/usr/lib/x86_64-linux-gnu/perl5/5.20/LibSBML.pod is in libsbml5-perl 5.10.0+dfsg-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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LibSBML -- interface to the libSBML library
=head1 SYNOPSIS
# Change the following path to wherever your copy is installed.
use lib '/usr/local/lib/perl5/site_perl';
use File::Spec;
use LibSBML;
use strict;
my $file = File::Spec->rel2abs('FOO.xml');
my $rd = new LibSBML::SBMLReader;
my $document = $rd->readSBML($file);
# Check for reading errors:
my $errors = $document->getNumErrors();
# Print errors, if any, to stderr.
if ($errors > 0) {
$document->printErrors();
die "Errors while reading $file";
}
my $model = $document->getModel() || die "No Model found in $file";
...
=head1 DESCRIPTION
The LibSBML.pm package gives access to almost all functions in libSBML
(http://sbml.org). The Perl wrapper is generated using SWIG
http://www.swig.org/ with relatively little manual intervention.
=head1 AUTHORS
Christoph Flamm <xtof@tbi.univie.ac.at>
Rainer Machne <raim@tbi.univie.ac.at>
=head1 FUNCTION INDEX
=over 8
=item getLibSBMLVersion
Returns the version number of this copy of libSBML as an integer.
@return the libSBML version as an integer; version 1.2.3 becomes 10203.
=item getLibSBMLDottedVersion
Returns the version number of this copy of libSBML as a string.
@return the libSBML version as a string; version 1.2.3 becomes
"1.2.3".
@see getLibSBMLVersionString()
=item getLibSBMLVersionString
Returns the version number of this copy of libSBML as a string without
periods.
@return the libSBML version as a string: version 1.2.3 becomes "10203".
@see getLibSBMLDottedVersion()
=item isLibSBMLCompiledWith
Returns an indication whether libSBML has been compiled with
against a specific library.
@param option the library to test against, this can be one of
"expat", "libxml", "xerces-c", "bzip2", "zip"
@return 0 in case the libSBML has not been compiled against
that library and non-zero otherwise (for libraries
that define an integer version number that number will
be returned).
@see getLibSBMLDependencyVersionOf(const char option)
=item getLibSBMLDependencyVersionOf
Returns the version string for the dependency library used.
@param option the library for which the version
should be retrieved, this can be one of
"expat", "libxml", "xerces-c", "bzip2", "zip"
@return NULL in case libSBML has not been compiled against
that library and a version string otherwise.
@see isLibSBMLCompiledWith(const char option)
=item OperationReturnValue_toString
This method takes an SBML operation return value and returns a string representing
the code.
@param returnValue the operation return value to convert to a string
@return a human readable name for the given
@if clike #OperationReturnValues_t value@else operation return value @endif.
@note The caller does not own the returned string and is therefore not
allowed to modify it.
=back
=head2 IdList
@sbmlpackage{core}
@htmlinclude pkg-marker-core.html Maintains a list of SIds.
@internal
=over
=item IdList::append
@internal
Appends id to the list of ids.
=item IdList::contains
@internal
Returns true if id is already in this IdList, false otherwise.
@return true if id is already in this IdList, false otherwise.
=item IdList::removeIdsBefore
@internal
Removes all ids in this IdList before the given C<id>.
=item IdList::size
@internal
Returns the number of ids in this IdList.
@return the number of ids in this IdList.
=back
=head2 IdentifierTransformer
@sbmlpackage{core}
@htmlinclude pkg-marker-core.html Base class for identifier transformers.
@internal
=over
=back
=head2 ElementFilter
@sbmlpackage{core}
@htmlinclude pkg-marker-core.html
@internal
=over
=back
=head2 SBMLReader
@sbmlpackage{core}
@htmlinclude pkg-marker-core.html Methods for reading SBML from files and text strings.
@htmlinclude not-sbml-warning.html
The SBMLReader class provides the main interface for reading SBML
content from files and strings. The methods for reading SBML all return
an SBMLDocument object representing the results.
In the case of failures (such as if the SBML contains errors or a file
cannot be read), the errors will be recorded with the SBMLErrorLog
object kept in the SBMLDocument returned by SBMLReader. Consequently,
immediately after calling a method on SBMLReader, callers should always
check for errors and warnings using the methods for this purpose
provided by SBMLDocument.
For convenience as well as easy access from other languages besides C++,
this file also defines two global functions,
libsbml::readSBML(@if java String filename@endif)
and libsbml::readSBMLFromString(@if java String xml@endif).
They are equivalent to creating an SBMLReader
object and then calling the
SBMLReader::readSBML(@if java String filename@endif) or
SBMLReader::readSBMLFromString(@if java String xml@endif)
methods, respectively.
@section compression Support for reading compressed files
LibSBML provides support for reading (as well as writing) compressed
SBML files. The process is transparent to the calling
application—the application does not need to do anything
deliberate to invoke the functionality. If a given SBML filename ends
with an extension for the I<gzip>, I<zip> or I<bzip2> compression
formats (respectively, @c .gz, @c .zip, or @c .bz2), then the methods
SBMLReader::readSBML(@if java String filename@endif) and
SBMLWriter::writeSBML(@if java SBMLDocument d, String filename@endif)
will automatically decompress and compress the file while writing and
reading it. If the filename has no such extension, it
will be read and written uncompressed as normal.
The compression feature requires that the I<zlib> (for I<gzip> and @em
zip formats) and/or I<bzip2> (for I<bzip2> format) be available on the
system running libSBML, and that libSBML was configured with their
support compiled-in. Please see the libSBML @if clike <a href="libsbml-installation.html">installation instructions</a> @endif@if python <a href="libsbml-installation.html">installation instructions</a> @endif@if java <a href="../../../libsbml-installation.html">installation instructions</a> @endif@~ for more information about this. The methods
@if java SBMLReader::hasZlib()@else hasZlib()@endif@~ and
@if java SBMLReader::hasBzip2()@else hasBzip2()@endif@~
can be used by an application to query at run-time whether support
for the compression libraries is available in the present copy of
libSBML.
Support for compression is not mandated by the SBML standard, but
applications may find it helpful, particularly when large SBML models
are being communicated across data links of limited bandwidth.
=over
=item SBMLReader::SBMLReader
Creates a new SBMLReader and returns it.
The libSBML SBMLReader objects offer methods for reading SBML in
XML form from files and text strings.
=item SBMLReader::readSBML
Reads an SBML document from a file.
This method is identical to SBMLReader::readSBMLFromFile(@if java String filename@endif).
If the file named C<filename> does not exist or its content is not
valid SBML, one or more errors will be logged with the SBMLDocument
object returned by this method. Callers can use the methods on
SBMLDocument such as SBMLDocument::getNumErrors() and
SBMLDocument::getError(@if java long n@endif) to get the errors. The object returned by
SBMLDocument::getError(@if java long n@endif) is an SBMLError object, and it has methods to
get the error code, category, and severity level of the problem, as
well as a textual description of the problem. The possible severity
levels range from informational messages to fatal errors; see the
documentation for SBMLError for more information.
If the file C<filename> could not be read, the file-reading error will
appear first. The error code @if clike (a value drawn from the enumeration
#XMLErrorCode_t) @endif@~ can provide a clue about what happened. For example,
a file might be unreadable (either because it does not actually exist
or because the user does not have the necessary access privileges to
read it) or some sort of file operation error may have been reported
by the underlying operating system. Callers can check for these
situations using a program fragment such as the following:
@if clike
@verbatim
SBMLReader reader;
SBMLDocument doc = reader.readSBMLFromFile(filename);
if (doc->getNumErrors() E<gt> 0)
{
if (doc->getError(0)->getErrorId() == XMLError::XMLFileUnreadable)
{
// Handle case of unreadable file here.
}
else if (doc->getError(0)->getErrorId() == XMLError::XMLFileOperationError)
{
// Handle case of other file operation error here.
}
else
{
// Handle other cases -- see error codes defined in XMLErrorCode_t
// for other possible cases to check.
}
}
@endverbatim
@endif@if java
@verbatim
SBMLReader reader = new SBMLReader();
SBMLDocument doc = reader.readSBMLFromFile(filename);
if (doc.getNumErrors() E<gt> 0)
{
if (doc.getError(0).getErrorId() == libsbmlConstants.XMLFileUnreadable)
{
// Handle case of unreadable file here.
}
else if (doc.getError(0).getErrorId() == libsbmlConstants.XMLFileOperationError)
{
// Handle case of other file operation error here.
}
else
{
// Handle other error cases.
}
}
@endverbatim
@endif@if python
@verbatim
reader = SBMLReader()
doc = reader.readSBMLFromFile(filename)
if doc.getNumErrors() E<gt> 0:
if doc.getError(0).getErrorId() == libsbml.XMLFileUnreadable:
# Handle case of unreadable file here.
elif doc.getError(0).getErrorId() == libsbml.XMLFileOperationError:
# Handle case of other file error here.
else:
# Handle other error cases here.
@endverbatim
@endif@if csharp
@verbatim
SBMLReader reader = new SBMLReader();
SBMLDocument doc = reader.readSBMLFromFile(filename);
if (doc.getNumErrors() E<gt> 0)
{
if (doc.getError(0).getErrorId() == libsbmlcs.libsbml.XMLFileUnreadable)
{
// Handle case of unreadable file here.
}
else if (doc.getError(0).getErrorId() == libsbmlcs.libsbml.XMLFileOperationError)
{
// Handle case of other file operation error here.
}
else
{
// Handle other cases -- see error codes defined in XMLErrorCode_t
// for other possible cases to check.
}
}
@endverbatim
@endif@~
C<opydetails> doc_sbmlreader_if_compressed
C<opydetails> doc_config_for_reading_zipped_files
@param filename the name or full pathname of the file to be read.
@return a pointer to the SBMLDocument created from the SBML content.
C<opydetails> doc_note_sbmlreader_error_handling
@see SBMLError
@see SBMLDocument
=item SBMLReader::readSBMLFromFile
Reads an SBML document from a file.
This method is identical to SBMLReader::readSBML(@if java String filename@endif).
If the file named C<filename> does not exist or its content is not
valid SBML, one or more errors will be logged with the SBMLDocument
object returned by this method. Callers can use the methods on
SBMLDocument such as SBMLDocument::getNumErrors() and
SBMLDocument::getError(@if java long n@endif) to get the errors. The object returned by
SBMLDocument::getError(@if java long n@endif) is an SBMLError object, and it has methods to
get the error code, category, and severity level of the problem, as
well as a textual description of the problem. The possible severity
levels range from informational messages to fatal errors; see the
documentation for SBMLError for more information.
If the file C<filename> could not be read, the file-reading error will
appear first. The error code @if clike (a value drawn from the enumeration
#XMLErrorCode_t)@endif@~ can provide a clue about what happened. For example,
a file might be unreadable (either because it does not actually exist
or because the user does not have the necessary access privileges to
read it) or some sort of file operation error may have been reported
by the underlying operating system. Callers can check for these
situations using a program fragment such as the following:
@if clike
@verbatim
SBMLReader reader = new SBMLReader();
SBMLDocument doc = reader.readSBML(filename);
if (doc->getNumErrors() E<gt> 0)
{
if (doc->getError(0)->getErrorId() == XMLError::FileUnreadable)
{
// Handle case of unreadable file here.
}
else if (doc->getError(0)->getErrorId() == XMLError::FileOperationError)
{
// Handle case of other file operation error here.
}
else
{
// Handle other cases -- see error codes defined in XMLErrorCode_t
// for other possible cases to check.
}
}
@endverbatim
@endif@if java
@verbatim
SBMLReader reader = new SBMLReader();
SBMLDocument doc = reader.readSBMLFromFile(filename);
if (doc.getNumErrors() E<gt> 0)
{
if (doc.getError(0).getErrorId() == libsbmlConstants.XMLFileUnreadable)
{
// Handle case of unreadable file here.
}
else if (doc.getError(0).getErrorId() == libsbmlConstants.XMLFileOperationError)
{
// Handle case of other file operation error here.
}
else
{
// Handle other error cases.
}
}
@endverbatim
@endif@if python
@verbatim
reader = SBMLReader()
doc = reader.readSBMLFromFile(filename)
if doc.getNumErrors() E<gt> 0:
if doc.getError(0).getErrorId() == libsbml.XMLFileUnreadable:
# Handle case of unreadable file here.
elif doc.getError(0).getErrorId() == libsbml.XMLFileOperationError:
# Handle case of other file error here.
else:
# Handle other error cases here.
@endverbatim
@endif@~
C<opydetails> doc_sbmlreader_if_compressed
C<opydetails> doc_config_for_reading_zipped_files
@param filename the name or full pathname of the file to be read.
@return a pointer to the SBMLDocument created from the SBML content.
C<opydetails> doc_note_sbmlreader_error_handling
@see SBMLError
@see SBMLDocument
=item SBMLReader::readSBMLFromString
Reads an SBML document from the given XML string.
This method is flexible with respect to the presence of an XML
declaration at the beginning of the string. In particular, if the
string in C<xml> does not begin with the XML declaration
C<<?xml version='1.0' encoding='UTF-8'?>>, then this
method will automatically prepend the declaration to C<xml>.
This method will log a fatal error if the content given in the
parameter C<xml> is not SBML. See the method documentation for
SBMLReader::readSBML(@if java String filename@endif)
for an example of code for testing the returned error code.
@param xml a string containing a full SBML model
@return a pointer to the SBMLDocument created from the SBML content.
@note When using this method to read an SBMLDocument that uses
the SBML L3 Hierarchical Model Composition package (comp) the
document location cannot be set automatically. Thus, if the model
contains references to ExternalModelDefinitions, it will be necessary
to manually set the document URI location (setLocationURI) in order
to facilitate resolving these models.
@see SBMLReader::readSBML(@if java String filename@endif)
=item SBMLReader::hasZlib
Static method; returns C<true> if this copy of libSBML supports
<i>gzip</I> and <i>zip</i> format compression.
@return C<true> if libSBML has been linked with the <i>zlib</i>
library, C<false> otherwise.
C<opydetails> doc_note_static_methods
@see @if clike hasBzip2() @else SBMLReader::hasBzip2() @endif@~
=item SBMLReader::hasBzip2
Static method; returns C<true> if this copy of libSBML supports
<i>bzip2</i> format compression.
@return C<true> if libSBML is linked with the <i>bzip2</i>
libraries, C<false> otherwise.
C<opydetails> doc_note_static_methods
@see @if clike hasZlib() @else SBMLReader::hasZlib() @endif@~
=item SBMLReader::readInternal
@internal
Used by readSBML() and readSBMLFromString().
@if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
=item readSBML
Reads an SBML document from the given file C<filename>.
If C<filename> does not exist, or it is not an SBML file, an error will
be logged in the error log of the SBMLDocument object returned by this
method. Calling programs can inspect this error log to determine
the nature of the problem. Please refer to the definition of
SBMLDocument_t for more information about the error reporting mechanism.
<code>
SBMLReader_t sr;\n
SBMLDocument_t d;
sr = SBMLReader_create();
d = SBMLReader_readSBML(reader, filename);
if (SBMLDocument_getNumErrors(d) E<gt> 0)\n
{\n
if (XMLError_getId(SBMLDocument_getError(d, 0))
== SBML_READ_ERROR_FILE_NOT_FOUND)\n
if (XMLError_getId(SBMLDocument_getError(d, 0))
== SBML_READ_ERROR_NOT_SBML)\n
}\n
</code>
If the filename ends with @em .gz, the file will be read as a I<gzip> file.
Similary, if the filename ends with @em .zip or @em .bz2, the file will be
read as a I<zip> or I<bzip2> file, respectively. Otherwise, the fill will be
read as an uncompressed file.
If the filename ends with @em .zip, only the first file in the archive will
be read if the zip archive contains two or more files.
To read a gzip/zip file, underlying libSBML needs to be linked with zlib
at compile time. Also, underlying libSBML needs to be linked with bzip2
to read a bzip2 file. File unreadable error will be logged if a compressed
file name is given and underlying libSBML is not linked with the corresponding
required library.
SBMLReader_hasZlib() and SBMLReader_hasBzip2() can be used to check
whether libSBML is linked with each library.
@return a pointer to the SBMLDocument read.
@if conly
@memberof SBMLReader_t
@endif
=item readSBMLFromFile
Reads an SBML document from the given file C<filename>.
If C<filename> does not exist, or it is not an SBML file, an error will
be logged in the error log of the SBMLDocument object returned by this
method. Calling programs can inspect this error log to determine
the nature of the problem. Please refer to the definition of
SBMLDocument_t for more information about the error reporting mechanism.
<code>
SBMLReader_t sr;\n
SBMLDocument_t d;
sr = SBMLReader_create();
d = SBMLReader_readSBML(reader, filename);
if (SBMLDocument_getNumErrors(d) E<gt> 0)\n
{\n
if (XMLError_getId(SBMLDocument_getError(d, 0))
== SBML_READ_ERROR_FILE_NOT_FOUND)\n
if (XMLError_getId(SBMLDocument_getError(d, 0))
== SBML_READ_ERROR_NOT_SBML)\n
}\n
</code>
If the filename ends with @em .gz, the file will be read as a I<gzip> file.
Similary, if the filename ends with @em .zip or @em .bz2, the file will be
read as a I<zip> or I<bzip2> file, respectively. Otherwise, the fill will be
read as an uncompressed file.
If the filename ends with @em .zip, only the first file in the archive will
be read if the zip archive contains two or more files.
To read a gzip/zip file, underlying libSBML needs to be linked with zlib
at compile time. Also, underlying libSBML needs to be linked with bzip2
to read a bzip2 file. File unreadable error will be logged if a compressed
file name is given and underlying libSBML is not linked with the corresponding
required library.
SBMLReader_hasZlib() and SBMLReader_hasBzip2() can be used to check
whether libSBML is linked with each library.
@return a pointer to the SBMLDocument read.
@if conly
@memberof SBMLReader_t
@endif
=item readSBMLFromString
Reads an SBML document from the given XML string C<xml>.
If the string does not begin with XML declaration,
@verbatim
<?xml version='1.0' encoding='UTF-8'?>
@endverbatim
an XML declaration string will be prepended.
This method will report an error if the given string C<xml> is not SBML.
The error will be logged in the error log of the SBMLDocument_t structure
returned by this method. Calling programs can inspect this error log to
determine the nature of the problem. Please refer to the definition of
SBMLDocument for more information about the error reporting mechanism.
@return a pointer to the SBMLDocument_t read.
@note When using this method to read an SBMLDocument that uses
the SBML L3 Hierarchical Model Composition package (comp) the
document location cannot be set automatically. Thus, if the model
contains references to ExternalModelDefinitions, it will be necessary
to manually set the document URI location (setLocationURI) in order
to facilitate resolving these models.
@if conly
@memberof SBMLReader_t
@endif
=back
=head2 SBMLWriter
@sbmlpackage{core}
@htmlinclude pkg-marker-core.html Methods for writing SBML to files and text strings.
@htmlinclude not-sbml-warning.html
The SBMLWriter class is the converse of SBMLReader, and provides the
main interface for serializing SBML models into XML and writing the
result to an output stream or to files and text strings. The methods
for writing SBML all take an SBMLDocument object and a destination.
They return a boolean or integer value to indicate success or failure.
@section compression Support for writing compressed files
LibSBML provides support for writing (as well as reading) compressed
SBML files. The process is transparent to the calling
application—the application does not need to do anything
deliberate to invoke the functionality. If a given SBML filename ends
with an extension for the I<gzip>, I<zip> or I<bzip2> compression
formats (respectively, C<".gz">,
C<".zip">, or C<".bz2">),
then the methods
SBMLWriter::writeSBML(@if java SBMLDocument d, String filename@endif)
and SBMLReader::readSBML(@if java String filename@endif)
will automatically compress and decompress the file while writing and
reading it. If the filename has no such extension, it
will be written and read uncompressed as normal.
The compression feature requires that the I<zlib> (for I<gzip> and @em
zip formats) and/or I<bzip2> (for I<bzip2> format) be available on the
system running libSBML, and that libSBML was configured with their
support compiled-in. Please see the libSBML @if clike <a href="libsbml-installation.html">installation instructions</a>@endif@if python <a href="libsbml-installation.html">installation instructions</a>@endif@if java <a href="../../../libsbml-installation.html">installation instructions</a>@endif@~ for
more information about this. The methods
SBMLWriter::hasZlib() and
SBMLWriter::hasBzip2()
can be used by an application to query at run-time whether support
for the compression libraries is available in the present copy of
libSBML.
Support for compression is not mandated by the SBML standard, but
applications may find it helpful, particularly when large SBML models
are being communicated across data links of limited bandwidth.
=over
=item SBMLWriter::SBMLWriter
Creates a new SBMLWriter.
The libSBML SBMLWriter objects offer methods for writing SBML in
XML form to files and text strings.
=item SBMLWriter::setProgramName
Sets the name of this program, i.e., the program that is about to
write out the SBMLDocument.
If the program name and version are set (see
SBMLWriter::setProgramVersion(@if java String version@endif)), the
following XML comment, intended for human consumption, will be written
at the beginning of the XML document:
@verbatim
<!-- Created by <program name> version <program version>
on yyyy-MM-dd HH:mm with libSBML version <libsbml version>. -->
@endverbatim
If the program name and version are not set at some point before
calling the writeSBML() methods, no such comment is written out.
@param name the name of this program (where "this program" refers to
program in which libSBML is embedded, not libSBML itself!)
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@see setProgramVersion(const std::string& version)
=item SBMLWriter::setProgramVersion
Sets the version of this program, i.e., the program that is about to
write out the SBMLDocument.
If the program version and name are set (see
SBMLWriter::setProgramName(@if java String name@endif)), the
following XML comment, intended for human consumption, will be written
at the beginning of the document:
@verbatim
<!-- Created by <program name> version <program version>
on yyyy-MM-dd HH:mm with libSBML version <libsbml version>. -->
@endverbatim
If the program version and name are not set at some point before
calling the writeSBML() methods, no such comment is written out.
@param version the version of this program (where "this program"
refers to program in which libSBML is embedded, not libSBML itself!)
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@see setProgramName(const std::string& name)
=item SBMLWriter::writeSBML
Writes the given SBML document to filename.
@htmlinclude assuming-compressed-file.html
@param d the SBML document to be written
@param filename the name or full pathname of the file where the SBML
is to be written.
@return C<true> on success and C<false> if the filename could not be
opened for writing.
@note @htmlinclude note-writing-zipped-files.html
@see setProgramVersion(const std::string& version)
@see setProgramName(const std::string& name)
=item SBMLWriter::writeSBML
Writes the given SBML document to the output stream.
@param d the SBML document to be written
@param stream the stream object where the SBML is to be written.
@return C<true> on success and C<false> if one of the underlying
parser components fail (rare).
@see setProgramVersion(const std::string& version)
@see setProgramName(const std::string& name)
=item SBMLWriter::writeToString
@internal
Writes the given SBML document to an in-memory string and returns a
pointer to it.
The string is owned by the caller and should be freed (with C<free>())
when no longer needed.
@param d the SBML document to be written
@return the string on success and C<0> if one of the underlying parser
components fail.
@see setProgramVersion(const std::string& version)
@see setProgramName(const std::string& name)
=item SBMLWriter::writeSBMLToFile
Writes the given SBML document to filename.
@htmlinclude assuming-compressed-file.html
@param d the SBML document to be written
@param filename the name or full pathname of the file where the SBML
is to be written.
@return C<true> on success and C<false> if the filename could not be
opened for writing.
