Static variable in interface org.biojava.bibliography.<a href="./org/biojava/bibliography/BibRefSupport.html" title="interface in org.biojava.bibliography">BibRefSupport</a></dt>
<dd>
<div class="block">A name of a provider type.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BibRefSupport.html#PROVIDER_SERVICE">PROVIDER_SERVICE</a></span> - Static variable in interface org.biojava.bibliography.<a href="./org/biojava/bibliography/BibRefSupport.html" title="interface in org.biojava.bibliography">BibRefSupport</a></dt>
<dd>
<div class="block">A name of a provider type.</div>
</dd>
<dt><a href="./org/biojava/directory/ProviderNotFoundException.html" title="class in org.biojava.directory"><span class="strong">ProviderNotFoundException</span></a> - Exception in <a href="./org/biojava/directory/package-summary.html">org.biojava.directory</a></dt>
<dd>
<div class="block"><code>ProviderNotFoundException</code> is thrown when a sequence
database provider can not be located.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/directory/ProviderNotFoundException.html#ProviderNotFoundException()">ProviderNotFoundException()</a></span> - Constructor for exception org.biojava.directory.<a href="./org/biojava/directory/ProviderNotFoundException.html" title="class in org.biojava.directory">ProviderNotFoundException</a></dt>
<dd>
<div class="block">Creates a <code>ProviderNotFoundException</code> with no detail
message.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/directory/ProviderNotFoundException.html#ProviderNotFoundException(java.lang.String)">ProviderNotFoundException(String)</a></span> - Constructor for exception org.biojava.directory.<a href="./org/biojava/directory/ProviderNotFoundException.html" title="class in org.biojava.directory">ProviderNotFoundException</a></dt>
<dd>
<div class="block">Creates a <code>ProviderNotFoundException</code> with the
specified detail message.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html#PTM">PTM</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html" title="class in org.biojavax.bio.seq.io">UniProtCommentParser</a></dt>
<dd>
<div class="block">A name for a comment type.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/io/CachingInputStream.html#ptr">ptr</a></span> - Variable in class org.biojava.utils.io.<a href="./org/biojava/utils/io/CachingInputStream.html" title="class in org.biojava.utils.io">CachingInputStream</a></dt>
<dd>
<div class="block">The 0-based index into cache of the _next_ byte to return.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BibRef.html#publisher">publisher</a></span> - Variable in class org.biojava.bibliography.<a href="./org/biojava/bibliography/BibRef.html" title="class in org.biojava.bibliography">BibRef</a></dt>
<dd>
<div class="block">A publisher is responsible for making the resource available.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.Terms.html#PUBMED_KEY">PUBMED_KEY</a></span> - Static variable in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.Terms.html" title="class in org.biojavax.bio.seq">RichSequence.Terms</a></dt>
<dd>
<div class="block">Holds a reference to the key that must be used to store PubMed
references.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/GenbankFormat.html#PUBMED_TAG">PUBMED_TAG</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/GenbankFormat.html" title="class in org.biojava.bio.seq.io">GenbankFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/GenbankFormat.html#PUBMED_TAG">PUBMED_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/GenbankFormat.html" title="class in org.biojavax.bio.seq.io">GenbankFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/INSDseqFormat.html#PUBMED_TAG">PUBMED_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/INSDseqFormat.html" title="class in org.biojavax.bio.seq.io">INSDseqFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/StAXFeatureHandler.html#push(org.biojava.bio.seq.io.agave.StAXContentHandler)">push(StAXContentHandler)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/StAXFeatureHandler.html" title="class in org.biojava.bio.seq.io.agave">StAXFeatureHandler</a></dt>
<dd>
<div class="block">Push StAXContentHandler object onto stack</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game/StAXFeatureHandler.html#push(org.biojava.utils.stax.StAXContentHandler)">push(StAXContentHandler)</a></span> - Method in class org.biojava.bio.seq.io.game.<a href="./org/biojava/bio/seq/io/game/StAXFeatureHandler.html" title="class in org.biojava.bio.seq.io.game">StAXFeatureHandler</a></dt>
<dd>
<div class="block">Push StAXContentHandler object onto stack</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/TagValueContext.html#pushParser(org.biojava.bio.program.tagvalue.TagValueParser, org.biojava.bio.program.tagvalue.TagValueListener)">pushParser(TagValueParser, TagValueListener)</a></span> - Method in interface org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/TagValueContext.html" title="interface in org.biojava.bio.program.tagvalue">TagValueContext</a></dt>
<dd>
<div class="block">
Push a parser and listener pair onto the parser stack.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/StateMachine.TransitionTable.html#put(java.lang.Object, org.biojava.bio.program.tagvalue.StateMachine.Transition)">put(Object, StateMachine.Transition)</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/StateMachine.TransitionTable.html" title="class in org.biojava.bio.program.tagvalue">StateMachine.TransitionTable</a></dt>
<dd>
<div class="block">set a Transition within this TransitionTable (2-argument form)</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/CodonPrefFilter.AcceptAll.html#put(org.biojava.bio.symbol.CodonPref)">put(CodonPref)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/CodonPrefFilter.AcceptAll.html" title="class in org.biojava.bio.symbol">CodonPrefFilter.AcceptAll</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/CodonPrefFilter.ByName.html#put(org.biojava.bio.symbol.CodonPref)">put(CodonPref)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/CodonPrefFilter.ByName.html" title="class in org.biojava.bio.symbol">CodonPrefFilter.ByName</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/CodonPrefFilter.EverythingToXML.html#put(org.biojava.bio.symbol.CodonPref)">put(CodonPref)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/CodonPrefFilter.EverythingToXML.html" title="class in org.biojava.bio.symbol">CodonPrefFilter.EverythingToXML</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/CodonPrefFilter.html#put(org.biojava.bio.symbol.CodonPref)">put(CodonPref)</a></span> - Method in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/CodonPrefFilter.html" title="interface in org.biojava.bio.symbol">CodonPrefFilter</a></dt>
<dd>
<div class="block">handles storage of a CodonPref object</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/SparseVector.html#put(int, double)">put(int, double)</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/SparseVector.html" title="class in org.biojava.stats.svm">SparseVector</a></dt>
<dd>
<div class="block">Set the value at a particular dimension.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/BeanAsMap.html#put(java.lang.Object, java.lang.Object)">put(Object, Object)</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/BeanAsMap.html" title="class in org.biojava.utils">BeanAsMap</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/cache/CacheMap.html#put(java.lang.Object, java.lang.Object)">put(Object, Object)</a></span> - Method in interface org.biojava.utils.cache.<a href="./org/biojava/utils/cache/CacheMap.html" title="interface in org.biojava.utils.cache">CacheMap</a></dt>
<dd>
<div class="block">Associate a value with a key.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/cache/ChangeableCache.html#put(java.lang.Object, java.lang.Object)">put(Object, Object)</a></span> - Method in class org.biojava.utils.cache.<a href="./org/biojava/utils/cache/ChangeableCache.html" title="class in org.biojava.utils.cache">ChangeableCache</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/cache/FixedSizeMap.html#put(java.lang.Object, java.lang.Object)">put(Object, Object)</a></span> - Method in class org.biojava.utils.cache.<a href="./org/biojava/utils/cache/FixedSizeMap.html" title="class in org.biojava.utils.cache">FixedSizeMap</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/cache/WeakCacheMap.html#put(java.lang.Object, java.lang.Object)">put(Object, Object)</a></span> - Method in class org.biojava.utils.cache.<a href="./org/biojava/utils/cache/WeakCacheMap.html" title="class in org.biojava.utils.cache">WeakCacheMap</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/cache/WeakValueHashMap.html#put(java.lang.Object, java.lang.Object)">put(Object, Object)</a></span> - Method in class org.biojava.utils.cache.<a href="./org/biojava/utils/cache/WeakValueHashMap.html" title="class in org.biojava.utils.cache">WeakValueHashMap</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/io/LargeBuffer.html#put(long, byte)">put(long, byte)</a></span> - Method in class org.biojava.utils.io.<a href="./org/biojava/utils/io/LargeBuffer.html" title="class in org.biojava.utils.io">LargeBuffer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/io/LargeBuffer.html#put(byte)">put(byte)</a></span> - Method in class org.biojava.utils.io.<a href="./org/biojava/utils/io/LargeBuffer.html" title="class in org.biojava.utils.io">LargeBuffer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/OverlayMap.html#put(java.lang.Object, java.lang.Object)">put(Object, Object)</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/OverlayMap.html" title="class in org.biojava.utils">OverlayMap</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/SmallMap.html#put(java.lang.Object, java.lang.Object)">put(Object, Object)</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/SmallMap.html" title="class in org.biojava.utils">SmallMap</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/io/LargeBuffer.html#putChar(long, char)">putChar(long, char)</a></span> - Method in class org.biojava.utils.io.<a href="./org/biojava/utils/io/LargeBuffer.html" title="class in org.biojava.utils.io">LargeBuffer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/io/LargeBuffer.html#putChar(char)">putChar(char)</a></span> - Method in class org.biojava.utils.io.<a href="./org/biojava/utils/io/LargeBuffer.html" title="class in org.biojava.utils.io">LargeBuffer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/AssembledSymbolList.html#putComponent(org.biojava.bio.seq.ComponentFeature)">putComponent(ComponentFeature)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/AssembledSymbolList.html" title="class in org.biojava.bio.seq.impl">AssembledSymbolList</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/AssembledSymbolList.html#putComponent(org.biojava.bio.symbol.Location, org.biojava.bio.symbol.SymbolList)">putComponent(Location, SymbolList)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/AssembledSymbolList.html" title="class in org.biojava.bio.seq.impl">AssembledSymbolList</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/NewAssembledSymbolList.html#putComponent(org.biojava.bio.seq.ComponentFeature)">putComponent(ComponentFeature)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/NewAssembledSymbolList.html" title="class in org.biojava.bio.seq.impl">NewAssembledSymbolList</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/JDBCConnectionPool.html#putConnection(java.sql.Connection)">putConnection(Connection)</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/JDBCConnectionPool.html" title="class in org.biojava.utils">JDBCConnectionPool</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/io/LargeBuffer.html#putDouble(long, double)">putDouble(long, double)</a></span> - Method in class org.biojava.utils.io.<a href="./org/biojava/utils/io/LargeBuffer.html" title="class in org.biojava.utils.io">LargeBuffer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/io/LargeBuffer.html#putDouble(double)">putDouble(double)</a></span> - Method in class org.biojava.utils.io.<a href="./org/biojava/utils/io/LargeBuffer.html" title="class in org.biojava.utils.io">LargeBuffer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/io/LargeBuffer.html#putFloat(long, float)">putFloat(long, float)</a></span> - Method in class org.biojava.utils.io.<a href="./org/biojava/utils/io/LargeBuffer.html" title="class in org.biojava.utils.io">LargeBuffer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/io/LargeBuffer.html#putFloat(float)">putFloat(float)</a></span> - Method in class org.biojava.utils.io.<a href="./org/biojava/utils/io/LargeBuffer.html" title="class in org.biojava.utils.io">LargeBuffer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/io/LargeBuffer.html#putInt(long, int)">putInt(long, int)</a></span> - Method in class org.biojava.utils.io.<a href="./org/biojava/utils/io/LargeBuffer.html" title="class in org.biojava.utils.io">LargeBuffer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/io/LargeBuffer.html#putInt(int)">putInt(int)</a></span> - Method in class org.biojava.utils.io.<a href="./org/biojava/utils/io/LargeBuffer.html" title="class in org.biojava.utils.io">LargeBuffer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/io/LargeBuffer.html#putLong(long, long)">putLong(long, long)</a></span> - Method in class org.biojava.utils.io.<a href="./org/biojava/utils/io/LargeBuffer.html" title="class in org.biojava.utils.io">LargeBuffer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/io/LargeBuffer.html#putLong(long)">putLong(long)</a></span> - Method in class org.biojava.utils.io.<a href="./org/biojava/utils/io/LargeBuffer.html" title="class in org.biojava.utils.io">LargeBuffer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/io/LargeBuffer.html#putShort(long, short)">putShort(long, short)</a></span> - Method in class org.biojava.utils.io.<a href="./org/biojava/utils/io/LargeBuffer.html" title="class in org.biojava.utils.io">LargeBuffer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/io/LargeBuffer.html#putShort(short)">putShort(short)</a></span> - Method in class org.biojava.utils.io.<a href="./org/biojava/utils/io/LargeBuffer.html" title="class in org.biojava.utils.io">LargeBuffer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/JDBCConnectionPool.html#putStatement(java.sql.Statement)">putStatement(Statement)</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/JDBCConnectionPool.html" title="class in org.biojava.utils">JDBCConnectionPool</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/biosql/TaxonSQL.html#putTaxon(java.sql.Connection, org.biojava.bio.seq.db.biosql.DBHelper, org.biojava.bio.taxa.Taxon)">putTaxon(Connection, DBHelper, Taxon)</a></span> - Static method in class org.biojava.bio.seq.db.biosql.<a href="./org/biojava/bio/seq/db/biosql/TaxonSQL.html" title="class in org.biojava.bio.seq.db.biosql">TaxonSQL</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Adds a <code>Taxon</code> (along with its parents) to the
database.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AbstractAlphabet.html#putTokenization(java.lang.String, org.biojava.bio.seq.io.SymbolTokenization)">putTokenization(String, SymbolTokenization)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AbstractAlphabet.html" title="class in org.biojava.bio.symbol">AbstractAlphabet</a></dt>
<dd>
<div class="block">
Assigns a symbol parser to a String object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/ProteinTools.html#pyl()">pyl()</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/ProteinTools.html" title="class in org.biojava.bio.seq">ProteinTools</a></dt>
<dd>
<div class="block">Returns the <code>AtomicSymbol</code> for the amino acid
Pyrrolysine (O)</div>
</dd>
</dl>
<a name="_Q_">
<!-- -->
</a>
<h2 class="title">Q</h2>
<dl>
<dt><span class="strong"><a href="./org/biojava/bio/seq/ProteinTools.html#q()">q()</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/ProteinTools.html" title="class in org.biojava.bio.seq">ProteinTools</a></dt>
<dd>
<div class="block">Returns the <code>AtomicSymbol</code> for the amino acid
Glutamine</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/jama/Matrix.html#qr()">qr()</a></span> - Method in class org.biojava.bio.structure.jama.<a href="./org/biojava/bio/structure/jama/Matrix.html" title="class in org.biojava.bio.structure.jama">Matrix</a></dt>
<dd>
<div class="block">QR Decomposition</div>
</dd>
<dt><a href="./org/biojava/bio/structure/jama/QRDecomposition.html" title="class in org.biojava.bio.structure.jama"><span class="strong">QRDecomposition</span></a> - Class in <a href="./org/biojava/bio/structure/jama/package-summary.html">org.biojava.bio.structure.jama</a></dt>
<dd>
<div class="block">QR Decomposition.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/jama/QRDecomposition.html#QRDecomposition(org.biojava.bio.structure.jama.Matrix)">QRDecomposition(Matrix)</a></span> - Constructor for class org.biojava.bio.structure.jama.<a href="./org/biojava/bio/structure/jama/QRDecomposition.html" title="class in org.biojava.bio.structure.jama">QRDecomposition</a></dt>
<dd>
<div class="block">QR Decomposition, computed by Householder reflections.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEProperty.html#QUALIFIER">QUALIFIER</a></span> - Static variable in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEProperty.html" title="class in org.biojava.bio.seq.io.agave">AGAVEProperty</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html#QUALIFIER_NAME_ATTR">QUALIFIER_NAME_ATTR</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html" title="class in org.biojavax.bio.seq.io">EMBLxmlFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html#QUALIFIER_TAG">QUALIFIER_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html" title="class in org.biojavax.bio.seq.io">EMBLxmlFormat</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/phred/Qualitative.html" title="interface in org.biojava.bio.program.phred"><span class="strong">Qualitative</span></a> - Interface in <a href="./org/biojava/bio/program/phred/package-summary.html">org.biojava.bio.program.phred</a></dt>
<dd>
<div class="block">Qualitative is an interface for classes wanting to hold quality
data in symbolic form such as Phred scores.</div>
</dd>
<dt><a href="./org/biojava/bio/alignment/QualitativeAlignment.html" title="interface in org.biojava.bio.alignment"><span class="strong">QualitativeAlignment</span></a> - Interface in <a href="./org/biojava/bio/alignment/package-summary.html">org.biojava.bio.alignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/abi/ABITools.html#QUALITY">QUALITY</a></span> - Static variable in class org.biojava.bio.program.abi.<a href="./org/biojava/bio/program/abi/ABITools.html" title="class in org.biojava.bio.program.abi">ABITools</a></dt>
<dd>
<div class="block">The quality alphabet.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/QualitativeAlignment.html#qualityAt(java.lang.Object, int)">qualityAt(Object, int)</a></span> - Method in interface org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/QualitativeAlignment.html" title="interface in org.biojava.bio.alignment">QualitativeAlignment</a></dt>
<dd>
<div class="block">Returns a quality score for label/position</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/phred/PhredTools.html#qualityFromP(double)">qualityFromP(double)</a></span> - Static method in class org.biojava.bio.program.phred.<a href="./org/biojava/bio/program/phred/PhredTools.html" title="class in org.biojava.bio.program.phred">PhredTools</a></dt>
<dd>
<div class="block">The quality value is related to the base call error probability
by the formula QV = - 10 * log_10( P_e )
where P_e is the probability that the base call is an error.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BibRefQuery.html#query(java.lang.String, java.util.Hashtable)">query(String, Hashtable)</a></span> - Method in interface org.biojava.bibliography.<a href="./org/biojava/bibliography/BibRefQuery.html" title="interface in org.biojava.bibliography">BibRefQuery</a></dt>
<dd>
<div class="block">
It queries the current collection using a query language.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BiblioCriterion.html#QUERY_CRITERION">QUERY_CRITERION</a></span> - Static variable in class org.biojava.bibliography.<a href="./org/biojava/bibliography/BiblioCriterion.html" title="class in org.biojava.bibliography">BiblioCriterion</a></dt>
<dd>
<div class="block">A query criterion.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SeqSimilaritySearchSubHit.html#QUERY_LABEL">QUERY_LABEL</a></span> - Static variable in interface org.biojava.bio.search.<a href="./org/biojava/bio/search/SeqSimilaritySearchSubHit.html" title="interface in org.biojava.bio.search">SeqSimilaritySearchSubHit</a></dt>
<dd>
<div class="block">This object is used as the label for the query sequence in the
alignment of the query sequence with this sub-hit sequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/homol/SimilarityPairFeature.html#QUERY_LABEL">QUERY_LABEL</a></span> - Static variable in interface org.biojava.bio.seq.homol.<a href="./org/biojava/bio/seq/homol/SimilarityPairFeature.html" title="interface in org.biojava.bio.seq.homol">SimilarityPairFeature</a></dt>
<dd>
<div class="block">Constant <code>QUERY_LABEL</code> is the alignment label used
for all query sequences.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/ViewSequenceFactory.html#querySeqHolder">querySeqHolder</a></span> - Variable in class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/ViewSequenceFactory.html" title="class in org.biojava.bio.program.ssbind">ViewSequenceFactory</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/ViewSequenceFactory.html#queryViewCache">queryViewCache</a></span> - Variable in class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/ViewSequenceFactory.html" title="class in org.biojava.bio.program.ssbind">ViewSequenceFactory</a></dt>
<dd> </dd>
</dl>
<a name="_R_">
<!-- -->
</a>
<h2 class="title">R</h2>
<dl>
<dt><span class="strong"><a href="./org/biojava/bio/seq/DNATools.html#r()">r()</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/DNATools.html" title="class in org.biojava.bio.seq">DNATools</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/NucleotideTools.html#r()">r()</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/NucleotideTools.html" title="class in org.biojava.bio.seq">NucleotideTools</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/ProteinTools.html#r()">r()</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/ProteinTools.html" title="class in org.biojava.bio.seq">ProteinTools</a></dt>
<dd>
<div class="block">Returns the <code>AtomicSymbol</code> for the amino acid
Arginine</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/Taxon.html#R_NORVEGICUS">R_NORVEGICUS</a></span> - Static variable in interface org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/Taxon.html" title="interface in org.biojava.bio.program.homologene">Taxon</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/stats/svm/RadialBaseKernel.html" title="class in org.biojava.stats.svm"><span class="strong">RadialBaseKernel</span></a> - Class in <a href="./org/biojava/stats/svm/package-summary.html">org.biojava.stats.svm</a></dt>
<dd>
<div class="block">This kernel computes the radial base kernel that corresponds to a gausian
distribution.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/RadialBaseKernel.html#RadialBaseKernel()">RadialBaseKernel()</a></span> - Constructor for class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/RadialBaseKernel.html" title="class in org.biojava.stats.svm">RadialBaseKernel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/RadialBaseKernel.html#RadialBaseKernel(org.biojava.stats.svm.SVMKernel, double)">RadialBaseKernel(SVMKernel, double)</a></span> - Constructor for class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/RadialBaseKernel.html" title="class in org.biojava.stats.svm">RadialBaseKernel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Calc.html#radiansPerDegree">radiansPerDegree</a></span> - Static variable in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Calc.html" title="class in org.biojava.bio.structure">Calc</a></dt>
<dd>
<div class="block">Radians per degree.</div>
</dd>
<dt><a href="./org/biojava/utils/io/RAF.html" title="class in org.biojava.utils.io"><span class="strong">RAF</span></a> - Class in <a href="./org/biojava/utils/io/package-summary.html">org.biojava.utils.io</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/io/RAF.html#RAF(java.io.File, java.lang.String)">RAF(File, String)</a></span> - Constructor for class org.biojava.utils.io.<a href="./org/biojava/utils/io/RAF.html" title="class in org.biojava.utils.io">RAF</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/io/RAF.html#RAF(java.lang.String, java.lang.String)">RAF(String, String)</a></span> - Constructor for class org.biojava.utils.io.<a href="./org/biojava/utils/io/RAF.html" title="class in org.biojava.utils.io">RAF</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/emblcd/EmblCDROMRandomAccess.html#raIndexFile">raIndexFile</a></span> - Variable in class org.biojava.bio.seq.db.emblcd.<a href="./org/biojava/bio/seq/db/emblcd/EmblCDROMRandomAccess.html" title="class in org.biojava.bio.seq.db.emblcd">EmblCDROMRandomAccess</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/jama/Matrix.html#random(int, int)">random(int, int)</a></span> - Static method in class org.biojava.bio.structure.jama.<a href="./org/biojava/bio/structure/jama/Matrix.html" title="class in org.biojava.bio.structure.jama">Matrix</a></dt>
<dd>
<div class="block">Generate matrix with random elements</div>
</dd>
<dt><a href="./org/biojava/utils/io/RandomAccessReader.html" title="class in org.biojava.utils.io"><span class="strong">RandomAccessReader</span></a> - Class in <a href="./org/biojava/utils/io/package-summary.html">org.biojava.utils.io</a></dt>
<dd>
<div class="block"><code>RandomAccessReader</code> extends <code>Reader</code> to
provide a means to create buffered <code>Reader</code>s from
<code>RandomAccessFile</code>s.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/io/RandomAccessReader.html#RandomAccessReader(java.io.RandomAccessFile)">RandomAccessReader(RandomAccessFile)</a></span> - Constructor for class org.biojava.utils.io.<a href="./org/biojava/utils/io/RandomAccessReader.html" title="class in org.biojava.utils.io">RandomAccessReader</a></dt>
<dd>
<div class="block">Creates a new <code>RandomAccessReader</code> wrapping the
<code>RandomAccessFile</code> and using a default-sized buffer
(8192 bytes).</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/io/RandomAccessReader.html#RandomAccessReader(java.io.RandomAccessFile, int)">RandomAccessReader(RandomAccessFile, int)</a></span> - Constructor for class org.biojava.utils.io.<a href="./org/biojava/utils/io/RandomAccessReader.html" title="class in org.biojava.utils.io">RandomAccessReader</a></dt>
<dd>
<div class="block">Creates a new <code>RandomAccessReader</code> wrapping the
<code>RandomAccessFile</code> and using a buffer of the
specified size.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/DistributionTools.html#randomizeDistribution(org.biojava.bio.dist.Distribution)">randomizeDistribution(Distribution)</a></span> - Static method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/DistributionTools.html" title="class in org.biojava.bio.dist">DistributionTools</a></dt>
<dd>
<div class="block">Randomizes the weights of a <code>Distribution</code>.</div>
</dd>
<dt><a href="./org/biojava/bio/symbol/RangeLocation.html" title="class in org.biojava.bio.symbol"><span class="strong">RangeLocation</span></a> - Class in <a href="./org/biojava/bio/symbol/package-summary.html">org.biojava.bio.symbol</a></dt>
<dd>
<div class="block">A simple implementation of Location that contains all points between
getMin and getMax inclusive.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/RangeLocation.html#RangeLocation(int, int)">RangeLocation(int, int)</a></span> - Constructor for class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/RangeLocation.html" title="class in org.biojava.bio.symbol">RangeLocation</a></dt>
<dd>
<div class="block">Construct a new RangeLocation from <code>min</code> to <code>max</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/events/AlignmentPositionListener.html#rangeSelected(org.biojava.bio.structure.gui.util.AlignedPosition, org.biojava.bio.structure.gui.util.AlignedPosition)">rangeSelected(AlignedPosition, AlignedPosition)</a></span> - Method in interface org.biojava.bio.structure.gui.events.<a href="./org/biojava/bio/structure/gui/events/AlignmentPositionListener.html" title="interface in org.biojava.bio.structure.gui.events">AlignmentPositionListener</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/events/JmolAlignedPositionListener.html#rangeSelected(org.biojava.bio.structure.gui.util.AlignedPosition, org.biojava.bio.structure.gui.util.AlignedPosition)">rangeSelected(AlignedPosition, AlignedPosition)</a></span> - Method in class org.biojava.bio.structure.gui.events.<a href="./org/biojava/bio/structure/gui/events/JmolAlignedPositionListener.html" title="class in org.biojava.bio.structure.gui.events">JmolAlignedPositionListener</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/jama/Matrix.html#rank()">rank()</a></span> - Method in class org.biojava.bio.structure.jama.<a href="./org/biojava/bio/structure/jama/Matrix.html" title="class in org.biojava.bio.structure.jama">Matrix</a></dt>
<dd>
<div class="block">Matrix rank</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/jama/SingularValueDecomposition.html#rank()">rank()</a></span> - Method in class org.biojava.bio.structure.jama.<a href="./org/biojava/bio/structure/jama/SingularValueDecomposition.html" title="class in org.biojava.bio.structure.jama">SingularValueDecomposition</a></dt>
<dd>
<div class="block">Effective numerical matrix rank</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/BioEntryRelationship.html#RANK">RANK</a></span> - Static variable in interface org.biojavax.bio.<a href="./org/biojavax/bio/BioEntryRelationship.html" title="interface in org.biojavax.bio">BioEntryRelationship</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichFeature.html#RANK">RANK</a></span> - Static variable in interface org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichFeature.html" title="interface in org.biojavax.bio.seq">RichFeature</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichFeatureRelationship.html#RANK">RANK</a></span> - Static variable in interface org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichFeatureRelationship.html" title="interface in org.biojavax.bio.seq">RichFeatureRelationship</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichLocation.html#RANK">RANK</a></span> - Static variable in interface org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichLocation.html" title="interface in org.biojavax.bio.seq">RichLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/Comment.html#RANK">RANK</a></span> - Static variable in interface org.biojavax.<a href="./org/biojavax/Comment.html" title="interface in org.biojavax">Comment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/Note.html#RANK">RANK</a></span> - Static variable in interface org.biojavax.<a href="./org/biojavax/Note.html" title="interface in org.biojavax">Note</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/RankedCrossRef.html#RANK">RANK</a></span> - Static variable in interface org.biojavax.<a href="./org/biojavax/RankedCrossRef.html" title="interface in org.biojavax">RankedCrossRef</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/RankedDocRef.html#RANK">RANK</a></span> - Static variable in interface org.biojavax.<a href="./org/biojavax/RankedDocRef.html" title="interface in org.biojavax">RankedDocRef</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/BioEntry.html#RANKEDCROSSREF">RANKEDCROSSREF</a></span> - Static variable in interface org.biojavax.bio.<a href="./org/biojavax/bio/BioEntry.html" title="interface in org.biojavax.bio">BioEntry</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ontology/ComparableTerm.html#RANKEDCROSSREF">RANKEDCROSSREF</a></span> - Static variable in interface org.biojavax.ontology.<a href="./org/biojavax/ontology/ComparableTerm.html" title="interface in org.biojavax.ontology">ComparableTerm</a></dt>
<dd> </dd>
<dt><a href="./org/biojavax/RankedCrossRef.html" title="interface in org.biojavax"><span class="strong">RankedCrossRef</span></a> - Interface in <a href="./org/biojavax/package-summary.html">org.biojavax</a></dt>
<dd>
<div class="block">Allows cross-references to other databases to be ranked.</div>
</dd>
<dt><a href="./org/biojavax/RankedCrossRefable.html" title="interface in org.biojavax"><span class="strong">RankedCrossRefable</span></a> - Interface in <a href="./org/biojavax/package-summary.html">org.biojavax</a></dt>
<dd>
<div class="block">Defines an object as being able to have ranked cross references associated
with it.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichFeature.Template.html#rankedCrossRefs">rankedCrossRefs</a></span> - Variable in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichFeature.Template.html" title="class in org.biojavax.bio.seq">RichFeature.Template</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/BioEntry.html#RANKEDDOCREF">RANKEDDOCREF</a></span> - Static variable in interface org.biojavax.bio.<a href="./org/biojavax/bio/BioEntry.html" title="interface in org.biojavax.bio">BioEntry</a></dt>
<dd> </dd>
<dt><a href="./org/biojavax/RankedDocRef.html" title="interface in org.biojavax"><span class="strong">RankedDocRef</span></a> - Interface in <a href="./org/biojavax/package-summary.html">org.biojavax</a></dt>
<dd>
<div class="block">Represents a documentary reference.</div>
</dd>
<dt><a href="./org/biojava/bio/structure/gui/RasmolCommandListener.html" title="class in org.biojava.bio.structure.gui"><span class="strong">RasmolCommandListener</span></a> - Class in <a href="./org/biojava/bio/structure/gui/package-summary.html">org.biojava.bio.structure.gui</a></dt>
<dd>
<div class="block">a utility class that listens to Ramsol script commands in the @link <a href="./org/biojava/bio/structure/gui/BiojavaJmol.html" title="class in org.biojava.bio.structure.gui"><code>BiojavaJmol</code></a> class</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/RasmolCommandListener.html#RasmolCommandListener(org.biojava.bio.structure.gui.BiojavaJmol.JmolPanel, javax.swing.JTextField)">RasmolCommandListener(BiojavaJmol.JmolPanel, JTextField)</a></span> - Constructor for class org.biojava.bio.structure.gui.<a href="./org/biojava/bio/structure/gui/RasmolCommandListener.html" title="class in org.biojava.bio.structure.gui">RasmolCommandListener</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/CodonPrefTools.html#RAT_NUCLEAR">RAT_NUCLEAR</a></span> - Static variable in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/CodonPrefTools.html" title="class in org.biojava.bio.symbol">CodonPrefTools</a></dt>
<dd>
<div class="block">Rattus norvegicus codon preferences</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/EllipticalBeadRenderer.html#RATIO">RATIO</a></span> - Static variable in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/EllipticalBeadRenderer.html" title="class in org.biojava.bio.gui.sequence">EllipticalBeadRenderer</a></dt>
<dd>
<div class="block">Constant <code>RATIO</code> indicating a change to the minimum
allowed ratio of long axis to short axis of the features.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/AlignIOConstants.html#RAW">RAW</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/AlignIOConstants.html" title="class in org.biojava.bio.seq.io">AlignIOConstants</a></dt>
<dd>
<div class="block"><code>RAW</code> indicates that the alignment format is raw
(symbols only).</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOConstants.html#RAW">RAW</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOConstants.html" title="class in org.biojava.bio.seq.io">SeqIOConstants</a></dt>
<dd>
<div class="block"><code>RAW</code> indicates that the sequence format is raw
(symbols only).</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/AlignIOConstants.html#RAW_AA">RAW_AA</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/AlignIOConstants.html" title="class in org.biojava.bio.seq.io">AlignIOConstants</a></dt>
<dd>
<div class="block"><code>RAW_AA</code> premade RAW | AA.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/AlignIOConstants.html#RAW_DNA">RAW_DNA</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/AlignIOConstants.html" title="class in org.biojava.bio.seq.io">AlignIOConstants</a></dt>
<dd>
<div class="block"><code>RAW_DNA</code> premade RAW | DNA.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/AlignIOConstants.html#RAW_RNA">RAW_RNA</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/AlignIOConstants.html" title="class in org.biojava.bio.seq.io">AlignIOConstants</a></dt>
<dd>
<div class="block"><code>RAW_RNA</code> premade RAW | RNA.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/FileAsList.html#rawGet(int)">rawGet(int)</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/FileAsList.html" title="class in org.biojava.utils">FileAsList</a></dt>
<dd>
<div class="block"><code>rawGet</code> reads the record at the specified index as
a raw byte array.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/tools/ClassifierExample.PointClassifier.html#rbfKernel">rbfKernel</a></span> - Static variable in class org.biojava.stats.svm.tools.<a href="./org/biojava/stats/svm/tools/ClassifierExample.PointClassifier.html" title="class in org.biojava.stats.svm.tools">ClassifierExample.PointClassifier</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtFormat.html#RC_LINE_TAG">RC_LINE_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtFormat.html" title="class in org.biojavax.bio.seq.io">UniProtFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#RC_LINE_TAG">RC_LINE_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#RC_PLASMID_TAG">RC_PLASMID_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#RC_SPECIES_TAG">RC_SPECIES_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#RC_STRAIN_TAG">RC_STRAIN_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#RC_TISSUE_TAG">RC_TISSUE_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#RC_TRANSP_TAG">RC_TRANSP_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/fastq/FastqReader.html#read(java.io.File)">read(File)</a></span> - Method in interface org.biojava.bio.program.fastq.<a href="./org/biojava/bio/program/fastq/FastqReader.html" title="interface in org.biojava.bio.program.fastq">FastqReader</a></dt>
<dd>
<div class="block">Read zero or more FASTQ formatted sequences from the specified file.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/fastq/FastqReader.html#read(java.net.URL)">read(URL)</a></span> - Method in interface org.biojava.bio.program.fastq.<a href="./org/biojava/bio/program/fastq/FastqReader.html" title="interface in org.biojava.bio.program.fastq">FastqReader</a></dt>
<dd>
<div class="block">Read zero or more FASTQ formatted sequences from the specified url.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/fastq/FastqReader.html#read(java.io.InputStream)">read(InputStream)</a></span> - Method in interface org.biojava.bio.program.fastq.<a href="./org/biojava/bio/program/fastq/FastqReader.html" title="interface in org.biojava.bio.program.fastq">FastqReader</a></dt>
<dd>
<div class="block">Read zero or more FASTQ formatted sequences from the specified input stream.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/Parser.html#read(java.io.BufferedReader, org.biojava.bio.program.tagvalue.TagValueParser, org.biojava.bio.program.tagvalue.TagValueListener)">read(BufferedReader, TagValueParser, TagValueListener)</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/Parser.html" title="class in org.biojava.bio.program.tagvalue">Parser</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/AlignmentFormat.html#read(java.io.BufferedReader)">read(BufferedReader)</a></span> - Method in interface org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/AlignmentFormat.html" title="interface in org.biojava.bio.seq.io">AlignmentFormat</a></dt>
<dd>
<div class="block">Read in an alignment from a buffered reader object</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/FastaAlignmentFormat.html#read(java.io.BufferedReader)">read(BufferedReader)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/FastaAlignmentFormat.html" title="class in org.biojava.bio.seq.io">FastaAlignmentFormat</a></dt>
<dd>
<div class="block">Reads an alignment in FASTA format.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/MSFAlignmentFormat.html#read(java.io.BufferedReader)">read(BufferedReader)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/MSFAlignmentFormat.html" title="class in org.biojava.bio.seq.io">MSFAlignmentFormat</a></dt>
<dd>
<div class="block">Reads an MSF Alignment File</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/jama/Matrix.html#read(java.io.BufferedReader)">read(BufferedReader)</a></span> - Static method in class org.biojava.bio.structure.jama.<a href="./org/biojava/bio/structure/jama/Matrix.html" title="class in org.biojava.bio.structure.jama">Matrix</a></dt>
<dd>
<div class="block">Read a matrix from a stream.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/io/CachingInputStream.html#read()">read()</a></span> - Method in class org.biojava.utils.io.<a href="./org/biojava/utils/io/CachingInputStream.html" title="class in org.biojava.utils.io">CachingInputStream</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/io/CachingInputStream.html#read(byte[], int, int)">read(byte[], int, int)</a></span> - Method in class org.biojava.utils.io.<a href="./org/biojava/utils/io/CachingInputStream.html" title="class in org.biojava.utils.io">CachingInputStream</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/io/CountedBufferedReader.html#read()">read()</a></span> - Method in class org.biojava.utils.io.<a href="./org/biojava/utils/io/CountedBufferedReader.html" title="class in org.biojava.utils.io">CountedBufferedReader</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/io/CountedBufferedReader.html#read(char[])">read(char[])</a></span> - Method in class org.biojava.utils.io.<a href="./org/biojava/utils/io/CountedBufferedReader.html" title="class in org.biojava.utils.io">CountedBufferedReader</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/io/CountedBufferedReader.html#read(char[], int, int)">read(char[], int, int)</a></span> - Method in class org.biojava.utils.io.<a href="./org/biojava/utils/io/CountedBufferedReader.html" title="class in org.biojava.utils.io">CountedBufferedReader</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/io/RandomAccessReader.html#read()">read()</a></span> - Method in class org.biojava.utils.io.<a href="./org/biojava/utils/io/RandomAccessReader.html" title="class in org.biojava.utils.io">RandomAccessReader</a></dt>
<dd>
<div class="block"><code>read</code> reads one byte from the underlying
<code>RandomAccessFile</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/io/RandomAccessReader.html#read(char[], int, int)">read(char[], int, int)</a></span> - Method in class org.biojava.utils.io.<a href="./org/biojava/utils/io/RandomAccessReader.html" title="class in org.biojava.utils.io">RandomAccessReader</a></dt>
<dd>
<div class="block"><code>read</code> reads from the underlying
<code>RandomAccessFile</code> into an array.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/io/UncompressInputStream.html#read()">read()</a></span> - Method in class org.biojava.utils.io.<a href="./org/biojava/utils/io/UncompressInputStream.html" title="class in org.biojava.utils.io">UncompressInputStream</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/io/UncompressInputStream.html#read(byte[], int, int)">read(byte[], int, int)</a></span> - Method in class org.biojava.utils.io.<a href="./org/biojava/utils/io/UncompressInputStream.html" title="class in org.biojava.utils.io">UncompressInputStream</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/DebuggingRichSeqIOListener.html#read()">read()</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/DebuggingRichSeqIOListener.html" title="class in org.biojavax.bio.seq.io">DebuggingRichSeqIOListener</a></dt>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLFormat.html#readableFileNames">readableFileNames</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLFormat.html" title="class in org.biojavax.bio.seq.io">EMBLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/FastaFormat.html#readableFiles">readableFiles</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/FastaFormat.html" title="class in org.biojavax.bio.seq.io">FastaFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/GenbankFormat.html#readableFiles">readableFiles</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/GenbankFormat.html" title="class in org.biojavax.bio.seq.io">GenbankFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/blast2html/SimpleAlignmentStyler.html#readColourMap()">readColourMap()</a></span> - Method in class org.biojava.bio.program.blast2html.<a href="./org/biojava/bio/program/blast2html/SimpleAlignmentStyler.html" title="class in org.biojava.bio.program.blast2html">SimpleAlignmentStyler</a></dt>
<dd>
<div class="block">Read the the properties file that specifies the character/colour mapping.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/blast2html/SimpleAlignmentStyler.html#readColourMapFromProperties(java.lang.String)">readColourMapFromProperties(String)</a></span> - Method in class org.biojava.bio.program.blast2html.<a href="./org/biojava/bio/program/blast2html/SimpleAlignmentStyler.html" title="class in org.biojava.bio.program.blast2html">SimpleAlignmentStyler</a></dt>
<dd>
<div class="block">Setup styles from java property file.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/emblcd/EmblCDROMIndexReader.html#readDBDate()">readDBDate()</a></span> - Method in class org.biojava.bio.seq.db.emblcd.<a href="./org/biojava/bio/seq/db/emblcd/EmblCDROMIndexReader.html" title="class in org.biojava.bio.seq.db.emblcd">EmblCDROMIndexReader</a></dt>
<dd>
<div class="block"><code>readDBDate</code> reads the date from the index
header.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/emblcd/EmblCDROMIndexReader.html#readDBName()">readDBName()</a></span> - Method in class org.biojava.bio.seq.db.emblcd.<a href="./org/biojava/bio/seq/db/emblcd/EmblCDROMIndexReader.html" title="class in org.biojava.bio.seq.db.emblcd">EmblCDROMIndexReader</a></dt>
<dd>
<div class="block"><code>readDBName</code> returns the database name from the
index header.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/emblcd/EmblCDROMIndexReader.html#readDBRelease()">readDBRelease()</a></span> - Method in class org.biojava.bio.seq.db.emblcd.<a href="./org/biojava/bio/seq/db/emblcd/EmblCDROMIndexReader.html" title="class in org.biojava.bio.seq.db.emblcd">EmblCDROMIndexReader</a></dt>
<dd>
<div class="block"><code>readDBRelease</code> returns the database release from
the index header.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOTools.html#readEmbl(java.io.BufferedReader)">readEmbl(BufferedReader)</a></span> - Static method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOTools.html" title="class in org.biojava.bio.seq.io">SeqIOTools</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Iterate over the sequences in an EMBL-format stream.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.IOTools.html#readEMBL(java.io.BufferedReader, org.biojava.bio.seq.io.SymbolTokenization, org.biojavax.bio.seq.io.RichSequenceBuilderFactory, org.biojavax.Namespace)">readEMBL(BufferedReader, SymbolTokenization, RichSequenceBuilderFactory, Namespace)</a></span> - Static method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.IOTools.html" title="class in org.biojavax.bio.seq">RichSequence.IOTools</a></dt>
<dd>
<div class="block">Read a EMBL file using a custom type of SymbolList.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.IOTools.html#readEMBLDNA(java.io.BufferedReader, org.biojavax.Namespace)">readEMBLDNA(BufferedReader, Namespace)</a></span> - Static method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.IOTools.html" title="class in org.biojavax.bio.seq">RichSequence.IOTools</a></dt>
<dd>
<div class="block">Iterate over the sequences in an EMBL-format stream of DNA sequences.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOTools.html#readEmblNucleotide(java.io.BufferedReader)">readEmblNucleotide(BufferedReader)</a></span> - Static method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOTools.html" title="class in org.biojava.bio.seq.io">SeqIOTools</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Iterate over the sequences in an EMBL-format stream.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.IOTools.html#readEMBLProtein(java.io.BufferedReader, org.biojavax.Namespace)">readEMBLProtein(BufferedReader, Namespace)</a></span> - Static method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.IOTools.html" title="class in org.biojavax.bio.seq">RichSequence.IOTools</a></dt>
<dd>
<div class="block">Iterate over the sequences in an EMBL-format stream of Protein
sequences.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOTools.html#readEmblRNA(java.io.BufferedReader)">readEmblRNA(BufferedReader)</a></span> - Static method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOTools.html" title="class in org.biojava.bio.seq.io">SeqIOTools</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Iterate over the sequences in an EMBL-format stream, but for RNA.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.IOTools.html#readEMBLRNA(java.io.BufferedReader, org.biojavax.Namespace)">readEMBLRNA(BufferedReader, Namespace)</a></span> - Static method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.IOTools.html" title="class in org.biojavax.bio.seq">RichSequence.IOTools</a></dt>
<dd>
<div class="block">Iterate over the sequences in an EMBL-format stream of RNA sequences.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.IOTools.html#readEMBLxml(java.io.BufferedReader, org.biojava.bio.seq.io.SymbolTokenization, org.biojavax.bio.seq.io.RichSequenceBuilderFactory, org.biojavax.Namespace)">readEMBLxml(BufferedReader, SymbolTokenization, RichSequenceBuilderFactory, Namespace)</a></span> - Static method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.IOTools.html" title="class in org.biojavax.bio.seq">RichSequence.IOTools</a></dt>
<dd>
<div class="block">Read a EMBLxml file using a custom type of SymbolList.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.IOTools.html#readEMBLxmlDNA(java.io.BufferedReader, org.biojavax.Namespace)">readEMBLxmlDNA(BufferedReader, Namespace)</a></span> - Static method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.IOTools.html" title="class in org.biojavax.bio.seq">RichSequence.IOTools</a></dt>
<dd>
<div class="block">Iterate over the sequences in an EMBLxml-format stream of DNA
sequences.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.IOTools.html#readEMBLxmlProtein(java.io.BufferedReader, org.biojavax.Namespace)">readEMBLxmlProtein(BufferedReader, Namespace)</a></span> - Static method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.IOTools.html" title="class in org.biojavax.bio.seq">RichSequence.IOTools</a></dt>
<dd>
<div class="block">Iterate over the sequences in an EMBLxml-format stream of Protein
sequences.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.IOTools.html#readEMBLxmlRNA(java.io.BufferedReader, org.biojavax.Namespace)">readEMBLxmlRNA(BufferedReader, Namespace)</a></span> - Static method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.IOTools.html" title="class in org.biojavax.bio.seq">RichSequence.IOTools</a></dt>
<dd>
<div class="block">Iterate over the sequences in an EMBLxml-format stream of RNA
sequences.</div>
</dd>
<dt><a href="./org/biojava/utils/process/ReaderInputHandler.html" title="class in org.biojava.utils.process"><span class="strong">ReaderInputHandler</span></a> - Class in <a href="./org/biojava/utils/process/package-summary.html">org.biojava.utils.process</a></dt>
<dd>
<div class="block">Reader <a href="./org/biojava/utils/process/InputHandler.html" title="interface in org.biojava.utils.process">input handler</a>
that reads the input for an external process from a
<a href="./org/biojava/utils/process/ReaderWriterPipe.html#getReader()">reader</a>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/process/ReaderInputHandler.html#ReaderInputHandler(java.io.Reader, java.lang.String)">ReaderInputHandler(Reader, String)</a></span> - Constructor for class org.biojava.utils.process.<a href="./org/biojava/utils/process/ReaderInputHandler.html" title="class in org.biojava.utils.process">ReaderInputHandler</a></dt>
<dd>
<div class="block">Initializes the reader input handler.</div>
</dd>
<dt><a href="./org/biojava/utils/process/ReaderWriterPipe.html" title="class in org.biojava.utils.process"><span class="strong">ReaderWriterPipe</span></a> - Class in <a href="./org/biojava/utils/process/package-summary.html">org.biojava.utils.process</a></dt>
<dd>
<div class="block">A multi threaded class
which pipes the contents of an input reader to an output
writer.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/process/ReaderWriterPipe.html#ReaderWriterPipe(java.io.Reader, java.io.Writer, java.lang.String)">ReaderWriterPipe(Reader, Writer, String)</a></span> - Constructor for class org.biojava.utils.process.<a href="./org/biojava/utils/process/ReaderWriterPipe.html" title="class in org.biojava.utils.process">ReaderWriterPipe</a></dt>
<dd>
<div class="block">Initializes the reader writer pipe.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOTools.html#readFasta(java.io.BufferedReader, org.biojava.bio.seq.io.SymbolTokenization)">readFasta(BufferedReader, SymbolTokenization)</a></span> - Static method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOTools.html" title="class in org.biojava.bio.seq.io">SeqIOTools</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Read a fasta file.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOTools.html#readFasta(java.io.BufferedReader, org.biojava.bio.seq.io.SymbolTokenization, org.biojava.bio.seq.io.SequenceBuilderFactory)">readFasta(BufferedReader, SymbolTokenization, SequenceBuilderFactory)</a></span> - Static method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOTools.html" title="class in org.biojava.bio.seq.io">SeqIOTools</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Read a fasta file using a custom type of SymbolList.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOTools.html#readFasta(java.io.InputStream, org.biojava.bio.symbol.Alphabet)">readFasta(InputStream, Alphabet)</a></span> - Static method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOTools.html" title="class in org.biojava.bio.seq.io">SeqIOTools</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Create a sequence database from a fasta file provided as an
input stream.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.IOTools.html#readFasta(java.io.BufferedReader, org.biojava.bio.seq.io.SymbolTokenization, org.biojavax.Namespace)">readFasta(BufferedReader, SymbolTokenization, Namespace)</a></span> - Static method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.IOTools.html" title="class in org.biojavax.bio.seq">RichSequence.IOTools</a></dt>
<dd>
<div class="block">Read a fasta file.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.IOTools.html#readFasta(java.io.BufferedReader, org.biojava.bio.seq.io.SymbolTokenization, org.biojavax.bio.seq.io.RichSequenceBuilderFactory, org.biojavax.Namespace)">readFasta(BufferedReader, SymbolTokenization, RichSequenceBuilderFactory, Namespace)</a></span> - Static method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.IOTools.html" title="class in org.biojavax.bio.seq">RichSequence.IOTools</a></dt>
<dd>
<div class="block">Read a fasta file building a custom type of <code>RichSequence</code>
.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOTools.html#readFastaDNA(java.io.BufferedReader)">readFastaDNA(BufferedReader)</a></span> - Static method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOTools.html" title="class in org.biojava.bio.seq.io">SeqIOTools</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Iterate over the sequences in an FASTA-format stream of DNA sequences.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.IOTools.html#readFastaDNA(java.io.BufferedReader, org.biojavax.Namespace)">readFastaDNA(BufferedReader, Namespace)</a></span> - Static method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.IOTools.html" title="class in org.biojavax.bio.seq">RichSequence.IOTools</a></dt>
<dd>
<div class="block">Iterate over the sequences in an FASTA-format stream of DNA
sequences.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOTools.html#readFastaProtein(java.io.BufferedReader)">readFastaProtein(BufferedReader)</a></span> - Static method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOTools.html" title="class in org.biojava.bio.seq.io">SeqIOTools</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Iterate over the sequences in an FASTA-format stream of Protein sequences.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.IOTools.html#readFastaProtein(java.io.BufferedReader, org.biojavax.Namespace)">readFastaProtein(BufferedReader, Namespace)</a></span> - Static method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.IOTools.html" title="class in org.biojavax.bio.seq">RichSequence.IOTools</a></dt>
<dd>
<div class="block">Iterate over the sequences in an FASTA-format stream of Protein
sequences.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOTools.html#readFastaRNA(java.io.BufferedReader)">readFastaRNA(BufferedReader)</a></span> - Static method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOTools.html" title="class in org.biojava.bio.seq.io">SeqIOTools</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Iterate over the sequences in an FASTA-format stream of RNA sequences.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.IOTools.html#readFastaRNA(java.io.BufferedReader, org.biojavax.Namespace)">readFastaRNA(BufferedReader, Namespace)</a></span> - Static method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.IOTools.html" title="class in org.biojavax.bio.seq">RichSequence.IOTools</a></dt>
<dd>
<div class="block">Iterate over the sequences in an FASTA-format stream of RNA
sequences.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.IOTools.html#readFile(java.io.File, org.biojavax.bio.seq.io.RichSequenceBuilderFactory, org.biojavax.Namespace)">readFile(File, RichSequenceBuilderFactory, Namespace)</a></span> - Static method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.IOTools.html" title="class in org.biojavax.bio.seq">RichSequence.IOTools</a></dt>
<dd>
<div class="block">Guess which format a file is then attempt to read it.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.IOTools.html#readFile(java.io.File, org.biojavax.Namespace)">readFile(File, Namespace)</a></span> - Static method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.IOTools.html" title="class in org.biojavax.bio.seq">RichSequence.IOTools</a></dt>
<dd>
<div class="block">Guess which format a file is then attempt to read it.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/emblcd/EmblCDROMIndexReader.html#readFileLength()">readFileLength()</a></span> - Method in class org.biojava.bio.seq.db.emblcd.<a href="./org/biojava/bio/seq/db/emblcd/EmblCDROMIndexReader.html" title="class in org.biojava.bio.seq.db.emblcd">EmblCDROMIndexReader</a></dt>
<dd>
<div class="block"><code>readFileLength</code> returns the file length in bytes
(stored within the file's header by the indexing program).</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/DistributionTools.html#readFromXML(java.io.InputStream)">readFromXML(InputStream)</a></span> - Static method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/DistributionTools.html" title="class in org.biojava.bio.dist">DistributionTools</a></dt>
<dd>
<div class="block">Read a distribution from XML.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/CodonPrefTools.html#readFromXML(java.io.InputStream, java.lang.String)">readFromXML(InputStream, String)</a></span> - Static method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/CodonPrefTools.html" title="class in org.biojava.bio.symbol">CodonPrefTools</a></dt>
<dd>
<div class="block">reads a specified CodonPref from an file.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/CodonPrefTools.html#readFromXML(java.io.InputStream)">readFromXML(InputStream)</a></span> - Static method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/CodonPrefTools.html" title="class in org.biojava.bio.symbol">CodonPrefTools</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/CodonPrefTools.html#readFromXML(java.io.InputStream, org.biojava.bio.symbol.CodonPrefFilter)">readFromXML(InputStream, CodonPrefFilter)</a></span> - Static method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/CodonPrefTools.html" title="class in org.biojava.bio.symbol">CodonPrefTools</a></dt>
<dd>
<div class="block">read an CodonPref XML stream and handle it with a CodonPrefFilter object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOTools.html#readGenbank(java.io.BufferedReader)">readGenbank(BufferedReader)</a></span> - Static method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOTools.html" title="class in org.biojava.bio.seq.io">SeqIOTools</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Iterate over the sequences in an Genbank-format stream.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.IOTools.html#readGenbank(java.io.BufferedReader, org.biojava.bio.seq.io.SymbolTokenization, org.biojavax.bio.seq.io.RichSequenceBuilderFactory, org.biojavax.Namespace)">readGenbank(BufferedReader, SymbolTokenization, RichSequenceBuilderFactory, Namespace)</a></span> - Static method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.IOTools.html" title="class in org.biojavax.bio.seq">RichSequence.IOTools</a></dt>
<dd>
<div class="block">Read a GenBank file using a custom type of SymbolList.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.IOTools.html#readGenbankDNA(java.io.BufferedReader, org.biojavax.Namespace)">readGenbankDNA(BufferedReader, Namespace)</a></span> - Static method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.IOTools.html" title="class in org.biojavax.bio.seq">RichSequence.IOTools</a></dt>
<dd>
<div class="block">Iterate over the sequences in an GenBank-format stream of DNA
sequences.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.IOTools.html#readGenbankProtein(java.io.BufferedReader, org.biojavax.Namespace)">readGenbankProtein(BufferedReader, Namespace)</a></span> - Static method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.IOTools.html" title="class in org.biojavax.bio.seq">RichSequence.IOTools</a></dt>
<dd>
<div class="block">Iterate over the sequences in an GenBank-format stream of Protein
sequences.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.IOTools.html#readGenbankRNA(java.io.BufferedReader, org.biojavax.Namespace)">readGenbankRNA(BufferedReader, Namespace)</a></span> - Static method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.IOTools.html" title="class in org.biojavax.bio.seq">RichSequence.IOTools</a></dt>
<dd>
<div class="block">Iterate over the sequences in an GenBank-format stream of RNA
sequences.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOTools.html#readGenbankXml(java.io.BufferedReader)">readGenbankXml(BufferedReader)</a></span> - Static method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOTools.html" title="class in org.biojava.bio.seq.io">SeqIOTools</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Iterate over the sequences in an GenbankXML-format stream.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOTools.html#readGenpept(java.io.BufferedReader)">readGenpept(BufferedReader)</a></span> - Static method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOTools.html" title="class in org.biojava.bio.seq.io">SeqIOTools</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Iterate over the sequences in an Genpept-format stream.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFTools.html#readGFF(java.lang.String)">readGFF(String)</a></span> - Static method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFTools.html" title="class in org.biojava.bio.program.gff">GFFTools</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>use: readGff(File)</i></div>
</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFTools.html#readGFF(java.lang.String, org.biojava.bio.program.gff.GFFRecordFilter)">readGFF(String, GFFRecordFilter)</a></span> - Static method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFTools.html" title="class in org.biojava.bio.program.gff">GFFTools</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>use: readGff(File,GFFRecordFilter)</i></div>
</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFTools.html#readGFF(java.io.File)">readGFF(File)</a></span> - Static method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFTools.html" title="class in org.biojava.bio.program.gff">GFFTools</a></dt>
<dd>
<div class="block">Reads a <code>GFFEntrySet</code> from a file with no filtering.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFTools.html#readGFF(java.io.File, org.biojava.bio.program.gff.GFFRecordFilter)">readGFF(File, GFFRecordFilter)</a></span> - Static method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFTools.html" title="class in org.biojava.bio.program.gff">GFFTools</a></dt>
<dd>
<div class="block">Reads a GFFEntrySet from a file with the specified filter.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFTools.html#readGFF(java.io.BufferedReader)">readGFF(BufferedReader)</a></span> - Static method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFTools.html" title="class in org.biojava.bio.program.gff">GFFTools</a></dt>
<dd>
<div class="block">Read all GFF entries from a buffered reader.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFTools.html#readGFF(java.io.BufferedReader, org.biojava.bio.program.gff.GFFRecordFilter)">readGFF(BufferedReader, GFFRecordFilter)</a></span> - Static method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFTools.html" title="class in org.biojava.bio.program.gff">GFFTools</a></dt>
<dd>
<div class="block">Read all GFF entries matching a filter from a buffered reader.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.IOTools.html#readHashedFastaDNA(java.io.BufferedInputStream, org.biojavax.Namespace)">readHashedFastaDNA(BufferedInputStream, Namespace)</a></span> - Static method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.IOTools.html" title="class in org.biojavax.bio.seq">RichSequence.IOTools</a></dt>
<dd>
<div class="block">Iterate over the sequences in an FASTA-format stream of DNA
sequences.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FramedFeature.Template.html#readingFrame">readingFrame</a></span> - Variable in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FramedFeature.Template.html" title="class in org.biojava.bio.seq">FramedFeature.Template</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.IOTools.html#readINSDseq(java.io.BufferedReader, org.biojava.bio.seq.io.SymbolTokenization, org.biojavax.bio.seq.io.RichSequenceBuilderFactory, org.biojavax.Namespace)">readINSDseq(BufferedReader, SymbolTokenization, RichSequenceBuilderFactory, Namespace)</a></span> - Static method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.IOTools.html" title="class in org.biojavax.bio.seq">RichSequence.IOTools</a></dt>
<dd>
<div class="block">Read a INSDseq file using a custom type of SymbolList.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.IOTools.html#readINSDseqDNA(java.io.BufferedReader, org.biojavax.Namespace)">readINSDseqDNA(BufferedReader, Namespace)</a></span> - Static method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.IOTools.html" title="class in org.biojavax.bio.seq">RichSequence.IOTools</a></dt>
<dd>
<div class="block">Iterate over the sequences in an INSDseq-format stream of DNA
sequences.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.IOTools.html#readINSDseqProtein(java.io.BufferedReader, org.biojavax.Namespace)">readINSDseqProtein(BufferedReader, Namespace)</a></span> - Static method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.IOTools.html" title="class in org.biojavax.bio.seq">RichSequence.IOTools</a></dt>
<dd>
<div class="block">Iterate over the sequences in an INSDseq-format stream of Protein
sequences.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.IOTools.html#readINSDseqRNA(java.io.BufferedReader, org.biojavax.Namespace)">readINSDseqRNA(BufferedReader, Namespace)</a></span> - Static method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.IOTools.html" title="class in org.biojavax.bio.seq">RichSequence.IOTools</a></dt>
<dd>
<div class="block">Iterate over the sequences in an INSDseq-format stream of RNA
sequences.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/io/CountedBufferedReader.html#readLine()">readLine()</a></span> - Method in class org.biojava.utils.io.<a href="./org/biojava/utils/io/CountedBufferedReader.html" title="class in org.biojava.utils.io">CountedBufferedReader</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/XmlMarkovModel.html#readMatrix(org.w3c.dom.Element)">readMatrix(Element)</a></span> - Static method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/XmlMarkovModel.html" title="class in org.biojava.bio.dp">XmlMarkovModel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/XmlMarkovModel.html#readModel(org.w3c.dom.Element)">readModel(Element)</a></span> - Static method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/XmlMarkovModel.html" title="class in org.biojava.bio.dp">XmlMarkovModel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/tools/SVM_Light.html#readModelFile(java.lang.String)">readModelFile(String)</a></span> - Static method in class org.biojava.stats.svm.tools.<a href="./org/biojava/stats/svm/tools/SVM_Light.html" title="class in org.biojava.stats.svm.tools">SVM_Light</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/taxa/io/NCBITaxonomyLoader.html#readName(java.io.BufferedReader)">readName(BufferedReader)</a></span> - Method in interface org.biojavax.bio.taxa.io.<a href="./org/biojavax/bio/taxa/io/NCBITaxonomyLoader.html" title="interface in org.biojavax.bio.taxa.io">NCBITaxonomyLoader</a></dt>
<dd>
<div class="block">Reads the next entry from the names.dmp file and returns the corresponding
NCBITaxon object with the name added in already.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/taxa/io/SimpleNCBITaxonomyLoader.html#readName(java.io.BufferedReader)">readName(BufferedReader)</a></span> - Method in class org.biojavax.bio.taxa.io.<a href="./org/biojavax/bio/taxa/io/SimpleNCBITaxonomyLoader.html" title="class in org.biojavax.bio.taxa.io">SimpleNCBITaxonomyLoader</a></dt>
<dd>
<div class="block">Reads the next entry from the names.dmp file and returns the corresponding
NCBITaxon object with the name added in already.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/taxa/io/NCBITaxonomyLoader.html#readNode(java.io.BufferedReader)">readNode(BufferedReader)</a></span> - Method in interface org.biojavax.bio.taxa.io.<a href="./org/biojavax/bio/taxa/io/NCBITaxonomyLoader.html" title="interface in org.biojavax.bio.taxa.io">NCBITaxonomyLoader</a></dt>
<dd>
<div class="block">Reads the next entry from the nodes.dmp file and returns the corresponding
NCBITaxon object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/taxa/io/SimpleNCBITaxonomyLoader.html#readNode(java.io.BufferedReader)">readNode(BufferedReader)</a></span> - Method in class org.biojavax.bio.taxa.io.<a href="./org/biojavax/bio/taxa/io/SimpleNCBITaxonomyLoader.html" title="class in org.biojavax.bio.taxa.io">SimpleNCBITaxonomyLoader</a></dt>
<dd>
<div class="block">Reads the next entry from the nodes.dmp file and returns the corresponding
NCBITaxon object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/phred/PhredTools.html#readPhredQuality(java.io.BufferedReader)">readPhredQuality(BufferedReader)</a></span> - Static method in class org.biojava.bio.program.phred.<a href="./org/biojava/bio/program/phred/PhredTools.html" title="class in org.biojava.bio.program.phred">PhredTools</a></dt>
<dd>
<div class="block">Constructs a StreamReader to read in Phred quality data in FASTA format.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/phred/PhredTools.html#readPhredSequence(java.io.BufferedReader)">readPhredSequence(BufferedReader)</a></span> - Static method in class org.biojava.bio.program.phred.<a href="./org/biojava/bio/program/phred/PhredTools.html" title="class in org.biojava.bio.program.phred">PhredTools</a></dt>
<dd>
<div class="block">Calls SeqIOTools.readFastaDNA(br), added here for convinience.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/obo/OboFileParser.html#readQuotedString(java.lang.String, int, int, char, boolean, boolean)">readQuotedString(String, int, int, char, boolean, boolean)</a></span> - Method in class org.biojava.ontology.obo.<a href="./org/biojava/ontology/obo/OboFileParser.html" title="class in org.biojava.ontology.obo">OboFileParser</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/emblcd/EmblCDROMIndexReader.html#readRawRecord()">readRawRecord()</a></span> - Method in class org.biojava.bio.seq.db.emblcd.<a href="./org/biojava/bio/seq/db/emblcd/EmblCDROMIndexReader.html" title="class in org.biojava.bio.seq.db.emblcd">EmblCDROMIndexReader</a></dt>
<dd>
<div class="block"><code>readRawRecord</code> returns the raw bytes of a single
record from the index.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/emblcd/AcnumHitReader.html#readRecord()">readRecord()</a></span> - Method in class org.biojava.bio.seq.db.emblcd.<a href="./org/biojava/bio/seq/db/emblcd/AcnumHitReader.html" title="class in org.biojava.bio.seq.db.emblcd">AcnumHitReader</a></dt>
<dd>
<div class="block"><code>readRecord</code> creates an array of Objects from the
raw byte array of a single record.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/emblcd/AcnumTrgReader.html#readRecord()">readRecord()</a></span> - Method in class org.biojava.bio.seq.db.emblcd.<a href="./org/biojava/bio/seq/db/emblcd/AcnumTrgReader.html" title="class in org.biojava.bio.seq.db.emblcd">AcnumTrgReader</a></dt>
<dd>
<div class="block"><code>readRecord</code> creates an array of Objects from the
raw byte array of a single record.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/emblcd/DivisionLkpReader.html#readRecord()">readRecord()</a></span> - Method in class org.biojava.bio.seq.db.emblcd.<a href="./org/biojava/bio/seq/db/emblcd/DivisionLkpReader.html" title="class in org.biojava.bio.seq.db.emblcd">DivisionLkpReader</a></dt>
<dd>
<div class="block"><code>readRecord</code> creates an array of Objects from the
raw byte array of a single record.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/emblcd/EmblCDROMIndexReader.html#readRecord()">readRecord()</a></span> - Method in class org.biojava.bio.seq.db.emblcd.<a href="./org/biojava/bio/seq/db/emblcd/EmblCDROMIndexReader.html" title="class in org.biojava.bio.seq.db.emblcd">EmblCDROMIndexReader</a></dt>
<dd>
<div class="block"><code>readRecord</code> returns an array of objects parsed from
a single record.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/emblcd/EmblCDROMRandomAccess.html#readRecord()">readRecord()</a></span> - Method in class org.biojava.bio.seq.db.emblcd.<a href="./org/biojava/bio/seq/db/emblcd/EmblCDROMRandomAccess.html" title="class in org.biojava.bio.seq.db.emblcd">EmblCDROMRandomAccess</a></dt>
<dd>
<div class="block"><code>readRecord</code> returns an array of objects parsed from
a single record.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/emblcd/EntryNamIdxReader.html#readRecord()">readRecord()</a></span> - Method in class org.biojava.bio.seq.db.emblcd.<a href="./org/biojava/bio/seq/db/emblcd/EntryNamIdxReader.html" title="class in org.biojava.bio.seq.db.emblcd">EntryNamIdxReader</a></dt>
<dd>
<div class="block"><code>readRecord</code> creates an array of Objects from the
raw byte array of a single record.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/emblcd/EntryNamRandomAccess.html#readRecord()">readRecord()</a></span> - Method in class org.biojava.bio.seq.db.emblcd.<a href="./org/biojava/bio/seq/db/emblcd/EntryNamRandomAccess.html" title="class in org.biojava.bio.seq.db.emblcd">EntryNamRandomAccess</a></dt>
<dd>
<div class="block"><code>readRecord</code> creates an array of Objects from the
raw byte array of a single record.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/emblcd/EmblCDROMIndexReader.html#readRecordCount()">readRecordCount()</a></span> - Method in class org.biojava.bio.seq.db.emblcd.<a href="./org/biojava/bio/seq/db/emblcd/EmblCDROMIndexReader.html" title="class in org.biojava.bio.seq.db.emblcd">EmblCDROMIndexReader</a></dt>
<dd>
<div class="block"><code>readRecordCount</code> returns the number of records in
the file.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/emblcd/EmblCDROMIndexReader.html#readRecordLength()">readRecordLength()</a></span> - Method in class org.biojava.bio.seq.db.emblcd.<a href="./org/biojava/bio/seq/db/emblcd/EmblCDROMIndexReader.html" title="class in org.biojava.bio.seq.db.emblcd">EmblCDROMIndexReader</a></dt>
<dd>
<div class="block"><code>readRecordLength</code> returns the record length
(bytes).</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/Protease.html#readResolve()">readResolve()</a></span> - Method in class org.biojava.bio.proteomics.<a href="./org/biojava/bio/proteomics/Protease.html" title="class in org.biojava.bio.proteomics">Protease</a></dt>
<dd>
<div class="block">Prevent duplication of the object during Serialization</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AbstractAlphabet.html#readResolve()">readResolve()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AbstractAlphabet.html" title="class in org.biojava.bio.symbol">AbstractAlphabet</a></dt>
<dd>
<div class="block">To prevent duplication of a what should be a
single instance of an existing alphabet.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/DoubleAlphabet.SubDoubleAlphabet.html#readResolve()">readResolve()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/DoubleAlphabet.SubDoubleAlphabet.html" title="class in org.biojava.bio.symbol">DoubleAlphabet.SubDoubleAlphabet</a></dt>
<dd>
<div class="block">To prevent duplication of a what should be a
single instance of an existing alphabet.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/StaticMemberPlaceHolder.html#readResolve()">readResolve()</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/StaticMemberPlaceHolder.html" title="class in org.biojava.utils">StaticMemberPlaceHolder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLFormat.html#readRichSequence(java.io.BufferedReader, org.biojava.bio.seq.io.SymbolTokenization, org.biojavax.bio.seq.io.RichSeqIOListener, org.biojavax.Namespace)">readRichSequence(BufferedReader, SymbolTokenization, RichSeqIOListener, Namespace)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLFormat.html" title="class in org.biojavax.bio.seq.io">EMBLFormat</a></dt>
<dd>
<div class="block">Reads a sequence from the given buffered reader using the given tokenizer to parse
sequence symbols.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html#readRichSequence(java.io.BufferedReader, org.biojava.bio.seq.io.SymbolTokenization, org.biojavax.bio.seq.io.RichSeqIOListener, org.biojavax.Namespace)">readRichSequence(BufferedReader, SymbolTokenization, RichSeqIOListener, Namespace)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html" title="class in org.biojavax.bio.seq.io">EMBLxmlFormat</a></dt>
<dd>
<div class="block">Reads a sequence from the given buffered reader using the given tokenizer to parse
sequence symbols.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/FastaFormat.html#readRichSequence(java.io.BufferedReader, org.biojava.bio.seq.io.SymbolTokenization, org.biojavax.bio.seq.io.RichSeqIOListener, org.biojavax.Namespace)">readRichSequence(BufferedReader, SymbolTokenization, RichSeqIOListener, Namespace)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/FastaFormat.html" title="class in org.biojavax.bio.seq.io">FastaFormat</a></dt>
<dd>
<div class="block">Reads a sequence from the given buffered reader using the given tokenizer to parse
sequence symbols.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/GenbankFormat.html#readRichSequence(java.io.BufferedReader, org.biojava.bio.seq.io.SymbolTokenization, org.biojavax.bio.seq.io.RichSeqIOListener, org.biojavax.Namespace)">readRichSequence(BufferedReader, SymbolTokenization, RichSeqIOListener, Namespace)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/GenbankFormat.html" title="class in org.biojavax.bio.seq.io">GenbankFormat</a></dt>
<dd>
<div class="block">Reads a sequence from the given buffered reader using the given tokenizer to parse
sequence symbols.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/INSDseqFormat.html#readRichSequence(java.io.BufferedReader, org.biojava.bio.seq.io.SymbolTokenization, org.biojavax.bio.seq.io.RichSeqIOListener, org.biojavax.Namespace)">readRichSequence(BufferedReader, SymbolTokenization, RichSeqIOListener, Namespace)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/INSDseqFormat.html" title="class in org.biojavax.bio.seq.io">INSDseqFormat</a></dt>
<dd>
<div class="block">Reads a sequence from the given buffered reader using the given tokenizer to parse
sequence symbols.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/RichSequenceFormat.html#readRichSequence(java.io.BufferedReader, org.biojava.bio.seq.io.SymbolTokenization, org.biojavax.bio.seq.io.RichSeqIOListener, org.biojavax.Namespace)">readRichSequence(BufferedReader, SymbolTokenization, RichSeqIOListener, Namespace)</a></span> - Method in interface org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/RichSequenceFormat.html" title="interface in org.biojavax.bio.seq.io">RichSequenceFormat</a></dt>
<dd>
<div class="block">Reads a sequence from the given buffered reader using the given tokenizer to parse
sequence symbols.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtFormat.html#readRichSequence(java.io.BufferedReader, org.biojava.bio.seq.io.SymbolTokenization, org.biojavax.bio.seq.io.RichSeqIOListener, org.biojavax.Namespace)">readRichSequence(BufferedReader, SymbolTokenization, RichSeqIOListener, Namespace)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtFormat.html" title="class in org.biojavax.bio.seq.io">UniProtFormat</a></dt>
<dd>
<div class="block">Reads a sequence from the given buffered reader using the given tokenizer to parse
sequence symbols.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#readRichSequence(java.io.BufferedReader, org.biojava.bio.seq.io.SymbolTokenization, org.biojavax.bio.seq.io.RichSeqIOListener, org.biojavax.Namespace)">readRichSequence(BufferedReader, SymbolTokenization, RichSeqIOListener, Namespace)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd>
<div class="block">Reads a sequence from the given buffered reader using the given tokenizer to parse
sequence symbols.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/phred/PhredFormat.html#readSequence(java.io.BufferedReader, org.biojava.bio.seq.io.SymbolTokenization, org.biojava.bio.seq.io.SeqIOListener)">readSequence(BufferedReader, SymbolTokenization, SeqIOListener)</a></span> - Method in class org.biojava.bio.program.phred.<a href="./org/biojava/bio/program/phred/PhredFormat.html" title="class in org.biojava.bio.program.phred">PhredFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/EmblLikeFormat.html#readSequence(java.io.BufferedReader, org.biojava.bio.seq.io.SymbolTokenization, org.biojava.bio.seq.io.SeqIOListener)">readSequence(BufferedReader, SymbolTokenization, SeqIOListener)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/EmblLikeFormat.html" title="class in org.biojava.bio.seq.io">EmblLikeFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/FastaFormat.html#readSequence(java.io.BufferedReader, org.biojava.bio.seq.io.SymbolTokenization, org.biojava.bio.seq.io.SeqIOListener)">readSequence(BufferedReader, SymbolTokenization, SeqIOListener)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/FastaFormat.html" title="class in org.biojava.bio.seq.io">FastaFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Reads information from a flatfile to a <code>SeqIOListener</code>
using a <code>SymbolTokenizer</code> to convert sequence strings
to <code>Symbol</code> objects.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/GAMEFormat.html#readSequence(java.io.BufferedReader, org.biojava.bio.seq.io.SymbolTokenization, org.biojava.bio.seq.io.SeqIOListener)">readSequence(BufferedReader, SymbolTokenization, SeqIOListener)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/GAMEFormat.html" title="class in org.biojava.bio.seq.io">GAMEFormat</a></dt>
<dd>
<div class="block">this version only reads annotations (no symbols)</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/GenbankFormat.html#readSequence(java.io.BufferedReader, org.biojava.bio.seq.io.SymbolTokenization, org.biojava.bio.seq.io.SeqIOListener)">readSequence(BufferedReader, SymbolTokenization, SeqIOListener)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/GenbankFormat.html" title="class in org.biojava.bio.seq.io">GenbankFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Reads a sequence from the specified reader using the Symbol
parser and Sequence Factory provided.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/GenbankXmlFormat.html#readSequence(java.io.BufferedReader, org.biojava.bio.seq.io.SymbolTokenization, org.biojava.bio.seq.io.SeqIOListener)">readSequence(BufferedReader, SymbolTokenization, SeqIOListener)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/GenbankXmlFormat.html" title="class in org.biojava.bio.seq.io">GenbankXmlFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SequenceFormat.html#readSequence(java.io.BufferedReader, org.biojava.bio.seq.io.SymbolTokenization, org.biojava.bio.seq.io.SeqIOListener)">readSequence(BufferedReader, SymbolTokenization, SeqIOListener)</a></span> - Method in interface org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SequenceFormat.html" title="interface in org.biojava.bio.seq.io">SequenceFormat</a></dt>
<dd>
<div class="block">Read a sequence and pass data on to a SeqIOListener.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLFormat.html#readSequence(java.io.BufferedReader, org.biojava.bio.seq.io.SymbolTokenization, org.biojava.bio.seq.io.SeqIOListener)">readSequence(BufferedReader, SymbolTokenization, SeqIOListener)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLFormat.html" title="class in org.biojavax.bio.seq.io">EMBLFormat</a></dt>
<dd>
<div class="block">Read a sequence and pass data on to a SeqIOListener.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html#readSequence(java.io.BufferedReader, org.biojava.bio.seq.io.SymbolTokenization, org.biojava.bio.seq.io.SeqIOListener)">readSequence(BufferedReader, SymbolTokenization, SeqIOListener)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html" title="class in org.biojavax.bio.seq.io">EMBLxmlFormat</a></dt>
<dd>
<div class="block">Read a sequence and pass data on to a SeqIOListener.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/FastaFormat.html#readSequence(java.io.BufferedReader, org.biojava.bio.seq.io.SymbolTokenization, org.biojava.bio.seq.io.SeqIOListener)">readSequence(BufferedReader, SymbolTokenization, SeqIOListener)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/FastaFormat.html" title="class in org.biojavax.bio.seq.io">FastaFormat</a></dt>
<dd>
<div class="block">Read a sequence and pass data on to a SeqIOListener.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/GenbankFormat.html#readSequence(java.io.BufferedReader, org.biojava.bio.seq.io.SymbolTokenization, org.biojava.bio.seq.io.SeqIOListener)">readSequence(BufferedReader, SymbolTokenization, SeqIOListener)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/GenbankFormat.html" title="class in org.biojavax.bio.seq.io">GenbankFormat</a></dt>
<dd>
<div class="block">Read a sequence and pass data on to a SeqIOListener.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/INSDseqFormat.html#readSequence(java.io.BufferedReader, org.biojava.bio.seq.io.SymbolTokenization, org.biojava.bio.seq.io.SeqIOListener)">readSequence(BufferedReader, SymbolTokenization, SeqIOListener)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/INSDseqFormat.html" title="class in org.biojavax.bio.seq.io">INSDseqFormat</a></dt>
<dd>
<div class="block">Read a sequence and pass data on to a SeqIOListener.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtFormat.html#readSequence(java.io.BufferedReader, org.biojava.bio.seq.io.SymbolTokenization, org.biojava.bio.seq.io.SeqIOListener)">readSequence(BufferedReader, SymbolTokenization, SeqIOListener)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtFormat.html" title="class in org.biojavax.bio.seq.io">UniProtFormat</a></dt>
<dd>
<div class="block">Read a sequence and pass data on to a SeqIOListener.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#readSequence(java.io.BufferedReader, org.biojava.bio.seq.io.SymbolTokenization, org.biojava.bio.seq.io.SeqIOListener)">readSequence(BufferedReader, SymbolTokenization, SeqIOListener)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd>
<div class="block">Read a sequence and pass data on to a SeqIOListener.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.IOTools.html#readStream(java.io.BufferedInputStream, org.biojavax.bio.seq.io.RichSequenceBuilderFactory, org.biojavax.Namespace)">readStream(BufferedInputStream, RichSequenceBuilderFactory, Namespace)</a></span> - Static method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.IOTools.html" title="class in org.biojavax.bio.seq">RichSequence.IOTools</a></dt>
<dd>
<div class="block">Guess which format a stream is then attempt to read it.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.IOTools.html#readStream(java.io.BufferedInputStream, org.biojavax.Namespace)">readStream(BufferedInputStream, Namespace)</a></span> - Static method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.IOTools.html" title="class in org.biojavax.bio.seq">RichSequence.IOTools</a></dt>
<dd>
<div class="block">Guess which format a stream is then attempt to read it.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOTools.html#readSwissprot(java.io.BufferedReader)">readSwissprot(BufferedReader)</a></span> - Static method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOTools.html" title="class in org.biojava.bio.seq.io">SeqIOTools</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Iterate over the sequences in an Swissprot-format stream.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SymbolReader.html#readSymbol()">readSymbol()</a></span> - Method in interface org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SymbolReader.html" title="interface in org.biojava.bio.seq.io">SymbolReader</a></dt>
<dd>
<div class="block">Return a single symbol from the stream.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SymbolReader.html#readSymbols(org.biojava.bio.symbol.Symbol[], int, int)">readSymbols(Symbol[], int, int)</a></span> - Method in interface org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SymbolReader.html" title="interface in org.biojava.bio.seq.io">SymbolReader</a></dt>
<dd>
<div class="block">Read one or more symbols from the stream.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.IOTools.html#readUniProt(java.io.BufferedReader, org.biojava.bio.seq.io.SymbolTokenization, org.biojavax.bio.seq.io.RichSequenceBuilderFactory, org.biojavax.Namespace)">readUniProt(BufferedReader, SymbolTokenization, RichSequenceBuilderFactory, Namespace)</a></span> - Static method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.IOTools.html" title="class in org.biojavax.bio.seq">RichSequence.IOTools</a></dt>
<dd>
<div class="block">Read a UniProt file using a custom type of SymbolList.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.IOTools.html#readUniProt(java.io.BufferedReader, org.biojavax.Namespace)">readUniProt(BufferedReader, Namespace)</a></span> - Static method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.IOTools.html" title="class in org.biojavax.bio.seq">RichSequence.IOTools</a></dt>
<dd>
<div class="block">Iterate over the sequences in an UniProt-format stream of RNA
sequences.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.IOTools.html#readUniProtXML(java.io.BufferedReader, org.biojava.bio.seq.io.SymbolTokenization, org.biojavax.bio.seq.io.RichSequenceBuilderFactory, org.biojavax.Namespace)">readUniProtXML(BufferedReader, SymbolTokenization, RichSequenceBuilderFactory, Namespace)</a></span> - Static method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.IOTools.html" title="class in org.biojavax.bio.seq">RichSequence.IOTools</a></dt>
<dd>
<div class="block">Read a UniProt XML file using a custom type of SymbolList.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.IOTools.html#readUniProtXML(java.io.BufferedReader, org.biojavax.Namespace)">readUniProtXML(BufferedReader, Namespace)</a></span> - Static method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.IOTools.html" title="class in org.biojavax.bio.seq">RichSequence.IOTools</a></dt>
<dd>
<div class="block">Iterate over the sequences in an UniProt XML-format stream of RNA
sequences.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/xff/XFFTools.html#readXFF(java.io.File, java.lang.String, org.biojava.bio.symbol.FiniteAlphabet)">readXFF(File, String, FiniteAlphabet)</a></span> - Static method in class org.biojava.bio.program.xff.<a href="./org/biojava/bio/program/xff/XFFTools.html" title="class in org.biojava.bio.program.xff">XFFTools</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/xff/XFFTools.html#readXFF(java.io.File, java.lang.String)">readXFF(File, String)</a></span> - Static method in class org.biojava.bio.program.xff.<a href="./org/biojava/bio/program/xff/XFFTools.html" title="class in org.biojava.bio.program.xff">XFFTools</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/utils/XMLTools.html#readXMLChunk(java.io.BufferedReader, org.xml.sax.helpers.DefaultHandler, java.lang.String)">readXMLChunk(BufferedReader, DefaultHandler, String)</a></span> - Static method in class org.biojavax.utils.<a href="./org/biojavax/utils/XMLTools.html" title="class in org.biojavax.utils">XMLTools</a></dt>
<dd>
<div class="block">Attempts to read XML file in chunks, passing each chunk to a SAX parser.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/io/CountedBufferedReader.html#ready()">ready()</a></span> - Method in class org.biojava.utils.io.<a href="./org/biojava/utils/io/CountedBufferedReader.html" title="class in org.biojava.utils.io">CountedBufferedReader</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/DASSequence.html#realizeFeature(org.biojava.bio.seq.FeatureHolder, org.biojava.bio.seq.Feature.Template)">realizeFeature(FeatureHolder, Feature.Template)</a></span> - Method in class org.biojava.bio.program.das.<a href="./org/biojava/bio/program/das/DASSequence.html" title="class in org.biojava.bio.program.das">DASSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureRealizer.html#realizeFeature(org.biojava.bio.seq.Sequence, org.biojava.bio.seq.FeatureHolder, org.biojava.bio.seq.Feature.Template)">realizeFeature(Sequence, FeatureHolder, Feature.Template)</a></span> - Method in interface org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureRealizer.html" title="interface in org.biojava.bio.seq">FeatureRealizer</a></dt>
<dd>
<div class="block">Install a feature on the specified sequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleFeature.html#realizeFeature(org.biojava.bio.seq.FeatureHolder, org.biojava.bio.seq.Feature.Template)">realizeFeature(FeatureHolder, Feature.Template)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleFeature.html" title="class in org.biojava.bio.seq.impl">SimpleFeature</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleSequence.html#realizeFeature(org.biojava.bio.seq.FeatureHolder, org.biojava.bio.seq.Feature.Template)">realizeFeature(FeatureHolder, Feature.Template)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleSequence.html" title="class in org.biojava.bio.seq.impl">SimpleSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/ViewSequence.html#realizeFeature(org.biojava.bio.seq.FeatureHolder, org.biojava.bio.seq.Feature.Template)">realizeFeature(FeatureHolder, Feature.Template)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/ViewSequence.html" title="class in org.biojava.bio.seq.impl">ViewSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/NewSimpleAssembly.html#realizeFeature(org.biojava.bio.seq.FeatureHolder, org.biojava.bio.seq.Feature.Template)">realizeFeature(FeatureHolder, Feature.Template)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/NewSimpleAssembly.html" title="class in org.biojava.bio.seq">NewSimpleAssembly</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/RealizingFeatureHolder.html#realizeFeature(org.biojava.bio.seq.FeatureHolder, org.biojava.bio.seq.Feature.Template)">realizeFeature(FeatureHolder, Feature.Template)</a></span> - Method in interface org.biojava.bio.seq.<a href="./org/biojava/bio/seq/RealizingFeatureHolder.html" title="interface in org.biojava.bio.seq">RealizingFeatureHolder</a></dt>
<dd>
<div class="block">Realize a feature template.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/SimpleAssembly.html#realizeFeature(org.biojava.bio.seq.FeatureHolder, org.biojava.bio.seq.Feature.Template)">realizeFeature(FeatureHolder, Feature.Template)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/SimpleAssembly.html" title="class in org.biojava.bio.seq">SimpleAssembly</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/SimpleFeatureRealizer.html#realizeFeature(org.biojava.bio.seq.Sequence, org.biojava.bio.seq.FeatureHolder, org.biojava.bio.seq.Feature.Template)">realizeFeature(Sequence, FeatureHolder, Feature.Template)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/SimpleFeatureRealizer.html" title="class in org.biojava.bio.seq">SimpleFeatureRealizer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/StAXFeatureHandler.html#realizeSubFeatures(org.biojava.bio.seq.Feature)">realizeSubFeatures(Feature)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/StAXFeatureHandler.html" title="class in org.biojava.bio.seq.io.agave">StAXFeatureHandler</a></dt>
<dd>
<div class="block">recursively attach children features to parent</div>
</dd>
<dt><a href="./org/biojava/bio/seq/RealizingFeatureHolder.html" title="interface in org.biojava.bio.seq"><span class="strong">RealizingFeatureHolder</span></a> - Interface in <a href="./org/biojava/bio/seq/package-summary.html">org.biojava.bio.seq</a></dt>
<dd>
<div class="block">Interface for <code>FeatureHolder</code> objects which know how to
instantiate new child Features.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/ChangeSupport.html#reapGarbageListeners()">reapGarbageListeners()</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/ChangeSupport.html" title="class in org.biojava.utils">ChangeSupport</a></dt>
<dd>
<div class="block">Remove all references to listeners which have been cleared by the
garbage collector.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/molbio/RestrictionEnzymeManager.html#REBASE_DATA_KEY">REBASE_DATA_KEY</a></span> - Static variable in class org.biojava.bio.molbio.<a href="./org/biojava/bio/molbio/RestrictionEnzymeManager.html" title="class in org.biojava.bio.molbio">RestrictionEnzymeManager</a></dt>
<dd>
<div class="block"><code>REBASE_DATA_KEY</code> the ResourceBundle key which
specifies the location of the REBASE flat file.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/molbio/RestrictionEnzymeManager.html#REBASE_TAG_COMM">REBASE_TAG_COMM</a></span> - Static variable in class org.biojava.bio.molbio.<a href="./org/biojava/bio/molbio/RestrictionEnzymeManager.html" title="class in org.biojava.bio.molbio">RestrictionEnzymeManager</a></dt>
<dd>
<div class="block"><code>REBASE_TAG_COMM</code> the REBASE tag containing the
commercial suppliers.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/molbio/RestrictionEnzymeManager.html#REBASE_TAG_ISZR">REBASE_TAG_ISZR</a></span> - Static variable in class org.biojava.bio.molbio.<a href="./org/biojava/bio/molbio/RestrictionEnzymeManager.html" title="class in org.biojava.bio.molbio">RestrictionEnzymeManager</a></dt>
<dd>
<div class="block"><code>REBASE_TAG_ISZR</code> the REBASE tag containing the
enzyme isoschizomers.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/molbio/RestrictionEnzymeManager.html#REBASE_TAG_METH">REBASE_TAG_METH</a></span> - Static variable in class org.biojava.bio.molbio.<a href="./org/biojava/bio/molbio/RestrictionEnzymeManager.html" title="class in org.biojava.bio.molbio">RestrictionEnzymeManager</a></dt>
<dd>
<div class="block"><code>REBASE_TAG_METH</code> the REBASE tag containing the
methylation site.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/molbio/RestrictionEnzymeManager.html#REBASE_TAG_NAME">REBASE_TAG_NAME</a></span> - Static variable in class org.biojava.bio.molbio.<a href="./org/biojava/bio/molbio/RestrictionEnzymeManager.html" title="class in org.biojava.bio.molbio">RestrictionEnzymeManager</a></dt>
<dd>
<div class="block"><code>REBASE_TAG_NAME</code> the REBASE tag containing the
enzyme name.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/molbio/RestrictionEnzymeManager.html#REBASE_TAG_ORGN">REBASE_TAG_ORGN</a></span> - Static variable in class org.biojava.bio.molbio.<a href="./org/biojava/bio/molbio/RestrictionEnzymeManager.html" title="class in org.biojava.bio.molbio">RestrictionEnzymeManager</a></dt>
<dd>
<div class="block"><code>REBASE_TAG_ORGN</code> the REBASE tag containing the
organism.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/molbio/RestrictionEnzymeManager.html#REBASE_TAG_REFS">REBASE_TAG_REFS</a></span> - Static variable in class org.biojava.bio.molbio.<a href="./org/biojava/bio/molbio/RestrictionEnzymeManager.html" title="class in org.biojava.bio.molbio">RestrictionEnzymeManager</a></dt>
<dd>
<div class="block"><code>REBASE_TAG_REFS</code> the REBASE tag containing the
references.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/molbio/RestrictionEnzymeManager.html#REBASE_TAG_SITE">REBASE_TAG_SITE</a></span> - Static variable in class org.biojava.bio.molbio.<a href="./org/biojava/bio/molbio/RestrictionEnzymeManager.html" title="class in org.biojava.bio.molbio">RestrictionEnzymeManager</a></dt>
<dd>
<div class="block"><code>REBASE_TAG_SITE</code> the REBASE tag containing the
enzyme site.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/molbio/RestrictionEnzymeManager.html#REBASE_TAG_SRCE">REBASE_TAG_SRCE</a></span> - Static variable in class org.biojava.bio.molbio.<a href="./org/biojava/bio/molbio/RestrictionEnzymeManager.html" title="class in org.biojava.bio.molbio">RestrictionEnzymeManager</a></dt>
<dd>
<div class="block"><code>REBASE_TAG_SRCE</code> the REBASE tag containing the
source.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/naming/ObdaContext.html#rebind(javax.naming.Name, java.lang.Object)">rebind(Name, Object)</a></span> - Method in class org.biojava.naming.<a href="./org/biojava/naming/ObdaContext.html" title="class in org.biojava.naming">ObdaContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/naming/ObdaContext.html#rebind(javax.naming.Name, java.lang.Object, javax.naming.directory.Attributes)">rebind(Name, Object, Attributes)</a></span> - Method in class org.biojava.naming.<a href="./org/biojava/naming/ObdaContext.html" title="class in org.biojava.naming">ObdaContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/naming/ObdaContext.html#rebind(java.lang.String, java.lang.Object)">rebind(String, Object)</a></span> - Method in class org.biojava.naming.<a href="./org/biojava/naming/ObdaContext.html" title="class in org.biojava.naming">ObdaContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/naming/ObdaContext.html#rebind(java.lang.String, java.lang.Object, javax.naming.directory.Attributes)">rebind(String, Object, Attributes)</a></span> - Method in class org.biojava.naming.<a href="./org/biojava/naming/ObdaContext.html" title="class in org.biojava.naming">ObdaContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/emblcd/EmblCDROMRandomAccess.html#recBytes">recBytes</a></span> - Variable in class org.biojava.bio.seq.db.emblcd.<a href="./org/biojava/bio/seq/db/emblcd/EmblCDROMRandomAccess.html" title="class in org.biojava.bio.seq.db.emblcd">EmblCDROMRandomAccess</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/phylo/io/phylip/PHYLIPFileBuilder.html#receiveSequence(java.lang.String)">receiveSequence(String)</a></span> - Method in class org.biojavax.bio.phylo.io.phylip.<a href="./org/biojavax/bio/phylo/io/phylip/PHYLIPFileBuilder.html" title="class in org.biojavax.bio.phylo.io.phylip">PHYLIPFileBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/phylo/io/phylip/PHYLIPFileListener.html#receiveSequence(java.lang.String)">receiveSequence(String)</a></span> - Method in interface org.biojavax.bio.phylo.io.phylip.<a href="./org/biojavax/bio/phylo/io/phylip/PHYLIPFileListener.html" title="interface in org.biojavax.bio.phylo.io.phylip">PHYLIPFileListener</a></dt>
<dd>
<div class="block">Receive sequence data for the current sequence.</div>
</dd>
<dt><a href="./org/biojava/bio/program/indexdb/Record.html" title="interface in org.biojava.bio.program.indexdb"><span class="strong">Record</span></a> - Interface in <a href="./org/biojava/bio/program/indexdb/package-summary.html">org.biojava.bio.program.indexdb</a></dt>
<dd>
<div class="block"><code>Record</code> represents a record within an indexed flat file
databank as defined by the OBDA standard.</div>
</dd>
<dt><a href="./org/biojava/bio/program/indexdb/Record.Impl.html" title="class in org.biojava.bio.program.indexdb"><span class="strong">Record.Impl</span></a> - Class in <a href="./org/biojava/bio/program/indexdb/package-summary.html">org.biojava.bio.program.indexdb</a></dt>
<dd>
<div class="block"><code>Impl</code> is the default implementation of Record.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/indexdb/Record.Impl.html#Record.Impl(java.lang.String, org.biojava.utils.io.RAF, long, int)">Record.Impl(String, RAF, long, int)</a></span> - Constructor for class org.biojava.bio.program.indexdb.<a href="./org/biojava/bio/program/indexdb/Record.Impl.html" title="class in org.biojava.bio.program.indexdb">Record.Impl</a></dt>
<dd>
<div class="block">Creates a new <code>Impl</code> record.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/HMMTrainer.html#recordEmittedSymbol(org.biojava.bio.dp.State, org.biojava.bio.symbol.Symbol, double)">recordEmittedSymbol(State, Symbol, double)</a></span> - Method in interface org.biojava.bio.dp.<a href="./org/biojava/bio/dp/HMMTrainer.html" title="interface in org.biojava.bio.dp">HMMTrainer</a></dt>
<dd>
<div class="block">record that the specified symbol was emitted from the specified state.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/SimpleHMMTrainer.html#recordEmittedSymbol(org.biojava.bio.dp.State, org.biojava.bio.symbol.Symbol, double)">recordEmittedSymbol(State, Symbol, double)</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/SimpleHMMTrainer.html" title="class in org.biojava.bio.dp">SimpleHMMTrainer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/abi/ABIFParser.TaggedDataRecord.html#recordLength">recordLength</a></span> - Variable in class org.biojava.bio.program.abi.<a href="./org/biojava/bio/program/abi/ABIFParser.TaggedDataRecord.html" title="class in org.biojava.bio.program.abi">ABIFParser.TaggedDataRecord</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFDocumentHandler.html#recordLine(org.biojava.bio.program.gff.GFFRecord)">recordLine(GFFRecord)</a></span> - Method in interface org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFDocumentHandler.html" title="interface in org.biojava.bio.program.gff">GFFDocumentHandler</a></dt>
<dd>
<div class="block">A record line has been encountered.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFFilterer.html#recordLine(org.biojava.bio.program.gff.GFFRecord)">recordLine(GFFRecord)</a></span> - Method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFFilterer.html" title="class in org.biojava.bio.program.gff">GFFFilterer</a></dt>
<dd>
<div class="block">Only forward the <span class="type">GFFRecord</span>s that match a filter.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFWriter.html#recordLine(org.biojava.bio.program.gff.GFFRecord)">recordLine(GFFRecord)</a></span> - Method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFWriter.html" title="class in org.biojava.bio.program.gff">GFFWriter</a></dt>
<dd>
<div class="block">Prints <span class="arg">record</span> to the <span class="type">PrintWriter</span>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff3/GFF3DocumentHandler.html#recordLine(org.biojava.bio.program.gff3.GFF3Record)">recordLine(GFF3Record)</a></span> - Method in interface org.biojava.bio.program.gff3.<a href="./org/biojava/bio/program/gff3/GFF3DocumentHandler.html" title="interface in org.biojava.bio.program.gff3">GFF3DocumentHandler</a></dt>
<dd>
<div class="block">A record line has been encountered.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/HMMTrainer.html#recordTransition(org.biojava.bio.dp.State, org.biojava.bio.dp.State, double)">recordTransition(State, State, double)</a></span> - Method in interface org.biojava.bio.dp.<a href="./org/biojava/bio/dp/HMMTrainer.html" title="interface in org.biojava.bio.dp">HMMTrainer</a></dt>
<dd>
<div class="block">record that a transition was observed between the specified states.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/SimpleHMMTrainer.html#recordTransition(org.biojava.bio.dp.State, org.biojava.bio.dp.State, double)">recordTransition(State, State, double)</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/SimpleHMMTrainer.html" title="class in org.biojava.bio.dp">SimpleHMMTrainer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/emblcd/EmblCDROMIndexReader.html#recParser">recParser</a></span> - Variable in class org.biojava.bio.seq.db.emblcd.<a href="./org/biojava/bio/seq/db/emblcd/EmblCDROMIndexReader.html" title="class in org.biojava.bio.seq.db.emblcd">EmblCDROMIndexReader</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/emblcd/EmblCDROMRandomAccess.html#recParser">recParser</a></span> - Variable in class org.biojava.bio.seq.db.emblcd.<a href="./org/biojava/bio/seq/db/emblcd/EmblCDROMRandomAccess.html" title="class in org.biojava.bio.seq.db.emblcd">EmblCDROMRandomAccess</a></dt>
<dd>
<div class="block">A <code>recParser</code> for implementing
<code>readRecord()</code> specific to each concrete subclass.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/ImageMap.html#RECT">RECT</a></span> - Static variable in interface org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/ImageMap.html" title="interface in org.biojava.bio.gui.sequence">ImageMap</a></dt>
<dd>
<div class="block"><code>RECT</code> indicates a rectangular image map hotspot.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/RectangularBeadRenderer.html#rect">rect</a></span> - Variable in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/RectangularBeadRenderer.html" title="class in org.biojava.bio.gui.sequence">RectangularBeadRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/RoundRectangularBeadRenderer.html#rect">rect</a></span> - Variable in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/RoundRectangularBeadRenderer.html" title="class in org.biojava.bio.gui.sequence">RoundRectangularBeadRenderer</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/gui/glyph/RectangleGlyph.html" title="class in org.biojava.bio.gui.glyph"><span class="strong">RectangleGlyph</span></a> - Class in <a href="./org/biojava/bio/gui/glyph/package-summary.html">org.biojava.bio.gui.glyph</a></dt>
<dd>
<div class="block">A Glyph that paints a rectangle shape within the bounds.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/glyph/RectangleGlyph.html#RectangleGlyph()">RectangleGlyph()</a></span> - Constructor for class org.biojava.bio.gui.glyph.<a href="./org/biojava/bio/gui/glyph/RectangleGlyph.html" title="class in org.biojava.bio.gui.glyph">RectangleGlyph</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/glyph/RectangleGlyph.html#RectangleGlyph(java.awt.geom.Rectangle2D.Float)">RectangleGlyph(Rectangle2D.Float)</a></span> - Constructor for class org.biojava.bio.gui.glyph.<a href="./org/biojava/bio/gui/glyph/RectangleGlyph.html" title="class in org.biojava.bio.gui.glyph">RectangleGlyph</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/glyph/RectangleGlyph.html#RectangleGlyph(java.awt.Paint)">RectangleGlyph(Paint)</a></span> - Constructor for class org.biojava.bio.gui.glyph.<a href="./org/biojava/bio/gui/glyph/RectangleGlyph.html" title="class in org.biojava.bio.gui.glyph">RectangleGlyph</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/gui/sequence/RectangularBeadRenderer.html" title="class in org.biojava.bio.gui.sequence"><span class="strong">RectangularBeadRenderer</span></a> - Class in <a href="./org/biojava/bio/gui/sequence/package-summary.html">org.biojava.bio.gui.sequence</a></dt>
<dd>
<div class="block"><code>RectangularBeadRenderer</code> renders features as simple
rectangles.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/RectangularBeadRenderer.html#RectangularBeadRenderer()">RectangularBeadRenderer()</a></span> - Constructor for class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/RectangularBeadRenderer.html" title="class in org.biojava.bio.gui.sequence">RectangularBeadRenderer</a></dt>
<dd>
<div class="block">Creates a new <code>RectangularBeadRenderer</code> with the
default settings.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/RectangularBeadRenderer.html#RectangularBeadRenderer(double, double, java.awt.Paint, java.awt.Paint, java.awt.Stroke)">RectangularBeadRenderer(double, double, Paint, Paint, Stroke)</a></span> - Constructor for class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/RectangularBeadRenderer.html" title="class in org.biojava.bio.gui.sequence">RectangularBeadRenderer</a></dt>
<dd>
<div class="block">Creates a new <code>RectangularBeadRenderer</code>.</div>
</dd>
<dt><a href="./org/biojava/bio/gui/sequence/RectangularImapRenderer.html" title="class in org.biojava.bio.gui.sequence"><span class="strong">RectangularImapRenderer</span></a> - Class in <a href="./org/biojava/bio/gui/sequence/package-summary.html">org.biojava.bio.gui.sequence</a></dt>
<dd>
<div class="block"><code>RectangularImapRenderer</code> is a decorator for
<code>RectangularBeadRenderer</code> which adds the ability to
create HTML image map coordinates which correspond to the feature
rendering produced by the <code>RectangularBeadRenderer</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/RectangularImapRenderer.html#RectangularImapRenderer(org.biojava.bio.gui.sequence.RectangularBeadRenderer, org.biojava.bio.gui.sequence.ImageMap, org.biojava.utils.net.URLFactory)">RectangularImapRenderer(RectangularBeadRenderer, ImageMap, URLFactory)</a></span> - Constructor for class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/RectangularImapRenderer.html" title="class in org.biojava.bio.gui.sequence">RectangularImapRenderer</a></dt>
<dd>
<div class="block">Creates a new <code>RectangularImapRenderer</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/FilteringRenderer.html#RECURSE">RECURSE</a></span> - Static variable in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/FilteringRenderer.html" title="class in org.biojava.bio.gui.sequence">FilteringRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/FilteringRenderer.html#recurse">recurse</a></span> - Variable in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/FilteringRenderer.html" title="class in org.biojava.bio.gui.sequence">FilteringRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PairwiseFilteringRenderer.html#RECURSE">RECURSE</a></span> - Static variable in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PairwiseFilteringRenderer.html" title="class in org.biojava.bio.gui.sequence">PairwiseFilteringRenderer</a></dt>
<dd>
<div class="block">Constant <code>RECURSE</code> indicating a change to the
renderer's filter recursion flag.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PairwiseFilteringRenderer.html#recurse">recurse</a></span> - Variable in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PairwiseFilteringRenderer.html" title="class in org.biojava.bio.gui.sequence">PairwiseFilteringRenderer</a></dt>
<dd>
<div class="block"><code>recurse</code> indicates whether the filter should
recurse through any subfeatures.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/FragmentJoiner.html#reduceFragments(java.util.List, org.biojava.bio.structure.align.pairwise.FragmentPair, org.biojava.bio.structure.jama.Matrix)">reduceFragments(List<FragmentPair>, FragmentPair, Matrix)</a></span> - Static method in class org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/FragmentJoiner.html" title="class in org.biojava.bio.structure.align.pairwise">FragmentJoiner</a></dt>
<dd>
<div class="block">In helices often many similar fragments can be found.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/StrucAligParameters.html#reduceInitialFragments()">reduceInitialFragments()</a></span> - Method in class org.biojava.bio.structure.align.<a href="./org/biojava/bio/structure/align/StrucAligParameters.html" title="class in org.biojava.bio.structure.align">StrucAligParameters</a></dt>
<dd>
<div class="block">if this is set to false, the time spent to joint the initial fragments (step 2)
is increased.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/EmblLikeFormat.html#REF_ACCESSION_TAG">REF_ACCESSION_TAG</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/EmblLikeFormat.html" title="class in org.biojava.bio.seq.io">EmblLikeFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/GenbankFormat.html#REF_ACCESSION_TAG">REF_ACCESSION_TAG</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/GenbankFormat.html" title="class in org.biojava.bio.seq.io">GenbankFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#REF_ATTR">REF_ATTR</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html#REF_POS_BEGIN_ATTR">REF_POS_BEGIN_ATTR</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html" title="class in org.biojavax.bio.seq.io">EMBLxmlFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html#REF_POS_END_ATTR">REF_POS_END_ATTR</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html" title="class in org.biojavax.bio.seq.io">EMBLxmlFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/EmblLikeFormat.html#REF_XREF_TAG">REF_XREF_TAG</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/EmblLikeFormat.html" title="class in org.biojava.bio.seq.io">EmblLikeFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/HomologeneBuilder.html#REFERENCE">REFERENCE</a></span> - Static variable in interface org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/HomologeneBuilder.html" title="interface in org.biojava.bio.program.homologene">HomologeneBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/INSDseqFormat.html#REFERENCE_LOCATION_TAG">REFERENCE_LOCATION_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/INSDseqFormat.html" title="class in org.biojavax.bio.seq.io">INSDseqFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLFormat.html#REFERENCE_POSITION_TAG">REFERENCE_POSITION_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLFormat.html" title="class in org.biojavax.bio.seq.io">EMBLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/INSDseqFormat.html#REFERENCE_POSITION_TAG">REFERENCE_POSITION_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/INSDseqFormat.html" title="class in org.biojavax.bio.seq.io">INSDseqFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/EmblLikeFormat.html#REFERENCE_TAG">REFERENCE_TAG</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/EmblLikeFormat.html" title="class in org.biojava.bio.seq.io">EmblLikeFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/GenbankFormat.html#REFERENCE_TAG">REFERENCE_TAG</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/GenbankFormat.html" title="class in org.biojava.bio.seq.io">GenbankFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLFormat.html#REFERENCE_TAG">REFERENCE_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLFormat.html" title="class in org.biojavax.bio.seq.io">EMBLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html#REFERENCE_TAG">REFERENCE_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html" title="class in org.biojavax.bio.seq.io">EMBLxmlFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/GenbankFormat.html#REFERENCE_TAG">REFERENCE_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/GenbankFormat.html" title="class in org.biojavax.bio.seq.io">GenbankFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/INSDseqFormat.html#REFERENCE_TAG">REFERENCE_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/INSDseqFormat.html" title="class in org.biojavax.bio.seq.io">INSDseqFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtFormat.html#REFERENCE_TAG">REFERENCE_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtFormat.html" title="class in org.biojavax.bio.seq.io">UniProtFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#REFERENCE_TAG">REFERENCE_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLFormat.html#REFERENCE_XREF_TAG">REFERENCE_XREF_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLFormat.html" title="class in org.biojavax.bio.seq.io">EMBLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtFormat.html#REFERENCE_XREF_TAG">REFERENCE_XREF_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtFormat.html" title="class in org.biojavax.bio.seq.io">UniProtFormat</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/io/ReferenceAnnotation.html" title="class in org.biojava.bio.seq.io"><span class="strong">ReferenceAnnotation</span></a> - Class in <a href="./org/biojava/bio/seq/io/package-summary.html">org.biojava.bio.seq.io</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>Use org.biojavax.bio.seq.io framework instead</i></div>
</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/ReferenceAnnotation.html#ReferenceAnnotation()">ReferenceAnnotation()</a></span> - Constructor for class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/ReferenceAnnotation.html" title="class in org.biojava.bio.seq.io">ReferenceAnnotation</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/INSDseqFormat.html#REFERENCES_GROUP_TAG">REFERENCES_GROUP_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/INSDseqFormat.html" title="class in org.biojavax.bio.seq.io">INSDseqFormat</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/das/ReferenceServer.html" title="class in org.biojava.bio.program.das"><span class="strong">ReferenceServer</span></a> - Class in <a href="./org/biojava/bio/program/das/package-summary.html">org.biojava.bio.program.das</a></dt>
<dd>
<div class="block">Reflects a reference server on the DAS network.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/AlternativeAlignment.html#refine(org.biojava.bio.structure.align.StrucAligParameters, org.biojava.bio.structure.Atom[], org.biojava.bio.structure.Atom[])">refine(StrucAligParameters, Atom[], Atom[])</a></span> - Method in class org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/AlternativeAlignment.html" title="class in org.biojava.bio.structure.align.pairwise">AlternativeAlignment</a></dt>
<dd>
<div class="block">Refinement procedure based on superposition and dynamic programming.</div>
</dd>
<dt><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model"><span class="strong">Refine</span></a> - Class in <a href="./org/biojava/bio/structure/io/mmcif/model/package-summary.html">org.biojava.bio.structure.io.mmcif.model</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#Refine()">Refine()</a></span> - Constructor for class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/OntoTools.html#REFLEXIVE">REFLEXIVE</a></span> - Static variable in class org.biojava.ontology.<a href="./org/biojava/ontology/OntoTools.html" title="class in org.biojava.ontology">OntoTools</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/GenbankFormat.html#refp">refp</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/GenbankFormat.html" title="class in org.biojavax.bio.seq.io">GenbankFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/GenbankFormat.html#refRange">refRange</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/GenbankFormat.html" title="class in org.biojavax.bio.seq.io">GenbankFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePanelWrapper.html#refreshSequencePanels()">refreshSequencePanels()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePanelWrapper.html" title="class in org.biojava.bio.gui.sequence">SequencePanelWrapper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOConstants.html#REFSEQ">REFSEQ</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOConstants.html" title="class in org.biojava.bio.seq.io">SeqIOConstants</a></dt>
<dd>
<div class="block"><code>REFSEQ</code> indicates that the sequence format is
REFSEQ.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOConstants.html#REFSEQ_AA">REFSEQ_AA</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOConstants.html" title="class in org.biojava.bio.seq.io">SeqIOConstants</a></dt>
<dd>
<div class="block"><code>REFSEQ_AA</code> premade REFSEQ | AA.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOConstants.html#REFSEQ_DNA">REFSEQ_DNA</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOConstants.html" title="class in org.biojava.bio.seq.io">SeqIOConstants</a></dt>
<dd>
<div class="block"><code>REFSEQ_DNA</code> premade REFSEQ | DNA.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOConstants.html#REFSEQ_RNA">REFSEQ_RNA</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOConstants.html" title="class in org.biojava.bio.seq.io">SeqIOConstants</a></dt>
<dd>
<div class="block"><code>REFSEQ_RNA</code> premade REFSEQ | RNA.</div>
</dd>
<dt><a href="./org/biojava/bio/program/tagvalue/RegexChanger.html" title="class in org.biojava.bio.program.tagvalue"><span class="strong">RegexChanger</span></a> - Class in <a href="./org/biojava/bio/program/tagvalue/package-summary.html">org.biojava.bio.program.tagvalue</a></dt>
<dd>
<div class="block">
A ValueChanger.Changer that returns a specific match value using a regex
Pattern.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/RegexChanger.html#RegexChanger(java.util.regex.Pattern, int)">RegexChanger(Pattern, int)</a></span> - Constructor for class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/RegexChanger.html" title="class in org.biojava.bio.program.tagvalue">RegexChanger</a></dt>
<dd>
<div class="block">Create a new RegexChanger with a pattern.</div>
</dd>
<dt><a href="./org/biojava/utils/regex/RegexException.html" title="class in org.biojava.utils.regex"><span class="strong">RegexException</span></a> - Exception in <a href="./org/biojava/utils/regex/package-summary.html">org.biojava.utils.regex</a></dt>
<dd>
<div class="block">An exception thrown by classes of this package.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/regex/RegexException.html#RegexException(java.lang.String)">RegexException(String)</a></span> - Constructor for exception org.biojava.utils.regex.<a href="./org/biojava/utils/regex/RegexException.html" title="class in org.biojava.utils.regex">RegexException</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/regex/RegexException.html#RegexException(java.lang.Throwable)">RegexException(Throwable)</a></span> - Constructor for exception org.biojava.utils.regex.<a href="./org/biojava/utils/regex/RegexException.html" title="class in org.biojava.utils.regex">RegexException</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/regex/RegexException.html#RegexException(java.lang.Throwable, java.lang.String)">RegexException(Throwable, String)</a></span> - Constructor for exception org.biojava.utils.regex.<a href="./org/biojava/utils/regex/RegexException.html" title="class in org.biojava.utils.regex">RegexException</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/tagvalue/RegexFieldFinder.html" title="class in org.biojava.bio.program.tagvalue"><span class="strong">RegexFieldFinder</span></a> - Class in <a href="./org/biojava/bio/program/tagvalue/package-summary.html">org.biojava.bio.program.tagvalue</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/RegexFieldFinder.html#RegexFieldFinder(org.biojava.bio.program.tagvalue.TagValueListener, java.util.regex.Pattern, java.lang.String[], boolean)">RegexFieldFinder(TagValueListener, Pattern, String[], boolean)</a></span> - Constructor for class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/RegexFieldFinder.html" title="class in org.biojava.bio.program.tagvalue">RegexFieldFinder</a></dt>
<dd>
<div class="block">Creates a new RegexFiledFinder.</div>
</dd>
<dt><a href="./org/biojava/bio/program/tagvalue/RegexParser.html" title="class in org.biojava.bio.program.tagvalue"><span class="strong">RegexParser</span></a> - Class in <a href="./org/biojava/bio/program/tagvalue/package-summary.html">org.biojava.bio.program.tagvalue</a></dt>
<dd>
<div class="block">
A TagValueParser that splits a line based upon a regular expression.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/RegexParser.html#RegexParser()">RegexParser()</a></span> - Constructor for class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/RegexParser.html" title="class in org.biojava.bio.program.tagvalue">RegexParser</a></dt>
<dd>
<div class="block">Create a new RegexParser with all boolean values set to false.</div>
</dd>
<dt><a href="./org/biojava/bio/program/tagvalue/RegexSplitter.html" title="class in org.biojava.bio.program.tagvalue"><span class="strong">RegexSplitter</span></a> - Class in <a href="./org/biojava/bio/program/tagvalue/package-summary.html">org.biojava.bio.program.tagvalue</a></dt>
<dd>
<div class="block">
A ValueChanger.Splitter that splits a line of text using a regular
expression, returning one value per match.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/RegexSplitter.html#RegexSplitter(java.util.regex.Pattern, int)">RegexSplitter(Pattern, int)</a></span> - Constructor for class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/RegexSplitter.html" title="class in org.biojava.bio.program.tagvalue">RegexSplitter</a></dt>
<dd>
<div class="block">Create a new RegexSplitter with a pattern.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/RemoteFeature.Template.html#regions">regions</a></span> - Variable in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/RemoteFeature.Template.html" title="class in org.biojava.bio.seq">RemoteFeature.Template</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/molbio/RestrictionEnzymeManager.html#register(org.biojava.bio.molbio.RestrictionEnzyme, java.util.Set)">register(RestrictionEnzyme, Set)</a></span> - Static method in class org.biojava.bio.molbio.<a href="./org/biojava/bio/molbio/RestrictionEnzymeManager.html" title="class in org.biojava.bio.molbio">RestrictionEnzymeManager</a></dt>
<dd>
<div class="block"><code>register</code> regisiters a new
<code>RestrictionEnzyme</code> with the manager.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AlphabetManager.html#registerAlphabet(java.lang.String, org.biojava.bio.symbol.Alphabet)">registerAlphabet(String, Alphabet)</a></span> - Static method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AlphabetManager.html" title="class in org.biojava.bio.symbol">AlphabetManager</a></dt>
<dd>
<div class="block">Register an alphabet by name.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AlphabetManager.html#registerAlphabet(java.lang.String[], org.biojava.bio.symbol.Alphabet)">registerAlphabet(String[], Alphabet)</a></span> - Static method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AlphabetManager.html" title="class in org.biojava.bio.symbol">AlphabetManager</a></dt>
<dd>
<div class="block">Register and Alphabet by more than one name.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/filterxml/XMLAnnotationTypeHandler.html#registerCollectionHandlerFactory(java.lang.String, java.lang.String, org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeHandler.CollectionConstraintHandlerFactory)">registerCollectionHandlerFactory(String, String, XMLAnnotationTypeHandler.CollectionConstraintHandlerFactory)</a></span> - Method in class org.biojava.bio.seq.io.filterxml.<a href="./org/biojava/bio/seq/io/filterxml/XMLAnnotationTypeHandler.html" title="class in org.biojava.bio.seq.io.filterxml">XMLAnnotationTypeHandler</a></dt>
<dd>
<div class="block">Register a factory used to create handlers for the specified tag in an
XML AnnotationType</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/DistributionTrainerContext.html#registerDistribution(org.biojava.bio.dist.Distribution)">registerDistribution(Distribution)</a></span> - Method in interface org.biojava.bio.dist.<a href="./org/biojava/bio/dist/DistributionTrainerContext.html" title="interface in org.biojava.bio.dist">DistributionTrainerContext</a></dt>
<dd>
<div class="block">
Register a distribution object with this context.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/SimpleDistributionTrainerContext.html#registerDistribution(org.biojava.bio.dist.Distribution)">registerDistribution(Distribution)</a></span> - Method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/SimpleDistributionTrainerContext.html" title="class in org.biojava.bio.dist">SimpleDistributionTrainerContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/ProteaseManager.html#registered(java.lang.String)">registered(String)</a></span> - Static method in class org.biojava.bio.proteomics.<a href="./org/biojava/bio/proteomics/ProteaseManager.html" title="class in org.biojava.bio.proteomics">ProteaseManager</a></dt>
<dd>
<div class="block">Has a Protease been registered with that name?</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AlphabetManager.html#registered(java.lang.String)">registered(String)</a></span> - Static method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AlphabetManager.html" title="class in org.biojava.bio.symbol">AlphabetManager</a></dt>
<dd>
<div class="block">Has an Alphabet been registered by that name</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/unigene/UnigeneTools.html#registerFactory(org.biojava.bio.program.unigene.UnigeneFactory)">registerFactory(UnigeneFactory)</a></span> - Static method in class org.biojava.bio.program.unigene.<a href="./org/biojava/bio/program/unigene/UnigeneTools.html" title="class in org.biojava.bio.program.unigene">UnigeneTools</a></dt>
<dd>
<div class="block">Register a UnigeneFactory.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.IOTools.html#registerFormat(java.lang.Class)">registerFormat(Class)</a></span> - Static method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.IOTools.html" title="class in org.biojavax.bio.seq">RichSequence.IOTools</a></dt>
<dd>
<div class="block">Register a new format with IOTools for auto-guessing.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/filterxml/XMLFilterHandler.html#registerHandlerFactory(java.lang.String, java.lang.String, org.biojava.bio.seq.io.filterxml.XMLFilterHandler.FilterHandlerFactory)">registerHandlerFactory(String, String, XMLFilterHandler.FilterHandlerFactory)</a></span> - Method in class org.biojava.bio.seq.io.filterxml.<a href="./org/biojava/bio/seq/io/filterxml/XMLFilterHandler.html" title="class in org.biojava.bio.seq.io.filterxml">XMLFilterHandler</a></dt>
<dd>
<div class="block">Register a factory used to create handlers for the specified tag name</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/ModelTrainer.html#registerModel(org.biojava.bio.dp.MarkovModel)">registerModel(MarkovModel)</a></span> - Method in interface org.biojava.bio.dp.<a href="./org/biojava/bio/dp/ModelTrainer.html" title="interface in org.biojava.bio.dp">ModelTrainer</a></dt>
<dd>
<div class="block">Registers an HMM with this trainer.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/SimpleModelTrainer.html#registerModel(org.biojava.bio.dp.MarkovModel)">registerModel(MarkovModel)</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/SimpleModelTrainer.html" title="class in org.biojava.bio.dp">SimpleModelTrainer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/filterxml/XMLAnnotationTypeHandler.html#registerPropertyHandlerFactory(java.lang.String, java.lang.String, org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeHandler.PropertyConstraintHandlerFactory)">registerPropertyHandlerFactory(String, String, XMLAnnotationTypeHandler.PropertyConstraintHandlerFactory)</a></span> - Method in class org.biojava.bio.seq.io.filterxml.<a href="./org/biojava/bio/seq/io/filterxml/XMLAnnotationTypeHandler.html" title="class in org.biojava.bio.seq.io.filterxml">XMLAnnotationTypeHandler</a></dt>
<dd>
<div class="block">Register a factory used to create handlers for the specified tag in an
XML AnnotationType</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/ProteaseManager.html#registerProtease(org.biojava.bio.proteomics.Protease)">registerProtease(Protease)</a></span> - Static method in class org.biojava.bio.proteomics.<a href="./org/biojava/bio/proteomics/ProteaseManager.html" title="class in org.biojava.bio.proteomics">ProteaseManager</a></dt>
<dd>
<div class="block">Registers a protease and ensures its flyweight status</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/DistributionTrainerContext.html#registerTrainer(org.biojava.bio.dist.Distribution, org.biojava.bio.dist.DistributionTrainer)">registerTrainer(Distribution, DistributionTrainer)</a></span> - Method in interface org.biojava.bio.dist.<a href="./org/biojava/bio/dist/DistributionTrainerContext.html" title="interface in org.biojava.bio.dist">DistributionTrainerContext</a></dt>
<dd>
<div class="block">
Register a Distribution and an associated DistributionTrainer object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/SimpleDistributionTrainerContext.html#registerTrainer(org.biojava.bio.dist.Distribution, org.biojava.bio.dist.DistributionTrainer)">registerTrainer(Distribution, DistributionTrainer)</a></span> - Method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/SimpleDistributionTrainerContext.html" title="class in org.biojava.bio.dist">SimpleDistributionTrainerContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/AbstractDistribution.html#registerWithTrainer(org.biojava.bio.dist.DistributionTrainerContext)">registerWithTrainer(DistributionTrainerContext)</a></span> - Method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/AbstractDistribution.html" title="class in org.biojava.bio.dist">AbstractDistribution</a></dt>
<dd>
<div class="block">Register an IgnoreCountsTrainer instance as the trainer for this
distribution.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/AbstractOrderNDistribution.html#registerWithTrainer(org.biojava.bio.dist.DistributionTrainerContext)">registerWithTrainer(DistributionTrainerContext)</a></span> - Method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/AbstractOrderNDistribution.html" title="class in org.biojava.bio.dist">AbstractOrderNDistribution</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/Distribution.html#registerWithTrainer(org.biojava.bio.dist.DistributionTrainerContext)">registerWithTrainer(DistributionTrainerContext)</a></span> - Method in interface org.biojava.bio.dist.<a href="./org/biojava/bio/dist/Distribution.html" title="interface in org.biojava.bio.dist">Distribution</a></dt>
<dd>
<div class="block">
Register this distribution with a training context.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/GapDistribution.html#registerWithTrainer(org.biojava.bio.dist.DistributionTrainerContext)">registerWithTrainer(DistributionTrainerContext)</a></span> - Method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/GapDistribution.html" title="class in org.biojava.bio.dist">GapDistribution</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/PairDistribution.html#registerWithTrainer(org.biojava.bio.dp.ModelTrainer)">registerWithTrainer(ModelTrainer)</a></span> - Method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/PairDistribution.html" title="class in org.biojava.bio.dist">PairDistribution</a></dt>
<dd>
<div class="block">Register this paired distribution with a model trainer.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/PairDistribution.html#registerWithTrainer(org.biojava.bio.dist.DistributionTrainerContext)">registerWithTrainer(DistributionTrainerContext)</a></span> - Method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/PairDistribution.html" title="class in org.biojava.bio.dist">PairDistribution</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/SimpleDistribution.html#registerWithTrainer(org.biojava.bio.dist.DistributionTrainerContext)">registerWithTrainer(DistributionTrainerContext)</a></span> - Method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/SimpleDistribution.html" title="class in org.biojava.bio.dist">SimpleDistribution</a></dt>
<dd>
<div class="block">Register an SimpleDistribution.Trainer instance as the trainer for this distribution.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/TranslatedDistribution.html#registerWithTrainer(org.biojava.bio.dist.DistributionTrainerContext)">registerWithTrainer(DistributionTrainerContext)</a></span> - Method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/TranslatedDistribution.html" title="class in org.biojava.bio.dist">TranslatedDistribution</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/UniformDistribution.html#registerWithTrainer(org.biojava.bio.dist.DistributionTrainerContext)">registerWithTrainer(DistributionTrainerContext)</a></span> - Method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/UniformDistribution.html" title="class in org.biojava.bio.dist">UniformDistribution</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/UntrainableDistribution.html#registerWithTrainer(org.biojava.bio.dist.DistributionTrainerContext)">registerWithTrainer(DistributionTrainerContext)</a></span> - Method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/UntrainableDistribution.html" title="class in org.biojava.bio.dist">UntrainableDistribution</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/SimpleEmissionState.html#registerWithTrainer(org.biojava.bio.dp.ModelTrainer)">registerWithTrainer(ModelTrainer)</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/SimpleEmissionState.html" title="class in org.biojava.bio.dp">SimpleEmissionState</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/Trainable.html#registerWithTrainer(org.biojava.bio.dp.ModelTrainer)">registerWithTrainer(ModelTrainer)</a></span> - Method in interface org.biojava.bio.dp.<a href="./org/biojava/bio/dp/Trainable.html" title="interface in org.biojava.bio.dp">Trainable</a></dt>
<dd>
<div class="block">Perform any registration that is necessary with mt.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/WMAsMM.html#registerWithTrainer(org.biojava.bio.dp.ModelTrainer)">registerWithTrainer(ModelTrainer)</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/WMAsMM.html" title="class in org.biojava.bio.dp">WMAsMM</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AlphabetManager.html#registrations()">registrations()</a></span> - Static method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AlphabetManager.html" title="class in org.biojava.bio.symbol">AlphabetManager</a></dt>
<dd>
<div class="block">A set of names under which Alphabets have been registered.</div>
</dd>
<dt><a href="./org/biojava/directory/Registry.html" title="class in org.biojava.directory"><span class="strong">Registry</span></a> - Class in <a href="./org/biojava/directory/package-summary.html">org.biojava.directory</a></dt>
<dd>
<div class="block"><code>Registry</code> is a factory which gets implementations of
the BioJava <code>SequenceDBLite</code> interface.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/directory/Registry.html#Registry(org.biojava.directory.RegistryConfiguration)">Registry(RegistryConfiguration)</a></span> - Constructor for class org.biojava.directory.<a href="./org/biojava/directory/Registry.html" title="class in org.biojava.directory">Registry</a></dt>
<dd>
<div class="block">Creates a new OBDA <code>Registry</code> with the specified
configuration.</div>
</dd>
<dt><a href="./org/biojava/directory/RegistryConfiguration.html" title="interface in org.biojava.directory"><span class="strong">RegistryConfiguration</span></a> - Interface in <a href="./org/biojava/directory/package-summary.html">org.biojava.directory</a></dt>
<dd>
<div class="block">The BioDirectory Registry is a simple system for specifying
where to find services which provide sequence databases.</div>
</dd>
<dt><a href="./org/biojava/directory/RegistryConfiguration.Composite.html" title="class in org.biojava.directory"><span class="strong">RegistryConfiguration.Composite</span></a> - Class in <a href="./org/biojava/directory/package-summary.html">org.biojava.directory</a></dt>
<dd>
<div class="block">A RegistryConfiguration that allows you to treat other
configurations as providing important or default configuration
information.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/directory/RegistryConfiguration.Composite.html#RegistryConfiguration.Composite()">RegistryConfiguration.Composite()</a></span> - Constructor for class org.biojava.directory.<a href="./org/biojava/directory/RegistryConfiguration.Composite.html" title="class in org.biojava.directory">RegistryConfiguration.Composite</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/directory/RegistryConfiguration.Impl.html" title="class in org.biojava.directory"><span class="strong">RegistryConfiguration.Impl</span></a> - Class in <a href="./org/biojava/directory/package-summary.html">org.biojava.directory</a></dt>
<dd>
<div class="block">A simple implementation of RegistryConfiguration backed by a Map.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/directory/RegistryConfiguration.Impl.html#RegistryConfiguration.Impl(java.lang.String, java.util.Map)">RegistryConfiguration.Impl(String, Map)</a></span> - Constructor for class org.biojava.directory.<a href="./org/biojava/directory/RegistryConfiguration.Impl.html" title="class in org.biojava.directory">RegistryConfiguration.Impl</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/directory/RegistryException.html" title="class in org.biojava.directory"><span class="strong">RegistryException</span></a> - Exception in <a href="./org/biojava/directory/package-summary.html">org.biojava.directory</a></dt>
<dd>
<div class="block">A <code>RegistryException</code> thrown when the registry cannot
find an implementation of a requested <code>SequenceDB</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/directory/RegistryException.html#RegistryException()">RegistryException()</a></span> - Constructor for exception org.biojava.directory.<a href="./org/biojava/directory/RegistryException.html" title="class in org.biojava.directory">RegistryException</a></dt>
<dd>
<div class="block">Creates a new <code>RegistryException</code> with no detail
message.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/directory/RegistryException.html#RegistryException(java.lang.String)">RegistryException(String)</a></span> - Constructor for exception org.biojava.directory.<a href="./org/biojava/directory/RegistryException.html" title="class in org.biojava.directory">RegistryException</a></dt>
<dd>
<div class="block">Creates a new <code>RegistryException</code> with the specified
detail message.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/directory/RegistryException.html#RegistryException(java.lang.Throwable)">RegistryException(Throwable)</a></span> - Constructor for exception org.biojava.directory.<a href="./org/biojava/directory/RegistryException.html" title="class in org.biojava.directory">RegistryException</a></dt>
<dd>
<div class="block">Creates a new <code>RegistryException</code> with no detail
message, wrapping another <code>Throwable</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/directory/RegistryException.html#RegistryException(java.lang.Throwable, java.lang.String)">RegistryException(Throwable, String)</a></span> - Constructor for exception org.biojava.directory.<a href="./org/biojava/directory/RegistryException.html" title="class in org.biojava.directory">RegistryException</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>use new RegistryException(message, cause)</i></div>
</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/directory/RegistryException.html#RegistryException(java.lang.String, java.lang.Throwable)">RegistryException(String, Throwable)</a></span> - Constructor for exception org.biojava.directory.<a href="./org/biojava/directory/RegistryException.html" title="class in org.biojava.directory">RegistryException</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/obo/OboFileHandler.html#REL_SYNONYM">REL_SYNONYM</a></span> - Static variable in class org.biojava.ontology.obo.<a href="./org/biojava/ontology/obo/OboFileHandler.html" title="class in org.biojava.ontology.obo">OboFileHandler</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/symbol/RelabeledAlignment.html" title="class in org.biojava.bio.symbol"><span class="strong">RelabeledAlignment</span></a> - Class in <a href="./org/biojava/bio/symbol/package-summary.html">org.biojava.bio.symbol</a></dt>
<dd>
<div class="block">An alignment that relabels another alignment.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/RelabeledAlignment.html#RelabeledAlignment(org.biojava.bio.symbol.Alignment)">RelabeledAlignment(Alignment)</a></span> - Constructor for class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/RelabeledAlignment.html" title="class in org.biojava.bio.symbol">RelabeledAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/Synonym.html#RELATED_SYNONYM">RELATED_SYNONYM</a></span> - Static variable in class org.biojava.ontology.<a href="./org/biojava/ontology/Synonym.html" title="class in org.biojava.ontology">Synonym</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/OntoTools.html#RELATION">RELATION</a></span> - Static variable in class org.biojava.ontology.<a href="./org/biojava/ontology/OntoTools.html" title="class in org.biojava.ontology">OntoTools</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichFeature.html#RELATION">RELATION</a></span> - Static variable in interface org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichFeature.html" title="interface in org.biojavax.bio.seq">RichFeature</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/BioEntry.html#RELATIONS">RELATIONS</a></span> - Static variable in interface org.biojavax.bio.<a href="./org/biojavax/bio/BioEntry.html" title="interface in org.biojavax.bio">BioEntry</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/obo/OboFileHandler.html#RELATIONSHIP">RELATIONSHIP</a></span> - Static variable in class org.biojava.ontology.obo.<a href="./org/biojava/ontology/obo/OboFileHandler.html" title="class in org.biojava.ontology.obo">OboFileHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/DocRef.html#REMARK">REMARK</a></span> - Static variable in interface org.biojavax.<a href="./org/biojavax/DocRef.html" title="interface in org.biojavax">DocRef</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLFormat.html#REMARK_TAG">REMARK_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLFormat.html" title="class in org.biojavax.bio.seq.io">EMBLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/GenbankFormat.html#REMARK_TAG">REMARK_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/GenbankFormat.html" title="class in org.biojavax.bio.seq.io">GenbankFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/INSDseqFormat.html#REMARK_TAG">REMARK_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/INSDseqFormat.html" title="class in org.biojavax.bio.seq.io">INSDseqFormat</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/RemoteFeature.html" title="interface in org.biojava.bio.seq"><span class="strong">RemoteFeature</span></a> - Interface in <a href="./org/biojava/bio/seq/package-summary.html">org.biojava.bio.seq</a></dt>
<dd>
<div class="block">A feature that indicates that there is some remote feature that can't be
represented entirely on a single Sequence.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/RemoteFeature.Region.html" title="class in org.biojava.bio.seq"><span class="strong">RemoteFeature.Region</span></a> - Class in <a href="./org/biojava/bio/seq/package-summary.html">org.biojava.bio.seq</a></dt>
<dd>
<div class="block">A tuple of Location and sequence ID.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/RemoteFeature.Region.html#RemoteFeature.Region(org.biojava.bio.symbol.Location, java.lang.String, boolean)">RemoteFeature.Region(Location, String, boolean)</a></span> - Constructor for class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/RemoteFeature.Region.html" title="class in org.biojava.bio.seq">RemoteFeature.Region</a></dt>
<dd>
<div class="block">Create a new Region.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/RemoteFeature.Resolver.html" title="interface in org.biojava.bio.seq"><span class="strong">RemoteFeature.Resolver</span></a> - Interface in <a href="./org/biojava/bio/seq/package-summary.html">org.biojava.bio.seq</a></dt>
<dd>
<div class="block">The interface for objects that actually can take a RemoteFeature and
return a Sequence object with the feature resolved into a real feature.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/RemoteFeature.Template.html" title="class in org.biojava.bio.seq"><span class="strong">RemoteFeature.Template</span></a> - Class in <a href="./org/biojava/bio/seq/package-summary.html">org.biojava.bio.seq</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/RemoteFeature.Template.html#RemoteFeature.Template()">RemoteFeature.Template()</a></span> - Constructor for class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/RemoteFeature.Template.html" title="class in org.biojava.bio.seq">RemoteFeature.Template</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/RemoteFeature.Template.html#RemoteFeature.Template(org.biojava.bio.seq.Feature.Template)">RemoteFeature.Template(Feature.Template)</a></span> - Constructor for class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/RemoteFeature.Template.html" title="class in org.biojava.bio.seq">RemoteFeature.Template</a></dt>
<dd>
<div class="block">Creates a RemoteFeature.Template that has the same values as the
template passed in.</div>
</dd>
<dt><a href="./org/biojava/ontology/RemoteTerm.html" title="interface in org.biojava.ontology"><span class="strong">RemoteTerm</span></a> - Interface in <a href="./org/biojava/ontology/package-summary.html">org.biojava.ontology</a></dt>
<dd>
<div class="block">A term in another ontology.</div>
</dd>
<dt><a href="./org/biojava/ontology/RemoteTerm.Impl.html" title="class in org.biojava.ontology"><span class="strong">RemoteTerm.Impl</span></a> - Class in <a href="./org/biojava/ontology/package-summary.html">org.biojava.ontology</a></dt>
<dd>
<div class="block">Simple in-memory implementation of a remote ontology term.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/RemoteTerm.Impl.html#RemoteTerm.Impl(org.biojava.ontology.Ontology, org.biojava.ontology.Term, java.lang.String)">RemoteTerm.Impl(Ontology, Term, String)</a></span> - Constructor for class org.biojava.ontology.<a href="./org/biojava/ontology/RemoteTerm.Impl.html" title="class in org.biojava.ontology">RemoteTerm.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/RemoteTerm.Impl.html#RemoteTerm.Impl(org.biojava.ontology.Ontology, org.biojava.ontology.Term, java.lang.String, java.lang.Object[])">RemoteTerm.Impl(Ontology, Term, String, Object[])</a></span> - Constructor for class org.biojava.ontology.<a href="./org/biojava/ontology/RemoteTerm.Impl.html" title="class in org.biojava.ontology">RemoteTerm.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/DP.ReverseIterator.html#remove()">remove()</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/DP.ReverseIterator.html" title="class in org.biojava.bio.dp">DP.ReverseIterator</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/AtomIterator.html#remove()">remove()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/AtomIterator.html" title="class in org.biojava.bio.structure">AtomIterator</a></dt>
<dd>
<div class="block">does nothing.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/GroupIterator.html#remove()">remove()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/GroupIterator.html" title="class in org.biojava.bio.structure">GroupIterator</a></dt>
<dd>
<div class="block">does nothing .</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/Alignment.SymbolListIterator.html#remove()">remove()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/Alignment.SymbolListIterator.html" title="class in org.biojava.bio.symbol">Alignment.SymbolListIterator</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/cache/CacheMap.html#remove(java.lang.Object)">remove(Object)</a></span> - Method in interface org.biojava.utils.cache.<a href="./org/biojava/utils/cache/CacheMap.html" title="interface in org.biojava.utils.cache">CacheMap</a></dt>
<dd>
<div class="block">Explicitly remove an object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/cache/FixedSizeMap.html#remove(java.lang.Object)">remove(Object)</a></span> - Method in class org.biojava.utils.cache.<a href="./org/biojava/utils/cache/FixedSizeMap.html" title="class in org.biojava.utils.cache">FixedSizeMap</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/cache/WeakCacheMap.html#remove(java.lang.Object)">remove(Object)</a></span> - Method in class org.biojava.utils.cache.<a href="./org/biojava/utils/cache/WeakCacheMap.html" title="class in org.biojava.utils.cache">WeakCacheMap</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/MergingIterator.html#remove()">remove()</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/MergingIterator.html" title="class in org.biojava.utils">MergingIterator</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/MergingSet.html#remove(java.lang.Object)">remove(Object)</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/MergingSet.html" title="class in org.biojava.utils">MergingSet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/util/WeightedSet.html#remove(java.lang.Object)">remove(Object)</a></span> - Method in class org.biojavax.ga.util.<a href="./org/biojavax/ga/util/WeightedSet.html" title="class in org.biojavax.ga.util">WeightedSet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/ARAlignment.html#REMOVE_LABEL">REMOVE_LABEL</a></span> - Static variable in interface org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/ARAlignment.html" title="interface in org.biojava.bio.alignment">ARAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/DAS.html#removeActivityListener(org.biojava.utils.ActivityListener)">removeActivityListener(ActivityListener)</a></span> - Static method in class org.biojava.bio.program.das.<a href="./org/biojava/bio/program/das/DAS.html" title="class in org.biojava.bio.program.das">DAS</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/impl/AbstractPopulation.html#removeAllOrganisms()">removeAllOrganisms()</a></span> - Method in class org.biojavax.ga.impl.<a href="./org/biojavax/ga/impl/AbstractPopulation.html" title="class in org.biojavax.ga.impl">AbstractPopulation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/Population.html#removeAllOrganisms()">removeAllOrganisms()</a></span> - Method in interface org.biojavax.ga.<a href="./org/biojavax/ga/Population.html" title="interface in org.biojavax.ga">Population</a></dt>
<dd>
<div class="block">Removes all the <code>Organisms</code> in this <code>Population</code></div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ga/impl/AbstractPopulation.html#removeAllOrganismsImpl()">removeAllOrganismsImpl()</a></span> - Method in class org.biojavax.ga.impl.<a href="./org/biojavax/ga/impl/AbstractPopulation.html" title="class in org.biojavax.ga.impl">AbstractPopulation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/impl/SimplePopulation.html#removeAllOrganismsImpl()">removeAllOrganismsImpl()</a></span> - Method in class org.biojavax.ga.impl.<a href="./org/biojavax/ga/impl/SimplePopulation.html" title="class in org.biojavax.ga.impl">SimplePopulation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/MergeAnnotation.html#removeAnnotation(org.biojava.bio.Annotation)">removeAnnotation(Annotation)</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/MergeAnnotation.html" title="class in org.biojava.bio">MergeAnnotation</a></dt>
<dd>
<div class="block">Remove an Annotation from the list.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/annodb/MergingAnnotationDB.html#removeAnnotationDB(org.biojava.bio.annodb.AnnotationDB)">removeAnnotationDB(AnnotationDB)</a></span> - Method in class org.biojava.bio.annodb.<a href="./org/biojava/bio/annodb/MergingAnnotationDB.html" title="class in org.biojava.bio.annodb">MergingAnnotationDB</a></dt>
<dd>
<div class="block">Remove a DB from this view.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/DASSequence.html#removeAnnotationSource(java.net.URL)">removeAnnotationSource(URL)</a></span> - Method in class org.biojava.bio.program.das.<a href="./org/biojava/bio/program/das/DASSequence.html" title="class in org.biojava.bio.program.das">DASSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/AbstractBioEntryDB.html#removeBioEntry(java.lang.String)">removeBioEntry(String)</a></span> - Method in class org.biojavax.bio.db.<a href="./org/biojavax/bio/db/AbstractBioEntryDB.html" title="class in org.biojavax.bio.db">AbstractBioEntryDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/AbstractRichSequenceDB.html#removeBioEntry(java.lang.String)">removeBioEntry(String)</a></span> - Method in class org.biojavax.bio.db.<a href="./org/biojavax/bio/db/AbstractRichSequenceDB.html" title="class in org.biojavax.bio.db">AbstractRichSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/BioEntryDBLite.html#removeBioEntry(java.lang.String)">removeBioEntry(String)</a></span> - Method in interface org.biojavax.bio.db.<a href="./org/biojavax/bio/db/BioEntryDBLite.html" title="interface in org.biojavax.bio.db">BioEntryDBLite</a></dt>
<dd>
<div class="block">Remove the BioEntry associated with an ID from the database.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLBioEntryDB.html#removeBioEntry(java.lang.String)">removeBioEntry(String)</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLBioEntryDB.html" title="class in org.biojavax.bio.db.biosql">BioSQLBioEntryDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/HashBioEntryDB.html#removeBioEntry(java.lang.String)">removeBioEntry(String)</a></span> - Method in class org.biojavax.bio.db.<a href="./org/biojavax/bio/db/HashBioEntryDB.html" title="class in org.biojavax.bio.db">HashBioEntryDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PairwiseSequencePanel.html#removeChangeListener(org.biojava.utils.ChangeListener)">removeChangeListener(ChangeListener)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PairwiseSequencePanel.html" title="class in org.biojava.bio.gui.sequence">PairwiseSequencePanel</a></dt>
<dd>
<div class="block"><code>removeChangeListener</code> removes a listener.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PairwiseSequencePanel.html#removeChangeListener(org.biojava.utils.ChangeListener, org.biojava.utils.ChangeType)">removeChangeListener(ChangeListener, ChangeType)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PairwiseSequencePanel.html" title="class in org.biojava.bio.gui.sequence">PairwiseSequencePanel</a></dt>
<dd>
<div class="block"><code>removeChangeListener</code> removes a listener.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePanel.html#removeChangeListener(org.biojava.utils.ChangeListener)">removeChangeListener(ChangeListener)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePanel.html" title="class in org.biojava.bio.gui.sequence">SequencePanel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePanel.html#removeChangeListener(org.biojava.utils.ChangeListener, org.biojava.utils.ChangeType)">removeChangeListener(ChangeListener, ChangeType)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePanel.html" title="class in org.biojava.bio.gui.sequence">SequencePanel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePoster.html#removeChangeListener(org.biojava.utils.ChangeListener)">removeChangeListener(ChangeListener)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePoster.html" title="class in org.biojava.bio.gui.sequence">SequencePoster</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePoster.html#removeChangeListener(org.biojava.utils.ChangeListener, org.biojava.utils.ChangeType)">removeChangeListener(ChangeListener, ChangeType)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePoster.html" title="class in org.biojava.bio.gui.sequence">SequencePoster</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/TranslatedSequencePanel.html#removeChangeListener(org.biojava.utils.ChangeListener)">removeChangeListener(ChangeListener)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/TranslatedSequencePanel.html" title="class in org.biojava.bio.gui.sequence">TranslatedSequencePanel</a></dt>
<dd>
<div class="block"><code>removeChangeListener</code> removes a listener.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/TranslatedSequencePanel.html#removeChangeListener(org.biojava.utils.ChangeListener, org.biojava.utils.ChangeType)">removeChangeListener(ChangeListener, ChangeType)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/TranslatedSequencePanel.html" title="class in org.biojava.bio.gui.sequence">TranslatedSequencePanel</a></dt>
<dd>
<div class="block"><code>removeChangeListener</code> removes a listener.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/ReferenceServer.html#removeChangeListener(org.biojava.utils.ChangeListener)">removeChangeListener(ChangeListener)</a></span> - Method in class org.biojava.bio.program.das.<a href="./org/biojava/bio/program/das/ReferenceServer.html" title="class in org.biojava.bio.program.das">ReferenceServer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/ReferenceServer.html#removeChangeListener(org.biojava.utils.ChangeListener, org.biojava.utils.ChangeType)">removeChangeListener(ChangeListener, ChangeType)</a></span> - Method in class org.biojava.bio.program.das.<a href="./org/biojava/bio/program/das/ReferenceServer.html" title="class in org.biojava.bio.program.das">ReferenceServer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/LazyFilterFeatureHolder.html#removeChangeListener(org.biojava.utils.ChangeListener)">removeChangeListener(ChangeListener)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/LazyFilterFeatureHolder.html" title="class in org.biojava.bio.seq.impl">LazyFilterFeatureHolder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/LazyFilterFeatureHolder.html#removeChangeListener(org.biojava.utils.ChangeListener, org.biojava.utils.ChangeType)">removeChangeListener(ChangeListener, ChangeType)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/LazyFilterFeatureHolder.html" title="class in org.biojava.bio.seq.impl">LazyFilterFeatureHolder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SubSequence.html#removeChangeListener(org.biojava.utils.ChangeListener, org.biojava.utils.ChangeType)">removeChangeListener(ChangeListener, ChangeType)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SubSequence.html" title="class in org.biojava.bio.seq.impl">SubSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SubSequence.html#removeChangeListener(org.biojava.utils.ChangeListener)">removeChangeListener(ChangeListener)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SubSequence.html" title="class in org.biojava.bio.seq.impl">SubSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/projection/ProjectedFeature.html#removeChangeListener(org.biojava.utils.ChangeListener)">removeChangeListener(ChangeListener)</a></span> - Method in class org.biojava.bio.seq.projection.<a href="./org/biojava/bio/seq/projection/ProjectedFeature.html" title="class in org.biojava.bio.seq.projection">ProjectedFeature</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/projection/ProjectedFeature.html#removeChangeListener(org.biojava.utils.ChangeListener, org.biojava.utils.ChangeType)">removeChangeListener(ChangeListener, ChangeType)</a></span> - Method in class org.biojava.bio.seq.projection.<a href="./org/biojava/bio/seq/projection/ProjectedFeature.html" title="class in org.biojava.bio.seq.projection">ProjectedFeature</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/projection/ProjectionContext.html#removeChangeListener(org.biojava.bio.seq.Feature, org.biojava.utils.ChangeListener, org.biojava.utils.ChangeType)">removeChangeListener(Feature, ChangeListener, ChangeType)</a></span> - Method in interface org.biojava.bio.seq.projection.<a href="./org/biojava/bio/seq/projection/ProjectionContext.html" title="interface in org.biojava.bio.seq.projection">ProjectionContext</a></dt>
<dd>
<div class="block">Remove a ChangeListener from a projected feature.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/projection/ReparentContext.html#removeChangeListener(org.biojava.bio.seq.Feature, org.biojava.utils.ChangeListener, org.biojava.utils.ChangeType)">removeChangeListener(Feature, ChangeListener, ChangeType)</a></span> - Method in class org.biojava.bio.seq.projection.<a href="./org/biojava/bio/seq/projection/ReparentContext.html" title="class in org.biojava.bio.seq.projection">ReparentContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/AbstractChangeable.html#removeChangeListener(org.biojava.utils.ChangeListener)">removeChangeListener(ChangeListener)</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/AbstractChangeable.html" title="class in org.biojava.utils">AbstractChangeable</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/AbstractChangeable.html#removeChangeListener(org.biojava.utils.ChangeListener, org.biojava.utils.ChangeType)">removeChangeListener(ChangeListener, ChangeType)</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/AbstractChangeable.html" title="class in org.biojava.utils">AbstractChangeable</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/Changeable.html#removeChangeListener(org.biojava.utils.ChangeListener)">removeChangeListener(ChangeListener)</a></span> - Method in interface org.biojava.utils.<a href="./org/biojava/utils/Changeable.html" title="interface in org.biojava.utils">Changeable</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>use removeChangeListener(cl, ChangeType.UNKNOWN)</i></div>
</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/Changeable.html#removeChangeListener(org.biojava.utils.ChangeListener, org.biojava.utils.ChangeType)">removeChangeListener(ChangeListener, ChangeType)</a></span> - Method in interface org.biojava.utils.<a href="./org/biojava/utils/Changeable.html" title="interface in org.biojava.utils">Changeable</a></dt>
<dd>
<div class="block">Remove a listener that was interested in a specific types of changes.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/ChangeSupport.html#removeChangeListener(org.biojava.utils.ChangeListener)">removeChangeListener(ChangeListener)</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/ChangeSupport.html" title="class in org.biojava.utils">ChangeSupport</a></dt>
<dd>
<div class="block">Remove a listener that was interested in all types of changes.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/ChangeSupport.html#removeChangeListener(org.biojava.utils.ChangeListener, org.biojava.utils.ChangeType)">removeChangeListener(ChangeListener, ChangeType)</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/ChangeSupport.html" title="class in org.biojava.utils">ChangeSupport</a></dt>
<dd>
<div class="block">Remove a listener that was interested in a specific types of changes.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/Unchangeable.html#removeChangeListener(org.biojava.utils.ChangeListener)">removeChangeListener(ChangeListener)</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/Unchangeable.html" title="class in org.biojava.utils">Unchangeable</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/Unchangeable.html#removeChangeListener(org.biojava.utils.ChangeListener, org.biojava.utils.ChangeType)">removeChangeListener(ChangeListener, ChangeType)</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/Unchangeable.html" title="class in org.biojava.utils">Unchangeable</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/InfinitelyAmbiguousSymbolList.html#removeChangeListener(org.biojava.utils.ChangeListener)">removeChangeListener(ChangeListener)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/InfinitelyAmbiguousSymbolList.html" title="class in org.biojavax.bio.seq">InfinitelyAmbiguousSymbolList</a></dt>
<dd>
<div class="block">Remove a listener that was interested in all types of changes.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/InfinitelyAmbiguousSymbolList.html#removeChangeListener(org.biojava.utils.ChangeListener, org.biojava.utils.ChangeType)">removeChangeListener(ChangeListener, ChangeType)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/InfinitelyAmbiguousSymbolList.html" title="class in org.biojavax.bio.seq">InfinitelyAmbiguousSymbolList</a></dt>
<dd>
<div class="block">Remove a listener that was interested in a specific types of changes.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ga/functions/CrossOverFunction.NoCross.html#removeChangeListener(org.biojava.utils.ChangeListener)">removeChangeListener(ChangeListener)</a></span> - Method in class org.biojavax.ga.functions.<a href="./org/biojavax/ga/functions/CrossOverFunction.NoCross.html" title="class in org.biojavax.ga.functions">CrossOverFunction.NoCross</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/functions/CrossOverFunction.NoCross.html#removeChangeListener(org.biojava.utils.ChangeListener, org.biojava.utils.ChangeType)">removeChangeListener(ChangeListener, ChangeType)</a></span> - Method in class org.biojavax.ga.functions.<a href="./org/biojavax/ga/functions/CrossOverFunction.NoCross.html" title="class in org.biojavax.ga.functions">CrossOverFunction.NoCross</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/functions/MutationFunction.NoMutation.html#removeChangeListener(org.biojava.utils.ChangeListener)">removeChangeListener(ChangeListener)</a></span> - Method in class org.biojavax.ga.functions.<a href="./org/biojavax/ga/functions/MutationFunction.NoMutation.html" title="class in org.biojavax.ga.functions">MutationFunction.NoMutation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/functions/MutationFunction.NoMutation.html#removeChangeListener(org.biojava.utils.ChangeListener, org.biojava.utils.ChangeType)">removeChangeListener(ChangeListener, ChangeType)</a></span> - Method in class org.biojavax.ga.functions.<a href="./org/biojavax/ga/functions/MutationFunction.NoMutation.html" title="class in org.biojavax.ga.functions">MutationFunction.NoMutation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/taxa/SimpleTaxonFactory.html#removeChild(org.biojava.bio.taxa.Taxon, org.biojava.bio.taxa.Taxon)">removeChild(Taxon, Taxon)</a></span> - Method in class org.biojava.bio.taxa.<a href="./org/biojava/bio/taxa/SimpleTaxonFactory.html" title="class in org.biojava.bio.taxa">SimpleTaxonFactory</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/taxa/TaxonFactory.html#removeChild(org.biojava.bio.taxa.Taxon, org.biojava.bio.taxa.Taxon)">removeChild(Taxon, Taxon)</a></span> - Method in interface org.biojava.bio.taxa.<a href="./org/biojava/bio/taxa/TaxonFactory.html" title="interface in org.biojava.bio.taxa">TaxonFactory</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Remove a Taxon as a child to this one.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/taxa/WeakTaxonFactory.html#removeChild(org.biojava.bio.taxa.Taxon, org.biojava.bio.taxa.Taxon)">removeChild(Taxon, Taxon)</a></span> - Method in class org.biojava.bio.taxa.<a href="./org/biojava/bio/taxa/WeakTaxonFactory.html" title="class in org.biojava.bio.taxa">WeakTaxonFactory</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/BioEntry.html#removeComment(org.biojavax.Comment)">removeComment(Comment)</a></span> - Method in interface org.biojavax.bio.<a href="./org/biojavax/bio/BioEntry.html" title="interface in org.biojavax.bio">BioEntry</a></dt>
<dd>
<div class="block">Removes a comment instance from this bioentry.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/SimpleBioEntry.html#removeComment(org.biojavax.Comment)">removeComment(Comment)</a></span> - Method in class org.biojavax.bio.<a href="./org/biojavax/bio/SimpleBioEntry.html" title="class in org.biojavax.bio">SimpleBioEntry</a></dt>
<dd>
<div class="block">Removes a comment instance from this bioentry.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/AssembledSymbolList.html#removeComponent(org.biojava.bio.symbol.Location)">removeComponent(Location)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/AssembledSymbolList.html" title="class in org.biojava.bio.seq.impl">AssembledSymbolList</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/NewAssembledSymbolList.html#removeComponent(org.biojava.bio.seq.ComponentFeature)">removeComponent(ComponentFeature)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/NewAssembledSymbolList.html" title="class in org.biojava.bio.seq.impl">NewAssembledSymbolList</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/distributed/DistributedSequenceDB.html#removeDataSource(org.biojava.bio.seq.distributed.DistDataSource)">removeDataSource(DistDataSource)</a></span> - Method in class org.biojava.bio.seq.distributed.<a href="./org/biojava/bio/seq/distributed/DistributedSequenceDB.html" title="class in org.biojava.bio.seq.distributed">DistributedSequenceDB</a></dt>
<dd>
<div class="block">Remove a distributed data source.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/AbstractBeadRenderer.html#removeDelegateRenderer(org.biojava.bio.seq.OptimizableFilter)">removeDelegateRenderer(OptimizableFilter)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/AbstractBeadRenderer.html" title="class in org.biojava.bio.gui.sequence">AbstractBeadRenderer</a></dt>
<dd>
<div class="block"><code>removeDelegateRenderer</code> removes any association
of the given <code>OptimizableFilter</code> with a
<code>BeadFeatureRenderer</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ontology/ComparableTriple.html#removeDescriptor(org.biojavax.ontology.ComparableTerm)">removeDescriptor(ComparableTerm)</a></span> - Method in interface org.biojavax.ontology.<a href="./org/biojavax/ontology/ComparableTriple.html" title="interface in org.biojavax.ontology">ComparableTriple</a></dt>
<dd>
<div class="block">Removes a descriptor.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ontology/SimpleComparableTriple.html#removeDescriptor(org.biojavax.ontology.ComparableTerm)">removeDescriptor(ComparableTerm)</a></span> - Method in class org.biojavax.ontology.<a href="./org/biojavax/ontology/SimpleComparableTriple.html" title="class in org.biojavax.ontology">SimpleComparableTriple</a></dt>
<dd>
<div class="block">Removes a descriptor.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/molbio/RestrictionMapper.html#removeEnzyme(org.biojava.bio.molbio.RestrictionEnzyme)">removeEnzyme(RestrictionEnzyme)</a></span> - Method in class org.biojava.bio.molbio.<a href="./org/biojava/bio/molbio/RestrictionMapper.html" title="class in org.biojava.bio.molbio">RestrictionMapper</a></dt>
<dd>
<div class="block"><code>removeEnzyme</code> removes an enzyme from those to be
searched for in the <code>Sequence</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/DASSequence.html#removeFeature(org.biojava.bio.seq.Feature)">removeFeature(Feature)</a></span> - Method in class org.biojava.bio.program.das.<a href="./org/biojava/bio/program/das/DASSequence.html" title="class in org.biojava.bio.program.das">DASSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/AbstractFeatureHolder.html#removeFeature(org.biojava.bio.seq.Feature)">removeFeature(Feature)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/AbstractFeatureHolder.html" title="class in org.biojava.bio.seq">AbstractFeatureHolder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureHolder.EmptyFeatureHolder.html#removeFeature(org.biojava.bio.seq.Feature)">removeFeature(Feature)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureHolder.EmptyFeatureHolder.html" title="class in org.biojava.bio.seq">FeatureHolder.EmptyFeatureHolder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureHolder.html#removeFeature(org.biojava.bio.seq.Feature)">removeFeature(Feature)</a></span> - Method in interface org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureHolder.html" title="interface in org.biojava.bio.seq">FeatureHolder</a></dt>
<dd>
<div class="block">Remove a feature from this FeatureHolder.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/DummySequence.html#removeFeature(org.biojava.bio.seq.Feature)">removeFeature(Feature)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/DummySequence.html" title="class in org.biojava.bio.seq.impl">DummySequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/LazyFilterFeatureHolder.html#removeFeature(org.biojava.bio.seq.Feature)">removeFeature(Feature)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/LazyFilterFeatureHolder.html" title="class in org.biojava.bio.seq.impl">LazyFilterFeatureHolder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/RevCompSequence.html#removeFeature(org.biojava.bio.seq.Feature)">removeFeature(Feature)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/RevCompSequence.html" title="class in org.biojava.bio.seq.impl">RevCompSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleFeature.html#removeFeature(org.biojava.bio.seq.Feature)">removeFeature(Feature)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleFeature.html" title="class in org.biojava.bio.seq.impl">SimpleFeature</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleGappedSequence.html#removeFeature(org.biojava.bio.seq.Feature)">removeFeature(Feature)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleGappedSequence.html" title="class in org.biojava.bio.seq.impl">SimpleGappedSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleSequence.html#removeFeature(org.biojava.bio.seq.Feature)">removeFeature(Feature)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleSequence.html" title="class in org.biojava.bio.seq.impl">SimpleSequence</a></dt>
<dd>
<div class="block">Remove a feature attached to this sequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SubSequence.html#removeFeature(org.biojava.bio.seq.Feature)">removeFeature(Feature)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SubSequence.html" title="class in org.biojava.bio.seq.impl">SubSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/ViewSequence.html#removeFeature(org.biojava.bio.seq.Feature)">removeFeature(Feature)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/ViewSequence.html" title="class in org.biojava.bio.seq.impl">ViewSequence</a></dt>
<dd>
<div class="block">Remove a feature from this sequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/LazyFeatureHolder.html#removeFeature(org.biojava.bio.seq.Feature)">removeFeature(Feature)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/LazyFeatureHolder.html" title="class in org.biojava.bio.seq">LazyFeatureHolder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/NewSimpleAssembly.html#removeFeature(org.biojava.bio.seq.Feature)">removeFeature(Feature)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/NewSimpleAssembly.html" title="class in org.biojava.bio.seq">NewSimpleAssembly</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/projection/ProjectedFeature.html#removeFeature(org.biojava.bio.seq.Feature)">removeFeature(Feature)</a></span> - Method in class org.biojava.bio.seq.projection.<a href="./org/biojava/bio/seq/projection/ProjectedFeature.html" title="class in org.biojava.bio.seq.projection">ProjectedFeature</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/projection/ProjectedFeatureHolder.html#removeFeature(org.biojava.bio.seq.Feature)">removeFeature(Feature)</a></span> - Method in class org.biojava.bio.seq.projection.<a href="./org/biojava/bio/seq/projection/ProjectedFeatureHolder.html" title="class in org.biojava.bio.seq.projection">ProjectedFeatureHolder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/projection/ProjectionContext.html#removeFeature(org.biojava.bio.seq.Feature)">removeFeature(Feature)</a></span> - Method in interface org.biojava.bio.seq.projection.<a href="./org/biojava/bio/seq/projection/ProjectionContext.html" title="interface in org.biojava.bio.seq.projection">ProjectionContext</a></dt>
<dd>
<div class="block">Remove the dying child.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/projection/ProjectionContext.html#removeFeature(org.biojava.bio.seq.Feature, org.biojava.bio.seq.Feature)">removeFeature(Feature, Feature)</a></span> - Method in interface org.biojava.bio.seq.projection.<a href="./org/biojava/bio/seq/projection/ProjectionContext.html" title="interface in org.biojava.bio.seq.projection">ProjectionContext</a></dt>
<dd>
<div class="block">Remove the dying child.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/projection/ReparentContext.html#removeFeature(org.biojava.bio.seq.Feature)">removeFeature(Feature)</a></span> - Method in class org.biojava.bio.seq.projection.<a href="./org/biojava/bio/seq/projection/ReparentContext.html" title="class in org.biojava.bio.seq.projection">ReparentContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/projection/ReparentContext.html#removeFeature(org.biojava.bio.seq.Feature, org.biojava.bio.seq.Feature)">removeFeature(Feature, Feature)</a></span> - Method in class org.biojava.bio.seq.projection.<a href="./org/biojava/bio/seq/projection/ReparentContext.html" title="class in org.biojava.bio.seq.projection">ReparentContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/SimpleAssembly.html#removeFeature(org.biojava.bio.seq.Feature)">removeFeature(Feature)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/SimpleAssembly.html" title="class in org.biojava.bio.seq">SimpleAssembly</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/SimpleFeatureHolder.html#removeFeature(org.biojava.bio.seq.Feature)">removeFeature(Feature)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/SimpleFeatureHolder.html" title="class in org.biojava.bio.seq">SimpleFeatureHolder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichFeature.html#removeFeature(org.biojava.bio.seq.Feature)">removeFeature(Feature)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichFeature.html" title="class in org.biojavax.bio.seq">SimpleRichFeature</a></dt>
<dd>
<div class="block">Remove a feature from this FeatureHolder.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/ThinRichSequence.html#removeFeature(org.biojava.bio.seq.Feature)">removeFeature(Feature)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/ThinRichSequence.html" title="class in org.biojavax.bio.seq">ThinRichSequence</a></dt>
<dd>
<div class="block">Remove a feature from this FeatureHolder.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/MergeFeatureHolder.html#removeFeatureHolder(org.biojava.bio.seq.FeatureHolder)">removeFeatureHolder(FeatureHolder)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/MergeFeatureHolder.html" title="class in org.biojava.bio.seq">MergeFeatureHolder</a></dt>
<dd>
<div class="block">Remove a FeatureHolder from the set of FeatureHolders which
are merged.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichFeatureRelationshipHolder.html#removeFeatureRelationship(org.biojavax.bio.seq.RichFeatureRelationship)">removeFeatureRelationship(RichFeatureRelationship)</a></span> - Method in interface org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichFeatureRelationshipHolder.html" title="interface in org.biojavax.bio.seq">RichFeatureRelationshipHolder</a></dt>
<dd>
<div class="block">Removes a relationship from this feature holder.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichFeature.html#removeFeatureRelationship(org.biojavax.bio.seq.RichFeatureRelationship)">removeFeatureRelationship(RichFeatureRelationship)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichFeature.html" title="class in org.biojavax.bio.seq">SimpleRichFeature</a></dt>
<dd>
<div class="block">Removes a relationship from this feature holder.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/GlyphFeatureRenderer.html#removeFilterWithGlyph(org.biojava.bio.seq.FeatureFilter)">removeFilterWithGlyph(FeatureFilter)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/GlyphFeatureRenderer.html" title="class in org.biojava.bio.gui.sequence">GlyphFeatureRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/Unchangeable.html#removeForwarder(org.biojava.utils.ChangeForwarder, org.biojava.utils.ChangeType)">removeForwarder(ChangeForwarder, ChangeType)</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/Unchangeable.html" title="class in org.biojava.utils">Unchangeable</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/naming/ObdaContext.html#removeFromEnvironment(java.lang.String)">removeFromEnvironment(String)</a></span> - Method in class org.biojava.naming.<a href="./org/biojava/naming/ObdaContext.html" title="class in org.biojava.naming">ObdaContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/GappedSymbolList.html#removeGap(int)">removeGap(int)</a></span> - Method in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/GappedSymbolList.html" title="interface in org.biojava.bio.symbol">GappedSymbolList</a></dt>
<dd>
<div class="block">Remove a single gap at position pos in this GappedSymbolList.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleGappedSymbolList.html#removeGap(int)">removeGap(int)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleGappedSymbolList.html" title="class in org.biojava.bio.symbol">SimpleGappedSymbolList</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/FlexibleAlignment.html#removeGaps(org.biojava.bio.symbol.GappedSymbolList, int, int)">removeGaps(GappedSymbolList, int, int)</a></span> - Method in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/FlexibleAlignment.html" title="class in org.biojava.bio.alignment">FlexibleAlignment</a></dt>
<dd>
<div class="block">because there is a bug in GappedSymbolList</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/GappedSymbolList.html#removeGaps(int, int)">removeGaps(int, int)</a></span> - Method in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/GappedSymbolList.html" title="interface in org.biojava.bio.symbol">GappedSymbolList</a></dt>
<dd>
<div class="block">Remove some gaps at position pos in this GappedSymbolList.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleGappedSymbolList.html#removeGaps(int, int)">removeGaps(int, int)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleGappedSymbolList.html" title="class in org.biojava.bio.symbol">SimpleGappedSymbolList</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/biosql/TaxonSQL.html#removeGeneticCodeID(java.sql.Connection, org.biojava.bio.seq.db.biosql.DBHelper, org.biojava.bio.taxa.Taxon)">removeGeneticCodeID(Connection, DBHelper, Taxon)</a></span> - Static method in class org.biojava.bio.seq.db.biosql.<a href="./org/biojava/bio/seq/db/biosql/TaxonSQL.html" title="class in org.biojava.bio.seq.db.biosql">TaxonSQL</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Deletes the genetic code annotation from the taxon in the database.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/AbstractSVMClassifierModel.html#removeItem(java.lang.Object)">removeItem(Object)</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/AbstractSVMClassifierModel.html" title="class in org.biojava.stats.svm">AbstractSVMClassifierModel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/AbstractSVMTarget.html#removeItem(java.lang.Object)">removeItem(Object)</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/AbstractSVMTarget.html" title="class in org.biojava.stats.svm">AbstractSVMTarget</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/SimpleSVMClassifierModel.html#removeItem(java.lang.Object)">removeItem(Object)</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/SimpleSVMClassifierModel.html" title="class in org.biojava.stats.svm">SimpleSVMClassifierModel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/SimpleSVMTarget.html#removeItem(java.lang.Object)">removeItem(Object)</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/SimpleSVMTarget.html" title="class in org.biojava.stats.svm">SimpleSVMTarget</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/SVMClassifierModel.html#removeItem(java.lang.Object)">removeItem(Object)</a></span> - Method in interface org.biojava.stats.svm.<a href="./org/biojava/stats/svm/SVMClassifierModel.html" title="interface in org.biojava.stats.svm">SVMClassifierModel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/SVMTarget.html#removeItem(java.lang.Object)">removeItem(Object)</a></span> - Method in interface org.biojava.stats.svm.<a href="./org/biojava/stats/svm/SVMTarget.html" title="interface in org.biojava.stats.svm">SVMTarget</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/indexdb/BioStoreFactory.html#removeKey(java.lang.String)">removeKey(String)</a></span> - Method in class org.biojava.bio.program.indexdb.<a href="./org/biojava/bio/program/indexdb/BioStoreFactory.html" title="class in org.biojava.bio.program.indexdb">BioStoreFactory</a></dt>
<dd>
<div class="block"><code>removeKey</code> removes the specified
key.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/Index2Model.html#removeKeyPath(java.lang.String)">removeKeyPath(String)</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/Index2Model.html" title="class in org.biojava.bio.program.tagvalue">Index2Model</a></dt>
<dd>
<div class="block">Remove a key.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/LabelledSequenceRenderer.html#removeLabelString(java.lang.String)">removeLabelString(String)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/LabelledSequenceRenderer.html" title="class in org.biojava.bio.gui.sequence">LabelledSequenceRenderer</a></dt>
<dd>
<div class="block">Remove a piece of text from the label</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/biosql/TaxonSQL.html#removeLeftValue(java.sql.Connection, org.biojava.bio.seq.db.biosql.DBHelper, org.biojava.bio.taxa.Taxon)">removeLeftValue(Connection, DBHelper, Taxon)</a></span> - Static method in class org.biojava.bio.seq.db.biosql.<a href="./org/biojava/bio/seq/db/biosql/TaxonSQL.html" title="class in org.biojava.bio.seq.db.biosql">TaxonSQL</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Deletes the left value from the specified taxon in the database.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/ChangeHub.html#removeListener(java.lang.Object, org.biojava.utils.ChangeListener, org.biojava.utils.ChangeType)">removeListener(Object, ChangeListener, ChangeType)</a></span> - Method in interface org.biojava.utils.<a href="./org/biojava/utils/ChangeHub.html" title="interface in org.biojava.utils">ChangeHub</a></dt>
<dd>
<div class="block">remove a ChangeListener associated with given key.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/IndexedChangeHub.html#removeListener(java.lang.Object, org.biojava.utils.ChangeListener, org.biojava.utils.ChangeType)">removeListener(Object, ChangeListener, ChangeType)</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/IndexedChangeHub.html" title="class in org.biojava.utils">IndexedChangeHub</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/biosql/TaxonSQL.html#removeMitochondrialGeneticCodeID(java.sql.Connection, org.biojava.bio.seq.db.biosql.DBHelper, org.biojava.bio.taxa.Taxon)">removeMitochondrialGeneticCodeID(Connection, DBHelper, Taxon)</a></span> - Static method in class org.biojava.bio.seq.db.biosql.<a href="./org/biojava/bio/seq/db/biosql/TaxonSQL.html" title="class in org.biojava.bio.seq.db.biosql">TaxonSQL</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Deletes the so called mitochondrial genetic code annotation from the given taxon.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/MMcifParser.html#removeMMcifConsumer(org.biojava.bio.structure.io.mmcif.MMcifConsumer)">removeMMcifConsumer(MMcifConsumer)</a></span> - Method in interface org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/MMcifParser.html" title="interface in org.biojava.bio.structure.io.mmcif">MMcifParser</a></dt>
<dd>
<div class="block">remove a single consumer from the parser</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/SimpleMMcifParser.html#removeMMcifConsumer(org.biojava.bio.structure.io.mmcif.MMcifConsumer)">removeMMcifConsumer(MMcifConsumer)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/SimpleMMcifParser.html" title="class in org.biojava.bio.structure.io.mmcif">SimpleMMcifParser</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/biosql/TaxonSQL.html#removeName(java.sql.Connection, org.biojava.bio.seq.db.biosql.DBHelper, org.biojava.bio.taxa.Taxon, java.lang.String, java.lang.String)">removeName(Connection, DBHelper, Taxon, String, String)</a></span> - Static method in class org.biojava.bio.seq.db.biosql.<a href="./org/biojava/bio/seq/db/biosql/TaxonSQL.html" title="class in org.biojava.bio.seq.db.biosql">TaxonSQL</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Deletes the specified name from of the taxon from the database.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/taxa/NCBITaxon.html#removeName(java.lang.String, java.lang.String)">removeName(String, String)</a></span> - Method in interface org.biojavax.bio.taxa.<a href="./org/biojavax/bio/taxa/NCBITaxon.html" title="interface in org.biojavax.bio.taxa">NCBITaxon</a></dt>
<dd>
<div class="block">Removes the name from the given name class.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/taxa/SimpleNCBITaxon.html#removeName(java.lang.String, java.lang.String)">removeName(String, String)</a></span> - Method in class org.biojavax.bio.taxa.<a href="./org/biojavax/bio/taxa/SimpleNCBITaxon.html" title="class in org.biojavax.bio.taxa">SimpleNCBITaxon</a></dt>
<dd>
<div class="block">Removes the name from the given name class.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/EmptyRichAnnotation.html#removeNote(org.biojavax.Note)">removeNote(Note)</a></span> - Method in class org.biojavax.<a href="./org/biojavax/EmptyRichAnnotation.html" title="class in org.biojavax">EmptyRichAnnotation</a></dt>
<dd>
<div class="block">Removes a note from this annotation.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/RichAnnotation.html#removeNote(org.biojavax.Note)">removeNote(Note)</a></span> - Method in interface org.biojavax.<a href="./org/biojavax/RichAnnotation.html" title="interface in org.biojavax">RichAnnotation</a></dt>
<dd>
<div class="block">Removes a note from this annotation.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleRichAnnotation.html#removeNote(org.biojavax.Note)">removeNote(Note)</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleRichAnnotation.html" title="class in org.biojavax">SimpleRichAnnotation</a></dt>
<dd>
<div class="block">Removes a note from this annotation.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ga/impl/AbstractPopulation.html#removeOrganism(org.biojavax.ga.Organism)">removeOrganism(Organism)</a></span> - Method in class org.biojavax.ga.impl.<a href="./org/biojavax/ga/impl/AbstractPopulation.html" title="class in org.biojavax.ga.impl">AbstractPopulation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/Population.html#removeOrganism(org.biojavax.ga.Organism)">removeOrganism(Organism)</a></span> - Method in interface org.biojavax.ga.<a href="./org/biojavax/ga/Population.html" title="interface in org.biojavax.ga">Population</a></dt>
<dd>
<div class="block">Kills off the organism</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ga/impl/AbstractPopulation.html#removeOrganismImpl(org.biojavax.ga.Organism)">removeOrganismImpl(Organism)</a></span> - Method in class org.biojavax.ga.impl.<a href="./org/biojavax/ga/impl/AbstractPopulation.html" title="class in org.biojavax.ga.impl">AbstractPopulation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/impl/SimplePopulation.html#removeOrganismImpl(org.biojavax.ga.Organism)">removeOrganismImpl(Organism)</a></span> - Method in class org.biojavax.ga.impl.<a href="./org/biojavax/ga/impl/SimplePopulation.html" title="class in org.biojavax.ga.impl">SimplePopulation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/impl/AbstractPopulation.html#removeOrganisms(org.biojavax.ga.Organism[])">removeOrganisms(Organism[])</a></span> - Method in class org.biojavax.ga.impl.<a href="./org/biojavax/ga/impl/AbstractPopulation.html" title="class in org.biojavax.ga.impl">AbstractPopulation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/impl/AbstractPopulation.html#removeOrganisms(java.util.Set)">removeOrganisms(Set)</a></span> - Method in class org.biojavax.ga.impl.<a href="./org/biojavax/ga/impl/AbstractPopulation.html" title="class in org.biojavax.ga.impl">AbstractPopulation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/Population.html#removeOrganisms(org.biojavax.ga.Organism[])">removeOrganisms(Organism[])</a></span> - Method in interface org.biojavax.ga.<a href="./org/biojavax/ga/Population.html" title="interface in org.biojavax.ga">Population</a></dt>
<dd>
<div class="block">Removes all the <code>Organisms</code> in <code>orgs</code></div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ga/Population.html#removeOrganisms(java.util.Set)">removeOrganisms(Set)</a></span> - Method in interface org.biojavax.ga.<a href="./org/biojavax/ga/Population.html" title="interface in org.biojavax.ga">Population</a></dt>
<dd>
<div class="block">Removes all the <code>Organisms</code> in <code>orgs</code></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/OrthologueSet.html#removeOrthologue(org.biojava.bio.program.homologene.Orthologue)">removeOrthologue(Orthologue)</a></span> - Method in interface org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/OrthologueSet.html" title="interface in org.biojava.bio.program.homologene">OrthologueSet</a></dt>
<dd>