@note @htmlinclude note-writing-zipped-files.html
@see setProgramVersion(const std::string& version)
@see setProgramName(const std::string& name)
=item SBMLWriter::writeSBMLToString
Writes the given SBML document to an in-memory string and returns a
pointer to it.
The string is owned by the caller and should be freed (with C<free>())
when no longer needed.
@param d the SBML document to be written
@return the string on success and C<0> if one of the underlying parser
components fail.
@see setProgramVersion(const std::string& version)
@see setProgramName(const std::string& name)
=item SBMLWriter::hasZlib
Predicate returning C<true> if this copy of libSBML has been linked
with the <em>zlib</em> library.
LibSBML supports reading and writing files compressed with either
bzip2 or zip/gzip compression. The facility depends on libSBML having
been compiled with the necessary support libraries. This method
allows a calling program to inquire whether that is the case for the
copy of libSBML it is using.
@return C<true> if libSBML is linked with zlib, C<false> otherwise.
C<opydetails> doc_note_static_methods
@see @if clike hasBzip2() @else SBMLWriter::hasBzip2() @endif@~
=item SBMLWriter::hasBzip2
Predicate returning C<true> if this copy of libSBML has been linked
with the <em>bzip2</em> library.
LibSBML supports reading and writing files compressed with either
bzip2 or zip/gzip compression. The facility depends on libSBML having
been compiled with the necessary support libraries. This method
allows a calling program to inquire whether that is the case for the
copy of libSBML it is using.
@return C<true> if libSBML is linked with bzip2, C<false> otherwise.
C<opydetails> doc_note_static_methods
@see @if clike hasZlib() @else SBMLWriter::hasZlib() @endif@~
=item writeSBML
Writes the given SBML document C<d> to the file named by C<filename>.
This convenience function is functionally equivalent to:
SBMLWriter_writeSBML(SBMLWriter_create(), d, filename);
@htmlinclude assuming-compressed-file.html
@param d the SBMLDocument object to be written out in XML format
@param filename a string giving the path to a file where the XML
content is to be written.
@return C<1> on success and C<0> (zero) if C<filename> could not be
written. Some possible reasons for failure include (a) being unable to
open the file, and (b) using a filename that indicates a compressed SBML
file (i.e., a filename ending in C<".zip"> or
similar) when the compression functionality has not been enabled in
the underlying copy of libSBML.
@see SBMLWriter::hasZlib()
@see SBMLWriter::hasBzip2()
@if conly
@memberof SBMLWriter_t
@endif
=item writeSBMLToString
Writes the given SBML document C<d> to an in-memory string and returns a
pointer to it. The string is owned by the caller and should be freed
(with free()) when no longer needed. This convenience function is
functionally equivalent to:
SBMLWriter_writeSBMLToString(SBMLWriter_create(), d);
but does not require the caller to create an SBMLWriter object first.
@param d an SBMLDocument object to be written out in XML format
@return the string on success and C<NULL> if one of the underlying parser
components fail.
@if clike @warning Note that the string is owned by the caller and
should be freed after it is no longer needed.@endif@~
@if conly
@memberof SBMLWriter_t
@endif
=item writeSBMLToFile
Writes the given SBML document C<d> to the file C<filename>.
This convenience function is functionally equivalent to:
SBMLWriter_writeSBMLToFile(SBMLWriter_create(), d, filename);
but that does not require the caller to create an SBMLWriter object first.
@htmlinclude assuming-compressed-file.html
@param d an SBMLDocument object to be written out in XML format
@param filename a string giving the path to a file where the XML
content is to be written.
@return C<1> on success and C<0> (zero) if C<filename> could not be
written. Some possible reasons for failure include (a) being unable to
open the file, and (b) using a filename that indicates a compressed SBML
file (i.e., a filename ending in C<".zip"> or
similar) when the compression functionality has not been enabled in
the underlying copy of libSBML.
@if clike @warning Note that the string is owned by the caller and
should be freed (with the normal string C<free()> C++
function) after it is no longer needed.@endif@~
@see SBMLWriter::hasZlib()
@see SBMLWriter::hasBzip2()
@if conly
@memberof SBMLWriter_t
@endif
=item SBMLTypeCode_toString
This method takes an SBML type code and returns a string representing
the code.
@if clike LibSBML attaches an identifying code to every kind of SBML
object. These are known as <em>SBML type codes</em>. The set of
possible type codes is defined in the enumeration #SBMLTypeCode_t.
The names of the type codes all begin with the characters @c
SBML_. @endif@if java LibSBML attaches an identifying code to every
kind of SBML object. These are known as <em>SBML type codes</em>. In
other languages, the set of type codes is stored in an enumeration; in
the Java language interface for libSBML, the type codes are defined as
static integer constants in the interface class {@link
libsbmlConstants}. The names of the type codes all begin with the
characters C<SBML_>. @endif@if python LibSBML attaches an identifying
code to every kind of SBML object. These are known as <em>SBML type
codes</em>. In the Python language interface for libSBML, the type
codes are defined as static integer constants in the interface class
@link libsbml@endlink. The names of the type codes all begin with the
characters C<SBML_>. @endif@if csharp LibSBML attaches an identifying
code to every kind of SBML object. These are known as <em>SBML type
codes</em>. In the C# language interface for libSBML, the type codes
are defined as static integer constants in the interface class @link
libsbml@endlink. The names of the type codes all begin with
the characters C<SBML_>. @endif@~
@return a human readable name for the given
@if clike #SBMLTypeCode_t value@else SBML type code@endif.
@note The caller does not own the returned string and is therefore not
allowed to modify it.
=back
=head2 SBase
@sbmlpackage{core}
@htmlinclude pkg-marker-core.html Implementation of SBase, the base class of most SBML
objects.
Most components in SBML are derived from a single abstract base type,
SBase. In addition to serving as the parent class for most other
classes of objects in SBML, this base type is designed to allow a
modeler or a software package to attach arbitrary information to each
major element or list in an SBML model.
SBase has an optional subelement called "notes". It is intended to
serve as a place for storing optional information intended to be seen by
humans. An example use of the "notes" element would be to contain
formatted user comments about the model element in which the "notes"
element is enclosed. There are certain conditions on the XHTML content
permitted inside the "notes" element; please consult the <a
target="_blank" href="http://sbml.org/Documents/Specifications">SBML
specification document</a> corresponding to the SBML Level and Version
of your model for more information about the requirements for "notes"
content.
SBase has another optional subelement called "annotation". Whereas the
"notes" element described above is a container for content to be shown
directly to humans, the "annotation" element is a container for optional
software-generated content I<not> meant to be shown to humans. The
element's content type is <a target="_blank"
href="http://www.w3.org/TR/2004/REC-xml-20040204/#elemdecls">XML type
"any"</a>, allowing essentially arbitrary data content. SBML places
only a few restrictions on the organization of the content; these are
intended to help software tools read and write the data as well as help
reduce conflicts between annotations added by different tools. As is
the case with "notes", it is important to refer to the <a
target="_blank" href="http://sbml.org/Documents/Specifications">SBML
specification document</a> corresponding to the SBML Level and Version
of your model for more information about the requirements for
"annotation" content.
It is worth pointing out that the "annotation" element in the definition
of SBase exists in order that software developers may attach optional
application-specific data to the elements in an SBML model. However, it
is important that this facility not be misused. In particular, it is
<em>critical</em> that data essential to a model definition or that can
be encoded in existing SBML elements is <em>not</em> stored in
"annotation". Parameter values, functional dependencies between model
elements, etc., should not be recorded as annotations. It is crucial to
keep in mind the fact that data placed in annotations can be freely
ignored by software applications. If such data affects the
interpretation of a model, then software interoperability is greatly
impeded.
SBML Level 2 introduced an optional SBase attribute named "metaid" for
supporting metadata annotations using RDF (<a target="_blank"
href="http://www.w3.org/RDF/">Resource Description Format</a>). The
attribute value has the data type <a
href="http://www.w3.org/TR/REC-xml/#id">XML ID</a>, the XML identifier
type, which means each "metaid" value must be globally unique within an
SBML file. (Importantly, this uniqueness criterion applies across any
attribute with type <a href="http://www.w3.org/TR/REC-xml/#id">XML
ID</a>, not just the "metaid" attribute used by SBML—something to
be aware of if your application-specific XML content inside the
"annotation" subelement happens to use <a
href="http://www.w3.org/TR/REC-xml/#id">XML ID</a>.) The "metaid" value
serves to identify a model component for purposes such as referencing
that component from metadata placed within "annotation" subelements.
Beginning with SBML Level 2 Version 3, SBase also has an optional
attribute named "sboTerm" for supporting the use of the Systems Biology
Ontology. In SBML proper, the data type of the attribute is a string of
the form "SBO:NNNNNNN", where "NNNNNNN" is a seven digit integer number;
libSBML simplifies the representation by only storing the "NNNNNNN"
integer portion. Thus, in libSBML, the "sboTerm" attribute on SBase has
data type C<int>, and SBO identifiers are stored simply as integers.
(For convenience, SBase offers methods for returning both the integer
form and a text-string form of the SBO identifier.) SBO terms are a
type of optional annotation, and each different class of SBML object
derived from SBase imposes its own requirements about the values
permitted for "sboTerm". Please consult the SBML Level 2
Version 4 specification for more information about the use of SBO
and the "sboTerm" attribute.
Finally, note that, in the list of methods on SBase, there is no public
constructor because SBase is an abstract class. The constructors reside
in the subclasses derived from SBase.
@section sbase-miriam Standard format for annotations linking data resources
SBML Level 2 Versions 2, 3 and 4, and Level 3, define a proposed
regular format for encoding two particular categories of annotations:
(a) references to controlled vocabulary terms and database identifiers
which define and describe biological and biochemical entities in a
model; and (b) descriptions of the provenance of a model, including its
author(s) and modification history.
=over
=item SBase::accept
Accepts the given SBMLVisitor for this SBase object.
@param v the SBMLVisitor instance to be used
@return the result of calling C<v.visit()>.
=item SBase::clone
Creates and returns a deep copy of this SBase object.
@return a (deep) copy of this SBase object.
=item SBase::getElementBySId
Returns the first child element found that has the given C<id> in the
model-wide C<SId> namespace, or C<NULL> if no such object is found.
@param id string representing the "id" attribute value of the object
to find.
@return pointer to the first element found with the given identifier.
=item SBase::getElementByMetaId
Returns the first child element it can find with a specific "metaid"
attribute value, or C<NULL> if no such object is found.
C<opydetails> doc_what_is_metaid
@param metaid string representing the "metaid" attribute value of the
object to find.
@return pointer to the first element found with the given meta-identifier.
=item SBase::getAllElements
Returns a List of all child SBase objects, including those nested to
an arbitrary depth.
@return a pointer to a List of pointers to all children objects.
=item SBase::renameSIdRefs
Renames all the C<SIdRef> attributes on this element, including any
found in MathML content (if such exists).
C<opydetails> doc_what_is_sidref
This method works by looking at all attributes and (if appropriate)
mathematical formulas, comparing the identifiers to the value of @p
oldid. If any matches are found, the matching identifiers are replaced
with C<newid>. The method does I<not> descend into child elements.
@param oldid the old identifier
@param newid the new identifier
=item SBase::renameMetaIdRefs
Renames all the meta-identifier attributes on this element.
C<opydetails> doc_what_is_metaidref
This method works by looking at all meta-identifier attribute values,
comparing the identifiers to the value of C<oldid>. If any matches are
found, the matching identifiers are replaced with C<newid>. The method
does I<not> descend into child elements.
@param oldid the old identifier
@param newid the new identifier
=item SBase::renameUnitSIdRefs
Renames all the C<UnitSIdRef> attributes on this element.
C<opydetails> doc_what_is_unitsidref
This method works by looking at all unit identifier attribute values
(including, if appropriate, inside mathematical formulas), comparing the
unit identifiers to the value of C<oldid>. If any matches are found,
the matching identifiers are replaced with C<newid>. The method does
I<not> descend into child elements.
@param oldid the old identifier
@param newid the new identifier
=item SBase::replaceSIDWithFunction
@internal
If this object has a child 'math' object (or anything with ASTNodes in
general), replace all nodes with the name 'id' with the provided
function.
@note This function does nothing itself—subclasses with ASTNode
subelements must override this function.
=item SBase::divideAssignmentsToSIdByFunction
@internal
If the function of this object is to assign a value has a child 'math'
object (or anything with ASTNodes in general), replace the 'math'
object with the function (existing/function).
@note This function does nothing itself—subclasses with ASTNode
subelements must override this function.
=item SBase::multiplyAssignmentsToSIdByFunction
@internal
If this assignment assigns a value to the 'id' element, replace the 'math' object with the function (existing function).
=item SBase::getElementFromPluginsBySId
@internal
Returns the first child element found that has the given C<id> in the
model-wide SId namespace from all plug-ins associated with this
element, or C<NULL> if no such object is found.
@param id string representing the id of objects to find
@return pointer to the first element found with the given C<id>.
=item SBase::getElementFromPluginsByMetaId
@internal
Returns the first child element it can find with the given C<metaid> from
all plug-ins associated with this element, or C<NULL> if no such object
is found.
@param metaid string representing the metaid of objects to find
@return pointer to the first element found with the given C<metaid>.
=item SBase::hasNonstandardIdentifierBeginningWith
@internal
Check to see if the given prefix is used by any of the IDs defined by
extension elements excluding 'id' and 'metaid' attributes (as, for
example, the spatial id attributes 'spid').
=item SBase::prependStringToAllIdentifiers
@internal
Add the given string to all identifiers in the object. If the string
is added to anything other than an id or a metaid, this code is
responsible for tracking down and renaming all idRefs in the package
extention that identifier comes from.
=item SBase::transformIdentifiers
@internal
=item SBase::getAllElementsFromPlugins
Returns a List of all child SBase objects contained in SBML package
plug-ins.
C<opydetails> doc_what_are_plugins
This method walks down the list of all SBML Level 3 packages used
by this object and returns all child objects defined by those packages.
@return a pointer to a List of pointers to all children objects from
plug-ins.
=item SBase::getMetaId
Returns the value of the "metaid" attribute of this object.
C<opydetails> doc_what_is_metaid
@return the meta-identifier of this SBML object.
@see isSetMetaId()
@see setMetaId(const std::string& metaid)
=item SBase::getMetaId
Returns the value of the "metaid" attribute of this object.
C<opydetails> doc_what_is_metaid
@return the meta-identifier of this SBML object, as a string.
@see isSetMetaId()
@see setMetaId(const std::string& metaid)
=item SBase::getId
@internal
=item SBase::getName
@internal
=item SBase::getNotes
Returns the content of the "notes" subelement of this object as
a tree of XMLNode objects.
C<opydetails> doc_what_are_notes
The "notes" element content returned by this method will be in XML
form, but libSBML does not provide an object model specifically for
the content of notes. Callers will need to traverse the XML tree
structure using the facilities available on XMLNode and related
objects. For an alternative method of accessing the notes, see
getNotesString().
@return the content of the "notes" subelement of this SBML object as a
tree structure composed of XMLNode objects.
@see getNotesString()
@see isSetNotes()
@see setNotes(const XMLNode notes)
@see setNotes(const std::string& notes, bool addXHTMLMarkup)
@see appendNotes(const XMLNode notes)
@see appendNotes(const std::string& notes)
@see unsetNotes()
@see SyntaxChecker::hasExpectedXHTMLSyntax(@if java XMLNode xhtml@endif)
=item SBase::getNotes
Returns the content of the "notes" subelement of this object as
a tree of XMLNode objects.
C<opydetails> doc_what_are_notes
The "notes" element content returned by this method will be in XML
form, but libSBML does not provide an object model specifically for
the content of notes. Callers will need to traverse the XML tree
structure using the facilities available on XMLNode and related
objects. For an alternative method of accessing the notes, see
getNotesString().
@return the content of the "notes" subelement of this SBML object as a
tree structure composed of XMLNode objects.
@see getNotesString()
@see isSetNotes()
@see setNotes(const XMLNode notes)
@see setNotes(const std::string& notes, bool addXHTMLMarkup)
@see appendNotes(const XMLNode notes)
@see appendNotes(const std::string& notes)
@see unsetNotes()
@see SyntaxChecker::hasExpectedXHTMLSyntax(@if java XMLNode xhtml@endif)
=item SBase::getNotesString
Returns the content of the "notes" subelement of this object as a
string.
C<opydetails> doc_what_are_notes
For an alternative method of accessing the notes, see getNotes(),
which returns the content as an XMLNode tree structure. Depending on
an application's needs, one or the other method may be more
convenient.
@return the content of the "notes" subelement of this SBML object as a
string.
@see getNotes()
@see isSetNotes()
@see setNotes(const XMLNode notes)
@see setNotes(const std::string& notes, bool addXHTMLMarkup)
@see appendNotes(const XMLNode notes)
@see appendNotes(const std::string& notes)
@see unsetNotes()
@see SyntaxChecker::hasExpectedXHTMLSyntax(@if java XMLNode xhtml@endif)
=item SBase::getNotesString
Returns the content of the "notes" subelement of this object as a
string.
C<opydetails> doc_what_are_notes
For an alternative method of accessing the notes, see getNotes(),
which returns the content as an XMLNode tree structure. Depending on
an application's needs, one or the other method may be more
convenient.
@return the content of the "notes" subelement of this SBML object as a
string.
@see getNotes()
@see isSetNotes()
@see setNotes(const XMLNode notes)
@see setNotes(const std::string& notes, bool addXHTMLMarkup)
@see appendNotes(const XMLNode notes)
@see appendNotes(const std::string& notes)
@see unsetNotes()
@see SyntaxChecker::hasExpectedXHTMLSyntax(@if java XMLNode xhtml@endif)
=item SBase::getAnnotation
Returns the content of the "annotation" subelement of this object as
a tree of XMLNode objects.
C<opydetails> doc_what_are_annotations
The annotations returned by this method will be in XML form. LibSBML
provides an object model and related interfaces for certain specific
kinds of annotations, namely model history information and RDF
content. See the ModelHistory, CVTerm and RDFAnnotationParser classes
for more information about the facilities available.
@return the annotation of this SBML object as a tree of XMLNode objects.
@see getAnnotationString()
@see isSetAnnotation()
@see setAnnotation(const XMLNode annotation)
@see setAnnotation(const std::string& annotation)
@see appendAnnotation(const XMLNode annotation)
@see appendAnnotation(const std::string& annotation)
@see unsetAnnotation()
=item SBase::getAnnotation
Returns the content of the "annotation" subelement of this object as
a tree of XMLNode objects.
C<opydetails> doc_what_are_annotations
The annotations returned by this method will be in XML form. LibSBML
provides an object model and related interfaces for certain specific
kinds of annotations, namely model history information and RDF
content. See the ModelHistory, CVTerm and RDFAnnotationParser classes
for more information about the facilities available.
@return the annotation of this SBML object as a tree of XMLNode objects.
@see getAnnotationString()
@see isSetAnnotation()
@see setAnnotation(const XMLNode annotation)
@see setAnnotation(const std::string& annotation)
@see appendAnnotation(const XMLNode annotation)
@see appendAnnotation(const std::string& annotation)
@see unsetAnnotation()
=item SBase::getAnnotationString
Returns the content of the "annotation" subelement of this object as a
character string.
C<opydetails> doc_what_are_annotations
The annotations returned by this method will be in string form. See the
method getAnnotation() for a version that returns annotations in XML form.
@return the annotation of this SBML object as a character string.
@see getAnnotation()
@see isSetAnnotation()
@see setAnnotation(const XMLNode annotation)
@see setAnnotation(const std::string& annotation)
@see appendAnnotation(const XMLNode annotation)
@see appendAnnotation(const std::string& annotation)
@see unsetAnnotation()
=item SBase::getAnnotationString
Returns the content of the "annotation" subelement of this object as a
character string.
C<opydetails> doc_what_are_annotations
The annotations returned by this method will be in string form. See the
method getAnnotation() for a version that returns annotations in XML form.
@return the annotation of this SBML object as a character string.
@see getAnnotation()
@see isSetAnnotation()
@see setAnnotation(const XMLNode annotation)
@see setAnnotation(const std::string& annotation)
@see appendAnnotation(const XMLNode annotation)
@see appendAnnotation(const std::string& annotation)
@see unsetAnnotation()
=item SBase::getNamespaces
Returns a list of the XML Namespaces declared on this SBML document.
The SBMLNamespaces object encapsulates SBML Level/Version/namespaces
information. It is used to communicate the SBML Level, Version, and (in
Level 3) packages used in addition to SBML Level 3 Core.
@return the XML Namespaces associated with this SBML object, or C<NULL>
in certain very usual circumstances where a namespace is not set.
@see getLevel()
@see getVersion()
=item SBase::getSBMLDocument
Returns the SBMLDocument object containing I<this> object instance.
C<opydetails> doc_what_is_SBMLDocument
This method allows the caller to obtain the SBMLDocument for the
current object.
@return the parent SBMLDocument object of this SBML object.
@see getParentSBMLObject()
@see getModel()
=item SBase::getSBMLDocument
Returns the SBMLDocument object containing I<this> object instance.
C<opydetails> doc_what_is_SBMLDocument
This method allows the caller to obtain the SBMLDocument for the
current object.
@return the parent SBMLDocument object of this SBML object.
@see getParentSBMLObject()
@see getModel()
=item SBase::getParentSBMLObject
Returns the parent SBML object containing this object.
This returns the immediately-containing object. This method is
convenient when holding an object nested inside other objects in an
SBML model.
@return the parent SBML object of this SBML object.
@see getSBMLDocument()
@see getModel()
=item SBase::getParentSBMLObject
Returns the parent SBML object containing this object.
This returns the immediately-containing object. This method is
convenient when holding an object nested inside other objects in an
SBML model.
@return the parent SBML object of this SBML object.
@see getSBMLDocument()
@see getModel()
=item SBase::getAncestorOfType
Returns the first ancestor object that has the given SBML type code from the given package.
@if clike LibSBML attaches an identifying code to every kind of SBML
object. These are known as <em>SBML type codes</em>. The set of
possible type codes is defined in the enumeration #SBMLTypeCode_t.
The names of the type codes all begin with the characters @c
SBML_. @endif@if java LibSBML attaches an identifying code to every
kind of SBML object. These are known as <em>SBML type codes</em>. In
other languages, the set of type codes is stored in an enumeration; in
the Java language interface for libSBML, the type codes are defined as
static integer constants in the interface class {@link
libsbmlConstants}. The names of the type codes all begin with the
characters C<SBML_>. @endif@if python LibSBML attaches an identifying
code to every kind of SBML object. These are known as <em>SBML type
codes</em>. In the Python language interface for libSBML, the type
codes are defined as static integer constants in the interface class
@link libsbml@endlink. The names of the type codes all begin with the
characters C<SBML_>. @endif@if csharp LibSBML attaches an identifying
code to every kind of SBML object. These are known as <em>SBML type
codes</em>. In the C# language interface for libSBML, the type codes
are defined as static integer constants in the interface class @link
libsbmlcs.libsbml libsbml@endlink. The names of the type codes all begin with
the characters C<SBML_>. @endif@~
This method searches the tree of objects that are parents of this
object, and returns the first one that has the given SBML type code from
the given C<pkgName>.
@param type the SBML type code of the object sought
@param pkgName (optional) the short name of an SBML Level 3
package to which the sought-after object must belong
@return the ancestor SBML object of this SBML object that corresponds
to the given @if clike #SBMLTypeCode_t value@else SBML object type
code@endif, or C<NULL> if no ancestor exists.