<div class="block">Remove an orthologue from the set.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/SimpleOrthologueSet.html#removeOrthologue(org.biojava.bio.program.homologene.Orthologue)">removeOrthologue(Orthologue)</a></span> - Method in class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/SimpleOrthologueSet.html" title="class in org.biojava.bio.program.homologene">SimpleOrthologueSet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/OrthoPairSet.html#removeOrthoPair(org.biojava.bio.program.homologene.OrthoPair)">removeOrthoPair(OrthoPair)</a></span> - Method in interface org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/OrthoPairSet.html" title="interface in org.biojava.bio.program.homologene">OrthoPairSet</a></dt>
<dd>
<div class="block">removes a specified OrthoPair relationship
from this group.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/SimpleOrthoPairSet.html#removeOrthoPair(org.biojava.bio.program.homologene.OrthoPair)">removeOrthoPair(OrthoPair)</a></span> - Method in class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/SimpleOrthoPairSet.html" title="class in org.biojava.bio.program.homologene">SimpleOrthoPairSet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/phred/PhredFormat.html#removeParseErrorListener(org.biojava.utils.ParseErrorListener)">removeParseErrorListener(ParseErrorListener)</a></span> - Method in class org.biojava.bio.program.phred.<a href="./org/biojava/bio/program/phred/PhredFormat.html" title="class in org.biojava.bio.program.phred">PhredFormat</a></dt>
<dd>
<div class="block">Removes a parse error listener from the list of listeners if it is
included.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/EmblLikeFormat.html#removeParseErrorListener(org.biojava.utils.ParseErrorListener)">removeParseErrorListener(ParseErrorListener)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/EmblLikeFormat.html" title="class in org.biojava.bio.seq.io">EmblLikeFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Removes a parse error listener from the list of listeners if it is
included.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/EmblProcessor.html#removeParseErrorListener(org.biojava.utils.ParseErrorListener)">removeParseErrorListener(ParseErrorListener)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/EmblProcessor.html" title="class in org.biojava.bio.seq.io">EmblProcessor</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Removes a parse error listener from the list of listeners if it is
included.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/FastaFormat.html#removeParseErrorListener(org.biojava.utils.ParseErrorListener)">removeParseErrorListener(ParseErrorListener)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/FastaFormat.html" title="class in org.biojava.bio.seq.io">FastaFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Removes a parse error listener from the list of listeners if it is
included.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/GenbankFormat.html#removeParseErrorListener(org.biojava.utils.ParseErrorListener)">removeParseErrorListener(ParseErrorListener)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/GenbankFormat.html" title="class in org.biojava.bio.seq.io">GenbankFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Removes a parse error listener from the list of listeners if it is
included.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/GenbankProcessor.html#removeParseErrorListener(org.biojava.utils.ParseErrorListener)">removeParseErrorListener(ParseErrorListener)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/GenbankProcessor.html" title="class in org.biojava.bio.seq.io">GenbankProcessor</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Removes a parse error listener from the list of listeners if it is
included.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SwissprotProcessor.html#removeParseErrorListener(org.biojava.utils.ParseErrorListener)">removeParseErrorListener(ParseErrorListener)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SwissprotProcessor.html" title="class in org.biojava.bio.seq.io">SwissprotProcessor</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Removes a parse error listener from the list of listeners if it is
included.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/ParseErrorSource.html#removeParseErrorListener(org.biojava.utils.ParseErrorListener)">removeParseErrorListener(ParseErrorListener)</a></span> - Method in interface org.biojava.utils.<a href="./org/biojava/utils/ParseErrorSource.html" title="interface in org.biojava.utils">ParseErrorSource</a></dt>
<dd>
<div class="block">Removes a parse error listener from the list of listeners.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/AbstractAnnotation.html#removeProperty(java.lang.Object)">removeProperty(Object)</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/AbstractAnnotation.html" title="class in org.biojava.bio">AbstractAnnotation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/Annotation.html#removeProperty(java.lang.Object)">removeProperty(Object)</a></span> - Method in interface org.biojava.bio.<a href="./org/biojava/bio/Annotation.html" title="interface in org.biojava.bio">Annotation</a></dt>
<dd>
<div class="block">Delete a property.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/AnnotationType.Abstract.html#removeProperty(org.biojava.bio.Annotation, java.lang.Object, java.lang.Object)">removeProperty(Annotation, Object, Object)</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/AnnotationType.Abstract.html" title="class in org.biojava.bio">AnnotationType.Abstract</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/AnnotationType.html#removeProperty(org.biojava.bio.Annotation, java.lang.Object, java.lang.Object)">removeProperty(Annotation, Object, Object)</a></span> - Method in interface org.biojava.bio.<a href="./org/biojava/bio/AnnotationType.html" title="interface in org.biojava.bio">AnnotationType</a></dt>
<dd>
<div class="block">Remove a value from the specified property slot.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/MergeAnnotation.html#removeProperty(java.lang.Object)">removeProperty(Object)</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/MergeAnnotation.html" title="class in org.biojava.bio">MergeAnnotation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/OverlayAnnotation.html#removeProperty(java.lang.Object)">removeProperty(Object)</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/OverlayAnnotation.html" title="class in org.biojava.bio">OverlayAnnotation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/EmptyRichAnnotation.html#removeProperty(java.lang.Object)">removeProperty(Object)</a></span> - Method in class org.biojavax.<a href="./org/biojavax/EmptyRichAnnotation.html" title="class in org.biojavax">EmptyRichAnnotation</a></dt>
<dd>
<div class="block">Delete a property.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleRichAnnotation.html#removeProperty(java.lang.Object)">removeProperty(Object)</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleRichAnnotation.html" title="class in org.biojavax">SimpleRichAnnotation</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span> </div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePanel.Border.html#removePropertyChangeListener(java.beans.PropertyChangeListener)">removePropertyChangeListener(PropertyChangeListener)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePanel.Border.html" title="class in org.biojava.bio.gui.sequence">SequencePanel.Border</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePoster.Border.html#removePropertyChangeListener(java.beans.PropertyChangeListener)">removePropertyChangeListener(PropertyChangeListener)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePoster.Border.html" title="class in org.biojava.bio.gui.sequence">SequencePoster.Border</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/StackedLogoPainter.html#removePropertyChangeListener(java.beans.PropertyChangeListener)">removePropertyChangeListener(PropertyChangeListener)</a></span> - Method in class org.biojava.bio.gui.<a href="./org/biojava/bio/gui/StackedLogoPainter.html" title="class in org.biojava.bio.gui">StackedLogoPainter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/StackedLogoPainter.html#removePropertyChangeListener(java.lang.String, java.beans.PropertyChangeListener)">removePropertyChangeListener(String, PropertyChangeListener)</a></span> - Method in class org.biojava.bio.gui.<a href="./org/biojava/bio/gui/StackedLogoPainter.html" title="class in org.biojava.bio.gui">StackedLogoPainter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/TextLogoPainter.html#removePropertyChangeListener(java.beans.PropertyChangeListener)">removePropertyChangeListener(PropertyChangeListener)</a></span> - Method in class org.biojava.bio.gui.<a href="./org/biojava/bio/gui/TextLogoPainter.html" title="class in org.biojava.bio.gui">TextLogoPainter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/TextLogoPainter.html#removePropertyChangeListener(java.lang.String, java.beans.PropertyChangeListener)">removePropertyChangeListener(String, PropertyChangeListener)</a></span> - Method in class org.biojava.bio.gui.<a href="./org/biojava/bio/gui/TextLogoPainter.html" title="class in org.biojava.bio.gui">TextLogoPainter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/biosql/TaxonSQL.html#removeRank(java.sql.Connection, org.biojava.bio.seq.db.biosql.DBHelper, org.biojava.bio.taxa.Taxon)">removeRank(Connection, DBHelper, Taxon)</a></span> - Static method in class org.biojava.bio.seq.db.biosql.<a href="./org/biojava/bio/seq/db/biosql/TaxonSQL.html" title="class in org.biojava.bio.seq.db.biosql">TaxonSQL</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Removes the rank persistently from the taxon in the database.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichFeature.html#removeRankedCrossRef(org.biojavax.RankedCrossRef)">removeRankedCrossRef(RankedCrossRef)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichFeature.html" title="class in org.biojavax.bio.seq">SimpleRichFeature</a></dt>
<dd>
<div class="block">Removes a ranked cross reference from the existing set.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/SimpleBioEntry.html#removeRankedCrossRef(org.biojavax.RankedCrossRef)">removeRankedCrossRef(RankedCrossRef)</a></span> - Method in class org.biojavax.bio.<a href="./org/biojavax/bio/SimpleBioEntry.html" title="class in org.biojavax.bio">SimpleBioEntry</a></dt>
<dd>
<div class="block">Removes a ranked cross reference from the existing set.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ontology/SimpleComparableTerm.html#removeRankedCrossRef(org.biojavax.RankedCrossRef)">removeRankedCrossRef(RankedCrossRef)</a></span> - Method in class org.biojavax.ontology.<a href="./org/biojavax/ontology/SimpleComparableTerm.html" title="class in org.biojavax.ontology">SimpleComparableTerm</a></dt>
<dd>
<div class="block">Removes a ranked cross reference from the existing set.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/RankedCrossRefable.html#removeRankedCrossRef(org.biojavax.RankedCrossRef)">removeRankedCrossRef(RankedCrossRef)</a></span> - Method in interface org.biojavax.<a href="./org/biojavax/RankedCrossRefable.html" title="interface in org.biojavax">RankedCrossRefable</a></dt>
<dd>
<div class="block">Removes a ranked cross reference from the existing set.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/BioEntry.html#removeRankedDocRef(org.biojavax.RankedDocRef)">removeRankedDocRef(RankedDocRef)</a></span> - Method in interface org.biojavax.bio.<a href="./org/biojavax/bio/BioEntry.html" title="interface in org.biojavax.bio">BioEntry</a></dt>
<dd>
<div class="block">Removes a ranked docref instance from this bioentry.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/SimpleBioEntry.html#removeRankedDocRef(org.biojavax.RankedDocRef)">removeRankedDocRef(RankedDocRef)</a></span> - Method in class org.biojavax.bio.<a href="./org/biojavax/bio/SimpleBioEntry.html" title="class in org.biojavax.bio">SimpleBioEntry</a></dt>
<dd>
<div class="block">Removes a ranked docref instance from this bioentry.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/BioEntry.html#removeRelationship(org.biojavax.bio.BioEntryRelationship)">removeRelationship(BioEntryRelationship)</a></span> - Method in interface org.biojavax.bio.<a href="./org/biojavax/bio/BioEntry.html" title="interface in org.biojavax.bio">BioEntry</a></dt>
<dd>
<div class="block">Removes a relation instance from this bioentry.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/SimpleBioEntry.html#removeRelationship(org.biojavax.bio.BioEntryRelationship)">removeRelationship(BioEntryRelationship)</a></span> - Method in class org.biojavax.bio.<a href="./org/biojavax/bio/SimpleBioEntry.html" title="class in org.biojavax.bio">SimpleBioEntry</a></dt>
<dd>
<div class="block">Removes a relation instance from this bioentry.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/CircularMLR.html#removeRenderer(org.biojava.bio.gui.sequence.CircularRenderer)">removeRenderer(CircularRenderer)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/CircularMLR.html" title="class in org.biojava.bio.gui.sequence">CircularMLR</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/MultiLineRenderer.html#removeRenderer(org.biojava.bio.gui.sequence.SequenceRenderer)">removeRenderer(SequenceRenderer)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/MultiLineRenderer.html" title="class in org.biojava.bio.gui.sequence">MultiLineRenderer</a></dt>
<dd>
<div class="block"><code>removeRenderer</code> removes a renderer.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PairwiseOverlayRenderer.html#removeRenderer(org.biojava.bio.gui.sequence.PairwiseSequenceRenderer)">removeRenderer(PairwiseSequenceRenderer)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PairwiseOverlayRenderer.html" title="class in org.biojava.bio.gui.sequence">PairwiseOverlayRenderer</a></dt>
<dd>
<div class="block"><code>removeRenderer</code> removes a renderer.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/StackedFeatureRenderer.html#removeRenderer(org.biojava.bio.gui.sequence.FeatureRenderer)">removeRenderer(FeatureRenderer)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/StackedFeatureRenderer.html" title="class in org.biojava.bio.gui.sequence">StackedFeatureRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureTypes.html#removeRepository(org.biojava.bio.seq.FeatureTypes.Repository)">removeRepository(FeatureTypes.Repository)</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureTypes.html" title="class in org.biojava.bio.seq">FeatureTypes</a></dt>
<dd>
<div class="block">Remove a repository from FeaturTypes.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/AbstractRichSequenceDB.html#removeRichSequence(java.lang.String)">removeRichSequence(String)</a></span> - Method in class org.biojavax.bio.db.<a href="./org/biojavax/bio/db/AbstractRichSequenceDB.html" title="class in org.biojavax.bio.db">AbstractRichSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLRichSequenceDB.html#removeRichSequence(java.lang.String)">removeRichSequence(String)</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLRichSequenceDB.html" title="class in org.biojavax.bio.db.biosql">BioSQLRichSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/RichSequenceDBLite.html#removeRichSequence(java.lang.String)">removeRichSequence(String)</a></span> - Method in interface org.biojavax.bio.db.<a href="./org/biojavax/bio/db/RichSequenceDBLite.html" title="interface in org.biojavax.bio.db">RichSequenceDBLite</a></dt>
<dd>
<div class="block">Remove the RichSequence associated with an ID from the database.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/biosql/TaxonSQL.html#removeRightValue(java.sql.Connection, org.biojava.bio.seq.db.biosql.DBHelper, org.biojava.bio.taxa.Taxon)">removeRightValue(Connection, DBHelper, Taxon)</a></span> - Static method in class org.biojava.bio.seq.db.biosql.<a href="./org/biojava/bio/seq/db/biosql/TaxonSQL.html" title="class in org.biojava.bio.seq.db.biosql">TaxonSQL</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Deletes the right value from the specified taxon in the database.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/Indexer.html#removeSecondaryKey(java.lang.String)">removeSecondaryKey(String)</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/Indexer.html" title="class in org.biojava.bio.program.tagvalue">Indexer</a></dt>
<dd>
<div class="block">Remove a secondary key.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/ARAlignment.html#removeSequence(java.lang.Object)">removeSequence(Object)</a></span> - Method in interface org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/ARAlignment.html" title="interface in org.biojava.bio.alignment">ARAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/FlexibleAlignment.html#removeSequence(java.lang.Object)">removeSequence(Object)</a></span> - Method in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/FlexibleAlignment.html" title="class in org.biojava.bio.alignment">FlexibleAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/DASSequenceDB.html#removeSequence(java.lang.String)">removeSequence(String)</a></span> - Method in class org.biojava.bio.program.das.<a href="./org/biojava/bio/program/das/DASSequenceDB.html" title="class in org.biojava.bio.program.das">DASSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/AbstractSequenceDB.html#removeSequence(java.lang.String)">removeSequence(String)</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/AbstractSequenceDB.html" title="class in org.biojava.bio.seq.db">AbstractSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/biofetch/BioFetchSequenceDB.html#removeSequence(java.lang.String)">removeSequence(String)</a></span> - Method in class org.biojava.bio.seq.db.biofetch.<a href="./org/biojava/bio/seq/db/biofetch/BioFetchSequenceDB.html" title="class in org.biojava.bio.seq.db.biofetch">BioFetchSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/biosql/BioSQLSequenceDB.html#removeSequence(java.lang.String)">removeSequence(String)</a></span> - Method in class org.biojava.bio.seq.db.biosql.<a href="./org/biojava/bio/seq/db/biosql/BioSQLSequenceDB.html" title="class in org.biojava.bio.seq.db.biosql">BioSQLSequenceDB</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/DummySequenceDB.html#removeSequence(java.lang.String)">removeSequence(String)</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/DummySequenceDB.html" title="class in org.biojava.bio.seq.db">DummySequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/flat/FlatSequenceDB.html#removeSequence(java.lang.String)">removeSequence(String)</a></span> - Method in class org.biojava.bio.seq.db.flat.<a href="./org/biojava/bio/seq/db/flat/FlatSequenceDB.html" title="class in org.biojava.bio.seq.db.flat">FlatSequenceDB</a></dt>
<dd>
<div class="block"><code>removeSequence</code> always throws a
<code>ChangeVetoException</code> as this implementation is
immutable.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/HashSequenceDB.html#removeSequence(java.lang.String)">removeSequence(String)</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/HashSequenceDB.html" title="class in org.biojava.bio.seq.db">HashSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/SequenceDBLite.html#removeSequence(java.lang.String)">removeSequence(String)</a></span> - Method in interface org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/SequenceDBLite.html" title="interface in org.biojava.bio.seq.db">SequenceDBLite</a></dt>
<dd>
<div class="block">Remove the sequence associated with an ID from the database.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/WebSequenceDB.html#removeSequence(java.lang.String)">removeSequence(String)</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/WebSequenceDB.html" title="class in org.biojava.bio.seq.db">WebSequenceDB</a></dt>
<dd>
<div class="block">Not supported, you can't remove a sequence from a WebDB!</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/distributed/DistributedSequenceDB.html#removeSequence(java.lang.String)">removeSequence(String)</a></span> - Method in class org.biojava.bio.seq.distributed.<a href="./org/biojava/bio/seq/distributed/DistributedSequenceDB.html" title="class in org.biojava.bio.seq.distributed">DistributedSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/AbstractRichSequenceDB.html#removeSequence(java.lang.String)">removeSequence(String)</a></span> - Method in class org.biojavax.bio.db.<a href="./org/biojavax/bio/db/AbstractRichSequenceDB.html" title="class in org.biojavax.bio.db">AbstractRichSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/HashRichSequenceDB.html#removeSequence(java.lang.String)">removeSequence(String)</a></span> - Method in class org.biojavax.bio.db.<a href="./org/biojavax/bio/db/HashRichSequenceDB.html" title="class in org.biojavax.bio.db">HashRichSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PairwiseSequencePanel.html#removeSequenceViewerListener(org.biojava.bio.gui.sequence.SequenceViewerListener)">removeSequenceViewerListener(SequenceViewerListener)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PairwiseSequencePanel.html" title="class in org.biojava.bio.gui.sequence">PairwiseSequencePanel</a></dt>
<dd>
<div class="block"><code>removeSequenceViewerListener</code> removes a listener
for mouse click <code>SequenceViewerEvent</code>s.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePanel.html#removeSequenceViewerListener(org.biojava.bio.gui.sequence.SequenceViewerListener)">removeSequenceViewerListener(SequenceViewerListener)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePanel.html" title="class in org.biojava.bio.gui.sequence">SequencePanel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePanelWrapper.html#removeSequenceViewerListener(org.biojava.bio.gui.sequence.SequenceViewerListener)">removeSequenceViewerListener(SequenceViewerListener)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePanelWrapper.html" title="class in org.biojava.bio.gui.sequence">SequencePanelWrapper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePoster.html#removeSequenceViewerListener(org.biojava.bio.gui.sequence.SequenceViewerListener)">removeSequenceViewerListener(SequenceViewerListener)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePoster.html" title="class in org.biojava.bio.gui.sequence">SequencePoster</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequenceViewerSupport.html#removeSequenceViewerListener(org.biojava.bio.gui.sequence.SequenceViewerListener)">removeSequenceViewerListener(SequenceViewerListener)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequenceViewerSupport.html" title="class in org.biojava.bio.gui.sequence">SequenceViewerSupport</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/TranslatedSequencePanel.html#removeSequenceViewerListener(org.biojava.bio.gui.sequence.SequenceViewerListener)">removeSequenceViewerListener(SequenceViewerListener)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/TranslatedSequencePanel.html" title="class in org.biojava.bio.gui.sequence">TranslatedSequencePanel</a></dt>
<dd>
<div class="block"><code>removeSequenceViewerListener</code> removes a listener
for mouse click <code>SequenceViewerEvent</code>s.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PairwiseSequencePanel.html#removeSequenceViewerMotionListener(org.biojava.bio.gui.sequence.SequenceViewerMotionListener)">removeSequenceViewerMotionListener(SequenceViewerMotionListener)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PairwiseSequencePanel.html" title="class in org.biojava.bio.gui.sequence">PairwiseSequencePanel</a></dt>
<dd>
<div class="block"><code>addSequenceViewerMotionListener</code> removes a listener for
mouse motion <code>SequenceViewerEvent</code>s.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePanel.html#removeSequenceViewerMotionListener(org.biojava.bio.gui.sequence.SequenceViewerMotionListener)">removeSequenceViewerMotionListener(SequenceViewerMotionListener)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePanel.html" title="class in org.biojava.bio.gui.sequence">SequencePanel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePanelWrapper.html#removeSequenceViewerMotionListener(org.biojava.bio.gui.sequence.SequenceViewerMotionListener)">removeSequenceViewerMotionListener(SequenceViewerMotionListener)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePanelWrapper.html" title="class in org.biojava.bio.gui.sequence">SequencePanelWrapper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePoster.html#removeSequenceViewerMotionListener(org.biojava.bio.gui.sequence.SequenceViewerMotionListener)">removeSequenceViewerMotionListener(SequenceViewerMotionListener)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePoster.html" title="class in org.biojava.bio.gui.sequence">SequencePoster</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequenceViewerMotionSupport.html#removeSequenceViewerMotionListener(org.biojava.bio.gui.sequence.SequenceViewerMotionListener)">removeSequenceViewerMotionListener(SequenceViewerMotionListener)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequenceViewerMotionSupport.html" title="class in org.biojava.bio.gui.sequence">SequenceViewerMotionSupport</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/TranslatedSequencePanel.html#removeSequenceViewerMotionListener(org.biojava.bio.gui.sequence.SequenceViewerMotionListener)">removeSequenceViewerMotionListener(SequenceViewerMotionListener)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/TranslatedSequencePanel.html" title="class in org.biojava.bio.gui.sequence">TranslatedSequencePanel</a></dt>
<dd>
<div class="block"><code>addSequenceViewerMotionListener</code> removes a listener for
mouse motion <code>SequenceViewerEvent</code>s.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/MergingSet.html#removeSet(java.util.Set)">removeSet(Set)</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/MergingSet.html" title="class in org.biojava.utils">MergingSet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/MarkovModel.html#removeState(org.biojava.bio.dp.State)">removeState(State)</a></span> - Method in interface org.biojava.bio.dp.<a href="./org/biojava/bio/dp/MarkovModel.html" title="interface in org.biojava.bio.dp">MarkovModel</a></dt>
<dd>
<div class="block">Remove a state from the model.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/SimpleMarkovModel.html#removeState(org.biojava.bio.dp.State)">removeState(State)</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/SimpleMarkovModel.html" title="class in org.biojava.bio.dp">SimpleMarkovModel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/WMAsMM.html#removeState(org.biojava.bio.dp.State)">removeState(State)</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/WMAsMM.html" title="class in org.biojava.bio.dp">WMAsMM</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/FiniteAlphabet.html#removeSymbol(org.biojava.bio.symbol.Symbol)">removeSymbol(Symbol)</a></span> - Method in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/FiniteAlphabet.html" title="interface in org.biojava.bio.symbol">FiniteAlphabet</a></dt>
<dd>
<div class="block">Remove a symbol from this alphabet.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/IntegerAlphabet.SubIntegerAlphabet.html#removeSymbol(org.biojava.bio.symbol.Symbol)">removeSymbol(Symbol)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/IntegerAlphabet.SubIntegerAlphabet.html" title="class in org.biojava.bio.symbol">IntegerAlphabet.SubIntegerAlphabet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleAlphabet.html#removeSymbol(org.biojava.bio.symbol.Symbol)">removeSymbol(Symbol)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleAlphabet.html" title="class in org.biojava.bio.symbol">SimpleAlphabet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SingletonAlphabet.html#removeSymbol(org.biojava.bio.symbol.Symbol)">removeSymbol(Symbol)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SingletonAlphabet.html" title="class in org.biojava.bio.symbol">SingletonAlphabet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SoftMaskedAlphabet.html#removeSymbol(org.biojava.bio.symbol.Symbol)">removeSymbol(Symbol)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SoftMaskedAlphabet.html" title="class in org.biojava.bio.symbol">SoftMaskedAlphabet</a></dt>
<dd>
<div class="block"><code>SoftMaskedAlphabet</code>s cannot remove <code>Symbol</code>s.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/IntegerOntology.IntTerm.html#removeSynonym(java.lang.Object)">removeSynonym(Object)</a></span> - Method in class org.biojava.ontology.<a href="./org/biojava/ontology/IntegerOntology.IntTerm.html" title="class in org.biojava.ontology">IntegerOntology.IntTerm</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/OntologyTerm.Impl.html#removeSynonym(java.lang.Object)">removeSynonym(Object)</a></span> - Method in class org.biojava.ontology.<a href="./org/biojava/ontology/OntologyTerm.Impl.html" title="class in org.biojava.ontology">OntologyTerm.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/RemoteTerm.Impl.html#removeSynonym(java.lang.Object)">removeSynonym(Object)</a></span> - Method in class org.biojava.ontology.<a href="./org/biojava/ontology/RemoteTerm.Impl.html" title="class in org.biojava.ontology">RemoteTerm.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/Term.Impl.html#removeSynonym(java.lang.Object)">removeSynonym(Object)</a></span> - Method in class org.biojava.ontology.<a href="./org/biojava/ontology/Term.Impl.html" title="class in org.biojava.ontology">Term.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/Term.html#removeSynonym(java.lang.Object)">removeSynonym(Object)</a></span> - Method in interface org.biojava.ontology.<a href="./org/biojava/ontology/Term.html" title="interface in org.biojava.ontology">Term</a></dt>
<dd>
<div class="block">Remove a synonym for this term.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/Triple.Impl.html#removeSynonym(java.lang.Object)">removeSynonym(Object)</a></span> - Method in class org.biojava.ontology.<a href="./org/biojava/ontology/Triple.Impl.html" title="class in org.biojava.ontology">Triple.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ontology/SimpleComparableTerm.html#removeSynonym(java.lang.Object)">removeSynonym(Object)</a></span> - Method in class org.biojavax.ontology.<a href="./org/biojavax/ontology/SimpleComparableTerm.html" title="class in org.biojavax.ontology">SimpleComparableTerm</a></dt>
<dd>
<div class="block">Remove a synonym for this term.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ontology/SimpleComparableTriple.html#removeSynonym(java.lang.Object)">removeSynonym(Object)</a></span> - Method in class org.biojavax.ontology.<a href="./org/biojavax/ontology/SimpleComparableTriple.html" title="class in org.biojavax.ontology">SimpleComparableTriple</a></dt>
<dd>
<div class="block">Remove a synonym for this term.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/TagDropper.html#removeTag(java.lang.Object)">removeTag(Object)</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/TagDropper.html" title="class in org.biojava.bio.program.tagvalue">TagDropper</a></dt>
<dd>
<div class="block">Remove a tag so that it will not be retained.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/biosql/TaxonSQL.html#removeTaxon(java.sql.Connection, org.biojava.bio.seq.db.biosql.DBHelper, java.lang.String)">removeTaxon(Connection, DBHelper, String)</a></span> - Static method in class org.biojava.bio.seq.db.biosql.<a href="./org/biojava/bio/seq/db/biosql/TaxonSQL.html" title="class in org.biojava.bio.seq.db.biosql">TaxonSQL</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Deletes a taxon specified by one of it's names with all it's different
names, annotations and sequences from the database.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/biosql/TaxonSQL.html#removeTaxon(java.sql.Connection, int, org.biojava.bio.seq.db.biosql.DBHelper)">removeTaxon(Connection, int, DBHelper)</a></span> - Static method in class org.biojava.bio.seq.db.biosql.<a href="./org/biojava/bio/seq/db/biosql/TaxonSQL.html" title="class in org.biojava.bio.seq.db.biosql">TaxonSQL</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Deletes the taxon given by it's NCBI-Taxon-ID from the database and returns the
removed taxon.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/MassCalc.html#removeVariableModifications(char)">removeVariableModifications(char)</a></span> - Method in class org.biojava.bio.proteomics.<a href="./org/biojava/bio/proteomics/MassCalc.html" title="class in org.biojava.bio.proteomics">MassCalc</a></dt>
<dd>
<div class="block">Remove all variable modifications assocaited with this residue.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/MassCalc.html#removeVariableModifications(org.biojava.bio.symbol.Symbol)">removeVariableModifications(Symbol)</a></span> - Method in class org.biojava.bio.proteomics.<a href="./org/biojava/bio/proteomics/MassCalc.html" title="class in org.biojava.bio.proteomics">MassCalc</a></dt>
<dd>
<div class="block">Remove all variable modifications assocaited with this residue.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/naming/ObdaContext.html#rename(javax.naming.Name, javax.naming.Name)">rename(Name, Name)</a></span> - Method in class org.biojava.naming.<a href="./org/biojava/naming/ObdaContext.html" title="class in org.biojava.naming">ObdaContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/naming/ObdaContext.html#rename(java.lang.String, java.lang.String)">rename(String, String)</a></span> - Method in class org.biojava.naming.<a href="./org/biojava/naming/ObdaContext.html" title="class in org.biojava.naming">ObdaContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/glyph/ArrowGlyph.html#render(java.awt.Graphics2D)">render(Graphics2D)</a></span> - Method in class org.biojava.bio.gui.glyph.<a href="./org/biojava/bio/gui/glyph/ArrowGlyph.html" title="class in org.biojava.bio.gui.glyph">ArrowGlyph</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/glyph/Glyph.html#render(java.awt.Graphics2D)">render(Graphics2D)</a></span> - Method in interface org.biojava.bio.gui.glyph.<a href="./org/biojava/bio/gui/glyph/Glyph.html" title="interface in org.biojava.bio.gui.glyph">Glyph</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/glyph/HelixGlyph.html#render(java.awt.Graphics2D)">render(Graphics2D)</a></span> - Method in class org.biojava.bio.gui.glyph.<a href="./org/biojava/bio/gui/glyph/HelixGlyph.html" title="class in org.biojava.bio.gui.glyph">HelixGlyph</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/glyph/RectangleGlyph.html#render(java.awt.Graphics2D)">render(Graphics2D)</a></span> - Method in class org.biojava.bio.gui.glyph.<a href="./org/biojava/bio/gui/glyph/RectangleGlyph.html" title="class in org.biojava.bio.gui.glyph">RectangleGlyph</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/glyph/TurnGlyph.html#render(java.awt.Graphics2D)">render(Graphics2D)</a></span> - Method in class org.biojava.bio.gui.glyph.<a href="./org/biojava/bio/gui/glyph/TurnGlyph.html" title="class in org.biojava.bio.gui.glyph">TurnGlyph</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/glyph/TwoHeadedArrowGlyph.html#render(java.awt.Graphics2D)">render(Graphics2D)</a></span> - Method in class org.biojava.bio.gui.glyph.<a href="./org/biojava/bio/gui/glyph/TwoHeadedArrowGlyph.html" title="class in org.biojava.bio.gui.glyph">TwoHeadedArrowGlyph</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/LabelRenderer.html#RENDER_NOTHING">RENDER_NOTHING</a></span> - Static variable in interface org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/LabelRenderer.html" title="interface in org.biojava.bio.gui.sequence">LabelRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/AbstractBeadRenderer.html#renderBead(java.awt.Graphics2D, org.biojava.bio.seq.Feature, org.biojava.bio.gui.sequence.SequenceRenderContext)">renderBead(Graphics2D, Feature, SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/AbstractBeadRenderer.html" title="class in org.biojava.bio.gui.sequence">AbstractBeadRenderer</a></dt>
<dd>
<div class="block"><code>renderBead</code> should be overridden by the concrete
<code>BeadRenderer</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/BeadFeatureRenderer.html#renderBead(java.awt.Graphics2D, org.biojava.bio.seq.Feature, org.biojava.bio.gui.sequence.SequenceRenderContext)">renderBead(Graphics2D, Feature, SequenceRenderContext)</a></span> - Method in interface org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/BeadFeatureRenderer.html" title="interface in org.biojava.bio.gui.sequence">BeadFeatureRenderer</a></dt>
<dd>
<div class="block"><code>renderBead</code> should implement rendering for this
bead type only.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/EllipticalBeadRenderer.html#renderBead(java.awt.Graphics2D, org.biojava.bio.seq.Feature, org.biojava.bio.gui.sequence.SequenceRenderContext)">renderBead(Graphics2D, Feature, SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/EllipticalBeadRenderer.html" title="class in org.biojava.bio.gui.sequence">EllipticalBeadRenderer</a></dt>
<dd>
<div class="block"><code>renderBead</code> renders features as simple ellipse.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/RectangularBeadRenderer.html#renderBead(java.awt.Graphics2D, org.biojava.bio.seq.Feature, org.biojava.bio.gui.sequence.SequenceRenderContext)">renderBead(Graphics2D, Feature, SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/RectangularBeadRenderer.html" title="class in org.biojava.bio.gui.sequence">RectangularBeadRenderer</a></dt>
<dd>
<div class="block"><code>renderBead</code> renders features as simple rectangle.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/RectangularImapRenderer.html#renderBead(java.awt.Graphics2D, org.biojava.bio.seq.Feature, org.biojava.bio.gui.sequence.SequenceRenderContext)">renderBead(Graphics2D, Feature, SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/RectangularImapRenderer.html" title="class in org.biojava.bio.gui.sequence">RectangularImapRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/RoundRectangularBeadRenderer.html#renderBead(java.awt.Graphics2D, org.biojava.bio.seq.Feature, org.biojava.bio.gui.sequence.SequenceRenderContext)">renderBead(Graphics2D, Feature, SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/RoundRectangularBeadRenderer.html" title="class in org.biojava.bio.gui.sequence">RoundRectangularBeadRenderer</a></dt>
<dd>
<div class="block"><code>renderBead</code> renders features as a rectangle with
rounded corners.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/LabelledSequenceRenderer.html#RENDERER">RENDERER</a></span> - Static variable in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/LabelledSequenceRenderer.html" title="class in org.biojava.bio.gui.sequence">LabelledSequenceRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/OverlayRendererWrapper.html#RENDERER">RENDERER</a></span> - Static variable in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/OverlayRendererWrapper.html" title="class in org.biojava.bio.gui.sequence">OverlayRendererWrapper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PairwiseFilteringRenderer.html#RENDERER">RENDERER</a></span> - Static variable in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PairwiseFilteringRenderer.html" title="class in org.biojava.bio.gui.sequence">PairwiseFilteringRenderer</a></dt>
<dd>
<div class="block">Constant <code>RENDERER</code> indicating a change to the
renderer.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PairwiseSequencePanel.html#RENDERER">RENDERER</a></span> - Static variable in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PairwiseSequencePanel.html" title="class in org.biojava.bio.gui.sequence">PairwiseSequencePanel</a></dt>
<dd>
<div class="block">Constant <code>RENDERER</code> is a <code>ChangeType</code>
which indicates a change to the renderer, requiring a layout
update.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePanel.html#RENDERER">RENDERER</a></span> - Static variable in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePanel.html" title="class in org.biojava.bio.gui.sequence">SequencePanel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePoster.html#RENDERER">RENDERER</a></span> - Static variable in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePoster.html" title="class in org.biojava.bio.gui.sequence">SequencePoster</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequenceRendererWrapper.html#RENDERER">RENDERER</a></span> - Static variable in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequenceRendererWrapper.html" title="class in org.biojava.bio.gui.sequence">SequenceRendererWrapper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/TranslatedSequencePanel.html#RENDERER">RENDERER</a></span> - Static variable in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/TranslatedSequencePanel.html" title="class in org.biojava.bio.gui.sequence">TranslatedSequencePanel</a></dt>
<dd>
<div class="block">Constant <code>RENDERER</code> is a <code>ChangeType</code>
which indicates a change to the renderer, requiring a layout
update.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/MultiLineRenderer.html#RENDERERS">RENDERERS</a></span> - Static variable in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/MultiLineRenderer.html" title="class in org.biojava.bio.gui.sequence">MultiLineRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/MultiLineRenderer.html#renderers">renderers</a></span> - Variable in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/MultiLineRenderer.html" title="class in org.biojava.bio.gui.sequence">MultiLineRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PairwiseOverlayRenderer.html#RENDERERS">RENDERERS</a></span> - Static variable in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PairwiseOverlayRenderer.html" title="class in org.biojava.bio.gui.sequence">PairwiseOverlayRenderer</a></dt>
<dd>
<div class="block">Constant <code>RENDERERS</code> indicating a change to the
renderers handled by the overlay.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/StackedFeatureRenderer.html#RENDERERS">RENDERERS</a></span> - Static variable in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/StackedFeatureRenderer.html" title="class in org.biojava.bio.gui.sequence">StackedFeatureRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/AbstractBeadRenderer.html#renderFeature(java.awt.Graphics2D, org.biojava.bio.seq.Feature, org.biojava.bio.gui.sequence.SequenceRenderContext)">renderFeature(Graphics2D, Feature, SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/AbstractBeadRenderer.html" title="class in org.biojava.bio.gui.sequence">AbstractBeadRenderer</a></dt>
<dd>
<div class="block"><code>renderFeature</code> draws a feature using the supplied
graphics context.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/ArrowedFeatureRenderer.html#renderFeature(java.awt.Graphics2D, org.biojava.bio.seq.Feature, org.biojava.bio.gui.sequence.SequenceRenderContext)">renderFeature(Graphics2D, Feature, SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/ArrowedFeatureRenderer.html" title="class in org.biojava.bio.gui.sequence">ArrowedFeatureRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/BasicFeatureRenderer.html#renderFeature(java.awt.Graphics2D, org.biojava.bio.seq.Feature, org.biojava.bio.gui.sequence.SequenceRenderContext)">renderFeature(Graphics2D, Feature, SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/BasicFeatureRenderer.html" title="class in org.biojava.bio.gui.sequence">BasicFeatureRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/BasicImapRenderer.html#renderFeature(java.awt.Graphics2D, org.biojava.bio.seq.Feature, org.biojava.bio.gui.sequence.SequenceRenderContext)">renderFeature(Graphics2D, Feature, SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/BasicImapRenderer.html" title="class in org.biojava.bio.gui.sequence">BasicImapRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/CircularFeatureRenderer.html#renderFeature(java.awt.Graphics2D, org.biojava.bio.seq.Feature, org.biojava.bio.gui.sequence.CircularRendererContext)">renderFeature(Graphics2D, Feature, CircularRendererContext)</a></span> - Method in interface org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/CircularFeatureRenderer.html" title="interface in org.biojava.bio.gui.sequence">CircularFeatureRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/FeatureLabelRenderer.html#renderFeature(java.awt.Graphics2D, org.biojava.bio.seq.Feature, org.biojava.bio.gui.sequence.SequenceRenderContext)">renderFeature(Graphics2D, Feature, SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/FeatureLabelRenderer.html" title="class in org.biojava.bio.gui.sequence">FeatureLabelRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/FeatureRenderer.html#renderFeature(java.awt.Graphics2D, org.biojava.bio.seq.Feature, org.biojava.bio.gui.sequence.SequenceRenderContext)">renderFeature(Graphics2D, Feature, SequenceRenderContext)</a></span> - Method in interface org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/FeatureRenderer.html" title="interface in org.biojava.bio.gui.sequence">FeatureRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/GlyphFeatureRenderer.html#renderFeature(java.awt.Graphics2D, org.biojava.bio.seq.Feature, org.biojava.bio.gui.sequence.SequenceRenderContext)">renderFeature(Graphics2D, Feature, SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/GlyphFeatureRenderer.html" title="class in org.biojava.bio.gui.sequence">GlyphFeatureRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/RectangularImapRenderer.html#renderFeature(java.awt.Graphics2D, org.biojava.bio.seq.Feature, org.biojava.bio.gui.sequence.SequenceRenderContext)">renderFeature(Graphics2D, Feature, SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/RectangularImapRenderer.html" title="class in org.biojava.bio.gui.sequence">RectangularImapRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SixFrameZiggyRenderer.html#renderFeature(java.awt.Graphics2D, org.biojava.bio.seq.Feature, org.biojava.bio.gui.sequence.SequenceRenderContext)">renderFeature(Graphics2D, Feature, SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SixFrameZiggyRenderer.html" title="class in org.biojava.bio.gui.sequence">SixFrameZiggyRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/StackedFeatureRenderer.html#renderFeature(java.awt.Graphics2D, org.biojava.bio.seq.Feature, org.biojava.bio.gui.sequence.SequenceRenderContext)">renderFeature(Graphics2D, Feature, SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/StackedFeatureRenderer.html" title="class in org.biojava.bio.gui.sequence">StackedFeatureRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/TickFeatureRenderer.html#renderFeature(java.awt.Graphics2D, org.biojava.bio.seq.Feature, org.biojava.bio.gui.sequence.SequenceRenderContext)">renderFeature(Graphics2D, Feature, SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/TickFeatureRenderer.html" title="class in org.biojava.bio.gui.sequence">TickFeatureRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/ZiggyFeatureRenderer.html#renderFeature(java.awt.Graphics2D, org.biojava.bio.seq.Feature, org.biojava.bio.gui.sequence.SequenceRenderContext)">renderFeature(Graphics2D, Feature, SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/ZiggyFeatureRenderer.html" title="class in org.biojava.bio.gui.sequence">ZiggyFeatureRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/ZiggyImapRenderer.html#renderFeature(java.awt.Graphics2D, org.biojava.bio.seq.Feature, org.biojava.bio.gui.sequence.SequenceRenderContext)">renderFeature(Graphics2D, Feature, SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/ZiggyImapRenderer.html" title="class in org.biojava.bio.gui.sequence">ZiggyImapRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/BasicImapRenderer.html#renderImageMap(java.awt.Graphics2D, org.biojava.bio.seq.Feature, org.biojava.bio.gui.sequence.SequenceRenderContext)">renderImageMap(Graphics2D, Feature, SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/BasicImapRenderer.html" title="class in org.biojava.bio.gui.sequence">BasicImapRenderer</a></dt>
<dd>
<div class="block"><code>renderImageMap</code> writes a set of image map
coordinates corresponding to the rectangle sections drawn by
the renderer.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/ImageMapRenderer.html#renderImageMap(java.awt.Graphics2D, org.biojava.bio.seq.Feature, org.biojava.bio.gui.sequence.SequenceRenderContext)">renderImageMap(Graphics2D, Feature, SequenceRenderContext)</a></span> - Method in interface org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/ImageMapRenderer.html" title="interface in org.biojava.bio.gui.sequence">ImageMapRenderer</a></dt>
<dd>
<div class="block"><code>renderImageMap</code> renders the <code>Feature</code> as
set of image map hotspots.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/RectangularImapRenderer.html#renderImageMap(java.awt.Graphics2D, org.biojava.bio.seq.Feature, org.biojava.bio.gui.sequence.SequenceRenderContext)">renderImageMap(Graphics2D, Feature, SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/RectangularImapRenderer.html" title="class in org.biojava.bio.gui.sequence">RectangularImapRenderer</a></dt>
<dd>
<div class="block"><code>renderImageMap</code> writes a set of image map
coordinates corresponding to the rectangle drawn by the
renderer.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/ZiggyImapRenderer.html#renderImageMap(java.awt.Graphics2D, org.biojava.bio.seq.Feature, org.biojava.bio.gui.sequence.SequenceRenderContext)">renderImageMap(Graphics2D, Feature, SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/ZiggyImapRenderer.html" title="class in org.biojava.bio.gui.sequence">ZiggyImapRenderer</a></dt>
<dd>
<div class="block"><code>renderImageMap</code> writes a set of image map
coordinates corresponding to the rectangle sections drawn by
the renderer.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SixFrameRenderer.html#renderLocation(java.awt.Graphics2D, org.biojava.bio.gui.sequence.SequenceRenderContext, org.biojava.bio.symbol.Location)">renderLocation(Graphics2D, SequenceRenderContext, Location)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SixFrameRenderer.html" title="class in org.biojava.bio.gui.sequence">SixFrameRenderer</a></dt>
<dd>
<div class="block">Render another "exon" in the correct translation frame.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleGappedSymbolList.html#renumber(int, int)">renumber(int, int)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleGappedSymbolList.html" title="class in org.biojava.bio.symbol">SimpleGappedSymbolList</a></dt>
<dd>
<div class="block">Renumber the view indexes from block, adding delta to each offset.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequenceRenderContext.html#REPAINT">REPAINT</a></span> - Static variable in interface org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequenceRenderContext.html" title="interface in org.biojava.bio.gui.sequence">SequenceRenderContext</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/projection/ReparentContext.html" title="class in org.biojava.bio.seq.projection"><span class="strong">ReparentContext</span></a> - Class in <a href="./org/biojava/bio/seq/projection/package-summary.html">org.biojava.bio.seq.projection</a></dt>
<dd>
<div class="block">A good base class to implement ProjectionContext from.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/projection/ReparentContext.html#ReparentContext(org.biojava.bio.seq.FeatureHolder, org.biojava.bio.seq.FeatureHolder)">ReparentContext(FeatureHolder, FeatureHolder)</a></span> - Constructor for class org.biojava.bio.seq.projection.<a href="./org/biojava/bio/seq/projection/ReparentContext.html" title="class in org.biojava.bio.seq.projection">ReparentContext</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/utils/RepeatedCharSequence.html" title="class in org.biojava.utils"><span class="strong">RepeatedCharSequence</span></a> - Class in <a href="./org/biojava/utils/package-summary.html">org.biojava.utils</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/RepeatedCharSequence.html#RepeatedCharSequence(int, char)">RepeatedCharSequence(int, char)</a></span> - Constructor for class org.biojava.utils.<a href="./org/biojava/utils/RepeatedCharSequence.html" title="class in org.biojava.utils">RepeatedCharSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/RepeatedCharSequence.html#RepeatedCharSequence()">RepeatedCharSequence()</a></span> - Constructor for class org.biojava.utils.<a href="./org/biojava/utils/RepeatedCharSequence.html" title="class in org.biojava.utils">RepeatedCharSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/Edit.html#replacement">replacement</a></span> - Variable in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/Edit.html" title="class in org.biojava.bio.symbol">Edit</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/impl/SimpleOrganism.html#replicate(java.lang.String)">replicate(String)</a></span> - Method in class org.biojavax.ga.impl.<a href="./org/biojavax/ga/impl/SimpleOrganism.html" title="class in org.biojavax.ga.impl">SimpleOrganism</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/Organism.html#replicate(java.lang.String)">replicate(String)</a></span> - Method in interface org.biojavax.ga.<a href="./org/biojavax/ga/Organism.html" title="interface in org.biojavax.ga">Organism</a></dt>
<dd>
<div class="block">Creates a replica of this <code>Organism</code> with a new name.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEBioSeqCallbackItf.html#reportDna(java.lang.String)">reportDna(String)</a></span> - Method in interface org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEBioSeqCallbackItf.html" title="interface in org.biojava.bio.seq.io.agave">AGAVEBioSeqCallbackItf</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEBioSeqHandler.html#reportDna(java.lang.String)">reportDna(String)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEBioSeqHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEBioSeqHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEContigCallbackItf.html#reportDna(java.lang.String)">reportDna(String)</a></span> - Method in interface org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEContigCallbackItf.html" title="interface in org.biojava.bio.seq.io.agave">AGAVEContigCallbackItf</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEContigHandler.html#reportDna(java.lang.String)">reportDna(String)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEContigHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEContigHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game/GAMEFeatureSetHandler.html#reportExon(org.biojava.bio.symbol.RangeLocation, org.biojava.bio.seq.StrandedFeature.Strand)">reportExon(RangeLocation, StrandedFeature.Strand)</a></span> - Method in class org.biojava.bio.seq.io.game.<a href="./org/biojava/bio/seq/io/game/GAMEFeatureSetHandler.html" title="class in org.biojava.bio.seq.io.game">GAMEFeatureSetHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game/GAMETranscriptCallbackItf.html#reportExon(org.biojava.bio.symbol.RangeLocation, org.biojava.bio.seq.StrandedFeature.Strand)">reportExon(RangeLocation, StrandedFeature.Strand)</a></span> - Method in interface org.biojava.bio.seq.io.game.<a href="./org/biojava/bio/seq/io/game/GAMETranscriptCallbackItf.html" title="interface in org.biojava.bio.seq.io.game">GAMETranscriptCallbackItf</a></dt>
<dd>
<div class="block">Allows nesting class that manages a transcript template
to gain information about its extent from nested
elements that represent exons.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEBioSeqCallbackItf.html#reportFeature(org.biojava.bio.symbol.Location)">reportFeature(Location)</a></span> - Method in interface org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEBioSeqCallbackItf.html" title="interface in org.biojava.bio.seq.io.agave">AGAVEBioSeqCallbackItf</a></dt>
<dd>
<div class="block">Allows nesting class that manages a gene template
to gain information about its extent from nested
elements.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEBioSeqHandler.html#reportFeature(org.biojava.bio.symbol.Location)">reportFeature(Location)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEBioSeqHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEBioSeqHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEBioSequenceHandler.html#reportFeature(org.biojava.bio.symbol.Location)">reportFeature(Location)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEBioSequenceHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEBioSequenceHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVECompResultHandler.html#reportFeature(org.biojava.bio.symbol.Location)">reportFeature(Location)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVECompResultHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVECompResultHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEFeatureCallbackItf.html#reportFeature(org.biojava.bio.symbol.Location)">reportFeature(Location)</a></span> - Method in interface org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEFeatureCallbackItf.html" title="interface in org.biojava.bio.seq.io.agave">AGAVEFeatureCallbackItf</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEFragmentOrderHandler.html#reportFeature(org.biojava.bio.symbol.Location)">reportFeature(Location)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEFragmentOrderHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEFragmentOrderHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEFragmentOrientationHandler.html#reportFeature(org.biojava.bio.symbol.Location)">reportFeature(Location)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEFragmentOrientationHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEFragmentOrientationHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEGeneHandler.html#reportFeature(org.biojava.bio.symbol.Location)">reportFeature(Location)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEGeneHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEGeneHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVESeqFeatureHandler.html#reportFeature(org.biojava.bio.symbol.Location)">reportFeature(Location)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVESeqFeatureHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVESeqFeatureHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game/GAMEAnnotationHandler.html#reportFeature(org.biojava.bio.symbol.Location)">reportFeature(Location)</a></span> - Method in class org.biojava.bio.seq.io.game.<a href="./org/biojava/bio/seq/io/game/GAMEAnnotationHandler.html" title="class in org.biojava.bio.seq.io.game">GAMEAnnotationHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game/GAMEFeatureCallbackItf.html#reportFeature(org.biojava.bio.symbol.Location)">reportFeature(Location)</a></span> - Method in interface org.biojava.bio.seq.io.game.<a href="./org/biojava/bio/seq/io/game/GAMEFeatureCallbackItf.html" title="interface in org.biojava.bio.seq.io.game">GAMEFeatureCallbackItf</a></dt>
<dd>
<div class="block">Allows nesting class that manages a gene template
to gain information about its extent from nested
elements.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/regex/Search.Listener.html#reportMatch(org.biojava.bio.symbol.SymbolList, org.biojava.utils.regex.Pattern, int, int)">reportMatch(SymbolList, Pattern, int, int)</a></span> - Method in interface org.biojava.utils.regex.<a href="./org/biojava/utils/regex/Search.Listener.html" title="interface in org.biojava.utils.regex">Search.Listener</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVECallbackItf.html#reportSequence(org.biojava.bio.seq.Sequence)">reportSequence(Sequence)</a></span> - Method in interface org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVECallbackItf.html" title="interface in org.biojava.bio.seq.io.agave">AGAVECallbackItf</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEChromosomeCallbackItf.html#reportSequence(org.biojava.bio.seq.Sequence)">reportSequence(Sequence)</a></span> - Method in interface org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEChromosomeCallbackItf.html" title="interface in org.biojava.bio.seq.io.agave">AGAVEChromosomeCallbackItf</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEChromosomeHandler.html#reportSequence(org.biojava.bio.seq.Sequence)">reportSequence(Sequence)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEChromosomeHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEChromosomeHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEContigCallbackItf.html#reportSequence(org.biojava.bio.seq.Sequence)">reportSequence(Sequence)</a></span> - Method in interface org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEContigCallbackItf.html" title="interface in org.biojava.bio.seq.io.agave">AGAVEContigCallbackItf</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEContigHandler.html#reportSequence(org.biojava.bio.seq.Sequence)">reportSequence(Sequence)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEContigHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEContigHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEHandler.html#reportSequence(org.biojava.bio.seq.Sequence)">reportSequence(Sequence)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEBioSeqCallbackItf.html#reportStrand(org.biojava.bio.seq.StrandedFeature.Strand)">reportStrand(StrandedFeature.Strand)</a></span> - Method in interface org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEBioSeqCallbackItf.html" title="interface in org.biojava.bio.seq.io.agave">AGAVEBioSeqCallbackItf</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEBioSeqHandler.html#reportStrand(org.biojava.bio.seq.StrandedFeature.Strand)">reportStrand(StrandedFeature.Strand)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEBioSeqHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEBioSeqHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEBioSequenceHandler.html#reportStrand(org.biojava.bio.seq.StrandedFeature.Strand)">reportStrand(StrandedFeature.Strand)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEBioSequenceHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEBioSequenceHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVECompResultHandler.html#reportStrand(org.biojava.bio.seq.StrandedFeature.Strand)">reportStrand(StrandedFeature.Strand)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVECompResultHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVECompResultHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEFeatureCallbackItf.html#reportStrand(org.biojava.bio.seq.StrandedFeature.Strand)">reportStrand(StrandedFeature.Strand)</a></span> - Method in interface org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEFeatureCallbackItf.html" title="interface in org.biojava.bio.seq.io.agave">AGAVEFeatureCallbackItf</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEFragmentOrderHandler.html#reportStrand(org.biojava.bio.seq.StrandedFeature.Strand)">reportStrand(StrandedFeature.Strand)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEFragmentOrderHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEFragmentOrderHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEFragmentOrientationHandler.html#reportStrand(org.biojava.bio.seq.StrandedFeature.Strand)">reportStrand(StrandedFeature.Strand)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEFragmentOrientationHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEFragmentOrientationHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEGeneHandler.html#reportStrand(org.biojava.bio.seq.StrandedFeature.Strand)">reportStrand(StrandedFeature.Strand)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEGeneHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEGeneHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVESeqFeatureHandler.html#reportStrand(org.biojava.bio.seq.StrandedFeature.Strand)">reportStrand(StrandedFeature.Strand)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVESeqFeatureHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVESeqFeatureHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game/GAMEAnnotationHandler.html#reportStrand(org.biojava.bio.seq.StrandedFeature.Strand)">reportStrand(StrandedFeature.Strand)</a></span> - Method in class org.biojava.bio.seq.io.game.<a href="./org/biojava/bio/seq/io/game/GAMEAnnotationHandler.html" title="class in org.biojava.bio.seq.io.game">GAMEAnnotationHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game/GAMEFeatureCallbackItf.html#reportStrand(org.biojava.bio.seq.StrandedFeature.Strand)">reportStrand(StrandedFeature.Strand)</a></span> - Method in interface org.biojava.bio.seq.io.game.<a href="./org/biojava/bio/seq/io/game/GAMEFeatureCallbackItf.html" title="interface in org.biojava.bio.seq.io.game">GAMEFeatureCallbackItf</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BibRefSupport.html#REPOSITORY_SUBSETS">REPOSITORY_SUBSETS</a></span> - Static variable in interface org.biojava.bibliography.<a href="./org/biojava/bibliography/BibRefSupport.html" title="interface in org.biojava.bibliography">BibRefSupport</a></dt>
<dd>
<div class="block">A vocabulary name.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BiblioEntryStatus.html#repositorySubset">repositorySubset</a></span> - Variable in class org.biojava.bibliography.<a href="./org/biojava/bibliography/BiblioEntryStatus.html" title="class in org.biojava.bibliography">BiblioEntryStatus</a></dt>
<dd>
<div class="block">
Some bibliographic repositories consist of several, or even
many, databases.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/server/SimpleStructureServer.html#requestNextStructure(org.biojava.bio.structure.server.StructureListener)">requestNextStructure(StructureListener)</a></span> - Method in class org.biojava.bio.structure.server.<a href="./org/biojava/bio/structure/server/SimpleStructureServer.html" title="class in org.biojava.bio.structure.server">SimpleStructureServer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/server/StructureServer.html#requestNextStructure(org.biojava.bio.structure.server.StructureListener)">requestNextStructure(StructureListener)</a></span> - Method in interface org.biojava.bio.structure.server.<a href="./org/biojava/bio/structure/server/StructureServer.html" title="interface in org.biojava.bio.structure.server">StructureServer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/SimpleThreadPool.html#requestsQueued()">requestsQueued()</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/SimpleThreadPool.html" title="class in org.biojava.utils">SimpleThreadPool</a></dt>
<dd>
<div class="block"><code>requestsQueued</code> returns the number of
<code>Runnable</code>s currently queued.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssaha/SequenceStreamer.FileStreamer.html#reset()">reset()</a></span> - Method in class org.biojava.bio.program.ssaha.<a href="./org/biojava/bio/program/ssaha/SequenceStreamer.FileStreamer.html" title="class in org.biojava.bio.program.ssaha">SequenceStreamer.FileStreamer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssaha/SequenceStreamer.html#reset()">reset()</a></span> - Method in interface org.biojava.bio.program.ssaha.<a href="./org/biojava/bio/program/ssaha/SequenceStreamer.html" title="interface in org.biojava.bio.program.ssaha">SequenceStreamer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssaha/SequenceStreamer.SequenceDBStreamer.html#reset()">reset()</a></span> - Method in class org.biojava.bio.program.ssaha.<a href="./org/biojava/bio/program/ssaha/SequenceStreamer.SequenceDBStreamer.html" title="class in org.biojava.bio.program.ssaha">SequenceStreamer.SequenceDBStreamer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/BlastLikeSearchFilter.AbstractBlastLikeSearchFilter.html#reset()">reset()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/BlastLikeSearchFilter.AbstractBlastLikeSearchFilter.html" title="class in org.biojava.bio.search">BlastLikeSearchFilter.AbstractBlastLikeSearchFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/BlastLikeSearchFilter.html#reset()">reset()</a></span> - Method in interface org.biojava.bio.search.<a href="./org/biojava/bio/search/BlastLikeSearchFilter.html" title="interface in org.biojava.bio.search">BlastLikeSearchFilter</a></dt>
<dd>
<div class="block">resets the internal state of this filter including
any cached evaluations.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/io/CountedBufferedReader.html#reset()">reset()</a></span> - Method in class org.biojava.utils.io.<a href="./org/biojava/utils/io/CountedBufferedReader.html" title="class in org.biojava.utils.io">CountedBufferedReader</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/regex/Matcher.html#reset()">reset()</a></span> - Method in class org.biojava.utils.regex.<a href="./org/biojava/utils/regex/Matcher.html" title="class in org.biojava.utils.regex">Matcher</a></dt>
<dd>
<div class="block">Resets this matcher.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/regex/Matcher.html#reset(org.biojava.bio.symbol.SymbolList)">reset(SymbolList)</a></span> - Method in class org.biojava.utils.regex.<a href="./org/biojava/utils/regex/Matcher.html" title="class in org.biojava.utils.regex">Matcher</a></dt>
<dd>
<div class="block">Resets this matcher with a new input SymbolList.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/utils/CRC64Checksum.html#reset()">reset()</a></span> - Method in class org.biojavax.utils.<a href="./org/biojavax/utils/CRC64Checksum.html" title="class in org.biojavax.utils">CRC64Checksum</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/FlexibleAlignment.html#resetRange()">resetRange()</a></span> - Method in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/FlexibleAlignment.html" title="class in org.biojava.bio.alignment">FlexibleAlignment</a></dt>
<dd>
<div class="block">check that begining is at 1 otherwise shift everything over</div>
</dd>
<dt><a href="./org/biojava/bio/structure/io/mmcif/chem/ResidueType.html" title="enum in org.biojava.bio.structure.io.mmcif.chem"><span class="strong">ResidueType</span></a> - Enum in <a href="./org/biojava/bio/structure/io/mmcif/chem/package-summary.html">org.biojava.bio.structure.io.mmcif.chem</a></dt>
<dd>
<div class="block">Enumerates the possible classifications of residues.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PairwiseSequencePanel.html#resizeAndValidate()">resizeAndValidate()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PairwiseSequencePanel.html" title="class in org.biojava.bio.gui.sequence">PairwiseSequencePanel</a></dt>
<dd>
<div class="block"><code>resizeAndValidate</code> sets the minimum, preferred and
maximum sizes of the component according to the current visible
symbol count.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePanel.html#resizeAndValidate()">resizeAndValidate()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePanel.html" title="class in org.biojava.bio.gui.sequence">SequencePanel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePanelWrapper.html#resizeAndValidate()">resizeAndValidate()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePanelWrapper.html" title="class in org.biojava.bio.gui.sequence">SequencePanelWrapper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePoster.html#resizeAndValidate()">resizeAndValidate()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePoster.html" title="class in org.biojava.bio.gui.sequence">SequencePoster</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/TranslatedSequencePanel.html#resizeAndValidate()">resizeAndValidate()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/TranslatedSequencePanel.html" title="class in org.biojava.bio.gui.sequence">TranslatedSequencePanel</a></dt>
<dd>
<div class="block"><code>resizeAndValidate</code> sets the minimum, preferred and
maximum sizes of the component according to the current leading
and trailing borders, renderer depth and visible symbol count.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/FragmentJoiner.html#resizeArray(java.lang.Object, int)">resizeArray(Object, int)</a></span> - Static method in class org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/FragmentJoiner.html" title="class in org.biojava.bio.structure.align.pairwise">FragmentJoiner</a></dt>
<dd>
<div class="block">Reallocates an array with a new size, and copies the contents
of the old array to the new array.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleRemoteFeature.DBResolver.html#resolve(org.biojava.bio.seq.RemoteFeature)">resolve(RemoteFeature)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleRemoteFeature.DBResolver.html" title="class in org.biojava.bio.seq.impl">SimpleRemoteFeature.DBResolver</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/RemoteFeature.Resolver.html#resolve(org.biojava.bio.seq.RemoteFeature)">resolve(RemoteFeature)</a></span> - Method in interface org.biojava.bio.seq.<a href="./org/biojava/bio/seq/RemoteFeature.Resolver.html" title="interface in org.biojava.bio.seq">RemoteFeature.Resolver</a></dt>
<dd>
<div class="block">Resolve rFeat.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/FuzzyPointLocation.PointResolver.html#resolve(org.biojava.bio.symbol.FuzzyPointLocation)">resolve(FuzzyPointLocation)</a></span> - Method in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/FuzzyPointLocation.PointResolver.html" title="interface in org.biojava.bio.symbol">FuzzyPointLocation.PointResolver</a></dt>
<dd>
<div class="block">Return the actual point that the specified location should claim to
occupy.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/FuzzyLocation.html#RESOLVE_AVERAGE">RESOLVE_AVERAGE</a></span> - Static variable in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/FuzzyLocation.html" title="class in org.biojava.bio.symbol">FuzzyLocation</a></dt>
<dd>
<div class="block">Use the arithmetic mean of the `inner' and `outer' values, unless the
outer value is unbounded.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/FuzzyPointLocation.html#RESOLVE_AVERAGE">RESOLVE_AVERAGE</a></span> - Static variable in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/FuzzyPointLocation.html" title="class in org.biojava.bio.symbol">FuzzyPointLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/FuzzyLocation.html#RESOLVE_INNER">RESOLVE_INNER</a></span> - Static variable in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/FuzzyLocation.html" title="class in org.biojava.bio.symbol">FuzzyLocation</a></dt>
<dd>
<div class="block">Always use the `inner' values.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/FuzzyPointLocation.html#RESOLVE_MAX">RESOLVE_MAX</a></span> - Static variable in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/FuzzyPointLocation.html" title="class in org.biojava.bio.symbol">FuzzyPointLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/FuzzyPointLocation.html#RESOLVE_MIN">RESOLVE_MIN</a></span> - Static variable in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/FuzzyPointLocation.html" title="class in org.biojava.bio.symbol">FuzzyPointLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/FuzzyLocation.html#RESOLVE_OUTER">RESOLVE_OUTER</a></span> - Static variable in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/FuzzyLocation.html" title="class in org.biojava.bio.symbol">FuzzyLocation</a></dt>
<dd>
<div class="block">Use the `outer' values, unless they are unbounded in which case the
`inner' values are used.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/AlphabetResolver.html#resolveAlphabet(java.lang.String)">resolveAlphabet(String)</a></span> - Static method in class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/AlphabetResolver.html" title="class in org.biojava.bio.program.ssbind">AlphabetResolver</a></dt>
<dd>
<div class="block"><code>resolveAlphabet</code> returns an appropriate
<code>Alphabet</code> for an arbitrary identifier.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/process/ExternalProcess.html#resolveCommands(java.lang.String, java.util.Properties)">resolveCommands(String, Properties)</a></span> - Static method in class org.biojava.utils.process.<a href="./org/biojava/utils/process/ExternalProcess.html" title="class in org.biojava.utils.process">ExternalProcess</a></dt>
<dd>
<div class="block">Resolves the given command line by replacing all placeholder of the
format <code>%NAME%</code> with the values from the given properties
for the corresponding keys of the format <code>NAME</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/xml/ResourceEntityResolver.html#resolveEntity(java.lang.String, java.lang.String)">resolveEntity(String, String)</a></span> - Method in class org.biojava.utils.xml.<a href="./org/biojava/utils/xml/ResourceEntityResolver.html" title="class in org.biojava.utils.xml">ResourceEntityResolver</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/IntegerOntology.html#resolveInt(int)">resolveInt(int)</a></span> - Method in class org.biojava.ontology.<a href="./org/biojava/ontology/IntegerOntology.html" title="class in org.biojava.ontology">IntegerOntology</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/FuzzyLocation.RangeResolver.html#resolveMax(org.biojava.bio.symbol.FuzzyLocation)">resolveMax(FuzzyLocation)</a></span> - Method in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/FuzzyLocation.RangeResolver.html" title="interface in org.biojava.bio.symbol">FuzzyLocation.RangeResolver</a></dt>
<dd>
<div class="block">Delegate for the getMax() method.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/FuzzyLocation.RangeResolver.html#resolveMin(org.biojava.bio.symbol.FuzzyLocation)">resolveMin(FuzzyLocation)</a></span> - Method in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/FuzzyLocation.RangeResolver.html" title="interface in org.biojava.bio.symbol">FuzzyLocation.RangeResolver</a></dt>
<dd>
<div class="block">Delegate for the getMin() method.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/RemoteFeature.Template.html#resolver">resolver</a></span> - Variable in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/RemoteFeature.Template.html" title="class in org.biojava.bio.seq">RemoteFeature.Template</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BibRefSupport.html#RESOURCE_TYPES">RESOURCE_TYPES</a></span> - Static variable in interface org.biojava.bibliography.<a href="./org/biojava/bibliography/BibRefSupport.html" title="interface in org.biojava.bibliography">BibRefSupport</a></dt>
<dd>
<div class="block">A vocabulary name.</div>
</dd>
<dt><a href="./org/biojava/utils/xml/ResourceEntityResolver.html" title="class in org.biojava.utils.xml"><span class="strong">ResourceEntityResolver</span></a> - Class in <a href="./org/biojava/utils/xml/package-summary.html">org.biojava.utils.xml</a></dt>
<dd>
<div class="block">SAX EntityResolve which looks up system IDs as resources
from a Java ClassLoader.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/xml/ResourceEntityResolver.html#ResourceEntityResolver(java.lang.String)">ResourceEntityResolver(String)</a></span> - Constructor for class org.biojava.utils.xml.<a href="./org/biojava/utils/xml/ResourceEntityResolver.html" title="class in org.biojava.utils.xml">ResourceEntityResolver</a></dt>
<dd>
<div class="block">Construct a resolver which searches for resources in the specified
path relative to the current classloader.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/xml/ResourceEntityResolver.html#ResourceEntityResolver(java.lang.String[])">ResourceEntityResolver(String[])</a></span> - Constructor for class org.biojava.utils.xml.<a href="./org/biojava/utils/xml/ResourceEntityResolver.html" title="class in org.biojava.utils.xml">ResourceEntityResolver</a></dt>
<dd>
<div class="block">Construct a resolver which searches for resources in the specified
list of directories relative to the current classloader.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/xml/ResourceEntityResolver.html#ResourceEntityResolver(java.lang.String[], java.lang.ClassLoader)">ResourceEntityResolver(String[], ClassLoader)</a></span> - Constructor for class org.biojava.utils.xml.<a href="./org/biojava/utils/xml/ResourceEntityResolver.html" title="class in org.biojava.utils.xml">ResourceEntityResolver</a></dt>
<dd>
<div class="block">Construct a resolver which searches for resources in the specified
list of directories relative to the supplied classloader.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/xml/ResourceEntityResolver.html#ResourceEntityResolver(java.lang.String, java.lang.ClassLoader)">ResourceEntityResolver(String, ClassLoader)</a></span> - Constructor for class org.biojava.utils.xml.<a href="./org/biojava/utils/xml/ResourceEntityResolver.html" title="class in org.biojava.utils.xml">ResourceEntityResolver</a></dt>
<dd>
<div class="block">Construct a resolver which searches for resources in the specified
path relative to the supplied classloader.</div>
</dd>
<dt><a href="./org/biojava/bio/molbio/RestrictionEnzyme.html" title="class in org.biojava.bio.molbio"><span class="strong">RestrictionEnzyme</span></a> - Class in <a href="./org/biojava/bio/molbio/package-summary.html">org.biojava.bio.molbio</a></dt>
<dd>
<div class="block"><code>RestrictionEnzyme</code> represents a restriction enzyme
according to the REBASE standard.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/molbio/RestrictionEnzyme.html#RestrictionEnzyme(java.lang.String, org.biojava.bio.symbol.SymbolList, int, int)">RestrictionEnzyme(String, SymbolList, int, int)</a></span> - Constructor for class org.biojava.bio.molbio.<a href="./org/biojava/bio/molbio/RestrictionEnzyme.html" title="class in org.biojava.bio.molbio">RestrictionEnzyme</a></dt>
<dd>
<div class="block">Creates a new <code>RestrictionEnzyme</code> which cuts within
or downstream of the recognition site.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/molbio/RestrictionEnzyme.html#RestrictionEnzyme(java.lang.String, org.biojava.bio.symbol.SymbolList, int, int, int, int)">RestrictionEnzyme(String, SymbolList, int, int, int, int)</a></span> - Constructor for class org.biojava.bio.molbio.<a href="./org/biojava/bio/molbio/RestrictionEnzyme.html" title="class in org.biojava.bio.molbio">RestrictionEnzyme</a></dt>
<dd>
<div class="block">Creates a new <code>RestrictionEnzyme</code> of the unusual
type which cuts both upstream and downstream of its recognition
site.</div>
</dd>
<dt><a href="./org/biojava/bio/molbio/RestrictionEnzymeManager.html" title="class in org.biojava.bio.molbio"><span class="strong">RestrictionEnzymeManager</span></a> - Class in <a href="./org/biojava/bio/molbio/package-summary.html">org.biojava.bio.molbio</a></dt>
<dd>
<div class="block"><code>RestrictionEnzymeManager</code> manages collections of
static <code>RestrictionEnzyme</code> instances.</div>
</dd>
<dt><a href="./org/biojava/bio/molbio/RestrictionMapper.html" title="class in org.biojava.bio.molbio"><span class="strong">RestrictionMapper</span></a> - Class in <a href="./org/biojava/bio/molbio/package-summary.html">org.biojava.bio.molbio</a></dt>
<dd>
<div class="block"><code>RestrictionMapper</code> is a class for annotating
<code>Sequence</code>s with <code>Feature</code>s which represent
restriction sites.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/molbio/RestrictionMapper.html#RestrictionMapper(org.biojava.utils.ThreadPool)">RestrictionMapper(ThreadPool)</a></span> - Constructor for class org.biojava.bio.molbio.<a href="./org/biojava/bio/molbio/RestrictionMapper.html" title="class in org.biojava.bio.molbio">RestrictionMapper</a></dt>
<dd>
<div class="block">Creates a new <code>RestrictionMapper</code> which will use
the specified <code>ThreadPool</code>.</div>
</dd>
<dt><a href="./org/biojava/bio/molbio/RestrictionSite.html" title="interface in org.biojava.bio.molbio"><span class="strong">RestrictionSite</span></a> - Interface in <a href="./org/biojava/bio/molbio/package-summary.html">org.biojava.bio.molbio</a></dt>
<dd>
<div class="block"><code>RestrictionSite</code> represents the recognition site of a
restriction enzyme.</div>
</dd>
<dt><a href="./org/biojava/bio/molbio/RestrictionSite.Template.html" title="class in org.biojava.bio.molbio"><span class="strong">RestrictionSite.Template</span></a> - Class in <a href="./org/biojava/bio/molbio/package-summary.html">org.biojava.bio.molbio</a></dt>
<dd>
<div class="block"><code>Template</code> for construction of
<code>RestrictionSite</code>s.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/molbio/RestrictionSite.Template.html#RestrictionSite.Template()">RestrictionSite.Template()</a></span> - Constructor for class org.biojava.bio.molbio.<a href="./org/biojava/bio/molbio/RestrictionSite.Template.html" title="class in org.biojava.bio.molbio">RestrictionSite.Template</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEProperty.html#RESULT_PROPERTY">RESULT_PROPERTY</a></span> - Static variable in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEProperty.html" title="class in org.biojava.bio.seq.io.agave">AGAVEProperty</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/util/WeightedSet.html#retainAll(java.util.Collection)">retainAll(Collection)</a></span> - Method in class org.biojavax.ga.util.<a href="./org/biojavax/ga/util/WeightedSet.html" title="class in org.biojavax.ga.util">WeightedSet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game12/StAXFeatureHandler.html#returnData(java.lang.Object)">returnData(Object)</a></span> - Method in class org.biojava.bio.seq.io.game12.<a href="./org/biojava/bio/seq/io/game12/StAXFeatureHandler.html" title="class in org.biojava.bio.seq.io.game12">StAXFeatureHandler</a></dt>
<dd>
<div class="block">provides a standardised way of returning an
object that represents the result of parsing the
child element</div>
</dd>
<dt><a href="./org/biojava/bio/seq/impl/RevCompSequence.html" title="class in org.biojava.bio.seq.impl"><span class="strong">RevCompSequence</span></a> - Class in <a href="./org/biojava/bio/seq/impl/package-summary.html">org.biojava.bio.seq.impl</a></dt>
<dd>
<div class="block">A reverse complement view onto <code>Sequence</code> interface.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/RevCompSequence.html#RevCompSequence(org.biojava.bio.seq.Sequence)">RevCompSequence(Sequence)</a></span> - Constructor for class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/RevCompSequence.html" title="class in org.biojava.bio.seq.impl">RevCompSequence</a></dt>
<dd>
<div class="block">URN, Name and Annotation are copied as is from the original Sequence, unless you use the
the other contructor that sets these.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/RevCompSequence.html#RevCompSequence(org.biojava.bio.seq.Sequence, java.lang.String, java.lang.String, org.biojava.bio.Annotation)">RevCompSequence(Sequence, String, String, Annotation)</a></span> - Constructor for class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/RevCompSequence.html" title="class in org.biojava.bio.seq.impl">RevCompSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/AbstractChromatogram.html#reverse(int[])">reverse(int[])</a></span> - Static method in class org.biojava.bio.chromatogram.<a href="./org/biojava/bio/chromatogram/AbstractChromatogram.html" title="class in org.biojava.bio.chromatogram">AbstractChromatogram</a></dt>
<dd>
<div class="block">Utility method for reversing an int[] array.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SymbolListViews.html#reverse(org.biojava.bio.symbol.SymbolList)">reverse(SymbolList)</a></span> - Static method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SymbolListViews.html" title="class in org.biojava.bio.symbol">SymbolListViews</a></dt>
<dd>
<div class="block">A reversed view onto a SymbolList.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/AbstractChromatogram.html#reverseComplement()">reverseComplement()</a></span> - Method in class org.biojava.bio.chromatogram.<a href="./org/biojava/bio/chromatogram/AbstractChromatogram.html" title="class in org.biojava.bio.chromatogram">AbstractChromatogram</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/Chromatogram.html#reverseComplement()">reverseComplement()</a></span> - Method in interface org.biojava.bio.chromatogram.<a href="./org/biojava/bio/chromatogram/Chromatogram.html" title="interface in org.biojava.bio.chromatogram">Chromatogram</a></dt>
<dd>
<div class="block">Returns a new <code>Chromatogram</code> representing the reverse
complement of this one.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/DNATools.html#reverseComplement(org.biojava.bio.symbol.SymbolList)">reverseComplement(SymbolList)</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/DNATools.html" title="class in org.biojava.bio.seq">DNATools</a></dt>
<dd>
<div class="block">Retrieve a reverse-complement view of list.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/NucleotideTools.html#reverseComplement(org.biojava.bio.symbol.SymbolList)">reverseComplement(SymbolList)</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/NucleotideTools.html" title="class in org.biojava.bio.seq">NucleotideTools</a></dt>
<dd>
<div class="block">Retrieve a reverse-complement view of list.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/RNATools.html#reverseComplement(org.biojava.bio.symbol.SymbolList)">reverseComplement(SymbolList)</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/RNATools.html" title="class in org.biojava.bio.seq">RNATools</a></dt>
<dd>
<div class="block">Retrieve a reverse-complement view of list.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/SequenceTools.html#reverseComplement(org.biojava.bio.seq.Sequence)">reverseComplement(Sequence)</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/SequenceTools.html" title="class in org.biojava.bio.seq">SequenceTools</a></dt>
<dd>
<div class="block">Reverse-complement a sequence, and flip all of its features.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/AbstractChromatogram.html#reverseComplementBaseCallList(java.lang.Object)">reverseComplementBaseCallList(Object)</a></span> - Method in class org.biojava.bio.chromatogram.<a href="./org/biojava/bio/chromatogram/AbstractChromatogram.html" title="class in org.biojava.bio.chromatogram">AbstractChromatogram</a></dt>
<dd>
<div class="block">Return a symbol list containing the reverse complement of the base call
data for the given label.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/scf/SCF.html#reverseComplementBaseCallList(java.lang.Object)">reverseComplementBaseCallList(Object)</a></span> - Method in class org.biojava.bio.program.scf.<a href="./org/biojava/bio/program/scf/SCF.html" title="class in org.biojava.bio.program.scf">SCF</a></dt>
<dd>
<div class="block">Overrides <a href="./org/biojava/bio/chromatogram/AbstractChromatogram.html#reverseComplementBaseCallList(java.lang.Object)"><code>AbstractChromatogram.reverseComplementBaseCallList(java.lang.Object)</code></a> to
support the 7 quality values from the SCF.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/AbstractChromatogram.html#reverseComplementBaseCalls()">reverseComplementBaseCalls()</a></span> - Method in class org.biojava.bio.chromatogram.<a href="./org/biojava/bio/chromatogram/AbstractChromatogram.html" title="class in org.biojava.bio.chromatogram">AbstractChromatogram</a></dt>
<dd>
<div class="block">Returns a new base call alignment that is the reverse complement of
one in this chromatogram.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/AbstractChromatogram.html#reverseComplementInstance()">reverseComplementInstance()</a></span> - Method in class org.biojava.bio.chromatogram.<a href="./org/biojava/bio/chromatogram/AbstractChromatogram.html" title="class in org.biojava.bio.chromatogram">AbstractChromatogram</a></dt>
<dd>
<div class="block">Returns a new instance of this AbstractChromatogram subclass for use in
<a href="./org/biojava/bio/chromatogram/AbstractChromatogram.html#reverseComplement()"><code>AbstractChromatogram.reverseComplement()</code></a>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/SimpleChromatogram.html#reverseComplementInstance()">reverseComplementInstance()</a></span> - Method in class org.biojava.bio.chromatogram.<a href="./org/biojava/bio/chromatogram/SimpleChromatogram.html" title="class in org.biojava.bio.chromatogram">SimpleChromatogram</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/abi/ABIFChromatogram.html#reverseComplementInstance()">reverseComplementInstance()</a></span> - Method in class org.biojava.bio.program.abi.<a href="./org/biojava/bio/program/abi/ABIFChromatogram.html" title="class in org.biojava.bio.program.abi">ABIFChromatogram</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/scf/SCF.html#reverseComplementInstance()">reverseComplementInstance()</a></span> - Method in class org.biojava.bio.program.scf.<a href="./org/biojava/bio/program/scf/SCF.html" title="class in org.biojava.bio.program.scf">SCF</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/molbio/RestrictionEnzyme.html#reverseRegex">reverseRegex</a></span> - Variable in class org.biojava.bio.molbio.<a href="./org/biojava/bio/molbio/RestrictionEnzyme.html" title="class in org.biojava.bio.molbio">RestrictionEnzyme</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/symbol/ReversibleTranslationTable.html" title="interface in org.biojava.bio.symbol"><span class="strong">ReversibleTranslationTable</span></a> - Interface in <a href="./org/biojava/bio/symbol/package-summary.html">org.biojava.bio.symbol</a></dt>
<dd>
<div class="block">A translation table that can also translate from the target to source
alphabet.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SubSequence.SubProjectedFeatureContext.html#revertFeature(org.biojava.bio.seq.Feature)">revertFeature(Feature)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SubSequence.SubProjectedFeatureContext.html" title="class in org.biojava.bio.seq.impl">SubSequence.SubProjectedFeatureContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/projection/ProjectionContext.html#revertFeature(org.biojava.bio.seq.Feature)">revertFeature(Feature)</a></span> - Method in interface org.biojava.bio.seq.projection.<a href="./org/biojava/bio/seq/projection/ProjectionContext.html" title="interface in org.biojava.bio.seq.projection">ProjectionContext</a></dt>
<dd>
<div class="block">Unproject a feature.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/projection/ReparentContext.html#revertFeature(org.biojava.bio.seq.Feature)">revertFeature(Feature)</a></span> - Method in class org.biojava.bio.seq.projection.<a href="./org/biojava/bio/seq/projection/ReparentContext.html" title="class in org.biojava.bio.seq.projection">ReparentContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/projection/ProjectionContext.html#revertFilter(org.biojava.bio.seq.FeatureFilter)">revertFilter(FeatureFilter)</a></span> - Method in interface org.biojava.bio.seq.projection.<a href="./org/biojava/bio/seq/projection/ProjectionContext.html" title="interface in org.biojava.bio.seq.projection">ProjectionContext</a></dt>
<dd>
<div class="block">Transform a filter on projected features so that it applies to unprojected
features.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/projection/ReparentContext.html#revertFilter(org.biojava.bio.seq.FeatureFilter)">revertFilter(FeatureFilter)</a></span> - Method in class org.biojava.bio.seq.projection.<a href="./org/biojava/bio/seq/projection/ReparentContext.html" title="class in org.biojava.bio.seq.projection">ReparentContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleGappedSequence.GappedContext.html#revertLocation(org.biojava.bio.symbol.Location)">revertLocation(Location)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleGappedSequence.GappedContext.html" title="class in org.biojava.bio.seq.impl">SimpleGappedSequence.GappedContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/projection/ProjectionUtils.html#revertLocation(org.biojava.bio.symbol.Location, int, boolean)">revertLocation(Location, int, boolean)</a></span> - Static method in class org.biojava.bio.seq.projection.<a href="./org/biojava/bio/seq/projection/ProjectionUtils.html" title="class in org.biojava.bio.seq.projection">ProjectionUtils</a></dt>
<dd>
<div class="block">Revert a location, translating and flipping as required.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/projection/TranslateFlipContext.html#revertLocation(org.biojava.bio.symbol.Location)">revertLocation(Location)</a></span> - Method in class org.biojava.bio.seq.projection.<a href="./org/biojava/bio/seq/projection/TranslateFlipContext.html" title="class in org.biojava.bio.seq.projection">TranslateFlipContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/projection/TranslateFlipContext.html#revertStrand(org.biojava.bio.seq.StrandedFeature.Strand)">revertStrand(StrandedFeature.Strand)</a></span> - Method in class org.biojava.bio.seq.projection.<a href="./org/biojava/bio/seq/projection/TranslateFlipContext.html" title="class in org.biojava.bio.seq.projection">TranslateFlipContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/projection/ProjectionEngine.html#revertTemplate(org.biojava.bio.seq.Feature.Template, org.biojava.bio.seq.projection.ProjectionContext)">revertTemplate(Feature.Template, ProjectionContext)</a></span> - Method in class org.biojava.bio.seq.projection.<a href="./org/biojava/bio/seq/projection/ProjectionEngine.html" title="class in org.biojava.bio.seq.projection">ProjectionEngine</a></dt>
<dd>
<div class="block">Revert a template so that it can be used on the original feature-space.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/projection/ProjectionEngine.TemplateProjector.html#revertTemplate(org.biojava.bio.seq.projection.ProjectionContext, org.biojava.bio.seq.Feature.Template)">revertTemplate(ProjectionContext, Feature.Template)</a></span> - Method in interface org.biojava.bio.seq.projection.<a href="./org/biojava/bio/seq/projection/ProjectionEngine.TemplateProjector.html" title="interface in org.biojava.bio.seq.projection">ProjectionEngine.TemplateProjector</a></dt>
<dd> </dd>
<dt><a href="./org/biojavax/RichAnnotatable.html" title="interface in org.biojavax"><span class="strong">RichAnnotatable</span></a> - Interface in <a href="./org/biojavax/package-summary.html">org.biojavax</a></dt>
<dd>
<div class="block">Annotatable objects that can have rich annotations.</div>
</dd>
<dt><a href="./org/biojavax/RichAnnotation.html" title="interface in org.biojavax"><span class="strong">RichAnnotation</span></a> - Interface in <a href="./org/biojavax/package-summary.html">org.biojavax</a></dt>
<dd>
<div class="block">An annotation collection which stores annotations as Note objects.</div>
</dd>
<dt><a href="./org/biojavax/bio/seq/RichFeature.html" title="interface in org.biojavax.bio.seq"><span class="strong">RichFeature</span></a> - Interface in <a href="./org/biojavax/bio/seq/package-summary.html">org.biojavax.bio.seq</a></dt>
<dd>
<div class="block">Represents a feature that can be given name and rank and be
moved from one sequence to another.</div>
</dd>
<dt><a href="./org/biojavax/bio/seq/RichFeature.Template.html" title="class in org.biojavax.bio.seq"><span class="strong">RichFeature.Template</span></a> - Class in <a href="./org/biojavax/bio/seq/package-summary.html">org.biojavax.bio.seq</a></dt>
<dd>
<div class="block">Added-value extension of Feature.Template including bits we're
interested in, eg.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichFeature.Template.html#RichFeature.Template()">RichFeature.Template()</a></span> - Constructor for class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichFeature.Template.html" title="class in org.biojavax.bio.seq">RichFeature.Template</a></dt>
<dd> </dd>
<dt><a href="./org/biojavax/bio/seq/RichFeature.Tools.html" title="class in org.biojavax.bio.seq"><span class="strong">RichFeature.Tools</span></a> - Class in <a href="./org/biojavax/bio/seq/package-summary.html">org.biojavax.bio.seq</a></dt>
<dd>
<div class="block">Some useful tools for working with features.</div>
</dd>
<dt><a href="./org/biojavax/bio/seq/RichFeatureRelationship.html" title="interface in org.biojavax.bio.seq"><span class="strong">RichFeatureRelationship</span></a> - Interface in <a href="./org/biojavax/bio/seq/package-summary.html">org.biojavax.bio.seq</a></dt>
<dd>
<div class="block">Represents the relation between two features.</div>
</dd>
<dt><a href="./org/biojavax/bio/seq/RichFeatureRelationshipHolder.html" title="interface in org.biojavax.bio.seq"><span class="strong">RichFeatureRelationshipHolder</span></a> - Interface in <a href="./org/biojavax/bio/seq/package-summary.html">org.biojavax.bio.seq</a></dt>
<dd>
<div class="block">Holds feature relationships.</div>
</dd>
<dt><a href="./org/biojavax/bio/seq/RichLocation.html" title="interface in org.biojavax.bio.seq"><span class="strong">RichLocation</span></a> - Interface in <a href="./org/biojavax/bio/seq/package-summary.html">org.biojavax.bio.seq</a></dt>
<dd>
<div class="block">Describes locations, and adds the concepts of circularity, fuzziness,
annotations, and cross-references to other databases.</div>
</dd>
<dt><a href="./org/biojavax/bio/seq/RichLocation.Strand.html" title="class in org.biojavax.bio.seq"><span class="strong">RichLocation.Strand</span></a> - Class in <a href="./org/biojavax/bio/seq/package-summary.html">org.biojavax.bio.seq</a></dt>
<dd>
<div class="block">This class represents a strand on which a location may lie.</div>
</dd>
<dt><a href="./org/biojavax/bio/seq/RichLocation.Tools.html" title="class in org.biojavax.bio.seq"><span class="strong">RichLocation.Tools</span></a> - Class in <a href="./org/biojavax/bio/seq/package-summary.html">org.biojavax.bio.seq</a></dt>
<dd>
<div class="block">Some useful tools for working with Locations.</div>
</dd>
<dt><a href="./org/biojavax/RichObjectBuilder.html" title="interface in org.biojavax"><span class="strong">RichObjectBuilder</span></a> - Interface in <a href="./org/biojavax/package-summary.html">org.biojavax</a></dt>
<dd>
<div class="block">This interface allows a class to generate Rich objects based on a class
name and some parameters.</div>
</dd>
<dt><a href="./org/biojavax/RichObjectFactory.html" title="class in org.biojavax"><span class="strong">RichObjectFactory</span></a> - Class in <a href="./org/biojavax/package-summary.html">org.biojavax</a></dt>
<dd>
<div class="block">Runs a service that builds rich objects, and provides some default values
for things like default ontology, default namespace, etc.</div>
</dd>
<dt><a href="./org/biojavax/bio/seq/io/RichSeqIOAdapter.html" title="class in org.biojavax.bio.seq.io"><span class="strong">RichSeqIOAdapter</span></a> - Class in <a href="./org/biojavax/bio/seq/io/package-summary.html">org.biojavax.bio.seq.io</a></dt>
<dd>
<div class="block">This class implements all methods of RichSeqIOListener and takes no action.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/RichSeqIOAdapter.html#RichSeqIOAdapter()">RichSeqIOAdapter()</a></span> - Constructor for class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/RichSeqIOAdapter.html" title="class in org.biojavax.bio.seq.io">RichSeqIOAdapter</a></dt>
<dd>
<div class="block">Creates a new instance of RichSeqIOAdapter</div>
</dd>
<dt><a href="./org/biojavax/bio/seq/io/RichSeqIOListener.html" title="interface in org.biojavax.bio.seq.io"><span class="strong">RichSeqIOListener</span></a> - Interface in <a href="./org/biojavax/bio/seq/io/package-summary.html">org.biojavax.bio.seq.io</a></dt>
<dd>
<div class="block">An interface for classes that listen to BioEntry or
RichSequence I/O streams.</div>
</dd>
<dt><a href="./org/biojavax/bio/seq/RichSequence.html" title="interface in org.biojavax.bio.seq"><span class="strong">RichSequence</span></a> - Interface in <a href="./org/biojavax/bio/seq/package-summary.html">org.biojavax.bio.seq</a></dt>
<dd>
<div class="block">A rich sequence is a combination of a org.biojavax.bio.Bioentry and a
Sequence.</div>
</dd>
<dt><a href="./org/biojavax/bio/seq/RichSequence.IOTools.html" title="class in org.biojavax.bio.seq"><span class="strong">RichSequence.IOTools</span></a> - Class in <a href="./org/biojavax/bio/seq/package-summary.html">org.biojavax.bio.seq</a></dt>
<dd>
<div class="block">A set of convenience methods for handling common file formats.</div>
</dd>
<dt><a href="./org/biojavax/bio/seq/RichSequence.IOTools.SingleRichSeqIterator.html" title="class in org.biojavax.bio.seq"><span class="strong">RichSequence.IOTools.SingleRichSeqIterator</span></a> - Class in <a href="./org/biojavax/bio/seq/package-summary.html">org.biojavax.bio.seq</a></dt>
<dd>
<div class="block">Used to iterate over a single rich sequence</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.IOTools.SingleRichSeqIterator.html#RichSequence.IOTools.SingleRichSeqIterator(org.biojava.bio.seq.Sequence)">RichSequence.IOTools.SingleRichSeqIterator(Sequence)</a></span> - Constructor for class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.IOTools.SingleRichSeqIterator.html" title="class in org.biojavax.bio.seq">RichSequence.IOTools.SingleRichSeqIterator</a></dt>
<dd>
<div class="block">Creates an iterator over a single sequence.</div>
</dd>
<dt><a href="./org/biojavax/bio/seq/RichSequence.Terms.html" title="class in org.biojavax.bio.seq"><span class="strong">RichSequence.Terms</span></a> - Class in <a href="./org/biojavax/bio/seq/package-summary.html">org.biojavax.bio.seq</a></dt>
<dd>
<div class="block">Stores a number of useful terms used across many sequence formats for
consistency's sake.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.Terms.html#RichSequence.Terms()">RichSequence.Terms()</a></span> - Constructor for class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.Terms.html" title="class in org.biojavax.bio.seq">RichSequence.Terms</a></dt>
<dd> </dd>
<dt><a href="./org/biojavax/bio/seq/RichSequence.Tools.html" title="class in org.biojavax.bio.seq"><span class="strong">RichSequence.Tools</span></a> - Class in <a href="./org/biojavax/bio/seq/package-summary.html">org.biojavax.bio.seq</a></dt>
<dd>
<div class="block">Some useful tools for working with RichSequence objects.</div>
</dd>
<dt><a href="./org/biojavax/bio/seq/io/RichSequenceBuilder.html" title="interface in org.biojavax.bio.seq.io"><span class="strong">RichSequenceBuilder</span></a> - Interface in <a href="./org/biojavax/bio/seq/io/package-summary.html">org.biojavax.bio.seq.io</a></dt>
<dd>
<div class="block">An interface for objects that can build RichSequences.</div>
</dd>
<dt><a href="./org/biojavax/bio/seq/io/RichSequenceBuilderFactory.html" title="interface in org.biojavax.bio.seq.io"><span class="strong">RichSequenceBuilderFactory</span></a> - Interface in <a href="./org/biojavax/bio/seq/io/package-summary.html">org.biojavax.bio.seq.io</a></dt>
<dd>
<div class="block">Simple factory for constructing new RichSequenceBuilder objects.</div>
</dd>
<dt><a href="./org/biojavax/bio/db/RichSequenceDB.html" title="interface in org.biojavax.bio.db"><span class="strong">RichSequenceDB</span></a> - Interface in <a href="./org/biojavax/bio/db/package-summary.html">org.biojavax.bio.db</a></dt>
<dd>
<div class="block">A database of RichSequences with accessible keys and iterators over all
sequences.</div>
</dd>
<dt><a href="./org/biojavax/bio/db/RichSequenceDBLite.html" title="interface in org.biojavax.bio.db"><span class="strong">RichSequenceDBLite</span></a> - Interface in <a href="./org/biojavax/bio/db/package-summary.html">org.biojavax.bio.db</a></dt>
<dd>
<div class="block">A database of RichSequences.</div>
</dd>
<dt><a href="./org/biojavax/bio/seq/io/RichSequenceFormat.html" title="interface in org.biojavax.bio.seq.io"><span class="strong">RichSequenceFormat</span></a> - Interface in <a href="./org/biojavax/bio/seq/io/package-summary.html">org.biojavax.bio.seq.io</a></dt>
<dd>
<div class="block">Allows a file format to be read/written as RichSequences.</div>
</dd>
<dt><a href="./org/biojavax/bio/seq/io/RichSequenceFormat.BasicFormat.html" title="class in org.biojavax.bio.seq.io"><span class="strong">RichSequenceFormat.BasicFormat</span></a> - Class in <a href="./org/biojavax/bio/seq/io/package-summary.html">org.biojavax.bio.seq.io</a></dt>
<dd>
<div class="block">Provides a basic format with simple things like line-widths precoded.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/RichSequenceFormat.BasicFormat.html#RichSequenceFormat.BasicFormat()">RichSequenceFormat.BasicFormat()</a></span> - Constructor for class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/RichSequenceFormat.BasicFormat.html" title="class in org.biojavax.bio.seq.io">RichSequenceFormat.BasicFormat</a></dt>
<dd> </dd>
<dt><a href="./org/biojavax/bio/seq/io/RichSequenceFormat.HeaderlessFormat.html" title="class in org.biojavax.bio.seq.io"><span class="strong">RichSequenceFormat.HeaderlessFormat</span></a> - Class in <a href="./org/biojavax/bio/seq/io/package-summary.html">org.biojavax.bio.seq.io</a></dt>
<dd>
<div class="block">Provides the basic implementation required for simple header/footer-less files such as Genbank.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/RichSequenceFormat.HeaderlessFormat.html#RichSequenceFormat.HeaderlessFormat()">RichSequenceFormat.HeaderlessFormat()</a></span> - Constructor for class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/RichSequenceFormat.HeaderlessFormat.html" title="class in org.biojavax.bio.seq.io">RichSequenceFormat.HeaderlessFormat</a></dt>
<dd> </dd>
<dt><a href="./org/biojavax/bio/seq/RichSequenceHandler.html" title="interface in org.biojavax.bio.seq"><span class="strong">RichSequenceHandler</span></a> - Interface in <a href="./org/biojavax/bio/seq/package-summary.html">org.biojavax.bio.seq</a></dt>
<dd>
<div class="block">An interface for classes that know how to handle subsequence operations.</div>
</dd>
<dt><a href="./org/biojavax/bio/seq/RichSequenceIterator.html" title="interface in org.biojavax.bio.seq"><span class="strong">RichSequenceIterator</span></a> - Interface in <a href="./org/biojavax/bio/seq/package-summary.html">org.biojavax.bio.seq</a></dt>
<dd>
<div class="block">Essentially the same as SequenceIterator.</div>
</dd>
<dt><a href="./org/biojavax/bio/seq/io/RichStreamReader.html" title="class in org.biojavax.bio.seq.io"><span class="strong">RichStreamReader</span></a> - Class in <a href="./org/biojavax/bio/seq/io/package-summary.html">org.biojavax.bio.seq.io</a></dt>
<dd>
<div class="block">Parses a stream into sequences.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/RichStreamReader.html#RichStreamReader(java.io.InputStream, org.biojavax.bio.seq.io.RichSequenceFormat, org.biojava.bio.seq.io.SymbolTokenization, org.biojavax.bio.seq.io.RichSequenceBuilderFactory, org.biojavax.Namespace)">RichStreamReader(InputStream, RichSequenceFormat, SymbolTokenization, RichSequenceBuilderFactory, Namespace)</a></span> - Constructor for class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/RichStreamReader.html" title="class in org.biojavax.bio.seq.io">RichStreamReader</a></dt>
<dd>
<div class="block">Creates a new stream reader on the given input stream, which will attempt to read
sequences in the given format, having symbols from the given tokenization, and
pass them to the given factory to be transformed into RichSequence objects in
the given namespace.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/RichStreamReader.html#RichStreamReader(java.io.BufferedReader, org.biojavax.bio.seq.io.RichSequenceFormat, org.biojava.bio.seq.io.SymbolTokenization, org.biojavax.bio.seq.io.RichSequenceBuilderFactory, org.biojavax.Namespace)">RichStreamReader(BufferedReader, RichSequenceFormat, SymbolTokenization, RichSequenceBuilderFactory, Namespace)</a></span> - Constructor for class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/RichStreamReader.html" title="class in org.biojavax.bio.seq.io">RichStreamReader</a></dt>
<dd>
<div class="block">Creates a new stream reader on the given reader, which will attempt to read
sequences in the given format, having symbols from the given tokenization, and
pass them to the given factory to be transformed into RichSequence objects in
the given namespace.</div>
</dd>
<dt><a href="./org/biojavax/bio/seq/io/RichStreamWriter.html" title="class in org.biojavax.bio.seq.io"><span class="strong">RichStreamWriter</span></a> - Class in <a href="./org/biojavax/bio/seq/io/package-summary.html">org.biojavax.bio.seq.io</a></dt>
<dd>
<div class="block">Writes all of the sequences from a SequenceIterator to a stream with a
particular format.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/RichStreamWriter.html#RichStreamWriter(java.io.OutputStream, org.biojavax.bio.seq.io.RichSequenceFormat)">RichStreamWriter(OutputStream, RichSequenceFormat)</a></span> - Constructor for class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/RichStreamWriter.html" title="class in org.biojavax.bio.seq.io">RichStreamWriter</a></dt>
<dd>
<div class="block">Generate a new RichStreamWriter to the stream os and using format.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/AbstractULAlignment.html#rightMost()">rightMost()</a></span> - Method in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/AbstractULAlignment.html" title="class in org.biojava.bio.alignment">AbstractULAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/utils/StringTools.html#rightPad(java.lang.String, int)">rightPad(String, int)</a></span> - Static method in class org.biojavax.utils.<a href="./org/biojavax/utils/StringTools.html" title="class in org.biojavax.utils">StringTools</a></dt>
<dd>
<div class="block">Pads a string to be a certain width by appending spaces.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/utils/StringTools.html#rightPad(java.lang.String, char, int)">rightPad(String, char, int)</a></span> - Static method in class org.biojavax.utils.<a href="./org/biojavax/utils/StringTools.html" title="class in org.biojavax.utils">StringTools</a></dt>
<dd>
<div class="block">Pads a string to be a certain width by appending given symbols.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BibRef.html#rights">rights</a></span> - Variable in class org.biojava.bibliography.<a href="./org/biojava/bibliography/BibRef.html" title="class in org.biojava.bibliography">BibRef</a></dt>
<dd>
<div class="block">
It specifies information about rights over the cited resource.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/taxa/NCBITaxon.html#RIGHTVALUE">RIGHTVALUE</a></span> - Static variable in interface org.biojavax.bio.taxa.<a href="./org/biojavax/bio/taxa/NCBITaxon.html" title="interface in org.biojavax.bio.taxa">NCBITaxon</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/helper/AlignTools.html#rms_dk_diag(double[], double[], int, int, int, int)">rms_dk_diag(double[], double[], int, int, int, int)</a></span> - Static method in class org.biojava.bio.structure.align.helper.<a href="./org/biojava/bio/structure/align/helper/AlignTools.html" title="class in org.biojava.bio.structure.align.helper">AlignTools</a></dt>
<dd>
<div class="block">Given distance matrix diagonals dk1, dk2, get the rmsd of a fpair.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOConstants.html#RNA">RNA</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOConstants.html" title="class in org.biojava.bio.seq.io">SeqIOConstants</a></dt>
<dd>
<div class="block"><code>RNA</code> indicates that a sequence contains RNA
(ribonucleic acid) symbols.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/chem/PolymerType.html#RNA_ONLY">RNA_ONLY</a></span> - Static variable in enum org.biojava.bio.structure.io.mmcif.chem.<a href="./org/biojava/bio/structure/io/mmcif/chem/PolymerType.html" title="enum in org.biojava.bio.structure.io.mmcif.chem">PolymerType</a></dt>
<dd>
<div class="block">Convenience <tt>Set</tt> of polymer types classified as RNA.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/RNATools.html" title="class in org.biojava.bio.seq"><span class="strong">RNATools</span></a> - Class in <a href="./org/biojava/bio/seq/package-summary.html">org.biojava.bio.seq</a></dt>
<dd>
<div class="block">Useful functionality for processing DNA and RNA sequences.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BibRefSupport.html#ROLE_ATTR_QUERYABLE">ROLE_ATTR_QUERYABLE</a></span> - Static variable in interface org.biojava.bibliography.<a href="./org/biojava/bibliography/BibRefSupport.html" title="interface in org.biojava.bibliography">BibRefSupport</a></dt>
<dd>
<div class="block">
A role of an attribute.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BibRefSupport.html#ROLE_ATTR_RETRIEVABLE">ROLE_ATTR_RETRIEVABLE</a></span> - Static variable in interface org.biojava.bibliography.<a href="./org/biojava/bibliography/BibRefSupport.html" title="interface in org.biojava.bibliography">BibRefSupport</a></dt>
<dd>
<div class="block">
A role of an attribute.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/BioIndex.html#rollback()">rollback()</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/BioIndex.html" title="class in org.biojava.bio.seq.db">BioIndex</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/EmblCDROMIndexStore.html#rollback()">rollback()</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/EmblCDROMIndexStore.html" title="class in org.biojava.bio.seq.db">EmblCDROMIndexStore</a></dt>
<dd>
<div class="block"><code>rollback</code> rolls back changes made since the last
<code>commit</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/IndexStore.html#rollback()">rollback()</a></span> - Method in interface org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/IndexStore.html" title="interface in org.biojava.bio.seq.db">IndexStore</a></dt>
<dd>
<div class="block">Discard all uncommited changes.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/TabIndexStore.html#rollback()">rollback()</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/TabIndexStore.html" title="class in org.biojava.bio.seq.db">TabIndexStore</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/Commitable.html#rollback()">rollback()</a></span> - Method in interface org.biojava.utils.<a href="./org/biojava/utils/Commitable.html" title="interface in org.biojava.utils">Commitable</a></dt>
<dd>
<div class="block"><code>rollback</code> reverses pending changes to restore
initial (or prior commit) state.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/FileAsList.html#rollback()">rollback()</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/FileAsList.html" title="class in org.biojava.utils">FileAsList</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Calc.html#rotate(org.biojava.bio.structure.Atom, double[][])">rotate(Atom, double[][])</a></span> - Static method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Calc.html" title="class in org.biojava.bio.structure">Calc</a></dt>
<dd>
<div class="block">rotate a single atom aroud a rotation matrix.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Calc.html#rotate(org.biojava.bio.structure.Structure, double[][])">rotate(Structure, double[][])</a></span> - Static method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Calc.html" title="class in org.biojava.bio.structure">Calc</a></dt>
<dd>
<div class="block">Rotate a structure.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Calc.html#rotate(org.biojava.bio.structure.Group, double[][])">rotate(Group, double[][])</a></span> - Static method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Calc.html" title="class in org.biojava.bio.structure">Calc</a></dt>
<dd>
<div class="block">rotate a structure .</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Calc.html#rotate(org.biojava.bio.structure.Atom, org.biojava.bio.structure.jama.Matrix)">rotate(Atom, Matrix)</a></span> - Static method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Calc.html" title="class in org.biojava.bio.structure">Calc</a></dt>
<dd>
<div class="block">Rotate an atom around a Matrix object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Calc.html#rotate(org.biojava.bio.structure.Group, org.biojava.bio.structure.jama.Matrix)">rotate(Group, Matrix)</a></span> - Static method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Calc.html" title="class in org.biojava.bio.structure">Calc</a></dt>
<dd>
<div class="block">Rotate a group object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Calc.html#rotate(org.biojava.bio.structure.Structure, org.biojava.bio.structure.jama.Matrix)">rotate(Structure, Matrix)</a></span> - Static method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Calc.html" title="class in org.biojava.bio.structure">Calc</a></dt>
<dd>
<div class="block">Rotate a structure object.</div>
</dd>
<dt><a href="./org/biojava/bio/gui/sequence/RoundRectangularBeadRenderer.html" title="class in org.biojava.bio.gui.sequence"><span class="strong">RoundRectangularBeadRenderer</span></a> - Class in <a href="./org/biojava/bio/gui/sequence/package-summary.html">org.biojava.bio.gui.sequence</a></dt>
<dd>
<div class="block"><code>RoundRectangularBeadRenderer</code> renders features
as rectangles with rounded corners.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/RoundRectangularBeadRenderer.html#RoundRectangularBeadRenderer()">RoundRectangularBeadRenderer()</a></span> - Constructor for class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/RoundRectangularBeadRenderer.html" title="class in org.biojava.bio.gui.sequence">RoundRectangularBeadRenderer</a></dt>
<dd>
<div class="block">Creates a new <code>RoundRectangularBeadRenderer</code>
object with the default settings.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/RoundRectangularBeadRenderer.html#RoundRectangularBeadRenderer(double, double, java.awt.Paint, java.awt.Paint, java.awt.Stroke, double, double)">RoundRectangularBeadRenderer(double, double, Paint, Paint, Stroke, double, double)</a></span> - Constructor for class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/RoundRectangularBeadRenderer.html" title="class in org.biojava.bio.gui.sequence">RoundRectangularBeadRenderer</a></dt>
<dd>
<div class="block">Creates a new <code>RoundRectangularBeadRenderer</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/SubstitutionMatrix.html#rowSymbols">rowSymbols</a></span> - Variable in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/SubstitutionMatrix.html" title="class in org.biojava.bio.alignment">SubstitutionMatrix</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtFormat.html#RP_LINE_TAG">RP_LINE_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtFormat.html" title="class in org.biojavax.bio.seq.io">UniProtFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#RP_LINE_TAG">RP_LINE_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLFormat.html#rpp">rpp</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLFormat.html" title="class in org.biojavax.bio.seq.io">EMBLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtFormat.html#rppat">rppat</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtFormat.html" title="class in org.biojavax.bio.seq.io">UniProtFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#rppat">rppat</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/gui/sequence/RulerRenderer.html" title="class in org.biojava.bio.gui.sequence"><span class="strong">RulerRenderer</span></a> - Class in <a href="./org/biojava/bio/gui/sequence/package-summary.html">org.biojava.bio.gui.sequence</a></dt>
<dd>
<div class="block"><code>RulerRenderer</code> renders numerical scales in sequence
coordinates.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/RulerRenderer.html#RulerRenderer()">RulerRenderer()</a></span> - Constructor for class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/RulerRenderer.html" title="class in org.biojava.bio.gui.sequence">RulerRenderer</a></dt>
<dd>
<div class="block">Creates a new <code>RulerRenderer</code> with the default
setting of ticks pointing downwards.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/RulerRenderer.html#RulerRenderer(int)">RulerRenderer(int)</a></span> - Constructor for class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/RulerRenderer.html" title="class in org.biojava.bio.gui.sequence">RulerRenderer</a></dt>
<dd>
<div class="block">Creates a new <code>RulerRenderer</code> with the specified
tick direction.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/util/AlignmentCalc.html#run()">run()</a></span> - Method in class org.biojava.bio.structure.gui.util.<a href="./org/biojava/bio/structure/gui/util/AlignmentCalc.html" title="class in org.biojava.bio.structure.gui.util">AlignmentCalc</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/server/DemoStructureServer.html#run()">run()</a></span> - Method in class org.biojava.bio.structure.server.<a href="./org/biojava/bio/structure/server/DemoStructureServer.html" title="class in org.biojava.bio.structure.server">DemoStructureServer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/server/StructureFetcherRunnable.html#run()">run()</a></span> - Method in class org.biojava.bio.structure.server.<a href="./org/biojava/bio/structure/server/StructureFetcherRunnable.html" title="class in org.biojava.bio.structure.server">StructureFetcherRunnable</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/process/ReaderInputHandler.html#run()">run()</a></span> - Method in class org.biojava.utils.process.<a href="./org/biojava/utils/process/ReaderInputHandler.html" title="class in org.biojava.utils.process">ReaderInputHandler</a></dt>
<dt><span class="strong"><a href="./org/biojava/utils/process/ReaderWriterPipe.html#run()">run()</a></span> - Method in class org.biojava.utils.process.<a href="./org/biojava/utils/process/ReaderWriterPipe.html" title="class in org.biojava.utils.process">ReaderWriterPipe</a></dt>
<dt><span class="strong"><a href="./org/biojava/utils/process/SimpleInputHandler.html#run()">run()</a></span> - Method in class org.biojava.utils.process.<a href="./org/biojava/utils/process/SimpleInputHandler.html" title="class in org.biojava.utils.process">SimpleInputHandler</a></dt>
<dt><span class="strong"><a href="./org/biojava/utils/process/StreamPipe.html#run()">run()</a></span> - Method in class org.biojava.utils.process.<a href="./org/biojava/utils/process/StreamPipe.html" title="class in org.biojava.utils.process">StreamPipe</a></dt>
<dt><span class="strong"><a href="./org/biojavax/ga/GeneticAlgorithm.html#run(org.biojavax.ga.GAStoppingCriteria)">run(GAStoppingCriteria)</a></span> - Method in interface org.biojavax.ga.<a href="./org/biojavax/ga/GeneticAlgorithm.html" title="interface in org.biojavax.ga">GeneticAlgorithm</a></dt>
<dd>
<div class="block">Iterates the Algorithm until the stopping criteria are met.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ga/impl/SimpleGeneticAlgorithm.html#run(org.biojavax.ga.GAStoppingCriteria)">run(GAStoppingCriteria)</a></span> - Method in class org.biojavax.ga.impl.<a href="./org/biojavax/ga/impl/SimpleGeneticAlgorithm.html" title="class in org.biojavax.ga.impl">SimpleGeneticAlgorithm</a></dt>
<dd> </dd>
</dl>
<a name="_S_">
<!-- -->
</a>
<h2 class="title">S</h2>
<dl>
<dt><span class="strong"><a href="./org/biojava/bio/seq/DNATools.html#s()">s()</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/DNATools.html" title="class in org.biojava.bio.seq">DNATools</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/NucleotideTools.html#s()">s()</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/NucleotideTools.html" title="class in org.biojava.bio.seq">NucleotideTools</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/ProteinTools.html#s()">s()</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/ProteinTools.html" title="class in org.biojava.bio.seq">ProteinTools</a></dt>
<dd>
<div class="block">Returns the <code>AtomicSymbol</code> for the amino acid
Serine</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/Taxon.html#S_SCROFA">S_SCROFA</a></span> - Static variable in interface org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/Taxon.html" title="interface in org.biojava.bio.program.homologene">Taxon</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/util/WeightedSet.html#sample()">sample()</a></span> - Method in class org.biojavax.ga.util.<a href="./org/biojavax/ga/util/WeightedSet.html" title="class in org.biojavax.ga.util">WeightedSet</a></dt>
<dd>
<div class="block">Randomly samples an <code>Object</code> from the <code>Set</code> according
to its weight.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/AbstractDistribution.html#sampleSymbol()">sampleSymbol()</a></span> - Method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/AbstractDistribution.html" title="class in org.biojava.bio.dist">AbstractDistribution</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/Distribution.html#sampleSymbol()">sampleSymbol()</a></span> - Method in interface org.biojava.bio.dist.<a href="./org/biojava/bio/dist/Distribution.html" title="interface in org.biojava.bio.dist">Distribution</a></dt>
<dd>
<div class="block">Sample a symbol from this state's probability distribution.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/GapDistribution.html#sampleSymbol()">sampleSymbol()</a></span> - Method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/GapDistribution.html" title="class in org.biojava.bio.dist">GapDistribution</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/PairDistribution.html#sampleSymbol()">sampleSymbol()</a></span> - Method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/PairDistribution.html" title="class in org.biojava.bio.dist">PairDistribution</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/TranslatedDistribution.html#sampleSymbol()">sampleSymbol()</a></span> - Method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/TranslatedDistribution.html" title="class in org.biojava.bio.dist">TranslatedDistribution</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/fastq/SangerFastqReader.html" title="class in org.biojava.bio.program.fastq"><span class="strong">SangerFastqReader</span></a> - Class in <a href="./org/biojava/bio/program/fastq/package-summary.html">org.biojava.bio.program.fastq</a></dt>
<dd>
<div class="block">Reader for <a href="./org/biojava/bio/program/fastq/FastqVariant.html#FASTQ_SANGER"><code>FastqVariant.FASTQ_SANGER</code></a> formatted sequences.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/fastq/SangerFastqReader.html#SangerFastqReader()">SangerFastqReader()</a></span> - Constructor for class org.biojava.bio.program.fastq.<a href="./org/biojava/bio/program/fastq/SangerFastqReader.html" title="class in org.biojava.bio.program.fastq">SangerFastqReader</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/fastq/SangerFastqWriter.html" title="class in org.biojava.bio.program.fastq"><span class="strong">SangerFastqWriter</span></a> - Class in <a href="./org/biojava/bio/program/fastq/package-summary.html">org.biojava.bio.program.fastq</a></dt>
<dd>
<div class="block">Writer for <a href="./org/biojava/bio/program/fastq/FastqVariant.html#FASTQ_SANGER"><code>FastqVariant.FASTQ_SANGER</code></a> formatted sequences.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/fastq/SangerFastqWriter.html#SangerFastqWriter()">SangerFastqWriter()</a></span> - Constructor for class org.biojava.bio.program.fastq.<a href="./org/biojava/bio/program/fastq/SangerFastqWriter.html" title="class in org.biojava.bio.program.fastq">SangerFastqWriter</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/io/agave/SAX2StAXAdaptor.html" title="class in org.biojava.bio.seq.io.agave"><span class="strong">SAX2StAXAdaptor</span></a> - Class in <a href="./org/biojava/bio/seq/io/agave/package-summary.html">org.biojava.bio.seq.io.agave</a></dt>
<dd>
<div class="block">Lightweight adaptor which translates SAX content events into
StAX form, and provides delegation services.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/SAX2StAXAdaptor.html#SAX2StAXAdaptor(org.biojava.bio.seq.io.agave.StAXContentHandler)">SAX2StAXAdaptor(StAXContentHandler)</a></span> - Constructor for class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/SAX2StAXAdaptor.html" title="class in org.biojava.bio.seq.io.agave">SAX2StAXAdaptor</a></dt>
<dd>
<div class="block">Construct a new SAX Content handler which wraps a StAX
handler.</div>
</dd>
<dt><a href="./org/biojava/utils/stax/SAX2StAXAdaptor.html" title="class in org.biojava.utils.stax"><span class="strong">SAX2StAXAdaptor</span></a> - Class in <a href="./org/biojava/utils/stax/package-summary.html">org.biojava.utils.stax</a></dt>
<dd>
<div class="block">Lightweight adaptor which translates SAX content events into
StAX form, and provides delegation services.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/stax/SAX2StAXAdaptor.html#SAX2StAXAdaptor(org.biojava.utils.stax.StAXContentHandler)">SAX2StAXAdaptor(StAXContentHandler)</a></span> - Constructor for class org.biojava.utils.stax.<a href="./org/biojava/utils/stax/SAX2StAXAdaptor.html" title="class in org.biojava.utils.stax">SAX2StAXAdaptor</a></dt>
<dd>
<div class="block">Construct a new SAX Content handler which wraps a StAX
handler.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/emblcd/EmblCDROMIndexReader.html#sb">sb</a></span> - Variable in class org.biojava.bio.seq.db.emblcd.<a href="./org/biojava/bio/seq/db/emblcd/EmblCDROMIndexReader.html" title="class in org.biojava.bio.seq.db.emblcd">EmblCDROMIndexReader</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/graphic/ChromatogramNonlinearScaler.Identity.html#scale(org.biojava.bio.chromatogram.Chromatogram, int)">scale(Chromatogram, int)</a></span> - Method in class org.biojava.bio.chromatogram.graphic.<a href="./org/biojava/bio/chromatogram/graphic/ChromatogramNonlinearScaler.Identity.html" title="class in org.biojava.bio.chromatogram.graphic">ChromatogramNonlinearScaler.Identity</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/graphic/ChromatogramNonlinearScaler.html#scale(org.biojava.bio.chromatogram.Chromatogram, int)">scale(Chromatogram, int)</a></span> - Method in interface org.biojava.bio.chromatogram.graphic.<a href="./org/biojava/bio/chromatogram/graphic/ChromatogramNonlinearScaler.html" title="interface in org.biojava.bio.chromatogram.graphic">ChromatogramNonlinearScaler</a></dt>
<dd>
<div class="block">Returns the remapped coordinate for the provided trace sample index of the
given chromatogram.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/graphic/FixedBaseWidthScaler.html#scale(org.biojava.bio.chromatogram.Chromatogram, int)">scale(Chromatogram, int)</a></span> - Method in class org.biojava.bio.chromatogram.graphic.<a href="./org/biojava/bio/chromatogram/graphic/FixedBaseWidthScaler.html" title="class in org.biojava.bio.chromatogram.graphic">FixedBaseWidthScaler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/util/SequenceScalePanel.html#SCALE_COLOR">SCALE_COLOR</a></span> - Static variable in class org.biojava.bio.structure.gui.util.<a href="./org/biojava/bio/structure/gui/util/SequenceScalePanel.html" title="class in org.biojava.bio.structure.gui.util">SequenceScalePanel</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/structure/gui/ScaleableMatrixPanel.html" title="class in org.biojava.bio.structure.gui"><span class="strong">ScaleableMatrixPanel</span></a> - Class in <a href="./org/biojava/bio/structure/gui/package-summary.html">org.biojava.bio.structure.gui</a></dt>
<dd>
<div class="block">A JPanel that can display the underlying distance matrix
data of the protein structure alignment algorithm.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/ScaleableMatrixPanel.html#ScaleableMatrixPanel()">ScaleableMatrixPanel()</a></span> - Constructor for class org.biojava.bio.structure.gui.<a href="./org/biojava/bio/structure/gui/ScaleableMatrixPanel.html" title="class in org.biojava.bio.structure.gui">ScaleableMatrixPanel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/RectangularBeadRenderer.html#scaleHeight">scaleHeight</a></span> - Variable in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/RectangularBeadRenderer.html" title="class in org.biojava.bio.gui.sequence">RectangularBeadRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/TranslationTable.html#SCENE_MITO">SCENE_MITO</a></span> - Static variable in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/TranslationTable.html" title="interface in org.biojava.bio.symbol">TranslationTable</a></dt>
<dd>
<div class="block">Translation table name for the scenedesmus obliquus mitochondrial genetic
code.</div>
</dd>
<dt><a href="./org/biojava/bio/program/scf/SCF.html" title="class in org.biojava.bio.program.scf"><span class="strong">SCF</span></a> - Class in <a href="./org/biojava/bio/program/scf/package-summary.html">org.biojava.bio.program.scf</a></dt>
<dd>
<div class="block">A <a href="./org/biojava/bio/chromatogram/Chromatogram.html" title="interface in org.biojava.bio.chromatogram"><code>Chromatogram</code></a> as loaded from an
SCF v2 or v3 file.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/scf/SCF.html#SCF()">SCF()</a></span> - Constructor for class org.biojava.bio.program.scf.<a href="./org/biojava/bio/program/scf/SCF.html" title="class in org.biojava.bio.program.scf">SCF</a></dt>
<dd>
<div class="block">Creates a new, completely empty SCF.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/ChromatogramFactory.html#SCF_MAGIC">SCF_MAGIC</a></span> - Static variable in class org.biojava.bio.chromatogram.<a href="./org/biojava/bio/chromatogram/ChromatogramFactory.html" title="class in org.biojava.bio.chromatogram">ChromatogramFactory</a></dt>
<dd>
<div class="block">The magic number for SCF files.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureHolder.html#SCHEMA">SCHEMA</a></span> - Static variable in interface org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureHolder.html" title="interface in org.biojava.bio.seq">FeatureHolder</a></dt>
<dd>
<div class="block">Signals that the schema of this FeatureHolder has changed.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEProperty.html#SCI_PROPERTY">SCI_PROPERTY</a></span> - Static variable in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEProperty.html" title="class in org.biojava.bio.seq.io.agave">AGAVEProperty</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/taxa/NCBITaxon.html#SCIENTIFIC">SCIENTIFIC</a></span> - Static variable in interface org.biojavax.bio.taxa.<a href="./org/biojavax/bio/taxa/NCBITaxon.html" title="interface in org.biojavax.bio.taxa">NCBITaxon</a></dt>
<dd>
<div class="block">Use this to define scientific names for things.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.Terms.html#SCIENTIFIC_NAME_KEY">SCIENTIFIC_NAME_KEY</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.Terms.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat.Terms</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html#SCINAME_TAG">SCINAME_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html" title="class in org.biojavax.bio.seq.io">EMBLxmlFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/BasicFeatureRenderer.html#SCOOP">SCOOP</a></span> - Static variable in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/BasicFeatureRenderer.html" title="class in org.biojava.bio.gui.sequence">BasicFeatureRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/BackPointer.html#score">score</a></span> - Variable in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/BackPointer.html" title="class in org.biojava.bio.dp">BackPointer</a></dt>
<dd>
<div class="block">The score of this element of the DP matrix.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/onehead/SingleDPMatrix.html#score">score</a></span> - Variable in class org.biojava.bio.dp.onehead.<a href="./org/biojava/bio/dp/onehead/SingleDPMatrix.html" title="class in org.biojava.bio.dp.onehead">SingleDPMatrix</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/homol/SimilarityPairFeature.Template.html#score">score</a></span> - Variable in class org.biojava.bio.seq.homol.<a href="./org/biojava/bio/seq/homol/SimilarityPairFeature.Template.html" title="class in org.biojava.bio.seq.homol">SimilarityPairFeature.Template</a></dt>
<dd>
<div class="block"><code>score</code> of the search which produced the
alignment.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/onehead/SingleDPMatrix.html#scores">scores</a></span> - Variable in class org.biojava.bio.dp.onehead.<a href="./org/biojava/bio/dp/onehead/SingleDPMatrix.html" title="class in org.biojava.bio.dp.onehead">SingleDPMatrix</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/StatePath.html#SCORES">SCORES</a></span> - Static variable in interface org.biojava.bio.dp.<a href="./org/biojava/bio/dp/StatePath.html" title="interface in org.biojava.bio.dp">StatePath</a></dt>
<dd>
<div class="block">Alignment label for the likelyhood at each step.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/twohead/Cell.html#scores">scores</a></span> - Variable in class org.biojava.bio.dp.twohead.<a href="./org/biojava/bio/dp/twohead/Cell.html" title="class in org.biojava.bio.dp.twohead">Cell</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/dp/ScoreType.html" title="interface in org.biojava.bio.dp"><span class="strong">ScoreType</span></a> - Interface in <a href="./org/biojava/bio/dp/package-summary.html">org.biojava.bio.dp</a></dt>
<dd>
<div class="block">This class computes the score that is used to be used
in a DP optimisation.</div>
</dd>
<dt><a href="./org/biojava/bio/dp/ScoreType.NullModel.html" title="class in org.biojava.bio.dp"><span class="strong">ScoreType.NullModel</span></a> - Class in <a href="./org/biojava/bio/dp/package-summary.html">org.biojava.bio.dp</a></dt>
<dd>
<div class="block">In this class, calculateScore returns the probability of
a Symbol being emitted by the null model.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/ScoreType.NullModel.html#ScoreType.NullModel()">ScoreType.NullModel()</a></span> - Constructor for class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/ScoreType.NullModel.html" title="class in org.biojava.bio.dp">ScoreType.NullModel</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/dp/ScoreType.Odds.html" title="class in org.biojava.bio.dp"><span class="strong">ScoreType.Odds</span></a> - Class in <a href="./org/biojava/bio/dp/package-summary.html">org.biojava.bio.dp</a></dt>
<dd>
<div class="block">In this class, calculateScore returns the odds ratio
of a symbol being emitted.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/ScoreType.Odds.html#ScoreType.Odds()">ScoreType.Odds()</a></span> - Constructor for class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/ScoreType.Odds.html" title="class in org.biojava.bio.dp">ScoreType.Odds</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/dp/ScoreType.Probability.html" title="class in org.biojava.bio.dp"><span class="strong">ScoreType.Probability</span></a> - Class in <a href="./org/biojava/bio/dp/package-summary.html">org.biojava.bio.dp</a></dt>
<dd>
<div class="block">In this class, calculateScore returns the probability
of a Symbol being emitted.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/ScoreType.Probability.html#ScoreType.Probability()">ScoreType.Probability()</a></span> - Constructor for class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/ScoreType.Probability.html" title="class in org.biojava.bio.dp">ScoreType.Probability</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/DP.html#scoreWeightMatrix(org.biojava.bio.dp.WeightMatrix, org.biojava.bio.symbol.SymbolList, int)">scoreWeightMatrix(WeightMatrix, SymbolList, int)</a></span> - Static method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/DP.html" title="class in org.biojava.bio.dp">DP</a></dt>
<dd>
<div class="block">Scores the SymbolList from symbol start to symbol (start+columns) with a
weight matrix.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/DP.html#scoreWeightMatrix(org.biojava.bio.dp.WeightMatrix, org.biojava.bio.symbol.SymbolList, org.biojava.bio.dp.ScoreType, int)">scoreWeightMatrix(WeightMatrix, SymbolList, ScoreType, int)</a></span> - Static method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/DP.html" title="class in org.biojava.bio.dp">DP</a></dt>
<dd>
<div class="block">Scores the SymbolList from symbol start to symbol (start+columns) with a
weight matrix using a particular ScoreType.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/annodb/AnnotationDB.html#search(org.biojava.bio.AnnotationType)">search(AnnotationType)</a></span> - Method in interface org.biojava.bio.annodb.<a href="./org/biojava/bio/annodb/AnnotationDB.html" title="interface in org.biojava.bio.annodb">AnnotationDB</a></dt>
<dd>
<div class="block">Find all Annotation instances in this DB and any Annotations that are child
properties of these that match an AnnotationType.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/annodb/IndexedAnnotationDB.html#search(org.biojava.bio.AnnotationType)">search(AnnotationType)</a></span> - Method in class org.biojava.bio.annodb.<a href="./org/biojava/bio/annodb/IndexedAnnotationDB.html" title="class in org.biojava.bio.annodb">IndexedAnnotationDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/annodb/LazyFilteredAnnotationDB.html#search(org.biojava.bio.AnnotationType)">search(AnnotationType)</a></span> - Method in class org.biojava.bio.annodb.<a href="./org/biojava/bio/annodb/LazyFilteredAnnotationDB.html" title="class in org.biojava.bio.annodb">LazyFilteredAnnotationDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/annodb/LazySearchedAnnotationDB.html#search(org.biojava.bio.AnnotationType)">search(AnnotationType)</a></span> - Method in class org.biojava.bio.annodb.<a href="./org/biojava/bio/annodb/LazySearchedAnnotationDB.html" title="class in org.biojava.bio.annodb">LazySearchedAnnotationDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/annodb/MergingAnnotationDB.html#search(org.biojava.bio.AnnotationType)">search(AnnotationType)</a></span> - Method in class org.biojava.bio.annodb.<a href="./org/biojava/bio/annodb/MergingAnnotationDB.html" title="class in org.biojava.bio.annodb">MergingAnnotationDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/annodb/SimpleAnnotationDB.html#search(org.biojava.bio.AnnotationType)">search(AnnotationType)</a></span> - Method in class org.biojava.bio.annodb.<a href="./org/biojava/bio/annodb/SimpleAnnotationDB.html" title="class in org.biojava.bio.annodb">SimpleAnnotationDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssaha/CompactedDataStore.html#search(java.lang.String, org.biojava.bio.symbol.SymbolList, org.biojava.bio.program.ssaha.SearchListener)">search(String, SymbolList, SearchListener)</a></span> - Method in class org.biojava.bio.program.ssaha.<a href="./org/biojava/bio/program/ssaha/CompactedDataStore.html" title="class in org.biojava.bio.program.ssaha">CompactedDataStore</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssaha/DataStore.html#search(java.lang.String, org.biojava.bio.symbol.SymbolList, org.biojava.bio.program.ssaha.SearchListener)">search(String, SymbolList, SearchListener)</a></span> - Method in interface org.biojava.bio.program.ssaha.<a href="./org/biojava/bio/program/ssaha/DataStore.html" title="interface in org.biojava.bio.program.ssaha">DataStore</a></dt>
<dd>
<div class="block">Search the DataStore with a symbol list.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SeqSimilaritySearcher.html#search(org.biojava.bio.symbol.SymbolList, org.biojava.bio.seq.db.SequenceDB, java.util.Map)">search(SymbolList, SequenceDB, Map)</a></span> - Method in interface org.biojava.bio.search.<a href="./org/biojava/bio/search/SeqSimilaritySearcher.html" title="interface in org.biojava.bio.search">SeqSimilaritySearcher</a></dt>
<dd>
<div class="block">Using this sequence similarity searcher, search with the given
sequence against the given sequence database.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/taxa/SimpleTaxonFactory.html#search(java.lang.Object)">search(Object)</a></span> - Method in class org.biojava.bio.taxa.<a href="./org/biojava/bio/taxa/SimpleTaxonFactory.html" title="class in org.biojava.bio.taxa">SimpleTaxonFactory</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/taxa/TaxonFactory.html#search(java.lang.Object)">search(Object)</a></span> - Method in interface org.biojava.bio.taxa.<a href="./org/biojava/bio/taxa/TaxonFactory.html" title="interface in org.biojava.bio.taxa">TaxonFactory</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Retrieve a Taxon that matches some ID.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/taxa/WeakTaxonFactory.html#search(java.lang.Object)">search(Object)</a></span> - Method in class org.biojava.bio.taxa.<a href="./org/biojava/bio/taxa/WeakTaxonFactory.html" title="class in org.biojava.bio.taxa">WeakTaxonFactory</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/naming/ObdaContext.html#search(javax.naming.Name, javax.naming.directory.Attributes)">search(Name, Attributes)</a></span> - Method in class org.biojava.naming.<a href="./org/biojava/naming/ObdaContext.html" title="class in org.biojava.naming">ObdaContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/naming/ObdaContext.html#search(javax.naming.Name, java.lang.String, java.lang.Object[], javax.naming.directory.SearchControls)">search(Name, String, Object[], SearchControls)</a></span> - Method in class org.biojava.naming.<a href="./org/biojava/naming/ObdaContext.html" title="class in org.biojava.naming">ObdaContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/naming/ObdaContext.html#search(javax.naming.Name, javax.naming.directory.Attributes, java.lang.String[])">search(Name, Attributes, String[])</a></span> - Method in class org.biojava.naming.<a href="./org/biojava/naming/ObdaContext.html" title="class in org.biojava.naming">ObdaContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/naming/ObdaContext.html#search(javax.naming.Name, java.lang.String, javax.naming.directory.SearchControls)">search(Name, String, SearchControls)</a></span> - Method in class org.biojava.naming.<a href="./org/biojava/naming/ObdaContext.html" title="class in org.biojava.naming">ObdaContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/naming/ObdaContext.html#search(java.lang.String, javax.naming.directory.Attributes, java.lang.String[])">search(String, Attributes, String[])</a></span> - Method in class org.biojava.naming.<a href="./org/biojava/naming/ObdaContext.html" title="class in org.biojava.naming">ObdaContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/naming/ObdaContext.html#search(java.lang.String, javax.naming.directory.Attributes)">search(String, Attributes)</a></span> - Method in class org.biojava.naming.<a href="./org/biojava/naming/ObdaContext.html" title="class in org.biojava.naming">ObdaContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/naming/ObdaContext.html#search(java.lang.String, java.lang.String, javax.naming.directory.SearchControls)">search(String, String, SearchControls)</a></span> - Method in class org.biojava.naming.<a href="./org/biojava/naming/ObdaContext.html" title="class in org.biojava.naming">ObdaContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/naming/ObdaContext.html#search(java.lang.String, java.lang.String, java.lang.Object[], javax.naming.directory.SearchControls)">search(String, String, Object[], SearchControls)</a></span> - Method in class org.biojava.naming.<a href="./org/biojava/naming/ObdaContext.html" title="class in org.biojava.naming">ObdaContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/automata/PatternBlitz.html#search(org.biojava.bio.symbol.SymbolList)">search(SymbolList)</a></span> - Method in class org.biojava.utils.automata.<a href="./org/biojava/utils/automata/PatternBlitz.html" title="class in org.biojava.utils.automata">PatternBlitz</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/utils/regex/Search.html" title="class in org.biojava.utils.regex"><span class="strong">Search</span></a> - Class in <a href="./org/biojava/utils/regex/package-summary.html">org.biojava.utils.regex</a></dt>
<dd>
<div class="block">A utility class to make searching a Sequence with many regex patterns
easier.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/regex/Search.html#Search(org.biojava.bio.symbol.FiniteAlphabet)">Search(FiniteAlphabet)</a></span> - Constructor for class org.biojava.utils.regex.<a href="./org/biojava/utils/regex/Search.html" title="class in org.biojava.utils.regex">Search</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/regex/Search.html#search(org.biojava.bio.symbol.SymbolList)">search(SymbolList)</a></span> - Method in class org.biojava.utils.regex.<a href="./org/biojava/utils/regex/Search.html" title="class in org.biojava.utils.regex">Search</a></dt>
<dd>
<div class="block">search the Sequence with the patterns already registered with this object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/regex/Search.html#search(org.biojava.bio.symbol.SymbolList, int, int)">search(SymbolList, int, int)</a></span> - Method in class org.biojava.utils.regex.<a href="./org/biojava/utils/regex/Search.html" title="class in org.biojava.utils.regex">Search</a></dt>
<dd>
<div class="block">search part of the SymbolList with the patterns already registered with this object.</div>
</dd>
<dt><a href="./org/biojava/utils/regex/Search.Listener.html" title="interface in org.biojava.utils.regex"><span class="strong">Search.Listener</span></a> - Interface in <a href="./org/biojava/utils/regex/package-summary.html">org.biojava.utils.regex</a></dt>
<dd>
<div class="block">Interface for a class that will recieve match information
from this class.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/AnnotationTools.html#searchAnnotation(org.biojava.bio.Annotation, org.biojava.bio.AnnotationType)">searchAnnotation(Annotation, AnnotationType)</a></span> - Static method in class org.biojava.bio.<a href="./org/biojava/bio/AnnotationTools.html" title="class in org.biojava.bio">AnnotationTools</a></dt>
<dd>
<div class="block">
Scans an Annotation with an AnnotationType and returns all Annotation
instances matching a Type.</div>
</dd>
<dt><a href="./org/biojava/bio/search/SearchBuilder.html" title="interface in org.biojava.bio.search"><span class="strong">SearchBuilder</span></a> - Interface in <a href="./org/biojava/bio/search/package-summary.html">org.biojava.bio.search</a></dt>
<dd>
<div class="block">The <code>SearchBuilder</code> interface is to be used by objects
which accumulate state via a <code>SearchContentHandler</code> and
then construct a <code>SeqSimilaritySearchResult</code> object.</div>
</dd>
<dt><a href="./org/biojava/bio/search/SearchContentAdapter.html" title="class in org.biojava.bio.search"><span class="strong">SearchContentAdapter</span></a> - Class in <a href="./org/biojava/bio/search/package-summary.html">org.biojava.bio.search</a></dt>
<dd>
<div class="block">
An adapter for SearchContentHandler.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SearchContentAdapter.html#SearchContentAdapter()">SearchContentAdapter()</a></span> - Constructor for class org.biojava.bio.search.<a href="./org/biojava/bio/search/SearchContentAdapter.html" title="class in org.biojava.bio.search">SearchContentAdapter</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/search/SearchContentFilter.html" title="class in org.biojava.bio.search"><span class="strong">SearchContentFilter</span></a> - Class in <a href="./org/biojava/bio/search/package-summary.html">org.biojava.bio.search</a></dt>
<dd>
<div class="block">
Filtering implementation of SearchContentHandler that by default passes
all messages on to the next delegate in the chain.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SearchContentFilter.html#SearchContentFilter(org.biojava.bio.search.SearchContentHandler)">SearchContentFilter(SearchContentHandler)</a></span> - Constructor for class org.biojava.bio.search.<a href="./org/biojava/bio/search/SearchContentFilter.html" title="class in org.biojava.bio.search">SearchContentFilter</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/search/SearchContentHandler.html" title="interface in org.biojava.bio.search"><span class="strong">SearchContentHandler</span></a> - Interface in <a href="./org/biojava/bio/search/package-summary.html">org.biojava.bio.search</a></dt>
<dd>
<div class="block"><code>SearchContentHandler</code> is a notification interface for
objects which listen to search stream parsers.</div>
</dd>
<dt><a href="./org/biojava/bio/search/SearchContentHandlerDebugger.html" title="class in org.biojava.bio.search"><span class="strong">SearchContentHandlerDebugger</span></a> - Class in <a href="./org/biojava/bio/search/package-summary.html">org.biojava.bio.search</a></dt>
<dd>
<div class="block">This class prints to a PrintStream
calls to the SearchContentHandler interface
in human readable form.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SearchContentHandlerDebugger.html#SearchContentHandlerDebugger()">SearchContentHandlerDebugger()</a></span> - Constructor for class org.biojava.bio.search.<a href="./org/biojava/bio/search/SearchContentHandlerDebugger.html" title="class in org.biojava.bio.search">SearchContentHandlerDebugger</a></dt>
<dd>
<div class="block">Create an instance that dumps to System.out.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SearchContentHandlerDebugger.html#SearchContentHandlerDebugger(java.io.PrintStream)">SearchContentHandlerDebugger(PrintStream)</a></span> - Constructor for class org.biojava.bio.search.<a href="./org/biojava/bio/search/SearchContentHandlerDebugger.html" title="class in org.biojava.bio.search">SearchContentHandlerDebugger</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/ssaha/SearchException.html" title="class in org.biojava.bio.program.ssaha"><span class="strong">SearchException</span></a> - Exception in <a href="./org/biojava/bio/program/ssaha/package-summary.html">org.biojava.bio.program.ssaha</a></dt>
<dd>
<div class="block">There has been some failure that prevents a search from completing.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssaha/SearchException.html#SearchException(java.lang.String)">SearchException(String)</a></span> - Constructor for exception org.biojava.bio.program.ssaha.<a href="./org/biojava/bio/program/ssaha/SearchException.html" title="class in org.biojava.bio.program.ssaha">SearchException</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssaha/SearchException.html#SearchException(java.lang.Throwable)">SearchException(Throwable)</a></span> - Constructor for exception org.biojava.bio.program.ssaha.<a href="./org/biojava/bio/program/ssaha/SearchException.html" title="class in org.biojava.bio.program.ssaha">SearchException</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssaha/SearchException.html#SearchException(java.lang.String, java.lang.Throwable)">SearchException(String, Throwable)</a></span> - Constructor for exception org.biojava.bio.program.ssaha.<a href="./org/biojava/bio/program/ssaha/SearchException.html" title="class in org.biojava.bio.program.ssaha">SearchException</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/ssaha/SearchListener.html" title="interface in org.biojava.bio.program.ssaha"><span class="strong">SearchListener</span></a> - Interface in <a href="./org/biojava/bio/program/ssaha/package-summary.html">org.biojava.bio.program.ssaha</a></dt>
<dd>
<div class="block">The interface used to inform interested parties that some sequence has
been searched and something found.</div>
</dd>
<dt><a href="./org/biojava/bio/program/ssaha/SearchListener.Echo.html" title="class in org.biojava.bio.program.ssaha"><span class="strong">SearchListener.Echo</span></a> - Class in <a href="./org/biojava/bio/program/ssaha/package-summary.html">org.biojava.bio.program.ssaha</a></dt>
<dd>
<div class="block">A SearchListener that prints events out to a PrintStream.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssaha/SearchListener.Echo.html#SearchListener.Echo(java.io.PrintStream)">SearchListener.Echo(PrintStream)</a></span> - Constructor for class org.biojava.bio.program.ssaha.<a href="./org/biojava/bio/program/ssaha/SearchListener.Echo.html" title="class in org.biojava.bio.program.ssaha">SearchListener.Echo</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/ssaha/SearchListener.FilterByLength.html" title="class in org.biojava.bio.program.ssaha"><span class="strong">SearchListener.FilterByLength</span></a> - Class in <a href="./org/biojava/bio/program/ssaha/package-summary.html">org.biojava.bio.program.ssaha</a></dt>
<dd>
<div class="block">A simple listener that filters out all hits that are too short.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssaha/SearchListener.FilterByLength.html#SearchListener.FilterByLength(org.biojava.bio.program.ssaha.SearchListener, int)">SearchListener.FilterByLength(SearchListener, int)</a></span> - Constructor for class org.biojava.bio.program.ssaha.<a href="./org/biojava/bio/program/ssaha/SearchListener.FilterByLength.html" title="class in org.biojava.bio.program.ssaha">SearchListener.FilterByLength</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/ssaha/SearchListener.Tee.html" title="class in org.biojava.bio.program.ssaha"><span class="strong">SearchListener.Tee</span></a> - Class in <a href="./org/biojava/bio/program/ssaha/package-summary.html">org.biojava.bio.program.ssaha</a></dt>
<dd>
<div class="block">A SearchListener that passes events on to two delegate listeners.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssaha/SearchListener.Tee.html#SearchListener.Tee(org.biojava.bio.program.ssaha.SearchListener, org.biojava.bio.program.ssaha.SearchListener)">SearchListener.Tee(SearchListener, SearchListener)</a></span> - Constructor for class org.biojava.bio.program.ssaha.<a href="./org/biojava/bio/program/ssaha/SearchListener.Tee.html" title="class in org.biojava.bio.program.ssaha">SearchListener.Tee</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/ssaha/SearchListener.Wrapper.html" title="class in org.biojava.bio.program.ssaha"><span class="strong">SearchListener.Wrapper</span></a> - Class in <a href="./org/biojava/bio/program/ssaha/package-summary.html">org.biojava.bio.program.ssaha</a></dt>
<dd>
<div class="block">A simple wrapper implementation.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssaha/SearchListener.Wrapper.html#SearchListener.Wrapper(org.biojava.bio.program.ssaha.SearchListener)">SearchListener.Wrapper(SearchListener)</a></span> - Constructor for class org.biojava.bio.program.ssaha.<a href="./org/biojava/bio/program/ssaha/SearchListener.Wrapper.html" title="class in org.biojava.bio.program.ssaha">SearchListener.Wrapper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/ProteinTools.html#sec()">sec()</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/ProteinTools.html" title="class in org.biojava.bio.seq">ProteinTools</a></dt>
<dd>
<div class="block">Returns the <code>AtomicSymbol</code> for the amino acid
Selenocysteine (U)</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html#SEC_ACC_TAG">SEC_ACC_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html" title="class in org.biojavax.bio.seq.io">EMBLxmlFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/INSDseqFormat.html#SECONDARY_ACCESSION_TAG">SECONDARY_ACCESSION_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/INSDseqFormat.html" title="class in org.biojavax.bio.seq.io">INSDseqFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/INSDseqFormat.html#SECONDARY_ACCESSIONS_GROUP_TAG">SECONDARY_ACCESSIONS_GROUP_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/INSDseqFormat.html" title="class in org.biojavax.bio.seq.io">INSDseqFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PairwiseRenderContext.html#secondarySequenceToGraphics(int)">secondarySequenceToGraphics(int)</a></span> - Method in interface org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PairwiseRenderContext.html" title="interface in org.biojava.bio.gui.sequence">PairwiseRenderContext</a></dt>
<dd>
<div class="block"><code>secondarySequenceToGraphics</code> converts a sequence
coordinate on the secondary sequence to a graphical position.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PairwiseSequencePanel.html#secondarySequenceToGraphics(int)">secondarySequenceToGraphics(int)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PairwiseSequencePanel.html" title="class in org.biojava.bio.gui.sequence">PairwiseSequencePanel</a></dt>
<dd>
<div class="block"><code>secondarySequenceToGraphics</code> converts a sequence
index to a graphical position.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SubPairwiseRenderContext.html#secondarySequenceToGraphics(int)">secondarySequenceToGraphics(int)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SubPairwiseRenderContext.html" title="class in org.biojava.bio.gui.sequence">SubPairwiseRenderContext</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/gui/sequence/SecondaryStructureFeatureRenderer.html" title="class in org.biojava.bio.gui.sequence"><span class="strong">SecondaryStructureFeatureRenderer</span></a> - Class in <a href="./org/biojava/bio/gui/sequence/package-summary.html">org.biojava.bio.gui.sequence</a></dt>
<dd>
<div class="block">A GlyphRenderer subclass that specificatlly handles Features pertaining to Secondary Structure
(Helices, Turns and Strands).</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SecondaryStructureFeatureRenderer.html#SecondaryStructureFeatureRenderer()">SecondaryStructureFeatureRenderer()</a></span> - Constructor for class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SecondaryStructureFeatureRenderer.html" title="class in org.biojava.bio.gui.sequence">SecondaryStructureFeatureRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/GenbankFormat.html#sectp">sectp</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/GenbankFormat.html" title="class in org.biojavax.bio.seq.io">GenbankFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/io/CachingInputStream.html#seek(long)">seek(long)</a></span> - Method in class org.biojava.utils.io.<a href="./org/biojava/utils/io/CachingInputStream.html" title="class in org.biojava.utils.io">CachingInputStream</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/io/RandomAccessReader.html#seek(long)">seek(long)</a></span> - Method in class org.biojava.utils.io.<a href="./org/biojava/utils/io/RandomAccessReader.html" title="class in org.biojava.utils.io">RandomAccessReader</a></dt>
<dd>
<div class="block"><code>seek</code> moves the pointer to the specified position.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/io/Seekable.html#seek(long)">seek(long)</a></span> - Method in interface org.biojava.utils.io.<a href="./org/biojava/utils/io/Seekable.html" title="interface in org.biojava.utils.io">Seekable</a></dt>
<dd>
<div class="block">Moves the pointer in the inputstream such that the byte starting at
<code>pos</code> are returned by the next read.</div>
</dd>
<dt><a href="./org/biojava/utils/io/Seekable.html" title="interface in org.biojava.utils.io"><span class="strong">Seekable</span></a> - Interface in <a href="./org/biojava/utils/io/package-summary.html">org.biojava.utils.io</a></dt>
<dd>
<div class="block">This interface provides a collective name for IO classes that implement a
seek function (e.g., <code>RandomAccessFile</code>).</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ga/functions/ProportionalSelection.html#select(org.biojavax.ga.Population, org.biojavax.ga.GeneticAlgorithm)">select(Population, GeneticAlgorithm)</a></span> - Method in class org.biojavax.ga.functions.<a href="./org/biojavax/ga/functions/ProportionalSelection.html" title="class in org.biojavax.ga.functions">ProportionalSelection</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/functions/SelectionFunction.html#select(org.biojavax.ga.Population, org.biojavax.ga.GeneticAlgorithm)">select(Population, GeneticAlgorithm)</a></span> - Method in interface org.biojavax.ga.functions.<a href="./org/biojavax/ga/functions/SelectionFunction.html" title="interface in org.biojavax.ga.functions">SelectionFunction</a></dt>
<dd>
<div class="block">Selects a <code>Population</code> of <code>Organisms</code> for
replication based on their fitness.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ga/functions/SelectionFunction.SelectAll.html#select(org.biojavax.ga.Population, org.biojavax.ga.GeneticAlgorithm)">select(Population, GeneticAlgorithm)</a></span> - Method in class org.biojavax.ga.functions.<a href="./org/biojavax/ga/functions/SelectionFunction.SelectAll.html" title="class in org.biojavax.ga.functions">SelectionFunction.SelectAll</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/functions/SelectionFunction.Threshold.html#select(org.biojavax.ga.Population, org.biojavax.ga.GeneticAlgorithm)">select(Population, GeneticAlgorithm)</a></span> - Method in class org.biojavax.ga.functions.<a href="./org/biojavax/ga/functions/SelectionFunction.Threshold.html" title="class in org.biojavax.ga.functions">SelectionFunction.Threshold</a></dt>
<dd>
<div class="block">Selects individuals whose fitness (as determined by the
<code>FitnessFunction</code>) is more than the cutoff.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ga/functions/TournamentSelection.html#select(org.biojavax.ga.Population, org.biojavax.ga.GeneticAlgorithm)">select(Population, GeneticAlgorithm)</a></span> - Method in class org.biojavax.ga.functions.<a href="./org/biojavax/ga/functions/TournamentSelection.html" title="class in org.biojavax.ga.functions">TournamentSelection</a></dt>
<dd>
<div class="block">Standard call to select organisms, will select a number of Organisms
corresponding to 75 % of the population.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ga/GeneticAlgorithm.html#SELECTION_FUNCTION">SELECTION_FUNCTION</a></span> - Static variable in interface org.biojavax.ga.<a href="./org/biojavax/ga/GeneticAlgorithm.html" title="interface in org.biojavax.ga">GeneticAlgorithm</a></dt>
<dd> </dd>
<dt><a href="./org/biojavax/ga/functions/SelectionFunction.html" title="interface in org.biojavax.ga.functions"><span class="strong">SelectionFunction</span></a> - Interface in <a href="./org/biojavax/ga/functions/package-summary.html">org.biojavax.ga.functions</a></dt>
<dd>
<div class="block">Selects Organisms for Replication and returns the offspring.</div>
</dd>
<dt><a href="./org/biojavax/ga/functions/SelectionFunction.SelectAll.html" title="class in org.biojavax.ga.functions"><span class="strong">SelectionFunction.SelectAll</span></a> - Class in <a href="./org/biojavax/ga/functions/package-summary.html">org.biojavax.ga.functions</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/functions/SelectionFunction.SelectAll.html#SelectionFunction.SelectAll()">SelectionFunction.SelectAll()</a></span> - Constructor for class org.biojavax.ga.functions.<a href="./org/biojavax/ga/functions/SelectionFunction.SelectAll.html" title="class in org.biojavax.ga.functions">SelectionFunction.SelectAll</a></dt>
<dd> </dd>
<dt><a href="./org/biojavax/ga/functions/SelectionFunction.Threshold.html" title="class in org.biojavax.ga.functions"><span class="strong">SelectionFunction.Threshold</span></a> - Class in <a href="./org/biojavax/ga/functions/package-summary.html">org.biojavax.ga.functions</a></dt>
<dd>
<div class="block">
Selects individuals who's fitness exceeds a threshold value.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ga/functions/SelectionFunction.Threshold.html#SelectionFunction.Threshold(double)">SelectionFunction.Threshold(double)</a></span> - Constructor for class org.biojavax.ga.functions.<a href="./org/biojavax/ga/functions/SelectionFunction.Threshold.html" title="class in org.biojavax.ga.functions">SelectionFunction.Threshold</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/events/AlignmentPositionListener.html#selectionLocked()">selectionLocked()</a></span> - Method in interface org.biojava.bio.structure.gui.events.<a href="./org/biojava/bio/structure/gui/events/AlignmentPositionListener.html" title="interface in org.biojava.bio.structure.gui.events">AlignmentPositionListener</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/events/JmolAlignedPositionListener.html#selectionLocked()">selectionLocked()</a></span> - Method in class org.biojava.bio.structure.gui.events.<a href="./org/biojava/bio/structure/gui/events/JmolAlignedPositionListener.html" title="class in org.biojava.bio.structure.gui.events">JmolAlignedPositionListener</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/events/AlignmentPositionListener.html#selectionUnlocked()">selectionUnlocked()</a></span> - Method in interface org.biojava.bio.structure.gui.events.<a href="./org/biojava/bio/structure/gui/events/AlignmentPositionListener.html" title="interface in org.biojava.bio.structure.gui.events">AlignmentPositionListener</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/events/JmolAlignedPositionListener.html#selectionUnlocked()">selectionUnlocked()</a></span> - Method in class org.biojava.bio.structure.gui.events.<a href="./org/biojava/bio/structure/gui/events/JmolAlignedPositionListener.html" title="class in org.biojava.bio.structure.gui.events">JmolAlignedPositionListener</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/functions/TournamentSelection.html#selectNIndividuals(org.biojavax.ga.Population, org.biojavax.ga.GeneticAlgorithm, int)">selectNIndividuals(Population, GeneticAlgorithm, int)</a></span> - Method in class org.biojavax.ga.functions.<a href="./org/biojavax/ga/functions/TournamentSelection.html" title="class in org.biojavax.ga.functions">TournamentSelection</a></dt>
<dd>
<div class="block">This method selects n Organism from the population it is given, using the
tournament selection method</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SymbolTokenization.html#SEPARATED">SEPARATED</a></span> - Static variable in interface org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SymbolTokenization.html" title="interface in org.biojava.bio.seq.io">SymbolTokenization</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.Option.html#SEPARATOR_COLOR">SEPARATOR_COLOR</a></span> - Static variable in class org.biojava.bio.chromatogram.graphic.<a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.Option.html" title="class in org.biojava.bio.chromatogram.graphic">ChromatogramGraphic.Option</a></dt>
<dd>
<div class="block">Option indicating the color that the call separators
should be.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.Option.html#SEPARATOR_STROKE">SEPARATOR_STROKE</a></span> - Static variable in class org.biojava.bio.chromatogram.graphic.<a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.Option.html" title="class in org.biojava.bio.chromatogram.graphic">ChromatogramGraphic.Option</a></dt>
<dd>
<div class="block">Option providing the the stroke to use for drawing
call separators.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/EmblLikeFormat.html#SEPARATOR_TAG">SEPARATOR_TAG</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/EmblLikeFormat.html" title="class in org.biojava.bio.seq.io">EmblLikeFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/SimpleAlignmentElement.html#seq">seq</a></span> - Variable in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/SimpleAlignmentElement.html" title="class in org.biojava.bio.alignment">SimpleAlignmentElement</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SequenceBuilderBase.html#seq">seq</a></span> - Variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SequenceBuilderBase.html" title="class in org.biojava.bio.seq.io">SequenceBuilderBase</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/search/SeqContentPattern.html" title="class in org.biojava.bio.search"><span class="strong">SeqContentPattern</span></a> - Class in <a href="./org/biojava/bio/search/package-summary.html">org.biojava.bio.search</a></dt>
<dd>
<div class="block">A pattern that can be used to find regions with given sequence content.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SeqContentPattern.html#SeqContentPattern(org.biojava.bio.symbol.FiniteAlphabet)">SeqContentPattern(FiniteAlphabet)</a></span> - Constructor for class org.biojava.bio.search.<a href="./org/biojava/bio/search/SeqContentPattern.html" title="class in org.biojava.bio.search">SeqContentPattern</a></dt>
<dd>
<div class="block">Create a new SeqContentPattern over an alphabet.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/SeqFileFormer.html" title="interface in org.biojava.bio.seq.io"><span class="strong">SeqFileFormer</span></a> - Interface in <a href="./org/biojava/bio/seq/io/package-summary.html">org.biojava.bio.seq.io</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>Use org.biojavax.bio.seq.io framework instead</i></div>
</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/util/SequenceScalePanel.html#seqFont">seqFont</a></span> - Static variable in class org.biojava.bio.structure.gui.util.<a href="./org/biojava/bio/structure/gui/util/SequenceScalePanel.html" title="class in org.biojava.bio.structure.gui.util">SequenceScalePanel</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/io/SeqIOAdapter.html" title="class in org.biojava.bio.seq.io"><span class="strong">SeqIOAdapter</span></a> - Class in <a href="./org/biojava/bio/seq/io/package-summary.html">org.biojava.bio.seq.io</a></dt>
<dd>
<div class="block">Adapter class for SeqIOListener that has empty methods.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOAdapter.html#SeqIOAdapter()">SeqIOAdapter()</a></span> - Constructor for class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOAdapter.html" title="class in org.biojava.bio.seq.io">SeqIOAdapter</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/io/SeqIOConstants.html" title="class in org.biojava.bio.seq.io"><span class="strong">SeqIOConstants</span></a> - Class in <a href="./org/biojava/bio/seq/io/package-summary.html">org.biojava.bio.seq.io</a></dt>
<dd>
<div class="block"><code>SeqIOConstants</code> contains constants used to identify
sequence formats, alphabets etc, in the context of reading and
writing sequences.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOConstants.html#SeqIOConstants()">SeqIOConstants()</a></span> - Constructor for class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOConstants.html" title="class in org.biojava.bio.seq.io">SeqIOConstants</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/io/SeqIOEventEmitter.html" title="class in org.biojava.bio.seq.io"><span class="strong">SeqIOEventEmitter</span></a> - Class in <a href="./org/biojava/bio/seq/io/package-summary.html">org.biojava.bio.seq.io</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>Use org.biojavax.bio.seq.io framework instead</i></div>
</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOEventEmitter.html#SeqIOEventEmitter(java.util.Comparator, java.util.Comparator)">SeqIOEventEmitter(Comparator, Comparator)</a></span> - Constructor for class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOEventEmitter.html" title="class in org.biojava.bio.seq.io">SeqIOEventEmitter</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/SeqIOFilter.html" title="class in org.biojava.bio.seq.io"><span class="strong">SeqIOFilter</span></a> - Class in <a href="./org/biojava/bio/seq/io/package-summary.html">org.biojava.bio.seq.io</a></dt>
<dd>
<div class="block">Base-class for listeners that pass filtered events onto another listener.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOFilter.html#SeqIOFilter(org.biojava.bio.seq.io.SeqIOListener)">SeqIOFilter(SeqIOListener)</a></span> - Constructor for class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOFilter.html" title="class in org.biojava.bio.seq.io">SeqIOFilter</a></dt>
<dd>
<div class="block">Create a new SeqIOFilter that will forward events on to another listener.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/SeqIOListener.html" title="interface in org.biojava.bio.seq.io"><span class="strong">SeqIOListener</span></a> - Interface in <a href="./org/biojava/bio/seq/io/package-summary.html">org.biojava.bio.seq.io</a></dt>
<dd>
<div class="block">Notification interface for objects which listen to a sequence stream
parser.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/SeqIOTools.html" title="class in org.biojava.bio.seq.io"><span class="strong">SeqIOTools</span></a> - Class in <a href="./org/biojava/bio/seq/io/package-summary.html">org.biojava.bio.seq.io</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>use org.biojavax.bio.seq.RichSequence.IOTools</i></div>
</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssaha/CompactedDataStore.html#seqNameForID(int)">seqNameForID(int)</a></span> - Method in class org.biojava.bio.program.ssaha.<a href="./org/biojava/bio/program/ssaha/CompactedDataStore.html" title="class in org.biojava.bio.program.ssaha">CompactedDataStore</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssaha/DataStore.html#seqNameForID(int)">seqNameForID(int)</a></span> - Method in interface org.biojava.bio.program.ssaha.<a href="./org/biojava/bio/program/ssaha/DataStore.html" title="interface in org.biojava.bio.program.ssaha">DataStore</a></dt>
<dd>
<div class="block">Resolve an ID to a sequence name.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePanelWrapper.html#seqPanels">seqPanels</a></span> - Variable in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePanelWrapper.html" title="class in org.biojava.bio.gui.sequence">SequencePanelWrapper</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/structure/io/SeqRes2AtomAligner.html" title="class in org.biojava.bio.structure.io"><span class="strong">SeqRes2AtomAligner</span></a> - Class in <a href="./org/biojava/bio/structure/io/package-summary.html">org.biojava.bio.structure.io</a></dt>
<dd>
<div class="block">Aligns the SEQRES residues to the ATOM residues.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/SeqRes2AtomAligner.html#SeqRes2AtomAligner()">SeqRes2AtomAligner()</a></span> - Constructor for class org.biojava.bio.structure.io.<a href="./org/biojava/bio/structure/io/SeqRes2AtomAligner.html" title="class in org.biojava.bio.structure.io">SeqRes2AtomAligner</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/AminoAcid.html#SEQRESRECORD">SEQRESRECORD</a></span> - Static variable in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/AminoAcid.html" title="interface in org.biojava.bio.structure">AminoAcid</a></dt>
<dd>
<div class="block">Field to distribguish AminoAcids that have been created from SEQRES records and ATOM records.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/twohead/AbstractMatrixPairDPCursor.html#seqs">seqs</a></span> - Variable in class org.biojava.bio.dp.twohead.<a href="./org/biojava/bio/dp/twohead/AbstractMatrixPairDPCursor.html" title="class in org.biojava.bio.dp.twohead">AbstractMatrixPairDPCursor</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/ssbind/SeqSimilarityAdapter.html" title="class in org.biojava.bio.program.ssbind"><span class="strong">SeqSimilarityAdapter</span></a> - Class in <a href="./org/biojava/bio/program/ssbind/package-summary.html">org.biojava.bio.program.ssbind</a></dt>
<dd>
<div class="block">A <code>SeqSimilarityAdapter</code> converts SAX events into method
calls on a <code>SearchContentHandler</code> implementation.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/SeqSimilarityAdapter.html#SeqSimilarityAdapter()">SeqSimilarityAdapter()</a></span> - Constructor for class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/SeqSimilarityAdapter.html" title="class in org.biojava.bio.program.ssbind">SeqSimilarityAdapter</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/search/SeqSimilaritySearcher.html" title="interface in org.biojava.bio.search"><span class="strong">SeqSimilaritySearcher</span></a> - Interface in <a href="./org/biojava/bio/search/package-summary.html">org.biojava.bio.search</a></dt>
<dd>
<div class="block">Objects of this type represent one particular installation (not
just implementation) of a sequence similarity searcher such as
BLASTP.</div>
</dd>
<dt><a href="./org/biojava/bio/search/SeqSimilaritySearchHit.html" title="interface in org.biojava.bio.search"><span class="strong">SeqSimilaritySearchHit</span></a> - Interface in <a href="./org/biojava/bio/search/package-summary.html">org.biojava.bio.search</a></dt>
<dd>
<div class="block">Objects of this type represent one particular hit (sequence and
associated information) from a sequence similarity search.</div>
</dd>
<dt><a href="./org/biojava/bio/search/SeqSimilaritySearchHit.ByScoreComparator.html" title="class in org.biojava.bio.search"><span class="strong">SeqSimilaritySearchHit.ByScoreComparator</span></a> - Class in <a href="./org/biojava/bio/search/package-summary.html">org.biojava.bio.search</a></dt>
<dd>
<div class="block"><code>ByScoreComparator</code> compares
<code>SeqSimilaritySearchHit</code>s by their score.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SeqSimilaritySearchHit.ByScoreComparator.html#SeqSimilaritySearchHit.ByScoreComparator()">SeqSimilaritySearchHit.ByScoreComparator()</a></span> - Constructor for class org.biojava.bio.search.<a href="./org/biojava/bio/search/SeqSimilaritySearchHit.ByScoreComparator.html" title="class in org.biojava.bio.search">SeqSimilaritySearchHit.ByScoreComparator</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/search/SeqSimilaritySearchHit.BySubHitCountComparator.html" title="class in org.biojava.bio.search"><span class="strong">SeqSimilaritySearchHit.BySubHitCountComparator</span></a> - Class in <a href="./org/biojava/bio/search/package-summary.html">org.biojava.bio.search</a></dt>
<dd>
<div class="block"><code>BySubHitCountComparator</code> compares
<code>SeqSimilaritySearchHit</code>s by their number of
sub-hits.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SeqSimilaritySearchHit.BySubHitCountComparator.html#SeqSimilaritySearchHit.BySubHitCountComparator()">SeqSimilaritySearchHit.BySubHitCountComparator()</a></span> - Constructor for class org.biojava.bio.search.<a href="./org/biojava/bio/search/SeqSimilaritySearchHit.BySubHitCountComparator.html" title="class in org.biojava.bio.search">SeqSimilaritySearchHit.BySubHitCountComparator</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/search/SeqSimilaritySearchResult.html" title="interface in org.biojava.bio.search"><span class="strong">SeqSimilaritySearchResult</span></a> - Interface in <a href="./org/biojava/bio/search/package-summary.html">org.biojava.bio.search</a></dt>
<dd>
<div class="block">Objects of this type represent one particular result of a sequence
similarity search.</div>
</dd>
<dt><a href="./org/biojava/bio/search/SeqSimilaritySearchSubHit.html" title="interface in org.biojava.bio.search"><span class="strong">SeqSimilaritySearchSubHit</span></a> - Interface in <a href="./org/biojava/bio/search/package-summary.html">org.biojava.bio.search</a></dt>
<dd>
<div class="block">Objects of this type represent one particular sub-hit (one concrete
sequence stretch within a sequence and associated information) from
a sequence similarity search hit.</div>
</dd>
<dt><a href="./org/biojava/bio/search/SeqSimilaritySearchSubHit.ByScoreComparator.html" title="class in org.biojava.bio.search"><span class="strong">SeqSimilaritySearchSubHit.ByScoreComparator</span></a> - Class in <a href="./org/biojava/bio/search/package-summary.html">org.biojava.bio.search</a></dt>
<dd>
<div class="block"><code>ByScoreComparator</code> compares
<code>SeqSimilaritySearchSubHit</code>s by their score.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SeqSimilaritySearchSubHit.ByScoreComparator.html#SeqSimilaritySearchSubHit.ByScoreComparator()">SeqSimilaritySearchSubHit.ByScoreComparator()</a></span> - Constructor for class org.biojava.bio.search.<a href="./org/biojava/bio/search/SeqSimilaritySearchSubHit.ByScoreComparator.html" title="class in org.biojava.bio.search">SeqSimilaritySearchSubHit.ByScoreComparator</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/search/SeqSimilaritySearchSubHit.BySubjectStartComparator.html" title="class in org.biojava.bio.search"><span class="strong">SeqSimilaritySearchSubHit.BySubjectStartComparator</span></a> - Class in <a href="./org/biojava/bio/search/package-summary.html">org.biojava.bio.search</a></dt>
<dd>
<div class="block"><code>BySubjectStartComparator</code> compares
<code>SeqSimilaritySearchSubHit</code>s by their start position
on the subject sequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SeqSimilaritySearchSubHit.BySubjectStartComparator.html#SeqSimilaritySearchSubHit.BySubjectStartComparator()">SeqSimilaritySearchSubHit.BySubjectStartComparator()</a></span> - Constructor for class org.biojava.bio.search.<a href="./org/biojava/bio/search/SeqSimilaritySearchSubHit.BySubjectStartComparator.html" title="class in org.biojava.bio.search">SeqSimilaritySearchSubHit.BySubjectStartComparator</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/ssbind/SeqSimilarityStAXAdapter.html" title="class in org.biojava.bio.program.ssbind"><span class="strong">SeqSimilarityStAXAdapter</span></a> - Class in <a href="./org/biojava/bio/program/ssbind/package-summary.html">org.biojava.bio.program.ssbind</a></dt>
<dd>
<div class="block"><code>SeqSimilarityStAXAdapter</code> is a handler for XML
conforming to the BioJava BlastLike DTD.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/SeqSimilarityStAXAdapter.html#SeqSimilarityStAXAdapter()">SeqSimilarityStAXAdapter()</a></span> - Constructor for class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/SeqSimilarityStAXAdapter.html" title="class in org.biojava.bio.program.ssbind">SeqSimilarityStAXAdapter</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/ssbind/SeqSimilarityStAXHandler.html" title="class in org.biojava.bio.program.ssbind"><span class="strong">SeqSimilarityStAXHandler</span></a> - Class in <a href="./org/biojava/bio/program/ssbind/package-summary.html">org.biojava.bio.program.ssbind</a></dt>
<dd>
<div class="block"><code>SeqSimilarityStAXHandler</code> is a base class for creating
modular StAX handlers which send callbacks to a
<code>SeqSimilarityStAXAdapter</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/SeqSimilarityStAXHandler.html#SeqSimilarityStAXHandler(org.biojava.bio.program.ssbind.SeqSimilarityStAXAdapter)">SeqSimilarityStAXHandler(SeqSimilarityStAXAdapter)</a></span> - Constructor for class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/SeqSimilarityStAXHandler.html" title="class in org.biojava.bio.program.ssbind">SeqSimilarityStAXHandler</a></dt>
<dd>
<div class="block">Creates a new <code>SeqSimilarityStAXHandler</code> which
simply maintains a list of <code>StAXHandlerBinding</code>s and
delegates to any suitable <code>StAXContentHandler</code> bound
by one of them.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/SimpleStatePath.html#seqString()">seqString()</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/SimpleStatePath.html" title="class in org.biojava.bio.dp">SimpleStatePath</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/DASSequence.html#seqString()">seqString()</a></span> - Method in class org.biojava.bio.program.das.<a href="./org/biojava/bio/program/das/DASSequence.html" title="class in org.biojava.bio.program.das">DASSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/homol/SimilarityPairFeature.EmptyPairwiseAlignment.html#seqString()">seqString()</a></span> - Method in class org.biojava.bio.seq.homol.<a href="./org/biojava/bio/seq/homol/SimilarityPairFeature.EmptyPairwiseAlignment.html" title="class in org.biojava.bio.seq.homol">SimilarityPairFeature.EmptyPairwiseAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/DummySequence.html#seqString()">seqString()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/DummySequence.html" title="class in org.biojava.bio.seq.impl">DummySequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleSequence.html#seqString()">seqString()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleSequence.html" title="class in org.biojava.bio.seq.impl">SimpleSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SubSequence.html#seqString()">seqString()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SubSequence.html" title="class in org.biojava.bio.seq.impl">SubSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/ViewSequence.html#seqString()">seqString()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/ViewSequence.html" title="class in org.biojava.bio.seq.impl">ViewSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/NewSimpleAssembly.html#seqString()">seqString()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/NewSimpleAssembly.html" title="class in org.biojava.bio.seq">NewSimpleAssembly</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/SimpleAssembly.html#seqString()">seqString()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/SimpleAssembly.html" title="class in org.biojava.bio.seq">SimpleAssembly</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AbstractSymbolList.html#seqString()">seqString()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AbstractSymbolList.html" title="class in org.biojava.bio.symbol">AbstractSymbolList</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/RelabeledAlignment.html#seqString()">seqString()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/RelabeledAlignment.html" title="class in org.biojava.bio.symbol">RelabeledAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SymbolList.html#seqString()">seqString()</a></span> - Method in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SymbolList.html" title="interface in org.biojava.bio.symbol">SymbolList</a></dt>
<dd>
<div class="block">Stringify this symbol list.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLRichSequenceHandler.html#seqString(org.biojavax.bio.seq.RichSequence)">seqString(RichSequence)</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLRichSequenceHandler.html" title="class in org.biojavax.bio.db.biosql">BioSQLRichSequenceHandler</a></dt>
<dd>
<div class="block">Stringify this Sequences.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/DummyRichSequenceHandler.html#seqString(org.biojavax.bio.seq.RichSequence)">seqString(RichSequence)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/DummyRichSequenceHandler.html" title="class in org.biojavax.bio.seq">DummyRichSequenceHandler</a></dt>
<dd>
<div class="block">Stringify this Sequences.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/InfinitelyAmbiguousSymbolList.html#seqString()">seqString()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/InfinitelyAmbiguousSymbolList.html" title="class in org.biojavax.bio.seq">InfinitelyAmbiguousSymbolList</a></dt>
<dd>
<div class="block">Stringify this symbol list.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequenceHandler.html#seqString(org.biojavax.bio.seq.RichSequence)">seqString(RichSequence)</a></span> - Method in interface org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequenceHandler.html" title="interface in org.biojavax.bio.seq">RichSequenceHandler</a></dt>
<dd>
<div class="block">Stringify this Sequences.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/ThinRichSequence.html#seqString()">seqString()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/ThinRichSequence.html" title="class in org.biojavax.bio.seq">ThinRichSequence</a></dt>
<dd>
<div class="block">Stringify this symbol list.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/StatePath.html#SEQUENCE">SEQUENCE</a></span> - Static variable in interface org.biojava.bio.dp.<a href="./org/biojava/bio/dp/StatePath.html" title="interface in org.biojava.bio.dp">StatePath</a></dt>
<dd>
<div class="block">Alignment label for the emitted sequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/abi/ABITools.html#SEQUENCE">SEQUENCE</a></span> - Static variable in class org.biojava.bio.program.abi.<a href="./org/biojava/bio/program/abi/ABITools.html" title="class in org.biojava.bio.program.abi">ABITools</a></dt>
<dd>
<div class="block">Alignment label for the DNA sequence row.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEBioSeqHandler.html#sequence">sequence</a></span> - Variable in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEBioSeqHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEBioSeqHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEContigHandler.html#sequence">sequence</a></span> - Variable in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEContigHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEContigHandler</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/Sequence.html" title="interface in org.biojava.bio.seq"><span class="strong">Sequence</span></a> - Interface in <a href="./org/biojava/bio/seq/package-summary.html">org.biojava.bio.seq</a></dt>
<dd>
<div class="block">
A biological sequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html#SEQUENCE_CAUTION">SEQUENCE_CAUTION</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html" title="class in org.biojavax.bio.seq.io">UniProtCommentParser</a></dt>
<dd>
<div class="block">A name for a comment type.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#SEQUENCE_CHECKSUM_ATTR">SEQUENCE_CHECKSUM_ATTR</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/util/SequenceScalePanel.html#SEQUENCE_COLOR">SEQUENCE_COLOR</a></span> - Static variable in class org.biojava.bio.structure.gui.util.<a href="./org/biojava/bio/structure/gui/util/SequenceScalePanel.html" title="class in org.biojava.bio.structure.gui.util">SequenceScalePanel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/indexdb/BioStoreFactory.html#SEQUENCE_FORMAT">SEQUENCE_FORMAT</a></span> - Static variable in class org.biojava.bio.program.indexdb.<a href="./org/biojava/bio/program/indexdb/BioStoreFactory.html" title="class in org.biojava.bio.program.indexdb">BioStoreFactory</a></dt>
<dd>
<div class="block"><code>SEQUENCE_FORMAT</code> is the key used to identify the
format of the indexed sequence files represented by the store
in the OBDA config.dat files.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html#SEQUENCE_LENGTH_ATTR">SEQUENCE_LENGTH_ATTR</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html" title="class in org.biojavax.bio.seq.io">EMBLxmlFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#SEQUENCE_LENGTH_ATTR">SEQUENCE_LENGTH_ATTR</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#SEQUENCE_MASS_ATTR">SEQUENCE_MASS_ATTR</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#SEQUENCE_MODIFIED_ATTR">SEQUENCE_MODIFIED_ATTR</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html#SEQUENCE_TAG">SEQUENCE_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html" title="class in org.biojavax.bio.seq.io">EMBLxmlFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/INSDseqFormat.html#SEQUENCE_TAG">SEQUENCE_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/INSDseqFormat.html" title="class in org.biojavax.bio.seq.io">INSDseqFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#SEQUENCE_TAG">SEQUENCE_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html#SEQUENCE_TOPOLOGY_ATTR">SEQUENCE_TOPOLOGY_ATTR</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html" title="class in org.biojavax.bio.seq.io">EMBLxmlFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html#SEQUENCE_TYPE_ATTR">SEQUENCE_TYPE_ATTR</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html" title="class in org.biojavax.bio.seq.io">EMBLxmlFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html#SEQUENCE_VER_ATTR">SEQUENCE_VER_ATTR</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html" title="class in org.biojavax.bio.seq.io">EMBLxmlFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#SEQUENCE_VERSION_ATTR">SEQUENCE_VERSION_ATTR</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/alignment/SequenceAlignment.html" title="class in org.biojava.bio.alignment"><span class="strong">SequenceAlignment</span></a> - Class in <a href="./org/biojava/bio/alignment/package-summary.html">org.biojava.bio.alignment</a></dt>
<dd>
<div class="block">This Interface provides methods for the alignment of bio-sequences.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/SequenceAlignment.html#SequenceAlignment()">SequenceAlignment()</a></span> - Constructor for class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/SequenceAlignment.html" title="class in org.biojava.bio.alignment">SequenceAlignment</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/sax/SequenceAlignmentSAXParser.html" title="class in org.biojava.bio.program.sax"><span class="strong">SequenceAlignmentSAXParser</span></a> - Class in <a href="./org/biojava/bio/program/sax/package-summary.html">org.biojava.bio.program.sax</a></dt>
<dd>
<div class="block">A SAX2 parser for dealing with a sequence alignments.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/sax/SequenceAlignmentSAXParser.html#SequenceAlignmentSAXParser()">SequenceAlignmentSAXParser()</a></span> - Constructor for class org.biojava.bio.program.sax.<a href="./org/biojava/bio/program/sax/SequenceAlignmentSAXParser.html" title="class in org.biojava.bio.program.sax">SequenceAlignmentSAXParser</a></dt>
<dd>
<div class="block">Initialises internal state
Sets namespace prefix to "biojava"</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/fastq/FastqBuilder.html#sequenceAndQualityLengthsMatch()">sequenceAndQualityLengthsMatch()</a></span> - Method in class org.biojava.bio.program.fastq.<a href="./org/biojava/bio/program/fastq/FastqBuilder.html" title="class in org.biojava.bio.program.fastq">FastqBuilder</a></dt>
<dd>
<div class="block">Return true if the sequence and quality scores for this FASTQ formatted sequence builder are equal in length.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/SequenceAnnotator.html" title="interface in org.biojava.bio.seq"><span class="strong">SequenceAnnotator</span></a> - Interface in <a href="./org/biojava/bio/seq/package-summary.html">org.biojava.bio.seq</a></dt>
<dd>
<div class="block">An object which adds some additional information to a Sequence.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/SequenceBuilder.html" title="interface in org.biojava.bio.seq.io"><span class="strong">SequenceBuilder</span></a> - Interface in <a href="./org/biojava/bio/seq/io/package-summary.html">org.biojava.bio.seq.io</a></dt>
<dd>
<div class="block">Interface for objects which accumulate state via SeqIOListener,
then construct a Sequence object.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/SequenceBuilderBase.html" title="class in org.biojava.bio.seq.io"><span class="strong">SequenceBuilderBase</span></a> - Class in <a href="./org/biojava/bio/seq/io/package-summary.html">org.biojava.bio.seq.io</a></dt>
<dd>
<div class="block">Basic SequenceBuilder implementation which accumulates all
notified information.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SequenceBuilderBase.html#SequenceBuilderBase()">SequenceBuilderBase()</a></span> - Constructor for class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SequenceBuilderBase.html" title="class in org.biojava.bio.seq.io">SequenceBuilderBase</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/io/SequenceBuilderFactory.html" title="interface in org.biojava.bio.seq.io"><span class="strong">SequenceBuilderFactory</span></a> - Interface in <a href="./org/biojava/bio/seq/io/package-summary.html">org.biojava.bio.seq.io</a></dt>
<dd>
<div class="block">Simple factory for constructing new SequenceBuilder objects.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/SequenceBuilderFilter.html" title="class in org.biojava.bio.seq.io"><span class="strong">SequenceBuilderFilter</span></a> - Class in <a href="./org/biojava/bio/seq/io/package-summary.html">org.biojava.bio.seq.io</a></dt>
<dd>
<div class="block">Base-class for builders that pass filtered events onto another builder.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SequenceBuilderFilter.html#SequenceBuilderFilter(org.biojava.bio.seq.io.SequenceBuilder)">SequenceBuilderFilter(SequenceBuilder)</a></span> - Constructor for class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SequenceBuilderFilter.html" title="class in org.biojava.bio.seq.io">SequenceBuilderFilter</a></dt>
<dd>
<div class="block">Create a new SeqIOFilter that will forward events on to another listener.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/game/SequenceContentHandlerBase.html" title="class in org.biojava.bio.seq.io.game"><span class="strong">SequenceContentHandlerBase</span></a> - Class in <a href="./org/biojava/bio/seq/io/game/package-summary.html">org.biojava.bio.seq.io.game</a></dt>
<dd>
<div class="block">StAX handler for elements containing sequence</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game/SequenceContentHandlerBase.html#SequenceContentHandlerBase()">SequenceContentHandlerBase()</a></span> - Constructor for class org.biojava.bio.seq.io.game.<a href="./org/biojava/bio/seq/io/game/SequenceContentHandlerBase.html" title="class in org.biojava.bio.seq.io.game">SequenceContentHandlerBase</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/db/SequenceDB.html" title="interface in org.biojava.bio.seq.db"><span class="strong">SequenceDB</span></a> - Interface in <a href="./org/biojava/bio/seq/db/package-summary.html">org.biojava.bio.seq.db</a></dt>
<dd>
<div class="block">A database of sequences with accessible keys and iterators over all
sequences.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/distributed/SequenceDBDataSource.html" title="class in org.biojava.bio.seq.distributed"><span class="strong">SequenceDBDataSource</span></a> - Class in <a href="./org/biojava/bio/seq/distributed/package-summary.html">org.biojava.bio.seq.distributed</a></dt>
<dd>
<div class="block">Turn an entire SequenceDB instance into a DistDataSource.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/distributed/SequenceDBDataSource.html#SequenceDBDataSource(org.biojava.bio.seq.db.SequenceDB)">SequenceDBDataSource(SequenceDB)</a></span> - Constructor for class org.biojava.bio.seq.distributed.<a href="./org/biojava/bio/seq/distributed/SequenceDBDataSource.html" title="class in org.biojava.bio.seq.distributed">SequenceDBDataSource</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/db/SequenceDBInstallation.html" title="interface in org.biojava.bio.seq.db"><span class="strong">SequenceDBInstallation</span></a> - Interface in <a href="./org/biojava/bio/seq/db/package-summary.html">org.biojava.bio.seq.db</a></dt>
<dd>
<div class="block">
A SequenceDBInstallation has the functionality of a factory for
SequenceDB objects and additionally manages the SequenceDB objects
created by itself such that the minimum number of SequenceDB
objects is created by a particular SequenceDBInstallation
object.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/db/SequenceDBLite.html" title="interface in org.biojava.bio.seq.db"><span class="strong">SequenceDBLite</span></a> - Interface in <a href="./org/biojava/bio/seq/db/package-summary.html">org.biojava.bio.seq.db</a></dt>
<dd>
<div class="block">A database of sequences.</div>
</dd>
<dt><a href="./org/biojava/directory/SequenceDBProvider.html" title="interface in org.biojava.directory"><span class="strong">SequenceDBProvider</span></a> - Interface in <a href="./org/biojava/directory/package-summary.html">org.biojava.directory</a></dt>
<dd>
<div class="block">Interfaces for named resources that can provide sequences via a
database given some configuration information as defined by the
OBDA standard.</div>
</dd>
<dt><a href="./org/biojava/bio/search/SequenceDBSearchHit.html" title="class in org.biojava.bio.search"><span class="strong">SequenceDBSearchHit</span></a> - Class in <a href="./org/biojava/bio/search/package-summary.html">org.biojava.bio.search</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>SimpleSeqSimilaritySearchHit has been made Annotatable
and is now functionally identical.</i></div>
</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SequenceDBSearchHit.html#SequenceDBSearchHit(double, double, double, int, int, org.biojava.bio.seq.StrandedFeature.Strand, int, int, org.biojava.bio.seq.StrandedFeature.Strand, java.lang.String, org.biojava.bio.Annotation, java.util.List)">SequenceDBSearchHit(double, double, double, int, int, StrandedFeature.Strand, int, int, StrandedFeature.Strand, String, Annotation, List)</a></span> - Constructor for class org.biojava.bio.search.<a href="./org/biojava/bio/search/SequenceDBSearchHit.html" title="class in org.biojava.bio.search">SequenceDBSearchHit</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Creates a new <code>SequenceDBSearchHit</code> object.</div>
</dd>
<dt><a href="./org/biojava/bio/search/SequenceDBSearchResult.html" title="class in org.biojava.bio.search"><span class="strong">SequenceDBSearchResult</span></a> - Class in <a href="./org/biojava/bio/search/package-summary.html">org.biojava.bio.search</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>SimpleSeqSimilaritySearchResult has been made
Annotatable and is now functionally identical.</i></div>
</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SequenceDBSearchResult.html#SequenceDBSearchResult(org.biojava.bio.seq.Sequence, org.biojava.bio.seq.db.SequenceDB, java.util.Map, java.util.List, org.biojava.bio.Annotation)">SequenceDBSearchResult(Sequence, SequenceDB, Map, List, Annotation)</a></span> - Constructor for class org.biojava.bio.search.<a href="./org/biojava/bio/search/SequenceDBSearchResult.html" title="class in org.biojava.bio.search">SequenceDBSearchResult</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Creates a new <code>SequenceDBSearchResult</code>.</div>
</dd>
<dt><a href="./org/biojava/bio/search/SequenceDBSearchSubHit.html" title="class in org.biojava.bio.search"><span class="strong">SequenceDBSearchSubHit</span></a> - Class in <a href="./org/biojava/bio/search/package-summary.html">org.biojava.bio.search</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>SimpleSeqSimilaritySearchSubHit has been made
Annotatable and is now functionally identical.</i></div>
</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SequenceDBSearchSubHit.html#SequenceDBSearchSubHit(double, double, double, int, int, org.biojava.bio.seq.StrandedFeature.Strand, int, int, org.biojava.bio.seq.StrandedFeature.Strand, org.biojava.bio.symbol.Alignment, org.biojava.bio.Annotation)">SequenceDBSearchSubHit(double, double, double, int, int, StrandedFeature.Strand, int, int, StrandedFeature.Strand, Alignment, Annotation)</a></span> - Constructor for class org.biojava.bio.search.<a href="./org/biojava/bio/search/SequenceDBSearchSubHit.html" title="class in org.biojava.bio.search">SequenceDBSearchSubHit</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Creates a new <code>SequenceDBSearchSubHit</code> object.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/SequenceDBSequenceBuilder.html" title="class in org.biojava.bio.seq.io"><span class="strong">SequenceDBSequenceBuilder</span></a> - Class in <a href="./org/biojava/bio/seq/io/package-summary.html">org.biojava.bio.seq.io</a></dt>
<dd>
<div class="block">This SequenceBuilder has a variety of modes of operation.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SequenceDBSequenceBuilder.html#SequenceDBSequenceBuilder(org.biojava.bio.seq.db.SequenceDB, int)">SequenceDBSequenceBuilder(SequenceDB, int)</a></span> - Constructor for class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SequenceDBSequenceBuilder.html" title="class in org.biojava.bio.seq.io">SequenceDBSequenceBuilder</a></dt>
<dd>
<div class="block">constructor</div>
</dd>
<dt><a href="./org/biojava/bio/seq/db/SequenceDBWrapper.html" title="class in org.biojava.bio.seq.db"><span class="strong">SequenceDBWrapper</span></a> - Class in <a href="./org/biojava/bio/seq/db/package-summary.html">org.biojava.bio.seq.db</a></dt>
<dd>
<div class="block">An abstract implementation of SequenceDB that wraps up another database.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/SequenceDBWrapper.html#SequenceDBWrapper(org.biojava.bio.seq.db.SequenceDB)">SequenceDBWrapper(SequenceDB)</a></span> - Constructor for class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/SequenceDBWrapper.html" title="class in org.biojava.bio.seq.db">SequenceDBWrapper</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/db/SequenceDBWrapper.SequencesForwarder.html" title="class in org.biojava.bio.seq.db"><span class="strong">SequenceDBWrapper.SequencesForwarder</span></a> - Class in <a href="./org/biojava/bio/seq/db/package-summary.html">org.biojava.bio.seq.db</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/SequenceDBWrapper.SequencesForwarder.html#SequenceDBWrapper.SequencesForwarder(java.lang.Object, org.biojava.utils.ChangeSupport)">SequenceDBWrapper.SequencesForwarder(Object, ChangeSupport)</a></span> - Constructor for class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/SequenceDBWrapper.SequencesForwarder.html" title="class in org.biojava.bio.seq.db">SequenceDBWrapper.SequencesForwarder</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/structure/gui/SequenceDisplay.html" title="class in org.biojava.bio.structure.gui"><span class="strong">SequenceDisplay</span></a> - Class in <a href="./org/biojava/bio/structure/gui/package-summary.html">org.biojava.bio.structure.gui</a></dt>
<dd>
<div class="block">A sequence display that can show the results of a protein structure alignment.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/SequenceDisplay.html#SequenceDisplay(org.biojava.bio.structure.align.StructurePairAligner)">SequenceDisplay(StructurePairAligner)</a></span> - Constructor for class org.biojava.bio.structure.gui.<a href="./org/biojava/bio/structure/gui/SequenceDisplay.html" title="class in org.biojava.bio.structure.gui">SequenceDisplay</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SixFrameRenderer.html#sequenceExtentOfPixels(org.biojava.bio.gui.sequence.SequenceRenderContext)">sequenceExtentOfPixels(SequenceRenderContext)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SixFrameRenderer.html" title="class in org.biojava.bio.gui.sequence">SixFrameRenderer</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/SequenceFactory.html" title="interface in org.biojava.bio.seq"><span class="strong">SequenceFactory</span></a> - Interface in <a href="./org/biojava/bio/seq/package-summary.html">org.biojava.bio.seq</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>use org.biojavax.bio.seq.io.RichSequenceBuilder or
use org.biojavax.bio.seq.io.SequenceBuilder</i></div>
</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/SequenceFormat.html" title="interface in org.biojava.bio.seq.io"><span class="strong">SequenceFormat</span></a> - Interface in <a href="./org/biojava/bio/seq/io/package-summary.html">org.biojava.bio.seq.io</a></dt>
<dd>
<div class="block">Defines what a sequence format does.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/agave/SequenceHandler.html" title="interface in org.biojava.bio.seq.io.agave"><span class="strong">SequenceHandler</span></a> - Interface in <a href="./org/biojava/bio/seq/io/agave/package-summary.html">org.biojava.bio.seq.io.agave</a></dt>
<dd>
<div class="block">mark interface</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/DASSequenceDB.html#sequenceIterator()">sequenceIterator()</a></span> - Method in class org.biojava.bio.program.das.<a href="./org/biojava/bio/program/das/DASSequenceDB.html" title="class in org.biojava.bio.program.das">DASSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/AbstractSequenceDB.html#sequenceIterator()">sequenceIterator()</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/AbstractSequenceDB.html" title="class in org.biojava.bio.seq.db">AbstractSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/AnnotatedSequenceDB.html#sequenceIterator()">sequenceIterator()</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/AnnotatedSequenceDB.html" title="class in org.biojava.bio.seq.db">AnnotatedSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/biosql/BioSQLSequenceDB.html#sequenceIterator()">sequenceIterator()</a></span> - Method in class org.biojava.bio.seq.db.biosql.<a href="./org/biojava/bio/seq/db/biosql/BioSQLSequenceDB.html" title="class in org.biojava.bio.seq.db.biosql">BioSQLSequenceDB</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/DummySequenceDB.html#sequenceIterator()">sequenceIterator()</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/DummySequenceDB.html" title="class in org.biojava.bio.seq.db">DummySequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/HashSequenceDB.html#sequenceIterator()">sequenceIterator()</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/HashSequenceDB.html" title="class in org.biojava.bio.seq.db">HashSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/IndexedSequenceDB.html#sequenceIterator()">sequenceIterator()</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/IndexedSequenceDB.html" title="class in org.biojava.bio.seq.db">IndexedSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/SequenceDB.html#sequenceIterator()">sequenceIterator()</a></span> - Method in interface org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/SequenceDB.html" title="interface in org.biojava.bio.seq.db">SequenceDB</a></dt>
<dd>
<div class="block">Returns a SequenceIterator over all sequences in the database.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/SequenceIterator.html" title="interface in org.biojava.bio.seq"><span class="strong">SequenceIterator</span></a> - Interface in <a href="./org/biojava/bio/seq/package-summary.html">org.biojava.bio.seq</a></dt>
<dd>
<div class="block">An iterator over a bag of sequences.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/AbstractRichSequenceDB.html#sequenceIterator()">sequenceIterator()</a></span> - Method in class org.biojavax.bio.db.<a href="./org/biojavax/bio/db/AbstractRichSequenceDB.html" title="class in org.biojavax.bio.db">AbstractRichSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/RichSequenceDB.html#sequenceIterator()">sequenceIterator()</a></span> - Method in interface org.biojavax.bio.db.<a href="./org/biojavax/bio/db/RichSequenceDB.html" title="interface in org.biojavax.bio.db">RichSequenceDB</a></dt>
<dd>
<div class="block">Returns a SequenceIterator over all sequences in the database.</div>
</dd>
<dt><a href="./org/biojava/bio/structure/gui/util/SequenceMouseListener.html" title="class in org.biojava.bio.structure.gui.util"><span class="strong">SequenceMouseListener</span></a> - Class in <a href="./org/biojava/bio/structure/gui/util/package-summary.html">org.biojava.bio.structure.gui.util</a></dt>
<dd>
<div class="block">a mouse listener for the AbstractChainRenderer class
it listens to all mouse events and triggeres appropriate
SequenceListener and FeatureListener events</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/util/SequenceMouseListener.html#SequenceMouseListener(org.biojava.bio.structure.gui.SequenceDisplay)">SequenceMouseListener(SequenceDisplay)</a></span> - Constructor for class org.biojava.bio.structure.gui.util.<a href="./org/biojava/bio/structure/gui/util/SequenceMouseListener.html" title="class in org.biojava.bio.structure.gui.util">SequenceMouseListener</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/gui/sequence/SequencePanel.html" title="class in org.biojava.bio.gui.sequence"><span class="strong">SequencePanel</span></a> - Class in <a href="./org/biojava/bio/gui/sequence/package-summary.html">org.biojava.bio.gui.sequence</a></dt>
<dd>
<div class="block">A panel that displays a Sequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePanel.html#SequencePanel()">SequencePanel()</a></span> - Constructor for class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePanel.html" title="class in org.biojava.bio.gui.sequence">SequencePanel</a></dt>
<dd>
<div class="block">Create a new SequencePanel.</div>
</dd>
<dt><a href="./org/biojava/bio/gui/sequence/SequencePanel.Border.html" title="class in org.biojava.bio.gui.sequence"><span class="strong">SequencePanel.Border</span></a> - Class in <a href="./org/biojava/bio/gui/sequence/package-summary.html">org.biojava.bio.gui.sequence</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/gui/sequence/SequencePanelWrapper.html" title="class in org.biojava.bio.gui.sequence"><span class="strong">SequencePanelWrapper</span></a> - Class in <a href="./org/biojava/bio/gui/sequence/package-summary.html">org.biojava.bio.gui.sequence</a></dt>
<dd>
<div class="block">Handles multiple SequencePanels and Ranges so that a Sequence can be wrapped
over more than one line on screen.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePanelWrapper.html#SequencePanelWrapper()">SequencePanelWrapper()</a></span> - Constructor for class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePanelWrapper.html" title="class in org.biojava.bio.gui.sequence">SequencePanelWrapper</a></dt>
<dd>
<div class="block">Creates a new instance of WrappedSequencePanel</div>
</dd>
<dt><a href="./org/biojava/bio/gui/sequence/SequencePoster.html" title="class in org.biojava.bio.gui.sequence"><span class="strong">SequencePoster</span></a> - Class in <a href="./org/biojava/bio/gui/sequence/package-summary.html">org.biojava.bio.gui.sequence</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>This doesn't handle loads of stuff. Use SequencePoster.</i></div>
</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePoster.html#SequencePoster()">SequencePoster()</a></span> - Constructor for class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePoster.html" title="class in org.biojava.bio.gui.sequence">SequencePoster</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Create a new SeqeuncePanel.</div>
</dd>
<dt><a href="./org/biojava/bio/gui/sequence/SequencePoster.Border.html" title="class in org.biojava.bio.gui.sequence"><span class="strong">SequencePoster.Border</span></a> - Class in <a href="./org/biojava/bio/gui/sequence/package-summary.html">org.biojava.bio.gui.sequence</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><a href="./org/biojava/bio/gui/sequence/SequenceRenderContext.html" title="interface in org.biojava.bio.gui.sequence"><span class="strong">SequenceRenderContext</span></a> - Interface in <a href="./org/biojava/bio/gui/sequence/package-summary.html">org.biojava.bio.gui.sequence</a></dt>
<dd>
<div class="block">A context within which sequence information may be rendered.</div>
</dd>
<dt><a href="./org/biojava/bio/gui/sequence/SequenceRenderContext.Border.html" title="class in org.biojava.bio.gui.sequence"><span class="strong">SequenceRenderContext.Border</span></a> - Class in <a href="./org/biojava/bio/gui/sequence/package-summary.html">org.biojava.bio.gui.sequence</a></dt>
<dd>
<div class="block">The metric object for the 'border' area - the area between the extent of
the rendered area and the beginning or end of the sequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequenceRenderContext.Border.html#SequenceRenderContext.Border()">SequenceRenderContext.Border()</a></span> - Constructor for class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequenceRenderContext.Border.html" title="class in org.biojava.bio.gui.sequence">SequenceRenderContext.Border</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/gui/sequence/SequenceRenderer.html" title="interface in org.biojava.bio.gui.sequence"><span class="strong">SequenceRenderer</span></a> - Interface in <a href="./org/biojava/bio/gui/sequence/package-summary.html">org.biojava.bio.gui.sequence</a></dt>
<dd>
<div class="block">The interface for things that can render a line of information about a
sequence.</div>
</dd>
<dt><a href="./org/biojava/bio/gui/sequence/SequenceRenderer.RendererForwarder.html" title="class in org.biojava.bio.gui.sequence"><span class="strong">SequenceRenderer.RendererForwarder</span></a> - Class in <a href="./org/biojava/bio/gui/sequence/package-summary.html">org.biojava.bio.gui.sequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequenceRenderer.RendererForwarder.html#SequenceRenderer.RendererForwarder(org.biojava.bio.gui.sequence.SequenceRenderer, org.biojava.utils.ChangeSupport)">SequenceRenderer.RendererForwarder(SequenceRenderer, ChangeSupport)</a></span> - Constructor for class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequenceRenderer.RendererForwarder.html" title="class in org.biojava.bio.gui.sequence">SequenceRenderer.RendererForwarder</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/gui/sequence/SequenceRendererWrapper.html" title="class in org.biojava.bio.gui.sequence"><span class="strong">SequenceRendererWrapper</span></a> - Class in <a href="./org/biojava/bio/gui/sequence/package-summary.html">org.biojava.bio.gui.sequence</a></dt>
<dd>
<div class="block">An implementation of SequenceRenderer that delegates rendering to another
renderer.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequenceRendererWrapper.html#SequenceRendererWrapper()">SequenceRendererWrapper()</a></span> - Constructor for class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequenceRendererWrapper.html" title="class in org.biojava.bio.gui.sequence">SequenceRendererWrapper</a></dt>
<dd>
<div class="block">Create a new renderer with no wrapped renderer.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequenceRendererWrapper.html#SequenceRendererWrapper(org.biojava.bio.gui.sequence.SequenceRenderer)">SequenceRendererWrapper(SequenceRenderer)</a></span> - Constructor for class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequenceRendererWrapper.html" title="class in org.biojava.bio.gui.sequence">SequenceRendererWrapper</a></dt>
<dd>
<div class="block">Create a new wrapper with a wrapped renderer</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/SequenceDBLite.html#SEQUENCES">SEQUENCES</a></span> - Static variable in interface org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/SequenceDBLite.html" title="interface in org.biojava.bio.seq.db">SequenceDBLite</a></dt>
<dd>
<div class="block">Signals that sequences are being added to or remove from the database.</div>
</dd>
<dt><a href="./org/biojava/bio/program/gff/SequencesAsGFF.html" title="class in org.biojava.bio.program.gff"><span class="strong">SequencesAsGFF</span></a> - Class in <a href="./org/biojava/bio/program/gff/package-summary.html">org.biojava.bio.program.gff</a></dt>
<dd>
<div class="block">Turns a sequence database into a GFF event stream.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/SequencesAsGFF.html#SequencesAsGFF()">SequencesAsGFF()</a></span> - Constructor for class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/SequencesAsGFF.html" title="class in org.biojava.bio.program.gff">SequencesAsGFF</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/structure/gui/util/SequenceScalePanel.html" title="class in org.biojava.bio.structure.gui.util"><span class="strong">SequenceScalePanel</span></a> - Class in <a href="./org/biojava/bio/structure/gui/util/package-summary.html">org.biojava.bio.structure.gui.util</a></dt>
<dd>
<div class="block">A class that draws a Sequence as a rectangle, a scale display over it.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/util/SequenceScalePanel.html#SequenceScalePanel(int)">SequenceScalePanel(int)</a></span> - Constructor for class org.biojava.bio.structure.gui.util.<a href="./org/biojava/bio/structure/gui/util/SequenceScalePanel.html" title="class in org.biojava.bio.structure.gui.util">SequenceScalePanel</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/ssaha/SequenceStreamer.html" title="interface in org.biojava.bio.program.ssaha"><span class="strong">SequenceStreamer</span></a> - Interface in <a href="./org/biojava/bio/program/ssaha/package-summary.html">org.biojava.bio.program.ssaha</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/ssaha/SequenceStreamer.FileStreamer.html" title="class in org.biojava.bio.program.ssaha"><span class="strong">SequenceStreamer.FileStreamer</span></a> - Class in <a href="./org/biojava/bio/program/ssaha/package-summary.html">org.biojava.bio.program.ssaha</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssaha/SequenceStreamer.FileStreamer.html#SequenceStreamer.FileStreamer(org.biojava.bio.seq.io.SequenceFormat, org.biojava.bio.seq.io.SymbolTokenization, java.util.List)">SequenceStreamer.FileStreamer(SequenceFormat, SymbolTokenization, List)</a></span> - Constructor for class org.biojava.bio.program.ssaha.<a href="./org/biojava/bio/program/ssaha/SequenceStreamer.FileStreamer.html" title="class in org.biojava.bio.program.ssaha">SequenceStreamer.FileStreamer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssaha/SequenceStreamer.FileStreamer.html#SequenceStreamer.FileStreamer(org.biojava.bio.seq.io.SequenceFormat, org.biojava.bio.seq.io.SymbolTokenization, java.io.File)">SequenceStreamer.FileStreamer(SequenceFormat, SymbolTokenization, File)</a></span> - Constructor for class org.biojava.bio.program.ssaha.<a href="./org/biojava/bio/program/ssaha/SequenceStreamer.FileStreamer.html" title="class in org.biojava.bio.program.ssaha">SequenceStreamer.FileStreamer</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/ssaha/SequenceStreamer.SequenceDBStreamer.html" title="class in org.biojava.bio.program.ssaha"><span class="strong">SequenceStreamer.SequenceDBStreamer</span></a> - Class in <a href="./org/biojava/bio/program/ssaha/package-summary.html">org.biojava.bio.program.ssaha</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssaha/SequenceStreamer.SequenceDBStreamer.html#SequenceStreamer.SequenceDBStreamer(org.biojava.bio.seq.db.SequenceDB)">SequenceStreamer.SequenceDBStreamer(SequenceDB)</a></span> - Constructor for class org.biojava.bio.program.ssaha.<a href="./org/biojava/bio/program/ssaha/SequenceStreamer.SequenceDBStreamer.html" title="class in org.biojava.bio.program.ssaha">SequenceStreamer.SequenceDBStreamer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/HeadlessRenderContext.html#sequenceToGraphics(int)">sequenceToGraphics(int)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/HeadlessRenderContext.html" title="class in org.biojava.bio.gui.sequence">HeadlessRenderContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PairwiseSequencePanel.html#sequenceToGraphics(int)">sequenceToGraphics(int)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PairwiseSequencePanel.html" title="class in org.biojava.bio.gui.sequence">PairwiseSequencePanel</a></dt>
<dd>
<div class="block"><code>sequenceToGraphics</code> converts a sequence index
to a graphical position.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePanel.html#sequenceToGraphics(int)">sequenceToGraphics(int)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePanel.html" title="class in org.biojava.bio.gui.sequence">SequencePanel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePoster.html#sequenceToGraphics(int)">sequenceToGraphics(int)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePoster.html" title="class in org.biojava.bio.gui.sequence">SequencePoster</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequenceRenderContext.html#sequenceToGraphics(int)">sequenceToGraphics(int)</a></span> - Method in interface org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequenceRenderContext.html" title="interface in org.biojava.bio.gui.sequence">SequenceRenderContext</a></dt>
<dd>
<div class="block">Converts a sequence index into a graphical coordinate.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SubPairwiseRenderContext.html#sequenceToGraphics(int)">sequenceToGraphics(int)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SubPairwiseRenderContext.html" title="class in org.biojava.bio.gui.sequence">SubPairwiseRenderContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SubSequenceRenderContext.html#sequenceToGraphics(int)">sequenceToGraphics(int)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SubSequenceRenderContext.html" title="class in org.biojava.bio.gui.sequence">SubSequenceRenderContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/TranslatedSequencePanel.html#sequenceToGraphics(int)">sequenceToGraphics(int)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/TranslatedSequencePanel.html" title="class in org.biojava.bio.gui.sequence">TranslatedSequencePanel</a></dt>
<dd>
<div class="block"><code>sequenceToGraphics</code> converts a sequence index to a
graphical position.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/SequenceTools.html" title="class in org.biojava.bio.seq"><span class="strong">SequenceTools</span></a> - Class in <a href="./org/biojava/bio/seq/package-summary.html">org.biojava.bio.seq</a></dt>
<dd>
<div class="block">Methods for manipulating sequences.</div>
</dd>
<dt><a href="./org/biojava/bio/gui/sequence/SequenceViewerEvent.html" title="class in org.biojava.bio.gui.sequence"><span class="strong">SequenceViewerEvent</span></a> - Class in <a href="./org/biojava/bio/gui/sequence/package-summary.html">org.biojava.bio.gui.sequence</a></dt>
<dd>
<div class="block">An event indicating that a mouse gesture was recognised within a widget that
renders sequences.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequenceViewerEvent.html#SequenceViewerEvent(java.lang.Object, java.lang.Object, int, java.awt.event.MouseEvent, java.util.List)">SequenceViewerEvent(Object, Object, int, MouseEvent, List)</a></span> - Constructor for class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequenceViewerEvent.html" title="class in org.biojava.bio.gui.sequence">SequenceViewerEvent</a></dt>
<dd>
<div class="block">Construct a SequenceViewerEvent with the given source, target, mouseEvent
and path.</div>
</dd>
<dt><a href="./org/biojava/bio/gui/sequence/SequenceViewerListener.html" title="interface in org.biojava.bio.gui.sequence"><span class="strong">SequenceViewerListener</span></a> - Interface in <a href="./org/biojava/bio/gui/sequence/package-summary.html">org.biojava.bio.gui.sequence</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/gui/sequence/SequenceViewerMotionListener.html" title="interface in org.biojava.bio.gui.sequence"><span class="strong">SequenceViewerMotionListener</span></a> - Interface in <a href="./org/biojava/bio/gui/sequence/package-summary.html">org.biojava.bio.gui.sequence</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/gui/sequence/SequenceViewerMotionSupport.html" title="class in org.biojava.bio.gui.sequence"><span class="strong">SequenceViewerMotionSupport</span></a> - Class in <a href="./org/biojava/bio/gui/sequence/package-summary.html">org.biojava.bio.gui.sequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequenceViewerMotionSupport.html#SequenceViewerMotionSupport()">SequenceViewerMotionSupport()</a></span> - Constructor for class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequenceViewerMotionSupport.html" title="class in org.biojava.bio.gui.sequence">SequenceViewerMotionSupport</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/gui/sequence/SequenceViewerSupport.html" title="class in org.biojava.bio.gui.sequence"><span class="strong">SequenceViewerSupport</span></a> - Class in <a href="./org/biojava/bio/gui/sequence/package-summary.html">org.biojava.bio.gui.sequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequenceViewerSupport.html#SequenceViewerSupport()">SequenceViewerSupport()</a></span> - Constructor for class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequenceViewerSupport.html" title="class in org.biojava.bio.gui.sequence">SequenceViewerSupport</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/BioEntry.html#SEQVERSION">SEQVERSION</a></span> - Static variable in interface org.biojavax.bio.<a href="./org/biojavax/bio/BioEntry.html" title="interface in org.biojavax.bio">BioEntry</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/ProteinTools.html#ser()">ser()</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/ProteinTools.html" title="class in org.biojava.bio.seq">ProteinTools</a></dt>
<dd>
<div class="block">Returns the <code>AtomicSymbol</code> for the amino acid
Serine (S)</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/taxa/EbiFormat.html#serialize(org.biojava.bio.taxa.Taxon)">serialize(Taxon)</a></span> - Method in class org.biojava.bio.taxa.<a href="./org/biojava/bio/taxa/EbiFormat.html" title="class in org.biojava.bio.taxa">EbiFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/taxa/TaxonParser.html#serialize(org.biojava.bio.taxa.Taxon)">serialize(Taxon)</a></span> - Method in interface org.biojava.bio.taxa.<a href="./org/biojava/bio/taxa/TaxonParser.html" title="interface in org.biojava.bio.taxa">TaxonParser</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Convert a Taxon into a stringified representation.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/taxa/EbiFormat.html#serializeSource(org.biojava.bio.taxa.Taxon)">serializeSource(Taxon)</a></span> - Method in class org.biojava.bio.taxa.<a href="./org/biojava/bio/taxa/EbiFormat.html" title="class in org.biojava.bio.taxa">EbiFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/taxa/EbiFormat.html#serializeXRef(org.biojava.bio.taxa.Taxon)">serializeXRef(Taxon)</a></span> - Method in class org.biojava.bio.taxa.<a href="./org/biojava/bio/taxa/EbiFormat.html" title="class in org.biojava.bio.taxa">EbiFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/SimpleMarkovModel.html#serialVersionUID">serialVersionUID</a></span> - Static variable in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/SimpleMarkovModel.html" title="class in org.biojava.bio.dp">SimpleMarkovModel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/PDBParseException.html#serialVersionUID">serialVersionUID</a></span> - Static variable in exception org.biojava.bio.structure.io.<a href="./org/biojava/bio/structure/io/PDBParseException.html" title="class in org.biojava.bio.structure.io">PDBParseException</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/StructureException.html#serialVersionUID">serialVersionUID</a></span> - Static variable in exception org.biojava.bio.structure.<a href="./org/biojava/bio/structure/StructureException.html" title="class in org.biojava.bio.structure">StructureException</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AbstractAlphabet.html#serialVersionUID">serialVersionUID</a></span> - Static variable in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AbstractAlphabet.html" title="class in org.biojava.bio.symbol">AbstractAlphabet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BiblioBook.html#series">series</a></span> - Variable in class org.biojava.bibliography.<a href="./org/biojava/bibliography/BiblioBook.html" title="class in org.biojava.bibliography">BiblioBook</a></dt>
<dd>
<div class="block">Book series.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/server/DemoStructureServer.html#server">server</a></span> - Variable in class org.biojava.bio.structure.server.<a href="./org/biojava/bio/structure/server/DemoStructureServer.html" title="class in org.biojava.bio.structure.server">DemoStructureServer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/DAS.html#SERVERS">SERVERS</a></span> - Static variable in class org.biojava.bio.program.das.<a href="./org/biojava/bio/program/das/DAS.html" title="class in org.biojava.bio.program.das">DAS</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/utils/Services.html" title="class in org.biojava.utils"><span class="strong">Services</span></a> - Class in <a href="./org/biojava/utils/package-summary.html">org.biojava.utils</a></dt>
<dd>
<div class="block">Utility methods for handling META-INF/services files</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/Services.html#Services()">Services()</a></span> - Constructor for class org.biojava.utils.<a href="./org/biojava/utils/Services.html" title="class in org.biojava.utils">Services</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/jama/Matrix.html#set(int, int, double)">set(int, int, double)</a></span> - Method in class org.biojava.bio.structure.jama.<a href="./org/biojava/bio/structure/jama/Matrix.html" title="class in org.biojava.bio.structure.jama">Matrix</a></dt>
<dd>
<div class="block">Set a single element.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/FileAsList.html#set(int, java.lang.Object)">set(int, Object)</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/FileAsList.html" title="class in org.biojava.utils">FileAsList</a></dt>
<dd>
<div class="block">This always returns null, not the previous object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/ListTools.Doublet.html#set(java.lang.Object, java.lang.Object)">set(Object, Object)</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/ListTools.Doublet.html" title="class in org.biojava.utils">ListTools.Doublet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ListTools.Triplet.html#set(java.lang.Object, java.lang.Object, java.lang.Object)">set(Object, Object, Object)</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/ListTools.Triplet.html" title="class in org.biojava.utils">ListTools.Triplet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ListTools.Doublet.html#setA(java.lang.Object)">setA(Object)</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/ListTools.Doublet.html" title="class in org.biojava.utils">ListTools.Doublet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ListTools.Triplet.html#setA(java.lang.Object)">setA(Object)</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/ListTools.Triplet.html" title="class in org.biojava.utils">ListTools.Triplet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Exptl.html#setAbsorpt_coefficient_mu(java.lang.String)">setAbsorpt_coefficient_mu(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Exptl.html" title="class in org.biojava.bio.structure.io.mmcif.model">Exptl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Exptl.html#setAbsorpt_correction_T_max(java.lang.String)">setAbsorpt_correction_T_max(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Exptl.html" title="class in org.biojava.bio.structure.io.mmcif.model">Exptl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Exptl.html#setAbsorpt_correction_T_min(java.lang.String)">setAbsorpt_correction_T_min(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Exptl.html" title="class in org.biojava.bio.structure.io.mmcif.model">Exptl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Exptl.html#setAbsorpt_correction_type(java.lang.String)">setAbsorpt_correction_type(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Exptl.html" title="class in org.biojava.bio.structure.io.mmcif.model">Exptl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Exptl.html#setAbsorpt_process_details(java.lang.String)">setAbsorpt_process_details(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Exptl.html" title="class in org.biojava.bio.structure.io.mmcif.model">Exptl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html#setAbsorptionMax(java.lang.String)">setAbsorptionMax(String)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html" title="class in org.biojavax.bio.seq.io">UniProtCommentParser</a></dt>
<dd>
<div class="block">Setter for property absorptionMax.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html#setAbsorptionNote(java.lang.String)">setAbsorptionNote(String)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html" title="class in org.biojavax.bio.seq.io">UniProtCommentParser</a></dt>
<dd>
<div class="block">Setter for property absorptionNote.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/DebuggingRichSeqIOListener.html#setAccession(java.lang.String)">setAccession(String)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/DebuggingRichSeqIOListener.html" title="class in org.biojavax.bio.seq.io">DebuggingRichSeqIOListener</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/RichSeqIOAdapter.html#setAccession(java.lang.String)">setAccession(String)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/RichSeqIOAdapter.html" title="class in org.biojavax.bio.seq.io">RichSeqIOAdapter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/RichSeqIOListener.html#setAccession(java.lang.String)">setAccession(String)</a></span> - Method in interface org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/RichSeqIOListener.html" title="interface in org.biojavax.bio.seq.io">RichSeqIOListener</a></dt>
<dd>
<div class="block">Call back method so the event emitter can tell the listener
the accession of the record being read.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/SimpleRichSequenceBuilder.html#setAccession(java.lang.String)">setAccession(String)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/SimpleRichSequenceBuilder.html" title="class in org.biojavax.bio.seq.io">SimpleRichSequenceBuilder</a></dt>
<dd>
<div class="block">Call back method so the event emitter can tell the listener
the accession of the record being read.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/Namespace.html#setAcronym(java.lang.String)">setAcronym(String)</a></span> - Method in interface org.biojavax.<a href="./org/biojavax/Namespace.html" title="interface in org.biojavax">Namespace</a></dt>
<dd>
<div class="block">Sets an optional acronym for the namespace.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleNamespace.html#setAcronym(java.lang.String)">setAcronym(String)</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleNamespace.html" title="class in org.biojavax">SimpleNamespace</a></dt>
<dd>
<div class="block">Sets an optional acronym for the namespace.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/tools/ClassifierExample.PointClassifier.html#setAddPos(boolean)">setAddPos(boolean)</a></span> - Method in class org.biojava.stats.svm.tools.<a href="./org/biojava/stats/svm/tools/ClassifierExample.PointClassifier.html" title="class in org.biojava.stats.svm.tools">ClassifierExample.PointClassifier</a></dt>
<dd>
<div class="block">Set a flag so that newly added points will be in the positive class or
negative class, depending on wether addPos is true or false respectively.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/EmissionState.html#setAdvance(int[])">setAdvance(int[])</a></span> - Method in interface org.biojava.bio.dp.<a href="./org/biojava/bio/dp/EmissionState.html" title="interface in org.biojava.bio.dp">EmissionState</a></dt>
<dd>
<div class="block">Set the advance array.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/SimpleEmissionState.html#setAdvance(int[])">setAdvance(int[])</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/SimpleEmissionState.html" title="class in org.biojava.bio.dp">SimpleEmissionState</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/util/SequenceScalePanel.html#setAligMap(java.util.List)">setAligMap(List<AlignedPosition>)</a></span> - Method in class org.biojava.bio.structure.gui.util.<a href="./org/biojava/bio/structure/gui/util/SequenceScalePanel.html" title="class in org.biojava.bio.structure.gui.util">SequenceScalePanel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/Alignable.html#setAligMat(org.biojava.bio.structure.align.helper.AligMatEl[][])">setAligMat(AligMatEl[][])</a></span> - Method in interface org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/Alignable.html" title="interface in org.biojava.bio.structure.align.pairwise">Alignable</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/StrCompAlignment.html#setAligMat(int, int, org.biojava.bio.structure.align.helper.AligMatEl)">setAligMat(int, int, AligMatEl)</a></span> - Method in class org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/StrCompAlignment.html" title="class in org.biojava.bio.structure.align.pairwise">StrCompAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/StrCompAlignment.html#setAligMat(org.biojava.bio.structure.align.helper.AligMatEl[][])">setAligMat(AligMatEl[][])</a></span> - Method in class org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/StrCompAlignment.html" title="class in org.biojava.bio.structure.align.pairwise">StrCompAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/StructRefSeq.html#setAlign_id(java.lang.String)">setAlign_id(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/StructRefSeq.html" title="class in org.biojava.bio.structure.io.mmcif.model">StructRefSeq</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePanel.Border.html#setAlignment(int)">setAlignment(int)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePanel.Border.html" title="class in org.biojava.bio.gui.sequence">SequencePanel.Border</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePoster.Border.html#setAlignment(int)">setAlignment(int)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePoster.Border.html" title="class in org.biojava.bio.gui.sequence">SequencePoster.Border</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequenceRenderContext.Border.html#setAlignment(int)">setAlignment(int)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequenceRenderContext.Border.html" title="class in org.biojava.bio.gui.sequence">SequenceRenderContext.Border</a></dt>
<dd>
<div class="block">Sets the Alignment attribute of the Border object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/homol/SimpleHomology.html#setAlignment(org.biojava.bio.symbol.Alignment)">setAlignment(Alignment)</a></span> - Method in class org.biojava.bio.seq.homol.<a href="./org/biojava/bio/seq/homol/SimpleHomology.html" title="class in org.biojava.bio.seq.homol">SimpleHomology</a></dt>
<dd>
<div class="block"><code>setAlignment</code> sets the alignment which describes
the homology.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/SimpleMMcifConsumer.html#setAlignSeqRes(boolean)">setAlignSeqRes(boolean)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/SimpleMMcifConsumer.html" title="class in org.biojava.bio.structure.io.mmcif">SimpleMMcifConsumer</a></dt>
<dd>
<div class="block">define if the SEQRES in the structure should be aligned with the ATOM records
if yes, the AminoAcids in structure.getSeqRes will have the coordinates set.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/PDBFileParser.html#setAlignSeqRes(boolean)">setAlignSeqRes(boolean)</a></span> - Method in class org.biojava.bio.structure.io.<a href="./org/biojava/bio/structure/io/PDBFileParser.html" title="class in org.biojava.bio.structure.io">PDBFileParser</a></dt>
<dd>
<div class="block">define if the SEQRES in the structure should be aligned with the ATOM records
if yes, the AminoAcids in structure.getSeqRes will have the coordinates set.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/PDBFileReader.html#setAlignSeqRes(boolean)">setAlignSeqRes(boolean)</a></span> - Method in class org.biojava.bio.structure.io.<a href="./org/biojava/bio/structure/io/PDBFileReader.html" title="class in org.biojava.bio.structure.io">PDBFileReader</a></dt>
<dd>
<div class="block">set the flag if the SEQRES and ATOM amino acids should be aligned and linked</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/AbstractSVMClassifierModel.html#setAlpha(java.lang.Object, double)">setAlpha(Object, double)</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/AbstractSVMClassifierModel.html" title="class in org.biojava.stats.svm">AbstractSVMClassifierModel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/SimpleSVMClassifierModel.html#setAlpha(java.lang.Object, double)">setAlpha(Object, double)</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/SimpleSVMClassifierModel.html" title="class in org.biojava.stats.svm">SimpleSVMClassifierModel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/SVMClassifierModel.html#setAlpha(java.lang.Object, double)">setAlpha(Object, double)</a></span> - Method in interface org.biojava.stats.svm.<a href="./org/biojava/stats/svm/SVMClassifierModel.html" title="interface in org.biojava.stats.svm">SVMClassifierModel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/SVMRegressionModel.html#setAlpha(int, double)">setAlpha(int, double)</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/SVMRegressionModel.html" title="class in org.biojava.stats.svm">SVMRegressionModel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichSequence.html#setAlphabetName(java.lang.String)">setAlphabetName(String)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichSequence.html" title="class in org.biojavax.bio.seq">SimpleRichSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/ThinRichSequence.html#setAlphabetName(java.lang.String)">setAlphabetName(String)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/ThinRichSequence.html" title="class in org.biojavax.bio.seq">ThinRichSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/SVMRegressionModel.html#setAlphaStar(int, double)">setAlphaStar(int, double)</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/SVMRegressionModel.html" title="class in org.biojava.stats.svm">SVMRegressionModel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/AlternativeAlignment.html#setAltAligNumber(int)">setAltAligNumber(int)</a></span> - Method in class org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/AlternativeAlignment.html" title="class in org.biojava.bio.structure.align.pairwise">AlternativeAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/SequenceDisplay.html#setAlternativeAlignment(org.biojava.bio.structure.align.pairwise.AlternativeAlignment)">setAlternativeAlignment(AlternativeAlignment)</a></span> - Method in class org.biojava.bio.structure.gui.<a href="./org/biojava/bio/structure/gui/SequenceDisplay.html" title="class in org.biojava.bio.structure.gui">SequenceDisplay</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/util/AlternativeAlignmentFrame.html#setAlternativeAlignments(org.biojava.bio.structure.align.pairwise.AlternativeAlignment[])">setAlternativeAlignments(AlternativeAlignment[])</a></span> - Method in class org.biojava.bio.structure.gui.util.<a href="./org/biojava/bio/structure/gui/util/AlternativeAlignmentFrame.html" title="class in org.biojava.bio.structure.gui.util">AlternativeAlignmentFrame</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/JMatrixPanel.html#setAlternativeAligs(org.biojava.bio.structure.align.pairwise.AlternativeAlignment[])">setAlternativeAligs(AlternativeAlignment[])</a></span> - Method in class org.biojava.bio.structure.gui.<a href="./org/biojava/bio/structure/gui/JMatrixPanel.html" title="class in org.biojava.bio.structure.gui">JMatrixPanel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/ScaleableMatrixPanel.html#setAlternativeAligs(org.biojava.bio.structure.align.pairwise.AlternativeAlignment[])">setAlternativeAligs(AlternativeAlignment[])</a></span> - Method in class org.biojava.bio.structure.gui.<a href="./org/biojava/bio/structure/gui/ScaleableMatrixPanel.html" title="class in org.biojava.bio.structure.gui">ScaleableMatrixPanel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Atom.html#setAltLoc(java.lang.Character)">setAltLoc(Character)</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Atom.html" title="interface in org.biojava.bio.structure">Atom</a></dt>
<dd>
<div class="block">get set alternate Location.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/AtomImpl.html#setAltLoc(java.lang.Character)">setAltLoc(Character)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/AtomImpl.html" title="class in org.biojava.bio.structure">AtomImpl</a></dt>
<dd>
<div class="block">set alternate Location.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/AminoAcid.html#setAminoType(java.lang.Character)">setAminoType(Character)</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/AminoAcid.html" title="interface in org.biojava.bio.structure">AminoAcid</a></dt>
<dd>
<div class="block">set the name of the AA, in single letter code .</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/AminoAcidImpl.html#setAminoType(java.lang.Character)">setAminoType(Character)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/AminoAcidImpl.html" title="class in org.biojava.bio.structure">AminoAcidImpl</a></dt>
<dd>
<div class="block">set the name of the AA, in single letter code .</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/StrucAligParameters.html#setAngleDiff(int)">setAngleDiff(int)</a></span> - Method in class org.biojava.bio.structure.align.<a href="./org/biojava/bio/structure/align/StrucAligParameters.html" title="class in org.biojava.bio.structure.align">StrucAligParameters</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#setAniso_B(java.lang.String[][])">setAniso_B(String[][])</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/SimpleEmissionState.html#setAnnotation(org.biojava.bio.Annotation)">setAnnotation(Annotation)</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/SimpleEmissionState.html" title="class in org.biojava.bio.dp">SimpleEmissionState</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Chain.html#setAnnotation(org.biojava.bio.Annotation)">setAnnotation(Annotation)</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Chain.html" title="interface in org.biojava.bio.structure">Chain</a></dt>
<dd>
<div class="block">get/set the Annotation of a Chain.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/ChainImpl.html#setAnnotation(org.biojava.bio.Annotation)">setAnnotation(Annotation)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/ChainImpl.html" title="class in org.biojava.bio.structure">ChainImpl</a></dt>
<dd>
<div class="block">get/set the Annotation of a Chain.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/Term.Impl.html#setAnnotation(org.biojava.bio.Annotation)">setAnnotation(Annotation)</a></span> - Method in class org.biojava.ontology.<a href="./org/biojava/ontology/Term.Impl.html" title="class in org.biojava.ontology">Term.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/RichObjectFactory.html#setApplicationClass(java.lang.Class, java.lang.Class)">setApplicationClass(Class, Class)</a></span> - Static method in class org.biojavax.<a href="./org/biojavax/RichObjectFactory.html" title="class in org.biojavax">RichObjectFactory</a></dt>
<dd>
<div class="block">Allow application to override the default biojava class created in getObject - subclass restriction is checked in the builder.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/ArrowedFeatureRenderer.html#setArrowHeadSize(double)">setArrowHeadSize(double)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/ArrowedFeatureRenderer.html" title="class in org.biojava.bio.gui.sequence">ArrowedFeatureRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/ArrowedFeatureRenderer.html#setArrowScoop(double)">setArrowScoop(double)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/ArrowedFeatureRenderer.html" title="class in org.biojava.bio.gui.sequence">ArrowedFeatureRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/BasicFeatureRenderer.html#setArrowScoop(double)">setArrowScoop(double)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/BasicFeatureRenderer.html" title="class in org.biojava.bio.gui.sequence">BasicFeatureRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/ArrowedFeatureRenderer.html#setArrowSize(double)">setArrowSize(double)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/ArrowedFeatureRenderer.html" title="class in org.biojava.bio.gui.sequence">ArrowedFeatureRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/BasicFeatureRenderer.html#setArrowSize(double)">setArrowSize(double)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/BasicFeatureRenderer.html" title="class in org.biojava.bio.gui.sequence">BasicFeatureRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/aaindex/AAindex.html#setArticleAuthors(java.lang.String)">setArticleAuthors(String)</a></span> - Method in class org.biojava.bio.proteomics.aaindex.<a href="./org/biojava/bio/proteomics/aaindex/AAindex.html" title="class in org.biojava.bio.proteomics.aaindex">AAindex</a></dt>
<dd>
<div class="block">Sets the names of the authors which first published an article about the
AAindex entry.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/aaindex/AAindex.html#setArticleTitle(java.lang.String)">setArticleTitle(String)</a></span> - Method in class org.biojava.bio.proteomics.aaindex.<a href="./org/biojava/bio/proteomics/aaindex/AAindex.html" title="class in org.biojava.bio.proteomics.aaindex">AAindex</a></dt>
<dd>
<div class="block">Sets the title of the article which describes the AAindex entry.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/PdbxNonPolyScheme.html#setAsym_id(java.lang.String)">setAsym_id(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/PdbxNonPolyScheme.html" title="class in org.biojava.bio.structure.io.mmcif.model">PdbxNonPolyScheme</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/PdbxPolySeqScheme.html#setAsym_id(java.lang.String)">setAsym_id(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/PdbxPolySeqScheme.html" title="class in org.biojava.bio.structure.io.mmcif.model">PdbxPolySeqScheme</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Compound.html#setAtcc(java.lang.String)">setAtcc(String)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure">Compound</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Chain.html#setAtomGroups(java.util.List)">setAtomGroups(List<Group>)</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Chain.html" title="interface in org.biojava.bio.structure">Chain</a></dt>
<dd>
<div class="block">Set all groups that have been specified in the ATOM section of this chain .</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/ChainImpl.html#setAtomGroups(java.util.List)">setAtomGroups(List<Group>)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/ChainImpl.html" title="class in org.biojava.bio.structure">ChainImpl</a></dt>
<dd>
<div class="block">Set all groups that have been specified in the ATOM section of this chain .</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Group.html#setAtoms(java.util.List)">setAtoms(List<Atom>)</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Group.html" title="interface in org.biojava.bio.structure">Group</a></dt>
<dd>
<div class="block">Set the atoms of this group.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/HetatomImpl.html#setAtoms(java.util.List)">setAtoms(List<Atom>)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/HetatomImpl.html" title="class in org.biojava.bio.structure">HetatomImpl</a></dt>
<dd>
<div class="block">set the atoms of this group</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html#setAuth_asym_id(java.lang.String)">setAuth_asym_id(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html" title="class in org.biojava.bio.structure.io.mmcif.model">AtomSite</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html#setAuth_atom_id(java.lang.String)">setAuth_atom_id(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html" title="class in org.biojava.bio.structure.io.mmcif.model">AtomSite</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html#setAuth_comp_id(java.lang.String)">setAuth_comp_id(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html" title="class in org.biojava.bio.structure.io.mmcif.model">AtomSite</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/PdbxNonPolyScheme.html#setAuth_mon_id(java.lang.String)">setAuth_mon_id(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/PdbxNonPolyScheme.html" title="class in org.biojava.bio.structure.io.mmcif.model">PdbxNonPolyScheme</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/PdbxPolySeqScheme.html#setAuth_mon_id(java.lang.String)">setAuth_mon_id(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/PdbxPolySeqScheme.html" title="class in org.biojava.bio.structure.io.mmcif.model">PdbxPolySeqScheme</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html#setAuth_seq_id(java.lang.String)">setAuth_seq_id(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html" title="class in org.biojava.bio.structure.io.mmcif.model">AtomSite</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/PdbxNonPolyScheme.html#setAuth_seq_num(java.lang.String)">setAuth_seq_num(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/PdbxNonPolyScheme.html" title="class in org.biojava.bio.structure.io.mmcif.model">PdbxNonPolyScheme</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/PdbxPolySeqScheme.html#setAuth_seq_num(java.lang.String)">setAuth_seq_num(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/PdbxPolySeqScheme.html" title="class in org.biojava.bio.structure.io.mmcif.model">PdbxPolySeqScheme</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/Namespace.html#setAuthority(java.lang.String)">setAuthority(String)</a></span> - Method in interface org.biojavax.<a href="./org/biojavax/Namespace.html" title="interface in org.biojavax">Namespace</a></dt>
<dd>
<div class="block">This method sets the authority that governs the namespace.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleNamespace.html#setAuthority(java.lang.String)">setAuthority(String)</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleNamespace.html" title="class in org.biojavax">SimpleNamespace</a></dt>
<dd>
<div class="block">This method sets the authority that governs the namespace.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/JournalArticle.html#setAuthorList(java.util.List)">setAuthorList(List<Author>)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/JournalArticle.html" title="class in org.biojava.bio.structure">JournalArticle</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/MMCIFFileReader.html#setAutoFetch(boolean)">setAutoFetch(boolean)</a></span> - Method in class org.biojava.bio.structure.io.<a href="./org/biojava/bio/structure/io/MMCIFFileReader.html" title="class in org.biojava.bio.structure.io">MMCIFFileReader</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/PDBFileReader.html#setAutoFetch(boolean)">setAutoFetch(boolean)</a></span> - Method in class org.biojava.bio.structure.io.<a href="./org/biojava/bio/structure/io/PDBFileReader.html" title="class in org.biojava.bio.structure.io">PDBFileReader</a></dt>
<dd>
<div class="block">tell the parser to fetch missing PDB files from the EBI FTP server automatically.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/StructureIOFile.html#setAutoFetch(boolean)">setAutoFetch(boolean)</a></span> - Method in interface org.biojava.bio.structure.io.<a href="./org/biojava/bio/structure/io/StructureIOFile.html" title="interface in org.biojava.bio.structure.io">StructureIOFile</a></dt>
<dd>
<div class="block">Tell the parser to fetch missing PDB files from the FTP server automatically.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/server/MMCIFFileInstallation.html#setAutoFetch(boolean)">setAutoFetch(boolean)</a></span> - Method in class org.biojava.bio.structure.server.<a href="./org/biojava/bio/structure/server/MMCIFFileInstallation.html" title="class in org.biojava.bio.structure.server">MMCIFFileInstallation</a></dt>
<dd>
<div class="block">tell the parser to fetch missing mmCif files from the RCSB FTP server automatically.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/ListTools.Doublet.html#setB(java.lang.Object)">setB(Object)</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/ListTools.Doublet.html" title="class in org.biojava.utils">ListTools.Doublet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ListTools.Triplet.html#setB(java.lang.Object)">setB(Object)</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/ListTools.Triplet.html" title="class in org.biojava.utils">ListTools.Triplet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#setB_iso_max(java.lang.String)">setB_iso_max(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#setB_iso_mean(java.lang.String)">setB_iso_mean(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#setB_iso_min(java.lang.String)">setB_iso_min(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html#setB_iso_or_equiv(java.lang.String)">setB_iso_or_equiv(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html" title="class in org.biojava.bio.structure.io.mmcif.model">AtomSite</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html#setB_iso_or_equiv_esd(java.lang.String)">setB_iso_or_equiv_esd(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html" title="class in org.biojava.bio.structure.io.mmcif.model">AtomSite</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/AbstractChromatogram.html#setBaseCallAlignment(org.biojava.bio.symbol.Alignment)">setBaseCallAlignment(Alignment)</a></span> - Method in class org.biojava.bio.chromatogram.<a href="./org/biojava/bio/chromatogram/AbstractChromatogram.html" title="class in org.biojava.bio.chromatogram">AbstractChromatogram</a></dt>
<dd>
<div class="block">Provides the list of base calls.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.html#setBaseColor(org.biojava.bio.symbol.Symbol, java.awt.Color)">setBaseColor(Symbol, Color)</a></span> - Method in class org.biojava.bio.chromatogram.graphic.<a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.html" title="class in org.biojava.bio.chromatogram.graphic">ChromatogramGraphic</a></dt>
<dd>
<div class="block">Maps a color to a DNA symbol.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/AbstractBeadRenderer.html#setBeadDepth(double)">setBeadDepth(double)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/AbstractBeadRenderer.html" title="class in org.biojava.bio.gui.sequence">AbstractBeadRenderer</a></dt>
<dd>
<div class="block"><code>setBeadDepth</code> sets the depth of a single bead
produced by this renderer.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/AbstractBeadRenderer.html#setBeadDisplacement(double)">setBeadDisplacement(double)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/AbstractBeadRenderer.html" title="class in org.biojava.bio.gui.sequence">AbstractBeadRenderer</a></dt>
<dd>
<div class="block"><code>setBeadDisplacement</code> sets the displacement of
beads from the centre line of the renderer.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/AbstractBeadRenderer.html#setBeadFill(java.awt.Paint)">setBeadFill(Paint)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/AbstractBeadRenderer.html" title="class in org.biojava.bio.gui.sequence">AbstractBeadRenderer</a></dt>
<dd>
<div class="block"><code>setBeadFill</code> sets the bead fill paint.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/AbstractBeadRenderer.html#setBeadOutline(java.awt.Paint)">setBeadOutline(Paint)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/AbstractBeadRenderer.html" title="class in org.biojava.bio.gui.sequence">AbstractBeadRenderer</a></dt>
<dd>
<div class="block"><code>setBeadOutline</code> sets the bead outline paint.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/AbstractBeadRenderer.html#setBeadStroke(java.awt.Stroke)">setBeadStroke(Stroke)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/AbstractBeadRenderer.html" title="class in org.biojava.bio.gui.sequence">AbstractBeadRenderer</a></dt>
<dd>
<div class="block"><code>setBeadStroke</code> sets the bead outline stroke.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/StructRef.html#setBiol_id(java.lang.String)">setBiol_id(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/StructRef.html" title="class in org.biojava.bio.structure.io.mmcif.model">StructRef</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Compound.html#setBiologicalUnit(java.lang.String)">setBiologicalUnit(String)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure">Compound</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/AbstractChromatogram.html#setBits(int)">setBits(int)</a></span> - Method in class org.biojava.bio.chromatogram.<a href="./org/biojava/bio/chromatogram/AbstractChromatogram.html" title="class in org.biojava.bio.chromatogram">AbstractChromatogram</a></dt>
<dd>
<div class="block">Sets the number of significant bits in the trace samples.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SixFrameZiggyRenderer.html#setBlockDepth(double)">setBlockDepth(double)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SixFrameZiggyRenderer.html" title="class in org.biojava.bio.gui.sequence">SixFrameZiggyRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/ZiggyFeatureRenderer.html#setBlockDepth(double)">setBlockDepth(double)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/ZiggyFeatureRenderer.html" title="class in org.biojava.bio.gui.sequence">ZiggyFeatureRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/DistributionLogo.html#setBlockPainter(org.biojava.bio.gui.BlockPainter)">setBlockPainter(BlockPainter)</a></span> - Method in class org.biojava.bio.gui.<a href="./org/biojava/bio/gui/DistributionLogo.html" title="class in org.biojava.bio.gui">DistributionLogo</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SixFrameRenderer.html#setBlockWidth(double)">setBlockWidth(double)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SixFrameRenderer.html" title="class in org.biojava.bio.gui.sequence">SixFrameRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/stax/BooleanElementHandlerBase.html#setBooleanValue(boolean)">setBooleanValue(boolean)</a></span> - Method in class org.biojava.utils.stax.<a href="./org/biojava/utils/stax/BooleanElementHandlerBase.html" title="class in org.biojava.utils.stax">BooleanElementHandlerBase</a></dt>
<dd>
<div class="block">
Override this method to do something useful with the
boolean we collect.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/Aggregator.html#setBoundaryFinder(org.biojava.bio.program.tagvalue.BoundaryFinder)">setBoundaryFinder(BoundaryFinder)</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/Aggregator.html" title="class in org.biojava.bio.program.tagvalue">Aggregator</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/glyph/ArrowGlyph.html#setBounds(java.awt.geom.Rectangle2D.Float)">setBounds(Rectangle2D.Float)</a></span> - Method in class org.biojava.bio.gui.glyph.<a href="./org/biojava/bio/gui/glyph/ArrowGlyph.html" title="class in org.biojava.bio.gui.glyph">ArrowGlyph</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/glyph/Glyph.html#setBounds(java.awt.geom.Rectangle2D.Float)">setBounds(Rectangle2D.Float)</a></span> - Method in interface org.biojava.bio.gui.glyph.<a href="./org/biojava/bio/gui/glyph/Glyph.html" title="interface in org.biojava.bio.gui.glyph">Glyph</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/glyph/HelixGlyph.html#setBounds(java.awt.geom.Rectangle2D.Float)">setBounds(Rectangle2D.Float)</a></span> - Method in class org.biojava.bio.gui.glyph.<a href="./org/biojava/bio/gui/glyph/HelixGlyph.html" title="class in org.biojava.bio.gui.glyph">HelixGlyph</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/glyph/RectangleGlyph.html#setBounds(java.awt.geom.Rectangle2D.Float)">setBounds(Rectangle2D.Float)</a></span> - Method in class org.biojava.bio.gui.glyph.<a href="./org/biojava/bio/gui/glyph/RectangleGlyph.html" title="class in org.biojava.bio.gui.glyph">RectangleGlyph</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/glyph/TurnGlyph.html#setBounds(java.awt.geom.Rectangle2D.Float)">setBounds(Rectangle2D.Float)</a></span> - Method in class org.biojava.bio.gui.glyph.<a href="./org/biojava/bio/gui/glyph/TurnGlyph.html" title="class in org.biojava.bio.gui.glyph">TurnGlyph</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/glyph/TwoHeadedArrowGlyph.html#setBounds(java.awt.geom.Rectangle2D.Float)">setBounds(Rectangle2D.Float)</a></span> - Method in class org.biojava.bio.gui.glyph.<a href="./org/biojava/bio/gui/glyph/TwoHeadedArrowGlyph.html" title="class in org.biojava.bio.gui.glyph">TwoHeadedArrowGlyph</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/stax/ByteElementHandlerBase.html#setByteValue(byte)">setByteValue(byte)</a></span> - Method in class org.biojava.utils.stax.<a href="./org/biojava/utils/stax/ByteElementHandlerBase.html" title="class in org.biojava.utils.stax">ByteElementHandlerBase</a></dt>
<dd>
<div class="block">
Override this method to do something useful with the
byte we collect.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/SMORegressionTrainer.html#setC(double)">setC(double)</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/SMORegressionTrainer.html" title="class in org.biojava.stats.svm">SMORegressionTrainer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/SMOTrainer.html#setC(double)">setC(double)</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/SMOTrainer.html" title="class in org.biojava.stats.svm">SMOTrainer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ListTools.Triplet.html#setC(java.lang.Object)">setC(Object)</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/ListTools.Triplet.html" title="class in org.biojava.utils">ListTools.Triplet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/server/SimpleStructureServer.html#setCacheSize(int)">setCacheSize(int)</a></span> - Method in class org.biojava.bio.structure.server.<a href="./org/biojava/bio/structure/server/SimpleStructureServer.html" title="class in org.biojava.bio.structure.server">SimpleStructureServer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/server/StructureServer.html#setCacheSize(int)">setCacheSize(int)</a></span> - Method in interface org.biojava.bio.structure.server.<a href="./org/biojava/bio/structure/server/StructureServer.html" title="interface in org.biojava.bio.structure.server">StructureServer</a></dt>
<dd>
<div class="block">set how many structures should be kept in memory - for quicker access</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html#setCartn_x(java.lang.String)">setCartn_x(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html" title="class in org.biojava.bio.structure.io.mmcif.model">AtomSite</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html#setCartn_x_esd(java.lang.String)">setCartn_x_esd(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html" title="class in org.biojava.bio.structure.io.mmcif.model">AtomSite</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html#setCartn_y(java.lang.String)">setCartn_y(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html" title="class in org.biojava.bio.structure.io.mmcif.model">AtomSite</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html#setCartn_y_esd(java.lang.String)">setCartn_y_esd(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html" title="class in org.biojava.bio.structure.io.mmcif.model">AtomSite</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html#setCartn_z(java.lang.String)">setCartn_z(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html" title="class in org.biojava.bio.structure.io.mmcif.model">AtomSite</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html#setCartn_z_esd(java.lang.String)">setCartn_z_esd(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html" title="class in org.biojava.bio.structure.io.mmcif.model">AtomSite</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/Synonym.html#setCategory(java.lang.String)">setCategory(String)</a></span> - Method in class org.biojava.ontology.<a href="./org/biojava/ontology/Synonym.html" title="class in org.biojava.ontology">Synonym</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Compound.html#setCell(java.lang.String)">setCell(String)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure">Compound</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Compound.html#setCellLine(java.lang.String)">setCellLine(String)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure">Compound</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Compound.html#setCellularLocation(java.lang.String)">setCellularLocation(String)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure">Compound</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/FragmentPair.html#setCenter1(org.biojava.bio.structure.Atom)">setCenter1(Atom)</a></span> - Method in class org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/FragmentPair.html" title="class in org.biojava.bio.structure.align.pairwise">FragmentPair</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/FragmentPair.html#setCenter2(org.biojava.bio.structure.Atom)">setCenter2(Atom)</a></span> - Method in class org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/FragmentPair.html" title="class in org.biojava.bio.structure.align.pairwise">FragmentPair</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/util/SequenceMouseListener.html#setChain(org.biojava.bio.structure.Chain)">setChain(Chain)</a></span> - Method in class org.biojava.bio.structure.gui.util.<a href="./org/biojava/bio/structure/gui/util/SequenceMouseListener.html" title="class in org.biojava.bio.structure.gui.util">SequenceMouseListener</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/util/SequenceScalePanel.html#setChain(org.biojava.bio.structure.Chain)">setChain(Chain)</a></span> - Method in class org.biojava.bio.structure.gui.util.<a href="./org/biojava/bio/structure/gui/util/SequenceScalePanel.html" title="class in org.biojava.bio.structure.gui.util">SequenceScalePanel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Compound.html#setChainId(java.util.List)">setChainId(List<String>)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure">Compound</a></dt>
<dd>
<div class="block">Sets the list of chain IDs.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/DBRef.html#setChainId(java.lang.Character)">setChainId(Character)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/DBRef.html" title="class in org.biojava.bio.structure">DBRef</a></dt>
<dd>
<div class="block">The chain ID of the corresponding chain.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/SSBond.html#setChainID1(java.lang.String)">setChainID1(String)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/SSBond.html" title="class in org.biojava.bio.structure">SSBond</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/SSBond.html#setChainID2(java.lang.String)">setChainID2(String)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/SSBond.html" title="class in org.biojava.bio.structure">SSBond</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/server/FlatFileInstallation.html#setChainInfoFile(java.io.File)">setChainInfoFile(File)</a></span> - Method in class org.biojava.bio.structure.server.<a href="./org/biojava/bio/structure/server/FlatFileInstallation.html" title="class in org.biojava.bio.structure.server">FlatFileInstallation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Compound.html#setChains(java.util.List)">setChains(List<Chain>)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure">Compound</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Structure.html#setChains(java.util.List)">setChains(List<Chain>)</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Structure.html" title="interface in org.biojava.bio.structure">Structure</a></dt>
<dd>
<div class="block">set the chains of a structure, if this is a NMR structure,
this will only set model 0.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Structure.html#setChains(int, java.util.List)">setChains(int, List<Chain>)</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Structure.html" title="interface in org.biojava.bio.structure">Structure</a></dt>
<dd>
<div class="block">set the chains for a model</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/StructureImpl.html#setChains(java.util.List)">setChains(List<Chain>)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/StructureImpl.html" title="class in org.biojava.bio.structure">StructureImpl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/StructureImpl.html#setChains(int, java.util.List)">setChains(int, List<Chain>)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/StructureImpl.html" title="class in org.biojava.bio.structure">StructureImpl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/ChangeTable.html#setChanger(java.lang.Object, org.biojava.bio.program.tagvalue.ChangeTable.Changer)">setChanger(Object, ChangeTable.Changer)</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/ChangeTable.html" title="class in org.biojava.bio.program.tagvalue">ChangeTable</a></dt>
<dd>
<div class="block">Set the Changer to be used for all values of a particular tag.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/ValueChanger.html#setChangeTable(org.biojava.bio.program.tagvalue.ChangeTable)">setChangeTable(ChangeTable)</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/ValueChanger.html" title="class in org.biojava.bio.program.tagvalue">ValueChanger</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/RepeatedCharSequence.html#setCharacter(char)">setCharacter(char)</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/RepeatedCharSequence.html" title="class in org.biojava.utils">RepeatedCharSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/stax/CharElementHandlerBase.html#setCharValue(char)">setCharValue(char)</a></span> - Method in class org.biojava.utils.stax.<a href="./org/biojava/utils/stax/CharElementHandlerBase.html" title="class in org.biojava.utils.stax">CharElementHandlerBase</a></dt>
<dd>
<div class="block">
Override this method to do something useful with the
char we collect.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/taxa/WeakTaxon.html#setChildrenRaw(java.util.Set)">setChildrenRaw(Set)</a></span> - Method in class org.biojava.bio.taxa.<a href="./org/biojava/bio/taxa/WeakTaxon.html" title="class in org.biojava.bio.taxa">WeakTaxon</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.html#setChromatogram(org.biojava.bio.chromatogram.Chromatogram)">setChromatogram(Chromatogram)</a></span> - Method in class org.biojava.bio.chromatogram.graphic.<a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.html" title="class in org.biojava.bio.chromatogram.graphic">ChromatogramGraphic</a></dt>
<dd>
<div class="block">Sets the chromatogram to draw.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ga/impl/AbstractOrganism.html#setChromImpl(org.biojava.bio.symbol.SymbolList[])">setChromImpl(SymbolList[])</a></span> - Method in class org.biojavax.ga.impl.<a href="./org/biojavax/ga/impl/AbstractOrganism.html" title="class in org.biojavax.ga.impl">AbstractOrganism</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/impl/SimpleOrganism.html#setChromImpl(org.biojava.bio.symbol.SymbolList[])">setChromImpl(SymbolList[])</a></span> - Method in class org.biojavax.ga.impl.<a href="./org/biojavax/ga/impl/SimpleOrganism.html" title="class in org.biojavax.ga.impl">SimpleOrganism</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEMapLocation.html#setChromosome(java.lang.String)">setChromosome(String)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEMapLocation.html" title="class in org.biojava.bio.seq.io.agave">AGAVEMapLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/impl/AbstractOrganism.html#setChromosomes(org.biojava.bio.symbol.SymbolList[])">setChromosomes(SymbolList[])</a></span> - Method in class org.biojavax.ga.impl.<a href="./org/biojavax/ga/impl/AbstractOrganism.html" title="class in org.biojavax.ga.impl">AbstractOrganism</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/Organism.html#setChromosomes(org.biojava.bio.symbol.SymbolList[])">setChromosomes(SymbolList[])</a></span> - Method in interface org.biojavax.ga.<a href="./org/biojavax/ga/Organism.html" title="interface in org.biojavax.ga">Organism</a></dt>
<dd>
<div class="block">Sets the organisms 'chromosome' sequences.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/DebuggingRichSeqIOListener.html#setCircular(boolean)">setCircular(boolean)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/DebuggingRichSeqIOListener.html" title="class in org.biojavax.bio.seq.io">DebuggingRichSeqIOListener</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/RichSeqIOAdapter.html#setCircular(boolean)">setCircular(boolean)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/RichSeqIOAdapter.html" title="class in org.biojavax.bio.seq.io">RichSeqIOAdapter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/RichSeqIOListener.html#setCircular(boolean)">setCircular(boolean)</a></span> - Method in interface org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/RichSeqIOListener.html" title="interface in org.biojavax.bio.seq.io">RichSeqIOListener</a></dt>
<dd>
<div class="block">Defined this sequence being parser as circular.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/SimpleRichSequenceBuilder.html#setCircular(boolean)">setCircular(boolean)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/SimpleRichSequenceBuilder.html" title="class in org.biojavax.bio.seq.io">SimpleRichSequenceBuilder</a></dt>
<dd>
<div class="block">Defined this sequence being parser as circular.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.html#setCircular(boolean)">setCircular(boolean)</a></span> - Method in interface org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.html" title="interface in org.biojavax.bio.seq">RichSequence</a></dt>
<dd>
<div class="block">Circularises the <code>Sequence</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/ThinRichSequence.html#setCircular(boolean)">setCircular(boolean)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/ThinRichSequence.html" title="class in org.biojavax.bio.seq">ThinRichSequence</a></dt>
<dd>
<div class="block">Circularises the <code>Sequence</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/CompoundRichLocation.html#setCircularLength(int)">setCircularLength(int)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/CompoundRichLocation.html" title="class in org.biojavax.bio.seq">CompoundRichLocation</a></dt>
<dd>
<div class="block">Sets the circular length of this location.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/EmptyRichLocation.html#setCircularLength(int)">setCircularLength(int)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/EmptyRichLocation.html" title="class in org.biojavax.bio.seq">EmptyRichLocation</a></dt>
<dd>
<div class="block">Sets the circular length of this location.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/MultiSourceCompoundRichLocation.html#setCircularLength(int)">setCircularLength(int)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/MultiSourceCompoundRichLocation.html" title="class in org.biojavax.bio.seq">MultiSourceCompoundRichLocation</a></dt>
<dd>
<div class="block">Sets the circular length of this location.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichLocation.html#setCircularLength(int)">setCircularLength(int)</a></span> - Method in interface org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichLocation.html" title="interface in org.biojavax.bio.seq">RichLocation</a></dt>
<dd>
<div class="block">Sets the circular length of this location.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichLocation.html#setCircularLength(int)">setCircularLength(int)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichLocation.html" title="class in org.biojavax.bio.seq">SimpleRichLocation</a></dt>
<dd>
<div class="block">Sets the circular length of this location.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/PDBHeader.html#setClassification(java.lang.String)">setClassification(String)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/PDBHeader.html" title="class in org.biojava.bio.structure">PDBHeader</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/AlternativeAlignment.html#setCluster(int)">setCluster(int)</a></span> - Method in class org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/AlternativeAlignment.html" title="class in org.biojava.bio.structure.align.pairwise">AlternativeAlignment</a></dt>
<dd>
<div class="block">set the number of the cluster this alignment belongs to.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/FragmentPair.html#setCluster(int)">setCluster(int)</a></span> - Method in class org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/FragmentPair.html" title="class in org.biojava.bio.structure.align.pairwise">FragmentPair</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/helper/IndexPair.html#setCol(short)">setCol(short)</a></span> - Method in class org.biojava.bio.structure.align.helper.<a href="./org/biojava/bio/structure/align/helper/IndexPair.html" title="class in org.biojava.bio.structure.align.helper">IndexPair</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/FeatureBlockSequenceRenderer.html#setCollapsing(boolean)">setCollapsing(boolean)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/FeatureBlockSequenceRenderer.html" title="class in org.biojava.bio.gui.sequence">FeatureBlockSequenceRenderer</a></dt>
<dd>
<div class="block">Specifies if the renderer should collapse to zero depth when no
features are visible (default <code>true</code>).</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/process/ExternalProcess.html#setCommands(java.lang.String)">setCommands(String)</a></span> - Method in class org.biojava.utils.process.<a href="./org/biojava/utils/process/ExternalProcess.html" title="class in org.biojava.utils.process">ExternalProcess</a></dt>
<dd>
<div class="block">Sets the command line including the path or name of the external program
and its command line arguments.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/AnnotationType.Impl.html#setComment(java.lang.String)">setComment(String)</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/AnnotationType.Impl.html" title="class in org.biojava.bio">AnnotationType.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/AnnotationType.Impl.html#setComment(java.lang.Object, java.lang.String)">setComment(Object, String)</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/AnnotationType.Impl.html" title="class in org.biojava.bio">AnnotationType.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/AnnotationType.html#setComment(java.lang.String)">setComment(String)</a></span> - Method in interface org.biojava.bio.<a href="./org/biojava/bio/AnnotationType.html" title="interface in org.biojava.bio">AnnotationType</a></dt>
<dd>
<div class="block">Set the comment for the whole AnnotationType.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/AnnotationType.html#setComment(java.lang.Object, java.lang.String)">setComment(Object, String)</a></span> - Method in interface org.biojava.bio.<a href="./org/biojava/bio/AnnotationType.html" title="interface in org.biojava.bio">AnnotationType</a></dt>
<dd>
<div class="block">Set the comment for a particular property.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/SimpleGFFRecord.html#setComment(java.lang.String)">setComment(String)</a></span> - Method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/SimpleGFFRecord.html" title="class in org.biojava.bio.program.gff">SimpleGFFRecord</a></dt>
<dd>
<div class="block">Set the comment to <span class="arg">comment</source>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/aaindex/AAindex.html#setComment(java.lang.String)">setComment(String)</a></span> - Method in class org.biojava.bio.proteomics.aaindex.<a href="./org/biojava/bio/proteomics/aaindex/AAindex.html" title="class in org.biojava.bio.proteomics.aaindex">AAindex</a></dt>
<dd>
<div class="block">Sets the user comment for the AAindex entry.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/DebuggingRichSeqIOListener.html#setComment(java.lang.String)">setComment(String)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/DebuggingRichSeqIOListener.html" title="class in org.biojavax.bio.seq.io">DebuggingRichSeqIOListener</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/RichSeqIOAdapter.html#setComment(java.lang.String)">setComment(String)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/RichSeqIOAdapter.html" title="class in org.biojavax.bio.seq.io">RichSeqIOAdapter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/RichSeqIOListener.html#setComment(java.lang.String)">setComment(String)</a></span> - Method in interface org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/RichSeqIOListener.html" title="interface in org.biojavax.bio.seq.io">RichSeqIOListener</a></dt>
<dd>
<div class="block">Call back method so the event emitter can tell the listener
about a comment in the record being read.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/SimpleRichSequenceBuilder.html#setComment(java.lang.String)">setComment(String)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/SimpleRichSequenceBuilder.html" title="class in org.biojavax.bio.seq.io">SimpleRichSequenceBuilder</a></dt>
<dd>
<div class="block">Call back method so the event emitter can tell the listener
about a comment in the record being read.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtCommentParser.Event.html#setComment(java.lang.String)">setComment(String)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtCommentParser.Event.html" title="class in org.biojavax.bio.seq.io">UniProtCommentParser.Event</a></dt>
<dd>
<div class="block">Setter for property comment.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleComment.html#setComment(java.lang.String)">setComment(String)</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleComment.html" title="class in org.biojavax">SimpleComment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html#setCommentType(java.lang.String)">setCommentType(String)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html" title="class in org.biojavax.bio.seq.io">UniProtCommentParser</a></dt>
<dd>
<div class="block">Setter for property commentType.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/biosql/TaxonSQL.html#setCommonName(java.sql.Connection, org.biojava.bio.taxa.Taxon, java.lang.String)">setCommonName(Connection, Taxon, String)</a></span> - Static method in class org.biojava.bio.seq.db.biosql.<a href="./org/biojava/bio/seq/db/biosql/TaxonSQL.html" title="class in org.biojava.bio.seq.db.biosql">TaxonSQL</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">With this method the common name of the given taxon can be changed or created,
if there was none before.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/taxa/AbstractTaxon.html#setCommonName(java.lang.String)">setCommonName(String)</a></span> - Method in class org.biojava.bio.taxa.<a href="./org/biojava/bio/taxa/AbstractTaxon.html" title="class in org.biojava.bio.taxa">AbstractTaxon</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/taxa/Taxon.html#setCommonName(java.lang.String)">setCommonName(String)</a></span> - Method in interface org.biojava.bio.taxa.<a href="./org/biojava/bio/taxa/Taxon.html" title="interface in org.biojava.bio.taxa">Taxon</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Set the new common name of this Taxon.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/PdbxEntityNonPoly.html#setComp_id(java.lang.String)">setComp_id(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/PdbxEntityNonPoly.html" title="class in org.biojava.bio.structure.io.mmcif.model">PdbxEntityNonPoly</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Structure.html#setCompounds(java.util.List)">setCompounds(List<Compound>)</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Structure.html" title="interface in org.biojava.bio.structure">Structure</a></dt>
<dd>
<div class="block">set the compounts</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/StructureImpl.html#setCompounds(java.util.List)">setCompounds(List<Compound>)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/StructureImpl.html" title="class in org.biojava.bio.structure">StructureImpl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Structure.html#setConnections(java.util.List)">setConnections(List<Map<String, Integer>>)</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Structure.html" title="interface in org.biojava.bio.structure">Structure</a></dt>
<dd>
<div class="block">sets/gets an List of Maps which corresponds to the CONECT lines in the PDB file:</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/StructureImpl.html#setConnections(java.util.List)">setConnections(List<Map<String, Integer>>)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/StructureImpl.html" title="class in org.biojava.bio.structure">StructureImpl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/PolynomialKernel.html#setConstant(double)">setConstant(double)</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/PolynomialKernel.html" title="class in org.biojava.stats.svm">PolynomialKernel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/SigmoidKernel.html#setConstant(double)">setConstant(double)</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/SigmoidKernel.html" title="class in org.biojava.stats.svm">SigmoidKernel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/AnnotationType.Impl.html#setConstraint(java.lang.Object, org.biojava.bio.CollectionConstraint)">setConstraint(Object, CollectionConstraint)</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/AnnotationType.Impl.html" title="class in org.biojava.bio">AnnotationType.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/AnnotationType.html#setConstraint(java.lang.Object, org.biojava.bio.CollectionConstraint)">setConstraint(Object, CollectionConstraint)</a></span> - Method in interface org.biojava.bio.<a href="./org/biojava/bio/AnnotationType.html" title="interface in org.biojava.bio">AnnotationType</a></dt>
<dd>
<div class="block">Specifies the constraint to apply to the specified property.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/AnnotationType.Abstract.html#setConstraints(java.lang.Object, org.biojava.bio.PropertyConstraint, org.biojava.bio.symbol.Location)">setConstraints(Object, PropertyConstraint, Location)</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/AnnotationType.Abstract.html" title="class in org.biojava.bio">AnnotationType.Abstract</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/AnnotationType.html#setConstraints(java.lang.Object, org.biojava.bio.PropertyConstraint, org.biojava.bio.symbol.Location)">setConstraints(Object, PropertyConstraint, Location)</a></span> - Method in interface org.biojava.bio.<a href="./org/biojava/bio/AnnotationType.html" title="interface in org.biojava.bio">AnnotationType</a></dt>
<dd>
<div class="block">Set the constraints associated with a property.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/FragmentPair.html#setContacts(int)">setContacts(int)</a></span> - Method in class org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/FragmentPair.html" title="class in org.biojava.bio.structure.align.pairwise">FragmentPair</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/sax/blastxml/BlastXMLParser.html#setContentHandler(org.xml.sax.ContentHandler)">setContentHandler(ContentHandler)</a></span> - Method in class org.biojava.bio.program.sax.blastxml.<a href="./org/biojava/bio/program/sax/blastxml/BlastXMLParser.html" title="class in org.biojava.bio.program.sax.blastxml">BlastXMLParser</a></dt>
<dd>
<div class="block">sets the ContentHandler for this object</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/sax/blastxml/BlastXMLParserFacade.html#setContentHandler(org.xml.sax.ContentHandler)">setContentHandler(ContentHandler)</a></span> - Method in class org.biojava.bio.program.sax.blastxml.<a href="./org/biojava/bio/program/sax/blastxml/BlastXMLParserFacade.html" title="class in org.biojava.bio.program.sax.blastxml">BlastXMLParserFacade</a></dt>
<dd>
<div class="block">this sets the ContentHandler that receives
SAX events from the internal Blast XML parser which
is the actual ContentHandler.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/helper/AligMatEl.html#setContig(int)">setContig(int)</a></span> - Method in class org.biojava.bio.structure.align.helper.<a href="./org/biojava/bio/structure/align/helper/AligMatEl.html" title="class in org.biojava.bio.structure.align.helper">AligMatEl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/LineSplitParser.html#setContinueOnEmptyTag(boolean)">setContinueOnEmptyTag(boolean)</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/LineSplitParser.html" title="class in org.biojava.bio.program.tagvalue">LineSplitParser</a></dt>
<dd>
<div class="block">Choose whether to treat empty tags as a continuation of previous tags or as a
new tag with the value of the empty string.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/RegexParser.html#setContinueOnEmptyTag(boolean)">setContinueOnEmptyTag(boolean)</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/RegexParser.html" title="class in org.biojava.bio.program.tagvalue">RegexParser</a></dt>
<dd>
<div class="block">Decide whether to treat empty tags as continuations of the previous non
-empty tag.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Atom.html#setCoords(double[])">setCoords(double[])</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Atom.html" title="interface in org.biojava.bio.structure">Atom</a></dt>
<dd>
<div class="block">set the coordinates.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/AtomImpl.html#setCoords(double[])">setCoords(double[])</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/AtomImpl.html" title="class in org.biojava.bio.structure">AtomImpl</a></dt>
<dd>
<div class="block">the coordinates.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#setCorrelation_coeff_Fo_to_Fc(java.lang.String)">setCorrelation_coeff_Fo_to_Fc(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#setCorrelation_coeff_Fo_to_Fc_free(java.lang.String)">setCorrelation_coeff_Fo_to_Fc_free(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/Count.html#setCount(org.biojava.bio.symbol.AtomicSymbol, double)">setCount(AtomicSymbol, double)</a></span> - Method in interface org.biojava.bio.dist.<a href="./org/biojava/bio/dist/Count.html" title="interface in org.biojava.bio.dist">Count</a></dt>
<dd>
<div class="block">Set the count for the Symbol s.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/IndexedCount.html#setCount(org.biojava.bio.symbol.AtomicSymbol, double)">setCount(AtomicSymbol, double)</a></span> - Method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/IndexedCount.html" title="class in org.biojava.bio.dist">IndexedCount</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/Count.html#setCounts(org.biojava.bio.dist.Count)">setCounts(Count)</a></span> - Method in interface org.biojava.bio.dist.<a href="./org/biojava/bio/dist/Count.html" title="interface in org.biojava.bio.dist">Count</a></dt>
<dd>
<div class="block">Set the counts in this Counts to be equal to the counts in c.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/IndexedCount.html#setCounts(org.biojava.bio.dist.Count)">setCounts(Count)</a></span> - Method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/IndexedCount.html" title="class in org.biojava.bio.dist">IndexedCount</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/FragmentPair.html#setCovered(int)">setCovered(int)</a></span> - Method in class org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/FragmentPair.html" title="class in org.biojava.bio.structure.align.pairwise">FragmentPair</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/StrucAligParameters.html#setCreate_co(float)">setCreate_co(float)</a></span> - Method in class org.biojava.bio.structure.align.<a href="./org/biojava/bio/structure/align/StrucAligParameters.html" title="class in org.biojava.bio.structure.align">StrucAligParameters</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleGappedSequence.html#setCreateOnUnderlyingSequence(boolean)">setCreateOnUnderlyingSequence(boolean)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleGappedSequence.html" title="class in org.biojava.bio.seq.impl">SimpleGappedSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/GeneticAlgorithm.html#setCrossOverFunction(org.biojavax.ga.functions.CrossOverFunction)">setCrossOverFunction(CrossOverFunction)</a></span> - Method in interface org.biojavax.ga.<a href="./org/biojavax/ga/GeneticAlgorithm.html" title="interface in org.biojavax.ga">GeneticAlgorithm</a></dt>
<dd>
<div class="block">Changes the <code>CrossOverFunction</code> used to CrossOver Chromosomes</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ga/impl/AbstractGeneticAlgorithm.html#setCrossOverFunction(org.biojavax.ga.functions.CrossOverFunction)">setCrossOverFunction(CrossOverFunction)</a></span> - Method in class org.biojavax.ga.impl.<a href="./org/biojavax/ga/impl/AbstractGeneticAlgorithm.html" title="class in org.biojavax.ga.impl">AbstractGeneticAlgorithm</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/functions/AbstractCrossOverFunction.html#setCrossOverProbs(double[])">setCrossOverProbs(double[])</a></span> - Method in class org.biojavax.ga.functions.<a href="./org/biojavax/ga/functions/AbstractCrossOverFunction.html" title="class in org.biojavax.ga.functions">AbstractCrossOverFunction</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/functions/CrossOverFunction.NoCross.html#setCrossOverProbs(double[])">setCrossOverProbs(double[])</a></span> - Method in class org.biojavax.ga.functions.<a href="./org/biojavax/ga/functions/CrossOverFunction.NoCross.html" title="class in org.biojavax.ga.functions">CrossOverFunction.NoCross</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/functions/CrossOverFunction.html#setCrossOverProbs(double[])">setCrossOverProbs(double[])</a></span> - Method in interface org.biojavax.ga.functions.<a href="./org/biojavax/ga/functions/CrossOverFunction.html" title="interface in org.biojavax.ga.functions">CrossOverFunction</a></dt>
<dd>
<div class="block">Sets the probability of crossing at each base.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichLocation.html#setCrossRef(org.biojavax.CrossRef)">setCrossRef(CrossRef)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichLocation.html" title="class in org.biojavax.bio.seq">SimpleRichLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/DocRef.html#setCrossref(org.biojavax.CrossRef)">setCrossref(CrossRef)</a></span> - Method in interface org.biojavax.<a href="./org/biojavax/DocRef.html" title="interface in org.biojavax">DocRef</a></dt>
<dd>
<div class="block">The document reference may refer to an object in another database.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleDocRef.html#setCrossref(org.biojavax.CrossRef)">setCrossref(CrossRef)</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleDocRef.html" title="class in org.biojavax">SimpleDocRef</a></dt>
<dd>
<div class="block">The document reference may refer to an object in another database.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/CompoundRichLocation.html#setCrossRefResolver(org.biojavax.CrossReferenceResolver)">setCrossRefResolver(CrossReferenceResolver)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/CompoundRichLocation.html" title="class in org.biojavax.bio.seq">CompoundRichLocation</a></dt>
<dd>
<div class="block">Sets the cross ref resolver to use when retrieving remote symbols.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/EmptyRichLocation.html#setCrossRefResolver(org.biojavax.CrossReferenceResolver)">setCrossRefResolver(CrossReferenceResolver)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/EmptyRichLocation.html" title="class in org.biojavax.bio.seq">EmptyRichLocation</a></dt>
<dd>
<div class="block">Sets the cross ref resolver to use when retrieving remote symbols.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichLocation.html#setCrossRefResolver(org.biojavax.CrossReferenceResolver)">setCrossRefResolver(CrossReferenceResolver)</a></span> - Method in interface org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichLocation.html" title="interface in org.biojavax.bio.seq">RichLocation</a></dt>
<dd>
<div class="block">Sets the cross ref resolver to use when retrieving remote symbols.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichLocation.html#setCrossRefResolver(org.biojavax.CrossReferenceResolver)">setCrossRefResolver(CrossReferenceResolver)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichLocation.html" title="class in org.biojavax.bio.seq">SimpleRichLocation</a></dt>
<dd>
<div class="block">Sets the cross ref resolver to use when retrieving remote symbols.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Exptl.html#setCrystals_number(java.lang.String)">setCrystals_number(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Exptl.html" title="class in org.biojava.bio.structure.io.mmcif.model">Exptl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/phylo/io/phylip/PHYLIPFileBuilder.html#setCurrentSequenceName(java.lang.String)">setCurrentSequenceName(String)</a></span> - Method in class org.biojavax.bio.phylo.io.phylip.<a href="./org/biojavax/bio/phylo/io/phylip/PHYLIPFileBuilder.html" title="class in org.biojavax.bio.phylo.io.phylip">PHYLIPFileBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/phylo/io/phylip/PHYLIPFileListener.html#setCurrentSequenceName(java.lang.String)">setCurrentSequenceName(String)</a></span> - Method in interface org.biojavax.bio.phylo.io.phylip.<a href="./org/biojavax/bio/phylo/io/phylip/PHYLIPFileListener.html" title="interface in org.biojavax.bio.phylo.io.phylip">PHYLIPFileListener</a></dt>
<dd>
<div class="block">Set the name of the sequence which is about to be received.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/NCBISequenceDB.html#setDatabase(java.lang.String)">setDatabase(String)</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/NCBISequenceDB.html" title="class in org.biojava.bio.seq.db">NCBISequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/DBRef.html#setDatabase(java.lang.String)">setDatabase(String)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/DBRef.html" title="class in org.biojava.bio.structure">DBRef</a></dt>
<dd>
<div class="block">Specifies the database value.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/sax/FastaSearchSAXParser.html#setDatabaseID(java.lang.String)">setDatabaseID(String)</a></span> - Method in class org.biojava.bio.program.sax.<a href="./org/biojava/bio/program/sax/FastaSearchSAXParser.html" title="class in org.biojava.bio.program.sax">FastaSearchSAXParser</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/BlastLikeSearchBuilder.html#setDatabaseID(java.lang.String)">setDatabaseID(String)</a></span> - Method in class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/BlastLikeSearchBuilder.html" title="class in org.biojava.bio.program.ssbind">BlastLikeSearchBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/ViewSequenceFactory.html#setDatabaseID(java.lang.String)">setDatabaseID(String)</a></span> - Method in class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/ViewSequenceFactory.html" title="class in org.biojava.bio.program.ssbind">ViewSequenceFactory</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/FilteringContentHandler.html#setDatabaseID(java.lang.String)">setDatabaseID(String)</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/FilteringContentHandler.html" title="class in org.biojava.bio.search">FilteringContentHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SearchContentAdapter.html#setDatabaseID(java.lang.String)">setDatabaseID(String)</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SearchContentAdapter.html" title="class in org.biojava.bio.search">SearchContentAdapter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SearchContentFilter.html#setDatabaseID(java.lang.String)">setDatabaseID(String)</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SearchContentFilter.html" title="class in org.biojava.bio.search">SearchContentFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SearchContentHandler.html#setDatabaseID(java.lang.String)">setDatabaseID(String)</a></span> - Method in interface org.biojava.bio.search.<a href="./org/biojava/bio/search/SearchContentHandler.html" title="interface in org.biojava.bio.search">SearchContentHandler</a></dt>
<dd>
<div class="block"><code>setDatabaseID</code> identifies the database searched by
a name, ID or URN.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SearchContentHandlerDebugger.html#setDatabaseID(java.lang.String)">setDatabaseID(String)</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SearchContentHandlerDebugger.html" title="class in org.biojava.bio.search">SearchContentHandlerDebugger</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html#setDatabaseName(java.lang.String)">setDatabaseName(String)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html" title="class in org.biojavax.bio.seq.io">UniProtCommentParser</a></dt>
<dd>
<div class="block">Setter for property databaseName.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/DatabasePDBrev.html#setDate(java.lang.String)">setDate(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/DatabasePDBrev.html" title="class in org.biojava.bio.structure.io.mmcif.model">DatabasePDBrev</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/DatabasePDBrev.html#setDate_original(java.lang.String)">setDate_original(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/DatabasePDBrev.html" title="class in org.biojava.bio.structure.io.mmcif.model">DatabasePDBrev</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/StructRefSeq.html#setDb_align_beg(java.lang.String)">setDb_align_beg(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/StructRefSeq.html" title="class in org.biojava.bio.structure.io.mmcif.model">StructRefSeq</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/StructRefSeq.html#setDb_align_end(java.lang.String)">setDb_align_end(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/StructRefSeq.html" title="class in org.biojava.bio.structure.io.mmcif.model">StructRefSeq</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/StructRef.html#setDb_code(java.lang.String)">setDb_code(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/StructRef.html" title="class in org.biojava.bio.structure.io.mmcif.model">StructRef</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/StructRef.html#setDb_name(java.lang.String)">setDb_name(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/StructRef.html" title="class in org.biojava.bio.structure.io.mmcif.model">StructRef</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/DBRef.html#setDbAccession(java.lang.String)">setDbAccession(String)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/DBRef.html" title="class in org.biojava.bio.structure">DBRef</a></dt>
<dd>
<div class="block">Sequence database accession code.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEDbId.html#setDbCode(java.lang.String)">setDbCode(String)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEDbId.html" title="class in org.biojava.bio.seq.io.agave">AGAVEDbId</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/PDBMSDReader.html#setDBConnection(java.lang.String, java.lang.String, java.lang.String, java.lang.String)">setDBConnection(String, String, String, String)</a></span> - Method in class org.biojava.bio.structure.io.<a href="./org/biojava/bio/structure/io/PDBMSDReader.html" title="class in org.biojava.bio.structure.io">PDBMSDReader</a></dt>
<dd>
<div class="block">open a database conenction to the MSD search database</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEMatchRegion.html#setDbId(org.biojava.bio.seq.io.agave.AGAVEDbId)">setDbId(AGAVEDbId)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEMatchRegion.html" title="class in org.biojava.bio.seq.io.agave">AGAVEMatchRegion</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEQueryRegion.html#setDbId(org.biojava.bio.seq.io.agave.AGAVEDbId)">setDbId(AGAVEDbId)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEQueryRegion.html" title="class in org.biojava.bio.seq.io.agave">AGAVEQueryRegion</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEXref.html#setDbId(org.biojava.bio.seq.io.agave.AGAVEDbId)">setDbId(AGAVEDbId)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEXref.html" title="class in org.biojava.bio.seq.io.agave">AGAVEXref</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/DBRef.html#setDbIdCode(java.lang.String)">setDbIdCode(String)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/DBRef.html" title="class in org.biojava.bio.structure">DBRef</a></dt>
<dd>
<div class="block">Sequence database identification code.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Structure.html#setDBRefs(java.util.List)">setDBRefs(List<DBRef>)</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Structure.html" title="interface in org.biojava.bio.structure">Structure</a></dt>
<dd>
<div class="block">set the list of database references for this structure</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/StructureImpl.html#setDBRefs(java.util.List)">setDBRefs(List<DBRef>)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/StructureImpl.html" title="class in org.biojava.bio.structure">StructureImpl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/DBRef.html#setDbSeqBegin(int)">setDbSeqBegin(int)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/DBRef.html" title="class in org.biojava.bio.structure">DBRef</a></dt>
<dd>
<div class="block">Initial sequence number of the
database seqment.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/DBRef.html#setDbSeqEnd(int)">setDbSeqEnd(int)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/DBRef.html" title="class in org.biojava.bio.structure">DBRef</a></dt>
<dd>
<div class="block">The begin of the sequence position in the database</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/StructurePairAligner.html#setDebug(boolean)">setDebug(boolean)</a></span> - Method in class org.biojava.bio.structure.align.<a href="./org/biojava/bio/structure/align/StructurePairAligner.html" title="class in org.biojava.bio.structure.align">StructurePairAligner</a></dt>
<dd>
<div class="block">set the debug flag</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/SeqRes2AtomAligner.html#setDEBUG(boolean)">setDEBUG(boolean)</a></span> - Method in class org.biojava.bio.structure.io.<a href="./org/biojava/bio/structure/io/SeqRes2AtomAligner.html" title="class in org.biojava.bio.structure.io">SeqRes2AtomAligner</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/ValueChanger.html#setDefaultChanger(org.biojava.bio.program.tagvalue.ChangeTable.Changer)">setDefaultChanger(ChangeTable.Changer)</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/ValueChanger.html" title="class in org.biojava.bio.program.tagvalue">ValueChanger</a></dt>
<dd>
<div class="block">The changer that will be applied to the values of tags not registered
explicitly to any changer or splitter instance.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/AnnotationType.Impl.html#setDefaultConstraint(org.biojava.bio.CollectionConstraint)">setDefaultConstraint(CollectionConstraint)</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/AnnotationType.Impl.html" title="class in org.biojava.bio">AnnotationType.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/AnnotationType.html#setDefaultConstraint(org.biojava.bio.CollectionConstraint)">setDefaultConstraint(CollectionConstraint)</a></span> - Method in interface org.biojava.bio.<a href="./org/biojava/bio/AnnotationType.html" title="interface in org.biojava.bio">AnnotationType</a></dt>
<dd>
<div class="block">Specifies the default constraint to apply to properties where no
other constraint is specified.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/AnnotationType.Abstract.html#setDefaultConstraints(org.biojava.bio.PropertyConstraint, org.biojava.bio.symbol.Location)">setDefaultConstraints(PropertyConstraint, Location)</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/AnnotationType.Abstract.html" title="class in org.biojava.bio">AnnotationType.Abstract</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/AnnotationType.html#setDefaultConstraints(org.biojava.bio.PropertyConstraint, org.biojava.bio.symbol.Location)">setDefaultConstraints(PropertyConstraint, Location)</a></span> - Method in interface org.biojava.bio.<a href="./org/biojava/bio/AnnotationType.html" title="interface in org.biojava.bio">AnnotationType</a></dt>
<dd>
<div class="block">Set the constraints that will apply to all properties without an
explicitly defined set of constraints.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/RichObjectFactory.html#setDefaultCrossReferenceResolver(org.biojavax.CrossReferenceResolver)">setDefaultCrossReferenceResolver(CrossReferenceResolver)</a></span> - Static method in class org.biojavax.<a href="./org/biojavax/RichObjectFactory.html" title="class in org.biojavax">RichObjectFactory</a></dt>
<dd>
<div class="block">Sets the default crossref resolver to use when resolving remote entries.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/RichObjectFactory.html#setDefaultNamespaceName(java.lang.String)">setDefaultNamespaceName(String)</a></span> - Static method in class org.biojavax.<a href="./org/biojavax/RichObjectFactory.html" title="class in org.biojavax">RichObjectFactory</a></dt>
<dd>
<div class="block">Sets the default namespace name to use when loading sequences.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/RichObjectFactory.html#setDefaultOntologyName(java.lang.String)">setDefaultOntologyName(String)</a></span> - Static method in class org.biojavax.<a href="./org/biojavax/RichObjectFactory.html" title="class in org.biojavax">RichObjectFactory</a></dt>
<dd>
<div class="block">Sets the default ontology name to use when loading sequences.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PeptideDigestRenderer.html#setDefaultPaint(java.awt.Paint)">setDefaultPaint(Paint)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PeptideDigestRenderer.html" title="class in org.biojava.bio.gui.sequence">PeptideDigestRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/RichObjectFactory.html#setDefaultPositionResolver(org.biojavax.bio.seq.PositionResolver)">setDefaultPositionResolver(PositionResolver)</a></span> - Static method in class org.biojavax.<a href="./org/biojavax/RichObjectFactory.html" title="class in org.biojavax">RichObjectFactory</a></dt>
<dd>
<div class="block">Sets the default position resolver to use when creating new rich feature locations.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/RichObjectFactory.html#setDefaultRichSequenceHandler(org.biojavax.bio.seq.RichSequenceHandler)">setDefaultRichSequenceHandler(RichSequenceHandler)</a></span> - Static method in class org.biojavax.<a href="./org/biojavax/RichObjectFactory.html" title="class in org.biojavax">RichObjectFactory</a></dt>
<dd>
<div class="block">Sets the default sequence handler to use when performing sequence manipulation.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/ValueChanger.html#setDefaultSplitter(org.biojava.bio.program.tagvalue.ChangeTable.Splitter)">setDefaultSplitter(ChangeTable.Splitter)</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/ValueChanger.html" title="class in org.biojava.bio.program.tagvalue">ValueChanger</a></dt>
<dd>
<div class="block">The splitter that will be applied to the values of tags not registered
explicitly to any changer or splitter instance.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/StateMachine.BasicState.html#setDefaultTransitions(org.biojava.bio.program.tagvalue.StateMachine.TransitionTable)">setDefaultTransitions(StateMachine.TransitionTable)</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/StateMachine.BasicState.html" title="class in org.biojava.bio.program.tagvalue">StateMachine.BasicState</a></dt>
<dd>
<div class="block">specify fallback TransitionTable for this State</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/AbstractWrapper.html#setDelegate(org.biojava.bio.program.tagvalue.TagValueListener)">setDelegate(TagValueListener)</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/AbstractWrapper.html" title="class in org.biojava.bio.program.tagvalue">AbstractWrapper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/SimpleTagValueWrapper.html#setDelegate(org.biojava.bio.program.tagvalue.TagValueListener)">setDelegate(TagValueListener)</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/SimpleTagValueWrapper.html" title="class in org.biojava.bio.program.tagvalue">SimpleTagValueWrapper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/StateMachine.html#setDelegate(org.biojava.bio.program.tagvalue.TagValueListener)">setDelegate(TagValueListener)</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/StateMachine.html" title="class in org.biojava.bio.program.tagvalue">StateMachine</a></dt>
<dd>
<div class="block">TagValueWrapper interface</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/TagValueWrapper.html#setDelegate(org.biojava.bio.program.tagvalue.TagValueListener)">setDelegate(TagValueListener)</a></span> - Method in interface org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/TagValueWrapper.html" title="interface in org.biojava.bio.program.tagvalue">TagValueWrapper</a></dt>
<dd>
<div class="block">set listener to which all calls will be delegated</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/TagDelegator.html#setDelegateParser(org.biojava.bio.program.tagvalue.TagValueParser)">setDelegateParser(TagValueParser)</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/TagDelegator.html" title="class in org.biojava.bio.program.tagvalue">TagDelegator</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/AbstractBeadRenderer.html#setDelegateRenderer(org.biojava.bio.seq.OptimizableFilter, org.biojava.bio.gui.sequence.BeadFeatureRenderer)">setDelegateRenderer(OptimizableFilter, BeadFeatureRenderer)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/AbstractBeadRenderer.html" title="class in org.biojava.bio.gui.sequence">AbstractBeadRenderer</a></dt>
<dd>
<div class="block"><code>setDelegateRenderer</code> associates an
<code>OptimizableFilter</code> with a
<code>BeadFeatureRenderer</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/BeadFeatureRenderer.html#setDelegateRenderer(org.biojava.bio.seq.OptimizableFilter, org.biojava.bio.gui.sequence.BeadFeatureRenderer)">setDelegateRenderer(OptimizableFilter, BeadFeatureRenderer)</a></span> - Method in interface org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/BeadFeatureRenderer.html" title="interface in org.biojava.bio.gui.sequence">BeadFeatureRenderer</a></dt>
<dd>
<div class="block"><code>setDelegateRenderer</code> associates an
<code>OptimizableFilter</code> with a
<code>BeadFeatureRenderer</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/RectangularImapRenderer.html#setDelegateRenderer(org.biojava.bio.seq.OptimizableFilter, org.biojava.bio.gui.sequence.BeadFeatureRenderer)">setDelegateRenderer(OptimizableFilter, BeadFeatureRenderer)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/RectangularImapRenderer.html" title="class in org.biojava.bio.gui.sequence">RectangularImapRenderer</a></dt>
<dd>
<div class="block"><code>setDelegateRenderer</code> for the specified filter.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/NeedlemanWunsch.html#setDelete(short)">setDelete(short)</a></span> - Method in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/NeedlemanWunsch.html" title="class in org.biojava.bio.alignment">NeedlemanWunsch</a></dt>
<dd>
<div class="block">Sets the penalty for a delete operation to the specified value.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/SmithWaterman.html#setDelete(short)">setDelete(short)</a></span> - Method in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/SmithWaterman.html" title="class in org.biojava.bio.alignment">SmithWaterman</a></dt>
<dd>
<div class="block">Overrides the method inherited from the NeedlemanWunsch and sets the
penalty for a delete operation to the specified value.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/StrucAligParameters.html#setDensityCutoff(float)">setDensityCutoff(float)</a></span> - Method in class org.biojava.bio.structure.align.<a href="./org/biojava/bio/structure/align/StrucAligParameters.html" title="class in org.biojava.bio.structure.align">StrucAligParameters</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/PDBHeader.html#setDepDate(java.util.Date)">setDepDate(Date)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/PDBHeader.html" title="class in org.biojava.bio.structure">PDBHeader</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/AbiTraceRenderer.html#setDepth(double)">setDepth(double)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/AbiTraceRenderer.html" title="class in org.biojava.bio.gui.sequence">AbiTraceRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/GlyphFeatureRenderer.html#setDepth(double)">setDepth(double)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/GlyphFeatureRenderer.html" title="class in org.biojava.bio.gui.sequence">GlyphFeatureRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/LineInfo.html#setDepth(org.biojava.bio.gui.sequence.SequenceRenderer, double)">setDepth(SequenceRenderer, double)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/LineInfo.html" title="class in org.biojava.bio.gui.sequence">LineInfo</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/TickFeatureRenderer.html#setDepth(double)">setDepth(double)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/TickFeatureRenderer.html" title="class in org.biojava.bio.gui.sequence">TickFeatureRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/tools/SuffixTreeKernel.html#setDepthScaler(org.biojava.stats.svm.tools.SuffixTreeKernel.DepthScaler)">setDepthScaler(SuffixTreeKernel.DepthScaler)</a></span> - Method in class org.biojava.stats.svm.tools.<a href="./org/biojava/stats/svm/tools/SuffixTreeKernel.html" title="class in org.biojava.stats.svm.tools">SuffixTreeKernel</a></dt>
<dd>
<div class="block">Change the current <span class="type">DepthScaler</span> to
<span class="arg">depthScaler</span>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/SubstitutionMatrix.html#setDescription(java.lang.String)">setDescription(String)</a></span> - Method in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/SubstitutionMatrix.html" title="class in org.biojava.bio.alignment">SubstitutionMatrix</a></dt>
<dd>
<div class="block">Sets the description to the given value.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/aaindex/AAindex.html#setDescription(java.lang.String)">setDescription(String)</a></span> - Method in class org.biojava.bio.proteomics.aaindex.<a href="./org/biojava/bio/proteomics/aaindex/AAindex.html" title="class in org.biojava.bio.proteomics.aaindex">AAindex</a></dt>
<dd>
<div class="block">Sets the description for the AAindex entry.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/PDBHeader.html#setDescription(java.lang.String)">setDescription(String)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/PDBHeader.html" title="class in org.biojava.bio.structure">PDBHeader</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleGeneticCodeTable.html#setDescription(java.lang.String)">setDescription(String)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleGeneticCodeTable.html" title="class in org.biojava.bio.symbol">SimpleGeneticCodeTable</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/AbstractTerm.html#setDescription(java.lang.String)">setDescription(String)</a></span> - Method in class org.biojava.ontology.<a href="./org/biojava/ontology/AbstractTerm.html" title="class in org.biojava.ontology">AbstractTerm</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/IntegerOntology.IntTerm.html#setDescription(java.lang.String)">setDescription(String)</a></span> - Method in class org.biojava.ontology.<a href="./org/biojava/ontology/IntegerOntology.IntTerm.html" title="class in org.biojava.ontology">IntegerOntology.IntTerm</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/IntegerOntology.html#setDescription(java.lang.String)">setDescription(String)</a></span> - Method in class org.biojava.ontology.<a href="./org/biojava/ontology/IntegerOntology.html" title="class in org.biojava.ontology">IntegerOntology</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/Ontology.Impl.html#setDescription(java.lang.String)">setDescription(String)</a></span> - Method in class org.biojava.ontology.<a href="./org/biojava/ontology/Ontology.Impl.html" title="class in org.biojava.ontology">Ontology.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/Ontology.html#setDescription(java.lang.String)">setDescription(String)</a></span> - Method in interface org.biojava.ontology.<a href="./org/biojava/ontology/Ontology.html" title="interface in org.biojava.ontology">Ontology</a></dt>
<dd>
<div class="block">set the description of this ontology</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/OntologyTerm.Impl.html#setDescription(java.lang.String)">setDescription(String)</a></span> - Method in class org.biojava.ontology.<a href="./org/biojava/ontology/OntologyTerm.Impl.html" title="class in org.biojava.ontology">OntologyTerm.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/Term.html#setDescription(java.lang.String)">setDescription(String)</a></span> - Method in interface org.biojava.ontology.<a href="./org/biojava/ontology/Term.html" title="interface in org.biojava.ontology">Term</a></dt>
<dd>
<div class="block">set the description of the term;</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/Triple.Impl.html#setDescription(java.lang.String)">setDescription(String)</a></span> - Method in class org.biojava.ontology.<a href="./org/biojava/ontology/Triple.Impl.html" title="class in org.biojava.ontology">Triple.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/BioEntry.html#setDescription(java.lang.String)">setDescription(String)</a></span> - Method in interface org.biojavax.bio.<a href="./org/biojavax/bio/BioEntry.html" title="interface in org.biojavax.bio">BioEntry</a></dt>
<dd>
<div class="block">Sets the description for this bioentry.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/DebuggingRichSeqIOListener.html#setDescription(java.lang.String)">setDescription(String)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/DebuggingRichSeqIOListener.html" title="class in org.biojavax.bio.seq.io">DebuggingRichSeqIOListener</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/RichSeqIOAdapter.html#setDescription(java.lang.String)">setDescription(String)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/RichSeqIOAdapter.html" title="class in org.biojavax.bio.seq.io">RichSeqIOAdapter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/RichSeqIOListener.html#setDescription(java.lang.String)">setDescription(String)</a></span> - Method in interface org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/RichSeqIOListener.html" title="interface in org.biojavax.bio.seq.io">RichSeqIOListener</a></dt>
<dd>
<div class="block">Call back method so the event emitter can tell the listener
the description of the record being read.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/SimpleRichSequenceBuilder.html#setDescription(java.lang.String)">setDescription(String)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/SimpleRichSequenceBuilder.html" title="class in org.biojavax.bio.seq.io">SimpleRichSequenceBuilder</a></dt>
<dd>
<div class="block">Call back method so the event emitter can tell the listener
the description of the record being read.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/SimpleBioEntry.html#setDescription(java.lang.String)">setDescription(String)</a></span> - Method in class org.biojavax.bio.<a href="./org/biojavax/bio/SimpleBioEntry.html" title="class in org.biojavax.bio">SimpleBioEntry</a></dt>
<dd>
<div class="block">Sets the description for this bioentry.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/Namespace.html#setDescription(java.lang.String)">setDescription(String)</a></span> - Method in interface org.biojavax.<a href="./org/biojavax/Namespace.html" title="interface in org.biojavax">Namespace</a></dt>
<dd>
<div class="block">This method sets a description for the namespace.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ontology/ComparableOntology.html#setDescription(java.lang.String)">setDescription(String)</a></span> - Method in interface org.biojavax.ontology.<a href="./org/biojavax/ontology/ComparableOntology.html" title="interface in org.biojavax.ontology">ComparableOntology</a></dt>
<dd>
<div class="block">Sets a human-readable description of this ontology.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ontology/ComparableTerm.html#setDescription(java.lang.String)">setDescription(String)</a></span> - Method in interface org.biojavax.ontology.<a href="./org/biojavax/ontology/ComparableTerm.html" title="interface in org.biojavax.ontology">ComparableTerm</a></dt>
<dd>
<div class="block">Sets the description associated with this term.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ontology/SimpleComparableOntology.html#setDescription(java.lang.String)">setDescription(String)</a></span> - Method in class org.biojavax.ontology.<a href="./org/biojavax/ontology/SimpleComparableOntology.html" title="class in org.biojavax.ontology">SimpleComparableOntology</a></dt>
<dd>
<div class="block">Sets a human-readable description of this ontology.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ontology/SimpleComparableTerm.html#setDescription(java.lang.String)">setDescription(String)</a></span> - Method in class org.biojavax.ontology.<a href="./org/biojavax/ontology/SimpleComparableTerm.html" title="class in org.biojavax.ontology">SimpleComparableTerm</a></dt>
<dd>
<div class="block">Sets the description associated with this term.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ontology/SimpleComparableTriple.html#setDescription(java.lang.String)">setDescription(String)</a></span> - Method in class org.biojavax.ontology.<a href="./org/biojavax/ontology/SimpleComparableTriple.html" title="class in org.biojavax.ontology">SimpleComparableTriple</a></dt>
<dd>
<div class="block">set the description of the term;</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleNamespace.html#setDescription(java.lang.String)">setDescription(String)</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleNamespace.html" title="class in org.biojavax">SimpleNamespace</a></dt>
<dd>
<div class="block">This method sets a description for the namespace.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ontology/ComparableTriple.html#setDescriptors(java.util.Set)">setDescriptors(Set)</a></span> - Method in interface org.biojavax.ontology.<a href="./org/biojavax/ontology/ComparableTriple.html" title="interface in org.biojavax.ontology">ComparableTriple</a></dt>
<dd>
<div class="block">Clears the current set of descriptors and replaces it with the content of
the set passed.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ontology/SimpleComparableTriple.html#setDescriptors(java.util.Set)">setDescriptors(Set)</a></span> - Method in class org.biojavax.ontology.<a href="./org/biojavax/ontology/SimpleComparableTriple.html" title="class in org.biojavax.ontology">SimpleComparableTriple</a></dt>
<dd>
<div class="block">Clears the current set of descriptors and replaces it with the content of
the set passed.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Compound.html#setDetails(java.lang.String)">setDetails(String)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure">Compound</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Entity.html#setDetails(java.lang.String)">setDetails(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Entity.html" title="class in org.biojava.bio.structure.io.mmcif.model">Entity</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Exptl.html#setDetails(java.lang.String)">setDetails(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Exptl.html" title="class in org.biojava.bio.structure.io.mmcif.model">Exptl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#setDetails(java.lang.String)">setDetails(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/StructAsym.html#setDetails(java.lang.String)">setDetails(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/StructAsym.html" title="class in org.biojava.bio.structure.io.mmcif.model">StructAsym</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/StructRefSeq.html#setDetails(java.lang.String)">setDetails(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/StructRefSeq.html" title="class in org.biojava.bio.structure.io.mmcif.model">StructRefSeq</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/StrucAligParameters.html#setDiagonalDistance(int)">setDiagonalDistance(int)</a></span> - Method in class org.biojava.bio.structure.align.<a href="./org/biojava/bio/structure/align/StrucAligParameters.html" title="class in org.biojava.bio.structure.align">StrucAligParameters</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/StrucAligParameters.html#setDiagonalDistance2(int)">setDiagonalDistance2(int)</a></span> - Method in class org.biojava.bio.structure.align.<a href="./org/biojava/bio/structure/align/StrucAligParameters.html" title="class in org.biojava.bio.structure.align">StrucAligParameters</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/EllipticalBeadRenderer.html#setDimensionRatio(double)">setDimensionRatio(double)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/EllipticalBeadRenderer.html" title="class in org.biojava.bio.gui.sequence">EllipticalBeadRenderer</a></dt>
<dd>
<div class="block"><code>setDimensionRatio</code> sets the minimum ratio of
long dimension to short dimension of the bead.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/glyph/ArrowGlyph.html#setDirection(int)">setDirection(int)</a></span> - Method in class org.biojava.bio.gui.glyph.<a href="./org/biojava/bio/gui/glyph/ArrowGlyph.html" title="class in org.biojava.bio.gui.glyph">ArrowGlyph</a></dt>
<dd>
<div class="block">This method allows you to decide in which direction the arrow has to point.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PairwiseSequencePanel.html#setDirection(int)">setDirection(int)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PairwiseSequencePanel.html" title="class in org.biojava.bio.gui.sequence">PairwiseSequencePanel</a></dt>
<dd>
<div class="block"><code>setDirection</code> sets the direction in which this
context will render the sequence - HORIZONTAL or VERTICAL.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePanel.html#setDirection(int)">setDirection(int)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePanel.html" title="class in org.biojava.bio.gui.sequence">SequencePanel</a></dt>
<dd>
<div class="block">Set the direction that this SequencePanel renders in.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePanelWrapper.html#setDirection(int)">setDirection(int)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePanelWrapper.html" title="class in org.biojava.bio.gui.sequence">SequencePanelWrapper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePoster.html#setDirection(int)">setDirection(int)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePoster.html" title="class in org.biojava.bio.gui.sequence">SequencePoster</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Set the direction that this SequencePoster renders in.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/TranslatedSequencePanel.html#setDirection(int)">setDirection(int)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/TranslatedSequencePanel.html" title="class in org.biojava.bio.gui.sequence">TranslatedSequencePanel</a></dt>
<dd>
<div class="block"><code>setDirection</code> sets the direction in which this
context will render sequences - HORIZONTAL or VERTICAL.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/AbstractPeptideDigestRenderer.html#setDistanceBetweenFeatures(int)">setDistanceBetweenFeatures(int)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/AbstractPeptideDigestRenderer.html" title="class in org.biojava.bio.gui.sequence">AbstractPeptideDigestRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/AlternativeAlignment.html#setDistanceMatrix(org.biojava.bio.structure.jama.Matrix)">setDistanceMatrix(Matrix)</a></span> - Method in class org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/AlternativeAlignment.html" title="class in org.biojava.bio.structure.align.pairwise">AlternativeAlignment</a></dt>
<dd>
<div class="block">The distance matrix this alignment is based on</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/OrderNDistribution.html#setDistribution(org.biojava.bio.symbol.Symbol, org.biojava.bio.dist.Distribution)">setDistribution(Symbol, Distribution)</a></span> - Method in interface org.biojava.bio.dist.<a href="./org/biojava/bio/dist/OrderNDistribution.html" title="interface in org.biojava.bio.dist">OrderNDistribution</a></dt>
<dd>
<div class="block">Set the distribution assocated with a symbol.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/EmissionState.html#setDistribution(org.biojava.bio.dist.Distribution)">setDistribution(Distribution)</a></span> - Method in interface org.biojava.bio.dp.<a href="./org/biojava/bio/dp/EmissionState.html" title="interface in org.biojava.bio.dp">EmissionState</a></dt>
<dd>
<div class="block">Set the Distribution associated with this state.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/SimpleEmissionState.html#setDistribution(org.biojava.bio.dist.Distribution)">setDistribution(Distribution)</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/SimpleEmissionState.html" title="class in org.biojava.bio.dp">SimpleEmissionState</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/DistributionLogo.html#setDistribution(org.biojava.bio.dist.Distribution)">setDistribution(Distribution)</a></span> - Method in class org.biojava.bio.gui.<a href="./org/biojava/bio/gui/DistributionLogo.html" title="class in org.biojava.bio.gui">DistributionLogo</a></dt>
<dd>
<div class="block">
Set the dist to render.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/BioEntry.html#setDivision(java.lang.String)">setDivision(String)</a></span> - Method in interface org.biojavax.bio.<a href="./org/biojavax/bio/BioEntry.html" title="interface in org.biojavax.bio">BioEntry</a></dt>
<dd>
<div class="block">Sets the division of this bioentry.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/DebuggingRichSeqIOListener.html#setDivision(java.lang.String)">setDivision(String)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/DebuggingRichSeqIOListener.html" title="class in org.biojavax.bio.seq.io">DebuggingRichSeqIOListener</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/RichSeqIOAdapter.html#setDivision(java.lang.String)">setDivision(String)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/RichSeqIOAdapter.html" title="class in org.biojavax.bio.seq.io">RichSeqIOAdapter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/RichSeqIOListener.html#setDivision(java.lang.String)">setDivision(String)</a></span> - Method in interface org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/RichSeqIOListener.html" title="interface in org.biojavax.bio.seq.io">RichSeqIOListener</a></dt>
<dd>
<div class="block">Call back method so the event emitter can tell the listener
the division of the record being read.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/SimpleRichSequenceBuilder.html#setDivision(java.lang.String)">setDivision(String)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/SimpleRichSequenceBuilder.html" title="class in org.biojavax.bio.seq.io">SimpleRichSequenceBuilder</a></dt>
<dd>
<div class="block">Call back method so the event emitter can tell the listener
the division of the record being read.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/SimpleBioEntry.html#setDivision(java.lang.String)">setDivision(String)</a></span> - Method in class org.biojavax.bio.<a href="./org/biojavax/bio/SimpleBioEntry.html" title="class in org.biojavax.bio">SimpleBioEntry</a></dt>
<dd>
<div class="block">Sets the division of this bioentry.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/StrucAligParameters.html#setDoAngleCheck(boolean)">setDoAngleCheck(boolean)</a></span> - Method in class org.biojava.bio.structure.align.<a href="./org/biojava/bio/structure/align/StrucAligParameters.html" title="class in org.biojava.bio.structure.align">StrucAligParameters</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/SeqSimilarityAdapter.html#setDocumentLocator(org.xml.sax.Locator)">setDocumentLocator(Locator)</a></span> - Method in class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/SeqSimilarityAdapter.html" title="class in org.biojava.bio.program.ssbind">SeqSimilarityAdapter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/SAX2StAXAdaptor.html#setDocumentLocator(org.xml.sax.Locator)">setDocumentLocator(Locator)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/SAX2StAXAdaptor.html" title="class in org.biojava.bio.seq.io.agave">SAX2StAXAdaptor</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/StAXContentHandler.html#setDocumentLocator(org.xml.sax.Locator)">setDocumentLocator(Locator)</a></span> - Method in interface org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/StAXContentHandler.html" title="interface in org.biojava.bio.seq.io.agave">StAXContentHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/StAXContentHandlerBase.html#setDocumentLocator(org.xml.sax.Locator)">setDocumentLocator(Locator)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/StAXContentHandlerBase.html" title="class in org.biojava.bio.seq.io.agave">StAXContentHandlerBase</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/stax/SAX2StAXAdaptor.html#setDocumentLocator(org.xml.sax.Locator)">setDocumentLocator(Locator)</a></span> - Method in class org.biojava.utils.stax.<a href="./org/biojava/utils/stax/SAX2StAXAdaptor.html" title="class in org.biojava.utils.stax">SAX2StAXAdaptor</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/stax/StAXContentHandler.html#setDocumentLocator(org.xml.sax.Locator)">setDocumentLocator(Locator)</a></span> - Method in interface org.biojava.utils.stax.<a href="./org/biojava/utils/stax/StAXContentHandler.html" title="interface in org.biojava.utils.stax">StAXContentHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/stax/StAXContentHandlerBase.html#setDocumentLocator(org.xml.sax.Locator)">setDocumentLocator(Locator)</a></span> - Method in class org.biojava.utils.stax.<a href="./org/biojava/utils/stax/StAXContentHandlerBase.html" title="class in org.biojava.utils.stax">StAXContentHandlerBase</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/StrucAligParameters.html#setDoDensityCheck(boolean)">setDoDensityCheck(boolean)</a></span> - Method in class org.biojava.bio.structure.align.<a href="./org/biojava/bio/structure/align/StrucAligParameters.html" title="class in org.biojava.bio.structure.align">StrucAligParameters</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/StrucAligParameters.html#setDoDistanceCheck(boolean)">setDoDistanceCheck(boolean)</a></span> - Method in class org.biojava.bio.structure.align.<a href="./org/biojava/bio/structure/align/StrucAligParameters.html" title="class in org.biojava.bio.structure.align">StrucAligParameters</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/JournalArticle.html#setDoi(java.lang.String)">setDoi(String)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/JournalArticle.html" title="class in org.biojava.bio.structure">JournalArticle</a></dt>
<dd>
<div class="block">Set the value of doi</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/StrucAligParameters.html#setDoRMSCheck(boolean)">setDoRMSCheck(boolean)</a></span> - Method in class org.biojava.bio.structure.align.<a href="./org/biojava/bio/structure/align/StrucAligParameters.html" title="class in org.biojava.bio.structure.align">StrucAligParameters</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleSymbolPropertyTable.html#setDoubleProperty(org.biojava.bio.symbol.Symbol, java.lang.String)">setDoubleProperty(Symbol, String)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleSymbolPropertyTable.html" title="class in org.biojava.bio.symbol">SimpleSymbolPropertyTable</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/stax/DoubleElementHandlerBase.html#setDoubleValue(double)">setDoubleValue(double)</a></span> - Method in class org.biojava.utils.stax.<a href="./org/biojava/utils/stax/DoubleElementHandlerBase.html" title="class in org.biojava.utils.stax">DoubleElementHandlerBase</a></dt>
<dd>
<div class="block">
Override this method to do something useful with the
double we collect.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/sax/blastxml/BlastXMLParserFacade.html#setDTDHandler(org.xml.sax.DTDHandler)">setDTDHandler(DTDHandler)</a></span> - Method in class org.biojava.bio.program.sax.blastxml.<a href="./org/biojava/bio/program/sax/blastxml/BlastXMLParserFacade.html" title="class in org.biojava.bio.program.sax.blastxml">BlastXMLParserFacade</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Compound.html#setEcNums(java.util.List)">setEcNums(List<String>)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure">Compound</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/JournalArticle.html#setEditorList(java.util.List)">setEditorList(List<Author>)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/JournalArticle.html" title="class in org.biojava.bio.structure">JournalArticle</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEMatchRegion.html#setElementId(java.lang.String)">setElementId(String)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEMatchRegion.html" title="class in org.biojava.bio.seq.io.agave">AGAVEMatchRegion</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/RichSequenceFormat.BasicFormat.html#setElideComments(boolean)">setElideComments(boolean)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/RichSequenceFormat.BasicFormat.html" title="class in org.biojavax.bio.seq.io">RichSequenceFormat.BasicFormat</a></dt>
<dd>
<div class="block">Use this method to toggle reading of comments data.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/RichSequenceFormat.html#setElideComments(boolean)">setElideComments(boolean)</a></span> - Method in interface org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/RichSequenceFormat.html" title="interface in org.biojavax.bio.seq.io">RichSequenceFormat</a></dt>
<dd>
<div class="block">Use this method to toggle reading of comments data.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/RichSequenceFormat.BasicFormat.html#setElideFeatures(boolean)">setElideFeatures(boolean)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/RichSequenceFormat.BasicFormat.html" title="class in org.biojavax.bio.seq.io">RichSequenceFormat.BasicFormat</a></dt>
<dd>
<div class="block">Use this method to toggle reading of feature data.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/RichSequenceFormat.html#setElideFeatures(boolean)">setElideFeatures(boolean)</a></span> - Method in interface org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/RichSequenceFormat.html" title="interface in org.biojavax.bio.seq.io">RichSequenceFormat</a></dt>
<dd>
<div class="block">Use this method to toggle reading of feature data.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/RichSequenceFormat.BasicFormat.html#setElideReferences(boolean)">setElideReferences(boolean)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/RichSequenceFormat.BasicFormat.html" title="class in org.biojavax.bio.seq.io">RichSequenceFormat.BasicFormat</a></dt>
<dd>
<div class="block">Use this method to toggle reading of bibliographic reference data.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/RichSequenceFormat.html#setElideReferences(boolean)">setElideReferences(boolean)</a></span> - Method in interface org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/RichSequenceFormat.html" title="interface in org.biojavax.bio.seq.io">RichSequenceFormat</a></dt>
<dd>
<div class="block">Use this method to toggle reading of bibliographic reference data.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/EmblLikeFormat.html#setElideSymbols(boolean)">setElideSymbols(boolean)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/EmblLikeFormat.html" title="class in org.biojava.bio.seq.io">EmblLikeFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Specifies whether the symbols (SQ) part of the entry should
be ignored.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/GenbankFormat.html#setElideSymbols(boolean)">setElideSymbols(boolean)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/GenbankFormat.html" title="class in org.biojava.bio.seq.io">GenbankFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Use this method to toggle reading of sequence data.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/RichSequenceFormat.BasicFormat.html#setElideSymbols(boolean)">setElideSymbols(boolean)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/RichSequenceFormat.BasicFormat.html" title="class in org.biojavax.bio.seq.io">RichSequenceFormat.BasicFormat</a></dt>
<dd>
<div class="block">Use this method to toggle reading of sequence data.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/RichSequenceFormat.html#setElideSymbols(boolean)">setElideSymbols(boolean)</a></span> - Method in interface org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/RichSequenceFormat.html" title="interface in org.biojavax.bio.seq.io">RichSequenceFormat</a></dt>
<dd>
<div class="block">Use this method to toggle reading of sequence data.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/SimpleGFFRecord.html#setEnd(int)">setEnd(int)</a></span> - Method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/SimpleGFFRecord.html" title="class in org.biojava.bio.program.gff">SimpleGFFRecord</a></dt>
<dd>
<div class="block">Set the end coordinate to <span class="arg">end</source>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff3/GFF3Record.Impl.html#setEnd(int)">setEnd(int)</a></span> - Method in class org.biojava.bio.program.gff3.<a href="./org/biojava/bio/program/gff3/GFF3Record.Impl.html" title="class in org.biojava.bio.program.gff3">GFF3Record.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEMatchRegion.html#setEnd(int)">setEnd(int)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEMatchRegion.html" title="class in org.biojava.bio.seq.io.agave">AGAVEMatchRegion</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEQueryRegion.html#setEnd(int)">setEnd(int)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEQueryRegion.html" title="class in org.biojava.bio.seq.io.agave">AGAVEQueryRegion</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/LineSplitParser.html#setEndOfRecord(java.lang.String)">setEndOfRecord(String)</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/LineSplitParser.html" title="class in org.biojava.bio.program.tagvalue">LineSplitParser</a></dt>
<dd>
<div class="block">Set the string indicating that a record has ended.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/RegexParser.html#setEndOfRecord(java.lang.String)">setEndOfRecord(String)</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/RegexParser.html" title="class in org.biojava.bio.program.tagvalue">RegexParser</a></dt>
<dd>
<div class="block">Set the explicit end-of-record string.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Compound.html#setEngineered(java.lang.String)">setEngineered(String)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure">Compound</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/EntityPolySeq.html#setEntity_id(java.lang.String)">setEntity_id(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/EntityPolySeq.html" title="class in org.biojava.bio.structure.io.mmcif.model">EntityPolySeq</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/PdbxEntityNonPoly.html#setEntity_id(java.lang.String)">setEntity_id(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/PdbxEntityNonPoly.html" title="class in org.biojava.bio.structure.io.mmcif.model">PdbxEntityNonPoly</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/PdbxNonPolyScheme.html#setEntity_id(java.lang.String)">setEntity_id(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/PdbxNonPolyScheme.html" title="class in org.biojava.bio.structure.io.mmcif.model">PdbxNonPolyScheme</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/PdbxPolySeqScheme.html#setEntity_id(java.lang.String)">setEntity_id(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/PdbxPolySeqScheme.html" title="class in org.biojava.bio.structure.io.mmcif.model">PdbxPolySeqScheme</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/StructAsym.html#setEntity_id(java.lang.String)">setEntity_id(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/StructAsym.html" title="class in org.biojava.bio.structure.io.mmcif.model">StructAsym</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/StructRef.html#setEntity_id(java.lang.String)">setEntity_id(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/StructRef.html" title="class in org.biojava.bio.structure.io.mmcif.model">StructRef</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/sax/blastxml/BlastXMLParserFacade.html#setEntityResolver(org.xml.sax.EntityResolver)">setEntityResolver(EntityResolver)</a></span> - Method in class org.biojava.bio.program.sax.blastxml.<a href="./org/biojava/bio/program/sax/blastxml/BlastXMLParserFacade.html" title="class in org.biojava.bio.program.sax.blastxml">BlastXMLParserFacade</a></dt>
<dd>
<div class="block">This class has an EntityResolver that
resolves the public ID specifying the
NCBI DTDs to resource files within the
BioJava libraries.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Exptl.html#setEntry_id(java.lang.String)">setEntry_id(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Exptl.html" title="class in org.biojava.bio.structure.io.mmcif.model">Exptl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#setEntry_id(java.lang.String)">setEntry_id(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Struct.html#setEntry_id(java.lang.String)">setEntry_id(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Struct.html" title="class in org.biojava.bio.structure.io.mmcif.model">Struct</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/StructKeywords.html#setEntry_id(java.lang.String)">setEntry_id(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/StructKeywords.html" title="class in org.biojava.bio.structure.io.mmcif.model">StructKeywords</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/process/ExternalProcess.html#setEnvironmentProperties(java.lang.String[])">setEnvironmentProperties(String[])</a></span> - Method in class org.biojava.utils.process.<a href="./org/biojava/utils/process/ExternalProcess.html" title="class in org.biojava.utils.process">ExternalProcess</a></dt>
<dd>
<div class="block">Sets environment variables for the external process.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/SMORegressionTrainer.html#setEpsilon(double)">setEpsilon(double)</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/SMORegressionTrainer.html" title="class in org.biojava.stats.svm">SMORegressionTrainer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/SMOTrainer.html#setEpsilon(double)">setEpsilon(double)</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/SMOTrainer.html" title="class in org.biojava.stats.svm">SMOTrainer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/util/AlignedPosition.html#setEquivalent(int)">setEquivalent(int)</a></span> - Method in class org.biojava.bio.structure.gui.util.<a href="./org/biojava/bio/structure/gui/util/AlignedPosition.html" title="class in org.biojava.bio.structure.gui.util">AlignedPosition</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFParser.html#setErrorHandler(org.biojava.bio.program.gff.GFFErrorHandler)">setErrorHandler(GFFErrorHandler)</a></span> - Method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFParser.html" title="class in org.biojava.bio.program.gff">GFFParser</a></dt>
<dd>
<div class="block">Set the error handler used by this parser.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff3/GFF3Parser.html#setErrorHandler(org.biojava.bio.program.gff.GFFErrorHandler)">setErrorHandler(GFFErrorHandler)</a></span> - Method in class org.biojava.bio.program.gff3.<a href="./org/biojava/bio/program/gff3/GFF3Parser.html" title="class in org.biojava.bio.program.gff3">GFF3Parser</a></dt>
<dd>
<div class="block">Set the error handler used by this parser.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/sax/blastxml/BlastXMLParserFacade.html#setErrorHandler(org.xml.sax.ErrorHandler)">setErrorHandler(ErrorHandler)</a></span> - Method in class org.biojava.bio.program.sax.blastxml.<a href="./org/biojava/bio/program/sax/blastxml/BlastXMLParserFacade.html" title="class in org.biojava.bio.program.sax.blastxml">BlastXMLParserFacade</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/process/ExternalProcess.html#setErrorHandler(org.biojava.utils.process.OutputHandler)">setErrorHandler(OutputHandler)</a></span> - Method in class org.biojava.utils.process.<a href="./org/biojava/utils/process/ExternalProcess.html" title="class in org.biojava.utils.process">ExternalProcess</a></dt>
<dd>
<div class="block">Sets the output error handler which is responsible for the standard error
output of the external process.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/StrucAligParameters.html#setEvalCutoff(float)">setEvalCutoff(float)</a></span> - Method in class org.biojava.bio.structure.align.<a href="./org/biojava/bio/structure/align/StrucAligParameters.html" title="class in org.biojava.bio.structure.align">StrucAligParameters</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html#setEvents(java.util.List)">setEvents(List)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html" title="class in org.biojavax.bio.seq.io">UniProtCommentParser</a></dt>
<dd>
<div class="block">Setter for property events.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/StateMachine.SimpleStateListener.html#setExceptionOnNullDelegate(boolean)">setExceptionOnNullDelegate(boolean)</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/StateMachine.SimpleStateListener.html" title="class in org.biojava.bio.program.tagvalue">StateMachine.SimpleStateListener</a></dt>
<dd>
<div class="block">determines if an exception is thrown when an event
arrives without the delegate being set.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Compound.html#setExpressionSystem(java.lang.String)">setExpressionSystem(String)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure">Compound</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Compound.html#setExpressionSystemAtccNumber(java.lang.String)">setExpressionSystemAtccNumber(String)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure">Compound</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Compound.html#setExpressionSystemCell(java.lang.String)">setExpressionSystemCell(String)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure">Compound</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Compound.html#setExpressionSystemCellLine(java.lang.String)">setExpressionSystemCellLine(String)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure">Compound</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Compound.html#setExpressionSystemCellularLocation(java.lang.String)">setExpressionSystemCellularLocation(String)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure">Compound</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Compound.html#setExpressionSystemGene(java.lang.String)">setExpressionSystemGene(String)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure">Compound</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Compound.html#setExpressionSystemOrgan(java.lang.String)">setExpressionSystemOrgan(String)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure">Compound</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Compound.html#setExpressionSystemOrganelle(java.lang.String)">setExpressionSystemOrganelle(String)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure">Compound</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Compound.html#setExpressionSystemOtherDetails(java.lang.String)">setExpressionSystemOtherDetails(String)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure">Compound</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Compound.html#setExpressionSystemPlasmid(java.lang.String)">setExpressionSystemPlasmid(String)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure">Compound</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Compound.html#setExpressionSystemStrain(java.lang.String)">setExpressionSystemStrain(String)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure">Compound</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Compound.html#setExpressionSystemTaxId(java.lang.String)">setExpressionSystemTaxId(String)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure">Compound</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Compound.html#setExpressionSystemTissue(java.lang.String)">setExpressionSystemTissue(String)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure">Compound</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Compound.html#setExpressionSystemVariant(java.lang.String)">setExpressionSystemVariant(String)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure">Compound</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Compound.html#setExpressionSystemVector(java.lang.String)">setExpressionSystemVector(String)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure">Compound</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Compound.html#setExpressionSystemVectorType(java.lang.String)">setExpressionSystemVectorType(String)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure">Compound</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/ncbi/GenbankRichSequenceDB.html#setFactory(org.biojavax.bio.seq.io.RichSequenceBuilderFactory)">setFactory(RichSequenceBuilderFactory)</a></span> - Method in class org.biojavax.bio.db.ncbi.<a href="./org/biojavax/bio/db/ncbi/GenbankRichSequenceDB.html" title="class in org.biojavax.bio.db.ncbi">GenbankRichSequenceDB</a></dt>
<dd>
<div class="block">Setter for property factory.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/ncbi/GenpeptRichSequenceDB.html#setFactory(org.biojavax.bio.seq.io.RichSequenceBuilderFactory)">setFactory(RichSequenceBuilderFactory)</a></span> - Method in class org.biojavax.bio.db.ncbi.<a href="./org/biojavax/bio/db/ncbi/GenpeptRichSequenceDB.html" title="class in org.biojavax.bio.db.ncbi">GenpeptRichSequenceDB</a></dt>
<dd>
<div class="block">Setter for property factory.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/StateMachine.TransitionTable.html#setFallback(org.biojava.bio.program.tagvalue.StateMachine.TransitionTable)">setFallback(StateMachine.TransitionTable)</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/StateMachine.TransitionTable.html" title="class in org.biojava.bio.program.tagvalue">StateMachine.TransitionTable</a></dt>
<dd>
<div class="block">set the specified TransitionTable to be looked
looked up if the Transition cannot be found in
this one.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFRecordFilter.FeatureFilter.html#setFeature(java.lang.String)">setFeature(String)</a></span> - Method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFRecordFilter.FeatureFilter.html" title="class in org.biojava.bio.program.gff">GFFRecordFilter.FeatureFilter</a></dt>
<dd>
<div class="block">Set the feature to <span class="arg">feature</span>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/SimpleGFFRecord.html#setFeature(java.lang.String)">setFeature(String)</a></span> - Method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/SimpleGFFRecord.html" title="class in org.biojava.bio.program.gff">SimpleGFFRecord</a></dt>
<dd>
<div class="block">Set the feature type to <span class="arg">type</source>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/sax/blastxml/BlastXMLParserFacade.html#setFeature(java.lang.String, boolean)">setFeature(String, boolean)</a></span> - Method in class org.biojava.bio.program.sax.blastxml.<a href="./org/biojava/bio/program/sax/blastxml/BlastXMLParserFacade.html" title="class in org.biojava.bio.program.sax.blastxml">BlastXMLParserFacade</a></dt>
<dd>
<div class="block">by default, we set the parser to non-validating.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/CompoundRichLocation.html#setFeature(org.biojavax.bio.seq.RichFeature)">setFeature(RichFeature)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/CompoundRichLocation.html" title="class in org.biojavax.bio.seq">CompoundRichLocation</a></dt>
<dd>
<div class="block">Sets the feature this location is associated with.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/EmptyRichLocation.html#setFeature(org.biojavax.bio.seq.RichFeature)">setFeature(RichFeature)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/EmptyRichLocation.html" title="class in org.biojavax.bio.seq">EmptyRichLocation</a></dt>
<dd>
<div class="block">Sets the feature this location is associated with.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichLocation.html#setFeature(org.biojavax.bio.seq.RichFeature)">setFeature(RichFeature)</a></span> - Method in interface org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichLocation.html" title="interface in org.biojavax.bio.seq">RichLocation</a></dt>
<dd>
<div class="block">Sets the feature this location is associated with.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichLocation.html#setFeature(org.biojavax.bio.seq.RichFeature)">setFeature(RichFeature)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichLocation.html" title="class in org.biojavax.bio.seq">SimpleRichLocation</a></dt>
<dd>
<div class="block">Sets the feature this location is associated with.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/SequencesAsGFF.html#setFeatureFilter(org.biojava.bio.seq.FeatureFilter)">setFeatureFilter(FeatureFilter)</a></span> - Method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/SequencesAsGFF.html" title="class in org.biojava.bio.program.gff">SequencesAsGFF</a></dt>
<dd>
<div class="block">Replace the current <span class="type">FeatureFilter</span> with
<span class="arg">filter</span>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/xff/XFFFeatureSetHandler.html#setFeatureListener(org.biojava.bio.seq.io.SeqIOListener)">setFeatureListener(SeqIOListener)</a></span> - Method in class org.biojava.bio.program.xff.<a href="./org/biojava/bio/program/xff/XFFFeatureSetHandler.html" title="class in org.biojava.bio.program.xff">XFFFeatureSetHandler</a></dt>
<dd>
<div class="block">Set the object which receives startFeature/endFeature notifications.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/StAXFeatureHandler.html#setFeatureListener(org.biojava.bio.seq.io.SeqIOListener)">setFeatureListener(SeqIOListener)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/StAXFeatureHandler.html" title="class in org.biojava.bio.seq.io.agave">StAXFeatureHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game/StAXFeatureHandler.html#setFeatureListener(org.biojava.bio.seq.io.SeqIOListener)">setFeatureListener(SeqIOListener)</a></span> - Method in class org.biojava.bio.seq.io.game.<a href="./org/biojava/bio/seq/io/game/StAXFeatureHandler.html" title="class in org.biojava.bio.seq.io.game">StAXFeatureHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/xff/FeatureHandler.html#setFeatureProperty(java.lang.Object, java.lang.Object)">setFeatureProperty(Object, Object)</a></span> - Method in class org.biojava.bio.program.xff.<a href="./org/biojava/bio/program/xff/FeatureHandler.html" title="class in org.biojava.bio.program.xff">FeatureHandler</a></dt>
<dd>
<div class="block">Set a property.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleSequenceFactory.html#setFeatureRealizer(org.biojava.bio.seq.FeatureRealizer)">setFeatureRealizer(FeatureRealizer)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleSequenceFactory.html" title="class in org.biojava.bio.seq.impl">SimpleSequenceFactory</a></dt>
<dd>
<div class="block">Set the FeatureRealizer used by new sequences created by this
factory.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichFeatureRelationshipHolder.html#setFeatureRelationshipSet(java.util.Set)">setFeatureRelationshipSet(Set)</a></span> - Method in interface org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichFeatureRelationshipHolder.html" title="interface in org.biojavax.bio.seq">RichFeatureRelationshipHolder</a></dt>
<dd>
<div class="block">Clears the relations from this feautre holder and replaces them with a new set.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichFeature.html#setFeatureRelationshipSet(java.util.Set)">setFeatureRelationshipSet(Set)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichFeature.html" title="class in org.biojavax.bio.seq">SimpleRichFeature</a></dt>
<dd>
<div class="block">Clears the relations from this feautre holder and replaces them with a new set.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/FeatureBlockSequenceRenderer.html#setFeatureRenderer(org.biojava.bio.gui.sequence.FeatureRenderer)">setFeatureRenderer(FeatureRenderer)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/FeatureBlockSequenceRenderer.html" title="class in org.biojava.bio.gui.sequence">FeatureBlockSequenceRenderer</a></dt>
<dd>
<div class="block"><code>setFeatureRenderer</code> sets the renderer to be used.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.html#setFeatureSet(java.util.Set)">setFeatureSet(Set<Feature>)</a></span> - Method in interface org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.html" title="interface in org.biojavax.bio.seq">RichSequence</a></dt>
<dd>
<div class="block">Sets the features of this sequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/ThinRichSequence.html#setFeatureSet(java.util.Set)">setFeatureSet(Set<Feature>)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/ThinRichSequence.html" title="class in org.biojavax.bio.seq">ThinRichSequence</a></dt>
<dd>
<div class="block">Sets the features of this sequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/AbstractPeptideDigestRenderer.html#setFeatureSource(org.biojava.bio.gui.sequence.FeatureSource)">setFeatureSource(FeatureSource)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/AbstractPeptideDigestRenderer.html" title="class in org.biojava.bio.gui.sequence">AbstractPeptideDigestRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/server/FlatFileInstallation.html#setFilePath(java.io.File)">setFilePath(File)</a></span> - Method in class org.biojava.bio.structure.server.<a href="./org/biojava/bio/structure/server/FlatFileInstallation.html" title="class in org.biojava.bio.structure.server">FlatFileInstallation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/ArrowedFeatureRenderer.html#setFill(java.awt.Paint)">setFill(Paint)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/ArrowedFeatureRenderer.html" title="class in org.biojava.bio.gui.sequence">ArrowedFeatureRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/BasicFeatureRenderer.html#setFill(java.awt.Paint)">setFill(Paint)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/BasicFeatureRenderer.html" title="class in org.biojava.bio.gui.sequence">BasicFeatureRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SixFrameRenderer.html#setFill(java.awt.Paint)">setFill(Paint)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SixFrameRenderer.html" title="class in org.biojava.bio.gui.sequence">SixFrameRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SixFrameZiggyRenderer.html#setFill(java.awt.Paint)">setFill(Paint)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SixFrameZiggyRenderer.html" title="class in org.biojava.bio.gui.sequence">SixFrameZiggyRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/TickFeatureRenderer.html#setFill(java.awt.Paint)">setFill(Paint)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/TickFeatureRenderer.html" title="class in org.biojava.bio.gui.sequence">TickFeatureRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/ZiggyFeatureRenderer.html#setFill(java.awt.Paint)">setFill(Paint)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/ZiggyFeatureRenderer.html" title="class in org.biojava.bio.gui.sequence">ZiggyFeatureRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/LabelledSequenceRenderer.html#setFillColor(java.awt.Color)">setFillColor(Color)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/LabelledSequenceRenderer.html" title="class in org.biojava.bio.gui.sequence">LabelledSequenceRenderer</a></dt>
<dd>
<div class="block">Set the background color of the label area.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/DNAStyle.html#setFillPaint(org.biojava.bio.symbol.Symbol, java.awt.Paint)">setFillPaint(Symbol, Paint)</a></span> - Method in class org.biojava.bio.gui.<a href="./org/biojava/bio/gui/DNAStyle.html" title="class in org.biojava.bio.gui">DNAStyle</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/glyph/ArrowGlyph.html#setFillPaint(java.awt.Paint)">setFillPaint(Paint)</a></span> - Method in class org.biojava.bio.gui.glyph.<a href="./org/biojava/bio/gui/glyph/ArrowGlyph.html" title="class in org.biojava.bio.gui.glyph">ArrowGlyph</a></dt>
<dd>
<div class="block">Allows you to set the paint properties of this glyph.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/SimpleSymbolStyle.html#setFillPaint(org.biojava.bio.symbol.Symbol, java.awt.Paint)">setFillPaint(Symbol, Paint)</a></span> - Method in class org.biojava.bio.gui.<a href="./org/biojava/bio/gui/SimpleSymbolStyle.html" title="class in org.biojava.bio.gui">SimpleSymbolStyle</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/AbstractPeptideDigestRenderer.html#setFilter(org.biojava.bio.seq.FeatureFilter)">setFilter(FeatureFilter)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/AbstractPeptideDigestRenderer.html" title="class in org.biojava.bio.gui.sequence">AbstractPeptideDigestRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/FilteringRenderer.html#setFilter(org.biojava.bio.seq.FeatureFilter)">setFilter(FeatureFilter)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/FilteringRenderer.html" title="class in org.biojava.bio.gui.sequence">FilteringRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PairwiseFilteringRenderer.html#setFilter(org.biojava.bio.seq.FeatureFilter)">setFilter(FeatureFilter)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PairwiseFilteringRenderer.html" title="class in org.biojava.bio.gui.sequence">PairwiseFilteringRenderer</a></dt>
<dd>
<div class="block"><code>setFilter</code> sets the filter.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFRecordFilter.NotFilter.html#setFilter(org.biojava.bio.program.gff.GFFRecordFilter)">setFilter(GFFRecordFilter)</a></span> - Method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFRecordFilter.NotFilter.html" title="class in org.biojava.bio.program.gff">GFFRecordFilter.NotFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtCommentParser.Interaction.html#setFirstIntActID(java.lang.String)">setFirstIntActID(String)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtCommentParser.Interaction.html" title="class in org.biojavax.bio.seq.io">UniProtCommentParser.Interaction</a></dt>
<dd>
<div class="block">Setter for property firstIntActID.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ga/impl/AbstractOrganism.html#setFitness(double[])">setFitness(double[])</a></span> - Method in class org.biojavax.ga.impl.<a href="./org/biojavax/ga/impl/AbstractOrganism.html" title="class in org.biojavax.ga.impl">AbstractOrganism</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/Organism.html#setFitness(double[])">setFitness(double[])</a></span> - Method in interface org.biojavax.ga.<a href="./org/biojavax/ga/Organism.html" title="interface in org.biojavax.ga">Organism</a></dt>
<dd>
<div class="block">This method allows to set the fitness of this organism to the specified
value.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ga/functions/SelectionFunction.SelectAll.html#setFitnessFunction(org.biojavax.ga.functions.FitnessFunction)">setFitnessFunction(FitnessFunction)</a></span> - Method in class org.biojavax.ga.functions.<a href="./org/biojavax/ga/functions/SelectionFunction.SelectAll.html" title="class in org.biojavax.ga.functions">SelectionFunction.SelectAll</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/GeneticAlgorithm.html#setFitnessFunction(org.biojavax.ga.functions.FitnessFunction)">setFitnessFunction(FitnessFunction)</a></span> - Method in interface org.biojavax.ga.<a href="./org/biojavax/ga/GeneticAlgorithm.html" title="interface in org.biojavax.ga">GeneticAlgorithm</a></dt>
<dd>
<div class="block">The fitness function that will be used to compute the fitness of each
organism.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ga/impl/AbstractGeneticAlgorithm.html#setFitnessFunction(org.biojavax.ga.functions.FitnessFunction)">setFitnessFunction(FitnessFunction)</a></span> - Method in class org.biojavax.ga.impl.<a href="./org/biojavax/ga/impl/AbstractGeneticAlgorithm.html" title="class in org.biojavax.ga.impl">AbstractGeneticAlgorithm</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/stax/FloatElementHandlerBase.html#setFloatValue(float)">setFloatValue(float)</a></span> - Method in class org.biojava.utils.stax.<a href="./org/biojava/utils/stax/FloatElementHandlerBase.html" title="class in org.biojava.utils.stax">FloatElementHandlerBase</a></dt>
<dd>
<div class="block">Override this method to do something useful with the
float we collect.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePanelWrapper.html#setFont(java.awt.Font)">setFont(Font)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePanelWrapper.html" title="class in org.biojava.bio.gui.sequence">SequencePanelWrapper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html#setFormula(java.lang.String)">setFormula(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html" title="class in org.biojava.bio.structure.io.mmcif.model">ChemComp</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html#setFormula_weight(java.lang.String)">setFormula_weight(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html" title="class in org.biojava.bio.structure.io.mmcif.model">ChemComp</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Entity.html#setFormula_weight(java.lang.String)">setFormula_weight(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Entity.html" title="class in org.biojava.bio.structure.io.mmcif.model">Entity</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/StrucAligParameters.html#setFragCompat(float)">setFragCompat(float)</a></span> - Method in class org.biojava.bio.structure.align.<a href="./org/biojava/bio/structure/align/StrucAligParameters.html" title="class in org.biojava.bio.structure.align">StrucAligParameters</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Compound.html#setFragment(java.lang.String)">setFragment(String)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure">Compound</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/StrucAligParameters.html#setFragmentLength(int)">setFragmentLength(int)</a></span> - Method in class org.biojava.bio.structure.align.<a href="./org/biojava/bio/structure/align/StrucAligParameters.html" title="class in org.biojava.bio.structure.align">StrucAligParameters</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/StrucAligParameters.html#setFragmentMiniDistance(float)">setFragmentMiniDistance(float)</a></span> - Method in class org.biojava.bio.structure.align.<a href="./org/biojava/bio/structure/align/StrucAligParameters.html" title="class in org.biojava.bio.structure.align">StrucAligParameters</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/StructurePairAligner.html#setFragmentPairs(org.biojava.bio.structure.align.pairwise.FragmentPair[])">setFragmentPairs(FragmentPair[])</a></span> - Method in class org.biojava.bio.structure.align.<a href="./org/biojava/bio/structure/align/StructurePairAligner.html" title="class in org.biojava.bio.structure.align">StructurePairAligner</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/JMatrixPanel.html#setFragmentPairs(org.biojava.bio.structure.align.pairwise.FragmentPair[])">setFragmentPairs(FragmentPair[])</a></span> - Method in class org.biojava.bio.structure.gui.<a href="./org/biojava/bio/structure/gui/JMatrixPanel.html" title="class in org.biojava.bio.structure.gui">JMatrixPanel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/ScaleableMatrixPanel.html#setFragmentPairs(org.biojava.bio.structure.align.pairwise.FragmentPair[])">setFragmentPairs(FragmentPair[])</a></span> - Method in class org.biojava.bio.structure.gui.<a href="./org/biojava/bio/structure/gui/ScaleableMatrixPanel.html" title="class in org.biojava.bio.structure.gui">ScaleableMatrixPanel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFRecordFilter.FrameFilter.html#setFrame(int)">setFrame(int)</a></span> - Method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFRecordFilter.FrameFilter.html" title="class in org.biojava.bio.program.gff">GFFRecordFilter.FrameFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/SimpleGFFRecord.html#setFrame(int)">setFrame(int)</a></span> - Method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/SimpleGFFRecord.html" title="class in org.biojava.bio.program.gff">SimpleGFFRecord</a></dt>
<dd>
<div class="block">Set the frame to <span class="arg">frame</source>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Atom.html#setFullName(java.lang.String)">setFullName(String)</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Atom.html" title="interface in org.biojava.bio.structure">Atom</a></dt>
<dd>
<div class="block">set full name of atom e.g.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/AtomImpl.html#setFullName(java.lang.String)">setFullName(String)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/AtomImpl.html" title="class in org.biojava.bio.structure">AtomImpl</a></dt>
<dd>
<div class="block">set full name of atom e.g.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/NeedlemanWunsch.html#setGapExt(short)">setGapExt(short)</a></span> - Method in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/NeedlemanWunsch.html" title="class in org.biojava.bio.alignment">NeedlemanWunsch</a></dt>
<dd>
<div class="block">Sets the penalty for an extension of any gap (insert or delete) to the
specified value.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/SmithWaterman.html#setGapExt(short)">setGapExt(short)</a></span> - Method in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/SmithWaterman.html" title="class in org.biojava.bio.alignment">SmithWaterman</a></dt>
<dd>
<div class="block">Overrides the method inherited from the NeedlemanWunsch and sets the
penalty for an extension of any gap (insert or delete) to the specified
value.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/Alignable.html#setGapExtCol(float)">setGapExtCol(float)</a></span> - Method in interface org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/Alignable.html" title="interface in org.biojava.bio.structure.align.pairwise">Alignable</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/StrCompAlignment.html#setGapExtCol(float)">setGapExtCol(float)</a></span> - Method in class org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/StrCompAlignment.html" title="class in org.biojava.bio.structure.align.pairwise">StrCompAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/StrucAligParameters.html#setGapExtension(float)">setGapExtension(float)</a></span> - Method in class org.biojava.bio.structure.align.<a href="./org/biojava/bio/structure/align/StrucAligParameters.html" title="class in org.biojava.bio.structure.align">StrucAligParameters</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/Alignable.html#setGapExtRow(float)">setGapExtRow(float)</a></span> - Method in interface org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/Alignable.html" title="interface in org.biojava.bio.structure.align.pairwise">Alignable</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/StrCompAlignment.html#setGapExtRow(float)">setGapExtRow(float)</a></span> - Method in class org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/StrCompAlignment.html" title="class in org.biojava.bio.structure.align.pairwise">StrCompAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/StrucAligParameters.html#setGapOpen(float)">setGapOpen(float)</a></span> - Method in class org.biojava.bio.structure.align.<a href="./org/biojava/bio/structure/align/StrucAligParameters.html" title="class in org.biojava.bio.structure.align">StrucAligParameters</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/Alignable.html#setGapOpenCol(float)">setGapOpenCol(float)</a></span> - Method in interface org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/Alignable.html" title="interface in org.biojava.bio.structure.align.pairwise">Alignable</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/StrCompAlignment.html#setGapOpenCol(float)">setGapOpenCol(float)</a></span> - Method in class org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/StrCompAlignment.html" title="class in org.biojava.bio.structure.align.pairwise">StrCompAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/Alignable.html#setGapOpenRow(float)">setGapOpenRow(float)</a></span> - Method in interface org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/Alignable.html" title="interface in org.biojava.bio.structure.align.pairwise">Alignable</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/StrCompAlignment.html#setGapOpenRow(float)">setGapOpenRow(float)</a></span> - Method in class org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/StrCompAlignment.html" title="class in org.biojava.bio.structure.align.pairwise">StrCompAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Compound.html#setGene(java.lang.String)">setGene(String)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure">Compound</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/SequencesAsGFF.html#setGenerateSequenceHeader(boolean)">setGenerateSequenceHeader(boolean)</a></span> - Method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/SequencesAsGFF.html" title="class in org.biojava.bio.program.gff">SequencesAsGFF</a></dt>
<dd>
<div class="block">Specify whether a per-sequence header line, giving the length of the
sequence, should be generated.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/taxa/NCBITaxon.html#setGeneticCode(java.lang.Integer)">setGeneticCode(Integer)</a></span> - Method in interface org.biojavax.bio.taxa.<a href="./org/biojavax/bio/taxa/NCBITaxon.html" title="interface in org.biojavax.bio.taxa">NCBITaxon</a></dt>
<dd>
<div class="block">Sets the genetic code of this taxon, which may be null, which will unset it.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/taxa/SimpleNCBITaxon.html#setGeneticCode(java.lang.Integer)">setGeneticCode(Integer)</a></span> - Method in class org.biojavax.bio.taxa.<a href="./org/biojavax/bio/taxa/SimpleNCBITaxon.html" title="class in org.biojavax.bio.taxa">SimpleNCBITaxon</a></dt>
<dd>
<div class="block">Sets the genetic code of this taxon, which may be null, which will unset it.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/biosql/TaxonSQL.html#setGeneticCodeID(java.sql.Connection, org.biojava.bio.taxa.Taxon, int)">setGeneticCodeID(Connection, Taxon, int)</a></span> - Static method in class org.biojava.bio.seq.db.biosql.<a href="./org/biojava/bio/seq/db/biosql/TaxonSQL.html" title="class in org.biojava.bio.seq.db.biosql">TaxonSQL</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Updates the taxon in the database and sets its genetic code id to the specified value.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/GlyphFeatureRenderer.html#setGlyphForFilter(org.biojava.bio.seq.FeatureFilter, org.biojava.bio.gui.glyph.Glyph)">setGlyphForFilter(FeatureFilter, Glyph)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/GlyphFeatureRenderer.html" title="class in org.biojava.bio.gui.sequence">GlyphFeatureRenderer</a></dt>
<dd>
<div class="block">Allows setting another <a href="./org/biojava/bio/gui/glyph/Glyph.html" title="interface in org.biojava.bio.gui.glyph"><code>Glyph</code></a> object to be painted for the given
FeatureFilter.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html#setGroup_PDB(java.lang.String)">setGroup_PDB(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html" title="class in org.biojava.bio.structure.io.mmcif.model">AtomSite</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/SimpleGFFRecord.html#setGroupAttributes(java.util.Map)">setGroupAttributes(Map)</a></span> - Method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/SimpleGFFRecord.html" title="class in org.biojava.bio.program.gff">SimpleGFFRecord</a></dt>
<dd>
<div class="block">Replace the group-attribute <span class="type">Map</span> with
<span class="arg">ga</span>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/StAXFeatureHandler.html#setHandlerCharacteristics(java.lang.String, boolean)">setHandlerCharacteristics(String, boolean)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/StAXFeatureHandler.html" title="class in org.biojava.bio.seq.io.agave">StAXFeatureHandler</a></dt>
<dd>
<div class="block">Sets the element name that the class responds to.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/StAXPropertyHandler.html#setHandlerCharacteristics(java.lang.String, boolean)">setHandlerCharacteristics(String, boolean)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/StAXPropertyHandler.html" title="class in org.biojava.bio.seq.io.agave">StAXPropertyHandler</a></dt>
<dd>
<div class="block">Sets the element name that the class responds to.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game/StAXFeatureHandler.html#setHandlerCharacteristics(java.lang.String, boolean)">setHandlerCharacteristics(String, boolean)</a></span> - Method in class org.biojava.bio.seq.io.game.<a href="./org/biojava/bio/seq/io/game/StAXFeatureHandler.html" title="class in org.biojava.bio.seq.io.game">StAXFeatureHandler</a></dt>
<dd>
<div class="block">Sets the element name that the class responds to.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game/StAXPropertyHandler.html#setHandlerCharacteristics(java.lang.String, boolean)">setHandlerCharacteristics(String, boolean)</a></span> - Method in class org.biojava.bio.seq.io.game.<a href="./org/biojava/bio/seq/io/game/StAXPropertyHandler.html" title="class in org.biojava.bio.seq.io.game">StAXPropertyHandler</a></dt>
<dd>
<div class="block">Sets the element name that the class responds to.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Chain.html#setHeader(org.biojava.bio.structure.Compound)">setHeader(Compound)</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Chain.html" title="interface in org.biojava.bio.structure">Chain</a></dt>
<dd>
<div class="block">Set the Header from the PDB file.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/ChainImpl.html#setHeader(org.biojava.bio.structure.Compound)">setHeader(Compound)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/ChainImpl.html" title="class in org.biojava.bio.structure">ChainImpl</a></dt>
<dd>
<div class="block">Set the Header from the PDB file.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Structure.html#setHeader(java.util.Map)">setHeader(Map<String, Object>)</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Structure.html" title="interface in org.biojava.bio.structure">Structure</a></dt>
<dd>
<div class="block">set the Header data .</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/StructureImpl.html#setHeader(java.util.Map)">setHeader(Map<String, Object>)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/StructureImpl.html" title="class in org.biojava.bio.structure">StructureImpl</a></dt>
<dd>
<div class="block">set the Header data.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/FastaFormat.html#setHeader(org.biojavax.bio.seq.io.FastaHeader)">setHeader(FastaHeader)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/FastaFormat.html" title="class in org.biojavax.bio.seq.io">FastaFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Compound.html#setHeaderVars(java.lang.String)">setHeaderVars(String)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure">Compound</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.html#setHeight(int)">setHeight(int)</a></span> - Method in class org.biojava.bio.chromatogram.graphic.<a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.html" title="class in org.biojava.bio.chromatogram.graphic">ChromatogramGraphic</a></dt>
<dd>
<div class="block">Sets the height (in pixels).</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/RectangularBeadRenderer.html#setHeightScaling(boolean)">setHeightScaling(boolean)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/RectangularBeadRenderer.html" title="class in org.biojava.bio.gui.sequence">RectangularBeadRenderer</a></dt>
<dd>
<div class="block"><code>setHeightScaling</code> sets the height scaling
policy.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/RectangularImapRenderer.html#setHeightScaling(boolean)">setHeightScaling(boolean)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/RectangularImapRenderer.html" title="class in org.biojava.bio.gui.sequence">RectangularImapRenderer</a></dt>
<dd>
<div class="block"><code>setHeightScaling</code> sets the height scaling
policy.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/EntityPolySeq.html#setHetero(java.lang.String)">setHetero(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/EntityPolySeq.html" title="class in org.biojava.bio.structure.io.mmcif.model">EntityPolySeq</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/PdbxPolySeqScheme.html#setHetero(java.lang.String)">setHetero(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/PdbxPolySeqScheme.html" title="class in org.biojava.bio.structure.io.mmcif.model">PdbxPolySeqScheme</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.html#setHorizontalScale(float)">setHorizontalScale(float)</a></span> - Method in class org.biojava.bio.chromatogram.graphic.<a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.html" title="class in org.biojava.bio.chromatogram.graphic">ChromatogramGraphic</a></dt>
<dd>
<div class="block">Sets the horizontal scale (proportional).</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEDbId.html#setId(java.lang.String)">setId(String)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEDbId.html" title="class in org.biojava.bio.seq.io.agave">AGAVEDbId</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/AtomImpl.html#setId(long)">setId(long)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/AtomImpl.html" title="class in org.biojava.bio.structure">AtomImpl</a></dt>
<dd>
<div class="block">Set the Hibernate database ID.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Chain.html#setId(java.lang.Long)">setId(Long)</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Chain.html" title="interface in org.biojava.bio.structure">Chain</a></dt>
<dd>
<div class="block">Set the ID used by Hibernate.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/ChainImpl.html#setId(java.lang.Long)">setId(Long)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/ChainImpl.html" title="class in org.biojava.bio.structure">ChainImpl</a></dt>
<dd>