@warning The optional argument C<pkgName> must be used for all type codes
from SBML Level 3 packages. Otherwise, the function will search the
"core" namespace alone, not find any corresponding elements, and return
NULL.
@if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
=item SBase::getAncestorOfType
Returns the first ancestor object that has the given SBML type code from the given package.
@if clike LibSBML attaches an identifying code to every kind of SBML
object. These are known as <em>SBML type codes</em>. The set of
possible type codes is defined in the enumeration #SBMLTypeCode_t.
The names of the type codes all begin with the characters @c
SBML_. @endif@if java LibSBML attaches an identifying code to every
kind of SBML object. These are known as <em>SBML type codes</em>. In
other languages, the set of type codes is stored in an enumeration; in
the Java language interface for libSBML, the type codes are defined as
static integer constants in the interface class {@link
libsbmlConstants}. The names of the type codes all begin with the
characters C<SBML_>. @endif@if python LibSBML attaches an identifying
code to every kind of SBML object. These are known as <em>SBML type
codes</em>. In the Python language interface for libSBML, the type
codes are defined as static integer constants in the interface class
@link libsbml@endlink. The names of the type codes all begin with the
characters C<SBML_>. @endif@if csharp LibSBML attaches an identifying
code to every kind of SBML object. These are known as <em>SBML type
codes</em>. In the C# language interface for libSBML, the type codes
are defined as static integer constants in the interface class @link
libsbmlcs.libsbml libsbml@endlink. The names of the type codes all begin with
the characters C<SBML_>. @endif@~
This method searches the tree of objects that are parents of this
object, and returns the first one that has the given SBML type code from
the given C<pkgName>.
@param type the SBML type code of the object sought
@param pkgName (optional) the short name of an SBML Level 3
package to which the sought-after object must belong
@return the ancestor SBML object of this SBML object that corresponds
to the given @if clike #SBMLTypeCode_t value@else SBML object type
code@endif, or C<NULL> if no ancestor exists.
@warning The optional argument C<pkgName> must be used for all type codes
from SBML Level 3 packages. Otherwise, the function will search the
"core" namespace alone, not find any corresponding elements, and return
NULL.
@if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
=item SBase::getSBOTerm
Returns the integer portion of the value of the "sboTerm" attribute of
this object.
Beginning with SBML Level 2 Version 3, objects derived from SBase have
an optional attribute named "sboTerm" for supporting the use of the
Systems Biology Ontology. In SBML proper, the data type of the
attribute is a string of the form "SBO:NNNNNNN", where "NNNNNNN" is a
seven digit integer number; libSBML simplifies the representation by
only storing the "NNNNNNN" integer portion. Thus, in libSBML, the
"sboTerm" attribute on SBase has data type C<int>, and SBO identifiers
are stored simply as integers. (For convenience, libSBML offers
methods for returning both the integer form and a text-string form of
the SBO identifier.)
SBO terms are a type of optional annotation, and each different class
of SBML object derived from SBase imposes its own requirements about
the values permitted for "sboTerm". Please consult the SBML
Level 2 Version 4 specification for more information about
the use of SBO and the "sboTerm" attribute.
@return the value of the "sboTerm" attribute as an integer, or C<-1>
if the value is not set.
=item SBase::getSBOTermID
Returns the string representation of the "sboTerm" attribute of
this object.
Beginning with SBML Level 2 Version 3, objects derived from SBase have
an optional attribute named "sboTerm" for supporting the use of the
Systems Biology Ontology. In SBML proper, the data type of the
attribute is a string of the form "SBO:NNNNNNN", where "NNNNNNN" is a
seven digit integer number; libSBML simplifies the representation by
only storing the "NNNNNNN" integer portion. Thus, in libSBML, the
"sboTerm" attribute on SBase has data type C<int>, and SBO identifiers
are stored simply as integers. This method returns the entire SBO
identifier as a text string in the form "SBO:NNNNNNN".
SBO terms are a type of optional annotation, and each different class
of SBML object derived from SBase imposes its own requirements about
the values permitted for "sboTerm". Please consult the SBML
Level 2 Version 4 specification for more information about
the use of SBO and the "sboTerm" attribute.
@return the value of the "sboTerm" attribute as a string (its value
will be of the form "SBO:NNNNNNN"), or an empty string if
the value is not set.
=item SBase::getSBOTermAsURL
Returns the identifiers.org URL representation of the "sboTerm" attribute of
this object.
This method returns the entire SBO
identifier as a text string in the form
"http://identifiers.org/biomodels.sbo/SBO:NNNNNNN".
SBO terms are a type of optional annotation, and each different class
of SBML object derived from SBase imposes its own requirements about
the values permitted for "sboTerm". Please consult the SBML
Level 2 Version 4 specification for more information about
the use of SBO and the "sboTerm" attribute.
@return the value of the "sboTerm" attribute as an identifiers.org URL
(its value will be of the form
"http://identifiers.org/biomodels.sbo/SBO:NNNNNNN"), or an empty string if
the value is not set.
=item SBase::getLine
Returns the line number on which this object first appears in the XML
representation of the SBML document.
@return the line number of this SBML object.
@note The line number for each construct in an SBML model is set upon
reading the model. The accuracy of the line number depends on the
correctness of the XML representation of the model, and on the
particular XML parser library being used. The former limitation
relates to the following problem: if the model is actually invalid
XML, then the parser may not be able to interpret the data correctly
and consequently may not be able to establish the real line number.
The latter limitation is simply that different parsers seem to have
their own accuracy limitations, and out of all the parsers supported
by libSBML, none have been 100% accurate in all situations. (At this
time, libSBML supports the use of <a target="_blank"
href="http://xmlsoft.org">libxml2</a>, <a target="_blank"
href="http://expat.sourceforge.net/">Expat</a> and <a target="_blank"
href="http://xerces.apache.org/xerces-c/">Xerces</a>.)
@see getColumn()
=item SBase::getColumn
Returns the column number on which this object first appears in the XML
representation of the SBML document.
@return the column number of this SBML object.
@note The column number for each construct in an SBML model is set
upon reading the model. The accuracy of the column number depends on
the correctness of the XML representation of the model, and on the
particular XML parser library being used. The former limitation
relates to the following problem: if the model is actually invalid
XML, then the parser may not be able to interpret the data correctly
and consequently may not be able to establish the real column number.
The latter limitation is simply that different parsers seem to have
their own accuracy limitations, and out of all the parsers supported
by libSBML, none have been 100% accurate in all situations. (At this
time, libSBML supports the use of <a target="_blank"
href="http://xmlsoft.org">libxml2</a>, <a target="_blank"
href="http://expat.sourceforge.net/">Expat</a> and <a target="_blank"
href="http://xerces.apache.org/xerces-c/">Xerces</a>.)
@see getLine()
=item SBase::getModelHistory
Returns the ModelHistory object, if any, attached to this object.
@return the ModelHistory object attached to this object, or C<NULL> if
none exist.
@note In SBML Level 2, model history annotations were only
permitted on the Model element. In SBML Level 3, they are
permitted on all SBML components derived from SBase.
=item SBase::getModelHistory
Returns the ModelHistory object, if any, attached to this object.
@return the ModelHistory object attached to this object, or C<NULL> if
none exist.
@note In SBML Level 2, model history annotations were only
permitted on the Model element. In SBML Level 3, they are
permitted on all SBML components derived from SBase.
=item SBase::isSetMetaId
Predicate returning C<true> if this object's "metaid" attribute is set.
C<opydetails> doc_what_is_metaid
@return C<true> if the "metaid" attribute of this SBML object is
set, C<false> otherwise.
@see getMetaId()
@see setMetaId(const std::string& metaid)
=item SBase::isSetId
@internal
=item SBase::isSetName
@internal
=item SBase::isSetNotes
Predicate returning C<true> if this
object's "notes" subelement exists and has content.
The optional SBML element named "notes", present on every major SBML
component type, is intended as a place for storing optional
information intended to be seen by humans. An example use of the
"notes" element would be to contain formatted user comments about the
model element in which the "notes" element is enclosed. Every object
derived directly or indirectly from type SBase can have a separate
value for "notes", allowing users considerable freedom when adding
comments to their models.
The format of "notes" elements must be <a target="_blank"
href="http://www.w3.org/TR/xhtml1/">XHTML 1.0</a>. To help
verify the formatting of "notes" content, libSBML provides the static
utility method SyntaxChecker::hasExpectedXHTMLSyntax(@if java XMLNode xhtml@endif); however,
readers are urged to consult the appropriate <a target="_blank"
href="http://sbml.org/Documents/Specifications">SBML specification
document</a> for the Level and Version of their model for more
in-depth explanations. The SBML Level 2 and 3
specifications have considerable detail about how "notes" element
content must be structured.
@return C<true> if a "notes" subelement exists, C<false> otherwise.
@see getNotes()
@see getNotesString()
@see setNotes(const XMLNode notes)
@see setNotes(const std::string& notes, bool addXHTMLMarkup)
@see appendNotes(const XMLNode notes)
@see appendNotes(const std::string& notes)
@see unsetNotes()
@see SyntaxChecker::hasExpectedXHTMLSyntax(@if java XMLNode xhtml@endif)
=item SBase::isSetAnnotation
Predicate returning C<true> if this
object's "annotation" subelement exists and has content.
Whereas the SBase "notes" subelement is a container for content to be
shown directly to humans, the "annotation" element is a container for
optional software-generated content I<not> meant to be shown to
humans. Every object derived from SBase can have its own value for
"annotation". The element's content type is <a target="_blank"
href="http://www.w3.org/TR/2004/REC-xml-20040204/#elemdecls">XML type
"any"</a>, allowing essentially arbitrary well-formed XML data
content.
SBML places a few restrictions on the organization of the content of
annotations; these are intended to help software tools read and write
the data as well as help reduce conflicts between annotations added by
different tools. Please see the SBML specifications for more details.
@return C<true> if a "annotation" subelement exists, C<false>
otherwise.
@see getAnnotation()
@see getAnnotationString()
@see setAnnotation(const XMLNode annotation)
@see setAnnotation(const std::string& annotation)
@see appendAnnotation(const XMLNode annotation)
@see appendAnnotation(const std::string& annotation)
@see unsetAnnotation()
=item SBase::isSetSBOTerm
Predicate returning C<true> if this
object's "sboTerm" attribute is set.
@return C<true> if the "sboTerm" attribute of this SBML object is
set, C<false> otherwise.
=item SBase::setMetaId
Sets the value of the meta-identifier attribute of this object.
C<opydetails> doc_what_is_metaid
The string C<metaid> is copied.
@param metaid the identifier string to use as the value of the
"metaid" attribute
@return integer value indicating success/failure of the
function. The possible values returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
@li @link OperationReturnValues_t#LIBSBML_UNEXPECTED_ATTRIBUTE LIBSBML_UNEXPECTED_ATTRIBUTE @endlink
@see getMetaId()
@see isSetMetaId()
=item SBase::isSetModelHistory
Predicate returning C<true> if this
object has a ModelHistory object attached to it.
@return C<true> if the ModelHistory of this object is set, @c
false otherwise.
@note In SBML Level 2, model history annotations were only
permitted on the Model element. In SBML Level 3, they are
permitted on all SBML components derived from SBase.
=item SBase::setId
@internal
=item SBase::setName
@internal
=item SBase::setAnnotation
Sets the value of the "annotation" subelement of this SBML object.
The content of C<annotation> is copied, and any previous content of
this object's "annotation" subelement is deleted.
Whereas the SBase "notes" subelement is a container for content to be
shown directly to humans, the "annotation" element is a container for
optional software-generated content I<not> meant to be shown to
humans. Every object derived from SBase can have its own value for
"annotation". The element's content type is <a target="_blank"
href="http://www.w3.org/TR/2004/REC-xml-20040204/#elemdecls">XML type
"any"</a>, allowing essentially arbitrary well-formed XML data
content.
SBML places a few restrictions on the organization of the content of
annotations; these are intended to help software tools read and write
the data as well as help reduce conflicts between annotations added by
different tools. Please see the SBML specifications for more details.
Call this method will result in any existing content of the
"annotation" subelement to be discarded. Unless you have taken steps
to first copy and reconstitute any existing annotations into the @p
annotation that is about to be assigned, it is likely that performing
such wholesale replacement is unfriendly towards other software
applications whose annotations are discarded. An alternative may be
to use SBase::appendAnnotation(const XMLNode annotation) or
SBase::appendAnnotation(const std::string& annotation).
@param annotation an XML structure that is to be used as the new content
of the "annotation" subelement of this object
@return integer value indicating success/failure of the
function. The possible values returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@see getAnnotationString()
@see isSetAnnotation()
@see setAnnotation(const std::string& annotation)
@see appendAnnotation(const XMLNode annotation)
@see appendAnnotation(const std::string& annotation)
@see unsetAnnotation()
=item SBase::setAnnotation
Sets the value of the "annotation" subelement of this SBML object.
The content of C<annotation> is copied, and any previous content of
this object's "annotation" subelement is deleted.
Whereas the SBase "notes" subelement is a container for content to be
shown directly to humans, the "annotation" element is a container for
optional software-generated content I<not> meant to be shown to
humans. Every object derived from SBase can have its own value for
"annotation". The element's content type is <a target="_blank"
href="http://www.w3.org/TR/2004/REC-xml-20040204/#elemdecls">XML type
"any"</a>, allowing essentially arbitrary well-formed XML data
content.
SBML places a few restrictions on the organization of the content of
annotations; these are intended to help software tools read and write
the data as well as help reduce conflicts between annotations added by
different tools. Please see the SBML specifications for more details.
Call this method will result in any existing content of the
"annotation" subelement to be discarded. Unless you have taken steps
to first copy and reconstitute any existing annotations into the @p
annotation that is about to be assigned, it is likely that performing
such wholesale replacement is unfriendly towards other software
applications whose annotations are discarded. An alternative may be
to use SBase::appendAnnotation(const XMLNode annotation) or
SBase::appendAnnotation(const std::string& annotation).
@param annotation an XML string that is to be used as the content
of the "annotation" subelement of this object
@return integer value indicating success/failure of the
function. The possible values returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
@see getAnnotationString()
@see isSetAnnotation()
@see setAnnotation(const XMLNode annotation)
@see appendAnnotation(const XMLNode annotation)
@see appendAnnotation(const std::string& annotation)
@see unsetAnnotation()
=item SBase::appendAnnotation
Appends the given C<annotation> to the "annotation" subelement of this
object.
Whereas the SBase "notes" subelement is a container for content to be
shown directly to humans, the "annotation" element is a container for
optional software-generated content I<not> meant to be shown to
humans. Every object derived from SBase can have its own value for
"annotation". The element's content type is <a
target="_blank"
href="http://www.w3.org/TR/2004/REC-xml-20040204/#elemdecls">XML type "any"</a>,
allowing essentially arbitrary well-formed XML data content.
SBML places a few restrictions on the organization of the content of
annotations; these are intended to help software tools read and write
the data as well as help reduce conflicts between annotations added by
different tools. Please see the SBML specifications for more details.
Unlike SBase::setAnnotation(const XMLNode annotation) or
SBase::setAnnotation(const std::string& annotation), this method
allows other annotations to be preserved when an application adds its
own data.
@param annotation an XML structure that is to be copied and appended
to the content of the "annotation" subelement of this object
@return integer value indicating success/failure of the
function. The possible values returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
@see getAnnotationString()
@see isSetAnnotation()
@see setAnnotation(const XMLNode annotation)
@see setAnnotation(const std::string& annotation)
@see appendAnnotation(const std::string& annotation)
@see unsetAnnotation()
=item SBase::appendAnnotation
Appends the given C<annotation> to the "annotation" subelement of this
object.
Whereas the SBase "notes" subelement is a container for content to be
shown directly to humans, the "annotation" element is a container for
optional software-generated content I<not> meant to be shown to
humans. Every object derived from SBase can have its own value for
"annotation". The element's content type is <a
target="_blank"
href="http://www.w3.org/TR/2004/REC-xml-20040204/#elemdecls">XML type "any"</a>,
allowing essentially arbitrary well-formed XML data content.
SBML places a few restrictions on the organization of the content of
annotations; these are intended to help software tools read and write
the data as well as help reduce conflicts between annotations added by
different tools. Please see the SBML specifications for more details.
Unlike SBase::setAnnotation(const XMLNode annotation) or
SBase::setAnnotation(const std::string& annotation), this method
allows other annotations to be preserved when an application adds its
own data.
@param annotation an XML string that is to be copied and appended
to the content of the "annotation" subelement of this object
@return integer value indicating success/failure of the
function. The possible values returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
@see getAnnotationString()
@see isSetAnnotation()
@see setAnnotation(const XMLNode annotation)
@see setAnnotation(const std::string& annotation)
@see appendAnnotation(const XMLNode annotation)
@see unsetAnnotation()
=item SBase::removeTopLevelAnnotationElement
Removes the top-level element within the "annotation" subelement of this
SBML object with the given name and optional URI.
SBML places a few restrictions on the organization of the content of
annotations; these are intended to help software tools read and write
the data as well as help reduce conflicts between annotations added by
different tools. Please see the SBML specifications for more details.
Calling this method allows a particular annotation element to be removed
whilst the remaining annotations remain intact.
@param elementName a string representing the name of the top level
annotation element that is to be removed
@param elementURI an optional string that is used to check both the name
and URI of the top level element to be removed
@param removeEmpty if after removing of the element, the annotation is
empty, and the removeEmpty argument is true, the annotation node will be
deleted (default).
@return integer value indicating success/failure of the
function. The possible values returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
@li @link OperationReturnValues_t#LIBSBML_ANNOTATION_NAME_NOT_FOUND LIBSBML_ANNOTATION_NAME_NOT_FOUND @endlink
@li @link OperationReturnValues_t#LIBSBML_ANNOTATION_NS_NOT_FOUND LIBSBML_ANNOTATION_NS_NOT_FOUND @endlink
@see replaceTopLevelAnnotationElement(const XMLNode )
@see replaceTopLevelAnnotationElement(const std::string&)
=item SBase::replaceTopLevelAnnotationElement
Replaces the given top-level element within the "annotation"
subelement of this SBML object and with the annotation element supplied.
SBML places a few restrictions on the organization of the content of
annotations; these are intended to help software tools read and write
the data as well as help reduce conflicts between annotations added by
different tools. Please see the SBML specifications for more details.
This method determines the name of the element to be replaced from the
annotation argument. Functionally it is equivalent to calling C<
removeTopLevelAnnotationElement(name)> followed by calling
C<appendAnnotation(annotation_with_name)>, with the exception
that the placement of the annotation element remains the same.
@param annotation XMLNode representing the replacement top level annotation
@return integer value indicating success/failure of the
function. The possible values returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT @endlink
@see removeTopLevelAnnotationElement(const std::string elementName, const std::string elementURI)
@see replaceTopLevelAnnotationElement(const std::string&)
=item SBase::replaceTopLevelAnnotationElement
Replaces the given top-level element within the "annotation"
subelement of this SBML object and with the annotation element supplied.
SBML places a few restrictions on the organization of the content of
annotations; these are intended to help software tools read and write
the data as well as help reduce conflicts between annotations added by
different tools. Please see the SBML specifications for more details.
This method determines the name of the element to be replaced from the
annotation argument. Functionally it is equivalent to calling C<
removeTopLevelAnnotationElement(name)> followed by calling
C<appendAnnotation(annotation_with_name)>, with the exception
that the placement of the annotation element remains the same.
@param annotation string representing the replacement top level annotation
@return integer value indicating success/failure of the
function. The possible values returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT @endlink
@see removeTopLevelAnnotationElement(const std::string elementName, const std::string elementURI)
@see replaceTopLevelAnnotationElement(const XMLNode )
=item SBase::setNotes
Sets the value of the "notes" subelement of this SBML object.
The content of C<notes> is copied, and any existing content of this
object's "notes" subelement is deleted.
The optional SBML element named "notes", present on every major SBML
component type, is intended as a place for storing optional
information intended to be seen by humans. An example use of the
"notes" element would be to contain formatted user comments about the
model element in which the "notes" element is enclosed. Every object
derived directly or indirectly from type SBase can have a separate
value for "notes", allowing users considerable freedom when adding
comments to their models.
The format of "notes" elements must be <a target="_blank"
href="http://www.w3.org/TR/xhtml1/">XHTML 1.0</a>. To help
verify the formatting of "notes" content, libSBML provides the static
utility method SyntaxChecker::hasExpectedXHTMLSyntax(@if java XMLNode xhtml@endif); however,
readers are urged to consult the appropriate <a target="_blank"
href="http://sbml.org/Documents/Specifications">SBML specification
document</a> for the Level and Version of their model for more
in-depth explanations. The SBML Level 2 and 3
specifications have considerable detail about how "notes" element
content must be structured.
@param notes an XML structure that is to be used as the content of the
"notes" subelement of this object
@return integer value indicating success/failure of the
function. The possible values returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT @endlink
@see getNotesString()
@see isSetNotes()
@see setNotes(const std::string& notes, bool addXHTMLMarkup)
@see appendNotes(const XMLNode notes)
@see appendNotes(const std::string& notes)
@see unsetNotes()
@see SyntaxChecker::hasExpectedXHTMLSyntax(@if java XMLNode xhtml@endif)
=item SBase::setNotes
Sets the value of the "notes" subelement of this SBML object to a copy
of the string C<notes>.
The content of C<notes> is copied, and any existing content of this
object's "notes" subelement is deleted.
The optional SBML element named "notes", present on every major SBML
component type, is intended as a place for storing optional
information intended to be seen by humans. An example use of the
"notes" element would be to contain formatted user comments about the
model element in which the "notes" element is enclosed. Every object
derived directly or indirectly from type SBase can have a separate
value for "notes", allowing users considerable freedom when adding
comments to their models.
The format of "notes" elements must be <a target="_blank"
href="http://www.w3.org/TR/xhtml1/">XHTML 1.0</a>. To help
verify the formatting of "notes" content, libSBML provides the static
utility method SyntaxChecker::hasExpectedXHTMLSyntax(@if java XMLNode xhtml@endif); however,
readers are urged to consult the appropriate <a target="_blank"
href="http://sbml.org/Documents/Specifications">SBML specification
document</a> for the Level and Version of their model for more
in-depth explanations. The SBML Level 2 and 3
specifications have considerable detail about how "notes" element
content must be structured.
The following code illustrates a very simple way of setting the notes
using this method. Here, the object being annotated is the whole SBML
document, but that is for illustration purposes only; you could of
course use this same approach to annotate any other SBML component.
@if clike
@verbatim
SBMLDocument s = new SBMLDocument(3, 1);
s->setNotes("<body xmlns='http://www.w3.org/1999/xhtml'><p>here is my note</p></body>");
@endverbatim
@endif@if java
@verbatim
SBMLDocument s = new SBMLDocument(3, 1);
s.setNotes("<body xmlns='http://www.w3.org/1999/xhtml'><p>here is my note</p></body>");
@endverbatim
@endif@if csharp
@verbatim
SBMLDocument s = new SBMLDocument(3, 1);
s.setNotes("<body xmlns='http://www.w3.org/1999/xhtml'><p>here is my note</p></body>");
@endverbatim
@endif@~
@param notes an XML string that is to be used as the content of the
"notes" subelement of this object
@param addXHTMLMarkup a boolean indicating whether to wrap the contents
of the C<notes> argument with XHTML paragraph (C<<p>>)
tags. This is appropriate when the string in C<notes> does not already
containg the appropriate XHTML markup.
@return integer value indicating success/failure of the
function. The possible values returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
@see getNotesString()
@see isSetNotes()
@see setNotes(const XMLNode notes)
@see appendNotes(const XMLNode notes)
@see appendNotes(const std::string& notes)
@see unsetNotes()
@see SyntaxChecker::hasExpectedXHTMLSyntax(@if java XMLNode xhtml@endif)
=item SBase::appendNotes
Appends the given C<notes> to the "notes" subelement of this object.
The content of C<notes> is copied.
The optional SBML element named "notes", present on every major SBML
component type, is intended as a place for storing optional
information intended to be seen by humans. An example use of the
"notes" element would be to contain formatted user comments about the
model element in which the "notes" element is enclosed. Every object
derived directly or indirectly from type SBase can have a separate
value for "notes", allowing users considerable freedom when adding
comments to their models.
The format of "notes" elements must be <a target="_blank"
href="http://www.w3.org/TR/xhtml1/">XHTML 1.0</a>. To help
verify the formatting of "notes" content, libSBML provides the static
utility method SyntaxChecker::hasExpectedXHTMLSyntax(@if java XMLNode xhtml@endif); however,
readers are urged to consult the appropriate <a target="_blank"
href="http://sbml.org/Documents/Specifications">SBML specification
document</a> for the Level and Version of their model for more
in-depth explanations. The SBML Level 2 and 3
specifications have considerable detail about how "notes" element
content must be structured.
@param notes an XML node structure that is to appended to the content
of the "notes" subelement of this object
@return integer value indicating success/failure of the
function. The possible values returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
@see getNotesString()
@see isSetNotes()
@see setNotes(const XMLNode notes)
@see setNotes(const std::string& notes, bool addXHTMLMarkup)
@see appendNotes(const std::string& notes)
@see unsetNotes()
@see SyntaxChecker::hasExpectedXHTMLSyntax(@if java XMLNode xhtml@endif)
=item SBase::appendNotes
Appends the given C<notes> to the "notes" subelement of this object.
The content of the parameter C<notes> is copied.
The optional SBML element named "notes", present on every major SBML
component type, is intended as a place for storing optional
information intended to be seen by humans. An example use of the
"notes" element would be to contain formatted user comments about the
model element in which the "notes" element is enclosed. Every object
derived directly or indirectly from type SBase can have a separate
value for "notes", allowing users considerable freedom when adding
comments to their models.
The format of "notes" elements must be <a target="_blank"
href="http://www.w3.org/TR/xhtml1/">XHTML 1.0</a>. To help
verify the formatting of "notes" content, libSBML provides the static
utility method SyntaxChecker::hasExpectedXHTMLSyntax(@if java XMLNode xhtml@endif); however,
readers are urged to consult the appropriate <a target="_blank"
href="http://sbml.org/Documents/Specifications">SBML specification
document</a> for the Level and Version of their model for more
in-depth explanations. The SBML Level 2 and 3
specifications have considerable detail about how "notes" element
content must be structured.
@param notes an XML string that is to appended to the content of
the "notes" subelement of this object
@return integer value indicating success/failure of the
function. The possible values returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
@see getNotesString()
@see isSetNotes()
@see setNotes(const XMLNode notes)
@see setNotes(const std::string& notes, bool addXHTMLMarkup)
@see appendNotes(const XMLNode notes)
@see unsetNotes()
@see SyntaxChecker::hasExpectedXHTMLSyntax(@if java XMLNode xhtml@endif)
=item SBase::setModelHistory
Sets the ModelHistory of this object.
The content of C<history> is copied, and this object's existing model
history content is deleted.
@param history ModelHistory of this object.
@return integer value indicating success/failure of the
function. The possible values returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_UNEXPECTED_ATTRIBUTE LIBSBML_UNEXPECTED_ATTRIBUTE @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT @endlink
@note In SBML Level 2, model history annotations were only
permitted on the Model element. In SBML Level 3, they are
permitted on all SBML components derived from SBase.
=item SBase::setSBMLDocument
@internal
Sets the parent SBMLDocument of this SBML object.
C<opydetails> doc_what_is_SBMLDocument
@param d the SBMLDocument object to use
@see connectToChild()
@if clike
@see enablePackageInternal()
@endif@~
=item SBase::connectToParent
@internal
Sets the parent SBML object of this SBML object.
(Creates a child-parent relationship by the child)
This function is called when a child element is
set/added/created by its parent element (e.g. by setXXX,
addXXX, createXXX, and connectToChild functions of the
parent element).
@param parent the SBML object to use
=item SBase::connectToChild
@internal
Sets this SBML object to child SBML objects (if any).
(Creates a child-parent relationship by the parent)
Subclasses must override this function if they define
one ore more child elements.
Basically, this function needs to be called in
constructor, copy constructor, assignment operator.
@if clike
@see setSBMLDocument()
@see enablePackageInternal()
@endif@~
=item SBase::setSBOTerm
Sets the value of the "sboTerm" attribute.
Beginning with SBML Level 2 Version 3, objects derived from SBase have
an optional attribute named "sboTerm" for supporting the use of the
Systems Biology Ontology. In SBML proper, the data type of the
attribute is a string of the form "SBO:NNNNNNN", where "NNNNNNN" is a
seven digit integer number; libSBML simplifies the representation by
only storing the "NNNNNNN" integer portion. Thus, in libSBML, the
"sboTerm" attribute on SBase has data type C<int>, and SBO identifiers
are stored simply as integers.
SBO terms are a type of optional annotation, and each different class
of SBML object derived from SBase imposes its own requirements about
the values permitted for "sboTerm". Please consult the SBML
Level 2 Version 4 specification for more information about
the use of SBO and the "sboTerm" attribute.
@param value the NNNNNNN integer portion of the SBO identifier
@return integer value indicating success/failure of the
function. The possible values returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
@li @link OperationReturnValues_t#LIBSBML_UNEXPECTED_ATTRIBUTE LIBSBML_UNEXPECTED_ATTRIBUTE @endlink
@see setSBOTerm(@if java String sbo_id@else const std::string &sboid@endif)
=item SBase::setSBOTerm
Sets the value of the "sboTerm" attribute by string.
Beginning with SBML Level 2 Version 3, objects derived from SBase have
an optional attribute named "sboTerm" for supporting the use of the
Systems Biology Ontology. In SBML proper, the data type of the
attribute is a string of the form "SBO:NNNNNNN", where "NNNNNNN" is a
seven digit integer number; libSBML simplifies the representation by
only storing the "NNNNNNN" integer portion. Thus, in libSBML, the
"sboTerm" attribute on SBase has data type C<int>, and SBO identifiers
are stored simply as integers. This method lets you set the value of
"sboTerm" as a complete string of the form "SBO:NNNNNNN", whereas
setSBOTerm(int value) allows you to set it using the integer form.
SBO terms are a type of optional annotation, and each different class
of SBML object derived from SBase imposes its own requirements about
the values permitted for "sboTerm". Please consult the SBML
Level 2 Version 4 specification for more information about
the use of SBO and the "sboTerm" attribute.
@param sboid the SBO identifier string of the form "SBO:NNNNNNN"
@return integer value indicating success/failure of the
function. The possible values returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
@li @link OperationReturnValues_t#LIBSBML_UNEXPECTED_ATTRIBUTE LIBSBML_UNEXPECTED_ATTRIBUTE @endlink
@see setSBOTerm(int value)
=item SBase::setNamespaces
Sets the namespaces relevant of this SBML object.
The content of C<xmlns> is copied, and this object's existing
namespace content is deleted.
The SBMLNamespaces object encapsulates SBML Level/Version/namespaces
information. It is used to communicate the SBML Level, Version, and
(in Level 3) packages used in addition to SBML Level 3 Core.
@param xmlns the namespaces to set
@return integer value indicating success/failure of the
function. The possible values returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
=item SBase::unsetMetaId
Unsets the value of the "metaid" attribute of this SBML object.
C<opydetails> doc_what_is_metaid
@return integer value indicating success/failure of the
function. The possible values returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_UNEXPECTED_ATTRIBUTE LIBSBML_UNEXPECTED_ATTRIBUTE @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item SBase::unsetId
Unsets the value of the "id" attribute of this SBML object.
Most (but not all) objects in SBML include two common attributes: "id"
and "name". The identifier given by an object's "id" attribute value
is used to identify the object within the SBML model definition.
Other objects can refer to the component using this identifier.
@return integer value indicating success/failure of the
function. The possible values returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item SBase::unsetName
Unsets the value of the "name" attribute of this SBML object.
Most (but not all) objects in SBML include two common attributes: "id"
and "name". In contrast to the "id" attribute, the "name" attribute is
optional and is not intended to be used for cross-referencing purposes
within a model. Its purpose instead is to provide a human-readable
label for the component. The data type of "name" is the type
C<string> defined in XML Schema. SBML imposes no
restrictions as to the content of "name" attributes beyond those
restrictions defined by the C<string> type in XML Schema.
The recommended practice for handling "name" is as follows. If a
software tool has the capability for displaying the content of "name"
attributes, it should display this content to the user as a
component's label instead of the component's "id". If the user
interface does not have this capability (e.g., because it cannot
display or use special characters in symbol names), or if the "name"
attribute is missing on a given component, then the user interface
should display the value of the "id" attribute instead. (Script
language interpreters are especially likely to display "id" instead of
"name".)
As a consequence of the above, authors of systems that automatically
generate the values of "id" attributes should be aware some systems
may display the "id"'s to the user. Authors therefore may wish to
take some care to have their software create "id" values that are: (a)
reasonably easy for humans to type and read; and (b) likely to be
meaningful, for example by making the "id" attribute be an abbreviated
form of the name attribute value.
An additional point worth mentioning is although there are
restrictions on the uniqueness of "id" values, there are no
restrictions on the uniqueness of "name" values in a model. This
allows software applications leeway in assigning component identifiers.
@return integer value indicating success/failure of the
function. The possible values returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item SBase::unsetNotes
Unsets the value of the "notes" subelement of this SBML object.
The optional SBML element named "notes", present on every major SBML
component type, is intended as a place for storing optional
information intended to be seen by humans. An example use of the
"notes" element would be to contain formatted user comments about the
model element in which the "notes" element is enclosed. Every object
derived directly or indirectly from type SBase can have a separate
value for "notes", allowing users considerable freedom when adding
comments to their models.
The format of "notes" elements must be <a target="_blank"
href="http://www.w3.org/TR/xhtml1/">XHTML 1.0</a>. To help
verify the formatting of "notes" content, libSBML provides the static
utility method SyntaxChecker::hasExpectedXHTMLSyntax(@if java XMLNode xhtml@endif); however,
readers are urged to consult the appropriate <a target="_blank"
href="http://sbml.org/Documents/Specifications">SBML specification
document</a> for the Level and Version of their model for more
in-depth explanations. The SBML Level 2 and 3
specifications have considerable detail about how "notes" element
content must be structured.
@return integer value indicating success/failure of the
function. The possible values returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@see getNotesString()
@see isSetNotes()
@see setNotes(const XMLNode notes)
@see setNotes(const std::string& notes, bool addXHTMLMarkup)
@see appendNotes(const XMLNode notes)
@see appendNotes(const std::string& notes)
@see SyntaxChecker::hasExpectedXHTMLSyntax(@if java XMLNode xhtml@endif)
=item SBase::unsetAnnotation
Unsets the value of the "annotation" subelement of this SBML object.
Whereas the SBase "notes" subelement is a container for content to be
shown directly to humans, the "annotation" element is a container for
optional software-generated content I<not> meant to be shown to
humans. Every object derived from SBase can have its own value for
"annotation". The element's content type is <a target="_blank"
href="http://www.w3.org/TR/2004/REC-xml-20040204/#elemdecls">XML type
"any"</a>, allowing essentially arbitrary well-formed XML data
content.
SBML places a few restrictions on the organization of the content of
annotations; these are intended to help software tools read and write
the data as well as help reduce conflicts between annotations added by
different tools. Please see the SBML specifications for more details.
@return integer value indicating success/failure of the
function. The possible values returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@see getAnnotation()
@see getAnnotationString()
@see isSetAnnotation()
@see setAnnotation(const XMLNode annotation)
@see setAnnotation(const std::string& annotation)
@see appendAnnotation(const XMLNode annotation)
@see appendAnnotation(const std::string& annotation)
=item SBase::unsetSBOTerm
Unsets the value of the "sboTerm" attribute of this SBML object.
@return integer value indicating success/failure of the
function. The possible values returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_UNEXPECTED_ATTRIBUTE LIBSBML_UNEXPECTED_ATTRIBUTE @endlink
=item SBase::addCVTerm
Adds a copy of the given CVTerm object to this SBML object.
@param term the CVTerm to assign.
@param newBag if C<true>, creates a new RDF bag with the same identifier
as a previous bag, and if C<false>, adds the term to an existing
RDF bag with the same type of qualifier as the term being added.
@return integer value indicating success/failure of the
function. The possible values returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
@li @link OperationReturnValues_t#LIBSBML_UNEXPECTED_ATTRIBUTE LIBSBML_UNEXPECTED_ATTRIBUTE @endlink, if
this object lacks a "metaid" attribute
@li @link OperationReturnValues_t#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT @endlink
@note Since the CV Term uses the "metaid" attribute of the object as a
reference, if the object has no "metaid" attribute value set, then the
CVTerm will not be added.
C<opydetails> doc_note_object_is_copied
@if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
=item SBase::getCVTerms
Returns a list of CVTerm objects in the annotations of this SBML
object.
@return the list of CVTerms for this SBML object.
=item SBase::getCVTerms
Returns a list of CVTerm objects in the annotations of this SBML
object.
@return the list of CVTerms for this SBML object.
=item SBase::getNumCVTerms
Returns the number of CVTerm objects in the annotations of this SBML
object.
@return the number of CVTerms for this SBML object.
=item SBase::getCVTerm
Returns the nth CVTerm in the list of CVTerms of this SBML
object.
@param n unsigned int the index of the CVTerm to retrieve
@return the nth CVTerm in the list of CVTerms for this SBML object.
=item SBase::unsetCVTerms
Clears the list of CVTerm objects attached to this SBML object.
@return integer value indicating success/failure of the
function. The possible values returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item SBase::unsetModelHistory
Unsets the ModelHistory object attached to this object.
@return integer value indicating success/failure of the
function. The possible values returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_UNEXPECTED_ATTRIBUTE LIBSBML_UNEXPECTED_ATTRIBUTE @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
@note In SBML Level 2, model history annotations were only
permitted on the Model element. In SBML Level 3, they are
permitted on all SBML components derived from SBase.
=item SBase::getResourceBiologicalQualifier
Returns the MIRIAM <em>biological qualifier</em> associated with the
given resource.
In <a target="_blank" href="http://biomodels.net/miriam">MIRIAM</a>,
qualifiers are an optional means of indicating the relationship
between a model component and its annotations. There are two broad
kinds of annotations: <em>model</em> and <em>biological</em>. The
latter kind is used to qualify the relationship between a model
component and a biological entity which it represents. Examples of
relationships include "is" and "has part", but many others are
possible. MIRIAM defines <a target="_blank"
href="http://www.ebi.ac.uk/miriam/main/qualifiers/">numerous
relationship qualifiers</a> to enable different software tools to
qualify biological annotations in the same standardized way. In
libSBML, the MIRIAM controlled-vocabulary annotations on an SBML model
element are represented using lists of CVTerm objects, and the
the MIRIAM biological qualifiers are represented using
values @if clike from the enumeration
type #BiolQualifierType_t.@endif@if python whose
names begin with C<BQB_> in the interface class
@link libsbml libsbml@endlink.@endif@if java whose
names begin with C<BQB_> in the interface class
{@link libsbmlConstants}.@endif@if csharp whose
names begin with C<BQB_> in the interface class
@link libsbmlcs.libsbml libsbml@endlink.@endif@~
This method searches the controlled-vocabulary annotations
(i.e., the list of CVTerm objects) on the present object, then out of
those that have biological qualifiers, looks for an annotation to the
given C<resource>. If such an annotation is found, it returns the
type of biological qualifier associated with that resource as a
value @if clike from the enumeration type
#BiolQualifierType_t.@endif@if python whose name begins with
C<BQB_> from the interface
class @link libsbml libsbml@endlink.@endif@if java whose name
begins with C<BQB_> from the interface
class {@link libsbmlConstants}.@endif@if csharp whose
names begin with C<BQB_> in the interface class
@link libsbmlcs.libsbml libsbml@endlink.@endif@~
@param resource string representing the resource; e.g.,
C<"http://www.geneontology.org/#GO:0005892">.
@return the qualifier associated with the resource,
or @link BiolQualifierType_t#BQB_UNKNOWN BQB_UNKNOWN@endlink if the
resource does not exist.
@if clike
@note The set of MIRIAM biological qualifiers grows over
time, although relatively slowly. The values in the enumeration
#BiolQualifierType_t are up to date with MIRIAM at the time of a given
libSBML release. The set of values may be expanded in later libSBML
releases, to match the values defined by MIRIAM at that later time.
@endif@if python
@note The set of MIRIAM biological qualifiers grows over
time, although relatively slowly. The values are up to date with
MIRIAM at the time of a given libSBML release. The set of values in
list of C<BQB_> constants defined in @link libsbml
libsbml@endlink may be expanded in later libSBML releases, to match
the values defined by MIRIAM at that later time.
@endif@if java
@note The set of MIRIAM biological qualifiers grows over
time, although relatively slowly. The values are up to date with
MIRIAM at the time of a given libSBML release. The set of values in
list of C<BQB_> constants defined in {@link libsbmlConstants}
may be expanded in later libSBML releases, to match
the values defined by MIRIAM at that later time.
@endif@if csharp
@note The set of MIRIAM biological qualifiers grows over
time, although relatively slowly. The values are up to date with
MIRIAM at the time of a given libSBML release. The set of values in
list of C<BQB_> constants defined in @link libsbmlcs.libsbml libsbml@endlink
may be expanded in later libSBML releases, to match
the values defined by MIRIAM at that later time.
@endif@~
=item SBase::getResourceModelQualifier
Returns the MIRIAM <em>model qualifier</em> associated with the
given resource.
In <a target="_blank" href="http://biomodels.net/miriam">MIRIAM</a>,
qualifiers are an optional means of indicating the relationship
between a model component and its annotations. There are two broad
kinds of annotations: <em>model</em> and <em>biological</em>. The
former kind is used to qualify the relationship between a model
component and another modeling object. An example qualifier is
"isDerivedFrom", to indicate that a given component of the model is
derived from the modeling object represented by the referenced
resource. MIRIAM defines <a target="_blank"
href="http://www.ebi.ac.uk/miriam/main/qualifiers/">numerous
relationship qualifiers</a> to enable different software tools to
qualify model annotations in the same standardized way. In libSBML,
the MIRIAM controlled-vocabulary annotations on an SBML model element
are represented using lists of CVTerm objects, and the
the MIRIAM model qualifiers are represented using
values @if clike from the enumeration
type #ModelQualifierType_t.@endif@if python whose
names begin with C<BQM_> in the interface class
@link libsbml libsbml@endlink.@endif@if java whose
names begin with C<BQM_> in the interface class
{@link libsbmlConstants}.@endif@if csharp whose
names begin with C<BQB_> in the interface class
@link libsbmlcs.libsbml libsbml@endlink.@endif@~
This method method searches the controlled-vocabulary annotations
(i.e., the list of CVTerm objects) on the present object, then out of
those that have model qualifiers, looks for an annotation to the given
C<resource>. If such an annotation is found, it returns the type of
type of model qualifier associated with that resource as a
value @if clike from the enumeration type
#ModelQualifierType_t.@endif@if python whose name begins with
C<BQM_> from the interface
class @link libsbml libsbml@endlink.@endif@if java whose name
begins with C<BQM_> from the interface
class {@link libsbmlConstants}.@endif@if csharp whose
names begin with C<BQB_> in the interface class
@link libsbmlcs.libsbml libsbml@endlink.@endif@~
@param resource string representing the resource; e.g.,
C<"http://www.geneontology.org/#GO:0005892">.
@return the @if clike #ModelQualifierType_t value@else model qualifier
type@endif@~ associated with the resource, or @link
ModelQualifierType_t#BQM_UNKNOWN BQM_UNKNOWN@endlink if the resource
does not exist.
@if clike
@note The set of MIRIAM biological qualifiers grows over
time, although relatively slowly. The values in the enumeration
#ModelQualifierType_t are up to date with MIRIAM at the time of a given
libSBML release. The set of values may be expanded in later libSBML
releases, to match the values defined by MIRIAM at that later time.
@endif@if python
@note The set of MIRIAM model qualifiers grows over
time, although relatively slowly. The values are up to date with
MIRIAM at the time of a given libSBML release. The set of values in
list of C<BQM_> constants defined in @link libsbml
libsbml@endlink may be expanded in later libSBML releases, to match
the values defined by MIRIAM at that later time.
@endif@if java
@note The set of MIRIAM model qualifiers grows over
time, although relatively slowly. The values are up to date with
MIRIAM at the time of a given libSBML release. The set of values in
list of C<BQM_> constants defined in {@link libsbmlConstants}
may be expanded in later libSBML releases, to match
the values defined by MIRIAM at that later time.
@endif@if csharp
@note The set of MIRIAM model qualifiers grows over
time, although relatively slowly. The values are up to date with
MIRIAM at the time of a given libSBML release. The set of values in
list of C<BQM_> constants defined in @link libsbmlcs.libsbml libsbml@endlink
may be expanded in later libSBML releases, to match
the values defined by MIRIAM at that later time.
@endif@~
=item SBase::getModel
Returns the Model object for the SBML Document in which the current object is located.
@return the Model object for the SBML Document of this SBML object.
@see getParentSBMLObject()
@see getSBMLDocument()
=item SBase::getLevel
Returns the SBML Level of the SBMLDocument object containing this
object.
C<opydetails> doc_what_is_SBMLDocument
@return the SBML level of this SBML object.
@see getVersion()
@see getNamespaces()
@see getPackageVersion()
=item SBase::getVersion
Returns the Version within the SBML Level of the SBMLDocument object
containing this object.
C<opydetails> doc_what_is_SBMLDocument
@return the SBML version of this SBML object.
@see getLevel()
@see getNamespaces()
=item SBase::getPackageVersion
Returns the Version of the SBML Level 3 package to which this
element belongs to.
@return the version of the SBML Level 3 package to which this
element belongs. The value C<0> will be returned if this element
belongs to the SBML Level 3 Core package.
@see getLevel()
@see getVersion()
=item SBase::getPackageName
Returns the name of the SBML Level 3 package in which this
element is defined.
@return the name of the SBML package in which this element is defined.
The string C<"core"> will be returned if this
element is defined in SBML Level 3 Core. The string
C<"unknown"> will be returned if this element is
not defined in any SBML package.
=item SBase::getTypeCode
Returns the libSBML type code for this object.
This method may return the type code of this SBML object, or it may
return @link SBMLTypeCode_t#SBML_UNKNOWN SBML_UNKNOWN@endlink. This
is because subclasses of SBase are not required to implement this
method to return a type code. This method is meant primarily for the
LibSBML C interface, in which class and subclass information is not
readily available.
@return the @if clike #SBMLTypeCode_t value@else SBML object type code@endif@~
of this SBML object or
@link SBMLTypeCode_t#SBML_UNKNOWN SBML_UNKNOWN@endlink (the default).
C<opydetails> doc_warning_typecodes_not_unique
@see getElementName()
@see getPackageName()
=item SBase::hasValidLevelVersionNamespaceCombination
Predicate returning C<true> if this
object's level/version and namespace values correspond to a valid
SBML specification.