<div class="block">Set the ID used by Hibernate.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Compound.html#setId(java.lang.Long)">setId(Long)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure">Compound</a></dt>
<dd>
<div class="block">set the ID used by Hibernate</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/DBRef.html#setId(java.lang.Long)">setId(Long)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/DBRef.html" title="class in org.biojava.bio.structure">DBRef</a></dt>
<dd>
<div class="block">Set the ID used by Hibernate.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/HetatomImpl.html#setId(long)">setId(long)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/HetatomImpl.html" title="class in org.biojava.bio.structure">HetatomImpl</a></dt>
<dd>
<div class="block">the Hibernate database ID</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html#setId(java.lang.String)">setId(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html" title="class in org.biojava.bio.structure.io.mmcif.model">AtomSite</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html#setId(java.lang.String)">setId(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html" title="class in org.biojava.bio.structure.io.mmcif.model">ChemComp</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/DatabasePDBremark.html#setId(java.lang.String)">setId(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/DatabasePDBremark.html" title="class in org.biojava.bio.structure.io.mmcif.model">DatabasePDBremark</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Entity.html#setId(java.lang.String)">setId(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Entity.html" title="class in org.biojava.bio.structure.io.mmcif.model">Entity</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/StructAsym.html#setId(java.lang.String)">setId(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/StructAsym.html" title="class in org.biojava.bio.structure.io.mmcif.model">StructAsym</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/StructRef.html#setId(java.lang.String)">setId(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/StructRef.html" title="class in org.biojava.bio.structure.io.mmcif.model">StructRef</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Structure.html#setId(java.lang.Long)">setId(Long)</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Structure.html" title="interface in org.biojava.bio.structure">Structure</a></dt>
<dd>
<div class="block">set the ID used by Hibernate</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/StructureImpl.html#setId(java.lang.Long)">setId(Long)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/StructureImpl.html" title="class in org.biojava.bio.structure">StructureImpl</a></dt>
<dd>
<div class="block">set the ID used by Hibernate</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtCommentParser.Interaction.html#setID(java.lang.String)">setID(String)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtCommentParser.Interaction.html" title="class in org.biojavax.bio.seq.io">UniProtCommentParser.Interaction</a></dt>
<dd>
<div class="block">Setter for property ID.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimplePosition.html#setId(java.lang.Integer)">setId(Integer)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimplePosition.html" title="class in org.biojavax.bio.seq">SimplePosition</a></dt>
<dd>
<div class="block">Sets the Hibernate ID.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichFeature.html#setId(java.lang.Integer)">setId(Integer)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichFeature.html" title="class in org.biojavax.bio.seq">SimpleRichFeature</a></dt>
<dd>
<div class="block">Sets the Hibernate ID.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichFeatureRelationship.html#setId(java.lang.Integer)">setId(Integer)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichFeatureRelationship.html" title="class in org.biojavax.bio.seq">SimpleRichFeatureRelationship</a></dt>
<dd>
<div class="block">Sets the Hibernate ID.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichLocation.html#setId(java.lang.Integer)">setId(Integer)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichLocation.html" title="class in org.biojavax.bio.seq">SimpleRichLocation</a></dt>
<dd>
<div class="block">Sets the Hibernate ID.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/SimpleBioEntry.html#setId(java.lang.Integer)">setId(Integer)</a></span> - Method in class org.biojavax.bio.<a href="./org/biojavax/bio/SimpleBioEntry.html" title="class in org.biojavax.bio">SimpleBioEntry</a></dt>
<dd>
<div class="block">Sets the Hibernate ID.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/SimpleBioEntryRelationship.html#setId(java.lang.Integer)">setId(Integer)</a></span> - Method in class org.biojavax.bio.<a href="./org/biojavax/bio/SimpleBioEntryRelationship.html" title="class in org.biojavax.bio">SimpleBioEntryRelationship</a></dt>
<dd>
<div class="block">Sets the Hibernate ID.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/taxa/SimpleNCBITaxon.html#setId(java.lang.Integer)">setId(Integer)</a></span> - Method in class org.biojavax.bio.taxa.<a href="./org/biojavax/bio/taxa/SimpleNCBITaxon.html" title="class in org.biojavax.bio.taxa">SimpleNCBITaxon</a></dt>
<dd>
<div class="block">Sets the Hibernate ID.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ontology/SimpleComparableOntology.html#setId(java.lang.Integer)">setId(Integer)</a></span> - Method in class org.biojavax.ontology.<a href="./org/biojavax/ontology/SimpleComparableOntology.html" title="class in org.biojavax.ontology">SimpleComparableOntology</a></dt>
<dd>
<div class="block">Sets the Hibernate ID.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ontology/SimpleComparableTerm.html#setId(java.lang.Integer)">setId(Integer)</a></span> - Method in class org.biojavax.ontology.<a href="./org/biojavax/ontology/SimpleComparableTerm.html" title="class in org.biojavax.ontology">SimpleComparableTerm</a></dt>
<dd>
<div class="block">Sets the Hibernate ID.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ontology/SimpleComparableTriple.html#setId(java.lang.Integer)">setId(Integer)</a></span> - Method in class org.biojavax.ontology.<a href="./org/biojavax/ontology/SimpleComparableTriple.html" title="class in org.biojavax.ontology">SimpleComparableTriple</a></dt>
<dd>
<div class="block">Sets the Hibernate ID.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleComment.html#setId(java.lang.Integer)">setId(Integer)</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleComment.html" title="class in org.biojavax">SimpleComment</a></dt>
<dd>
<div class="block">Sets the Hibernate ID.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleCrossRef.html#setId(java.lang.Integer)">setId(Integer)</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleCrossRef.html" title="class in org.biojavax">SimpleCrossRef</a></dt>
<dd>
<div class="block">Sets the Hibernate ID.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleDocRef.html#setId(java.lang.Integer)">setId(Integer)</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleDocRef.html" title="class in org.biojavax">SimpleDocRef</a></dt>
<dd>
<div class="block">Sets the Hibernate ID.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleNamespace.html#setId(java.lang.Integer)">setId(Integer)</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleNamespace.html" title="class in org.biojavax">SimpleNamespace</a></dt>
<dd>
<div class="block">Sets the Hibernate ID.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/DBRef.html#setIdbnsBegin(char)">setIdbnsBegin(char)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/DBRef.html" title="class in org.biojava.bio.structure">DBRef</a></dt>
<dd>
<div class="block">Insertion code of initial residue of the segment, if PDB is the
reference.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/DBRef.html#setIdbnsEnd(char)">setIdbnsEnd(char)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/DBRef.html" title="class in org.biojava.bio.structure">DBRef</a></dt>
<dd>
<div class="block">Insertion code of the ending
residue of the segment, if PDB is
the reference.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/DBRef.html#setIdCode(java.lang.String)">setIdCode(String)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/DBRef.html" title="class in org.biojava.bio.structure">DBRef</a></dt>
<dd>
<div class="block">Set the idCode for this entry.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/PDBHeader.html#setIdCode(java.lang.String)">setIdCode(String)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/PDBHeader.html" title="class in org.biojava.bio.structure">PDBHeader</a></dt>
<dd>
<div class="block">The PDB code for this protein structure.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/BioEntry.html#setIdentifier(java.lang.String)">setIdentifier(String)</a></span> - Method in interface org.biojavax.bio.<a href="./org/biojavax/bio/BioEntry.html" title="interface in org.biojavax.bio">BioEntry</a></dt>
<dd>
<div class="block">Sets the identifier of this bioentry.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/DebuggingRichSeqIOListener.html#setIdentifier(java.lang.String)">setIdentifier(String)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/DebuggingRichSeqIOListener.html" title="class in org.biojavax.bio.seq.io">DebuggingRichSeqIOListener</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/RichSeqIOAdapter.html#setIdentifier(java.lang.String)">setIdentifier(String)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/RichSeqIOAdapter.html" title="class in org.biojavax.bio.seq.io">RichSeqIOAdapter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/RichSeqIOListener.html#setIdentifier(java.lang.String)">setIdentifier(String)</a></span> - Method in interface org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/RichSeqIOListener.html" title="interface in org.biojavax.bio.seq.io">RichSeqIOListener</a></dt>
<dd>
<div class="block">Call back method so the event emitter can tell the listener
the identifier of the record being read.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/SimpleRichSequenceBuilder.html#setIdentifier(java.lang.String)">setIdentifier(String)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/SimpleRichSequenceBuilder.html" title="class in org.biojavax.bio.seq.io">SimpleRichSequenceBuilder</a></dt>
<dd>
<div class="block">Call back method so the event emitter can tell the listener
the identifier of the record being read.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/SimpleBioEntry.html#setIdentifier(java.lang.String)">setIdentifier(String)</a></span> - Method in class org.biojavax.bio.<a href="./org/biojavax/bio/SimpleBioEntry.html" title="class in org.biojavax.bio">SimpleBioEntry</a></dt>
<dd>
<div class="block">Sets the identifier of this bioentry.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ontology/ComparableTerm.html#setIdentifier(java.lang.String)">setIdentifier(String)</a></span> - Method in interface org.biojavax.ontology.<a href="./org/biojavax/ontology/ComparableTerm.html" title="interface in org.biojavax.ontology">ComparableTerm</a></dt>
<dd>
<div class="block">Sets the (optional) identifier associated with this term.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ontology/SimpleComparableTerm.html#setIdentifier(java.lang.String)">setIdentifier(String)</a></span> - Method in class org.biojavax.ontology.<a href="./org/biojavax/ontology/SimpleComparableTerm.html" title="class in org.biojavax.ontology">SimpleComparableTerm</a></dt>
<dd>
<div class="block">Sets the (optional) identifier associated with this term.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/helper/JointFragments.html#setIdxlist(java.util.List)">setIdxlist(List<int[]>)</a></span> - Method in class org.biojava.bio.structure.align.helper.<a href="./org/biojava/bio/structure/align/helper/JointFragments.html" title="class in org.biojava.bio.structure.align.helper">JointFragments</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/BasicImapRenderer.html#setImageMap(org.biojava.bio.gui.sequence.ImageMap)">setImageMap(ImageMap)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/BasicImapRenderer.html" title="class in org.biojava.bio.gui.sequence">BasicImapRenderer</a></dt>
<dd>
<div class="block"><code>setImageMap</code> sets the current image map.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/RectangularImapRenderer.html#setImageMap(org.biojava.bio.gui.sequence.ImageMap)">setImageMap(ImageMap)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/RectangularImapRenderer.html" title="class in org.biojava.bio.gui.sequence">RectangularImapRenderer</a></dt>
<dd>
<div class="block"><code>setImageMap</code> sets the current image map.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/ZiggyImapRenderer.html#setImageMap(org.biojava.bio.gui.sequence.ImageMap)">setImageMap(ImageMap)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/ZiggyImapRenderer.html" title="class in org.biojava.bio.gui.sequence">ZiggyImapRenderer</a></dt>
<dd>
<div class="block"><code>setImageMap</code> sets the current image map.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/helper/GapArray.html#setIndex(int)">setIndex(int)</a></span> - Method in class org.biojava.bio.structure.align.helper.<a href="./org/biojava/bio/structure/align/helper/GapArray.html" title="class in org.biojava.bio.structure.align.helper">GapArray</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/StrucAligParameters.html#setInitialK(int)">setInitialK(int)</a></span> - Method in class org.biojava.bio.structure.align.<a href="./org/biojava/bio/structure/align/StrucAligParameters.html" title="class in org.biojava.bio.structure.align">StrucAligParameters</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Author.html#setInitials(java.lang.String)">setInitials(String)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Author.html" title="class in org.biojava.bio.structure">Author</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/process/OutputHandler.html#setInput(java.io.InputStream)">setInput(InputStream)</a></span> - Method in interface org.biojava.utils.process.<a href="./org/biojava/utils/process/OutputHandler.html" title="interface in org.biojava.utils.process">OutputHandler</a></dt>
<dd>
<div class="block">Sets the input stream.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/process/StreamPipe.html#setInput(java.io.InputStream)">setInput(InputStream)</a></span> - Method in class org.biojava.utils.process.<a href="./org/biojava/utils/process/StreamPipe.html" title="class in org.biojava.utils.process">StreamPipe</a></dt>
<dd>
<div class="block">Sets the input stream</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/process/WriterOutputHandler.html#setInput(java.io.InputStream)">setInput(InputStream)</a></span> - Method in class org.biojava.utils.process.<a href="./org/biojava/utils/process/WriterOutputHandler.html" title="class in org.biojava.utils.process">WriterOutputHandler</a></dt>
<dd>
<div class="block">Sets the input stream.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/process/ExternalProcess.html#setInputHandler(org.biojava.utils.process.InputHandler)">setInputHandler(InputHandler)</a></span> - Method in class org.biojava.utils.process.<a href="./org/biojava/utils/process/ExternalProcess.html" title="class in org.biojava.utils.process">ExternalProcess</a></dt>
<dd>
<div class="block">Sets the input handler which is responsible for the standard input
of the external process.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/SSBond.html#setInsCode1(java.lang.String)">setInsCode1(String)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/SSBond.html" title="class in org.biojava.bio.structure">SSBond</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/SSBond.html#setInsCode2(java.lang.String)">setInsCode2(String)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/SSBond.html" title="class in org.biojava.bio.structure">SSBond</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/NeedlemanWunsch.html#setInsert(short)">setInsert(short)</a></span> - Method in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/NeedlemanWunsch.html" title="class in org.biojava.bio.alignment">NeedlemanWunsch</a></dt>
<dd>
<div class="block">Sets the penalty for an insert operation to the specified value.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/SmithWaterman.html#setInsert(short)">setInsert(short)</a></span> - Method in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/SmithWaterman.html" title="class in org.biojava.bio.alignment">SmithWaterman</a></dt>
<dd>
<div class="block">Overrides the method inherited from the NeedlemanWunsch and sets the
penalty for an insert operation to the specified value.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/DBRef.html#setInsertBegin(char)">setInsertBegin(char)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/DBRef.html" title="class in org.biojava.bio.structure">DBRef</a></dt>
<dd>
<div class="block">Initial insertion code of the PDB sequence segment.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/DBRef.html#setInsertEnd(char)">setInsertEnd(char)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/DBRef.html" title="class in org.biojava.bio.structure">DBRef</a></dt>
<dd>
<div class="block">Ending insertion code of the PDB sequence segment.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html#setInteractions(java.util.List)">setInteractions(List)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html" title="class in org.biojavax.bio.seq.io">UniProtCommentParser</a></dt>
<dd>
<div class="block">Setter for property interactions.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/stax/IntElementHandlerBase.html#setIntValue(int)">setIntValue(int)</a></span> - Method in class org.biojava.utils.stax.<a href="./org/biojava/utils/stax/IntElementHandlerBase.html" title="class in org.biojava.utils.stax">IntElementHandlerBase</a></dt>
<dd>
<div class="block">Override this method to do something useful with the
int we collect.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html#setIsoforms(java.util.List)">setIsoforms(List)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html" title="class in org.biojavax.bio.seq.io">UniProtCommentParser</a></dt>
<dd>
<div class="block">Setter for property isoforms.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtCommentParser.Isoform.html#setIsoIDs(java.util.List)">setIsoIDs(List)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtCommentParser.Isoform.html" title="class in org.biojavax.bio.seq.io">UniProtCommentParser.Isoform</a></dt>
<dd>
<div class="block">Setter for property isoIDs.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/JournalArticle.html#setIsPublished(java.lang.Boolean)">setIsPublished(Boolean)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/JournalArticle.html" title="class in org.biojava.bio.structure">JournalArticle</a></dt>
<dd>
<div class="block">Sets the publication state of a JournalArticle - TO BE PUBLISHED == false</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/filterxml/XMLAnnotationTypeWriter.html#setIsStrict(boolean)">setIsStrict(boolean)</a></span> - Method in class org.biojava.bio.seq.io.filterxml.<a href="./org/biojava/bio/seq/io/filterxml/XMLAnnotationTypeWriter.html" title="class in org.biojava.bio.seq.io.filterxml">XMLAnnotationTypeWriter</a></dt>
<dd>
<div class="block">Selects strict mode.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/filterxml/XMLFilterWriter.html#setIsStrict(boolean)">setIsStrict(boolean)</a></span> - Method in class org.biojava.bio.seq.io.filterxml.<a href="./org/biojava/bio/seq/io/filterxml/XMLFilterWriter.html" title="class in org.biojava.bio.seq.io.filterxml">XMLFilterWriter</a></dt>
<dd>
<div class="block">Selects strict mode.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/Aggregator.html#setJoiner(java.lang.String)">setJoiner(String)</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/Aggregator.html" title="class in org.biojava.bio.program.tagvalue">Aggregator</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/StrucAligParameters.html#setJoinPlo(boolean)">setJoinPlo(boolean)</a></span> - Method in class org.biojava.bio.structure.align.<a href="./org/biojava/bio/structure/align/StrucAligParameters.html" title="class in org.biojava.bio.structure.align">StrucAligParameters</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/StrucAligParameters.html#setJoinRMSCutoff(double)">setJoinRMSCutoff(double)</a></span> - Method in class org.biojava.bio.structure.align.<a href="./org/biojava/bio/structure/align/StrucAligParameters.html" title="class in org.biojava.bio.structure.align">StrucAligParameters</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Structure.html#setJournalArticle(org.biojava.bio.structure.JournalArticle)">setJournalArticle(JournalArticle)</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Structure.html" title="interface in org.biojava.bio.structure">Structure</a></dt>
<dd>
<div class="block">set the associated publication as defined by the JRNL records in a PDB
file.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/StructureImpl.html#setJournalArticle(org.biojava.bio.structure.JournalArticle)">setJournalArticle(JournalArticle)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/StructureImpl.html" title="class in org.biojava.bio.structure">StructureImpl</a></dt>
<dd>
<div class="block">set the associated publication as defined by the JRNL records in a PDB
file.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/JournalArticle.html#setJournalName(java.lang.String)">setJournalName(String)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/JournalArticle.html" title="class in org.biojava.bio.structure">JournalArticle</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/aaindex/AAindex.html#setJournalReference(java.lang.String)">setJournalReference(String)</a></span> - Method in class org.biojava.bio.proteomics.aaindex.<a href="./org/biojava/bio/proteomics/aaindex/AAindex.html" title="class in org.biojava.bio.proteomics.aaindex">AAindex</a></dt>
<dd>
<div class="block">Sets a reference to the journal which published the article about the
AAindex entry.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/SVMRegressionModel.html#setKernel(org.biojava.stats.svm.SVMKernel)">setKernel(SVMKernel)</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/SVMRegressionModel.html" title="class in org.biojava.stats.svm">SVMRegressionModel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/tools/ClassifierExample.PointClassifier.html#setKernel(org.biojava.stats.svm.SVMKernel)">setKernel(SVMKernel)</a></span> - Method in class org.biojava.stats.svm.tools.<a href="./org/biojava/stats/svm/tools/ClassifierExample.PointClassifier.html" title="class in org.biojava.stats.svm.tools">ClassifierExample.PointClassifier</a></dt>
<dd>
<div class="block">Set the kernel used for classification.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/FeatureLabelRenderer.AnnotationLabelMaker.html#setKey(java.lang.Object)">setKey(Object)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/FeatureLabelRenderer.AnnotationLabelMaker.html" title="class in org.biojava.bio.gui.sequence">FeatureLabelRenderer.AnnotationLabelMaker</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html#setKineticsNote(java.lang.String)">setKineticsNote(String)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html" title="class in org.biojavax.bio.seq.io">UniProtCommentParser</a></dt>
<dd>
<div class="block">Setter for property kineticsNote.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html#setKMs(java.util.List)">setKMs(List)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html" title="class in org.biojavax.bio.seq.io">UniProtCommentParser</a></dt>
<dd>
<div class="block">Setter for property KMs.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/AlignmentRenderer.html#setLabel(java.lang.Object)">setLabel(Object)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/AlignmentRenderer.html" title="class in org.biojava.bio.gui.sequence">AlignmentRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SimpleLabelRenderer.html#setLabel(java.lang.String)">setLabel(String)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SimpleLabelRenderer.html" title="class in org.biojava.bio.gui.sequence">SimpleLabelRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtCommentParser.Interaction.html#setLabel(java.lang.String)">setLabel(String)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtCommentParser.Interaction.html" title="class in org.biojavax.bio.seq.io">UniProtCommentParser.Interaction</a></dt>
<dd>
<div class="block">Setter for property label.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html#setLabel_alt_id(java.lang.String)">setLabel_alt_id(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html" title="class in org.biojava.bio.structure.io.mmcif.model">AtomSite</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html#setLabel_asym_id(java.lang.String)">setLabel_asym_id(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html" title="class in org.biojava.bio.structure.io.mmcif.model">AtomSite</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html#setLabel_atom_id(java.lang.String)">setLabel_atom_id(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html" title="class in org.biojava.bio.structure.io.mmcif.model">AtomSite</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html#setLabel_comp_id(java.lang.String)">setLabel_comp_id(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html" title="class in org.biojava.bio.structure.io.mmcif.model">AtomSite</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html#setLabel_entity_id(java.lang.String)">setLabel_entity_id(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html" title="class in org.biojava.bio.structure.io.mmcif.model">AtomSite</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html#setLabel_seq_id(java.lang.String)">setLabel_seq_id(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html" title="class in org.biojava.bio.structure.io.mmcif.model">AtomSite</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/FeatureLabelRenderer.html#setLabelMaker(org.biojava.bio.gui.sequence.FeatureLabelRenderer.LabelMaker)">setLabelMaker(FeatureLabelRenderer.LabelMaker)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/FeatureLabelRenderer.html" title="class in org.biojava.bio.gui.sequence">FeatureLabelRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/DiagonalAddKernel.html#setLambda(double)">setLambda(double)</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/DiagonalAddKernel.html" title="class in org.biojava.stats.svm">DiagonalAddKernel</a></dt>
<dd>
<div class="block">Set the scale factor.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/BumpedRenderer.html#setLeadingPixles(int)">setLeadingPixles(int)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/BumpedRenderer.html" title="class in org.biojava.bio.gui.sequence">BumpedRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/biosql/TaxonSQL.html#setLeftValue(java.sql.Connection, org.biojava.bio.taxa.Taxon, int)">setLeftValue(Connection, Taxon, int)</a></span> - Static method in class org.biojava.bio.seq.db.biosql.<a href="./org/biojava/bio/seq/db/biosql/TaxonSQL.html" title="class in org.biojava.bio.seq.db.biosql">TaxonSQL</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Updates the taxon and sets the left value to the specified value.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/taxa/NCBITaxon.html#setLeftValue(java.lang.Integer)">setLeftValue(Integer)</a></span> - Method in interface org.biojavax.bio.taxa.<a href="./org/biojavax/bio/taxa/NCBITaxon.html" title="interface in org.biojavax.bio.taxa">NCBITaxon</a></dt>
<dd>
<div class="block">Sets the left value.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/taxa/SimpleNCBITaxon.html#setLeftValue(java.lang.Integer)">setLeftValue(Integer)</a></span> - Method in class org.biojavax.bio.taxa.<a href="./org/biojavax/bio/taxa/SimpleNCBITaxon.html" title="class in org.biojavax.bio.taxa">SimpleNCBITaxon</a></dt>
<dd>
<div class="block">Sets the left value.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SeqContentPattern.html#setLength(int)">setLength(int)</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SeqContentPattern.html" title="class in org.biojava.bio.search">SeqContentPattern</a></dt>
<dd>
<div class="block">Set the pattern length.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/AssembledSymbolList.html#setLength(int)">setLength(int)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/AssembledSymbolList.html" title="class in org.biojava.bio.seq.impl">AssembledSymbolList</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/NewAssembledSymbolList.html#setLength(int)">setLength(int)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/NewAssembledSymbolList.html" title="class in org.biojava.bio.seq.impl">NewAssembledSymbolList</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/FragmentPair.html#setLength(int)">setLength(int)</a></span> - Method in class org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/FragmentPair.html" title="class in org.biojava.bio.structure.align.pairwise">FragmentPair</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/util/CoordManager.html#setLength(int)">setLength(int)</a></span> - Method in class org.biojava.bio.structure.gui.util.<a href="./org/biojava/bio/structure/gui/util/CoordManager.html" title="class in org.biojava.bio.structure.gui.util">CoordManager</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/RepeatedCharSequence.html#setLength(int)">setLength(int)</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/RepeatedCharSequence.html" title="class in org.biojava.utils">RepeatedCharSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/cache/FixedSizeCache.html#setLimit(int)">setLimit(int)</a></span> - Method in class org.biojava.utils.cache.<a href="./org/biojava/utils/cache/FixedSizeCache.html" title="class in org.biojava.utils.cache">FixedSizeCache</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePoster.html#setLines(int)">setLines(int)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePoster.html" title="class in org.biojava.bio.gui.sequence">SequencePoster</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Set the absolute number of lines that the sequence will be rendered on.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/phred/PhredFormat.html#setLineWidth(int)">setLineWidth(int)</a></span> - Method in class org.biojava.bio.program.phred.<a href="./org/biojava/bio/program/phred/PhredFormat.html" title="class in org.biojava.bio.program.phred">PhredFormat</a></dt>
<dd>
<div class="block">Set the line width.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/FastaFormat.html#setLineWidth(int)">setLineWidth(int)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/FastaFormat.html" title="class in org.biojava.bio.seq.io">FastaFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Set the line width.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/RichSequenceFormat.BasicFormat.html#setLineWidth(int)">setLineWidth(int)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/RichSequenceFormat.BasicFormat.html" title="class in org.biojavax.bio.seq.io">RichSequenceFormat.BasicFormat</a></dt>
<dd>
<div class="block">Set the line width.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/RichSequenceFormat.html#setLineWidth(int)">setLineWidth(int)</a></span> - Method in interface org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/RichSequenceFormat.html" title="interface in org.biojavax.bio.seq.io">RichSequenceFormat</a></dt>
<dd>
<div class="block">Set the line width.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/StateMachine.BasicState.html#setListener(org.biojava.bio.program.tagvalue.TagValueListener)">setListener(TagValueListener)</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/StateMachine.BasicState.html" title="class in org.biojava.bio.program.tagvalue">StateMachine.BasicState</a></dt>
<dd>
<div class="block">set a TagValueListener for this State.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/TagDelegator.html#setListener(java.lang.Object, org.biojava.bio.program.tagvalue.TagValueListener)">setListener(Object, TagValueListener)</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/TagDelegator.html" title="class in org.biojava.bio.program.tagvalue">TagDelegator</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/automata/PatternBlitz.html#setListener(org.biojava.utils.automata.PatternListener)">setListener(PatternListener)</a></span> - Method in class org.biojava.utils.automata.<a href="./org/biojava/utils/automata/PatternBlitz.html" title="class in org.biojava.utils.automata">PatternBlitz</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/automata/StateMachineFactory.html#setListener(org.biojava.utils.automata.PatternListener)">setListener(PatternListener)</a></span> - Method in interface org.biojava.utils.automata.<a href="./org/biojava/utils/automata/StateMachineFactory.html" title="interface in org.biojava.utils.automata">StateMachineFactory</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/regex/Search.html#setListener(org.biojava.utils.regex.Search.Listener)">setListener(Search.Listener)</a></span> - Method in class org.biojava.utils.regex.<a href="./org/biojava/utils/regex/Search.html" title="class in org.biojava.utils.regex">Search</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/aaindex/AAindex.html#setLITDBEntryNumbers(java.lang.String[])">setLITDBEntryNumbers(String[])</a></span> - Method in class org.biojava.bio.proteomics.aaindex.<a href="./org/biojava/bio/proteomics/aaindex/AAindex.html" title="class in org.biojava.bio.proteomics.aaindex">AAindex</a></dt>
<dd>
<div class="block">Sets the list of literature database identifiers for the AAindex entry.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/AlignmentElement.html#setLoc(org.biojava.bio.symbol.Location)">setLoc(Location)</a></span> - Method in interface org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/AlignmentElement.html" title="interface in org.biojava.bio.alignment">AlignmentElement</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/SimpleAlignmentElement.html#setLoc(org.biojava.bio.symbol.Location)">setLoc(Location)</a></span> - Method in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/SimpleAlignmentElement.html" title="class in org.biojava.bio.alignment">SimpleAlignmentElement</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/Feature.html#setLocation(org.biojava.bio.symbol.Location)">setLocation(Location)</a></span> - Method in interface org.biojava.bio.seq.<a href="./org/biojava/bio/seq/Feature.html" title="interface in org.biojava.bio.seq">Feature</a></dt>
<dd>
<div class="block">The new location for this feature.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleFeature.html#setLocation(org.biojava.bio.symbol.Location)">setLocation(Location)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleFeature.html" title="class in org.biojava.bio.seq.impl">SimpleFeature</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichFeature.html#setLocation(org.biojava.bio.symbol.Location)">setLocation(Location)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichFeature.html" title="class in org.biojavax.bio.seq">SimpleRichFeature</a></dt>
<dd>
<div class="block">The new location for this feature.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/RankedDocRef.html#setLocation(org.biojavax.bio.seq.RichLocation)">setLocation(RichLocation)</a></span> - Method in interface org.biojavax.<a href="./org/biojavax/RankedDocRef.html" title="interface in org.biojavax">RankedDocRef</a></dt>
<dd>
<div class="block">Set the location of this reference.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleRankedDocRef.html#setLocation(org.biojavax.bio.seq.RichLocation)">setLocation(RichLocation)</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleRankedDocRef.html" title="class in org.biojavax">SimpleRankedDocRef</a></dt>
<dd>
<div class="block">Set the location of this reference.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/xff/LocationHandlerBase.html#setLocationValue(org.biojava.bio.symbol.Location)">setLocationValue(Location)</a></span> - Method in class org.biojava.bio.program.xff.<a href="./org/biojava/bio/program/xff/LocationHandlerBase.html" title="class in org.biojava.bio.program.xff">LocationHandlerBase</a></dt>
<dd>
<div class="block">Override this method to do something useful with the
location we collect.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/TextBlock.html#setLogoFont(java.awt.Font)">setLogoFont(Font)</a></span> - Method in class org.biojava.bio.gui.<a href="./org/biojava/bio/gui/TextBlock.html" title="class in org.biojava.bio.gui">TextBlock</a></dt>
<dd>
<div class="block">Set the current logo font.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/TextLogoPainter.html#setLogoFont(java.awt.Font)">setLogoFont(Font)</a></span> - Method in class org.biojava.bio.gui.<a href="./org/biojava/bio/gui/TextLogoPainter.html" title="class in org.biojava.bio.gui">TextLogoPainter</a></dt>
<dd>
<div class="block">Set the current logo font.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/DistributionLogo.html#setLogoPainter(org.biojava.bio.gui.LogoPainter)">setLogoPainter(LogoPainter)</a></span> - Method in class org.biojava.bio.gui.<a href="./org/biojava/bio/gui/DistributionLogo.html" title="class in org.biojava.bio.gui">DistributionLogo</a></dt>
<dd>
<div class="block">
Set the logo painter.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/stax/LongElementHandlerBase.html#setLongValue(long)">setLongValue(long)</a></span> - Method in class org.biojava.utils.stax.<a href="./org/biojava/utils/stax/LongElementHandlerBase.html" title="class in org.biojava.utils.stax">LongElementHandlerBase</a></dt>
<dd>
<div class="block">Override this method to do something useful with the
long we collect.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/RichObjectFactory.html#setLRUCacheSize(int)">setLRUCacheSize(int)</a></span> - Static method in class org.biojavax.<a href="./org/biojavax/RichObjectFactory.html" title="class in org.biojavax">RichObjectFactory</a></dt>
<dd>
<div class="block">Sets the size of the LRU cache.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/RichObjectFactory.html#setLRUCacheSize(java.lang.Class, int)">setLRUCacheSize(Class, int)</a></span> - Static method in class org.biojavax.<a href="./org/biojavax/RichObjectFactory.html" title="class in org.biojavax">RichObjectFactory</a></dt>
<dd>
<div class="block">Sets the size of the LRU cache.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#setLs_d_res_high(java.lang.String)">setLs_d_res_high(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#setLs_d_res_low(java.lang.String)">setLs_d_res_low(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#setLs_number_parameters(java.lang.String)">setLs_number_parameters(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#setLs_number_reflns_all(java.lang.String)">setLs_number_reflns_all(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#setLs_number_reflns_obs(java.lang.String)">setLs_number_reflns_obs(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#setLs_number_reflns_R_free(java.lang.String)">setLs_number_reflns_R_free(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#setLs_number_restraints(java.lang.String)">setLs_number_restraints(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#setLs_percent_reflns_obs(java.lang.String)">setLs_percent_reflns_obs(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#setLs_percent_reflns_R_free(java.lang.String)">setLs_percent_reflns_R_free(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#setLs_R_factor_all(java.lang.String)">setLs_R_factor_all(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#setLs_R_factor_obs(java.lang.String)">setLs_R_factor_obs(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#setLs_R_factor_R_free(java.lang.String)">setLs_R_factor_R_free(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#setLs_R_factor_R_free_error(java.lang.String)">setLs_R_factor_R_free_error(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#setLs_R_factor_R_free_error_details(java.lang.String)">setLs_R_factor_R_free_error_details(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#setLs_R_factor_R_work(java.lang.String)">setLs_R_factor_R_work(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#setLs_redundancy_reflns_obs(java.lang.String)">setLs_redundancy_reflns_obs(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#setLs_wR_factor_R_free(java.lang.String)">setLs_wR_factor_R_free(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#setLs_wR_factor_R_work(java.lang.String)">setLs_wR_factor_R_work(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/molbio/RestrictionMapper.html#setMapAll(boolean)">setMapAll(boolean)</a></span> - Method in class org.biojava.bio.molbio.<a href="./org/biojava/bio/molbio/RestrictionMapper.html" title="class in org.biojava.bio.molbio">RestrictionMapper</a></dt>
<dd>
<div class="block"><code>setMapAll</code> sets whether all sites should be marked,
including those which have recognition sites within the
sequence, but cut outside it.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEMapLocation.html#setMapType(java.lang.String)">setMapType(String)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEMapLocation.html" title="class in org.biojava.bio.seq.io.agave">AGAVEMapLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/NeedlemanWunsch.html#setMatch(short)">setMatch(short)</a></span> - Method in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/NeedlemanWunsch.html" title="class in org.biojava.bio.alignment">NeedlemanWunsch</a></dt>
<dd>
<div class="block">Sets the penalty for a match operation to the specified value.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/SmithWaterman.html#setMatch(short)">setMatch(short)</a></span> - Method in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/SmithWaterman.html" title="class in org.biojava.bio.alignment">SmithWaterman</a></dt>
<dd>
<div class="block">Overrides the method inherited from the NeedlemanWunsch and sets the
penalty for a match operation to the specified value.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/JMatrixPanel.html#setMatrix(org.biojava.bio.structure.jama.Matrix)">setMatrix(Matrix)</a></span> - Method in class org.biojava.bio.structure.gui.<a href="./org/biojava/bio/structure/gui/JMatrixPanel.html" title="class in org.biojava.bio.structure.gui">JMatrixPanel</a></dt>
<dd>
<div class="block">sets the distance matrix to be displayed</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/ScaleableMatrixPanel.html#setMatrix(org.biojava.bio.structure.jama.Matrix)">setMatrix(Matrix)</a></span> - Method in class org.biojava.bio.structure.gui.<a href="./org/biojava/bio/structure/gui/ScaleableMatrixPanel.html" title="class in org.biojava.bio.structure.gui">ScaleableMatrixPanel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/jama/Matrix.html#setMatrix(int, int, int, int, org.biojava.bio.structure.jama.Matrix)">setMatrix(int, int, int, int, Matrix)</a></span> - Method in class org.biojava.bio.structure.jama.<a href="./org/biojava/bio/structure/jama/Matrix.html" title="class in org.biojava.bio.structure.jama">Matrix</a></dt>
<dd>
<div class="block">Set a submatrix.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/jama/Matrix.html#setMatrix(int[], int[], org.biojava.bio.structure.jama.Matrix)">setMatrix(int[], int[], Matrix)</a></span> - Method in class org.biojava.bio.structure.jama.<a href="./org/biojava/bio/structure/jama/Matrix.html" title="class in org.biojava.bio.structure.jama">Matrix</a></dt>
<dd>
<div class="block">Set a submatrix.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/jama/Matrix.html#setMatrix(int[], int, int, org.biojava.bio.structure.jama.Matrix)">setMatrix(int[], int, int, Matrix)</a></span> - Method in class org.biojava.bio.structure.jama.<a href="./org/biojava/bio/structure/jama/Matrix.html" title="class in org.biojava.bio.structure.jama">Matrix</a></dt>
<dd>
<div class="block">Set a submatrix.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/jama/Matrix.html#setMatrix(int, int, int[], org.biojava.bio.structure.jama.Matrix)">setMatrix(int, int, int[], Matrix)</a></span> - Method in class org.biojava.bio.structure.jama.<a href="./org/biojava/bio/structure/jama/Matrix.html" title="class in org.biojava.bio.structure.jama">Matrix</a></dt>
<dd>
<div class="block">Set a submatrix.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SeqContentPattern.html#setMaxCounts(org.biojava.bio.symbol.AtomicSymbol, int)">setMaxCounts(AtomicSymbol, int)</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SeqContentPattern.html" title="class in org.biojava.bio.search">SeqContentPattern</a></dt>
<dd>
<div class="block">Set the maximum counts required for a symbol.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ga/functions/AbstractCrossOverFunction.html#setMaxCrossOvers(int)">setMaxCrossOvers(int)</a></span> - Method in class org.biojavax.ga.functions.<a href="./org/biojavax/ga/functions/AbstractCrossOverFunction.html" title="class in org.biojavax.ga.functions">AbstractCrossOverFunction</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/functions/CrossOverFunction.NoCross.html#setMaxCrossOvers(int)">setMaxCrossOvers(int)</a></span> - Method in class org.biojavax.ga.functions.<a href="./org/biojavax/ga/functions/CrossOverFunction.NoCross.html" title="class in org.biojavax.ga.functions">CrossOverFunction.NoCross</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/functions/CrossOverFunction.html#setMaxCrossOvers(int)">setMaxCrossOvers(int)</a></span> - Method in interface org.biojavax.ga.functions.<a href="./org/biojavax/ga/functions/CrossOverFunction.html" title="interface in org.biojavax.ga.functions">CrossOverFunction</a></dt>
<dd>
<div class="block">Sets an upper limit on the number of crosses.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/StrucAligParameters.html#setMaxIter(int)">setMaxIter(int)</a></span> - Method in class org.biojava.bio.structure.align.<a href="./org/biojava/bio/structure/align/StrucAligParameters.html" title="class in org.biojava.bio.structure.align">StrucAligParameters</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/Digest.html#setMaxMissedCleavages(int)">setMaxMissedCleavages(int)</a></span> - Method in class org.biojava.bio.proteomics.<a href="./org/biojava/bio/proteomics/Digest.html" title="class in org.biojava.bio.proteomics">Digest</a></dt>
<dd>
<div class="block">Sets the maximum number of partial digest products to be annotated.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichLocation.html#setMaxPosition(org.biojavax.bio.seq.Position)">setMaxPosition(Position)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichLocation.html" title="class in org.biojavax.bio.seq">SimpleRichLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/StrucAligParameters.html#setMaxrefine(int)">setMaxrefine(int)</a></span> - Method in class org.biojava.bio.structure.align.<a href="./org/biojava/bio/structure/align/StrucAligParameters.html" title="class in org.biojava.bio.structure.align">StrucAligParameters</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ExecRunner.html#setMaxRunTimeSecs(int)">setMaxRunTimeSecs(int)</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/ExecRunner.html" title="class in org.biojava.utils">ExecRunner</a></dt>
<dd>
<div class="block">Sets the maximum run time in seconds.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/xff/XFFFeatureSetHandler.html#setMergeAnnotation(org.biojava.bio.Annotation)">setMergeAnnotation(Annotation)</a></span> - Method in class org.biojava.bio.program.xff.<a href="./org/biojava/bio/program/xff/XFFFeatureSetHandler.html" title="class in org.biojava.bio.program.xff">XFFFeatureSetHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/LineSplitParser.html#setMergeSameTag(boolean)">setMergeSameTag(boolean)</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/LineSplitParser.html" title="class in org.biojava.bio.program.tagvalue">LineSplitParser</a></dt>
<dd>
<div class="block">Enable or disable treating runs of identical tags as a single tag start
event with multiple values or each as a separate tag start, value, and tag
end.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/RegexParser.html#setMergeSameTag(boolean)">setMergeSameTag(boolean)</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/RegexParser.html" title="class in org.biojava.bio.program.tagvalue">RegexParser</a></dt>
<dd>
<div class="block">Decide if multiple examples of a single tag should be merged into a single
start/endTag pair with multiple values, or multiple start/endTag pairs each
with a single value.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Exptl.html#setMethod(java.lang.String)">setMethod(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Exptl.html" title="class in org.biojava.bio.structure.io.mmcif.model">Exptl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/PDBHeader.html#setMethod(java.lang.String)">setMethod(String)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/PDBHeader.html" title="class in org.biojava.bio.structure">PDBHeader</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Exptl.html#setMethod_details(java.lang.String)">setMethod_details(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Exptl.html" title="class in org.biojava.bio.structure.io.mmcif.model">Exptl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SeqContentPattern.html#setMinCounts(org.biojava.bio.symbol.AtomicSymbol, int)">setMinCounts(AtomicSymbol, int)</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SeqContentPattern.html" title="class in org.biojava.bio.search">SeqContentPattern</a></dt>
<dd>
<div class="block">Set the minimum counts required for a symbol.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichLocation.html#setMinPosition(org.biojavax.bio.seq.Position)">setMinPosition(Position)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichLocation.html" title="class in org.biojavax.bio.seq">SimpleRichLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/MaxMismatchPattern.html#setMismatches(int)">setMismatches(int)</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/MaxMismatchPattern.html" title="class in org.biojava.bio.search">MaxMismatchPattern</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/biosql/TaxonSQL.html#setMitochondrialGeneticCodeID(java.sql.Connection, org.biojava.bio.taxa.Taxon, int)">setMitochondrialGeneticCodeID(Connection, Taxon, int)</a></span> - Static method in class org.biojava.bio.seq.db.biosql.<a href="./org/biojava/bio/seq/db/biosql/TaxonSQL.html" title="class in org.biojava.bio.seq.db.biosql">TaxonSQL</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Updates the given taxon and sets it's so called mitochondrial genetic code id to
the specified value.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/taxa/NCBITaxon.html#setMitoGeneticCode(java.lang.Integer)">setMitoGeneticCode(Integer)</a></span> - Method in interface org.biojavax.bio.taxa.<a href="./org/biojavax/bio/taxa/NCBITaxon.html" title="interface in org.biojavax.bio.taxa">NCBITaxon</a></dt>
<dd>
<div class="block">Sets the mitochondrial genetic code of this taxon, which may be null,
which will unset it.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/taxa/SimpleNCBITaxon.html#setMitoGeneticCode(java.lang.Integer)">setMitoGeneticCode(Integer)</a></span> - Method in class org.biojavax.bio.taxa.<a href="./org/biojavax/bio/taxa/SimpleNCBITaxon.html" title="class in org.biojavax.bio.taxa">SimpleNCBITaxon</a></dt>
<dd>
<div class="block">Sets the mitochondrial genetic code of this taxon, which may be null,
which will unset it.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/DatabasePDBrev.html#setMod_type(java.lang.String)">setMod_type(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/DatabasePDBrev.html" title="class in org.biojava.bio.structure.io.mmcif.model">DatabasePDBrev</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/PDBHeader.html#setModDate(java.util.Date)">setModDate(Date)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/PDBHeader.html" title="class in org.biojava.bio.structure">PDBHeader</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/DP.html#setModel(org.biojava.bio.dp.MarkovModel)">setModel(MarkovModel)</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/DP.html" title="class in org.biojava.bio.dp">DP</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Structure.html#setModel(int, java.util.List)">setModel(int, List<Chain>)</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Structure.html" title="interface in org.biojava.bio.structure">Structure</a></dt>
<dd>
<div class="block">a convenience function if one wants to edit and replace the
models in a structure.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/StructureImpl.html#setModel(int, java.util.List)">setModel(int, List<Chain>)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/StructureImpl.html" title="class in org.biojava.bio.structure">StructureImpl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/BlastLikeToXMLConverter.html#setModeLazy()">setModeLazy()</a></span> - Method in class org.biojava.bio.program.<a href="./org/biojava/bio/program/BlastLikeToXMLConverter.html" title="class in org.biojava.bio.program">BlastLikeToXMLConverter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/sax/BlastLikeSAXParser.html#setModeLazy()">setModeLazy()</a></span> - Method in class org.biojava.bio.program.sax.<a href="./org/biojava/bio/program/sax/BlastLikeSAXParser.html" title="class in org.biojava.bio.program.sax">BlastLikeSAXParser</a></dt>
<dd>
<div class="block">Setting the mode to lazy means that, if the program is recognised,
e.g.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/BlastLikeToXMLConverter.html#setModeStrict()">setModeStrict()</a></span> - Method in class org.biojava.bio.program.<a href="./org/biojava/bio/program/BlastLikeToXMLConverter.html" title="class in org.biojava.bio.program">BlastLikeToXMLConverter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/sax/BlastLikeSAXParser.html#setModeStrict()">setModeStrict()</a></span> - Method in class org.biojava.bio.program.sax.<a href="./org/biojava/bio/program/sax/BlastLikeSAXParser.html" title="class in org.biojava.bio.program.sax">BlastLikeSAXParser</a></dt>
<dd>
<div class="block">This is the default, parsing will be attempted only if both
the program e.g.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html#setMolecularWeight(int)">setMolecularWeight(int)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html" title="class in org.biojavax.bio.seq.io">UniProtCommentParser</a></dt>
<dd>
<div class="block">Setter for property molecularWeight.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Compound.html#setMolId(java.lang.String)">setMolId(String)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure">Compound</a></dt>
<dd>
<div class="block">Set the mol id value.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Compound.html#setMolName(java.lang.String)">setMolName(String)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure">Compound</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html#setMolWeightError(java.lang.Integer)">setMolWeightError(Integer)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html" title="class in org.biojavax.bio.seq.io">UniProtCommentParser</a></dt>
<dd>
<div class="block">Setter for property molWeightError.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html#setMolWeightMethod(java.lang.String)">setMolWeightMethod(String)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html" title="class in org.biojavax.bio.seq.io">UniProtCommentParser</a></dt>
<dd>
<div class="block">Setter for property molWeightMethod.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html#setMolWeightRangeEnd(int)">setMolWeightRangeEnd(int)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html" title="class in org.biojavax.bio.seq.io">UniProtCommentParser</a></dt>
<dd>
<div class="block">Setter for property molWeightRangeEnd.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html#setMolWeightRangeStart(int)">setMolWeightRangeStart(int)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html" title="class in org.biojavax.bio.seq.io">UniProtCommentParser</a></dt>
<dd>
<div class="block">Setter for property molWeightRangeStart.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/EntityPolySeq.html#setMon_id(java.lang.String)">setMon_id(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/EntityPolySeq.html" title="class in org.biojava.bio.structure.io.mmcif.model">EntityPolySeq</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/PdbxNonPolyScheme.html#setMon_id(java.lang.String)">setMon_id(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/PdbxNonPolyScheme.html" title="class in org.biojava.bio.structure.io.mmcif.model">PdbxNonPolyScheme</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/PdbxPolySeqScheme.html#setMon_id(java.lang.String)">setMon_id(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/PdbxPolySeqScheme.html" title="class in org.biojava.bio.structure.io.mmcif.model">PdbxPolySeqScheme</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html#setMon_nstd_flag(java.lang.String)">setMon_nstd_flag(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html" title="class in org.biojava.bio.structure.io.mmcif.model">ChemComp</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html#setMon_nstd_parent_comp_id(java.lang.String)">setMon_nstd_parent_comp_id(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html" title="class in org.biojava.bio.structure.io.mmcif.model">ChemComp</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/sax/FastaSearchSAXParser.html#setMoreSearches(boolean)">setMoreSearches(boolean)</a></span> - Method in class org.biojava.bio.program.sax.<a href="./org/biojava/bio/program/sax/FastaSearchSAXParser.html" title="class in org.biojava.bio.program.sax">FastaSearchSAXParser</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/BlastLikeHomologyBuilder.html#setMoreSearches(boolean)">setMoreSearches(boolean)</a></span> - Method in class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/BlastLikeHomologyBuilder.html" title="class in org.biojava.bio.program.ssbind">BlastLikeHomologyBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/BlastLikeSearchBuilder.html#setMoreSearches(boolean)">setMoreSearches(boolean)</a></span> - Method in class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/BlastLikeSearchBuilder.html" title="class in org.biojava.bio.program.ssbind">BlastLikeSearchBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/SimilarityPairBuilder.html#setMoreSearches(boolean)">setMoreSearches(boolean)</a></span> - Method in class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/SimilarityPairBuilder.html" title="class in org.biojava.bio.program.ssbind">SimilarityPairBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SearchContentAdapter.html#setMoreSearches(boolean)">setMoreSearches(boolean)</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SearchContentAdapter.html" title="class in org.biojava.bio.search">SearchContentAdapter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SearchContentFilter.html#setMoreSearches(boolean)">setMoreSearches(boolean)</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SearchContentFilter.html" title="class in org.biojava.bio.search">SearchContentFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SearchContentHandler.html#setMoreSearches(boolean)">setMoreSearches(boolean)</a></span> - Method in interface org.biojava.bio.search.<a href="./org/biojava/bio/search/SearchContentHandler.html" title="interface in org.biojava.bio.search">SearchContentHandler</a></dt>
<dd>
<div class="block"><code>setMoreSearches</code> sets the state of the
<code>SearchContentHandler</code>'s expectation of receiving
more results.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SearchContentHandlerDebugger.html#setMoreSearches(boolean)">setMoreSearches(boolean)</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SearchContentHandlerDebugger.html" title="class in org.biojava.bio.search">SearchContentHandlerDebugger</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/PolynomialKernel.html#setMultiplier(double)">setMultiplier(double)</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/PolynomialKernel.html" title="class in org.biojava.stats.svm">PolynomialKernel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/SigmoidKernel.html#setMultiplier(double)">setMultiplier(double)</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/SigmoidKernel.html" title="class in org.biojava.stats.svm">SigmoidKernel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Compound.html#setMutation(java.lang.String)">setMutation(String)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure">Compound</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/GeneticAlgorithm.html#setMutationFunction(org.biojavax.ga.functions.MutationFunction)">setMutationFunction(MutationFunction)</a></span> - Method in interface org.biojavax.ga.<a href="./org/biojavax/ga/GeneticAlgorithm.html" title="interface in org.biojavax.ga">GeneticAlgorithm</a></dt>
<dd>
<div class="block">Sets the current <code>MutationFunction</code></div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ga/impl/AbstractGeneticAlgorithm.html#setMutationFunction(org.biojavax.ga.functions.MutationFunction)">setMutationFunction(MutationFunction)</a></span> - Method in class org.biojavax.ga.impl.<a href="./org/biojavax/ga/impl/AbstractGeneticAlgorithm.html" title="class in org.biojavax.ga.impl">AbstractGeneticAlgorithm</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/functions/AbstractMutationFunction.html#setMutationProbs(double[])">setMutationProbs(double[])</a></span> - Method in class org.biojavax.ga.functions.<a href="./org/biojavax/ga/functions/AbstractMutationFunction.html" title="class in org.biojavax.ga.functions">AbstractMutationFunction</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/functions/MutationFunction.NoMutation.html#setMutationProbs(double[])">setMutationProbs(double[])</a></span> - Method in class org.biojavax.ga.functions.<a href="./org/biojavax/ga/functions/MutationFunction.NoMutation.html" title="class in org.biojavax.ga.functions">MutationFunction.NoMutation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/functions/MutationFunction.html#setMutationProbs(double[])">setMutationProbs(double[])</a></span> - Method in interface org.biojavax.ga.functions.<a href="./org/biojavax/ga/functions/MutationFunction.html" title="interface in org.biojavax.ga.functions">MutationFunction</a></dt>
<dd>
<div class="block">Set the probability of a mutation occuring at a certain position
Position 0 in the array corresponds to the
probability of the first residue of <code>seq</code> mutating.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ga/functions/AbstractMutationFunction.html#setMutationSpectrum(org.biojava.bio.dist.OrderNDistribution)">setMutationSpectrum(OrderNDistribution)</a></span> - Method in class org.biojavax.ga.functions.<a href="./org/biojavax/ga/functions/AbstractMutationFunction.html" title="class in org.biojavax.ga.functions">AbstractMutationFunction</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/functions/MutationFunction.NoMutation.html#setMutationSpectrum(org.biojava.bio.dist.OrderNDistribution)">setMutationSpectrum(OrderNDistribution)</a></span> - Method in class org.biojavax.ga.functions.<a href="./org/biojavax/ga/functions/MutationFunction.NoMutation.html" title="class in org.biojavax.ga.functions">MutationFunction.NoMutation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/functions/MutationFunction.html#setMutationSpectrum(org.biojava.bio.dist.OrderNDistribution)">setMutationSpectrum(OrderNDistribution)</a></span> - Method in interface org.biojavax.ga.functions.<a href="./org/biojavax/ga/functions/MutationFunction.html" title="interface in org.biojavax.ga.functions">MutationFunction</a></dt>
<dd>
<div class="block">Sets the <code>Distribution</code> of <code>Symbols</code> that will be selected
from when a mutation occurs.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/SimpleEmissionState.html#setName(java.lang.String)">setName(String)</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/SimpleEmissionState.html" title="class in org.biojava.bio.dp">SimpleEmissionState</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/OrthoPairSet.html#setName(java.lang.String)">setName(String)</a></span> - Method in interface org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/OrthoPairSet.html" title="interface in org.biojava.bio.program.homologene">OrthoPairSet</a></dt>
<dd>
<div class="block">set the name of this group.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/SimpleOrthoPairSet.html#setName(java.lang.String)">setName(String)</a></span> - Method in class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/SimpleOrthoPairSet.html" title="class in org.biojava.bio.program.homologene">SimpleOrthoPairSet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleSequence.html#setName(java.lang.String)">setName(String)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleSequence.html" title="class in org.biojava.bio.seq.impl">SimpleSequence</a></dt>
<dd>
<div class="block">Assign a name to this sequence</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/EmblFileFormer.html#setName(java.lang.String)">setName(String)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/EmblFileFormer.html" title="class in org.biojava.bio.seq.io">EmblFileFormer</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/GenbankFileFormer.html#setName(java.lang.String)">setName(String)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/GenbankFileFormer.html" title="class in org.biojava.bio.seq.io">GenbankFileFormer</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOAdapter.html#setName(java.lang.String)">setName(String)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOAdapter.html" title="class in org.biojava.bio.seq.io">SeqIOAdapter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOFilter.html#setName(java.lang.String)">setName(String)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOFilter.html" title="class in org.biojava.bio.seq.io">SeqIOFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOListener.html#setName(java.lang.String)">setName(String)</a></span> - Method in interface org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOListener.html" title="interface in org.biojava.bio.seq.io">SeqIOListener</a></dt>
<dd>
<div class="block">Notify the listener that the current sequence is generally known
by a particular name.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SequenceBuilderBase.html#setName(java.lang.String)">setName(String)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SequenceBuilderBase.html" title="class in org.biojava.bio.seq.io">SequenceBuilderBase</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SequenceBuilderFilter.html#setName(java.lang.String)">setName(String)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SequenceBuilderFilter.html" title="class in org.biojava.bio.seq.io">SequenceBuilderFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SwissprotFileFormer.html#setName(java.lang.String)">setName(String)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SwissprotFileFormer.html" title="class in org.biojava.bio.seq.io">SwissprotFileFormer</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">The name is printed out as part of the identifier line.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Atom.html#setName(java.lang.String)">setName(String)</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Atom.html" title="interface in org.biojava.bio.structure">Atom</a></dt>
<dd>
<div class="block">set trimmed version of atom name, e.g.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/AtomImpl.html#setName(java.lang.String)">setName(String)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/AtomImpl.html" title="class in org.biojava.bio.structure">AtomImpl</a></dt>
<dd>
<div class="block">trimmed version of atom name, e.g.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Chain.html#setName(java.lang.String)">setName(String)</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Chain.html" title="interface in org.biojava.bio.structure">Chain</a></dt>
<dd>
<div class="block">get and set the name of this chain (Chain id in PDB file ).</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/ChainImpl.html#setName(java.lang.String)">setName(String)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/ChainImpl.html" title="class in org.biojava.bio.structure">ChainImpl</a></dt>
<dd>
<div class="block">get and set the name of this chain (Chain id in PDB file ).</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html#setName(java.lang.String)">setName(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html" title="class in org.biojava.bio.structure.io.mmcif.model">ChemComp</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/PdbxEntityNonPoly.html#setName(java.lang.String)">setName(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/PdbxEntityNonPoly.html" title="class in org.biojava.bio.structure.io.mmcif.model">PdbxEntityNonPoly</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Structure.html#setName(java.lang.String)">setName(String)</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Structure.html" title="interface in org.biojava.bio.structure">Structure</a></dt>
<dd>
<div class="block">set biological name of Structure .</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/StructureImpl.html#setName(java.lang.String)">setName(String)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/StructureImpl.html" title="class in org.biojava.bio.structure">StructureImpl</a></dt>
<dd>
<div class="block">set biological name of Structure.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleAlphabet.html#setName(java.lang.String)">setName(String)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleAlphabet.html" title="class in org.biojava.bio.symbol">SimpleAlphabet</a></dt>
<dd>
<div class="block">Assign a name to the alphabet</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/IntegerOntology.html#setName(java.lang.String)">setName(String)</a></span> - Method in class org.biojava.ontology.<a href="./org/biojava/ontology/IntegerOntology.html" title="class in org.biojava.ontology">IntegerOntology</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/Ontology.Impl.html#setName(java.lang.String)">setName(String)</a></span> - Method in class org.biojava.ontology.<a href="./org/biojava/ontology/Ontology.Impl.html" title="class in org.biojava.ontology">Ontology.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/Ontology.html#setName(java.lang.String)">setName(String)</a></span> - Method in interface org.biojava.ontology.<a href="./org/biojava/ontology/Ontology.html" title="interface in org.biojava.ontology">Ontology</a></dt>
<dd>
<div class="block">Set the name for this ontology</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/Synonym.html#setName(java.lang.String)">setName(String)</a></span> - Method in class org.biojava.ontology.<a href="./org/biojava/ontology/Synonym.html" title="class in org.biojava.ontology">Synonym</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/DebuggingRichSeqIOListener.html#setName(java.lang.String)">setName(String)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/DebuggingRichSeqIOListener.html" title="class in org.biojavax.bio.seq.io">DebuggingRichSeqIOListener</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/RichSeqIOAdapter.html#setName(java.lang.String)">setName(String)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/RichSeqIOAdapter.html" title="class in org.biojavax.bio.seq.io">RichSeqIOAdapter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/SimpleRichSequenceBuilder.html#setName(java.lang.String)">setName(String)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/SimpleRichSequenceBuilder.html" title="class in org.biojavax.bio.seq.io">SimpleRichSequenceBuilder</a></dt>
<dd>
<div class="block">Notify the listener that the current sequence is generally known
by a particular name.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichFeature.html#setName(java.lang.String)">setName(String)</a></span> - Method in interface org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichFeature.html" title="interface in org.biojavax.bio.seq">RichFeature</a></dt>
<dd>
<div class="block">Sets the name of this feature.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichFeature.html#setName(java.lang.String)">setName(String)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichFeature.html" title="class in org.biojavax.bio.seq">SimpleRichFeature</a></dt>
<dd>
<div class="block">Sets the name of this feature.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/taxa/SimpleNCBITaxonName.html#setName(java.lang.String)">setName(String)</a></span> - Method in class org.biojavax.bio.taxa.<a href="./org/biojavax/bio/taxa/SimpleNCBITaxonName.html" title="class in org.biojavax.bio.taxa">SimpleNCBITaxonName</a></dt>
<dd>
<div class="block">Changes the name.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ga/impl/AbstractOrganism.html#setName(java.lang.String)">setName(String)</a></span> - Method in class org.biojavax.ga.impl.<a href="./org/biojavax/ga/impl/AbstractOrganism.html" title="class in org.biojavax.ga.impl">AbstractOrganism</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/impl/AbstractPopulation.html#setName(java.lang.String)">setName(String)</a></span> - Method in class org.biojavax.ga.impl.<a href="./org/biojavax/ga/impl/AbstractPopulation.html" title="class in org.biojavax.ga.impl">AbstractPopulation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/Organism.html#setName(java.lang.String)">setName(String)</a></span> - Method in interface org.biojavax.ga.<a href="./org/biojavax/ga/Organism.html" title="interface in org.biojavax.ga">Organism</a></dt>
<dd>
<div class="block">Sets the organisms name</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ga/Population.html#setName(java.lang.String)">setName(String)</a></span> - Method in interface org.biojavax.ga.<a href="./org/biojavax/ga/Population.html" title="interface in org.biojavax.ga">Population</a></dt>
<dd>
<div class="block">Sets the name of the population</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ontology/SimpleComparableOntology.html#setName(java.lang.String)">setName(String)</a></span> - Method in class org.biojavax.ontology.<a href="./org/biojavax/ontology/SimpleComparableOntology.html" title="class in org.biojavax.ontology">SimpleComparableOntology</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/taxa/SimpleNCBITaxonName.html#setNameClass(java.lang.String)">setNameClass(String)</a></span> - Method in class org.biojavax.bio.taxa.<a href="./org/biojavax/bio/taxa/SimpleNCBITaxonName.html" title="class in org.biojavax.bio.taxa">SimpleNCBITaxonName</a></dt>
<dd>
<div class="block">Changes the class of this name.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtCommentParser.Event.html#setNamedIsoforms(int)">setNamedIsoforms(int)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtCommentParser.Event.html" title="class in org.biojavax.bio.seq.io">UniProtCommentParser.Event</a></dt>
<dd>
<div class="block">Setter for property namedIsoforms.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtCommentParser.Isoform.html#setNames(java.util.List)">setNames(List)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtCommentParser.Isoform.html" title="class in org.biojavax.bio.seq.io">UniProtCommentParser.Isoform</a></dt>
<dd>
<div class="block">Setter for property names.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/ncbi/GenbankRichSequenceDB.html#setNamespace(org.biojavax.Namespace)">setNamespace(Namespace)</a></span> - Method in class org.biojavax.bio.db.ncbi.<a href="./org/biojavax/bio/db/ncbi/GenbankRichSequenceDB.html" title="class in org.biojavax.bio.db.ncbi">GenbankRichSequenceDB</a></dt>
<dd>
<div class="block">Setter for property namespace.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/ncbi/GenpeptRichSequenceDB.html#setNamespace(org.biojavax.Namespace)">setNamespace(Namespace)</a></span> - Method in class org.biojavax.bio.db.ncbi.<a href="./org/biojavax/bio/db/ncbi/GenpeptRichSequenceDB.html" title="class in org.biojavax.bio.db.ncbi">GenpeptRichSequenceDB</a></dt>
<dd>
<div class="block">Setter for property namespace.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/DebuggingRichSeqIOListener.html#setNamespace(org.biojavax.Namespace)">setNamespace(Namespace)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/DebuggingRichSeqIOListener.html" title="class in org.biojavax.bio.seq.io">DebuggingRichSeqIOListener</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/RichSeqIOAdapter.html#setNamespace(org.biojavax.Namespace)">setNamespace(Namespace)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/RichSeqIOAdapter.html" title="class in org.biojavax.bio.seq.io">RichSeqIOAdapter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/RichSeqIOListener.html#setNamespace(org.biojavax.Namespace)">setNamespace(Namespace)</a></span> - Method in interface org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/RichSeqIOListener.html" title="interface in org.biojavax.bio.seq.io">RichSeqIOListener</a></dt>
<dd>
<div class="block">Call back method so the event emitter can tell the listener
the namespace of the record being read.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/SimpleRichSequenceBuilder.html#setNamespace(org.biojavax.Namespace)">setNamespace(Namespace)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/SimpleRichSequenceBuilder.html" title="class in org.biojavax.bio.seq.io">SimpleRichSequenceBuilder</a></dt>
<dd>
<div class="block">Call back method so the event emitter can tell the listener
the namespace of the record being read.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/PdbxNonPolyScheme.html#setNdb_seq_num(java.lang.String)">setNdb_seq_num(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/PdbxNonPolyScheme.html" title="class in org.biojava.bio.structure.io.mmcif.model">PdbxNonPolyScheme</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/PdbxPolySeqScheme.html#setNdb_seq_num(java.lang.String)">setNdb_seq_num(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/PdbxPolySeqScheme.html" title="class in org.biojava.bio.structure.io.mmcif.model">PdbxPolySeqScheme</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/tools/ClassifierExample.PointClassifier.html#setNegShape(java.awt.Shape)">setNegShape(Shape)</a></span> - Method in class org.biojava.stats.svm.tools.<a href="./org/biojava/stats/svm/tools/ClassifierExample.PointClassifier.html" title="class in org.biojava.stats.svm.tools">ClassifierExample.PointClassifier</a></dt>
<dd>
<div class="block">Set the Shape to represent the negative points.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/CachingKernel.html#setNestedKernel(org.biojava.stats.svm.SVMKernel)">setNestedKernel(SVMKernel)</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/CachingKernel.html" title="class in org.biojava.stats.svm">CachingKernel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/DiagonalCachingKernel.html#setNestedKernel(org.biojava.stats.svm.SVMKernel)">setNestedKernel(SVMKernel)</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/DiagonalCachingKernel.html" title="class in org.biojava.stats.svm">DiagonalCachingKernel</a></dt>
<dd>
<div class="block">
Set the kernel to nest.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/NestedKernel.html#setNestedKernel(org.biojava.stats.svm.SVMKernel)">setNestedKernel(SVMKernel)</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/NestedKernel.html" title="class in org.biojava.stats.svm">NestedKernel</a></dt>
<dd>
<div class="block">Set the <span class="type">SVMKernel</span> to nest to
<span class="arg">k</span>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/TagMapper.html#setNewTag(java.lang.Object, java.lang.Object)">setNewTag(Object, Object)</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/TagMapper.html" title="class in org.biojava.bio.program.tagvalue">TagMapper</a></dt>
<dd>
<div class="block"><code>setNewTag</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Structure.html#setNmr(boolean)">setNmr(boolean)</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Structure.html" title="interface in org.biojava.bio.structure">Structure</a></dt>
<dd>
<div class="block">set NMR flag.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/StructureImpl.html#setNmr(boolean)">setNmr(boolean)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/StructureImpl.html" title="class in org.biojava.bio.structure">StructureImpl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/taxa/NCBITaxon.html#setNodeRank(java.lang.String)">setNodeRank(String)</a></span> - Method in interface org.biojavax.bio.taxa.<a href="./org/biojavax/bio/taxa/NCBITaxon.html" title="interface in org.biojavax.bio.taxa">NCBITaxon</a></dt>
<dd>
<div class="block">Sets the node rank of this taxon.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/taxa/SimpleNCBITaxon.html#setNodeRank(java.lang.String)">setNodeRank(String)</a></span> - Method in class org.biojavax.bio.taxa.<a href="./org/biojavax/bio/taxa/SimpleNCBITaxon.html" title="class in org.biojavax.bio.taxa">SimpleNCBITaxon</a></dt>
<dd>
<div class="block">Setter for property nodeRank.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/SparseVector.NormalizingKernel.html#setNormalizingVector(org.biojava.stats.svm.SparseVector)">setNormalizingVector(SparseVector)</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/SparseVector.NormalizingKernel.html" title="class in org.biojava.stats.svm">SparseVector.NormalizingKernel</a></dt>
<dd>
<div class="block">Set the normalizing vector.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtCommentParser.Isoform.html#setNote(java.lang.String)">setNote(String)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtCommentParser.Isoform.html" title="class in org.biojavax.bio.seq.io">UniProtCommentParser.Isoform</a></dt>
<dd>
<div class="block">Setter for property note.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtCommentParser.SeqCaution.html#setNote(java.lang.String)">setNote(String)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtCommentParser.SeqCaution.html" title="class in org.biojavax.bio.seq.io">UniProtCommentParser.SeqCaution</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html#setNote(java.lang.String)">setNote(String)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html" title="class in org.biojavax.bio.seq.io">UniProtCommentParser</a></dt>
<dd>
<div class="block">Setter for property note.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/CompoundRichLocation.html#setNoteSet(java.util.Set)">setNoteSet(Set)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/CompoundRichLocation.html" title="class in org.biojavax.bio.seq">CompoundRichLocation</a></dt>
<dd>
<div class="block">Clears the notes associated with this object and replaces them with
the contents of this set.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/EmptyRichLocation.html#setNoteSet(java.util.Set)">setNoteSet(Set)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/EmptyRichLocation.html" title="class in org.biojavax.bio.seq">EmptyRichLocation</a></dt>
<dd>
<div class="block">Clears the notes associated with this object and replaces them with
the contents of this set.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichFeature.html#setNoteSet(java.util.Set)">setNoteSet(Set)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichFeature.html" title="class in org.biojavax.bio.seq">SimpleRichFeature</a></dt>
<dd>
<div class="block">Clears the notes associated with this object and replaces them with
the contents of this set.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichLocation.html#setNoteSet(java.util.Set)">setNoteSet(Set)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichLocation.html" title="class in org.biojavax.bio.seq">SimpleRichLocation</a></dt>
<dd>
<div class="block">Clears the notes associated with this object and replaces them with
the contents of this set.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/SimpleBioEntry.html#setNoteSet(java.util.Set)">setNoteSet(Set)</a></span> - Method in class org.biojavax.bio.<a href="./org/biojavax/bio/SimpleBioEntry.html" title="class in org.biojavax.bio">SimpleBioEntry</a></dt>
<dd>
<div class="block">Clears the notes associated with this object and replaces them with
the contents of this set.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/EmptyRichAnnotation.html#setNoteSet(java.util.Set)">setNoteSet(Set)</a></span> - Method in class org.biojavax.<a href="./org/biojavax/EmptyRichAnnotation.html" title="class in org.biojavax">EmptyRichAnnotation</a></dt>
<dd>
<div class="block">Clears the notes from this annotation and replaces them with
those from the given set.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/RichAnnotatable.html#setNoteSet(java.util.Set)">setNoteSet(Set)</a></span> - Method in interface org.biojavax.<a href="./org/biojavax/RichAnnotatable.html" title="interface in org.biojavax">RichAnnotatable</a></dt>
<dd>
<div class="block">Clears the notes associated with this object and replaces them with
the contents of this set.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/RichAnnotation.html#setNoteSet(java.util.Set)">setNoteSet(Set)</a></span> - Method in interface org.biojavax.<a href="./org/biojavax/RichAnnotation.html" title="interface in org.biojavax">RichAnnotation</a></dt>
<dd>
<div class="block">Clears the notes from this annotation and replaces them with
those from the given set.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleCrossRef.html#setNoteSet(java.util.Set)">setNoteSet(Set)</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleCrossRef.html" title="class in org.biojavax">SimpleCrossRef</a></dt>
<dd>
<div class="block">Clears the notes associated with this object and replaces them with
the contents of this set.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleRichAnnotation.html#setNoteSet(java.util.Set)">setNoteSet(Set)</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleRichAnnotation.html" title="class in org.biojavax">SimpleRichAnnotation</a></dt>
<dd>
<div class="block">Clears the notes from this annotation and replaces them with
those from the given set.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/AbstractDistribution.html#setNullModel(org.biojava.bio.dist.Distribution)">setNullModel(Distribution)</a></span> - Method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/AbstractDistribution.html" title="class in org.biojava.bio.dist">AbstractDistribution</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/Distribution.html#setNullModel(org.biojava.bio.dist.Distribution)">setNullModel(Distribution)</a></span> - Method in interface org.biojava.bio.dist.<a href="./org/biojava/bio/dist/Distribution.html" title="interface in org.biojava.bio.dist">Distribution</a></dt>
<dd>
<div class="block">Set the null model Distribution that this Distribution recognizes.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/GapDistribution.html#setNullModel(org.biojava.bio.dist.Distribution)">setNullModel(Distribution)</a></span> - Method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/GapDistribution.html" title="class in org.biojava.bio.dist">GapDistribution</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/PairDistribution.html#setNullModel(org.biojava.bio.dist.Distribution)">setNullModel(Distribution)</a></span> - Method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/PairDistribution.html" title="class in org.biojava.bio.dist">PairDistribution</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/TranslatedDistribution.html#setNullModel(org.biojava.bio.dist.Distribution)">setNullModel(Distribution)</a></span> - Method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/TranslatedDistribution.html" title="class in org.biojava.bio.dist">TranslatedDistribution</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/AbstractDistribution.html#setNullModelImpl(org.biojava.bio.dist.Distribution)">setNullModelImpl(Distribution)</a></span> - Method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/AbstractDistribution.html" title="class in org.biojava.bio.dist">AbstractDistribution</a></dt>
<dd>
<div class="block">Implement this to set the null model.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/AbstractOrderNDistribution.html#setNullModelImpl(org.biojava.bio.dist.Distribution)">setNullModelImpl(Distribution)</a></span> - Method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/AbstractOrderNDistribution.html" title="class in org.biojava.bio.dist">AbstractOrderNDistribution</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/SimpleDistribution.html#setNullModelImpl(org.biojava.bio.dist.Distribution)">setNullModelImpl(Distribution)</a></span> - Method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/SimpleDistribution.html" title="class in org.biojava.bio.dist">SimpleDistribution</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/UniformDistribution.html#setNullModelImpl(org.biojava.bio.dist.Distribution)">setNullModelImpl(Distribution)</a></span> - Method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/UniformDistribution.html" title="class in org.biojava.bio.dist">UniformDistribution</a></dt>
<dd>
<div class="block">Assign a background distribution.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/DistributionTrainerContext.html#setNullModelWeight(double)">setNullModelWeight(double)</a></span> - Method in interface org.biojava.bio.dist.<a href="./org/biojava/bio/dist/DistributionTrainerContext.html" title="interface in org.biojava.bio.dist">DistributionTrainerContext</a></dt>
<dd>
<div class="block">Set the number of pseudocounts to add when training the distribution.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/SimpleDistributionTrainerContext.html#setNullModelWeight(double)">setNullModelWeight(double)</a></span> - Method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/SimpleDistributionTrainerContext.html" title="class in org.biojava.bio.dist">SimpleDistributionTrainerContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/DatabasePDBrev.html#setNum(java.lang.String)">setNum(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/DatabasePDBrev.html" title="class in org.biojava.bio.structure.io.mmcif.model">DatabasePDBrev</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/EntityPolySeq.html#setNum(java.lang.String)">setNum(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/EntityPolySeq.html" title="class in org.biojava.bio.structure.io.mmcif.model">EntityPolySeq</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SuffixTree.SuffixNode.html#setNumber(float)">setNumber(float)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SuffixTree.SuffixNode.html" title="class in org.biojava.bio.symbol">SuffixTree.SuffixNode</a></dt>
<dd>
<div class="block">Set the number associated with this node.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtCommentParser.Interaction.html#setNumberExperiments(int)">setNumberExperiments(int)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtCommentParser.Interaction.html" title="class in org.biojavax.bio.seq.io">UniProtCommentParser.Interaction</a></dt>
<dd>
<div class="block">Setter for property numberExperiments.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Compound.html#setNumRes(java.lang.String)">setNumRes(String)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure">Compound</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ontology/ComparableTerm.html#setObsolete(java.lang.Boolean)">setObsolete(Boolean)</a></span> - Method in interface org.biojavax.ontology.<a href="./org/biojavax/ontology/ComparableTerm.html" title="interface in org.biojavax.ontology">ComparableTerm</a></dt>
<dd>
<div class="block">Sets the obsolescence flag associated with this term.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ontology/SimpleComparableTerm.html#setObsolete(java.lang.Boolean)">setObsolete(Boolean)</a></span> - Method in class org.biojavax.ontology.<a href="./org/biojavax/ontology/SimpleComparableTerm.html" title="class in org.biojavax.ontology">SimpleComparableTerm</a></dt>
<dd>
<div class="block">Sets the obsolescence flag associated with this term.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Atom.html#setOccupancy(double)">setOccupancy(double)</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Atom.html" title="interface in org.biojava.bio.structure">Atom</a></dt>
<dd>
<div class="block">set occupancy.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/AtomImpl.html#setOccupancy(double)">setOccupancy(double)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/AtomImpl.html" title="class in org.biojava.bio.structure">AtomImpl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html#setOccupancy(java.lang.String)">setOccupancy(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html" title="class in org.biojava.bio.structure.io.mmcif.model">AtomSite</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html#setOccupancy_esd(java.lang.String)">setOccupancy_esd(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html" title="class in org.biojava.bio.structure.io.mmcif.model">AtomSite</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#setOccupancy_max(java.lang.String)">setOccupancy_max(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#setOccupancy_min(java.lang.String)">setOccupancy_min(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/CircularRendererPanel.html#setOffset(double)">setOffset(double)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/CircularRendererPanel.html" title="class in org.biojava.bio.gui.sequence">CircularRendererPanel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html#setOne_letter_code(java.lang.String)">setOne_letter_code(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html" title="class in org.biojava.bio.structure.io.mmcif.model">ChemComp</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.html#setOption(org.biojava.bio.chromatogram.graphic.ChromatogramGraphic.Option, java.lang.Object)">setOption(ChromatogramGraphic.Option, Object)</a></span> - Method in class org.biojava.bio.chromatogram.graphic.<a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.html" title="class in org.biojava.bio.chromatogram.graphic">ChromatogramGraphic</a></dt>
<dd>
<div class="block">Sets a new value for the specified option.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/PolynomialKernel.html#setOrder(double)">setOrder(double)</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/PolynomialKernel.html" title="class in org.biojava.stats.svm">PolynomialKernel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Compound.html#setOrgan(java.lang.String)">setOrgan(String)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure">Compound</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Compound.html#setOrganelle(java.lang.String)">setOrganelle(String)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure">Compound</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Compound.html#setOrganismCommon(java.lang.String)">setOrganismCommon(String)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure">Compound</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Compound.html#setOrganismScientific(java.lang.String)">setOrganismScientific(String)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure">Compound</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtCommentParser.Interaction.html#setOrganismsDiffer(boolean)">setOrganismsDiffer(boolean)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtCommentParser.Interaction.html" title="class in org.biojavax.bio.seq.io">UniProtCommentParser.Interaction</a></dt>
<dd>
<div class="block">Setter for property organismsDiffer.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Compound.html#setOrganismTaxId(java.lang.String)">setOrganismTaxId(String)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure">Compound</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEMapLocation.html#setOrientation(java.lang.String)">setOrientation(String)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEMapLocation.html" title="class in org.biojava.bio.seq.io.agave">AGAVEMapLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/glyph/ArrowGlyph.html#setOuterPaint(java.awt.Paint)">setOuterPaint(Paint)</a></span> - Method in class org.biojava.bio.gui.glyph.<a href="./org/biojava/bio/gui/glyph/ArrowGlyph.html" title="class in org.biojava.bio.gui.glyph">ArrowGlyph</a></dt>
<dd>
<div class="block">Allows setting the paint properties of the outer line of this glyph to the
given value.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/ArrowedFeatureRenderer.html#setOutline(java.awt.Paint)">setOutline(Paint)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/ArrowedFeatureRenderer.html" title="class in org.biojava.bio.gui.sequence">ArrowedFeatureRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/BasicFeatureRenderer.html#setOutline(java.awt.Paint)">setOutline(Paint)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/BasicFeatureRenderer.html" title="class in org.biojava.bio.gui.sequence">BasicFeatureRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/CrosshairRenderer.html#setOutline(java.awt.Paint)">setOutline(Paint)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/CrosshairRenderer.html" title="class in org.biojava.bio.gui.sequence">CrosshairRenderer</a></dt>
<dd>
<div class="block"><code>setOutline</code> sets the the colour used to draw the
lines.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PairwiseDiagonalRenderer.html#setOutline(java.awt.Paint)">setOutline(Paint)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PairwiseDiagonalRenderer.html" title="class in org.biojava.bio.gui.sequence">PairwiseDiagonalRenderer</a></dt>
<dd>
<div class="block"><code>setOutline</code> sets the the colour used to draw the
lines.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SixFrameRenderer.html#setOutline(java.awt.Paint)">setOutline(Paint)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SixFrameRenderer.html" title="class in org.biojava.bio.gui.sequence">SixFrameRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SixFrameZiggyRenderer.html#setOutline(java.awt.Paint)">setOutline(Paint)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SixFrameZiggyRenderer.html" title="class in org.biojava.bio.gui.sequence">SixFrameZiggyRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/TickFeatureRenderer.html#setOutline(java.awt.Paint)">setOutline(Paint)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/TickFeatureRenderer.html" title="class in org.biojava.bio.gui.sequence">TickFeatureRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/ZiggyFeatureRenderer.html#setOutline(java.awt.Paint)">setOutline(Paint)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/ZiggyFeatureRenderer.html" title="class in org.biojava.bio.gui.sequence">ZiggyFeatureRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/DNAStyle.html#setOutlinePaint(org.biojava.bio.symbol.Symbol, java.awt.Paint)">setOutlinePaint(Symbol, Paint)</a></span> - Method in class org.biojava.bio.gui.<a href="./org/biojava/bio/gui/DNAStyle.html" title="class in org.biojava.bio.gui">DNAStyle</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/SimpleSymbolStyle.html#setOutlinePaint(org.biojava.bio.symbol.Symbol, java.awt.Paint)">setOutlinePaint(Symbol, Paint)</a></span> - Method in class org.biojava.bio.gui.<a href="./org/biojava/bio/gui/SimpleSymbolStyle.html" title="class in org.biojava.bio.gui">SimpleSymbolStyle</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/process/InputHandler.html#setOutput(java.io.OutputStream)">setOutput(OutputStream)</a></span> - Method in interface org.biojava.utils.process.<a href="./org/biojava/utils/process/InputHandler.html" title="interface in org.biojava.utils.process">InputHandler</a></dt>
<dd>
<div class="block">Sets the output stream.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/process/ReaderInputHandler.html#setOutput(java.io.OutputStream)">setOutput(OutputStream)</a></span> - Method in class org.biojava.utils.process.<a href="./org/biojava/utils/process/ReaderInputHandler.html" title="class in org.biojava.utils.process">ReaderInputHandler</a></dt>
<dd>
<div class="block">Sets the output stream.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/process/StreamPipe.html#setOutput(java.io.OutputStream)">setOutput(OutputStream)</a></span> - Method in class org.biojava.utils.process.<a href="./org/biojava/utils/process/StreamPipe.html" title="class in org.biojava.utils.process">StreamPipe</a></dt>
<dd>
<div class="block">Sets the output stream</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/process/ExternalProcess.html#setOutputHandler(org.biojava.utils.process.OutputHandler)">setOutputHandler(OutputHandler)</a></span> - Method in class org.biojava.utils.process.<a href="./org/biojava/utils/process/ExternalProcess.html" title="class in org.biojava.utils.process">ExternalProcess</a></dt>
<dd>
<div class="block">Sets the output handler which is responsible for the standard output
of the external process.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#setOverall_FOM_free_R_set(java.lang.String)">setOverall_FOM_free_R_set(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#setOverall_FOM_work_R_set(java.lang.String)">setOverall_FOM_work_R_set(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#setOverall_SU_B(java.lang.String)">setOverall_SU_B(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#setOverall_SU_ML(java.lang.String)">setOverall_SU_ML(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#setOverall_SU_R_Cruickshank_DPI(java.lang.String)">setOverall_SU_R_Cruickshank_DPI(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#setOverall_SU_R_free(java.lang.String)">setOverall_SU_R_free(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PaddingRenderer.html#setPadding(double)">setPadding(double)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PaddingRenderer.html" title="class in org.biojava.bio.gui.sequence">PaddingRenderer</a></dt>
<dd>
<div class="block">Set the padding.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/glyph/RectangleGlyph.html#setPaint(java.awt.Paint)">setPaint(Paint)</a></span> - Method in class org.biojava.bio.gui.glyph.<a href="./org/biojava/bio/gui/glyph/RectangleGlyph.html" title="class in org.biojava.bio.gui.glyph">RectangleGlyph</a></dt>
<dd>
<div class="block">Allows you to set the paint properties of this glyph, i.e., its color.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/glyph/TurnGlyph.html#setPaint(java.awt.Paint)">setPaint(Paint)</a></span> - Method in class org.biojava.bio.gui.glyph.<a href="./org/biojava/bio/gui/glyph/TurnGlyph.html" title="class in org.biojava.bio.gui.glyph">TurnGlyph</a></dt>
<dd>
<div class="block">Allows you to set the paint properties of this glyph, i.e., its color.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/util/SequenceScalePanel.html#setPaintDefaults(java.awt.Graphics2D)">setPaintDefaults(Graphics2D)</a></span> - Method in class org.biojava.bio.structure.gui.util.<a href="./org/biojava/bio/structure/gui/util/SequenceScalePanel.html" title="class in org.biojava.bio.structure.gui.util">SequenceScalePanel</a></dt>
<dd>
<div class="block">set some default rendering hints, like text antialiasing on</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/StructurePairAligner.html#setParams(org.biojava.bio.structure.align.StrucAligParameters)">setParams(StrucAligParameters)</a></span> - Method in class org.biojava.bio.structure.align.<a href="./org/biojava/bio/structure/align/StructurePairAligner.html" title="class in org.biojava.bio.structure.align">StructurePairAligner</a></dt>
<dd>
<div class="block">set the parameters to be used for the algorithm</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/biosql/TaxonSQL.html#setParent(java.sql.Connection, org.biojava.bio.taxa.Taxon, org.biojava.bio.taxa.Taxon)">setParent(Connection, Taxon, Taxon)</a></span> - Static method in class org.biojava.bio.seq.db.biosql.<a href="./org/biojava/bio/seq/db/biosql/TaxonSQL.html" title="class in org.biojava.bio.seq.db.biosql">TaxonSQL</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">This updates the taxonomic tree in the database and sets the parent of the given
child taxon to the parent taxon.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Atom.html#setParent(org.biojava.bio.structure.Group)">setParent(Group)</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Atom.html" title="interface in org.biojava.bio.structure">Atom</a></dt>
<dd>
<div class="block">Sets the back-reference to its parent Group.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/AtomImpl.html#setParent(org.biojava.bio.structure.Group)">setParent(Group)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/AtomImpl.html" title="class in org.biojava.bio.structure">AtomImpl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Chain.html#setParent(org.biojava.bio.structure.Structure)">setParent(Structure)</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Chain.html" title="interface in org.biojava.bio.structure">Chain</a></dt>
<dd>
<div class="block">Set the back-reference to its parent Structure.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/ChainImpl.html#setParent(org.biojava.bio.structure.Structure)">setParent(Structure)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/ChainImpl.html" title="class in org.biojava.bio.structure">ChainImpl</a></dt>
<dd>
<div class="block">Set the back-reference to its parent Structure.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/DBRef.html#setParent(org.biojava.bio.structure.Structure)">setParent(Structure)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/DBRef.html" title="class in org.biojava.bio.structure">DBRef</a></dt>
<dd>
<div class="block">Set the structure object that this DBRef relates to.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Group.html#setParent(org.biojava.bio.structure.Chain)">setParent(Chain)</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Group.html" title="interface in org.biojava.bio.structure">Group</a></dt>
<dd>
<div class="block">Set the back-reference (to its parent Chain).</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/HetatomImpl.html#setParent(org.biojava.bio.structure.Chain)">setParent(Chain)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/HetatomImpl.html" title="class in org.biojava.bio.structure">HetatomImpl</a></dt>
<dd>
<div class="block">Set the back-reference (to its parent Chain)</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichFeature.html#setParent(org.biojava.bio.seq.FeatureHolder)">setParent(FeatureHolder)</a></span> - Method in interface org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichFeature.html" title="interface in org.biojavax.bio.seq">RichFeature</a></dt>
<dd>
<div class="block">Sets the parent of this feature.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichFeature.html#setParent(org.biojava.bio.seq.FeatureHolder)">setParent(FeatureHolder)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichFeature.html" title="class in org.biojavax.bio.seq">SimpleRichFeature</a></dt>
<dd>
<div class="block">Sets the parent of this feature.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/taxa/NCBITaxon.html#setParentNCBITaxID(java.lang.Integer)">setParentNCBITaxID(Integer)</a></span> - Method in interface org.biojavax.bio.taxa.<a href="./org/biojavax/bio/taxa/NCBITaxon.html" title="interface in org.biojavax.bio.taxa">NCBITaxon</a></dt>
<dd>
<div class="block">Sets the parent NCBI taxon ID.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/taxa/SimpleNCBITaxon.html#setParentNCBITaxID(java.lang.Integer)">setParentNCBITaxID(Integer)</a></span> - Method in class org.biojavax.bio.taxa.<a href="./org/biojavax/bio/taxa/SimpleNCBITaxon.html" title="class in org.biojavax.bio.taxa">SimpleNCBITaxon</a></dt>
<dd>
<div class="block">Sets the parent NCBI taxon ID.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/SimpleMMcifConsumer.html#setParseCAOnly(boolean)">setParseCAOnly(boolean)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/SimpleMMcifConsumer.html" title="class in org.biojava.bio.structure.io.mmcif">SimpleMMcifConsumer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/PDBFileParser.html#setParseCAOnly(boolean)">setParseCAOnly(boolean)</a></span> - Method in class org.biojava.bio.structure.io.<a href="./org/biojava/bio/structure/io/PDBFileParser.html" title="class in org.biojava.bio.structure.io">PDBFileParser</a></dt>
<dd>
<div class="block">the flag if only the C-alpha atoms of the structure should be parsed.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/PDBFileReader.html#setParseCAOnly(boolean)">setParseCAOnly(boolean)</a></span> - Method in class org.biojava.bio.structure.io.<a href="./org/biojava/bio/structure/io/PDBFileReader.html" title="class in org.biojava.bio.structure.io">PDBFileReader</a></dt>
<dd>
<div class="block">only the CA atoms should be parsed from the PDB file</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/TagDelegator.html#setParserListener(java.lang.Object, org.biojava.bio.program.tagvalue.TagValueParser, org.biojava.bio.program.tagvalue.TagValueListener)">setParserListener(Object, TagValueParser, TagValueListener)</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/TagDelegator.html" title="class in org.biojava.bio.program.tagvalue">TagDelegator</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/PDBFileParser.html#setParseSecStruc(boolean)">setParseSecStruc(boolean)</a></span> - Method in class org.biojava.bio.structure.io.<a href="./org/biojava/bio/structure/io/PDBFileParser.html" title="class in org.biojava.bio.structure.io">PDBFileParser</a></dt>
<dd>
<div class="block">a flag to tell the parser to parse the Author's secondary structure assignment from the file
default is set to false, i.e.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/PDBFileReader.html#setParseSecStruc(boolean)">setParseSecStruc(boolean)</a></span> - Method in class org.biojava.bio.structure.io.<a href="./org/biojava/bio/structure/io/PDBFileReader.html" title="class in org.biojava.bio.structure.io">PDBFileReader</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/Alignable.html#setPath(org.biojava.bio.structure.align.helper.IndexPair[])">setPath(IndexPair[])</a></span> - Method in interface org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/Alignable.html" title="interface in org.biojava.bio.structure.align.pairwise">Alignable</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/StrCompAlignment.html#setPath(org.biojava.bio.structure.align.helper.IndexPair[])">setPath(IndexPair[])</a></span> - Method in class org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/StrCompAlignment.html" title="class in org.biojava.bio.structure.align.pairwise">StrCompAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/MMCIFFileReader.html#setPath(java.lang.String)">setPath(String)</a></span> - Method in class org.biojava.bio.structure.io.<a href="./org/biojava/bio/structure/io/MMCIFFileReader.html" title="class in org.biojava.bio.structure.io">MMCIFFileReader</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/PDBFileReader.html#setPath(java.lang.String)">setPath(String)</a></span> - Method in class org.biojava.bio.structure.io.<a href="./org/biojava/bio/structure/io/PDBFileReader.html" title="class in org.biojava.bio.structure.io">PDBFileReader</a></dt>
<dd>
<div class="block">directory where to find PDB files</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/StructureIOFile.html#setPath(java.lang.String)">setPath(String)</a></span> - Method in interface org.biojava.bio.structure.io.<a href="./org/biojava/bio/structure/io/StructureIOFile.html" title="interface in org.biojava.bio.structure.io">StructureIOFile</a></dt>
<dd>
<div class="block">Set path to file / connection string to db.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/EmblCDROMIndexStore.html#setPathPrefix(java.io.File)">setPathPrefix(File)</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/EmblCDROMIndexStore.html" title="class in org.biojava.bio.seq.db">EmblCDROMIndexStore</a></dt>
<dd>
<div class="block"><code>setPathPrefix</code> sets the abstract path to be
appended to sequence database filenames retrieved from the
binary index.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/Alignable.html#setPathSize(int)">setPathSize(int)</a></span> - Method in interface org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/Alignable.html" title="interface in org.biojava.bio.structure.align.pairwise">Alignable</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/StrCompAlignment.html#setPathSize(int)">setPathSize(int)</a></span> - Method in class org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/StrCompAlignment.html" title="class in org.biojava.bio.structure.align.pairwise">StrCompAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/RegexParser.html#setPattern(java.util.regex.Pattern)">setPattern(Pattern)</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/RegexParser.html" title="class in org.biojava.bio.program.tagvalue">RegexParser</a></dt>
<dd>
<div class="block">Set the Pattern used to split lines.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/MaxMismatchPattern.html#setPattern(org.biojava.bio.symbol.SymbolList)">setPattern(SymbolList)</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/MaxMismatchPattern.html" title="class in org.biojava.bio.search">MaxMismatchPattern</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/PdbxNonPolyScheme.html#setPdb_ins_code(java.lang.String)">setPdb_ins_code(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/PdbxNonPolyScheme.html" title="class in org.biojava.bio.structure.io.mmcif.model">PdbxNonPolyScheme</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/PdbxPolySeqScheme.html#setPdb_ins_code(java.lang.String)">setPdb_ins_code(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/PdbxPolySeqScheme.html" title="class in org.biojava.bio.structure.io.mmcif.model">PdbxPolySeqScheme</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/PdbxNonPolyScheme.html#setPdb_mon_id(java.lang.String)">setPdb_mon_id(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/PdbxNonPolyScheme.html" title="class in org.biojava.bio.structure.io.mmcif.model">PdbxNonPolyScheme</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/PdbxPolySeqScheme.html#setPdb_mon_id(java.lang.String)">setPdb_mon_id(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/PdbxPolySeqScheme.html" title="class in org.biojava.bio.structure.io.mmcif.model">PdbxPolySeqScheme</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/PdbxNonPolyScheme.html#setPdb_seq_num(java.lang.String)">setPdb_seq_num(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/PdbxNonPolyScheme.html" title="class in org.biojava.bio.structure.io.mmcif.model">PdbxNonPolyScheme</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/PdbxPolySeqScheme.html#setPdb_seq_num(java.lang.String)">setPdb_seq_num(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/PdbxPolySeqScheme.html" title="class in org.biojava.bio.structure.io.mmcif.model">PdbxPolySeqScheme</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/PdbxNonPolyScheme.html#setPdb_strand_id(java.lang.String)">setPdb_strand_id(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/PdbxNonPolyScheme.html" title="class in org.biojava.bio.structure.io.mmcif.model">PdbxNonPolyScheme</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/PdbxPolySeqScheme.html#setPdb_strand_id(java.lang.String)">setPdb_strand_id(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/PdbxPolySeqScheme.html" title="class in org.biojava.bio.structure.io.mmcif.model">PdbxPolySeqScheme</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Group.html#setPDBCode(java.lang.String)">setPDBCode(String)</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Group.html" title="interface in org.biojava.bio.structure">Group</a></dt>
<dd>
<div class="block">Specifies the PDBCode (residue number + insertion code) value.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/HetatomImpl.html#setPDBCode(java.lang.String)">setPDBCode(String)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/HetatomImpl.html" title="class in org.biojava.bio.structure">HetatomImpl</a></dt>
<dd>
<div class="block">set the PDB code.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/server/StructureEvent.html#setPDBCode(java.lang.String)">setPDBCode(String)</a></span> - Method in interface org.biojava.bio.structure.server.<a href="./org/biojava/bio/structure/server/StructureEvent.html" title="interface in org.biojava.bio.structure.server">StructureEvent</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/server/StructureEventImpl.html#setPDBCode(java.lang.String)">setPDBCode(String)</a></span> - Method in class org.biojava.bio.structure.server.<a href="./org/biojava/bio/structure/server/StructureEventImpl.html" title="class in org.biojava.bio.structure.server">StructureEventImpl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Structure.html#setPDBCode(java.lang.String)">setPDBCode(String)</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Structure.html" title="interface in org.biojava.bio.structure">Structure</a></dt>
<dd>
<div class="block">set PDB code of structure .</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/StructureImpl.html#setPDBCode(java.lang.String)">setPDBCode(String)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/StructureImpl.html" title="class in org.biojava.bio.structure">StructureImpl</a></dt>
<dd>
<div class="block">set PDB code of structure .</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Group.html#setPDBFlag(boolean)">setPDBFlag(boolean)</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Group.html" title="interface in org.biojava.bio.structure">Group</a></dt>
<dd>
<div class="block">flag if group has 3D data .</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/HetatomImpl.html#setPDBFlag(boolean)">setPDBFlag(boolean)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/HetatomImpl.html" title="class in org.biojava.bio.structure">HetatomImpl</a></dt>
<dd>
<div class="block">flag if group has 3D data.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Structure.html#setPDBHeader(org.biojava.bio.structure.PDBHeader)">setPDBHeader(PDBHeader)</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Structure.html" title="interface in org.biojava.bio.structure">Structure</a></dt>
<dd>
<div class="block">the the header information for this PDB file</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/StructureImpl.html#setPDBHeader(org.biojava.bio.structure.PDBHeader)">setPDBHeader(PDBHeader)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/StructureImpl.html" title="class in org.biojava.bio.structure">StructureImpl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/server/FlatFileInstallation.html#setPDBInfoFile(java.io.File)">setPDBInfoFile(File)</a></span> - Method in class org.biojava.bio.structure.server.<a href="./org/biojava/bio/structure/server/FlatFileInstallation.html" title="class in org.biojava.bio.structure.server">FlatFileInstallation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/server/SimpleStructureServer.html#setPDBInstallation(org.biojava.bio.structure.server.PDBInstallation)">setPDBInstallation(PDBInstallation)</a></span> - Method in class org.biojava.bio.structure.server.<a href="./org/biojava/bio/structure/server/SimpleStructureServer.html" title="class in org.biojava.bio.structure.server">SimpleStructureServer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/server/StructureServer.html#setPDBInstallation(org.biojava.bio.structure.server.PDBInstallation)">setPDBInstallation(PDBInstallation)</a></span> - Method in interface org.biojava.bio.structure.server.<a href="./org/biojava/bio/structure/server/StructureServer.html" title="interface in org.biojava.bio.structure.server">StructureServer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Atom.html#setPDBline(java.lang.String)">setPDBline(String)</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Atom.html" title="interface in org.biojava.bio.structure">Atom</a></dt>
<dd>
<div class="block">store the whole line.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/AtomImpl.html#setPDBline(java.lang.String)">setPDBline(String)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/AtomImpl.html" title="class in org.biojava.bio.structure">AtomImpl</a></dt>
<dd>
<div class="block">store the whole line.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/AminoAcidImpl.html#setPDBName(java.lang.String)">setPDBName(String)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/AminoAcidImpl.html" title="class in org.biojava.bio.structure">AminoAcidImpl</a></dt>
<dd>
<div class="block">set three character name of AminoAcid.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Group.html#setPDBName(java.lang.String)">setPDBName(String)</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Group.html" title="interface in org.biojava.bio.structure">Group</a></dt>
<dd>
<div class="block">Set the PDB 3 letter name for this group.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/HetatomImpl.html#setPDBName(java.lang.String)">setPDBName(String)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/HetatomImpl.html" title="class in org.biojava.bio.structure">HetatomImpl</a></dt>
<dd>
<div class="block">set three character name of Group .</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/AlternativeAlignment.html#setPDBresnum1(java.lang.String[])">setPDBresnum1(String[])</a></span> - Method in class org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/AlternativeAlignment.html" title="class in org.biojava.bio.structure.align.pairwise">AlternativeAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/AlternativeAlignment.html#setPDBresnum2(java.lang.String[])">setPDBresnum2(String[])</a></span> - Method in class org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/AlternativeAlignment.html" title="class in org.biojava.bio.structure.align.pairwise">AlternativeAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Atom.html#setPDBserial(int)">setPDBserial(int)</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Atom.html" title="interface in org.biojava.bio.structure">Atom</a></dt>
<dd>
<div class="block">set PDB atom number.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/AtomImpl.html#setPDBserial(int)">setPDBserial(int)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/AtomImpl.html" title="class in org.biojava.bio.structure">AtomImpl</a></dt>
<dd>
<div class="block">set PDB atom number.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/StructRef.html#setPdbx_align_begin(java.lang.String)">setPdbx_align_begin(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/StructRef.html" title="class in org.biojava.bio.structure.io.mmcif.model">StructRef</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html#setPdbx_ambiguous_flag(java.lang.String)">setPdbx_ambiguous_flag(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html" title="class in org.biojava.bio.structure.io.mmcif.model">ChemComp</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/StructRefSeq.html#setPdbx_auth_seq_align_beg(java.lang.String)">setPdbx_auth_seq_align_beg(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/StructRefSeq.html" title="class in org.biojava.bio.structure.io.mmcif.model">StructRefSeq</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/StructRefSeq.html#setPdbx_auth_seq_align_end(java.lang.String)">setPdbx_auth_seq_align_end(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/StructRefSeq.html" title="class in org.biojava.bio.structure.io.mmcif.model">StructRefSeq</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/StructAsym.html#setPdbx_blank_PDB_chainid_flag(java.lang.String)">setPdbx_blank_PDB_chainid_flag(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/StructAsym.html" title="class in org.biojava.bio.structure.io.mmcif.model">StructAsym</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#setPdbx_data_cutoff_high_absF(java.lang.String)">setPdbx_data_cutoff_high_absF(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#setPdbx_data_cutoff_high_rms_absF(java.lang.String)">setPdbx_data_cutoff_high_rms_absF(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#setPdbx_data_cutoff_low_absF(java.lang.String)">setPdbx_data_cutoff_low_absF(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/StructRef.html#setPdbx_db_accession(java.lang.String)">setPdbx_db_accession(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/StructRef.html" title="class in org.biojava.bio.structure.io.mmcif.model">StructRef</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/StructRefSeq.html#setPdbx_db_accession(java.lang.String)">setPdbx_db_accession(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/StructRefSeq.html" title="class in org.biojava.bio.structure.io.mmcif.model">StructRefSeq</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/StructRefSeq.html#setPdbx_db_align_beg_ins_code(java.lang.String)">setPdbx_db_align_beg_ins_code(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/StructRefSeq.html" title="class in org.biojava.bio.structure.io.mmcif.model">StructRefSeq</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/StructRefSeq.html#setPdbx_db_align_end_ins_code(java.lang.String)">setPdbx_db_align_end_ins_code(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/StructRefSeq.html" title="class in org.biojava.bio.structure.io.mmcif.model">StructRefSeq</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Entity.html#setPdbx_description(java.lang.String)">setPdbx_description(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Entity.html" title="class in org.biojava.bio.structure.io.mmcif.model">Entity</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Struct.html#setPdbx_descriptor(java.lang.String)">setPdbx_descriptor(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Struct.html" title="class in org.biojava.bio.structure.io.mmcif.model">Struct</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Entity.html#setPdbx_ec(java.lang.String)">setPdbx_ec(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Entity.html" title="class in org.biojava.bio.structure.io.mmcif.model">Entity</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html#setPdbx_formal_charge(java.lang.String)">setPdbx_formal_charge(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html" title="class in org.biojava.bio.structure.io.mmcif.model">AtomSite</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html#setPdbx_formal_charge(java.lang.String)">setPdbx_formal_charge(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html" title="class in org.biojava.bio.structure.io.mmcif.model">ChemComp</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Entity.html#setPdbx_fragment(java.lang.String)">setPdbx_fragment(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Entity.html" title="class in org.biojava.bio.structure.io.mmcif.model">Entity</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html#setPdbx_ideal_coordinates_details(java.lang.String)">setPdbx_ideal_coordinates_details(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html" title="class in org.biojava.bio.structure.io.mmcif.model">ChemComp</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html#setPdbx_ideal_coordinates_missing_flag(java.lang.String)">setPdbx_ideal_coordinates_missing_flag(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html" title="class in org.biojava.bio.structure.io.mmcif.model">ChemComp</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html#setPdbx_initial_date(java.lang.String)">setPdbx_initial_date(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html" title="class in org.biojava.bio.structure.io.mmcif.model">ChemComp</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#setPdbx_isotropic_thermal_model(java.lang.String)">setPdbx_isotropic_thermal_model(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/StructKeywords.html#setPdbx_keywords(java.lang.String)">setPdbx_keywords(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/StructKeywords.html" title="class in org.biojava.bio.structure.io.mmcif.model">StructKeywords</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#setPdbx_ls_cross_valid_method(java.lang.String)">setPdbx_ls_cross_valid_method(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#setPdbx_ls_sigma_F(java.lang.String)">setPdbx_ls_sigma_F(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#setPdbx_ls_sigma_I(java.lang.String)">setPdbx_ls_sigma_I(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#setPdbx_method_to_determine_struct(java.lang.String)">setPdbx_method_to_determine_struct(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html#setPdbx_model_coordinates_db_code(java.lang.String)">setPdbx_model_coordinates_db_code(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html" title="class in org.biojava.bio.structure.io.mmcif.model">ChemComp</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html#setPdbx_model_coordinates_details(java.lang.String)">setPdbx_model_coordinates_details(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html" title="class in org.biojava.bio.structure.io.mmcif.model">ChemComp</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html#setPdbx_model_coordinates_missing_flag(java.lang.String)">setPdbx_model_coordinates_missing_flag(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html" title="class in org.biojava.bio.structure.io.mmcif.model">ChemComp</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Struct.html#setPdbx_model_details(java.lang.String)">setPdbx_model_details(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Struct.html" title="class in org.biojava.bio.structure.io.mmcif.model">Struct</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Struct.html#setPdbx_model_type_details(java.lang.String)">setPdbx_model_type_details(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Struct.html" title="class in org.biojava.bio.structure.io.mmcif.model">Struct</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/StructAsym.html#setPdbx_modified(java.lang.String)">setPdbx_modified(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/StructAsym.html" title="class in org.biojava.bio.structure.io.mmcif.model">StructAsym</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html#setPdbx_modified_date(java.lang.String)">setPdbx_modified_date(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html" title="class in org.biojava.bio.structure.io.mmcif.model">ChemComp</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Entity.html#setPdbx_mutation(java.lang.String)">setPdbx_mutation(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Entity.html" title="class in org.biojava.bio.structure.io.mmcif.model">Entity</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Entity.html#setPdbx_number_of_molecules(java.lang.String)">setPdbx_number_of_molecules(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Entity.html" title="class in org.biojava.bio.structure.io.mmcif.model">Entity</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#setPdbx_overall_ESU_R(java.lang.String)">setPdbx_overall_ESU_R(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#setPdbx_overall_ESU_R_Free(java.lang.String)">setPdbx_overall_ESU_R_Free(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#setPdbx_overall_phase_error(java.lang.String)">setPdbx_overall_phase_error(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/StructRefSeq.html#setPdbx_PDB_id_code(java.lang.String)">setPdbx_PDB_id_code(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/StructRefSeq.html" title="class in org.biojava.bio.structure.io.mmcif.model">StructRefSeq</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html#setPdbx_PDB_ins_code(java.lang.String)">setPdbx_PDB_ins_code(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html" title="class in org.biojava.bio.structure.io.mmcif.model">AtomSite</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html#setPdbx_PDB_model_num(java.lang.String)">setPdbx_PDB_model_num(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html" title="class in org.biojava.bio.structure.io.mmcif.model">AtomSite</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html#setPdbx_processing_site(java.lang.String)">setPdbx_processing_site(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html" title="class in org.biojava.bio.structure.io.mmcif.model">ChemComp</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#setPdbx_R_Free_selection_details(java.lang.String)">setPdbx_R_Free_selection_details(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#setPdbx_refine_id(java.lang.String)">setPdbx_refine_id(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html#setPdbx_release_status(java.lang.String)">setPdbx_release_status(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html" title="class in org.biojava.bio.structure.io.mmcif.model">ChemComp</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html#setPdbx_replaced_by(java.lang.String)">setPdbx_replaced_by(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html" title="class in org.biojava.bio.structure.io.mmcif.model">ChemComp</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html#setPdbx_replaces(java.lang.String)">setPdbx_replaces(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html" title="class in org.biojava.bio.structure.io.mmcif.model">ChemComp</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/StructRefSeq.html#setPdbx_seq_align_beg_ins_code(java.lang.String)">setPdbx_seq_align_beg_ins_code(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/StructRefSeq.html" title="class in org.biojava.bio.structure.io.mmcif.model">StructRefSeq</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/StructRefSeq.html#setPdbx_seq_align_end_ins_code(java.lang.String)">setPdbx_seq_align_end_ins_code(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/StructRefSeq.html" title="class in org.biojava.bio.structure.io.mmcif.model">StructRefSeq</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/StructRef.html#setPdbx_seq_one_letter_code(java.lang.String)">setPdbx_seq_one_letter_code(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/StructRef.html" title="class in org.biojava.bio.structure.io.mmcif.model">StructRef</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#setPdbx_solvent_ion_probe_radii(java.lang.String)">setPdbx_solvent_ion_probe_radii(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#setPdbx_solvent_shrinkage_radii(java.lang.String)">setPdbx_solvent_shrinkage_radii(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#setPdbx_solvent_vdw_probe_radii(java.lang.String)">setPdbx_solvent_vdw_probe_radii(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#setPdbx_starting_model(java.lang.String)">setPdbx_starting_model(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#setPdbx_stereochem_target_val_spec_case(java.lang.String)">setPdbx_stereochem_target_val_spec_case(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#setPdbx_stereochemistry_target_values(java.lang.String)">setPdbx_stereochemistry_target_values(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/StructRefSeq.html#setPdbx_strand_id(java.lang.String)">setPdbx_strand_id(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/StructRefSeq.html" title="class in org.biojava.bio.structure.io.mmcif.model">StructRefSeq</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html#setPdbx_subcomponent_list(java.lang.String)">setPdbx_subcomponent_list(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html" title="class in org.biojava.bio.structure.io.mmcif.model">ChemComp</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html#setPdbx_synonyms(java.lang.String)">setPdbx_synonyms(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html" title="class in org.biojava.bio.structure.io.mmcif.model">ChemComp</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html#setPdbx_type(java.lang.String)">setPdbx_type(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html" title="class in org.biojava.bio.structure.io.mmcif.model">ChemComp</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/AlternativeAlignment.html#setPercId(int)">setPercId(int)</a></span> - Method in class org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/AlternativeAlignment.html" title="class in org.biojava.bio.structure.align.pairwise">AlternativeAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/StrucAligParameters.html#setPermutationSize(int)">setPermutationSize(int)</a></span> - Method in class org.biojava.bio.structure.align.<a href="./org/biojava/bio/structure/align/StrucAligParameters.html" title="class in org.biojava.bio.structure.align">StrucAligParameters</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff3/GFF3Record.Impl.html#setPhase(int)">setPhase(int)</a></span> - Method in class org.biojava.bio.program.gff3.<a href="./org/biojava/bio/program/gff3/GFF3Record.Impl.html" title="class in org.biojava.bio.program.gff3">GFF3Record.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html#setPHDependence(java.lang.String)">setPHDependence(String)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html" title="class in org.biojavax.bio.seq.io">UniProtCommentParser</a></dt>
<dd>
<div class="block">Setter for property PHDependence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/JournalArticle.html#setPmid(java.lang.String)">setPmid(String)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/JournalArticle.html" title="class in org.biojava.bio.structure">JournalArticle</a></dt>
<dd>
<div class="block">Set the value of pmid</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html#setPolymerType(org.biojava.bio.structure.io.mmcif.chem.PolymerType)">setPolymerType(PolymerType)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html" title="class in org.biojava.bio.structure.io.mmcif.model">ChemComp</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/GeneticAlgorithm.html#setPopulation(org.biojavax.ga.Population)">setPopulation(Population)</a></span> - Method in interface org.biojavax.ga.<a href="./org/biojavax/ga/GeneticAlgorithm.html" title="interface in org.biojavax.ga">GeneticAlgorithm</a></dt>
<dd>
<div class="block">Sets the <code>Population</code> of <code>Organisms</code> to the
Algorithm.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ga/impl/AbstractGeneticAlgorithm.html#setPopulation(org.biojavax.ga.Population)">setPopulation(Population)</a></span> - Method in class org.biojavax.ga.impl.<a href="./org/biojavax/ga/impl/AbstractGeneticAlgorithm.html" title="class in org.biojavax.ga.impl">AbstractGeneticAlgorithm</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEMapPosition.html#setPos(java.lang.String)">setPos(String)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEMapPosition.html" title="class in org.biojava.bio.seq.io.agave">AGAVEMapPosition</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/util/AlignedPosition.html#setPos(int, int)">setPos(int, int)</a></span> - Method in class org.biojava.bio.structure.gui.util.<a href="./org/biojava/bio/structure/gui/util/AlignedPosition.html" title="class in org.biojava.bio.structure.gui.util">AlignedPosition</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/FragmentPair.html#setPos1(int)">setPos1(int)</a></span> - Method in class org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/FragmentPair.html" title="class in org.biojava.bio.structure.align.pairwise">FragmentPair</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/util/AlignedPosition.html#setPos1(int)">setPos1(int)</a></span> - Method in class org.biojava.bio.structure.gui.util.<a href="./org/biojava/bio/structure/gui/util/AlignedPosition.html" title="class in org.biojava.bio.structure.gui.util">AlignedPosition</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/FragmentPair.html#setPos2(int)">setPos2(int)</a></span> - Method in class org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/FragmentPair.html" title="class in org.biojava.bio.structure.align.pairwise">FragmentPair</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/util/AlignedPosition.html#setPos2(int)">setPos2(int)</a></span> - Method in class org.biojava.bio.structure.gui.util.<a href="./org/biojava/bio/structure/gui/util/AlignedPosition.html" title="class in org.biojava.bio.structure.gui.util">AlignedPosition</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/EmptyRichLocation.html#setPositionResolver(org.biojavax.bio.seq.PositionResolver)">setPositionResolver(PositionResolver)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/EmptyRichLocation.html" title="class in org.biojavax.bio.seq">EmptyRichLocation</a></dt>
<dd>
<div class="block">Sets the resolver to use when working out actual base coordinates from
fuzzy positions.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichLocation.html#setPositionResolver(org.biojavax.bio.seq.PositionResolver)">setPositionResolver(PositionResolver)</a></span> - Method in interface org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichLocation.html" title="interface in org.biojavax.bio.seq">RichLocation</a></dt>
<dd>
<div class="block">Sets the resolver to use when working out actual base coordinates from
fuzzy positions.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichLocation.html#setPositionResolver(org.biojavax.bio.seq.PositionResolver)">setPositionResolver(PositionResolver)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichLocation.html" title="class in org.biojavax.bio.seq">SimpleRichLocation</a></dt>
<dd>
<div class="block">Sets the resolver to use when working out actual base coordinates from
fuzzy positions.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtCommentParser.SeqCaution.html#setPositions(java.lang.String)">setPositions(String)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtCommentParser.SeqCaution.html" title="class in org.biojavax.bio.seq.io">UniProtCommentParser.SeqCaution</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/tools/ClassifierExample.PointClassifier.html#setPosShape(java.awt.Shape)">setPosShape(Shape)</a></span> - Method in class org.biojava.stats.svm.tools.<a href="./org/biojava/stats/svm/tools/ClassifierExample.PointClassifier.html" title="class in org.biojava.stats.svm.tools">ClassifierExample.PointClassifier</a></dt>
<dd>
<div class="block">Set the Shape to represent the positive points.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/JMatrixPanel.html#setPreferredSize()">setPreferredSize()</a></span> - Method in class org.biojava.bio.structure.gui.<a href="./org/biojava/bio/structure/gui/JMatrixPanel.html" title="class in org.biojava.bio.structure.gui">JMatrixPanel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/indexdb/BioStoreFactory.html#setPrimaryKey(java.lang.String)">setPrimaryKey(String)</a></span> - Method in class org.biojava.bio.program.indexdb.<a href="./org/biojava/bio/program/indexdb/BioStoreFactory.html" title="class in org.biojava.bio.program.indexdb">BioStoreFactory</a></dt>
<dd>
<div class="block"><code>setPrimaryKey</code> sets the primary identifier
namespace.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/Index2Model.html#setPrimaryKeyName(java.lang.String)">setPrimaryKeyName(String)</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/Index2Model.html" title="class in org.biojava.bio.program.tagvalue">Index2Model</a></dt>
<dd>
<div class="block">
Set the tag to use as a primary key in the index.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/Indexer.html#setPrimaryKeyName(java.lang.String)">setPrimaryKeyName(String)</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/Indexer.html" title="class in org.biojava.bio.program.tagvalue">Indexer</a></dt>
<dd>
<div class="block">
Set the tag to use as a primary key in the index.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/FileConvert.html#setPrintConnections(boolean)">setPrintConnections(boolean)</a></span> - Method in class org.biojava.bio.structure.io.<a href="./org/biojava/bio/structure/io/FileConvert.html" title="class in org.biojava.bio.structure.io">FileConvert</a></dt>
<dd>
<div class="block">enable/disable printing of connections
connections are sometimes buggy in PDB files
so there are some cases where one might turn this off.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/EmblFileFormer.html#setPrintStream(java.io.PrintStream)">setPrintStream(PrintStream)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/EmblFileFormer.html" title="class in org.biojava.bio.seq.io">EmblFileFormer</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/GenbankFileFormer.html#setPrintStream(java.io.PrintStream)">setPrintStream(PrintStream)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/GenbankFileFormer.html" title="class in org.biojava.bio.seq.io">GenbankFileFormer</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqFileFormer.html#setPrintStream(java.io.PrintStream)">setPrintStream(PrintStream)</a></span> - Method in interface org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqFileFormer.html" title="interface in org.biojava.bio.seq.io">SeqFileFormer</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block"><code>setPrintStream</code> informs an instance which
<code>PrintStream</code> to use.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SwissprotFileFormer.html#setPrintStream(java.io.PrintStream)">setPrintStream(PrintStream)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SwissprotFileFormer.html" title="class in org.biojava.bio.seq.io">SwissprotFileFormer</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block"><code>setPrintStream</code> informs an instance which
<code>PrintStream</code> to use.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/RichSequenceFormat.BasicFormat.html#setPrintStream(java.io.PrintStream)">setPrintStream(PrintStream)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/RichSequenceFormat.BasicFormat.html" title="class in org.biojavax.bio.seq.io">RichSequenceFormat.BasicFormat</a></dt>
<dd>
<div class="block">Sets the stream to write to.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/RichSequenceFormat.html#setPrintStream(java.io.PrintStream)">setPrintStream(PrintStream)</a></span> - Method in interface org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/RichSequenceFormat.html" title="interface in org.biojavax.bio.seq.io">RichSequenceFormat</a></dt>
<dd>
<div class="block">Sets the stream to write to.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/blast2html/HTMLRenderer.html#setPrintWriter(java.io.PrintWriter)">setPrintWriter(PrintWriter)</a></span> - Method in class org.biojava.bio.program.blast2html.<a href="./org/biojava/bio/program/blast2html/HTMLRenderer.html" title="class in org.biojava.bio.program.blast2html">HTMLRenderer</a></dt>
<dd>
<div class="block">Set the <CODE>PrintWriter</CODE> to output the HTML
to.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/hmmer/HmmerProfileParser.html#setProfileHMM()">setProfileHMM()</a></span> - Method in class org.biojava.bio.program.hmmer.<a href="./org/biojava/bio/program/hmmer/HmmerProfileParser.html" title="class in org.biojava.bio.program.hmmer">HmmerProfileParser</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Group.html#setProperties(java.util.Map)">setProperties(Map<String, Object>)</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Group.html" title="interface in org.biojava.bio.structure">Group</a></dt>
<dd>
<div class="block">properties of this amino acid.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/HetatomImpl.html#setProperties(java.util.Map)">setProperties(Map<String, Object>)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/HetatomImpl.html" title="class in org.biojava.bio.structure">HetatomImpl</a></dt>
<dd>
<div class="block">properties of this amino acid.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/AbstractAnnotation.html#setProperty(java.lang.Object, java.lang.Object)">setProperty(Object, Object)</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/AbstractAnnotation.html" title="class in org.biojava.bio">AbstractAnnotation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/Annotation.html#setProperty(java.lang.Object, java.lang.Object)">setProperty(Object, Object)</a></span> - Method in interface org.biojava.bio.<a href="./org/biojava/bio/Annotation.html" title="interface in org.biojava.bio">Annotation</a></dt>
<dd>
<div class="block">
Set the value of a property.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/AnnotationType.Abstract.html#setProperty(org.biojava.bio.Annotation, java.lang.Object, java.lang.Object)">setProperty(Annotation, Object, Object)</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/AnnotationType.Abstract.html" title="class in org.biojava.bio">AnnotationType.Abstract</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/AnnotationType.html#setProperty(org.biojava.bio.Annotation, java.lang.Object, java.lang.Object)">setProperty(Annotation, Object, Object)</a></span> - Method in interface org.biojava.bio.<a href="./org/biojava/bio/AnnotationType.html" title="interface in org.biojava.bio">AnnotationType</a></dt>
<dd>
<div class="block">Set the property in an annotation bundle according to the type we believe
it should be.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/MergeAnnotation.html#setProperty(java.lang.Object, java.lang.Object)">setProperty(Object, Object)</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/MergeAnnotation.html" title="class in org.biojava.bio">MergeAnnotation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/OverlayAnnotation.html#setProperty(java.lang.Object, java.lang.Object)">setProperty(Object, Object)</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/OverlayAnnotation.html" title="class in org.biojava.bio">OverlayAnnotation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/sax/blastxml/BlastXMLParserFacade.html#setProperty(java.lang.String, java.lang.Object)">setProperty(String, Object)</a></span> - Method in class org.biojava.bio.program.sax.blastxml.<a href="./org/biojava/bio/program/sax/blastxml/BlastXMLParserFacade.html" title="class in org.biojava.bio.program.sax.blastxml">BlastXMLParserFacade</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/StAXFeatureHandler.html#setProperty(java.lang.String, java.lang.String, boolean)">setProperty(String, String, boolean)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/StAXFeatureHandler.html" title="class in org.biojava.bio.seq.io.agave">StAXFeatureHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/StAXPropertyHandler.html#setProperty(java.lang.String, java.lang.String)">setProperty(String, String)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/StAXPropertyHandler.html" title="class in org.biojava.bio.seq.io.agave">StAXPropertyHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Group.html#setProperty(java.lang.String, java.lang.Object)">setProperty(String, Object)</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Group.html" title="interface in org.biojava.bio.structure">Group</a></dt>
<dd>
<div class="block">set a single property .</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/HetatomImpl.html#setProperty(java.lang.String, java.lang.Object)">setProperty(String, Object)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/HetatomImpl.html" title="class in org.biojava.bio.structure">HetatomImpl</a></dt>
<dd>
<div class="block">set a single property .</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/EmptyRichAnnotation.html#setProperty(java.lang.Object, java.lang.Object)">setProperty(Object, Object)</a></span> - Method in class org.biojavax.<a href="./org/biojavax/EmptyRichAnnotation.html" title="class in org.biojavax">EmptyRichAnnotation</a></dt>
<dd>
<div class="block">
Set the value of a property.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleRichAnnotation.html#setProperty(java.lang.Object, java.lang.Object)">setProperty(Object, Object)</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleRichAnnotation.html" title="class in org.biojavax">SimpleRichAnnotation</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span> </div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/Digest.html#setProtease(org.biojava.bio.proteomics.Protease)">setProtease(Protease)</a></span> - Method in class org.biojava.bio.proteomics.<a href="./org/biojava/bio/proteomics/Digest.html" title="class in org.biojava.bio.proteomics">Digest</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/JournalArticle.html#setPublicationDate(int)">setPublicationDate(int)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/JournalArticle.html" title="class in org.biojava.bio.structure">JournalArticle</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/JournalArticle.html#setPublished(boolean)">setPublished(boolean)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/JournalArticle.html" title="class in org.biojava.bio.structure">JournalArticle</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/JournalArticle.html#setPublisher(java.lang.String)">setPublisher(String)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/JournalArticle.html" title="class in org.biojava.bio.structure">JournalArticle</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/dasalignment/DASAlignmentClient.html#setQuery(java.lang.String)">setQuery(String)</a></span> - Method in class org.biojava.bio.program.das.dasalignment.<a href="./org/biojava/bio/program/das/dasalignment/DASAlignmentClient.html" title="class in org.biojava.bio.program.das.dasalignment">DASAlignmentClient</a></dt>
<dd>
<div class="block">Specifies the query.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/sax/FastaSearchSAXParser.html#setQueryID(java.lang.String)">setQueryID(String)</a></span> - Method in class org.biojava.bio.program.sax.<a href="./org/biojava/bio/program/sax/FastaSearchSAXParser.html" title="class in org.biojava.bio.program.sax">FastaSearchSAXParser</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/BlastLikeHomologyBuilder.html#setQueryID(java.lang.String)">setQueryID(String)</a></span> - Method in class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/BlastLikeHomologyBuilder.html" title="class in org.biojava.bio.program.ssbind">BlastLikeHomologyBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/BlastLikeSearchBuilder.html#setQueryID(java.lang.String)">setQueryID(String)</a></span> - Method in class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/BlastLikeSearchBuilder.html" title="class in org.biojava.bio.program.ssbind">BlastLikeSearchBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/SimilarityPairBuilder.html#setQueryID(java.lang.String)">setQueryID(String)</a></span> - Method in class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/SimilarityPairBuilder.html" title="class in org.biojava.bio.program.ssbind">SimilarityPairBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/FilteringContentHandler.html#setQueryID(java.lang.String)">setQueryID(String)</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/FilteringContentHandler.html" title="class in org.biojava.bio.search">FilteringContentHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SearchContentAdapter.html#setQueryID(java.lang.String)">setQueryID(String)</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SearchContentAdapter.html" title="class in org.biojava.bio.search">SearchContentAdapter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SearchContentFilter.html#setQueryID(java.lang.String)">setQueryID(String)</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SearchContentFilter.html" title="class in org.biojava.bio.search">SearchContentFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SearchContentHandler.html#setQueryID(java.lang.String)">setQueryID(String)</a></span> - Method in interface org.biojava.bio.search.<a href="./org/biojava/bio/search/SearchContentHandler.html" title="interface in org.biojava.bio.search">SearchContentHandler</a></dt>
<dd>
<div class="block"><code>setQueryID</code> identifies the query sequence by a
name, ID or URN.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SearchContentHandlerDebugger.html#setQueryID(java.lang.String)">setQueryID(String)</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SearchContentHandlerDebugger.html" title="class in org.biojava.bio.search">SearchContentHandlerDebugger</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/sax/FastaSearchSAXParser.html#setQuerySeq(java.lang.String)">setQuerySeq(String)</a></span> - Method in class org.biojava.bio.program.sax.<a href="./org/biojava/bio/program/sax/FastaSearchSAXParser.html" title="class in org.biojava.bio.program.sax">FastaSearchSAXParser</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>use <code>setQueryID</code> instead.</i></div>
</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/BlastLikeSearchBuilder.html#setQuerySeqHolder(org.biojava.bio.seq.db.SequenceDB)">setQuerySeqHolder(SequenceDB)</a></span> - Method in class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/BlastLikeSearchBuilder.html" title="class in org.biojava.bio.program.ssbind">BlastLikeSearchBuilder</a></dt>
<dd>
<div class="block"><code>setQuerySeqHolder</code> sets the query sequence holder
to a specific database.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/ViewSequenceFactory.html#setQuerySeqHolder(org.biojava.bio.seq.db.SequenceDB)">setQuerySeqHolder(SequenceDB)</a></span> - Method in class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/ViewSequenceFactory.html" title="class in org.biojava.bio.program.ssbind">ViewSequenceFactory</a></dt>
<dd>
<div class="block"><code>setQuerySeqHolder</code> sets the query sequence holder
to a specific database.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/CircularRendererPanel.html#setRadius(double)">setRadius(double)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/CircularRendererPanel.html" title="class in org.biojava.bio.gui.sequence">CircularRendererPanel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePanel.html#setRange(org.biojava.bio.symbol.RangeLocation)">setRange(RangeLocation)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePanel.html" title="class in org.biojava.bio.gui.sequence">SequencePanel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePanelWrapper.html#setRange(org.biojava.bio.symbol.RangeLocation)">setRange(RangeLocation)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePanelWrapper.html" title="class in org.biojava.bio.gui.sequence">SequencePanelWrapper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/tracklayout/SimpleTrackLayout.html#setRange(org.biojava.bio.symbol.RangeLocation)">setRange(RangeLocation)</a></span> - Method in class org.biojava.bio.gui.sequence.tracklayout.<a href="./org/biojava/bio/gui/sequence/tracklayout/SimpleTrackLayout.html" title="class in org.biojava.bio.gui.sequence.tracklayout">SimpleTrackLayout</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/tracklayout/TrackLayout.html#setRange(org.biojava.bio.symbol.RangeLocation)">setRange(RangeLocation)</a></span> - Method in interface org.biojava.bio.gui.sequence.tracklayout.<a href="./org/biojava/bio/gui/sequence/tracklayout/TrackLayout.html" title="interface in org.biojava.bio.gui.sequence.tracklayout">TrackLayout</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/tracklayout/UserDefinedTrackLayout.html#setRange(org.biojava.bio.symbol.RangeLocation)">setRange(RangeLocation)</a></span> - Method in class org.biojava.bio.gui.sequence.tracklayout.<a href="./org/biojava/bio/gui/sequence/tracklayout/UserDefinedTrackLayout.html" title="class in org.biojava.bio.gui.sequence.tracklayout">UserDefinedTrackLayout</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/biosql/TaxonSQL.html#setRank(java.sql.Connection, org.biojava.bio.taxa.Taxon, java.lang.String)">setRank(Connection, Taxon, String)</a></span> - Static method in class org.biojava.bio.seq.db.biosql.<a href="./org/biojava/bio/seq/db/biosql/TaxonSQL.html" title="class in org.biojava.bio.seq.db.biosql">TaxonSQL</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Updates a taxon and sets it's rank to the specified <code>String</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/BioEntryRelationship.html#setRank(java.lang.Integer)">setRank(Integer)</a></span> - Method in interface org.biojavax.bio.<a href="./org/biojavax/bio/BioEntryRelationship.html" title="interface in org.biojavax.bio">BioEntryRelationship</a></dt>
<dd>
<div class="block">Sets the rank of this relationship.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/EmptyRichLocation.html#setRank(int)">setRank(int)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/EmptyRichLocation.html" title="class in org.biojavax.bio.seq">EmptyRichLocation</a></dt>
<dd>
<div class="block">Sets the rank for this location.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichFeature.html#setRank(int)">setRank(int)</a></span> - Method in interface org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichFeature.html" title="interface in org.biojavax.bio.seq">RichFeature</a></dt>
<dd>
<div class="block">Sets the rank of this feature.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichFeatureRelationship.html#setRank(int)">setRank(int)</a></span> - Method in interface org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichFeatureRelationship.html" title="interface in org.biojavax.bio.seq">RichFeatureRelationship</a></dt>
<dd>
<div class="block">Sets the rank of this relationship.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichLocation.html#setRank(int)">setRank(int)</a></span> - Method in interface org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichLocation.html" title="interface in org.biojavax.bio.seq">RichLocation</a></dt>
<dd>
<div class="block">Sets the rank for this location.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichFeature.html#setRank(int)">setRank(int)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichFeature.html" title="class in org.biojavax.bio.seq">SimpleRichFeature</a></dt>
<dd>
<div class="block">Sets the rank of this feature.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichFeatureRelationship.html#setRank(int)">setRank(int)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichFeatureRelationship.html" title="class in org.biojavax.bio.seq">SimpleRichFeatureRelationship</a></dt>
<dd>
<div class="block">Sets the rank of this relationship.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichLocation.html#setRank(int)">setRank(int)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichLocation.html" title="class in org.biojavax.bio.seq">SimpleRichLocation</a></dt>
<dd>
<div class="block">Sets the rank for this location.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/SimpleBioEntryRelationship.html#setRank(java.lang.Integer)">setRank(Integer)</a></span> - Method in class org.biojavax.bio.<a href="./org/biojavax/bio/SimpleBioEntryRelationship.html" title="class in org.biojavax.bio">SimpleBioEntryRelationship</a></dt>
<dd>
<div class="block">Sets the rank of this relationship.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/Comment.html#setRank(int)">setRank(int)</a></span> - Method in interface org.biojavax.<a href="./org/biojavax/Comment.html" title="interface in org.biojavax">Comment</a></dt>
<dd>
<div class="block">Sets the rank of this comment.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/Note.html#setRank(int)">setRank(int)</a></span> - Method in interface org.biojavax.<a href="./org/biojavax/Note.html" title="interface in org.biojavax">Note</a></dt>
<dd>
<div class="block">Sets the rank for this note.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/RankedCrossRef.html#setRank(int)">setRank(int)</a></span> - Method in interface org.biojavax.<a href="./org/biojavax/RankedCrossRef.html" title="interface in org.biojavax">RankedCrossRef</a></dt>
<dd>
<div class="block">Set the rank associated with the cross reference.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/RankedDocRef.html#setRank(int)">setRank(int)</a></span> - Method in interface org.biojavax.<a href="./org/biojavax/RankedDocRef.html" title="interface in org.biojavax">RankedDocRef</a></dt>
<dd>
<div class="block">Set the rank of this reference.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleComment.html#setRank(int)">setRank(int)</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleComment.html" title="class in org.biojavax">SimpleComment</a></dt>
<dd>
<div class="block">Sets the rank of this comment.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleNote.html#setRank(int)">setRank(int)</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleNote.html" title="class in org.biojavax">SimpleNote</a></dt>
<dd>
<div class="block">Sets the rank for this note.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleRankedCrossRef.html#setRank(int)">setRank(int)</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleRankedCrossRef.html" title="class in org.biojavax">SimpleRankedCrossRef</a></dt>
<dd>
<div class="block">Set the rank associated with the cross reference.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleRankedDocRef.html#setRank(int)">setRank(int)</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleRankedDocRef.html" title="class in org.biojavax">SimpleRankedDocRef</a></dt>
<dd>
<div class="block">Set the rank of this reference.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/DebuggingRichSeqIOListener.html#setRankedCrossRef(org.biojavax.RankedCrossRef)">setRankedCrossRef(RankedCrossRef)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/DebuggingRichSeqIOListener.html" title="class in org.biojavax.bio.seq.io">DebuggingRichSeqIOListener</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/RichSeqIOAdapter.html#setRankedCrossRef(org.biojavax.RankedCrossRef)">setRankedCrossRef(RankedCrossRef)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/RichSeqIOAdapter.html" title="class in org.biojavax.bio.seq.io">RichSeqIOAdapter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/RichSeqIOListener.html#setRankedCrossRef(org.biojavax.RankedCrossRef)">setRankedCrossRef(RankedCrossRef)</a></span> - Method in interface org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/RichSeqIOListener.html" title="interface in org.biojavax.bio.seq.io">RichSeqIOListener</a></dt>
<dd>
<div class="block">Call back method so the event emitter can tell the listener about a cross reference.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/SimpleRichSequenceBuilder.html#setRankedCrossRef(org.biojavax.RankedCrossRef)">setRankedCrossRef(RankedCrossRef)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/SimpleRichSequenceBuilder.html" title="class in org.biojavax.bio.seq.io">SimpleRichSequenceBuilder</a></dt>
<dd>
<div class="block">Call back method so the event emitter can tell the listener about a cross reference.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichFeature.html#setRankedCrossRefs(java.util.Set)">setRankedCrossRefs(Set)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichFeature.html" title="class in org.biojavax.bio.seq">SimpleRichFeature</a></dt>
<dd>
<div class="block">Sets the ranked cross references associated with an object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/SimpleBioEntry.html#setRankedCrossRefs(java.util.Set)">setRankedCrossRefs(Set)</a></span> - Method in class org.biojavax.bio.<a href="./org/biojavax/bio/SimpleBioEntry.html" title="class in org.biojavax.bio">SimpleBioEntry</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ontology/SimpleComparableTerm.html#setRankedCrossRefs(java.util.Set)">setRankedCrossRefs(Set)</a></span> - Method in class org.biojavax.ontology.<a href="./org/biojavax/ontology/SimpleComparableTerm.html" title="class in org.biojavax.ontology">SimpleComparableTerm</a></dt>
<dd>
<div class="block">Sets the ranked cross references associated with an object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/RankedCrossRefable.html#setRankedCrossRefs(java.util.Set)">setRankedCrossRefs(Set)</a></span> - Method in interface org.biojavax.<a href="./org/biojavax/RankedCrossRefable.html" title="interface in org.biojavax">RankedCrossRefable</a></dt>
<dd>
<div class="block">Sets the ranked cross references associated with an object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/DebuggingRichSeqIOListener.html#setRankedDocRef(org.biojavax.RankedDocRef)">setRankedDocRef(RankedDocRef)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/DebuggingRichSeqIOListener.html" title="class in org.biojavax.bio.seq.io">DebuggingRichSeqIOListener</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/RichSeqIOAdapter.html#setRankedDocRef(org.biojavax.RankedDocRef)">setRankedDocRef(RankedDocRef)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/RichSeqIOAdapter.html" title="class in org.biojavax.bio.seq.io">RichSeqIOAdapter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/RichSeqIOListener.html#setRankedDocRef(org.biojavax.RankedDocRef)">setRankedDocRef(RankedDocRef)</a></span> - Method in interface org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/RichSeqIOListener.html" title="interface in org.biojavax.bio.seq.io">RichSeqIOListener</a></dt>
<dd>
<div class="block">Call back method so the event emitter can tell the listener
about a literature reference in the record being read.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/SimpleRichSequenceBuilder.html#setRankedDocRef(org.biojavax.RankedDocRef)">setRankedDocRef(RankedDocRef)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/SimpleRichSequenceBuilder.html" title="class in org.biojavax.bio.seq.io">SimpleRichSequenceBuilder</a></dt>
<dd>
<div class="block">Call back method so the event emitter can tell the listener
about a literature reference in the record being read.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/process/ReaderWriterPipe.html#setReader(java.io.Reader)">setReader(Reader)</a></span> - Method in class org.biojava.utils.process.<a href="./org/biojava/utils/process/ReaderWriterPipe.html" title="class in org.biojava.utils.process">ReaderWriterPipe</a></dt>
<dd>
<div class="block">Sets the reader.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/AminoAcid.html#setRecordType(java.lang.String)">setRecordType(String)</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/AminoAcid.html" title="interface in org.biojava.bio.structure">AminoAcid</a></dt>
<dd>
<div class="block">Allows to distinguish between amino acids that are provided
as ATOM records and a SEQRES records.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/AminoAcidImpl.html#setRecordType(java.lang.String)">setRecordType(String)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/AminoAcidImpl.html" title="class in org.biojava.bio.structure">AminoAcidImpl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/FilteringRenderer.html#setRecurse(boolean)">setRecurse(boolean)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/FilteringRenderer.html" title="class in org.biojava.bio.gui.sequence">FilteringRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PairwiseFilteringRenderer.html#setRecurse(boolean)">setRecurse(boolean)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PairwiseFilteringRenderer.html" title="class in org.biojava.bio.gui.sequence">PairwiseFilteringRenderer</a></dt>
<dd>
<div class="block"><code>setRecurse</code> sets the recursion flag on the filter.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/SequencesAsGFF.html#setRecurse(boolean)">setRecurse(boolean)</a></span> - Method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/SequencesAsGFF.html" title="class in org.biojava.bio.program.gff">SequencesAsGFF</a></dt>
<dd>
<div class="block">Set whether features will be filtered recursively to
<span class="arg">recurse</span>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/DelegationManager.html#setRecursive(boolean)">setRecursive(boolean)</a></span> - Method in interface org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/DelegationManager.html" title="interface in org.biojava.bio.seq.io.agave">DelegationManager</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html#setRedoxPotential(java.lang.String)">setRedoxPotential(String)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html" title="class in org.biojavax.bio.seq.io">UniProtCommentParser</a></dt>
<dd>
<div class="block">Setter for property redoxPotential.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/StrucAligParameters.html#setReduceInitialFragments(boolean)">setReduceInitialFragments(boolean)</a></span> - Method in class org.biojava.bio.structure.align.<a href="./org/biojava/bio/structure/align/StrucAligParameters.html" title="class in org.biojava.bio.structure.align">StrucAligParameters</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/JournalArticle.html#setRef(java.lang.String)">setRef(String)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/JournalArticle.html" title="class in org.biojava.bio.structure">JournalArticle</a></dt>
<dd>
<div class="block">Set the value of the ref.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/StructRefSeq.html#setRef_id(java.lang.String)">setRef_id(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/StructRefSeq.html" title="class in org.biojava.bio.structure.io.mmcif.model">StructRefSeq</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Compound.html#setRefChainId(java.lang.String)">setRefChainId(String)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure">Compound</a></dt>
<dd>
<div class="block">Returns the ref chain id value.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/JournalArticle.html#setRefn(java.lang.String)">setRefn(String)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/JournalArticle.html" title="class in org.biojava.bio.structure">JournalArticle</a></dt>
<dd>
<div class="block">Set the value of the refn</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVERelatedAnnot.html#setRel(java.lang.String)">setRel(String)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVERelatedAnnot.html" title="class in org.biojava.bio.seq.io.agave">AGAVERelatedAnnot</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEXref.html#setRel(java.lang.String)">setRel(String)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEXref.html" title="class in org.biojava.bio.seq.io.agave">AGAVEXref</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/DebuggingRichSeqIOListener.html#setRelationship(org.biojavax.bio.BioEntryRelationship)">setRelationship(BioEntryRelationship)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/DebuggingRichSeqIOListener.html" title="class in org.biojavax.bio.seq.io">DebuggingRichSeqIOListener</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/RichSeqIOAdapter.html#setRelationship(org.biojavax.bio.BioEntryRelationship)">setRelationship(BioEntryRelationship)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/RichSeqIOAdapter.html" title="class in org.biojavax.bio.seq.io">RichSeqIOAdapter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/RichSeqIOListener.html#setRelationship(org.biojavax.bio.BioEntryRelationship)">setRelationship(BioEntryRelationship)</a></span> - Method in interface org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/RichSeqIOListener.html" title="interface in org.biojavax.bio.seq.io">RichSeqIOListener</a></dt>
<dd>
<div class="block">Call back method so the event emitter can tell the listener
about a relationship between the bioentry or sequence in the
record being read and another bioentry.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/SimpleRichSequenceBuilder.html#setRelationship(org.biojavax.bio.BioEntryRelationship)">setRelationship(BioEntryRelationship)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/SimpleRichSequenceBuilder.html" title="class in org.biojavax.bio.seq.io">SimpleRichSequenceBuilder</a></dt>
<dd>
<div class="block">Call back method so the event emitter can tell the listener
about a relationship between the bioentry or sequence in the
record being read and another bioentry.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/DocRef.html#setRemark(java.lang.String)">setRemark(String)</a></span> - Method in interface org.biojavax.<a href="./org/biojavax/DocRef.html" title="interface in org.biojavax">DocRef</a></dt>
<dd>
<div class="block">Set the remarks for this document reference using this method.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleDocRef.html#setRemark(java.lang.String)">setRemark(String)</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleDocRef.html" title="class in org.biojavax">SimpleDocRef</a></dt>
<dd>
<div class="block">Set the remarks for this document reference using this method.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/CircularFeaturesRenderer.html#setRenderer(org.biojava.bio.gui.sequence.CircularFeatureRenderer)">setRenderer(CircularFeatureRenderer)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/CircularFeaturesRenderer.html" title="class in org.biojava.bio.gui.sequence">CircularFeaturesRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/CircularRendererPanel.html#setRenderer(org.biojava.bio.gui.sequence.CircularRenderer)">setRenderer(CircularRenderer)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/CircularRendererPanel.html" title="class in org.biojava.bio.gui.sequence">CircularRendererPanel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/LabelledSequenceRenderer.html#setRenderer(org.biojava.bio.gui.sequence.SequenceRenderer)">setRenderer(SequenceRenderer)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/LabelledSequenceRenderer.html" title="class in org.biojava.bio.gui.sequence">LabelledSequenceRenderer</a></dt>
<dd>
<div class="block">Set the child renderer responsible for drawing the contents of this track</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/OverlayRendererWrapper.html#setRenderer(org.biojava.bio.gui.sequence.SequenceRenderer)">setRenderer(SequenceRenderer)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/OverlayRendererWrapper.html" title="class in org.biojava.bio.gui.sequence">OverlayRendererWrapper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PairwiseFilteringRenderer.html#setRenderer(org.biojava.bio.gui.sequence.PairwiseSequenceRenderer)">setRenderer(PairwiseSequenceRenderer)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PairwiseFilteringRenderer.html" title="class in org.biojava.bio.gui.sequence">PairwiseFilteringRenderer</a></dt>
<dd>
<div class="block"><code>setRenderer</code> sets the renderer.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PairwiseSequencePanel.html#setRenderer(org.biojava.bio.gui.sequence.PairwiseSequenceRenderer)">setRenderer(PairwiseSequenceRenderer)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PairwiseSequencePanel.html" title="class in org.biojava.bio.gui.sequence">PairwiseSequencePanel</a></dt>
<dd>
<div class="block"><code>setRenderer</code> sets the current
<code>PairwiseSequenceRenderer</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePanel.html#setRenderer(org.biojava.bio.gui.sequence.SequenceRenderer)">setRenderer(SequenceRenderer)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePanel.html" title="class in org.biojava.bio.gui.sequence">SequencePanel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePanelWrapper.html#setRenderer(org.biojava.bio.gui.sequence.SequenceRenderer)">setRenderer(SequenceRenderer)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePanelWrapper.html" title="class in org.biojava.bio.gui.sequence">SequencePanelWrapper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePoster.html#setRenderer(org.biojava.bio.gui.sequence.SequenceRenderer)">setRenderer(SequenceRenderer)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePoster.html" title="class in org.biojava.bio.gui.sequence">SequencePoster</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequenceRendererWrapper.html#setRenderer(org.biojava.bio.gui.sequence.SequenceRenderer)">setRenderer(SequenceRenderer)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequenceRendererWrapper.html" title="class in org.biojava.bio.gui.sequence">SequenceRendererWrapper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/TranslatedSequencePanel.html#setRenderer(org.biojava.bio.gui.sequence.SequenceRenderer)">setRenderer(SequenceRenderer)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/TranslatedSequencePanel.html" title="class in org.biojava.bio.gui.sequence">TranslatedSequencePanel</a></dt>
<dd>
<div class="block"><code>setRenderer</code> sets the current
<code>SequenceRenderer</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/DistributionLogo.html#setRenderingHints(java.awt.RenderingHints)">setRenderingHints(RenderingHints)</a></span> - Method in class org.biojava.bio.gui.<a href="./org/biojava/bio/gui/DistributionLogo.html" title="class in org.biojava.bio.gui">DistributionLogo</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PairwiseSequencePanel.html#setRenderingHints(java.awt.RenderingHints)">setRenderingHints(RenderingHints)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PairwiseSequencePanel.html" title="class in org.biojava.bio.gui.sequence">PairwiseSequencePanel</a></dt>
<dd>
<div class="block"><code>setRenderingHints</code> sets the
<code>RenderingHints</code> which will be used by the
<code>Graphics2D</code> instances of delegate renderers.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePanel.html#setRenderingHints(java.awt.RenderingHints)">setRenderingHints(RenderingHints)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePanel.html" title="class in org.biojava.bio.gui.sequence">SequencePanel</a></dt>
<dd>
<div class="block">Use this to switch on effects like Anti-aliasing etc</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePanelWrapper.html#setRenderingHints(java.awt.RenderingHints)">setRenderingHints(RenderingHints)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePanelWrapper.html" title="class in org.biojava.bio.gui.sequence">SequencePanelWrapper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePoster.html#setRenderingHints(java.awt.RenderingHints)">setRenderingHints(RenderingHints)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePoster.html" title="class in org.biojava.bio.gui.sequence">SequencePoster</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Use this to switch on effects like Anti-aliasing etc</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/TranslatedSequencePanel.html#setRenderingHints(java.awt.RenderingHints)">setRenderingHints(RenderingHints)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/TranslatedSequencePanel.html" title="class in org.biojava.bio.gui.sequence">TranslatedSequencePanel</a></dt>
<dd>
<div class="block"><code>setRenderingHints</code> sets the
<code>RenderingHints</code> which will be used by the
<code>Graphics2D</code> instances of delegate renderers.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/NeedlemanWunsch.html#setReplace(short)">setReplace(short)</a></span> - Method in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/NeedlemanWunsch.html" title="class in org.biojava.bio.alignment">NeedlemanWunsch</a></dt>
<dd>
<div class="block">Sets the penalty for a replace operation to the specified value.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/SmithWaterman.html#setReplace(short)">setReplace(short)</a></span> - Method in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/SmithWaterman.html" title="class in org.biojava.bio.alignment">SmithWaterman</a></dt>
<dd>
<div class="block">Overrides the method inherited from the NeedlemanWunsch and sets the
penalty for a replace operation to the specified value.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/DatabasePDBrev.html#setReplaces(java.lang.String)">setReplaces(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/DatabasePDBrev.html" title="class in org.biojava.bio.structure.io.mmcif.model">DatabasePDBrev</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html#setResidueType(org.biojava.bio.structure.io.mmcif.chem.ResidueType)">setResidueType(ResidueType)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html" title="class in org.biojava.bio.structure.io.mmcif.model">ChemComp</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Compound.html#setResNames(java.lang.String)">setResNames(String)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure">Compound</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/SSBond.html#setResnum1(java.lang.String)">setResnum1(String)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/SSBond.html" title="class in org.biojava.bio.structure">SSBond</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/SSBond.html#setResnum2(java.lang.String)">setResnum2(String)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/SSBond.html" title="class in org.biojava.bio.structure">SSBond</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/PDBHeader.html#setResolution(float)">setResolution(float)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/PDBHeader.html" title="class in org.biojava.bio.structure">PDBHeader</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/TagDropper.html#setRetain(boolean)">setRetain(boolean)</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/TagDropper.html" title="class in org.biojava.bio.program.tagvalue">TagDropper</a></dt>
<dd>
<div class="block">Set wether known tags are to be retained or dropped.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/RichObjectFactory.html#setRichObjectBuilder(org.biojavax.RichObjectBuilder)">setRichObjectBuilder(RichObjectBuilder)</a></span> - Static method in class org.biojavax.<a href="./org/biojavax/RichObjectFactory.html" title="class in org.biojavax">RichObjectFactory</a></dt>
<dd>
<div class="block">Sets the builder to use when instantiating new Rich objects.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/biosql/TaxonSQL.html#setRightValue(java.sql.Connection, org.biojava.bio.taxa.Taxon, int)">setRightValue(Connection, Taxon, int)</a></span> - Static method in class org.biojava.bio.seq.db.biosql.<a href="./org/biojava/bio/seq/db/biosql/TaxonSQL.html" title="class in org.biojava.bio.seq.db.biosql">TaxonSQL</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Updates the taxon in the database and sets the right value to the specified value.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/taxa/NCBITaxon.html#setRightValue(java.lang.Integer)">setRightValue(Integer)</a></span> - Method in interface org.biojavax.bio.taxa.<a href="./org/biojavax/bio/taxa/NCBITaxon.html" title="interface in org.biojavax.bio.taxa">NCBITaxon</a></dt>
<dd>
<div class="block">Sets the right value.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/taxa/SimpleNCBITaxon.html#setRightValue(java.lang.Integer)">setRightValue(Integer)</a></span> - Method in class org.biojavax.bio.taxa.<a href="./org/biojavax/bio/taxa/SimpleNCBITaxon.html" title="class in org.biojavax.bio.taxa">SimpleNCBITaxon</a></dt>
<dd>
<div class="block">Sets the right value.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/helper/JointFragments.html#setRms(double)">setRms(double)</a></span> - Method in class org.biojava.bio.structure.align.helper.<a href="./org/biojava/bio/structure/align/helper/JointFragments.html" title="class in org.biojava.bio.structure.align.helper">JointFragments</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/AlternativeAlignment.html#setRms(double)">setRms(double)</a></span> - Method in class org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/AlternativeAlignment.html" title="class in org.biojava.bio.structure.align.pairwise">AlternativeAlignment</a></dt>
<dd>
<div class="block">the rms in the structurally equivalent regions</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/FragmentPair.html#setRms(double)">setRms(double)</a></span> - Method in class org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/FragmentPair.html" title="class in org.biojava.bio.structure.align.pairwise">FragmentPair</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/FragmentPair.html#setRot(org.biojava.bio.structure.jama.Matrix)">setRot(Matrix)</a></span> - Method in class org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/FragmentPair.html" title="class in org.biojava.bio.structure.align.pairwise">FragmentPair</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/helper/IndexPair.html#setRow(short)">setRow(short)</a></span> - Method in class org.biojava.bio.structure.align.helper.<a href="./org/biojava/bio/structure/align/helper/IndexPair.html" title="class in org.biojava.bio.structure.align.helper">IndexPair</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/JMatrixPanel.html#setSaturation(float)">setSaturation(float)</a></span> - Method in class org.biojava.bio.structure.gui.<a href="./org/biojava/bio/structure/gui/JMatrixPanel.html" title="class in org.biojava.bio.structure.gui">JMatrixPanel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PairwiseSequencePanel.html#setScale(double)">setScale(double)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PairwiseSequencePanel.html" title="class in org.biojava.bio.gui.sequence">PairwiseSequencePanel</a></dt>
<dd>
<div class="block"><code>setScale</code> sets the scale in pixels per
<code>Symbol</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePanel.html#setScale(double)">setScale(double)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePanel.html" title="class in org.biojava.bio.gui.sequence">SequencePanel</a></dt>
<dd>
<div class="block">Set the scale.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePanelWrapper.html#setScale(double)">setScale(double)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePanelWrapper.html" title="class in org.biojava.bio.gui.sequence">SequencePanelWrapper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePoster.html#setScale(double)">setScale(double)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePoster.html" title="class in org.biojava.bio.gui.sequence">SequencePoster</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Set the scale.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/TranslatedSequencePanel.html#setScale(double)">setScale(double)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/TranslatedSequencePanel.html" title="class in org.biojava.bio.gui.sequence">TranslatedSequencePanel</a></dt>
<dd>
<div class="block"><code>setScale</code> sets the scale in pixels per
<code>Symbol</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/JMatrixPanel.html#setScale(float)">setScale(float)</a></span> - Method in class org.biojava.bio.structure.gui.<a href="./org/biojava/bio/structure/gui/JMatrixPanel.html" title="class in org.biojava.bio.structure.gui">JMatrixPanel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/util/CoordManager.html#setScale(float)">setScale(float)</a></span> - Method in class org.biojava.bio.structure.gui.util.<a href="./org/biojava/bio/structure/gui/util/CoordManager.html" title="class in org.biojava.bio.structure.gui.util">CoordManager</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/util/SequenceScalePanel.html#setScale(float)">setScale(float)</a></span> - Method in class org.biojava.bio.structure.gui.util.<a href="./org/biojava/bio/structure/gui/util/SequenceScalePanel.html" title="class in org.biojava.bio.structure.gui.util">SequenceScalePanel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/DistributionLogo.html#setScaleByInformation(boolean)">setScaleByInformation(boolean)</a></span> - Method in class org.biojava.bio.gui.<a href="./org/biojava/bio/gui/DistributionLogo.html" title="class in org.biojava.bio.gui">DistributionLogo</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/JMatrixPanel.html#setScalevalue(float)">setScalevalue(float)</a></span> - Method in class org.biojava.bio.structure.gui.<a href="./org/biojava/bio/structure/gui/JMatrixPanel.html" title="class in org.biojava.bio.structure.gui">JMatrixPanel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/biosql/TaxonSQL.html#setScientificName(java.sql.Connection, org.biojava.bio.taxa.Taxon, java.lang.String)">setScientificName(Connection, Taxon, String)</a></span> - Static method in class org.biojava.bio.seq.db.biosql.<a href="./org/biojava/bio/seq/db/biosql/TaxonSQL.html" title="class in org.biojava.bio.seq.db.biosql">TaxonSQL</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">This changes the scientific name of the given taxon and stores the new name persistent
in the database.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/taxa/AbstractTaxon.html#setScientificName(java.lang.String)">setScientificName(String)</a></span> - Method in class org.biojava.bio.taxa.<a href="./org/biojava/bio/taxa/AbstractTaxon.html" title="class in org.biojava.bio.taxa">AbstractTaxon</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/taxa/Taxon.html#setScientificName(java.lang.String)">setScientificName(String)</a></span> - Method in interface org.biojava.bio.taxa.<a href="./org/biojava/bio/taxa/Taxon.html" title="interface in org.biojava.bio.taxa">Taxon</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Change the scientific name of this species.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/Synonym.html#setScope(int)">setScope(int)</a></span> - Method in class org.biojava.ontology.<a href="./org/biojava/ontology/Synonym.html" title="class in org.biojava.ontology">Synonym</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/onehead/SingleDPMatrix.html#setScore(double)">setScore(double)</a></span> - Method in class org.biojava.bio.dp.onehead.<a href="./org/biojava/bio/dp/onehead/SingleDPMatrix.html" title="class in org.biojava.bio.dp.onehead">SingleDPMatrix</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/SimpleGFFRecord.html#setScore(double)">setScore(double)</a></span> - Method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/SimpleGFFRecord.html" title="class in org.biojava.bio.program.gff">SimpleGFFRecord</a></dt>
<dd>
<div class="block">Set the score to <span class="arg">score</source>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff3/GFF3Record.Impl.html#setScore(double)">setScore(double)</a></span> - Method in class org.biojava.bio.program.gff3.<a href="./org/biojava/bio/program/gff3/GFF3Record.Impl.html" title="class in org.biojava.bio.program.gff3">GFF3Record.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVERelatedAnnot.html#setScore(java.lang.String)">setScore(String)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVERelatedAnnot.html" title="class in org.biojava.bio.seq.io.agave">AGAVERelatedAnnot</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/Alignable.html#setScore(float)">setScore(float)</a></span> - Method in interface org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/Alignable.html" title="interface in org.biojava.bio.structure.align.pairwise">Alignable</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/AlternativeAlignment.html#setScore(float)">setScore(float)</a></span> - Method in class org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/AlternativeAlignment.html" title="class in org.biojava.bio.structure.align.pairwise">AlternativeAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/StrCompAlignment.html#setScore(float)">setScore(float)</a></span> - Method in class org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/StrCompAlignment.html" title="class in org.biojava.bio.structure.align.pairwise">StrCompAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/SeqSimilarityAdapter.html#setSearchContentHandler(org.biojava.bio.search.SearchContentHandler)">setSearchContentHandler(SearchContentHandler)</a></span> - Method in class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/SeqSimilarityAdapter.html" title="class in org.biojava.bio.program.ssbind">SeqSimilarityAdapter</a></dt>
<dd>
<div class="block"><code>setSearchContentHandler</code> sets the handler which
will recieve the method calls generated by the adapter.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/SeqSimilarityStAXAdapter.html#setSearchContentHandler(org.biojava.bio.search.SearchContentHandler)">setSearchContentHandler(SearchContentHandler)</a></span> - Method in class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/SeqSimilarityStAXAdapter.html" title="class in org.biojava.bio.program.ssbind">SeqSimilarityStAXAdapter</a></dt>
<dd>
<div class="block"><code>setSearchContentHandler</code> sets the handler which
will recieve the method calls generated by the adapter.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/FilteringContentHandler.html#setSearchContentHandler(org.biojava.bio.search.SearchContentHandler)">setSearchContentHandler(SearchContentHandler)</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/FilteringContentHandler.html" title="class in org.biojava.bio.search">FilteringContentHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PairwiseSequencePanel.html#setSecondarySequence(org.biojava.bio.seq.Sequence)">setSecondarySequence(Sequence)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PairwiseSequencePanel.html" title="class in org.biojava.bio.gui.sequence">PairwiseSequencePanel</a></dt>
<dd>
<div class="block"><code>setSecondarySequence</code> sets the secondary
<code>Sequence</code> to be rendered.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PairwiseSequencePanel.html#setSecondarySymbolTranslation(int)">setSecondarySymbolTranslation(int)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PairwiseSequencePanel.html" title="class in org.biojava.bio.gui.sequence">PairwiseSequencePanel</a></dt>
<dd>
<div class="block"><code>setSecondarySymbolTranslation</code> sets the translation
in <code>Symbol</code>s which will be applied when
rendering.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtCommentParser.Interaction.html#setSecondIntActID(java.lang.String)">setSecondIntActID(String)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtCommentParser.Interaction.html" title="class in org.biojavax.bio.seq.io">UniProtCommentParser.Interaction</a></dt>
<dd>
<div class="block">Setter for property secondIntActID.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Compound.html#setSecretion(java.lang.String)">setSecretion(String)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure">Compound</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/AminoAcid.html#setSecStruc(java.util.Map)">setSecStruc(Map<String, String>)</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/AminoAcid.html" title="interface in org.biojava.bio.structure">AminoAcid</a></dt>
<dd>
<div class="block">Specifies the secondary structure as a Map.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/AminoAcidImpl.html#setSecStruc(java.util.Map)">setSecStruc(Map<String, String>)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/AminoAcidImpl.html" title="class in org.biojava.bio.structure">AminoAcidImpl</a></dt>
<dd>
<div class="block">set the secondary structure data for this amino acid.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/StrucAligParameters.html#setSeedFragmentLength(int)">setSeedFragmentLength(int)</a></span> - Method in class org.biojava.bio.structure.align.<a href="./org/biojava/bio/structure/align/StrucAligParameters.html" title="class in org.biojava.bio.structure.align">StrucAligParameters</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/StrucAligParameters.html#setSeedRmsdCutoff(float)">setSeedRmsdCutoff(float)</a></span> - Method in class org.biojava.bio.structure.align.<a href="./org/biojava/bio/structure/align/StrucAligParameters.html" title="class in org.biojava.bio.structure.align">StrucAligParameters</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/JMatrixPanel.html#setSelectedAlignmentPos(int)">setSelectedAlignmentPos(int)</a></span> - Method in class org.biojava.bio.structure.gui.<a href="./org/biojava/bio/structure/gui/JMatrixPanel.html" title="class in org.biojava.bio.structure.gui">JMatrixPanel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/GeneticAlgorithm.html#setSelectionFunction(org.biojavax.ga.functions.SelectionFunction)">setSelectionFunction(SelectionFunction)</a></span> - Method in interface org.biojavax.ga.<a href="./org/biojavax/ga/GeneticAlgorithm.html" title="interface in org.biojavax.ga">GeneticAlgorithm</a></dt>
<dd>
<div class="block">Changes the <code>SelectionFunction</code> used to select candidates for
the next generation</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ga/impl/AbstractGeneticAlgorithm.html#setSelectionFunction(org.biojavax.ga.functions.SelectionFunction)">setSelectionFunction(SelectionFunction)</a></span> - Method in class org.biojavax.ga.impl.<a href="./org/biojavax/ga/impl/AbstractGeneticAlgorithm.html" title="class in org.biojavax.ga.impl">AbstractGeneticAlgorithm</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/functions/TournamentSelection.html#setSelectionPressure(int)">setSelectionPressure(int)</a></span> - Method in class org.biojavax.ga.functions.<a href="./org/biojavax/ga/functions/TournamentSelection.html" title="class in org.biojavax.ga.functions">TournamentSelection</a></dt>
<dd>
<div class="block">sets the parameter controlling selection pressure</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/StructRefSeq.html#setSeq_align_beg(java.lang.String)">setSeq_align_beg(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/StructRefSeq.html" title="class in org.biojava.bio.structure.io.mmcif.model">StructRefSeq</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/StructRefSeq.html#setSeq_align_end(java.lang.String)">setSeq_align_end(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/StructRefSeq.html" title="class in org.biojava.bio.structure.io.mmcif.model">StructRefSeq</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/PdbxNonPolyScheme.html#setSeq_id(java.lang.String)">setSeq_id(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/PdbxNonPolyScheme.html" title="class in org.biojava.bio.structure.io.mmcif.model">PdbxNonPolyScheme</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/PdbxPolySeqScheme.html#setSeq_id(java.lang.String)">setSeq_id(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/PdbxPolySeqScheme.html" title="class in org.biojava.bio.structure.io.mmcif.model">PdbxPolySeqScheme</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/DBRef.html#setSeqBegin(int)">setSeqBegin(int)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/DBRef.html" title="class in org.biojava.bio.structure">DBRef</a></dt>
<dd>
<div class="block">Initial sequence number of the PDB sequence segment.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html#setSeqCautions(java.util.List)">setSeqCautions(List)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html" title="class in org.biojavax.bio.seq.io">UniProtCommentParser</a></dt>
<dd>