The valid combinations of SBML Level, Version and Namespace as of this
release of libSBML are the following:
\n=over\n
\n=item\n\nLevel 1 Version 2: C<"http://www.sbml.org/sbml/level1">
\n=item\n\nLevel 2 Version 1: C<"http://www.sbml.org/sbml/level2">
\n=item\n\nLevel 2 Version 2: C<"http://www.sbml.org/sbml/level2/version2">
\n=item\n\nLevel 2 Version 3: C<"http://www.sbml.org/sbml/level2/version3">
\n=item\n\nLevel 2 Version 4: C<"http://www.sbml.org/sbml/level2/version4">
\n=item\n\nLevel 3 Version 1 Core: C<"http://www.sbml.org/sbml/level3/version1/core">
\n=back\n
@return C<true> if the level, version and namespace values of this
SBML object correspond to a valid set of values, C<false> otherwise.
=item SBase::getElementName
Returns the XML element name of this object.
This is overridden by subclasses to return a string appropriate to the
SBML component. For example, Model defines it as returning @c
"model", CompartmentType defines it as returning C<"compartmentType">,
and so on.
=item SBase::toSBML
Returns a string consisting of a partial SBML corresponding to just
this object.
@return the partial SBML that describes this SBML object.
@warning <span class="warning">This is primarily provided for testing
and debugging purposes. It may be removed in a future version of
libSBML.</span>
=item SBase::toXMLNode
Returns this element as an XMLNode.
@return this element as an XMLNode.
@warning <span class="warning">This operation is computationally
expensive, because the element has to be fully serialized to a string
and then parsed into the XMLNode structure. Attempting to convert a
large tree structure (e.g., a large Model) may consume significant
computer memory and time.</span>
=item SBase::read
Reads (initializes) this SBML object by reading from the given XMLNode.
@param node The XMLNode to read from.
@param flag An optional flag that determines how how errors are logged
during the reading process.
@warning <span class="warning">This method is computationally expensive,
because the given node has to be serialized to a string first.
Attempting to serialize a large tree structure (e.g., a large Model) may
consume significant computer memory and time.</span>
=item SBase::getPlugin
Returns a plug-in object (extension interface) for an SBML Level 3
package extension with the given package name or URI.
C<opydetails> doc_what_are_plugins
@param package the name or URI of the package
@return the plug-in object (the libSBML extension interface) of
a package extension with the given package name or URI.
=item SBase::getPlugin
Returns a plug-in object (extension interface) for an SBML Level 3
package extension with the given package name or URI.
C<opydetails> doc_what_are_plugins
@param package the name or URI of the package
@return the plug-in object (the libSBML extension interface) of a
package extension with the given package name or URI.
=item SBase::getPlugin
Returns the nth plug-in object (extension interface) for an SBML Level 3
package extension.
C<opydetails> doc_what_are_plugins
@param n the index of the plug-in to return
@return the plug-in object (the libSBML extension interface) of
a package extension with the given package name or URI.
=item SBase::getPlugin
Returns the nth plug-in object (extension interface) for an SBML Level 3
package extension.
C<opydetails> doc_what_are_plugins
@param n the index of the plug-in to return
@return the plug-in object (the libSBML extension interface) of a
package extension with the given package name or URI.
=item SBase::getNumPlugins
Returns the number of plug-in objects (extenstion interfaces) for SBML
Level 3 package extensions known.
C<opydetails> doc_what_are_plugins
@return the number of plug-in objects (extension interfaces) of
package extensions known by this instance of libSBML.
=item SBase::enablePackage
Enables or disables the given SBML Level 3 package on this object.
This method enables the specified package on this object and other
objects connected by child-parent links in the same SBMLDocument object.
This method is the converse of
SBase::disablePackage(const std::string& pkgURI, const std::string& pkgPrefix).
@param pkgURI the URI of the package.
@param pkgPrefix the XML prefix of the package
@param flag whether to enable (C<true>) or disable (C<false>) the package
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif@~ The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_PKG_UNKNOWN LIBSBML_PKG_UNKNOWN @endlink
@li @link OperationReturnValues_t#LIBSBML_PKG_VERSION_MISMATCH LIBSBML_PKG_VERSION_MISMATCH @endlink
@li @link OperationReturnValues_t#LIBSBML_PKG_CONFLICTED_VERSION LIBSBML_PKG_CONFLICTED_VERSION @endlink
@see disablePackage(const std::string& pkgURI, const std::string& pkgPrefix)
=item SBase::disablePackage
Disables the given SBML Level 3 package on this object.
This method disables the specified package on this object
and other objects connected by child-parent links in the same
SBMLDocument object.
An example of when this may be useful is during construction of model
components when mixing existing and new models. Suppose your
application read an SBML document containing a model that used the SBML
Hierarchical Model Composition (“comp”) package, and
extracted parts of that model in order to construct a new model in
memory. The new, in-memory model will not accept a component drawn from
another SBMLDocument with different package namespace declarations.
You could reconstruct the same namespaces in the in-memory model first,
but as a shortcut, you could also disable the package namespace on the
object being added. Here is a code example to help clarify this:
@if clike @verbatim
// We read in an SBML L3V1 model that uses the 'comp' package namespace
doc = readSBML("sbml-file-with-comp-elements.xml");
// We extract one of the species from the model we just read in.
Species s1 = doc->getModel()->getSpecies(0);
// We construct a new model. This model does not use the 'comp' package.
Model newModel = new Model(3,1);
// The following will fail with an error, because addSpecies() will
// first check that the parent of the given object has namespaces
// declared, and will discover that s1 does but newModel does not.
// newModel->addSpecies(s1);
// However, if we disable the 'comp' package on s1, then the call
// to addSpecies will work.
s1->disablePackage("http://www.sbml.org/sbml/level3/version1/comp/version1",
"comp");
newModel->addSpecies(s1);
@endverbatim
@endif@if python
@verbatim
import sys
import os.path
from libsbml import
# We read in an SBML L3V1 model that uses the 'comp' package namespace
doc = readSBML("sbml-file-with-comp-elements.xml");
# We extract one of the species from the model we just read in.
s1 = doc.getModel().getSpecies(0);
# We construct a new model. This model does not use the 'comp' package.
newDoc = SBMLDocument(3, 1);
newModel = newDoc.createModel();
# The following would fail with an error, because addSpecies() would
# first check that the parent of the given object has namespaces
# declared, and will discover that s1 does but newModel does not.
# newModel.addSpecies(s1);
# However, if we disable the 'comp' package on s1, then the call
# to addSpecies will work.
s1.disablePackage("http://www.sbml.org/sbml/level3/version1/comp/version1",
"comp");
newModel.addSpecies(s1);
@endverbatim
@endif@if java
@verbatim
// We read in an SBML L3V1 model that uses the 'comp' package namespace
SBMLReader reader = new SBMLReader();
SBMLDocument doc = reader.readSBML("sbml-file-with-comp-elements.xml");
// We extract one of the species from the model we just read in.
Species s1 = doc.getModel().getSpecies(0);
// We construct a new model. This model does not use the 'comp' package.
Model newModel = new Model(3,1);
// The following will fail with an error, because addSpecies() will
// first check that the parent of the given object has namespaces
// declared, and will discover that s1 does but newModel does not.
// newModel->addSpecies(s1);
// However, if we disable the 'comp' package on s1, then the call
// to addSpecies will work.
s1->disablePackage("http://www.sbml.org/sbml/level3/version1/comp/version1",
"comp");
newModel.addSpecies(s1);
@endverbatim
@endif
@param pkgURI the URI of the package
@param pkgPrefix the XML prefix of the package
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif@~ The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_PKG_UNKNOWN LIBSBML_PKG_UNKNOWN @endlink
@li @link OperationReturnValues_t#LIBSBML_PKG_VERSION_MISMATCH LIBSBML_PKG_VERSION_MISMATCH @endlink
@li @link OperationReturnValues_t#LIBSBML_PKG_CONFLICTED_VERSION LIBSBML_PKG_CONFLICTED_VERSION @endlink
@see enablePackage(const std::string& pkgURI, const std::string& pkgPrefix, bool flag)
=item SBase::enablePackageInternal
@internal
Enables/Disables the given package with this element and child
elements (if any).
(This is an internal implementation for enablePackage function)
@note Subclasses in which one or more child elements are defined
must override this function.
@if clike
@see setSBMLDocument()
@endif@~
@see connectToChild()
=item SBase::isPackageURIEnabled
Predicate returning C<true> if an SBML Level 3 package with the
given URI is enabled with this object.
@param pkgURI the URI of the package
@return C<true> if the given package is enabled within this object, @c
false otherwise.
@see isPackageEnabled(@if java String pkgName@endif)
=item SBase::isPackageEnabled
Predicate returning C<true> if the given SBML Level 3 package is
enabled with this object.
The search ignores the package version.
@param pkgName the name of the package
@return C<true> if the given package is enabled within this object, @c
false otherwise.
@see isPackageURIEnabled(@if java String pkgURI@endif)
=item SBase::isPkgURIEnabled
Predicate returning C<true> if an SBML Level 3 package with the
given URI is enabled with this object.
@param pkgURI the URI of the package
@return C<true> if the given package is enabled within this object, @c
false otherwise.
@see isPkgEnabled(@if java String pkgName@endif)
@deprecated Replaced in libSBML 5.2.0 by
isPackageURIEnabled(@if java String pkgURI@endif)
=item SBase::isPkgEnabled
Predicate returning C<true> if the given SBML Level 3 package is
enabled with this object.
The search ignores the package version.
@param pkgName the name of the package
@return C<true> if the given package is enabled within this object, @c
false otherwise.
@see isPkgURIEnabled(@if java String pkgURI@endif)
@deprecated Replaced in libSBML 5.2.0 by
isPackageEnabled(@if java String pkgName@endif)
=item SBase::writeExtensionElements
@internal
Writes out contained SBML objects of package extensions (if any)
as XML elements.
=item SBase::read
@internal
Reads (initializes) this SBML object by reading from XMLInputStream.
=item SBase::write
@internal
Writes (serializes) this SBML object by writing it to XMLOutputStream.
=item SBase::writeElements
@internal
Subclasses should override this method to write out their contained
SBML objects as XML elements. Be sure to call your parents
implementation of this method as well. For example:@if clike
<pre>
SBase::writeElements();
mReactants.write(stream);
mProducts.write(stream);
...
</pre>@endif@~
=item SBase::hasRequiredAttributes
@internal
=item SBase::hasRequiredElements
@internal
=item SBase::checkCompatibility
@internal
=item SBase::setSBMLNamespaces
@internal
=item SBase::setSBMLNamespacesAndOwn
@internal
=item SBase::getSBMLNamespaces
@internal
=item SBase::removeDuplicateAnnotations
@internal
=item SBase::checkMathMLNamespace
@internal
=item SBase::getDerivedUnitDefinition
@internal
=item SBase::containsUndeclaredUnits
@internal
=item SBase::removeFromParentAndDelete
Removes this object from its parent.
If the parent was storing this object as a pointer, it is deleted. If
not, it is simply cleared (as in ListOf objects). This is a pure
virtual method, as every SBase element has different parents, and
therefore different methods of removing itself. Will fail (and not
delete itself) if it has no parent object. This function is designed to
be overridden, but for all objects whose parent is of the class ListOf,
the default implementation will work.
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif@~ The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item SBase::matchesSBMLNamespaces
Returns C<true> if this object's set of XML namespaces are the same
as the given object's XML namespaces.
C<opydetails> doc_what_are_sbmlnamespaces
@param sb an object to compare with respect to namespaces
@return boolean, C<true> if this object's collection of namespaces is
the same as C<sb's>, C<false> otherwise.
=item SBase::matchesSBMLNamespaces
Returns C<true> if this object's set of XML namespaces are the same
as the given object's XML namespaces.
C<opydetails> doc_what_are_sbmlnamespaces
@param sb an object to compare with respect to namespaces
@return boolean, C<true> if this object's collection of namespaces is
the same as C<sb's>, C<false> otherwise.
=item SBase::matchesRequiredSBMLNamespacesForAddition
Returns C<true> if this object's set of XML namespaces are a subset
of the given object's XML namespaces.
C<opydetails> doc_what_are_sbmlnamespaces
@param sb an object to compare with respect to namespaces
@return boolean, C<true> if this object's collection of namespaces is
a subset of C<sb's>, C<false> otherwise.
=item SBase::matchesRequiredSBMLNamespacesForAddition
Returns C<true> if this object's set of XML namespaces are a subset
of the given object's XML namespaces.
C<opydetails> doc_what_are_sbmlnamespaces
@param sb an object to compare with respect to namespaces
@return boolean, C<true> if this object's collection of namespaces is
a subset of C<sb's>, C<false> otherwise.
=item SBase::setUserData
Sets the user data of this element.
C<opydetails> doc_sbase_what_is_user_data
@param userData specifies the new user data.
@return integer value indicating success/failure of the
function. The possible values returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item SBase::*getUserData
Returns the user data that has been previously set via setUserData().
C<opydetails> doc_sbase_what_is_user_data
@return the user data of this node, or C<NULL> if no user data has been set.
@if clike
@see ASTNode::setUserData(void userData)
@endif@~
=item SBase::getURI
Gets the namespace URI to which this element belongs to.
For example, all elements that belong to SBML Level 3 Version 1 Core
must would have the URI "http://www.sbml.org/sbml/level3/version1/core";
all elements that belong to Layout Extension Version 1 for SBML Level 3
Version 1 Core must would have the URI
"http://www.sbml.org/sbml/level3/version1/layout/version1/"
This function first returns the URI for this element by looking into the
SBMLNamespaces object of the document with the its package name. If not
found, it will @if clike return the result of getElementNamespace()@else
return the XML namespace to which this element belongs@endif.
@return the URI of this element
@see getSBMLDocument()
@see getPackageName()
@if clike @see getElementNamespace() @endif
=item SBase::getPrefix
Returns the namespace prefix of this element.
=item SBase::setElementText
When overridden allows SBase elements to use the text included in between
the elements tags. The default implementation does nothing.
@param text the text string found between the element tags.
=item SBase::matchesCoreSBMLNamespace
@internal
=item SBase::matchesCoreSBMLNamespace
@internal
=item SBase::SBase
@internal
Creates a new SBase object with the given SBML level, version.
=item SBase::SBase
@internal
Creates a new SBase object with the given SBMLNamespaces.
Only subclasses may create SBase objects.
=item SBase::SBase
@internal
Copy constructor. Creates a copy of this SBase object.
@param orig the object to copy.
@throws @if python ValueError @else SBMLConstructorException @endif@~
Thrown if the argument C<orig> is C<NULL>.
=item SBase::createObject
@internal
Subclasses should override this method to create, store, and then
return an SBML object corresponding to the next XMLToken in the
XMLInputStream.
@return the SBML object corresponding to next XMLToken in the
XMLInputStream or C<NULL> if the token was not recognized.
=item SBase::hasValidLevelVersionNamespaceCombination
@internal
Predicate returning C<true> if this
object's level/version and namespace values correspond to a valid
SBML specification.
The valid combinations of SBML Level, Version and Namespace as of this
release of libSBML are the following:
\n=over\n
\n=item\n\nLevel 1 Version 2: C<"http://www.sbml.org/sbml/level1">
\n=item\n\nLevel 2 Version 1: C<"http://www.sbml.org/sbml/level2">
\n=item\n\nLevel 2 Version 2: C<"http://www.sbml.org/sbml/level2/version2">
\n=item\n\nLevel 2 Version 3: C<"http://www.sbml.org/sbml/level2/version3">
\n=item\n\nLevel 2 Version 4: C<"http://www.sbml.org/sbml/level2/version4">
\n=item\n\nLevel 3 Version 1 Core: C<"http://www.sbml.org/sbml/level3/version1/core">
\n=back\n
@param typecode the typecode for this element
@param xmlns the namespaces used by this element.
@note This function is provided as convenience method to be called from constructors. This
allows to use it in scenarios where the namespaces or typecode have not yet been initialized.
@return C<true> if the level, version and namespace values of this
SBML object correspond to a valid set of values, C<false> otherwise.
=item SBase::readOtherXML
@internal
Subclasses should override this method to read (and store) XHTML,
MathML, etc. directly from the XMLInputStream.
@return true if the subclass read from the stream, false otherwise.
=item SBase::getElementPosition
@internal
The SBML XML Schema is written such that the order of child elements
is significant. LibSBML can read elements out of order. If you
override this method to indicate the ordinal position of element with
respect to its siblings, libSBML will log an error if the element is
read out of order.
@return the ordinal position of the element with respect to its
siblings or C<-1> (the default) to indicate the position is not
significant.
=item SBase::getErrorLog
@internal
Returns the SBMLErrorLog used to log errors while reading and
validating SBML.
@return the SBMLErrorLog used to log errors while reading and
validating SBML.
=item SBase::logError
@internal
Convenience method for easily logging problems from within method
implementations.
This is essentially a short form of getErrorLog()->logError(...)
@if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
=item SBase::logUnknownAttribute
@internal
Helper to log a common type of error.
=item SBase::logUnknownElement
@internal
Helper to log a common type of error.
=item SBase::logEmptyString
@internal
Helper to log a common type of error.
=item SBase::addExpectedAttributes
@internal
Subclasses should override this method to add the list of
expected attributes. Be sure to call your parents implementation
of this method as well.
=item SBase::readAttributes
@internal
Subclasses should override this method to read values from the given
XMLAttributes set into their specific fields. Be sure to call your
parents implementation of this method as well.
=item SBase::writeAttributes
@internal
Subclasses should override this method to write their XML attributes
to the XMLOutputStream. Be sure to call your parents implementation
of this method as well. For example:
SBase::writeAttributes(stream);
stream.writeAttribute( "id" , mId );
stream.writeAttribute( "name", mName );
...
(NOTICE) this function doesn't write xmlns attributes.
Be sure to implement wirteXMLNS() function to write xmlns attributes.
=item SBase::writeXMLNS
@internal
Subclasses should override this method to write their xmlns attriubutes
(if any) to the XMLOutputStream.
=item SBase::syncAnnotation
@internal
Synchronizes the annotation of this SBML object.
Annotation element (XMLNode mAnnotation) is synchronized with the
current CVTerm objects (List mCVTerm).
Currently, this method is called in getAnnotation, isSetAnnotation,
and writeElements methods.
=item SBase::reconstructRDFAnnotation
@internal
=item SBase::checkOrderAndLogError
@internal
Checks that the SBML element appears in the expected order.
If C<object> is not in the expected position, an error is logged.
=item SBase::checkListOfPopulated
@internal
Checks that an SBML ListOf element is populated.
If a listOf element has been declared with no elements,
an error is logged.
=item SBase::checkDefaultNamespace
@internal
Checks that the given default namespace in the given element is valid.
If the given default namespace is not valid, an error is logged.
=item SBase::checkAnnotation
@internal
Checks the annotation does not declare an sbml namespace.
If the annotation declares an sbml namespace an error is logged.
=item SBase::checkXHTML
@internal
Checks that the XHTML is valid.
If the xhtml does not conform to the specification of valid xhtml within
an sbml document, an error is logged.
=item SBase::loadPlugins
@internal
=item SBase::createExtensionObject
@internal
Create, store, and then return an SBML object of package extensions
corresponding to the next XMLToken in the XMLInputStream.
@return the SBML object of package extensions corresponding to next
XMLToken in the XMLInputStream or C<NULL> if the token was not recognized.
=item SBase::setElementNamespace
@internal
Sets the XML namespace to which this element belongs to.
For example, all elements that belong to SBML Level 3 Version 1 Core
must set the namespace to "http://www.sbml.org/sbml/level3/version1/core";
all elements that belong to Layout Extension Version 1 for SBML Level 3
Version 1 Core must set the namespace to
"http://www.sbml.org/sbml/level3/version1/layout/version1/"
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif@~ The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item SBase::getElementNamespace
@internal
Gets the XML namespace (URI) to which this element belongs to.
=item SBase::readExtensionAttributes
@internal
Read attributes of package extensions from the given XMLAttributes
set into their specific fields.
Be sure to call your parents implementation of this function as well.
For example:
@if clike
@verbatim
SBase::readExtensionAttributes(attributes, expectedAttributes);
@endverbatim
@endif@if java
@verbatim
SBase.readExtensionAttributes(attributes, expectedAttributes);
@endverbatim
@endif@if java
@verbatim
SBase.readExtensionAttributes(attributes, expectedAttributes);
@endverbatim
@endif@if python
@verbatim
SBase.readExtensionAttributes(attributes, expectedAttributes);
@endverbatim
@endif@~
=item SBase::writeExtensionAttributes
@internal
Write attributes of package extensions to the XMLOutputStream.
Be sure to call your parents implementation of this function as well.
For example:
SBase::writeExtensionAttributes(stream);
=item SBase::storeUnknownExtAttribute
@internal
Stores the given attribute to the list of ignored attributes if
the given attribute belongs to some unknown package extension.
Unknown attribute error will be logged if the "required" attribute
of the package is "true" in SBMLDocument element.
The stored attributes will be written out as-is when writing the
SBMLDocument to a string or a file (i.e. Attributes and elements of
unknown package extensions will not be lost when reading/writing
a file/sting containing them.)
@param element the string of element which contains the given attribute
@param xattr the XMLAttributes object which is contained in the given
element
@param index the index of the target attribute in the given XMLAttributes
object.
@return true will be returned if the given attribute belongs
to some unknown package extension, otherwise false will be returned.
=item SBase::storeUnknownExtElement
@internal
Stores the element of next token if the element belongs to some
unknown package extension. Unknown element error will be logged if
the "required" attribute of the package is "true" in SBMLDocument
element.
The stored elements will be written out as-is when writing the
SBMLDocument to a string or a file (i.e. Attributes and elements of
unknown package extensions will not be lost when reading/writing
a file/sting containing them.)
@return true will be returned if the element of next token belongs
to some unknown package extension, otherwise false will be returned.
=item SBase::getSBMLPrefix
@internal
Return the SBML prefix of this element. This will be the same as getPrefix()
unless the element in question is an element of an SBML extension class.
=item SBase::getRootElement
@internal
Returns the root element of the node tree to which this element is connected.
@note The root element may not be an SBMLDocument element. For example,
this element is the root element if this element doesn't have a parent
SBML object (i.e. mParentSBMLObject is NULL)
@see enablePackageInternal
=item SBase::getHasBeenDeleted
@internal
=item SBase::setSBaseFields
@internal
Stores the location (line and column) and any XML namespaces (for
roundtripping) declared on this SBML (XML) element.
=item SBase::readAnnotation
@internal
Reads an annotation from the stream and returns true if successful.
@return true if read an <annotation> element from the stream
=item SBase::removeDuplicatedResources
@internal
removes resources from the term object that alread exist on this object
=item SBase::addTermToExistingBag
@internal
adds the given term to an existing bag. Returns 1 if added, 0 otherwise.
=item SBase::readNotes
@internal
Reads the notes from the stream and returns true if successful.
@return true if read a <notes> element from the stream
=back
=head2 ListOf
@sbmlpackage{core}
@htmlinclude pkg-marker-core.html Parent class for libSBML's "ListOfXYZ" classes.
@htmlinclude not-sbml-warning.html
The ListOf class in libSBML is a utility class that serves as the parent
class for implementing the ListOf__ classes. It provides methods for
working generically with the various SBML lists of objects in a program.
LibSBML uses this separate list class rather than ordinary
@if conly C@endif@if cpp C++; @endif@if java Java@endif@if python Python@endif@~ lists,
so that it can provide the methods and features associated with SBase.
C<opydetails> doc_what_is_listof
=over
=item ListOf::ListOf
Creates a new ListOf object.