<div class="block">Setter for property seqCautions.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/DBRef.html#setSeqEnd(int)">setSeqEnd(int)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/DBRef.html" title="class in org.biojava.bio.structure">DBRef</a></dt>
<dd>
<div class="block">Ending sequence number of the PDB sequence segment.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/FeatureTableParser.html#setSeqID(java.lang.String)">setSeqID(String)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/FeatureTableParser.html" title="class in org.biojava.bio.seq.io">FeatureTableParser</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFRecordFilter.SequenceFilter.html#setSeqName(java.lang.String)">setSeqName(String)</a></span> - Method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFRecordFilter.SequenceFilter.html" title="class in org.biojava.bio.program.gff">GFFRecordFilter.SequenceFilter</a></dt>
<dd>
<div class="block">Set the sequence name to <span class="arg">seqName</span>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/SimpleGFFRecord.html#setSeqName(java.lang.String)">setSeqName(String)</a></span> - Method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/SimpleGFFRecord.html" title="class in org.biojava.bio.program.gff">SimpleGFFRecord</a></dt>
<dd>
<div class="block">Set the sequence name to <span class="arg">seqName</span>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Chain.html#setSeqResGroups(java.util.List)">setSeqResGroups(List<Group>)</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Chain.html" title="interface in org.biojava.bio.structure">Chain</a></dt>
<dd>
<div class="block">Set the list of SeqResGroups for this chain.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/ChainImpl.html#setSeqResGroups(java.util.List)">setSeqResGroups(List<Group>)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/ChainImpl.html" title="class in org.biojava.bio.structure">ChainImpl</a></dt>
<dd>
<div class="block">Set the list of SeqResGroups for this chain.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/CircularRendererPanel.html#setSequence(org.biojava.bio.symbol.SymbolList)">setSequence(SymbolList)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/CircularRendererPanel.html" title="class in org.biojava.bio.gui.sequence">CircularRendererPanel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PairwiseSequencePanel.html#setSequence(org.biojava.bio.seq.Sequence)">setSequence(Sequence)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PairwiseSequencePanel.html" title="class in org.biojava.bio.gui.sequence">PairwiseSequencePanel</a></dt>
<dd>
<div class="block"><code>setSequence</code> sets the <code>Sequence</code>
to be rendered.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePanel.html#setSequence(org.biojava.bio.symbol.SymbolList)">setSequence(SymbolList)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePanel.html" title="class in org.biojava.bio.gui.sequence">SequencePanel</a></dt>
<dd>
<div class="block">Set the SymboList to be rendered.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePanelWrapper.html#setSequence(org.biojava.bio.seq.Sequence)">setSequence(Sequence)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePanelWrapper.html" title="class in org.biojava.bio.gui.sequence">SequencePanelWrapper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePoster.html#setSequence(org.biojava.bio.seq.Sequence)">setSequence(Sequence)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePoster.html" title="class in org.biojava.bio.gui.sequence">SequencePoster</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Set the SymboList to be rendered.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/tracklayout/SimpleTrackLayout.html#setSequence(org.biojava.bio.seq.Sequence)">setSequence(Sequence)</a></span> - Method in class org.biojava.bio.gui.sequence.tracklayout.<a href="./org/biojava/bio/gui/sequence/tracklayout/SimpleTrackLayout.html" title="class in org.biojava.bio.gui.sequence.tracklayout">SimpleTrackLayout</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/tracklayout/TrackLayout.html#setSequence(org.biojava.bio.seq.Sequence)">setSequence(Sequence)</a></span> - Method in interface org.biojava.bio.gui.sequence.tracklayout.<a href="./org/biojava/bio/gui/sequence/tracklayout/TrackLayout.html" title="interface in org.biojava.bio.gui.sequence.tracklayout">TrackLayout</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/tracklayout/UserDefinedTrackLayout.html#setSequence(org.biojava.bio.seq.Sequence)">setSequence(Sequence)</a></span> - Method in class org.biojava.bio.gui.sequence.tracklayout.<a href="./org/biojava/bio/gui/sequence/tracklayout/UserDefinedTrackLayout.html" title="class in org.biojava.bio.gui.sequence.tracklayout">UserDefinedTrackLayout</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/TranslatedSequencePanel.html#setSequence(org.biojava.bio.symbol.SymbolList)">setSequence(SymbolList)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/TranslatedSequencePanel.html" title="class in org.biojava.bio.gui.sequence">TranslatedSequencePanel</a></dt>
<dd>
<div class="block"><code>setSequence</code> sets the <code>Sequence</code> to be
rendered.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/Digest.html#setSequence(org.biojava.bio.seq.Sequence)">setSequence(Sequence)</a></span> - Method in class org.biojava.bio.proteomics.<a href="./org/biojava/bio/proteomics/Digest.html" title="class in org.biojava.bio.proteomics">Digest</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtCommentParser.SeqCaution.html#setSequence(java.lang.String)">setSequence(String)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtCommentParser.SeqCaution.html" title="class in org.biojavax.bio.seq.io">UniProtCommentParser.SeqCaution</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/phylo/io/phylip/PHYLIPFileBuilder.html#setSequenceCount(int)">setSequenceCount(int)</a></span> - Method in class org.biojavax.bio.phylo.io.phylip.<a href="./org/biojavax/bio/phylo/io/phylip/PHYLIPFileBuilder.html" title="class in org.biojavax.bio.phylo.io.phylip">PHYLIPFileBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/phylo/io/phylip/PHYLIPFileListener.html#setSequenceCount(int)">setSequenceCount(int)</a></span> - Method in interface org.biojavax.bio.phylo.io.phylip.<a href="./org/biojavax/bio/phylo/io/phylip/PHYLIPFileListener.html" title="interface in org.biojavax.bio.phylo.io.phylip">PHYLIPFileListener</a></dt>
<dd>
<div class="block">Set the number of sequences in the alignment.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/FeatureTree.html#setSequenceDB(org.biojava.bio.seq.db.SequenceDB)">setSequenceDB(SequenceDB)</a></span> - Method in class org.biojava.bio.gui.<a href="./org/biojava/bio/gui/FeatureTree.html" title="class in org.biojava.bio.gui">FeatureTree</a></dt>
<dd>
<div class="block">Use this method to provide the sequences for the tree to work with.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/indexdb/BioStoreFactory.html#setSequenceFormat(org.biojava.utils.lsid.LifeScienceIdentifier)">setSequenceFormat(LifeScienceIdentifier)</a></span> - Method in class org.biojava.bio.program.indexdb.<a href="./org/biojava/bio/program/indexdb/BioStoreFactory.html" title="class in org.biojava.bio.program.indexdb">BioStoreFactory</a></dt>
<dd>
<div class="block"><code>setSequenceFormat</code> sets the sequence format name
which will be indicated in the index.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/NCBISequenceDB.html#setSequenceFormat(org.biojava.bio.seq.io.SequenceFormat)">setSequenceFormat(SequenceFormat)</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/NCBISequenceDB.html" title="class in org.biojava.bio.seq.db">NCBISequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff3/GFF3Record.Impl.html#setSequenceID(java.lang.String)">setSequenceID(String)</a></span> - Method in class org.biojava.bio.program.gff3.<a href="./org/biojava/bio/program/gff3/GFF3Record.Impl.html" title="class in org.biojava.bio.program.gff3">GFF3Record.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichSequence.html#setSequenceLength(int)">setSequenceLength(int)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichSequence.html" title="class in org.biojavax.bio.seq">SimpleRichSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/ThinRichSequence.html#setSequenceLength(int)">setSequenceLength(int)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/ThinRichSequence.html" title="class in org.biojavax.bio.seq">ThinRichSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/OffsetRulerRenderer.html#setSequenceOffset(int)">setSequenceOffset(int)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/OffsetRulerRenderer.html" title="class in org.biojava.bio.gui.sequence">OffsetRulerRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtCommentParser.Isoform.html#setSequenceRef(java.lang.String)">setSequenceRef(String)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtCommentParser.Isoform.html" title="class in org.biojavax.bio.seq.io">UniProtCommentParser.Isoform</a></dt>
<dd>
<div class="block">Setter for property sequenceRef.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtCommentParser.Isoform.html#setSequenceType(java.lang.String)">setSequenceType(String)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtCommentParser.Isoform.html" title="class in org.biojavax.bio.seq.io">UniProtCommentParser.Isoform</a></dt>
<dd>
<div class="block">Setter for property sequenceType.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/DebuggingRichSeqIOListener.html#setSeqVersion(java.lang.String)">setSeqVersion(String)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/DebuggingRichSeqIOListener.html" title="class in org.biojavax.bio.seq.io">DebuggingRichSeqIOListener</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/RichSeqIOAdapter.html#setSeqVersion(java.lang.String)">setSeqVersion(String)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/RichSeqIOAdapter.html" title="class in org.biojavax.bio.seq.io">RichSeqIOAdapter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/RichSeqIOListener.html#setSeqVersion(java.lang.String)">setSeqVersion(String)</a></span> - Method in interface org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/RichSeqIOListener.html" title="interface in org.biojavax.bio.seq.io">RichSeqIOListener</a></dt>
<dd>
<div class="block">Call back method so the event emitter can tell the listener
the version of the sequence of the record being read.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/SimpleRichSequenceBuilder.html#setSeqVersion(java.lang.String)">setSeqVersion(String)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/SimpleRichSequenceBuilder.html" title="class in org.biojavax.bio.seq.io">SimpleRichSequenceBuilder</a></dt>
<dd>
<div class="block">Call back method so the event emitter can tell the listener
the version of the sequence of the record being read.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.html#setSeqVersion(java.lang.Double)">setSeqVersion(Double)</a></span> - Method in interface org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.html" title="interface in org.biojavax.bio.seq">RichSequence</a></dt>
<dd>
<div class="block">Sets the version of the associated symbol list.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/ThinRichSequence.html#setSeqVersion(java.lang.Double)">setSeqVersion(Double)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/ThinRichSequence.html" title="class in org.biojavax.bio.seq">ThinRichSequence</a></dt>
<dd>
<div class="block">Sets the version of the associated symbol list.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/SSBond.html#setSerNum(int)">setSerNum(int)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/SSBond.html" title="class in org.biojava.bio.structure">SSBond</a></dt>
<dd>
<div class="block">get serial number of this SSBOND in PDB file</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/server/DemoStructureServer.html#setServer(org.biojava.bio.structure.server.StructureServer)">setServer(StructureServer)</a></span> - Method in class org.biojava.bio.structure.server.<a href="./org/biojava/bio/structure/server/DemoStructureServer.html" title="class in org.biojava.bio.structure.server">DemoStructureServer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/dasalignment/DASAlignmentCall.html#setServerurl(java.lang.String)">setServerurl(String)</a></span> - Method in class org.biojava.bio.program.das.dasalignment.<a href="./org/biojava/bio/program/das/dasalignment/DASAlignmentCall.html" title="class in org.biojava.bio.program.das.dasalignment">DASAlignmentCall</a></dt>
<dd>
<div class="block">set url of aligmnent service.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/dasstructure/DASStructureCall.html#setServerurl(java.lang.String)">setServerurl(String)</a></span> - Method in class org.biojava.bio.program.das.dasstructure.<a href="./org/biojava/bio/program/das/dasstructure/DASStructureCall.html" title="class in org.biojava.bio.program.das.dasstructure">DASStructureCall</a></dt>
<dd>
<div class="block">set url of structure service.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/SequencesAsGFF.html#setShatter(boolean)">setShatter(boolean)</a></span> - Method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/SequencesAsGFF.html" title="class in org.biojava.bio.program.gff">SequencesAsGFF</a></dt>
<dd>
<div class="block">Specify whether features with non-contiguous locations should be broken
up such that a GFF feature line is emitted for each contiguous block.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/FastaHeader.html#setShowAccession(boolean)">setShowAccession(boolean)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/FastaHeader.html" title="class in org.biojavax.bio.seq.io">FastaHeader</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/FastaHeader.html#setShowDescription(boolean)">setShowDescription(boolean)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/FastaHeader.html" title="class in org.biojavax.bio.seq.io">FastaHeader</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/FastaHeader.html#setShowIdentifier(boolean)">setShowIdentifier(boolean)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/FastaHeader.html" title="class in org.biojavax.bio.seq.io">FastaHeader</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/FastaHeader.html#setShowName(boolean)">setShowName(boolean)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/FastaHeader.html" title="class in org.biojavax.bio.seq.io">FastaHeader</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/FastaHeader.html#setShowNamespace(boolean)">setShowNamespace(boolean)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/FastaHeader.html" title="class in org.biojavax.bio.seq.io">FastaHeader</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/FastaHeader.html#setShowVersion(boolean)">setShowVersion(boolean)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/FastaHeader.html" title="class in org.biojavax.bio.seq.io">FastaHeader</a></dt>
<dd>
<div class="block">Determines if the version number of a sequence should be displayed.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/homol/SimilarityPairFeature.html#setSibling(org.biojava.bio.seq.homol.SimilarityPairFeature)">setSibling(SimilarityPairFeature)</a></span> - Method in interface org.biojava.bio.seq.homol.<a href="./org/biojava/bio/seq/homol/SimilarityPairFeature.html" title="interface in org.biojava.bio.seq.homol">SimilarityPairFeature</a></dt>
<dd>
<div class="block"><code>setSibling</code> sets the sibling feature of the
pair.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleSimilarityPairFeature.html#setSibling(org.biojava.bio.seq.homol.SimilarityPairFeature)">setSibling(SimilarityPairFeature)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleSimilarityPairFeature.html" title="class in org.biojava.bio.seq.impl">SimpleSimilarityPairFeature</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/SimpleChromatogram.html#setSignificantBits(int)">setSignificantBits(int)</a></span> - Method in class org.biojava.bio.chromatogram.<a href="./org/biojava/bio/chromatogram/SimpleChromatogram.html" title="class in org.biojava.bio.chromatogram">SimpleChromatogram</a></dt>
<dd>
<div class="block">Sets the number of significant bits in the data.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/phylo/io/phylip/PHYLIPFileBuilder.html#setSitesCount(int)">setSitesCount(int)</a></span> - Method in class org.biojavax.bio.phylo.io.phylip.<a href="./org/biojavax/bio/phylo/io/phylip/PHYLIPFileBuilder.html" title="class in org.biojavax.bio.phylo.io.phylip">PHYLIPFileBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/phylo/io/phylip/PHYLIPFileListener.html#setSitesCount(int)">setSitesCount(int)</a></span> - Method in interface org.biojavax.bio.phylo.io.phylip.<a href="./org/biojavax/bio/phylo/io/phylip/PHYLIPFileListener.html" title="interface in org.biojavax.bio.phylo.io.phylip">PHYLIPFileListener</a></dt>
<dd>
<div class="block">Set the number of sites in the alignment</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequenceRenderContext.Border.html#setSize(double)">setSize(double)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequenceRenderContext.Border.html" title="class in org.biojava.bio.gui.sequence">SequenceRenderContext.Border</a></dt>
<dd>
<div class="block">Sets the size of the border in number of pixels.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/process/ExternalProcess.html#setSleepTime(int)">setSleepTime(int)</a></span> - Method in class org.biojava.utils.process.<a href="./org/biojava/utils/process/ExternalProcess.html" title="class in org.biojava.utils.process">ExternalProcess</a></dt>
<dd>
<div class="block">Sets the number of milliseconds the <a href="./org/biojava/utils/process/ExternalProcess.html#execute(java.util.Properties)">ExternalProcess.execute(Properties)</a>
method should pauses after the external process is terminated.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#setSolvent_model_details(java.lang.String)">setSolvent_model_details(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#setSolvent_model_param_bsol(java.lang.String)">setSolvent_model_param_bsol(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html#setSolvent_model_param_ksol(java.lang.String)">setSolvent_model_param_ksol(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.bio.structure.io.mmcif.model">Refine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFRecordFilter.SourceFilter.html#setSource(java.lang.String)">setSource(String)</a></span> - Method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFRecordFilter.SourceFilter.html" title="class in org.biojava.bio.program.gff">GFFRecordFilter.SourceFilter</a></dt>
<dd>
<div class="block">Set the source to <span class="arg">source</span>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/SimpleGFFRecord.html#setSource(java.lang.String)">setSource(String)</a></span> - Method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/SimpleGFFRecord.html" title="class in org.biojava.bio.program.gff">SimpleGFFRecord</a></dt>
<dd>
<div class="block">Set the feature source to <span class="arg">source</source>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff3/GFF3Record.Impl.html#setSource(org.biojava.ontology.Term)">setSource(Term)</a></span> - Method in class org.biojava.bio.program.gff3.<a href="./org/biojava/bio/program/gff3/GFF3Record.Impl.html" title="class in org.biojava.bio.program.gff3">GFF3Record.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/Feature.html#setSource(java.lang.String)">setSource(String)</a></span> - Method in interface org.biojava.bio.seq.<a href="./org/biojava/bio/seq/Feature.html" title="interface in org.biojava.bio.seq">Feature</a></dt>
<dd>
<div class="block">Change the source of the Feature.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleFeature.html#setSource(java.lang.String)">setSource(String)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleFeature.html" title="class in org.biojava.bio.seq.impl">SimpleFeature</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEMapLocation.html#setSource(java.lang.String)">setSource(String)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEMapLocation.html" title="class in org.biojava.bio.seq.io.agave">AGAVEMapLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichFeature.html#setSource(java.lang.String)">setSource(String)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichFeature.html" title="class in org.biojavax.bio.seq">SimpleRichFeature</a></dt>
<dd>
<div class="block">Change the source of the Feature.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/Feature.html#setSourceTerm(org.biojava.ontology.Term)">setSourceTerm(Term)</a></span> - Method in interface org.biojava.bio.seq.<a href="./org/biojava/bio/seq/Feature.html" title="interface in org.biojava.bio.seq">Feature</a></dt>
<dd>
<div class="block">Set the source ontology-term for this feature.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleFeature.html#setSourceTerm(org.biojava.ontology.Term)">setSourceTerm(Term)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleFeature.html" title="class in org.biojava.bio.seq.impl">SimpleFeature</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichFeature.html#setSourceTerm(org.biojava.ontology.Term)">setSourceTerm(Term)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichFeature.html" title="class in org.biojavax.bio.seq">SimpleRichFeature</a></dt>
<dd>
<div class="block">Set the source ontology-term for this feature.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePoster.html#setSpacer(int)">setSpacer(int)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePoster.html" title="class in org.biojava.bio.gui.sequence">SequencePoster</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Set the number of pixels to leave blank between each block of sequence
information.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/LineSplitParser.html#setSplitOffset(int)">setSplitOffset(int)</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/LineSplitParser.html" title="class in org.biojava.bio.program.tagvalue">LineSplitParser</a></dt>
<dd>
<div class="block">Set the offset to split lines at.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/ChangeTable.html#setSplitter(java.lang.Object, org.biojava.bio.program.tagvalue.ChangeTable.Splitter)">setSplitter(Object, ChangeTable.Splitter)</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/ChangeTable.html" title="class in org.biojava.bio.program.tagvalue">ChangeTable</a></dt>
<dd>
<div class="block">Set the Splitter to be used for all values of a particular tag.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Entity.html#setSrc_method(java.lang.String)">setSrc_method(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Entity.html" title="class in org.biojava.bio.structure.io.mmcif.model">Entity</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Structure.html#setSSBonds(java.util.List)">setSSBonds(List<SSBond>)</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Structure.html" title="interface in org.biojava.bio.structure">Structure</a></dt>
<dd>
<div class="block">set the list of SSBonds for this structure</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/StructureImpl.html#setSSBonds(java.util.List)">setSSBonds(List<SSBond>)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/StructureImpl.html" title="class in org.biojava.bio.structure">StructureImpl</a></dt>
<dd>
<div class="block">set the list of SSBonds for this structure</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html#setStandard(boolean)">setStandard(boolean)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html" title="class in org.biojava.bio.structure.io.mmcif.model">ChemComp</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/SimpleGFFRecord.html#setStart(int)">setStart(int)</a></span> - Method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/SimpleGFFRecord.html" title="class in org.biojava.bio.program.gff">SimpleGFFRecord</a></dt>
<dd>
<div class="block">Set the start coordinate to <span class="arg">start</source>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff3/GFF3Record.Impl.html#setStart(int)">setStart(int)</a></span> - Method in class org.biojava.bio.program.gff3.<a href="./org/biojava/bio/program/gff3/GFF3Record.Impl.html" title="class in org.biojava.bio.program.gff3">GFF3Record.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEMatchRegion.html#setStart(int)">setStart(int)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEMatchRegion.html" title="class in org.biojava.bio.seq.io.agave">AGAVEMatchRegion</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEQueryRegion.html#setStart(int)">setStart(int)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEQueryRegion.html" title="class in org.biojava.bio.seq.io.agave">AGAVEQueryRegion</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/JournalArticle.html#setStartPage(java.lang.String)">setStartPage(String)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/JournalArticle.html" title="class in org.biojava.bio.structure">JournalArticle</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/DatabasePDBrev.html#setStatus(java.lang.String)">setStatus(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/DatabasePDBrev.html" title="class in org.biojava.bio.structure.io.mmcif.model">DatabasePDBrev</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/indexdb/BioStoreFactory.html#setStoreLocation(java.io.File)">setStoreLocation(File)</a></span> - Method in class org.biojava.bio.program.indexdb.<a href="./org/biojava/bio/program/indexdb/BioStoreFactory.html" title="class in org.biojava.bio.program.indexdb">BioStoreFactory</a></dt>
<dd>
<div class="block"><code>setStoreLocation</code> sets the directory of the new
index.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/indexdb/BioStoreFactory.html#setStoreName(java.lang.String)">setStoreName(String)</a></span> - Method in class org.biojava.bio.program.indexdb.<a href="./org/biojava/bio/program/indexdb/BioStoreFactory.html" title="class in org.biojava.bio.program.indexdb">BioStoreFactory</a></dt>
<dd>
<div class="block"><code>setStoreName</code> sets the name to be given to the new
index.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Compound.html#setStrain(java.lang.String)">setStrain(String)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure">Compound</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFRecordFilter.StrandFilter.html#setStrand(org.biojava.bio.seq.StrandedFeature.Strand)">setStrand(StrandedFeature.Strand)</a></span> - Method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFRecordFilter.StrandFilter.html" title="class in org.biojava.bio.program.gff">GFFRecordFilter.StrandFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/SimpleGFFRecord.html#setStrand(org.biojava.bio.seq.StrandedFeature.Strand)">setStrand(StrandedFeature.Strand)</a></span> - Method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/SimpleGFFRecord.html" title="class in org.biojava.bio.program.gff">SimpleGFFRecord</a></dt>
<dd>
<div class="block">Set the strand to <span class="arg">strand</source>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff3/GFF3Record.Impl.html#setStrand(org.biojava.bio.seq.StrandedFeature.Strand)">setStrand(StrandedFeature.Strand)</a></span> - Method in class org.biojava.bio.program.gff3.<a href="./org/biojava/bio/program/gff3/GFF3Record.Impl.html" title="class in org.biojava.bio.program.gff3">GFF3Record.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleStrandedFeature.html#setStrand(org.biojava.bio.seq.StrandedFeature.Strand)">setStrand(StrandedFeature.Strand)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleStrandedFeature.html" title="class in org.biojava.bio.seq.impl">SimpleStrandedFeature</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/StrandedFeature.html#setStrand(org.biojava.bio.seq.StrandedFeature.Strand)">setStrand(StrandedFeature.Strand)</a></span> - Method in interface org.biojava.bio.seq.<a href="./org/biojava/bio/seq/StrandedFeature.html" title="interface in org.biojava.bio.seq">StrandedFeature</a></dt>
<dd>
<div class="block">Set the strand that this feature lies upon.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichFeature.html#setStrand(org.biojava.bio.seq.StrandedFeature.Strand)">setStrand(StrandedFeature.Strand)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichFeature.html" title="class in org.biojavax.bio.seq">SimpleRichFeature</a></dt>
<dd>
<div class="block">Set the strand that this feature lies upon.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichLocation.html#setStrand(org.biojavax.bio.seq.RichLocation.Strand)">setStrand(RichLocation.Strand)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichLocation.html" title="class in org.biojavax.bio.seq">SimpleRichLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game/SequenceContentHandlerBase.html#setStreamParser(org.biojava.bio.seq.io.StreamParser)">setStreamParser(StreamParser)</a></span> - Method in class org.biojava.bio.seq.io.game.<a href="./org/biojava/bio/seq/io/game/SequenceContentHandlerBase.html" title="class in org.biojava.bio.seq.io.game">SequenceContentHandlerBase</a></dt>
<dd>
<div class="block">assign a StreamParser object to instance.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichSequence.html#setStringSequence(java.lang.String)">setStringSequence(String)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichSequence.html" title="class in org.biojavax.bio.seq">SimpleRichSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/xff/PropDetailHandler.html#setStringValue(java.lang.String)">setStringValue(String)</a></span> - Method in class org.biojava.bio.program.xff.<a href="./org/biojava/bio/program/xff/PropDetailHandler.html" title="class in org.biojava.bio.program.xff">PropDetailHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game/GAMEDescriptionPropHandler.html#setStringValue(java.lang.String)">setStringValue(String)</a></span> - Method in class org.biojava.bio.seq.io.game.<a href="./org/biojava/bio/seq/io/game/GAMEDescriptionPropHandler.html" title="class in org.biojava.bio.seq.io.game">GAMEDescriptionPropHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game/GAMENamePropHandler.html#setStringValue(java.lang.String)">setStringValue(String)</a></span> - Method in class org.biojava.bio.seq.io.game.<a href="./org/biojava/bio/seq/io/game/GAMENamePropHandler.html" title="class in org.biojava.bio.seq.io.game">GAMENamePropHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game/GAMETypePropHandler.html#setStringValue(java.lang.String)">setStringValue(String)</a></span> - Method in class org.biojava.bio.seq.io.game.<a href="./org/biojava/bio/seq/io/game/GAMETypePropHandler.html" title="class in org.biojava.bio.seq.io.game">GAMETypePropHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/stax/StringElementHandlerBase.html#setStringValue(java.lang.String)">setStringValue(String)</a></span> - Method in class org.biojava.utils.stax.<a href="./org/biojava/utils/stax/StringElementHandlerBase.html" title="class in org.biojava.utils.stax">StringElementHandlerBase</a></dt>
<dd>
<div class="block">Override this method to do something useful with the
string we collect.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/ChemCompConsumer.html#setStruct(org.biojava.bio.structure.io.mmcif.model.Struct)">setStruct(Struct)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/ChemCompConsumer.html" title="class in org.biojava.bio.structure.io.mmcif">ChemCompConsumer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/MMcifConsumer.html#setStruct(org.biojava.bio.structure.io.mmcif.model.Struct)">setStruct(Struct)</a></span> - Method in interface org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/MMcifConsumer.html" title="interface in org.biojava.bio.structure.io.mmcif">MMcifConsumer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/SimpleMMcifConsumer.html#setStruct(org.biojava.bio.structure.io.mmcif.model.Struct)">setStruct(Struct)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/SimpleMMcifConsumer.html" title="class in org.biojava.bio.structure.io.mmcif">SimpleMMcifConsumer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/BiojavaJmol.html#setStructure(org.biojava.bio.structure.Structure)">setStructure(Structure)</a></span> - Method in class org.biojava.bio.structure.gui.<a href="./org/biojava/bio/structure/gui/BiojavaJmol.html" title="class in org.biojava.bio.structure.gui">BiojavaJmol</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/events/JmolAlignedPositionListener.html#setStructure1(org.biojava.bio.structure.Structure)">setStructure1(Structure)</a></span> - Method in class org.biojava.bio.structure.gui.events.<a href="./org/biojava/bio/structure/gui/events/JmolAlignedPositionListener.html" title="class in org.biojava.bio.structure.gui.events">JmolAlignedPositionListener</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/SequenceDisplay.html#setStructure1(org.biojava.bio.structure.Structure)">setStructure1(Structure)</a></span> - Method in class org.biojava.bio.structure.gui.<a href="./org/biojava/bio/structure/gui/SequenceDisplay.html" title="class in org.biojava.bio.structure.gui">SequenceDisplay</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/events/JmolAlignedPositionListener.html#setStructure2(org.biojava.bio.structure.Structure)">setStructure2(Structure)</a></span> - Method in class org.biojava.bio.structure.gui.events.<a href="./org/biojava/bio/structure/gui/events/JmolAlignedPositionListener.html" title="class in org.biojava.bio.structure.gui.events">JmolAlignedPositionListener</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/SequenceDisplay.html#setStructure2(org.biojava.bio.structure.Structure)">setStructure2(Structure)</a></span> - Method in class org.biojava.bio.structure.gui.<a href="./org/biojava/bio/structure/gui/SequenceDisplay.html" title="class in org.biojava.bio.structure.gui">SequenceDisplay</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/SequenceDisplay.html#setStructurePairAligner(org.biojava.bio.structure.align.StructurePairAligner)">setStructurePairAligner(StructurePairAligner)</a></span> - Method in class org.biojava.bio.structure.gui.<a href="./org/biojava/bio/structure/gui/SequenceDisplay.html" title="class in org.biojava.bio.structure.gui">SequenceDisplay</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/util/AlternativeAlignmentFrame.html#setStructurePairAligner(org.biojava.bio.structure.align.StructurePairAligner)">setStructurePairAligner(StructurePairAligner)</a></span> - Method in class org.biojava.bio.structure.gui.util.<a href="./org/biojava/bio/structure/gui/util/AlternativeAlignmentFrame.html" title="class in org.biojava.bio.structure.gui.util">AlternativeAlignmentFrame</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/DistributionLogo.html#setStyle(org.biojava.bio.gui.SymbolStyle)">setStyle(SymbolStyle)</a></span> - Method in class org.biojava.bio.gui.<a href="./org/biojava/bio/gui/DistributionLogo.html" title="class in org.biojava.bio.gui">DistributionLogo</a></dt>
<dd>
<div class="block">
Set the symbol style.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/sax/FastaSearchSAXParser.html#setSubjectDB(java.lang.String)">setSubjectDB(String)</a></span> - Method in class org.biojava.bio.program.sax.<a href="./org/biojava/bio/program/sax/FastaSearchSAXParser.html" title="class in org.biojava.bio.program.sax">FastaSearchSAXParser</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>use <code>setDatabaseID</code> instead.</i></div>
</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/BlastLikeSearchBuilder.html#setSubjectDBInstallation(org.biojava.bio.seq.db.SequenceDBInstallation)">setSubjectDBInstallation(SequenceDBInstallation)</a></span> - Method in class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/BlastLikeSearchBuilder.html" title="class in org.biojava.bio.program.ssbind">BlastLikeSearchBuilder</a></dt>
<dd>
<div class="block"><code>setSubjectDBInstallation</code> sets the subject database
holder to a specific installation.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/ViewSequenceFactory.html#setSubjectDBInstallation(org.biojava.bio.seq.db.SequenceDBInstallation)">setSubjectDBInstallation(SequenceDBInstallation)</a></span> - Method in class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/ViewSequenceFactory.html" title="class in org.biojava.bio.program.ssbind">ViewSequenceFactory</a></dt>
<dd>
<div class="block"><code>setSubjectDBInstallation</code> sets the subject database
holder to a specific installation.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEMapLocation.html#setSubSeqStart(java.lang.String)">setSubSeqStart(String)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEMapLocation.html" title="class in org.biojava.bio.seq.io.agave">AGAVEMapLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/NeedlemanWunsch.html#setSubstitutionMatrix(org.biojava.bio.alignment.SubstitutionMatrix)">setSubstitutionMatrix(SubstitutionMatrix)</a></span> - Method in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/NeedlemanWunsch.html" title="class in org.biojava.bio.alignment">NeedlemanWunsch</a></dt>
<dd>
<div class="block">Sets the substitution matrix to be used to the specified one.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Author.html#setSurname(java.lang.String)">setSurname(String)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Author.html" title="class in org.biojava.bio.structure">Author</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Chain.html#setSwissprotId(java.lang.String)">setSwissprotId(String)</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Chain.html" title="interface in org.biojava.bio.structure">Chain</a></dt>
<dd>
<div class="block">Set the Swissprot id of this chain.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/ChainImpl.html#setSwissprotId(java.lang.String)">setSwissprotId(String)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/ChainImpl.html" title="class in org.biojava.bio.structure">ChainImpl</a></dt>
<dd>
<div class="block">set the Swissprot id of this chains .</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/molbio/Composition.html#setSymbolList(org.biojava.bio.symbol.SymbolList)">setSymbolList(SymbolList)</a></span> - Method in class org.biojava.bio.molbio.<a href="./org/biojava/bio/molbio/Composition.html" title="class in org.biojava.bio.molbio">Composition</a></dt>
<dd>
<div class="block">Set the <code>SymbolList</code> to calculation the composition of.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/SimpleChromatogram.html#setSymbolLists(org.biojava.bio.symbol.SymbolList, org.biojava.bio.symbol.SymbolList)">setSymbolLists(SymbolList, SymbolList)</a></span> - Method in class org.biojava.bio.chromatogram.<a href="./org/biojava/bio/chromatogram/SimpleChromatogram.html" title="class in org.biojava.bio.chromatogram">SimpleChromatogram</a></dt>
<dd>
<div class="block">Set the DNA and OFFSETS symbol lists for the basecall alignment.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/MassCalc.html#setSymbolModification(char, double)">setSymbolModification(char, double)</a></span> - Method in class org.biojava.bio.proteomics.<a href="./org/biojava/bio/proteomics/MassCalc.html" title="class in org.biojava.bio.proteomics">MassCalc</a></dt>
<dd>
<div class="block">Use this to set a post translational modification for the
<code>Symbol</code> represented by this character.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PairwiseSequencePanel.html#setSymbolTranslation(int)">setSymbolTranslation(int)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PairwiseSequencePanel.html" title="class in org.biojava.bio.gui.sequence">PairwiseSequencePanel</a></dt>
<dd>
<div class="block"><code>setSymbolTranslation</code> sets the translation in
<code>Symbol</code>s which will be applied when rendering.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/TranslatedSequencePanel.html#setSymbolTranslation(int)">setSymbolTranslation(int)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/TranslatedSequencePanel.html" title="class in org.biojava.bio.gui.sequence">TranslatedSequencePanel</a></dt>
<dd>
<div class="block"><code>setSymbolTranslation</code> sets the translation in
<code>Symbol</code>s which will be applied when rendering.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Compound.html#setSynonyms(java.util.List)">setSynonyms(List<String>)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure">Compound</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/Term.Impl.html#setSynonyms(java.util.Set)">setSynonyms(Set)</a></span> - Method in class org.biojava.ontology.<a href="./org/biojava/ontology/Term.Impl.html" title="class in org.biojava.ontology">Term.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Compound.html#setSynthetic(java.lang.String)">setSynthetic(String)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure">Compound</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleGeneticCodeTable.html#setTableNumber(int)">setTableNumber(int)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleGeneticCodeTable.html" title="class in org.biojava.bio.symbol">SimpleGeneticCodeTable</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/RegexParser.html#setTagGroup(int)">setTagGroup(int)</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/RegexParser.html" title="class in org.biojava.bio.program.tagvalue">RegexParser</a></dt>
<dd>
<div class="block">Set the group number that will match the tag.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/AbstractSVMTarget.html#setTarget(java.lang.Object, double)">setTarget(Object, double)</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/AbstractSVMTarget.html" title="class in org.biojava.stats.svm">AbstractSVMTarget</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/SimpleSVMTarget.html#setTarget(java.lang.Object, double)">setTarget(Object, double)</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/SimpleSVMTarget.html" title="class in org.biojava.stats.svm">SimpleSVMTarget</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/SVMTarget.html#setTarget(java.lang.Object, double)">setTarget(Object, double)</a></span> - Method in interface org.biojava.stats.svm.<a href="./org/biojava/stats/svm/SVMTarget.html" title="interface in org.biojava.stats.svm">SVMTarget</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/BioEntry.html#setTaxon(org.biojavax.bio.taxa.NCBITaxon)">setTaxon(NCBITaxon)</a></span> - Method in interface org.biojavax.bio.<a href="./org/biojavax/bio/BioEntry.html" title="interface in org.biojavax.bio">BioEntry</a></dt>
<dd>
<div class="block">Sets the taxon for this bioentry.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/DebuggingRichSeqIOListener.html#setTaxon(org.biojavax.bio.taxa.NCBITaxon)">setTaxon(NCBITaxon)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/DebuggingRichSeqIOListener.html" title="class in org.biojavax.bio.seq.io">DebuggingRichSeqIOListener</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/RichSeqIOAdapter.html#setTaxon(org.biojavax.bio.taxa.NCBITaxon)">setTaxon(NCBITaxon)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/RichSeqIOAdapter.html" title="class in org.biojavax.bio.seq.io">RichSeqIOAdapter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/RichSeqIOListener.html#setTaxon(org.biojavax.bio.taxa.NCBITaxon)">setTaxon(NCBITaxon)</a></span> - Method in interface org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/RichSeqIOListener.html" title="interface in org.biojavax.bio.seq.io">RichSeqIOListener</a></dt>
<dd>
<div class="block">Call back method so the event emitter can tell the listener
the Taxon of the record being read.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/SimpleRichSequenceBuilder.html#setTaxon(org.biojavax.bio.taxa.NCBITaxon)">setTaxon(NCBITaxon)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/SimpleRichSequenceBuilder.html" title="class in org.biojavax.bio.seq.io">SimpleRichSequenceBuilder</a></dt>
<dd>
<div class="block">Call back method so the event emitter can tell the listener
the Taxon of the record being read.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/SimpleBioEntry.html#setTaxon(org.biojavax.bio.taxa.NCBITaxon)">setTaxon(NCBITaxon)</a></span> - Method in class org.biojavax.bio.<a href="./org/biojavax/bio/SimpleBioEntry.html" title="class in org.biojavax.bio">SimpleBioEntry</a></dt>
<dd>
<div class="block">Sets the taxon for this bioentry.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/taxa/NCBITaxon.html#setTaxonHidden(boolean)">setTaxonHidden(boolean)</a></span> - Method in interface org.biojavax.bio.taxa.<a href="./org/biojavax/bio/taxa/NCBITaxon.html" title="interface in org.biojavax.bio.taxa">NCBITaxon</a></dt>
<dd>
<div class="block">determines whether this taxonomy level is displayed in etNameHierarchy()</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/taxa/SimpleNCBITaxon.html#setTaxonHidden(boolean)">setTaxonHidden(boolean)</a></span> - Method in class org.biojavax.bio.taxa.<a href="./org/biojavax/bio/taxa/SimpleNCBITaxon.html" title="class in org.biojavax.bio.taxa">SimpleNCBITaxon</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/PDBHeader.html#setTechnique(java.lang.String)">setTechnique(String)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/PDBHeader.html" title="class in org.biojava.bio.structure">PDBHeader</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html#setTemperatureDependence(java.lang.String)">setTemperatureDependence(String)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html" title="class in org.biojavax.bio.seq.io">UniProtCommentParser</a></dt>
<dd>
<div class="block">Setter for property temperatureDependence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Atom.html#setTempFactor(double)">setTempFactor(double)</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Atom.html" title="interface in org.biojava.bio.structure">Atom</a></dt>
<dd>
<div class="block">get set temp factor .</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/AtomImpl.html#setTempFactor(double)">setTempFactor(double)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/AtomImpl.html" title="class in org.biojava.bio.structure">AtomImpl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/CompoundRichLocation.html#setTerm(org.biojavax.ontology.ComparableTerm)">setTerm(ComparableTerm)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/CompoundRichLocation.html" title="class in org.biojavax.bio.seq">CompoundRichLocation</a></dt>
<dd>
<div class="block">Sets the term for this location.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/EmptyRichLocation.html#setTerm(org.biojavax.ontology.ComparableTerm)">setTerm(ComparableTerm)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/EmptyRichLocation.html" title="class in org.biojavax.bio.seq">EmptyRichLocation</a></dt>
<dd>
<div class="block">Sets the term for this location.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichLocation.html#setTerm(org.biojavax.ontology.ComparableTerm)">setTerm(ComparableTerm)</a></span> - Method in interface org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichLocation.html" title="interface in org.biojavax.bio.seq">RichLocation</a></dt>
<dd>
<div class="block">Sets the term for this location.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichLocation.html#setTerm(org.biojavax.ontology.ComparableTerm)">setTerm(ComparableTerm)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichLocation.html" title="class in org.biojavax.bio.seq">SimpleRichLocation</a></dt>
<dd>
<div class="block">Sets the term for this location.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/Note.html#setTerm(org.biojavax.ontology.ComparableTerm)">setTerm(ComparableTerm)</a></span> - Method in interface org.biojavax.<a href="./org/biojavax/Note.html" title="interface in org.biojavax">Note</a></dt>
<dd>
<div class="block">Sets the term for this note.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleNote.html#setTerm(org.biojavax.ontology.ComparableTerm)">setTerm(ComparableTerm)</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleNote.html" title="class in org.biojavax">SimpleNote</a></dt>
<dd>
<div class="block">Sets the term for this note.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ontology/ComparableOntology.html#setTermSet(java.util.Set)">setTermSet(Set)</a></span> - Method in interface org.biojavax.ontology.<a href="./org/biojavax/ontology/ComparableOntology.html" title="interface in org.biojavax.ontology">ComparableOntology</a></dt>
<dd>
<div class="block">Clears out all the terms and populates the ontology with the contents
of the set passed.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ontology/SimpleComparableOntology.html#setTermSet(java.util.Set)">setTermSet(Set)</a></span> - Method in class org.biojavax.ontology.<a href="./org/biojavax/ontology/SimpleComparableOntology.html" title="class in org.biojavax.ontology">SimpleComparableOntology</a></dt>
<dd>
<div class="block">Clears out all the terms and populates the ontology with the contents
of the set passed.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/DatabasePDBremark.html#setText(java.lang.String)">setText(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/DatabasePDBremark.html" title="class in org.biojava.bio.structure.io.mmcif.model">DatabasePDBremark</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/StructKeywords.html#setText(java.lang.String)">setText(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/StructKeywords.html" title="class in org.biojava.bio.structure.io.mmcif.model">StructKeywords</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html#setText(java.lang.String)">setText(String)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html" title="class in org.biojavax.bio.seq.io">UniProtCommentParser</a></dt>
<dd>
<div class="block">Setter for property text.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/LabelledSequenceRenderer.html#setTextColor(java.awt.Color)">setTextColor(Color)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/LabelledSequenceRenderer.html" title="class in org.biojava.bio.gui.sequence">LabelledSequenceRenderer</a></dt>
<dd>
<div class="block">Set the color of the label text</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/DAS.html#setThreadFetches(boolean)">setThreadFetches(boolean)</a></span> - Static method in class org.biojava.bio.program.das.<a href="./org/biojava/bio/program/das/DAS.html" title="class in org.biojava.bio.program.das">DAS</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html#setThree_letter_code(java.lang.String)">setThree_letter_code(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html" title="class in org.biojava.bio.structure.io.mmcif.model">ChemComp</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/AbstractSVMClassifierModel.html#setThreshold()">setThreshold()</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/AbstractSVMClassifierModel.html" title="class in org.biojava.stats.svm">AbstractSVMClassifierModel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/SimpleSVMClassifierModel.html#setThreshold(double)">setThreshold(double)</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/SimpleSVMClassifierModel.html" title="class in org.biojava.stats.svm">SimpleSVMClassifierModel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/SVMClassifierModel.html#setThreshold(double)">setThreshold(double)</a></span> - Method in interface org.biojava.stats.svm.<a href="./org/biojava/stats/svm/SVMClassifierModel.html" title="interface in org.biojava.stats.svm">SVMClassifierModel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/SVMRegressionModel.html#setThreshold(double)">setThreshold(double)</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/SVMRegressionModel.html" title="class in org.biojava.stats.svm">SVMRegressionModel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/OffsetRulerRenderer.html#setTickDirection(int)">setTickDirection(int)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/OffsetRulerRenderer.html" title="class in org.biojava.bio.gui.sequence">OffsetRulerRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Compound.html#setTissue(java.lang.String)">setTissue(String)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure">Compound</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/Orthologue.html#setTitle(java.lang.String)">setTitle(String)</a></span> - Method in interface org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/Orthologue.html" title="interface in org.biojava.bio.program.homologene">Orthologue</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/SimpleOrthologue.html#setTitle(java.lang.String)">setTitle(String)</a></span> - Method in class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/SimpleOrthologue.html" title="class in org.biojava.bio.program.homologene">SimpleOrthologue</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Compound.html#setTitle(java.lang.String)">setTitle(String)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure">Compound</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/BiojavaJmol.html#setTitle(java.lang.String)">setTitle(String)</a></span> - Method in class org.biojava.bio.structure.gui.<a href="./org/biojava/bio/structure/gui/BiojavaJmol.html" title="class in org.biojava.bio.structure.gui">BiojavaJmol</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Struct.html#setTitle(java.lang.String)">setTitle(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Struct.html" title="class in org.biojava.bio.structure.io.mmcif.model">Struct</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/JournalArticle.html#setTitle(java.lang.String)">setTitle(String)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/JournalArticle.html" title="class in org.biojava.bio.structure">JournalArticle</a></dt>
<dd>
<div class="block">Set the value of title</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/PDBHeader.html#setTitle(java.lang.String)">setTitle(String)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/PDBHeader.html" title="class in org.biojava.bio.structure">PDBHeader</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/AbstractChromatogram.html#setTrace(org.biojava.bio.symbol.AtomicSymbol, int[], int)">setTrace(AtomicSymbol, int[], int)</a></span> - Method in class org.biojava.bio.chromatogram.<a href="./org/biojava/bio/chromatogram/AbstractChromatogram.html" title="class in org.biojava.bio.chromatogram">AbstractChromatogram</a></dt>
<dd>
<div class="block">Provides the trace samples for a particular nucleotide.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/AbiTraceRenderer.html#setTrace(org.biojava.bio.program.abi.ABITrace)">setTrace(ABITrace)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/AbiTraceRenderer.html" title="class in org.biojava.bio.gui.sequence">AbiTraceRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/SimpleChromatogram.html#setTraceValues(org.biojava.bio.symbol.AtomicSymbol, int[], int)">setTraceValues(AtomicSymbol, int[], int)</a></span> - Method in class org.biojava.bio.chromatogram.<a href="./org/biojava/bio/chromatogram/SimpleChromatogram.html" title="class in org.biojava.bio.chromatogram">SimpleChromatogram</a></dt>
<dd>
<div class="block">Sets the trace array for one of the DNA nucleotides.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePanelWrapper.html#setTrackLayout(org.biojava.bio.gui.sequence.tracklayout.TrackLayout)">setTrackLayout(TrackLayout)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePanelWrapper.html" title="class in org.biojava.bio.gui.sequence">SequencePanelWrapper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/BumpedRenderer.html#setTrailingPixles(int)">setTrailingPixles(int)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/BumpedRenderer.html" title="class in org.biojava.bio.gui.sequence">BumpedRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/FragmentPair.html#setTrans(org.biojava.bio.structure.Atom)">setTrans(Atom)</a></span> - Method in class org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/FragmentPair.html" title="class in org.biojava.bio.structure.align.pairwise">FragmentPair</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/StateMachine.BasicState.html#setTransition(java.lang.Object, org.biojava.bio.program.tagvalue.StateMachine.State, boolean)">setTransition(Object, StateMachine.State, boolean)</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/StateMachine.BasicState.html" title="class in org.biojava.bio.program.tagvalue">StateMachine.BasicState</a></dt>
<dd>
<div class="block">set a Transition for this State</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/StateMachine.BasicState.html#setTransition(java.lang.Object, org.biojava.bio.program.tagvalue.StateMachine.State)">setTransition(Object, StateMachine.State)</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/StateMachine.BasicState.html" title="class in org.biojava.bio.program.tagvalue">StateMachine.BasicState</a></dt>
<dd>
<div class="block">set a Transition for this State setting notifyOnExit to false.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/StateMachine.TransitionTable.html#setTransition(java.lang.Object, org.biojava.bio.program.tagvalue.StateMachine.State, boolean)">setTransition(Object, StateMachine.State, boolean)</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/StateMachine.TransitionTable.html" title="class in org.biojava.bio.program.tagvalue">StateMachine.TransitionTable</a></dt>
<dd>
<div class="block">set a Transition within this TransitionTable (3-argument form)</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleManyToOneTranslationTable.html#setTranslation(org.biojava.bio.symbol.AtomicSymbol, org.biojava.bio.symbol.AtomicSymbol)">setTranslation(AtomicSymbol, AtomicSymbol)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleManyToOneTranslationTable.html" title="class in org.biojava.bio.symbol">SimpleManyToOneTranslationTable</a></dt>
<dd>
<div class="block">Alter the translation mapping.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleReversibleTranslationTable.html#setTranslation(org.biojava.bio.symbol.AtomicSymbol, org.biojava.bio.symbol.AtomicSymbol)">setTranslation(AtomicSymbol, AtomicSymbol)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleReversibleTranslationTable.html" title="class in org.biojava.bio.symbol">SimpleReversibleTranslationTable</a></dt>
<dd>
<div class="block">Alter the translation mapping.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleTranslationTable.html#setTranslation(org.biojava.bio.symbol.AtomicSymbol, org.biojava.bio.symbol.AtomicSymbol)">setTranslation(AtomicSymbol, AtomicSymbol)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleTranslationTable.html" title="class in org.biojava.bio.symbol">SimpleTranslationTable</a></dt>
<dd>
<div class="block">Alter the translation mapping.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/LineSplitParser.html#setTrimTag(boolean)">setTrimTag(boolean)</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/LineSplitParser.html" title="class in org.biojava.bio.program.tagvalue">LineSplitParser</a></dt>
<dd>
<div class="block">Enable or disable trimming of tags.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/RegexParser.html#setTrimTag(boolean)">setTrimTag(boolean)</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/RegexParser.html" title="class in org.biojava.bio.program.tagvalue">RegexParser</a></dt>
<dd>
<div class="block">Enable trimming of the tag using String.trim().</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/LineSplitParser.html#setTrimValue(boolean)">setTrimValue(boolean)</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/LineSplitParser.html" title="class in org.biojava.bio.program.tagvalue">LineSplitParser</a></dt>
<dd>
<div class="block">Enable or disable trimming of values.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/RegexParser.html#setTrimValue(boolean)">setTrimValue(boolean)</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/RegexParser.html" title="class in org.biojava.bio.program.tagvalue">RegexParser</a></dt>
<dd>
<div class="block">Enable trimming of the value using String.trim().</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ontology/ComparableOntology.html#setTripleSet(java.util.Set)">setTripleSet(Set)</a></span> - Method in interface org.biojavax.ontology.<a href="./org/biojavax/ontology/ComparableOntology.html" title="interface in org.biojavax.ontology">ComparableOntology</a></dt>
<dd>
<div class="block">Clears out all the triples and populates the ontology with the contents
of the set passed.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ontology/SimpleComparableOntology.html#setTripleSet(java.util.Set)">setTripleSet(Set)</a></span> - Method in class org.biojavax.ontology.<a href="./org/biojavax/ontology/SimpleComparableOntology.html" title="class in org.biojavax.ontology">SimpleComparableOntology</a></dt>
<dd>
<div class="block">Clears out all the triples and populates the ontology with the contents
of the set passed.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff3/GFF3Record.Impl.html#setType(org.biojava.ontology.Term)">setType(Term)</a></span> - Method in class org.biojava.bio.program.gff3.<a href="./org/biojava/bio/program/gff3/GFF3Record.Impl.html" title="class in org.biojava.bio.program.gff3">GFF3Record.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/Feature.html#setType(java.lang.String)">setType(String)</a></span> - Method in interface org.biojava.bio.seq.<a href="./org/biojava/bio/seq/Feature.html" title="interface in org.biojava.bio.seq">Feature</a></dt>
<dd>
<div class="block">Change the type of this feature.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ByAnnotationType.html#setType(org.biojava.bio.AnnotationType)">setType(AnnotationType)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ByAnnotationType.html" title="class in org.biojava.bio.seq">FeatureFilter.ByAnnotationType</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleFeature.html#setType(java.lang.String)">setType(String)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleFeature.html" title="class in org.biojava.bio.seq.impl">SimpleFeature</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html#setType(java.lang.String)">setType(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html" title="class in org.biojava.bio.structure.io.mmcif.model">ChemComp</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Entity.html#setType(java.lang.String)">setType(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Entity.html" title="class in org.biojava.bio.structure.io.mmcif.model">Entity</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtCommentParser.Event.html#setType(java.lang.String)">setType(String)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtCommentParser.Event.html" title="class in org.biojavax.bio.seq.io">UniProtCommentParser.Event</a></dt>
<dd>
<div class="block">Setter for property type.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtCommentParser.SeqCaution.html#setType(java.lang.String)">setType(String)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtCommentParser.SeqCaution.html" title="class in org.biojavax.bio.seq.io">UniProtCommentParser.SeqCaution</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichFeature.html#setType(java.lang.String)">setType(String)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichFeature.html" title="class in org.biojavax.bio.seq">SimpleRichFeature</a></dt>
<dd>
<div class="block">Change the type of this feature.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html#setType_symbol(java.lang.String)">setType_symbol(String)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/AtomSite.html" title="class in org.biojava.bio.structure.io.mmcif.model">AtomSite</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/Feature.html#setTypeTerm(org.biojava.ontology.Term)">setTypeTerm(Term)</a></span> - Method in interface org.biojava.bio.seq.<a href="./org/biojava/bio/seq/Feature.html" title="interface in org.biojava.bio.seq">Feature</a></dt>
<dd>
<div class="block">Set the type ontology-term for this feature.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleFeature.html#setTypeTerm(org.biojava.ontology.Term)">setTypeTerm(Term)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleFeature.html" title="class in org.biojava.bio.seq.impl">SimpleFeature</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichFeature.html#setTypeTerm(org.biojava.ontology.Term)">setTypeTerm(Term)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichFeature.html" title="class in org.biojavax.bio.seq">SimpleRichFeature</a></dt>
<dd>
<div class="block">Set the type ontology-term for this feature.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEMapLocation.html#setUnits(java.lang.String)">setUnits(String)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEMapLocation.html" title="class in org.biojava.bio.seq.io.agave">AGAVEMapLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/FragmentPair.html#setUnitv(org.biojava.bio.structure.Atom)">setUnitv(Atom)</a></span> - Method in class org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/FragmentPair.html" title="class in org.biojava.bio.structure.align.pairwise">FragmentPair</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/EmblFileFormer.html#setURI(java.lang.String)">setURI(String)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/EmblFileFormer.html" title="class in org.biojava.bio.seq.io">EmblFileFormer</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/GenbankFileFormer.html#setURI(java.lang.String)">setURI(String)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/GenbankFileFormer.html" title="class in org.biojava.bio.seq.io">GenbankFileFormer</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOAdapter.html#setURI(java.lang.String)">setURI(String)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOAdapter.html" title="class in org.biojava.bio.seq.io">SeqIOAdapter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOFilter.html#setURI(java.lang.String)">setURI(String)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOFilter.html" title="class in org.biojava.bio.seq.io">SeqIOFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOListener.html#setURI(java.lang.String)">setURI(String)</a></span> - Method in interface org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOListener.html" title="interface in org.biojava.bio.seq.io">SeqIOListener</a></dt>
<dd>
<div class="block">Notify the listener of a URI identifying the current sequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SequenceBuilderBase.html#setURI(java.lang.String)">setURI(String)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SequenceBuilderBase.html" title="class in org.biojava.bio.seq.io">SequenceBuilderBase</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SequenceBuilderFilter.html#setURI(java.lang.String)">setURI(String)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SequenceBuilderFilter.html" title="class in org.biojava.bio.seq.io">SequenceBuilderFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SwissprotFileFormer.html#setURI(java.lang.String)">setURI(String)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SwissprotFileFormer.html" title="class in org.biojava.bio.seq.io">SwissprotFileFormer</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Null implementation.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/DebuggingRichSeqIOListener.html#setURI(java.lang.String)">setURI(String)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/DebuggingRichSeqIOListener.html" title="class in org.biojavax.bio.seq.io">DebuggingRichSeqIOListener</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/RichSeqIOAdapter.html#setURI(java.lang.String)">setURI(String)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/RichSeqIOAdapter.html" title="class in org.biojavax.bio.seq.io">RichSeqIOAdapter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/RichSeqIOListener.html#setURI(java.lang.String)">setURI(String)</a></span> - Method in interface org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/RichSeqIOListener.html" title="interface in org.biojavax.bio.seq.io">RichSeqIOListener</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>There is no clear mapping between URI and BioSQL. This
method is no longer used or supported in biojavax. Don't use it. Calling
it may result in exceptions. Use instead setName(String name),
setAccession(String accession), setVersion(int version) etc as
appropriate.</i></div>
</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/SimpleRichSequenceBuilder.html#setURI(java.lang.String)">setURI(String)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/SimpleRichSequenceBuilder.html" title="class in org.biojavax.bio.seq.io">SimpleRichSequenceBuilder</a></dt>
<dd>
<div class="block">Notify the listener of a URI identifying the current sequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html#setUri(java.lang.String)">setUri(String)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html" title="class in org.biojavax.bio.seq.io">UniProtCommentParser</a></dt>
<dd>
<div class="block">Setter for property uri.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/Namespace.html#setURI(java.net.URI)">setURI(URI)</a></span> - Method in interface org.biojavax.<a href="./org/biojavax/Namespace.html" title="interface in org.biojavax">Namespace</a></dt>
<dd>
<div class="block">Sets an optional URI for the namespace.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleNamespace.html#setURI(java.net.URI)">setURI(URI)</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleNamespace.html" title="class in org.biojavax">SimpleNamespace</a></dt>
<dd>
<div class="block">Sets an optional URI for the namespace.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleSequence.html#setURN(java.lang.String)">setURN(String)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleSequence.html" title="class in org.biojava.bio.seq.impl">SimpleSequence</a></dt>
<dd>
<div class="block">Provide the URN for this sequence</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/FragmentPair.html#setUsed(int)">setUsed(int)</a></span> - Method in class org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/FragmentPair.html" title="class in org.biojava.bio.structure.align.pairwise">FragmentPair</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/StrucAligParameters.html#setUsedAtomNames(java.lang.String[])">setUsedAtomNames(String[])</a></span> - Method in class org.biojava.bio.structure.align.<a href="./org/biojava/bio/structure/align/StrucAligParameters.html" title="class in org.biojava.bio.structure.align">StrucAligParameters</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/ImageMap.HotSpot.html#setUserObject(java.lang.Object)">setUserObject(Object)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/ImageMap.HotSpot.html" title="class in org.biojava.bio.gui.sequence">ImageMap.HotSpot</a></dt>
<dd>
<div class="block"><code>setUserObject</code> sets the user object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/helper/AligMatEl.html#setValue(int)">setValue(int)</a></span> - Method in class org.biojava.bio.structure.align.helper.<a href="./org/biojava/bio/structure/align/helper/AligMatEl.html" title="class in org.biojava.bio.structure.align.helper">AligMatEl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/helper/GapArray.html#setValue(int)">setValue(int)</a></span> - Method in class org.biojava.bio.structure.align.helper.<a href="./org/biojava/bio/structure/align/helper/GapArray.html" title="class in org.biojava.bio.structure.align.helper">GapArray</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/ItemValue.html#setValue(double)">setValue(double)</a></span> - Method in interface org.biojava.stats.svm.<a href="./org/biojava/stats/svm/ItemValue.html" title="interface in org.biojava.stats.svm">ItemValue</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/SimpleItemValue.html#setValue(double)">setValue(double)</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/SimpleItemValue.html" title="class in org.biojava.stats.svm">SimpleItemValue</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/Note.html#setValue(java.lang.String)">setValue(String)</a></span> - Method in interface org.biojavax.<a href="./org/biojavax/Note.html" title="interface in org.biojavax">Note</a></dt>
<dd>
<div class="block">Sets the value for this note, or null for no value.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleNote.html#setValue(java.lang.String)">setValue(String)</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleNote.html" title="class in org.biojavax">SimpleNote</a></dt>
<dd>
<div class="block">Sets the value for this note, or null for no value.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/RegexParser.html#setValueGroup(int)">setValueGroup(int)</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/RegexParser.html" title="class in org.biojava.bio.program.tagvalue">RegexParser</a></dt>
<dd>
<div class="block">Set the group number that will match the value.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Compound.html#setVariant(java.lang.String)">setVariant(String)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure">Compound</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/GenbankFileFormer.html#setVectorNTISupport(boolean)">setVectorNTISupport(boolean)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/GenbankFileFormer.html" title="class in org.biojava.bio.seq.io">GenbankFileFormer</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">VectorNTI requires GenBank format to be a little more specific than
required by the GenBank definition.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEDbId.html#setVersion(java.lang.String)">setVersion(String)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEDbId.html" title="class in org.biojava.bio.seq.io.agave">AGAVEDbId</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/DebuggingRichSeqIOListener.html#setVersion(int)">setVersion(int)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/DebuggingRichSeqIOListener.html" title="class in org.biojavax.bio.seq.io">DebuggingRichSeqIOListener</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/RichSeqIOAdapter.html#setVersion(int)">setVersion(int)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/RichSeqIOAdapter.html" title="class in org.biojavax.bio.seq.io">RichSeqIOAdapter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/RichSeqIOListener.html#setVersion(int)">setVersion(int)</a></span> - Method in interface org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/RichSeqIOListener.html" title="interface in org.biojavax.bio.seq.io">RichSeqIOListener</a></dt>
<dd>
<div class="block">Call back method so the event emitter can tell the listener
the version of the record being read.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/SimpleRichSequenceBuilder.html#setVersion(int)">setVersion(int)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/SimpleRichSequenceBuilder.html" title="class in org.biojavax.bio.seq.io">SimpleRichSequenceBuilder</a></dt>
<dd>
<div class="block">Call back method so the event emitter can tell the listener
the version of the record being read.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.html#setVerticalScale(float)">setVerticalScale(float)</a></span> - Method in class org.biojava.bio.chromatogram.graphic.<a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.html" title="class in org.biojava.bio.chromatogram.graphic">ChromatogramGraphic</a></dt>
<dd>
<div class="block">Sets the vertical scale (proportional).</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html#setVMaxes(java.util.List)">setVMaxes(List)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html" title="class in org.biojavax.bio.seq.io">UniProtCommentParser</a></dt>
<dd>
<div class="block">Setter for property VMaxes.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/JournalArticle.html#setVolume(java.lang.String)">setVolume(String)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/JournalArticle.html" title="class in org.biojava.bio.structure">JournalArticle</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/AbstractDistribution.html#setWeight(org.biojava.bio.symbol.Symbol, double)">setWeight(Symbol, double)</a></span> - Method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/AbstractDistribution.html" title="class in org.biojava.bio.dist">AbstractDistribution</a></dt>
<dd>
<div class="block">Set the weight of a given symbol in this distribution.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/Distribution.html#setWeight(org.biojava.bio.symbol.Symbol, double)">setWeight(Symbol, double)</a></span> - Method in interface org.biojava.bio.dist.<a href="./org/biojava/bio/dist/Distribution.html" title="interface in org.biojava.bio.dist">Distribution</a></dt>
<dd>
<div class="block">Set the probability or odds that Symbol s is emitted by this state.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/GapDistribution.html#setWeight(org.biojava.bio.symbol.Symbol, double)">setWeight(Symbol, double)</a></span> - Method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/GapDistribution.html" title="class in org.biojava.bio.dist">GapDistribution</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/PairDistribution.html#setWeight(org.biojava.bio.symbol.Symbol, double)">setWeight(Symbol, double)</a></span> - Method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/PairDistribution.html" title="class in org.biojava.bio.dist">PairDistribution</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/TranslatedDistribution.html#setWeight(org.biojava.bio.symbol.Symbol, double)">setWeight(Symbol, double)</a></span> - Method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/TranslatedDistribution.html" title="class in org.biojava.bio.dist">TranslatedDistribution</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/util/WeightedSet.html#setWeight(java.lang.Object, double)">setWeight(Object, double)</a></span> - Method in class org.biojavax.ga.util.<a href="./org/biojavax/ga/util/WeightedSet.html" title="class in org.biojavax.ga.util">WeightedSet</a></dt>
<dd>
<div class="block">Sets the weight of an <code>Object</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/AbstractDistribution.html#setWeightImpl(org.biojava.bio.symbol.AtomicSymbol, double)">setWeightImpl(AtomicSymbol, double)</a></span> - Method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/AbstractDistribution.html" title="class in org.biojava.bio.dist">AbstractDistribution</a></dt>
<dd>
<div class="block">Implement this to actually set the weight.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/AbstractOrderNDistribution.html#setWeightImpl(org.biojava.bio.symbol.AtomicSymbol, double)">setWeightImpl(AtomicSymbol, double)</a></span> - Method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/AbstractOrderNDistribution.html" title="class in org.biojava.bio.dist">AbstractOrderNDistribution</a></dt>
<dd>
<div class="block">Set a weight in one of the conditioned distributions.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/SimpleDistribution.html#setWeightImpl(org.biojava.bio.symbol.AtomicSymbol, double)">setWeightImpl(AtomicSymbol, double)</a></span> - Method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/SimpleDistribution.html" title="class in org.biojava.bio.dist">SimpleDistribution</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/UniformDistribution.html#setWeightImpl(org.biojava.bio.symbol.AtomicSymbol, double)">setWeightImpl(AtomicSymbol, double)</a></span> - Method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/UniformDistribution.html" title="class in org.biojava.bio.dist">UniformDistribution</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/WeightMatrixAnnotator.html#setWeightMatrixID(java.lang.String)">setWeightMatrixID(String)</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/WeightMatrixAnnotator.html" title="class in org.biojava.bio.dp">WeightMatrixAnnotator</a></dt>
<dd>
<div class="block">Set the weight matrix id.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/MarkovModel.html#setWeights(org.biojava.bio.dp.State, org.biojava.bio.dist.Distribution)">setWeights(State, Distribution)</a></span> - Method in interface org.biojava.bio.dp.<a href="./org/biojava/bio/dp/MarkovModel.html" title="interface in org.biojava.bio.dp">MarkovModel</a></dt>
<dd>
<div class="block">Set the probability distribution over the transitions from 'source'.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/SimpleMarkovModel.html#setWeights(org.biojava.bio.dp.State, org.biojava.bio.dist.Distribution)">setWeights(State, Distribution)</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/SimpleMarkovModel.html" title="class in org.biojava.bio.dp">SimpleMarkovModel</a></dt>
<dd>
<div class="block">Use this methods to customize the transition probabilities.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/WMAsMM.html#setWeights(org.biojava.bio.dp.State, org.biojava.bio.dist.Distribution)">setWeights(State, Distribution)</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/WMAsMM.html" title="class in org.biojava.bio.dp">WMAsMM</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.html#setWidth(int)">setWidth(int)</a></span> - Method in class org.biojava.bio.chromatogram.graphic.<a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.html" title="class in org.biojava.bio.chromatogram.graphic">ChromatogramGraphic</a></dt>
<dd>
<div class="block">Sets the width of the whole graphic (in pixels).</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/RadialBaseKernel.html#setWidth(double)">setWidth(double)</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/RadialBaseKernel.html" title="class in org.biojava.stats.svm">RadialBaseKernel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/process/ExternalProcess.html#setWorkingDirectory(java.io.File)">setWorkingDirectory(File)</a></span> - Method in class org.biojava.utils.process.<a href="./org/biojava/utils/process/ExternalProcess.html" title="class in org.biojava.utils.process">ExternalProcess</a></dt>
<dd>
<div class="block">Sets the working directory for the external process.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePanelWrapper.html#setWrap(int)">setWrap(int)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePanelWrapper.html" title="class in org.biojava.bio.gui.sequence">SequencePanelWrapper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/tracklayout/SimpleTrackLayout.html#setWrap(int)">setWrap(int)</a></span> - Method in class org.biojava.bio.gui.sequence.tracklayout.<a href="./org/biojava/bio/gui/sequence/tracklayout/SimpleTrackLayout.html" title="class in org.biojava.bio.gui.sequence.tracklayout">SimpleTrackLayout</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/tracklayout/TrackLayout.html#setWrap(int)">setWrap(int)</a></span> - Method in interface org.biojava.bio.gui.sequence.tracklayout.<a href="./org/biojava/bio/gui/sequence/tracklayout/TrackLayout.html" title="interface in org.biojava.bio.gui.sequence.tracklayout">TrackLayout</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/tracklayout/UserDefinedTrackLayout.html#setWrap(int)">setWrap(int)</a></span> - Method in class org.biojava.bio.gui.sequence.tracklayout.<a href="./org/biojava/bio/gui/sequence/tracklayout/UserDefinedTrackLayout.html" title="class in org.biojava.bio.gui.sequence.tracklayout">UserDefinedTrackLayout</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/tracklayout/SimpleTrackLayout.html#setWrapIncrement(int)">setWrapIncrement(int)</a></span> - Method in class org.biojava.bio.gui.sequence.tracklayout.<a href="./org/biojava/bio/gui/sequence/tracklayout/SimpleTrackLayout.html" title="class in org.biojava.bio.gui.sequence.tracklayout">SimpleTrackLayout</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/tracklayout/TrackLayout.html#setWrapIncrement(int)">setWrapIncrement(int)</a></span> - Method in interface org.biojava.bio.gui.sequence.tracklayout.<a href="./org/biojava/bio/gui/sequence/tracklayout/TrackLayout.html" title="interface in org.biojava.bio.gui.sequence.tracklayout">TrackLayout</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/tracklayout/UserDefinedTrackLayout.html#setWrapIncrement(int)">setWrapIncrement(int)</a></span> - Method in class org.biojava.bio.gui.sequence.tracklayout.<a href="./org/biojava/bio/gui/sequence/tracklayout/UserDefinedTrackLayout.html" title="class in org.biojava.bio.gui.sequence.tracklayout">UserDefinedTrackLayout</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/SigmoidKernel.html#setWrappedKernel(org.biojava.stats.svm.SVMKernel)">setWrappedKernel(SVMKernel)</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/SigmoidKernel.html" title="class in org.biojava.stats.svm">SigmoidKernel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AgaveWriter.html#setWriteDocType(boolean)">setWriteDocType(boolean)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AgaveWriter.html" title="class in org.biojava.bio.seq.io.agave">AgaveWriter</a></dt>
<dd>
<div class="block">Set flag that determines if XML DOCTYPE is written
or not.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/process/ReaderWriterPipe.html#setWriter(java.io.Writer)">setWriter(Writer)</a></span> - Method in class org.biojava.utils.process.<a href="./org/biojava/utils/process/ReaderWriterPipe.html" title="class in org.biojava.utils.process">ReaderWriterPipe</a></dt>
<dd>
<div class="block">Sets the writer.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Atom.html#setX(double)">setX(double)</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Atom.html" title="interface in org.biojava.bio.structure">Atom</a></dt>
<dd>
<div class="block">Set the X coordinate.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/AtomImpl.html#setX(double)">setX(double)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/AtomImpl.html" title="class in org.biojava.bio.structure">AtomImpl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Atom.html#setY(double)">setY(double)</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Atom.html" title="interface in org.biojava.bio.structure">Atom</a></dt>
<dd>
<div class="block">Set the Y coordinate.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/AtomImpl.html#setY(double)">setY(double)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/AtomImpl.html" title="class in org.biojava.bio.structure">AtomImpl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Atom.html#setZ(double)">setZ(double)</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Atom.html" title="interface in org.biojava.bio.structure">Atom</a></dt>
<dd>
<div class="block">Set the Z coordinate.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/AtomImpl.html#setZ(double)">setZ(double)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/AtomImpl.html" title="class in org.biojava.bio.structure">AtomImpl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/LocationTools.html#shadow(org.biojava.bio.symbol.Location)">shadow(Location)</a></span> - Static method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/LocationTools.html" title="class in org.biojava.bio.symbol">LocationTools</a></dt>
<dd>
<div class="block">Return a contiguous location running from the minimum to the maximum points of
the specified location.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FilterUtils.html#shadowContainedByLocation(org.biojava.bio.symbol.Location)">shadowContainedByLocation(Location)</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FilterUtils.html" title="class in org.biojava.bio.seq">FilterUtils</a></dt>
<dd>
<div class="block">Construct a filter which matches features with locations where the interval
between the <code>min</code> and <code>max</code> positions are contained by
the specified <code>Location</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FilterUtils.html#shadowOverlapsLocation(org.biojava.bio.symbol.Location)">shadowOverlapsLocation(Location)</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FilterUtils.html" title="class in org.biojava.bio.seq">FilterUtils</a></dt>
<dd>
<div class="block">Construct a filter which matches features with locations where the interval
between the <code>min</code> and <code>max</code> positions are contained by or
overlap the specified <code>Location</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/DistributionTools.html#shannonEntropy(org.biojava.bio.dist.Distribution, double)">shannonEntropy(Distribution, double)</a></span> - Static method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/DistributionTools.html" title="class in org.biojava.bio.dist">DistributionTools</a></dt>
<dd>
<div class="block">A method to calculate the Shannon Entropy for a Distribution.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/FlexibleAlignment.html#shift(java.lang.Object, int)">shift(Object, int)</a></span> - Method in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/FlexibleAlignment.html" title="class in org.biojava.bio.alignment">FlexibleAlignment</a></dt>
<dd>
<div class="block">moves the whole sequence</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Calc.html#shift(org.biojava.bio.structure.Structure, org.biojava.bio.structure.Atom)">shift(Structure, Atom)</a></span> - Static method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Calc.html" title="class in org.biojava.bio.structure">Calc</a></dt>
<dd>
<div class="block">shift a structure with a vector.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Calc.html#shift(org.biojava.bio.structure.Atom, org.biojava.bio.structure.Atom)">shift(Atom, Atom)</a></span> - Static method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Calc.html" title="class in org.biojava.bio.structure">Calc</a></dt>
<dd>
<div class="block">Shift a vector.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Calc.html#shift(org.biojava.bio.structure.Group, org.biojava.bio.structure.Atom)">shift(Group, Atom)</a></span> - Static method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Calc.html" title="class in org.biojava.bio.structure">Calc</a></dt>
<dd>
<div class="block">Shift a Group with a vector.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/FlexibleAlignment.html#shiftAll(int)">shiftAll(int)</a></span> - Method in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/FlexibleAlignment.html" title="class in org.biojava.bio.alignment">FlexibleAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/EditableAlignment.html#shiftAtAlignmentLoc(java.lang.Object, org.biojava.bio.symbol.Location, int)">shiftAtAlignmentLoc(Object, Location, int)</a></span> - Method in interface org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/EditableAlignment.html" title="interface in org.biojava.bio.alignment">EditableAlignment</a></dt>
<dd>
<div class="block">loc in this case is the Alignment Location</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/FlexibleAlignment.html#shiftAtAlignmentLoc(java.lang.Object, org.biojava.bio.symbol.Location, int)">shiftAtAlignmentLoc(Object, Location, int)</a></span> - Method in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/FlexibleAlignment.html" title="class in org.biojava.bio.alignment">FlexibleAlignment</a></dt>
<dd>
<div class="block">loc in this case is the Alignment Location</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/EditableAlignment.html#shiftAtSequenceLoc(java.lang.Object, org.biojava.bio.symbol.Location, int)">shiftAtSequenceLoc(Object, Location, int)</a></span> - Method in interface org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/EditableAlignment.html" title="interface in org.biojava.bio.alignment">EditableAlignment</a></dt>
<dd>
<div class="block">loc in this case is the SymbolList Location</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/FlexibleAlignment.html#shiftAtSequenceLoc(java.lang.Object, org.biojava.bio.symbol.Location, int)">shiftAtSequenceLoc(Object, Location, int)</a></span> - Method in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/FlexibleAlignment.html" title="class in org.biojava.bio.alignment">FlexibleAlignment</a></dt>
<dd>
<div class="block">loc in this case is the SymbolList Location</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/scf/SCF.html#SHORT_MAX_VALUE">SHORT_MAX_VALUE</a></span> - Static variable in class org.biojava.bio.program.scf.<a href="./org/biojava/bio/program/scf/SCF.html" title="class in org.biojava.bio.program.scf">SCF</a></dt>
<dd>
<div class="block">Represents the maximum unsigned value
of a short for wrapping purposes</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/blast2html/SimpleAlignmentStyler.html#SHOW_ALL">SHOW_ALL</a></span> - Static variable in class org.biojava.bio.program.blast2html.<a href="./org/biojava/bio/program/blast2html/SimpleAlignmentStyler.html" title="class in org.biojava.bio.program.blast2html">SimpleAlignmentStyler</a></dt>
<dd>
<div class="block">Return default styles</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/blast2html/SimpleAlignmentStyler.html#SHOW_DIFF">SHOW_DIFF</a></span> - Static variable in class org.biojava.bio.program.blast2html.<a href="./org/biojava/bio/program/blast2html/SimpleAlignmentStyler.html" title="class in org.biojava.bio.program.blast2html">SimpleAlignmentStyler</a></dt>
<dd>
<div class="block">As NORMAL except only return if the two colour classes for
query and subject are the different</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/blast2html/SimpleAlignmentStyler.html#SHOW_SAME">SHOW_SAME</a></span> - Static variable in class org.biojava.bio.program.blast2html.<a href="./org/biojava/bio/program/blast2html/SimpleAlignmentStyler.html" title="class in org.biojava.bio.program.blast2html">SimpleAlignmentStyler</a></dt>
<dd>
<div class="block">Only return if the two colour classes for
query and subject are the same</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/util/AlternativeAlignmentFrame.html#showAlternative(int)">showAlternative(int)</a></span> - Method in class org.biojava.bio.structure.gui.util.<a href="./org/biojava/bio/structure/gui/util/AlternativeAlignmentFrame.html" title="class in org.biojava.bio.structure.gui.util">AlternativeAlignmentFrame</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Compound.html#showCompound()">showCompound()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure">Compound</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/util/AlternativeAlignmentFrame.html#showDistanceMatrix(int)">showDistanceMatrix(int)</a></span> - Method in class org.biojava.bio.structure.gui.util.<a href="./org/biojava/bio/structure/gui/util/AlternativeAlignmentFrame.html" title="class in org.biojava.bio.structure.gui.util">AlternativeAlignmentFrame</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Compound.html#showHeader()">showHeader()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure">Compound</a></dt>
<dd>
<div class="block">Print some debug statements to System.out</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Compound.html#showSource()">showSource()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure">Compound</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/homol/SimilarityPairFeature.html#SIBLING">SIBLING</a></span> - Static variable in interface org.biojava.bio.seq.homol.<a href="./org/biojava/bio/seq/homol/SimilarityPairFeature.html" title="interface in org.biojava.bio.seq.homol">SimilarityPairFeature</a></dt>
<dd>
<div class="block">The sibling of this feature has altered.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/homol/SimilarityPairFeature.Template.html#sibling">sibling</a></span> - Variable in class org.biojava.bio.seq.homol.<a href="./org/biojava/bio/seq/homol/SimilarityPairFeature.Template.html" title="class in org.biojava.bio.seq.homol">SimilarityPairFeature.Template</a></dt>
<dd>
<div class="block"><code>sibling</code> <code>SimilarityPairFeature</code>
field.</div>
</dd>
<dt><a href="./org/biojava/stats/svm/SigmoidKernel.html" title="class in org.biojava.stats.svm"><span class="strong">SigmoidKernel</span></a> - Class in <a href="./org/biojava/stats/svm/package-summary.html">org.biojava.stats.svm</a></dt>
<dd>
<div class="block">This kernel implements a three layer neural net.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/SigmoidKernel.html#SigmoidKernel()">SigmoidKernel()</a></span> - Constructor for class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/SigmoidKernel.html" title="class in org.biojava.stats.svm">SigmoidKernel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/tools/Classify.html#sign(double)">sign(double)</a></span> - Static method in class org.biojava.stats.svm.tools.<a href="./org/biojava/stats/svm/tools/Classify.html" title="class in org.biojava.stats.svm.tools">Classify</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/aaindex/AAindex.html#similarEntries()">similarEntries()</a></span> - Method in class org.biojava.bio.proteomics.aaindex.<a href="./org/biojava/bio/proteomics/aaindex/AAindex.html" title="class in org.biojava.bio.proteomics.aaindex">AAindex</a></dt>
<dd>
<div class="block">Returns a map with the names of similar AAindex entries and its
correlation coefficients.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/SimilarityPairBuilder.html#SIMILARITY_PAIR_FEATURE_TYPE">SIMILARITY_PAIR_FEATURE_TYPE</a></span> - Static variable in class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/SimilarityPairBuilder.html" title="class in org.biojava.bio.program.ssbind">SimilarityPairBuilder</a></dt>
<dd>
<div class="block">Constant <code>SIMILARITY_PAIR_FEATURE_TYPE</code> the type
String used by <code>SimilarityPairBuilder</code> when creating
<code>SimilarityPairFeature</code>s.</div>
</dd>
<dt><a href="./org/biojava/bio/program/ssbind/SimilarityPairBuilder.html" title="class in org.biojava.bio.program.ssbind"><span class="strong">SimilarityPairBuilder</span></a> - Class in <a href="./org/biojava/bio/program/ssbind/package-summary.html">org.biojava.bio.program.ssbind</a></dt>
<dd>
<div class="block"><code>SimilarityPairBuilder</code> annotates query and subject
<code>Sequence</code> with <code>SimilarityPairFeature</code>s
created from SAX events supplied via a
<code>SeqSimilarityAdapter</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/SimilarityPairBuilder.html#SimilarityPairBuilder()">SimilarityPairBuilder()</a></span> - Constructor for class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/SimilarityPairBuilder.html" title="class in org.biojava.bio.program.ssbind">SimilarityPairBuilder</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/homol/SimilarityPairFeature.html" title="interface in org.biojava.bio.seq.homol"><span class="strong">SimilarityPairFeature</span></a> - Interface in <a href="./org/biojava/bio/seq/homol/package-summary.html">org.biojava.bio.seq.homol</a></dt>
<dd>
<div class="block"><code>SimilarityPairFeature</code> describes a pairwise
similarity between two nucleotide sequences (as it extends
<code>StrandedFeature</code>).</div>
</dd>
<dt><a href="./org/biojava/bio/seq/homol/SimilarityPairFeature.EmptyPairwiseAlignment.html" title="class in org.biojava.bio.seq.homol"><span class="strong">SimilarityPairFeature.EmptyPairwiseAlignment</span></a> - Class in <a href="./org/biojava/bio/seq/homol/package-summary.html">org.biojava.bio.seq.homol</a></dt>
<dd>
<div class="block"><code>EmptyPairwiseAlignment</code> empty pairwise alignment
which has labels to empty symbol lists.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/homol/SimilarityPairFeature.Template.html" title="class in org.biojava.bio.seq.homol"><span class="strong">SimilarityPairFeature.Template</span></a> - Class in <a href="./org/biojava/bio/seq/homol/package-summary.html">org.biojava.bio.seq.homol</a></dt>
<dd>
<div class="block"><code>Template</code> for construction of
<code>SimilarityPairFeature</code>s.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/homol/SimilarityPairFeature.Template.html#SimilarityPairFeature.Template()">SimilarityPairFeature.Template()</a></span> - Constructor for class org.biojava.bio.seq.homol.<a href="./org/biojava/bio/seq/homol/SimilarityPairFeature.Template.html" title="class in org.biojava.bio.seq.homol">SimilarityPairFeature.Template</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/HomologeneBuilder.html#SIMILARITYTYPE">SIMILARITYTYPE</a></span> - Static variable in interface org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/HomologeneBuilder.html" title="interface in org.biojava.bio.program.homologene">HomologeneBuilder</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/homologene/SimilarityType.html" title="interface in org.biojava.bio.program.homologene"><span class="strong">SimilarityType</span></a> - Interface in <a href="./org/biojava/bio/program/homologene/package-summary.html">org.biojava.bio.program.homologene</a></dt>
<dd>
<div class="block">Each HomologeneEntry represents a single
Homologene record that relates two
presumptive orthologues.</div>
</dd>
<dt><a href="./org/biojava/bio/program/homologene/SimilarityType.PlaceHolder.html" title="class in org.biojava.bio.program.homologene"><span class="strong">SimilarityType.PlaceHolder</span></a> - Class in <a href="./org/biojava/bio/program/homologene/package-summary.html">org.biojava.bio.program.homologene</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/SimpleAnnotFilter.html#SIMPLE_ANNOT_FILTER_FACTORY">SIMPLE_ANNOT_FILTER_FACTORY</a></span> - Static variable in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/SimpleAnnotFilter.html" title="class in org.biojava.bio.seq.io.agave">SimpleAnnotFilter</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/symbol/SimpleAlignment.html" title="class in org.biojava.bio.symbol"><span class="strong">SimpleAlignment</span></a> - Class in <a href="./org/biojava/bio/symbol/package-summary.html">org.biojava.bio.symbol</a></dt>
<dd>
<div class="block">A simple implementation of an Alignment.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleAlignment.html#SimpleAlignment(java.util.Map)">SimpleAlignment(Map)</a></span> - Constructor for class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleAlignment.html" title="class in org.biojava.bio.symbol">SimpleAlignment</a></dt>
<dd>
<div class="block">Generate an alignment from a list of SymbolLists.</div>
</dd>
<dt><a href="./org/biojava/bio/alignment/SimpleAlignmentElement.html" title="class in org.biojava.bio.alignment"><span class="strong">SimpleAlignmentElement</span></a> - Class in <a href="./org/biojava/bio/alignment/package-summary.html">org.biojava.bio.alignment</a></dt>
<dd>
<div class="block">SimpleSimpleAlignment is a simple implementation of
AlignmentElement.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/SimpleAlignmentElement.html#SimpleAlignmentElement(java.lang.Object, org.biojava.bio.symbol.SymbolList, org.biojava.bio.symbol.Location)">SimpleAlignmentElement(Object, SymbolList, Location)</a></span> - Constructor for class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/SimpleAlignmentElement.html" title="class in org.biojava.bio.alignment">SimpleAlignmentElement</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/blast2html/SimpleAlignmentStyler.html" title="class in org.biojava.bio.program.blast2html"><span class="strong">SimpleAlignmentStyler</span></a> - Class in <a href="./org/biojava/bio/program/blast2html/package-summary.html">org.biojava.bio.program.blast2html</a></dt>
<dd>
<div class="block">Simple implementation for specifying markup styles.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/blast2html/SimpleAlignmentStyler.html#SimpleAlignmentStyler(int)">SimpleAlignmentStyler(int)</a></span> - Constructor for class org.biojava.bio.program.blast2html.<a href="./org/biojava/bio/program/blast2html/SimpleAlignmentStyler.html" title="class in org.biojava.bio.program.blast2html">SimpleAlignmentStyler</a></dt>
<dd>
<div class="block">Creates a new <CODE>SimpleAlignmentStyler</CODE> instance.</div>
</dd>
<dt><a href="./org/biojava/bio/symbol/SimpleAlphabet.html" title="class in org.biojava.bio.symbol"><span class="strong">SimpleAlphabet</span></a> - Class in <a href="./org/biojava/bio/symbol/package-summary.html">org.biojava.bio.symbol</a></dt>
<dd>
<div class="block">A simple no-frills implementation of the FiniteAlphabet interface.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleAlphabet.html#SimpleAlphabet()">SimpleAlphabet()</a></span> - Constructor for class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleAlphabet.html" title="class in org.biojava.bio.symbol">SimpleAlphabet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleAlphabet.html#SimpleAlphabet(java.util.Set)">SimpleAlphabet(Set)</a></span> - Constructor for class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleAlphabet.html" title="class in org.biojava.bio.symbol">SimpleAlphabet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleAlphabet.html#SimpleAlphabet(java.lang.String)">SimpleAlphabet(String)</a></span> - Constructor for class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleAlphabet.html" title="class in org.biojava.bio.symbol">SimpleAlphabet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleAlphabet.html#SimpleAlphabet(java.util.Set, java.lang.String)">SimpleAlphabet(Set, String)</a></span> - Constructor for class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleAlphabet.html" title="class in org.biojava.bio.symbol">SimpleAlphabet</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/SimpleAnnotation.html" title="class in org.biojava.bio"><span class="strong">SimpleAnnotation</span></a> - Class in <a href="./org/biojava/bio/package-summary.html">org.biojava.bio</a></dt>
<dd>
<div class="block">A no-frills implementation of Annotation that is just a wrapper
around a <code>LinkedHashMap</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/SimpleAnnotation.html#SimpleAnnotation()">SimpleAnnotation()</a></span> - Constructor for class org.biojava.bio.<a href="./org/biojava/bio/SimpleAnnotation.html" title="class in org.biojava.bio">SimpleAnnotation</a></dt>
<dd>
<div class="block">Create a new, empty SimpleAnnotation instance.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/SimpleAnnotation.html#SimpleAnnotation(org.biojava.bio.Annotation)">SimpleAnnotation(Annotation)</a></span> - Constructor for class org.biojava.bio.<a href="./org/biojava/bio/SimpleAnnotation.html" title="class in org.biojava.bio">SimpleAnnotation</a></dt>
<dd>
<div class="block">Create a new SimpleAnnotation by copying the properties from another
one.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/SimpleAnnotation.html#SimpleAnnotation(java.util.Map)">SimpleAnnotation(Map)</a></span> - Constructor for class org.biojava.bio.<a href="./org/biojava/bio/SimpleAnnotation.html" title="class in org.biojava.bio">SimpleAnnotation</a></dt>
<dd>
<div class="block">Create a new SimpleAnnotation using the values in a Map.</div>
</dd>
<dt><a href="./org/biojava/bio/annodb/SimpleAnnotationDB.html" title="class in org.biojava.bio.annodb"><span class="strong">SimpleAnnotationDB</span></a> - Class in <a href="./org/biojava/bio/annodb/package-summary.html">org.biojava.bio.annodb</a></dt>
<dd>
<div class="block">A no-frills implementation of AnnotationDB.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/annodb/SimpleAnnotationDB.html#SimpleAnnotationDB(java.lang.String, java.util.Set, org.biojava.bio.AnnotationType)">SimpleAnnotationDB(String, Set, AnnotationType)</a></span> - Constructor for class org.biojava.bio.annodb.<a href="./org/biojava/bio/annodb/SimpleAnnotationDB.html" title="class in org.biojava.bio.annodb">SimpleAnnotationDB</a></dt>
<dd>
<div class="block">Create a no-frills AnnotationDB instancec.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/agave/SimpleAnnotFilter.html" title="class in org.biojava.bio.seq.io.agave"><span class="strong">SimpleAnnotFilter</span></a> - Class in <a href="./org/biojava/bio/seq/io/agave/package-summary.html">org.biojava.bio.seq.io.agave</a></dt>
<dd>
<div class="block">Basic implementation of AGAVEAnnotFilter</div>
</dd>
<dt><a href="./org/biojava/bio/seq/SimpleAssembly.html" title="class in org.biojava.bio.seq"><span class="strong">SimpleAssembly</span></a> - Class in <a href="./org/biojava/bio/seq/package-summary.html">org.biojava.bio.seq</a></dt>
<dd>
<div class="block">A Sequence which is assembled from other sequences contained
in a set of ComponentFeature objects.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/SimpleAssembly.html#SimpleAssembly(int, java.lang.String, java.lang.String)">SimpleAssembly(int, String, String)</a></span> - Constructor for class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/SimpleAssembly.html" title="class in org.biojava.bio.seq">SimpleAssembly</a></dt>
<dd>
<div class="block">Construct a new SimpleAssembly using the DNA alphabet.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/SimpleAssembly.html#SimpleAssembly(java.lang.String, java.lang.String)">SimpleAssembly(String, String)</a></span> - Constructor for class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/SimpleAssembly.html" title="class in org.biojava.bio.seq">SimpleAssembly</a></dt>
<dd>
<div class="block">Construct a new SimpleAssembly using the DNA alphabet.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/SimpleAssemblyBuilder.html" title="class in org.biojava.bio.seq.io"><span class="strong">SimpleAssemblyBuilder</span></a> - Class in <a href="./org/biojava/bio/seq/io/package-summary.html">org.biojava.bio.seq.io</a></dt>
<dd>
<div class="block">Basic SequenceBuilder implementation which accumulates all
notified information and creates a SimpleAssembly.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SimpleAssemblyBuilder.html#SimpleAssemblyBuilder()">SimpleAssemblyBuilder()</a></span> - Constructor for class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SimpleAssemblyBuilder.html" title="class in org.biojava.bio.seq.io">SimpleAssemblyBuilder</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/symbol/SimpleAtomicSymbol.html" title="class in org.biojava.bio.symbol"><span class="strong">SimpleAtomicSymbol</span></a> - Class in <a href="./org/biojava/bio/symbol/package-summary.html">org.biojava.bio.symbol</a></dt>
<dd>
<div class="block">A basic implementation of AtomicSymbol.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleAtomicSymbol.html#SimpleAtomicSymbol(org.biojava.bio.Annotation, java.util.List)">SimpleAtomicSymbol(Annotation, List)</a></span> - Constructor for class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleAtomicSymbol.html" title="class in org.biojava.bio.symbol">SimpleAtomicSymbol</a></dt>
<dd> </dd>
<dt><a href="./org/biojavax/bio/SimpleBioEntry.html" title="class in org.biojavax.bio"><span class="strong">SimpleBioEntry</span></a> - Class in <a href="./org/biojavax/bio/package-summary.html">org.biojavax.bio</a></dt>
<dd>
<div class="block">Reference implementation of a BioEntry object which has no features or sequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/SimpleBioEntry.html#SimpleBioEntry(org.biojavax.Namespace, java.lang.String, java.lang.String, int)">SimpleBioEntry(Namespace, String, String, int)</a></span> - Constructor for class org.biojavax.bio.<a href="./org/biojavax/bio/SimpleBioEntry.html" title="class in org.biojavax.bio">SimpleBioEntry</a></dt>
<dd>
<div class="block">Creates a new bioentry representing the sequence in the given namespace
with the given name, accession and version.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/SimpleBioEntry.html#SimpleBioEntry()">SimpleBioEntry()</a></span> - Constructor for class org.biojavax.bio.<a href="./org/biojavax/bio/SimpleBioEntry.html" title="class in org.biojavax.bio">SimpleBioEntry</a></dt>
<dd> </dd>
<dt><a href="./org/biojavax/bio/SimpleBioEntryRelationship.html" title="class in org.biojavax.bio"><span class="strong">SimpleBioEntryRelationship</span></a> - Class in <a href="./org/biojavax/bio/package-summary.html">org.biojavax.bio</a></dt>
<dd>
<div class="block">Represents a relationship between two bioentries that is described by a term
and given a rank.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/SimpleBioEntryRelationship.html#SimpleBioEntryRelationship(org.biojavax.bio.BioEntry, org.biojavax.bio.BioEntry, org.biojavax.ontology.ComparableTerm, java.lang.Integer)">SimpleBioEntryRelationship(BioEntry, BioEntry, ComparableTerm, Integer)</a></span> - Constructor for class org.biojavax.bio.<a href="./org/biojavax/bio/SimpleBioEntryRelationship.html" title="class in org.biojavax.bio">SimpleBioEntryRelationship</a></dt>
<dd>
<div class="block">Creates a new instance of SimpleBioEntryRelationship.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/SimpleBioEntryRelationship.html#SimpleBioEntryRelationship()">SimpleBioEntryRelationship()</a></span> - Constructor for class org.biojavax.bio.<a href="./org/biojavax/bio/SimpleBioEntryRelationship.html" title="class in org.biojavax.bio">SimpleBioEntryRelationship</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/chromatogram/SimpleChromatogram.html" title="class in org.biojava.bio.chromatogram"><span class="strong">SimpleChromatogram</span></a> - Class in <a href="./org/biojava/bio/chromatogram/package-summary.html">org.biojava.bio.chromatogram</a></dt>
<dd>
<div class="block">A basic chromatogram implementation which provides public mutators
for setting the various attributes of the chromatogram.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/SimpleChromatogram.html#SimpleChromatogram()">SimpleChromatogram()</a></span> - Constructor for class org.biojava.bio.chromatogram.<a href="./org/biojava/bio/chromatogram/SimpleChromatogram.html" title="class in org.biojava.bio.chromatogram">SimpleChromatogram</a></dt>
<dd>
<div class="block">Creates a new instance of SimpleChromatogram.</div>
</dd>
<dt><a href="./org/biojava/bio/symbol/SimpleCodonPref.html" title="class in org.biojava.bio.symbol"><span class="strong">SimpleCodonPref</span></a> - Class in <a href="./org/biojava/bio/symbol/package-summary.html">org.biojava.bio.symbol</a></dt>
<dd>
<div class="block">a simple no-frills implementation of the
CodonPref object that encapsulates
codon preference data.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleCodonPref.html#SimpleCodonPref(java.lang.String, org.biojava.bio.dist.Distribution, java.lang.String)">SimpleCodonPref(String, Distribution, String)</a></span> - Constructor for class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleCodonPref.html" title="class in org.biojava.bio.symbol">SimpleCodonPref</a></dt>
<dd> </dd>
<dt><a href="./org/biojavax/SimpleComment.html" title="class in org.biojavax"><span class="strong">SimpleComment</span></a> - Class in <a href="./org/biojavax/package-summary.html">org.biojavax</a></dt>
<dd>
<div class="block">An implementaion of Comment.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleComment.html#SimpleComment(java.lang.String, int)">SimpleComment(String, int)</a></span> - Constructor for class org.biojavax.<a href="./org/biojavax/SimpleComment.html" title="class in org.biojavax">SimpleComment</a></dt>
<dd>
<div class="block">Constructs a new, immutable comment, given some text and a rank.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleComment.html#SimpleComment()">SimpleComment()</a></span> - Constructor for class org.biojavax.<a href="./org/biojavax/SimpleComment.html" title="class in org.biojavax">SimpleComment</a></dt>
<dd> </dd>
<dt><a href="./org/biojavax/ontology/SimpleComparableOntology.html" title="class in org.biojavax.ontology"><span class="strong">SimpleComparableOntology</span></a> - Class in <a href="./org/biojavax/ontology/package-summary.html">org.biojavax.ontology</a></dt>
<dd>
<div class="block">Represents an ontology that can be compared to other ontologies.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ontology/SimpleComparableOntology.html#SimpleComparableOntology(java.lang.String)">SimpleComparableOntology(String)</a></span> - Constructor for class org.biojavax.ontology.<a href="./org/biojavax/ontology/SimpleComparableOntology.html" title="class in org.biojavax.ontology">SimpleComparableOntology</a></dt>
<dd>
<div class="block">Creates a new instance of SimpleComparableOntology with the given,
immutable, non-nullable name.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ontology/SimpleComparableOntology.html#SimpleComparableOntology()">SimpleComparableOntology()</a></span> - Constructor for class org.biojavax.ontology.<a href="./org/biojavax/ontology/SimpleComparableOntology.html" title="class in org.biojavax.ontology">SimpleComparableOntology</a></dt>
<dd> </dd>
<dt><a href="./org/biojavax/ontology/SimpleComparableTerm.html" title="class in org.biojavax.ontology"><span class="strong">SimpleComparableTerm</span></a> - Class in <a href="./org/biojavax/ontology/package-summary.html">org.biojavax.ontology</a></dt>
<dd>
<div class="block">A Term object that can be compared and thus sorted.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ontology/SimpleComparableTerm.html#SimpleComparableTerm()">SimpleComparableTerm()</a></span> - Constructor for class org.biojavax.ontology.<a href="./org/biojavax/ontology/SimpleComparableTerm.html" title="class in org.biojavax.ontology">SimpleComparableTerm</a></dt>
<dd> </dd>
<dt><a href="./org/biojavax/ontology/SimpleComparableTriple.html" title="class in org.biojavax.ontology"><span class="strong">SimpleComparableTriple</span></a> - Class in <a href="./org/biojavax/ontology/package-summary.html">org.biojavax.ontology</a></dt>
<dd>
<div class="block">Basic comparable triple, BioSQL style.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ontology/SimpleComparableTriple.html#SimpleComparableTriple()">SimpleComparableTriple()</a></span> - Constructor for class org.biojavax.ontology.<a href="./org/biojavax/ontology/SimpleComparableTriple.html" title="class in org.biojavax.ontology">SimpleComparableTriple</a></dt>
<dd> </dd>
<dt><a href="./org/biojavax/ga/functions/SimpleCrossOverFunction.html" title="class in org.biojavax.ga.functions"><span class="strong">SimpleCrossOverFunction</span></a> - Class in <a href="./org/biojavax/ga/functions/package-summary.html">org.biojavax.ga.functions</a></dt>
<dd>
<div class="block">Simple Implementation of the <code>CrossOverFunction</code> interface</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ga/functions/SimpleCrossOverFunction.html#SimpleCrossOverFunction()">SimpleCrossOverFunction()</a></span> - Constructor for class org.biojavax.ga.functions.<a href="./org/biojavax/ga/functions/SimpleCrossOverFunction.html" title="class in org.biojavax.ga.functions">SimpleCrossOverFunction</a></dt>
<dd> </dd>
<dt><a href="./org/biojavax/SimpleCrossRef.html" title="class in org.biojavax"><span class="strong">SimpleCrossRef</span></a> - Class in <a href="./org/biojavax/package-summary.html">org.biojavax</a></dt>
<dd>
<div class="block">A basic CrossRef implementation.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleCrossRef.html#SimpleCrossRef(java.lang.String, java.lang.String, int)">SimpleCrossRef(String, String, int)</a></span> - Constructor for class org.biojavax.<a href="./org/biojavax/SimpleCrossRef.html" title="class in org.biojavax">SimpleCrossRef</a></dt>
<dd>
<div class="block">Creates a new instance of SimpleCrossRef with the values to use for
the immutable database name, accession and version.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleCrossRef.html#SimpleCrossRef(java.lang.String, java.lang.String, java.lang.Integer)">SimpleCrossRef(String, String, Integer)</a></span> - Constructor for class org.biojavax.<a href="./org/biojavax/SimpleCrossRef.html" title="class in org.biojavax">SimpleCrossRef</a></dt>
<dd>
<div class="block">Creates a new instance of SimpleCrossRef with the values to use for
the immutable database name, accession and version.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleCrossRef.html#SimpleCrossRef()">SimpleCrossRef()</a></span> - Constructor for class org.biojavax.<a href="./org/biojavax/SimpleCrossRef.html" title="class in org.biojavax">SimpleCrossRef</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/dist/SimpleDistribution.html" title="class in org.biojava.bio.dist"><span class="strong">SimpleDistribution</span></a> - Class in <a href="./org/biojava/bio/dist/package-summary.html">org.biojava.bio.dist</a></dt>
<dd>
<div class="block">A simple implementation of a distribution, which works with any finite alphabet.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/SimpleDistribution.html#SimpleDistribution(org.biojava.bio.symbol.FiniteAlphabet)">SimpleDistribution(FiniteAlphabet)</a></span> - Constructor for class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/SimpleDistribution.html" title="class in org.biojava.bio.dist">SimpleDistribution</a></dt>
<dd>
<div class="block">make an instance of SimpleDistribution for the specified Alphabet.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/SimpleDistribution.html#SimpleDistribution(org.biojava.bio.dist.Distribution)">SimpleDistribution(Distribution)</a></span> - Constructor for class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/SimpleDistribution.html" title="class in org.biojava.bio.dist">SimpleDistribution</a></dt>
<dd>
<div class="block">make an instance of SimpleDistribution with weights identical
to the specified Distribution.</div>
</dd>
<dt><a href="./org/biojava/bio/dist/SimpleDistribution.Trainer.html" title="class in org.biojava.bio.dist"><span class="strong">SimpleDistribution.Trainer</span></a> - Class in <a href="./org/biojava/bio/dist/package-summary.html">org.biojava.bio.dist</a></dt>
<dd>
<div class="block">A simple implementation of a trainer for this class.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/SimpleDistribution.Trainer.html#SimpleDistribution.Trainer()">SimpleDistribution.Trainer()</a></span> - Constructor for class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/SimpleDistribution.Trainer.html" title="class in org.biojava.bio.dist">SimpleDistribution.Trainer</a></dt>
<dd>
<div class="block">Create a new trainer.</div>
</dd>
<dt><a href="./org/biojava/bio/dist/SimpleDistributionTrainer.html" title="class in org.biojava.bio.dist"><span class="strong">SimpleDistributionTrainer</span></a> - Class in <a href="./org/biojava/bio/dist/package-summary.html">org.biojava.bio.dist</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>Distribution impls should be providing custom trainers.</i></div>
</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/SimpleDistributionTrainer.html#SimpleDistributionTrainer(org.biojava.bio.dist.Distribution)">SimpleDistributionTrainer(Distribution)</a></span> - Constructor for class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/SimpleDistributionTrainer.html" title="class in org.biojava.bio.dist">SimpleDistributionTrainer</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><a href="./org/biojava/bio/dist/SimpleDistributionTrainerContext.html" title="class in org.biojava.bio.dist"><span class="strong">SimpleDistributionTrainerContext</span></a> - Class in <a href="./org/biojava/bio/dist/package-summary.html">org.biojava.bio.dist</a></dt>
<dd>
<div class="block">A no-frills implementation of DistributionTrainerContext.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/SimpleDistributionTrainerContext.html#SimpleDistributionTrainerContext()">SimpleDistributionTrainerContext()</a></span> - Constructor for class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/SimpleDistributionTrainerContext.html" title="class in org.biojava.bio.dist">SimpleDistributionTrainerContext</a></dt>
<dd>
<div class="block">Create a new context with no initial distributions or trainers.</div>
</dd>
<dt><a href="./org/biojavax/SimpleDocRef.html" title="class in org.biojavax"><span class="strong">SimpleDocRef</span></a> - Class in <a href="./org/biojavax/package-summary.html">org.biojavax</a></dt>
<dd>
<div class="block">A basic DocRef implementation.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleDocRef.html#SimpleDocRef(java.util.List, java.lang.String)">SimpleDocRef(List, String)</a></span> - Constructor for class org.biojavax.<a href="./org/biojavax/SimpleDocRef.html" title="class in org.biojavax">SimpleDocRef</a></dt>
<dd>
<div class="block">Creates a new document reference from the given immutable authors and
location and title.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleDocRef.html#SimpleDocRef(java.lang.String, java.lang.String)">SimpleDocRef(String, String)</a></span> - Constructor for class org.biojavax.<a href="./org/biojavax/SimpleDocRef.html" title="class in org.biojavax">SimpleDocRef</a></dt>
<dd>
<div class="block">Creates a new document reference from the given immutable authors and
location and title.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleDocRef.html#SimpleDocRef(java.lang.String, java.lang.String, java.lang.String)">SimpleDocRef(String, String, String)</a></span> - Constructor for class org.biojavax.<a href="./org/biojavax/SimpleDocRef.html" title="class in org.biojavax">SimpleDocRef</a></dt>
<dd>
<div class="block">Creates a new document reference from the given immutable authors and
location and title.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleDocRef.html#SimpleDocRef(java.util.List, java.lang.String, java.lang.String)">SimpleDocRef(List, String, String)</a></span> - Constructor for class org.biojavax.<a href="./org/biojavax/SimpleDocRef.html" title="class in org.biojavax">SimpleDocRef</a></dt>
<dd>
<div class="block">Creates a new document reference from the given immutable authors and
location and title.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleDocRef.html#SimpleDocRef()">SimpleDocRef()</a></span> - Constructor for class org.biojavax.<a href="./org/biojavax/SimpleDocRef.html" title="class in org.biojavax">SimpleDocRef</a></dt>
<dd> </dd>
<dt><a href="./org/biojavax/SimpleDocRefAuthor.html" title="class in org.biojavax"><span class="strong">SimpleDocRefAuthor</span></a> - Class in <a href="./org/biojavax/package-summary.html">org.biojavax</a></dt>
<dd>
<div class="block">Represents an author of a documentary reference.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleDocRefAuthor.html#SimpleDocRefAuthor(java.lang.String, boolean, boolean)">SimpleDocRefAuthor(String, boolean, boolean)</a></span> - Constructor for class org.biojavax.<a href="./org/biojavax/SimpleDocRefAuthor.html" title="class in org.biojavax">SimpleDocRefAuthor</a></dt>
<dd>
<div class="block">Constructs a new author instance.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleDocRefAuthor.html#SimpleDocRefAuthor(java.lang.String)">SimpleDocRefAuthor(String)</a></span> - Constructor for class org.biojavax.<a href="./org/biojavax/SimpleDocRefAuthor.html" title="class in org.biojavax">SimpleDocRefAuthor</a></dt>
<dd>
<div class="block">Constructs a new author instance from a string.</div>
</dd>
<dt><a href="./org/biojava/bio/dp/SimpleDotState.html" title="class in org.biojava.bio.dp"><span class="strong">SimpleDotState</span></a> - Class in <a href="./org/biojava/bio/dp/package-summary.html">org.biojava.bio.dp</a></dt>
<dd>
<div class="block">A Dot state that you can make and use.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/SimpleDotState.html#SimpleDotState(char, java.lang.String, org.biojava.bio.Annotation)">SimpleDotState(char, String, Annotation)</a></span> - Constructor for class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/SimpleDotState.html" title="class in org.biojava.bio.dp">SimpleDotState</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>token is ignored since 1.2. Use the 2-arg constructor instead.</i></div>
</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/SimpleDotState.html#SimpleDotState(java.lang.String, org.biojava.bio.Annotation)">SimpleDotState(String, Annotation)</a></span> - Constructor for class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/SimpleDotState.html" title="class in org.biojava.bio.dp">SimpleDotState</a></dt>
<dd>
<div class="block">Construct a new state with the specified name and annotation</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/SimpleDotState.html#SimpleDotState(java.lang.String)">SimpleDotState(String)</a></span> - Constructor for class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/SimpleDotState.html" title="class in org.biojava.bio.dp">SimpleDotState</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/dp/SimpleEmissionState.html" title="class in org.biojava.bio.dp"><span class="strong">SimpleEmissionState</span></a> - Class in <a href="./org/biojava/bio/dp/package-summary.html">org.biojava.bio.dp</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/SimpleEmissionState.html#SimpleEmissionState(java.lang.String, org.biojava.bio.Annotation, int[], org.biojava.bio.dist.Distribution)">SimpleEmissionState(String, Annotation, int[], Distribution)</a></span> - Constructor for class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/SimpleEmissionState.html" title="class in org.biojava.bio.dp">SimpleEmissionState</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/impl/SimpleFeature.html" title="class in org.biojava.bio.seq.impl"><span class="strong">SimpleFeature</span></a> - Class in <a href="./org/biojava/bio/seq/impl/package-summary.html">org.biojava.bio.seq.impl</a></dt>
<dd>
<div class="block">A no-frills implementation of a feature.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleFeature.html#SimpleFeature(org.biojava.bio.seq.Sequence, org.biojava.bio.seq.FeatureHolder, org.biojava.bio.seq.Feature.Template)">SimpleFeature(Sequence, FeatureHolder, Feature.Template)</a></span> - Constructor for class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleFeature.html" title="class in org.biojava.bio.seq.impl">SimpleFeature</a></dt>
<dd>
<div class="block">Create a <code>SimpleFeature</code> on the given sequence.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/SimpleFeatureHolder.html" title="class in org.biojava.bio.seq"><span class="strong">SimpleFeatureHolder</span></a> - Class in <a href="./org/biojava/bio/seq/package-summary.html">org.biojava.bio.seq</a></dt>
<dd>
<div class="block">A no-frills implementation of FeatureHolder.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/SimpleFeatureHolder.html#SimpleFeatureHolder()">SimpleFeatureHolder()</a></span> - Constructor for class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/SimpleFeatureHolder.html" title="class in org.biojava.bio.seq">SimpleFeatureHolder</a></dt>
<dd>
<div class="block">Construct a new SimpleFeatureHolder with a non-informative schema.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/SimpleFeatureHolder.html#SimpleFeatureHolder(org.biojava.bio.seq.FeatureFilter)">SimpleFeatureHolder(FeatureFilter)</a></span> - Constructor for class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/SimpleFeatureHolder.html" title="class in org.biojava.bio.seq">SimpleFeatureHolder</a></dt>
<dd>
<div class="block">Construct a new SimpleFeatureHolder with the specified schema.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/SimpleFeatureRealizer.html" title="class in org.biojava.bio.seq"><span class="strong">SimpleFeatureRealizer</span></a> - Class in <a href="./org/biojava/bio/seq/package-summary.html">org.biojava.bio.seq</a></dt>
<dd>
<div class="block">FeatureRealizer which uses a lookup table to map template classes
to implementations.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/SimpleFeatureRealizer.html#SimpleFeatureRealizer()">SimpleFeatureRealizer()</a></span> - Constructor for class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/SimpleFeatureRealizer.html" title="class in org.biojava.bio.seq">SimpleFeatureRealizer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/SimpleFeatureRealizer.html#SimpleFeatureRealizer(org.biojava.bio.seq.FeatureRealizer)">SimpleFeatureRealizer(FeatureRealizer)</a></span> - Constructor for class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/SimpleFeatureRealizer.html" title="class in org.biojava.bio.seq">SimpleFeatureRealizer</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/impl/SimpleFramedFeature.html" title="class in org.biojava.bio.seq.impl"><span class="strong">SimpleFramedFeature</span></a> - Class in <a href="./org/biojava/bio/seq/impl/package-summary.html">org.biojava.bio.seq.impl</a></dt>
<dd>
<div class="block">Title: SimpleFramedFeature.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleFramedFeature.html#SimpleFramedFeature(org.biojava.bio.seq.Sequence, org.biojava.bio.seq.FeatureHolder, org.biojava.bio.seq.FramedFeature.Template)">SimpleFramedFeature(Sequence, FeatureHolder, FramedFeature.Template)</a></span> - Constructor for class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleFramedFeature.html" title="class in org.biojava.bio.seq.impl">SimpleFramedFeature</a></dt>
<dd> </dd>
<dt><a href="./org/biojavax/ga/functions/SimpleGACrossResult.html" title="class in org.biojavax.ga.functions"><span class="strong">SimpleGACrossResult</span></a> - Class in <a href="./org/biojavax/ga/functions/package-summary.html">org.biojavax.ga.functions</a></dt>
<dd>
<div class="block">Simple implementation of the <code>GACross</code> interface.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ga/functions/SimpleGACrossResult.html#SimpleGACrossResult(org.biojava.bio.symbol.PointLocation[], org.biojava.bio.symbol.SymbolList[])">SimpleGACrossResult(PointLocation[], SymbolList[])</a></span> - Constructor for class org.biojavax.ga.functions.<a href="./org/biojavax/ga/functions/SimpleGACrossResult.html" title="class in org.biojavax.ga.functions">SimpleGACrossResult</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/impl/SimpleGappedSequence.html" title="class in org.biojava.bio.seq.impl"><span class="strong">SimpleGappedSequence</span></a> - Class in <a href="./org/biojava/bio/seq/impl/package-summary.html">org.biojava.bio.seq.impl</a></dt>
<dd>
<div class="block">Simple implementation of GappedSequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleGappedSequence.html#SimpleGappedSequence(org.biojava.bio.seq.Sequence)">SimpleGappedSequence(Sequence)</a></span> - Constructor for class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleGappedSequence.html" title="class in org.biojava.bio.seq.impl">SimpleGappedSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleGappedSequence.html#SimpleGappedSequence(org.biojava.bio.seq.GappedSequence)">SimpleGappedSequence(GappedSequence)</a></span> - Constructor for class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleGappedSequence.html" title="class in org.biojava.bio.seq.impl">SimpleGappedSequence</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/impl/SimpleGappedSequence.GappedContext.html" title="class in org.biojava.bio.seq.impl"><span class="strong">SimpleGappedSequence.GappedContext</span></a> - Class in <a href="./org/biojava/bio/seq/impl/package-summary.html">org.biojava.bio.seq.impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleGappedSequence.GappedContext.html#SimpleGappedSequence.GappedContext()">SimpleGappedSequence.GappedContext()</a></span> - Constructor for class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleGappedSequence.GappedContext.html" title="class in org.biojava.bio.seq.impl">SimpleGappedSequence.GappedContext</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/symbol/SimpleGappedSymbolList.html" title="class in org.biojava.bio.symbol"><span class="strong">SimpleGappedSymbolList</span></a> - Class in <a href="./org/biojava/bio/symbol/package-summary.html">org.biojava.bio.symbol</a></dt>
<dd>
<div class="block">This implementation of GappedSymbolList wraps a SymbolList, allowing you to
insert gaps.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleGappedSymbolList.html#SimpleGappedSymbolList(org.biojava.bio.symbol.GappedSymbolList)">SimpleGappedSymbolList(GappedSymbolList)</a></span> - Constructor for class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleGappedSymbolList.html" title="class in org.biojava.bio.symbol">SimpleGappedSymbolList</a></dt>
<dd>
<div class="block">Create a new SimpleGappedSymbolList that will view source,
inheriting all existing gaps.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleGappedSymbolList.html#SimpleGappedSymbolList(org.biojava.bio.symbol.SymbolList)">SimpleGappedSymbolList(SymbolList)</a></span> - Constructor for class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleGappedSymbolList.html" title="class in org.biojava.bio.symbol">SimpleGappedSymbolList</a></dt>
<dd>
<div class="block">Create a new SimpleGappedSymbolList that will view source.</div>
</dd>
<dt><a href="./org/biojava/bio/symbol/SimpleGappedSymbolList.Block.html" title="class in org.biojava.bio.symbol"><span class="strong">SimpleGappedSymbolList.Block</span></a> - Class in <a href="./org/biojava/bio/symbol/package-summary.html">org.biojava.bio.symbol</a></dt>
<dd>
<div class="block">An aligned block.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleGappedSymbolList.Block.html#SimpleGappedSymbolList.Block(int, int, int, int)">SimpleGappedSymbolList.Block(int, int, int, int)</a></span> - Constructor for class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleGappedSymbolList.Block.html" title="class in org.biojava.bio.symbol">SimpleGappedSymbolList.Block</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleGappedSymbolList.Block.html#SimpleGappedSymbolList.Block(org.biojava.bio.symbol.SimpleGappedSymbolList.Block)">SimpleGappedSymbolList.Block(SimpleGappedSymbolList.Block)</a></span> - Constructor for class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleGappedSymbolList.Block.html" title="class in org.biojava.bio.symbol">SimpleGappedSymbolList.Block</a></dt>
<dd> </dd>
<dt><a href="./org/biojavax/ga/impl/SimpleGeneticAlgorithm.html" title="class in org.biojavax.ga.impl"><span class="strong">SimpleGeneticAlgorithm</span></a> - Class in <a href="./org/biojavax/ga/impl/package-summary.html">org.biojavax.ga.impl</a></dt>
<dd>
<div class="block">A simple implementation of the <code>GeneticAlgorithm</code> interface it
is not intended that this class be overidden, hence it is final.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ga/impl/SimpleGeneticAlgorithm.html#SimpleGeneticAlgorithm()">SimpleGeneticAlgorithm()</a></span> - Constructor for class org.biojavax.ga.impl.<a href="./org/biojavax/ga/impl/SimpleGeneticAlgorithm.html" title="class in org.biojavax.ga.impl">SimpleGeneticAlgorithm</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/impl/SimpleGeneticAlgorithm.html#SimpleGeneticAlgorithm(org.biojavax.ga.Population, org.biojavax.ga.functions.MutationFunction, org.biojavax.ga.functions.CrossOverFunction, org.biojavax.ga.functions.SelectionFunction)">SimpleGeneticAlgorithm(Population, MutationFunction, CrossOverFunction, SelectionFunction)</a></span> - Constructor for class org.biojavax.ga.impl.<a href="./org/biojavax/ga/impl/SimpleGeneticAlgorithm.html" title="class in org.biojavax.ga.impl">SimpleGeneticAlgorithm</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/symbol/SimpleGeneticCodeTable.html" title="class in org.biojava.bio.symbol"><span class="strong">SimpleGeneticCodeTable</span></a> - Class in <a href="./org/biojava/bio/symbol/package-summary.html">org.biojava.bio.symbol</a></dt>
<dd>
<div class="block">A genetic code translation table representing a translation table in the
DDBJ/EMBL/GenBank Feature Table (appendix V).</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleGeneticCodeTable.html#SimpleGeneticCodeTable(org.biojava.bio.symbol.FiniteAlphabet, org.biojava.bio.symbol.FiniteAlphabet)">SimpleGeneticCodeTable(FiniteAlphabet, FiniteAlphabet)</a></span> - Constructor for class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleGeneticCodeTable.html" title="class in org.biojava.bio.symbol">SimpleGeneticCodeTable</a></dt>
<dd>
<div class="block">Creates a new instance of SimpleGeneticCodeTable</div>
</dd>
<dt><a href="./org/biojava/bio/program/gff/SimpleGFFRecord.html" title="class in org.biojava.bio.program.gff"><span class="strong">SimpleGFFRecord</span></a> - Class in <a href="./org/biojava/bio/program/gff/package-summary.html">org.biojava.bio.program.gff</a></dt>
<dd>
<div class="block">A no-frills implementation of a <span class="type">GFFRecord</span>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/SimpleGFFRecord.html#SimpleGFFRecord(org.biojava.bio.program.gff.GFFRecord)">SimpleGFFRecord(GFFRecord)</a></span> - Constructor for class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/SimpleGFFRecord.html" title="class in org.biojava.bio.program.gff">SimpleGFFRecord</a></dt>
<dd>
<div class="block">Create a new SimpleGFFRecord from GFFRecord object</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/SimpleGFFRecord.html#SimpleGFFRecord(java.lang.String, java.lang.String, java.lang.String, int, int, double, org.biojava.bio.seq.StrandedFeature.Strand, int, java.lang.String, java.util.Map)">SimpleGFFRecord(String, String, String, int, int, double, StrandedFeature.Strand, int, String, Map)</a></span> - Constructor for class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/SimpleGFFRecord.html" title="class in org.biojava.bio.program.gff">SimpleGFFRecord</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/SimpleGFFRecord.html#SimpleGFFRecord()">SimpleGFFRecord()</a></span> - Constructor for class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/SimpleGFFRecord.html" title="class in org.biojava.bio.program.gff">SimpleGFFRecord</a></dt>
<dd>
<div class="block">Create a new SimpleGFFRecord with values set to null or zero</div>
</dd>
<dt><a href="./org/biojava/bio/dp/SimpleHMMTrainer.html" title="class in org.biojava.bio.dp"><span class="strong">SimpleHMMTrainer</span></a> - Class in <a href="./org/biojava/bio/dp/package-summary.html">org.biojava.bio.dp</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/SimpleHMMTrainer.html#SimpleHMMTrainer(org.biojava.bio.dp.MarkovModel)">SimpleHMMTrainer(MarkovModel)</a></span> - Constructor for class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/SimpleHMMTrainer.html" title="class in org.biojava.bio.dp">SimpleHMMTrainer</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/homologene/SimpleHomologeneBuilder.html" title="class in org.biojava.bio.program.homologene"><span class="strong">SimpleHomologeneBuilder</span></a> - Class in <a href="./org/biojava/bio/program/homologene/package-summary.html">org.biojava.bio.program.homologene</a></dt>
<dd>
<div class="block">A simple no-frills implementation of the HomologeneBuilder interface.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/SimpleHomologeneBuilder.html#SimpleHomologeneBuilder()">SimpleHomologeneBuilder()</a></span> - Constructor for class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/SimpleHomologeneBuilder.html" title="class in org.biojava.bio.program.homologene">SimpleHomologeneBuilder</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/homologene/SimpleHomologeneDB.html" title="class in org.biojava.bio.program.homologene"><span class="strong">SimpleHomologeneDB</span></a> - Class in <a href="./org/biojava/bio/program/homologene/package-summary.html">org.biojava.bio.program.homologene</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/SimpleHomologeneDB.html#SimpleHomologeneDB()">SimpleHomologeneDB()</a></span> - Constructor for class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/SimpleHomologeneDB.html" title="class in org.biojava.bio.program.homologene">SimpleHomologeneDB</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/homol/SimpleHomology.html" title="class in org.biojava.bio.seq.homol"><span class="strong">SimpleHomology</span></a> - Class in <a href="./org/biojava/bio/seq/homol/package-summary.html">org.biojava.bio.seq.homol</a></dt>
<dd>
<div class="block">A no-frills implementation of Homology.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/homol/SimpleHomology.html#SimpleHomology()">SimpleHomology()</a></span> - Constructor for class org.biojava.bio.seq.homol.<a href="./org/biojava/bio/seq/homol/SimpleHomology.html" title="class in org.biojava.bio.seq.homol">SimpleHomology</a></dt>
<dd>
<div class="block">Creates a new empty <code>SimpleHomology</code> containing no
<code>Alignment</code> and no <code>FeatureHolder</code>.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/impl/SimpleHomologyFeature.html" title="class in org.biojava.bio.seq.impl"><span class="strong">SimpleHomologyFeature</span></a> - Class in <a href="./org/biojava/bio/seq/impl/package-summary.html">org.biojava.bio.seq.impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleHomologyFeature.html#SimpleHomologyFeature(org.biojava.bio.seq.Sequence, org.biojava.bio.seq.FeatureHolder, org.biojava.bio.seq.homol.HomologyFeature.Template)">SimpleHomologyFeature(Sequence, FeatureHolder, HomologyFeature.Template)</a></span> - Constructor for class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleHomologyFeature.html" title="class in org.biojava.bio.seq.impl">SimpleHomologyFeature</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/db/SimpleIndex.html" title="class in org.biojava.bio.seq.db"><span class="strong">SimpleIndex</span></a> - Class in <a href="./org/biojava/bio/seq/db/package-summary.html">org.biojava.bio.seq.db</a></dt>
<dd>
<div class="block">This is a no-frills implementation of the Index interface.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/SimpleIndex.html#SimpleIndex(java.io.File, long, int, java.lang.String)">SimpleIndex(File, long, int, String)</a></span> - Constructor for class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/SimpleIndex.html" title="class in org.biojava.bio.seq.db">SimpleIndex</a></dt>
<dd>
<div class="block">Build the index using the given file, start and id</div>
</dd>
<dt><a href="./org/biojava/utils/process/SimpleInputHandler.html" title="class in org.biojava.utils.process"><span class="strong">SimpleInputHandler</span></a> - Class in <a href="./org/biojava/utils/process/package-summary.html">org.biojava.utils.process</a></dt>
<dd>
<div class="block">Simple <a href="./org/biojava/utils/process/InputHandler.html" title="interface in org.biojava.utils.process">input handler</a>
that reads the input for an external process from an
<a href="./org/biojava/utils/process/StreamPipe.html#getInput()">input stream</a>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/process/SimpleInputHandler.html#SimpleInputHandler(java.io.InputStream, java.lang.String)">SimpleInputHandler(InputStream, String)</a></span> - Constructor for class org.biojava.utils.process.<a href="./org/biojava/utils/process/SimpleInputHandler.html" title="class in org.biojava.utils.process">SimpleInputHandler</a></dt>
<dd>
<div class="block">Initializes the simple input handler.</div>
</dd>
<dt><a href="./org/biojava/stats/svm/SimpleItemValue.html" title="class in org.biojava.stats.svm"><span class="strong">SimpleItemValue</span></a> - Class in <a href="./org/biojava/stats/svm/package-summary.html">org.biojava.stats.svm</a></dt>
<dd>
<div class="block">A no-frills implementation of ItemValue.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/SimpleItemValue.html#SimpleItemValue(java.lang.Object, double)">SimpleItemValue(Object, double)</a></span> - Constructor for class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/SimpleItemValue.html" title="class in org.biojava.stats.svm">SimpleItemValue</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/gui/sequence/SimpleLabelRenderer.html" title="class in org.biojava.bio.gui.sequence"><span class="strong">SimpleLabelRenderer</span></a> - Class in <a href="./org/biojava/bio/gui/sequence/package-summary.html">org.biojava.bio.gui.sequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SimpleLabelRenderer.html#SimpleLabelRenderer()">SimpleLabelRenderer()</a></span> - Constructor for class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SimpleLabelRenderer.html" title="class in org.biojava.bio.gui.sequence">SimpleLabelRenderer</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/symbol/SimpleManyToOneTranslationTable.html" title="class in org.biojava.bio.symbol"><span class="strong">SimpleManyToOneTranslationTable</span></a> - Class in <a href="./org/biojava/bio/symbol/package-summary.html">org.biojava.bio.symbol</a></dt>
<dd>
<div class="block">A no-frills implementation of a translation table that
maps between two alphabets.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleManyToOneTranslationTable.html#SimpleManyToOneTranslationTable(org.biojava.bio.symbol.FiniteAlphabet, org.biojava.bio.symbol.FiniteAlphabet)">SimpleManyToOneTranslationTable(FiniteAlphabet, FiniteAlphabet)</a></span> - Constructor for class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleManyToOneTranslationTable.html" title="class in org.biojava.bio.symbol">SimpleManyToOneTranslationTable</a></dt>
<dd>
<div class="block">Construct a new translation table.</div>
</dd>
<dt><a href="./org/biojava/bio/dp/SimpleMarkovModel.html" title="class in org.biojava.bio.dp"><span class="strong">SimpleMarkovModel</span></a> - Class in <a href="./org/biojava/bio/dp/package-summary.html">org.biojava.bio.dp</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/SimpleMarkovModel.html#SimpleMarkovModel(int, org.biojava.bio.symbol.Alphabet, java.lang.String)">SimpleMarkovModel(int, Alphabet, String)</a></span> - Constructor for class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/SimpleMarkovModel.html" title="class in org.biojava.bio.dp">SimpleMarkovModel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/SimpleMarkovModel.html#SimpleMarkovModel(int, org.biojava.bio.symbol.Alphabet)">SimpleMarkovModel(int, Alphabet)</a></span> - Constructor for class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/SimpleMarkovModel.html" title="class in org.biojava.bio.dp">SimpleMarkovModel</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span> </div>
</dd>
<dt><a href="./org/biojava/bio/structure/io/mmcif/SimpleMMcifConsumer.html" title="class in org.biojava.bio.structure.io.mmcif"><span class="strong">SimpleMMcifConsumer</span></a> - Class in <a href="./org/biojava/bio/structure/io/mmcif/package-summary.html">org.biojava.bio.structure.io.mmcif</a></dt>
<dd>
<div class="block">A MMcifConsumer implementation that build a in-memory representation of the
content of a mmcif file as a BioJava Structure object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/SimpleMMcifConsumer.html#SimpleMMcifConsumer()">SimpleMMcifConsumer()</a></span> - Constructor for class org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/SimpleMMcifConsumer.html" title="class in org.biojava.bio.structure.io.mmcif">SimpleMMcifConsumer</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/structure/io/mmcif/SimpleMMcifParser.html" title="class in org.biojava.bio.structure.io.mmcif"><span class="strong">SimpleMMcifParser</span></a> - Class in <a href="./org/biojava/bio/structure/io/mmcif/package-summary.html">org.biojava.bio.structure.io.mmcif</a></dt>
<dd>
<div class="block">A simple mmCif file parser</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/SimpleMMcifParser.html#SimpleMMcifParser()">SimpleMMcifParser()</a></span> - Constructor for class org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/SimpleMMcifParser.html" title="class in org.biojava.bio.structure.io.mmcif">SimpleMMcifParser</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/dp/SimpleModelInState.html" title="class in org.biojava.bio.dp"><span class="strong">SimpleModelInState</span></a> - Class in <a href="./org/biojava/bio/dp/package-summary.html">org.biojava.bio.dp</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/SimpleModelInState.html#SimpleModelInState(org.biojava.bio.dp.MarkovModel, java.lang.String)">SimpleModelInState(MarkovModel, String)</a></span> - Constructor for class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/SimpleModelInState.html" title="class in org.biojava.bio.dp">SimpleModelInState</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/dp/SimpleModelTrainer.html" title="class in org.biojava.bio.dp"><span class="strong">SimpleModelTrainer</span></a> - Class in <a href="./org/biojava/bio/dp/package-summary.html">org.biojava.bio.dp</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/SimpleModelTrainer.html#SimpleModelTrainer()">SimpleModelTrainer()</a></span> - Constructor for class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/SimpleModelTrainer.html" title="class in org.biojava.bio.dp">SimpleModelTrainer</a></dt>
<dd> </dd>
<dt><a href="./org/biojavax/ga/functions/SimpleMutationFunction.html" title="class in org.biojavax.ga.functions"><span class="strong">SimpleMutationFunction</span></a> - Class in <a href="./org/biojavax/ga/functions/package-summary.html">org.biojavax.ga.functions</a></dt>
<dd>
<div class="block"> Simple no frills Implementation of the MutationFunction interface</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ga/functions/SimpleMutationFunction.html#SimpleMutationFunction()">SimpleMutationFunction()</a></span> - Constructor for class org.biojavax.ga.functions.<a href="./org/biojavax/ga/functions/SimpleMutationFunction.html" title="class in org.biojavax.ga.functions">SimpleMutationFunction</a></dt>
<dd> </dd>
<dt><a href="./org/biojavax/SimpleNamespace.html" title="class in org.biojavax"><span class="strong">SimpleNamespace</span></a> - Class in <a href="./org/biojavax/package-summary.html">org.biojavax</a></dt>
<dd>
<div class="block">A basic Namespace implemenation.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleNamespace.html#SimpleNamespace(java.lang.String)">SimpleNamespace(String)</a></span> - Constructor for class org.biojavax.<a href="./org/biojavax/SimpleNamespace.html" title="class in org.biojavax">SimpleNamespace</a></dt>
<dd>
<div class="block">Creates a new instance of SimpleNamespace with the given name,
which cannot be null.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleNamespace.html#SimpleNamespace()">SimpleNamespace()</a></span> - Constructor for class org.biojavax.<a href="./org/biojavax/SimpleNamespace.html" title="class in org.biojavax">SimpleNamespace</a></dt>
<dd> </dd>
<dt><a href="./org/biojavax/bio/taxa/SimpleNCBITaxon.html" title="class in org.biojavax.bio.taxa"><span class="strong">SimpleNCBITaxon</span></a> - Class in <a href="./org/biojavax/bio/taxa/package-summary.html">org.biojavax.bio.taxa</a></dt>
<dd>
<div class="block">Reference implementation of NCBITaxon.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/taxa/SimpleNCBITaxon.html#SimpleNCBITaxon(int)">SimpleNCBITaxon(int)</a></span> - Constructor for class org.biojavax.bio.taxa.<a href="./org/biojavax/bio/taxa/SimpleNCBITaxon.html" title="class in org.biojavax.bio.taxa">SimpleNCBITaxon</a></dt>
<dd>
<div class="block">Creates a new instance of SimpleNCBITaxon based on the given taxon ID.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/taxa/SimpleNCBITaxon.html#SimpleNCBITaxon(java.lang.Integer)">SimpleNCBITaxon(Integer)</a></span> - Constructor for class org.biojavax.bio.taxa.<a href="./org/biojavax/bio/taxa/SimpleNCBITaxon.html" title="class in org.biojavax.bio.taxa">SimpleNCBITaxon</a></dt>
<dd>
<div class="block">Creates a new instance of SimpleNCBITaxon based on the given taxon ID.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/taxa/SimpleNCBITaxon.html#SimpleNCBITaxon()">SimpleNCBITaxon()</a></span> - Constructor for class org.biojavax.bio.taxa.<a href="./org/biojavax/bio/taxa/SimpleNCBITaxon.html" title="class in org.biojavax.bio.taxa">SimpleNCBITaxon</a></dt>
<dd> </dd>
<dt><a href="./org/biojavax/bio/taxa/SimpleNCBITaxonName.html" title="class in org.biojavax.bio.taxa"><span class="strong">SimpleNCBITaxonName</span></a> - Class in <a href="./org/biojavax/bio/taxa/package-summary.html">org.biojavax.bio.taxa</a></dt>
<dd>
<div class="block">Represents a name class plus name combination for an NCBITaxon object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/taxa/SimpleNCBITaxonName.html#SimpleNCBITaxonName()">SimpleNCBITaxonName()</a></span> - Constructor for class org.biojavax.bio.taxa.<a href="./org/biojavax/bio/taxa/SimpleNCBITaxonName.html" title="class in org.biojavax.bio.taxa">SimpleNCBITaxonName</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/taxa/SimpleNCBITaxonName.html#SimpleNCBITaxonName(java.lang.String, java.lang.String)">SimpleNCBITaxonName(String, String)</a></span> - Constructor for class org.biojavax.bio.taxa.<a href="./org/biojavax/bio/taxa/SimpleNCBITaxonName.html" title="class in org.biojavax.bio.taxa">SimpleNCBITaxonName</a></dt>
<dd>
<div class="block">Creates a new taxon name based on the given class and name, both of
which cannot be null.</div>
</dd>
<dt><a href="./org/biojavax/bio/taxa/io/SimpleNCBITaxonomyLoader.html" title="class in org.biojavax.bio.taxa.io"><span class="strong">SimpleNCBITaxonomyLoader</span></a> - Class in <a href="./org/biojavax/bio/taxa/io/package-summary.html">org.biojavax.bio.taxa.io</a></dt>
<dd>
<div class="block">Loads NCBI taxon information from names.dmp and nodes.dmp, which are
two of the files in the archive downloadable at ftp://ftp.ncbi.nih.gov/pub/taxonomy/ .</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/taxa/io/SimpleNCBITaxonomyLoader.html#SimpleNCBITaxonomyLoader()">SimpleNCBITaxonomyLoader()</a></span> - Constructor for class org.biojavax.bio.taxa.io.<a href="./org/biojavax/bio/taxa/io/SimpleNCBITaxonomyLoader.html" title="class in org.biojavax.bio.taxa.io">SimpleNCBITaxonomyLoader</a></dt>
<dd> </dd>
<dt><a href="./org/biojavax/SimpleNote.html" title="class in org.biojavax"><span class="strong">SimpleNote</span></a> - Class in <a href="./org/biojavax/package-summary.html">org.biojavax</a></dt>
<dd>
<div class="block">Simple implementation of Note.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleNote.html#SimpleNote(org.biojavax.ontology.ComparableTerm, java.lang.String, int)">SimpleNote(ComparableTerm, String, int)</a></span> - Constructor for class org.biojavax.<a href="./org/biojavax/SimpleNote.html" title="class in org.biojavax">SimpleNote</a></dt>
<dd>
<div class="block">Creates a new instance of SimpleNote with a given term, value and rank.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleNote.html#SimpleNote()">SimpleNote()</a></span> - Constructor for class org.biojavax.<a href="./org/biojavax/SimpleNote.html" title="class in org.biojavax">SimpleNote</a></dt>
<dd> </dd>
<dt><a href="./org/biojavax/ga/impl/SimpleOrganism.html" title="class in org.biojavax.ga.impl"><span class="strong">SimpleOrganism</span></a> - Class in <a href="./org/biojavax/ga/impl/package-summary.html">org.biojavax.ga.impl</a></dt>
<dd>
<div class="block">A Simple Haploid Organism implementation</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ga/impl/SimpleOrganism.html#SimpleOrganism()">SimpleOrganism()</a></span> - Constructor for class org.biojavax.ga.impl.<a href="./org/biojavax/ga/impl/SimpleOrganism.html" title="class in org.biojavax.ga.impl">SimpleOrganism</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/impl/SimpleOrganism.html#SimpleOrganism(java.lang.String)">SimpleOrganism(String)</a></span> - Constructor for class org.biojavax.ga.impl.<a href="./org/biojavax/ga/impl/SimpleOrganism.html" title="class in org.biojavax.ga.impl">SimpleOrganism</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/impl/SimpleOrganism.html#SimpleOrganism(org.biojavax.ga.Organism, java.lang.String)">SimpleOrganism(Organism, String)</a></span> - Constructor for class org.biojavax.ga.impl.<a href="./org/biojavax/ga/impl/SimpleOrganism.html" title="class in org.biojavax.ga.impl">SimpleOrganism</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/homologene/SimpleOrthologue.html" title="class in org.biojava.bio.program.homologene"><span class="strong">SimpleOrthologue</span></a> - Class in <a href="./org/biojava/bio/program/homologene/package-summary.html">org.biojava.bio.program.homologene</a></dt>
<dd>
<div class="block">this entry contains data about the orthologue.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/SimpleOrthologue.html#SimpleOrthologue(org.biojava.bio.program.homologene.Taxon, java.lang.String, java.lang.String, java.lang.String)">SimpleOrthologue(Taxon, String, String, String)</a></span> - Constructor for class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/SimpleOrthologue.html" title="class in org.biojava.bio.program.homologene">SimpleOrthologue</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/SimpleOrthologue.html#SimpleOrthologue(int, java.lang.String, java.lang.String, java.lang.String)">SimpleOrthologue(int, String, String, String)</a></span> - Constructor for class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/SimpleOrthologue.html" title="class in org.biojava.bio.program.homologene">SimpleOrthologue</a></dt>
<dd>
<div class="block">this constructor does the Taxon lookup for you too</div>
</dd>
<dt><a href="./org/biojava/bio/program/homologene/SimpleOrthologueSet.html" title="class in org.biojava.bio.program.homologene"><span class="strong">SimpleOrthologueSet</span></a> - Class in <a href="./org/biojava/bio/program/homologene/package-summary.html">org.biojava.bio.program.homologene</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/SimpleOrthologueSet.html#SimpleOrthologueSet()">SimpleOrthologueSet()</a></span> - Constructor for class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/SimpleOrthologueSet.html" title="class in org.biojava.bio.program.homologene">SimpleOrthologueSet</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/homologene/SimpleOrthologueSet.Iterator.html" title="class in org.biojava.bio.program.homologene"><span class="strong">SimpleOrthologueSet.Iterator</span></a> - Class in <a href="./org/biojava/bio/program/homologene/package-summary.html">org.biojava.bio.program.homologene</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/homologene/SimpleOrthoPair.html" title="class in org.biojava.bio.program.homologene"><span class="strong">SimpleOrthoPair</span></a> - Class in <a href="./org/biojava/bio/program/homologene/package-summary.html">org.biojava.bio.program.homologene</a></dt>
<dd>
<div class="block">A no-frills implementation of the OrthoPair interface</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/SimpleOrthoPair.html#SimpleOrthoPair(org.biojava.bio.program.homologene.Orthologue, org.biojava.bio.program.homologene.Orthologue, org.biojava.bio.program.homologene.SimilarityType, double)">SimpleOrthoPair(Orthologue, Orthologue, SimilarityType, double)</a></span> - Constructor for class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/SimpleOrthoPair.html" title="class in org.biojava.bio.program.homologene">SimpleOrthoPair</a></dt>
<dd>
<div class="block">constructor for the computed form
of an orthology relationship.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/SimpleOrthoPair.html#SimpleOrthoPair(org.biojava.bio.program.homologene.Orthologue, org.biojava.bio.program.homologene.Orthologue, java.lang.String)">SimpleOrthoPair(Orthologue, Orthologue, String)</a></span> - Constructor for class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/SimpleOrthoPair.html" title="class in org.biojava.bio.program.homologene">SimpleOrthoPair</a></dt>
<dd>
<div class="block">constructor for the curated form
of an orthology relationship</div>
</dd>
<dt><a href="./org/biojava/bio/program/homologene/SimpleOrthoPairCollection.html" title="class in org.biojava.bio.program.homologene"><span class="strong">SimpleOrthoPairCollection</span></a> - Class in <a href="./org/biojava/bio/program/homologene/package-summary.html">org.biojava.bio.program.homologene</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/SimpleOrthoPairCollection.html#SimpleOrthoPairCollection()">SimpleOrthoPairCollection()</a></span> - Constructor for class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/SimpleOrthoPairCollection.html" title="class in org.biojava.bio.program.homologene">SimpleOrthoPairCollection</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/homologene/SimpleOrthoPairCollection.Iterator.html" title="class in org.biojava.bio.program.homologene"><span class="strong">SimpleOrthoPairCollection.Iterator</span></a> - Class in <a href="./org/biojava/bio/program/homologene/package-summary.html">org.biojava.bio.program.homologene</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/homologene/SimpleOrthoPairSet.html" title="class in org.biojava.bio.program.homologene"><span class="strong">SimpleOrthoPairSet</span></a> - Class in <a href="./org/biojava/bio/program/homologene/package-summary.html">org.biojava.bio.program.homologene</a></dt>
<dd>
<div class="block">a no-frills implementation of a Homologene Group</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/SimpleOrthoPairSet.html#SimpleOrthoPairSet()">SimpleOrthoPairSet()</a></span> - Constructor for class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/SimpleOrthoPairSet.html" title="class in org.biojava.bio.program.homologene">SimpleOrthoPairSet</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/homologene/SimpleOrthoPairSet.Iterator.html" title="class in org.biojava.bio.program.homologene"><span class="strong">SimpleOrthoPairSet.Iterator</span></a> - Class in <a href="./org/biojava/bio/program/homologene/package-summary.html">org.biojava.bio.program.homologene</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/utils/process/SimpleOutputHandler.html" title="class in org.biojava.utils.process"><span class="strong">SimpleOutputHandler</span></a> - Class in <a href="./org/biojava/utils/process/package-summary.html">org.biojava.utils.process</a></dt>
<dd>
<div class="block">Simple <a href="./org/biojava/utils/process/OutputHandler.html" title="interface in org.biojava.utils.process">output handler</a>
that pipes the output of an external process to an
<a href="./org/biojava/utils/process/StreamPipe.html#getOutput()">output stream</a>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/process/SimpleOutputHandler.html#SimpleOutputHandler(java.io.OutputStream, java.lang.String)">SimpleOutputHandler(OutputStream, String)</a></span> - Constructor for class org.biojava.utils.process.<a href="./org/biojava/utils/process/SimpleOutputHandler.html" title="class in org.biojava.utils.process">SimpleOutputHandler</a></dt>
<dd>
<div class="block">Initializes the simple output handler.</div>
</dd>
<dt><a href="./org/biojavax/ga/impl/SimplePopulation.html" title="class in org.biojavax.ga.impl"><span class="strong">SimplePopulation</span></a> - Class in <a href="./org/biojavax/ga/impl/package-summary.html">org.biojavax.ga.impl</a></dt>
<dd>
<div class="block">Simple concrete implementation of the <code>Population</code> interface</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ga/impl/SimplePopulation.html#SimplePopulation(java.lang.String)">SimplePopulation(String)</a></span> - Constructor for class org.biojavax.ga.impl.<a href="./org/biojavax/ga/impl/SimplePopulation.html" title="class in org.biojavax.ga.impl">SimplePopulation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/impl/SimplePopulation.html#SimplePopulation()">SimplePopulation()</a></span> - Constructor for class org.biojavax.ga.impl.<a href="./org/biojavax/ga/impl/SimplePopulation.html" title="class in org.biojavax.ga.impl">SimplePopulation</a></dt>
<dd> </dd>
<dt><a href="./org/biojavax/bio/seq/SimplePosition.html" title="class in org.biojavax.bio.seq"><span class="strong">SimplePosition</span></a> - Class in <a href="./org/biojavax/bio/seq/package-summary.html">org.biojavax.bio.seq</a></dt>
<dd>
<div class="block">A simple implementation of the Position interface.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimplePosition.html#SimplePosition(int)">SimplePosition(int)</a></span> - Constructor for class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimplePosition.html" title="class in org.biojavax.bio.seq">SimplePosition</a></dt>
<dd>
<div class="block">Constructs a point position, with no fuzzy start or
end.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimplePosition.html#SimplePosition(int, int)">SimplePosition(int, int)</a></span> - Constructor for class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimplePosition.html" title="class in org.biojavax.bio.seq">SimplePosition</a></dt>
<dd>
<div class="block">Constructs a range position, with no fuzzy start or
end.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimplePosition.html#SimplePosition(boolean, boolean, int)">SimplePosition(boolean, boolean, int)</a></span> - Constructor for class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimplePosition.html" title="class in org.biojavax.bio.seq">SimplePosition</a></dt>
<dd>
<div class="block">Constructs a point position, with optionally fuzzy start and
end.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimplePosition.html#SimplePosition(boolean, boolean, int, int, java.lang.String)">SimplePosition(boolean, boolean, int, int, String)</a></span> - Constructor for class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimplePosition.html" title="class in org.biojavax.bio.seq">SimplePosition</a></dt>
<dd>
<div class="block">Constructs a range position, with optionally fuzzy start and
end.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimplePosition.html#SimplePosition()">SimplePosition()</a></span> - Constructor for class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimplePosition.html" title="class in org.biojavax.bio.seq">SimplePosition</a></dt>
<dd> </dd>
<dt><a href="./org/biojavax/SimpleRankedCrossRef.html" title="class in org.biojavax"><span class="strong">SimpleRankedCrossRef</span></a> - Class in <a href="./org/biojavax/package-summary.html">org.biojavax</a></dt>
<dd>
<div class="block">Simple implementation of RankedCrossRef.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleRankedCrossRef.html#SimpleRankedCrossRef(org.biojavax.CrossRef, int)">SimpleRankedCrossRef(CrossRef, int)</a></span> - Constructor for class org.biojavax.<a href="./org/biojavax/SimpleRankedCrossRef.html" title="class in org.biojavax">SimpleRankedCrossRef</a></dt>
<dd>
<div class="block">Constructs a new crossref with a rank.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleRankedCrossRef.html#SimpleRankedCrossRef()">SimpleRankedCrossRef()</a></span> - Constructor for class org.biojavax.<a href="./org/biojavax/SimpleRankedCrossRef.html" title="class in org.biojavax">SimpleRankedCrossRef</a></dt>
<dd> </dd>
<dt><a href="./org/biojavax/SimpleRankedDocRef.html" title="class in org.biojavax"><span class="strong">SimpleRankedDocRef</span></a> - Class in <a href="./org/biojavax/package-summary.html">org.biojavax</a></dt>
<dd>
<div class="block">Represents a documentary reference.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleRankedDocRef.html#SimpleRankedDocRef(org.biojavax.DocRef, java.lang.Integer, java.lang.Integer, int)">SimpleRankedDocRef(DocRef, Integer, Integer, int)</a></span> - Constructor for class org.biojavax.<a href="./org/biojavax/SimpleRankedDocRef.html" title="class in org.biojavax">SimpleRankedDocRef</a></dt>
<dd>
<div class="block">Constructs a new docref for a given location.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleRankedDocRef.html#SimpleRankedDocRef(org.biojavax.DocRef, org.biojavax.bio.seq.RichLocation, int)">SimpleRankedDocRef(DocRef, RichLocation, int)</a></span> - Constructor for class org.biojavax.<a href="./org/biojavax/SimpleRankedDocRef.html" title="class in org.biojavax">SimpleRankedDocRef</a></dt>
<dd>
<div class="block">Constructs a new docref for a given location.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleRankedDocRef.html#SimpleRankedDocRef()">SimpleRankedDocRef()</a></span> - Constructor for class org.biojavax.<a href="./org/biojavax/SimpleRankedDocRef.html" title="class in org.biojavax">SimpleRankedDocRef</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/impl/SimpleRemoteFeature.html" title="class in org.biojava.bio.seq.impl"><span class="strong">SimpleRemoteFeature</span></a> - Class in <a href="./org/biojava/bio/seq/impl/package-summary.html">org.biojava.bio.seq.impl</a></dt>
<dd>
<div class="block">A no-frills implementation of a remote feature.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleRemoteFeature.html#SimpleRemoteFeature(org.biojava.bio.seq.Sequence, org.biojava.bio.seq.FeatureHolder, org.biojava.bio.seq.RemoteFeature.Template)">SimpleRemoteFeature(Sequence, FeatureHolder, RemoteFeature.Template)</a></span> - Constructor for class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleRemoteFeature.html" title="class in org.biojava.bio.seq.impl">SimpleRemoteFeature</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/impl/SimpleRemoteFeature.DBResolver.html" title="class in org.biojava.bio.seq.impl"><span class="strong">SimpleRemoteFeature.DBResolver</span></a> - Class in <a href="./org/biojava/bio/seq/impl/package-summary.html">org.biojava.bio.seq.impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleRemoteFeature.DBResolver.html#SimpleRemoteFeature.DBResolver(org.biojava.bio.seq.db.SequenceDB)">SimpleRemoteFeature.DBResolver(SequenceDB)</a></span> - Constructor for class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleRemoteFeature.DBResolver.html" title="class in org.biojava.bio.seq.impl">SimpleRemoteFeature.DBResolver</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/impl/SimpleRestrictionSite.html" title="class in org.biojava.bio.seq.impl"><span class="strong">SimpleRestrictionSite</span></a> - Class in <a href="./org/biojava/bio/seq/impl/package-summary.html">org.biojava.bio.seq.impl</a></dt>
<dd>
<div class="block"><code>SimpleRestrictionSite</code> represents the recognition site
of a restriction enzyme.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleRestrictionSite.html#SimpleRestrictionSite(org.biojava.bio.seq.Sequence, org.biojava.bio.seq.FeatureHolder, org.biojava.bio.molbio.RestrictionSite.Template)">SimpleRestrictionSite(Sequence, FeatureHolder, RestrictionSite.Template)</a></span> - Constructor for class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleRestrictionSite.html" title="class in org.biojava.bio.seq.impl">SimpleRestrictionSite</a></dt>
<dd>
<div class="block">Creates a new <code>SimpleRestrictionSite</code>.</div>
</dd>
<dt><a href="./org/biojava/bio/symbol/SimpleReversibleTranslationTable.html" title="class in org.biojava.bio.symbol"><span class="strong">SimpleReversibleTranslationTable</span></a> - Class in <a href="./org/biojava/bio/symbol/package-summary.html">org.biojava.bio.symbol</a></dt>
<dd>
<div class="block">A no-frills implementation of TranslationTable that uses a Map to map from
symbols in a finite source alphabet into a target alphabet.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleReversibleTranslationTable.html#SimpleReversibleTranslationTable(org.biojava.bio.symbol.FiniteAlphabet, org.biojava.bio.symbol.FiniteAlphabet)">SimpleReversibleTranslationTable(FiniteAlphabet, FiniteAlphabet)</a></span> - Constructor for class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleReversibleTranslationTable.html" title="class in org.biojava.bio.symbol">SimpleReversibleTranslationTable</a></dt>
<dd>
<div class="block">Construct a new translation table.</div>
</dd>
<dt><a href="./org/biojavax/SimpleRichAnnotation.html" title="class in org.biojavax"><span class="strong">SimpleRichAnnotation</span></a> - Class in <a href="./org/biojavax/package-summary.html">org.biojavax</a></dt>
<dd>
<div class="block">Simple annotation wrapper.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleRichAnnotation.html#SimpleRichAnnotation()">SimpleRichAnnotation()</a></span> - Constructor for class org.biojavax.<a href="./org/biojavax/SimpleRichAnnotation.html" title="class in org.biojavax">SimpleRichAnnotation</a></dt>
<dd>
<div class="block">Creates a new, empty instance of SimpleRichAnnotation</div>
</dd>
<dt><a href="./org/biojavax/bio/seq/SimpleRichFeature.html" title="class in org.biojavax.bio.seq"><span class="strong">SimpleRichFeature</span></a> - Class in <a href="./org/biojavax/bio/seq/package-summary.html">org.biojavax.bio.seq</a></dt>
<dd>
<div class="block">A simple implementation of RichFeature.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichFeature.html#SimpleRichFeature(org.biojava.bio.seq.FeatureHolder, org.biojava.bio.seq.Feature.Template)">SimpleRichFeature(FeatureHolder, Feature.Template)</a></span> - Constructor for class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichFeature.html" title="class in org.biojavax.bio.seq">SimpleRichFeature</a></dt>
<dd>
<div class="block">Creates a new instance of SimpleRichFeature based on a template.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichFeature.html#SimpleRichFeature()">SimpleRichFeature()</a></span> - Constructor for class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichFeature.html" title="class in org.biojavax.bio.seq">SimpleRichFeature</a></dt>
<dd> </dd>
<dt><a href="./org/biojavax/bio/seq/SimpleRichFeatureRelationship.html" title="class in org.biojavax.bio.seq"><span class="strong">SimpleRichFeatureRelationship</span></a> - Class in <a href="./org/biojavax/bio/seq/package-summary.html">org.biojavax.bio.seq</a></dt>
<dd>
<div class="block">Represents a relationship between two features that is described by a term.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichFeatureRelationship.html#SimpleRichFeatureRelationship(org.biojavax.bio.seq.RichFeature, org.biojavax.bio.seq.RichFeature, org.biojavax.ontology.ComparableTerm, int)">SimpleRichFeatureRelationship(RichFeature, RichFeature, ComparableTerm, int)</a></span> - Constructor for class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichFeatureRelationship.html" title="class in org.biojavax.bio.seq">SimpleRichFeatureRelationship</a></dt>
<dd>
<div class="block">Creates a new instance of SimpleRichFeatureRelationship.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichFeatureRelationship.html#SimpleRichFeatureRelationship()">SimpleRichFeatureRelationship()</a></span> - Constructor for class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichFeatureRelationship.html" title="class in org.biojavax.bio.seq">SimpleRichFeatureRelationship</a></dt>
<dd> </dd>
<dt><a href="./org/biojavax/bio/seq/SimpleRichLocation.html" title="class in org.biojavax.bio.seq"><span class="strong">SimpleRichLocation</span></a> - Class in <a href="./org/biojavax/bio/seq/package-summary.html">org.biojavax.bio.seq</a></dt>
<dd>
<div class="block">A simple implementation of RichLocation.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichLocation.html#SimpleRichLocation(org.biojavax.bio.seq.Position, int)">SimpleRichLocation(Position, int)</a></span> - Constructor for class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichLocation.html" title="class in org.biojavax.bio.seq">SimpleRichLocation</a></dt>
<dd>
<div class="block">Creates a new instance of SimpleRichSequenceLocation that points to a
single position on the positive strand.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichLocation.html#SimpleRichLocation(org.biojavax.bio.seq.Position, int, org.biojavax.bio.seq.RichLocation.Strand)">SimpleRichLocation(Position, int, RichLocation.Strand)</a></span> - Constructor for class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichLocation.html" title="class in org.biojavax.bio.seq">SimpleRichLocation</a></dt>
<dd>
<div class="block">Creates a new instance of SimpleRichSequenceLocation that points to a
single position.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichLocation.html#SimpleRichLocation(org.biojavax.bio.seq.Position, int, org.biojavax.bio.seq.RichLocation.Strand, org.biojavax.CrossRef)">SimpleRichLocation(Position, int, RichLocation.Strand, CrossRef)</a></span> - Constructor for class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichLocation.html" title="class in org.biojavax.bio.seq">SimpleRichLocation</a></dt>
<dd>
<div class="block">Creates a new instance of SimpleRichSequenceLocation that points to a
single position on another sequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichLocation.html#SimpleRichLocation(org.biojavax.bio.seq.Position, org.biojavax.bio.seq.Position, int)">SimpleRichLocation(Position, Position, int)</a></span> - Constructor for class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichLocation.html" title="class in org.biojavax.bio.seq">SimpleRichLocation</a></dt>
<dd>
<div class="block">Creates a new instance of SimpleRichSequenceLocation that points to a
range position on the positive strand.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichLocation.html#SimpleRichLocation(org.biojavax.bio.seq.Position, org.biojavax.bio.seq.Position, int, org.biojavax.bio.seq.RichLocation.Strand)">SimpleRichLocation(Position, Position, int, RichLocation.Strand)</a></span> - Constructor for class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichLocation.html" title="class in org.biojavax.bio.seq">SimpleRichLocation</a></dt>
<dd>
<div class="block">Creates a new instance of SimpleRichSequenceLocation that points to a
range position.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichLocation.html#SimpleRichLocation(org.biojavax.bio.seq.Position, org.biojavax.bio.seq.Position, int, org.biojavax.bio.seq.RichLocation.Strand, org.biojavax.CrossRef)">SimpleRichLocation(Position, Position, int, RichLocation.Strand, CrossRef)</a></span> - Constructor for class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichLocation.html" title="class in org.biojavax.bio.seq">SimpleRichLocation</a></dt>
<dd>
<div class="block">Creates a new instance of SimpleRichSequenceLocation that points to a
range position on another sequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichLocation.html#SimpleRichLocation()">SimpleRichLocation()</a></span> - Constructor for class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichLocation.html" title="class in org.biojavax.bio.seq">SimpleRichLocation</a></dt>
<dd> </dd>
<dt><a href="./org/biojavax/SimpleRichObjectBuilder.html" title="class in org.biojavax"><span class="strong">SimpleRichObjectBuilder</span></a> - Class in <a href="./org/biojavax/package-summary.html">org.biojavax</a></dt>
<dd>
<div class="block">Creates objects and returns them, and stores them in an internal
map of singletons for reference.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleRichObjectBuilder.html#SimpleRichObjectBuilder()">SimpleRichObjectBuilder()</a></span> - Constructor for class org.biojavax.<a href="./org/biojavax/SimpleRichObjectBuilder.html" title="class in org.biojavax">SimpleRichObjectBuilder</a></dt>
<dd> </dd>
<dt><a href="./org/biojavax/bio/seq/SimpleRichSequence.html" title="class in org.biojavax.bio.seq"><span class="strong">SimpleRichSequence</span></a> - Class in <a href="./org/biojavax/bio/seq/package-summary.html">org.biojavax.bio.seq</a></dt>
<dd>
<div class="block">A simple implementation of RichSequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichSequence.html#SimpleRichSequence(org.biojavax.Namespace, java.lang.String, java.lang.String, int, org.biojava.bio.symbol.SymbolList, java.lang.Double)">SimpleRichSequence(Namespace, String, String, int, SymbolList, Double)</a></span> - Constructor for class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichSequence.html" title="class in org.biojavax.bio.seq">SimpleRichSequence</a></dt>
<dd>
<div class="block">Creates a new instance of SimpleRichSequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichSequence.html#SimpleRichSequence()">SimpleRichSequence()</a></span> - Constructor for class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichSequence.html" title="class in org.biojavax.bio.seq">SimpleRichSequence</a></dt>
<dd> </dd>
<dt><a href="./org/biojavax/bio/seq/io/SimpleRichSequenceBuilder.html" title="class in org.biojavax.bio.seq.io"><span class="strong">SimpleRichSequenceBuilder</span></a> - Class in <a href="./org/biojavax/bio/seq/io/package-summary.html">org.biojavax.bio.seq.io</a></dt>
<dd>
<div class="block">Constructs BioEntry objects by listening to events.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/SimpleRichSequenceBuilder.html#SimpleRichSequenceBuilder()">SimpleRichSequenceBuilder()</a></span> - Constructor for class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/SimpleRichSequenceBuilder.html" title="class in org.biojavax.bio.seq.io">SimpleRichSequenceBuilder</a></dt>
<dd>
<div class="block">Creates a new instance of SimpleRichSequenceBuilder using a SimpleSymbolListFactory
with a threshold of zero.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/SimpleRichSequenceBuilder.html#SimpleRichSequenceBuilder(org.biojava.bio.symbol.SymbolListFactory)">SimpleRichSequenceBuilder(SymbolListFactory)</a></span> - Constructor for class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/SimpleRichSequenceBuilder.html" title="class in org.biojavax.bio.seq.io">SimpleRichSequenceBuilder</a></dt>
<dd>
<div class="block">Creates a new instance of SimpleRichSequenceBuilder with the
desired symbollistfactory and threshold of zero.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/SimpleRichSequenceBuilder.html#SimpleRichSequenceBuilder(org.biojava.bio.symbol.SymbolListFactory, int)">SimpleRichSequenceBuilder(SymbolListFactory, int)</a></span> - Constructor for class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/SimpleRichSequenceBuilder.html" title="class in org.biojavax.bio.seq.io">SimpleRichSequenceBuilder</a></dt>
<dd>
<div class="block">Creates a new instance of SimpleRichSequenceBuilder with the
desired symbollistfactory and threshold.</div>
</dd>
<dt><a href="./org/biojavax/bio/seq/io/SimpleRichSequenceBuilderFactory.html" title="class in org.biojavax.bio.seq.io"><span class="strong">SimpleRichSequenceBuilderFactory</span></a> - Class in <a href="./org/biojavax/bio/seq/io/package-summary.html">org.biojavax.bio.seq.io</a></dt>
<dd>
<div class="block">Generates RichSequenceBuilder objects.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/SimpleRichSequenceBuilderFactory.html#SimpleRichSequenceBuilderFactory()">SimpleRichSequenceBuilderFactory()</a></span> - Constructor for class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/SimpleRichSequenceBuilderFactory.html" title="class in org.biojavax.bio.seq.io">SimpleRichSequenceBuilderFactory</a></dt>
<dd>
<div class="block">Creates a new instance of SimpleRichSequenceBuilderFactory</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/SimpleRichSequenceBuilderFactory.html#SimpleRichSequenceBuilderFactory(org.biojava.bio.symbol.SymbolListFactory)">SimpleRichSequenceBuilderFactory(SymbolListFactory)</a></span> - Constructor for class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/SimpleRichSequenceBuilderFactory.html" title="class in org.biojavax.bio.seq.io">SimpleRichSequenceBuilderFactory</a></dt>
<dd>
<div class="block">Creates a new instance of SimpleRichSequenceBuilderFactory</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/SimpleRichSequenceBuilderFactory.html#SimpleRichSequenceBuilderFactory(org.biojava.bio.symbol.SymbolListFactory, int)">SimpleRichSequenceBuilderFactory(SymbolListFactory, int)</a></span> - Constructor for class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/SimpleRichSequenceBuilderFactory.html" title="class in org.biojavax.bio.seq.io">SimpleRichSequenceBuilderFactory</a></dt>
<dd>
<div class="block">Creates a new instance of SimpleRichSequenceBuilderFactory that uses
a specified factory for <code>SymbolLists</code> longer than a specified
length.</div>
</dd>
<dt><a href="./org/biojava/bio/search/SimpleSeqSimilaritySearchHit.html" title="class in org.biojava.bio.search"><span class="strong">SimpleSeqSimilaritySearchHit</span></a> - Class in <a href="./org/biojava/bio/search/package-summary.html">org.biojava.bio.search</a></dt>
<dd>
<div class="block"><code>SimpleSeqSimilaritySearchHit</code> objects represent a
similarity search hit of a query sequence to a sequence referenced
in a SequenceDB object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SimpleSeqSimilaritySearchHit.html#SimpleSeqSimilaritySearchHit(double, double, double, int, int, org.biojava.bio.seq.StrandedFeature.Strand, int, int, org.biojava.bio.seq.StrandedFeature.Strand, java.lang.String, org.biojava.bio.Annotation, java.util.List)">SimpleSeqSimilaritySearchHit(double, double, double, int, int, StrandedFeature.Strand, int, int, StrandedFeature.Strand, String, Annotation, List)</a></span> - Constructor for class org.biojava.bio.search.<a href="./org/biojava/bio/search/SimpleSeqSimilaritySearchHit.html" title="class in org.biojava.bio.search">SimpleSeqSimilaritySearchHit</a></dt>
<dd>
<div class="block">Creates a new <code>SimpleSeqSimilaritySearchHit</code> object.</div>
</dd>
<dt><a href="./org/biojava/bio/search/SimpleSeqSimilaritySearchResult.html" title="class in org.biojava.bio.search"><span class="strong">SimpleSeqSimilaritySearchResult</span></a> - Class in <a href="./org/biojava/bio/search/package-summary.html">org.biojava.bio.search</a></dt>
<dd>
<div class="block"><code>SimpleSeqSimilaritySearchResult</code> objects represent a
result of a search of a <code>SymbolList</code> against the
sequences within a <code>SequenceDB</code> object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SimpleSeqSimilaritySearchResult.html#SimpleSeqSimilaritySearchResult(org.biojava.bio.seq.Sequence, org.biojava.bio.seq.db.SequenceDB, java.util.Map, java.util.List, org.biojava.bio.Annotation)">SimpleSeqSimilaritySearchResult(Sequence, SequenceDB, Map, List, Annotation)</a></span> - Constructor for class org.biojava.bio.search.<a href="./org/biojava/bio/search/SimpleSeqSimilaritySearchResult.html" title="class in org.biojava.bio.search">SimpleSeqSimilaritySearchResult</a></dt>
<dd>
<div class="block">Creates a new <code>SimpleSeqSimilaritySearchResult</code>.</div>
</dd>
<dt><a href="./org/biojava/bio/search/SimpleSeqSimilaritySearchSubHit.html" title="class in org.biojava.bio.search"><span class="strong">SimpleSeqSimilaritySearchSubHit</span></a> - Class in <a href="./org/biojava/bio/search/package-summary.html">org.biojava.bio.search</a></dt>
<dd>
<div class="block"><code>SimpleSeqSimilaritySearchSubHit</code> objects represent
sub-hits which make up a hit.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SimpleSeqSimilaritySearchSubHit.html#SimpleSeqSimilaritySearchSubHit(double, double, double, int, int, org.biojava.bio.seq.StrandedFeature.Strand, int, int, org.biojava.bio.seq.StrandedFeature.Strand, org.biojava.bio.symbol.Alignment, org.biojava.bio.Annotation)">SimpleSeqSimilaritySearchSubHit(double, double, double, int, int, StrandedFeature.Strand, int, int, StrandedFeature.Strand, Alignment, Annotation)</a></span> - Constructor for class org.biojava.bio.search.<a href="./org/biojava/bio/search/SimpleSeqSimilaritySearchSubHit.html" title="class in org.biojava.bio.search">SimpleSeqSimilaritySearchSubHit</a></dt>
<dd>
<div class="block">Creates a new <code>SimpleSeqSimilaritySearchSubHit</code>
object.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/impl/SimpleSequence.html" title="class in org.biojava.bio.seq.impl"><span class="strong">SimpleSequence</span></a> - Class in <a href="./org/biojava/bio/seq/impl/package-summary.html">org.biojava.bio.seq.impl</a></dt>
<dd>
<div class="block">A basic implementation of the <code>Sequence</code> interface.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleSequence.html#SimpleSequence(org.biojava.bio.symbol.SymbolList, java.lang.String, java.lang.String, org.biojava.bio.Annotation)">SimpleSequence(SymbolList, String, String, Annotation)</a></span> - Constructor for class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleSequence.html" title="class in org.biojava.bio.seq.impl">SimpleSequence</a></dt>
<dd>
<div class="block">Create a SimpleSequence with the symbols and alphabet of sym, and the
sequence properties listed.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleSequence.html#SimpleSequence(org.biojava.bio.symbol.SymbolList, java.lang.String, java.lang.String, org.biojava.bio.Annotation, org.biojava.bio.seq.FeatureRealizer)">SimpleSequence(SymbolList, String, String, Annotation, FeatureRealizer)</a></span> - Constructor for class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleSequence.html" title="class in org.biojava.bio.seq.impl">SimpleSequence</a></dt>
<dd>
<div class="block">Create a SimpleSequence using a specified FeatureRealizer.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/SimpleSequenceBuilder.html" title="class in org.biojava.bio.seq.io"><span class="strong">SimpleSequenceBuilder</span></a> - Class in <a href="./org/biojava/bio/seq/io/package-summary.html">org.biojava.bio.seq.io</a></dt>
<dd>
<div class="block">Basic SequenceBuilder implementation which accumulates all
notified information and creates a SimpleSequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SimpleSequenceBuilder.html#SimpleSequenceBuilder()">SimpleSequenceBuilder()</a></span> - Constructor for class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SimpleSequenceBuilder.html" title="class in org.biojava.bio.seq.io">SimpleSequenceBuilder</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/db/SimpleSequenceDBInstallation.html" title="class in org.biojava.bio.seq.db"><span class="strong">SimpleSequenceDBInstallation</span></a> - Class in <a href="./org/biojava/bio/seq/db/package-summary.html">org.biojava.bio.seq.db</a></dt>
<dd>
<div class="block">This class is an implementation of interface SequenceDBInstallation
that manages a set of SequenceDB objects.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/SimpleSequenceDBInstallation.html#SimpleSequenceDBInstallation()">SimpleSequenceDBInstallation()</a></span> - Constructor for class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/SimpleSequenceDBInstallation.html" title="class in org.biojava.bio.seq.db">SimpleSequenceDBInstallation</a></dt>
<dd>
<div class="block">create an initially empty SimpleSequenceDBInstallation</div>
</dd>
<dt><a href="./org/biojava/bio/seq/impl/SimpleSequenceFactory.html" title="class in org.biojava.bio.seq.impl"><span class="strong">SimpleSequenceFactory</span></a> - Class in <a href="./org/biojava/bio/seq/impl/package-summary.html">org.biojava.bio.seq.impl</a></dt>
<dd>
<div class="block">A no-frills implementation of SequenceFactory that produces SimpleSequence
objects.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleSequenceFactory.html#SimpleSequenceFactory()">SimpleSequenceFactory()</a></span> - Constructor for class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleSequenceFactory.html" title="class in org.biojava.bio.seq.impl">SimpleSequenceFactory</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/impl/SimpleSimilarityPairFeature.html" title="class in org.biojava.bio.seq.impl"><span class="strong">SimpleSimilarityPairFeature</span></a> - Class in <a href="./org/biojava/bio/seq/impl/package-summary.html">org.biojava.bio.seq.impl</a></dt>
<dd>
<div class="block"><code>SimpleSimilarityPairFeature</code> represents a similarity
between a query sequence and a subject sequence as produced by a
search program.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleSimilarityPairFeature.html#SimpleSimilarityPairFeature(org.biojava.bio.seq.Sequence, org.biojava.bio.seq.FeatureHolder, org.biojava.bio.seq.homol.SimilarityPairFeature.Template)">SimpleSimilarityPairFeature(Sequence, FeatureHolder, SimilarityPairFeature.Template)</a></span> - Constructor for class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleSimilarityPairFeature.html" title="class in org.biojava.bio.seq.impl">SimpleSimilarityPairFeature</a></dt>
<dd>
<div class="block">Creates a new <code>SimpleSimilarityPairFeature</code>.</div>
</dd>
<dt><a href="./org/biojava/bio/dp/SimpleStatePath.html" title="class in org.biojava.bio.dp"><span class="strong">SimpleStatePath</span></a> - Class in <a href="./org/biojava/bio/dp/package-summary.html">org.biojava.bio.dp</a></dt>
<dd>
<div class="block">A no-frills implementation of StatePath.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/SimpleStatePath.html#SimpleStatePath(double, org.biojava.bio.symbol.SymbolList, org.biojava.bio.symbol.SymbolList, org.biojava.bio.symbol.SymbolList)">SimpleStatePath(double, SymbolList, SymbolList, SymbolList)</a></span> - Constructor for class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/SimpleStatePath.html" title="class in org.biojava.bio.dp">SimpleStatePath</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/impl/SimpleStrandedFeature.html" title="class in org.biojava.bio.seq.impl"><span class="strong">SimpleStrandedFeature</span></a> - Class in <a href="./org/biojava/bio/seq/impl/package-summary.html">org.biojava.bio.seq.impl</a></dt>
<dd>
<div class="block">A no-frills implementation of StrandedFeature.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleStrandedFeature.html#SimpleStrandedFeature(org.biojava.bio.seq.Sequence, org.biojava.bio.seq.FeatureHolder, org.biojava.bio.seq.StrandedFeature.Template)">SimpleStrandedFeature(Sequence, FeatureHolder, StrandedFeature.Template)</a></span> - Constructor for class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleStrandedFeature.html" title="class in org.biojava.bio.seq.impl">SimpleStrandedFeature</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/structure/server/SimpleStructureServer.html" title="class in org.biojava.bio.structure.server"><span class="strong">SimpleStructureServer</span></a> - Class in <a href="./org/biojava/bio/structure/server/package-summary.html">org.biojava.bio.structure.server</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/server/SimpleStructureServer.html#SimpleStructureServer()">SimpleStructureServer()</a></span> - Constructor for class org.biojava.bio.structure.server.<a href="./org/biojava/bio/structure/server/SimpleStructureServer.html" title="class in org.biojava.bio.structure.server">SimpleStructureServer</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/stats/svm/SimpleSVMClassifierModel.html" title="class in org.biojava.stats.svm"><span class="strong">SimpleSVMClassifierModel</span></a> - Class in <a href="./org/biojava/stats/svm/package-summary.html">org.biojava.stats.svm</a></dt>
<dd>
<div class="block">A no-frills implementation of an SVM classifier model.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/SimpleSVMClassifierModel.html#SimpleSVMClassifierModel(org.biojava.stats.svm.SVMKernel)">SimpleSVMClassifierModel(SVMKernel)</a></span> - Constructor for class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/SimpleSVMClassifierModel.html" title="class in org.biojava.stats.svm">SimpleSVMClassifierModel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/SimpleSVMClassifierModel.html#SimpleSVMClassifierModel(org.biojava.stats.svm.SVMKernel, java.util.Collection)">SimpleSVMClassifierModel(SVMKernel, Collection)</a></span> - Constructor for class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/SimpleSVMClassifierModel.html" title="class in org.biojava.stats.svm">SimpleSVMClassifierModel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/SimpleSVMClassifierModel.html#SimpleSVMClassifierModel(org.biojava.stats.svm.SVMKernel, org.biojava.stats.svm.SVMTarget)">SimpleSVMClassifierModel(SVMKernel, SVMTarget)</a></span> - Constructor for class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/SimpleSVMClassifierModel.html" title="class in org.biojava.stats.svm">SimpleSVMClassifierModel</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/stats/svm/SimpleSVMTarget.html" title="class in org.biojava.stats.svm"><span class="strong">SimpleSVMTarget</span></a> - Class in <a href="./org/biojava/stats/svm/package-summary.html">org.biojava.stats.svm</a></dt>
<dd>
<div class="block">No-frills implementation of SVMTarget.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/SimpleSVMTarget.html#SimpleSVMTarget()">SimpleSVMTarget()</a></span> - Constructor for class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/SimpleSVMTarget.html" title="class in org.biojava.stats.svm">SimpleSVMTarget</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/SimpleSVMTarget.html#SimpleSVMTarget(java.util.Collection)">SimpleSVMTarget(Collection)</a></span> - Constructor for class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/SimpleSVMTarget.html" title="class in org.biojava.stats.svm">SimpleSVMTarget</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/symbol/SimpleSymbolList.html" title="class in org.biojava.bio.symbol"><span class="strong">SimpleSymbolList</span></a> - Class in <a href="./org/biojava/bio/symbol/package-summary.html">org.biojava.bio.symbol</a></dt>
<dd>
<div class="block">Basic implementation of SymbolList.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleSymbolList.html#SimpleSymbolList(org.biojava.bio.symbol.Alphabet)">SimpleSymbolList(Alphabet)</a></span> - Constructor for class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleSymbolList.html" title="class in org.biojava.bio.symbol">SimpleSymbolList</a></dt>
<dd>
<div class="block">Construct an empty SimpleSymbolList.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleSymbolList.html#SimpleSymbolList(org.biojava.bio.symbol.Alphabet, java.util.List)">SimpleSymbolList(Alphabet, List)</a></span> - Constructor for class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleSymbolList.html" title="class in org.biojava.bio.symbol">SimpleSymbolList</a></dt>
<dd>
<div class="block">Construct a SymbolList containing the symbols in the specified list.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleSymbolList.html#SimpleSymbolList(org.biojava.bio.seq.io.SymbolTokenization, java.lang.String)">SimpleSymbolList(SymbolTokenization, String)</a></span> - Constructor for class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleSymbolList.html" title="class in org.biojava.bio.symbol">SimpleSymbolList</a></dt>
<dd>
<div class="block">Construct a SymbolList from a string.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleSymbolList.html#SimpleSymbolList(org.biojava.bio.symbol.SymbolList)">SimpleSymbolList(SymbolList)</a></span> - Constructor for class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleSymbolList.html" title="class in org.biojava.bio.symbol">SimpleSymbolList</a></dt>
<dd>
<div class="block">Construct a copy of an existing SymbolList.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleSymbolList.html#SimpleSymbolList(org.biojava.bio.symbol.Symbol[], int, org.biojava.bio.symbol.Alphabet)">SimpleSymbolList(Symbol[], int, Alphabet)</a></span> - Constructor for class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleSymbolList.html" title="class in org.biojava.bio.symbol">SimpleSymbolList</a></dt>
<dd>
<div class="block">Construct a SimpleSymbolList given the Symbol array that backs it.</div>
</dd>
<dt><a href="./org/biojava/bio/symbol/SimpleSymbolListFactory.html" title="class in org.biojava.bio.symbol"><span class="strong">SimpleSymbolListFactory</span></a> - Class in <a href="./org/biojava/bio/symbol/package-summary.html">org.biojava.bio.symbol</a></dt>
<dd>