@param level the SBML Level; if not assigned, defaults to the
value of SBMLDocument::getDefaultLevel().
@param version the Version within the SBML Level; if not assigned,
defaults to the value of SBMLDocument::getDefaultVersion().
@if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
=item ListOf::ListOf
Creates a new ListOf with SBMLNamespaces object.
@param sbmlns the set of SBML namespaces that this ListOf should
contain.
=item ListOf::ListOf
Copy constructor; creates a copy of this ListOf.
@param orig the ListOf instance to copy.
=item ListOf::accept
Accepts the given SBMLVisitor.
@param v the SBMLVisitor instance to be used.
@return the result of calling C<v.visit()>, which indicates
whether the Visitor would like to visit the next item in the
list.
=item ListOf::clone
Creates and returns a deep copy of this ListOf.
@return a (deep) copy of this ListOf.
=item ListOf::append
Adds an item to the end of this ListOf's list of items.
This method makes a clone of the C<item> handed to it. This means that
when the ListOf object is destroyed, the original items will not be
destroyed. For a method with an alternative ownership behavior, see the
ListOf::appendAndOwn(SBase item) method.
@param item the item to be added to the list.
@see appendAndOwn(SBase item)
@see appendFrom(const ListOf list)
=item ListOf::appendAndOwn
Adds an item to the end of this ListOf's list of items.
This method does not clone the C<item> handed to it; instead, it assumes
ownership of it. This means that when the ListOf is destroyed, the item
will be destroyed along with it. For a method with an alternative
ownership behavior, see the ListOf::append(SBase item) method.
@param item the item to be added to the list.
@see append(const SBase item)
@see appendFrom(const ListOf list)
=item ListOf::appendFrom
Adds a clone of a list of items to this ListOf's list.
Note that because this clones the objects handed to it, the original
items will not be destroyed when this ListOf object is destroyed.
@param list a list of items to be added.
@see append(const SBase item)
@see appendAndOwn(SBase item)
=item ListOf::insert
Inserts an item at a given position in this ListOf's list of items.
This variant of the method makes a clone of the C<item> handed to it.
This means that when the ListOf is destroyed, the original items will
not be destroyed. For an alternative method with different ownership
behavior, see insertAndOwn(int location, SBase item).
@param location the location in the list where to insert the item.
@param item the item to be inserted to the list.
@see insertAndOwn(int location, SBase item)
=item ListOf::insertAndOwn
Inserts an item at a given position in this ListOf's list of items.
This variant of the method makes a clone of the C<item> handet to it.
This means that when the ListOf is destroyed, the original items will
not be destroyed.
@param location the location where to insert the item
@param item the item to be inserted to the list
@see insert(int location, const SBase item)
=item ListOf::get
Get an item from the list.
@param n the index number of the item to get.
@return the nth item in this ListOf items.
@see size()
=item ListOf::get
Get an item from the list.
@param n the index number of the item to get.
@return the nth item in this ListOf items.
@see size()
=item ListOf::getElementBySId
Returns the first child element found that has the given identifier.
This method searches this ListOf's list of items for SBML objects based
on their "id" attribute value in the model-wide SId namespace.
@param id string representing the id of objects to find.
@return the first element found with the given C<id>, or C<NULL> if no
such object is found.
=item ListOf::getElementByMetaId
Returns the first child element found with the given C<metaid>.
@param metaid string representing the metaid of objects to find
@return the first element found with the given C<metaid>, or C<NULL> if
no such object is found.
=item ListOf::getAllElements
Returns a List of all child SBase objects.
The values returned include all children of the objects in this ListOf
list, nested to an arbitrary depth.
@return a List of pointers to all child objects.
=item ListOf::clear
Removes all items in this ListOf object.
If parameter C<doDelete> is C<true> (default), all items in this ListOf
object are deleted and cleared, and thus the caller doesn't have to
delete those items. Otherwise, all items are cleared only from this
ListOf object; the caller is still responsible for deleting all items.
(In the latter case, callers are advised to store pointers to all items
elsewhere before calling this function.)
@param doDelete if C<true> (default), all items are deleted and cleared.
Otherwise, all items are just cleared and not deleted.
@if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
=item ListOf::removeFromParentAndDelete
Because ListOf objects typically live as object children of their parent
object and not as pointer children, this function clears itself, but
does not attempt to do anything else.
If a particular ListOf subclass does indeed exist as a pointer only,
this function will need to be overridden.
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif@~ The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
=item ListOf::remove
Removes the <em>n</em>th item from this ListOf items and returns it.
The caller owns the returned item and is responsible for deleting it.
@param n the index of the item to remove
@see size()
=item ListOf::size
Returns number of items in this ListOf list.
@return the number of items in this ListOf items.
=item ListOf::setSBMLDocument
@internal
Sets the parent SBMLDocument of this SBML object.
@param d the SBMLDocument that should become the parent of this
ListOf.
=item ListOf::connectToChild
@internal
Sets this SBML object to child SBML objects (if any).
(Creates a child-parent relationship by the parent)
Subclasses must override this function if they define
one ore more child elements.
Basically, this function needs to be called in
constructor, copy constructor and assignment operator.
@if cpp
@see setSBMLDocument()
@see enablePackageInternal()
@endif
=item ListOf::getTypeCode
Returns the libSBML type code for this object, namely,
@link SBMLTypeCode_t#SBML_LIST_OF SBML_LIST_OF@endlink.
C<opydetails> doc_what_are_typecodes
@return the SBML type code for this object:
@link SBMLTypeCode_t#SBML_LIST_OF SBML_LIST_OF@endlink (default).
@note The various ListOf classes mostly differ from each other in what they
contain. Hence, one must call getItemTypeCode() to fully determine the
class of this SBML object.
C<opydetails> doc_warning_typecodes_not_unique
@see getItemTypeCode()
@see getElementName()
@see getPackageName()
=item ListOf::getItemTypeCode
Get the type code of the objects contained in this ListOf.
C<opydetails> doc_what_are_typecodes
Classes that inherit from the ListOf class should
override this function to return the SBML type code for
the objects contained in this ListOf. If they do not,
@link SBMLTypeCode_t#SBML_UNKNOWN SBML_UNKNOWN@endlink is returned.
@return The ListOf class itself contains no SBML objects, and
therefore returns @link SBMLTypeCode_t#SBML_UNKNOWN SBML_UNKNOWN@endlink.
@see getElementName()
@see getPackageName()
=item ListOf::getElementName
Returns the XML element name of this object, which for ListOf, is
always C<"listOf">.
@return the XML name of this element.
=item ListOf::writeElements
@internal
Subclasses should override this method to write out their contained
SBML objects as XML elements. Be sure to call your parents
implementation of this method as well.
=item ListOf::enablePackageInternal
@internal
Enables/Disables the given package with this element and child
elements (if any).
(This is an internal implementation for enablePackage function)
@note Subclasses of the SBML Core package in which one or more child
elements are defined must override this function.
=item ListOf::addExpectedAttributes
@internal
Subclasses should override this method to get the list of
expected attributes.
This function is invoked from corresponding readAttributes()
function.
=item ListOf::readAttributes
@internal
Subclasses should override this method to read values from the given
XMLAttributes set into their specific fields. Be sure to call your
parents implementation of this method as well.
=item ListOf::writeAttributes
@internal
Subclasses should override this method to write their XML attributes
to the XMLOutputStream. Be sure to call your parents implementation
of this method as well. For example:
SBase::writeAttributes(stream);
stream.writeAttribute( "id" , mId );
stream.writeAttribute( "name", mName );
...
=item ListOf::isValidTypeForList
@internal
=back
=head2 Model
@sbmlpackage{core}
@htmlinclude pkg-marker-core.html Implementation of SBML's Model construct.
In an SBML model definition, a single object of class Model serves as
the overall container for the lists of the various model components.
All of the lists are optional, but if a given list container is present
within the model, the list must not be empty; that is, it must have
length one or more. The following are the components and lists
permitted in different Levels and Versions of SBML in
version @htmlinclude libsbml-version.html
of libSBML:
\n=over\n
\n=item\n\nIn SBML Level 1, the components are: UnitDefinition, Compartment,
Species, Parameter, Rule, and Reaction. Instances of the classes are
placed inside instances of classes ListOfUnitDefinitions,
ListOfCompartments, ListOfSpecies, ListOfParameters, ListOfRules, and
ListOfReactions.
\n=item\n\nIn SBML Level 2 Version 1, the components are: FunctionDefinition,
UnitDefinition, Compartment, Species, Parameter, Rule, Reaction and
Event. Instances of the classes are placed inside instances of classes
ListOfFunctionDefinitions, ListOfUnitDefinitions, ListOfCompartments,
ListOfSpecies, ListOfParameters, ListOfRules, ListOfReactions, and
ListOfEvents.
\n=item\n\nIn SBML Level 2 Versions 2, 3 and 4, the components are:
FunctionDefinition, UnitDefinition, CompartmentType, SpeciesType,
Compartment, Species, Parameter, InitialAssignment, Rule, Constraint,
Reaction and Event. Instances of the classes are placed inside
instances of classes ListOfFunctionDefinitions, ListOfUnitDefinitions,
ListOfCompartmentTypes, ListOfSpeciesTypes, ListOfCompartments,
ListOfSpecies, ListOfParameters, ListOfInitialAssignments, ListOfRules,
ListOfConstraints, ListOfReactions, and ListOfEvents.
\n=item\n\nIn SBML Level 3 Version 1, the components are: FunctionDefinition,
UnitDefinition, Compartment, Species, Parameter, InitialAssignment,
Rule, Constraint, Reaction and Event. Instances of the classes are
placed inside instances of classes ListOfFunctionDefinitions,
ListOfUnitDefinitions, ListOfCompartments, ListOfSpecies,
ListOfParameters, ListOfInitialAssignments, ListOfRules,
ListOfConstraints, ListOfReactions, and ListOfEvents.
\n=back\n
Although all the lists are optional, there are dependencies between SBML
components such that defining some components requires defining others.
An example is that defining a species requires defining a compartment,
and defining a reaction requires defining a species. The dependencies
are explained in more detail in the SBML specifications.
In addition to the above lists and attributes, the Model class in both
SBML Level 2 and Level 3 has the usual two attributes of "id"
and "name", and both are optional. As is the case for other SBML
components with "id" and "name" attributes, they must be used according
to the guidelines described in the SBML specifications. (Within the
frameworks of SBML Level 2 and Level 3 Version 1 Core, a
Model object identifier has no assigned meaning, but extension packages
planned for SBML Level 3 are likely to make use of this
identifier.)
Finally, SBML Level 3 has introduced a number of additional Model
attributes. They are discussed in a separate section below.
@section approaches Approaches to creating objects using the libSBML API
LibSBML provides two main mechanisms for creating objects: class
constructors
(e.g., @if java <a href="org/sbml/libsbml/Species.html">Species()</a> @else Species::Species() @endif),
and <code>create<span class="placeholder"><em>Object</em></span>()</code>
methods (such as Model::createSpecies()) provided by certain <span
class="placeholder"><em>Object</em></span> classes such as Model. These
multiple mechanisms are provided by libSBML for flexibility and to
support different use-cases, but they also have different implications
for the overall model structure.
In general, the recommended approach is to use the <code>create<span
class="placeholder"><em>Object</em></span>()</code> methods. These
methods both create an object I<and> link it to the parent in one step.
Here is an example:@if clike
@verbatim
// Create an SBMLDocument object in Level 3 Version 1 format:
SBMLDocument sbmlDoc = new SBMLDocument(3, 1);
// Create a Model object inside the SBMLDocument object and set
// its identifier. The call returns a pointer to the Model object
// created, and methods called on that object affect the attributes
// of the object attached to the model (as expected).
Model model = sbmlDoc->createModel();
model->setId("BestModelEver");
// Create a Species object inside the Model and set its identifier.
// Similar to the lines above, this call returns a pointer to the Species
// object created, and methods called on that object affect the attributes
// of the object attached to the model (as expected).
Species sp = model->createSpecies();
sp->setId("MySpecies");
@endverbatim
@endif@if java
@verbatim
// Create an SBMLDocument object in Level 3 Version 1 format:
SBMLDocument sbmlDoc = new SBMLDocument(3, 1);
// Create a Model object inside the SBMLDocument object and set
// its identifier. The call returns a pointer to the Model object
// created, and methods called on that object affect the attributes
// of the object attached to the model (as expected). Note that
// the call to setId() returns a status code, and a real program
// should check this status code to make sure everything went okay.
Model model = sbmlDoc.createModel();
model.setId("BestModelEver");
// Create a Species object inside the Model and set its identifier.
// Similar to the lines above, this call returns a pointer to the Species
// object created, and methods called on that object affect the attributes
// of the object attached to the model (as expected). Note that, like
// with Model, the call to setId() returns a status code, and a real program
// should check this status code to make sure everything went okay.
Species sp = model.createSpecies();
sp.setId("BestSpeciesEver");
@endverbatim
@endif@if python
@verbatim
# Create an SBMLDocument object in Level 3 Version 1 format:
sbmlDoc = SBMLDocument(3, 1)
# Create a Model object inside the SBMLDocument object and set
# its identifier. The call to setId() returns a status code
# to indicate whether the assignment was successful. Code 0
# means success; see the documentation for Model's setId() for
# more information.
model = sbmlDoc.createModel()
model.setId("BestModelEver")
# Create a Species object inside the Model and set its identifier.
# Again, the setId() returns a status code to indicate whether the
# assignment was successful. Code 0 means success; see the
# documentation for Specie's setId() for more information.
sp = model.createSpecies()
sp.setId("BestSpeciesEver")
@endverbatim
@endif@if csharp
@verbatim
// Create an SBMLDocument object in Level 3 Version 1 format:
SBMLDocument sbmlDoc = new SBMLDocument(3, 1);
// Create a Model object inside the SBMLDocument object and set
// its identifier. The call returns a pointer to the Model object
// created, and methods called on that object affect the attributes
// of the object attached to the model (as expected).
Model model = sbmlDoc.createModel();
model.setId("BestModelEver");
// Create a Species object inside the Model and set its identifier.
// Similar to the lines above, this call returns a pointer to the Species
// object created, and methods called on that object affect the attributes
// of the object attached to the model (as expected).
Species sp = model.createSpecies();
sp.setId("MySpecies");
@endverbatim
@endif@~
The <code>create<span
class="placeholder"><em>Object</em></span>()</code> methods return a
pointer to the object created, but they also add the object to the
relevant list of object instances contained in the parent. (These lists
become the <code><listOf<span
class="placeholder"><em>Object</em></span>s></code> elements in the
finished XML rendition of SBML.) In the example above,
Model::createSpecies() adds the created species directly to the
C<<listOfSpecies>> list in the model. Subsequently,
methods called on the species change the species in the model (which is
what is expected in most situations).
@section checking Consistency and adherence to SBML specifications
To make it easier for applications to do whatever they need,
libSBML version @htmlinclude libsbml-version.html
is relatively lax when it comes to enforcing correctness and
completeness of models I<during> model construction and editing.
Essentially, libSBML I<will> I<not> in most cases check automatically
that a model's components have valid attribute values, or that the
overall model is consistent and free of errors—even obvious errors
such as duplication of identifiers. This allows applications great
leeway in how they build their models, but it means that software
authors must take deliberate steps to ensure that the model will be, in
the end, valid SBML. These steps include such things as keeping track
of the identifiers used in a model, manually performing updates in
certain situations where an entity is referenced in more than one place
(e.g., a species that is referenced by multiple SpeciesReference
objects), and so on.
That said, libSBML does provide powerful features for deliberately
performing validation of SBML when an application decides it is time to
do so. The interfaces to these facilities are on the SBMLDocument
class, in the form of SBMLDocument::checkInternalConsistency() and
SBMLDocument::checkConsistency(). Please refer to the documentation for
SBMLDocument for more information about this.
While applications may play fast and loose and live like free spirits
during the construction and editing of SBML models, they should always
make sure to call SBMLDocument::checkInternalConsistency() and/or
SBMLDocument::checkConsistency() before writing out the final version of
an SBML model.
@section model-l3-attrib Model attributes introduced in SBML Level 3
As mentioned above, the Model class has a number of optional attributes
in SBML Level 3 Version 1 Core. These are "substanceUnits",
"timeUnits", "volumeUnits", "areaUnits", "lengthUnits", "extentUnits",
and "conversionFactor. The following provide more information about
them.
@subsection model-l3-substanceunits The "substanceUnits" attribute
The "substanceUnits" attribute is used to specify the unit of
measurement associated with substance quantities of Species objects that
do not specify units explicitly. If a given Species object definition
does not specify its unit of substance quantity via the "substanceUnits"
attribute on the Species object instance, then that species inherits the
value of the Model "substanceUnits" attribute. If the Model does not
define a value for this attribute, then there is no unit to inherit, and
all species that do not specify individual "substanceUnits" attribute
values then have <em>no</em> declared units for their quantities. The
SBML Level 3 Version 1 Core specification provides more
details.
Note that when the identifier of a species appears in a model's
mathematical expressions, the unit of measurement associated with that
identifier is <em>not solely determined</em> by setting "substanceUnits"
on Model or Species. Please see the discussion about units given in
the documentation for the Species class.
@subsection model-l3-timeunits The "timeUnits" attribute
The "timeUnits" attribute on SBML Level 3's Model object is used to
specify the unit in which time is measured in the model. This attribute
on Model is the <em>only</em> way to specify a unit for time in a model.
It is a global attribute; time is measured in the model everywhere in
the same way. This is particularly relevant to Reaction and RateRule
objects in a model: all Reaction and RateRule objects in SBML define
per-time values, and the unit of time is given by the "timeUnits"
attribute on the Model object instance. If the Model "timeUnits"
attribute has no value, it means that the unit of time is not defined
for the model's reactions and rate rules. Leaving it unspecified in an
SBML model does not result in an invalid model in SBML Level 3;
however, as a matter of best practice, we strongly recommend that all
models specify units of measurement for time.
@subsection model-l3-voletc The "volumeUnits", "areaUnits", and "lengthUnits" attributes
The attributes "volumeUnits", "areaUnits" and "lengthUnits" together are
used to set the units of measurements for the sizes of Compartment
objects in an SBML Level 3 model when those objects do not
otherwise specify units. The three attributes correspond to the most
common cases of compartment dimensions: "volumeUnits" for compartments
having a "spatialDimensions" attribute value of C<"3">, "areaUnits" for
compartments having a "spatialDimensions" attribute value of C<"2">, and
"lengthUnits" for compartments having a "spatialDimensions" attribute
value of C<"1">. The attributes are not applicable to compartments
whose "spatialDimensions" attribute values are I<not> one of C<"1">, @c
"2" or C<"3">.
If a given Compartment object instance does not provide a value for its
"units" attribute, then the unit of measurement of that compartment's
size is inherited from the value specified by the Model "volumeUnits",
"areaUnits" or "lengthUnits" attribute, as appropriate based on the
Compartment object's "spatialDimensions" attribute value. If the Model
object does not define the relevant attribute, then there are no units
to inherit, and all Compartment objects that do not set a value for
their "units" attribute then have <em>no</em> units associated with
their compartment sizes.
The use of three separate attributes is a carry-over from SBML
Level 2. Note that it is entirely possible for a model to define a
value for two or more of the attributes "volumeUnits", "areaUnits" and
"lengthUnits" simultaneously, because SBML models may contain
compartments with different numbers of dimensions.
@subsection model-l3-extentunits The "extentUnits" attribute
Reactions are processes that occur over time. These processes involve
events of some sort, where a single ``reaction event'' is one in which
some set of entities (known as reactants, products and modifiers in
SBML) interact, once. The <em>extent</em> of a reaction is a measure of
how many times the reaction has occurred, while the time derivative of
the extent gives the instantaneous rate at which the reaction is
occurring. Thus, what is colloquially referred to as the "rate of the
reaction" is in fact equal to the rate of change of reaction extent.
In SBML Level 3, the combination of "extentUnits" and "timeUnits"
defines the units of kinetic laws in SBML and establishes how the
numerical value of each KineticLaw object's mathematical formula is
meant to be interpreted in a model. The units of the kinetic laws are
taken to be "extentUnits" divided by "timeUnits".
Note that this embodies an important principle in SBML Level 3
models: <em>all reactions in an SBML model must have the same units</em>
for the rate of change of extent. In other words, the units of all
reaction rates in the model <em>must be the same</em>. There is only
one global value for "extentUnits" and one global value for "timeUnits".
@subsection model-l3-convfactor The "conversionFactor" attribute
The attribute "conversionFactor" in SBML Level 3's Model object
defines a global value inherited by all Species object instances that do
not define separate values for their "conversionFactor" attributes. The
value of this attribute must refer to a Parameter object instance
defined in the model. The Parameter object in question must be a
constant; ie it must have its "constant" attribute value set to @c
"true".
If a given Species object definition does not specify a conversion
factor via the "conversionFactor" attribute on Species, then the species
inherits the conversion factor specified by the Model "conversionFactor"
attribute. If the Model does not define a value for this attribute,
then there is no conversion factor to inherit. More information about
conversion factors is provided in the SBML Level 3 Version 1
specification.
=over
=item Model::Model
Creates a new Model using the given SBML C<level> and C<version>
values.
@param level an unsigned int, the SBML Level to assign to this Model
@param version an unsigned int, the SBML Version to assign to this
Model
@throws @if python ValueError @else SBMLConstructorException @endif@~
Thrown if the given C<level> and C<version> combination, or this kind
of SBML object, are either invalid or mismatched with respect to the
parent SBMLDocument object.
C<opydetails> doc_note_model_setting_lv
=item Model::Model
Creates a new Model using the given SBMLNamespaces object
C<sbmlns>.
C<opydetails> doc_what_are_sbmlnamespaces
@param sbmlns an SBMLNamespaces object.
@throws @if python ValueError @else SBMLConstructorException @endif@~
Thrown if the given C<level> and C<version> combination, or this kind
of SBML object, are either invalid or mismatched with respect to the
parent SBMLDocument object.
C<opydetails> doc_note_model_setting_lv
=item Model::Model
Copy constructor; creates a (deep) copy of the given Model object.
@param orig the object to copy.
@throws @if python ValueError @else SBMLConstructorException @endif@~
Thrown if the argument C<orig> is C<NULL>.
=item Model::accept
Accepts the given SBMLVisitor for this instance of Constraint.
@param v the SBMLVisitor instance to be used.
@return the result of calling C<v.visit()>.
=item Model::clone
Creates and returns a deep copy of this Model object.
@return a (deep) copy of this Model.
=item Model::getElementBySId
Returns the first child element found that has the given C<id> in the
model-wide SId namespace, or C<NULL> if no such object is found.
@param id string representing the id of objects to find.
@return pointer to the first element found with the given C<id>.
=item Model::getElementByMetaId
Returns the first child element it can find with the given C<metaid>, or
NULL if no such object is found.
@param metaid string representing the metaid of objects to find
@return pointer to the first element found with the given C<metaid>.
=item Model::getAllElements
Returns a List of all child SBase objects, including those nested to an
arbitrary depth
@return a List of pointers to all children objects.
=item Model::getId
Returns the value of the "id" attribute of this Model.
@return the id of this Model.
=item Model::getName
Returns the value of the "name" attribute of this Model.
@return the name of this Model.
=item Model::getSubstanceUnits
Returns the value of the "substanceUnits" attribute of this Model.
@return the substanceUnits of this Model.
@note The "substanceUnits" attribute is available in
SBML Level 3 but is not present on Model in lower Levels of SBML.
=item Model::getTimeUnits
Returns the value of the "timeUnits" attribute of this Model.
@return the timeUnits of this Model.
@note The "timeUnits" attribute is available in
SBML Level 3 but is not present on Model in lower Levels of SBML.
=item Model::getVolumeUnits
Returns the value of the "volumeUnits" attribute of this Model.
@return the volumeUnits of this Model.
@note The "volumeUnits" attribute is available in
SBML Level 3 but is not present on Model in lower Levels of SBML.
=item Model::getAreaUnits
Returns the value of the "areaUnits" attribute of this Model.
@return the areaUnits of this Model.
@note The "areaUnits" attribute is available in
SBML Level 3 but is not present on Model in lower Levels of SBML.
=item Model::getLengthUnits
Returns the value of the "lengthUnits" attribute of this Model.
@return the lengthUnits of this Model.
@note The "lengthUnits" attribute is available in
SBML Level 3 but is not present on Model in lower Levels of SBML.
=item Model::getExtentUnits
Returns the value of the "extentUnits" attribute of this Model.
@return the extentUnits of this Model.
@note The "extentUnits" attribute is available in
SBML Level 3 but is not present on Model in lower Levels of SBML.
=item Model::getConversionFactor
Returns the value of the "conversionFactor" attribute of this Model.
@return the conversionFactor of this Model.
@note The "conversionFactor" attribute is available in
SBML Level 3 but is not present on Model in lower Levels of SBML.
=item Model::isSetId
Predicate returning C<true> if this
Model's "id" attribute is set.
@return C<true> if the "id" attribute of this Model is
set, C<false> otherwise.
=item Model::isSetName
Predicate returning C<true> if this
Model's "name" attribute is set.
@return C<true> if the "name" attribute of this Model is
set, C<false> otherwise.
=item Model::isSetSubstanceUnits
Predicate returning C<true> if this
Model's "substanceUnits" attribute is set.
@return C<true> if the "substanceUnits" attribute of this Model is
set, C<false> otherwise.
@note The "substanceUnits" attribute is available in
SBML Level 3 but is not present on Model in lower Levels of SBML.
=item Model::isSetTimeUnits
Predicate returning C<true> if this
Model's "timeUnits" attribute is set.
@return C<true> if the "timeUnits" attribute of this Model is
set, C<false> otherwise.
@note The "substanceUnits" attribute is available in
SBML Level 3 but is not present on Model in lower Levels of SBML.
=item Model::isSetVolumeUnits
Predicate returning C<true> if this
Model's "volumeUnits" attribute is set.
@return C<true> if the "volumeUnits" attribute of this Model is
set, C<false> otherwise.
@note The "volumeUnits" attribute is available in
SBML Level 3 but is not present on Model in lower Levels of SBML.
=item Model::isSetAreaUnits
Predicate returning C<true> if this
Model's "areaUnits" attribute is set.
@return C<true> if the "areaUnits" attribute of this Model is
set, C<false> otherwise.
@note The "areaUnits" attribute is available in
SBML Level 3 but is not present on Model in lower Levels of SBML.
=item Model::isSetLengthUnits
Predicate returning C<true> if this
Model's "lengthUnits" attribute is set.
@return C<true> if the "lengthUnits" attribute of this Model is
set, C<false> otherwise.
@note The "lengthUnits" attribute is available in
SBML Level 3 but is not present on Model in lower Levels of SBML.
=item Model::isSetExtentUnits
Predicate returning C<true> if this
Model's "extentUnits" attribute is set.
@return C<true> if the "extentUnits" attribute of this Model is
set, C<false> otherwise.
@note The "extentUnits" attribute is available in
SBML Level 3 but is not present on Model in lower Levels of SBML.
=item Model::isSetConversionFactor
Predicate returning C<true> if this
Model's "conversionFactor" attribute is set.
@return C<true> if the "conversionFactor" attribute of this Model is
set, C<false> otherwise.
@note The "conversionFactor" attribute is available in
SBML Level 3 but is not present on Model in lower Levels of SBML.
=item Model::setId
Sets the value of the "id" attribute of this Model.
The string C<sid> is copied.
C<opydetails> doc_id_syntax
@param sid the string to use as the identifier of this Model
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item Model::setName
Sets the value of the "name" attribute of this Model.
The string in C<name> is copied.
@param name the new name for the Model
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item Model::setSubstanceUnits
Sets the value of the "substanceUnits" attribute of this Model.
The string in C<units> is copied.
@param units the new substanceUnits for the Model
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_UNEXPECTED_ATTRIBUTE LIBSBML_UNEXPECTED_ATTRIBUTE @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
@note The "substanceUnits" attribute is available in
SBML Level 3 but is not present on Model in lower Levels of SBML.
=item Model::setTimeUnits
Sets the value of the "timeUnits" attribute of this Model.
The string in C<units> is copied.
@param units the new timeUnits for the Model
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_UNEXPECTED_ATTRIBUTE LIBSBML_UNEXPECTED_ATTRIBUTE @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
@note The "timeUnits" attribute is available in
SBML Level 3 but is not present on Model in lower Levels of SBML.
=item Model::setVolumeUnits
Sets the value of the "volumeUnits" attribute of this Model.
The string in C<units> is copied.
@param units the new volumeUnits for the Model
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_UNEXPECTED_ATTRIBUTE LIBSBML_UNEXPECTED_ATTRIBUTE @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
@note The "volumeUnits" attribute is available in
SBML Level 3 but is not present on Model in lower Levels of SBML.
=item Model::setAreaUnits
Sets the value of the "areaUnits" attribute of this Model.
The string in C<units> is copied.
@param units the new areaUnits for the Model
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_UNEXPECTED_ATTRIBUTE LIBSBML_UNEXPECTED_ATTRIBUTE @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
@note The "areaUnits" attribute is available in
SBML Level 3 but is not present on Model in lower Levels of SBML.
=item Model::setLengthUnits
Sets the value of the "lengthUnits" attribute of this Model.
The string in C<units> is copied.
@param units the new lengthUnits for the Model
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_UNEXPECTED_ATTRIBUTE LIBSBML_UNEXPECTED_ATTRIBUTE @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
@note The "lengthUnits" attribute is available in
SBML Level 3 but is not present on Model in lower Levels of SBML.
=item Model::setExtentUnits
Sets the value of the "extentUnits" attribute of this Model.
The string in C<units> is copied.
@param units the new extentUnits for the Model
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_UNEXPECTED_ATTRIBUTE LIBSBML_UNEXPECTED_ATTRIBUTE @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
@note The "extentUnits" attribute is available in
SBML Level 3 but is not present on Model in lower Levels of SBML.
=item Model::setConversionFactor
Sets the value of the "conversionFactor" attribute of this Model.
The string in C<units> is copied.
@param units the new conversionFactor for the Model
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_UNEXPECTED_ATTRIBUTE LIBSBML_UNEXPECTED_ATTRIBUTE @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
@note The "conversionFactor" attribute is available in
SBML Level 3 but is not present on Model in lower Levels of SBML.
=item Model::unsetId
Unsets the value of the "id" attribute of this Model.
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item Model::unsetName
Unsets the value of the "name" attribute of this Model.
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item Model::unsetSubstanceUnits
Unsets the value of the "substanceUnits" attribute of this Model.
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
@note The "substanceUnits" attribute is available in
SBML Level 3 but is not present on Model in lower Levels of SBML.
=item Model::unsetTimeUnits
Unsets the value of the "timeUnits" attribute of this Model.
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
@note The "timeUnits" attribute is available in
SBML Level 3 but is not present on Model in lower Levels of SBML.
=item Model::unsetVolumeUnits
Unsets the value of the "volumeUnits" attribute of this Model.
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
@note The "volumeUnits" attribute is available in
SBML Level 3 but is not present on Model in lower Levels of SBML.
=item Model::unsetAreaUnits
Unsets the value of the "areaUnits" attribute of this Model.
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_UNEXPECTED_ATTRIBUTE LIBSBML_UNEXPECTED_ATTRIBUTE @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
@note The "areaUnits" attribute is available in
SBML Level 3 but is not present on Model in lower Levels of SBML.
=item Model::unsetLengthUnits
Unsets the value of the "lengthUnits" attribute of this Model.
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_UNEXPECTED_ATTRIBUTE LIBSBML_UNEXPECTED_ATTRIBUTE @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
@note The "lengthUnits" attribute is available in
SBML Level 3 but is not present on Model in lower Levels of SBML.
=item Model::unsetExtentUnits
Unsets the value of the "extentUnits" attribute of this Model.
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_UNEXPECTED_ATTRIBUTE LIBSBML_UNEXPECTED_ATTRIBUTE @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
@note The "extentUnits" attribute is available in
SBML Level 3 but is not present on Model in lower Levels of SBML.
=item Model::unsetConversionFactor
Unsets the value of the "conversionFactor" attribute of this Model.
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_UNEXPECTED_ATTRIBUTE LIBSBML_UNEXPECTED_ATTRIBUTE @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
@note The "conversionFactor" attribute is available in
SBML Level 3 but is not present on Model in lower Levels of SBML.
=item Model::addFunctionDefinition
Adds a copy of the given FunctionDefinition object to this Model.
@param fd the FunctionDefinition to add
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_LEVEL_MISMATCH LIBSBML_LEVEL_MISMATCH @endlink
@li @link OperationReturnValues_t#LIBSBML_VERSION_MISMATCH LIBSBML_VERSION_MISMATCH @endlink
@li @link OperationReturnValues_t#LIBSBML_DUPLICATE_OBJECT_ID LIBSBML_DUPLICATE_OBJECT_ID @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
C<opydetails> doc_note_object_is_copied
@see createFunctionDefinition()
=item Model::addUnitDefinition
Adds a copy of the given UnitDefinition object to this Model.
@param ud the UnitDefinition object to add
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_LEVEL_MISMATCH LIBSBML_LEVEL_MISMATCH @endlink
@li @link OperationReturnValues_t#LIBSBML_VERSION_MISMATCH LIBSBML_VERSION_MISMATCH @endlink
@li @link OperationReturnValues_t#LIBSBML_DUPLICATE_OBJECT_ID LIBSBML_DUPLICATE_OBJECT_ID @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
C<opydetails> doc_note_object_is_copied
@see createUnitDefinition()
=item Model::addCompartmentType
Adds a copy of the given CompartmentType object to this Model.
@param ct the CompartmentType object to add
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_LEVEL_MISMATCH LIBSBML_LEVEL_MISMATCH @endlink
@li @link OperationReturnValues_t#LIBSBML_VERSION_MISMATCH LIBSBML_VERSION_MISMATCH @endlink
@li @link OperationReturnValues_t#LIBSBML_DUPLICATE_OBJECT_ID LIBSBML_DUPLICATE_OBJECT_ID @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
C<opydetails> doc_note_object_is_copied
@note The CompartmentType object class is only available in SBML
Level 2 Versions 2–4. It is not available in
Level 1 nor Level 3.
@see createCompartmentType()
=item Model::addSpeciesType
Adds a copy of the given SpeciesType object to this Model.
@param st the SpeciesType object to add
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_LEVEL_MISMATCH LIBSBML_LEVEL_MISMATCH @endlink
@li @link OperationReturnValues_t#LIBSBML_VERSION_MISMATCH LIBSBML_VERSION_MISMATCH @endlink
@li @link OperationReturnValues_t#LIBSBML_DUPLICATE_OBJECT_ID LIBSBML_DUPLICATE_OBJECT_ID @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
C<opydetails> doc_note_object_is_copied
@note The SpeciesType object class is only available in SBML
Level 2 Versions 2–4. It is not available in
Level 1 nor Level 3.
@see createSpeciesType()
=item Model::addCompartment
Adds a copy of the given Compartment object to this Model.
@param c the Compartment object to add
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_LEVEL_MISMATCH LIBSBML_LEVEL_MISMATCH @endlink
@li @link OperationReturnValues_t#LIBSBML_VERSION_MISMATCH LIBSBML_VERSION_MISMATCH @endlink
@li @link OperationReturnValues_t#LIBSBML_DUPLICATE_OBJECT_ID LIBSBML_DUPLICATE_OBJECT_ID @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
C<opydetails> doc_note_object_is_copied
@see createCompartment()
=item Model::addSpecies
Adds a copy of the given Species object to this Model.
@param s the Species object to add
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_LEVEL_MISMATCH LIBSBML_LEVEL_MISMATCH @endlink
@li @link OperationReturnValues_t#LIBSBML_VERSION_MISMATCH LIBSBML_VERSION_MISMATCH @endlink
@li @link OperationReturnValues_t#LIBSBML_DUPLICATE_OBJECT_ID LIBSBML_DUPLICATE_OBJECT_ID @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
C<opydetails> doc_note_object_is_copied
@see createSpecies()
=item Model::addParameter
Adds a copy of the given Parameter object to this Model.
@param p the Parameter object to add
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_LEVEL_MISMATCH LIBSBML_LEVEL_MISMATCH @endlink
@li @link OperationReturnValues_t#LIBSBML_VERSION_MISMATCH LIBSBML_VERSION_MISMATCH @endlink
@li @link OperationReturnValues_t#LIBSBML_DUPLICATE_OBJECT_ID LIBSBML_DUPLICATE_OBJECT_ID @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
C<opydetails> doc_note_object_is_copied
@see createParameter()
=item Model::addInitialAssignment
Adds a copy of the given InitialAssignment object to this Model.
@param ia the InitialAssignment object to add
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_LEVEL_MISMATCH LIBSBML_LEVEL_MISMATCH @endlink
@li @link OperationReturnValues_t#LIBSBML_VERSION_MISMATCH LIBSBML_VERSION_MISMATCH @endlink
@li @link OperationReturnValues_t#LIBSBML_DUPLICATE_OBJECT_ID LIBSBML_DUPLICATE_OBJECT_ID @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
C<opydetails> doc_note_object_is_copied
@see createInitialAssignment()
=item Model::addRule
Adds a copy of the given Rule object to this Model.
@param r the Rule object to add
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_LEVEL_MISMATCH LIBSBML_LEVEL_MISMATCH @endlink
@li @link OperationReturnValues_t#LIBSBML_VERSION_MISMATCH LIBSBML_VERSION_MISMATCH @endlink
@li @link OperationReturnValues_t#LIBSBML_DUPLICATE_OBJECT_ID LIBSBML_DUPLICATE_OBJECT_ID @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
C<opydetails> doc_note_object_is_copied
@see createAlgebraicRule()
@see createAssignmentRule()
@see createRateRule()
=item Model::addConstraint
Adds a copy of the given Constraint object to this Model.
@param c the Constraint object to add
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_LEVEL_MISMATCH LIBSBML_LEVEL_MISMATCH @endlink
@li @link OperationReturnValues_t#LIBSBML_VERSION_MISMATCH LIBSBML_VERSION_MISMATCH @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
C<opydetails> doc_note_object_is_copied
@see createConstraint()
=item Model::addReaction
Adds a copy of the given Reaction object to this Model.
@param r the Reaction object to add
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_LEVEL_MISMATCH LIBSBML_LEVEL_MISMATCH @endlink
@li @link OperationReturnValues_t#LIBSBML_VERSION_MISMATCH LIBSBML_VERSION_MISMATCH @endlink
@li @link OperationReturnValues_t#LIBSBML_DUPLICATE_OBJECT_ID LIBSBML_DUPLICATE_OBJECT_ID @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
C<opydetails> doc_note_object_is_copied
@see createReaction()
=item Model::addEvent
Adds a copy of the given Event object to this Model.
@param e the Event object to add
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_LEVEL_MISMATCH LIBSBML_LEVEL_MISMATCH @endlink
@li @link OperationReturnValues_t#LIBSBML_VERSION_MISMATCH LIBSBML_VERSION_MISMATCH @endlink
@li @link OperationReturnValues_t#LIBSBML_DUPLICATE_OBJECT_ID LIBSBML_DUPLICATE_OBJECT_ID @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
C<opydetails> doc_note_object_is_copied
@see createEvent()
=item Model::createFunctionDefinition
Creates a new FunctionDefinition inside this Model and returns it.
The SBML Level and Version of the enclosing Model object, as well as
any SBML package namespaces, are used to initialize this
object's corresponding attributes.
@return the FunctionDefinition object created
@see addFunctionDefinition(const FunctionDefinition fd)
=item Model::createUnitDefinition
Creates a new UnitDefinition inside this Model and returns it.
The SBML Level and Version of the enclosing Model object, as well as
any SBML package namespaces, are used to initialize this
object's corresponding attributes.
@return the UnitDefinition object created
@see addUnitDefinition(const UnitDefinition ud)
=item Model::createUnit
Creates a new Unit object within the last UnitDefinition object
created in this model and returns a pointer to it.
The SBML Level and Version of the enclosing Model object, as well as
any SBML package namespaces, are used to initialize this
object's corresponding attributes.
The mechanism by which the UnitDefinition was created is not
significant. If a UnitDefinition object does not exist in this model,
a new Unit is I<not> created and C<NULL> is returned instead.
@return the Unit object created
@see addUnitDefinition(const UnitDefinition ud)
=item Model::createCompartmentType
Creates a new CompartmentType inside this Model and returns it.
The SBML Level and Version of the enclosing Model object, as well as
any SBML package namespaces, are used to initialize this
object's corresponding attributes.
@return the CompartmentType object created
@note The CompartmentType object class is only available in SBML
Level 2 Versions 2–4. It is not available in
Level 1 nor Level 3.
@see addCompartmentType(const CompartmentType ct)
=item Model::createSpeciesType
Creates a new SpeciesType inside this Model and returns it.
The SBML Level and Version of the enclosing Model object, as well as
any SBML package namespaces, are used to initialize this
object's corresponding attributes.
@return the SpeciesType object created
@note The SpeciesType object class is only available in SBML
Level 2 Versions 2–4. It is not available in
Level 1 nor Level 3.
@see addSpeciesType(const SpeciesType st)
=item Model::createCompartment
Creates a new Compartment inside this Model and returns it.
The SBML Level and Version of the enclosing Model object, as well as
any SBML package namespaces, are used to initialize this
object's corresponding attributes.
@return the Compartment object created
@see addCompartment(const Compartment c)
=item Model::createSpecies
Creates a new Species inside this Model and returns it.
The SBML Level and Version of the enclosing Model object, as well as
any SBML package namespaces, are used to initialize this
object's corresponding attributes.
@return the Species object created
@see addSpecies(const Species s)
=item Model::createParameter
Creates a new Parameter inside this Model and returns it.
The SBML Level and Version of the enclosing Model object, as well as
any SBML package namespaces, are used to initialize this
object's corresponding attributes.
@return the Parameter object created
@see addParameter(const Parameter p)
=item Model::createInitialAssignment
Creates a new InitialAssignment inside this Model and returns it.
The SBML Level and Version of the enclosing Model object, as well as
any SBML package namespaces, are used to initialize this
object's corresponding attributes.
@return the InitialAssignment object created
@see addInitialAssignment(const InitialAssignment ia)
=item Model::createAlgebraicRule
Creates a new AlgebraicRule inside this Model and returns it.
The SBML Level and Version of the enclosing Model object, as well as
any SBML package namespaces, are used to initialize this
object's corresponding attributes.
@return the AlgebraicRule object created
@see addRule(const Rule r)
=item Model::createAssignmentRule
Creates a new AssignmentRule inside this Model and returns it.
The SBML Level and Version of the enclosing Model object, as well as
any SBML package namespaces, are used to initialize this
object's corresponding attributes.
@return the AssignmentRule object created
@see addRule(const Rule r)
=item Model::createRateRule
Creates a new RateRule inside this Model and returns it.
The SBML Level and Version of the enclosing Model object, as well as
any SBML package namespaces, are used to initialize this
object's corresponding attributes.
@return the RateRule object created
@see addRule(const Rule r)
=item Model::createConstraint
Creates a new Constraint inside this Model and returns it.
The SBML Level and Version of the enclosing Model object, as well as
any SBML package namespaces, are used to initialize this
object's corresponding attributes.
@return the Constraint object created
@see addConstraint(const Constraint c)
=item Model::createReaction
Creates a new Reaction inside this Model and returns it.
The SBML Level and Version of the enclosing Model object, as well as
any SBML package namespaces, are used to initialize this
object's corresponding attributes.
@return the Reaction object created
@see addReaction(const Reaction r)
=item Model::createReactant
Creates a new SpeciesReference object for a reactant inside the last
Reaction object in this Model, and returns a pointer to it.
The SBML Level and Version of the enclosing Model object, as well as
any SBML package namespaces, are used to initialize this
object's corresponding attributes.
The mechanism by which the last Reaction object was created and added
to this Model is not significant. It could have been created in a
variety of ways, for example using createReaction(). If a Reaction
does not exist for this model, a new SpeciesReference is I<not>
created and C<NULL> is returned instead.
@return the SpeciesReference object created
=item Model::createProduct
Creates a new SpeciesReference object for a product inside the last
Reaction object in this Model, and returns a pointer to it.
The SBML Level and Version of the enclosing Model object, as well as
any SBML package namespaces, are used to initialize this
object's corresponding attributes.
The mechanism by which the last Reaction object was created and added
to this Model is not significant. It could have been created in a
variety of ways, for example using createReaction(). If a Reaction
does not exist for this model, a new SpeciesReference is I<not>
created and C<NULL> is returned instead.
@return the SpeciesReference object created
=item Model::createModifier
Creates a new ModifierSpeciesReference object for a modifier species
inside the last Reaction object in this Model, and returns a pointer
to it.
The SBML Level and Version of the enclosing Model object, as well as
any SBML package namespaces, are used to initialize this
object's corresponding attributes.
The mechanism by which the last Reaction object was created and added
to this Model is not significant. It could have been created in a
variety of ways, for example using createReaction(). If a Reaction
does not exist for this model, a new ModifierSpeciesReference is @em
not created and C<NULL> is returned instead.
@return the SpeciesReference object created
=item Model::createKineticLaw
Creates a new KineticLaw inside the last Reaction object created in
this Model, and returns a pointer to it.
The SBML Level and Version of the enclosing Model object, as well as
any SBML package namespaces, are used to initialize this
object's corresponding attributes.
The mechanism by which the last Reaction object was created and added
to this Model is not significant. It could have been created in a
variety of ways, for example using createReaction(). If a Reaction
does not exist for this model, or a Reaction exists but already has a
KineticLaw, a new KineticLaw is I<not> created and C<NULL> is returned
instead.
@return the KineticLaw object created
=item Model::createKineticLawParameter
Creates a new local Parameter inside the KineticLaw object of the last
Reaction created inside this Model, and returns a pointer to it.
The SBML Level and Version of the enclosing Model object, as well as
any SBML package namespaces, are used to initialize this
object's corresponding attributes.
The last KineticLaw object in this Model could have been created in a
variety of ways. For example, it could have been added using
createKineticLaw(), or it could be the result of using
Reaction::createKineticLaw() on the Reaction object created by a
createReaction(). If a Reaction does not exist for this model, or the
last Reaction does not contain a KineticLaw object, a new Parameter is
I<not> created and C<NULL> is returned instead.
@return the Parameter object created
=item Model::createKineticLawLocalParameter
Creates a new LocalParameter inside the KineticLaw object of the last
Reaction created inside this Model, and returns a pointer to it.
The SBML Level and Version of the enclosing Model object, as well as
any SBML package namespaces, are used to initialize this
object's corresponding attributes.
The last KineticLaw object in this Model could have been created in a
variety of ways. For example, it could have been added using
createKineticLaw(), or it could be the result of using
Reaction::createKineticLaw() on the Reaction object created by a
createReaction(). If a Reaction does not exist for this model, or the
last Reaction does not contain a KineticLaw object, a new Parameter is
I<not> created and C<NULL> is returned instead.