<div class="block">This class makes SimpleSymbolLists.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleSymbolListFactory.html#SimpleSymbolListFactory()">SimpleSymbolListFactory()</a></span> - Constructor for class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleSymbolListFactory.html" title="class in org.biojava.bio.symbol">SimpleSymbolListFactory</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/symbol/SimpleSymbolPropertyTable.html" title="class in org.biojava.bio.symbol"><span class="strong">SimpleSymbolPropertyTable</span></a> - Class in <a href="./org/biojava/bio/symbol/package-summary.html">org.biojava.bio.symbol</a></dt>
<dd>
<div class="block">Class that implements the SymbolPropertyTable interface</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleSymbolPropertyTable.html#SimpleSymbolPropertyTable(org.biojava.bio.symbol.Alphabet, java.lang.String)">SimpleSymbolPropertyTable(Alphabet, String)</a></span> - Constructor for class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleSymbolPropertyTable.html" title="class in org.biojava.bio.symbol">SimpleSymbolPropertyTable</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/proteomics/aaindex/SimpleSymbolPropertyTableDB.html" title="class in org.biojava.bio.proteomics.aaindex"><span class="strong">SimpleSymbolPropertyTableDB</span></a> - Class in <a href="./org/biojava/bio/proteomics/aaindex/package-summary.html">org.biojava.bio.proteomics.aaindex</a></dt>
<dd>
<div class="block">A simple implementation of a symbol property table database.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/aaindex/SimpleSymbolPropertyTableDB.html#SimpleSymbolPropertyTableDB()">SimpleSymbolPropertyTableDB()</a></span> - Constructor for class org.biojava.bio.proteomics.aaindex.<a href="./org/biojava/bio/proteomics/aaindex/SimpleSymbolPropertyTableDB.html" title="class in org.biojava.bio.proteomics.aaindex">SimpleSymbolPropertyTableDB</a></dt>
<dd>
<div class="block">Initializes the database.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/aaindex/SimpleSymbolPropertyTableDB.html#SimpleSymbolPropertyTableDB(org.biojava.bio.proteomics.aaindex.SymbolPropertyTableIterator)">SimpleSymbolPropertyTableDB(SymbolPropertyTableIterator)</a></span> - Constructor for class org.biojava.bio.proteomics.aaindex.<a href="./org/biojava/bio/proteomics/aaindex/SimpleSymbolPropertyTableDB.html" title="class in org.biojava.bio.proteomics.aaindex">SimpleSymbolPropertyTableDB</a></dt>
<dd>
<div class="block">Initializes the database by copying all symbol property tables from
a given iterator into the database.</div>
</dd>
<dt><a href="./org/biojava/bio/gui/SimpleSymbolStyle.html" title="class in org.biojava.bio.gui"><span class="strong">SimpleSymbolStyle</span></a> - Class in <a href="./org/biojava/bio/gui/package-summary.html">org.biojava.bio.gui</a></dt>
<dd>
<div class="block">A no-frills implementation of SymbolStyle.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/SimpleSymbolStyle.html#SimpleSymbolStyle(org.biojava.bio.symbol.FiniteAlphabet)">SimpleSymbolStyle(FiniteAlphabet)</a></span> - Constructor for class org.biojava.bio.gui.<a href="./org/biojava/bio/gui/SimpleSymbolStyle.html" title="class in org.biojava.bio.gui">SimpleSymbolStyle</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/tagvalue/SimpleTagValueWrapper.html" title="class in org.biojava.bio.program.tagvalue"><span class="strong">SimpleTagValueWrapper</span></a> - Class in <a href="./org/biojava/bio/program/tagvalue/package-summary.html">org.biojava.bio.program.tagvalue</a></dt>
<dd>
<div class="block">
Helper class to wrap one TagValueListener inside another one.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/SimpleTagValueWrapper.html#SimpleTagValueWrapper(org.biojava.bio.program.tagvalue.TagValueListener)">SimpleTagValueWrapper(TagValueListener)</a></span> - Constructor for class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/SimpleTagValueWrapper.html" title="class in org.biojava.bio.program.tagvalue">SimpleTagValueWrapper</a></dt>
<dd>
<div class="block">Build a SimpleTagValueWrapper that will forward everything to a delegate.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/SimpleTagValueWrapper.html#SimpleTagValueWrapper()">SimpleTagValueWrapper()</a></span> - Constructor for class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/SimpleTagValueWrapper.html" title="class in org.biojava.bio.program.tagvalue">SimpleTagValueWrapper</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/taxa/SimpleTaxon.html" title="class in org.biojava.bio.taxa"><span class="strong">SimpleTaxon</span></a> - Class in <a href="./org/biojava/bio/taxa/package-summary.html">org.biojava.bio.taxa</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>replaced by classes in <a href="./org/biojavax/bio/taxa/package-summary.html"><code>org.biojavax.bio.taxa</code></a></i></div>
</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/taxa/SimpleTaxon.html#SimpleTaxon()">SimpleTaxon()</a></span> - Constructor for class org.biojava.bio.taxa.<a href="./org/biojava/bio/taxa/SimpleTaxon.html" title="class in org.biojava.bio.taxa">SimpleTaxon</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/taxa/SimpleTaxon.html#SimpleTaxon(java.lang.String, java.lang.String)">SimpleTaxon(String, String)</a></span> - Constructor for class org.biojava.bio.taxa.<a href="./org/biojava/bio/taxa/SimpleTaxon.html" title="class in org.biojava.bio.taxa">SimpleTaxon</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Create a new instance with no parent, no children and given
scientific and common names.</div>
</dd>
<dt><a href="./org/biojava/bio/taxa/SimpleTaxonFactory.html" title="class in org.biojava.bio.taxa"><span class="strong">SimpleTaxonFactory</span></a> - Class in <a href="./org/biojava/bio/taxa/package-summary.html">org.biojava.bio.taxa</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>replaced by classes in <a href="./org/biojavax/bio/taxa/package-summary.html"><code>org.biojavax.bio.taxa</code></a></i></div>
</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/taxa/SimpleTaxonFactory.html#SimpleTaxonFactory(java.lang.String)">SimpleTaxonFactory(String)</a></span> - Constructor for class org.biojava.bio.taxa.<a href="./org/biojava/bio/taxa/SimpleTaxonFactory.html" title="class in org.biojava.bio.taxa">SimpleTaxonFactory</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><a href="./org/biojava/utils/SimpleThreadPool.html" title="class in org.biojava.utils"><span class="strong">SimpleThreadPool</span></a> - Class in <a href="./org/biojava/utils/package-summary.html">org.biojava.utils</a></dt>
<dd>
<div class="block"><code>SimpleThreadPool</code> is a basic implementation of
<code>ThreadPool</code> for use where we don't wish to introduce a
dependency on a 3rd-party pool.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/SimpleThreadPool.html#SimpleThreadPool()">SimpleThreadPool()</a></span> - Constructor for class org.biojava.utils.<a href="./org/biojava/utils/SimpleThreadPool.html" title="class in org.biojava.utils">SimpleThreadPool</a></dt>
<dd>
<div class="block">Creates a new <code>SimpleThreadPool</code> containing 4
non-daemon threads and starts them.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/SimpleThreadPool.html#SimpleThreadPool(int, boolean)">SimpleThreadPool(int, boolean)</a></span> - Constructor for class org.biojava.utils.<a href="./org/biojava/utils/SimpleThreadPool.html" title="class in org.biojava.utils">SimpleThreadPool</a></dt>
<dd>
<div class="block">Creates a new <code>SimpleThreadPool</code> containing the
specified number of threads and starts them.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/SimpleThreadPool.html#SimpleThreadPool(int, boolean, int)">SimpleThreadPool(int, boolean, int)</a></span> - Constructor for class org.biojava.utils.<a href="./org/biojava/utils/SimpleThreadPool.html" title="class in org.biojava.utils">SimpleThreadPool</a></dt>
<dd>
<div class="block">Creates a new <code>SimpleThreadPool</code> containing the
specified number of threads and starts them.</div>
</dd>
<dt><a href="./org/biojava/bio/gui/sequence/tracklayout/SimpleTrackLayout.html" title="class in org.biojava.bio.gui.sequence.tracklayout"><span class="strong">SimpleTrackLayout</span></a> - Class in <a href="./org/biojava/bio/gui/sequence/tracklayout/package-summary.html">org.biojava.bio.gui.sequence.tracklayout</a></dt>
<dd>
<div class="block">A TrackLayout implenentation that wraps the sequence smoothly after a set number of residues</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/tracklayout/SimpleTrackLayout.html#SimpleTrackLayout()">SimpleTrackLayout()</a></span> - Constructor for class org.biojava.bio.gui.sequence.tracklayout.<a href="./org/biojava/bio/gui/sequence/tracklayout/SimpleTrackLayout.html" title="class in org.biojava.bio.gui.sequence.tracklayout">SimpleTrackLayout</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/tracklayout/SimpleTrackLayout.html#SimpleTrackLayout(org.biojava.bio.seq.Sequence, int)">SimpleTrackLayout(Sequence, int)</a></span> - Constructor for class org.biojava.bio.gui.sequence.tracklayout.<a href="./org/biojava/bio/gui/sequence/tracklayout/SimpleTrackLayout.html" title="class in org.biojava.bio.gui.sequence.tracklayout">SimpleTrackLayout</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/symbol/SimpleTranslationTable.html" title="class in org.biojava.bio.symbol"><span class="strong">SimpleTranslationTable</span></a> - Class in <a href="./org/biojava/bio/symbol/package-summary.html">org.biojava.bio.symbol</a></dt>
<dd>
<div class="block">A no-frills implementation of TranslationTable that uses a Map to map from
symbols in a finite source alphabet into a target alphabet.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleTranslationTable.html#SimpleTranslationTable(org.biojava.bio.symbol.FiniteAlphabet, org.biojava.bio.symbol.Alphabet)">SimpleTranslationTable(FiniteAlphabet, Alphabet)</a></span> - Constructor for class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleTranslationTable.html" title="class in org.biojava.bio.symbol">SimpleTranslationTable</a></dt>
<dd>
<div class="block">Create a new translation table that will translate symbols from source to
target.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleTranslationTable.html#SimpleTranslationTable(org.biojava.bio.symbol.FiniteAlphabet, org.biojava.bio.symbol.Alphabet, java.util.Map)">SimpleTranslationTable(FiniteAlphabet, Alphabet, Map)</a></span> - Constructor for class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleTranslationTable.html" title="class in org.biojava.bio.symbol">SimpleTranslationTable</a></dt>
<dd>
<div class="block">Create a new translation table that will translate symbols from source to
target.</div>
</dd>
<dt><a href="./org/biojava/bio/dp/SimpleWeightMatrix.html" title="class in org.biojava.bio.dp"><span class="strong">SimpleWeightMatrix</span></a> - Class in <a href="./org/biojava/bio/dp/package-summary.html">org.biojava.bio.dp</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/SimpleWeightMatrix.html#SimpleWeightMatrix(org.biojava.bio.symbol.Alphabet, int, org.biojava.bio.dist.DistributionFactory)">SimpleWeightMatrix(Alphabet, int, DistributionFactory)</a></span> - Constructor for class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/SimpleWeightMatrix.html" title="class in org.biojava.bio.dp">SimpleWeightMatrix</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/SimpleWeightMatrix.html#SimpleWeightMatrix(org.biojava.bio.dist.Distribution[])">SimpleWeightMatrix(Distribution[])</a></span> - Constructor for class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/SimpleWeightMatrix.html" title="class in org.biojava.bio.dp">SimpleWeightMatrix</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/xml/SimpleXMLEmitter.html" title="class in org.biojava.bio.program.xml"><span class="strong">SimpleXMLEmitter</span></a> - Class in <a href="./org/biojava/bio/program/xml/package-summary.html">org.biojava.bio.program.xml</a></dt>
<dd>
<div class="block">A simple XML DocumentHandler that processes SAX2 events
to create a sensibly formatted XML as it parsed
without populating objects with data.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/xml/SimpleXMLEmitter.html#SimpleXMLEmitter()">SimpleXMLEmitter()</a></span> - Constructor for class org.biojava.bio.program.xml.<a href="./org/biojava/bio/program/xml/SimpleXMLEmitter.html" title="class in org.biojava.bio.program.xml">SimpleXMLEmitter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/xml/SimpleXMLEmitter.html#SimpleXMLEmitter(boolean)">SimpleXMLEmitter(boolean)</a></span> - Constructor for class org.biojava.bio.program.xml.<a href="./org/biojava/bio/program/xml/SimpleXMLEmitter.html" title="class in org.biojava.bio.program.xml">SimpleXMLEmitter</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/dp/onehead/SingleDP.html" title="class in org.biojava.bio.dp.onehead"><span class="strong">SingleDP</span></a> - Class in <a href="./org/biojava/bio/dp/onehead/package-summary.html">org.biojava.bio.dp.onehead</a></dt>
<dd>
<div class="block">An implementation of DP that aligns a single sequence against a single model.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/onehead/SingleDP.html#SingleDP(org.biojava.bio.dp.MarkovModel)">SingleDP(MarkovModel)</a></span> - Constructor for class org.biojava.bio.dp.onehead.<a href="./org/biojava/bio/dp/onehead/SingleDP.html" title="class in org.biojava.bio.dp.onehead">SingleDP</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/dp/onehead/SingleDPMatrix.html" title="class in org.biojava.bio.dp.onehead"><span class="strong">SingleDPMatrix</span></a> - Class in <a href="./org/biojava/bio/dp/onehead/package-summary.html">org.biojava.bio.dp.onehead</a></dt>
<dd>
<div class="block">The dynamic programming matrix for a single sequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/onehead/SingleDPMatrix.html#SingleDPMatrix(org.biojava.bio.dp.DP, org.biojava.bio.symbol.SymbolList)">SingleDPMatrix(DP, SymbolList)</a></span> - Constructor for class org.biojava.bio.dp.onehead.<a href="./org/biojava/bio/dp/onehead/SingleDPMatrix.html" title="class in org.biojava.bio.dp.onehead">SingleDPMatrix</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/AbstractTrainer.html#singleSequenceIteration(org.biojava.bio.dp.ModelTrainer, org.biojava.bio.symbol.SymbolList)">singleSequenceIteration(ModelTrainer, SymbolList)</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/AbstractTrainer.html" title="class in org.biojava.bio.dp">AbstractTrainer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/BaumWelchSampler.html#singleSequenceIteration(org.biojava.bio.dp.ModelTrainer, org.biojava.bio.symbol.SymbolList)">singleSequenceIteration(ModelTrainer, SymbolList)</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/BaumWelchSampler.html" title="class in org.biojava.bio.dp">BaumWelchSampler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/BaumWelchSampler.html#singleSequenceIteration(org.biojava.bio.dp.ModelTrainer, org.biojava.bio.symbol.SymbolList, org.biojava.bio.dp.ScoreType)">singleSequenceIteration(ModelTrainer, SymbolList, ScoreType)</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/BaumWelchSampler.html" title="class in org.biojava.bio.dp">BaumWelchSampler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/BaumWelchTrainer.html#singleSequenceIteration(org.biojava.bio.dp.ModelTrainer, org.biojava.bio.symbol.SymbolList)">singleSequenceIteration(ModelTrainer, SymbolList)</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/BaumWelchTrainer.html" title="class in org.biojava.bio.dp">BaumWelchTrainer</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/symbol/SingletonAlphabet.html" title="class in org.biojava.bio.symbol"><span class="strong">SingletonAlphabet</span></a> - Class in <a href="./org/biojava/bio/symbol/package-summary.html">org.biojava.bio.symbol</a></dt>
<dd>
<div class="block">An alphabet that contains a single atomic symbol.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SingletonAlphabet.html#SingletonAlphabet(org.biojava.bio.symbol.AtomicSymbol)">SingletonAlphabet(AtomicSymbol)</a></span> - Constructor for class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SingletonAlphabet.html" title="class in org.biojava.bio.symbol">SingletonAlphabet</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/utils/SingletonList.html" title="class in org.biojava.utils"><span class="strong">SingletonList</span></a> - Class in <a href="./org/biojava/utils/package-summary.html">org.biojava.utils</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/SingletonList.html#SingletonList(java.lang.Object)">SingletonList(Object)</a></span> - Constructor for class org.biojava.utils.<a href="./org/biojava/utils/SingletonList.html" title="class in org.biojava.utils">SingletonList</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/structure/jama/SingularValueDecomposition.html" title="class in org.biojava.bio.structure.jama"><span class="strong">SingularValueDecomposition</span></a> - Class in <a href="./org/biojava/bio/structure/jama/package-summary.html">org.biojava.bio.structure.jama</a></dt>
<dd>
<div class="block">Singular Value Decomposition.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/jama/SingularValueDecomposition.html#SingularValueDecomposition(org.biojava.bio.structure.jama.Matrix)">SingularValueDecomposition(Matrix)</a></span> - Constructor for class org.biojava.bio.structure.jama.<a href="./org/biojava/bio/structure/jama/SingularValueDecomposition.html" title="class in org.biojava.bio.structure.jama">SingularValueDecomposition</a></dt>
<dd>
<div class="block">Construct the singular value decomposition.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/molbio/RestrictionEnzyme.html#site">site</a></span> - Variable in class org.biojava.bio.molbio.<a href="./org/biojava/bio/molbio/RestrictionEnzyme.html" title="class in org.biojava.bio.molbio">RestrictionEnzyme</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/molbio/RestrictionMapper.html#SITE_FEATURE_SOURCE">SITE_FEATURE_SOURCE</a></span> - Static variable in class org.biojava.bio.molbio.<a href="./org/biojava/bio/molbio/RestrictionMapper.html" title="class in org.biojava.bio.molbio">RestrictionMapper</a></dt>
<dd>
<div class="block"><code>SITE_FEATURE_SOURCE</code> the source <code>String</code>
used by <code>RestrictionMapper</code> when creating
restriction site <code>Feature</code>s.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/molbio/RestrictionMapper.html#SITE_FEATURE_TYPE">SITE_FEATURE_TYPE</a></span> - Static variable in class org.biojava.bio.molbio.<a href="./org/biojava/bio/molbio/RestrictionMapper.html" title="class in org.biojava.bio.molbio">RestrictionMapper</a></dt>
<dd>
<div class="block"><code>SITE_FEATURE_TYPE</code> the type <code>String</code>
used by <code>RestrictionMapper</code> when creating
restriction site <code>Feature</code>s.</div>
</dd>
<dt><a href="./org/biojava/bio/gui/sequence/SixFrameRenderer.html" title="class in org.biojava.bio.gui.sequence"><span class="strong">SixFrameRenderer</span></a> - Class in <a href="./org/biojava/bio/gui/sequence/package-summary.html">org.biojava.bio.gui.sequence</a></dt>
<dd>
<div class="block">Class that handles drawing in six frames for other
classes.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SixFrameRenderer.html#SixFrameRenderer()">SixFrameRenderer()</a></span> - Constructor for class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SixFrameRenderer.html" title="class in org.biojava.bio.gui.sequence">SixFrameRenderer</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/gui/sequence/SixFrameZiggyRenderer.html" title="class in org.biojava.bio.gui.sequence"><span class="strong">SixFrameZiggyRenderer</span></a> - Class in <a href="./org/biojava/bio/gui/sequence/package-summary.html">org.biojava.bio.gui.sequence</a></dt>
<dd>
<div class="block">A feature renderer that computes the data necessary to render
multi-exon transcripts without CDS data.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SixFrameZiggyRenderer.html#SixFrameZiggyRenderer(org.biojava.bio.gui.sequence.SixFrameRenderer)">SixFrameZiggyRenderer(SixFrameRenderer)</a></span> - Constructor for class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SixFrameZiggyRenderer.html" title="class in org.biojava.bio.gui.sequence">SixFrameZiggyRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/annodb/AnnotationDB.html#size()">size()</a></span> - Method in interface org.biojava.bio.annodb.<a href="./org/biojava/bio/annodb/AnnotationDB.html" title="interface in org.biojava.bio.annodb">AnnotationDB</a></dt>
<dd>
<div class="block">The number of Annotation instances in the DB.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/annodb/IndexedAnnotationDB.html#size()">size()</a></span> - Method in class org.biojava.bio.annodb.<a href="./org/biojava/bio/annodb/IndexedAnnotationDB.html" title="class in org.biojava.bio.annodb">IndexedAnnotationDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/annodb/LazyFilteredAnnotationDB.html#size()">size()</a></span> - Method in class org.biojava.bio.annodb.<a href="./org/biojava/bio/annodb/LazyFilteredAnnotationDB.html" title="class in org.biojava.bio.annodb">LazyFilteredAnnotationDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/annodb/LazySearchedAnnotationDB.html#size()">size()</a></span> - Method in class org.biojava.bio.annodb.<a href="./org/biojava/bio/annodb/LazySearchedAnnotationDB.html" title="class in org.biojava.bio.annodb">LazySearchedAnnotationDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/annodb/MergingAnnotationDB.html#size()">size()</a></span> - Method in class org.biojava.bio.annodb.<a href="./org/biojava/bio/annodb/MergingAnnotationDB.html" title="class in org.biojava.bio.annodb">MergingAnnotationDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/annodb/SimpleAnnotationDB.html#size()">size()</a></span> - Method in class org.biojava.bio.annodb.<a href="./org/biojava/bio/annodb/SimpleAnnotationDB.html" title="class in org.biojava.bio.annodb">SimpleAnnotationDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/BasicFeatureRenderer.html#SIZE">SIZE</a></span> - Static variable in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/BasicFeatureRenderer.html" title="class in org.biojava.bio.gui.sequence">BasicFeatureRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFEntrySet.html#size()">size()</a></span> - Method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFEntrySet.html" title="class in org.biojava.bio.program.gff">GFFEntrySet</a></dt>
<dd>
<div class="block">Return how many lines are in this set.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/OrthoPairSet.html#size()">size()</a></span> - Method in interface org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/OrthoPairSet.html" title="interface in org.biojava.bio.program.homologene">OrthoPairSet</a></dt>
<dd>
<div class="block">returns an iterator to the contents of the set.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/SimpleOrthoPairSet.html#size()">size()</a></span> - Method in class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/SimpleOrthoPairSet.html" title="class in org.biojava.bio.program.homologene">SimpleOrthoPairSet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Group.html#size()">size()</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Group.html" title="interface in org.biojava.bio.structure">Group</a></dt>
<dd>
<div class="block">getnumber of atoms.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/util/SequenceScalePanel.html#SIZE">SIZE</a></span> - Static variable in class org.biojava.bio.structure.gui.util.<a href="./org/biojava/bio/structure/gui/util/SequenceScalePanel.html" title="class in org.biojava.bio.structure.gui.util">SequenceScalePanel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/HetatomImpl.html#size()">size()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/HetatomImpl.html" title="class in org.biojava.bio.structure">HetatomImpl</a></dt>
<dd>
<div class="block">getnumber of atoms.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Structure.html#size()">size()</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Structure.html" title="interface in org.biojava.bio.structure">Structure</a></dt>
<dd>
<div class="block">return number of Chains in this Structure.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Structure.html#size(int)">size(int)</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Structure.html" title="interface in org.biojava.bio.structure">Structure</a></dt>
<dd>
<div class="block">return number of chains of model.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/StructureImpl.html#size()">size()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/StructureImpl.html" title="class in org.biojava.bio.structure">StructureImpl</a></dt>
<dd>
<div class="block">return number of chains , if NMR return number of chains of first model .</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/StructureImpl.html#size(int)">size(int)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/StructureImpl.html" title="class in org.biojava.bio.structure">StructureImpl</a></dt>
<dd>
<div class="block">return number of chains of model.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/FiniteAlphabet.html#size()">size()</a></span> - Method in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/FiniteAlphabet.html" title="interface in org.biojava.bio.symbol">FiniteAlphabet</a></dt>
<dd>
<div class="block">The number of symbols in the alphabet.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/IntegerAlphabet.SubIntegerAlphabet.html#size()">size()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/IntegerAlphabet.SubIntegerAlphabet.html" title="class in org.biojava.bio.symbol">IntegerAlphabet.SubIntegerAlphabet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleAlphabet.html#size()">size()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleAlphabet.html" title="class in org.biojava.bio.symbol">SimpleAlphabet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SingletonAlphabet.html#size()">size()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SingletonAlphabet.html" title="class in org.biojava.bio.symbol">SingletonAlphabet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SoftMaskedAlphabet.html#size()">size()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SoftMaskedAlphabet.html" title="class in org.biojava.bio.symbol">SoftMaskedAlphabet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/SparseVector.html#size()">size()</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/SparseVector.html" title="class in org.biojava.stats.svm">SparseVector</a></dt>
<dd>
<div class="block">The number of used dimensions.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/SVMRegressionModel.html#size()">size()</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/SVMRegressionModel.html" title="class in org.biojava.stats.svm">SVMRegressionModel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/BeanAsMap.html#size()">size()</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/BeanAsMap.html" title="class in org.biojava.utils">BeanAsMap</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/FileAsList.html#size()">size()</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/FileAsList.html" title="class in org.biojava.utils">FileAsList</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ListTools.Doublet.html#size()">size()</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/ListTools.Doublet.html" title="class in org.biojava.utils">ListTools.Doublet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ListTools.SeriesList.html#size()">size()</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/ListTools.SeriesList.html" title="class in org.biojava.utils">ListTools.SeriesList</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ListTools.Triplet.html#size()">size()</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/ListTools.Triplet.html" title="class in org.biojava.utils">ListTools.Triplet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/MergingSet.html#size()">size()</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/MergingSet.html" title="class in org.biojava.utils">MergingSet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/SingletonList.html#size()">size()</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/SingletonList.html" title="class in org.biojava.utils">SingletonList</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/SmallMap.html#size()">size()</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/SmallMap.html" title="class in org.biojava.utils">SmallMap</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/SmallSet.html#size()">size()</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/SmallSet.html" title="class in org.biojava.utils">SmallSet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/CompoundRichLocation.html#size">size</a></span> - Variable in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/CompoundRichLocation.html" title="class in org.biojavax.bio.seq">CompoundRichLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/impl/SimplePopulation.html#size()">size()</a></span> - Method in class org.biojavax.ga.impl.<a href="./org/biojavax/ga/impl/SimplePopulation.html" title="class in org.biojavax.ga.impl">SimplePopulation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/Population.html#size()">size()</a></span> - Method in interface org.biojavax.ga.<a href="./org/biojavax/ga/Population.html" title="interface in org.biojavax.ga">Population</a></dt>
<dd>
<div class="block">Gets the Size of the population</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ga/util/WeightedSet.html#size()">size()</a></span> - Method in class org.biojavax.ga.util.<a href="./org/biojavax/ga/util/WeightedSet.html" title="class in org.biojavax.ga.util">WeightedSet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/EmblLikeFormat.html#SIZE_TAG">SIZE_TAG</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/EmblLikeFormat.html" title="class in org.biojava.bio.seq.io">EmblLikeFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/GenbankFormat.html#SIZE_TAG">SIZE_TAG</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/GenbankFormat.html" title="class in org.biojava.bio.seq.io">GenbankFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/DASSequence.html#SIZE_THRESHOLD">SIZE_THRESHOLD</a></span> - Static variable in class org.biojava.bio.program.das.<a href="./org/biojava/bio/program/das/DASSequence.html" title="class in org.biojava.bio.program.das">DASSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Calc.html#skalarProduct(org.biojava.bio.structure.Atom, org.biojava.bio.structure.Atom)">skalarProduct(Atom, Atom)</a></span> - Static method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Calc.html" title="class in org.biojava.bio.structure">Calc</a></dt>
<dd>
<div class="block">skalar product.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/io/CachingInputStream.html#skip(long)">skip(long)</a></span> - Method in class org.biojava.utils.io.<a href="./org/biojava/utils/io/CachingInputStream.html" title="class in org.biojava.utils.io">CachingInputStream</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/io/CountedBufferedReader.html#skip(long)">skip(long)</a></span> - Method in class org.biojava.utils.io.<a href="./org/biojava/utils/io/CountedBufferedReader.html" title="class in org.biojava.utils.io">CountedBufferedReader</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/io/UncompressInputStream.html#skip(long)">skip(long)</a></span> - Method in class org.biojava.utils.io.<a href="./org/biojava/utils/io/UncompressInputStream.html" title="class in org.biojava.utils.io">UncompressInputStream</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFErrorHandler.html#SKIP_RECORD">SKIP_RECORD</a></span> - Static variable in interface org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFErrorHandler.html" title="interface in org.biojava.bio.program.gff">GFFErrorHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/SeqSimilarityAdapter.html#skippedEntity(java.lang.String)">skippedEntity(String)</a></span> - Method in class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/SeqSimilarityAdapter.html" title="class in org.biojava.bio.program.ssbind">SeqSimilarityAdapter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/SAX2StAXAdaptor.html#skippedEntity(java.lang.String)">skippedEntity(String)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/SAX2StAXAdaptor.html" title="class in org.biojava.bio.seq.io.agave">SAX2StAXAdaptor</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/StAXContentHandler.html#skippedEntity(java.lang.String)">skippedEntity(String)</a></span> - Method in interface org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/StAXContentHandler.html" title="interface in org.biojava.bio.seq.io.agave">StAXContentHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/StAXContentHandlerBase.html#skippedEntity(java.lang.String)">skippedEntity(String)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/StAXContentHandlerBase.html" title="class in org.biojava.bio.seq.io.agave">StAXContentHandlerBase</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/stax/SAX2StAXAdaptor.html#skippedEntity(java.lang.String)">skippedEntity(String)</a></span> - Method in class org.biojava.utils.stax.<a href="./org/biojava/utils/stax/SAX2StAXAdaptor.html" title="class in org.biojava.utils.stax">SAX2StAXAdaptor</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/stax/StAXContentHandler.html#skippedEntity(java.lang.String)">skippedEntity(String)</a></span> - Method in interface org.biojava.utils.stax.<a href="./org/biojava/utils/stax/StAXContentHandler.html" title="interface in org.biojava.utils.stax">StAXContentHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/stax/StAXContentHandlerBase.html#skippedEntity(java.lang.String)">skippedEntity(String)</a></span> - Method in class org.biojava.utils.stax.<a href="./org/biojava/utils/stax/StAXContentHandlerBase.html" title="class in org.biojava.utils.stax">StAXContentHandlerBase</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/process/ExternalProcess.html#SLEEP_TIME">SLEEP_TIME</a></span> - Static variable in class org.biojava.utils.process.<a href="./org/biojava/utils/process/ExternalProcess.html" title="class in org.biojava.utils.process">ExternalProcess</a></dt>
<dd>
<div class="block">Number of milliseconds the execute method should pauses after the
external process has finished the execution.</div>
</dd>
<dt><a href="./org/biojava/bio/SmallAnnotation.html" title="class in org.biojava.bio"><span class="strong">SmallAnnotation</span></a> - Class in <a href="./org/biojava/bio/package-summary.html">org.biojava.bio</a></dt>
<dd>
<div class="block">Annotation that is optimized for memory usage.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/SmallAnnotation.html#SmallAnnotation()">SmallAnnotation()</a></span> - Constructor for class org.biojava.bio.<a href="./org/biojava/bio/SmallAnnotation.html" title="class in org.biojava.bio">SmallAnnotation</a></dt>
<dd>
<div class="block">Return a new SmallAnnotation optimised for small sets of properties.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/SmallAnnotation.html#SmallAnnotation(org.biojava.bio.Annotation)">SmallAnnotation(Annotation)</a></span> - Constructor for class org.biojava.bio.<a href="./org/biojava/bio/SmallAnnotation.html" title="class in org.biojava.bio">SmallAnnotation</a></dt>
<dd>
<div class="block">Return a new SmallAnnotation that copies all values from another annoation.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/SmallAnnotation.html#SmallAnnotation(java.util.Map)">SmallAnnotation(Map)</a></span> - Constructor for class org.biojava.bio.<a href="./org/biojava/bio/SmallAnnotation.html" title="class in org.biojava.bio">SmallAnnotation</a></dt>
<dd>
<div class="block">Return a new SmallAnnotation that copies all values from a Map.</div>
</dd>
<dt><a href="./org/biojava/bio/dp/onehead/SmallCursor.html" title="class in org.biojava.bio.dp.onehead"><span class="strong">SmallCursor</span></a> - Class in <a href="./org/biojava/bio/dp/onehead/package-summary.html">org.biojava.bio.dp.onehead</a></dt>
<dd>
<div class="block">Constant-memory implementation of single-head DP cursor.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/onehead/SmallCursor.html#SmallCursor(org.biojava.bio.dp.State[], org.biojava.bio.symbol.SymbolList, java.util.Iterator)">SmallCursor(State[], SymbolList, Iterator)</a></span> - Constructor for class org.biojava.bio.dp.onehead.<a href="./org/biojava/bio/dp/onehead/SmallCursor.html" title="class in org.biojava.bio.dp.onehead">SmallCursor</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/utils/SmallMap.html" title="class in org.biojava.utils"><span class="strong">SmallMap</span></a> - Class in <a href="./org/biojava/utils/package-summary.html">org.biojava.utils</a></dt>
<dd>
<div class="block">Lightweight implementation of Map which uses little memory to store a
small number of mappings, at the expense of scalability.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/SmallMap.html#SmallMap()">SmallMap()</a></span> - Constructor for class org.biojava.utils.<a href="./org/biojava/utils/SmallMap.html" title="class in org.biojava.utils">SmallMap</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/SmallMap.html#SmallMap(int)">SmallMap(int)</a></span> - Constructor for class org.biojava.utils.<a href="./org/biojava/utils/SmallMap.html" title="class in org.biojava.utils">SmallMap</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/SmallMap.html#SmallMap(java.util.Map)">SmallMap(Map)</a></span> - Constructor for class org.biojava.utils.<a href="./org/biojava/utils/SmallMap.html" title="class in org.biojava.utils">SmallMap</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/utils/SmallSet.html" title="class in org.biojava.utils"><span class="strong">SmallSet</span></a> - Class in <a href="./org/biojava/utils/package-summary.html">org.biojava.utils</a></dt>
<dd>
<div class="block">Lightweight implementation of Set which uses little memory to store a small
number of items, at the expense of scalability.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/SmallSet.html#SmallSet()">SmallSet()</a></span> - Constructor for class org.biojava.utils.<a href="./org/biojava/utils/SmallSet.html" title="class in org.biojava.utils">SmallSet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/SmallSet.html#SmallSet(int)">SmallSet(int)</a></span> - Constructor for class org.biojava.utils.<a href="./org/biojava/utils/SmallSet.html" title="class in org.biojava.utils">SmallSet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/SmallSet.html#SmallSet(java.util.Collection)">SmallSet(Collection)</a></span> - Constructor for class org.biojava.utils.<a href="./org/biojava/utils/SmallSet.html" title="class in org.biojava.utils">SmallSet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/BiojavaJmol.html#smartAdapter">smartAdapter</a></span> - Static variable in class org.biojava.bio.structure.gui.<a href="./org/biojava/bio/structure/gui/BiojavaJmol.html" title="class in org.biojava.bio.structure.gui">BiojavaJmol</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/io/SmartSequenceBuilder.html" title="class in org.biojava.bio.seq.io"><span class="strong">SmartSequenceBuilder</span></a> - Class in <a href="./org/biojava/bio/seq/io/package-summary.html">org.biojava.bio.seq.io</a></dt>
<dd>
<div class="block">Basic SequenceBuilder implementation which accumulates all
notified information and chooses a sequence implementation
suited to the size of the sequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/twohead/AbstractMatrixPairDPCursor.html#sMatrix">sMatrix</a></span> - Variable in class org.biojava.bio.dp.twohead.<a href="./org/biojava/bio/dp/twohead/AbstractMatrixPairDPCursor.html" title="class in org.biojava.bio.dp.twohead">AbstractMatrixPairDPCursor</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/alignment/SmithWaterman.html" title="class in org.biojava.bio.alignment"><span class="strong">SmithWaterman</span></a> - Class in <a href="./org/biojava/bio/alignment/package-summary.html">org.biojava.bio.alignment</a></dt>
<dd>
<div class="block">Smith and Waterman developed an efficient dynamic programming algorithm to
perform local sequence alignments, which returns the most conserved region of
two sequences (longest common substring with modifications).</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/SmithWaterman.html#SmithWaterman(short, short, short, short, short, org.biojava.bio.alignment.SubstitutionMatrix)">SmithWaterman(short, short, short, short, short, SubstitutionMatrix)</a></span> - Constructor for class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/SmithWaterman.html" title="class in org.biojava.bio.alignment">SmithWaterman</a></dt>
<dd>
<div class="block">Constructs the new SmithWaterman alignment object.</div>
</dd>
<dt><a href="./org/biojava/stats/svm/SMORegressionTrainer.html" title="class in org.biojava.stats.svm"><span class="strong">SMORegressionTrainer</span></a> - Class in <a href="./org/biojava/stats/svm/package-summary.html">org.biojava.stats.svm</a></dt>
<dd>
<div class="block">Train a regression support vector machine using the Sequential Minimal
Optimization algorithm.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/SMORegressionTrainer.html#SMORegressionTrainer()">SMORegressionTrainer()</a></span> - Constructor for class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/SMORegressionTrainer.html" title="class in org.biojava.stats.svm">SMORegressionTrainer</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/stats/svm/SMOTrainer.html" title="class in org.biojava.stats.svm"><span class="strong">SMOTrainer</span></a> - Class in <a href="./org/biojava/stats/svm/package-summary.html">org.biojava.stats.svm</a></dt>
<dd>
<div class="block">Train a support vector machine using the Sequential Minimal
Optimization algorithm.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/SMOTrainer.html#SMOTrainer()">SMOTrainer()</a></span> - Constructor for class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/SMOTrainer.html" title="class in org.biojava.stats.svm">SMOTrainer</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/symbol/SoftMaskedAlphabet.html" title="class in org.biojava.bio.symbol"><span class="strong">SoftMaskedAlphabet</span></a> - Class in <a href="./org/biojava/bio/symbol/package-summary.html">org.biojava.bio.symbol</a></dt>
<dd>
<div class="block">Soft masking is usually displayed by making the masked regions somehow
different from the non masked regions.</div>
</dd>
<dt><a href="./org/biojava/bio/symbol/SoftMaskedAlphabet.CaseSensitiveTokenization.html" title="class in org.biojava.bio.symbol"><span class="strong">SoftMaskedAlphabet.CaseSensitiveTokenization</span></a> - Class in <a href="./org/biojava/bio/symbol/package-summary.html">org.biojava.bio.symbol</a></dt>
<dd>
<div class="block">This <code>SymbolTokenizer</code> works with a delegate to softmask
symbol tokenization as appropriate.</div>
</dd>
<dt><a href="./org/biojava/bio/symbol/SoftMaskedAlphabet.MaskingDetector.html" title="interface in org.biojava.bio.symbol"><span class="strong">SoftMaskedAlphabet.MaskingDetector</span></a> - Interface in <a href="./org/biojava/bio/symbol/package-summary.html">org.biojava.bio.symbol</a></dt>
<dd>
<div class="block">Implementations will define how soft masking looks.</div>
</dd>
<dt><a href="./org/biojava/bio/symbol/SoftMaskedAlphabet.MaskingDetector.DefaultMaskingDetector.html" title="class in org.biojava.bio.symbol"><span class="strong">SoftMaskedAlphabet.MaskingDetector.DefaultMaskingDetector</span></a> - Class in <a href="./org/biojava/bio/symbol/package-summary.html">org.biojava.bio.symbol</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SoftMaskedAlphabet.MaskingDetector.DefaultMaskingDetector.html#SoftMaskedAlphabet.MaskingDetector.DefaultMaskingDetector()">SoftMaskedAlphabet.MaskingDetector.DefaultMaskingDetector()</a></span> - Constructor for class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SoftMaskedAlphabet.MaskingDetector.DefaultMaskingDetector.html" title="class in org.biojava.bio.symbol">SoftMaskedAlphabet.MaskingDetector.DefaultMaskingDetector</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/utils/cache/SoftReferenceCache.html" title="class in org.biojava.utils.cache"><span class="strong">SoftReferenceCache</span></a> - Class in <a href="./org/biojava/utils/cache/package-summary.html">org.biojava.utils.cache</a></dt>
<dd>
<div class="block">Cache which is cleared according to memory pressure.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/cache/SoftReferenceCache.html#SoftReferenceCache()">SoftReferenceCache()</a></span> - Constructor for class org.biojava.utils.cache.<a href="./org/biojava/utils/cache/SoftReferenceCache.html" title="class in org.biojava.utils.cache">SoftReferenceCache</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/fastq/SolexaFastqReader.html" title="class in org.biojava.bio.program.fastq"><span class="strong">SolexaFastqReader</span></a> - Class in <a href="./org/biojava/bio/program/fastq/package-summary.html">org.biojava.bio.program.fastq</a></dt>
<dd>
<div class="block">Reader for <a href="./org/biojava/bio/program/fastq/FastqVariant.html#FASTQ_SOLEXA"><code>FastqVariant.FASTQ_SOLEXA</code></a> formatted sequences.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/fastq/SolexaFastqReader.html#SolexaFastqReader()">SolexaFastqReader()</a></span> - Constructor for class org.biojava.bio.program.fastq.<a href="./org/biojava/bio/program/fastq/SolexaFastqReader.html" title="class in org.biojava.bio.program.fastq">SolexaFastqReader</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/fastq/SolexaFastqWriter.html" title="class in org.biojava.bio.program.fastq"><span class="strong">SolexaFastqWriter</span></a> - Class in <a href="./org/biojava/bio/program/fastq/package-summary.html">org.biojava.bio.program.fastq</a></dt>
<dd>
<div class="block">Writer for <a href="./org/biojava/bio/program/fastq/FastqVariant.html#FASTQ_SOLEXA"><code>FastqVariant.FASTQ_SOLEXA</code></a> formatted sequences.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/fastq/SolexaFastqWriter.html#SolexaFastqWriter()">SolexaFastqWriter()</a></span> - Constructor for class org.biojava.bio.program.fastq.<a href="./org/biojava/bio/program/fastq/SolexaFastqWriter.html" title="class in org.biojava.bio.program.fastq">SolexaFastqWriter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/jama/CholeskyDecomposition.html#solve(org.biojava.bio.structure.jama.Matrix)">solve(Matrix)</a></span> - Method in class org.biojava.bio.structure.jama.<a href="./org/biojava/bio/structure/jama/CholeskyDecomposition.html" title="class in org.biojava.bio.structure.jama">CholeskyDecomposition</a></dt>
<dd>
<div class="block">Solve A*X = B</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/jama/LUDecomposition.html#solve(org.biojava.bio.structure.jama.Matrix)">solve(Matrix)</a></span> - Method in class org.biojava.bio.structure.jama.<a href="./org/biojava/bio/structure/jama/LUDecomposition.html" title="class in org.biojava.bio.structure.jama">LUDecomposition</a></dt>
<dd>
<div class="block">Solve A*X = B</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/jama/Matrix.html#solve(org.biojava.bio.structure.jama.Matrix)">solve(Matrix)</a></span> - Method in class org.biojava.bio.structure.jama.<a href="./org/biojava/bio/structure/jama/Matrix.html" title="class in org.biojava.bio.structure.jama">Matrix</a></dt>
<dd>
<div class="block">Solve A*X = B</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/jama/QRDecomposition.html#solve(org.biojava.bio.structure.jama.Matrix)">solve(Matrix)</a></span> - Method in class org.biojava.bio.structure.jama.<a href="./org/biojava/bio/structure/jama/QRDecomposition.html" title="class in org.biojava.bio.structure.jama">QRDecomposition</a></dt>
<dd>
<div class="block">Least squares solution of A*X = B</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/math/BinarySearch.html#solve(double, double, double, org.biojava.utils.math.ComputeObject)">solve(double, double, double, ComputeObject)</a></span> - Static method in class org.biojava.utils.math.<a href="./org/biojava/utils/math/BinarySearch.html" title="class in org.biojava.utils.math">BinarySearch</a></dt>
<dd>
<div class="block">method that will attempt solving the equation.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/jama/Matrix.html#solveTranspose(org.biojava.bio.structure.jama.Matrix)">solveTranspose(Matrix)</a></span> - Method in class org.biojava.bio.structure.jama.<a href="./org/biojava/bio/structure/jama/Matrix.html" title="class in org.biojava.bio.structure.jama">Matrix</a></dt>
<dd>
<div class="block">Solve X*A = B, which is also A'*X' = B'</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BibRefQuery.html#sort(java.lang.String[], java.util.Hashtable)">sort(String[], Hashtable)</a></span> - Method in interface org.biojava.bibliography.<a href="./org/biojava/bibliography/BibRefQuery.html" title="interface in org.biojava.bibliography">BibRefQuery</a></dt>
<dd>
<div class="block">
It sorts the current collection and returns another collection which is
a sorted copy of the current collection.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/CompoundRichLocation.html#sort()">sort()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/CompoundRichLocation.html" title="class in org.biojavax.bio.seq">CompoundRichLocation</a></dt>
<dd>
<div class="block">Sorts the member locations of a compound location.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/EmptyRichLocation.html#sort()">sort()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/EmptyRichLocation.html" title="class in org.biojavax.bio.seq">EmptyRichLocation</a></dt>
<dd>
<div class="block">Sorts the member locations of a compound location.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichLocation.html#sort()">sort()</a></span> - Method in interface org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichLocation.html" title="interface in org.biojavax.bio.seq">RichLocation</a></dt>
<dd>
<div class="block">Sorts the member locations of a compound location.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichLocation.html#sort()">sort()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichLocation.html" title="class in org.biojavax.bio.seq">SimpleRichLocation</a></dt>
<dd>
<div class="block">Sorts the member locations of a compound location.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BiblioCriterion.html#SORT_CRITERION">SORT_CRITERION</a></span> - Static variable in class org.biojava.bibliography.<a href="./org/biojava/bibliography/BiblioCriterion.html" title="class in org.biojava.bibliography">BiblioCriterion</a></dt>
<dd>
<div class="block">A sort criterion.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/AbstractPeptideDigestRenderer.html#sortPeptidesIntoLanes()">sortPeptidesIntoLanes()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/AbstractPeptideDigestRenderer.html" title="class in org.biojava.bio.gui.sequence">AbstractPeptideDigestRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/Feature.html#SOURCE">SOURCE</a></span> - Static variable in interface org.biojava.bio.seq.<a href="./org/biojava/bio/seq/Feature.html" title="interface in org.biojava.bio.seq">Feature</a></dt>
<dd>
<div class="block">The source of this feature has altered</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/Feature.Template.html#source">source</a></span> - Variable in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/Feature.Template.html" title="class in org.biojava.bio.seq">Feature.Template</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/EmblLikeFormat.html#SOURCE_TAG">SOURCE_TAG</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/EmblLikeFormat.html" title="class in org.biojava.bio.seq.io">EmblLikeFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/GenbankFormat.html#SOURCE_TAG">SOURCE_TAG</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/GenbankFormat.html" title="class in org.biojava.bio.seq.io">GenbankFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLFormat.html#SOURCE_TAG">SOURCE_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLFormat.html" title="class in org.biojavax.bio.seq.io">EMBLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/GenbankFormat.html#SOURCE_TAG">SOURCE_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/GenbankFormat.html" title="class in org.biojavax.bio.seq.io">GenbankFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/INSDseqFormat.html#SOURCE_TAG">SOURCE_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/INSDseqFormat.html" title="class in org.biojavax.bio.seq.io">INSDseqFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtFormat.html#SOURCE_TAG">SOURCE_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtFormat.html" title="class in org.biojavax.bio.seq.io">UniProtFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleGappedSymbolList.Block.html#sourceEnd">sourceEnd</a></span> - Variable in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleGappedSymbolList.Block.html" title="class in org.biojava.bio.symbol">SimpleGappedSymbolList.Block</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleGappedSymbolList.Block.html#sourceStart">sourceStart</a></span> - Variable in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleGappedSymbolList.Block.html" title="class in org.biojava.bio.symbol">SimpleGappedSymbolList.Block</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/Feature.html#SOURCETERM">SOURCETERM</a></span> - Static variable in interface org.biojava.bio.seq.<a href="./org/biojava/bio/seq/Feature.html" title="interface in org.biojava.bio.seq">Feature</a></dt>
<dd>
<div class="block">The ontological source of this feature has altered</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/Feature.Template.html#sourceTerm">sourceTerm</a></span> - Variable in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/Feature.Template.html" title="class in org.biojava.bio.seq">Feature.Template</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichFeature.html#SOURCETERM">SOURCETERM</a></span> - Static variable in interface org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichFeature.html" title="interface in org.biojavax.bio.seq">RichFeature</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/GappedSymbolList.html#sourceToView(int)">sourceToView(int)</a></span> - Method in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/GappedSymbolList.html" title="interface in org.biojava.bio.symbol">GappedSymbolList</a></dt>
<dd>
<div class="block">Coordinate conversion from source to view.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleGappedSymbolList.html#sourceToView(org.biojava.bio.symbol.SimpleGappedSymbolList.Block, int)">sourceToView(SimpleGappedSymbolList.Block, int)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleGappedSymbolList.html" title="class in org.biojava.bio.symbol">SimpleGappedSymbolList</a></dt>
<dd>
<div class="block">Coordinate conversion from source to view.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleGappedSymbolList.html#sourceToView(int)">sourceToView(int)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleGappedSymbolList.html" title="class in org.biojava.bio.symbol">SimpleGappedSymbolList</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/stats/svm/SparseVector.html" title="class in org.biojava.stats.svm"><span class="strong">SparseVector</span></a> - Class in <a href="./org/biojava/stats/svm/package-summary.html">org.biojava.stats.svm</a></dt>
<dd>
<div class="block">An implementation of a sparse vector.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/SparseVector.html#SparseVector()">SparseVector()</a></span> - Constructor for class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/SparseVector.html" title="class in org.biojava.stats.svm">SparseVector</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/SparseVector.html#SparseVector(int)">SparseVector(int)</a></span> - Constructor for class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/SparseVector.html" title="class in org.biojava.stats.svm">SparseVector</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/stats/svm/SparseVector.NormalizingKernel.html" title="class in org.biojava.stats.svm"><span class="strong">SparseVector.NormalizingKernel</span></a> - Class in <a href="./org/biojava/stats/svm/package-summary.html">org.biojava.stats.svm</a></dt>
<dd>
<div class="block">A version of the standard dot-product kernel that scales each column
independently.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/SparseVector.NormalizingKernel.html#SparseVector.NormalizingKernel(org.biojava.stats.svm.SparseVector)">SparseVector.NormalizingKernel(SparseVector)</a></span> - Constructor for class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/SparseVector.NormalizingKernel.html" title="class in org.biojava.stats.svm">SparseVector.NormalizingKernel</a></dt>
<dd>
<div class="block">Generate a normalizing kernel with the normalizing vector s.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/SparseVector.NormalizingKernel.html#SparseVector.NormalizingKernel(java.util.List)">SparseVector.NormalizingKernel(List)</a></span> - Constructor for class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/SparseVector.NormalizingKernel.html" title="class in org.biojava.stats.svm">SparseVector.NormalizingKernel</a></dt>
<dd>
<div class="block">Generate a normalizing kernel defined by the SparseVectors in vectors.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BiblioScope.html#spatialLocation">spatialLocation</a></span> - Variable in class org.biojava.bibliography.<a href="./org/biojava/bibliography/BiblioScope.html" title="class in org.biojava.bibliography">BiblioScope</a></dt>
<dd>
<div class="block">
It defines a spatial location of the cited resource.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.Terms.html#SPECIES_KEY">SPECIES_KEY</a></span> - Static variable in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.Terms.html" title="class in org.biojavax.bio.seq">RichSequence.Terms</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/ChangeTable.Splitter.html#split(java.lang.Object)">split(Object)</a></span> - Method in interface org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/ChangeTable.Splitter.html" title="interface in org.biojava.bio.program.tagvalue">ChangeTable.Splitter</a></dt>
<dd>
<div class="block">
Produce a list of values from an old value.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/RegexSplitter.html#split(java.lang.Object)">split(Object)</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/RegexSplitter.html" title="class in org.biojava.bio.program.tagvalue">RegexSplitter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/WordTokenization.html#splitString(java.lang.String)">splitString(String)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/WordTokenization.html" title="class in org.biojava.bio.seq.io">WordTokenization</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/unigene/SQLUnigeneFactory.html" title="class in org.biojava.bio.program.unigene"><span class="strong">SQLUnigeneFactory</span></a> - Class in <a href="./org/biojava/bio/program/unigene/package-summary.html">org.biojava.bio.program.unigene</a></dt>
<dd>
<div class="block">An implementatoin of UnigeneFactory that manages it's data in an SQL
database.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/unigene/SQLUnigeneFactory.html#SQLUnigeneFactory()">SQLUnigeneFactory()</a></span> - Constructor for class org.biojava.bio.program.unigene.<a href="./org/biojava/bio/program/unigene/SQLUnigeneFactory.html" title="class in org.biojava.bio.program.unigene">SQLUnigeneFactory</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/structure/SSBond.html" title="class in org.biojava.bio.structure"><span class="strong">SSBond</span></a> - Class in <a href="./org/biojava/bio/structure/package-summary.html">org.biojava.bio.structure</a></dt>
<dd>
<div class="block">A simple bean to store disulfid bridge information, the SSBOND records in the PDB files.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/SSBond.html#SSBond()">SSBond()</a></span> - Constructor for class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/SSBond.html" title="class in org.biojava.bio.structure">SSBond</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/SeqSimilarityStAXHandler.html#ssContext">ssContext</a></span> - Variable in class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/SeqSimilarityStAXHandler.html" title="class in org.biojava.bio.program.ssbind">SeqSimilarityStAXHandler</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/gui/sequence/StackedFeatureRenderer.html" title="class in org.biojava.bio.gui.sequence"><span class="strong">StackedFeatureRenderer</span></a> - Class in <a href="./org/biojava/bio/gui/sequence/package-summary.html">org.biojava.bio.gui.sequence</a></dt>
<dd>
<div class="block">Allows you to stack multiple feature renderers up (for example a label renderer and
a beaded renderer) and have them treated as a single renderer for layout.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/StackedFeatureRenderer.html#StackedFeatureRenderer()">StackedFeatureRenderer()</a></span> - Constructor for class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/StackedFeatureRenderer.html" title="class in org.biojava.bio.gui.sequence">StackedFeatureRenderer</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/gui/StackedLogoPainter.html" title="class in org.biojava.bio.gui"><span class="strong">StackedLogoPainter</span></a> - Class in <a href="./org/biojava/bio/gui/package-summary.html">org.biojava.bio.gui</a></dt>
<dd>
<div class="block">A logo painter that paints in stacked areas.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/StackedLogoPainter.html#StackedLogoPainter()">StackedLogoPainter()</a></span> - Constructor for class org.biojava.bio.gui.<a href="./org/biojava/bio/gui/StackedLogoPainter.html" title="class in org.biojava.bio.gui">StackedLogoPainter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/StAXFeatureHandler.html#stackLevel">stackLevel</a></span> - Variable in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/StAXFeatureHandler.html" title="class in org.biojava.bio.seq.io.agave">StAXFeatureHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game/StAXFeatureHandler.html#stackLevel">stackLevel</a></span> - Variable in class org.biojava.bio.seq.io.game.<a href="./org/biojava/bio/seq/io/game/StAXFeatureHandler.html" title="class in org.biojava.bio.seq.io.game">StAXFeatureHandler</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/structure/StandardAminoAcid.html" title="class in org.biojava.bio.structure"><span class="strong">StandardAminoAcid</span></a> - Class in <a href="./org/biojava/bio/structure/package-summary.html">org.biojava.bio.structure</a></dt>
<dd>
<div class="block">A class that provides a set of standard amino acids.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/StandardAminoAcid.html#StandardAminoAcid()">StandardAminoAcid()</a></span> - Constructor for class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/StandardAminoAcid.html" title="class in org.biojava.bio.structure">StandardAminoAcid</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ga/util/GATools.html#standardMutationDistribution(org.biojava.bio.symbol.FiniteAlphabet)">standardMutationDistribution(FiniteAlphabet)</a></span> - Static method in class org.biojavax.ga.util.<a href="./org/biojavax/ga/util/GATools.html" title="class in org.biojavax.ga.util">GATools</a></dt>
<dd>
<div class="block">Makes a mutation <code>Distribution</code> where the probability
of a <code>Symbol</code> being mutated to itself is zero and the
probability of it being changed to any other <code>Symbol</code> in
the <code>Alphabet a</code> is <code>1.0 / (a.size() - 1.0)</code></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/BioMatcher.html#start()">start()</a></span> - Method in interface org.biojava.bio.search.<a href="./org/biojava/bio/search/BioMatcher.html" title="interface in org.biojava.bio.search">BioMatcher</a></dt>
<dd>
<div class="block">Get the first symbol index that matches the pattern.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/MaxMismatchMatcher.html#start()">start()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/MaxMismatchMatcher.html" title="class in org.biojava.bio.search">MaxMismatchMatcher</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/automata/FiniteAutomaton.html#start">start</a></span> - Variable in class org.biojava.utils.automata.<a href="./org/biojava/utils/automata/FiniteAutomaton.html" title="class in org.biojava.utils.automata">FiniteAutomaton</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/regex/Matcher.html#start()">start()</a></span> - Method in class org.biojava.utils.regex.<a href="./org/biojava/utils/regex/Matcher.html" title="class in org.biojava.utils.regex">Matcher</a></dt>
<dd>
<div class="block">Returns the start index of the previous match.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/regex/Matcher.html#start(int)">start(int)</a></span> - Method in class org.biojava.utils.regex.<a href="./org/biojava/utils/regex/Matcher.html" title="class in org.biojava.utils.regex">Matcher</a></dt>
<dd>
<div class="block">Returns the start index of the subsequence captured by the given group during the previous match operation.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/xml/AppEntry.html#start(java.lang.String[])">start(String[])</a></span> - Method in interface org.biojava.utils.xml.<a href="./org/biojava/utils/xml/AppEntry.html" title="interface in org.biojava.utils.xml">AppEntry</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/StateMachine.html#START_RECORD_TAG">START_RECORD_TAG</a></span> - Static variable in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/StateMachine.html" title="class in org.biojava.bio.program.tagvalue">StateMachine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/EmblLikeFormat.html#START_SEQUENCE_TAG">START_SEQUENCE_TAG</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/EmblLikeFormat.html" title="class in org.biojava.bio.seq.io">EmblLikeFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/GenbankFormat.html#START_SEQUENCE_TAG">START_SEQUENCE_TAG</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/GenbankFormat.html" title="class in org.biojava.bio.seq.io">GenbankFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLFormat.html#START_SEQUENCE_TAG">START_SEQUENCE_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLFormat.html" title="class in org.biojavax.bio.seq.io">EMBLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/GenbankFormat.html#START_SEQUENCE_TAG">START_SEQUENCE_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/GenbankFormat.html" title="class in org.biojavax.bio.seq.io">GenbankFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtFormat.html#START_SEQUENCE_TAG">START_SEQUENCE_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtFormat.html" title="class in org.biojavax.bio.seq.io">UniProtFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/HMMTrainer.html#startCycle()">startCycle()</a></span> - Method in interface org.biojava.bio.dp.<a href="./org/biojava/bio/dp/HMMTrainer.html" title="interface in org.biojava.bio.dp">HMMTrainer</a></dt>
<dd>
<div class="block">called to put the trainer into an initial state for a new
round of training.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/SimpleHMMTrainer.html#startCycle()">startCycle()</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/SimpleHMMTrainer.html" title="class in org.biojava.bio.dp">SimpleHMMTrainer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/HomologeneBuilder.html#startDB()">startDB()</a></span> - Method in interface org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/HomologeneBuilder.html" title="interface in org.biojava.bio.program.homologene">HomologeneBuilder</a></dt>
<dd>
<div class="block">indicates start of data for a HomologeneDB</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/SimpleHomologeneBuilder.html#startDB()">startDB()</a></span> - Method in class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/SimpleHomologeneBuilder.html" title="class in org.biojava.bio.program.homologene">SimpleHomologeneBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/dasalignment/DASAlignmentXMLResponseParser.html#startDocument()">startDocument()</a></span> - Method in class org.biojava.bio.program.das.dasalignment.<a href="./org/biojava/bio/program/das/dasalignment/DASAlignmentXMLResponseParser.html" title="class in org.biojava.bio.program.das.dasalignment">DASAlignmentXMLResponseParser</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/dasstructure/DASStructureXMLResponseParser.html#startDocument()">startDocument()</a></span> - Method in class org.biojava.bio.program.das.dasstructure.<a href="./org/biojava/bio/program/das/dasstructure/DASStructureXMLResponseParser.html" title="class in org.biojava.bio.program.das.dasstructure">DASStructureXMLResponseParser</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFDocumentHandler.html#startDocument(java.lang.String)">startDocument(String)</a></span> - Method in interface org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFDocumentHandler.html" title="interface in org.biojava.bio.program.gff">GFFDocumentHandler</a></dt>
<dd>
<div class="block">Indicates that a new GFF document has been started.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFFilterer.html#startDocument(java.lang.String)">startDocument(String)</a></span> - Method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFFilterer.html" title="class in org.biojava.bio.program.gff">GFFFilterer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFWriter.html#startDocument(java.lang.String)">startDocument(String)</a></span> - Method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFWriter.html" title="class in org.biojava.bio.program.gff">GFFWriter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff3/GFF3DocumentHandler.html#startDocument(java.lang.String)">startDocument(String)</a></span> - Method in interface org.biojava.bio.program.gff3.<a href="./org/biojava/bio/program/gff3/GFF3DocumentHandler.html" title="interface in org.biojava.bio.program.gff3">GFF3DocumentHandler</a></dt>
<dd>
<div class="block">Indicates that a new GFF document has been started.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/SeqSimilarityAdapter.html#startDocument()">startDocument()</a></span> - Method in class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/SeqSimilarityAdapter.html" title="class in org.biojava.bio.program.ssbind">SeqSimilarityAdapter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/SAX2StAXAdaptor.html#startDocument()">startDocument()</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/SAX2StAXAdaptor.html" title="class in org.biojava.bio.seq.io.agave">SAX2StAXAdaptor</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/stax/SAX2StAXAdaptor.html#startDocument()">startDocument()</a></span> - Method in class org.biojava.utils.stax.<a href="./org/biojava/utils/stax/SAX2StAXAdaptor.html" title="class in org.biojava.utils.stax">SAX2StAXAdaptor</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/DAS.html#startedActivity(java.lang.Object)">startedActivity(Object)</a></span> - Static method in class org.biojava.bio.program.das.<a href="./org/biojava/bio/program/das/DAS.html" title="class in org.biojava.bio.program.das">DAS</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ActivityListener.html#startedActivity(java.lang.Object)">startedActivity(Object)</a></span> - Method in interface org.biojava.utils.<a href="./org/biojava/utils/ActivityListener.html" title="interface in org.biojava.utils">ActivityListener</a></dt>
<dd>
<div class="block">Notification that an activity has started.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/XMLDistributionReader.html#startElement(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes)">startElement(String, String, String, Attributes)</a></span> - Method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/XMLDistributionReader.html" title="class in org.biojava.bio.dist">XMLDistributionReader</a></dt>
<dd>
<div class="block">Required by SAXParser to be public.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/blast2html/Blast2HTMLHandler.html#startElement(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes)">startElement(String, String, String, Attributes)</a></span> - Method in class org.biojava.bio.program.blast2html.<a href="./org/biojava/bio/program/blast2html/Blast2HTMLHandler.html" title="class in org.biojava.bio.program.blast2html">Blast2HTMLHandler</a></dt>
<dd>
<div class="block">This is called when an element is entered.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/dasalignment/DASAlignmentXMLResponseParser.html#startElement(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes)">startElement(String, String, String, Attributes)</a></span> - Method in class org.biojava.bio.program.das.dasalignment.<a href="./org/biojava/bio/program/das/dasalignment/DASAlignmentXMLResponseParser.html" title="class in org.biojava.bio.program.das.dasalignment">DASAlignmentXMLResponseParser</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/dasstructure/DASStructureXMLResponseParser.html#startElement(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes)">startElement(String, String, String, Attributes)</a></span> - Method in class org.biojava.bio.program.das.dasstructure.<a href="./org/biojava/bio/program/das/dasstructure/DASStructureXMLResponseParser.html" title="class in org.biojava.bio.program.das.dasstructure">DASStructureXMLResponseParser</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/sax/blastxml/BlastXMLParser.html#startElement(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes, org.biojava.utils.stax.DelegationManager)">startElement(String, String, String, Attributes, DelegationManager)</a></span> - Method in class org.biojava.bio.program.sax.blastxml.<a href="./org/biojava/bio/program/sax/blastxml/BlastXMLParser.html" title="class in org.biojava.bio.program.sax.blastxml">BlastXMLParser</a></dt>
<dd>
<div class="block">we override the superclass startElement method so we can determine the
the start tag type and use it to set up delegation for the superclass.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/SeqSimilarityAdapter.html#startElement(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes)">startElement(String, String, String, Attributes)</a></span> - Method in class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/SeqSimilarityAdapter.html" title="class in org.biojava.bio.program.ssbind">SeqSimilarityAdapter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/SeqSimilarityStAXAdapter.html#startElement(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes, org.biojava.utils.stax.DelegationManager)">startElement(String, String, String, Attributes, DelegationManager)</a></span> - Method in class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/SeqSimilarityStAXAdapter.html" title="class in org.biojava.bio.program.ssbind">SeqSimilarityStAXAdapter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/SeqSimilarityStAXHandler.html#startElement(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes, org.biojava.utils.stax.DelegationManager)">startElement(String, String, String, Attributes, DelegationManager)</a></span> - Method in class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/SeqSimilarityStAXHandler.html" title="class in org.biojava.bio.program.ssbind">SeqSimilarityStAXHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/xff/FeatureHandler.html#startElement(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes, org.biojava.utils.stax.DelegationManager)">startElement(String, String, String, Attributes, DelegationManager)</a></span> - Method in class org.biojava.bio.program.xff.<a href="./org/biojava/bio/program/xff/FeatureHandler.html" title="class in org.biojava.bio.program.xff">FeatureHandler</a></dt>
<dd>
<div class="block">StAX callback for element starts.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/xff/LocationHandlerBase.html#startElement(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes, org.biojava.utils.stax.DelegationManager)">startElement(String, String, String, Attributes, DelegationManager)</a></span> - Method in class org.biojava.bio.program.xff.<a href="./org/biojava/bio/program/xff/LocationHandlerBase.html" title="class in org.biojava.bio.program.xff">LocationHandlerBase</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/xff/PropDetailHandler.html#startElement(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes, org.biojava.utils.stax.DelegationManager)">startElement(String, String, String, Attributes, DelegationManager)</a></span> - Method in class org.biojava.bio.program.xff.<a href="./org/biojava/bio/program/xff/PropDetailHandler.html" title="class in org.biojava.bio.program.xff">PropDetailHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/xff/StrandedFeatureHandler.html#startElement(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes, org.biojava.utils.stax.DelegationManager)">startElement(String, String, String, Attributes, DelegationManager)</a></span> - Method in class org.biojava.bio.program.xff.<a href="./org/biojava/bio/program/xff/StrandedFeatureHandler.html" title="class in org.biojava.bio.program.xff">StrandedFeatureHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/xff/XFFFeatureSetHandler.html#startElement(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes, org.biojava.utils.stax.DelegationManager)">startElement(String, String, String, Attributes, DelegationManager)</a></span> - Method in class org.biojava.bio.program.xff.<a href="./org/biojava/bio/program/xff/XFFFeatureSetHandler.html" title="class in org.biojava.bio.program.xff">XFFFeatureSetHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/xml/BaseXMLWriter.html#startElement(java.lang.String)">startElement(String)</a></span> - Method in class org.biojava.bio.program.xml.<a href="./org/biojava/bio/program/xml/BaseXMLWriter.html" title="class in org.biojava.bio.program.xml">BaseXMLWriter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/xml/BaseXMLWriter.html#startElement(java.lang.String, org.xml.sax.Attributes)">startElement(String, Attributes)</a></span> - Method in class org.biojava.bio.program.xml.<a href="./org/biojava/bio/program/xml/BaseXMLWriter.html" title="class in org.biojava.bio.program.xml">BaseXMLWriter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/xml/SimpleXMLEmitter.html#startElement(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes)">startElement(String, String, String, Attributes)</a></span> - Method in class org.biojava.bio.program.xml.<a href="./org/biojava/bio/program/xml/SimpleXMLEmitter.html" title="class in org.biojava.bio.program.xml">SimpleXMLEmitter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/SAX2StAXAdaptor.html#startElement(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes)">startElement(String, String, String, Attributes)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/SAX2StAXAdaptor.html" title="class in org.biojava.bio.seq.io.agave">SAX2StAXAdaptor</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/StAXContentHandler.html#startElement(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes, org.biojava.bio.seq.io.agave.DelegationManager)">startElement(String, String, String, Attributes, DelegationManager)</a></span> - Method in interface org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/StAXContentHandler.html" title="interface in org.biojava.bio.seq.io.agave">StAXContentHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/StAXContentHandlerBase.html#startElement(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes, org.biojava.bio.seq.io.agave.DelegationManager)">startElement(String, String, String, Attributes, DelegationManager)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/StAXContentHandlerBase.html" title="class in org.biojava.bio.seq.io.agave">StAXContentHandlerBase</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/StAXFeatureHandler.html#startElement(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes, org.biojava.bio.seq.io.agave.DelegationManager)">startElement(String, String, String, Attributes, DelegationManager)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/StAXFeatureHandler.html" title="class in org.biojava.bio.seq.io.agave">StAXFeatureHandler</a></dt>
<dd>
<div class="block">Handles basic entry processing for all feature handlers.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/StAXPropertyHandler.html#startElement(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes, org.biojava.bio.seq.io.agave.DelegationManager)">startElement(String, String, String, Attributes, DelegationManager)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/StAXPropertyHandler.html" title="class in org.biojava.bio.seq.io.agave">StAXPropertyHandler</a></dt>
<dd>
<div class="block">Override this to do any processing required but call this
prior to returning.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/filterxml/XMLAnnotationTypeHandler.html#startElement(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes, org.biojava.utils.stax.DelegationManager)">startElement(String, String, String, Attributes, DelegationManager)</a></span> - Method in class org.biojava.bio.seq.io.filterxml.<a href="./org/biojava/bio/seq/io/filterxml/XMLAnnotationTypeHandler.html" title="class in org.biojava.bio.seq.io.filterxml">XMLAnnotationTypeHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game/GAMEAspectPropHandler.html#startElement(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes, org.biojava.utils.stax.DelegationManager)">startElement(String, String, String, Attributes, DelegationManager)</a></span> - Method in class org.biojava.bio.seq.io.game.<a href="./org/biojava/bio/seq/io/game/GAMEAspectPropHandler.html" title="class in org.biojava.bio.seq.io.game">GAMEAspectPropHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game/GAMEDescriptionPropHandler.html#startElement(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes, org.biojava.utils.stax.DelegationManager)">startElement(String, String, String, Attributes, DelegationManager)</a></span> - Method in class org.biojava.bio.seq.io.game.<a href="./org/biojava/bio/seq/io/game/GAMEDescriptionPropHandler.html" title="class in org.biojava.bio.seq.io.game">GAMEDescriptionPropHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game/GAMENamePropHandler.html#startElement(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes, org.biojava.utils.stax.DelegationManager)">startElement(String, String, String, Attributes, DelegationManager)</a></span> - Method in class org.biojava.bio.seq.io.game.<a href="./org/biojava/bio/seq/io/game/GAMENamePropHandler.html" title="class in org.biojava.bio.seq.io.game">GAMENamePropHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game/GAMEResiduesPropHandler.html#startElement(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes, org.biojava.utils.stax.DelegationManager)">startElement(String, String, String, Attributes, DelegationManager)</a></span> - Method in class org.biojava.bio.seq.io.game.<a href="./org/biojava/bio/seq/io/game/GAMEResiduesPropHandler.html" title="class in org.biojava.bio.seq.io.game">GAMEResiduesPropHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game/GAMETypePropHandler.html#startElement(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes, org.biojava.utils.stax.DelegationManager)">startElement(String, String, String, Attributes, DelegationManager)</a></span> - Method in class org.biojava.bio.seq.io.game.<a href="./org/biojava/bio/seq/io/game/GAMETypePropHandler.html" title="class in org.biojava.bio.seq.io.game">GAMETypePropHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game/SequenceContentHandlerBase.html#startElement(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes, org.biojava.utils.stax.DelegationManager)">startElement(String, String, String, Attributes, DelegationManager)</a></span> - Method in class org.biojava.bio.seq.io.game.<a href="./org/biojava/bio/seq/io/game/SequenceContentHandlerBase.html" title="class in org.biojava.bio.seq.io.game">SequenceContentHandlerBase</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game/StAXFeatureHandler.html#startElement(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes, org.biojava.utils.stax.DelegationManager)">startElement(String, String, String, Attributes, DelegationManager)</a></span> - Method in class org.biojava.bio.seq.io.game.<a href="./org/biojava/bio/seq/io/game/StAXFeatureHandler.html" title="class in org.biojava.bio.seq.io.game">StAXFeatureHandler</a></dt>
<dd>
<div class="block">Handles basic entry processing for all feature handlers.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game/StAXPropertyHandler.html#startElement(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes, org.biojava.utils.stax.DelegationManager)">startElement(String, String, String, Attributes, DelegationManager)</a></span> - Method in class org.biojava.bio.seq.io.game.<a href="./org/biojava/bio/seq/io/game/StAXPropertyHandler.html" title="class in org.biojava.bio.seq.io.game">StAXPropertyHandler</a></dt>
<dd>
<div class="block">Override this to do any processing required but call this
prior to returning.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game12/StAXFeatureHandler.html#startElement(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes, org.biojava.utils.stax.DelegationManager)">startElement(String, String, String, Attributes, DelegationManager)</a></span> - Method in class org.biojava.bio.seq.io.game12.<a href="./org/biojava/bio/seq/io/game12/StAXFeatureHandler.html" title="class in org.biojava.bio.seq.io.game12">StAXFeatureHandler</a></dt>
<dd>
<div class="block">Handles basic entry processing for all feature handlers.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/stax/BooleanElementHandlerBase.html#startElement(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes, org.biojava.utils.stax.DelegationManager)">startElement(String, String, String, Attributes, DelegationManager)</a></span> - Method in class org.biojava.utils.stax.<a href="./org/biojava/utils/stax/BooleanElementHandlerBase.html" title="class in org.biojava.utils.stax">BooleanElementHandlerBase</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/stax/ByteElementHandlerBase.html#startElement(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes, org.biojava.utils.stax.DelegationManager)">startElement(String, String, String, Attributes, DelegationManager)</a></span> - Method in class org.biojava.utils.stax.<a href="./org/biojava/utils/stax/ByteElementHandlerBase.html" title="class in org.biojava.utils.stax">ByteElementHandlerBase</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/stax/CharElementHandlerBase.html#startElement(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes, org.biojava.utils.stax.DelegationManager)">startElement(String, String, String, Attributes, DelegationManager)</a></span> - Method in class org.biojava.utils.stax.<a href="./org/biojava/utils/stax/CharElementHandlerBase.html" title="class in org.biojava.utils.stax">CharElementHandlerBase</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/stax/DoubleElementHandlerBase.html#startElement(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes, org.biojava.utils.stax.DelegationManager)">startElement(String, String, String, Attributes, DelegationManager)</a></span> - Method in class org.biojava.utils.stax.<a href="./org/biojava/utils/stax/DoubleElementHandlerBase.html" title="class in org.biojava.utils.stax">DoubleElementHandlerBase</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/stax/FloatElementHandlerBase.html#startElement(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes, org.biojava.utils.stax.DelegationManager)">startElement(String, String, String, Attributes, DelegationManager)</a></span> - Method in class org.biojava.utils.stax.<a href="./org/biojava/utils/stax/FloatElementHandlerBase.html" title="class in org.biojava.utils.stax">FloatElementHandlerBase</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/stax/IntElementHandlerBase.html#startElement(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes, org.biojava.utils.stax.DelegationManager)">startElement(String, String, String, Attributes, DelegationManager)</a></span> - Method in class org.biojava.utils.stax.<a href="./org/biojava/utils/stax/IntElementHandlerBase.html" title="class in org.biojava.utils.stax">IntElementHandlerBase</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/stax/LongElementHandlerBase.html#startElement(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes, org.biojava.utils.stax.DelegationManager)">startElement(String, String, String, Attributes, DelegationManager)</a></span> - Method in class org.biojava.utils.stax.<a href="./org/biojava/utils/stax/LongElementHandlerBase.html" title="class in org.biojava.utils.stax">LongElementHandlerBase</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/stax/SAX2StAXAdaptor.html#startElement(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes)">startElement(String, String, String, Attributes)</a></span> - Method in class org.biojava.utils.stax.<a href="./org/biojava/utils/stax/SAX2StAXAdaptor.html" title="class in org.biojava.utils.stax">SAX2StAXAdaptor</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/stax/StAXContentHandler.html#startElement(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes, org.biojava.utils.stax.DelegationManager)">startElement(String, String, String, Attributes, DelegationManager)</a></span> - Method in interface org.biojava.utils.stax.<a href="./org/biojava/utils/stax/StAXContentHandler.html" title="interface in org.biojava.utils.stax">StAXContentHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/stax/StAXContentHandlerBase.html#startElement(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes, org.biojava.utils.stax.DelegationManager)">startElement(String, String, String, Attributes, DelegationManager)</a></span> - Method in class org.biojava.utils.stax.<a href="./org/biojava/utils/stax/StAXContentHandlerBase.html" title="class in org.biojava.utils.stax">StAXContentHandlerBase</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/stax/StringElementHandlerBase.html#startElement(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes, org.biojava.utils.stax.DelegationManager)">startElement(String, String, String, Attributes, DelegationManager)</a></span> - Method in class org.biojava.utils.stax.<a href="./org/biojava/utils/stax/StringElementHandlerBase.html" title="class in org.biojava.utils.stax">StringElementHandlerBase</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEBioSeqHandler.html#startElementHandler(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes)">startElementHandler(String, String, String, Attributes)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEBioSeqHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEBioSeqHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEBioSequenceHandler.html#startElementHandler(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes)">startElementHandler(String, String, String, Attributes)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEBioSequenceHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEBioSequenceHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVECdsHandler.html#startElementHandler(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes)">startElementHandler(String, String, String, Attributes)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVECdsHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVECdsHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEChromosomeHandler.html#startElementHandler(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes)">startElementHandler(String, String, String, Attributes)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEChromosomeHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEChromosomeHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEClassificationHandler.html#startElementHandler(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes)">startElementHandler(String, String, String, Attributes)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEClassificationHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEClassificationHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVECompResultHandler.html#startElementHandler(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes)">startElementHandler(String, String, String, Attributes)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVECompResultHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVECompResultHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEComputationHandler.html#startElementHandler(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes)">startElementHandler(String, String, String, Attributes)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEComputationHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEComputationHandler</a></dt>
<dd>
<div class="block">currently we do not handler >computation< as subtag of sciobj yet</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEContigHandler.html#startElementHandler(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes)">startElementHandler(String, String, String, Attributes)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEContigHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEContigHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEDbIdPropHandler.html#startElementHandler(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes)">startElementHandler(String, String, String, Attributes)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEDbIdPropHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEDbIdPropHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEElementIdPropHandler.html#startElementHandler(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes)">startElementHandler(String, String, String, Attributes)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEElementIdPropHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEElementIdPropHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEFragmentOrderHandler.html#startElementHandler(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes)">startElementHandler(String, String, String, Attributes)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEFragmentOrderHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEFragmentOrderHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEFragmentOrientationHandler.html#startElementHandler(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes)">startElementHandler(String, String, String, Attributes)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEFragmentOrientationHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEFragmentOrientationHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEGeneHandler.html#startElementHandler(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes)">startElementHandler(String, String, String, Attributes)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEGeneHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEGeneHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEHandler.html#startElementHandler(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes, org.biojava.bio.seq.io.agave.DelegationManager)">startElementHandler(String, String, String, Attributes, DelegationManager)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEIdAliasPropHandler.html#startElementHandler(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes)">startElementHandler(String, String, String, Attributes)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEIdAliasPropHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEIdAliasPropHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEMapLocationPropHandler.html#startElementHandler(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes)">startElementHandler(String, String, String, Attributes)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEMapLocationPropHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEMapLocationPropHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEMapPositionPropHandler.html#startElementHandler(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes)">startElementHandler(String, String, String, Attributes)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEMapPositionPropHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEMapPositionPropHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEMatchRegionPropHandler.html#startElementHandler(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes)">startElementHandler(String, String, String, Attributes)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEMatchRegionPropHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEMatchRegionPropHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEMrnaHandler.html#startElementHandler(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes)">startElementHandler(String, String, String, Attributes)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEMrnaHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEMrnaHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEPredictedProteinHandler.html#startElementHandler(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes)">startElementHandler(String, String, String, Attributes)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEPredictedProteinHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEPredictedProteinHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEQualifierPropHandler.html#startElementHandler(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes)">startElementHandler(String, String, String, Attributes)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEQualifierPropHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEQualifierPropHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEQueryRegionPropHandler.html#startElementHandler(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes)">startElementHandler(String, String, String, Attributes)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEQueryRegionPropHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEQueryRegionPropHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVERelatedAnnotPropHandler.html#startElementHandler(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes)">startElementHandler(String, String, String, Attributes)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVERelatedAnnotPropHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVERelatedAnnotPropHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEResultGroupHandler.html#startElementHandler(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes)">startElementHandler(String, String, String, Attributes)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEResultGroupHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEResultGroupHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEResultPropertyPropHandler.html#startElementHandler(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes)">startElementHandler(String, String, String, Attributes)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEResultPropertyPropHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEResultPropertyPropHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVESciPropertyPropHandler.html#startElementHandler(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes)">startElementHandler(String, String, String, Attributes)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVESciPropertyPropHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVESciPropertyPropHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVESeqFeatureHandler.html#startElementHandler(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes)">startElementHandler(String, String, String, Attributes)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVESeqFeatureHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVESeqFeatureHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVESeqLocationPropHandler.html#startElementHandler(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes)">startElementHandler(String, String, String, Attributes)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVESeqLocationPropHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVESeqLocationPropHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVESeqMapHandler.html#startElementHandler(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes)">startElementHandler(String, String, String, Attributes)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVESeqMapHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVESeqMapHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVETranscriptHandler.html#startElementHandler(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes)">startElementHandler(String, String, String, Attributes)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVETranscriptHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVETranscriptHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEViewPropHandler.html#startElementHandler(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes)">startElementHandler(String, String, String, Attributes)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEViewPropHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEViewPropHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEXrefPropPropHandler.html#startElementHandler(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes)">startElementHandler(String, String, String, Attributes)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEXrefPropPropHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEXrefPropPropHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/StAXFeatureHandler.html#startElementHandler(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes)">startElementHandler(String, String, String, Attributes)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/StAXFeatureHandler.html" title="class in org.biojava.bio.seq.io.agave">StAXFeatureHandler</a></dt>
<dd>
<div class="block">Element-specific handler.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/StAXPropertyHandler.html#startElementHandler(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes)">startElementHandler(String, String, String, Attributes)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/StAXPropertyHandler.html" title="class in org.biojava.bio.seq.io.agave">StAXPropertyHandler</a></dt>
<dd>
<div class="block">Element-specific handler.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game/GAMEAnnotationHandler.html#startElementHandler(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes)">startElementHandler(String, String, String, Attributes)</a></span> - Method in class org.biojava.bio.seq.io.game.<a href="./org/biojava/bio/seq/io/game/GAMEAnnotationHandler.html" title="class in org.biojava.bio.seq.io.game">GAMEAnnotationHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game/GAMEFeatureSetHandler.html#startElementHandler(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes)">startElementHandler(String, String, String, Attributes)</a></span> - Method in class org.biojava.bio.seq.io.game.<a href="./org/biojava/bio/seq/io/game/GAMEFeatureSetHandler.html" title="class in org.biojava.bio.seq.io.game">GAMEFeatureSetHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game/GAMEFeatureSpanHandler.html#startElementHandler(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes)">startElementHandler(String, String, String, Attributes)</a></span> - Method in class org.biojava.bio.seq.io.game.<a href="./org/biojava/bio/seq/io/game/GAMEFeatureSpanHandler.html" title="class in org.biojava.bio.seq.io.game">GAMEFeatureSpanHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game/GAMEGenePropHandler.html#startElementHandler(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes)">startElementHandler(String, String, String, Attributes)</a></span> - Method in class org.biojava.bio.seq.io.game.<a href="./org/biojava/bio/seq/io/game/GAMEGenePropHandler.html" title="class in org.biojava.bio.seq.io.game">GAMEGenePropHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game/GAMEHandler.html#startElementHandler(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes, org.biojava.utils.stax.DelegationManager)">startElementHandler(String, String, String, Attributes, DelegationManager)</a></span> - Method in class org.biojava.bio.seq.io.game.<a href="./org/biojava/bio/seq/io/game/GAMEHandler.html" title="class in org.biojava.bio.seq.io.game">GAMEHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game/GAMEMapPosPropHandler.html#startElementHandler(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes)">startElementHandler(String, String, String, Attributes)</a></span> - Method in class org.biojava.bio.seq.io.game.<a href="./org/biojava/bio/seq/io/game/GAMEMapPosPropHandler.html" title="class in org.biojava.bio.seq.io.game">GAMEMapPosPropHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game/GAMESeqPropHandler.html#startElementHandler(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes)">startElementHandler(String, String, String, Attributes)</a></span> - Method in class org.biojava.bio.seq.io.game.<a href="./org/biojava/bio/seq/io/game/GAMESeqPropHandler.html" title="class in org.biojava.bio.seq.io.game">GAMESeqPropHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game/StAXFeatureHandler.html#startElementHandler(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes)">startElementHandler(String, String, String, Attributes)</a></span> - Method in class org.biojava.bio.seq.io.game.<a href="./org/biojava/bio/seq/io/game/StAXFeatureHandler.html" title="class in org.biojava.bio.seq.io.game">StAXFeatureHandler</a></dt>
<dd>
<div class="block">Element-specific handler.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game/StAXPropertyHandler.html#startElementHandler(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes)">startElementHandler(String, String, String, Attributes)</a></span> - Method in class org.biojava.bio.seq.io.game.<a href="./org/biojava/bio/seq/io/game/StAXPropertyHandler.html" title="class in org.biojava.bio.seq.io.game">StAXPropertyHandler</a></dt>
<dd>
<div class="block">Element-specific handler.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game12/GAMEAnnotationHandler.html#startElementHandler(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes)">startElementHandler(String, String, String, Attributes)</a></span> - Method in class org.biojava.bio.seq.io.game12.<a href="./org/biojava/bio/seq/io/game12/GAMEAnnotationHandler.html" title="class in org.biojava.bio.seq.io.game12">GAMEAnnotationHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game12/GAMEFeatureSetHandler.html#startElementHandler(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes)">startElementHandler(String, String, String, Attributes)</a></span> - Method in class org.biojava.bio.seq.io.game12.<a href="./org/biojava/bio/seq/io/game12/GAMEFeatureSetHandler.html" title="class in org.biojava.bio.seq.io.game12">GAMEFeatureSetHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game12/GAMEFeatureSpanHandler.html#startElementHandler(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes)">startElementHandler(String, String, String, Attributes)</a></span> - Method in class org.biojava.bio.seq.io.game12.<a href="./org/biojava/bio/seq/io/game12/GAMEFeatureSpanHandler.html" title="class in org.biojava.bio.seq.io.game12">GAMEFeatureSpanHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game12/GAMEGeneHandler.html#startElementHandler(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes)">startElementHandler(String, String, String, Attributes)</a></span> - Method in class org.biojava.bio.seq.io.game12.<a href="./org/biojava/bio/seq/io/game12/GAMEGeneHandler.html" title="class in org.biojava.bio.seq.io.game12">GAMEGeneHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game12/GAMEHandler.html#startElementHandler(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes)">startElementHandler(String, String, String, Attributes)</a></span> - Method in class org.biojava.bio.seq.io.game12.<a href="./org/biojava/bio/seq/io/game12/GAMEHandler.html" title="class in org.biojava.bio.seq.io.game12">GAMEHandler</a></dt>
<dd>
<div class="block">Description of the Method</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game12/GAMESeqHandler.html#startElementHandler(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes)">startElementHandler(String, String, String, Attributes)</a></span> - Method in class org.biojava.bio.seq.io.game12.<a href="./org/biojava/bio/seq/io/game12/GAMESeqHandler.html" title="class in org.biojava.bio.seq.io.game12">GAMESeqHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game12/GAMESeqRelHandler.html#startElementHandler(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes)">startElementHandler(String, String, String, Attributes)</a></span> - Method in class org.biojava.bio.seq.io.game12.<a href="./org/biojava/bio/seq/io/game12/GAMESeqRelHandler.html" title="class in org.biojava.bio.seq.io.game12">GAMESeqRelHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game12/StAXFeatureHandler.html#startElementHandler(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes)">startElementHandler(String, String, String, Attributes)</a></span> - Method in class org.biojava.bio.seq.io.game12.<a href="./org/biojava/bio/seq/io/game12/StAXFeatureHandler.html" title="class in org.biojava.bio.seq.io.game12">StAXFeatureHandler</a></dt>
<dd>
<div class="block">Element-specific handler.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/EmblFileFormer.html#startFeature(org.biojava.bio.seq.Feature.Template)">startFeature(Feature.Template)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/EmblFileFormer.html" title="class in org.biojava.bio.seq.io">EmblFileFormer</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/FeatureTableParser.html#startFeature(java.lang.String)">startFeature(String)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/FeatureTableParser.html" title="class in org.biojava.bio.seq.io">FeatureTableParser</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/GenbankFileFormer.html#startFeature(org.biojava.bio.seq.Feature.Template)">startFeature(Feature.Template)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/GenbankFileFormer.html" title="class in org.biojava.bio.seq.io">GenbankFileFormer</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/ProteinRefSeqFileFormer.html#startFeature(org.biojava.bio.seq.Feature.Template)">startFeature(Feature.Template)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/ProteinRefSeqFileFormer.html" title="class in org.biojava.bio.seq.io">ProteinRefSeqFileFormer</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOAdapter.html#startFeature(org.biojava.bio.seq.Feature.Template)">startFeature(Feature.Template)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOAdapter.html" title="class in org.biojava.bio.seq.io">SeqIOAdapter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOFilter.html#startFeature(org.biojava.bio.seq.Feature.Template)">startFeature(Feature.Template)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOFilter.html" title="class in org.biojava.bio.seq.io">SeqIOFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOListener.html#startFeature(org.biojava.bio.seq.Feature.Template)">startFeature(Feature.Template)</a></span> - Method in interface org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOListener.html" title="interface in org.biojava.bio.seq.io">SeqIOListener</a></dt>
<dd>
<div class="block">Notify the listener that a new feature object is starting.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SequenceBuilderBase.html#startFeature(org.biojava.bio.seq.Feature.Template)">startFeature(Feature.Template)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SequenceBuilderBase.html" title="class in org.biojava.bio.seq.io">SequenceBuilderBase</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SequenceBuilderFilter.html#startFeature(org.biojava.bio.seq.Feature.Template)">startFeature(Feature.Template)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SequenceBuilderFilter.html" title="class in org.biojava.bio.seq.io">SequenceBuilderFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SwissprotFileFormer.html#startFeature(org.biojava.bio.seq.Feature.Template)">startFeature(Feature.Template)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SwissprotFileFormer.html" title="class in org.biojava.bio.seq.io">SwissprotFileFormer</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Null implementation.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/DebuggingRichSeqIOListener.html#startFeature(org.biojava.bio.seq.Feature.Template)">startFeature(Feature.Template)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/DebuggingRichSeqIOListener.html" title="class in org.biojavax.bio.seq.io">DebuggingRichSeqIOListener</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/RichSeqIOAdapter.html#startFeature(org.biojava.bio.seq.Feature.Template)">startFeature(Feature.Template)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/RichSeqIOAdapter.html" title="class in org.biojavax.bio.seq.io">RichSeqIOAdapter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/SimpleRichSequenceBuilder.html#startFeature(org.biojava.bio.seq.Feature.Template)">startFeature(Feature.Template)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/SimpleRichSequenceBuilder.html" title="class in org.biojavax.bio.seq.io">SimpleRichSequenceBuilder</a></dt>
<dd>
<div class="block">Notify the listener that a new feature object is starting.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/phylo/io/phylip/PHYLIPFileBuilder.html#startFile()">startFile()</a></span> - Method in class org.biojavax.bio.phylo.io.phylip.<a href="./org/biojavax/bio/phylo/io/phylip/PHYLIPFileBuilder.html" title="class in org.biojavax.bio.phylo.io.phylip">PHYLIPFileBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/phylo/io/phylip/PHYLIPFileListener.html#startFile()">startFile()</a></span> - Method in interface org.biojavax.bio.phylo.io.phylip.<a href="./org/biojavax/bio/phylo/io/phylip/PHYLIPFileListener.html" title="interface in org.biojavax.bio.phylo.io.phylip">PHYLIPFileListener</a></dt>
<dd>
<div class="block">About to start a new file.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/HomologeneBuilder.html#startGroup()">startGroup()</a></span> - Method in interface org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/HomologeneBuilder.html" title="interface in org.biojava.bio.program.homologene">HomologeneBuilder</a></dt>
<dd>
<div class="block">indicates start of data for a OrthoPairSet</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/SimpleHomologeneBuilder.html#startGroup()">startGroup()</a></span> - Method in class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/SimpleHomologeneBuilder.html" title="class in org.biojava.bio.program.homologene">SimpleHomologeneBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/sax/FastaSearchSAXParser.html#startHeader()">startHeader()</a></span> - Method in class org.biojava.bio.program.sax.<a href="./org/biojava/bio/program/sax/FastaSearchSAXParser.html" title="class in org.biojava.bio.program.sax">FastaSearchSAXParser</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/BlastLikeHomologyBuilder.html#startHeader()">startHeader()</a></span> - Method in class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/BlastLikeHomologyBuilder.html" title="class in org.biojava.bio.program.ssbind">BlastLikeHomologyBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/BlastLikeSearchBuilder.html#startHeader()">startHeader()</a></span> - Method in class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/BlastLikeSearchBuilder.html" title="class in org.biojava.bio.program.ssbind">BlastLikeSearchBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/SimilarityPairBuilder.html#startHeader()">startHeader()</a></span> - Method in class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/SimilarityPairBuilder.html" title="class in org.biojava.bio.program.ssbind">SimilarityPairBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/FilteringContentHandler.html#startHeader()">startHeader()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/FilteringContentHandler.html" title="class in org.biojava.bio.search">FilteringContentHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SearchContentAdapter.html#startHeader()">startHeader()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SearchContentAdapter.html" title="class in org.biojava.bio.search">SearchContentAdapter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SearchContentFilter.html#startHeader()">startHeader()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SearchContentFilter.html" title="class in org.biojava.bio.search">SearchContentFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SearchContentHandler.html#startHeader()">startHeader()</a></span> - Method in interface org.biojava.bio.search.<a href="./org/biojava/bio/search/SearchContentHandler.html" title="interface in org.biojava.bio.search">SearchContentHandler</a></dt>
<dd>
<div class="block">The <code>startHeader</code> method indicates the start of a
formatted header.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SearchContentHandlerDebugger.html#startHeader()">startHeader()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SearchContentHandlerDebugger.html" title="class in org.biojava.bio.search">SearchContentHandlerDebugger</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/sax/FastaSearchSAXParser.html#startHit()">startHit()</a></span> - Method in class org.biojava.bio.program.sax.<a href="./org/biojava/bio/program/sax/FastaSearchSAXParser.html" title="class in org.biojava.bio.program.sax">FastaSearchSAXParser</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/BlastLikeHomologyBuilder.html#startHit()">startHit()</a></span> - Method in class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/BlastLikeHomologyBuilder.html" title="class in org.biojava.bio.program.ssbind">BlastLikeHomologyBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/BlastLikeSearchBuilder.html#startHit()">startHit()</a></span> - Method in class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/BlastLikeSearchBuilder.html" title="class in org.biojava.bio.program.ssbind">BlastLikeSearchBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/SimilarityPairBuilder.html#startHit()">startHit()</a></span> - Method in class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/SimilarityPairBuilder.html" title="class in org.biojava.bio.program.ssbind">SimilarityPairBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/FilteringContentHandler.html#startHit()">startHit()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/FilteringContentHandler.html" title="class in org.biojava.bio.search">FilteringContentHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SearchContentAdapter.html#startHit()">startHit()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SearchContentAdapter.html" title="class in org.biojava.bio.search">SearchContentAdapter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SearchContentFilter.html#startHit()">startHit()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SearchContentFilter.html" title="class in org.biojava.bio.search">SearchContentFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SearchContentHandler.html#startHit()">startHit()</a></span> - Method in interface org.biojava.bio.search.<a href="./org/biojava/bio/search/SearchContentHandler.html" title="interface in org.biojava.bio.search">SearchContentHandler</a></dt>
<dd>
<div class="block">The <code>startHit</code> method indicates the start of a
formatted hit.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SearchContentHandlerDebugger.html#startHit()">startHit()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SearchContentHandlerDebugger.html" title="class in org.biojava.bio.search">SearchContentHandlerDebugger</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/automata/StateMachineFactory.html#startInstance(int, int)">startInstance(int, int)</a></span> - Method in interface org.biojava.utils.automata.<a href="./org/biojava/utils/automata/StateMachineFactory.html" title="interface in org.biojava.utils.automata">StateMachineFactory</a></dt>
<dd>
<div class="block">Return a StateMachineInstance if the Symbol represented
by the symbol index is valid as the initial symbol of
the pattern.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/StAXFeatureHandler.html#startLoc">startLoc</a></span> - Variable in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/StAXFeatureHandler.html" title="class in org.biojava.bio.seq.io.agave">StAXFeatureHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game/StAXFeatureHandler.html#startLoc">startLoc</a></span> - Variable in class org.biojava.bio.seq.io.game.<a href="./org/biojava/bio/seq/io/game/StAXFeatureHandler.html" title="class in org.biojava.bio.seq.io.game">StAXFeatureHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/HomologeneBuilder.html#startOrthologue()">startOrthologue()</a></span> - Method in interface org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/HomologeneBuilder.html" title="interface in org.biojava.bio.program.homologene">HomologeneBuilder</a></dt>
<dd>
<div class="block">indicates start of data for an orthologue</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/SimpleHomologeneBuilder.html#startOrthologue()">startOrthologue()</a></span> - Method in class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/SimpleHomologeneBuilder.html" title="class in org.biojava.bio.program.homologene">SimpleHomologeneBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/HomologeneBuilder.html#startOrthoPair()">startOrthoPair()</a></span> - Method in interface org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/HomologeneBuilder.html" title="interface in org.biojava.bio.program.homologene">HomologeneBuilder</a></dt>
<dd>
<div class="block">indicates start of data for an OrthoPair</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/SimpleHomologeneBuilder.html#startOrthoPair()">startOrthoPair()</a></span> - Method in class org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/SimpleHomologeneBuilder.html" title="class in org.biojava.bio.program.homologene">SimpleHomologeneBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/SeqSimilarityAdapter.html#startPrefixMapping(java.lang.String, java.lang.String)">startPrefixMapping(String, String)</a></span> - Method in class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/SeqSimilarityAdapter.html" title="class in org.biojava.bio.program.ssbind">SeqSimilarityAdapter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/SAX2StAXAdaptor.html#startPrefixMapping(java.lang.String, java.lang.String)">startPrefixMapping(String, String)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/SAX2StAXAdaptor.html" title="class in org.biojava.bio.seq.io.agave">SAX2StAXAdaptor</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/StAXContentHandler.html#startPrefixMapping(java.lang.String, java.lang.String)">startPrefixMapping(String, String)</a></span> - Method in interface org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/StAXContentHandler.html" title="interface in org.biojava.bio.seq.io.agave">StAXContentHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/StAXContentHandlerBase.html#startPrefixMapping(java.lang.String, java.lang.String)">startPrefixMapping(String, String)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/StAXContentHandlerBase.html" title="class in org.biojava.bio.seq.io.agave">StAXContentHandlerBase</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/stax/SAX2StAXAdaptor.html#startPrefixMapping(java.lang.String, java.lang.String)">startPrefixMapping(String, String)</a></span> - Method in class org.biojava.utils.stax.<a href="./org/biojava/utils/stax/SAX2StAXAdaptor.html" title="class in org.biojava.utils.stax">SAX2StAXAdaptor</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/stax/StAXContentHandler.html#startPrefixMapping(java.lang.String, java.lang.String)">startPrefixMapping(String, String)</a></span> - Method in interface org.biojava.utils.stax.<a href="./org/biojava/utils/stax/StAXContentHandler.html" title="interface in org.biojava.utils.stax">StAXContentHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/stax/StAXContentHandlerBase.html#startPrefixMapping(java.lang.String, java.lang.String)">startPrefixMapping(String, String)</a></span> - Method in class org.biojava.utils.stax.<a href="./org/biojava/utils/stax/StAXContentHandlerBase.html" title="class in org.biojava.utils.stax">StAXContentHandlerBase</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/AbstractWrapper.html#startRecord()">startRecord()</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/AbstractWrapper.html" title="class in org.biojava.bio.program.tagvalue">AbstractWrapper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/AnnotationBuilder.html#startRecord()">startRecord()</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/AnnotationBuilder.html" title="class in org.biojava.bio.program.tagvalue">AnnotationBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/Echo.html#startRecord()">startRecord()</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/Echo.html" title="class in org.biojava.bio.program.tagvalue">Echo</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/Indexer.html#startRecord()">startRecord()</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/Indexer.html" title="class in org.biojava.bio.program.tagvalue">Indexer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/Indexer2.html#startRecord()">startRecord()</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/Indexer2.html" title="class in org.biojava.bio.program.tagvalue">Indexer2</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/SimpleTagValueWrapper.html#startRecord()">startRecord()</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/SimpleTagValueWrapper.html" title="class in org.biojava.bio.program.tagvalue">SimpleTagValueWrapper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/StateMachine.SimpleStateListener.html#startRecord()">startRecord()</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/StateMachine.SimpleStateListener.html" title="class in org.biojava.bio.program.tagvalue">StateMachine.SimpleStateListener</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/StateMachine.html#startRecord()">startRecord()</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/StateMachine.html" title="class in org.biojava.bio.program.tagvalue">StateMachine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/TagValueListener.html#startRecord()">startRecord()</a></span> - Method in interface org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/TagValueListener.html" title="interface in org.biojava.bio.program.tagvalue">TagValueListener</a></dt>
<dd>
<div class="block">A new record is about to start.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/sax/FastaSearchSAXParser.html#startSearch()">startSearch()</a></span> - Method in class org.biojava.bio.program.sax.<a href="./org/biojava/bio/program/sax/FastaSearchSAXParser.html" title="class in org.biojava.bio.program.sax">FastaSearchSAXParser</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssaha/HitMerger.html#startSearch(java.lang.String)">startSearch(String)</a></span> - Method in class org.biojava.bio.program.ssaha.<a href="./org/biojava/bio/program/ssaha/HitMerger.html" title="class in org.biojava.bio.program.ssaha">HitMerger</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssaha/SearchListener.Echo.html#startSearch(java.lang.String)">startSearch(String)</a></span> - Method in class org.biojava.bio.program.ssaha.<a href="./org/biojava/bio/program/ssaha/SearchListener.Echo.html" title="class in org.biojava.bio.program.ssaha">SearchListener.Echo</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssaha/SearchListener.html#startSearch(java.lang.String)">startSearch(String)</a></span> - Method in interface org.biojava.bio.program.ssaha.<a href="./org/biojava/bio/program/ssaha/SearchListener.html" title="interface in org.biojava.bio.program.ssaha">SearchListener</a></dt>
<dd>
<div class="block">Indicates that a sequence is about to be searched against a DataStore.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssaha/SearchListener.Tee.html#startSearch(java.lang.String)">startSearch(String)</a></span> - Method in class org.biojava.bio.program.ssaha.<a href="./org/biojava/bio/program/ssaha/SearchListener.Tee.html" title="class in org.biojava.bio.program.ssaha">SearchListener.Tee</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssaha/SearchListener.Wrapper.html#startSearch(java.lang.String)">startSearch(String)</a></span> - Method in class org.biojava.bio.program.ssaha.<a href="./org/biojava/bio/program/ssaha/SearchListener.Wrapper.html" title="class in org.biojava.bio.program.ssaha">SearchListener.Wrapper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/BlastLikeHomologyBuilder.html#startSearch()">startSearch()</a></span> - Method in class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/BlastLikeHomologyBuilder.html" title="class in org.biojava.bio.program.ssbind">BlastLikeHomologyBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/BlastLikeSearchBuilder.html#startSearch()">startSearch()</a></span> - Method in class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/BlastLikeSearchBuilder.html" title="class in org.biojava.bio.program.ssbind">BlastLikeSearchBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/SimilarityPairBuilder.html#startSearch()">startSearch()</a></span> - Method in class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/SimilarityPairBuilder.html" title="class in org.biojava.bio.program.ssbind">SimilarityPairBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/FilteringContentHandler.html#startSearch()">startSearch()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/FilteringContentHandler.html" title="class in org.biojava.bio.search">FilteringContentHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SearchContentAdapter.html#startSearch()">startSearch()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SearchContentAdapter.html" title="class in org.biojava.bio.search">SearchContentAdapter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SearchContentFilter.html#startSearch()">startSearch()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SearchContentFilter.html" title="class in org.biojava.bio.search">SearchContentFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SearchContentHandler.html#startSearch()">startSearch()</a></span> - Method in interface org.biojava.bio.search.<a href="./org/biojava/bio/search/SearchContentHandler.html" title="interface in org.biojava.bio.search">SearchContentHandler</a></dt>
<dd>
<div class="block">The <code>startSearch</code> method indicates the start of
useful search information.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SearchContentHandlerDebugger.html#startSearch()">startSearch()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SearchContentHandlerDebugger.html" title="class in org.biojava.bio.search">SearchContentHandlerDebugger</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/EmblFileFormer.html#startSequence()">startSequence()</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/EmblFileFormer.html" title="class in org.biojava.bio.seq.io">EmblFileFormer</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/GenbankFileFormer.html#startSequence()">startSequence()</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/GenbankFileFormer.html" title="class in org.biojava.bio.seq.io">GenbankFileFormer</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOAdapter.html#startSequence()">startSequence()</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOAdapter.html" title="class in org.biojava.bio.seq.io">SeqIOAdapter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOFilter.html#startSequence()">startSequence()</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOFilter.html" title="class in org.biojava.bio.seq.io">SeqIOFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOListener.html#startSequence()">startSequence()</a></span> - Method in interface org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOListener.html" title="interface in org.biojava.bio.seq.io">SeqIOListener</a></dt>
<dd>
<div class="block">Start the processing of a sequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SequenceBuilderBase.html#startSequence()">startSequence()</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SequenceBuilderBase.html" title="class in org.biojava.bio.seq.io">SequenceBuilderBase</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SequenceBuilderFilter.html#startSequence()">startSequence()</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SequenceBuilderFilter.html" title="class in org.biojava.bio.seq.io">SequenceBuilderFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SwissprotFileFormer.html#startSequence()">startSequence()</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SwissprotFileFormer.html" title="class in org.biojava.bio.seq.io">SwissprotFileFormer</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Start the processing of a sequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/DebuggingRichSeqIOListener.html#startSequence()">startSequence()</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/DebuggingRichSeqIOListener.html" title="class in org.biojavax.bio.seq.io">DebuggingRichSeqIOListener</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/RichSeqIOAdapter.html#startSequence()">startSequence()</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/RichSeqIOAdapter.html" title="class in org.biojavax.bio.seq.io">RichSeqIOAdapter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/SimpleRichSequenceBuilder.html#startSequence()">startSequence()</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/SimpleRichSequenceBuilder.html" title="class in org.biojavax.bio.seq.io">SimpleRichSequenceBuilder</a></dt>
<dd>
<div class="block">Start the processing of a sequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/sax/FastaSearchSAXParser.html#startSubHit()">startSubHit()</a></span> - Method in class org.biojava.bio.program.sax.<a href="./org/biojava/bio/program/sax/FastaSearchSAXParser.html" title="class in org.biojava.bio.program.sax">FastaSearchSAXParser</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/BlastLikeHomologyBuilder.html#startSubHit()">startSubHit()</a></span> - Method in class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/BlastLikeHomologyBuilder.html" title="class in org.biojava.bio.program.ssbind">BlastLikeHomologyBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/BlastLikeSearchBuilder.html#startSubHit()">startSubHit()</a></span> - Method in class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/BlastLikeSearchBuilder.html" title="class in org.biojava.bio.program.ssbind">BlastLikeSearchBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/SimilarityPairBuilder.html#startSubHit()">startSubHit()</a></span> - Method in class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/SimilarityPairBuilder.html" title="class in org.biojava.bio.program.ssbind">SimilarityPairBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/FilteringContentHandler.html#startSubHit()">startSubHit()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/FilteringContentHandler.html" title="class in org.biojava.bio.search">FilteringContentHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SearchContentAdapter.html#startSubHit()">startSubHit()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SearchContentAdapter.html" title="class in org.biojava.bio.search">SearchContentAdapter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SearchContentFilter.html#startSubHit()">startSubHit()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SearchContentFilter.html" title="class in org.biojava.bio.search">SearchContentFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SearchContentHandler.html#startSubHit()">startSubHit()</a></span> - Method in interface org.biojava.bio.search.<a href="./org/biojava/bio/search/SearchContentHandler.html" title="interface in org.biojava.bio.search">SearchContentHandler</a></dt>
<dd>
<div class="block">The <code>startSubHit</code> method indicates the start of a
formatted subhit.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SearchContentHandlerDebugger.html#startSubHit()">startSubHit()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SearchContentHandlerDebugger.html" title="class in org.biojava.bio.search">SearchContentHandlerDebugger</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/AbstractWrapper.html#startTag(java.lang.Object)">startTag(Object)</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/AbstractWrapper.html" title="class in org.biojava.bio.program.tagvalue">AbstractWrapper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/Aggregator.html#startTag(java.lang.Object)">startTag(Object)</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/Aggregator.html" title="class in org.biojava.bio.program.tagvalue">Aggregator</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/AnnotationBuilder.html#startTag(java.lang.Object)">startTag(Object)</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/AnnotationBuilder.html" title="class in org.biojava.bio.program.tagvalue">AnnotationBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/Echo.html#startTag(java.lang.Object)">startTag(Object)</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/Echo.html" title="class in org.biojava.bio.program.tagvalue">Echo</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/Indexer.html#startTag(java.lang.Object)">startTag(Object)</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/Indexer.html" title="class in org.biojava.bio.program.tagvalue">Indexer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/Indexer2.html#startTag(java.lang.Object)">startTag(Object)</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/Indexer2.html" title="class in org.biojava.bio.program.tagvalue">Indexer2</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/MultiTagger.html#startTag(java.lang.Object)">startTag(Object)</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/MultiTagger.html" title="class in org.biojava.bio.program.tagvalue">MultiTagger</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/RegexFieldFinder.html#startTag(java.lang.Object)">startTag(Object)</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/RegexFieldFinder.html" title="class in org.biojava.bio.program.tagvalue">RegexFieldFinder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/SimpleTagValueWrapper.html#startTag(java.lang.Object)">startTag(Object)</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/SimpleTagValueWrapper.html" title="class in org.biojava.bio.program.tagvalue">SimpleTagValueWrapper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/StateMachine.SimpleStateListener.html#startTag(java.lang.Object)">startTag(Object)</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/StateMachine.SimpleStateListener.html" title="class in org.biojava.bio.program.tagvalue">StateMachine.SimpleStateListener</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/StateMachine.html#startTag(java.lang.Object)">startTag(Object)</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/StateMachine.html" title="class in org.biojava.bio.program.tagvalue">StateMachine</a></dt>
<dd>
<div class="block">TagValueListener interface</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/TagDelegator.html#startTag(java.lang.Object)">startTag(Object)</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/TagDelegator.html" title="class in org.biojava.bio.program.tagvalue">TagDelegator</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/TagDropper.html#startTag(java.lang.Object)">startTag(Object)</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/TagDropper.html" title="class in org.biojava.bio.program.tagvalue">TagDropper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/TagRenamer.html#startTag(java.lang.Object)">startTag(Object)</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/TagRenamer.html" title="class in org.biojava.bio.program.tagvalue">TagRenamer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/TagValueListener.html#startTag(java.lang.Object)">startTag(Object)</a></span> - Method in interface org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/TagValueListener.html" title="interface in org.biojava.bio.program.tagvalue">TagValueListener</a></dt>
<dd>
<div class="block">Start a new tag.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/ValueChanger.html#startTag(java.lang.Object)">startTag(Object)</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/ValueChanger.html" title="class in org.biojava.bio.program.tagvalue">ValueChanger</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/SimpleThreadPool.html#startThreads()">startThreads()</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/SimpleThreadPool.html" title="class in org.biojava.utils">SimpleThreadPool</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ThreadPool.html#startThreads()">startThreads()</a></span> - Method in interface org.biojava.utils.<a href="./org/biojava/utils/ThreadPool.html" title="interface in org.biojava.utils">ThreadPool</a></dt>
<dd>
<div class="block"><code>startThreads</code> starts all the threads running and
opens the pool to requests.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/StAXContentHandler.html#startTree()">startTree()</a></span> - Method in interface org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/StAXContentHandler.html" title="interface in org.biojava.bio.seq.io.agave">StAXContentHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/StAXContentHandlerBase.html#startTree()">startTree()</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/StAXContentHandlerBase.html" title="class in org.biojava.bio.seq.io.agave">StAXContentHandlerBase</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/stax/StAXContentHandler.html#startTree()">startTree()</a></span> - Method in interface org.biojava.utils.stax.<a href="./org/biojava/utils/stax/StAXContentHandler.html" title="interface in org.biojava.utils.stax">StAXContentHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/stax/StAXContentHandlerBase.html#startTree()">startTree()</a></span> - Method in class org.biojava.utils.stax.<a href="./org/biojava/utils/stax/StAXContentHandlerBase.html" title="class in org.biojava.utils.stax">StAXContentHandlerBase</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SixFrameRenderer.html#startZiggy(org.biojava.bio.seq.StrandedFeature.Strand)">startZiggy(StrandedFeature.Strand)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SixFrameRenderer.html" title="class in org.biojava.bio.gui.sequence">SixFrameRenderer</a></dt>
<dd>
<div class="block">Used to initialise the spliced transcript renderer for
a CDS feature where the ends of the feature define the
frame of the feature.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SixFrameRenderer.html#startZiggy(org.biojava.bio.seq.StrandedFeature.Strand, int)">startZiggy(StrandedFeature.Strand, int)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SixFrameRenderer.html" title="class in org.biojava.bio.gui.sequence">SixFrameRenderer</a></dt>
<dd>
<div class="block">This method is called to initialise the renderer for a
spliced transcript.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/BackPointer.html#state">state</a></span> - Variable in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/BackPointer.html" title="class in org.biojava.bio.dp">BackPointer</a></dt>
<dd>
<div class="block">The state with which this backpointer is associated.</div>
</dd>
<dt><a href="./org/biojava/bio/dp/State.html" title="interface in org.biojava.bio.dp"><span class="strong">State</span></a> - Interface in <a href="./org/biojava/bio/dp/package-summary.html">org.biojava.bio.dp</a></dt>
<dd>
<div class="block">A state in a markov process.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/MarkovModel.html#stateAlphabet()">stateAlphabet()</a></span> - Method in interface org.biojava.bio.dp.<a href="./org/biojava/bio/dp/MarkovModel.html" title="interface in org.biojava.bio.dp">MarkovModel</a></dt>
<dd>
<div class="block">FiniteAlphabet of the states.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/SimpleMarkovModel.html#stateAlphabet()">stateAlphabet()</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/SimpleMarkovModel.html" title="class in org.biojava.bio.dp">SimpleMarkovModel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/WMAsMM.html#stateAlphabet()">stateAlphabet()</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/WMAsMM.html" title="class in org.biojava.bio.dp">WMAsMM</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/ScaleableMatrixPanel.html#stateChanged(javax.swing.event.ChangeEvent)">stateChanged(ChangeEvent)</a></span> - Method in class org.biojava.bio.structure.gui.<a href="./org/biojava/bio/structure/gui/ScaleableMatrixPanel.html" title="class in org.biojava.bio.structure.gui">ScaleableMatrixPanel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/SequenceDisplay.html#stateChanged(javax.swing.event.ChangeEvent)">stateChanged(ChangeEvent)</a></span> - Method in class org.biojava.bio.structure.gui.<a href="./org/biojava/bio/structure/gui/SequenceDisplay.html" title="class in org.biojava.bio.structure.gui">SequenceDisplay</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/DP.html#stateList(org.biojava.bio.dp.MarkovModel)">stateList(MarkovModel)</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/DP.html" title="class in org.biojava.bio.dp">DP</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/tagvalue/StateMachine.html" title="class in org.biojava.bio.program.tagvalue"><span class="strong">StateMachine</span></a> - Class in <a href="./org/biojava/bio/program/tagvalue/package-summary.html">org.biojava.bio.program.tagvalue</a></dt>
<dd>
<div class="block">This class implements a state machine for parsing events from
the Parser class.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/StateMachine.html#StateMachine()">StateMachine()</a></span> - Constructor for class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/StateMachine.html" title="class in org.biojava.bio.program.tagvalue">StateMachine</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/tagvalue/StateMachine.BasicState.html" title="class in org.biojava.bio.program.tagvalue"><span class="strong">StateMachine.BasicState</span></a> - Class in <a href="./org/biojava/bio/program/tagvalue/package-summary.html">org.biojava.bio.program.tagvalue</a></dt>
<dd>
<div class="block">Implementation of a State in a state machine</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/StateMachine.BasicState.html#StateMachine.BasicState(java.lang.String)">StateMachine.BasicState(String)</a></span> - Constructor for class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/StateMachine.BasicState.html" title="class in org.biojava.bio.program.tagvalue">StateMachine.BasicState</a></dt>
<dd>
<div class="block">This is the default constructor</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/StateMachine.BasicState.html#StateMachine.BasicState(java.lang.String, org.biojava.bio.program.tagvalue.TagValueListener)">StateMachine.BasicState(String, TagValueListener)</a></span> - Constructor for class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/StateMachine.BasicState.html" title="class in org.biojava.bio.program.tagvalue">StateMachine.BasicState</a></dt>
<dd>
<div class="block">when this constructor is used, a fixed listener
is used with this state.</div>
</dd>
<dt><a href="./org/biojava/bio/program/tagvalue/StateMachine.ExitNotification.html" title="interface in org.biojava.bio.program.tagvalue"><span class="strong">StateMachine.ExitNotification</span></a> - Interface in <a href="./org/biojava/bio/program/tagvalue/package-summary.html">org.biojava.bio.program.tagvalue</a></dt>
<dd>
<div class="block">Interface implemented by State listeners that
want notification when a transition leaves the State.</div>
</dd>
<dt><a href="./org/biojava/bio/program/tagvalue/StateMachine.SimpleStateListener.html" title="class in org.biojava.bio.program.tagvalue"><span class="strong">StateMachine.SimpleStateListener</span></a> - Class in <a href="./org/biojava/bio/program/tagvalue/package-summary.html">org.biojava.bio.program.tagvalue</a></dt>
<dd>
<div class="block">a basic listener for a State.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/StateMachine.SimpleStateListener.html#StateMachine.SimpleStateListener()">StateMachine.SimpleStateListener()</a></span> - Constructor for class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/StateMachine.SimpleStateListener.html" title="class in org.biojava.bio.program.tagvalue">StateMachine.SimpleStateListener</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/tagvalue/StateMachine.State.html" title="interface in org.biojava.bio.program.tagvalue"><span class="strong">StateMachine.State</span></a> - Interface in <a href="./org/biojava/bio/program/tagvalue/package-summary.html">org.biojava.bio.program.tagvalue</a></dt>
<dd>
<div class="block">Interface for a State within this StateMachine</div>
</dd>
<dt><a href="./org/biojava/bio/program/tagvalue/StateMachine.Transition.html" title="class in org.biojava.bio.program.tagvalue"><span class="strong">StateMachine.Transition</span></a> - Class in <a href="./org/biojava/bio/program/tagvalue/package-summary.html">org.biojava.bio.program.tagvalue</a></dt>
<dd>
<div class="block">class to represent a State Transition</div>
</dd>
<dt><a href="./org/biojava/bio/program/tagvalue/StateMachine.TransitionTable.html" title="class in org.biojava.bio.program.tagvalue"><span class="strong">StateMachine.TransitionTable</span></a> - Class in <a href="./org/biojava/bio/program/tagvalue/package-summary.html">org.biojava.bio.program.tagvalue</a></dt>
<dd>
<div class="block">Table of Transition destination States
and their corresponding Tags.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/StateMachine.TransitionTable.html#StateMachine.TransitionTable()">StateMachine.TransitionTable()</a></span> - Constructor for class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/StateMachine.TransitionTable.html" title="class in org.biojava.bio.program.tagvalue">StateMachine.TransitionTable</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/utils/automata/StateMachineFactory.html" title="interface in org.biojava.utils.automata"><span class="strong">StateMachineFactory</span></a> - Interface in <a href="./org/biojava/utils/automata/package-summary.html">org.biojava.utils.automata</a></dt>
<dd>
<div class="block">Class that produces StateMachineInstance objects.</div>
</dd>
<dt><a href="./org/biojava/utils/automata/StateMachineInstance.html" title="interface in org.biojava.utils.automata"><span class="strong">StateMachineInstance</span></a> - Interface in <a href="./org/biojava/utils/automata/package-summary.html">org.biojava.utils.automata</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/dp/StatePath.html" title="interface in org.biojava.bio.dp"><span class="strong">StatePath</span></a> - Interface in <a href="./org/biojava/bio/dp/package-summary.html">org.biojava.bio.dp</a></dt>
<dd>
<div class="block">Extends the Alignment interface so that it is explicitly used to represent
a state path through an HMM, and the associated emitted sequence and
likelihoods.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/DPMatrix.html#states()">states()</a></span> - Method in interface org.biojava.bio.dp.<a href="./org/biojava/bio/dp/DPMatrix.html" title="interface in org.biojava.bio.dp">DPMatrix</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/onehead/SingleDPMatrix.html#states">states</a></span> - Variable in class org.biojava.bio.dp.onehead.<a href="./org/biojava/bio/dp/onehead/SingleDPMatrix.html" title="class in org.biojava.bio.dp.onehead">SingleDPMatrix</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/onehead/SingleDPMatrix.html#states()">states()</a></span> - Method in class org.biojava.bio.dp.onehead.<a href="./org/biojava/bio/dp/onehead/SingleDPMatrix.html" title="class in org.biojava.bio.dp.onehead">SingleDPMatrix</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/StatePath.html#STATES">STATES</a></span> - Static variable in interface org.biojava.bio.dp.<a href="./org/biojava/bio/dp/StatePath.html" title="interface in org.biojava.bio.dp">StatePath</a></dt>
<dd>
<div class="block">Alignment label for the state path.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/twohead/PairDPMatrix.html#states()">states()</a></span> - Method in class org.biojava.bio.dp.twohead.<a href="./org/biojava/bio/dp/twohead/PairDPMatrix.html" title="class in org.biojava.bio.dp.twohead">PairDPMatrix</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/utils/StaticMemberPlaceHolder.html" title="class in org.biojava.utils"><span class="strong">StaticMemberPlaceHolder</span></a> - Class in <a href="./org/biojava/utils/package-summary.html">org.biojava.utils</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/StaticMemberPlaceHolder.html#StaticMemberPlaceHolder(java.lang.reflect.Field)">StaticMemberPlaceHolder(Field)</a></span> - Constructor for class org.biojava.utils.<a href="./org/biojava/utils/StaticMemberPlaceHolder.html" title="class in org.biojava.utils">StaticMemberPlaceHolder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/StaticMemberPlaceHolder.html#StaticMemberPlaceHolder()">StaticMemberPlaceHolder()</a></span> - Constructor for class org.biojava.utils.<a href="./org/biojava/utils/StaticMemberPlaceHolder.html" title="class in org.biojava.utils">StaticMemberPlaceHolder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#STATUS_ATTR">STATUS_ATTR</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/io/agave/StAXContentHandler.html" title="interface in org.biojava.bio.seq.io.agave"><span class="strong">StAXContentHandler</span></a> - Interface in <a href="./org/biojava/bio/seq/io/agave/package-summary.html">org.biojava.bio.seq.io.agave</a></dt>
<dd>
<div class="block">Interface for StAX content handlers.</div>
</dd>
<dt><a href="./org/biojava/utils/stax/StAXContentHandler.html" title="interface in org.biojava.utils.stax"><span class="strong">StAXContentHandler</span></a> - Interface in <a href="./org/biojava/utils/stax/package-summary.html">org.biojava.utils.stax</a></dt>
<dd>
<div class="block">Interface for StAX content handlers.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/agave/StAXContentHandlerBase.html" title="class in org.biojava.bio.seq.io.agave"><span class="strong">StAXContentHandlerBase</span></a> - Class in <a href="./org/biojava/bio/seq/io/agave/package-summary.html">org.biojava.bio.seq.io.agave</a></dt>
<dd>
<div class="block">Simple implementation of the <code>StAXContentHandler</code>
interface, with empty implementations for all the methods.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/StAXContentHandlerBase.html#StAXContentHandlerBase()">StAXContentHandlerBase()</a></span> - Constructor for class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/StAXContentHandlerBase.html" title="class in org.biojava.bio.seq.io.agave">StAXContentHandlerBase</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/utils/stax/StAXContentHandlerBase.html" title="class in org.biojava.utils.stax"><span class="strong">StAXContentHandlerBase</span></a> - Class in <a href="./org/biojava/utils/stax/package-summary.html">org.biojava.utils.stax</a></dt>
<dd>
<div class="block">Simple implementation of the <code>StAXContentHandler</code>
interface, with empty implementations for all the methods.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/stax/StAXContentHandlerBase.html#StAXContentHandlerBase()">StAXContentHandlerBase()</a></span> - Constructor for class org.biojava.utils.stax.<a href="./org/biojava/utils/stax/StAXContentHandlerBase.html" title="class in org.biojava.utils.stax">StAXContentHandlerBase</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/StAXFeatureHandler.html#staxenv">staxenv</a></span> - Variable in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/StAXFeatureHandler.html" title="class in org.biojava.bio.seq.io.agave">StAXFeatureHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/StAXPropertyHandler.html#staxenv">staxenv</a></span> - Variable in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/StAXPropertyHandler.html" title="class in org.biojava.bio.seq.io.agave">StAXPropertyHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game/StAXPropertyHandler.html#staxenv">staxenv</a></span> - Variable in class org.biojava.bio.seq.io.game.<a href="./org/biojava/bio/seq/io/game/StAXPropertyHandler.html" title="class in org.biojava.bio.seq.io.game">StAXPropertyHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game12/StAXFeatureHandler.html#staxenv">staxenv</a></span> - Variable in class org.biojava.bio.seq.io.game12.<a href="./org/biojava/bio/seq/io/game12/StAXFeatureHandler.html" title="class in org.biojava.bio.seq.io.game12">StAXFeatureHandler</a></dt>
<dd>
<div class="block">Nesting class that provides callback interfaces to nested class</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/agave/StAXFeatureHandler.html" title="class in org.biojava.bio.seq.io.agave"><span class="strong">StAXFeatureHandler</span></a> - Class in <a href="./org/biojava/bio/seq/io/agave/package-summary.html">org.biojava.bio.seq.io.agave</a></dt>
<dd>
<div class="block">StAX handler shamelessly ripped off from Thomas Down's
XFFFeatureSetHandler.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/game/StAXFeatureHandler.html" title="class in org.biojava.bio.seq.io.game"><span class="strong">StAXFeatureHandler</span></a> - Class in <a href="./org/biojava/bio/seq/io/game/package-summary.html">org.biojava.bio.seq.io.game</a></dt>
<dd>
<div class="block">StAX handler shamelessly ripped off from Thomas Down's
XFFFeatureSetHandler.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/game/StAXFeatureHandler.html#StAXFeatureHandler()">StAXFeatureHandler()</a></span> - Constructor for class org.biojava.bio.seq.io.game.<a href="./org/biojava/bio/seq/io/game/StAXFeatureHandler.html" title="class in org.biojava.bio.seq.io.game">StAXFeatureHandler</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/io/game12/StAXFeatureHandler.html" title="class in org.biojava.bio.seq.io.game12"><span class="strong">StAXFeatureHandler</span></a> - Class in <a href="./org/biojava/bio/seq/io/game12/package-summary.html">org.biojava.bio.seq.io.game12</a></dt>
<dd>
<div class="block">StAX handler shamelessly ripped off from Thomas Down's XFFFeatureSetHandler.</div>
</dd>
<dt><a href="./org/biojava/bio/program/ssbind/StAXHandlerBinding.html" title="class in org.biojava.bio.program.ssbind"><span class="strong">StAXHandlerBinding</span></a> - Class in <a href="./org/biojava/bio/program/ssbind/package-summary.html">org.biojava.bio.program.ssbind</a></dt>
<dd>
<div class="block"><code>StAXHandlerBinding</code>s associates an
<code>ElementRecognizer</code> with a factory which creates
<code>StAXContentHandler</code>s for elements which it the
<code>ElementRecognizer</code> accepts.</div>
</dd>
<dt><a href="./org/biojava/bio/program/ssbind/StAXHandlerFactory.html" title="interface in org.biojava.bio.program.ssbind"><span class="strong">StAXHandlerFactory</span></a> - Interface in <a href="./org/biojava/bio/program/ssbind/package-summary.html">org.biojava.bio.program.ssbind</a></dt>
<dd>
<div class="block"><code>StAXHandlerFactory</code> is an interface for factories
producing <code>StAXContentHandler</code>s which are used by the
<code>SeqSimilarityStAXAdapter</code>.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/agave/StAXHandlerFactory.html" title="interface in org.biojava.bio.seq.io.agave"><span class="strong">StAXHandlerFactory</span></a> - Interface in <a href="./org/biojava/bio/seq/io/agave/package-summary.html">org.biojava.bio.seq.io.agave</a></dt>
<dd>
<div class="block">Factory for StAX content handlers.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/game/StAXHandlerFactory.html" title="interface in org.biojava.bio.seq.io.game"><span class="strong">StAXHandlerFactory</span></a> - Interface in <a href="./org/biojava/bio/seq/io/game/package-summary.html">org.biojava.bio.seq.io.game</a></dt>
<dd>
<div class="block">Factory for StAX content handlers.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/game12/StAXHandlerFactory.html" title="interface in org.biojava.bio.seq.io.game12"><span class="strong">StAXHandlerFactory</span></a> - Interface in <a href="./org/biojava/bio/seq/io/game12/package-summary.html">org.biojava.bio.seq.io.game12</a></dt>
<dd>
<div class="block">Factory for StAX content handlers.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/agave/StAXPropertyHandler.html" title="class in org.biojava.bio.seq.io.agave"><span class="strong">StAXPropertyHandler</span></a> - Class in <a href="./org/biojava/bio/seq/io/agave/package-summary.html">org.biojava.bio.seq.io.agave</a></dt>
<dd>
<div class="block">StAX handler shamelessly ripped off from Thomas Down's
XFFFeatureSetHandler.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/game/StAXPropertyHandler.html" title="class in org.biojava.bio.seq.io.game"><span class="strong">StAXPropertyHandler</span></a> - Class in <a href="./org/biojava/bio/seq/io/game/package-summary.html">org.biojava.bio.seq.io.game</a></dt>
<dd>
<div class="block">StAX handler shamelessly ripped off from Thomas Down's
XFFFeatureSetHandler.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ga/GAStoppingCriteria.MaximumGeneration.html#stop(org.biojavax.ga.GeneticAlgorithm)">stop(GeneticAlgorithm)</a></span> - Method in class org.biojavax.ga.<a href="./org/biojavax/ga/GAStoppingCriteria.MaximumGeneration.html" title="class in org.biojavax.ga">GAStoppingCriteria.MaximumGeneration</a></dt>
<dd>
<div class="block">Stops the Algorithm if the iterations are >= <code>maxGenerations</code></div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ga/GAStoppingCriteria.html#stop(org.biojavax.ga.GeneticAlgorithm)">stop(GeneticAlgorithm)</a></span> - Method in interface org.biojavax.ga.<a href="./org/biojavax/ga/GAStoppingCriteria.html" title="interface in org.biojavax.ga">GAStoppingCriteria</a></dt>
<dd>
<div class="block">Determines if an Algorithm should stop spawning new generations</div>
</dd>
<dt><a href="./org/biojava/bio/dp/StoppingCriteria.html" title="interface in org.biojava.bio.dp"><span class="strong">StoppingCriteria</span></a> - Interface in <a href="./org/biojava/bio/dp/package-summary.html">org.biojava.bio.dp</a></dt>
<dd>
<div class="block">A callback that is invoked during the training of an HMM.</div>
</dd>
<dt><a href="./org/biojava/bio/gui/sequence/StopRenderer.html" title="class in org.biojava.bio.gui.sequence"><span class="strong">StopRenderer</span></a> - Class in <a href="./org/biojava/bio/gui/sequence/package-summary.html">org.biojava.bio.gui.sequence</a></dt>
<dd>
<div class="block">Compute sites of stop codons.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/StopRenderer.html#StopRenderer(org.biojava.bio.gui.sequence.SixFrameRenderer, int, org.biojava.bio.seq.StrandedFeature.Strand)">StopRenderer(SixFrameRenderer, int, StrandedFeature.Strand)</a></span> - Constructor for class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/StopRenderer.html" title="class in org.biojava.bio.gui.sequence">StopRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/SimpleThreadPool.html#stopThreads()">stopThreads()</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/SimpleThreadPool.html" title="class in org.biojava.utils">SimpleThreadPool</a></dt>
<dd>
<div class="block">Waits for all working threads to return and then stops them.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/ThreadPool.html#stopThreads()">stopThreads()</a></span> - Method in interface org.biojava.utils.<a href="./org/biojava/utils/ThreadPool.html" title="interface in org.biojava.utils">ThreadPool</a></dt>
<dd>
<div class="block"><code>stopThreads</code> causes all running threads to stop
when their current task is complete.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/BioIndex.html#store(org.biojava.bio.seq.db.Index)">store(Index)</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/BioIndex.html" title="class in org.biojava.bio.seq.db">BioIndex</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/EmblCDROMIndexStore.html#store(org.biojava.bio.seq.db.Index)">store(Index)</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/EmblCDROMIndexStore.html" title="class in org.biojava.bio.seq.db">EmblCDROMIndexStore</a></dt>
<dd>
<div class="block"><code>store</code> adds an <code>Index</code> to the store.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/IndexStore.html#store(org.biojava.bio.seq.db.Index)">store(Index)</a></span> - Method in interface org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/IndexStore.html" title="interface in org.biojava.bio.seq.db">IndexStore</a></dt>
<dd>
<div class="block">Add the Index to the store.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/TabIndexStore.html#store(org.biojava.bio.seq.db.Index)">store(Index)</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/TabIndexStore.html" title="class in org.biojava.bio.seq.db">TabIndexStore</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/indexdb/BioStoreFactory.html#STORE_NAME">STORE_NAME</a></span> - Static variable in class org.biojava.bio.program.indexdb.<a href="./org/biojava/bio/program/indexdb/BioStoreFactory.html" title="class in org.biojava.bio.program.indexdb">BioStoreFactory</a></dt>
<dd>
<div class="block"><code>STORE_NAME</code> is the key used to identify the
arbitrary name of the store in the OBDA config.dat files.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/obo/OboFileParser.SOPair.html#str">str</a></span> - Variable in class org.biojava.ontology.obo.<a href="./org/biojava/ontology/obo/OboFileParser.SOPair.html" title="class in org.biojava.ontology.obo">OboFileParser.SOPair</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.Terms.html#STRAIN_KEY">STRAIN_KEY</a></span> - Static variable in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.Terms.html" title="class in org.biojavax.bio.seq">RichSequence.Terms</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/StrandedFeature.html#STRAND">STRAND</a></span> - Static variable in interface org.biojava.bio.seq.<a href="./org/biojava/bio/seq/StrandedFeature.html" title="interface in org.biojava.bio.seq">StrandedFeature</a></dt>
<dd>
<div class="block">The strand of this feature is being altered.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/StrandedFeature.Template.html#strand">strand</a></span> - Variable in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/StrandedFeature.Template.html" title="class in org.biojava.bio.seq">StrandedFeature.Template</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/PDBFileParser.html#STRAND">STRAND</a></span> - Static variable in class org.biojava.bio.structure.io.<a href="./org/biojava/bio/structure/io/PDBFileParser.html" title="class in org.biojava.bio.structure.io">PDBFileParser</a></dt>
<dd>
<div class="block">Strand secondary structure assignment.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/EmblLikeFormat.html#STRAND_NUMBER_TAG">STRAND_NUMBER_TAG</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/EmblLikeFormat.html" title="class in org.biojava.bio.seq.io">EmblLikeFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/GenbankFormat.html#STRAND_NUMBER_TAG">STRAND_NUMBER_TAG</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/GenbankFormat.html" title="class in org.biojava.bio.seq.io">GenbankFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/INSDseqFormat.html#STRANDED_TAG">STRANDED_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/INSDseqFormat.html" title="class in org.biojavax.bio.seq.io">INSDseqFormat</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/StrandedFeature.html" title="interface in org.biojava.bio.seq"><span class="strong">StrandedFeature</span></a> - Interface in <a href="./org/biojava/bio/seq/package-summary.html">org.biojava.bio.seq</a></dt>
<dd>
<div class="block">Adds the concept of 'strand' to features.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/StrandedFeature.Strand.html" title="class in org.biojava.bio.seq"><span class="strong">StrandedFeature.Strand</span></a> - Class in <a href="./org/biojava/bio/seq/package-summary.html">org.biojava.bio.seq</a></dt>
<dd>
<div class="block">Class to represent the 'strandedness' of a feature.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/StrandedFeature.Template.html" title="class in org.biojava.bio.seq"><span class="strong">StrandedFeature.Template</span></a> - Class in <a href="./org/biojava/bio/seq/package-summary.html">org.biojava.bio.seq</a></dt>
<dd>
<div class="block">Template class for parameterizing the creation of a new
<code>StrandedFeature</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/StrandedFeature.Template.html#StrandedFeature.Template()">StrandedFeature.Template()</a></span> - Constructor for class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/StrandedFeature.Template.html" title="class in org.biojava.bio.seq">StrandedFeature.Template</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/xff/StrandedFeatureHandler.html#STRANDEDFEATURE_HANDLER_FACTORY">STRANDEDFEATURE_HANDLER_FACTORY</a></span> - Static variable in class org.biojava.bio.program.xff.<a href="./org/biojava/bio/program/xff/StrandedFeatureHandler.html" title="class in org.biojava.bio.program.xff">StrandedFeatureHandler</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/xff/StrandedFeatureHandler.html" title="class in org.biojava.bio.program.xff"><span class="strong">StrandedFeatureHandler</span></a> - Class in <a href="./org/biojava/bio/program/xff/package-summary.html">org.biojava.bio.program.xff</a></dt>
<dd>
<div class="block">StAX handler for XFF strandedFeature type.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/xff/StrandedFeatureHandler.html#StrandedFeatureHandler(org.biojava.bio.program.xff.XFFFeatureSetHandler)">StrandedFeatureHandler(XFFFeatureSetHandler)</a></span> - Constructor for class org.biojava.bio.program.xff.<a href="./org/biojava/bio/program/xff/StrandedFeatureHandler.html" title="class in org.biojava.bio.program.xff">StrandedFeatureHandler</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/StrandParser.html" title="class in org.biojava.bio.seq"><span class="strong">StrandParser</span></a> - Class in <a href="./org/biojava/bio/seq/package-summary.html">org.biojava.bio.seq</a></dt>
<dd>
<div class="block">Process strings and return strand objects.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/StrandParser.html#StrandParser()">StrandParser()</a></span> - Constructor for class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/StrandParser.html" title="class in org.biojava.bio.seq">StrandParser</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/structure/align/pairwise/StrCompAlignment.html" title="class in org.biojava.bio.structure.align.pairwise"><span class="strong">StrCompAlignment</span></a> - Class in <a href="./org/biojava/bio/structure/align/pairwise/package-summary.html">org.biojava.bio.structure.align.pairwise</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/StrCompAlignment.html#StrCompAlignment(int, int)">StrCompAlignment(int, int)</a></span> - Constructor for class org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/StrCompAlignment.html" title="class in org.biojava.bio.structure.align.pairwise">StrCompAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssaha/SequenceStreamer.FileStreamer.html#streamNext(org.biojava.bio.seq.io.SeqIOListener)">streamNext(SeqIOListener)</a></span> - Method in class org.biojava.bio.program.ssaha.<a href="./org/biojava/bio/program/ssaha/SequenceStreamer.FileStreamer.html" title="class in org.biojava.bio.program.ssaha">SequenceStreamer.FileStreamer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssaha/SequenceStreamer.SequenceDBStreamer.html#streamNext(org.biojava.bio.seq.io.SeqIOListener)">streamNext(SeqIOListener)</a></span> - Method in class org.biojava.bio.program.ssaha.<a href="./org/biojava/bio/program/ssaha/SequenceStreamer.SequenceDBStreamer.html" title="class in org.biojava.bio.program.ssaha">SequenceStreamer.SequenceDBStreamer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssaha/SequenceStreamer.html#streamNext(org.biojava.bio.seq.io.SeqIOListener)">streamNext(SeqIOListener)</a></span> - Method in interface org.biojava.bio.program.ssaha.<a href="./org/biojava/bio/program/ssaha/SequenceStreamer.html" title="interface in org.biojava.bio.program.ssaha">SequenceStreamer</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/io/StreamParser.html" title="interface in org.biojava.bio.seq.io"><span class="strong">StreamParser</span></a> - Interface in <a href="./org/biojava/bio/seq/io/package-summary.html">org.biojava.bio.seq.io</a></dt>
<dd>
<div class="block">Parse a stream of characters into BioJava symbols.</div>
</dd>
<dt><a href="./org/biojava/utils/process/StreamPipe.html" title="class in org.biojava.utils.process"><span class="strong">StreamPipe</span></a> - Class in <a href="./org/biojava/utils/process/package-summary.html">org.biojava.utils.process</a></dt>
<dd>
<div class="block">A multi threaded class
which pipes the contents of an input stream to an output stream.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/process/StreamPipe.html#StreamPipe(java.io.InputStream, java.io.OutputStream, java.lang.String)">StreamPipe(InputStream, OutputStream, String)</a></span> - Constructor for class org.biojava.utils.process.<a href="./org/biojava/utils/process/StreamPipe.html" title="class in org.biojava.utils.process">StreamPipe</a></dt>
<dd>
<div class="block">Initializes the stream pipe.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/StreamReader.html" title="class in org.biojava.bio.seq.io"><span class="strong">StreamReader</span></a> - Class in <a href="./org/biojava/bio/seq/io/package-summary.html">org.biojava.bio.seq.io</a></dt>
<dd>
<div class="block">Parses a stream into sequences.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/StreamReader.html#StreamReader(java.io.InputStream, org.biojava.bio.seq.io.SequenceFormat, org.biojava.bio.seq.io.SymbolTokenization, org.biojava.bio.seq.io.SequenceBuilderFactory)">StreamReader(InputStream, SequenceFormat, SymbolTokenization, SequenceBuilderFactory)</a></span> - Constructor for class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/StreamReader.html" title="class in org.biojava.bio.seq.io">StreamReader</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/StreamReader.html#StreamReader(java.io.BufferedReader, org.biojava.bio.seq.io.SequenceFormat, org.biojava.bio.seq.io.SymbolTokenization, org.biojava.bio.seq.io.SequenceBuilderFactory)">StreamReader(BufferedReader, SequenceFormat, SymbolTokenization, SequenceBuilderFactory)</a></span> - Constructor for class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/StreamReader.html" title="class in org.biojava.bio.seq.io">StreamReader</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFEntrySet.html#streamRecords(org.biojava.bio.program.gff.GFFDocumentHandler)">streamRecords(GFFDocumentHandler)</a></span> - Method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFEntrySet.html" title="class in org.biojava.bio.program.gff">GFFEntrySet</a></dt>
<dd>
<div class="block">Write all records in this set out to a handler.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/StreamWriter.html" title="class in org.biojava.bio.seq.io"><span class="strong">StreamWriter</span></a> - Class in <a href="./org/biojava/bio/seq/io/package-summary.html">org.biojava.bio.seq.io</a></dt>
<dd>
<div class="block">Writes all of the sequences from a SequenceIterator to a stream with a
particular format.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/StreamWriter.html#StreamWriter(java.io.OutputStream, org.biojava.bio.seq.io.SequenceFormat)">StreamWriter(OutputStream, SequenceFormat)</a></span> - Constructor for class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/StreamWriter.html" title="class in org.biojava.bio.seq.io">StreamWriter</a></dt>
<dd>
<div class="block">Generate a new StreamWriter to the stream os and using format.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/SimpleMMcifParser.html#STRING_LIMIT">STRING_LIMIT</a></span> - Static variable in class org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/SimpleMMcifParser.html" title="class in org.biojava.bio.structure.io.mmcif">SimpleMMcifParser</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/ChangeTable.html#STRING_TO_INT">STRING_TO_INT</a></span> - Static variable in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/ChangeTable.html" title="class in org.biojava.bio.program.tagvalue">ChangeTable</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/utils/stax/StringElementHandlerBase.html" title="class in org.biojava.utils.stax"><span class="strong">StringElementHandlerBase</span></a> - Class in <a href="./org/biojava/utils/stax/package-summary.html">org.biojava.utils.stax</a></dt>
<dd>
<div class="block">StAX handler for any element which just contains a string.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/stax/StringElementHandlerBase.html#StringElementHandlerBase()">StringElementHandlerBase()</a></span> - Constructor for class org.biojava.utils.stax.<a href="./org/biojava/utils/stax/StringElementHandlerBase.html" title="class in org.biojava.utils.stax">StringElementHandlerBase</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/SimpleGFFRecord.html#stringifyAttributes(java.util.Map)">stringifyAttributes(Map)</a></span> - Static method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/SimpleGFFRecord.html" title="class in org.biojava.bio.program.gff">SimpleGFFRecord</a></dt>
<dd>
<div class="block">Create a <span class="type">String</span> representation of
<span class="arg">attMap</span>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/SubstitutionMatrix.html#stringnifyDescription()">stringnifyDescription()</a></span> - Method in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/SubstitutionMatrix.html" title="class in org.biojava.bio.alignment">SubstitutionMatrix</a></dt>
<dd>
<div class="block">Converts the description of the matrix to a String.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/SubstitutionMatrix.html#stringnifyMatrix()">stringnifyMatrix()</a></span> - Method in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/SubstitutionMatrix.html" title="class in org.biojava.bio.alignment">SubstitutionMatrix</a></dt>
<dd>
<div class="block">Creates a <code>String</code> representation of this matrix.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/biosql/OracleDBHelper.html#stringToClob(java.sql.Connection, java.sql.ResultSet, int, java.lang.String)">stringToClob(Connection, ResultSet, int, String)</a></span> - Method in class org.biojava.bio.seq.db.biosql.<a href="./org/biojava/bio/seq/db/biosql/OracleDBHelper.html" title="class in org.biojava.bio.seq.db.biosql">OracleDBHelper</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><a href="./org/biojavax/utils/StringTools.html" title="class in org.biojavax.utils"><span class="strong">StringTools</span></a> - Class in <a href="./org/biojavax/utils/package-summary.html">org.biojavax.utils</a></dt>
<dd>
<div class="block">Utility class for formatting strings into regular-sized blocks.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/AbstractBeadRenderer.html#STROKE">STROKE</a></span> - Static variable in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/AbstractBeadRenderer.html" title="class in org.biojava.bio.gui.sequence">AbstractBeadRenderer</a></dt>
<dd>
<div class="block">Constant <code>STROKE</code> indicating a change to the outline
stroke of the features.</div>
</dd>
<dt><a href="./org/biojava/bio/structure/align/StrucAligParameters.html" title="class in org.biojava.bio.structure.align"><span class="strong">StrucAligParameters</span></a> - Class in <a href="./org/biojava/bio/structure/align/package-summary.html">org.biojava.bio.structure.align</a></dt>
<dd>
<div class="block">A class that contains all the parameters of the structure alignment algorithm.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/StrucAligParameters.html#StrucAligParameters()">StrucAligParameters()</a></span> - Constructor for class org.biojava.bio.structure.align.<a href="./org/biojava/bio/structure/align/StrucAligParameters.html" title="class in org.biojava.bio.structure.align">StrucAligParameters</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/structure/io/mmcif/model/Struct.html" title="class in org.biojava.bio.structure.io.mmcif.model"><span class="strong">Struct</span></a> - Class in <a href="./org/biojava/bio/structure/io/mmcif/model/package-summary.html">org.biojava.bio.structure.io.mmcif.model</a></dt>
<dd>
<div class="block">a bean to contain the data of the _struct lines</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Struct.html#Struct()">Struct()</a></span> - Constructor for class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Struct.html" title="class in org.biojava.bio.structure.io.mmcif.model">Struct</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/structure/io/mmcif/model/StructAsym.html" title="class in org.biojava.bio.structure.io.mmcif.model"><span class="strong">StructAsym</span></a> - Class in <a href="./org/biojava/bio/structure/io/mmcif/model/package-summary.html">org.biojava.bio.structure.io.mmcif.model</a></dt>
<dd>
<div class="block">Contains the data for _struct_asym</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/StructAsym.html#StructAsym()">StructAsym()</a></span> - Constructor for class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/StructAsym.html" title="class in org.biojava.bio.structure.io.mmcif.model">StructAsym</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/structure/io/mmcif/model/StructKeywords.html" title="class in org.biojava.bio.structure.io.mmcif.model"><span class="strong">StructKeywords</span></a> - Class in <a href="./org/biojava/bio/structure/io/mmcif/model/package-summary.html">org.biojava.bio.structure.io.mmcif.model</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/StructKeywords.html#StructKeywords()">StructKeywords()</a></span> - Constructor for class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/StructKeywords.html" title="class in org.biojava.bio.structure.io.mmcif.model">StructKeywords</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/structure/io/mmcif/model/StructRef.html" title="class in org.biojava.bio.structure.io.mmcif.model"><span class="strong">StructRef</span></a> - Class in <a href="./org/biojava/bio/structure/io/mmcif/model/package-summary.html">org.biojava.bio.structure.io.mmcif.model</a></dt>
<dd>
<div class="block">A class to containt the _struct_ref field data</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/StructRef.html#StructRef()">StructRef()</a></span> - Constructor for class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/StructRef.html" title="class in org.biojava.bio.structure.io.mmcif.model">StructRef</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/structure/io/mmcif/model/StructRefSeq.html" title="class in org.biojava.bio.structure.io.mmcif.model"><span class="strong">StructRefSeq</span></a> - Class in <a href="./org/biojava/bio/structure/io/mmcif/model/package-summary.html">org.biojava.bio.structure.io.mmcif.model</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/StructRefSeq.html#StructRefSeq()">StructRefSeq()</a></span> - Constructor for class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/StructRefSeq.html" title="class in org.biojava.bio.structure.io.mmcif.model">StructRefSeq</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/structure/Structure.html" title="interface in org.biojava.bio.structure"><span class="strong">Structure</span></a> - Interface in <a href="./org/biojava/bio/structure/package-summary.html">org.biojava.bio.structure</a></dt>
<dd>
<div class="block">Interface for a structure object.</div>
</dd>
<dt><a href="./org/biojava/bio/structure/server/StructureEvent.html" title="interface in org.biojava.bio.structure.server"><span class="strong">StructureEvent</span></a> - Interface in <a href="./org/biojava/bio/structure/server/package-summary.html">org.biojava.bio.structure.server</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/structure/server/StructureEventImpl.html" title="class in org.biojava.bio.structure.server"><span class="strong">StructureEventImpl</span></a> - Class in <a href="./org/biojava/bio/structure/server/package-summary.html">org.biojava.bio.structure.server</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/server/StructureEventImpl.html#StructureEventImpl(org.biojava.bio.structure.Structure)">StructureEventImpl(Structure)</a></span> - Constructor for class org.biojava.bio.structure.server.<a href="./org/biojava/bio/structure/server/StructureEventImpl.html" title="class in org.biojava.bio.structure.server">StructureEventImpl</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/structure/StructureException.html" title="class in org.biojava.bio.structure"><span class="strong">StructureException</span></a> - Exception in <a href="./org/biojava/bio/structure/package-summary.html">org.biojava.bio.structure</a></dt>
<dd>
<div class="block">An exception during the parsing of a PDB file.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/StructureException.html#StructureException(java.lang.String)">StructureException(String)</a></span> - Constructor for exception org.biojava.bio.structure.<a href="./org/biojava/bio/structure/StructureException.html" title="class in org.biojava.bio.structure">StructureException</a></dt>
<dd>
<div class="block">Constructs a StructureException object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/StructureException.html#StructureException(java.lang.String, java.lang.Throwable)">StructureException(String, Throwable)</a></span> - Constructor for exception org.biojava.bio.structure.<a href="./org/biojava/bio/structure/StructureException.html" title="class in org.biojava.bio.structure">StructureException</a></dt>
<dd>
<div class="block">Constructs a StructureException object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/StructureException.html#StructureException(java.lang.Throwable, java.lang.String)">StructureException(Throwable, String)</a></span> - Constructor for exception org.biojava.bio.structure.<a href="./org/biojava/bio/structure/StructureException.html" title="class in org.biojava.bio.structure">StructureException</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>use new StructureException(message, ex) instead</i></div>
</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/StructureException.html#StructureException(java.lang.Throwable)">StructureException(Throwable)</a></span> - Constructor for exception org.biojava.bio.structure.<a href="./org/biojava/bio/structure/StructureException.html" title="class in org.biojava.bio.structure">StructureException</a></dt>
<dd>
<div class="block">Constructs a StructureException object.</div>
</dd>
<dt><a href="./org/biojava/bio/structure/server/StructureFetcherRunnable.html" title="class in org.biojava.bio.structure.server"><span class="strong">StructureFetcherRunnable</span></a> - Class in <a href="./org/biojava/bio/structure/server/package-summary.html">org.biojava.bio.structure.server</a></dt>
<dd>
<div class="block">a Runnable class that talks to a PDBInstallation and requests a new protein
structure.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/server/StructureFetcherRunnable.html#StructureFetcherRunnable(org.biojava.bio.structure.server.PDBInstallation)">StructureFetcherRunnable(PDBInstallation)</a></span> - Constructor for class org.biojava.bio.structure.server.<a href="./org/biojava/bio/structure/server/StructureFetcherRunnable.html" title="class in org.biojava.bio.structure.server">StructureFetcherRunnable</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/structure/StructureImpl.html" title="class in org.biojava.bio.structure"><span class="strong">StructureImpl</span></a> - Class in <a href="./org/biojava/bio/structure/package-summary.html">org.biojava.bio.structure</a></dt>
<dd>
<div class="block">Implementation of a PDB Structure.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/StructureImpl.html#StructureImpl()">StructureImpl()</a></span> - Constructor for class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/StructureImpl.html" title="class in org.biojava.bio.structure">StructureImpl</a></dt>
<dd>
<div class="block">Constructs a StructureImpl object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/StructureImpl.html#StructureImpl(org.biojava.bio.structure.Group)">StructureImpl(Group)</a></span> - Constructor for class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/StructureImpl.html" title="class in org.biojava.bio.structure">StructureImpl</a></dt>
<dd>
<div class="block">construct a Structure object that only contains a single group</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/StructureImpl.html#StructureImpl(org.biojava.bio.structure.Chain)">StructureImpl(Chain)</a></span> - Constructor for class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/StructureImpl.html" title="class in org.biojava.bio.structure">StructureImpl</a></dt>
<dd>
<div class="block">construct a Structure object that contains a particular chain</div>
</dd>
<dt><a href="./org/biojava/bio/structure/io/StructureIO.html" title="interface in org.biojava.bio.structure.io"><span class="strong">StructureIO</span></a> - Interface in <a href="./org/biojava/bio/structure/io/package-summary.html">org.biojava.bio.structure.io</a></dt>
<dd>
<div class="block">Defines the interface how to access Structure (- PDB file) input,output readers, writers.</div>
</dd>
<dt><a href="./org/biojava/bio/structure/io/StructureIOFile.html" title="interface in org.biojava.bio.structure.io"><span class="strong">StructureIOFile</span></a> - Interface in <a href="./org/biojava/bio/structure/io/package-summary.html">org.biojava.bio.structure.io</a></dt>
<dd>
<div class="block">interface StructureIOFile extends the StructureIO interface
and adds a few File specific methods.</div>
</dd>
<dt><a href="./org/biojava/bio/structure/server/StructureListener.html" title="interface in org.biojava.bio.structure.server"><span class="strong">StructureListener</span></a> - Interface in <a href="./org/biojava/bio/structure/server/package-summary.html">org.biojava.bio.structure.server</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/structure/align/StructurePairAligner.html" title="class in org.biojava.bio.structure.align"><span class="strong">StructurePairAligner</span></a> - Class in <a href="./org/biojava/bio/structure/align/package-summary.html">org.biojava.bio.structure.align</a></dt>
<dd>
<div class="block">Perform a pairwise protein structure superimposition.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/StructurePairAligner.html#StructurePairAligner()">StructurePairAligner()</a></span> - Constructor for class org.biojava.bio.structure.align.<a href="./org/biojava/bio/structure/align/StructurePairAligner.html" title="class in org.biojava.bio.structure.align">StructurePairAligner</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/structure/gui/util/StructurePairSelector.html" title="interface in org.biojava.bio.structure.gui.util"><span class="strong">StructurePairSelector</span></a> - Interface in <a href="./org/biojava/bio/structure/gui/util/package-summary.html">org.biojava.bio.structure.gui.util</a></dt>
<dd>
<div class="block">To be implemented by JPanels that are part of the GUI to trigger structure aligmnents.</div>
</dd>
<dt><a href="./org/biojava/bio/structure/server/StructureServer.html" title="interface in org.biojava.bio.structure.server"><span class="strong">StructureServer</span></a> - Interface in <a href="./org/biojava/bio/structure/server/package-summary.html">org.biojava.bio.structure.server</a></dt>
<dd>
<div class="block">a server that pre-loads PDB files in memory, for quicker processing by StructureListeners</div>
</dd>
<dt><a href="./org/biojava/bio/proteomics/StructureTools.html" title="class in org.biojava.bio.proteomics"><span class="strong">StructureTools</span></a> - Class in <a href="./org/biojava/bio/proteomics/package-summary.html">org.biojava.bio.proteomics</a></dt>
<dd>
<div class="block">Simple access to protein seccondary structure assignments.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/StructureTools.html#StructureTools()">StructureTools()</a></span> - Constructor for class org.biojava.bio.proteomics.<a href="./org/biojava/bio/proteomics/StructureTools.html" title="class in org.biojava.bio.proteomics">StructureTools</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/structure/StructureTools.html" title="class in org.biojava.bio.structure"><span class="strong">StructureTools</span></a> - Class in <a href="./org/biojava/bio/structure/package-summary.html">org.biojava.bio.structure</a></dt>
<dd>
<div class="block">A class that provides some tool methods.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/StructureTools.html#StructureTools()">StructureTools()</a></span> - Constructor for class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/StructureTools.html" title="class in org.biojava.bio.structure">StructureTools</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/AbstractULAlignment.html#subAlignment(java.util.Set, org.biojava.bio.symbol.Location)">subAlignment(Set, Location)</a></span> - Method in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/AbstractULAlignment.html" title="class in org.biojava.bio.alignment">AbstractULAlignment</a></dt>
<dd>
<div class="block">Retrieves a subalignment specified by the location.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/AbstractULAlignment.html#subAlignment(java.util.Set, int, int)">subAlignment(Set, int, int)</a></span> - Method in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/AbstractULAlignment.html" title="class in org.biojava.bio.alignment">AbstractULAlignment</a></dt>
<dd>
<div class="block">Retreives a subAlignment</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/AbstractULAlignment.SubULAlignment.html#subAlignment(java.util.Set, org.biojava.bio.symbol.Location)">subAlignment(Set, Location)</a></span> - Method in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/AbstractULAlignment.SubULAlignment.html" title="class in org.biojava.bio.alignment">AbstractULAlignment.SubULAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/SimpleStatePath.html#subAlignment(java.util.Set, org.biojava.bio.symbol.Location)">subAlignment(Set, Location)</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/SimpleStatePath.html" title="class in org.biojava.bio.dp">SimpleStatePath</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/homol/SimilarityPairFeature.EmptyPairwiseAlignment.html#subAlignment(java.util.Set, org.biojava.bio.symbol.Location)">subAlignment(Set, Location)</a></span> - Method in class org.biojava.bio.seq.homol.<a href="./org/biojava/bio/seq/homol/SimilarityPairFeature.EmptyPairwiseAlignment.html" title="class in org.biojava.bio.seq.homol">SimilarityPairFeature.EmptyPairwiseAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/Alignment.html#subAlignment(java.util.Set, org.biojava.bio.symbol.Location)">subAlignment(Set, Location)</a></span> - Method in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/Alignment.html" title="interface in org.biojava.bio.symbol">Alignment</a></dt>
<dd>
<div class="block">
Make a view onto this alignment.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/RelabeledAlignment.html#subAlignment(java.util.Set, org.biojava.bio.symbol.Location)">subAlignment(Set, Location)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/RelabeledAlignment.html" title="class in org.biojava.bio.symbol">RelabeledAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleAlignment.html#subAlignment(java.util.Set, org.biojava.bio.symbol.Location)">subAlignment(Set, Location)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleAlignment.html" title="class in org.biojava.bio.symbol">SimpleAlignment</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/gui/sequence/SubCircularRendererContext.html" title="class in org.biojava.bio.gui.sequence"><span class="strong">SubCircularRendererContext</span></a> - Class in <a href="./org/biojava/bio/gui/sequence/package-summary.html">org.biojava.bio.gui.sequence</a></dt>
<dd>
<div class="block">A renderer context that allows some or all properties of another context to
be over-ridden.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SubCircularRendererContext.html#SubCircularRendererContext(org.biojava.bio.gui.sequence.CircularRendererContext, org.biojava.bio.symbol.SymbolList, org.biojava.bio.seq.FeatureHolder, double)">SubCircularRendererContext(CircularRendererContext, SymbolList, FeatureHolder, double)</a></span> - Constructor for class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SubCircularRendererContext.html" title="class in org.biojava.bio.gui.sequence">SubCircularRendererContext</a></dt>
<dd>
<div class="block">Create a new sub context.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/CollectionConstraint.AllValuesIn.html#subConstraintOf(org.biojava.bio.CollectionConstraint)">subConstraintOf(CollectionConstraint)</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/CollectionConstraint.AllValuesIn.html" title="class in org.biojava.bio">CollectionConstraint.AllValuesIn</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/CollectionConstraint.And.html#subConstraintOf(org.biojava.bio.CollectionConstraint)">subConstraintOf(CollectionConstraint)</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/CollectionConstraint.And.html" title="class in org.biojava.bio">CollectionConstraint.And</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/CollectionConstraint.Contains.html#subConstraintOf(org.biojava.bio.CollectionConstraint)">subConstraintOf(CollectionConstraint)</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/CollectionConstraint.Contains.html" title="class in org.biojava.bio">CollectionConstraint.Contains</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/CollectionConstraint.Or.html#subConstraintOf(org.biojava.bio.CollectionConstraint)">subConstraintOf(CollectionConstraint)</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/CollectionConstraint.Or.html" title="class in org.biojava.bio">CollectionConstraint.Or</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/CollectionConstraint.html#subConstraintOf(org.biojava.bio.CollectionConstraint)">subConstraintOf(CollectionConstraint)</a></span> - Method in interface org.biojava.bio.<a href="./org/biojava/bio/CollectionConstraint.html" title="interface in org.biojava.bio">CollectionConstraint</a></dt>
<dd>
<div class="block"><code>subConstraintOf</code> returns true if the constraint
is a sub-constraint.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/PropertyConstraint.And.html#subConstraintOf(org.biojava.bio.PropertyConstraint)">subConstraintOf(PropertyConstraint)</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/PropertyConstraint.And.html" title="class in org.biojava.bio">PropertyConstraint.And</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/PropertyConstraint.ByAnnotationType.html#subConstraintOf(org.biojava.bio.PropertyConstraint)">subConstraintOf(PropertyConstraint)</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/PropertyConstraint.ByAnnotationType.html" title="class in org.biojava.bio">PropertyConstraint.ByAnnotationType</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/PropertyConstraint.ByClass.html#subConstraintOf(org.biojava.bio.PropertyConstraint)">subConstraintOf(PropertyConstraint)</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/PropertyConstraint.ByClass.html" title="class in org.biojava.bio">PropertyConstraint.ByClass</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/PropertyConstraint.Enumeration.html#subConstraintOf(org.biojava.bio.PropertyConstraint)">subConstraintOf(PropertyConstraint)</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/PropertyConstraint.Enumeration.html" title="class in org.biojava.bio">PropertyConstraint.Enumeration</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/PropertyConstraint.ExactValue.html#subConstraintOf(org.biojava.bio.PropertyConstraint)">subConstraintOf(PropertyConstraint)</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/PropertyConstraint.ExactValue.html" title="class in org.biojava.bio">PropertyConstraint.ExactValue</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/PropertyConstraint.Or.html#subConstraintOf(org.biojava.bio.PropertyConstraint)">subConstraintOf(PropertyConstraint)</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/PropertyConstraint.Or.html" title="class in org.biojava.bio">PropertyConstraint.Or</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/PropertyConstraint.html#subConstraintOf(org.biojava.bio.PropertyConstraint)">subConstraintOf(PropertyConstraint)</a></span> - Method in interface org.biojava.bio.<a href="./org/biojava/bio/PropertyConstraint.html" title="interface in org.biojava.bio">PropertyConstraint</a></dt>
<dd>
<div class="block"><code>subConstraintOf</code> returns true if the constraint
is a sub-constraint.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/StAXFeatureHandler.html#subFeatures">subFeatures</a></span> - Variable in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/StAXFeatureHandler.html" title="class in org.biojava.bio.seq.io.agave">StAXFeatureHandler</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/io/SubIntegerTokenization.html" title="class in org.biojava.bio.seq.io"><span class="strong">SubIntegerTokenization</span></a> - Class in <a href="./org/biojava/bio/seq/io/package-summary.html">org.biojava.bio.seq.io</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SubIntegerTokenization.html#SubIntegerTokenization(org.biojava.bio.symbol.IntegerAlphabet.SubIntegerAlphabet)">SubIntegerTokenization(IntegerAlphabet.SubIntegerAlphabet)</a></span> - Constructor for class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SubIntegerTokenization.html" title="class in org.biojava.bio.seq.io">SubIntegerTokenization</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BibRef.html#subject">subject</a></span> - Variable in class org.biojava.bibliography.<a href="./org/biojava/bibliography/BibRef.html" title="class in org.biojava.bibliography">BibRef</a></dt>
<dd>
<div class="block">It defines the topic of the content of the cited resource.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BibRefSupport.html#SUBJECT_HEADINGS">SUBJECT_HEADINGS</a></span> - Static variable in interface org.biojava.bibliography.<a href="./org/biojava/bibliography/BibRefSupport.html" title="interface in org.biojava.bibliography">BibRefSupport</a></dt>
<dd>
<div class="block">A vocabulary name.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/homol/SimilarityPairFeature.html#SUBJECT_LABEL">SUBJECT_LABEL</a></span> - Static variable in interface org.biojava.bio.seq.homol.<a href="./org/biojava/bio/seq/homol/SimilarityPairFeature.html" title="interface in org.biojava.bio.seq.homol">SimilarityPairFeature</a></dt>
<dd>
<div class="block">Constant <code>SUBJECT_LABEL</code> is the alignment label used
for all subject sequences.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/ViewSequenceFactory.html#subjectDBs">subjectDBs</a></span> - Variable in class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/ViewSequenceFactory.html" title="class in org.biojava.bio.program.ssbind">ViewSequenceFactory</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BiblioSubject.html#subjectHeadings">subjectHeadings</a></span> - Variable in class org.biojava.bibliography.<a href="./org/biojava/bibliography/BiblioSubject.html" title="class in org.biojava.bibliography">BiblioSubject</a></dt>
<dd>
<div class="block">The subject headings usually come from standard lists
such as <em>Sears List of Subject Headings</em>,
or <em>Library of Congress Subject Headings (LCSH)</em>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BiblioSubject.html#subjectHeadingsSource">subjectHeadingsSource</a></span> - Variable in class org.biojava.bibliography.<a href="./org/biojava/bibliography/BiblioSubject.html" title="class in org.biojava.bibliography">BiblioSubject</a></dt>
<dd>
<div class="block">The source of <a href="./org/biojava/bibliography/BiblioSubject.html#subjectHeadings"><code>subject headings</code></a>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/ViewSequenceFactory.html#subjectViewCache">subjectViewCache</a></span> - Variable in class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/ViewSequenceFactory.html" title="class in org.biojava.bio.program.ssbind">ViewSequenceFactory</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/SimpleStatePath.html#subList(int, int)">subList(int, int)</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/SimpleStatePath.html" title="class in org.biojava.bio.dp">SimpleStatePath</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/DASSequence.html#subList(int, int)">subList(int, int)</a></span> - Method in class org.biojava.bio.program.das.<a href="./org/biojava/bio/program/das/DASSequence.html" title="class in org.biojava.bio.program.das">DASSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/CircularView.html#subList(int, int)">subList(int, int)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/CircularView.html" title="class in org.biojava.bio.seq">CircularView</a></dt>
<dd>
<div class="block">
Over rides ViewSequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/homol/SimilarityPairFeature.EmptyPairwiseAlignment.html#subList(int, int)">subList(int, int)</a></span> - Method in class org.biojava.bio.seq.homol.<a href="./org/biojava/bio/seq/homol/SimilarityPairFeature.EmptyPairwiseAlignment.html" title="class in org.biojava.bio.seq.homol">SimilarityPairFeature.EmptyPairwiseAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/AssembledSymbolList.html#subList(int, int)">subList(int, int)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/AssembledSymbolList.html" title="class in org.biojava.bio.seq.impl">AssembledSymbolList</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/DummySequence.html#subList(int, int)">subList(int, int)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/DummySequence.html" title="class in org.biojava.bio.seq.impl">DummySequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/NewAssembledSymbolList.html#subList(int, int)">subList(int, int)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/NewAssembledSymbolList.html" title="class in org.biojava.bio.seq.impl">NewAssembledSymbolList</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleSequence.html#subList(int, int)">subList(int, int)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleSequence.html" title="class in org.biojava.bio.seq.impl">SimpleSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SubSequence.html#subList(int, int)">subList(int, int)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SubSequence.html" title="class in org.biojava.bio.seq.impl">SubSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/ViewSequence.html#subList(int, int)">subList(int, int)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/ViewSequence.html" title="class in org.biojava.bio.seq.impl">ViewSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/NewSimpleAssembly.html#subList(int, int)">subList(int, int)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/NewSimpleAssembly.html" title="class in org.biojava.bio.seq">NewSimpleAssembly</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/SimpleAssembly.html#subList(int, int)">subList(int, int)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/SimpleAssembly.html" title="class in org.biojava.bio.seq">SimpleAssembly</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AbstractSymbolList.html#subList(int, int)">subList(int, int)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AbstractSymbolList.html" title="class in org.biojava.bio.symbol">AbstractSymbolList</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/ChunkedSymbolList.html#subList(int, int)">subList(int, int)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/ChunkedSymbolList.html" title="class in org.biojava.bio.symbol">ChunkedSymbolList</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/RelabeledAlignment.html#subList(int, int)">subList(int, int)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/RelabeledAlignment.html" title="class in org.biojava.bio.symbol">RelabeledAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleSymbolList.html#subList(int, int)">subList(int, int)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleSymbolList.html" title="class in org.biojava.bio.symbol">SimpleSymbolList</a></dt>
<dd>
<div class="block">create a subList of the original, this will be a view until
either the original symbolList or the sublist is edited</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SymbolList.html#subList(int, int)">subList(int, int)</a></span> - Method in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SymbolList.html" title="interface in org.biojava.bio.symbol">SymbolList</a></dt>
<dd>
<div class="block">Return a new SymbolList for the symbols start to end inclusive.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SymbolListViews.html#subList(org.biojava.bio.symbol.SymbolList, int, int)">subList(SymbolList, int, int)</a></span> - Static method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SymbolListViews.html" title="class in org.biojava.bio.symbol">SymbolListViews</a></dt>
<dd>
<div class="block">View a portion of a SymbolList.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLRichSequenceHandler.html#subList(org.biojavax.bio.seq.RichSequence, int, int)">subList(RichSequence, int, int)</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLRichSequenceHandler.html" title="class in org.biojavax.bio.db.biosql">BioSQLRichSequenceHandler</a></dt>
<dd>
<div class="block">Return a new SymbolList for the symbols start to end inclusive.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/DummyRichSequenceHandler.html#subList(org.biojavax.bio.seq.RichSequence, int, int)">subList(RichSequence, int, int)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/DummyRichSequenceHandler.html" title="class in org.biojavax.bio.seq">DummyRichSequenceHandler</a></dt>
<dd>
<div class="block">Return a new SymbolList for the symbols start to end inclusive.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/InfinitelyAmbiguousSymbolList.html#subList(int, int)">subList(int, int)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/InfinitelyAmbiguousSymbolList.html" title="class in org.biojavax.bio.seq">InfinitelyAmbiguousSymbolList</a></dt>
<dd>
<div class="block">Return a new SymbolList for the symbols start to end inclusive.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequenceHandler.html#subList(org.biojavax.bio.seq.RichSequence, int, int)">subList(RichSequence, int, int)</a></span> - Method in interface org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequenceHandler.html" title="interface in org.biojavax.bio.seq">RichSequenceHandler</a></dt>
<dd>
<div class="block">Return a new SymbolList for the symbols start to end inclusive.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/ThinRichSequence.html#subList(int, int)">subList(int, int)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/ThinRichSequence.html" title="class in org.biojavax.bio.seq">ThinRichSequence</a></dt>
<dd>
<div class="block">Return a new SymbolList for the symbols start to end inclusive.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/NeedlemanWunsch.html#subMatrix">subMatrix</a></span> - Variable in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/NeedlemanWunsch.html" title="class in org.biojava.bio.alignment">NeedlemanWunsch</a></dt>
<dd>
<div class="block">A matrix with the size length(alphabet) times length(alphabet)</div>
</dd>
<dt><a href="./org/biojava/bio/gui/sequence/SubPairwiseRenderContext.html" title="class in org.biojava.bio.gui.sequence"><span class="strong">SubPairwiseRenderContext</span></a> - Class in <a href="./org/biojava/bio/gui/sequence/package-summary.html">org.biojava.bio.gui.sequence</a></dt>
<dd>
<div class="block"><code>SubPairwiseRenderContext</code> is a rendering context
which wraps a delegate context and effectively hides some of the
delegate's properties with its own.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SubPairwiseRenderContext.html#SubPairwiseRenderContext(org.biojava.bio.gui.sequence.PairwiseRenderContext, org.biojava.bio.symbol.SymbolList, org.biojava.bio.symbol.SymbolList, org.biojava.bio.seq.FeatureHolder, org.biojava.bio.seq.FeatureHolder, org.biojava.bio.symbol.RangeLocation, org.biojava.bio.symbol.RangeLocation)">SubPairwiseRenderContext(PairwiseRenderContext, SymbolList, SymbolList, FeatureHolder, FeatureHolder, RangeLocation, RangeLocation)</a></span> - Constructor for class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SubPairwiseRenderContext.html" title="class in org.biojava.bio.gui.sequence">SubPairwiseRenderContext</a></dt>
<dd>
<div class="block">Creates a new <code>SubPairwiseRenderContext</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.Option.html#SUBPATH_LENGTH">SUBPATH_LENGTH</a></span> - Static variable in class org.biojava.bio.chromatogram.graphic.<a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.Option.html" title="class in org.biojava.bio.chromatogram.graphic">ChromatogramGraphic.Option</a></dt>
<dd>
<div class="block">To improve performance, the drawing objects for the chromatogram
traces are precomputed.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.html#subpathsValid">subpathsValid</a></span> - Variable in class org.biojava.bio.chromatogram.graphic.<a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.html" title="class in org.biojava.bio.chromatogram.graphic">ChromatogramGraphic</a></dt>
<dd>
<div class="block">Flag for subpaths.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/impl/SubSequence.html" title="class in org.biojava.bio.seq.impl"><span class="strong">SubSequence</span></a> - Class in <a href="./org/biojava/bio/seq/impl/package-summary.html">org.biojava.bio.seq.impl</a></dt>
<dd>
<div class="block">View a sub-section of a given sequence object, including all the
features intersecting that region.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SubSequence.html#SubSequence(org.biojava.bio.seq.Sequence, int, int, java.lang.String)">SubSequence(Sequence, int, int, String)</a></span> - Constructor for class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SubSequence.html" title="class in org.biojava.bio.seq.impl">SubSequence</a></dt>
<dd>
<div class="block">Construct a new SubSequence of the specified sequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SubSequence.html#SubSequence(org.biojava.bio.seq.Sequence, int, int)">SubSequence(Sequence, int, int)</a></span> - Constructor for class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SubSequence.html" title="class in org.biojava.bio.seq.impl">SubSequence</a></dt>
<dd>
<div class="block">Construct a new SubSequence of the specified sequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SymbolListCharSequence.html#subSequence(int, int)">subSequence(int, int)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SymbolListCharSequence.html" title="class in org.biojava.bio.seq.io">SymbolListCharSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/SequenceTools.html#subSequence(org.biojava.bio.seq.Sequence, int, int)">subSequence(Sequence, int, int)</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/SequenceTools.html" title="class in org.biojava.bio.seq">SequenceTools</a></dt>
<dd>
<div class="block">Extract a sub-sequence from a sequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/SequenceTools.html#subSequence(org.biojava.bio.seq.Sequence, int, int, java.lang.String)">subSequence(Sequence, int, int, String)</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/SequenceTools.html" title="class in org.biojava.bio.seq">SequenceTools</a></dt>
<dd>
<div class="block">Extract a sub-sequence from a sequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/SequenceTools.html#subSequence(org.biojava.bio.seq.Sequence, int, int, java.lang.String, org.biojava.bio.seq.StrandedFeature.Strand)">subSequence(Sequence, int, int, String, StrandedFeature.Strand)</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/SequenceTools.html" title="class in org.biojava.bio.seq">SequenceTools</a></dt>
<dd>
<div class="block">Extract a sub-sequence from a sequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/RepeatedCharSequence.html#subSequence(int, int)">subSequence(int, int)</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/RepeatedCharSequence.html" title="class in org.biojava.utils">RepeatedCharSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.Tools.html#subSequence(org.biojavax.bio.seq.RichSequence, int, int, org.biojavax.Namespace, java.lang.String, java.lang.String, java.lang.String, int, java.lang.Double)">subSequence(RichSequence, int, int, Namespace, String, String, String, int, Double)</a></span> - Static method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.Tools.html" title="class in org.biojavax.bio.seq">RichSequence.Tools</a></dt>
<dd>
<div class="block">
Creates a new sequence from a subregion of another sequence.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/impl/SubSequence.SubProjectedFeatureContext.html" title="class in org.biojava.bio.seq.impl"><span class="strong">SubSequence.SubProjectedFeatureContext</span></a> - Class in <a href="./org/biojava/bio/seq/impl/package-summary.html">org.biojava.bio.seq.impl</a></dt>
<dd>
<div class="block">TargetContext that implements the mapping between the parent sequence and this
sub-sequence.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/db/SubSequenceDB.html" title="class in org.biojava.bio.seq.db"><span class="strong">SubSequenceDB</span></a> - Class in <a href="./org/biojava/bio/seq/db/package-summary.html">org.biojava.bio.seq.db</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/SubSequenceDB.html#SubSequenceDB(org.biojava.bio.seq.db.SequenceDB, java.util.Set)">SubSequenceDB(SequenceDB, Set)</a></span> - Constructor for class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/SubSequenceDB.html" title="class in org.biojava.bio.seq.db">SubSequenceDB</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/gui/sequence/SubSequenceRenderContext.html" title="class in org.biojava.bio.gui.sequence"><span class="strong">SubSequenceRenderContext</span></a> - Class in <a href="./org/biojava/bio/gui/sequence/package-summary.html">org.biojava.bio.gui.sequence</a></dt>
<dd>
<div class="block">Allows a new renderer to "wrap" another one, replacing one or more values.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SubSequenceRenderContext.html#SubSequenceRenderContext(org.biojava.bio.gui.sequence.SequenceRenderContext, org.biojava.bio.symbol.SymbolList, org.biojava.bio.seq.FeatureHolder, org.biojava.bio.symbol.RangeLocation)">SubSequenceRenderContext(SequenceRenderContext, SymbolList, FeatureHolder, RangeLocation)</a></span> - Constructor for class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SubSequenceRenderContext.html" title="class in org.biojava.bio.gui.sequence">SubSequenceRenderContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SubSequenceRenderContext.html#SubSequenceRenderContext(org.biojava.bio.gui.sequence.SequenceRenderContext, org.biojava.bio.symbol.SymbolList, org.biojava.bio.seq.FeatureHolder, org.biojava.bio.symbol.RangeLocation, int)">SubSequenceRenderContext(SequenceRenderContext, SymbolList, FeatureHolder, RangeLocation, int)</a></span> - Constructor for class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SubSequenceRenderContext.html" title="class in org.biojava.bio.gui.sequence">SubSequenceRenderContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/obo/OboFileHandler.html#SUBSET">SUBSET</a></span> - Static variable in class org.biojava.ontology.obo.<a href="./org/biojava/ontology/obo/OboFileHandler.html" title="class in org.biojava.ontology.obo">OboFileHandler</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/alignment/SubstitutionMatrix.html" title="class in org.biojava.bio.alignment"><span class="strong">SubstitutionMatrix</span></a> - Class in <a href="./org/biojava/bio/alignment/package-summary.html">org.biojava.bio.alignment</a></dt>
<dd>
<div class="block">
This object is able to read a substitution matrix file and constructs a short
matrix in memory.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/SubstitutionMatrix.html#SubstitutionMatrix(org.biojava.bio.symbol.FiniteAlphabet, java.io.File)">SubstitutionMatrix(FiniteAlphabet, File)</a></span> - Constructor for class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/SubstitutionMatrix.html" title="class in org.biojava.bio.alignment">SubstitutionMatrix</a></dt>
<dd>
<div class="block">This constructs a <code>SubstitutionMatrix</code> object that contains
two <code>Map</code> data structures having BioJava symbols as keys and
the value being the index of the matrix containing the substitution score.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/SubstitutionMatrix.html#SubstitutionMatrix(org.biojava.bio.symbol.FiniteAlphabet, java.lang.String, java.lang.String)">SubstitutionMatrix(FiniteAlphabet, String, String)</a></span> - Constructor for class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/SubstitutionMatrix.html" title="class in org.biojava.bio.alignment">SubstitutionMatrix</a></dt>
<dd>
<div class="block">With this constructor it is possible to construct a SubstitutionMatrix
object from a substitution matrix file.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/SubstitutionMatrix.html#SubstitutionMatrix(org.biojava.bio.symbol.FiniteAlphabet, short, short)">SubstitutionMatrix(FiniteAlphabet, short, short)</a></span> - Constructor for class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/SubstitutionMatrix.html" title="class in org.biojava.bio.alignment">SubstitutionMatrix</a></dt>
<dd>
<div class="block">Constructs a SubstitutionMatrix with every Match and every Replace having
the same expenses given by the parameters.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/SubstitutionMatrix.html#SubstitutionMatrix(java.io.File)">SubstitutionMatrix(File)</a></span> - Constructor for class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/SubstitutionMatrix.html" title="class in org.biojava.bio.alignment">SubstitutionMatrix</a></dt>
<dd>
<div class="block">This constructor can be used to guess the alphabet of this substitution
matrix.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/SimpleStatePath.html#subStr(int, int)">subStr(int, int)</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/SimpleStatePath.html" title="class in org.biojava.bio.dp">SimpleStatePath</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/DASSequence.html#subStr(int, int)">subStr(int, int)</a></span> - Method in class org.biojava.bio.program.das.<a href="./org/biojava/bio/program/das/DASSequence.html" title="class in org.biojava.bio.program.das">DASSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/CircularView.html#subStr(int, int)">subStr(int, int)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/CircularView.html" title="class in org.biojava.bio.seq">CircularView</a></dt>
<dd>
<div class="block">
Over rides ViewSequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/homol/SimilarityPairFeature.EmptyPairwiseAlignment.html#subStr(int, int)">subStr(int, int)</a></span> - Method in class org.biojava.bio.seq.homol.<a href="./org/biojava/bio/seq/homol/SimilarityPairFeature.EmptyPairwiseAlignment.html" title="class in org.biojava.bio.seq.homol">SimilarityPairFeature.EmptyPairwiseAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/AssembledSymbolList.html#subStr(int, int)">subStr(int, int)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/AssembledSymbolList.html" title="class in org.biojava.bio.seq.impl">AssembledSymbolList</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/DummySequence.html#subStr(int, int)">subStr(int, int)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/DummySequence.html" title="class in org.biojava.bio.seq.impl">DummySequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleSequence.html#subStr(int, int)">subStr(int, int)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleSequence.html" title="class in org.biojava.bio.seq.impl">SimpleSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SubSequence.html#subStr(int, int)">subStr(int, int)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SubSequence.html" title="class in org.biojava.bio.seq.impl">SubSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/ViewSequence.html#subStr(int, int)">subStr(int, int)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/ViewSequence.html" title="class in org.biojava.bio.seq.impl">ViewSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/NewSimpleAssembly.html#subStr(int, int)">subStr(int, int)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/NewSimpleAssembly.html" title="class in org.biojava.bio.seq">NewSimpleAssembly</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/SimpleAssembly.html#subStr(int, int)">subStr(int, int)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/SimpleAssembly.html" title="class in org.biojava.bio.seq">SimpleAssembly</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AbstractSymbolList.html#subStr(int, int)">subStr(int, int)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AbstractSymbolList.html" title="class in org.biojava.bio.symbol">AbstractSymbolList</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/RelabeledAlignment.html#subStr(int, int)">subStr(int, int)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/RelabeledAlignment.html" title="class in org.biojava.bio.symbol">RelabeledAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SymbolList.html#subStr(int, int)">subStr(int, int)</a></span> - Method in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SymbolList.html" title="interface in org.biojava.bio.symbol">SymbolList</a></dt>
<dd>
<div class="block">Return a region of this symbol list as a String.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLRichSequenceHandler.html#subStr(org.biojavax.bio.seq.RichSequence, int, int)">subStr(RichSequence, int, int)</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLRichSequenceHandler.html" title="class in org.biojavax.bio.db.biosql">BioSQLRichSequenceHandler</a></dt>
<dd>
<div class="block">Return a region of this sequence as a String.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/DummyRichSequenceHandler.html#subStr(org.biojavax.bio.seq.RichSequence, int, int)">subStr(RichSequence, int, int)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/DummyRichSequenceHandler.html" title="class in org.biojavax.bio.seq">DummyRichSequenceHandler</a></dt>
<dd>
<div class="block">Return a region of this sequence as a String.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/InfinitelyAmbiguousSymbolList.html#subStr(int, int)">subStr(int, int)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/InfinitelyAmbiguousSymbolList.html" title="class in org.biojavax.bio.seq">InfinitelyAmbiguousSymbolList</a></dt>
<dd>
<div class="block">Return a region of this symbol list as a String.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequenceHandler.html#subStr(org.biojavax.bio.seq.RichSequence, int, int)">subStr(RichSequence, int, int)</a></span> - Method in interface org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequenceHandler.html" title="interface in org.biojavax.bio.seq">RichSequenceHandler</a></dt>
<dd>
<div class="block">Return a region of this sequence as a String.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/ThinRichSequence.html#subStr(int, int)">subStr(int, int)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/ThinRichSequence.html" title="class in org.biojavax.bio.seq">ThinRichSequence</a></dt>
<dd>
<div class="block">Return a region of this symbol list as a String.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Calc.html#substract(org.biojava.bio.structure.Atom, org.biojava.bio.structure.Atom)">substract(Atom, Atom)</a></span> - Static method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Calc.html" title="class in org.biojava.bio.structure">Calc</a></dt>
<dd>
<div class="block">substract two atoms ( a - b).</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/UkkonenSuffixTree.html#subStringExists(java.lang.String)">subStringExists(String)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/UkkonenSuffixTree.html" title="class in org.biojava.bio.symbol">UkkonenSuffixTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/LocationTools.html#subtract(org.biojava.bio.symbol.Location, org.biojava.bio.symbol.Location)">subtract(Location, Location)</a></span> - Static method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/LocationTools.html" title="class in org.biojava.bio.symbol">LocationTools</a></dt>
<dd>
<div class="block">Subtract one location from another.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/AnnotationType.Abstract.html#subTypeOf(org.biojava.bio.AnnotationType)">subTypeOf(AnnotationType)</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/AnnotationType.Abstract.html" title="class in org.biojava.bio">AnnotationType.Abstract</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/AnnotationType.html#subTypeOf(org.biojava.bio.AnnotationType)">subTypeOf(AnnotationType)</a></span> - Method in interface org.biojava.bio.<a href="./org/biojava/bio/AnnotationType.html" title="interface in org.biojava.bio">AnnotationType</a></dt>
<dd>
<div class="block">See if an AnnotationType is a specialisation of this type.</div>
</dd>
<dt><a href="./org/biojava/bio/symbol/SuffixTree.html" title="class in org.biojava.bio.symbol"><span class="strong">SuffixTree</span></a> - Class in <a href="./org/biojava/bio/symbol/package-summary.html">org.biojava.bio.symbol</a></dt>
<dd>
<div class="block">Suffix tree implementation.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SuffixTree.html#SuffixTree(org.biojava.bio.symbol.FiniteAlphabet)">SuffixTree(FiniteAlphabet)</a></span> - Constructor for class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SuffixTree.html" title="class in org.biojava.bio.symbol">SuffixTree</a></dt>
<dd>
<div class="block">Construct a new SuffixTree to contain motifs over the
specified alphabet.</div>
</dd>
<dt><a href="./org/biojava/bio/symbol/SuffixTree.SuffixNode.html" title="class in org.biojava.bio.symbol"><span class="strong">SuffixTree.SuffixNode</span></a> - Class in <a href="./org/biojava/bio/symbol/package-summary.html">org.biojava.bio.symbol</a></dt>
<dd>
<div class="block">A node in the suffix tree.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SuffixTree.SuffixNode.html#SuffixTree.SuffixNode()">SuffixTree.SuffixNode()</a></span> - Constructor for class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SuffixTree.SuffixNode.html" title="class in org.biojava.bio.symbol">SuffixTree.SuffixNode</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/stats/svm/tools/SuffixTreeKernel.html" title="class in org.biojava.stats.svm.tools"><span class="strong">SuffixTreeKernel</span></a> - Class in <a href="./org/biojava/stats/svm/tools/package-summary.html">org.biojava.stats.svm.tools</a></dt>
<dd>
<div class="block">Computes the dot-product of two suffix-trees as the sum of the products
of the counts of all nodes they have in common.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/tools/SuffixTreeKernel.html#SuffixTreeKernel()">SuffixTreeKernel()</a></span> - Constructor for class org.biojava.stats.svm.tools.<a href="./org/biojava/stats/svm/tools/SuffixTreeKernel.html" title="class in org.biojava.stats.svm.tools">SuffixTreeKernel</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/stats/svm/tools/SuffixTreeKernel.DepthScaler.html" title="interface in org.biojava.stats.svm.tools"><span class="strong">SuffixTreeKernel.DepthScaler</span></a> - Interface in <a href="./org/biojava/stats/svm/tools/package-summary.html">org.biojava.stats.svm.tools</a></dt>
<dd>
<div class="block">Encapsulates the scale factor to apply at a given depth.</div>
</dd>
<dt><a href="./org/biojava/stats/svm/tools/SuffixTreeKernel.MultipleScalar.html" title="class in org.biojava.stats.svm.tools"><span class="strong">SuffixTreeKernel.MultipleScalar</span></a> - Class in <a href="./org/biojava/stats/svm/tools/package-summary.html">org.biojava.stats.svm.tools</a></dt>
<dd>
<div class="block">Scale using a multiple of two <span class="type">DepthScaler</span>s.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/tools/SuffixTreeKernel.MultipleScalar.html#SuffixTreeKernel.MultipleScalar(org.biojava.stats.svm.tools.SuffixTreeKernel.DepthScaler, org.biojava.stats.svm.tools.SuffixTreeKernel.DepthScaler)">SuffixTreeKernel.MultipleScalar(SuffixTreeKernel.DepthScaler, SuffixTreeKernel.DepthScaler)</a></span> - Constructor for class org.biojava.stats.svm.tools.<a href="./org/biojava/stats/svm/tools/SuffixTreeKernel.MultipleScalar.html" title="class in org.biojava.stats.svm.tools">SuffixTreeKernel.MultipleScalar</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/stats/svm/tools/SuffixTreeKernel.NullModelScaler.html" title="class in org.biojava.stats.svm.tools"><span class="strong">SuffixTreeKernel.NullModelScaler</span></a> - Class in <a href="./org/biojava/stats/svm/tools/package-summary.html">org.biojava.stats.svm.tools</a></dt>
<dd>
<div class="block">Scales by 4^depth - equivalent to dividing by a probablistic flatt prior
null model</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/tools/SuffixTreeKernel.NullModelScaler.html#SuffixTreeKernel.NullModelScaler()">SuffixTreeKernel.NullModelScaler()</a></span> - Constructor for class org.biojava.stats.svm.tools.<a href="./org/biojava/stats/svm/tools/SuffixTreeKernel.NullModelScaler.html" title="class in org.biojava.stats.svm.tools">SuffixTreeKernel.NullModelScaler</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/stats/svm/tools/SuffixTreeKernel.SelectionScalar.html" title="class in org.biojava.stats.svm.tools"><span class="strong">SuffixTreeKernel.SelectionScalar</span></a> - Class in <a href="./org/biojava/stats/svm/tools/package-summary.html">org.biojava.stats.svm.tools</a></dt>
<dd>
<div class="block">Scale using a <span class="type">BitSet</span> to allow/disallow depths.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/tools/SuffixTreeKernel.SelectionScalar.html#SuffixTreeKernel.SelectionScalar(java.util.BitSet)">SuffixTreeKernel.SelectionScalar(BitSet)</a></span> - Constructor for class org.biojava.stats.svm.tools.<a href="./org/biojava/stats/svm/tools/SuffixTreeKernel.SelectionScalar.html" title="class in org.biojava.stats.svm.tools">SuffixTreeKernel.SelectionScalar</a></dt>
<dd>
<div class="block">Make a new <span class="type">SelectionScalar</span> that masks in different
depths.</div>
</dd>
<dt><a href="./org/biojava/stats/svm/tools/SuffixTreeKernel.UniformScaler.html" title="class in org.biojava.stats.svm.tools"><span class="strong">SuffixTreeKernel.UniformScaler</span></a> - Class in <a href="./org/biojava/stats/svm/tools/package-summary.html">org.biojava.stats.svm.tools</a></dt>
<dd>
<div class="block">Scale all depths by 1.0</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/tools/SuffixTreeKernel.UniformScaler.html#SuffixTreeKernel.UniformScaler()">SuffixTreeKernel.UniformScaler()</a></span> - Constructor for class org.biojava.stats.svm.tools.<a href="./org/biojava/stats/svm/tools/SuffixTreeKernel.UniformScaler.html" title="class in org.biojava.stats.svm.tools">SuffixTreeKernel.UniformScaler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/abi/ABITools.html#SUPPORT">SUPPORT</a></span> - Static variable in class org.biojava.bio.program.abi.<a href="./org/biojava/bio/program/abi/ABITools.html" title="class in org.biojava.bio.program.abi">ABITools</a></dt>
<dd>
<div class="block">Alignment label for the support row.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BiblioPerson.html#surname">surname</a></span> - Variable in class org.biojava.bibliography.<a href="./org/biojava/bibliography/BiblioPerson.html" title="class in org.biojava.bibliography">BiblioPerson</a></dt>
<dd>
<div class="block">The person's sirname (family name).</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/jama/Matrix.html#svd()">svd()</a></span> - Method in class org.biojava.bio.structure.jama.<a href="./org/biojava/bio/structure/jama/Matrix.html" title="class in org.biojava.bio.structure.jama">Matrix</a></dt>
<dd>
<div class="block">Singular Value Decomposition</div>
</dd>
<dt><a href="./org/biojava/bio/structure/SVDSuperimposer.html" title="class in org.biojava.bio.structure"><span class="strong">SVDSuperimposer</span></a> - Class in <a href="./org/biojava/bio/structure/package-summary.html">org.biojava.bio.structure</a></dt>
<dd>
<div class="block">A class that calculates the superimposition between two sets of atoms
inspired by the biopython SVDSuperimposer class...</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/SVDSuperimposer.html#SVDSuperimposer(org.biojava.bio.structure.Atom[], org.biojava.bio.structure.Atom[])">SVDSuperimposer(Atom[], Atom[])</a></span> - Constructor for class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/SVDSuperimposer.html" title="class in org.biojava.bio.structure">SVDSuperimposer</a></dt>
<dd>
<div class="block">Create a SVDSuperimposer object and calculate a SVD superimposition of two sets of atoms.</div>
</dd>
<dt><a href="./org/biojava/stats/svm/tools/SVM_Light.html" title="class in org.biojava.stats.svm.tools"><span class="strong">SVM_Light</span></a> - Class in <a href="./org/biojava/stats/svm/tools/package-summary.html">org.biojava.stats.svm.tools</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/tools/SVM_Light.html#SVM_Light()">SVM_Light()</a></span> - Constructor for class org.biojava.stats.svm.tools.<a href="./org/biojava/stats/svm/tools/SVM_Light.html" title="class in org.biojava.stats.svm.tools">SVM_Light</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/stats/svm/tools/SVM_Light.LabelledVector.html" title="class in org.biojava.stats.svm.tools"><span class="strong">SVM_Light.LabelledVector</span></a> - Class in <a href="./org/biojava/stats/svm/tools/package-summary.html">org.biojava.stats.svm.tools</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/tools/SVM_Light.LabelledVector.html#SVM_Light.LabelledVector(org.biojava.stats.svm.SparseVector, double)">SVM_Light.LabelledVector(SparseVector, double)</a></span> - Constructor for class org.biojava.stats.svm.tools.<a href="./org/biojava/stats/svm/tools/SVM_Light.LabelledVector.html" title="class in org.biojava.stats.svm.tools">SVM_Light.LabelledVector</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/tools/SVM_Light.LabelledVector.html#SVM_Light.LabelledVector(org.biojava.stats.svm.SparseVector, double, java.lang.String)">SVM_Light.LabelledVector(SparseVector, double, String)</a></span> - Constructor for class org.biojava.stats.svm.tools.<a href="./org/biojava/stats/svm/tools/SVM_Light.LabelledVector.html" title="class in org.biojava.stats.svm.tools">SVM_Light.LabelledVector</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/stats/svm/SVMClassifierModel.html" title="interface in org.biojava.stats.svm"><span class="strong">SVMClassifierModel</span></a> - Interface in <a href="./org/biojava/stats/svm/package-summary.html">org.biojava.stats.svm</a></dt>
<dd>
<div class="block">An SVM classifier model.</div>
</dd>
<dt><a href="./org/biojava/stats/svm/SVMKernel.html" title="interface in org.biojava.stats.svm"><span class="strong">SVMKernel</span></a> - Interface in <a href="./org/biojava/stats/svm/package-summary.html">org.biojava.stats.svm</a></dt>
<dd>
<div class="block">Kernel for support vector machines and related methods.</div>
</dd>
<dt><a href="./org/biojava/stats/svm/SVMRegressionModel.html" title="class in org.biojava.stats.svm"><span class="strong">SVMRegressionModel</span></a> - Class in <a href="./org/biojava/stats/svm/package-summary.html">org.biojava.stats.svm</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/SVMRegressionModel.html#SVMRegressionModel()">SVMRegressionModel()</a></span> - Constructor for class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/SVMRegressionModel.html" title="class in org.biojava.stats.svm">SVMRegressionModel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/SVMRegressionModel.html#SVMRegressionModel(int)">SVMRegressionModel(int)</a></span> - Constructor for class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/SVMRegressionModel.html" title="class in org.biojava.stats.svm">SVMRegressionModel</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/stats/svm/SVMTarget.html" title="interface in org.biojava.stats.svm"><span class="strong">SVMTarget</span></a> - Interface in <a href="./org/biojava/stats/svm/package-summary.html">org.biojava.stats.svm</a></dt>
<dd>
<div class="block">An SVM classifier model.</div>
</dd>
<dt><a href="./org/biojavax/ga/functions/SwapMutationFunction.html" title="class in org.biojavax.ga.functions"><span class="strong">SwapMutationFunction</span></a> - Class in <a href="./org/biojavax/ga/functions/package-summary.html">org.biojavax.ga.functions</a></dt>
<dd>
<div class="block">This class does a sort of mutation by exchanging two positions on the
chromosome.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ga/functions/SwapMutationFunction.html#SwapMutationFunction(double[])">SwapMutationFunction(double[])</a></span> - Constructor for class org.biojavax.ga.functions.<a href="./org/biojavax/ga/functions/SwapMutationFunction.html" title="class in org.biojavax.ga.functions">SwapMutationFunction</a></dt>
<dd>
<div class="block">Sets the mutation probabilities to the designated values.</div>
</dd>
<dt><a href="./org/biojava/bio/program/formats/Swissprot.html" title="class in org.biojava.bio.program.formats"><span class="strong">Swissprot</span></a> - Class in <a href="./org/biojava/bio/program/formats/package-summary.html">org.biojava.bio.program.formats</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/formats/Swissprot.html#Swissprot()">Swissprot()</a></span> - Constructor for class org.biojava.bio.program.formats.<a href="./org/biojava/bio/program/formats/Swissprot.html" title="class in org.biojava.bio.program.formats">Swissprot</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOConstants.html#SWISSPROT">SWISSPROT</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOConstants.html" title="class in org.biojava.bio.seq.io">SeqIOConstants</a></dt>
<dd>
<div class="block"><code>SWISSPROT</code> indicates that the sequence format is
SWISSPROT.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/Formats.html#SWISSPROT_TYPE">SWISSPROT_TYPE</a></span> - Static variable in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/Formats.html" title="class in org.biojava.bio.program.tagvalue">Formats</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/io/SwissprotFileFormer.html" title="class in org.biojava.bio.seq.io"><span class="strong">SwissprotFileFormer</span></a> - Class in <a href="./org/biojava/bio/seq/io/package-summary.html">org.biojava.bio.seq.io</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>Use org.biojavax.bio.seq.io framework instead</i></div>
</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SwissprotFileFormer.html#SwissprotFileFormer()">SwissprotFileFormer()</a></span> - Constructor for class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SwissprotFileFormer.html" title="class in org.biojava.bio.seq.io">SwissprotFileFormer</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Creates a new <code>SwissprotFileFormer</code> using
<code>System.out</code> stream.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SwissprotFileFormer.html#SwissprotFileFormer(java.io.PrintStream)">SwissprotFileFormer(PrintStream)</a></span> - Constructor for class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SwissprotFileFormer.html" title="class in org.biojava.bio.seq.io">SwissprotFileFormer</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Creates a new <code>SwissprotFileFormer</code> using the
specified stream.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/SwissprotProcessor.html" title="class in org.biojava.bio.seq.io"><span class="strong">SwissprotProcessor</span></a> - Class in <a href="./org/biojava/bio/seq/io/package-summary.html">org.biojava.bio.seq.io</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>Use org.biojavax.bio.seq.io framework instead</i></div>
</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SwissprotProcessor.html#SwissprotProcessor(org.biojava.bio.seq.io.SequenceBuilder, java.lang.String)">SwissprotProcessor(SequenceBuilder, String)</a></span> - Constructor for class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SwissprotProcessor.html" title="class in org.biojava.bio.seq.io">SwissprotProcessor</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Constructor that sets the source of the feature to theSource.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SwissprotProcessor.html#SwissprotProcessor(org.biojava.bio.seq.io.SequenceBuilder)">SwissprotProcessor(SequenceBuilder)</a></span> - Constructor for class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SwissprotProcessor.html" title="class in org.biojava.bio.seq.io">SwissprotProcessor</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/SwissprotProcessor.Factory.html" title="class in org.biojava.bio.seq.io"><span class="strong">SwissprotProcessor.Factory</span></a> - Class in <a href="./org/biojava/bio/seq/io/package-summary.html">org.biojava.bio.seq.io</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Factory which wraps SequenceBuilders in a SwissprotProcessor</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SwissprotProcessor.Factory.html#SwissprotProcessor.Factory(org.biojava.bio.seq.io.SequenceBuilderFactory)">SwissprotProcessor.Factory(SequenceBuilderFactory)</a></span> - Constructor for class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SwissprotProcessor.Factory.html" title="class in org.biojava.bio.seq.io">SwissprotProcessor.Factory</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><a href="./org/biojava/bio/seq/db/SwissprotSequenceDB.html" title="class in org.biojava.bio.seq.db"><span class="strong">SwissprotSequenceDB</span></a> - Class in <a href="./org/biojava/bio/seq/db/package-summary.html">org.biojava.bio.seq.db</a></dt>
<dd>
<div class="block">This class contains functions accessing sequences in swiss-prot.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/SwissprotSequenceDB.html#SwissprotSequenceDB()">SwissprotSequenceDB()</a></span> - Constructor for class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/SwissprotSequenceDB.html" title="class in org.biojava.bio.seq.db">SwissprotSequenceDB</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/symbol/Symbol.html" title="interface in org.biojava.bio.symbol"><span class="strong">Symbol</span></a> - Interface in <a href="./org/biojava/bio/symbol/package-summary.html">org.biojava.bio.symbol</a></dt>
<dd>
<div class="block">A single symbol.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/AbstractULAlignment.SubULAlignment.html#symbolAt(java.lang.Object, int)">symbolAt(Object, int)</a></span> - Method in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/AbstractULAlignment.SubULAlignment.html" title="class in org.biojava.bio.alignment">AbstractULAlignment.SubULAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/AbstractULAlignment.SubULAlignment.html#symbolAt(int)">symbolAt(int)</a></span> - Method in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/AbstractULAlignment.SubULAlignment.html" title="class in org.biojava.bio.alignment">AbstractULAlignment.SubULAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/AbstractULAlignment.html#symbolAt(int)">symbolAt(int)</a></span> - Method in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/AbstractULAlignment.html" title="class in org.biojava.bio.alignment">AbstractULAlignment</a></dt>
<dd>
<div class="block">this will return the ambiguity symbol associated with all symbols in that column</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/FlexibleAlignment.html#symbolAt(java.lang.Object, int)">symbolAt(Object, int)</a></span> - Method in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/FlexibleAlignment.html" title="class in org.biojava.bio.alignment">FlexibleAlignment</a></dt>
<dd>
<div class="block">This gets the symbol for an individual sequence at position in the overall alignment
If the sequence is not aligned at that location it returns null</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/SimpleStatePath.html#symbolAt(int)">symbolAt(int)</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/SimpleStatePath.html" title="class in org.biojava.bio.dp">SimpleStatePath</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/SimpleStatePath.html#symbolAt(java.lang.Object, int)">symbolAt(Object, int)</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/SimpleStatePath.html" title="class in org.biojava.bio.dp">SimpleStatePath</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/DASSequence.html#symbolAt(int)">symbolAt(int)</a></span> - Method in class org.biojava.bio.program.das.<a href="./org/biojava/bio/program/das/DASSequence.html" title="class in org.biojava.bio.program.das">DASSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/CircularView.html#symbolAt(int)">symbolAt(int)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/CircularView.html" title="class in org.biojava.bio.seq">CircularView</a></dt>
<dd>
<div class="block">
Over rides ViewSequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/homol/SimilarityPairFeature.EmptyPairwiseAlignment.html#symbolAt(java.lang.Object, int)">symbolAt(Object, int)</a></span> - Method in class org.biojava.bio.seq.homol.<a href="./org/biojava/bio/seq/homol/SimilarityPairFeature.EmptyPairwiseAlignment.html" title="class in org.biojava.bio.seq.homol">SimilarityPairFeature.EmptyPairwiseAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/homol/SimilarityPairFeature.EmptyPairwiseAlignment.html#symbolAt(int)">symbolAt(int)</a></span> - Method in class org.biojava.bio.seq.homol.<a href="./org/biojava/bio/seq/homol/SimilarityPairFeature.EmptyPairwiseAlignment.html" title="class in org.biojava.bio.seq.homol">SimilarityPairFeature.EmptyPairwiseAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/AssembledSymbolList.html#symbolAt(int)">symbolAt(int)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/AssembledSymbolList.html" title="class in org.biojava.bio.seq.impl">AssembledSymbolList</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/DummySequence.html#symbolAt(int)">symbolAt(int)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/DummySequence.html" title="class in org.biojava.bio.seq.impl">DummySequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/NewAssembledSymbolList.html#symbolAt(int)">symbolAt(int)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/NewAssembledSymbolList.html" title="class in org.biojava.bio.seq.impl">NewAssembledSymbolList</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleSequence.html#symbolAt(int)">symbolAt(int)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleSequence.html" title="class in org.biojava.bio.seq.impl">SimpleSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SubSequence.html#symbolAt(int)">symbolAt(int)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SubSequence.html" title="class in org.biojava.bio.seq.impl">SubSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/ViewSequence.html#symbolAt(int)">symbolAt(int)</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/ViewSequence.html" title="class in org.biojava.bio.seq.impl">ViewSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/NewSimpleAssembly.html#symbolAt(int)">symbolAt(int)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/NewSimpleAssembly.html" title="class in org.biojava.bio.seq">NewSimpleAssembly</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/SimpleAssembly.html#symbolAt(int)">symbolAt(int)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/SimpleAssembly.html" title="class in org.biojava.bio.seq">SimpleAssembly</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/Alignment.html#symbolAt(java.lang.Object, int)">symbolAt(Object, int)</a></span> - Method in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/Alignment.html" title="interface in org.biojava.bio.symbol">Alignment</a></dt>
<dd>
<div class="block">Retrieve a symbol by label and column.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/ChunkedSymbolList.html#symbolAt(int)">symbolAt(int)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/ChunkedSymbolList.html" title="class in org.biojava.bio.symbol">ChunkedSymbolList</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/DummySymbolList.html#symbolAt(int)">symbolAt(int)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/DummySymbolList.html" title="class in org.biojava.bio.symbol">DummySymbolList</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/PackedSymbolList.html#symbolAt(int)">symbolAt(int)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/PackedSymbolList.html" title="class in org.biojava.bio.symbol">PackedSymbolList</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/RelabeledAlignment.html#symbolAt(java.lang.Object, int)">symbolAt(Object, int)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/RelabeledAlignment.html" title="class in org.biojava.bio.symbol">RelabeledAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/RelabeledAlignment.html#symbolAt(int)">symbolAt(int)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/RelabeledAlignment.html" title="class in org.biojava.bio.symbol">RelabeledAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleAlignment.html#symbolAt(int)">symbolAt(int)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleAlignment.html" title="class in org.biojava.bio.symbol">SimpleAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleAlignment.html#symbolAt(java.lang.Object, int)">symbolAt(Object, int)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleAlignment.html" title="class in org.biojava.bio.symbol">SimpleAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleGappedSymbolList.html#symbolAt(int)">symbolAt(int)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleGappedSymbolList.html" title="class in org.biojava.bio.symbol">SimpleGappedSymbolList</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleSymbolList.html#symbolAt(int)">symbolAt(int)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleSymbolList.html" title="class in org.biojava.bio.symbol">SimpleSymbolList</a></dt>
<dd>
<div class="block">Find a symbol at a specified offset in the SymbolList.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SymbolList.html#symbolAt(int)">symbolAt(int)</a></span> - Method in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SymbolList.html" title="interface in org.biojava.bio.symbol">SymbolList</a></dt>
<dd>
<div class="block">Return the symbol at index, counting from 1.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLRichSequenceHandler.html#symbolAt(org.biojavax.bio.seq.RichSequence, int)">symbolAt(RichSequence, int)</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLRichSequenceHandler.html" title="class in org.biojavax.bio.db.biosql">BioSQLRichSequenceHandler</a></dt>
<dd>
<div class="block">Return the symbol at index, counting from 1.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/DummyRichSequenceHandler.html#symbolAt(org.biojavax.bio.seq.RichSequence, int)">symbolAt(RichSequence, int)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/DummyRichSequenceHandler.html" title="class in org.biojavax.bio.seq">DummyRichSequenceHandler</a></dt>
<dd>
<div class="block">Return the symbol at index, counting from 1.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/InfinitelyAmbiguousSymbolList.html#symbolAt(int)">symbolAt(int)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/InfinitelyAmbiguousSymbolList.html" title="class in org.biojavax.bio.seq">InfinitelyAmbiguousSymbolList</a></dt>
<dd>
<div class="block">Return the symbol at index, counting from 1.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequenceHandler.html#symbolAt(org.biojavax.bio.seq.RichSequence, int)">symbolAt(RichSequence, int)</a></span> - Method in interface org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequenceHandler.html" title="interface in org.biojavax.bio.seq">RichSequenceHandler</a></dt>
<dd>
<div class="block">Return the symbol at index, counting from 1.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/ThinRichSequence.html#symbolAt(int)">symbolAt(int)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/ThinRichSequence.html" title="class in org.biojavax.bio.seq">ThinRichSequence</a></dt>
<dd>
<div class="block">Return the symbol at index, counting from 1.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AlphabetIndex.html#symbolForIndex(int)">symbolForIndex(int)</a></span> - Method in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AlphabetIndex.html" title="interface in org.biojava.bio.symbol">AlphabetIndex</a></dt>
<dd>
<div class="block">Retrieve the symbol for an index.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AlphabetManager.html#symbolForLifeScienceID(org.biojava.utils.lsid.LifeScienceIdentifier)">symbolForLifeScienceID(LifeScienceIdentifier)</a></span> - Static method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AlphabetManager.html" title="class in org.biojava.bio.symbol">AlphabetManager</a></dt>
<dd>
<div class="block">Retreives the Symbol for the LSID</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AlphabetManager.html#symbolForName(java.lang.String)">symbolForName(String)</a></span> - Static method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AlphabetManager.html" title="class in org.biojava.bio.symbol">AlphabetManager</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>use symbolForLifeScienceID() instead</i></div>
</div>
</dd>
<dt><a href="./org/biojava/bio/symbol/SymbolList.html" title="interface in org.biojava.bio.symbol"><span class="strong">SymbolList</span></a> - Interface in <a href="./org/biojava/bio/symbol/package-summary.html">org.biojava.bio.symbol</a></dt>
<dd>
<div class="block">A sequence of symbols that belong to an alphabet.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/SymbolListCharSequence.html" title="class in org.biojava.bio.seq.io"><span class="strong">SymbolListCharSequence</span></a> - Class in <a href="./org/biojava/bio/seq/io/package-summary.html">org.biojava.bio.seq.io</a></dt>
<dd>
<div class="block"><code>SymbolListCharSequence</code> is a <code>CharSequence</code>
implementation which wraps a <code>SymbolList</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SymbolListCharSequence.html#SymbolListCharSequence(org.biojava.bio.symbol.SymbolList)">SymbolListCharSequence(SymbolList)</a></span> - Constructor for class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SymbolListCharSequence.html" title="class in org.biojava.bio.seq.io">SymbolListCharSequence</a></dt>
<dd>
<div class="block">Creates a new <code>SymbolListCharSequence</code> wrapping a
<code>SymbolList</code>.</div>
</dd>
<dt><a href="./org/biojava/bio/symbol/SymbolListFactory.html" title="interface in org.biojava.bio.symbol"><span class="strong">SymbolListFactory</span></a> - Interface in <a href="./org/biojava/bio/symbol/package-summary.html">org.biojava.bio.symbol</a></dt>
<dd>
<div class="block">This interface exists to hide implementational details
of SymbolLists when making chunked symbol lists.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/AbstractULAlignment.SubULAlignment.html#symbolListForLabel(java.lang.Object)">symbolListForLabel(Object)</a></span> - Method in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/AbstractULAlignment.SubULAlignment.html" title="class in org.biojava.bio.alignment">AbstractULAlignment.SubULAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/FlexibleAlignment.html#symbolListForLabel(java.lang.Object)">symbolListForLabel(Object)</a></span> - Method in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/FlexibleAlignment.html" title="class in org.biojava.bio.alignment">FlexibleAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/SimpleStatePath.html#symbolListForLabel(java.lang.Object)">symbolListForLabel(Object)</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/SimpleStatePath.html" title="class in org.biojava.bio.dp">SimpleStatePath</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/homol/SimilarityPairFeature.EmptyPairwiseAlignment.html#symbolListForLabel(java.lang.Object)">symbolListForLabel(Object)</a></span> - Method in class org.biojava.bio.seq.homol.<a href="./org/biojava/bio/seq/homol/SimilarityPairFeature.EmptyPairwiseAlignment.html" title="class in org.biojava.bio.seq.homol">SimilarityPairFeature.EmptyPairwiseAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/Alignment.html#symbolListForLabel(java.lang.Object)">symbolListForLabel(Object)</a></span> - Method in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/Alignment.html" title="interface in org.biojava.bio.symbol">Alignment</a></dt>
<dd>
<div class="block">Retrieve a single row of the alignment by label.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/RelabeledAlignment.html#symbolListForLabel(java.lang.Object)">symbolListForLabel(Object)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/RelabeledAlignment.html" title="class in org.biojava.bio.symbol">RelabeledAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleAlignment.html#symbolListForLabel(java.lang.Object)">symbolListForLabel(Object)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleAlignment.html" title="class in org.biojava.bio.symbol">SimpleAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/AbstractULAlignment.SubULAlignment.html#symbolListIterator()">symbolListIterator()</a></span> - Method in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/AbstractULAlignment.SubULAlignment.html" title="class in org.biojava.bio.alignment">AbstractULAlignment.SubULAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/AbstractULAlignment.html#symbolListIterator()">symbolListIterator()</a></span> - Method in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/AbstractULAlignment.html" title="class in org.biojava.bio.alignment">AbstractULAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/SimpleStatePath.html#symbolListIterator()">symbolListIterator()</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/SimpleStatePath.html" title="class in org.biojava.bio.dp">SimpleStatePath</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/homol/SimilarityPairFeature.EmptyPairwiseAlignment.html#symbolListIterator()">symbolListIterator()</a></span> - Method in class org.biojava.bio.seq.homol.<a href="./org/biojava/bio/seq/homol/SimilarityPairFeature.EmptyPairwiseAlignment.html" title="class in org.biojava.bio.seq.homol">SimilarityPairFeature.EmptyPairwiseAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/Alignment.html#symbolListIterator()">symbolListIterator()</a></span> - Method in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/Alignment.html" title="interface in org.biojava.bio.symbol">Alignment</a></dt>
<dd>
<div class="block">Creates an Iterator over the SymbolLists in the alignment.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/RelabeledAlignment.html#symbolListIterator()">symbolListIterator()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/RelabeledAlignment.html" title="class in org.biojava.bio.symbol">RelabeledAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleAlignment.html#symbolListIterator()">symbolListIterator()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleAlignment.html" title="class in org.biojava.bio.symbol">SimpleAlignment</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/symbol/SymbolListViews.html" title="class in org.biojava.bio.symbol"><span class="strong">SymbolListViews</span></a> - Class in <a href="./org/biojava/bio/symbol/package-summary.html">org.biojava.bio.symbol</a></dt>
<dd>
<div class="block">Tools class for constructing views of <code>SymbolList</code> objects.</div>
</dd>
<dt><a href="./org/biojava/bio/symbol/SymbolPropertyTable.html" title="interface in org.biojava.bio.symbol"><span class="strong">SymbolPropertyTable</span></a> - Interface in <a href="./org/biojava/bio/symbol/package-summary.html">org.biojava.bio.symbol</a></dt>
<dd>
<div class="block">class for maintaining properties associated with a symbol</div>
</dd>
<dt><a href="./org/biojava/bio/proteomics/aaindex/SymbolPropertyTableDB.html" title="interface in org.biojava.bio.proteomics.aaindex"><span class="strong">SymbolPropertyTableDB</span></a> - Interface in <a href="./org/biojava/bio/proteomics/aaindex/package-summary.html">org.biojava.bio.proteomics.aaindex</a></dt>
<dd>
<div class="block">Database of <a href="./org/biojava/bio/symbol/SymbolPropertyTable.html" title="interface in org.biojava.bio.symbol"><code>SymbolPropertyTable</code></a> objects.</div>
</dd>
<dt><a href="./org/biojava/bio/proteomics/aaindex/SymbolPropertyTableIterator.html" title="interface in org.biojava.bio.proteomics.aaindex"><span class="strong">SymbolPropertyTableIterator</span></a> - Interface in <a href="./org/biojava/bio/proteomics/aaindex/package-summary.html">org.biojava.bio.proteomics.aaindex</a></dt>
<dd>
<div class="block">Iterator over <a href="./org/biojava/bio/symbol/SymbolPropertyTable.html" title="interface in org.biojava.bio.symbol"><code>SymbolPropertyTable</code></a> objects.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/SymbolReader.html" title="interface in org.biojava.bio.seq.io"><span class="strong">SymbolReader</span></a> - Interface in <a href="./org/biojava/bio/seq/io/package-summary.html">org.biojava.bio.seq.io</a></dt>
<dd>
<div class="block">Encapsulate a stream of Symbols being parsed from some input
stream.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AbstractLocationDecorator.html#symbols(org.biojava.bio.symbol.SymbolList)">symbols(SymbolList)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AbstractLocationDecorator.html" title="class in org.biojava.bio.symbol">AbstractLocationDecorator</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AbstractRangeLocation.html#symbols(org.biojava.bio.symbol.SymbolList)">symbols(SymbolList)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AbstractRangeLocation.html" title="class in org.biojava.bio.symbol">AbstractRangeLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/Alphabet.html#SYMBOLS">SYMBOLS</a></span> - Static variable in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/Alphabet.html" title="interface in org.biojava.bio.symbol">Alphabet</a></dt>
<dd>
<div class="block">
This ChangeType indicates that some symbols have been added or removed from
the alphabet.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/CircularLocation.html#symbols(org.biojava.bio.symbol.SymbolList)">symbols(SymbolList)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/CircularLocation.html" title="class in org.biojava.bio.symbol">CircularLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/FuzzyPointLocation.html#symbols(org.biojava.bio.symbol.SymbolList)">symbols(SymbolList)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/FuzzyPointLocation.html" title="class in org.biojava.bio.symbol">FuzzyPointLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/Location.html#symbols(org.biojava.bio.symbol.SymbolList)">symbols(SymbolList)</a></span> - Method in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/Location.html" title="interface in org.biojava.bio.symbol">Location</a></dt>
<dd>
<div class="block">Return the symbols in a sequence that fall within this range.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/CompoundRichLocation.html#symbols(org.biojava.bio.symbol.SymbolList)">symbols(SymbolList)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/CompoundRichLocation.html" title="class in org.biojavax.bio.seq">CompoundRichLocation</a></dt>
<dd>
<div class="block">Return the symbols in a sequence that fall within this range.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/EmptyRichLocation.html#symbols(org.biojava.bio.symbol.SymbolList)">symbols(SymbolList)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/EmptyRichLocation.html" title="class in org.biojavax.bio.seq">EmptyRichLocation</a></dt>
<dd>
<div class="block">Return the symbols in a sequence that fall within this range.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichLocation.html#symbols(org.biojava.bio.symbol.SymbolList)">symbols(SymbolList)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichLocation.html" title="class in org.biojavax.bio.seq">SimpleRichLocation</a></dt>
<dd>
<div class="block">Return the symbols in a sequence that fall within this range.</div>
</dd>
<dt><a href="./org/biojava/bio/gui/sequence/SymbolSequenceRenderer.html" title="class in org.biojava.bio.gui.sequence"><span class="strong">SymbolSequenceRenderer</span></a> - Class in <a href="./org/biojava/bio/gui/sequence/package-summary.html">org.biojava.bio.gui.sequence</a></dt>
<dd>
<div class="block"><code>SymbolSequenceRenderer</code> renders symbols of a
<code>SymbolList</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SymbolSequenceRenderer.html#SymbolSequenceRenderer()">SymbolSequenceRenderer()</a></span> - Constructor for class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SymbolSequenceRenderer.html" title="class in org.biojava.bio.gui.sequence">SymbolSequenceRenderer</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/gui/SymbolStyle.html" title="interface in org.biojava.bio.gui"><span class="strong">SymbolStyle</span></a> - Interface in <a href="./org/biojava/bio/gui/package-summary.html">org.biojava.bio.gui</a></dt>
<dd>
<div class="block">The interface for things that say how to paint a symbol.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/SymbolTokenization.html" title="interface in org.biojava.bio.seq.io"><span class="strong">SymbolTokenization</span></a> - Interface in <a href="./org/biojava/bio/seq/io/package-summary.html">org.biojava.bio.seq.io</a></dt>
<dd>
<div class="block">Encapsulate a mapping between BioJava Symbol objects and
some string representation.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/SymbolTokenization.TokenType.html" title="class in org.biojava.bio.seq.io"><span class="strong">SymbolTokenization.TokenType</span></a> - Class in <a href="./org/biojava/bio/seq/io/package-summary.html">org.biojava.bio.seq.io</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/DPMatrix.html#symList()">symList()</a></span> - Method in interface org.biojava.bio.dp.<a href="./org/biojava/bio/dp/DPMatrix.html" title="interface in org.biojava.bio.dp">DPMatrix</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/onehead/DPCursor.html#symList()">symList()</a></span> - Method in interface org.biojava.bio.dp.onehead.<a href="./org/biojava/bio/dp/onehead/DPCursor.html" title="interface in org.biojava.bio.dp.onehead">DPCursor</a></dt>
<dd>
<div class="block">The symbol list being looped over.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/onehead/SingleDPMatrix.html#symList">symList</a></span> - Variable in class org.biojava.bio.dp.onehead.<a href="./org/biojava/bio/dp/onehead/SingleDPMatrix.html" title="class in org.biojava.bio.dp.onehead">SingleDPMatrix</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/onehead/SingleDPMatrix.html#symList()">symList()</a></span> - Method in class org.biojava.bio.dp.onehead.<a href="./org/biojava/bio/dp/onehead/SingleDPMatrix.html" title="class in org.biojava.bio.dp.onehead">SingleDPMatrix</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/onehead/SmallCursor.html#symList()">symList()</a></span> - Method in class org.biojava.bio.dp.onehead.<a href="./org/biojava/bio/dp/onehead/SmallCursor.html" title="class in org.biojava.bio.dp.onehead">SmallCursor</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/twohead/PairDPMatrix.html#symList()">symList()</a></span> - Method in class org.biojava.bio.dp.twohead.<a href="./org/biojava/bio/dp/twohead/PairDPMatrix.html" title="class in org.biojava.bio.dp.twohead">PairDPMatrix</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.html#SYMLISTVERSION">SYMLISTVERSION</a></span> - Static variable in interface org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.html" title="interface in org.biojavax.bio.seq">RichSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/OntoTools.html#SYMMETRIC">SYMMETRIC</a></span> - Static variable in class org.biojava.ontology.<a href="./org/biojava/ontology/OntoTools.html" title="class in org.biojava.ontology">OntoTools</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/obo/OboFileHandler.html#SYNONYM">SYNONYM</a></span> - Static variable in class org.biojava.ontology.obo.<a href="./org/biojava/ontology/obo/OboFileHandler.html" title="class in org.biojava.ontology.obo">OboFileHandler</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/ontology/Synonym.html" title="class in org.biojava.ontology"><span class="strong">Synonym</span></a> - Class in <a href="./org/biojava/ontology/package-summary.html">org.biojava.ontology</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/Synonym.html#Synonym()">Synonym()</a></span> - Constructor for class org.biojava.ontology.<a href="./org/biojava/ontology/Synonym.html" title="class in org.biojava.ontology">Synonym</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/taxa/NCBITaxon.html#SYNONYM">SYNONYM</a></span> - Static variable in interface org.biojavax.bio.taxa.<a href="./org/biojavax/bio/taxa/NCBITaxon.html" title="interface in org.biojavax.bio.taxa">NCBITaxon</a></dt>
<dd>
<div class="block">Use this to define common names for things.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.Terms.html#SYNONYM_NAME_KEY">SYNONYM_NAME_KEY</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.Terms.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat.Terms</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/directory/SystemRegistry.html" title="class in org.biojava.directory"><span class="strong">SystemRegistry</span></a> - Class in <a href="./org/biojava/directory/package-summary.html">org.biojava.directory</a></dt>
<dd>
<div class="block">A registry that loads up the standard biodirectory files.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/directory/SystemRegistry.html#SystemRegistry()">SystemRegistry()</a></span> - Constructor for class org.biojava.directory.<a href="./org/biojava/directory/SystemRegistry.html" title="class in org.biojava.directory">SystemRegistry</a></dt>
<dd> </dd>
</dl>
<a name="_T_">
<!-- -->
</a>
<h2 class="title">T</h2>
<dl>
<dt><span class="strong"><a href="./org/biojava/bio/seq/DNATools.html#t()">t()</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/DNATools.html" title="class in org.biojava.bio.seq">DNATools</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/NucleotideTools.html#t()">t()</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/NucleotideTools.html" title="class in org.biojava.bio.seq">NucleotideTools</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/ProteinTools.html#t()">t()</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/ProteinTools.html" title="class in org.biojava.bio.seq">ProteinTools</a></dt>
<dd>
<div class="block">Returns the <code>AtomicSymbol</code> for the amino acid
Threonine</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/Taxon.html#T_AESTIVUM">T_AESTIVUM</a></span> - Static variable in interface org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/Taxon.html" title="interface in org.biojava.bio.program.homologene">Taxon</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/ontology/io/TabDelimParser.html" title="class in org.biojava.ontology.io"><span class="strong">TabDelimParser</span></a> - Class in <a href="./org/biojava/ontology/io/package-summary.html">org.biojava.ontology.io</a></dt>
<dd>
<div class="block">Parse tab-delimited ontology files into Ontology objects.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/io/TabDelimParser.html#TabDelimParser()">TabDelimParser()</a></span> - Constructor for class org.biojava.ontology.io.<a href="./org/biojava/ontology/io/TabDelimParser.html" title="class in org.biojava.ontology.io">TabDelimParser</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/db/TabIndexStore.html" title="class in org.biojava.bio.seq.db"><span class="strong">TabIndexStore</span></a> - Class in <a href="./org/biojava/bio/seq/db/package-summary.html">org.biojava.bio.seq.db</a></dt>
<dd>
<div class="block">
Implements IndexStore as a serialized file for the java data and a
tab-delimited file of offsets.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/TabIndexStore.html#TabIndexStore(java.io.File, java.io.File, java.lang.String, org.biojava.bio.seq.io.SequenceFormat, org.biojava.bio.seq.io.SequenceBuilderFactory, org.biojava.bio.seq.io.SymbolTokenization)">TabIndexStore(File, File, String, SequenceFormat, SequenceBuilderFactory, SymbolTokenization)</a></span> - Constructor for class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/TabIndexStore.html" title="class in org.biojava.bio.seq.db">TabIndexStore</a></dt>
<dd>
<div class="block">Create a new TabIndexStore.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/aaindex/SimpleSymbolPropertyTableDB.html#table(java.lang.String)">table(String)</a></span> - Method in class org.biojava.bio.proteomics.aaindex.<a href="./org/biojava/bio/proteomics/aaindex/SimpleSymbolPropertyTableDB.html" title="class in org.biojava.bio.proteomics.aaindex">SimpleSymbolPropertyTableDB</a></dt>
<dd>
<div class="block">Returns the table with the specified name.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/aaindex/SymbolPropertyTableDB.html#table(java.lang.String)">table(String)</a></span> - Method in interface org.biojava.bio.proteomics.aaindex.<a href="./org/biojava/bio/proteomics/aaindex/SymbolPropertyTableDB.html" title="interface in org.biojava.bio.proteomics.aaindex">SymbolPropertyTableDB</a></dt>
<dd>
<div class="block">Returns the table with the specified name.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/aaindex/SimpleSymbolPropertyTableDB.html#tableIterator()">tableIterator()</a></span> - Method in class org.biojava.bio.proteomics.aaindex.<a href="./org/biojava/bio/proteomics/aaindex/SimpleSymbolPropertyTableDB.html" title="class in org.biojava.bio.proteomics.aaindex">SimpleSymbolPropertyTableDB</a></dt>
<dd>
<div class="block">Returns an iterator over
<a href="./org/biojava/bio/symbol/SymbolPropertyTable.html" title="interface in org.biojava.bio.symbol"><code>SymbolPropertyTable</code></a> objects.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/aaindex/SymbolPropertyTableDB.html#tableIterator()">tableIterator()</a></span> - Method in interface org.biojava.bio.proteomics.aaindex.<a href="./org/biojava/bio/proteomics/aaindex/SymbolPropertyTableDB.html" title="interface in org.biojava.bio.proteomics.aaindex">SymbolPropertyTableDB</a></dt>
<dd>
<div class="block">Returns an iterator over
<a href="./org/biojava/bio/symbol/SymbolPropertyTable.html" title="interface in org.biojava.bio.symbol"><code>SymbolPropertyTable</code></a> objects.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BiblioDescription.html#tableOfContents">tableOfContents</a></span> - Variable in class org.biojava.bibliography.<a href="./org/biojava/bibliography/BiblioDescription.html" title="class in org.biojava.bibliography">BiblioDescription</a></dt>
<dd>
<div class="block">
It is a table of contents of the cited resource.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BiblioDescription.html#tableOfContentsType">tableOfContentsType</a></span> - Variable in class org.biojava.bibliography.<a href="./org/biojava/bibliography/BiblioDescription.html" title="class in org.biojava.bibliography">BiblioDescription</a></dt>
<dd>
<div class="block">
It specifies how <a href="./org/biojava/bibliography/BiblioDescription.html#tableOfContents"><code>BiblioDescription.tableOfContents</code></a> is coded.</div>
</dd>
<dt><a href="./org/biojava/bio/program/tagvalue/TagDelegator.html" title="class in org.biojava.bio.program.tagvalue"><span class="strong">TagDelegator</span></a> - Class in <a href="./org/biojava/bio/program/tagvalue/package-summary.html">org.biojava.bio.program.tagvalue</a></dt>
<dd>
<div class="block">
Pushes a new parser and listener, or delegate to a listener depending on the
tag.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/TagDelegator.html#TagDelegator()">TagDelegator()</a></span> - Constructor for class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/TagDelegator.html" title="class in org.biojava.bio.program.tagvalue">TagDelegator</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/TagDelegator.html#TagDelegator(org.biojava.bio.program.tagvalue.TagValueListener)">TagDelegator(TagValueListener)</a></span> - Constructor for class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/TagDelegator.html" title="class in org.biojava.bio.program.tagvalue">TagDelegator</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/tagvalue/TagDropper.html" title="class in org.biojava.bio.program.tagvalue"><span class="strong">TagDropper</span></a> - Class in <a href="./org/biojava/bio/program/tagvalue/package-summary.html">org.biojava.bio.program.tagvalue</a></dt>
<dd>
<div class="block">Silently drop all tags except those specified, and pass the rest onto a
delegate.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/TagDropper.html#TagDropper()">TagDropper()</a></span> - Constructor for class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/TagDropper.html" title="class in org.biojava.bio.program.tagvalue">TagDropper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/TagDropper.html#TagDropper(org.biojava.bio.program.tagvalue.TagValueListener)">TagDropper(TagValueListener)</a></span> - Constructor for class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/TagDropper.html" title="class in org.biojava.bio.program.tagvalue">TagDropper</a></dt>
<dd>
<div class="block">Create a new TagDropper that will pass on all retained tags and values to
tvl.</div>
</dd>
<dt><a href="./org/biojava/bio/program/tagvalue/TagMapper.html" title="class in org.biojava.bio.program.tagvalue"><span class="strong">TagMapper</span></a> - Class in <a href="./org/biojava/bio/program/tagvalue/package-summary.html">org.biojava.bio.program.tagvalue</a></dt>
<dd>
<div class="block">
<code>TagMapper</code> maps arbitrary object keys to new keys.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/TagMapper.html#TagMapper()">TagMapper()</a></span> - Constructor for class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/TagMapper.html" title="class in org.biojava.bio.program.tagvalue">TagMapper</a></dt>
<dd>
<div class="block">Creates a new, empty <code>TagMapper</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/abi/ABIFParser.TaggedDataRecord.html#tagName">tagName</a></span> - Variable in class org.biojava.bio.program.abi.<a href="./org/biojava/bio/program/abi/ABIFParser.TaggedDataRecord.html" title="class in org.biojava.bio.program.abi">ABIFParser.TaggedDataRecord</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/abi/ABIFParser.TaggedDataRecord.html#tagNumber">tagNumber</a></span> - Variable in class org.biojava.bio.program.abi.<a href="./org/biojava/bio/program/abi/ABIFParser.TaggedDataRecord.html" title="class in org.biojava.bio.program.abi">ABIFParser.TaggedDataRecord</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/tagvalue/TagRenamer.html" title="class in org.biojava.bio.program.tagvalue"><span class="strong">TagRenamer</span></a> - Class in <a href="./org/biojava/bio/program/tagvalue/package-summary.html">org.biojava.bio.program.tagvalue</a></dt>
<dd>
<div class="block">
Rename tags using a TagMapper.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/TagRenamer.html#TagRenamer(org.biojava.bio.program.tagvalue.TagValueListener, org.biojava.bio.program.tagvalue.PropertyChanger)">TagRenamer(TagValueListener, PropertyChanger)</a></span> - Constructor for class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/TagRenamer.html" title="class in org.biojava.bio.program.tagvalue">TagRenamer</a></dt>
<dd>
<div class="block">Build a new TagRenamer with a delegate and mapper.</div>
</dd>
<dt><a href="./org/biojava/bio/program/tagvalue/TagValue.html" title="class in org.biojava.bio.program.tagvalue"><span class="strong">TagValue</span></a> - Class in <a href="./org/biojava/bio/program/tagvalue/package-summary.html">org.biojava.bio.program.tagvalue</a></dt>
<dd>
<div class="block">
Utility class for representing tag-value pairs for TagValueParser
implementors.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/TagValue.html#TagValue(java.lang.Object, java.lang.Object, boolean)">TagValue(Object, Object, boolean)</a></span> - Constructor for class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/TagValue.html" title="class in org.biojava.bio.program.tagvalue">TagValue</a></dt>
<dd>
<div class="block">Build a new TagValue with a tag, a value and a flag indicating if this is a
new example of this tag or a continuation of an old example.</div>
</dd>
<dt><a href="./org/biojava/bio/program/tagvalue/TagValueContext.html" title="interface in org.biojava.bio.program.tagvalue"><span class="strong">TagValueContext</span></a> - Interface in <a href="./org/biojava/bio/program/tagvalue/package-summary.html">org.biojava.bio.program.tagvalue</a></dt>
<dd>
<div class="block">Communication interface between Parser and a TagValueListener that allows
listeners to request that a parser/listener pair be pushed onto the stack to
handle the current tag.</div>
</dd>
<dt><a href="./org/biojava/bio/program/tagvalue/TagValueListener.html" title="interface in org.biojava.bio.program.tagvalue"><span class="strong">TagValueListener</span></a> - Interface in <a href="./org/biojava/bio/program/tagvalue/package-summary.html">org.biojava.bio.program.tagvalue</a></dt>
<dd>
<div class="block">
An object that wishes to be informed of events during the parsing of a file.</div>
</dd>
<dt><a href="./org/biojava/bio/program/tagvalue/TagValueParser.html" title="interface in org.biojava.bio.program.tagvalue"><span class="strong">TagValueParser</span></a> - Interface in <a href="./org/biojava/bio/program/tagvalue/package-summary.html">org.biojava.bio.program.tagvalue</a></dt>
<dd>
<div class="block">
Tokenize single records (lines of text, objects) into a tag and a value.</div>
</dd>
<dt><a href="./org/biojava/bio/program/tagvalue/TagValueWrapper.html" title="interface in org.biojava.bio.program.tagvalue"><span class="strong">TagValueWrapper</span></a> - Interface in <a href="./org/biojava/bio/program/tagvalue/package-summary.html">org.biojava.bio.program.tagvalue</a></dt>
<dd>
<div class="block">
Interface for TagValueListeners that wrap other TagValueListeners</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/JDBCConnectionPool.html#takeConnection()">takeConnection()</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/JDBCConnectionPool.html" title="class in org.biojava.utils">JDBCConnectionPool</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/JDBCConnectionPool.html#takeStatement()">takeStatement()</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/JDBCConnectionPool.html" title="class in org.biojava.utils">JDBCConnectionPool</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/SigmoidKernel.html#tanh(double)">tanh(double)</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/SigmoidKernel.html" title="class in org.biojava.stats.svm">SigmoidKernel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/Taxon.html#taxa">taxa</a></span> - Static variable in interface org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/Taxon.html" title="interface in org.biojava.bio.program.homologene">Taxon</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html#TAXID_TAG">TAXID_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html" title="class in org.biojavax.bio.seq.io">EMBLxmlFormat</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/homologene/Taxon.html" title="interface in org.biojava.bio.program.homologene"><span class="strong">Taxon</span></a> - Interface in <a href="./org/biojava/bio/program/homologene/package-summary.html">org.biojava.bio.program.homologene</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/taxa/Taxon.html" title="interface in org.biojava.bio.taxa"><span class="strong">Taxon</span></a> - Interface in <a href="./org/biojava/bio/taxa/package-summary.html">org.biojava.bio.taxa</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>replaced by classes in <a href="./org/biojavax/bio/taxa/package-summary.html"><code>org.biojavax.bio.taxa</code></a></i></div>
</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/BioEntry.html#TAXON">TAXON</a></span> - Static variable in interface org.biojavax.bio.<a href="./org/biojavax/bio/BioEntry.html" title="interface in org.biojavax.bio">BioEntry</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/homologene/Taxon.TaxonStub.html" title="class in org.biojava.bio.program.homologene"><span class="strong">Taxon.TaxonStub</span></a> - Class in <a href="./org/biojava/bio/program/homologene/package-summary.html">org.biojava.bio.program.homologene</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html#TAXON_TAG">TAXON_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html" title="class in org.biojavax.bio.seq.io">EMBLxmlFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtFormat.html#TAXON_TAG">TAXON_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtFormat.html" title="class in org.biojavax.bio.seq.io">UniProtFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#TAXON_TAG">TAXON_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/taxa/TaxonFactory.html" title="interface in org.biojava.bio.taxa"><span class="strong">TaxonFactory</span></a> - Interface in <a href="./org/biojava/bio/taxa/package-summary.html">org.biojava.bio.taxa</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>replaced by classes in <a href="./org/biojavax/bio/taxa/package-summary.html"><code>org.biojavax.bio.taxa</code></a></i></div>
</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/HomologeneBuilder.html#TAXONID">TAXONID</a></span> - Static variable in interface org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/HomologeneBuilder.html" title="interface in org.biojava.bio.program.homologene">HomologeneBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/INSDseqFormat.html#TAXONOMY_TAG">TAXONOMY_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/INSDseqFormat.html" title="class in org.biojavax.bio.seq.io">INSDseqFormat</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/taxa/TaxonParser.html" title="interface in org.biojava.bio.taxa"><span class="strong">TaxonParser</span></a> - Interface in <a href="./org/biojava/bio/taxa/package-summary.html">org.biojava.bio.taxa</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>replaced by classes in <a href="./org/biojavax/bio/taxa/package-summary.html"><code>org.biojavax.bio.taxa</code></a></i></div>
</div>
</dd>
<dt><a href="./org/biojava/bio/seq/db/biosql/TaxonSQL.html" title="class in org.biojava.bio.seq.db.biosql"><span class="strong">TaxonSQL</span></a> - Class in <a href="./org/biojava/bio/seq/db/biosql/package-summary.html">org.biojava.bio.seq.db.biosql</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>Use hibernate and org.biojavax.bio.db.*</i></div>
</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/biosql/TaxonSQL.html#TaxonSQL()">TaxonSQL()</a></span> - Constructor for class org.biojava.bio.seq.db.biosql.<a href="./org/biojava/bio/seq/db/biosql/TaxonSQL.html" title="class in org.biojava.bio.seq.db.biosql">TaxonSQL</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/obo/OboFileParser.html#tempBuffer">tempBuffer</a></span> - Variable in class org.biojava.ontology.obo.<a href="./org/biojava/ontology/obo/OboFileParser.html" title="class in org.biojava.ontology.obo">OboFileParser</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/impl/TemplateUtils.html" title="class in org.biojava.bio.seq.impl"><span class="strong">TemplateUtils</span></a> - Class in <a href="./org/biojava/bio/seq/impl/package-summary.html">org.biojava.bio.seq.impl</a></dt>
<dd>
<div class="block">Common things you may want to do with feature templates.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BiblioScope.html#temporalPeriod">temporalPeriod</a></span> - Variable in class org.biojava.bibliography.<a href="./org/biojava/bibliography/BiblioScope.html" title="class in org.biojava.bibliography">BiblioScope</a></dt>
<dd>
<div class="block">It defines temporal period of the cited resource.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/ProteinTools.html#ter()">ter()</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/ProteinTools.html" title="class in org.biojava.bio.seq">ProteinTools</a></dt>
<dd>
<div class="block">Returns the <code>AtomicSymbol</code> for the termination (*)
placeholder</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/obo/OboFileHandler.html#TERM">TERM</a></span> - Static variable in class org.biojava.ontology.obo.<a href="./org/biojava/ontology/obo/OboFileHandler.html" title="class in org.biojava.ontology.obo">OboFileHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/Ontology.html#TERM">TERM</a></span> - Static variable in interface org.biojava.ontology.<a href="./org/biojava/ontology/Ontology.html" title="interface in org.biojava.ontology">Ontology</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/ontology/Term.html" title="interface in org.biojava.ontology"><span class="strong">Term</span></a> - Interface in <a href="./org/biojava/ontology/package-summary.html">org.biojava.ontology</a></dt>
<dd>
<div class="block">A term in an ontology.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichLocation.html#TERM">TERM</a></span> - Static variable in interface org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichLocation.html" title="interface in org.biojavax.bio.seq">RichLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichLocation.html#term">term</a></span> - Variable in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichLocation.html" title="class in org.biojavax.bio.seq">SimpleRichLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/Note.html#TERM">TERM</a></span> - Static variable in interface org.biojavax.<a href="./org/biojavax/Note.html" title="interface in org.biojavax">Note</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/ontology/ComparableOntology.html#TERM">TERM</a></span> - Static variable in interface org.biojavax.ontology.<a href="./org/biojavax/ontology/ComparableOntology.html" title="interface in org.biojavax.ontology">ComparableOntology</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/ontology/Term.Impl.html" title="class in org.biojava.ontology"><span class="strong">Term.Impl</span></a> - Class in <a href="./org/biojava/ontology/package-summary.html">org.biojava.ontology</a></dt>
<dd>
<div class="block">Simple in-memory implementation of an ontology term.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/Term.Impl.html#Term.Impl(org.biojava.ontology.Ontology, java.lang.String)">Term.Impl(Ontology, String)</a></span> - Constructor for class org.biojava.ontology.<a href="./org/biojava/ontology/Term.Impl.html" title="class in org.biojava.ontology">Term.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/Term.Impl.html#Term.Impl(org.biojava.ontology.Ontology, java.lang.String, java.lang.String)">Term.Impl(Ontology, String, String)</a></span> - Constructor for class org.biojava.ontology.<a href="./org/biojava/ontology/Term.Impl.html" title="class in org.biojava.ontology">Term.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/Term.Impl.html#Term.Impl(org.biojava.ontology.Ontology, java.lang.String, java.lang.String, java.lang.Object[])">Term.Impl(Ontology, String, String, Object[])</a></span> - Constructor for class org.biojava.ontology.<a href="./org/biojava/ontology/Term.Impl.html" title="class in org.biojava.ontology">Term.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/util/SequenceScalePanel.html#TEXT_SCALE_COLOR">TEXT_SCALE_COLOR</a></span> - Static variable in class org.biojava.bio.structure.gui.util.<a href="./org/biojava/bio/structure/gui/util/SequenceScalePanel.html" title="class in org.biojava.bio.structure.gui.util">SequenceScalePanel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#TEXT_TAG">TEXT_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/gui/TextBlock.html" title="class in org.biojava.bio.gui"><span class="strong">TextBlock</span></a> - Class in <a href="./org/biojava/bio/gui/package-summary.html">org.biojava.bio.gui</a></dt>
<dd>
<div class="block">A BlockPainter that renders letters in proportion to the size of the signal.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/TextBlock.html#TextBlock()">TextBlock()</a></span> - Constructor for class org.biojava.bio.gui.<a href="./org/biojava/bio/gui/TextBlock.html" title="class in org.biojava.bio.gui">TextBlock</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/gui/TextLogoPainter.html" title="class in org.biojava.bio.gui"><span class="strong">TextLogoPainter</span></a> - Class in <a href="./org/biojava/bio/gui/package-summary.html">org.biojava.bio.gui</a></dt>
<dd>
<div class="block">A logo painter that paints in stacked letters.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/TextLogoPainter.html#TextLogoPainter()">TextLogoPainter()</a></span> - Constructor for class org.biojava.bio.gui.<a href="./org/biojava/bio/gui/TextLogoPainter.html" title="class in org.biojava.bio.gui">TextLogoPainter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BiblioDescription.html#theAbstract">theAbstract</a></span> - Variable in class org.biojava.bibliography.<a href="./org/biojava/bibliography/BiblioDescription.html" title="class in org.biojava.bibliography">BiblioDescription</a></dt>
<dd>
<div class="block">
It is an abstract of the cited resource.</div>
</dd>
<dt><a href="./org/biojavax/bio/seq/ThinRichSequence.html" title="class in org.biojavax.bio.seq"><span class="strong">ThinRichSequence</span></a> - Class in <a href="./org/biojavax/bio/seq/package-summary.html">org.biojavax.bio.seq</a></dt>
<dd>
<div class="block">A simple implementation of RichSequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/ThinRichSequence.html#ThinRichSequence(org.biojavax.Namespace, java.lang.String, java.lang.String, int, org.biojava.bio.symbol.Alphabet, java.lang.Double)">ThinRichSequence(Namespace, String, String, int, Alphabet, Double)</a></span> - Constructor for class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/ThinRichSequence.html" title="class in org.biojavax.bio.seq">ThinRichSequence</a></dt>
<dd>
<div class="block">Creates a new instance of ThinRichSequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/ThinRichSequence.html#ThinRichSequence()">ThinRichSequence()</a></span> - Constructor for class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/ThinRichSequence.html" title="class in org.biojavax.bio.seq">ThinRichSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/ProteinTools.html#thr()">thr()</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/ProteinTools.html" title="class in org.biojava.bio.seq">ProteinTools</a></dt>
<dd>
<div class="block">Returns the <code>AtomicSymbol</code> for the amino acid
Threonine (T)</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/process/ExternalProcess.html#THREAD_POOL_SIZE">THREAD_POOL_SIZE</a></span> - Static variable in class org.biojava.utils.process.<a href="./org/biojava/utils/process/ExternalProcess.html" title="class in org.biojava.utils.process">ExternalProcess</a></dt>
<dd>
<div class="block">Size of the thread pool for the static execute methods.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/process/ExternalProcess.html#threadPool()">threadPool()</a></span> - Method in class org.biojava.utils.process.<a href="./org/biojava/utils/process/ExternalProcess.html" title="class in org.biojava.utils.process">ExternalProcess</a></dt>
<dd>
<div class="block">Gets the thread pool which is used for the input and output handlers.</div>
</dd>
<dt><a href="./org/biojava/utils/ThreadPool.html" title="interface in org.biojava.utils"><span class="strong">ThreadPool</span></a> - Interface in <a href="./org/biojava/utils/package-summary.html">org.biojava.utils</a></dt>
<dd>
<div class="block"><code>ThreadPool</code> specifies basic thread-pooling
operations such that third-party implementations may be used
without requiring changes to BioJava.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/SimpleThreadPool.html#threads">threads</a></span> - Variable in class org.biojava.utils.<a href="./org/biojava/utils/SimpleThreadPool.html" title="class in org.biojava.utils">SimpleThreadPool</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/SimpleThreadPool.html#threadsAlive()">threadsAlive()</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/SimpleThreadPool.html" title="class in org.biojava.utils">SimpleThreadPool</a></dt>
<dd>
<div class="block"><code>threadsAlive</code> returns the number of threads
currently alive.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/SimpleThreadPool.html#threadsIdle()">threadsIdle()</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/SimpleThreadPool.html" title="class in org.biojava.utils">SimpleThreadPool</a></dt>
<dd>
<div class="block"><code>threadsIdle</code> returns the number of threads
currently waiting for work.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/SimpleThreadPool.html#threadsWorking()">threadsWorking()</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/SimpleThreadPool.html" title="class in org.biojava.utils">SimpleThreadPool</a></dt>
<dd>
<div class="block"><code>threadsWorking</code> returns the number of threads
currently performing work.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/RichSequenceBuilderFactory.html#THRESHOLD">THRESHOLD</a></span> - Static variable in interface org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/RichSequenceBuilderFactory.html" title="interface in org.biojavax.bio.seq.io">RichSequenceBuilderFactory</a></dt>
<dd>
<div class="block">Accessor for a factory that produces builders that compress the
<code>SymbolList</code> of a <code>RichSequence</code> when the length of the
<code>SymbolList</code> exceeds <code>THRESHOLD</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/RichSequenceBuilderFactory.html#THRESHOLD_VALUE">THRESHOLD_VALUE</a></span> - Static variable in interface org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/RichSequenceBuilderFactory.html" title="interface in org.biojavax.bio.seq.io">RichSequenceBuilderFactory</a></dt>
<dd>
<div class="block">The value that will be used as a threshold for the <code>THRESHOLD</code>
builder.</div>
</dd>
<dt><a href="./org/biojava/bio/gui/sequence/TickFeatureRenderer.html" title="class in org.biojava.bio.gui.sequence"><span class="strong">TickFeatureRenderer</span></a> - Class in <a href="./org/biojava/bio/gui/sequence/package-summary.html">org.biojava.bio.gui.sequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/TickFeatureRenderer.html#TickFeatureRenderer()">TickFeatureRenderer()</a></span> - Constructor for class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/TickFeatureRenderer.html" title="class in org.biojava.bio.gui.sequence">TickFeatureRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/OffsetRulerRenderer.html#TICKS">TICKS</a></span> - Static variable in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/OffsetRulerRenderer.html" title="class in org.biojava.bio.gui.sequence">OffsetRulerRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/OffsetRulerRenderer.html#TICKS_DOWN">TICKS_DOWN</a></span> - Static variable in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/OffsetRulerRenderer.html" title="class in org.biojava.bio.gui.sequence">OffsetRulerRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/RulerRenderer.html#TICKS_DOWN">TICKS_DOWN</a></span> - Static variable in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/RulerRenderer.html" title="class in org.biojava.bio.gui.sequence">RulerRenderer</a></dt>
<dd>
<div class="block"><code>TICKS_DOWN</code> indicates that the ticks will point
downwards from a baseline.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/OffsetRulerRenderer.html#TICKS_UP">TICKS_UP</a></span> - Static variable in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/OffsetRulerRenderer.html" title="class in org.biojava.bio.gui.sequence">OffsetRulerRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/RulerRenderer.html#TICKS_UP">TICKS_UP</a></span> - Static variable in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/RulerRenderer.html" title="class in org.biojava.bio.gui.sequence">RulerRenderer</a></dt>
<dd>
<div class="block"><code>TICKS_UP</code> indicates that the ticks will point
upwards from a baseline.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/jama/Matrix.html#times(double)">times(double)</a></span> - Method in class org.biojava.bio.structure.jama.<a href="./org/biojava/bio/structure/jama/Matrix.html" title="class in org.biojava.bio.structure.jama">Matrix</a></dt>
<dd>
<div class="block">Multiply a matrix by a scalar, C = s*A</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/jama/Matrix.html#times(org.biojava.bio.structure.jama.Matrix)">times(Matrix)</a></span> - Method in class org.biojava.bio.structure.jama.<a href="./org/biojava/bio/structure/jama/Matrix.html" title="class in org.biojava.bio.structure.jama">Matrix</a></dt>
<dd>
<div class="block">Linear algebraic matrix multiplication, A * B</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/jama/Matrix.html#timesEquals(double)">timesEquals(double)</a></span> - Method in class org.biojava.bio.structure.jama.<a href="./org/biojava/bio/structure/jama/Matrix.html" title="class in org.biojava.bio.structure.jama">Matrix</a></dt>
<dd>
<div class="block">Multiply a matrix by a scalar in place, A = s*A</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.Terms.html#TISSUE_KEY">TISSUE_KEY</a></span> - Static variable in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.Terms.html" title="class in org.biojavax.bio.seq">RichSequence.Terms</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BibRef.html#title">title</a></span> - Variable in class org.biojava.bibliography.<a href="./org/biojava/bibliography/BibRef.html" title="class in org.biojava.bibliography">BibRef</a></dt>
<dd>
<div class="block">A title given to the cited resource (a name by which the resource is formally known).</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/EmblLikeFormat.html#TITLE_TAG">TITLE_TAG</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/EmblLikeFormat.html" title="class in org.biojava.bio.seq.io">EmblLikeFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/GenbankFormat.html#TITLE_TAG">TITLE_TAG</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/GenbankFormat.html" title="class in org.biojava.bio.seq.io">GenbankFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLFormat.html#TITLE_TAG">TITLE_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLFormat.html" title="class in org.biojavax.bio.seq.io">EMBLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html#TITLE_TAG">TITLE_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html" title="class in org.biojavax.bio.seq.io">EMBLxmlFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/GenbankFormat.html#TITLE_TAG">TITLE_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/GenbankFormat.html" title="class in org.biojavax.bio.seq.io">GenbankFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/INSDseqFormat.html#TITLE_TAG">TITLE_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/INSDseqFormat.html" title="class in org.biojavax.bio.seq.io">INSDseqFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtFormat.html#TITLE_TAG">TITLE_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtFormat.html" title="class in org.biojavax.bio.seq.io">UniProtFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#TITLE_TAG">TITLE_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/TrainerTransition.html#to">to</a></span> - Variable in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/TrainerTransition.html" title="class in org.biojava.bio.dp">TrainerTransition</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/Transition.html#to">to</a></span> - Variable in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/Transition.html" title="class in org.biojava.bio.dp">Transition</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/UkkonenSuffixTree.html#TO_A_LEAF">TO_A_LEAF</a></span> - Static variable in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/UkkonenSuffixTree.html" title="class in org.biojava.bio.symbol">UkkonenSuffixTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.Option.html#TO_TRACE_SAMPLE">TO_TRACE_SAMPLE</a></span> - Static variable in class org.biojava.bio.chromatogram.graphic.<a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.Option.html" title="class in org.biojava.bio.chromatogram.graphic">ChromatogramGraphic.Option</a></dt>
<dd>
<div class="block">Option indicating the highest (rightmost) trace sample that should be
drawn.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ga/util/WeightedSet.html#toArray()">toArray()</a></span> - Method in class org.biojavax.ga.util.<a href="./org/biojavax/ga/util/WeightedSet.html" title="class in org.biojavax.ga.util">WeightedSet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/FileConvert.html#toDASStructure(org.biojava.utils.xml.XMLWriter)">toDASStructure(XMLWriter)</a></span> - Method in class org.biojava.bio.structure.io.<a href="./org/biojava/bio/structure/io/FileConvert.html" title="class in org.biojava.bio.structure.io">FileConvert</a></dt>
<dd>
<div class="block">convert a protein Structure to a DAS Structure XML response .</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/LabelledSequenceRenderer.html#toggleSelectionStatus()">toggleSelectionStatus()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/LabelledSequenceRenderer.html" title="class in org.biojava.bio.gui.sequence">LabelledSequenceRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/AlternateTokenization.html#tokenizeSymbol(org.biojava.bio.symbol.Symbol)">tokenizeSymbol(Symbol)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/AlternateTokenization.html" title="class in org.biojava.bio.seq.io">AlternateTokenization</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/CharacterTokenization.html#tokenizeSymbol(org.biojava.bio.symbol.Symbol)">tokenizeSymbol(Symbol)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/CharacterTokenization.html" title="class in org.biojava.bio.seq.io">CharacterTokenization</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/CrossProductTokenization.html#tokenizeSymbol(org.biojava.bio.symbol.Symbol)">tokenizeSymbol(Symbol)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/CrossProductTokenization.html" title="class in org.biojava.bio.seq.io">CrossProductTokenization</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/DoubleTokenization.html#tokenizeSymbol(org.biojava.bio.symbol.Symbol)">tokenizeSymbol(Symbol)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/DoubleTokenization.html" title="class in org.biojava.bio.seq.io">DoubleTokenization</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/IntegerTokenization.html#tokenizeSymbol(org.biojava.bio.symbol.Symbol)">tokenizeSymbol(Symbol)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/IntegerTokenization.html" title="class in org.biojava.bio.seq.io">IntegerTokenization</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/NameTokenization.html#tokenizeSymbol(org.biojava.bio.symbol.Symbol)">tokenizeSymbol(Symbol)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/NameTokenization.html" title="class in org.biojava.bio.seq.io">NameTokenization</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SubIntegerTokenization.html#tokenizeSymbol(org.biojava.bio.symbol.Symbol)">tokenizeSymbol(Symbol)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SubIntegerTokenization.html" title="class in org.biojava.bio.seq.io">SubIntegerTokenization</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SymbolTokenization.html#tokenizeSymbol(org.biojava.bio.symbol.Symbol)">tokenizeSymbol(Symbol)</a></span> - Method in interface org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SymbolTokenization.html" title="interface in org.biojava.bio.seq.io">SymbolTokenization</a></dt>
<dd>
<div class="block">Return a token representing a single symbol.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SoftMaskedAlphabet.CaseSensitiveTokenization.html#tokenizeSymbol(org.biojava.bio.symbol.Symbol)">tokenizeSymbol(Symbol)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SoftMaskedAlphabet.CaseSensitiveTokenization.html" title="class in org.biojava.bio.symbol">SoftMaskedAlphabet.CaseSensitiveTokenization</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/AlternateTokenization.html#tokenizeSymbolList(org.biojava.bio.symbol.SymbolList)">tokenizeSymbolList(SymbolList)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/AlternateTokenization.html" title="class in org.biojava.bio.seq.io">AlternateTokenization</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/CharacterTokenization.html#tokenizeSymbolList(org.biojava.bio.symbol.SymbolList)">tokenizeSymbolList(SymbolList)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/CharacterTokenization.html" title="class in org.biojava.bio.seq.io">CharacterTokenization</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SymbolTokenization.html#tokenizeSymbolList(org.biojava.bio.symbol.SymbolList)">tokenizeSymbolList(SymbolList)</a></span> - Method in interface org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SymbolTokenization.html" title="interface in org.biojava.bio.seq.io">SymbolTokenization</a></dt>
<dd>
<div class="block">Return a string representation of a list of symbols.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/WordTokenization.html#tokenizeSymbolList(org.biojava.bio.symbol.SymbolList)">tokenizeSymbolList(SymbolList)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/WordTokenization.html" title="class in org.biojava.bio.seq.io">WordTokenization</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SoftMaskedAlphabet.CaseSensitiveTokenization.html#tokenizeSymbolList(org.biojava.bio.symbol.SymbolList)">tokenizeSymbolList(SymbolList)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SoftMaskedAlphabet.CaseSensitiveTokenization.html" title="class in org.biojava.bio.symbol">SoftMaskedAlphabet.CaseSensitiveTokenization</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/blast2html/DatabaseURLGenerator.html#toLink(java.lang.String, java.util.Properties)">toLink(String, Properties)</a></span> - Method in interface org.biojava.bio.program.blast2html.<a href="./org/biojava/bio/program/blast2html/DatabaseURLGenerator.html" title="interface in org.biojava.bio.program.blast2html">DatabaseURLGenerator</a></dt>
<dd>
<div class="block">Returns a full <a href=./org/biojava/bio/program/blast2html/_____>retrieve item</a> anchor
for the given database id.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/blast2html/EbiDatabaseURLGenerator.html#toLink(java.lang.String, java.util.Properties)">toLink(String, Properties)</a></span> - Method in class org.biojava.bio.program.blast2html.<a href="./org/biojava/bio/program/blast2html/EbiDatabaseURLGenerator.html" title="class in org.biojava.bio.program.blast2html">EbiDatabaseURLGenerator</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/blast2html/NcbiDatabaseURLGenerator.html#toLink(java.lang.String, java.util.Properties)">toLink(String, Properties)</a></span> - Method in class org.biojava.bio.program.blast2html.<a href="./org/biojava/bio/program/blast2html/NcbiDatabaseURLGenerator.html" title="class in org.biojava.bio.program.blast2html">NcbiDatabaseURLGenerator</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/SimpleStatePath.html#toList()">toList()</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/SimpleStatePath.html" title="class in org.biojava.bio.dp">SimpleStatePath</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/DASSequence.html#toList()">toList()</a></span> - Method in class org.biojava.bio.program.das.<a href="./org/biojava/bio/program/das/DASSequence.html" title="class in org.biojava.bio.program.das">DASSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/homol/SimilarityPairFeature.EmptyPairwiseAlignment.html#toList()">toList()</a></span> - Method in class org.biojava.bio.seq.homol.<a href="./org/biojava/bio/seq/homol/SimilarityPairFeature.EmptyPairwiseAlignment.html" title="class in org.biojava.bio.seq.homol">SimilarityPairFeature.EmptyPairwiseAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/DummySequence.html#toList()">toList()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/DummySequence.html" title="class in org.biojava.bio.seq.impl">DummySequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleSequence.html#toList()">toList()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleSequence.html" title="class in org.biojava.bio.seq.impl">SimpleSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SubSequence.html#toList()">toList()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SubSequence.html" title="class in org.biojava.bio.seq.impl">SubSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/ViewSequence.html#toList()">toList()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/ViewSequence.html" title="class in org.biojava.bio.seq.impl">ViewSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/NewSimpleAssembly.html#toList()">toList()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/NewSimpleAssembly.html" title="class in org.biojava.bio.seq">NewSimpleAssembly</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/SimpleAssembly.html#toList()">toList()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/SimpleAssembly.html" title="class in org.biojava.bio.seq">SimpleAssembly</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AbstractSymbolList.html#toList()">toList()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AbstractSymbolList.html" title="class in org.biojava.bio.symbol">AbstractSymbolList</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/RelabeledAlignment.html#toList()">toList()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/RelabeledAlignment.html" title="class in org.biojava.bio.symbol">RelabeledAlignment</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SymbolList.html#toList()">toList()</a></span> - Method in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SymbolList.html" title="interface in org.biojava.bio.symbol">SymbolList</a></dt>
<dd>
<div class="block">Returns a List of symbols.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLRichSequenceHandler.html#toList(org.biojavax.bio.seq.RichSequence)">toList(RichSequence)</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLRichSequenceHandler.html" title="class in org.biojavax.bio.db.biosql">BioSQLRichSequenceHandler</a></dt>
<dd>
<div class="block">Returns a List of symbols.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/DummyRichSequenceHandler.html#toList(org.biojavax.bio.seq.RichSequence)">toList(RichSequence)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/DummyRichSequenceHandler.html" title="class in org.biojavax.bio.seq">DummyRichSequenceHandler</a></dt>
<dd>
<div class="block">Returns a List of symbols.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/InfinitelyAmbiguousSymbolList.html#toList()">toList()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/InfinitelyAmbiguousSymbolList.html" title="class in org.biojavax.bio.seq">InfinitelyAmbiguousSymbolList</a></dt>
<dd>
<div class="block">Returns a List of symbols.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequenceHandler.html#toList(org.biojavax.bio.seq.RichSequence)">toList(RichSequence)</a></span> - Method in interface org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequenceHandler.html" title="interface in org.biojavax.bio.seq">RichSequenceHandler</a></dt>
<dd>
<div class="block">Returns a List of symbols.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/ThinRichSequence.html#toList()">toList()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/ThinRichSequence.html" title="class in org.biojavax.bio.seq">ThinRichSequence</a></dt>
<dd>
<div class="block">Returns a List of symbols.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.html#top_level">top_level</a></span> - Static variable in interface org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.html" title="interface in org.biojava.bio.seq">FeatureFilter</a></dt>
<dd>
<div class="block">A filter which accepts only top-level Features.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/AlternativeAlignment.html#toPDB(org.biojava.bio.structure.Structure, org.biojava.bio.structure.Structure)">toPDB(Structure, Structure)</a></span> - Method in class org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/AlternativeAlignment.html" title="class in org.biojava.bio.structure.align.pairwise">AlternativeAlignment</a></dt>
<dd>
<div class="block">converts the alignment to a PDB file
each of the structures will be represented as a model.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/DBRef.html#toPDB()">toPDB()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/DBRef.html" title="class in org.biojava.bio.structure">DBRef</a></dt>
<dd>
<div class="block">Convert the DBRef object to a DBREF record as it is used in PDB files</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/DBRef.html#toPDB(java.lang.StringBuffer)">toPDB(StringBuffer)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/DBRef.html" title="class in org.biojava.bio.structure">DBRef</a></dt>
<dd>
<div class="block">Append the PDB representation of this DBRef to the provided StringBuffer</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/FileConvert.html#toPDB()">toPDB()</a></span> - Method in class org.biojava.bio.structure.io.<a href="./org/biojava/bio/structure/io/FileConvert.html" title="class in org.biojava.bio.structure.io">FileConvert</a></dt>
<dd>
<div class="block">Convert a structure into a PDB file.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/PDBHeader.html#toPDB()">toPDB()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/PDBHeader.html" title="class in org.biojava.bio.structure">PDBHeader</a></dt>
<dd>
<div class="block">Return a PDB representation of the PDB Header</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/PDBHeader.html#toPDB(java.lang.StringBuffer)">toPDB(StringBuffer)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/PDBHeader.html" title="class in org.biojava.bio.structure">PDBHeader</a></dt>
<dd>
<div class="block">Appends a PDB representation of the PDB header to the provided StringBuffer</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/PDBRecord.html#toPDB()">toPDB()</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/PDBRecord.html" title="interface in org.biojava.bio.structure">PDBRecord</a></dt>
<dd>
<div class="block">Returns a PDB file like representation of this record.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/PDBRecord.html#toPDB(java.lang.StringBuffer)">toPDB(StringBuffer)</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/PDBRecord.html" title="interface in org.biojava.bio.structure">PDBRecord</a></dt>
<dd>
<div class="block">Appends a PDB file like representation of this record to the provided StringBuffer.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/SSBond.html#toPDB()">toPDB()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/SSBond.html" title="class in org.biojava.bio.structure">SSBond</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/SSBond.html#toPDB(java.lang.StringBuffer)">toPDB(StringBuffer)</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/SSBond.html" title="class in org.biojava.bio.structure">SSBond</a></dt>
<dd>
<div class="block">append the PDB representation of this SSBOND to the provided StringBUffer</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Structure.html#toPDB()">toPDB()</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Structure.html" title="interface in org.biojava.bio.structure">Structure</a></dt>
<dd>
<div class="block">create a String that contains the contents of a PDB file .</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/StructureImpl.html#toPDB()">toPDB()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/StructureImpl.html" title="class in org.biojava.bio.structure">StructureImpl</a></dt>
<dd>
<div class="block">create a String that contains the contents of a PDB file.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FilterUtils.html#topLevel()">topLevel()</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FilterUtils.html" title="class in org.biojava.bio.seq">FilterUtils</a></dt>
<dd>
<div class="block">Return a filter which matches all top-level features.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/INSDseqFormat.html#TOPOLOGY_TAG">TOPOLOGY_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/INSDseqFormat.html" title="class in org.biojavax.bio.seq.io">INSDseqFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/DNATools.html#toProtein(org.biojava.bio.symbol.SymbolList)">toProtein(SymbolList)</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/DNATools.html" title="class in org.biojava.bio.seq">DNATools</a></dt>
<dd>
<div class="block">Convenience method that directly converts a DNA sequence to RNA then to
protein.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/DNATools.html#toProtein(org.biojava.bio.symbol.SymbolList, int, int)">toProtein(SymbolList, int, int)</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/DNATools.html" title="class in org.biojava.bio.seq">DNATools</a></dt>
<dd>
<div class="block">Convenience method to translate a region of a DNA sequence directly into
protein.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/DNATools.html#toRNA(org.biojava.bio.symbol.SymbolList)">toRNA(SymbolList)</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/DNATools.html" title="class in org.biojava.bio.seq">DNATools</a></dt>
<dd>
<div class="block">Converts a <code>SymbolList</code> from the DNA <code>Alphabet</code> to the
RNA <code>Alphabet</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Calc.html#torsionAngle(org.biojava.bio.structure.Atom, org.biojava.bio.structure.Atom, org.biojava.bio.structure.Atom, org.biojava.bio.structure.Atom)">torsionAngle(Atom, Atom, Atom, Atom)</a></span> - Static method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Calc.html" title="class in org.biojava.bio.structure">Calc</a></dt>
<dd>
<div class="block">torsion angle
= angle between the normal vectors of the
two plains a-b-c and b-c-d.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/AbstractAnnotation.html#toString()">toString()</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/AbstractAnnotation.html" title="class in org.biojava.bio">AbstractAnnotation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/alignment/SubstitutionMatrix.html#toString()">toString()</a></span> - Method in class org.biojava.bio.alignment.<a href="./org/biojava/bio/alignment/SubstitutionMatrix.html" title="class in org.biojava.bio.alignment">SubstitutionMatrix</a></dt>
<dd>
<div class="block">Overrides the inherited method.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/AnnotationType.Abstract.html#toString()">toString()</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/AnnotationType.Abstract.html" title="class in org.biojava.bio">AnnotationType.Abstract</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.Option.html#toString()">toString()</a></span> - Method in class org.biojava.bio.chromatogram.graphic.<a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.Option.html" title="class in org.biojava.bio.chromatogram.graphic">ChromatogramGraphic.Option</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/CollectionConstraint.AllValuesIn.html#toString()">toString()</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/CollectionConstraint.AllValuesIn.html" title="class in org.biojava.bio">CollectionConstraint.AllValuesIn</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/CollectionConstraint.And.html#toString()">toString()</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/CollectionConstraint.And.html" title="class in org.biojava.bio">CollectionConstraint.And</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/CollectionConstraint.Contains.html#toString()">toString()</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/CollectionConstraint.Contains.html" title="class in org.biojava.bio">CollectionConstraint.Contains</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/CollectionConstraint.Or.html#toString()">toString()</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/CollectionConstraint.Or.html" title="class in org.biojava.bio">CollectionConstraint.Or</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/SimpleMarkovModel.html#toString()">toString()</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/SimpleMarkovModel.html" title="class in org.biojava.bio.dp">SimpleMarkovModel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/EcNumber.Impl.html#toString()">toString()</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/EcNumber.Impl.html" title="class in org.biojava.bio">EcNumber.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/FilteringRenderer.html#toString()">toString()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/FilteringRenderer.html" title="class in org.biojava.bio.gui.sequence">FilteringRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/ImageMap.ClientSide.html#toString()">toString()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/ImageMap.ClientSide.html" title="class in org.biojava.bio.gui.sequence">ImageMap.ClientSide</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/ImageMap.HotSpot.html#toString()">toString()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/ImageMap.HotSpot.html" title="class in org.biojava.bio.gui.sequence">ImageMap.HotSpot</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/ImageMap.ServerSide.html#toString()">toString()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/ImageMap.ServerSide.html" title="class in org.biojava.bio.gui.sequence">ImageMap.ServerSide</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PaddingRenderer.html#toString()">toString()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PaddingRenderer.html" title="class in org.biojava.bio.gui.sequence">PaddingRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequenceViewerEvent.html#toString()">toString()</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequenceViewerEvent.html" title="class in org.biojava.bio.gui.sequence">SequenceViewerEvent</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/molbio/RestrictionEnzyme.html#toString()">toString()</a></span> - Method in class org.biojava.bio.molbio.<a href="./org/biojava/bio/molbio/RestrictionEnzyme.html" title="class in org.biojava.bio.molbio">RestrictionEnzyme</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/abi/ABIFParser.TaggedDataRecord.html#toString()">toString()</a></span> - Method in class org.biojava.bio.program.abi.<a href="./org/biojava/bio/program/abi/ABIFParser.TaggedDataRecord.html" title="class in org.biojava.bio.program.abi">ABIFParser.TaggedDataRecord</a></dt>
<dd>
<div class="block">A very verbose <code>toString</code> that dumps all of the
data in this record in a human-readable format.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/das/dasalignment/Alignment.html#toString()">toString()</a></span> - Method in class org.biojava.bio.program.das.dasalignment.<a href="./org/biojava/bio/program/das/dasalignment/Alignment.html" title="class in org.biojava.bio.program.das.dasalignment">Alignment</a></dt>
<dd>
<div class="block">convert to String.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/xff/ElementRecognizer.AllElementRecognizer.html#toString()">toString()</a></span> - Method in class org.biojava.bio.program.xff.<a href="./org/biojava/bio/program/xff/ElementRecognizer.AllElementRecognizer.html" title="class in org.biojava.bio.program.xff">ElementRecognizer.AllElementRecognizer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/xff/ElementRecognizer.ByLocalName.html#toString()">toString()</a></span> - Method in class org.biojava.bio.program.xff.<a href="./org/biojava/bio/program/xff/ElementRecognizer.ByLocalName.html" title="class in org.biojava.bio.program.xff">ElementRecognizer.ByLocalName</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/xff/ElementRecognizer.ByNSName.html#toString()">toString()</a></span> - Method in class org.biojava.bio.program.xff.<a href="./org/biojava/bio/program/xff/ElementRecognizer.ByNSName.html" title="class in org.biojava.bio.program.xff">ElementRecognizer.ByNSName</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/xff/ElementRecognizer.HasAttribute.html#toString()">toString()</a></span> - Method in class org.biojava.bio.program.xff.<a href="./org/biojava/bio/program/xff/ElementRecognizer.HasAttribute.html" title="class in org.biojava.bio.program.xff">ElementRecognizer.HasAttribute</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/PropertyConstraint.And.html#toString()">toString()</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/PropertyConstraint.And.html" title="class in org.biojava.bio">PropertyConstraint.And</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/PropertyConstraint.ByAnnotationType.html#toString()">toString()</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/PropertyConstraint.ByAnnotationType.html" title="class in org.biojava.bio">PropertyConstraint.ByAnnotationType</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/PropertyConstraint.ByClass.html#toString()">toString()</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/PropertyConstraint.ByClass.html" title="class in org.biojava.bio">PropertyConstraint.ByClass</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/PropertyConstraint.Enumeration.html#toString()">toString()</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/PropertyConstraint.Enumeration.html" title="class in org.biojava.bio">PropertyConstraint.Enumeration</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/PropertyConstraint.ExactValue.html#toString()">toString()</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/PropertyConstraint.ExactValue.html" title="class in org.biojava.bio">PropertyConstraint.ExactValue</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/PropertyConstraint.Or.html#toString()">toString()</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/PropertyConstraint.Or.html" title="class in org.biojava.bio">PropertyConstraint.Or</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SequenceDBSearchHit.html#toString()">toString()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SequenceDBSearchHit.html" title="class in org.biojava.bio.search">SequenceDBSearchHit</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SequenceDBSearchResult.html#toString()">toString()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SequenceDBSearchResult.html" title="class in org.biojava.bio.search">SequenceDBSearchResult</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SequenceDBSearchSubHit.html#toString()">toString()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SequenceDBSearchSubHit.html" title="class in org.biojava.bio.search">SequenceDBSearchSubHit</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SimpleSeqSimilaritySearchHit.html#toString()">toString()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SimpleSeqSimilaritySearchHit.html" title="class in org.biojava.bio.search">SimpleSeqSimilaritySearchHit</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SimpleSeqSimilaritySearchResult.html#toString()">toString()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SimpleSeqSimilaritySearchResult.html" title="class in org.biojava.bio.search">SimpleSeqSimilaritySearchResult</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/search/SimpleSeqSimilaritySearchSubHit.html#toString()">toString()</a></span> - Method in class org.biojava.bio.search.<a href="./org/biojava/bio/search/SimpleSeqSimilaritySearchSubHit.html" title="class in org.biojava.bio.search">SimpleSeqSimilaritySearchSubHit</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/biosql/DBHelper.BioSequenceStyle.html#toString()">toString()</a></span> - Method in class org.biojava.bio.seq.db.biosql.<a href="./org/biojava/bio/seq/db/biosql/DBHelper.BioSequenceStyle.html" title="class in org.biojava.bio.seq.db.biosql">DBHelper.BioSequenceStyle</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/biosql/DBHelper.DeleteStyle.html#toString()">toString()</a></span> - Method in class org.biojava.bio.seq.db.biosql.<a href="./org/biojava/bio/seq/db/biosql/DBHelper.DeleteStyle.html" title="class in org.biojava.bio.seq.db.biosql">DBHelper.DeleteStyle</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/biosql/DBHelper.JoinStyle.html#toString()">toString()</a></span> - Method in class org.biojava.bio.seq.db.biosql.<a href="./org/biojava/bio/seq/db/biosql/DBHelper.JoinStyle.html" title="class in org.biojava.bio.seq.db.biosql">DBHelper.JoinStyle</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/SimpleSequenceDBInstallation.html#toString()">toString()</a></span> - Method in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/SimpleSequenceDBInstallation.html" title="class in org.biojava.bio.seq.db">SimpleSequenceDBInstallation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/Feature.Template.html#toString()">toString()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/Feature.Template.html" title="class in org.biojava.bio.seq">Feature.Template</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.And.html#toString()">toString()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.And.html" title="class in org.biojava.bio.seq">FeatureFilter.And</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ByAncestor.html#toString()">toString()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ByAncestor.html" title="class in org.biojava.bio.seq">FeatureFilter.ByAncestor</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ByAnnotationType.html#toString()">toString()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ByAnnotationType.html" title="class in org.biojava.bio.seq">FeatureFilter.ByAnnotationType</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ByClass.html#toString()">toString()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ByClass.html" title="class in org.biojava.bio.seq">FeatureFilter.ByClass</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ByComponentName.html#toString()">toString()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ByComponentName.html" title="class in org.biojava.bio.seq">FeatureFilter.ByComponentName</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ByPairwiseScore.html#toString()">toString()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ByPairwiseScore.html" title="class in org.biojava.bio.seq">FeatureFilter.ByPairwiseScore</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.BySource.html#toString()">toString()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.BySource.html" title="class in org.biojava.bio.seq">FeatureFilter.BySource</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ByType.html#toString()">toString()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ByType.html" title="class in org.biojava.bio.seq">FeatureFilter.ByType</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ContainedByLocation.html#toString()">toString()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ContainedByLocation.html" title="class in org.biojava.bio.seq">FeatureFilter.ContainedByLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.Not.html#toString()">toString()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.Not.html" title="class in org.biojava.bio.seq">FeatureFilter.Not</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.OnlyChildren.html#toString()">toString()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.OnlyChildren.html" title="class in org.biojava.bio.seq">FeatureFilter.OnlyChildren</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.Or.html#toString()">toString()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.Or.html" title="class in org.biojava.bio.seq">FeatureFilter.Or</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.OverlapsLocation.html#toString()">toString()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.OverlapsLocation.html" title="class in org.biojava.bio.seq">FeatureFilter.OverlapsLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ShadowContainedByLocation.html#toString()">toString()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ShadowContainedByLocation.html" title="class in org.biojava.bio.seq">FeatureFilter.ShadowContainedByLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.ShadowOverlapsLocation.html#toString()">toString()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.ShadowOverlapsLocation.html" title="class in org.biojava.bio.seq">FeatureFilter.ShadowOverlapsLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureFilter.StrandFilter.html#toString()">toString()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureFilter.StrandFilter.html" title="class in org.biojava.bio.seq">FeatureFilter.StrandFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FramedFeature.ReadingFrame.html#toString()">toString()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FramedFeature.ReadingFrame.html" title="class in org.biojava.bio.seq">FramedFeature.ReadingFrame</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/homol/SimpleHomology.html#toString()">toString()</a></span> - Method in class org.biojava.bio.seq.homol.<a href="./org/biojava/bio/seq/homol/SimpleHomology.html" title="class in org.biojava.bio.seq.homol">SimpleHomology</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleFeature.html#toString()">toString()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleFeature.html" title="class in org.biojava.bio.seq.impl">SimpleFeature</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleFramedFeature.html#toString()">toString()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleFramedFeature.html" title="class in org.biojava.bio.seq.impl">SimpleFramedFeature</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleHomologyFeature.html#toString()">toString()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleHomologyFeature.html" title="class in org.biojava.bio.seq.impl">SimpleHomologyFeature</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleRestrictionSite.html#toString()">toString()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleRestrictionSite.html" title="class in org.biojava.bio.seq.impl">SimpleRestrictionSite</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleSequence.html#toString()">toString()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleSequence.html" title="class in org.biojava.bio.seq.impl">SimpleSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleSimilarityPairFeature.html#toString()">toString()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleSimilarityPairFeature.html" title="class in org.biojava.bio.seq.impl">SimpleSimilarityPairFeature</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/SimpleStrandedFeature.html#toString()">toString()</a></span> - Method in class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/SimpleStrandedFeature.html" title="class in org.biojava.bio.seq.impl">SimpleStrandedFeature</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEDbId.html#toString(java.lang.String, java.lang.String)">toString(String, String)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEDbId.html" title="class in org.biojava.bio.seq.io.agave">AGAVEDbId</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEDbId.html#toString()">toString()</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEDbId.html" title="class in org.biojava.bio.seq.io.agave">AGAVEDbId</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEIdAlias.html#toString(java.lang.String, java.lang.String)">toString(String, String)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEIdAlias.html" title="class in org.biojava.bio.seq.io.agave">AGAVEIdAlias</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEIdAlias.html#toString()">toString()</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEIdAlias.html" title="class in org.biojava.bio.seq.io.agave">AGAVEIdAlias</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEMapLocation.html#toString(java.lang.String, java.lang.String)">toString(String, String)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEMapLocation.html" title="class in org.biojava.bio.seq.io.agave">AGAVEMapLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEMapLocation.html#toString()">toString()</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEMapLocation.html" title="class in org.biojava.bio.seq.io.agave">AGAVEMapLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEMapPosition.html#toString(java.lang.String, java.lang.String)">toString(String, String)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEMapPosition.html" title="class in org.biojava.bio.seq.io.agave">AGAVEMapPosition</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEMapPosition.html#toString()">toString()</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEMapPosition.html" title="class in org.biojava.bio.seq.io.agave">AGAVEMapPosition</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEMatchRegion.html#toString(java.lang.String, java.lang.String)">toString(String, String)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEMatchRegion.html" title="class in org.biojava.bio.seq.io.agave">AGAVEMatchRegion</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEMatchRegion.html#toString()">toString()</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEMatchRegion.html" title="class in org.biojava.bio.seq.io.agave">AGAVEMatchRegion</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEProperty.html#toString(java.lang.String, java.lang.String)">toString(String, String)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEProperty.html" title="class in org.biojava.bio.seq.io.agave">AGAVEProperty</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEProperty.html#toString()">toString()</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEProperty.html" title="class in org.biojava.bio.seq.io.agave">AGAVEProperty</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEQueryRegion.html#toString(java.lang.String, java.lang.String)">toString(String, String)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEQueryRegion.html" title="class in org.biojava.bio.seq.io.agave">AGAVEQueryRegion</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEQueryRegion.html#toString()">toString()</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEQueryRegion.html" title="class in org.biojava.bio.seq.io.agave">AGAVEQueryRegion</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVERelatedAnnot.html#toString(java.lang.String, java.lang.String)">toString(String, String)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVERelatedAnnot.html" title="class in org.biojava.bio.seq.io.agave">AGAVERelatedAnnot</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVERelatedAnnot.html#toString()">toString()</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVERelatedAnnot.html" title="class in org.biojava.bio.seq.io.agave">AGAVERelatedAnnot</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AgaveWriter.Indent.html#toString()">toString()</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AgaveWriter.Indent.html" title="class in org.biojava.bio.seq.io.agave">AgaveWriter.Indent</a></dt>
<dd>
<div class="block">Return the current indent</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEXref.html#toString(java.lang.String, java.lang.String)">toString(String, String)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEXref.html" title="class in org.biojava.bio.seq.io.agave">AGAVEXref</a></dt>
<dd>
<div class="block">return the agave xml representation of this instance</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEXref.html#toString()">toString()</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEXref.html" title="class in org.biojava.bio.seq.io.agave">AGAVEXref</a></dt>
<dd>
<div class="block">return the agave xml representation of this instance</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEXrefs.html#toString(java.lang.String, java.lang.String)">toString(String, String)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEXrefs.html" title="class in org.biojava.bio.seq.io.agave">AGAVEXrefs</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEXrefs.html#toString()">toString()</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEXrefs.html" title="class in org.biojava.bio.seq.io.agave">AGAVEXrefs</a></dt>
<dd>
<div class="block">the agave xml representation of xrefs</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SymbolListCharSequence.html#toString()">toString()</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SymbolListCharSequence.html" title="class in org.biojava.bio.seq.io">SymbolListCharSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SymbolTokenization.TokenType.html#toString()">toString()</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SymbolTokenization.TokenType.html" title="class in org.biojava.bio.seq.io">SymbolTokenization.TokenType</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/StrandedFeature.Strand.html#toString()">toString()</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/StrandedFeature.Strand.html" title="class in org.biojava.bio.seq">StrandedFeature.Strand</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/helper/AligMatEl.html#toString()">toString()</a></span> - Method in class org.biojava.bio.structure.align.helper.<a href="./org/biojava/bio/structure/align/helper/AligMatEl.html" title="class in org.biojava.bio.structure.align.helper">AligMatEl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/helper/IndexPair.html#toString()">toString()</a></span> - Method in class org.biojava.bio.structure.align.helper.<a href="./org/biojava/bio/structure/align/helper/IndexPair.html" title="class in org.biojava.bio.structure.align.helper">IndexPair</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/helper/JointFragments.html#toString()">toString()</a></span> - Method in class org.biojava.bio.structure.align.helper.<a href="./org/biojava/bio/structure/align/helper/JointFragments.html" title="class in org.biojava.bio.structure.align.helper">JointFragments</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/pairwise/AlternativeAlignment.html#toString()">toString()</a></span> - Method in class org.biojava.bio.structure.align.pairwise.<a href="./org/biojava/bio/structure/align/pairwise/AlternativeAlignment.html" title="class in org.biojava.bio.structure.align.pairwise">AlternativeAlignment</a></dt>
<dd>
<div class="block">print the idx positions of this alignment</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/StrucAligParameters.html#toString()">toString()</a></span> - Method in class org.biojava.bio.structure.align.<a href="./org/biojava/bio/structure/align/StrucAligParameters.html" title="class in org.biojava.bio.structure.align">StrucAligParameters</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/AminoAcid.html#toString()">toString()</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/AminoAcid.html" title="interface in org.biojava.bio.structure">AminoAcid</a></dt>
<dd>
<div class="block">string representation.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/AminoAcidImpl.html#toString()">toString()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/AminoAcidImpl.html" title="class in org.biojava.bio.structure">AminoAcidImpl</a></dt>
<dd>
<div class="block">string representation.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/AtomImpl.html#toString()">toString()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/AtomImpl.html" title="class in org.biojava.bio.structure">AtomImpl</a></dt>
<dd>
<div class="block">string representation.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Author.html#toString()">toString()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Author.html" title="class in org.biojava.bio.structure">Author</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Chain.html#toString()">toString()</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Chain.html" title="interface in org.biojava.bio.structure">Chain</a></dt>
<dd>
<div class="block">string representation.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/ChainImpl.html#toString()">toString()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/ChainImpl.html" title="class in org.biojava.bio.structure">ChainImpl</a></dt>
<dd>
<div class="block">String representation.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Compound.html#toString()">toString()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Compound.html" title="class in org.biojava.bio.structure">Compound</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/DBRef.html#toString()">toString()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/DBRef.html" title="class in org.biojava.bio.structure">DBRef</a></dt>
<dd>
<div class="block">String representation of a DBRef.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/util/AlignedPosition.html#toString()">toString()</a></span> - Method in class org.biojava.bio.structure.gui.util.<a href="./org/biojava/bio/structure/gui/util/AlignedPosition.html" title="class in org.biojava.bio.structure.gui.util">AlignedPosition</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/HetatomImpl.html#toString()">toString()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/HetatomImpl.html" title="class in org.biojava.bio.structure">HetatomImpl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/AbstractBean.html#toString()">toString()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/AbstractBean.html" title="class in org.biojava.bio.structure.io.mmcif.model">AbstractBean</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html#toString()">toString()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/ChemComp.html" title="class in org.biojava.bio.structure.io.mmcif.model">ChemComp</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/DatabasePDBrev.html#toString()">toString()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/DatabasePDBrev.html" title="class in org.biojava.bio.structure.io.mmcif.model">DatabasePDBrev</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Entity.html#toString()">toString()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Entity.html" title="class in org.biojava.bio.structure.io.mmcif.model">Entity</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/model/Struct.html#toString()">toString()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.model.<a href="./org/biojava/bio/structure/io/mmcif/model/Struct.html" title="class in org.biojava.bio.structure.io.mmcif.model">Struct</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/JournalArticle.html#toString()">toString()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/JournalArticle.html" title="class in org.biojava.bio.structure">JournalArticle</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/NucleotideImpl.html#toString()">toString()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/NucleotideImpl.html" title="class in org.biojava.bio.structure">NucleotideImpl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/PDBHeader.html#toString()">toString()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/PDBHeader.html" title="class in org.biojava.bio.structure">PDBHeader</a></dt>
<dd>
<div class="block">String representation</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Structure.html#toString()">toString()</a></span> - Method in interface org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Structure.html" title="interface in org.biojava.bio.structure">Structure</a></dt>
<dd>
<div class="block">String representation of object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/StructureImpl.html#toString()">toString()</a></span> - Method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/StructureImpl.html" title="class in org.biojava.bio.structure">StructureImpl</a></dt>
<dd>
<div class="block">string representation.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AbstractAlphabet.html#toString()">toString()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AbstractAlphabet.html" title="class in org.biojava.bio.symbol">AbstractAlphabet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AbstractSymbol.html#toString()">toString()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AbstractSymbol.html" title="class in org.biojava.bio.symbol">AbstractSymbol</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AbstractSymbolList.html#toString()">toString()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AbstractSymbolList.html" title="class in org.biojava.bio.symbol">AbstractSymbolList</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/CircularLocation.html#toString()">toString()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/CircularLocation.html" title="class in org.biojava.bio.symbol">CircularLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/FuzzyLocation.html#toString()">toString()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/FuzzyLocation.html" title="class in org.biojava.bio.symbol">FuzzyLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/FuzzyPointLocation.html#toString()">toString()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/FuzzyPointLocation.html" title="class in org.biojava.bio.symbol">FuzzyPointLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/PointLocation.html#toString()">toString()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/PointLocation.html" title="class in org.biojava.bio.symbol">PointLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/RangeLocation.html#toString()">toString()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/RangeLocation.html" title="class in org.biojava.bio.symbol">RangeLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleGappedSymbolList.Block.html#toString()">toString()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleGappedSymbolList.Block.html" title="class in org.biojava.bio.symbol">SimpleGappedSymbolList.Block</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/taxa/AbstractTaxon.html#toString()">toString()</a></span> - Method in class org.biojava.bio.taxa.<a href="./org/biojava/bio/taxa/AbstractTaxon.html" title="class in org.biojava.bio.taxa">AbstractTaxon</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/Ontology.Impl.html#toString()">toString()</a></span> - Method in class org.biojava.ontology.<a href="./org/biojava/ontology/Ontology.Impl.html" title="class in org.biojava.ontology">Ontology.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/OntologyTerm.Impl.html#toString()">toString()</a></span> - Method in class org.biojava.ontology.<a href="./org/biojava/ontology/OntologyTerm.Impl.html" title="class in org.biojava.ontology">OntologyTerm.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/RemoteTerm.Impl.html#toString()">toString()</a></span> - Method in class org.biojava.ontology.<a href="./org/biojava/ontology/RemoteTerm.Impl.html" title="class in org.biojava.ontology">RemoteTerm.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/Synonym.html#toString()">toString()</a></span> - Method in class org.biojava.ontology.<a href="./org/biojava/ontology/Synonym.html" title="class in org.biojava.ontology">Synonym</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/Term.Impl.html#toString()">toString()</a></span> - Method in class org.biojava.ontology.<a href="./org/biojava/ontology/Term.Impl.html" title="class in org.biojava.ontology">Term.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/Triple.Impl.html#toString()">toString()</a></span> - Method in class org.biojava.ontology.<a href="./org/biojava/ontology/Triple.Impl.html" title="class in org.biojava.ontology">Triple.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/CachingKernel.html#toString()">toString()</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/CachingKernel.html" title="class in org.biojava.stats.svm">CachingKernel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/DiagonalAddKernel.html#toString()">toString()</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/DiagonalAddKernel.html" title="class in org.biojava.stats.svm">DiagonalAddKernel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/DiagonalCachingKernel.html#toString()">toString()</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/DiagonalCachingKernel.html" title="class in org.biojava.stats.svm">DiagonalCachingKernel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/ListSumKernel.html#toString()">toString()</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/ListSumKernel.html" title="class in org.biojava.stats.svm">ListSumKernel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/NormalizingKernel.html#toString()">toString()</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/NormalizingKernel.html" title="class in org.biojava.stats.svm">NormalizingKernel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/PolynomialKernel.html#toString()">toString()</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/PolynomialKernel.html" title="class in org.biojava.stats.svm">PolynomialKernel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/RadialBaseKernel.html#toString()">toString()</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/RadialBaseKernel.html" title="class in org.biojava.stats.svm">RadialBaseKernel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/SigmoidKernel.html#toString()">toString()</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/SigmoidKernel.html" title="class in org.biojava.stats.svm">SigmoidKernel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/SparseVector.NormalizingKernel.html#toString()">toString()</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/SparseVector.NormalizingKernel.html" title="class in org.biojava.stats.svm">SparseVector.NormalizingKernel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/tools/SuffixTreeKernel.html#toString()">toString()</a></span> - Method in class org.biojava.stats.svm.tools.<a href="./org/biojava/stats/svm/tools/SuffixTreeKernel.html" title="class in org.biojava.stats.svm.tools">SuffixTreeKernel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/automata/FiniteAutomaton.html#toString()">toString()</a></span> - Method in class org.biojava.utils.automata.<a href="./org/biojava/utils/automata/FiniteAutomaton.html" title="class in org.biojava.utils.automata">FiniteAutomaton</a></dt>
<dd>
<div class="block">dumps internal data of Nodes and Transitions that describe
this FiniteAutomaton.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/automata/NfaBuilder.html#toString()">toString()</a></span> - Method in interface org.biojava.utils.automata.<a href="./org/biojava/utils/automata/NfaBuilder.html" title="interface in org.biojava.utils.automata">NfaBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/automata/NfaSubModel.html#toString()">toString()</a></span> - Method in class org.biojava.utils.automata.<a href="./org/biojava/utils/automata/NfaSubModel.html" title="class in org.biojava.utils.automata">NfaSubModel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/candy/CandyEntry.html#toString()">toString()</a></span> - Method in class org.biojava.utils.candy.<a href="./org/biojava/utils/candy/CandyEntry.html" title="class in org.biojava.utils.candy">CandyEntry</a></dt>
<dd>
<div class="block">It prints the entry contents.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/ChangeEvent.html#toString()">toString()</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/ChangeEvent.html" title="class in org.biojava.utils">ChangeEvent</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ChangeType.html#toString()">toString()</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/ChangeType.html" title="class in org.biojava.utils">ChangeType</a></dt>
<dd>
<div class="block">Return a string representation of this change.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/lsid/LifeScienceIdentifier.html#toString()">toString()</a></span> - Method in class org.biojava.utils.lsid.<a href="./org/biojava/utils/lsid/LifeScienceIdentifier.html" title="class in org.biojava.utils.lsid">LifeScienceIdentifier</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ParseErrorEvent.html#toString()">toString()</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/ParseErrorEvent.html" title="class in org.biojava.utils">ParseErrorEvent</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ParserException.html#toString()">toString()</a></span> - Method in exception org.biojava.utils.<a href="./org/biojava/utils/ParserException.html" title="class in org.biojava.utils">ParserException</a></dt>
<dd>
<div class="block">Represent this exception as a string.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/RepeatedCharSequence.html#toString()">toString()</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/RepeatedCharSequence.html" title="class in org.biojava.utils">RepeatedCharSequence</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/TypedProperties.html#toString()">toString()</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/TypedProperties.html" title="class in org.biojava.utils">TypedProperties</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLAcceptAllFilter.html#toString()">toString()</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLAcceptAllFilter.html" title="class in org.biojavax.bio.db.biosql">BioSQLAcceptAllFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLAcceptNoneFilter.html#toString()">toString()</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLAcceptNoneFilter.html" title="class in org.biojavax.bio.db.biosql">BioSQLAcceptNoneFilter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.And.html#toString()">toString()</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.And.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.And</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByName.html#toString()">toString()</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByName.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.ByName</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByNote.html#toString()">toString()</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByNote.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.ByNote</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByNoteTermOnly.html#toString()">toString()</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByNoteTermOnly.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.ByNoteTermOnly</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByRank.html#toString()">toString()</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByRank.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.ByRank</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.BySourceTerm.html#toString()">toString()</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.BySourceTerm.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.BySourceTerm</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.BySourceTermName.html#toString()">toString()</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.BySourceTermName.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.BySourceTermName</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByStrand.html#toString()">toString()</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByStrand.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.ByStrand</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByTypeTerm.html#toString()">toString()</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByTypeTerm.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.ByTypeTerm</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByTypeTermName.html#toString()">toString()</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByTypeTermName.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.ByTypeTermName</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ContainedByRichLocation.html#toString()">toString()</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ContainedByRichLocation.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.ContainedByRichLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.Not.html#toString()">toString()</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.Not.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.Not</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.Or.html#toString()">toString()</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.Or.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.Or</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.OverlapsRichLocation.html#toString()">toString()</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLFeatureFilter.OverlapsRichLocation.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.OverlapsRichLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/CompoundRichLocation.html#toString()">toString()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/CompoundRichLocation.html" title="class in org.biojavax.bio.seq">CompoundRichLocation</a></dt>
<dd>
<div class="block">
Form: "start..end" or just "point" for point locations</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/EmptyRichLocation.html#toString()">toString()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/EmptyRichLocation.html" title="class in org.biojavax.bio.seq">EmptyRichLocation</a></dt>
<dd>
<div class="block">
ALWAYS RETURNS "empty"</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichLocation.Strand.html#toString()">toString()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichLocation.Strand.html" title="class in org.biojavax.bio.seq">RichLocation.Strand</a></dt>
<dd>
<div class="block"> Form: "symbol" (eg.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimplePosition.html#toString()">toString()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimplePosition.html" title="class in org.biojavax.bio.seq">SimplePosition</a></dt>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichFeature.html#toString()">toString()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichFeature.html" title="class in org.biojavax.bio.seq">SimpleRichFeature</a></dt>
<dd>
<div class="block">
Form: "(#rank) parent:type,source(location)"</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichFeatureRelationship.html#toString()">toString()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichFeatureRelationship.html" title="class in org.biojavax.bio.seq">SimpleRichFeatureRelationship</a></dt>
<dd>
<div class="block">
Form: "(#rank) term(object,subject)"</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichLocation.html#toString()">toString()</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichLocation.html" title="class in org.biojavax.bio.seq">SimpleRichLocation</a></dt>
<dd>
<div class="block">
Form: "start..end" or just "point" for point locations</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/SimpleBioEntry.html#toString()">toString()</a></span> - Method in class org.biojavax.bio.<a href="./org/biojavax/bio/SimpleBioEntry.html" title="class in org.biojavax.bio">SimpleBioEntry</a></dt>
<dd>
<div class="block">
Form: namespace:name/accession.version</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/SimpleBioEntryRelationship.html#toString()">toString()</a></span> - Method in class org.biojavax.bio.<a href="./org/biojavax/bio/SimpleBioEntryRelationship.html" title="class in org.biojavax.bio">SimpleBioEntryRelationship</a></dt>
<dd>
<div class="block">
Form is "(#rank) term(object,subject)"</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/taxa/SimpleNCBITaxon.html#toString()">toString()</a></span> - Method in class org.biojavax.bio.taxa.<a href="./org/biojavax/bio/taxa/SimpleNCBITaxon.html" title="class in org.biojavax.bio.taxa">SimpleNCBITaxon</a></dt>
<dd>
<div class="block">
Form: "taxid:[name,name...]"</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/taxa/SimpleNCBITaxonName.html#toString()">toString()</a></span> - Method in class org.biojavax.bio.taxa.<a href="./org/biojavax/bio/taxa/SimpleNCBITaxonName.html" title="class in org.biojavax.bio.taxa">SimpleNCBITaxonName</a></dt>
<dd>
<div class="block">
Form: "class:name"</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ontology/SimpleComparableOntology.html#toString()">toString()</a></span> - Method in class org.biojavax.ontology.<a href="./org/biojavax/ontology/SimpleComparableOntology.html" title="class in org.biojavax.ontology">SimpleComparableOntology</a></dt>
<dd>
<div class="block">
Form: "name"</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ontology/SimpleComparableTerm.html#toString()">toString()</a></span> - Method in class org.biojavax.ontology.<a href="./org/biojavax/ontology/SimpleComparableTerm.html" title="class in org.biojavax.ontology">SimpleComparableTerm</a></dt>
<dd>
<div class="block">
Form: "ontology:name [obsolete]" where [obsolete] is optional</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ontology/SimpleComparableTriple.html#toString()">toString()</a></span> - Method in class org.biojavax.ontology.<a href="./org/biojavax/ontology/SimpleComparableTriple.html" title="class in org.biojavax.ontology">SimpleComparableTriple</a></dt>
<dd>
<div class="block">
Form: "ontology:predicate(subject,object)"</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleComment.html#toString()">toString()</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleComment.html" title="class in org.biojavax">SimpleComment</a></dt>
<dd>
<div class="block">
Form: "(#rank) comment"</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleCrossRef.html#toString()">toString()</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleCrossRef.html" title="class in org.biojavax">SimpleCrossRef</a></dt>
<dd>
<div class="block">
Form: "dbname:accession.version"</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleDocRef.html#toString()">toString()</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleDocRef.html" title="class in org.biojavax">SimpleDocRef</a></dt>
<dd>
<div class="block">
Form: "authors; location"</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleDocRefAuthor.html#toString()">toString()</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleDocRefAuthor.html" title="class in org.biojavax">SimpleDocRefAuthor</a></dt>
<dd>
<div class="block">
Form: "name (consortium) (ed.)" where sections in brackets are optional.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleNamespace.html#toString()">toString()</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleNamespace.html" title="class in org.biojavax">SimpleNamespace</a></dt>
<dd>
<div class="block">
Form: "name"</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleNote.html#toString()">toString()</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleNote.html" title="class in org.biojavax">SimpleNote</a></dt>
<dd>
<div class="block">
Form: "(#rank) term: value"</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleRankedCrossRef.html#toString()">toString()</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleRankedCrossRef.html" title="class in org.biojavax">SimpleRankedCrossRef</a></dt>
<dd>
<div class="block">
Form: "(#rank) crossref"</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleRankedDocRef.html#toString()">toString()</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleRankedDocRef.html" title="class in org.biojavax">SimpleRankedDocRef</a></dt>
<dd>
<div class="block">
Form: "(#rank) docref"</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/SimpleRichAnnotation.html#toString()">toString()</a></span> - Method in class org.biojavax.<a href="./org/biojavax/SimpleRichAnnotation.html" title="class in org.biojavax">SimpleRichAnnotation</a></dt>
<dd>
<div class="block">
Form: list of "[note]" values separated by commas</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/utils/CRC64Checksum.html#toString()">toString()</a></span> - Method in class org.biojavax.utils.<a href="./org/biojavax/utils/CRC64Checksum.html" title="class in org.biojavax.utils">CRC64Checksum</a></dt>
<dd>
<div class="block">Returns a zero-padded 16 character wide string containing the current
value of this checksum in uppercase hexadecimal format.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/DistributionLogo.html#totalBits(org.biojava.bio.dist.Distribution)">totalBits(Distribution)</a></span> - Static method in class org.biojava.bio.gui.<a href="./org/biojava/bio/gui/DistributionLogo.html" title="class in org.biojava.bio.gui">DistributionLogo</a></dt>
<dd>
<div class="block">Retrieve the maximal number of bits possible for this type of dist.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/DistributionTools.html#totalEntropy(org.biojava.bio.dist.Distribution)">totalEntropy(Distribution)</a></span> - Static method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/DistributionTools.html" title="class in org.biojava.bio.dist">DistributionTools</a></dt>
<dd>
<div class="block">Calculates the total Entropy for a Distribution.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/DistributionLogo.html#totalInformation(org.biojava.bio.dist.Distribution)">totalInformation(Distribution)</a></span> - Static method in class org.biojava.bio.gui.<a href="./org/biojava/bio/gui/DistributionLogo.html" title="class in org.biojava.bio.gui">DistributionLogo</a></dt>
<dd>
<div class="block">
Calculates the total information of the dist in bits.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/obo/OboFileParser.html#totalSize">totalSize</a></span> - Variable in class org.biojava.ontology.obo.<a href="./org/biojava/ontology/obo/OboFileParser.html" title="class in org.biojava.ontology.obo">OboFileParser</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/blast2html/DatabaseURLGenerator.html#toURL(java.lang.String, java.util.Properties)">toURL(String, Properties)</a></span> - Method in interface org.biojava.bio.program.blast2html.<a href="./org/biojava/bio/program/blast2html/DatabaseURLGenerator.html" title="interface in org.biojava.bio.program.blast2html">DatabaseURLGenerator</a></dt>
<dd>
<div class="block">Returns a string representation of a URL to the
specified ID.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/blast2html/EbiDatabaseURLGenerator.html#toURL(java.lang.String, java.util.Properties)">toURL(String, Properties)</a></span> - Method in class org.biojava.bio.program.blast2html.<a href="./org/biojava/bio/program/blast2html/EbiDatabaseURLGenerator.html" title="class in org.biojava.bio.program.blast2html">EbiDatabaseURLGenerator</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/blast2html/NcbiDatabaseURLGenerator.html#toURL(java.lang.String, java.util.Properties)">toURL(String, Properties)</a></span> - Method in class org.biojava.bio.program.blast2html.<a href="./org/biojava/bio/program/blast2html/NcbiDatabaseURLGenerator.html" title="class in org.biojava.bio.program.blast2html">NcbiDatabaseURLGenerator</a></dt>
<dd> </dd>
<dt><a href="./org/biojavax/ga/functions/TournamentSelection.html" title="class in org.biojavax.ga.functions"><span class="strong">TournamentSelection</span></a> - Class in <a href="./org/biojavax/ga/functions/package-summary.html">org.biojavax.ga.functions</a></dt>
<dd>
<div class="block">Tournament Selection chooses the best organisms from n random subsets of a
given population.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ga/functions/TournamentSelection.html#TournamentSelection()">TournamentSelection()</a></span> - Constructor for class org.biojavax.ga.functions.<a href="./org/biojavax/ga/functions/TournamentSelection.html" title="class in org.biojavax.ga.functions">TournamentSelection</a></dt>
<dd>
<div class="block">Default constructor: sets the selection pressure to the value of 10.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLFormat.html#TPA_TAG">TPA_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLFormat.html" title="class in org.biojavax.bio.seq.io">EMBLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/AbiTraceRenderer.html#TRACE">TRACE</a></span> - Static variable in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/AbiTraceRenderer.html" title="class in org.biojava.bio.gui.sequence">AbiTraceRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/jama/Matrix.html#trace()">trace()</a></span> - Method in class org.biojava.bio.structure.jama.<a href="./org/biojava/bio/structure/jama/Matrix.html" title="class in org.biojava.bio.structure.jama">Matrix</a></dt>
<dd>
<div class="block">Matrix trace.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.Option.html#TRACE_STROKE">TRACE_STROKE</a></span> - Static variable in class org.biojava.bio.chromatogram.graphic.<a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.Option.html" title="class in org.biojava.bio.chromatogram.graphic">ChromatogramGraphic.Option</a></dt>
<dd>
<div class="block">Option providing the the stroke to use for drawing
the chromatogram traces.</div>
</dd>
<dt><a href="./org/biojava/bio/gui/sequence/tracklayout/TrackLayout.html" title="interface in org.biojava.bio.gui.sequence.tracklayout"><span class="strong">TrackLayout</span></a> - Interface in <a href="./org/biojava/bio/gui/sequence/tracklayout/package-summary.html">org.biojava.bio.gui.sequence.tracklayout</a></dt>
<dd>
<div class="block">An interface for the handling of the layout of a WrappedSequencePanel.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/DistributionTrainer.html#train(org.biojava.bio.dist.DistributionTrainerContext, double)">train(DistributionTrainerContext, double)</a></span> - Method in interface org.biojava.bio.dist.<a href="./org/biojava/bio/dist/DistributionTrainer.html" title="interface in org.biojava.bio.dist">DistributionTrainer</a></dt>
<dd>
<div class="block">
Trains the Distribution, given a null model.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/DistributionTrainerContext.html#train()">train()</a></span> - Method in interface org.biojava.bio.dist.<a href="./org/biojava/bio/dist/DistributionTrainerContext.html" title="interface in org.biojava.bio.dist">DistributionTrainerContext</a></dt>
<dd>
<div class="block">
Trains the Distribution, given a null model.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/IgnoreCountsTrainer.html#train(org.biojava.bio.dist.DistributionTrainerContext, double)">train(DistributionTrainerContext, double)</a></span> - Method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/IgnoreCountsTrainer.html" title="class in org.biojava.bio.dist">IgnoreCountsTrainer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/SimpleDistribution.Trainer.html#train(org.biojava.bio.dist.DistributionTrainerContext, double)">train(DistributionTrainerContext, double)</a></span> - Method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/SimpleDistribution.Trainer.html" title="class in org.biojava.bio.dist">SimpleDistribution.Trainer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/SimpleDistributionTrainer.html#train(org.biojava.bio.dist.DistributionTrainerContext, double)">train(DistributionTrainerContext, double)</a></span> - Method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/SimpleDistributionTrainer.html" title="class in org.biojava.bio.dist">SimpleDistributionTrainer</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/SimpleDistributionTrainerContext.html#train()">train()</a></span> - Method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/SimpleDistributionTrainerContext.html" title="class in org.biojava.bio.dist">SimpleDistributionTrainerContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/AbstractTrainer.html#train(org.biojava.bio.seq.db.SequenceDB, double, org.biojava.bio.dp.StoppingCriteria)">train(SequenceDB, double, StoppingCriteria)</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/AbstractTrainer.html" title="class in org.biojava.bio.dp">AbstractTrainer</a></dt>
<dd>
<div class="block">Trains the sequences in db until stopper says to finnish.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/TrainingAlgorithm.html#train(org.biojava.bio.seq.db.SequenceDB, double, org.biojava.bio.dp.StoppingCriteria)">train(SequenceDB, double, StoppingCriteria)</a></span> - Method in interface org.biojava.bio.dp.<a href="./org/biojava/bio/dp/TrainingAlgorithm.html" title="interface in org.biojava.bio.dp">TrainingAlgorithm</a></dt>
<dd>
<div class="block">Trains the sequences in db untill stopper says to finnish.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/TransitionTrainer.html#train(double, double)">train(double, double)</a></span> - Method in interface org.biojava.bio.dp.<a href="./org/biojava/bio/dp/TransitionTrainer.html" title="interface in org.biojava.bio.dp">TransitionTrainer</a></dt>
<dd>
<div class="block">Trains the transition, given an expected probability, and a weight for
that probability.</div>
</dd>
<dt><a href="./org/biojava/stats/svm/tools/Train.html" title="class in org.biojava.stats.svm.tools"><span class="strong">Train</span></a> - Class in <a href="./org/biojava/stats/svm/tools/package-summary.html">org.biojava.stats.svm.tools</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/tools/Train.html#Train()">Train()</a></span> - Constructor for class org.biojava.stats.svm.tools.<a href="./org/biojava/stats/svm/tools/Train.html" title="class in org.biojava.stats.svm.tools">Train</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/dp/Trainable.html" title="interface in org.biojava.bio.dp"><span class="strong">Trainable</span></a> - Interface in <a href="./org/biojava/bio/dp/package-summary.html">org.biojava.bio.dp</a></dt>
<dd>
<div class="block">Flags an object as being able to register itself with a model trainer.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/TrainerTransition.html#trainer">trainer</a></span> - Variable in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/TrainerTransition.html" title="class in org.biojava.bio.dp">TrainerTransition</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/tools/ClassifierExample.PointClassifier.html#trainer">trainer</a></span> - Static variable in class org.biojava.stats.svm.tools.<a href="./org/biojava/stats/svm/tools/ClassifierExample.PointClassifier.html" title="class in org.biojava.stats.svm.tools">ClassifierExample.PointClassifier</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/dp/TrainerTransition.html" title="class in org.biojava.bio.dp"><span class="strong">TrainerTransition</span></a> - Class in <a href="./org/biojava/bio/dp/package-summary.html">org.biojava.bio.dp</a></dt>
<dd>
<div class="block">This is a small and ugly class for storing a trainer and a transition.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/TrainerTransition.html#TrainerTransition(org.biojava.bio.dp.TransitionTrainer, org.biojava.bio.dp.State, org.biojava.bio.dp.State)">TrainerTransition(TransitionTrainer, State, State)</a></span> - Constructor for class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/TrainerTransition.html" title="class in org.biojava.bio.dp">TrainerTransition</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/SimpleDistribution.Trainer.html#trainImpl(org.biojava.bio.dist.DistributionTrainerContext, double)">trainImpl(DistributionTrainerContext, double)</a></span> - Method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/SimpleDistribution.Trainer.html" title="class in org.biojava.bio.dist">SimpleDistribution.Trainer</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/dp/TrainingAlgorithm.html" title="interface in org.biojava.bio.dp"><span class="strong">TrainingAlgorithm</span></a> - Interface in <a href="./org/biojava/bio/dp/package-summary.html">org.biojava.bio.dp</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/TrainingListener.html#trainingComplete(org.biojava.stats.svm.TrainingEvent)">trainingComplete(TrainingEvent)</a></span> - Method in interface org.biojava.stats.svm.<a href="./org/biojava/stats/svm/TrainingListener.html" title="interface in org.biojava.stats.svm">TrainingListener</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/stats/svm/TrainingContext.html" title="interface in org.biojava.stats.svm"><span class="strong">TrainingContext</span></a> - Interface in <a href="./org/biojava/stats/svm/package-summary.html">org.biojava.stats.svm</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/TrainingListener.html#trainingCycleComplete(org.biojava.stats.svm.TrainingEvent)">trainingCycleComplete(TrainingEvent)</a></span> - Method in interface org.biojava.stats.svm.<a href="./org/biojava/stats/svm/TrainingListener.html" title="interface in org.biojava.stats.svm">TrainingListener</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/stats/svm/TrainingEvent.html" title="class in org.biojava.stats.svm"><span class="strong">TrainingEvent</span></a> - Class in <a href="./org/biojava/stats/svm/package-summary.html">org.biojava.stats.svm</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/TrainingEvent.html#TrainingEvent(org.biojava.stats.svm.TrainingContext)">TrainingEvent(TrainingContext)</a></span> - Constructor for class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/TrainingEvent.html" title="class in org.biojava.stats.svm">TrainingEvent</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/stats/svm/TrainingListener.html" title="interface in org.biojava.stats.svm"><span class="strong">TrainingListener</span></a> - Interface in <a href="./org/biojava/stats/svm/package-summary.html">org.biojava.stats.svm</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/SMORegressionTrainer.html#trainModel(org.biojava.stats.svm.SVMRegressionModel, double[])">trainModel(SVMRegressionModel, double[])</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/SMORegressionTrainer.html" title="class in org.biojava.stats.svm">SMORegressionTrainer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/SMOTrainer.html#trainModel(org.biojava.stats.svm.SVMTarget, org.biojava.stats.svm.SVMKernel, org.biojava.stats.svm.TrainingListener)">trainModel(SVMTarget, SVMKernel, TrainingListener)</a></span> - Method in class org.biojava.stats.svm.<a href="./org/biojava/stats/svm/SMOTrainer.html" title="class in org.biojava.stats.svm">SMOTrainer</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/stats/svm/tools/TrainRegression.html" title="class in org.biojava.stats.svm.tools"><span class="strong">TrainRegression</span></a> - Class in <a href="./org/biojava/stats/svm/tools/package-summary.html">org.biojava.stats.svm.tools</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/tools/TrainRegression.html#TrainRegression()">TrainRegression()</a></span> - Constructor for class org.biojava.stats.svm.tools.<a href="./org/biojava/stats/svm/tools/TrainRegression.html" title="class in org.biojava.stats.svm.tools">TrainRegression</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/GeneticCodes.html#transcribe(org.biojava.bio.symbol.SymbolList)">transcribe(SymbolList)</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/GeneticCodes.html" title="class in org.biojava.bio.seq">GeneticCodes</a></dt>
<dd>
<div class="block">Transcribe DNA into RNA.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/RNATools.html#transcribe(org.biojava.bio.symbol.SymbolList)">transcribe(SymbolList)</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/RNATools.html" title="class in org.biojava.bio.seq">RNATools</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>The naming of this method is confusing and inconsistent use either DNATools.toRNA(SymbolList list) or
DNATools.transcribeToRNA(SymbolList list) depending on the desired behaivour.</i></div>
</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/DNATools.html#transcribeToRNA(org.biojava.bio.symbol.SymbolList)">transcribeToRNA(SymbolList)</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/DNATools.html" title="class in org.biojava.bio.seq">DNATools</a></dt>
<dd>
<div class="block">Transcribes DNA to RNA.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/RNATools.html#transcriptionTable()">transcriptionTable()</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/RNATools.html" title="class in org.biojava.bio.seq">RNATools</a></dt>
<dd>
<div class="block">Get a translation table for converting DNA to RNA.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FilterUtils.DelegatingTransformer.html#transform(org.biojava.bio.seq.FeatureFilter)">transform(FeatureFilter)</a></span> - Method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FilterUtils.DelegatingTransformer.html" title="class in org.biojava.bio.seq">FilterUtils.DelegatingTransformer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FilterUtils.FilterTransformer.html#transform(org.biojava.bio.seq.FeatureFilter)">transform(FeatureFilter)</a></span> - Method in interface org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FilterUtils.FilterTransformer.html" title="interface in org.biojava.bio.seq">FilterUtils.FilterTransformer</a></dt>
<dd>
<div class="block">Transform a filter, or return null if it can not be transformed.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FilterUtils.html#transformFilter(org.biojava.bio.seq.FeatureFilter, org.biojava.bio.seq.FilterUtils.FilterTransformer)">transformFilter(FeatureFilter, FilterUtils.FilterTransformer)</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FilterUtils.html" title="class in org.biojava.bio.seq">FilterUtils</a></dt>
<dd>
<div class="block">This is a general framework method for transforming one filter into another.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/projection/ProjectionUtils.html#transformLocation(org.biojava.bio.symbol.Location, int, boolean)">transformLocation(Location, int, boolean)</a></span> - Static method in class org.biojava.bio.seq.projection.<a href="./org/biojava/bio/seq/projection/ProjectionUtils.html" title="class in org.biojava.bio.seq.projection">ProjectionUtils</a></dt>
<dd>
<div class="block">Transform a location, translating and flipping as required.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/StateMachine.BasicState.html#transit(java.lang.Object)">transit(Object)</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/StateMachine.BasicState.html" title="class in org.biojava.bio.program.tagvalue">StateMachine.BasicState</a></dt>
<dd>
<div class="block">Find the destination State when the specified tag
is encountered.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/StateMachine.State.html#transit(java.lang.Object)">transit(Object)</a></span> - Method in interface org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/StateMachine.State.html" title="interface in org.biojava.bio.program.tagvalue">StateMachine.State</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/automata/StateMachineInstance.html#transit(int)">transit(int)</a></span> - Method in interface org.biojava.utils.automata.<a href="./org/biojava/utils/automata/StateMachineInstance.html" title="interface in org.biojava.utils.automata">StateMachineInstance</a></dt>
<dd>
<div class="block">invoke transition from current state indicated by Symbol represented by symbol index.</div>
</dd>
<dt><a href="./org/biojava/bio/dp/Transition.html" title="class in org.biojava.bio.dp"><span class="strong">Transition</span></a> - Class in <a href="./org/biojava/bio/dp/package-summary.html">org.biojava.bio.dp</a></dt>
<dd>
<div class="block">This is a small and ugly class for storing a transition.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/Transition.html#Transition(org.biojava.bio.dp.State, org.biojava.bio.dp.State)">Transition(State, State)</a></span> - Constructor for class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/Transition.html" title="class in org.biojava.bio.dp">Transition</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/automata/FiniteAutomaton.html#transitions">transitions</a></span> - Variable in class org.biojava.utils.automata.<a href="./org/biojava/utils/automata/FiniteAutomaton.html" title="class in org.biojava.utils.automata">FiniteAutomaton</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/MarkovModel.html#transitionsFrom(org.biojava.bio.dp.State)">transitionsFrom(State)</a></span> - Method in interface org.biojava.bio.dp.<a href="./org/biojava/bio/dp/MarkovModel.html" title="interface in org.biojava.bio.dp">MarkovModel</a></dt>
<dd>
<div class="block">Returns the FiniteAlphabet of all states that have a transition from 'source'.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/SimpleMarkovModel.html#transitionsFrom(org.biojava.bio.dp.State)">transitionsFrom(State)</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/SimpleMarkovModel.html" title="class in org.biojava.bio.dp">SimpleMarkovModel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/WMAsMM.html#transitionsFrom(org.biojava.bio.dp.State)">transitionsFrom(State)</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/WMAsMM.html" title="class in org.biojava.bio.dp">WMAsMM</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/MarkovModel.html#transitionsTo(org.biojava.bio.dp.State)">transitionsTo(State)</a></span> - Method in interface org.biojava.bio.dp.<a href="./org/biojava/bio/dp/MarkovModel.html" title="interface in org.biojava.bio.dp">MarkovModel</a></dt>
<dd>
<div class="block">Returns the FiniteAlphabet of all states that have a transition to 'dest'.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/SimpleMarkovModel.html#transitionsTo(org.biojava.bio.dp.State)">transitionsTo(State)</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/SimpleMarkovModel.html" title="class in org.biojava.bio.dp">SimpleMarkovModel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/WMAsMM.html#transitionsTo(org.biojava.bio.dp.State)">transitionsTo(State)</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/WMAsMM.html" title="class in org.biojava.bio.dp">WMAsMM</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/dp/TransitionTrainer.html" title="interface in org.biojava.bio.dp"><span class="strong">TransitionTrainer</span></a> - Interface in <a href="./org/biojava/bio/dp/package-summary.html">org.biojava.bio.dp</a></dt>
<dd>
<div class="block">An object that can be used to train the transitions within a MarkovModel.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/OntoTools.html#TRANSITIVE">TRANSITIVE</a></span> - Static variable in class org.biojava.ontology.<a href="./org/biojava/ontology/OntoTools.html" title="class in org.biojava.ontology">OntoTools</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/GeneticCodes.html#translate(org.biojava.bio.symbol.SymbolList)">translate(SymbolList)</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/GeneticCodes.html" title="class in org.biojava.bio.seq">GeneticCodes</a></dt>
<dd>
<div class="block">Translate RNA into protein (with termination symbols).</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/RNATools.html#translate(org.biojava.bio.symbol.SymbolList)">translate(SymbolList)</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/RNATools.html" title="class in org.biojava.bio.seq">RNATools</a></dt>
<dd>
<div class="block">Translate RNA into protein (with termination symbols).</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AbstractLocationDecorator.html#translate(int)">translate(int)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AbstractLocationDecorator.html" title="class in org.biojava.bio.symbol">AbstractLocationDecorator</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/FuzzyLocation.html#translate(int)">translate(int)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/FuzzyLocation.html" title="class in org.biojava.bio.symbol">FuzzyLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/FuzzyPointLocation.html#translate(int)">translate(int)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/FuzzyPointLocation.html" title="class in org.biojava.bio.symbol">FuzzyPointLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/Location.html#translate(int)">translate(int)</a></span> - Method in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/Location.html" title="interface in org.biojava.bio.symbol">Location</a></dt>
<dd>
<div class="block">Create a location that is a translation of this location.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/PointLocation.html#translate(int)">translate(int)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/PointLocation.html" title="class in org.biojava.bio.symbol">PointLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/RangeLocation.html#translate(int)">translate(int)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/RangeLocation.html" title="class in org.biojava.bio.symbol">RangeLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SymbolListViews.html#translate(org.biojava.bio.symbol.SymbolList, org.biojava.bio.symbol.TranslationTable)">translate(SymbolList, TranslationTable)</a></span> - Static method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SymbolListViews.html" title="class in org.biojava.bio.symbol">SymbolListViews</a></dt>
<dd>
<div class="block">Provides a 'translated' view of an underlying SymbolList.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/TranslationTable.html#translate(org.biojava.bio.symbol.Symbol)">translate(Symbol)</a></span> - Method in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/TranslationTable.html" title="interface in org.biojava.bio.symbol">TranslationTable</a></dt>
<dd>
<div class="block">Translate a single symbol from source alphabet to the target alphabet.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/CompoundRichLocation.html#translate(int)">translate(int)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/CompoundRichLocation.html" title="class in org.biojavax.bio.seq">CompoundRichLocation</a></dt>
<dd>
<div class="block">Create a location that is a translation of this location.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/EmptyRichLocation.html#translate(int)">translate(int)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/EmptyRichLocation.html" title="class in org.biojavax.bio.seq">EmptyRichLocation</a></dt>
<dd>
<div class="block">Create a location that is a translation of this location.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/MultiSourceCompoundRichLocation.html#translate(int)">translate(int)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/MultiSourceCompoundRichLocation.html" title="class in org.biojavax.bio.seq">MultiSourceCompoundRichLocation</a></dt>
<dd>
<div class="block">Create a location that is a translation of this location.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/Position.html#translate(int)">translate(int)</a></span> - Method in interface org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/Position.html" title="interface in org.biojavax.bio.seq">Position</a></dt>
<dd>
<div class="block">Takes this position and returns a copy translated by 'distance' bases.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimplePosition.html#translate(int)">translate(int)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimplePosition.html" title="class in org.biojavax.bio.seq">SimplePosition</a></dt>
<dd>
<div class="block">Takes this position and returns a copy translated by 'distance' bases.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichLocation.html#translate(int)">translate(int)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichLocation.html" title="class in org.biojavax.bio.seq">SimpleRichLocation</a></dt>
<dd>
<div class="block">Create a location that is a translation of this location.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/CodonPrefTools.html#translateCUD(java.io.InputStream, java.io.OutputStream)">translateCUD(InputStream, OutputStream)</a></span> - Static method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/CodonPrefTools.html" title="class in org.biojava.bio.symbol">CodonPrefTools</a></dt>
<dd>
<div class="block">reads in a file in Codon Usage Database format and
translate it into our XML format
These can be obtained from the
<a href="http://www.kazusa.or.jp/codon/">Codon Usage Database</a>.</div>
</dd>
<dt><a href="./org/biojava/bio/dist/TranslatedDistribution.html" title="class in org.biojava.bio.dist"><span class="strong">TranslatedDistribution</span></a> - Class in <a href="./org/biojava/bio/dist/package-summary.html">org.biojava.bio.dist</a></dt>
<dd>
<div class="block">A translated view of some underlying distribution.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/TranslatedDistribution.html#TranslatedDistribution(org.biojava.bio.symbol.ReversibleTranslationTable, org.biojava.bio.dist.Distribution, org.biojava.bio.dist.DistributionFactory)">TranslatedDistribution(ReversibleTranslationTable, Distribution, DistributionFactory)</a></span> - Constructor for class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/TranslatedDistribution.html" title="class in org.biojava.bio.dist">TranslatedDistribution</a></dt>
<dd>
<div class="block">Create a new TranslatedDistribution.</div>
</dd>
<dt><a href="./org/biojava/bio/gui/sequence/TranslatedSequencePanel.html" title="class in org.biojava.bio.gui.sequence"><span class="strong">TranslatedSequencePanel</span></a> - Class in <a href="./org/biojava/bio/gui/sequence/package-summary.html">org.biojava.bio.gui.sequence</a></dt>
<dd>
<div class="block"><code>TranslatedSequencePanel</code> is a panel that displays a
Sequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/TranslatedSequencePanel.html#TranslatedSequencePanel()">TranslatedSequencePanel()</a></span> - Constructor for class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/TranslatedSequencePanel.html" title="class in org.biojava.bio.gui.sequence">TranslatedSequencePanel</a></dt>
<dd>
<div class="block">Creates a new <code>TranslatedSequencePanel</code> with the
default settings (direction HORIZONTAL, scale 10.0 pixels per
symbol, symbol translation 0, leading border 0.0, trailing
border 0.0, 12 point sanserif font).</div>
</dd>
<dt><a href="./org/biojava/bio/seq/projection/TranslateFlipContext.html" title="class in org.biojava.bio.seq.projection"><span class="strong">TranslateFlipContext</span></a> - Class in <a href="./org/biojava/bio/seq/projection/package-summary.html">org.biojava.bio.seq.projection</a></dt>
<dd>
<div class="block">A ProjectionContext that translates and optionaly flips features.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/projection/TranslateFlipContext.html#TranslateFlipContext(org.biojava.bio.seq.FeatureHolder, org.biojava.bio.seq.FeatureHolder, int, boolean)">TranslateFlipContext(FeatureHolder, FeatureHolder, int, boolean)</a></span> - Constructor for class org.biojava.bio.seq.projection.<a href="./org/biojava/bio/seq/projection/TranslateFlipContext.html" title="class in org.biojava.bio.seq.projection">TranslateFlipContext</a></dt>
<dd>
<div class="block">Create a new TranslateFlipContext with explicit translation and flip.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/projection/TranslateFlipContext.html#TranslateFlipContext(org.biojava.bio.seq.FeatureHolder, org.biojava.bio.seq.FeatureHolder, int, int)">TranslateFlipContext(FeatureHolder, FeatureHolder, int, int)</a></span> - Constructor for class org.biojava.bio.seq.projection.<a href="./org/biojava/bio/seq/projection/TranslateFlipContext.html" title="class in org.biojava.bio.seq.projection">TranslateFlipContext</a></dt>
<dd>
<div class="block">Create a new TranslateFlipContext that flips all featurs arround min and
max.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/projection/TranslateFlipContext.html#TranslateFlipContext(org.biojava.bio.seq.FeatureHolder, org.biojava.bio.seq.FeatureHolder, int)">TranslateFlipContext(FeatureHolder, FeatureHolder, int)</a></span> - Constructor for class org.biojava.bio.seq.projection.<a href="./org/biojava/bio/seq/projection/TranslateFlipContext.html" title="class in org.biojava.bio.seq.projection">TranslateFlipContext</a></dt>
<dd>
<div class="block">Create a new TranslateFlipContext with translation only.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PairwiseSequencePanel.html#TRANSLATION">TRANSLATION</a></span> - Static variable in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PairwiseSequencePanel.html" title="class in org.biojava.bio.gui.sequence">PairwiseSequencePanel</a></dt>
<dd>
<div class="block">Constant <code>TRANSLATION</code> is a <code>ChangeType</code>
which indicates a change to the translation, requiring a paint
update.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/TranslatedSequencePanel.html#TRANSLATION">TRANSLATION</a></span> - Static variable in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/TranslatedSequencePanel.html" title="class in org.biojava.bio.gui.sequence">TranslatedSequencePanel</a></dt>
<dd>
<div class="block">Constant <code>TRANSLATION</code> is a <code>ChangeType</code>
which indicates a change to the translation, requiring a paint
update.</div>
</dd>
<dt><a href="./org/biojava/bio/symbol/TranslationTable.html" title="interface in org.biojava.bio.symbol"><span class="strong">TranslationTable</span></a> - Interface in <a href="./org/biojava/bio/symbol/package-summary.html">org.biojava.bio.symbol</a></dt>
<dd>
<div class="block">Encapsulates the mapping from a source to a destination
alphabet.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/jama/Matrix.html#transpose()">transpose()</a></span> - Method in class org.biojava.bio.structure.jama.<a href="./org/biojava/bio/structure/jama/Matrix.html" title="class in org.biojava.bio.structure.jama">Matrix</a></dt>
<dd>
<div class="block">Matrix transpose.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.Terms.html#TRANSPOSON_KEY">TRANSPOSON_KEY</a></span> - Static variable in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.Terms.html" title="class in org.biojavax.bio.seq">RichSequence.Terms</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/hmmer/HmmerProfileHMM.html#transScore(org.biojava.bio.dp.State, org.biojava.bio.dp.State, org.biojava.bio.symbol.Symbol, org.biojava.bio.symbol.Symbol)">transScore(State, State, Symbol, Symbol)</a></span> - Method in class org.biojava.bio.program.hmmer.<a href="./org/biojava/bio/program/hmmer/HmmerProfileHMM.html" title="class in org.biojava.bio.program.hmmer">HmmerProfileHMM</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/TranslationTable.html#TREMA_MITO">TREMA_MITO</a></span> - Static variable in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/TranslationTable.html" title="interface in org.biojava.bio.symbol">TranslationTable</a></dt>
<dd>
<div class="block">Translation table name for the trematode mitochondrial genetic
code.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/SimpleMMcifParser.html#triggerDocumentEnd()">triggerDocumentEnd()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/SimpleMMcifParser.html" title="class in org.biojava.bio.structure.io.mmcif">SimpleMMcifParser</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/SimpleMMcifParser.html#triggerDocumentStart()">triggerDocumentStart()</a></span> - Method in class org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/SimpleMMcifParser.html" title="class in org.biojava.bio.structure.io.mmcif">SimpleMMcifParser</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/SimpleMMcifParser.html#triggerGeneric(java.lang.String, java.util.List, java.util.List)">triggerGeneric(String, List<String>, List<String>)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/SimpleMMcifParser.html" title="class in org.biojava.bio.structure.io.mmcif">SimpleMMcifParser</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/util/SequenceMouseListener.html#triggerMouseOverPosition(int, int)">triggerMouseOverPosition(int, int)</a></span> - Method in class org.biojava.bio.structure.gui.util.<a href="./org/biojava/bio/structure/gui/util/SequenceMouseListener.html" title="class in org.biojava.bio.structure.gui.util">SequenceMouseListener</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/SimpleMMcifParser.html#triggerNewChemComp(org.biojava.bio.structure.io.mmcif.model.ChemComp)">triggerNewChemComp(ChemComp)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/SimpleMMcifParser.html" title="class in org.biojava.bio.structure.io.mmcif">SimpleMMcifParser</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/SimpleMMcifParser.html#triggerNewEntity(org.biojava.bio.structure.io.mmcif.model.Entity)">triggerNewEntity(Entity)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/SimpleMMcifParser.html" title="class in org.biojava.bio.structure.io.mmcif">SimpleMMcifParser</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/SimpleMMcifParser.html#triggerNewEntityPolySeq(org.biojava.bio.structure.io.mmcif.model.EntityPolySeq)">triggerNewEntityPolySeq(EntityPolySeq)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/SimpleMMcifParser.html" title="class in org.biojava.bio.structure.io.mmcif">SimpleMMcifParser</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/SimpleMMcifParser.html#triggerNewPdbxEntityNonPoly(org.biojava.bio.structure.io.mmcif.model.PdbxEntityNonPoly)">triggerNewPdbxEntityNonPoly(PdbxEntityNonPoly)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/SimpleMMcifParser.html" title="class in org.biojava.bio.structure.io.mmcif">SimpleMMcifParser</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/SimpleMMcifParser.html#triggerNewRefine(org.biojava.bio.structure.io.mmcif.model.Refine)">triggerNewRefine(Refine)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/SimpleMMcifParser.html" title="class in org.biojava.bio.structure.io.mmcif">SimpleMMcifParser</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/SimpleMMcifParser.html#triggerNewStructAsym(org.biojava.bio.structure.io.mmcif.model.StructAsym)">triggerNewStructAsym(StructAsym)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/SimpleMMcifParser.html" title="class in org.biojava.bio.structure.io.mmcif">SimpleMMcifParser</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/SimpleMMcifParser.html#triggerNewStructKeywords(org.biojava.bio.structure.io.mmcif.model.StructKeywords)">triggerNewStructKeywords(StructKeywords)</a></span> - Method in class org.biojava.bio.structure.io.mmcif.<a href="./org/biojava/bio/structure/io/mmcif/SimpleMMcifParser.html" title="class in org.biojava.bio.structure.io.mmcif">SimpleMMcifParser</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/Ontology.html#TRIPLE">TRIPLE</a></span> - Static variable in interface org.biojava.ontology.<a href="./org/biojava/ontology/Ontology.html" title="interface in org.biojava.ontology">Ontology</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/ontology/Triple.html" title="interface in org.biojava.ontology"><span class="strong">Triple</span></a> - Interface in <a href="./org/biojava/ontology/package-summary.html">org.biojava.ontology</a></dt>
<dd>
<div class="block">A triple in an ontology.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ontology/ComparableOntology.html#TRIPLE">TRIPLE</a></span> - Static variable in interface org.biojavax.ontology.<a href="./org/biojavax/ontology/ComparableOntology.html" title="interface in org.biojavax.ontology">ComparableOntology</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/ontology/Triple.Impl.html" title="class in org.biojava.ontology"><span class="strong">Triple.Impl</span></a> - Class in <a href="./org/biojava/ontology/package-summary.html">org.biojava.ontology</a></dt>
<dd>
<div class="block">Basic in-memory implementation of a Triple in an ontology
This can be used to implement Ontology.createTriple</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/Triple.Impl.html#Triple.Impl(org.biojava.ontology.Term, org.biojava.ontology.Term, org.biojava.ontology.Term)">Triple.Impl(Term, Term, Term)</a></span> - Constructor for class org.biojava.ontology.<a href="./org/biojava/ontology/Triple.Impl.html" title="class in org.biojava.ontology">Triple.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/Triple.Impl.html#Triple.Impl(org.biojava.ontology.Term, org.biojava.ontology.Term, org.biojava.ontology.Term, java.lang.Object[])">Triple.Impl(Term, Term, Term, Object[])</a></span> - Constructor for class org.biojava.ontology.<a href="./org/biojava/ontology/Triple.Impl.html" title="class in org.biojava.ontology">Triple.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/Triple.Impl.html#Triple.Impl(org.biojava.ontology.Term, org.biojava.ontology.Term, org.biojava.ontology.Term, java.lang.String, java.lang.String)">Triple.Impl(Term, Term, Term, String, String)</a></span> - Constructor for class org.biojava.ontology.<a href="./org/biojava/ontology/Triple.Impl.html" title="class in org.biojava.ontology">Triple.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/Triple.Impl.html#Triple.Impl(org.biojava.ontology.Term, org.biojava.ontology.Term, org.biojava.ontology.Term, java.lang.String, java.lang.String, java.lang.Object[])">Triple.Impl(Term, Term, Term, String, String, Object[])</a></span> - Constructor for class org.biojava.ontology.<a href="./org/biojava/ontology/Triple.Impl.html" title="class in org.biojava.ontology">Triple.Impl</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/utils/TriState.html" title="class in org.biojava.utils"><span class="strong">TriState</span></a> - Class in <a href="./org/biojava/utils/package-summary.html">org.biojava.utils</a></dt>
<dd>
<div class="block">Class that represents the tristate values possible in
a logical operation: true, false and indeterminate.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/ProteinTools.html#trp()">trp()</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/ProteinTools.html" title="class in org.biojava.bio.seq">ProteinTools</a></dt>
<dd>
<div class="block">Returns the <code>AtomicSymbol</code> for the amino acid
Tryptophan (W)</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/TriState.html#TRUE">TRUE</a></span> - Static variable in class org.biojava.utils.<a href="./org/biojava/utils/TriState.html" title="class in org.biojava.utils">TriState</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/Protease.html#TRYPSIN">TRYPSIN</a></span> - Static variable in class org.biojava.bio.proteomics.<a href="./org/biojava/bio/proteomics/Protease.html" title="class in org.biojava.bio.proteomics">Protease</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/proteomics/ProteaseManager.html#TRYPSIN">TRYPSIN</a></span> - Static variable in class org.biojava.bio.proteomics.<a href="./org/biojava/bio/proteomics/ProteaseManager.html" title="class in org.biojava.bio.proteomics">ProteaseManager</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/PDBFileParser.html#TURN">TURN</a></span> - Static variable in class org.biojava.bio.structure.io.<a href="./org/biojava/bio/structure/io/PDBFileParser.html" title="class in org.biojava.bio.structure.io">PDBFileParser</a></dt>
<dd>
<div class="block">Turn secondary structure assignment.</div>
</dd>
<dt><a href="./org/biojava/bio/gui/glyph/TurnGlyph.html" title="class in org.biojava.bio.gui.glyph"><span class="strong">TurnGlyph</span></a> - Class in <a href="./org/biojava/bio/gui/glyph/package-summary.html">org.biojava.bio.gui.glyph</a></dt>
<dd>
<div class="block">A Glyph that paints a wide 'H' line within the bounds</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/glyph/TurnGlyph.html#TurnGlyph()">TurnGlyph()</a></span> - Constructor for class org.biojava.bio.gui.glyph.<a href="./org/biojava/bio/gui/glyph/TurnGlyph.html" title="class in org.biojava.bio.gui.glyph">TurnGlyph</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/glyph/TurnGlyph.html#TurnGlyph(java.awt.geom.Rectangle2D.Float)">TurnGlyph(Rectangle2D.Float)</a></span> - Constructor for class org.biojava.bio.gui.glyph.<a href="./org/biojava/bio/gui/glyph/TurnGlyph.html" title="class in org.biojava.bio.gui.glyph">TurnGlyph</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/glyph/TurnGlyph.html#TurnGlyph(java.awt.Paint, java.awt.Stroke)">TurnGlyph(Paint, Stroke)</a></span> - Constructor for class org.biojava.bio.gui.glyph.<a href="./org/biojava/bio/gui/glyph/TurnGlyph.html" title="class in org.biojava.bio.gui.glyph">TurnGlyph</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/HomologeneBuilder.html#TWIN">TWIN</a></span> - Static variable in interface org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/HomologeneBuilder.html" title="interface in org.biojava.bio.program.homologene">HomologeneBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/SimilarityType.html#TWIN">TWIN</a></span> - Static variable in interface org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/SimilarityType.html" title="interface in org.biojava.bio.program.homologene">SimilarityType</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/gui/glyph/TwoHeadedArrowGlyph.html" title="class in org.biojava.bio.gui.glyph"><span class="strong">TwoHeadedArrowGlyph</span></a> - Class in <a href="./org/biojava/bio/gui/glyph/package-summary.html">org.biojava.bio.gui.glyph</a></dt>
<dd>
<div class="block">A Glyph that paints a two headed arrow within the bounds</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/glyph/TwoHeadedArrowGlyph.html#TwoHeadedArrowGlyph()">TwoHeadedArrowGlyph()</a></span> - Constructor for class org.biojava.bio.gui.glyph.<a href="./org/biojava/bio/gui/glyph/TwoHeadedArrowGlyph.html" title="class in org.biojava.bio.gui.glyph">TwoHeadedArrowGlyph</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/glyph/TwoHeadedArrowGlyph.html#TwoHeadedArrowGlyph(java.awt.geom.Rectangle2D.Float)">TwoHeadedArrowGlyph(Rectangle2D.Float)</a></span> - Constructor for class org.biojava.bio.gui.glyph.<a href="./org/biojava/bio/gui/glyph/TwoHeadedArrowGlyph.html" title="class in org.biojava.bio.gui.glyph">TwoHeadedArrowGlyph</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BiblioCriterion.html#type">type</a></span> - Variable in class org.biojava.bibliography.<a href="./org/biojava/bibliography/BiblioCriterion.html" title="class in org.biojava.bibliography">BiblioCriterion</a></dt>
<dd>
<div class="block">The criteria can be used for defining rules for matching
(type <a href="./org/biojava/bibliography/BiblioCriterion.html#QUERY_CRITERION"><code>BiblioCriterion.QUERY_CRITERION</code></a>), or for ordering (type <a href="./org/biojava/bibliography/BiblioCriterion.html#SORT_CRITERION"><code>BiblioCriterion.SORT_CRITERION</code></a>).</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BibRef.html#type">type</a></span> - Variable in class org.biojava.bibliography.<a href="./org/biojava/bibliography/BibRef.html" title="class in org.biojava.bibliography">BibRef</a></dt>
<dd>
<div class="block">
It defines the nature or genre of the cited resource.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/Feature.Template.html#type">type</a></span> - Variable in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/Feature.Template.html" title="class in org.biojava.bio.seq">Feature.Template</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/Feature.html#TYPE">TYPE</a></span> - Static variable in interface org.biojava.bio.seq.<a href="./org/biojava/bio/seq/Feature.html" title="interface in org.biojava.bio.seq">Feature</a></dt>
<dd>
<div class="block">The type of this feature has altered.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/AminoAcidImpl.html#type">type</a></span> - Static variable in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/AminoAcidImpl.html" title="class in org.biojava.bio.structure">AminoAcidImpl</a></dt>
<dd>
<div class="block">this is an Amino acid.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/HetatomImpl.html#type">type</a></span> - Static variable in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/HetatomImpl.html" title="class in org.biojava.bio.structure">HetatomImpl</a></dt>
<dd>
<div class="block">this is a "hetatm".</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/NucleotideImpl.html#type">type</a></span> - Static variable in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/NucleotideImpl.html" title="class in org.biojava.bio.structure">NucleotideImpl</a></dt>
<dd>
<div class="block">this is a "nucleotide", a special occurance of a Hetatom.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/IndexedChangeHub.ListenerMemento.html#type">type</a></span> - Variable in class org.biojava.utils.<a href="./org/biojava/utils/IndexedChangeHub.ListenerMemento.html" title="class in org.biojava.utils">IndexedChangeHub.ListenerMemento</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BibRefSupport.html#TYPE_ARTICLE">TYPE_ARTICLE</a></span> - Static variable in interface org.biojava.bibliography.<a href="./org/biojava/bibliography/BibRefSupport.html" title="interface in org.biojava.bibliography">BibRefSupport</a></dt>
<dd>
<div class="block">A name of a bibliographic resource type.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#TYPE_ATTR">TYPE_ATTR</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BibRefSupport.html#TYPE_BOOK">TYPE_BOOK</a></span> - Static variable in interface org.biojava.bibliography.<a href="./org/biojava/bibliography/BibRefSupport.html" title="interface in org.biojava.bibliography">BibRefSupport</a></dt>
<dd>
<div class="block">A name of a bibliographic resource type.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BibRefSupport.html#TYPE_BOOK_ARTICLE">TYPE_BOOK_ARTICLE</a></span> - Static variable in interface org.biojava.bibliography.<a href="./org/biojava/bibliography/BibRefSupport.html" title="interface in org.biojava.bibliography">BibRefSupport</a></dt>
<dd>
<div class="block">A name of a bibliographic resource type.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BibRefSupport.html#TYPE_JOURNAL_ARTICLE">TYPE_JOURNAL_ARTICLE</a></span> - Static variable in interface org.biojava.bibliography.<a href="./org/biojava/bibliography/BibRefSupport.html" title="interface in org.biojava.bibliography">BibRefSupport</a></dt>
<dd>
<div class="block">A name of a bibliographic resource type.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BibRefSupport.html#TYPE_PATENT">TYPE_PATENT</a></span> - Static variable in interface org.biojava.bibliography.<a href="./org/biojava/bibliography/BibRefSupport.html" title="interface in org.biojava.bibliography">BibRefSupport</a></dt>
<dd>
<div class="block">A name of a bibliographic resource type.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BibRefSupport.html#TYPE_PROCEEDING">TYPE_PROCEEDING</a></span> - Static variable in interface org.biojava.bibliography.<a href="./org/biojava/bibliography/BibRefSupport.html" title="interface in org.biojava.bibliography">BibRefSupport</a></dt>
<dd>
<div class="block">A name of a bibliographic resource type.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/EmblLikeFormat.html#TYPE_TAG">TYPE_TAG</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/EmblLikeFormat.html" title="class in org.biojava.bio.seq.io">EmblLikeFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/GenbankFormat.html#TYPE_TAG">TYPE_TAG</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/GenbankFormat.html" title="class in org.biojava.bio.seq.io">GenbankFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BibRefSupport.html#TYPE_TECH_REPORT">TYPE_TECH_REPORT</a></span> - Static variable in interface org.biojava.bibliography.<a href="./org/biojava/bibliography/BibRefSupport.html" title="interface in org.biojava.bibliography">BibRefSupport</a></dt>
<dd>
<div class="block">A name of a bibliographic resource type.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BibRefSupport.html#TYPE_THESIS">TYPE_THESIS</a></span> - Static variable in interface org.biojava.bibliography.<a href="./org/biojava/bibliography/BibRefSupport.html" title="interface in org.biojava.bibliography">BibRefSupport</a></dt>
<dd>
<div class="block">A name of a bibliographic resource type.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BibRefSupport.html#TYPE_WEB_RESOURCE">TYPE_WEB_RESOURCE</a></span> - Static variable in interface org.biojava.bibliography.<a href="./org/biojava/bibliography/BibRefSupport.html" title="interface in org.biojava.bibliography">BibRefSupport</a></dt>
<dd>
<div class="block">A name of a bibliographic resource type.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/obo/OboFileHandler.html#TYPEDEF">TYPEDEF</a></span> - Static variable in class org.biojava.ontology.obo.<a href="./org/biojava/ontology/obo/OboFileHandler.html" title="class in org.biojava.ontology.obo">OboFileHandler</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/utils/TypedProperties.html" title="class in org.biojava.utils"><span class="strong">TypedProperties</span></a> - Class in <a href="./org/biojava/utils/package-summary.html">org.biojava.utils</a></dt>
<dd>
<div class="block">a sub-class of java.util.Properties that provides the same constructors, adds two convenient load methods to load
the properties from files and, most importantly, adds getPropertyAsXXX() methods to get a property as an object of
type XXX.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/TypedProperties.html#TypedProperties()">TypedProperties()</a></span> - Constructor for class org.biojava.utils.<a href="./org/biojava/utils/TypedProperties.html" title="class in org.biojava.utils">TypedProperties</a></dt>
<dd>
<div class="block">Creates an empty property list with no default values.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/TypedProperties.html#TypedProperties(java.util.Properties)">TypedProperties(Properties)</a></span> - Constructor for class org.biojava.utils.<a href="./org/biojava/utils/TypedProperties.html" title="class in org.biojava.utils">TypedProperties</a></dt>
<dd>
<div class="block">Creates an empty property list with the specified defaults.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/Feature.Template.html#typeTerm">typeTerm</a></span> - Variable in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/Feature.Template.html" title="class in org.biojava.bio.seq">Feature.Template</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/Feature.html#TYPETERM">TYPETERM</a></span> - Static variable in interface org.biojava.bio.seq.<a href="./org/biojava/bio/seq/Feature.html" title="interface in org.biojava.bio.seq">Feature</a></dt>
<dd>
<div class="block">The ontological type of this feature has altered.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichFeature.html#TYPETERM">TYPETERM</a></span> - Static variable in interface org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichFeature.html" title="interface in org.biojavax.bio.seq">RichFeature</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/ProteinTools.html#tyr()">tyr()</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/ProteinTools.html" title="class in org.biojava.bio.seq">ProteinTools</a></dt>
<dd>
<div class="block">Returns the <code>AtomicSymbol</code> for the amino acid
Tyrosine (Y)</div>
</dd>
</dl>
<a name="_U_">
<!-- -->
</a>
<h2 class="title">U</h2>
<dl>
<dt><span class="strong"><a href="./org/biojava/bio/seq/NucleotideTools.html#u()">u()</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/NucleotideTools.html" title="class in org.biojava.bio.seq">NucleotideTools</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/ProteinTools.html#u()">u()</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/ProteinTools.html" title="class in org.biojava.bio.seq">ProteinTools</a></dt>
<dd>
<div class="block">Returns the <code>AtomicSymbol</code> for the amino acid
Selenocysteine</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/RNATools.html#u()">u()</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/RNATools.html" title="class in org.biojava.bio.seq">RNATools</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/symbol/UkkonenSuffixTree.html" title="class in org.biojava.bio.symbol"><span class="strong">UkkonenSuffixTree</span></a> - Class in <a href="./org/biojava/bio/symbol/package-summary.html">org.biojava.bio.symbol</a></dt>
<dd>
<div class="block">
A suffix tree is an efficient method for encoding the frequencies
of motifs in a sequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/UkkonenSuffixTree.html#UkkonenSuffixTree()">UkkonenSuffixTree()</a></span> - Constructor for class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/UkkonenSuffixTree.html" title="class in org.biojava.bio.symbol">UkkonenSuffixTree</a></dt>
<dd>
<div class="block">Initializes a new <code>UkkonenSuffixTree</code> instance.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/UkkonenSuffixTree.html#UkkonenSuffixTree(java.lang.String)">UkkonenSuffixTree(String)</a></span> - Constructor for class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/UkkonenSuffixTree.html" title="class in org.biojava.bio.symbol">UkkonenSuffixTree</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/UkkonenSuffixTree.html#UkkonenSuffixTree(org.biojava.bio.symbol.FiniteAlphabet)">UkkonenSuffixTree(FiniteAlphabet)</a></span> - Constructor for class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/UkkonenSuffixTree.html" title="class in org.biojava.bio.symbol">UkkonenSuffixTree</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/symbol/UkkonenSuffixTree.SuffixNode.html" title="class in org.biojava.bio.symbol"><span class="strong">UkkonenSuffixTree.SuffixNode</span></a> - Class in <a href="./org/biojava/bio/symbol/package-summary.html">org.biojava.bio.symbol</a></dt>
<dd>
<div class="block">end Tree modification methods</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/UkkonenSuffixTree.SuffixNode.html#UkkonenSuffixTree.SuffixNode()">UkkonenSuffixTree.SuffixNode()</a></span> - Constructor for class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/UkkonenSuffixTree.SuffixNode.html" title="class in org.biojava.bio.symbol">UkkonenSuffixTree.SuffixNode</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/jama/Matrix.html#uminus()">uminus()</a></span> - Method in class org.biojava.bio.structure.jama.<a href="./org/biojava/bio/structure/jama/Matrix.html" title="class in org.biojava.bio.structure.jama">Matrix</a></dt>
<dd>
<div class="block">Unary minus</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/naming/ObdaContext.html#unbind(javax.naming.Name)">unbind(Name)</a></span> - Method in class org.biojava.naming.<a href="./org/biojava/naming/ObdaContext.html" title="class in org.biojava.naming">ObdaContext</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/naming/ObdaContext.html#unbind(java.lang.String)">unbind(String)</a></span> - Method in class org.biojava.naming.<a href="./org/biojava/naming/ObdaContext.html" title="class in org.biojava.naming">ObdaContext</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/utils/Unchangeable.html" title="class in org.biojava.utils"><span class="strong">Unchangeable</span></a> - Class in <a href="./org/biojava/utils/package-summary.html">org.biojava.utils</a></dt>
<dd>
<div class="block">This is a utility implementation of Changeable that doesn't fire any events
or keep references to any listeners.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/Unchangeable.html#Unchangeable()">Unchangeable()</a></span> - Constructor for class org.biojava.utils.<a href="./org/biojava/utils/Unchangeable.html" title="class in org.biojava.utils">Unchangeable</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/EcNumber.html#UNCLASSIFIED">UNCLASSIFIED</a></span> - Static variable in interface org.biojava.bio.<a href="./org/biojava/bio/EcNumber.html" title="interface in org.biojava.bio">EcNumber</a></dt>
<dd>
<div class="block">Constant that represents EC number components that are as yet unclassified.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/io/UncompressInputStream.html#uncompress(java.lang.String, java.io.FileOutputStream)">uncompress(String, FileOutputStream)</a></span> - Static method in class org.biojava.utils.io.<a href="./org/biojava/utils/io/UncompressInputStream.html" title="class in org.biojava.utils.io">UncompressInputStream</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/utils/io/UncompressInputStream.html" title="class in org.biojava.utils.io"><span class="strong">UncompressInputStream</span></a> - Class in <a href="./org/biojava/utils/io/package-summary.html">org.biojava.utils.io</a></dt>
<dd>
<div class="block">This class decompresses an input stream containing data compressed with
the unix "compress" utility (LZC, a LZW variant).</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/io/UncompressInputStream.html#UncompressInputStream(java.io.InputStream)">UncompressInputStream(InputStream)</a></span> - Constructor for class org.biojava.utils.io.<a href="./org/biojava/utils/io/UncompressInputStream.html" title="class in org.biojava.utils.io">UncompressInputStream</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/EcNumber.html#UNDEFINED">UNDEFINED</a></span> - Static variable in interface org.biojava.bio.<a href="./org/biojava/bio/EcNumber.html" title="interface in org.biojava.bio">EcNumber</a></dt>
<dd>
<div class="block">Constant that represents EC number components that are not defined.</div>
</dd>
<dt><a href="./org/biojava/bio/alignment/UnequalLengthAlignment.html" title="interface in org.biojava.bio.alignment"><span class="strong">UnequalLengthAlignment</span></a> - Interface in <a href="./org/biojava/bio/alignment/package-summary.html">org.biojava.bio.alignment</a></dt>
<dd>
<div class="block">UnequalLengthAlignment has the following behavior.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/obo/OboFileParser.html#unescape(java.lang.String)">unescape(String)</a></span> - Method in class org.biojava.ontology.obo.<a href="./org/biojava/ontology/obo/OboFileParser.html" title="class in org.biojava.ontology.obo">OboFileParser</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/obo/OboFileParser.html#unescape(java.lang.String, char, int, boolean)">unescape(String, char, int, boolean)</a></span> - Method in class org.biojava.ontology.obo.<a href="./org/biojava/ontology/obo/OboFileParser.html" title="class in org.biojava.ontology.obo">OboFileParser</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/obo/OboFileParser.html#unescape(java.lang.String, char, int, int, boolean)">unescape(String, char, int, int, boolean)</a></span> - Method in class org.biojava.ontology.obo.<a href="./org/biojava/ontology/obo/OboFileParser.html" title="class in org.biojava.ontology.obo">OboFileParser</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/obo/OboFileParser.html#unescapeChars">unescapeChars</a></span> - Static variable in class org.biojava.ontology.obo.<a href="./org/biojava/ontology/obo/OboFileParser.html" title="class in org.biojava.ontology.obo">OboFileParser</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/dist/UniformDistribution.html" title="class in org.biojava.bio.dist"><span class="strong">UniformDistribution</span></a> - Class in <a href="./org/biojava/bio/dist/package-summary.html">org.biojava.bio.dist</a></dt>
<dd>
<div class="block">An implementation of an uniform distribution</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/UniformDistribution.html#UniformDistribution(org.biojava.bio.symbol.FiniteAlphabet)">UniformDistribution(FiniteAlphabet)</a></span> - Constructor for class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/UniformDistribution.html" title="class in org.biojava.bio.dist">UniformDistribution</a></dt>
<dd>
<div class="block">Create a new UniformDistribution.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ga/util/GATools.html#uniformMutationDistribution(org.biojava.bio.symbol.FiniteAlphabet)">uniformMutationDistribution(FiniteAlphabet)</a></span> - Static method in class org.biojavax.ga.util.<a href="./org/biojavax/ga/util/GATools.html" title="class in org.biojavax.ga.util">GATools</a></dt>
<dd>
<div class="block">Makes a 1st order distribution which is infact uniform (equivalent to a
uniform zero order distribution).</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/unigene/UnigeneTools.html#UNIGENE_ANNOTATION">UNIGENE_ANNOTATION</a></span> - Static variable in class org.biojava.bio.program.unigene.<a href="./org/biojava/bio/program/unigene/UnigeneTools.html" title="class in org.biojava.bio.program.unigene">UnigeneTools</a></dt>
<dd>
<div class="block">
Annotation schema for all UnigeneCluster instances.</div>
</dd>
<dt><a href="./org/biojava/bio/program/unigene/UnigeneCluster.html" title="interface in org.biojava.bio.program.unigene"><span class="strong">UnigeneCluster</span></a> - Interface in <a href="./org/biojava/bio/program/unigene/package-summary.html">org.biojava.bio.program.unigene</a></dt>
<dd>
<div class="block">
A single unigene cluster.</div>
</dd>
<dt><a href="./org/biojava/bio/program/unigene/UnigeneDB.html" title="interface in org.biojava.bio.program.unigene"><span class="strong">UnigeneDB</span></a> - Interface in <a href="./org/biojava/bio/program/unigene/package-summary.html">org.biojava.bio.program.unigene</a></dt>
<dd>
<div class="block">A database of Unigene clusters.</div>
</dd>
<dt><a href="./org/biojava/bio/program/unigene/UnigeneFactory.html" title="interface in org.biojava.bio.program.unigene"><span class="strong">UnigeneFactory</span></a> - Interface in <a href="./org/biojava/bio/program/unigene/package-summary.html">org.biojava.bio.program.unigene</a></dt>
<dd>
<div class="block">Objects that can be used to produce a <code>UnigeneDB</code> instance
given a URL.</div>
</dd>
<dt><a href="./org/biojava/bio/program/unigene/UnigeneTools.html" title="class in org.biojava.bio.program.unigene"><span class="strong">UnigeneTools</span></a> - Class in <a href="./org/biojava/bio/program/unigene/package-summary.html">org.biojava.bio.program.unigene</a></dt>
<dd>
<div class="block">Usefull tools for working with Unigene.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/unigene/UnigeneTools.html#UnigeneTools()">UnigeneTools()</a></span> - Constructor for class org.biojava.bio.program.unigene.<a href="./org/biojava/bio/program/unigene/UnigeneTools.html" title="class in org.biojava.bio.program.unigene">UnigeneTools</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AgaveWriter.Indent.html#unIndent()">unIndent()</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AgaveWriter.Indent.html" title="class in org.biojava.bio.seq.io.agave">AgaveWriter.Indent</a></dt>
<dd>
<div class="block">Remove a level of indentation</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BibRefSupport.html#union(org.biojava.bibliography.BibRefQuery[], java.util.Hashtable)">union(BibRefQuery[], Hashtable)</a></span> - Method in interface org.biojava.bibliography.<a href="./org/biojava/bibliography/BibRefSupport.html" title="interface in org.biojava.bibliography">BibRefSupport</a></dt>
<dd>
<div class="block">
It merges all given collections together.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/AnnotationTools.html#union(org.biojava.bio.AnnotationType, org.biojava.bio.AnnotationType)">union(AnnotationType, AnnotationType)</a></span> - Static method in class org.biojava.bio.<a href="./org/biojava/bio/AnnotationTools.html" title="class in org.biojava.bio">AnnotationTools</a></dt>
<dd>
<div class="block">Create an AnnotationType that matches all Anntotations that are accepted
by two others.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/AnnotationTools.html#union(org.biojava.bio.PropertyConstraint, org.biojava.bio.PropertyConstraint)">union(PropertyConstraint, PropertyConstraint)</a></span> - Static method in class org.biojava.bio.<a href="./org/biojava/bio/AnnotationTools.html" title="class in org.biojava.bio">AnnotationTools</a></dt>
<dd>
<div class="block">Create a PropertyConstraint that matches all Objects that are accepted
by two others.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/AnnotationTools.html#union(org.biojava.bio.CollectionConstraint, org.biojava.bio.CollectionConstraint)">union(CollectionConstraint, CollectionConstraint)</a></span> - Static method in class org.biojava.bio.<a href="./org/biojava/bio/AnnotationTools.html" title="class in org.biojava.bio">AnnotationTools</a></dt>
<dd>
<div class="block">Calculate a CollectionConstaint that will accept all items accepted by
either constraint.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureHolderUtils.html#union(org.biojava.bio.seq.FeatureHolder, org.biojava.bio.seq.FeatureHolder)">union(FeatureHolder, FeatureHolder)</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureHolderUtils.html" title="class in org.biojava.bio.seq">FeatureHolderUtils</a></dt>
<dd>
<div class="block">Operator: Union of FeatureHolder1 and FeatureHolder2</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AbstractLocation.html#union(org.biojava.bio.symbol.Location)">union(Location)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AbstractLocation.html" title="class in org.biojava.bio.symbol">AbstractLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AbstractLocationDecorator.html#union(org.biojava.bio.symbol.Location)">union(Location)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AbstractLocationDecorator.html" title="class in org.biojava.bio.symbol">AbstractLocationDecorator</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/CircularLocation.html#union(org.biojava.bio.symbol.Location)">union(Location)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/CircularLocation.html" title="class in org.biojava.bio.symbol">CircularLocation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/Location.html#union(org.biojava.bio.symbol.Location)">union(Location)</a></span> - Method in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/Location.html" title="interface in org.biojava.bio.symbol">Location</a></dt>
<dd>
<div class="block">Return a Location containing all points in either ranges.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/LocationTools.html#union(org.biojava.bio.symbol.Location, org.biojava.bio.symbol.Location)">union(Location, Location)</a></span> - Static method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/LocationTools.html" title="class in org.biojava.bio.symbol">LocationTools</a></dt>
<dd>
<div class="block">Return the union of two locations.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/LocationTools.html#union(java.util.Collection)">union(Collection)</a></span> - Static method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/LocationTools.html" title="class in org.biojava.bio.symbol">LocationTools</a></dt>
<dd>
<div class="block">The n-way union of a Collection of locations.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/CompoundRichLocation.html#union(org.biojava.bio.symbol.Location)">union(Location)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/CompoundRichLocation.html" title="class in org.biojavax.bio.seq">CompoundRichLocation</a></dt>
<dd>
<div class="block">Return a Location containing all points in either ranges.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/EmptyRichLocation.html#union(org.biojava.bio.symbol.Location)">union(Location)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/EmptyRichLocation.html" title="class in org.biojavax.bio.seq">EmptyRichLocation</a></dt>
<dd>
<div class="block">Return a Location containing all points in either ranges.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/SimpleRichLocation.html#union(org.biojava.bio.symbol.Location)">union(Location)</a></span> - Method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/SimpleRichLocation.html" title="class in org.biojavax.bio.seq">SimpleRichLocation</a></dt>
<dd>
<div class="block">Return a Location containing all points in either ranges.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtFormat.html#UNIPROT_FORMAT">UNIPROT_FORMAT</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtFormat.html" title="class in org.biojavax.bio.seq.io">UniProtFormat</a></dt>
<dd>
<div class="block">The name of this format</div>
</dd>
<dt><a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html" title="class in org.biojavax.bio.seq.io"><span class="strong">UniProtCommentParser</span></a> - Class in <a href="./org/biojavax/bio/seq/io/package-summary.html">org.biojavax.bio.seq.io</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html#UniProtCommentParser()">UniProtCommentParser()</a></span> - Constructor for class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtCommentParser.html" title="class in org.biojavax.bio.seq.io">UniProtCommentParser</a></dt>
<dd>
<div class="block">Creates a new instance of UniProtCommentParser.</div>
</dd>
<dt><a href="./org/biojavax/bio/seq/io/UniProtCommentParser.Event.html" title="class in org.biojavax.bio.seq.io"><span class="strong">UniProtCommentParser.Event</span></a> - Class in <a href="./org/biojavax/bio/seq/io/package-summary.html">org.biojavax.bio.seq.io</a></dt>
<dd>
<div class="block">A class to describe events for alternative product comments.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtCommentParser.Event.html#UniProtCommentParser.Event()">UniProtCommentParser.Event()</a></span> - Constructor for class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtCommentParser.Event.html" title="class in org.biojavax.bio.seq.io">UniProtCommentParser.Event</a></dt>
<dd> </dd>
<dt><a href="./org/biojavax/bio/seq/io/UniProtCommentParser.Interaction.html" title="class in org.biojavax.bio.seq.io"><span class="strong">UniProtCommentParser.Interaction</span></a> - Class in <a href="./org/biojavax/bio/seq/io/package-summary.html">org.biojavax.bio.seq.io</a></dt>
<dd>
<div class="block">A class to describe protein-protein interactions.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtCommentParser.Interaction.html#UniProtCommentParser.Interaction()">UniProtCommentParser.Interaction()</a></span> - Constructor for class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtCommentParser.Interaction.html" title="class in org.biojavax.bio.seq.io">UniProtCommentParser.Interaction</a></dt>
<dd> </dd>
<dt><a href="./org/biojavax/bio/seq/io/UniProtCommentParser.Isoform.html" title="class in org.biojavax.bio.seq.io"><span class="strong">UniProtCommentParser.Isoform</span></a> - Class in <a href="./org/biojavax/bio/seq/io/package-summary.html">org.biojavax.bio.seq.io</a></dt>
<dd>
<div class="block">A class to describe isoforms for alternative product comments.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtCommentParser.Isoform.html#UniProtCommentParser.Isoform()">UniProtCommentParser.Isoform()</a></span> - Constructor for class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtCommentParser.Isoform.html" title="class in org.biojavax.bio.seq.io">UniProtCommentParser.Isoform</a></dt>
<dd>
<div class="block">Creates a new instance.</div>
</dd>
<dt><a href="./org/biojavax/bio/seq/io/UniProtCommentParser.SeqCaution.html" title="class in org.biojavax.bio.seq.io"><span class="strong">UniProtCommentParser.SeqCaution</span></a> - Class in <a href="./org/biojavax/bio/seq/io/package-summary.html">org.biojavax.bio.seq.io</a></dt>
<dd>
<div class="block">A class to describe seq caution entries.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtCommentParser.SeqCaution.html#UniProtCommentParser.SeqCaution()">UniProtCommentParser.SeqCaution()</a></span> - Constructor for class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtCommentParser.SeqCaution.html" title="class in org.biojavax.bio.seq.io">UniProtCommentParser.SeqCaution</a></dt>
<dd>
<div class="block">Creates a new instance.</div>
</dd>
<dt><a href="./org/biojavax/bio/seq/io/UniProtFormat.html" title="class in org.biojavax.bio.seq.io"><span class="strong">UniProtFormat</span></a> - Class in <a href="./org/biojavax/bio/seq/io/package-summary.html">org.biojavax.bio.seq.io</a></dt>
<dd>
<div class="block">Format reader for UniProt files.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtFormat.html#UniProtFormat()">UniProtFormat()</a></span> - Constructor for class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtFormat.html" title="class in org.biojavax.bio.seq.io">UniProtFormat</a></dt>
<dd> </dd>
<dt><a href="./org/biojavax/bio/seq/io/UniProtFormat.Terms.html" title="class in org.biojavax.bio.seq.io"><span class="strong">UniProtFormat.Terms</span></a> - Class in <a href="./org/biojavax/bio/seq/io/package-summary.html">org.biojavax.bio.seq.io</a></dt>
<dd>
<div class="block">Implements some UniProt-specific terms.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtFormat.Terms.html#UniProtFormat.Terms()">UniProtFormat.Terms()</a></span> - Constructor for class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtFormat.Terms.html" title="class in org.biojavax.bio.seq.io">UniProtFormat.Terms</a></dt>
<dd> </dd>
<dt><a href="./org/biojavax/bio/seq/io/UniProtLocationParser.html" title="class in org.biojavax.bio.seq.io"><span class="strong">UniProtLocationParser</span></a> - Class in <a href="./org/biojavax/bio/seq/io/package-summary.html">org.biojavax.bio.seq.io</a></dt>
<dd>
<div class="block">Parses UniProt location strings into RichLocation objects.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#UNIPROTXML_FORMAT">UNIPROTXML_FORMAT</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd>
<div class="block">The name of this format</div>
</dd>
<dt><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io"><span class="strong">UniProtXMLFormat</span></a> - Class in <a href="./org/biojavax/bio/seq/io/package-summary.html">org.biojavax.bio.seq.io</a></dt>
<dd>
<div class="block">Format reader for UniProtXML files.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#UniProtXMLFormat()">UniProtXMLFormat()</a></span> - Constructor for class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd> </dd>
<dt><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.Terms.html" title="class in org.biojavax.bio.seq.io"><span class="strong">UniProtXMLFormat.Terms</span></a> - Class in <a href="./org/biojavax/bio/seq/io/package-summary.html">org.biojavax.bio.seq.io</a></dt>
<dd>
<div class="block">Implements some UniProtXML-specific terms.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.Terms.html#UniProtXMLFormat.Terms()">UniProtXMLFormat.Terms()</a></span> - Constructor for class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.Terms.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat.Terms</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Calc.html#unitVector(org.biojava.bio.structure.Atom)">unitVector(Atom)</a></span> - Static method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Calc.html" title="class in org.biojava.bio.structure">Calc</a></dt>
<dd>
<div class="block">return the unit vector of vector a .</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/TranslationTable.html#UNIVERSAL">UNIVERSAL</a></span> - Static variable in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/TranslationTable.html" title="interface in org.biojava.bio.symbol">TranslationTable</a></dt>
<dd>
<div class="block">Translation table name for the universal genetic code.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/AlignIOConstants.html#UNKNOWN">UNKNOWN</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/AlignIOConstants.html" title="class in org.biojava.bio.seq.io">AlignIOConstants</a></dt>
<dd>
<div class="block"><code>UNKNOWN</code> indicates that the alignment format is
unknown.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOConstants.html#UNKNOWN">UNKNOWN</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOConstants.html" title="class in org.biojava.bio.seq.io">SeqIOConstants</a></dt>
<dd>
<div class="block"><code>UNKNOWN</code> indicates that the sequence format is
unknown.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SymbolTokenization.html#UNKNOWN">UNKNOWN</a></span> - Static variable in interface org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SymbolTokenization.html" title="interface in org.biojava.bio.seq.io">SymbolTokenization</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/StrandedFeature.html#UNKNOWN">UNKNOWN</a></span> - Static variable in interface org.biojava.bio.seq.<a href="./org/biojava/bio/seq/StrandedFeature.html" title="interface in org.biojava.bio.seq">StrandedFeature</a></dt>
<dd>
<div class="block">Flag to indicate that a feature has an unknown strand.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/ChangeType.html#UNKNOWN">UNKNOWN</a></span> - Static variable in class org.biojava.utils.<a href="./org/biojava/utils/ChangeType.html" title="class in org.biojava.utils">ChangeType</a></dt>
<dd>
<div class="block">Constant ChangeType field which indicates that a change has
occured which can't otherwise be represented.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/StructureTools.html#UNKNOWN_GROUP_LABEL">UNKNOWN_GROUP_LABEL</a></span> - Static variable in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/StructureTools.html" title="class in org.biojava.bio.structure">StructureTools</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/Synonym.html#UNKNOWN_SCOPE">UNKNOWN_SCOPE</a></span> - Static variable in class org.biojava.ontology.<a href="./org/biojava/ontology/Synonym.html" title="class in org.biojava.ontology">Synonym</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichLocation.Strand.html#UNKNOWN_STRAND">UNKNOWN_STRAND</a></span> - Static variable in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichLocation.Strand.html" title="class in org.biojavax.bio.seq">RichLocation.Strand</a></dt>
<dd>
<div class="block">The unknown strand is represented by the symbol '?' and has the
number 0.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/db/biosql/UnknownDBHelper.html" title="class in org.biojava.bio.seq.db.biosql"><span class="strong">UnknownDBHelper</span></a> - Class in <a href="./org/biojava/bio/seq/db/biosql/package-summary.html">org.biojava.bio.seq.db.biosql</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>Use hibernate and org.biojavax.bio.db.*</i></div>
</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/biosql/UnknownDBHelper.html#UnknownDBHelper()">UnknownDBHelper()</a></span> - Constructor for class org.biojava.bio.seq.db.biosql.<a href="./org/biojava/bio/seq/db/biosql/UnknownDBHelper.html" title="class in org.biojava.bio.seq.db.biosql">UnknownDBHelper</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/DP.html#unlockModel()">unlockModel()</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/DP.html" title="class in org.biojava.bio.dp">DP</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SoftMaskedAlphabet.MaskingDetector.DefaultMaskingDetector.html#unmask(java.lang.String)">unmask(String)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SoftMaskedAlphabet.MaskingDetector.DefaultMaskingDetector.html" title="class in org.biojava.bio.symbol">SoftMaskedAlphabet.MaskingDetector.DefaultMaskingDetector</a></dt>
<dd>
<div class="block">Un-masks the token by making it upper case.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SoftMaskedAlphabet.MaskingDetector.html#unmask(java.lang.String)">unmask(String)</a></span> - Method in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SoftMaskedAlphabet.MaskingDetector.html" title="interface in org.biojava.bio.symbol">SoftMaskedAlphabet.MaskingDetector</a></dt>
<dd>
<div class="block">Present the token for a <code>Symbol</code> as it would appear if
it wasn't softmasked</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/DNAAmbPack.html#unpack(byte)">unpack(byte)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/DNAAmbPack.html" title="class in org.biojava.bio.symbol">DNAAmbPack</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/DNANoAmbPack.html#unpack(byte)">unpack(byte)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/DNANoAmbPack.html" title="class in org.biojava.bio.symbol">DNANoAmbPack</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/Packing.html#unpack(byte)">unpack(byte)</a></span> - Method in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/Packing.html" title="interface in org.biojava.bio.symbol">Packing</a></dt>
<dd>
<div class="block">
Return the symbol for a packing.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/unigene/UnigeneTools.html#unregisterFactory(org.biojava.bio.program.unigene.UnigeneFactory)">unregisterFactory(UnigeneFactory)</a></span> - Static method in class org.biojava.bio.program.unigene.<a href="./org/biojava/bio/program/unigene/UnigeneTools.html" title="class in org.biojava.bio.program.unigene">UnigeneTools</a></dt>
<dd>
<div class="block">Register a UnigeneFactory.</div>
</dd>
<dt><a href="./org/biojava/bio/chromatogram/UnsupportedChromatogramFormatException.html" title="class in org.biojava.bio.chromatogram"><span class="strong">UnsupportedChromatogramFormatException</span></a> - Exception in <a href="./org/biojava/bio/chromatogram/package-summary.html">org.biojava.bio.chromatogram</a></dt>
<dd>
<div class="block">Exception indicating that some provided data does not represent
a supported chromatogram format.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/UnsupportedChromatogramFormatException.html#UnsupportedChromatogramFormatException()">UnsupportedChromatogramFormatException()</a></span> - Constructor for exception org.biojava.bio.chromatogram.<a href="./org/biojava/bio/chromatogram/UnsupportedChromatogramFormatException.html" title="class in org.biojava.bio.chromatogram">UnsupportedChromatogramFormatException</a></dt>
<dd>
<div class="block">Create a new UnsupportedChromatogramFormatException.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/UnsupportedChromatogramFormatException.html#UnsupportedChromatogramFormatException(java.lang.String)">UnsupportedChromatogramFormatException(String)</a></span> - Constructor for exception org.biojava.bio.chromatogram.<a href="./org/biojava/bio/chromatogram/UnsupportedChromatogramFormatException.html" title="class in org.biojava.bio.chromatogram">UnsupportedChromatogramFormatException</a></dt>
<dd>
<div class="block">Create a new UnsupportedChromatogramFormatException with a message.</div>
</dd>
<dt><a href="./org/biojava/bio/dist/UntrainableDistribution.html" title="class in org.biojava.bio.dist"><span class="strong">UntrainableDistribution</span></a> - Class in <a href="./org/biojava/bio/dist/package-summary.html">org.biojava.bio.dist</a></dt>
<dd>
<div class="block">A distribution which does not interact with the training framework.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/UntrainableDistribution.html#UntrainableDistribution(org.biojava.bio.symbol.FiniteAlphabet)">UntrainableDistribution(FiniteAlphabet)</a></span> - Constructor for class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/UntrainableDistribution.html" title="class in org.biojava.bio.dist">UntrainableDistribution</a></dt>
<dd>
<div class="block">Construct a new untrainable distribution over the specified alphabet.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AbstractManyToOneTranslationTable.html#untranslate(org.biojava.bio.symbol.Symbol)">untranslate(Symbol)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AbstractManyToOneTranslationTable.html" title="class in org.biojava.bio.symbol">AbstractManyToOneTranslationTable</a></dt>
<dd>
<div class="block">returns a Set of Atomic Symbols that are the reverse translation
of the specified Symbol in the target alphabet.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AbstractReversibleTranslationTable.html#untranslate(org.biojava.bio.symbol.Symbol)">untranslate(Symbol)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AbstractReversibleTranslationTable.html" title="class in org.biojava.bio.symbol">AbstractReversibleTranslationTable</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/ManyToOneTranslationTable.html#untranslate(org.biojava.bio.symbol.Symbol)">untranslate(Symbol)</a></span> - Method in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/ManyToOneTranslationTable.html" title="interface in org.biojava.bio.symbol">ManyToOneTranslationTable</a></dt>
<dd>
<div class="block">Translate a single symbol from target alphabet to the source alphabet.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/ReversibleTranslationTable.html#untranslate(org.biojava.bio.symbol.Symbol)">untranslate(Symbol)</a></span> - Method in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/ReversibleTranslationTable.html" title="interface in org.biojava.bio.symbol">ReversibleTranslationTable</a></dt>
<dd>
<div class="block">Translate a single symbol from target alphabet to the source alphabet.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/DP.html#update()">update()</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/DP.html" title="class in org.biojava.bio.dp">DP</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/onehead/SingleDP.html#update()">update()</a></span> - Method in class org.biojava.bio.dp.onehead.<a href="./org/biojava/bio/dp/onehead/SingleDP.html" title="class in org.biojava.bio.dp.onehead">SingleDP</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/twohead/PairwiseDP.html#update()">update()</a></span> - Method in class org.biojava.bio.dp.twohead.<a href="./org/biojava/bio/dp/twohead/PairwiseDP.html" title="class in org.biojava.bio.dp.twohead">PairwiseDP</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/utils/CRC64Checksum.html#update(int)">update(int)</a></span> - Method in class org.biojavax.utils.<a href="./org/biojavax/utils/CRC64Checksum.html" title="class in org.biojavax.utils">CRC64Checksum</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/utils/CRC64Checksum.html#update(byte[], int, int)">update(byte[], int, int)</a></span> - Method in class org.biojavax.utils.<a href="./org/biojavax/utils/CRC64Checksum.html" title="class in org.biojavax.utils">CRC64Checksum</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/utils/CRC64Checksum.html#update(java.lang.String)">update(String)</a></span> - Method in class org.biojavax.utils.<a href="./org/biojavax/utils/CRC64Checksum.html" title="class in org.biojavax.utils">CRC64Checksum</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/INSDseqFormat.html#UPDATE_DATE_TAG">UPDATE_DATE_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/INSDseqFormat.html" title="class in org.biojavax.bio.seq.io">INSDseqFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/INSDseqFormat.html#UPDATE_REL_TAG">UPDATE_REL_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/INSDseqFormat.html" title="class in org.biojavax.bio.seq.io">INSDseqFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/SequenceDisplay.html#updateDisplay()">updateDisplay()</a></span> - Method in class org.biojava.bio.structure.gui.<a href="./org/biojava/bio/structure/gui/SequenceDisplay.html" title="class in org.biojava.bio.structure.gui">SequenceDisplay</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SequenceBuilderBase.html#uri">uri</a></span> - Variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SequenceBuilderBase.html" title="class in org.biojava.bio.seq.io">SequenceBuilderBase</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/Namespace.html#URI">URI</a></span> - Static variable in interface org.biojavax.<a href="./org/biojavax/Namespace.html" title="interface in org.biojavax">Namespace</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FeatureTypes.html#URI_PREFIX">URI_PREFIX</a></span> - Static variable in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FeatureTypes.html" title="class in org.biojava.bio.seq">FeatureTypes</a></dt>
<dd>
<div class="block">The standard prefix for all type URIs</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BiblioWebResource.html#url">url</a></span> - Variable in class org.biojava.bibliography.<a href="./org/biojava/bibliography/BiblioWebResource.html" title="class in org.biojava.bibliography">BiblioWebResource</a></dt>
<dd>
<div class="block">The URL of the resource.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/GenbankSequenceDB.html#urlBatchSequences">urlBatchSequences</a></span> - Static variable in class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/GenbankSequenceDB.html" title="class in org.biojava.bio.seq.db">GenbankSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/ncbi/GenbankRichSequenceDB.html#urlBatchSequences">urlBatchSequences</a></span> - Static variable in class org.biojavax.bio.db.ncbi.<a href="./org/biojavax/bio/db/ncbi/GenbankRichSequenceDB.html" title="class in org.biojavax.bio.db.ncbi">GenbankRichSequenceDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/ncbi/GenpeptRichSequenceDB.html#urlBatchSequences">urlBatchSequences</a></span> - Static variable in class org.biojavax.bio.db.ncbi.<a href="./org/biojavax/bio/db/ncbi/GenpeptRichSequenceDB.html" title="class in org.biojavax.bio.db.ncbi">GenpeptRichSequenceDB</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/utils/net/URLFactory.html" title="interface in org.biojava.utils.net"><span class="strong">URLFactory</span></a> - Interface in <a href="./org/biojava/utils/net/package-summary.html">org.biojava.utils.net</a></dt>
<dd>
<div class="block"><code>URLFactory</code> defines a means of obtaining a URL
associated with an object.</div>
</dd>
<dt><a href="./org/biojava/bio/program/blast2html/URLGeneratorFactory.html" title="interface in org.biojava.bio.program.blast2html"><span class="strong">URLGeneratorFactory</span></a> - Interface in <a href="./org/biojava/bio/program/blast2html/package-summary.html">org.biojava.bio.program.blast2html</a></dt>
<dd>
<div class="block">Interface for a factory method to return a list of
0, 1 or more <code>DatabaseURLGenerator</code> instances.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/molbio/RestrictionEnzyme.html#usCutPositions">usCutPositions</a></span> - Variable in class org.biojava.bio.molbio.<a href="./org/biojava/bio/molbio/RestrictionEnzyme.html" title="class in org.biojava.bio.molbio">RestrictionEnzyme</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.Option.html#USE_CUSTOM_STROKE">USE_CUSTOM_STROKE</a></span> - Static variable in class org.biojava.bio.chromatogram.graphic.<a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.Option.html" title="class in org.biojava.bio.chromatogram.graphic">ChromatogramGraphic.Option</a></dt>
<dd>
<div class="block">Option indicating whether to use custom strokes when
drawing traces and separators.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.Option.html#USE_PER_SHAPE_TRANSFORM">USE_PER_SHAPE_TRANSFORM</a></span> - Static variable in class org.biojava.bio.chromatogram.graphic.<a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.Option.html" title="class in org.biojava.bio.chromatogram.graphic">ChromatogramGraphic.Option</a></dt>
<dd>
<div class="block">Option indicating whether to apply scaling and translation
transforms to each shape individually or to apply a single
transform to the graphics context.</div>
</dd>
<dt><a href="./org/biojava/bio/gui/sequence/tracklayout/UserDefinedTrackLayout.html" title="class in org.biojava.bio.gui.sequence.tracklayout"><span class="strong">UserDefinedTrackLayout</span></a> - Class in <a href="./org/biojava/bio/gui/sequence/tracklayout/package-summary.html">org.biojava.bio.gui.sequence.tracklayout</a></dt>
<dd>
<div class="block">An implementation of TrackLayout that that wraps a sequence over an arbitrary set of ranges</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/tracklayout/UserDefinedTrackLayout.html#UserDefinedTrackLayout(org.biojava.bio.symbol.RangeLocation[])">UserDefinedTrackLayout(RangeLocation[])</a></span> - Constructor for class org.biojava.bio.gui.sequence.tracklayout.<a href="./org/biojava/bio/gui/sequence/tracklayout/UserDefinedTrackLayout.html" title="class in org.biojava.bio.gui.sequence.tracklayout">UserDefinedTrackLayout</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/ChunkedSymbolListFactory.html#useSuppliedSymListFactory()">useSuppliedSymListFactory()</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/ChunkedSymbolListFactory.html" title="class in org.biojava.bio.seq.io">ChunkedSymbolListFactory</a></dt>
<dd>
<div class="block">Call this to convert from default SymbolList implementation
to user-supplied implementation.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/agave/UtilHelper.html" title="class in org.biojava.bio.seq.io.agave"><span class="strong">UtilHelper</span></a> - Class in <a href="./org/biojava/bio/seq/io/agave/package-summary.html">org.biojava.bio.seq.io.agave</a></dt>
<dd>
<div class="block">Just make the property follow the common case</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/UtilHelper.html#UtilHelper()">UtilHelper()</a></span> - Constructor for class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/UtilHelper.html" title="class in org.biojava.bio.seq.io.agave">UtilHelper</a></dt>
<dd> </dd>
</dl>
<a name="_V_">
<!-- -->
</a>
<h2 class="title">V</h2>
<dl>
<dt><span class="strong"><a href="./org/biojava/bio/seq/DNATools.html#v()">v()</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/DNATools.html" title="class in org.biojava.bio.seq">DNATools</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/NucleotideTools.html#v()">v()</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/NucleotideTools.html" title="class in org.biojava.bio.seq">NucleotideTools</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/ProteinTools.html#v()">v()</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/ProteinTools.html" title="class in org.biojava.bio.seq">ProteinTools</a></dt>
<dd>
<div class="block">Returns the <code>AtomicSymbol</code> for the amino acid
Valine</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/ProteinTools.html#val()">val()</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/ProteinTools.html" title="class in org.biojava.bio.seq">ProteinTools</a></dt>
<dd>
<div class="block">Returns the <code>AtomicSymbol</code> for the amino acid Valine (V)</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/fastq/IlluminaFastqWriter.html#validate(org.biojava.bio.program.fastq.Fastq)">validate(Fastq)</a></span> - Method in class org.biojava.bio.program.fastq.<a href="./org/biojava/bio/program/fastq/IlluminaFastqWriter.html" title="class in org.biojava.bio.program.fastq">IlluminaFastqWriter</a></dt>
<dd>
<div class="block">Validate the specified FASTQ formatted sequence for writing.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/fastq/SangerFastqWriter.html#validate(org.biojava.bio.program.fastq.Fastq)">validate(Fastq)</a></span> - Method in class org.biojava.bio.program.fastq.<a href="./org/biojava/bio/program/fastq/SangerFastqWriter.html" title="class in org.biojava.bio.program.fastq">SangerFastqWriter</a></dt>
<dd>
<div class="block">Validate the specified FASTQ formatted sequence for writing.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/fastq/SolexaFastqWriter.html#validate(org.biojava.bio.program.fastq.Fastq)">validate(Fastq)</a></span> - Method in class org.biojava.bio.program.fastq.<a href="./org/biojava/bio/program/fastq/SolexaFastqWriter.html" title="class in org.biojava.bio.program.fastq">SolexaFastqWriter</a></dt>
<dd>
<div class="block">Validate the specified FASTQ formatted sequence for writing.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/AbstractAlphabet.html#validate(org.biojava.bio.symbol.Symbol)">validate(Symbol)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/AbstractAlphabet.html" title="class in org.biojava.bio.symbol">AbstractAlphabet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/Alphabet.html#validate(org.biojava.bio.symbol.Symbol)">validate(Symbol)</a></span> - Method in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/Alphabet.html" title="interface in org.biojava.bio.symbol">Alphabet</a></dt>
<dd>
<div class="block">
Throws a precanned IllegalSymbolException if the symbol is not contained
within this Alphabet.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/DoubleAlphabet.SubDoubleAlphabet.html#validate(org.biojava.bio.symbol.Symbol)">validate(Symbol)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/DoubleAlphabet.SubDoubleAlphabet.html" title="class in org.biojava.bio.symbol">DoubleAlphabet.SubDoubleAlphabet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/DoubleAlphabet.html#validate(org.biojava.bio.symbol.Symbol)">validate(Symbol)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/DoubleAlphabet.html" title="class in org.biojava.bio.symbol">DoubleAlphabet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/IntegerAlphabet.html#validate(org.biojava.bio.symbol.Symbol)">validate(Symbol)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/IntegerAlphabet.html" title="class in org.biojava.bio.symbol">IntegerAlphabet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SoftMaskedAlphabet.html#validate(org.biojava.bio.symbol.Symbol)">validate(Symbol)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SoftMaskedAlphabet.html" title="class in org.biojava.bio.symbol">SoftMaskedAlphabet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/CollectionConstraint.AllValuesIn.html#validateAddValue(java.util.Collection, java.lang.Object)">validateAddValue(Collection, Object)</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/CollectionConstraint.AllValuesIn.html" title="class in org.biojava.bio">CollectionConstraint.AllValuesIn</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/CollectionConstraint.And.html#validateAddValue(java.util.Collection, java.lang.Object)">validateAddValue(Collection, Object)</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/CollectionConstraint.And.html" title="class in org.biojava.bio">CollectionConstraint.And</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/CollectionConstraint.Contains.html#validateAddValue(java.util.Collection, java.lang.Object)">validateAddValue(Collection, Object)</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/CollectionConstraint.Contains.html" title="class in org.biojava.bio">CollectionConstraint.Contains</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/CollectionConstraint.Or.html#validateAddValue(java.util.Collection, java.lang.Object)">validateAddValue(Collection, Object)</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/CollectionConstraint.Or.html" title="class in org.biojava.bio">CollectionConstraint.Or</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/CollectionConstraint.html#validateAddValue(java.util.Collection, java.lang.Object)">validateAddValue(Collection, Object)</a></span> - Method in interface org.biojava.bio.<a href="./org/biojava/bio/CollectionConstraint.html" title="interface in org.biojava.bio">CollectionConstraint</a></dt>
<dd>
<div class="block">Return <code>true</code> iff the Collection formed by adding
<code>newValue</code> to <code>current</code> would be accepted
by this constraint.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/fastq/IlluminaFastqReader.html#validateDescription(org.biojava.bio.program.fastq.FastqBuilder, java.lang.String, int)">validateDescription(FastqBuilder, String, int)</a></span> - Method in class org.biojava.bio.program.fastq.<a href="./org/biojava/bio/program/fastq/IlluminaFastqReader.html" title="class in org.biojava.bio.program.fastq">IlluminaFastqReader</a></dt>
<dd>
<div class="block">Validate the specified description.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/fastq/SangerFastqReader.html#validateDescription(org.biojava.bio.program.fastq.FastqBuilder, java.lang.String, int)">validateDescription(FastqBuilder, String, int)</a></span> - Method in class org.biojava.bio.program.fastq.<a href="./org/biojava/bio/program/fastq/SangerFastqReader.html" title="class in org.biojava.bio.program.fastq">SangerFastqReader</a></dt>
<dd>
<div class="block">Validate the specified description.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/fastq/SolexaFastqReader.html#validateDescription(org.biojava.bio.program.fastq.FastqBuilder, java.lang.String, int)">validateDescription(FastqBuilder, String, int)</a></span> - Method in class org.biojava.bio.program.fastq.<a href="./org/biojava/bio/program/fastq/SolexaFastqReader.html" title="class in org.biojava.bio.program.fastq">SolexaFastqReader</a></dt>
<dd>
<div class="block">Validate the specified description.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/fastq/IlluminaFastqReader.html#validateQuality(org.biojava.bio.program.fastq.FastqBuilder, java.lang.String, int)">validateQuality(FastqBuilder, String, int)</a></span> - Method in class org.biojava.bio.program.fastq.<a href="./org/biojava/bio/program/fastq/IlluminaFastqReader.html" title="class in org.biojava.bio.program.fastq">IlluminaFastqReader</a></dt>
<dd>
<div class="block">Validate the specified quality scores.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/fastq/SangerFastqReader.html#validateQuality(org.biojava.bio.program.fastq.FastqBuilder, java.lang.String, int)">validateQuality(FastqBuilder, String, int)</a></span> - Method in class org.biojava.bio.program.fastq.<a href="./org/biojava/bio/program/fastq/SangerFastqReader.html" title="class in org.biojava.bio.program.fastq">SangerFastqReader</a></dt>
<dd>
<div class="block">Validate the specified quality scores.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/fastq/SolexaFastqReader.html#validateQuality(org.biojava.bio.program.fastq.FastqBuilder, java.lang.String, int)">validateQuality(FastqBuilder, String, int)</a></span> - Method in class org.biojava.bio.program.fastq.<a href="./org/biojava/bio/program/fastq/SolexaFastqReader.html" title="class in org.biojava.bio.program.fastq">SolexaFastqReader</a></dt>
<dd>
<div class="block">Validate the specified quality scores.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/CollectionConstraint.AllValuesIn.html#validateRemoveValue(java.util.Collection, java.lang.Object)">validateRemoveValue(Collection, Object)</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/CollectionConstraint.AllValuesIn.html" title="class in org.biojava.bio">CollectionConstraint.AllValuesIn</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/CollectionConstraint.And.html#validateRemoveValue(java.util.Collection, java.lang.Object)">validateRemoveValue(Collection, Object)</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/CollectionConstraint.And.html" title="class in org.biojava.bio">CollectionConstraint.And</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/CollectionConstraint.Contains.html#validateRemoveValue(java.util.Collection, java.lang.Object)">validateRemoveValue(Collection, Object)</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/CollectionConstraint.Contains.html" title="class in org.biojava.bio">CollectionConstraint.Contains</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/CollectionConstraint.Or.html#validateRemoveValue(java.util.Collection, java.lang.Object)">validateRemoveValue(Collection, Object)</a></span> - Method in class org.biojava.bio.<a href="./org/biojava/bio/CollectionConstraint.Or.html" title="class in org.biojava.bio">CollectionConstraint.Or</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/CollectionConstraint.html#validateRemoveValue(java.util.Collection, java.lang.Object)">validateRemoveValue(Collection, Object)</a></span> - Method in interface org.biojava.bio.<a href="./org/biojava/bio/CollectionConstraint.html" title="interface in org.biojava.bio">CollectionConstraint</a></dt>
<dd>
<div class="block">Return <code>true</code> iff the Collection formed by removing
<code>newValue</code> from <code>current</code> would be accepted
by this constraint.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/fastq/IlluminaFastqReader.html#validateRepeatDescription(org.biojava.bio.program.fastq.FastqBuilder, java.lang.String, int)">validateRepeatDescription(FastqBuilder, String, int)</a></span> - Method in class org.biojava.bio.program.fastq.<a href="./org/biojava/bio/program/fastq/IlluminaFastqReader.html" title="class in org.biojava.bio.program.fastq">IlluminaFastqReader</a></dt>
<dd>
<div class="block">Validate the specified repeat description.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/fastq/SangerFastqReader.html#validateRepeatDescription(org.biojava.bio.program.fastq.FastqBuilder, java.lang.String, int)">validateRepeatDescription(FastqBuilder, String, int)</a></span> - Method in class org.biojava.bio.program.fastq.<a href="./org/biojava/bio/program/fastq/SangerFastqReader.html" title="class in org.biojava.bio.program.fastq">SangerFastqReader</a></dt>
<dd>
<div class="block">Validate the specified repeat description.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/fastq/SolexaFastqReader.html#validateRepeatDescription(org.biojava.bio.program.fastq.FastqBuilder, java.lang.String, int)">validateRepeatDescription(FastqBuilder, String, int)</a></span> - Method in class org.biojava.bio.program.fastq.<a href="./org/biojava/bio/program/fastq/SolexaFastqReader.html" title="class in org.biojava.bio.program.fastq">SolexaFastqReader</a></dt>
<dd>
<div class="block">Validate the specified repeat description.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/fastq/IlluminaFastqReader.html#validateSequence(org.biojava.bio.program.fastq.FastqBuilder, java.lang.String, int)">validateSequence(FastqBuilder, String, int)</a></span> - Method in class org.biojava.bio.program.fastq.<a href="./org/biojava/bio/program/fastq/IlluminaFastqReader.html" title="class in org.biojava.bio.program.fastq">IlluminaFastqReader</a></dt>
<dd>
<div class="block">Validate the specified sequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/fastq/SangerFastqReader.html#validateSequence(org.biojava.bio.program.fastq.FastqBuilder, java.lang.String, int)">validateSequence(FastqBuilder, String, int)</a></span> - Method in class org.biojava.bio.program.fastq.<a href="./org/biojava/bio/program/fastq/SangerFastqReader.html" title="class in org.biojava.bio.program.fastq">SangerFastqReader</a></dt>
<dd>
<div class="block">Validate the specified sequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/fastq/SolexaFastqReader.html#validateSequence(org.biojava.bio.program.fastq.FastqBuilder, java.lang.String, int)">validateSequence(FastqBuilder, String, int)</a></span> - Method in class org.biojava.bio.program.fastq.<a href="./org/biojava/bio/program/fastq/SolexaFastqReader.html" title="class in org.biojava.bio.program.fastq">SolexaFastqReader</a></dt>
<dd>
<div class="block">Validate the specified sequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/io/CachingInputStream.html#validLen">validLen</a></span> - Variable in class org.biojava.utils.io.<a href="./org/biojava/utils/io/CachingInputStream.html" title="class in org.biojava.utils.io">CachingInputStream</a></dt>
<dd>
<div class="block">A count of the number of bytes in <a href="./org/biojava/utils/io/CachingInputStream.html#cache"><code>CachingInputStream.cache</code></a> that contain
data read from the stream.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/AbstractWrapper.html#value(org.biojava.bio.program.tagvalue.TagValueContext, java.lang.Object)">value(TagValueContext, Object)</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/AbstractWrapper.html" title="class in org.biojava.bio.program.tagvalue">AbstractWrapper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/Aggregator.html#value(org.biojava.bio.program.tagvalue.TagValueContext, java.lang.Object)">value(TagValueContext, Object)</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/Aggregator.html" title="class in org.biojava.bio.program.tagvalue">Aggregator</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/AnnotationBuilder.html#value(org.biojava.bio.program.tagvalue.TagValueContext, java.lang.Object)">value(TagValueContext, Object)</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/AnnotationBuilder.html" title="class in org.biojava.bio.program.tagvalue">AnnotationBuilder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/Echo.html#value(org.biojava.bio.program.tagvalue.TagValueContext, java.lang.Object)">value(TagValueContext, Object)</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/Echo.html" title="class in org.biojava.bio.program.tagvalue">Echo</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/Indexer.html#value(org.biojava.bio.program.tagvalue.TagValueContext, java.lang.Object)">value(TagValueContext, Object)</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/Indexer.html" title="class in org.biojava.bio.program.tagvalue">Indexer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/Indexer2.html#value(org.biojava.bio.program.tagvalue.TagValueContext, java.lang.Object)">value(TagValueContext, Object)</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/Indexer2.html" title="class in org.biojava.bio.program.tagvalue">Indexer2</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/MultiTagger.html#value(org.biojava.bio.program.tagvalue.TagValueContext, java.lang.Object)">value(TagValueContext, Object)</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/MultiTagger.html" title="class in org.biojava.bio.program.tagvalue">MultiTagger</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/RegexFieldFinder.html#value(org.biojava.bio.program.tagvalue.TagValueContext, java.lang.Object)">value(TagValueContext, Object)</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/RegexFieldFinder.html" title="class in org.biojava.bio.program.tagvalue">RegexFieldFinder</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/SimpleTagValueWrapper.html#value(org.biojava.bio.program.tagvalue.TagValueContext, java.lang.Object)">value(TagValueContext, Object)</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/SimpleTagValueWrapper.html" title="class in org.biojava.bio.program.tagvalue">SimpleTagValueWrapper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/StateMachine.SimpleStateListener.html#value(org.biojava.bio.program.tagvalue.TagValueContext, java.lang.Object)">value(TagValueContext, Object)</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/StateMachine.SimpleStateListener.html" title="class in org.biojava.bio.program.tagvalue">StateMachine.SimpleStateListener</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/StateMachine.html#value(org.biojava.bio.program.tagvalue.TagValueContext, java.lang.Object)">value(TagValueContext, Object)</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/StateMachine.html" title="class in org.biojava.bio.program.tagvalue">StateMachine</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/TagDelegator.html#value(org.biojava.bio.program.tagvalue.TagValueContext, java.lang.Object)">value(TagValueContext, Object)</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/TagDelegator.html" title="class in org.biojava.bio.program.tagvalue">TagDelegator</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/TagDropper.html#value(org.biojava.bio.program.tagvalue.TagValueContext, java.lang.Object)">value(TagValueContext, Object)</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/TagDropper.html" title="class in org.biojava.bio.program.tagvalue">TagDropper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/TagValueListener.html#value(org.biojava.bio.program.tagvalue.TagValueContext, java.lang.Object)">value(TagValueContext, Object)</a></span> - Method in interface org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/TagValueListener.html" title="interface in org.biojava.bio.program.tagvalue">TagValueListener</a></dt>
<dd>
<div class="block">A value has been seen.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/ValueChanger.html#value(org.biojava.bio.program.tagvalue.TagValueContext, java.lang.Object)">value(TagValueContext, Object)</a></span> - Method in class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/ValueChanger.html" title="class in org.biojava.bio.program.tagvalue">ValueChanger</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/align/helper/GapArray.html#value">value</a></span> - Variable in class org.biojava.bio.structure.align.helper.<a href="./org/biojava/bio/structure/align/helper/GapArray.html" title="class in org.biojava.bio.structure.align.helper">GapArray</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/Note.html#VALUE">VALUE</a></span> - Static variable in interface org.biojavax.<a href="./org/biojavax/Note.html" title="interface in org.biojavax">Note</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#VALUE_ATTR">VALUE_ATTR</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/tagvalue/ValueChanger.html" title="class in org.biojava.bio.program.tagvalue"><span class="strong">ValueChanger</span></a> - Class in <a href="./org/biojava/bio/program/tagvalue/package-summary.html">org.biojava.bio.program.tagvalue</a></dt>
<dd>
<div class="block">
Intercept the values associated with some tags and change them
systematically.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/ValueChanger.html#ValueChanger(org.biojava.bio.program.tagvalue.TagValueListener)">ValueChanger(TagValueListener)</a></span> - Constructor for class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/ValueChanger.html" title="class in org.biojava.bio.program.tagvalue">ValueChanger</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/tagvalue/ValueChanger.html#ValueChanger(org.biojava.bio.program.tagvalue.TagValueListener, org.biojava.bio.program.tagvalue.ChangeTable)">ValueChanger(TagValueListener, ChangeTable)</a></span> - Constructor for class org.biojava.bio.program.tagvalue.<a href="./org/biojava/bio/program/tagvalue/ValueChanger.html" title="class in org.biojava.bio.program.tagvalue">ValueChanger</a></dt>
<dd>
<div class="block">Create a new changer that will pass the modified event stream to a
delegate.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/EcNumber.Impl.html#valueOf(java.lang.String)">valueOf(String)</a></span> - Static method in class org.biojava.bio.<a href="./org/biojava/bio/EcNumber.Impl.html" title="class in org.biojava.bio">EcNumber.Impl</a></dt>
<dd>
<div class="block">Process a string into an EcNumber.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/fastq/FastqVariant.html#valueOf(java.lang.String)">valueOf(String)</a></span> - Static method in enum org.biojava.bio.program.fastq.<a href="./org/biojava/bio/program/fastq/FastqVariant.html" title="enum in org.biojava.bio.program.fastq">FastqVariant</a></dt>
<dd>
<div class="block">Returns the enum constant of this type with the specified name.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/chem/PolymerType.html#valueOf(java.lang.String)">valueOf(String)</a></span> - Static method in enum org.biojava.bio.structure.io.mmcif.chem.<a href="./org/biojava/bio/structure/io/mmcif/chem/PolymerType.html" title="enum in org.biojava.bio.structure.io.mmcif.chem">PolymerType</a></dt>
<dd>
<div class="block">Returns the enum constant of this type with the specified name.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/chem/ResidueType.html#valueOf(java.lang.String)">valueOf(String)</a></span> - Static method in enum org.biojava.bio.structure.io.mmcif.chem.<a href="./org/biojava/bio/structure/io/mmcif/chem/ResidueType.html" title="enum in org.biojava.bio.structure.io.mmcif.chem">ResidueType</a></dt>
<dd>
<div class="block">Returns the enum constant of this type with the specified name.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/lsid/LifeScienceIdentifier.html#valueOf(java.lang.String)">valueOf(String)</a></span> - Static method in class org.biojava.utils.lsid.<a href="./org/biojava/utils/lsid/LifeScienceIdentifier.html" title="class in org.biojava.utils.lsid">LifeScienceIdentifier</a></dt>
<dd>
<div class="block">Create a new LifeScienceIdentifier parsed
from the properly formatted string <code>lsid</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/lsid/LifeScienceIdentifier.html#valueOf(java.lang.String, java.lang.String, java.lang.String, java.lang.String)">valueOf(String, String, String, String)</a></span> - Static method in class org.biojava.utils.lsid.<a href="./org/biojava/utils/lsid/LifeScienceIdentifier.html" title="class in org.biojava.utils.lsid">LifeScienceIdentifier</a></dt>
<dd>
<div class="block">Create a new LifeScienceIdentifier from the
specified parameters.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/lsid/LifeScienceIdentifier.html#valueOf(java.lang.String, java.lang.String, java.lang.String)">valueOf(String, String, String)</a></span> - Static method in class org.biojava.utils.lsid.<a href="./org/biojava/utils/lsid/LifeScienceIdentifier.html" title="class in org.biojava.utils.lsid">LifeScienceIdentifier</a></dt>
<dd>
<div class="block">Create a new LifeScienceIdentifier from the
specified parameters.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/LabelledSequenceRenderer.html#VALUES">VALUES</a></span> - Static variable in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/LabelledSequenceRenderer.html" title="class in org.biojava.bio.gui.sequence">LabelledSequenceRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/fastq/FastqVariant.html#values()">values()</a></span> - Static method in enum org.biojava.bio.program.fastq.<a href="./org/biojava/bio/program/fastq/FastqVariant.html" title="enum in org.biojava.bio.program.fastq">FastqVariant</a></dt>
<dd>
<div class="block">Returns an array containing the constants of this enum type, in
the order they are declared.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/chem/PolymerType.html#values()">values()</a></span> - Static method in enum org.biojava.bio.structure.io.mmcif.chem.<a href="./org/biojava/bio/structure/io/mmcif/chem/PolymerType.html" title="enum in org.biojava.bio.structure.io.mmcif.chem">PolymerType</a></dt>
<dd>
<div class="block">Returns an array containing the constants of this enum type, in
the order they are declared.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/io/mmcif/chem/ResidueType.html#values()">values()</a></span> - Static method in enum org.biojava.bio.structure.io.mmcif.chem.<a href="./org/biojava/bio/structure/io/mmcif/chem/ResidueType.html" title="enum in org.biojava.bio.structure.io.mmcif.chem">ResidueType</a></dt>
<dd>
<div class="block">Returns an array containing the constants of this enum type, in
the order they are declared.</div>
</dd>
<dt><a href="./org/biojava/ontology/Variable.html" title="interface in org.biojava.ontology"><span class="strong">Variable</span></a> - Interface in <a href="./org/biojava/ontology/package-summary.html">org.biojava.ontology</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/ontology/Variable.Impl.html" title="class in org.biojava.ontology"><span class="strong">Variable.Impl</span></a> - Class in <a href="./org/biojava/ontology/package-summary.html">org.biojava.ontology</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/Variable.Impl.html#Variable.Impl(org.biojava.ontology.Ontology, java.lang.String, java.lang.String)">Variable.Impl(Ontology, String, String)</a></span> - Constructor for class org.biojava.ontology.<a href="./org/biojava/ontology/Variable.Impl.html" title="class in org.biojava.ontology">Variable.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/ontology/Variable.Impl.html#Variable.Impl(org.biojava.ontology.Ontology, java.lang.String, java.lang.String, java.lang.Object[])">Variable.Impl(Ontology, String, String, Object[])</a></span> - Constructor for class org.biojava.ontology.<a href="./org/biojava/ontology/Variable.Impl.html" title="class in org.biojava.ontology">Variable.Impl</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/Calc.html#vectorProduct(org.biojava.bio.structure.Atom, org.biojava.bio.structure.Atom)">vectorProduct(Atom, Atom)</a></span> - Static method in class org.biojava.bio.structure.<a href="./org/biojava/bio/structure/Calc.html" title="class in org.biojava.bio.structure">Calc</a></dt>
<dd>
<div class="block">Vector product .</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/tools/SVM_Light.html#vectorToString(org.biojava.stats.svm.SparseVector)">vectorToString(SparseVector)</a></span> - Static method in class org.biojava.stats.svm.tools.<a href="./org/biojava/stats/svm/tools/SVM_Light.html" title="class in org.biojava.stats.svm.tools">SVM_Light</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/EmblLikeFormat.html#VERSION_TAG">VERSION_TAG</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/EmblLikeFormat.html" title="class in org.biojava.bio.seq.io">EmblLikeFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/GenbankFormat.html#VERSION_TAG">VERSION_TAG</a></span> - Static variable in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/GenbankFormat.html" title="class in org.biojava.bio.seq.io">GenbankFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLFormat.html#VERSION_TAG">VERSION_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLFormat.html" title="class in org.biojavax.bio.seq.io">EMBLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/GenbankFormat.html#VERSION_TAG">VERSION_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/GenbankFormat.html" title="class in org.biojavax.bio.seq.io">GenbankFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/TranslationTable.html#VERT_MITO">VERT_MITO</a></span> - Static variable in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/TranslationTable.html" title="interface in org.biojava.bio.symbol">TranslationTable</a></dt>
<dd>
<div class="block">Translation table name for the vertebrate mitochondrial genetic
code.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/SequenceTools.html#view(org.biojava.bio.seq.Sequence)">view(Sequence)</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/SequenceTools.html" title="class in org.biojava.bio.seq">SequenceTools</a></dt>
<dd>
<div class="block">Create a new sequence that has all of the data in the original, but allows
new features and top-level annotations to be added independantly.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/SequenceTools.html#view(org.biojava.bio.seq.Sequence, java.lang.String)">view(Sequence, String)</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/SequenceTools.html" title="class in org.biojava.bio.seq">SequenceTools</a></dt>
<dd>
<div class="block">Create a new sequence that has all of the data in the original, but allows
new features and top-level annotations to be added independantly.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/SequenceTools.html#view(org.biojava.bio.seq.Sequence, org.biojava.bio.seq.FeatureRealizer)">view(Sequence, FeatureRealizer)</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/SequenceTools.html" title="class in org.biojava.bio.seq">SequenceTools</a></dt>
<dd>
<div class="block">Creates a new Sequence with the data of the old but with a different
FeatureRealizer that will be applied to new Features.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleGappedSymbolList.Block.html#viewEnd">viewEnd</a></span> - Variable in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleGappedSymbolList.Block.html" title="class in org.biojava.bio.symbol">SimpleGappedSymbolList.Block</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/structure/gui/BiojavaJmol.html#viewer">viewer</a></span> - Static variable in class org.biojava.bio.structure.gui.<a href="./org/biojava/bio/structure/gui/BiojavaJmol.html" title="class in org.biojava.bio.structure.gui">BiojavaJmol</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/db/ViewingSequenceDB.html" title="class in org.biojava.bio.seq.db"><span class="strong">ViewingSequenceDB</span></a> - Class in <a href="./org/biojava/bio/seq/db/package-summary.html">org.biojava.bio.seq.db</a></dt>
<dd>
<div class="block">SequenceDB implementation that returns new SequenceView instances
wrapping the sequences in an underlying database.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/ViewingSequenceDB.html#ViewingSequenceDB(org.biojava.bio.seq.db.SequenceDB)">ViewingSequenceDB(SequenceDB)</a></span> - Constructor for class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/ViewingSequenceDB.html" title="class in org.biojava.bio.seq.db">ViewingSequenceDB</a></dt>
<dd>
<div class="block">Create a new ViewingSequenceDB that views the sequences in parent.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/impl/ViewSequence.html" title="class in org.biojava.bio.seq.impl"><span class="strong">ViewSequence</span></a> - Class in <a href="./org/biojava/bio/seq/impl/package-summary.html">org.biojava.bio.seq.impl</a></dt>
<dd>
<div class="block">A view onto another Sequence object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/ViewSequence.html#ViewSequence(org.biojava.bio.seq.Sequence, java.lang.String)">ViewSequence(Sequence, String)</a></span> - Constructor for class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/ViewSequence.html" title="class in org.biojava.bio.seq.impl">ViewSequence</a></dt>
<dd>
<div class="block">Construct a view onto an existing sequence and give it a new
name.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/ViewSequence.html#ViewSequence(org.biojava.bio.seq.Sequence)">ViewSequence(Sequence)</a></span> - Constructor for class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/ViewSequence.html" title="class in org.biojava.bio.seq.impl">ViewSequence</a></dt>
<dd>
<div class="block">Construct a view onto an existing sequence which takes on that
sequence's name.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/impl/ViewSequence.html#ViewSequence(org.biojava.bio.seq.Sequence, org.biojava.bio.seq.FeatureRealizer)">ViewSequence(Sequence, FeatureRealizer)</a></span> - Constructor for class org.biojava.bio.seq.impl.<a href="./org/biojava/bio/seq/impl/ViewSequence.html" title="class in org.biojava.bio.seq.impl">ViewSequence</a></dt>
<dd>
<div class="block">Construct a view onto a sequence, using a specific FeatureRealizer.</div>
</dd>
<dt><a href="./org/biojava/bio/program/ssbind/ViewSequenceFactory.html" title="class in org.biojava.bio.program.ssbind"><span class="strong">ViewSequenceFactory</span></a> - Class in <a href="./org/biojava/bio/program/ssbind/package-summary.html">org.biojava.bio.program.ssbind</a></dt>
<dd>
<div class="block"><code>ViewSequenceFactory</code> is a base class for creating
search handlers which create and cache views on the query and
subject sequences.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/ssbind/ViewSequenceFactory.html#ViewSequenceFactory()">ViewSequenceFactory()</a></span> - Constructor for class org.biojava.bio.program.ssbind.<a href="./org/biojava/bio/program/ssbind/ViewSequenceFactory.html" title="class in org.biojava.bio.program.ssbind">ViewSequenceFactory</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleGappedSymbolList.Block.html#viewStart">viewStart</a></span> - Variable in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleGappedSymbolList.Block.html" title="class in org.biojava.bio.symbol">SimpleGappedSymbolList.Block</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/GappedSymbolList.html#viewToSource(int)">viewToSource(int)</a></span> - Method in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/GappedSymbolList.html" title="interface in org.biojava.bio.symbol">GappedSymbolList</a></dt>
<dd>
<div class="block">Coordinate conversion from view to source.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleGappedSymbolList.html#viewToSource(org.biojava.bio.symbol.SimpleGappedSymbolList.Block, int)">viewToSource(SimpleGappedSymbolList.Block, int)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleGappedSymbolList.html" title="class in org.biojava.bio.symbol">SimpleGappedSymbolList</a></dt>
<dd>
<div class="block">Coordinate conversion from view to source.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SimpleGappedSymbolList.html#viewToSource(int)">viewToSource(int)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SimpleGappedSymbolList.html" title="class in org.biojava.bio.symbol">SimpleGappedSymbolList</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/FilterUtils.html#visitFilter(org.biojava.bio.seq.FeatureFilter, org.biojava.utils.walker.Visitor)">visitFilter(FeatureFilter, Visitor)</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/FilterUtils.html" title="class in org.biojava.bio.seq">FilterUtils</a></dt>
<dd>
<div class="block">Applies a visitor to a filter, and returns the visitor's result or null.</div>
</dd>
<dt><a href="./org/biojava/utils/walker/Visitor.html" title="interface in org.biojava.utils.walker"><span class="strong">Visitor</span></a> - Interface in <a href="./org/biojava/utils/walker/package-summary.html">org.biojava.utils.walker</a></dt>
<dd>
<div class="block">Things that will be shown filters.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/DP.html#viterbi(org.biojava.bio.symbol.SymbolList[], org.biojava.bio.dp.ScoreType)">viterbi(SymbolList[], ScoreType)</a></span> - Method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/DP.html" title="class in org.biojava.bio.dp">DP</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/onehead/SingleDP.html#viterbi(org.biojava.bio.symbol.SymbolList[], org.biojava.bio.dp.ScoreType)">viterbi(SymbolList[], ScoreType)</a></span> - Method in class org.biojava.bio.dp.onehead.<a href="./org/biojava/bio/dp/onehead/SingleDP.html" title="class in org.biojava.bio.dp.onehead">SingleDP</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/twohead/CellCalculatorFactory.html#viterbi(org.biojava.bio.dp.ScoreType, org.biojava.bio.dp.BackPointer)">viterbi(ScoreType, BackPointer)</a></span> - Method in interface org.biojava.bio.dp.twohead.<a href="./org/biojava/bio/dp/twohead/CellCalculatorFactory.html" title="interface in org.biojava.bio.dp.twohead">CellCalculatorFactory</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/twohead/DPInterpreter.html#viterbi(org.biojava.bio.dp.ScoreType, org.biojava.bio.dp.BackPointer)">viterbi(ScoreType, BackPointer)</a></span> - Method in class org.biojava.bio.dp.twohead.<a href="./org/biojava/bio/dp/twohead/DPInterpreter.html" title="class in org.biojava.bio.dp.twohead">DPInterpreter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/twohead/PairwiseDP.html#viterbi(org.biojava.bio.symbol.SymbolList[], org.biojava.bio.dp.ScoreType)">viterbi(SymbolList[], ScoreType)</a></span> - Method in class org.biojava.bio.dp.twohead.<a href="./org/biojava/bio/dp/twohead/PairwiseDP.html" title="class in org.biojava.bio.dp.twohead">PairwiseDP</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BiblioBook.html#volume">volume</a></span> - Variable in class org.biojava.bibliography.<a href="./org/biojava/bibliography/BiblioBook.html" title="class in org.biojava.bibliography">BiblioBook</a></dt>
<dd>
<div class="block">Book volume.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bibliography/BiblioJournalArticle.html#volume">volume</a></span> - Variable in class org.biojava.bibliography.<a href="./org/biojava/bibliography/BiblioJournalArticle.html" title="class in org.biojava.bibliography">BiblioJournalArticle</a></dt>
<dd>
<div class="block">The journal volume.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLFormat.html#vp">vp</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLFormat.html" title="class in org.biojavax.bio.seq.io">EMBLFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/GenbankFormat.html#vp">vp</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/GenbankFormat.html" title="class in org.biojavax.bio.seq.io">GenbankFormat</a></dt>
<dd> </dd>
</dl>
<a name="_W_">
<!-- -->
</a>
<h2 class="title">W</h2>
<dl>
<dt><span class="strong"><a href="./org/biojava/bio/seq/DNATools.html#w()">w()</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/DNATools.html" title="class in org.biojava.bio.seq">DNATools</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/NucleotideTools.html#w()">w()</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/NucleotideTools.html" title="class in org.biojava.bio.seq">NucleotideTools</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/ProteinTools.html#w()">w()</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/ProteinTools.html" title="class in org.biojava.bio.seq">ProteinTools</a></dt>
<dd>
<div class="block">Returns the <code>AtomicSymbol</code> for the amino acid
Tryptophan</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/SimpleThreadPool.html#waitForThreads()">waitForThreads()</a></span> - Method in class org.biojava.utils.<a href="./org/biojava/utils/SimpleThreadPool.html" title="class in org.biojava.utils">SimpleThreadPool</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/ThreadPool.html#waitForThreads()">waitForThreads()</a></span> - Method in interface org.biojava.utils.<a href="./org/biojava/utils/ThreadPool.html" title="interface in org.biojava.utils">ThreadPool</a></dt>
<dd>
<div class="block"><code>waitForThreads</code> temporarily closes the pool to new
requests until such time as the current request queue has been
emptied and all running tasks completed.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/walker/Walker.html#walk(java.lang.Object, org.biojava.utils.walker.Visitor)">walk(Object, Visitor)</a></span> - Method in interface org.biojava.utils.walker.<a href="./org/biojava/utils/walker/Walker.html" title="interface in org.biojava.utils.walker">Walker</a></dt>
<dd>
<div class="block">This walks the feature tree, showing the visitor each filter in
the expression.</div>
</dd>
<dt><a href="./org/biojava/utils/walker/Walker.html" title="interface in org.biojava.utils.walker"><span class="strong">Walker</span></a> - Interface in <a href="./org/biojava/utils/walker/package-summary.html">org.biojava.utils.walker</a></dt>
<dd>
<div class="block">Objects that can walk over a filter expression, showing each element to a
visitor.</div>
</dd>
<dt><a href="./org/biojava/utils/walker/WalkerFactory.html" title="class in org.biojava.utils.walker"><span class="strong">WalkerFactory</span></a> - Class in <a href="./org/biojava/utils/walker/package-summary.html">org.biojava.utils.walker</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/UkkonenSuffixTree.html#walkTo(org.biojava.bio.symbol.UkkonenSuffixTree.SuffixNode, java.lang.String, int, int)">walkTo(UkkonenSuffixTree.SuffixNode, String, int, int)</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/UkkonenSuffixTree.html" title="class in org.biojava.bio.symbol">UkkonenSuffixTree</a></dt>
<dd>
<div class="block">This method is used to walk down the tree, from a given node.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/blast2html/HTMLRenderer.html#wasEmpty()">wasEmpty()</a></span> - Method in class org.biojava.bio.program.blast2html.<a href="./org/biojava/bio/program/blast2html/HTMLRenderer.html" title="class in org.biojava.bio.program.blast2html">HTMLRenderer</a></dt>
<dd>
<div class="block">Returns true if no HitSummary and no Hit elements were
encountered</div>
</dd>
<dt><a href="./org/biojava/utils/cache/WeakCacheMap.html" title="class in org.biojava.utils.cache"><span class="strong">WeakCacheMap</span></a> - Class in <a href="./org/biojava/utils/cache/package-summary.html">org.biojava.utils.cache</a></dt>
<dd>
<div class="block">A cache which retains weak references to objects</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/cache/WeakCacheMap.html#WeakCacheMap()">WeakCacheMap()</a></span> - Constructor for class org.biojava.utils.cache.<a href="./org/biojava/utils/cache/WeakCacheMap.html" title="class in org.biojava.utils.cache">WeakCacheMap</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/taxa/WeakTaxon.html" title="class in org.biojava.bio.taxa"><span class="strong">WeakTaxon</span></a> - Class in <a href="./org/biojava/bio/taxa/package-summary.html">org.biojava.bio.taxa</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>replaced by classes in <a href="./org/biojavax/bio/taxa/package-summary.html"><code>org.biojavax.bio.taxa</code></a></i></div>
</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/taxa/WeakTaxon.html#WeakTaxon()">WeakTaxon()</a></span> - Constructor for class org.biojava.bio.taxa.<a href="./org/biojava/bio/taxa/WeakTaxon.html" title="class in org.biojava.bio.taxa">WeakTaxon</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/taxa/WeakTaxon.html#WeakTaxon(java.lang.String, java.lang.String)">WeakTaxon(String, String)</a></span> - Constructor for class org.biojava.bio.taxa.<a href="./org/biojava/bio/taxa/WeakTaxon.html" title="class in org.biojava.bio.taxa">WeakTaxon</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><a href="./org/biojava/bio/taxa/WeakTaxonFactory.html" title="class in org.biojava.bio.taxa"><span class="strong">WeakTaxonFactory</span></a> - Class in <a href="./org/biojava/bio/taxa/package-summary.html">org.biojava.bio.taxa</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>replaced by classes in <a href="./org/biojavax/bio/taxa/package-summary.html"><code>org.biojavax.bio.taxa</code></a></i></div>
</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/taxa/WeakTaxonFactory.html#WeakTaxonFactory(java.lang.String)">WeakTaxonFactory(String)</a></span> - Constructor for class org.biojava.bio.taxa.<a href="./org/biojava/bio/taxa/WeakTaxonFactory.html" title="class in org.biojava.bio.taxa">WeakTaxonFactory</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><a href="./org/biojava/utils/cache/WeakValueHashMap.html" title="class in org.biojava.utils.cache"><span class="strong">WeakValueHashMap</span></a> - Class in <a href="./org/biojava/utils/cache/package-summary.html">org.biojava.utils.cache</a></dt>
<dd>
<div class="block">Map implementation which keeps weak references to values.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/cache/WeakValueHashMap.html#WeakValueHashMap()">WeakValueHashMap()</a></span> - Constructor for class org.biojava.utils.cache.<a href="./org/biojava/utils/cache/WeakValueHashMap.html" title="class in org.biojava.utils.cache">WeakValueHashMap</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/db/WebSequenceDB.html" title="class in org.biojava.bio.seq.db"><span class="strong">WebSequenceDB</span></a> - Class in <a href="./org/biojava/bio/seq/db/package-summary.html">org.biojava.bio.seq.db</a></dt>
<dd>
<div class="block">Functions for access to a web based database that returns sequences
in a variety of formats.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/db/WebSequenceDB.html#WebSequenceDB()">WebSequenceDB()</a></span> - Constructor for class org.biojava.bio.seq.db.<a href="./org/biojava/bio/seq/db/WebSequenceDB.html" title="class in org.biojava.bio.seq.db">WebSequenceDB</a></dt>
<dd> </dd>
<dt><a href="./org/biojavax/ga/util/WeightedSet.html" title="class in org.biojavax.ga.util"><span class="strong">WeightedSet</span></a> - Class in <a href="./org/biojavax/ga/util/package-summary.html">org.biojavax.ga.util</a></dt>
<dd>
<div class="block">Inspred by the BioJava Distribution objects the WeightedSet is a map from
a Key to a Weight.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ga/util/WeightedSet.html#WeightedSet()">WeightedSet()</a></span> - Constructor for class org.biojavax.ga.util.<a href="./org/biojavax/ga/util/WeightedSet.html" title="class in org.biojavax.ga.util">WeightedSet</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/AbstractOrderNDistribution.html#weightForwarder">weightForwarder</a></span> - Variable in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/AbstractOrderNDistribution.html" title="class in org.biojava.bio.dist">AbstractOrderNDistribution</a></dt>
<dd>
<div class="block">The listener that will forward events from the underlying distributions to
listeners for this distribution.</div>
</dd>
<dt><a href="./org/biojava/bio/dp/WeightMatrix.html" title="interface in org.biojava.bio.dp"><span class="strong">WeightMatrix</span></a> - Interface in <a href="./org/biojava/bio/dp/package-summary.html">org.biojava.bio.dp</a></dt>
<dd>
<div class="block">A log odds weight matrix.</div>
</dd>
<dt><a href="./org/biojava/bio/dp/WeightMatrixAnnotator.html" title="class in org.biojava.bio.dp"><span class="strong">WeightMatrixAnnotator</span></a> - Class in <a href="./org/biojava/bio/dp/package-summary.html">org.biojava.bio.dp</a></dt>
<dd>
<div class="block">Annotates a sequence with hits to a weight-matrix.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/WeightMatrixAnnotator.html#WeightMatrixAnnotator(org.biojava.bio.dp.WeightMatrix, org.biojava.bio.dp.ScoreType, double, java.lang.String)">WeightMatrixAnnotator(WeightMatrix, ScoreType, double, String)</a></span> - Constructor for class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/WeightMatrixAnnotator.html" title="class in org.biojava.bio.dp">WeightMatrixAnnotator</a></dt>
<dd>
<div class="block">Create a new annotator that uses the PROBABILITY score type and an ID
for the weight matrix.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/WeightMatrixAnnotator.html#WeightMatrixAnnotator(org.biojava.bio.dp.WeightMatrix, double)">WeightMatrixAnnotator(WeightMatrix, double)</a></span> - Constructor for class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/WeightMatrixAnnotator.html" title="class in org.biojava.bio.dp">WeightMatrixAnnotator</a></dt>
<dd>
<div class="block">Create a new annotator that uses PROBABILITY score type.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/WeightMatrixAnnotator.html#WeightMatrixAnnotator(org.biojava.bio.dp.WeightMatrix, org.biojava.bio.dp.ScoreType, double)">WeightMatrixAnnotator(WeightMatrix, ScoreType, double)</a></span> - Constructor for class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/WeightMatrixAnnotator.html" title="class in org.biojava.bio.dp">WeightMatrixAnnotator</a></dt>
<dd>
<div class="block">Create a new annotator that uses a specific score type.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/Distribution.html#WEIGHTS">WEIGHTS</a></span> - Static variable in interface org.biojava.bio.dist.<a href="./org/biojava/bio/dist/Distribution.html" title="interface in org.biojava.bio.dist">Distribution</a></dt>
<dd>
<div class="block">
Whenever a distribution changes the values that would be returned by
getWeight, they should fire a ChangeEvent with this object as the type.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.Option.html#WIDTH_IS_AUTHORITATIVE">WIDTH_IS_AUTHORITATIVE</a></span> - Static variable in class org.biojava.bio.chromatogram.graphic.<a href="./org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.Option.html" title="class in org.biojava.bio.chromatogram.graphic">ChromatogramGraphic.Option</a></dt>
<dd>
<div class="block">Option indicating whether width or horizontal scale is
the authoritative measure.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/SymbolListViews.html#windowedSymbolList(org.biojava.bio.symbol.SymbolList, int)">windowedSymbolList(SymbolList, int)</a></span> - Static method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/SymbolListViews.html" title="class in org.biojava.bio.symbol">SymbolListViews</a></dt>
<dd>
<div class="block">A view of windows onto another SymbolList.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/fastq/FastqBuilder.html#withDescription(java.lang.String)">withDescription(String)</a></span> - Method in class org.biojava.bio.program.fastq.<a href="./org/biojava/bio/program/fastq/FastqBuilder.html" title="class in org.biojava.bio.program.fastq">FastqBuilder</a></dt>
<dd>
<div class="block">Return this FASTQ formatted sequence builder configured with the specified description.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/fastq/FastqBuilder.html#withQuality(java.lang.String)">withQuality(String)</a></span> - Method in class org.biojava.bio.program.fastq.<a href="./org/biojava/bio/program/fastq/FastqBuilder.html" title="class in org.biojava.bio.program.fastq">FastqBuilder</a></dt>
<dd>
<div class="block">Return this FASTQ formatted sequence builder configured with the specified quality scores.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/fastq/FastqBuilder.html#withSequence(java.lang.String)">withSequence(String)</a></span> - Method in class org.biojava.bio.program.fastq.<a href="./org/biojava/bio/program/fastq/FastqBuilder.html" title="class in org.biojava.bio.program.fastq">FastqBuilder</a></dt>
<dd>
<div class="block">Return this FASTQ formatted sequence builder configured with the specified sequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/fastq/FastqBuilder.html#withVariant(org.biojava.bio.program.fastq.FastqVariant)">withVariant(FastqVariant)</a></span> - Method in class org.biojava.bio.program.fastq.<a href="./org/biojava/bio/program/fastq/FastqBuilder.html" title="class in org.biojava.bio.program.fastq">FastqBuilder</a></dt>
<dd>
<div class="block">Return this FASTQ formatted sequence builder configured with the specified FASTQ sequence format variant.</div>
</dd>
<dt><a href="./org/biojava/bio/dp/WMAsMM.html" title="class in org.biojava.bio.dp"><span class="strong">WMAsMM</span></a> - Class in <a href="./org/biojava/bio/dp/package-summary.html">org.biojava.bio.dp</a></dt>
<dd>
<div class="block">Wraps a weight matrix up so that it appears to be a very simple HMM.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/WMAsMM.html#WMAsMM(org.biojava.bio.dp.WeightMatrix)">WMAsMM(WeightMatrix)</a></span> - Constructor for class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/WMAsMM.html" title="class in org.biojava.bio.dp">WMAsMM</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/symbol/WobbleDistribution.html" title="interface in org.biojava.bio.symbol"><span class="strong">WobbleDistribution</span></a> - Interface in <a href="./org/biojava/bio/symbol/package-summary.html">org.biojava.bio.symbol</a></dt>
<dd>
<div class="block">an object to return statistics about
the frequency of the wobble base
in a set of synonymous codons.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/DNAAmbPack.html#wordSize()">wordSize()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/DNAAmbPack.html" title="class in org.biojava.bio.symbol">DNAAmbPack</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/DNANoAmbPack.html#wordSize()">wordSize()</a></span> - Method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/DNANoAmbPack.html" title="class in org.biojava.bio.symbol">DNANoAmbPack</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/Packing.html#wordSize()">wordSize()</a></span> - Method in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/Packing.html" title="interface in org.biojava.bio.symbol">Packing</a></dt>
<dd>
<div class="block">
The number of bits required to pack a symbol.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/WordTokenization.html" title="class in org.biojava.bio.seq.io"><span class="strong">WordTokenization</span></a> - Class in <a href="./org/biojava/bio/seq/io/package-summary.html">org.biojava.bio.seq.io</a></dt>
<dd>
<div class="block">Base class for tokenizations which accept whitespace-separated
`words'.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/WordTokenization.html#WordTokenization(org.biojava.bio.symbol.Alphabet)">WordTokenization(Alphabet)</a></span> - Constructor for class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/WordTokenization.html" title="class in org.biojava.bio.seq.io">WordTokenization</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/utils/StringTools.html#wordWrap(java.lang.String, java.lang.String, int)">wordWrap(String, String, int)</a></span> - Static method in class org.biojavax.utils.<a href="./org/biojavax/utils/StringTools.html" title="class in org.biojavax.utils">StringTools</a></dt>
<dd>
<div class="block">Word-wraps a string into an array of lines of no more than the given width.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/CodonPrefTools.html#WORM_NUCLEAR">WORM_NUCLEAR</a></span> - Static variable in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/CodonPrefTools.html" title="class in org.biojava.bio.symbol">CodonPrefTools</a></dt>
<dd>
<div class="block">Caenorhabditis elegans codon preferences</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/fastq/FastqWriter.html#write(java.io.File, org.biojava.bio.program.fastq.Fastq...)">write(File, Fastq...)</a></span> - Method in interface org.biojava.bio.program.fastq.<a href="./org/biojava/bio/program/fastq/FastqWriter.html" title="interface in org.biojava.bio.program.fastq">FastqWriter</a></dt>
<dd>
<div class="block">Write the specified FASTQ formatted sequences to the specified file.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/fastq/FastqWriter.html#write(java.io.File, java.lang.Iterable)">write(File, Iterable<Fastq>)</a></span> - Method in interface org.biojava.bio.program.fastq.<a href="./org/biojava/bio/program/fastq/FastqWriter.html" title="interface in org.biojava.bio.program.fastq">FastqWriter</a></dt>
<dd>
<div class="block">Write the specified FASTQ formatted sequences to the specified file.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/fastq/FastqWriter.html#write(java.io.OutputStream, org.biojava.bio.program.fastq.Fastq...)">write(OutputStream, Fastq...)</a></span> - Method in interface org.biojava.bio.program.fastq.<a href="./org/biojava/bio/program/fastq/FastqWriter.html" title="interface in org.biojava.bio.program.fastq">FastqWriter</a></dt>
<dd>
<div class="block">Write the specified FASTQ formatted sequences to the specified output stream.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/fastq/FastqWriter.html#write(java.io.OutputStream, java.lang.Iterable)">write(OutputStream, Iterable<Fastq>)</a></span> - Method in interface org.biojava.bio.program.fastq.<a href="./org/biojava/bio/program/fastq/FastqWriter.html" title="interface in org.biojava.bio.program.fastq">FastqWriter</a></dt>
<dd>
<div class="block">Write the specified FASTQ formatted sequences to the specified output stream.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AgaveWriter.html#write(org.biojava.bio.seq.Sequence)">write(Sequence)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AgaveWriter.html" title="class in org.biojava.bio.seq.io.agave">AgaveWriter</a></dt>
<dd>
<div class="block">Writing Sequence.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/FastaAlignmentFormat.html#write(java.io.OutputStream, org.biojava.bio.symbol.Alignment, int)">write(OutputStream, Alignment, int)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/FastaAlignmentFormat.html" title="class in org.biojava.bio.seq.io">FastaAlignmentFormat</a></dt>
<dd>
<div class="block">Writes out the alignment to an FASTA file.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/MSFAlignmentFormat.html#write(java.io.OutputStream, org.biojava.bio.symbol.Alignment, int)">write(OutputStream, Alignment, int)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/MSFAlignmentFormat.html" title="class in org.biojava.bio.seq.io">MSFAlignmentFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AgaveWriter.html#writeAnnotations(org.biojava.bio.seq.FeatureHolder)">writeAnnotations(FeatureHolder)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AgaveWriter.html" title="class in org.biojava.bio.seq.io.agave">AgaveWriter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/filterxml/XMLAnnotationTypeWriter.html#writeAnnotationType(org.biojava.bio.AnnotationType, org.biojava.utils.xml.XMLWriter)">writeAnnotationType(AnnotationType, XMLWriter)</a></span> - Method in class org.biojava.bio.seq.io.filterxml.<a href="./org/biojava/bio/seq/io/filterxml/XMLAnnotationTypeWriter.html" title="class in org.biojava.bio.seq.io.filterxml">XMLAnnotationTypeWriter</a></dt>
<dd>
<div class="block">Write an <code>AnnotationType</code> to the specified XMLWriter.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AgaveWriter.html#writeAssembly(org.biojava.bio.Annotatable)">writeAssembly(Annotatable)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AgaveWriter.html" title="class in org.biojava.bio.seq.io.agave">AgaveWriter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AgaveWriter.html#writeBioSequence(org.biojava.bio.Annotatable)">writeBioSequence(Annotatable)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AgaveWriter.html" title="class in org.biojava.bio.seq.io.agave">AgaveWriter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AgaveWriter.html#writeClassification(org.biojava.bio.Annotatable)">writeClassification(Annotatable)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AgaveWriter.html" title="class in org.biojava.bio.seq.io.agave">AgaveWriter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/filterxml/XMLAnnotationTypeWriter.XMLCollectionConstraintWriter.html#writeCollectionConstraint(org.biojava.bio.CollectionConstraint, org.biojava.utils.xml.XMLWriter, org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeWriter)">writeCollectionConstraint(CollectionConstraint, XMLWriter, XMLAnnotationTypeWriter)</a></span> - Method in interface org.biojava.bio.seq.io.filterxml.<a href="./org/biojava/bio/seq/io/filterxml/XMLAnnotationTypeWriter.XMLCollectionConstraintWriter.html" title="interface in org.biojava.bio.seq.io.filterxml">XMLAnnotationTypeWriter.XMLCollectionConstraintWriter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AgaveWriter.html#writeCompResult(org.biojava.bio.Annotatable)">writeCompResult(Annotatable)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AgaveWriter.html" title="class in org.biojava.bio.seq.io.agave">AgaveWriter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AgaveWriter.html#writeContig(org.biojava.bio.Annotatable)">writeContig(Annotatable)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AgaveWriter.html" title="class in org.biojava.bio.seq.io.agave">AgaveWriter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/xff/BasicXFFHelper.html#writeDetails(org.biojava.utils.xml.XMLWriter, org.biojava.bio.seq.Feature)">writeDetails(XMLWriter, Feature)</a></span> - Method in class org.biojava.bio.program.xff.<a href="./org/biojava/bio/program/xff/BasicXFFHelper.html" title="class in org.biojava.bio.program.xff">BasicXFFHelper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/xff/PropertyWriter.html#writeDetails(org.biojava.utils.xml.XMLWriter, org.biojava.bio.seq.Feature)">writeDetails(XMLWriter, Feature)</a></span> - Method in class org.biojava.bio.program.xff.<a href="./org/biojava/bio/program/xff/PropertyWriter.html" title="class in org.biojava.bio.program.xff">PropertyWriter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/xff/XFFHelper.html#writeDetails(org.biojava.utils.xml.XMLWriter, org.biojava.bio.seq.Feature)">writeDetails(XMLWriter, Feature)</a></span> - Method in interface org.biojava.bio.program.xff.<a href="./org/biojava/bio/program/xff/XFFHelper.html" title="interface in org.biojava.bio.program.xff">XFFHelper</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/XMLDistributionWriter.html#writeDistribution(org.biojava.bio.dist.Distribution, java.io.OutputStream)">writeDistribution(Distribution, OutputStream)</a></span> - Method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/XMLDistributionWriter.html" title="class in org.biojava.bio.dist">XMLDistributionWriter</a></dt>
<dd>
<div class="block">Writes an OrderNDistribution or simple Distribution to an XML file.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/FastaAlignmentFormat.html#writeDna(java.io.OutputStream, org.biojava.bio.symbol.Alignment)">writeDna(OutputStream, Alignment)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/FastaAlignmentFormat.html" title="class in org.biojava.bio.seq.io">FastaAlignmentFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/MSFAlignmentFormat.html#writeDna(java.io.OutputStream, org.biojava.bio.symbol.Alignment)">writeDna(OutputStream, Alignment)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/MSFAlignmentFormat.html" title="class in org.biojava.bio.seq.io">MSFAlignmentFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOTools.html#writeEmbl(java.io.OutputStream, org.biojava.bio.seq.SequenceIterator)">writeEmbl(OutputStream, SequenceIterator)</a></span> - Static method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOTools.html" title="class in org.biojava.bio.seq.io">SeqIOTools</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Writes a stream of Sequences to an OutputStream in EMBL format.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOTools.html#writeEmbl(java.io.OutputStream, org.biojava.bio.seq.Sequence)">writeEmbl(OutputStream, Sequence)</a></span> - Static method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOTools.html" title="class in org.biojava.bio.seq.io">SeqIOTools</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Writes a single Sequence to an OutputStream in EMBL format.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.IOTools.html#writeEMBL(java.io.OutputStream, org.biojava.bio.seq.SequenceIterator, org.biojavax.Namespace)">writeEMBL(OutputStream, SequenceIterator, Namespace)</a></span> - Static method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.IOTools.html" title="class in org.biojavax.bio.seq">RichSequence.IOTools</a></dt>
<dd>
<div class="block">Writes sequences from a <code>SequenceIterator</code> to an
<code>OutputStream </code>in EMBL Format.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.IOTools.html#writeEMBL(java.io.OutputStream, org.biojava.bio.seq.Sequence, org.biojavax.Namespace)">writeEMBL(OutputStream, Sequence, Namespace)</a></span> - Static method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.IOTools.html" title="class in org.biojavax.bio.seq">RichSequence.IOTools</a></dt>
<dd>
<div class="block">Writes a single <code>Sequence</code> to an <code>OutputStream</code>
in EMBL format.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.IOTools.html#writeEMBLxml(java.io.OutputStream, org.biojava.bio.seq.SequenceIterator, org.biojavax.Namespace)">writeEMBLxml(OutputStream, SequenceIterator, Namespace)</a></span> - Static method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.IOTools.html" title="class in org.biojavax.bio.seq">RichSequence.IOTools</a></dt>
<dd>
<div class="block">Writes sequences from a <code>SequenceIterator</code> to an
<code>OutputStream </code>in EMBLxml Format.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.IOTools.html#writeEMBLxml(java.io.OutputStream, org.biojava.bio.seq.Sequence, org.biojavax.Namespace)">writeEMBLxml(OutputStream, Sequence, Namespace)</a></span> - Static method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.IOTools.html" title="class in org.biojavax.bio.seq">RichSequence.IOTools</a></dt>
<dd>
<div class="block">Writes a single <code>Sequence</code> to an <code>OutputStream</code>
in EMBLxml format.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/xml/BaseXMLWriter.html#writeEmptyElement(java.lang.String)">writeEmptyElement(String)</a></span> - Method in class org.biojava.bio.program.xml.<a href="./org/biojava/bio/program/xml/BaseXMLWriter.html" title="class in org.biojava.bio.program.xml">BaseXMLWriter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/xml/BaseXMLWriter.html#writeEmptyElement(java.lang.String, org.xml.sax.Attributes)">writeEmptyElement(String, Attributes)</a></span> - Method in class org.biojava.bio.program.xml.<a href="./org/biojava/bio/program/xml/BaseXMLWriter.html" title="class in org.biojava.bio.program.xml">BaseXMLWriter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOTools.html#writeFasta(java.io.OutputStream, org.biojava.bio.seq.db.SequenceDB)">writeFasta(OutputStream, SequenceDB)</a></span> - Static method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOTools.html" title="class in org.biojava.bio.seq.io">SeqIOTools</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Write a sequenceDB to an output stream in fasta format.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOTools.html#writeFasta(java.io.OutputStream, org.biojava.bio.seq.SequenceIterator)">writeFasta(OutputStream, SequenceIterator)</a></span> - Static method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOTools.html" title="class in org.biojava.bio.seq.io">SeqIOTools</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Writes sequences from a SequenceIterator to an OutputStream in
Fasta Format.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOTools.html#writeFasta(java.io.OutputStream, org.biojava.bio.seq.Sequence)">writeFasta(OutputStream, Sequence)</a></span> - Static method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOTools.html" title="class in org.biojava.bio.seq.io">SeqIOTools</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Writes a single Sequence to an OutputStream in Fasta format.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.IOTools.html#writeFasta(java.io.OutputStream, org.biojava.bio.seq.SequenceIterator, org.biojavax.Namespace, org.biojavax.bio.seq.io.FastaHeader)">writeFasta(OutputStream, SequenceIterator, Namespace, FastaHeader)</a></span> - Static method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.IOTools.html" title="class in org.biojavax.bio.seq">RichSequence.IOTools</a></dt>
<dd>
<div class="block">Writes <CODE>Sequence</CODE>s from a <code>SequenceIterator</code> to
an <code>OutputStream </code>in Fasta Format.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.IOTools.html#writeFasta(java.io.OutputStream, org.biojava.bio.seq.SequenceIterator, org.biojavax.Namespace)">writeFasta(OutputStream, SequenceIterator, Namespace)</a></span> - Static method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.IOTools.html" title="class in org.biojavax.bio.seq">RichSequence.IOTools</a></dt>
<dd>
<div class="block">Writes <CODE>Sequence</CODE>s from a <code>SequenceIterator</code> to
an <code>OutputStream </code>in Fasta Format.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.IOTools.html#writeFasta(java.io.OutputStream, org.biojava.bio.seq.Sequence, org.biojavax.Namespace)">writeFasta(OutputStream, Sequence, Namespace)</a></span> - Static method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.IOTools.html" title="class in org.biojavax.bio.seq">RichSequence.IOTools</a></dt>
<dd>
<div class="block">Writes a single <code>Sequence</code> to an <code>OutputStream</code>
in Fasta format.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.IOTools.html#writeFasta(java.io.OutputStream, org.biojava.bio.seq.Sequence, org.biojavax.Namespace, org.biojavax.bio.seq.io.FastaHeader)">writeFasta(OutputStream, Sequence, Namespace, FastaHeader)</a></span> - Static method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.IOTools.html" title="class in org.biojavax.bio.seq">RichSequence.IOTools</a></dt>
<dd>
<div class="block">Writes a single <code>Sequence</code> to an <code>OutputStream</code>
in Fasta format.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/xff/XFFWriter.html#writeFeatureSet(org.biojava.bio.seq.FeatureHolder, org.biojava.utils.xml.XMLWriter)">writeFeatureSet(FeatureHolder, XMLWriter)</a></span> - Method in class org.biojava.bio.program.xff.<a href="./org/biojava/bio/program/xff/XFFWriter.html" title="class in org.biojava.bio.program.xff">XFFWriter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/phylo/io/phylip/PHYLIPFileFormat.html#writeFile(java.io.File, org.biojava.bio.symbol.Alignment)">writeFile(File, Alignment)</a></span> - Static method in class org.biojavax.bio.phylo.io.phylip.<a href="./org/biojavax/bio/phylo/io/phylip/PHYLIPFileFormat.html" title="class in org.biojavax.bio.phylo.io.phylip">PHYLIPFileFormat</a></dt>
<dd>
<div class="block">Writes the given Alignment in PHYLIP format to a file.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/filterxml/XMLFilterWriter.FilterWriter.html#writeFilter(org.biojava.bio.seq.FeatureFilter, org.biojava.utils.xml.XMLWriter, org.biojava.bio.seq.io.filterxml.XMLFilterWriter)">writeFilter(FeatureFilter, XMLWriter, XMLFilterWriter)</a></span> - Method in interface org.biojava.bio.seq.io.filterxml.<a href="./org/biojava/bio/seq/io/filterxml/XMLFilterWriter.FilterWriter.html" title="interface in org.biojava.bio.seq.io.filterxml">XMLFilterWriter.FilterWriter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/filterxml/XMLFilterWriter.html#writeFilter(org.biojava.bio.seq.FeatureFilter, org.biojava.utils.xml.XMLWriter)">writeFilter(FeatureFilter, XMLWriter)</a></span> - Method in class org.biojava.bio.seq.io.filterxml.<a href="./org/biojava/bio/seq/io/filterxml/XMLFilterWriter.html" title="class in org.biojava.bio.seq.io.filterxml">XMLFilterWriter</a></dt>
<dd>
<div class="block">Write a FeatureFilter to the supplied XMLWriter</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AgaveWriter.html#writeFooter()">writeFooter()</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AgaveWriter.html" title="class in org.biojava.bio.seq.io.agave">AgaveWriter</a></dt>
<dd>
<div class="block">Write </sciobj></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOTools.html#writeGenbank(java.io.OutputStream, org.biojava.bio.seq.SequenceIterator)">writeGenbank(OutputStream, SequenceIterator)</a></span> - Static method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOTools.html" title="class in org.biojava.bio.seq.io">SeqIOTools</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Writes a stream of Sequences to an OutputStream in Genbank
format.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOTools.html#writeGenbank(java.io.OutputStream, org.biojava.bio.seq.Sequence)">writeGenbank(OutputStream, Sequence)</a></span> - Static method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOTools.html" title="class in org.biojava.bio.seq.io">SeqIOTools</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Writes a single Sequence to an OutputStream in Genbank format.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.IOTools.html#writeGenbank(java.io.OutputStream, org.biojava.bio.seq.SequenceIterator, org.biojavax.Namespace)">writeGenbank(OutputStream, SequenceIterator, Namespace)</a></span> - Static method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.IOTools.html" title="class in org.biojavax.bio.seq">RichSequence.IOTools</a></dt>
<dd>
<div class="block">Writes sequences from a <code>SequenceIterator</code> to an
<code>OutputStream </code>in GenBank Format.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.IOTools.html#writeGenbank(java.io.OutputStream, org.biojava.bio.seq.Sequence, org.biojavax.Namespace)">writeGenbank(OutputStream, Sequence, Namespace)</a></span> - Static method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.IOTools.html" title="class in org.biojavax.bio.seq">RichSequence.IOTools</a></dt>
<dd>
<div class="block">Writes a single <code>Sequence</code> to an <code>OutputStream</code>
in GenBank format.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AgaveWriter.html#writeGene(org.biojava.bio.Annotatable)">writeGene(Annotatable)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AgaveWriter.html" title="class in org.biojava.bio.seq.io.agave">AgaveWriter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOTools.html#writeGenpept(java.io.OutputStream, org.biojava.bio.seq.SequenceIterator)">writeGenpept(OutputStream, SequenceIterator)</a></span> - Static method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOTools.html" title="class in org.biojava.bio.seq.io">SeqIOTools</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Writes a stream of Sequences to an OutputStream in Genpept
format.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOTools.html#writeGenpept(java.io.OutputStream, org.biojava.bio.seq.Sequence)">writeGenpept(OutputStream, Sequence)</a></span> - Static method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOTools.html" title="class in org.biojava.bio.seq.io">SeqIOTools</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Writes a single Sequence to an OutputStream in Genpept format.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFTools.html#writeGFF(java.lang.String, org.biojava.bio.program.gff.GFFEntrySet)">writeGFF(String, GFFEntrySet)</a></span> - Static method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFTools.html" title="class in org.biojava.bio.program.gff">GFFTools</a></dt>
<dd>
<div class="block">Writes a GFFEntrySet to a file.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFTools.html#writeGFF(java.io.File, org.biojava.bio.program.gff.GFFEntrySet)">writeGFF(File, GFFEntrySet)</a></span> - Static method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFTools.html" title="class in org.biojava.bio.program.gff">GFFTools</a></dt>
<dd>
<div class="block">Writes a GFFEntrySet to a file.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/gff/GFFTools.html#writeGFF(java.io.PrintWriter, org.biojava.bio.program.gff.GFFEntrySet)">writeGFF(PrintWriter, GFFEntrySet)</a></span> - Static method in class org.biojava.bio.program.gff.<a href="./org/biojava/bio/program/gff/GFFTools.html" title="class in org.biojava.bio.program.gff">GFFTools</a></dt>
<dd>
<div class="block">Writes a GFFEntrySet to a PrintWriter.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/xml/BaseXMLWriter.html#writeHeader()">writeHeader()</a></span> - Method in class org.biojava.bio.program.xml.<a href="./org/biojava/bio/program/xml/BaseXMLWriter.html" title="class in org.biojava.bio.program.xml">BaseXMLWriter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AgaveWriter.html#writeHeader()">writeHeader()</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AgaveWriter.html" title="class in org.biojava.bio.seq.io.agave">AgaveWriter</a></dt>
<dd>
<div class="block">Write <sciobj></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/xml/PrettyXMLWriter.html#writeIndent()">writeIndent()</a></span> - Method in class org.biojava.utils.xml.<a href="./org/biojava/utils/xml/PrettyXMLWriter.html" title="class in org.biojava.utils.xml">PrettyXMLWriter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.IOTools.html#writeINSDseq(java.io.OutputStream, org.biojava.bio.seq.SequenceIterator, org.biojavax.Namespace)">writeINSDseq(OutputStream, SequenceIterator, Namespace)</a></span> - Static method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.IOTools.html" title="class in org.biojavax.bio.seq">RichSequence.IOTools</a></dt>
<dd>
<div class="block">Writes sequences from a <code>SequenceIterator</code> to an
<code>OutputStream </code>in INSDseq Format.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.IOTools.html#writeINSDseq(java.io.OutputStream, org.biojava.bio.seq.Sequence, org.biojavax.Namespace)">writeINSDseq(OutputStream, Sequence, Namespace)</a></span> - Static method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.IOTools.html" title="class in org.biojavax.bio.seq">RichSequence.IOTools</a></dt>
<dd>
<div class="block">Writes a single <code>Sequence</code> to an <code>OutputStream</code>
in INSDseq format.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/utils/StringTools.html#writeKeyValueLine(java.lang.String, java.lang.String, int, int, java.io.PrintStream)">writeKeyValueLine(String, String, int, int, PrintStream)</a></span> - Static method in class org.biojavax.utils.<a href="./org/biojavax/utils/StringTools.html" title="class in org.biojavax.utils">StringTools</a></dt>
<dd>
<div class="block">Writes some text to the output stream in the following format:
key text
continuation of text
where the key/wrappedKey column is keyWidth wide, and the total line width is lineWidth,
and the text is split over multiple lines at the nearest occurrence of whitespace.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/utils/StringTools.html#writeKeyValueLine(java.lang.String, java.lang.String, int, int, java.lang.String, java.io.PrintStream)">writeKeyValueLine(String, String, int, int, String, PrintStream)</a></span> - Static method in class org.biojavax.utils.<a href="./org/biojavax/utils/StringTools.html" title="class in org.biojavax.utils">StringTools</a></dt>
<dd>
<div class="block">Writes some text to the output stream in the following format:
key text
continuation of text
where the key/wrappedKey column is keyWidth wide, and the total line width is lineWidth,
and the text is split over multiple lines at the nearest occurrence of separator sep.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/utils/StringTools.html#writeKeyValueLine(java.lang.String, java.lang.String, int, int, java.lang.String, java.lang.String, java.io.PrintStream)">writeKeyValueLine(String, String, int, int, String, String, PrintStream)</a></span> - Static method in class org.biojavax.utils.<a href="./org/biojavax/utils/StringTools.html" title="class in org.biojavax.utils">StringTools</a></dt>
<dd>
<div class="block">Writes some text to the output stream in the following format:
key text
wrappedKey continuation of text
where the key/wrappedKey column is keyWidth wide, and the total line width is lineWidth,
and the text is split over multiple lines at the nearest occurrence of separator sep.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/GenbankLocationParser.html#writeLocation(org.biojavax.bio.seq.RichLocation)">writeLocation(RichLocation)</a></span> - Static method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/GenbankLocationParser.html" title="class in org.biojavax.bio.seq.io">GenbankLocationParser</a></dt>
<dd>
<div class="block">Writes a location in Genbank format.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtLocationParser.html#writeLocation(org.biojavax.bio.seq.RichLocation)">writeLocation(RichLocation)</a></span> - Static method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtLocationParser.html" title="class in org.biojavax.bio.seq.io">UniProtLocationParser</a></dt>
<dd>
<div class="block">Writes a location in UniProt format.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/XmlMarkovModel.html#writeMatrix(org.biojava.bio.dp.WeightMatrix, java.io.PrintStream)">writeMatrix(WeightMatrix, PrintStream)</a></span> - Static method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/XmlMarkovModel.html" title="class in org.biojava.bio.dp">XmlMarkovModel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/XmlMarkovModel.html#writeModel(org.biojava.bio.dp.MarkovModel, java.io.PrintStream)">writeModel(MarkovModel, PrintStream)</a></span> - Static method in class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/XmlMarkovModel.html" title="class in org.biojava.bio.dp">XmlMarkovModel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/stats/svm/tools/SVM_Light.html#writeModelFile(org.biojava.stats.svm.SVMClassifierModel, java.lang.String)">writeModelFile(SVMClassifierModel, String)</a></span> - Static method in class org.biojava.stats.svm.tools.<a href="./org/biojava/stats/svm/tools/SVM_Light.html" title="class in org.biojava.stats.svm.tools">SVM_Light</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/xml/BaseXMLWriter.html#writePCData(java.lang.String)">writePCData(String)</a></span> - Method in class org.biojava.bio.program.xml.<a href="./org/biojava/bio/program/xml/BaseXMLWriter.html" title="class in org.biojava.bio.program.xml">BaseXMLWriter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/phred/PhredTools.html#writePhredQuality(java.io.OutputStream, java.io.OutputStream, org.biojava.bio.seq.db.SequenceDB)">writePhredQuality(OutputStream, OutputStream, SequenceDB)</a></span> - Static method in class org.biojava.bio.program.phred.<a href="./org/biojava/bio/program/phred/PhredTools.html" title="class in org.biojava.bio.program.phred">PhredTools</a></dt>
<dd>
<div class="block">Writes Phred quality data in a Fasta type format.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/filterxml/XMLAnnotationTypeWriter.XMLPropertyConstraintWriter.html#writePropertyConstraint(org.biojava.bio.PropertyConstraint, org.biojava.utils.xml.XMLWriter, org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeWriter)">writePropertyConstraint(PropertyConstraint, XMLWriter, XMLAnnotationTypeWriter)</a></span> - Method in interface org.biojava.bio.seq.io.filterxml.<a href="./org/biojava/bio/seq/io/filterxml/XMLAnnotationTypeWriter.XMLPropertyConstraintWriter.html" title="interface in org.biojava.bio.seq.io.filterxml">XMLAnnotationTypeWriter.XMLPropertyConstraintWriter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/FastaAlignmentFormat.html#writeProtein(java.io.OutputStream, org.biojava.bio.symbol.Alignment)">writeProtein(OutputStream, Alignment)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/FastaAlignmentFormat.html" title="class in org.biojava.bio.seq.io">FastaAlignmentFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/MSFAlignmentFormat.html#writeProtein(java.io.OutputStream, org.biojava.bio.symbol.Alignment)">writeProtein(OutputStream, Alignment)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/MSFAlignmentFormat.html" title="class in org.biojava.bio.seq.io">MSFAlignmentFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/indexdb/BioStore.html#writeRecord(org.biojava.utils.io.RAF, long, int, java.lang.String, java.util.Map)">writeRecord(RAF, long, int, String, Map)</a></span> - Method in class org.biojava.bio.program.indexdb.<a href="./org/biojava/bio/program/indexdb/BioStore.html" title="class in org.biojava.bio.program.indexdb">BioStore</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/indexdb/IndexStore.html#writeRecord(org.biojava.utils.io.RAF, long, int, java.lang.String, java.util.Map)">writeRecord(RAF, long, int, String, Map)</a></span> - Method in interface org.biojava.bio.program.indexdb.<a href="./org/biojava/bio/program/indexdb/IndexStore.html" title="interface in org.biojava.bio.program.indexdb">IndexStore</a></dt>
<dd>
<div class="block"><code>writeRecord</code> creates and writes a new
<code>Record</code></div>
</dd>
<dt><a href="./org/biojava/utils/process/WriterOutputHandler.html" title="class in org.biojava.utils.process"><span class="strong">WriterOutputHandler</span></a> - Class in <a href="./org/biojava/utils/process/package-summary.html">org.biojava.utils.process</a></dt>
<dd>
<div class="block">Simple <a href="./org/biojava/utils/process/OutputHandler.html" title="interface in org.biojava.utils.process">output handler</a>
that writes the output of an external process to an
<a href="./org/biojava/utils/process/ReaderWriterPipe.html#getWriter()">writer</a>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/process/WriterOutputHandler.html#WriterOutputHandler(java.io.Writer, java.lang.String)">WriterOutputHandler(Writer, String)</a></span> - Constructor for class org.biojava.utils.process.<a href="./org/biojava/utils/process/WriterOutputHandler.html" title="class in org.biojava.utils.process">WriterOutputHandler</a></dt>
<dd>
<div class="block">Initializes the writer output handler.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AgaveWriter.html#writeSeqFeature(org.biojava.bio.Annotatable)">writeSeqFeature(Annotatable)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AgaveWriter.html" title="class in org.biojava.bio.seq.io.agave">AgaveWriter</a></dt>
<dd>
<div class="block">Write SeqFeature XML</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/phred/PhredFormat.html#writeSequence(org.biojava.bio.seq.Sequence, java.io.PrintStream)">writeSequence(Sequence, PrintStream)</a></span> - Method in class org.biojava.bio.program.phred.<a href="./org/biojava/bio/program/phred/PhredFormat.html" title="class in org.biojava.bio.program.phred">PhredFormat</a></dt>
<dd>
<div class="block">This method will print symbols to the line width followed by a
new line etc.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/phred/PhredFormat.html#writeSequence(org.biojava.bio.seq.Sequence, java.lang.String, java.io.PrintStream)">writeSequence(Sequence, String, PrintStream)</a></span> - Method in class org.biojava.bio.program.phred.<a href="./org/biojava/bio/program/phred/PhredFormat.html" title="class in org.biojava.bio.program.phred">PhredFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>use writeSequence(Sequence seq, PrintStream os)</i></div>
</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AgaveWriter.html#writeSequence(org.biojava.bio.seq.Sequence, java.io.PrintStream)">writeSequence(Sequence, PrintStream)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AgaveWriter.html" title="class in org.biojava.bio.seq.io.agave">AgaveWriter</a></dt>
<dd>
<div class="block">Write sequence into AGAVE XML format.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/EmblLikeFormat.html#writeSequence(org.biojava.bio.seq.Sequence, java.io.PrintStream)">writeSequence(Sequence, PrintStream)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/EmblLikeFormat.html" title="class in org.biojava.bio.seq.io">EmblLikeFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/EmblLikeFormat.html#writeSequence(org.biojava.bio.seq.Sequence, java.lang.String, java.io.PrintStream)">writeSequence(Sequence, String, PrintStream)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/EmblLikeFormat.html" title="class in org.biojava.bio.seq.io">EmblLikeFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>use writeSequence(Sequence seq, PrintStream os)</i></div>
</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/FastaFormat.html#writeSequence(org.biojava.bio.seq.Sequence, java.io.PrintStream)">writeSequence(Sequence, PrintStream)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/FastaFormat.html" title="class in org.biojava.bio.seq.io">FastaFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Writes a <code>Sequence</code> or <code>RichSequence</code> to a
<code>PrintStream</code> in FASTA format.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/FastaFormat.html#writeSequence(org.biojava.bio.seq.Sequence, java.lang.String, java.io.PrintStream)">writeSequence(Sequence, String, PrintStream)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/FastaFormat.html" title="class in org.biojava.bio.seq.io">FastaFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>use writeSequence(Sequence seq, PrintStream os)</i></div>
</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/GAMEFormat.html#writeSequence(org.biojava.bio.seq.Sequence, java.io.PrintStream)">writeSequence(Sequence, PrintStream)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/GAMEFormat.html" title="class in org.biojava.bio.seq.io">GAMEFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/GAMEFormat.html#writeSequence(org.biojava.bio.seq.Sequence, java.lang.String, java.io.PrintStream)">writeSequence(Sequence, String, PrintStream)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/GAMEFormat.html" title="class in org.biojava.bio.seq.io">GAMEFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/GenbankFormat.html#writeSequence(org.biojava.bio.seq.Sequence, java.io.PrintStream)">writeSequence(Sequence, PrintStream)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/GenbankFormat.html" title="class in org.biojava.bio.seq.io">GenbankFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/GenbankFormat.html#writeSequence(org.biojava.bio.seq.Sequence, java.lang.String, java.io.PrintStream)">writeSequence(Sequence, String, PrintStream)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/GenbankFormat.html" title="class in org.biojava.bio.seq.io">GenbankFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>use writeSequence(Sequence seq, PrintStream os)</i></div>
</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SequenceFormat.html#writeSequence(org.biojava.bio.seq.Sequence, java.io.PrintStream)">writeSequence(Sequence, PrintStream)</a></span> - Method in interface org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SequenceFormat.html" title="interface in org.biojava.bio.seq.io">SequenceFormat</a></dt>
<dd>
<div class="block"><code>writeSequence</code> writes a sequence to the specified
PrintStream, using the default format.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SequenceFormat.html#writeSequence(org.biojava.bio.seq.Sequence, java.lang.String, java.io.PrintStream)">writeSequence(Sequence, String, PrintStream)</a></span> - Method in interface org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SequenceFormat.html" title="interface in org.biojava.bio.seq.io">SequenceFormat</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span>
<div class="block"><i>use writeSequence(Sequence seq, PrintStream os)</i></div>
</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLFormat.html#writeSequence(org.biojava.bio.seq.Sequence, java.io.PrintStream)">writeSequence(Sequence, PrintStream)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLFormat.html" title="class in org.biojavax.bio.seq.io">EMBLFormat</a></dt>
<dd>
<div class="block"><code>writeSequence</code> writes a sequence to the specified
PrintStream, using the default format.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLFormat.html#writeSequence(org.biojava.bio.seq.Sequence, java.lang.String, java.io.PrintStream)">writeSequence(Sequence, String, PrintStream)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLFormat.html" title="class in org.biojavax.bio.seq.io">EMBLFormat</a></dt>
<dd>
<div class="block"><code>writeSequence</code> writes a sequence to the specified
<code>PrintStream</code>, using the specified format.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLFormat.html#writeSequence(org.biojava.bio.seq.Sequence, org.biojavax.Namespace)">writeSequence(Sequence, Namespace)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLFormat.html" title="class in org.biojavax.bio.seq.io">EMBLFormat</a></dt>
<dd>
<div class="block">Writes a sequence out to the outputstream given by beginWriting() using the default format of the
implementing class.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLFormat.html#writeSequence(org.biojava.bio.seq.Sequence, java.lang.String, org.biojavax.Namespace)">writeSequence(Sequence, String, Namespace)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLFormat.html" title="class in org.biojavax.bio.seq.io">EMBLFormat</a></dt>
<dd>
<div class="block">As per <a href="./org/biojavax/bio/seq/io/EMBLFormat.html#writeSequence(org.biojava.bio.seq.Sequence, org.biojavax.Namespace)"><code>EMBLFormat.writeSequence(Sequence, Namespace)</code></a>, except
that it also takes a format parameter.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html#writeSequence(org.biojava.bio.seq.Sequence, java.io.PrintStream)">writeSequence(Sequence, PrintStream)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html" title="class in org.biojavax.bio.seq.io">EMBLxmlFormat</a></dt>
<dd>
<div class="block"><code>writeSequence</code> writes a sequence to the specified
PrintStream, using the default format.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html#writeSequence(org.biojava.bio.seq.Sequence, java.lang.String, java.io.PrintStream)">writeSequence(Sequence, String, PrintStream)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html" title="class in org.biojavax.bio.seq.io">EMBLxmlFormat</a></dt>
<dd>
<div class="block"><code>writeSequence</code> writes a sequence to the specified
<code>PrintStream</code>, using the specified format.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html#writeSequence(org.biojava.bio.seq.Sequence, org.biojavax.Namespace)">writeSequence(Sequence, Namespace)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html" title="class in org.biojavax.bio.seq.io">EMBLxmlFormat</a></dt>
<dd>
<div class="block">Writes a sequence out to the outputstream given by beginWriting() using the default format of the
implementing class.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/FastaFormat.html#writeSequence(org.biojava.bio.seq.Sequence, java.io.PrintStream)">writeSequence(Sequence, PrintStream)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/FastaFormat.html" title="class in org.biojavax.bio.seq.io">FastaFormat</a></dt>
<dd>
<div class="block"><code>writeSequence</code> writes a sequence to the specified
PrintStream, using the default format.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/FastaFormat.html#writeSequence(org.biojava.bio.seq.Sequence, java.lang.String, java.io.PrintStream)">writeSequence(Sequence, String, PrintStream)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/FastaFormat.html" title="class in org.biojavax.bio.seq.io">FastaFormat</a></dt>
<dd>
<div class="block"><code>writeSequence</code> writes a sequence to the specified
<code>PrintStream</code>, using the specified format.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/FastaFormat.html#writeSequence(org.biojava.bio.seq.Sequence, org.biojavax.Namespace)">writeSequence(Sequence, Namespace)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/FastaFormat.html" title="class in org.biojavax.bio.seq.io">FastaFormat</a></dt>
<dd>
<div class="block">Writes a sequence out to the outputstream given by beginWriting() using the default format of the
implementing class.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/GenbankFormat.html#writeSequence(org.biojava.bio.seq.Sequence, java.io.PrintStream)">writeSequence(Sequence, PrintStream)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/GenbankFormat.html" title="class in org.biojavax.bio.seq.io">GenbankFormat</a></dt>
<dd>
<div class="block"><code>writeSequence</code> writes a sequence to the specified
PrintStream, using the default format.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/GenbankFormat.html#writeSequence(org.biojava.bio.seq.Sequence, java.lang.String, java.io.PrintStream)">writeSequence(Sequence, String, PrintStream)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/GenbankFormat.html" title="class in org.biojavax.bio.seq.io">GenbankFormat</a></dt>
<dd>
<div class="block"><code>writeSequence</code> writes a sequence to the specified
<code>PrintStream</code>, using the specified format.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/GenbankFormat.html#writeSequence(org.biojava.bio.seq.Sequence, org.biojavax.Namespace)">writeSequence(Sequence, Namespace)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/GenbankFormat.html" title="class in org.biojavax.bio.seq.io">GenbankFormat</a></dt>
<dd>
<div class="block">Writes a sequence out to the outputstream given by beginWriting() using the default format of the
implementing class.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/INSDseqFormat.html#writeSequence(org.biojava.bio.seq.Sequence, java.io.PrintStream)">writeSequence(Sequence, PrintStream)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/INSDseqFormat.html" title="class in org.biojavax.bio.seq.io">INSDseqFormat</a></dt>
<dd>
<div class="block"><code>writeSequence</code> writes a sequence to the specified
PrintStream, using the default format.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/INSDseqFormat.html#writeSequence(org.biojava.bio.seq.Sequence, java.lang.String, java.io.PrintStream)">writeSequence(Sequence, String, PrintStream)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/INSDseqFormat.html" title="class in org.biojavax.bio.seq.io">INSDseqFormat</a></dt>
<dd>
<div class="block"><code>writeSequence</code> writes a sequence to the specified
<code>PrintStream</code>, using the specified format.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/INSDseqFormat.html#writeSequence(org.biojava.bio.seq.Sequence, org.biojavax.Namespace)">writeSequence(Sequence, Namespace)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/INSDseqFormat.html" title="class in org.biojavax.bio.seq.io">INSDseqFormat</a></dt>
<dd>
<div class="block">Writes a sequence out to the outputstream given by beginWriting() using the default format of the
implementing class.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/RichSequenceFormat.html#writeSequence(org.biojava.bio.seq.Sequence, org.biojavax.Namespace)">writeSequence(Sequence, Namespace)</a></span> - Method in interface org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/RichSequenceFormat.html" title="interface in org.biojavax.bio.seq.io">RichSequenceFormat</a></dt>
<dd>
<div class="block">Writes a sequence out to the outputstream given by beginWriting() using the default format of the
implementing class.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtFormat.html#writeSequence(org.biojava.bio.seq.Sequence, java.io.PrintStream)">writeSequence(Sequence, PrintStream)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtFormat.html" title="class in org.biojavax.bio.seq.io">UniProtFormat</a></dt>
<dd>
<div class="block"><code>writeSequence</code> writes a sequence to the specified
PrintStream, using the default format.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtFormat.html#writeSequence(org.biojava.bio.seq.Sequence, java.lang.String, java.io.PrintStream)">writeSequence(Sequence, String, PrintStream)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtFormat.html" title="class in org.biojavax.bio.seq.io">UniProtFormat</a></dt>
<dd>
<div class="block"><code>writeSequence</code> writes a sequence to the specified
<code>PrintStream</code>, using the specified format.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtFormat.html#writeSequence(org.biojava.bio.seq.Sequence, org.biojavax.Namespace)">writeSequence(Sequence, Namespace)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtFormat.html" title="class in org.biojavax.bio.seq.io">UniProtFormat</a></dt>
<dd>
<div class="block">Writes a sequence out to the outputstream given by beginWriting() using the default format of the
implementing class.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#writeSequence(org.biojava.bio.seq.Sequence, java.io.PrintStream)">writeSequence(Sequence, PrintStream)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd>
<div class="block"><code>writeSequence</code> writes a sequence to the specified
PrintStream, using the default format.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#writeSequence(org.biojava.bio.seq.Sequence, java.lang.String, java.io.PrintStream)">writeSequence(Sequence, String, PrintStream)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd>
<div class="block"><code>writeSequence</code> writes a sequence to the specified
<code>PrintStream</code>, using the specified format.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#writeSequence(org.biojava.bio.seq.Sequence, org.biojavax.Namespace)">writeSequence(Sequence, Namespace)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd>
<div class="block">Writes a sequence out to the outputstream given by beginWriting() using the default format of the
implementing class.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AgaveWriter.html#writeSequenceMap(org.biojava.bio.Annotatable)">writeSequenceMap(Annotatable)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AgaveWriter.html" title="class in org.biojava.bio.seq.io.agave">AgaveWriter</a></dt>
<dd>
<div class="block">group sequence_map by getSource()</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AgaveWriter.html#writeSequenceMap2(org.biojava.bio.Annotatable)">writeSequenceMap2(Annotatable)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AgaveWriter.html" title="class in org.biojava.bio.seq.io.agave">AgaveWriter</a></dt>
<dd>
<div class="block">Write SequenceMap XML</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/StreamWriter.html#writeStream(org.biojava.bio.seq.SequenceIterator)">writeStream(SequenceIterator)</a></span> - Method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/StreamWriter.html" title="class in org.biojava.bio.seq.io">StreamWriter</a></dt>
<dd>
<div class="block">Write each of the sequences in ss to the stream in the given format.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/phylo/io/phylip/PHYLIPFileFormat.html#writeStream(java.io.OutputStream, org.biojava.bio.symbol.Alignment)">writeStream(OutputStream, Alignment)</a></span> - Static method in class org.biojavax.bio.phylo.io.phylip.<a href="./org/biojavax/bio/phylo/io/phylip/PHYLIPFileFormat.html" title="class in org.biojavax.bio.phylo.io.phylip">PHYLIPFileFormat</a></dt>
<dd>
<div class="block">Writes the given Alignment in PHYLIP format to a stream.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/RichStreamWriter.html#writeStream(org.biojava.bio.seq.SequenceIterator, org.biojavax.Namespace)">writeStream(SequenceIterator, Namespace)</a></span> - Method in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/RichStreamWriter.html" title="class in org.biojavax.bio.seq.io">RichStreamWriter</a></dt>
<dd>
<div class="block">Write each of the sequences in ss to the stream in the given format.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOTools.html#writeSwissprot(java.io.OutputStream, org.biojava.bio.seq.SequenceIterator)">writeSwissprot(OutputStream, SequenceIterator)</a></span> - Static method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOTools.html" title="class in org.biojava.bio.seq.io">SeqIOTools</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Writes a stream of Sequences to an OutputStream in SwissProt
format.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/SeqIOTools.html#writeSwissprot(java.io.OutputStream, org.biojava.bio.seq.Sequence)">writeSwissprot(OutputStream, Sequence)</a></span> - Static method in class org.biojava.bio.seq.io.<a href="./org/biojava/bio/seq/io/SeqIOTools.html" title="class in org.biojava.bio.seq.io">SeqIOTools</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
<div class="block">Writes a single Sequence to an OutputStream in SwissProt format.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/DistributionTools.html#writeToXML(org.biojava.bio.dist.Distribution, java.io.OutputStream)">writeToXML(Distribution, OutputStream)</a></span> - Static method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/DistributionTools.html" title="class in org.biojava.bio.dist">DistributionTools</a></dt>
<dd>
<div class="block">Writes a Distribution to XML that can be read with the readFromXML method.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/CodonPrefTools.html#writeToXML(org.biojava.bio.symbol.CodonPref, java.io.PrintWriter)">writeToXML(CodonPref, PrintWriter)</a></span> - Static method in class org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/CodonPrefTools.html" title="class in org.biojava.bio.symbol">CodonPrefTools</a></dt>
<dd>
<div class="block">write out a specified CodonPref object in XML format.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AgaveWriter.html#writeTranscript(org.biojava.bio.Annotatable)">writeTranscript(Annotatable)</a></span> - Method in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AgaveWriter.html" title="class in org.biojava.bio.seq.io.agave">AgaveWriter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.IOTools.html#writeUniProt(java.io.OutputStream, org.biojava.bio.seq.SequenceIterator, org.biojavax.Namespace)">writeUniProt(OutputStream, SequenceIterator, Namespace)</a></span> - Static method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.IOTools.html" title="class in org.biojavax.bio.seq">RichSequence.IOTools</a></dt>
<dd>
<div class="block">Writes sequences from a <code>SequenceIterator</code> to an
<code>OutputStream </code>in UniProt Format.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.IOTools.html#writeUniProt(java.io.OutputStream, org.biojava.bio.seq.Sequence, org.biojavax.Namespace)">writeUniProt(OutputStream, Sequence, Namespace)</a></span> - Static method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.IOTools.html" title="class in org.biojavax.bio.seq">RichSequence.IOTools</a></dt>
<dd>
<div class="block">Writes a single <code>Sequence</code> to an <code>OutputStream</code>
in UniProt format.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.IOTools.html#writeUniProtXML(java.io.OutputStream, org.biojava.bio.seq.SequenceIterator, org.biojavax.Namespace)">writeUniProtXML(OutputStream, SequenceIterator, Namespace)</a></span> - Static method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.IOTools.html" title="class in org.biojavax.bio.seq">RichSequence.IOTools</a></dt>
<dd>
<div class="block">Writes sequences from a <code>SequenceIterator</code> to an
<code>OutputStream </code>in UniProt XML Format.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/RichSequence.IOTools.html#writeUniProtXML(java.io.OutputStream, org.biojava.bio.seq.Sequence, org.biojavax.Namespace)">writeUniProtXML(OutputStream, Sequence, Namespace)</a></span> - Static method in class org.biojavax.bio.seq.<a href="./org/biojavax/bio/seq/RichSequence.IOTools.html" title="class in org.biojavax.bio.seq">RichSequence.IOTools</a></dt>
<dd>
<div class="block">Writes a single <code>Sequence</code> to an <code>OutputStream</code>
in UniProt XML format.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/phylo/io/phylip/PHYLIPFileFormat.html#writeWriter(java.io.Writer, org.biojava.bio.symbol.Alignment)">writeWriter(Writer, Alignment)</a></span> - Static method in class org.biojavax.bio.phylo.io.phylip.<a href="./org/biojavax/bio/phylo/io/phylip/PHYLIPFileFormat.html" title="class in org.biojavax.bio.phylo.io.phylip">PHYLIPFileFormat</a></dt>
<dd>
<div class="block">Writes the given Alignment in PHYLIP format to a writer.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/xff/XFFTools.html#writeXFF(java.io.File, org.biojava.bio.seq.FeatureHolder)">writeXFF(File, FeatureHolder)</a></span> - Static method in class org.biojava.bio.program.xff.<a href="./org/biojava/bio/program/xff/XFFTools.html" title="class in org.biojava.bio.program.xff">XFFTools</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/xff/XFFTools.html#writeXFF(java.io.PrintWriter, org.biojava.bio.seq.FeatureHolder)">writeXFF(PrintWriter, FeatureHolder)</a></span> - Static method in class org.biojava.bio.program.xff.<a href="./org/biojava/bio/program/xff/XFFTools.html" title="class in org.biojava.bio.program.xff">XFFTools</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/utils/xml/XMLWritable.html#writeXML(org.biojava.utils.xml.XMLWriter)">writeXML(XMLWriter)</a></span> - Method in interface org.biojava.utils.xml.<a href="./org/biojava/utils/xml/XMLWritable.html" title="interface in org.biojava.utils.xml">XMLWritable</a></dt>
<dd> </dd>
</dl>
<a name="_X_">
<!-- -->
</a>
<h2 class="title">X</h2>
<dl>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/Taxon.html#X_LAEVIS">X_LAEVIS</a></span> - Static variable in interface org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/Taxon.html" title="interface in org.biojava.bio.program.homologene">Taxon</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/xff/XFFTools.html#XFF_BIOJAVA_NS">XFF_BIOJAVA_NS</a></span> - Static variable in class org.biojava.bio.program.xff.<a href="./org/biojava/bio/program/xff/XFFTools.html" title="class in org.biojava.bio.program.xff">XFFTools</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/xff/XFFTools.html#XFF_NS">XFF_NS</a></span> - Static variable in class org.biojava.bio.program.xff.<a href="./org/biojava/bio/program/xff/XFFTools.html" title="class in org.biojava.bio.program.xff">XFFTools</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/xff/XFFFeatureSetHandler.html" title="class in org.biojava.bio.program.xff"><span class="strong">XFFFeatureSetHandler</span></a> - Class in <a href="./org/biojava/bio/program/xff/package-summary.html">org.biojava.bio.program.xff</a></dt>
<dd>
<div class="block">StAX handler which converts and stream of parse events for an XFF
featureSet element into BioJava SeqIO events.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/xff/XFFFeatureSetHandler.html#XFFFeatureSetHandler()">XFFFeatureSetHandler()</a></span> - Constructor for class org.biojava.bio.program.xff.<a href="./org/biojava/bio/program/xff/XFFFeatureSetHandler.html" title="class in org.biojava.bio.program.xff">XFFFeatureSetHandler</a></dt>
<dd>
<div class="block">Construct a new XFFFeatureSetHandler with the default set of handlers.</div>
</dd>
<dt><a href="./org/biojava/bio/program/xff/XFFHelper.html" title="interface in org.biojava.bio.program.xff"><span class="strong">XFFHelper</span></a> - Interface in <a href="./org/biojava/bio/program/xff/package-summary.html">org.biojava.bio.program.xff</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/xff/XFFPartHandlerFactory.html" title="interface in org.biojava.bio.program.xff"><span class="strong">XFFPartHandlerFactory</span></a> - Interface in <a href="./org/biojava/bio/program/xff/package-summary.html">org.biojava.bio.program.xff</a></dt>
<dd>
<div class="block">Factory for StAX content handlers.</div>
</dd>
<dt><a href="./org/biojava/bio/program/xff/XFFTools.html" title="class in org.biojava.bio.program.xff"><span class="strong">XFFTools</span></a> - Class in <a href="./org/biojava/bio/program/xff/package-summary.html">org.biojava.bio.program.xff</a></dt>
<dd>
<div class="block">Common functionality for manipulating XFF.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/xff/XFFTools.html#XFFTools()">XFFTools()</a></span> - Constructor for class org.biojava.bio.program.xff.<a href="./org/biojava/bio/program/xff/XFFTools.html" title="class in org.biojava.bio.program.xff">XFFTools</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/program/xff/XFFWriter.html" title="class in org.biojava.bio.program.xff"><span class="strong">XFFWriter</span></a> - Class in <a href="./org/biojava/bio/program/xff/package-summary.html">org.biojava.bio.program.xff</a></dt>
<dd>
<div class="block">Simple XFF writing code, ripped off from Dazzle 0.08.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/xff/XFFWriter.html#XFFWriter()">XFFWriter()</a></span> - Constructor for class org.biojava.bio.program.xff.<a href="./org/biojava/bio/program/xff/XFFWriter.html" title="class in org.biojava.bio.program.xff">XFFWriter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/xff/XFFWriter.html#XFFWriter(org.biojava.bio.program.xff.XFFHelper)">XFFWriter(XFFHelper)</a></span> - Constructor for class org.biojava.bio.program.xff.<a href="./org/biojava/bio/program/xff/XFFWriter.html" title="class in org.biojava.bio.program.xff">XFFWriter</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/CrosshairRenderer.html#xHair">xHair</a></span> - Variable in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/CrosshairRenderer.html" title="class in org.biojava.bio.gui.sequence">CrosshairRenderer</a></dt>
<dd>
<div class="block"><code>xHair</code> is the vertical line positioned along the
X-axis.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/filterxml/XMLAnnotationTypeWriter.html#XML_ANNOTATIONTYPE_NS">XML_ANNOTATIONTYPE_NS</a></span> - Static variable in class org.biojava.bio.seq.io.filterxml.<a href="./org/biojava/bio/seq/io/filterxml/XMLAnnotationTypeWriter.html" title="class in org.biojava.bio.seq.io.filterxml">XMLAnnotationTypeWriter</a></dt>
<dd>
<div class="block">XML namespace string used to the AnnotationType representation</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/filterxml/XMLFilterWriter.html#XML_FILTER_NS">XML_FILTER_NS</a></span> - Static variable in class org.biojava.bio.seq.io.filterxml.<a href="./org/biojava/bio/seq/io/filterxml/XMLFilterWriter.html" title="class in org.biojava.bio.seq.io.filterxml">XMLFilterWriter</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/io/filterxml/XMLAnnotationTypeHandler.html" title="class in org.biojava.bio.seq.io.filterxml"><span class="strong">XMLAnnotationTypeHandler</span></a> - Class in <a href="./org/biojava/bio/seq/io/filterxml/package-summary.html">org.biojava.bio.seq.io.filterxml</a></dt>
<dd>
<div class="block">StAX handler for parsing AnnotationTypes in FilterXML documents.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/filterxml/XMLAnnotationTypeHandler.html#XMLAnnotationTypeHandler()">XMLAnnotationTypeHandler()</a></span> - Constructor for class org.biojava.bio.seq.io.filterxml.<a href="./org/biojava/bio/seq/io/filterxml/XMLAnnotationTypeHandler.html" title="class in org.biojava.bio.seq.io.filterxml">XMLAnnotationTypeHandler</a></dt>
<dd>
<div class="block">Construct a new XMLAnnotationTypeHandler which can parse the builtin PropertyConstraints.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/filterxml/XMLAnnotationTypeHandler.CollectionConstraintHandler.html" title="interface in org.biojava.bio.seq.io.filterxml"><span class="strong">XMLAnnotationTypeHandler.CollectionConstraintHandler</span></a> - Interface in <a href="./org/biojava/bio/seq/io/filterxml/package-summary.html">org.biojava.bio.seq.io.filterxml</a></dt>
<dd>
<div class="block">Handler for an individual <code>CollectionConstraint</code> in an AnnotationType.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/filterxml/XMLAnnotationTypeHandler.CollectionConstraintHandlerFactory.html" title="interface in org.biojava.bio.seq.io.filterxml"><span class="strong">XMLAnnotationTypeHandler.CollectionConstraintHandlerFactory</span></a> - Interface in <a href="./org/biojava/bio/seq/io/filterxml/package-summary.html">org.biojava.bio.seq.io.filterxml</a></dt>
<dd>
<div class="block">Handler Factory for a <code>CollectionConstraint</code> in an AnnotationType.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/filterxml/XMLAnnotationTypeHandler.PropertyConstraintHandler.html" title="interface in org.biojava.bio.seq.io.filterxml"><span class="strong">XMLAnnotationTypeHandler.PropertyConstraintHandler</span></a> - Interface in <a href="./org/biojava/bio/seq/io/filterxml/package-summary.html">org.biojava.bio.seq.io.filterxml</a></dt>
<dd>
<div class="block">Handler for an individual <code>PropertyConstraint</code> in an AnnotationType.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/filterxml/XMLAnnotationTypeHandler.PropertyConstraintHandlerFactory.html" title="interface in org.biojava.bio.seq.io.filterxml"><span class="strong">XMLAnnotationTypeHandler.PropertyConstraintHandlerFactory</span></a> - Interface in <a href="./org/biojava/bio/seq/io/filterxml/package-summary.html">org.biojava.bio.seq.io.filterxml</a></dt>
<dd>
<div class="block">Handler Factory for a <code>PropertyConstraint</code> in an AnnotationType.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/filterxml/XMLAnnotationTypeWriter.html" title="class in org.biojava.bio.seq.io.filterxml"><span class="strong">XMLAnnotationTypeWriter</span></a> - Class in <a href="./org/biojava/bio/seq/io/filterxml/package-summary.html">org.biojava.bio.seq.io.filterxml</a></dt>
<dd>
<div class="block">Main class for writing AnnotationTypes as XML.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/filterxml/XMLAnnotationTypeWriter.html#XMLAnnotationTypeWriter()">XMLAnnotationTypeWriter()</a></span> - Constructor for class org.biojava.bio.seq.io.filterxml.<a href="./org/biojava/bio/seq/io/filterxml/XMLAnnotationTypeWriter.html" title="class in org.biojava.bio.seq.io.filterxml">XMLAnnotationTypeWriter</a></dt>
<dd>
<div class="block">Construct a new AnnotationTypeWriter which knows about the builtin types of PropertyConstraint</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/filterxml/XMLAnnotationTypeWriter.XMLCollectionConstraintWriter.html" title="interface in org.biojava.bio.seq.io.filterxml"><span class="strong">XMLAnnotationTypeWriter.XMLCollectionConstraintWriter</span></a> - Interface in <a href="./org/biojava/bio/seq/io/filterxml/package-summary.html">org.biojava.bio.seq.io.filterxml</a></dt>
<dd>
<div class="block">Writer for types of CollectionConstraint.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/filterxml/XMLAnnotationTypeWriter.XMLPropertyConstraintWriter.html" title="interface in org.biojava.bio.seq.io.filterxml"><span class="strong">XMLAnnotationTypeWriter.XMLPropertyConstraintWriter</span></a> - Interface in <a href="./org/biojava/bio/seq/io/filterxml/package-summary.html">org.biojava.bio.seq.io.filterxml</a></dt>
<dd>
<div class="block">Writer for types of PropertyConstraint.</div>
</dd>
<dt><a href="./org/biojava/utils/xml/XMLBeans.html" title="class in org.biojava.utils.xml"><span class="strong">XMLBeans</span></a> - Class in <a href="./org/biojava/utils/xml/package-summary.html">org.biojava.utils.xml</a></dt>
<dd>
<div class="block">Construct java beans from XML elements</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/utils/xml/XMLBeans.html#XMLBeans()">XMLBeans()</a></span> - Constructor for class org.biojava.utils.xml.<a href="./org/biojava/utils/xml/XMLBeans.html" title="class in org.biojava.utils.xml">XMLBeans</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/dist/XMLDistributionReader.html" title="class in org.biojava.bio.dist"><span class="strong">XMLDistributionReader</span></a> - Class in <a href="./org/biojava/bio/dist/package-summary.html">org.biojava.bio.dist</a></dt>
<dd>
<div class="block">A SAX parser that reads an XML representation of a
Distribution from a file and recreates it as a Distribution Object.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/XMLDistributionReader.html#XMLDistributionReader()">XMLDistributionReader()</a></span> - Constructor for class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/XMLDistributionReader.html" title="class in org.biojava.bio.dist">XMLDistributionReader</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/dist/XMLDistributionWriter.html" title="class in org.biojava.bio.dist"><span class="strong">XMLDistributionWriter</span></a> - Class in <a href="./org/biojava/bio/dist/package-summary.html">org.biojava.bio.dist</a></dt>
<dd>
<div class="block">Writes an OrderNDistribution or simple Distribution to an XML file.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/XMLDistributionWriter.html#XMLDistributionWriter()">XMLDistributionWriter()</a></span> - Constructor for class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/XMLDistributionWriter.html" title="class in org.biojava.bio.dist">XMLDistributionWriter</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/seq/io/filterxml/XMLFilterHandler.html" title="class in org.biojava.bio.seq.io.filterxml"><span class="strong">XMLFilterHandler</span></a> - Class in <a href="./org/biojava/bio/seq/io/filterxml/package-summary.html">org.biojava.bio.seq.io.filterxml</a></dt>
<dd>
<div class="block">Factory producing content handlers for parsing FilterXML elements.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/filterxml/XMLFilterHandler.html#XMLFilterHandler()">XMLFilterHandler()</a></span> - Constructor for class org.biojava.bio.seq.io.filterxml.<a href="./org/biojava/bio/seq/io/filterxml/XMLFilterHandler.html" title="class in org.biojava.bio.seq.io.filterxml">XMLFilterHandler</a></dt>
<dd>
<div class="block">Construct a new XMLFilterHandler which can parse the builtin types of <code>FeatureFilter</code>.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/filterxml/XMLFilterHandler.FilterHandler.html" title="interface in org.biojava.bio.seq.io.filterxml"><span class="strong">XMLFilterHandler.FilterHandler</span></a> - Interface in <a href="./org/biojava/bio/seq/io/filterxml/package-summary.html">org.biojava.bio.seq.io.filterxml</a></dt>
<dd>
<div class="block">StAXContentHandler for a particular type of FeatureFilter.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/filterxml/XMLFilterHandler.FilterHandlerFactory.html" title="interface in org.biojava.bio.seq.io.filterxml"><span class="strong">XMLFilterHandler.FilterHandlerFactory</span></a> - Interface in <a href="./org/biojava/bio/seq/io/filterxml/package-summary.html">org.biojava.bio.seq.io.filterxml</a></dt>
<dd>
<div class="block">Factory of StAXContentHandlers for a particular type of FeatureFilter.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/filterxml/XMLFilterWriter.html" title="class in org.biojava.bio.seq.io.filterxml"><span class="strong">XMLFilterWriter</span></a> - Class in <a href="./org/biojava/bio/seq/io/filterxml/package-summary.html">org.biojava.bio.seq.io.filterxml</a></dt>
<dd>
<div class="block">Write FeatureFilters in XML format.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/filterxml/XMLFilterWriter.html#XMLFilterWriter()">XMLFilterWriter()</a></span> - Constructor for class org.biojava.bio.seq.io.filterxml.<a href="./org/biojava/bio/seq/io/filterxml/XMLFilterWriter.html" title="class in org.biojava.bio.seq.io.filterxml">XMLFilterWriter</a></dt>
<dd>
<div class="block">Construct a new <code>XMLFilterWriter</code> which can serialize the buildin types of
<code>FeatureFilter</code>.</div>
</dd>
<dt><a href="./org/biojava/bio/seq/io/filterxml/XMLFilterWriter.FilterWriter.html" title="interface in org.biojava.bio.seq.io.filterxml"><span class="strong">XMLFilterWriter.FilterWriter</span></a> - Interface in <a href="./org/biojava/bio/seq/io/filterxml/package-summary.html">org.biojava.bio.seq.io.filterxml</a></dt>
<dd>
<div class="block">Interface for an object which can write a FeatureFilter as XML.</div>
</dd>
<dt><a href="./org/biojava/bio/dp/XmlMarkovModel.html" title="class in org.biojava.bio.dp"><span class="strong">XmlMarkovModel</span></a> - Class in <a href="./org/biojava/bio/dp/package-summary.html">org.biojava.bio.dp</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/XmlMarkovModel.html#XmlMarkovModel()">XmlMarkovModel()</a></span> - Constructor for class org.biojava.bio.dp.<a href="./org/biojava/bio/dp/XmlMarkovModel.html" title="class in org.biojava.bio.dp">XmlMarkovModel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html#xmlSchema">xmlSchema</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/EMBLxmlFormat.html" title="class in org.biojavax.bio.seq.io">EMBLxmlFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/INSDseqFormat.html#xmlSchema">xmlSchema</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/INSDseqFormat.html" title="class in org.biojavax.bio.seq.io">INSDseqFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html#xmlSchema">xmlSchema</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/UniProtXMLFormat.html" title="class in org.biojavax.bio.seq.io">UniProtXMLFormat</a></dt>
<dd> </dd>
<dt><a href="./org/biojavax/utils/XMLTools.html" title="class in org.biojavax.utils"><span class="strong">XMLTools</span></a> - Class in <a href="./org/biojavax/utils/package-summary.html">org.biojavax.utils</a></dt>
<dd>
<div class="block">Utility class for reading chunks of XML files and feeding them to SAX.</div>
</dd>
<dt><a href="./org/biojava/utils/xml/XMLWritable.html" title="interface in org.biojava.utils.xml"><span class="strong">XMLWritable</span></a> - Interface in <a href="./org/biojava/utils/xml/package-summary.html">org.biojava.utils.xml</a></dt>
<dd>
<div class="block">Object which knows how to represent itself as an XML element.</div>
</dd>
<dt><a href="./org/biojava/utils/xml/XMLWriter.html" title="interface in org.biojava.utils.xml"><span class="strong">XMLWriter</span></a> - Interface in <a href="./org/biojava/utils/xml/package-summary.html">org.biojava.utils.xml</a></dt>
<dd>
<div class="block">Simple interface for building XML documents.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/ontology/obo/OboFileHandler.html#XREF_ANALOG">XREF_ANALOG</a></span> - Static variable in class org.biojava.ontology.obo.<a href="./org/biojava/ontology/obo/OboFileHandler.html" title="class in org.biojava.ontology.obo">OboFileHandler</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/INSDseqFormat.html#XREF_DBNAME_TAG">XREF_DBNAME_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/INSDseqFormat.html" title="class in org.biojavax.bio.seq.io">INSDseqFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/INSDseqFormat.html#XREF_ID_TAG">XREF_ID_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/INSDseqFormat.html" title="class in org.biojavax.bio.seq.io">INSDseqFormat</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/io/agave/AGAVEProperty.html#XREF_PROPERTY">XREF_PROPERTY</a></span> - Static variable in class org.biojava.bio.seq.io.agave.<a href="./org/biojava/bio/seq/io/agave/AGAVEProperty.html" title="class in org.biojava.bio.seq.io.agave">AGAVEProperty</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojavax/bio/seq/io/INSDseqFormat.html#XREF_TAG">XREF_TAG</a></span> - Static variable in class org.biojavax.bio.seq.io.<a href="./org/biojavax/bio/seq/io/INSDseqFormat.html" title="class in org.biojavax.bio.seq.io">INSDseqFormat</a></dt>
<dd> </dd>
</dl>
<a name="_Y_">
<!-- -->
</a>
<h2 class="title">Y</h2>
<dl>
<dt><span class="strong"><a href="./org/biojava/bio/seq/DNATools.html#y()">y()</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/DNATools.html" title="class in org.biojava.bio.seq">DNATools</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/NucleotideTools.html#y()">y()</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/NucleotideTools.html" title="class in org.biojava.bio.seq">NucleotideTools</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/seq/ProteinTools.html#y()">y()</a></span> - Static method in class org.biojava.bio.seq.<a href="./org/biojava/bio/seq/ProteinTools.html" title="class in org.biojava.bio.seq">ProteinTools</a></dt>
<dd>
<div class="block">Returns the <code>AtomicSymbol</code> for the amino acid
Tyrosine</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/symbol/TranslationTable.html#YEAST_MITO">YEAST_MITO</a></span> - Static variable in interface org.biojava.bio.symbol.<a href="./org/biojava/bio/symbol/TranslationTable.html" title="interface in org.biojava.bio.symbol">TranslationTable</a></dt>
<dd>
<div class="block">Translation table name for the yeast mitochondrial genetic
code.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/CrosshairRenderer.html#yHair">yHair</a></span> - Variable in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/CrosshairRenderer.html" title="class in org.biojava.bio.gui.sequence">CrosshairRenderer</a></dt>
<dd>
<div class="block"><code>yHair</code> is the horizontal line positioned along the
Y-axis.</div>
</dd>
</dl>
<a name="_Z_">
<!-- -->
</a>
<h2 class="title">Z</h2>
<dl>
<dt><span class="strong"><a href="./org/biojava/bio/program/homologene/Taxon.html#Z_MAYS">Z_MAYS</a></span> - Static variable in interface org.biojava.bio.program.homologene.<a href="./org/biojava/bio/program/homologene/Taxon.html" title="interface in org.biojava.bio.program.homologene">Taxon</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/CardinalityConstraint.html#ZERO">ZERO</a></span> - Static variable in class org.biojava.bio.<a href="./org/biojava/bio/CardinalityConstraint.html" title="class in org.biojava.bio">CardinalityConstraint</a></dt>
<dd>
<div class="block">The property should have zero values.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/ga/util/GATools.html#zero()">zero()</a></span> - Static method in class org.biojavax.ga.util.<a href="./org/biojavax/ga/util/GATools.html" title="class in org.biojavax.ga.util">GATools</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/CardinalityConstraint.html#ZERO_OR_ONE">ZERO_OR_ONE</a></span> - Static variable in class org.biojava.bio.<a href="./org/biojava/bio/CardinalityConstraint.html" title="class in org.biojava.bio">CardinalityConstraint</a></dt>
<dd>
<div class="block">The property should have zero or one values.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/twohead/AbstractMatrixPairDPCursor.html#zeroCol">zeroCol</a></span> - Variable in class org.biojava.bio.dp.twohead.<a href="./org/biojava/bio/dp/twohead/AbstractMatrixPairDPCursor.html" title="class in org.biojava.bio.dp.twohead">AbstractMatrixPairDPCursor</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/dp/twohead/LightPairDPCursor.html#zeroCol">zeroCol</a></span> - Variable in class org.biojava.bio.dp.twohead.<a href="./org/biojava/bio/dp/twohead/LightPairDPCursor.html" title="class in org.biojava.bio.dp.twohead">LightPairDPCursor</a></dt>
<dd>
<div class="block">Description of the Field</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/Count.html#zeroCounts()">zeroCounts()</a></span> - Method in interface org.biojava.bio.dist.<a href="./org/biojava/bio/dist/Count.html" title="interface in org.biojava.bio.dist">Count</a></dt>
<dd>
<div class="block">Reset all the counts to zero.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/dist/IndexedCount.html#zeroCounts()">zeroCounts()</a></span> - Method in class org.biojava.bio.dist.<a href="./org/biojava/bio/dist/IndexedCount.html" title="class in org.biojava.bio.dist">IndexedCount</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/gui/sequence/ZiggyFeatureRenderer.html" title="class in org.biojava.bio.gui.sequence"><span class="strong">ZiggyFeatureRenderer</span></a> - Class in <a href="./org/biojava/bio/gui/sequence/package-summary.html">org.biojava.bio.gui.sequence</a></dt>
<dd>
<div class="block">A feature renderer that draws non-contiguous features as a set of boxes
joined by zig-zags.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/ZiggyFeatureRenderer.html#ZiggyFeatureRenderer()">ZiggyFeatureRenderer()</a></span> - Constructor for class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/ZiggyFeatureRenderer.html" title="class in org.biojava.bio.gui.sequence">ZiggyFeatureRenderer</a></dt>
<dd> </dd>
<dt><a href="./org/biojava/bio/gui/sequence/ZiggyImapRenderer.html" title="class in org.biojava.bio.gui.sequence"><span class="strong">ZiggyImapRenderer</span></a> - Class in <a href="./org/biojava/bio/gui/sequence/package-summary.html">org.biojava.bio.gui.sequence</a></dt>
<dd>
<div class="block"><code>ZiggyImapRenderer</code> is a decorator for
<code>ZiggyFeatureRenderer</code> which adds the ability to create
HTML image map coordinates which correspond to the feature
rendering produced by the <code>ZiggyFeatureRenderer</code>.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/ZiggyImapRenderer.html#ZiggyImapRenderer(org.biojava.bio.gui.sequence.ZiggyFeatureRenderer, org.biojava.bio.gui.sequence.ImageMap, org.biojava.utils.net.URLFactory)">ZiggyImapRenderer(ZiggyFeatureRenderer, ImageMap, URLFactory)</a></span> - Constructor for class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/ZiggyImapRenderer.html" title="class in org.biojava.bio.gui.sequence">ZiggyImapRenderer</a></dt>
<dd>
<div class="block">Creates a new <code>ZiggyImapRenderer</code>.</div>
</dd>
</dl>
<a name="___">
<!-- -->
</a>
<h2 class="title">_</h2>
<dl>
<dt><span class="strong"><a href="./org/biojava/bio/program/abi/ABITools.html#_0">_0</a></span> - Static variable in class org.biojava.bio.program.abi.<a href="./org/biojava/bio/program/abi/ABITools.html" title="class in org.biojava.bio.program.abi">ABITools</a></dt>
<dd>
<div class="block">The poorly supported symbol.</div>
</dd>
<dt><span class="strong"><a href="./org/biojava/bio/program/abi/ABITools.html#_1">_1</a></span> - Static variable in class org.biojava.bio.program.abi.<a href="./org/biojava/bio/program/abi/ABITools.html" title="class in org.biojava.bio.program.abi">ABITools</a></dt>
<dd>
<div class="block">The well supported symbol.</div>
</dd>
<dt><span class="strong"><a href="./org/biojavax/bio/db/biosql/BioSQLBioEntryDB.html#_addBioEntry(org.biojavax.bio.BioEntry)">_addBioEntry(BioEntry)</a></span> - Method in class org.biojavax.bio.db.biosql.<a href="./org/biojavax/bio/db/biosql/BioSQLBioEntryDB.html" title="class in org.biojavax.bio.db.biosql">BioSQLBioEntryDB</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/MultiLineRenderer.html#_addRenderer(org.biojava.bio.gui.sequence.SequenceRenderer)">_addRenderer(SequenceRenderer)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/MultiLineRenderer.html" title="class in org.biojava.bio.gui.sequence">MultiLineRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PairwiseOverlayRenderer.html#_addRenderer(org.biojava.bio.gui.sequence.PairwiseSequenceRenderer)">_addRenderer(PairwiseSequenceRenderer)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PairwiseOverlayRenderer.html" title="class in org.biojava.bio.gui.sequence">PairwiseOverlayRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/MultiLineRenderer.html#_removeRenderer(org.biojava.bio.gui.sequence.SequenceRenderer)">_removeRenderer(SequenceRenderer)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/MultiLineRenderer.html" title="class in org.biojava.bio.gui.sequence">MultiLineRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/PairwiseOverlayRenderer.html#_removeRenderer(org.biojava.bio.gui.sequence.PairwiseSequenceRenderer)">_removeRenderer(PairwiseSequenceRenderer)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/PairwiseOverlayRenderer.html" title="class in org.biojava.bio.gui.sequence">PairwiseOverlayRenderer</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePanel.html#_setRenderer(org.biojava.bio.gui.sequence.SequenceRenderer)">_setRenderer(SequenceRenderer)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePanel.html" title="class in org.biojava.bio.gui.sequence">SequencePanel</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="./org/biojava/bio/gui/sequence/SequencePoster.html#_setRenderer(org.biojava.bio.gui.sequence.SequenceRenderer)">_setRenderer(SequenceRenderer)</a></span> - Method in class org.biojava.bio.gui.sequence.<a href="./org/biojava/bio/gui/sequence/SequencePoster.html" title="class in org.biojava.bio.gui.sequence">SequencePoster</a></dt>
<dd>
<div class="block"><span class="strong">Deprecated.</span></div>
</dd>
</dl>
<a href="#_A_">A</a> <a href="#_B_">B</a> <a href="#_C_">C</a> <a href="#_D_">D</a> <a href="#_E_">E</a> <a href="#_F_">F</a> <a href="#_G_">G</a> <a href="#_H_">H</a> <a href="#_I_">I</a> <a href="#_J_">J</a> <a href="#_K_">K</a> <a href="#_L_">L</a> <a href="#_M_">M</a> <a href="#_N_">N</a> <a href="#_O_">O</a> <a href="#_P_">P</a> <a href="#_Q_">Q</a> <a href="#_R_">R</a> <a href="#_S_">S</a> <a href="#_T_">T</a> <a href="#_U_">U</a> <a href="#_V_">V</a> <a href="#_W_">W</a> <a href="#_X_">X</a> <a href="#_Y_">Y</a> <a href="#_Z_">Z</a> <a href="#___">_</a> </div>
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