@return the Parameter object created
=item Model::createEvent
Creates a new Event inside this Model and returns it.
The SBML Level and Version of the enclosing Model object, as well as
any SBML package namespaces, are used to initialize this
object's corresponding attributes.
@return the Event object created
=item Model::createEventAssignment
Creates a new EventAssignment inside the last Event object created in
this Model, and returns a pointer to it.
The SBML Level and Version of the enclosing Model object, as well as
any SBML package namespaces, are used to initialize this
object's corresponding attributes.
The mechanism by which the last Event object in this model was created
is not significant. It could have been created in a variety of ways,
for example by using createEvent(). If no Event object exists in this
Model object, a new EventAssignment is I<not> created and C<NULL> is
returned instead.
@return the EventAssignment object created
=item Model::createTrigger
Creates a new Trigger inside the last Event object created in
this Model, and returns a pointer to it.
The SBML Level and Version of the enclosing Model object, as well as
any SBML package namespaces, are used to initialize this
object's corresponding attributes.
The mechanism by which the last Event object in this model was created
is not significant. It could have been created in a variety of ways,
for example by using createEvent(). If no Event object exists in this
Model object, a new Trigger is I<not> created and C<NULL> is
returned instead.
@return the Trigger object created
=item Model::createDelay
Creates a new Delay inside the last Event object created in
this Model, and returns a pointer to it.
The SBML Level and Version of the enclosing Model object, as well as
any SBML package namespaces, are used to initialize this
object's corresponding attributes.
The mechanism by which the last Event object in this model was created
is not significant. It could have been created in a variety of ways,
for example by using createEvent(). If no Event object exists in this
Model object, a new Delay is I<not> created and C<NULL> is
returned instead.
@return the Delay object created
=item Model::setAnnotation
Sets the value of the "annotation" subelement of this SBML object to a
copy of C<annotation>.
Any existing content of the "annotation" subelement is discarded.
Unless you have taken steps to first copy and reconstitute any
existing annotations into the C<annotation> that is about to be
assigned, it is likely that performing such wholesale replacement is
unfriendly towards other software applications whose annotations are
discarded. An alternative may be to use appendAnnotation().
@param annotation an XML structure that is to be used as the content
of the "annotation" subelement of this object
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@see appendAnnotation(const XMLNode annotation)
=item Model::setAnnotation
Sets the value of the "annotation" subelement of this SBML object to a
copy of C<annotation>.
Any existing content of the "annotation" subelement is discarded.
Unless you have taken steps to first copy and reconstitute any
existing annotations into the C<annotation> that is about to be
assigned, it is likely that performing such wholesale replacement is
unfriendly towards other software applications whose annotations are
discarded. An alternative may be to use appendAnnotation().
@param annotation an XML string that is to be used as the content
of the "annotation" subelement of this object
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
@see appendAnnotation(const std::string& annotation)
=item Model::appendAnnotation
Appends annotation content to any existing content in the "annotation"
subelement of this object.
The content in C<annotation> is copied. Unlike setAnnotation(), this
method allows other annotations to be preserved when an application
adds its own data.
@param annotation an XML structure that is to be copied and appended
to the content of the "annotation" subelement of this object
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
@see setAnnotation(const XMLNode annotation)
=item Model::appendAnnotation
Appends annotation content to any existing content in the "annotation"
subelement of this object.
The content in C<annotation> is copied. Unlike setAnnotation(), this
method allows other annotations to be preserved when an application
adds its own data.
@param annotation an XML string that is to be copied and appended
to the content of the "annotation" subelement of this object
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
@see setAnnotation(const std::string& annotation)
=item Model::getListOfFunctionDefinitions
Get the ListOfFunctionDefinitions object in this Model.
@return the list of FunctionDefinitions for this Model.
=item Model::getListOfFunctionDefinitions
Get the ListOfFunctionDefinitions object in this Model.
@return the list of FunctionDefinitions for this Model.
=item Model::getListOfUnitDefinitions
Get the ListOfUnitDefinitions object in this Model.
@return the list of UnitDefinitions for this Model.
=item Model::getListOfUnitDefinitions
Get the ListOfUnitDefinitions object in this Model.
@return the list of UnitDefinitions for this Model.
=item Model::getListOfCompartmentTypes
Get the ListOfCompartmentTypes object in this Model.
@return the list of CompartmentTypes for this Model.
@note The CompartmentType object class is only available in SBML
Level 2 Versions 2–4. It is not available in
Level 1 nor Level 3.
=item Model::getListOfCompartmentTypes
Get the ListOfCompartmentTypes object in this Model.
@return the list of CompartmentTypes for this Model.
@note The CompartmentType object class is only available in SBML
Level 2 Versions 2–4. It is not available in
Level 1 nor Level 3.
=item Model::getListOfSpeciesTypes
Get the ListOfSpeciesTypes object in this Model.
@return the list of SpeciesTypes for this Model.
@note The SpeciesType object class is only available in SBML
Level 2 Versions 2–4. It is not available in
Level 1 nor Level 3.
=item Model::getListOfSpeciesTypes
Get the ListOfSpeciesTypes object in this Model.
@return the list of SpeciesTypes for this Model.
@note The SpeciesType object class is only available in SBML
Level 2 Versions 2–4. It is not available in
Level 1 nor Level 3.
=item Model::getListOfCompartments
Get the ListOfCompartments object in this Model.
@return the list of Compartments for this Model.
=item Model::getListOfCompartments
Get the ListOfCompartments object in this Model.
@return the list of Compartments for this Model.
=item Model::getListOfSpecies
Get the ListOfSpecies object in this Model.
@return the list of Species for this Model.
=item Model::getListOfSpecies
Get the ListOfSpecies object in this Model.
@return the list of Species for this Model.
=item Model::getListOfParameters
Get the ListOfParameters object in this Model.
@return the list of Parameters for this Model.
=item Model::getListOfParameters
Get the ListOfParameters object in this Model.
@return the list of Parameters for this Model.
=item Model::getListOfInitialAssignments
Get the ListOfInitialAssignments object in this Model.
@return the list of InitialAssignments for this Model.
=item Model::getListOfInitialAssignments
Get the ListOfInitialAssignments object in this Model.
@return the list of InitialAssignment for this Model.
=item Model::getListOfRules
Get the ListOfRules object in this Model.
@return the list of Rules for this Model.
=item Model::getListOfRules
Get the ListOfRules object in this Model.
@return the list of Rules for this Model.
=item Model::getListOfConstraints
Get the ListOfConstraints object in this Model.
@return the list of Constraints for this Model.
=item Model::getListOfConstraints
Get the ListOfConstraints object in this Model.
@return the list of Constraints for this Model.
=item Model::getListOfReactions
Get the ListOfReactions object in this Model.
@return the list of Reactions for this Model.
=item Model::getListOfReactions
Get the ListOfReactions object in this Model.
@return the list of Reactions for this Model.
=item Model::getListOfEvents
Get the ListOfEvents object in this Model.
@return the list of Events for this Model.
=item Model::getListOfEvents
Get the ListOfEvents object in this Model.
@return the list of Events for this Model.
=item Model::getFunctionDefinition
Get the nth FunctionDefinitions object in this Model.
@return the nth FunctionDefinition of this Model.
=item Model::getFunctionDefinition
Get the nth FunctionDefinitions object in this Model.
@return the nth FunctionDefinition of this Model.
=item Model::getFunctionDefinition
Get a FunctionDefinition object based on its identifier.
@return the FunctionDefinition in this Model with the identifier
C<sid> or C<NULL> if no such FunctionDefinition exists.
=item Model::getFunctionDefinition
Get a FunctionDefinition object based on its identifier.
@return the FunctionDefinition in this Model with the identifier
C<sid> or C<NULL> if no such FunctionDefinition exists.
=item Model::getUnitDefinition
Get the nth UnitDefinition object in this Model.
@return the nth UnitDefinition of this Model.
=item Model::getUnitDefinition
Get the nth UnitDefinition object in this Model.
@return the nth UnitDefinition of this Model.
=item Model::getUnitDefinition
Get a UnitDefinition based on its identifier.
@return the UnitDefinition in this Model with the identifier C<sid> or
C<NULL> if no such UnitDefinition exists.
=item Model::getUnitDefinition
Get a UnitDefinition based on its identifier.
@return the UnitDefinition in this Model with the identifier C<sid> or
C<NULL> if no such UnitDefinition exists.
=item Model::getCompartmentType
Get the nth CompartmentType object in this Model.
@return the nth CompartmentType of this Model.
@note The CompartmentType object class is only available in SBML
Level 2 Versions 2–4. It is not available in
Level 1 nor Level 3.
=item Model::getCompartmentType
Get the nth CompartmentType object in this Model.
@return the nth CompartmentType of this Model.
@note The CompartmentType object class is only available in SBML
Level 2 Versions 2–4. It is not available in
Level 1 nor Level 3.
=item Model::getCompartmentType
Get a CompartmentType object based on its identifier.
@return the CompartmentType in this Model with the identifier C<sid>
or C<NULL> if no such CompartmentType exists.
@note The CompartmentType object class is only available in SBML
Level 2 Versions 2–4. It is not available in
Level 1 nor Level 3.
=item Model::getCompartmentType
Get a CompartmentType object based on its identifier.
@return the CompartmentType in this Model with the identifier C<sid>
or C<NULL> if no such CompartmentType exists.
@note The CompartmentType object class is only available in SBML
Level 2 Versions 2–4. It is not available in
Level 1 nor Level 3.
=item Model::getSpeciesType
Get the nth SpeciesType object in this Model.
@return the nth SpeciesType of this Model.
@note The SpeciesType object class is only available in SBML
Level 2 Versions 2–4. It is not available in
Level 1 nor Level 3.
=item Model::getSpeciesType
Get the nth SpeciesType object in this Model.
@return the nth SpeciesType of this Model.
@note The SpeciesType object class is only available in SBML
Level 2 Versions 2–4. It is not available in
Level 1 nor Level 3.
=item Model::getSpeciesType
Get a SpeciesType object based on its identifier.
@return the SpeciesType in this Model with the identifier C<sid> or
C<NULL> if no such SpeciesType exists.
@note The SpeciesType object class is only available in SBML
Level 2 Versions 2–4. It is not available in
Level 1 nor Level 3.
=item Model::getSpeciesType
Get a SpeciesType object based on its identifier.
@return the SpeciesType in this Model with the identifier C<sid> or
C<NULL> if no such SpeciesType exists.
@note The SpeciesType object class is only available in SBML
Level 2 Versions 2–4. It is not available in
Level 1 nor Level 3.
=item Model::getCompartment
Get the nth Compartment object in this Model.
@return the nth Compartment of this Model.
=item Model::getCompartment
Get the nth Compartment object in this Model.
@return the nth Compartment of this Model.
=item Model::getCompartment
Get a Compartment object based on its identifier.
@return the Compartment in this Model with the identifier C<sid> or
C<NULL> if no such Compartment exists.
=item Model::getCompartment
Get a Compartment object based on its identifier.
@return the Compartment in this Model with the identifier C<sid> or
C<NULL> if no such Compartment exists.
=item Model::getSpecies
Get the nth Species object in this Model.
@return the nth Species of this Model.
=item Model::getSpecies
Get the nth Species object in this Model.
@return the nth Species of this Model.
=item Model::getSpecies
Get a Species object based on its identifier.
@return the Species in this Model with the identifier C<sid> or C<NULL>
if no such Species exists.
=item Model::getSpecies
Get a Species object based on its identifier.
@return the Species in this Model with the identifier C<sid> or C<NULL>
if no such Species exists.
=item Model::getParameter
Get the nth Parameter object in this Model.
@return the nth Parameter of this Model.
=item Model::getParameter
Get the nth Parameter object in this Model.
@return the nth Parameter of this Model.
=item Model::getParameter
Get a Parameter object based on its identifier.
@return the Parameter in this Model with the identifier C<sid> or C<NULL>
if no such Parameter exists.
=item Model::getParameter
Get a Parameter object based on its identifier.
@return the Parameter in this Model with the identifier C<sid> or C<NULL>
if no such Parameter exists.
=item Model::getInitialAssignment
Get the nth InitialAssignment object in this Model.
@return the nth InitialAssignment of this Model.
=item Model::getInitialAssignment
Get the nth InitialAssignment object in this Model.
@return the nth InitialAssignment of this Model.
=item Model::getInitialAssignment
Get an InitialAssignment object based on the symbol to which it
assigns a value.
@return the InitialAssignment in this Model with the given "symbol"
attribute value or C<NULL> if no such InitialAssignment exists.
=item Model::getInitialAssignmentBySymbol
Get an InitialAssignment object based on the symbol to which it
assigns a value.
@return the InitialAssignment in this Model with the given "symbol"
attribute value or C<NULL> if no such InitialAssignment exists.
=item Model::getInitialAssignment
Get an InitialAssignment object based on the symbol to which it
assigns a value.
@return the InitialAssignment in this Model with the given "symbol"
attribute value or C<NULL> if no such InitialAssignment exists.
=item Model::getInitialAssignmentBySymbol
Get an InitialAssignment object based on the symbol to which it
assigns a value.
@return the InitialAssignment in this Model with the given "symbol"
attribute value or C<NULL> if no such InitialAssignment exists.
=item Model::getRule
Get the nth Rule object in this Model.
@return the nth Rule of this Model.
=item Model::getRule
Get the nth Rule object in this Model.
@return the nth Rule of this Model.
=item Model::getRule
Get a Rule object based on the variable to which it assigns a value.
@return the Rule in this Model with the given "variable" attribute
value or C<NULL> if no such Rule exists.
=item Model::getRule
Get a Rule object based on the variable to which it assigns a value.
@return the Rule in this Model with the given "variable" attribute
value or C<NULL> if no such Rule exists.
=item Model::getRuleByVariable
Get a Rule object based on the variable to which it assigns a value.
@return the Rule in this Model with the given "variable" attribute
value or C<NULL> if no such Rule exists.
=item Model::getRuleByVariable
Get a Rule object based on the variable to which it assigns a value.
@return the Rule in this Model with the given "variable" attribute
value or C<NULL> if no such Rule exists.
=item Model::getAssignmentRule
Get a Rule object based on the variable to which it assigns a value.
@return the Rule in this Model with the given "variable" attribute
value or C<NULL> if no such Rule exists.
=item Model::getAssignmentRule
Get a Rule object based on the variable to which it assigns a value.
@return the Rule in this Model with the given "variable" attribute
value or C<NULL> if no such Rule exists.
=item Model::getRateRule
Get a Rule object based on the variable to which it assigns a value.
@return the Rule in this Model with the given "variable" attribute
value or C<NULL> if no such Rule exists.
=item Model::getRateRule
Get a Rule object based on the variable to which it assigns a value.
@return the Rule in this Model with the given "variable" attribute
value or C<NULL> if no such Rule exists.
=item Model::getAssignmentRuleByVariable
Get a Rule object based on the variable to which it assigns a value.
@return the Rule in this Model with the given "variable" attribute
value or C<NULL> if no such Rule exists.
=item Model::getAssignmentRuleByVariable
Get a Rule object based on the variable to which it assigns a value.
@return the Rule in this Model with the given "variable" attribute
value or C<NULL> if no such Rule exists.
=item Model::getRateRuleByVariable
Get a Rule object based on the variable to which it assigns a value.
@return the Rule in this Model with the given "variable" attribute
value or C<NULL> if no such Rule exists.
=item Model::getRateRuleByVariable
Get a Rule object based on the variable to which it assigns a value.
@return the Rule in this Model with the given "variable" attribute
value or C<NULL> if no such Rule exists.
=item Model::getConstraint
Get the nth Constraint object in this Model.
@return the nth Constraint of this Model.
=item Model::getConstraint
Get the nth Constraint object in this Model.
@return the nth Constraint of this Model.
=item Model::getReaction
Get the nth Reaction object in this Model.
@return the nth Reaction of this Model.
=item Model::getReaction
Get the nth Reaction object in this Model.
@return the nth Reaction of this Model.
=item Model::getReaction
Get a Reaction object based on its identifier.
@return the Reaction in this Model with the identifier C<sid> or C<NULL>
if no such Reaction exists.
=item Model::getReaction
Get a Reaction object based on its identifier.
@return the Reaction in this Model with the identifier C<sid> or C<NULL>
if no such Reaction exists.
=item Model::getSpeciesReference
Get a SpeciesReference object based on its identifier.
@return the SpeciesReference in this Model with the identifier C<sid> or C<NULL>
if no such SpeciesReference exists.
=item Model::getSpeciesReference
Get a SpeciesReference object based on its identifier.
@return the SpeciesReference in this Model with the identifier C<sid> or C<NULL>
if no such SpeciesReference exists.
=item Model::getModifierSpeciesReference
Get a ModifierSpeciesReference object based on its identifier.
@return the ModifierSpeciesReference in this Model with the
identifier C<sid> or C<NULL>
if no such ModifierSpeciesReference exists.
=item Model::getModifierSpeciesReference
Get a ModifierSpeciesReference object based on its identifier.
@return the ModifierSpeciesReference in this Model with the
identifier C<sid> or C<NULL>
if no such ModifierSpeciesReference exists.
=item Model::getEvent
Get the nth Event object in this Model.
@return the nth Event of this Model.
=item Model::getEvent
Get the nth Event object in this Model.
@return the nth Event of this Model.
=item Model::getEvent
Get an Event object based on its identifier.
@return the Event in this Model with the identifier C<sid> or C<NULL> if
no such Event exists.
=item Model::getEvent
Get an Event object based on its identifier.
@return the Event in this Model with the identifier C<sid> or C<NULL> if
no such Event exists.
=item Model::getNumFunctionDefinitions
Get the number of FunctionDefinition objects in this Model.
@return the number of FunctionDefinitions in this Model.
=item Model::getNumUnitDefinitions
Get the number of UnitDefinition objects in this Model.
@return the number of UnitDefinitions in this Model.
=item Model::getNumCompartmentTypes
Get the number of CompartmentType objects in this Model.
@return the number of CompartmentTypes in this Model.
@note The CompartmentType object class is only available in SBML
Level 2 Versions 2–4. It is not available in
Level 1 nor Level 3.
=item Model::getNumSpeciesTypes
Get the number of SpeciesType objects in this Model.
@return the number of SpeciesTypes in this Model.
@note The SpeciesType object class is only available in SBML
Level 2 Versions 2–4. It is not available in
Level 1 nor Level 3.
=item Model::getNumCompartments
Get the number of Compartment objects in this Model.
@return the number of Compartments in this Model.
=item Model::getNumSpecies
Get the number of Specie objects in this Model.
@return the number of Species in this Model.
=item Model::getNumSpeciesWithBoundaryCondition
Get the number of Species in this Model having their
"boundaryCondition" attribute value set to C<true>.
@return the number of Species in this Model with boundaryCondition set
to true.
=item Model::getNumParameters
Get the number of Parameter objects in this Model.
@return the number of Parameters in this Model. Parameters defined in
KineticLaws are not included.
=item Model::getNumInitialAssignments
Get the number of InitialAssignment objects in this Model.
@return the number of InitialAssignments in this Model.
=item Model::getNumRules
Get the number of Rule objects in this Model.
@return the number of Rules in this Model.
=item Model::getNumConstraints
Get the number of Constraint objects in this Model.
@return the number of Constraints in this Model.
=item Model::getNumReactions
Get the number of Reaction objects in this Model.
@return the number of Reactions in this Model.
=item Model::getNumEvents
Get the number of Event objects in this Model.
@return the number of Events in this Model.
=item Model::removeFromParentAndDelete
Finds this Model's parent SBMLDocument and calls setModel(NULL) on it,
indirectly deleting itself. Overridden from the SBase function since
the parent is not a ListOf.
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif@~ The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item Model::renameAllIds
@internal
=item Model::renameIDs
@internal
=item Model::renameSIdRefs
Renames all the C<SIdRef> attributes on this element, including any
found in MathML.
C<opydetails> doc_what_is_sidref
This method works by looking at all attributes and (if appropriate)
mathematical formulas, comparing the identifiers to the value of @p
oldid. If any matches are found, the matching identifiers are replaced
with C<newid>. The method does I<not> descend into child elements.
@param oldid the old identifier
@param newid the new identifier
=item Model::renameUnitSIdRefs
Renames all the C<UnitSIdRef> attributes on this element.
C<opydetails> doc_what_is_unitsidref
This method works by looking at all unit identifier attribute values
(including, if appropriate, inside mathematical formulas), comparing the
unit identifiers to the value of C<oldid>. If any matches are found,
the matching identifiers are replaced with C<newid>. The method does
I<not> descend into child elements.
@param oldid the old identifier
@param newid the new identifier
=item Model::isBoolean
@internal
Predicate returning C<true> if the
given ASTNode is a boolean.
Often times, this question can be answered with the ASTNode's own
isBoolean() method, but if the AST is an expression that calls a
function defined in the Model's ListOfFunctionDefinitions, the model
is needed for lookup context.
@return true if the given ASTNode is a boolean.
=item Model::convertL1ToL2
@internal
=item Model::convertL1ToL3
@internal
=item Model::convertL2ToL3
@internal
=item Model::convertL2ToL1
@internal
=item Model::convertL3ToL1
@internal
=item Model::convertL3ToL2
@internal
=item Model::addModifiers
@internal
=item Model::addConstantAttribute
@internal
=item Model::setSpatialDimensions
@internal
=item Model::addDefinitionsForDefaultUnits
@internal
=item Model::convertParametersToLocals
@internal
=item Model::setSpeciesReferenceConstantValueAndStoichiometry
@internal
=item Model::removeMetaId
@internal
=item Model::removeSBOTerms
@internal
=item Model::removeHasOnlySubstanceUnits
@internal
=item Model::removeSBOTermsNotInL2V2
@internal
=item Model::removeDuplicateTopLevelAnnotations
@internal
=item Model::removeParameterRuleUnits
@internal
=item Model::convertStoichiometryMath
@internal
=item Model::assignRequiredValues
@internal
=item Model::dealWithModelUnits
@internal
=item Model::dealWithStoichiometry
@internal
=item Model::dealWithEvents
@internal
=item Model::convertToL2Strict
@internal
=item Model::setSBMLDocument
@internal
=item Model::connectToChild
@internal
Sets this SBML object to child SBML objects (if any).
(Creates a child-parent relationship by the parent)
Subclasses must override this function if they define
one ore more child elements.
Basically, this function needs to be called in
constructor, copy constructor and assignment operator.
@see setSBMLDocument
@see enablePackageInternal
=item Model::getTypeCode
Returns the libSBML type code for this SBML object.
C<opydetails> doc_what_are_typecodes
@return the SBML type code for this object:
@link SBMLTypeCode_t#SBML_MODEL SBML_MODEL@endlink (default).
C<opydetails> doc_warning_typecodes_not_unique
@see getElementName()
@see getPackageName()
=item Model::getElementName
Returns the XML element name of this object, which for Model, is
always C<"model">.
@return the name of this element, i.e., C<"model">.
=item Model::getElementPosition
@internal
Return the position of this element.
@return the ordinal position of the element with respect to its
siblings or -1 (default) to indicate the position is not significant.
=item Model::writeElements
@internal
Subclasses should override this method to write out their contained
SBML objects as XML elements. Be sure to call your parents
implementation of this method as well.
=item Model::populateListFormulaUnitsData
Populates the list of FormulaDataUnits with the units derived
for the model. The list contains elements of class
FormulaUnitsData.
The first element of the list refers to the default units
of 'substance per time' derived from the model and has the
unitReferenceId 'subs_per_time'. This facilitates the comparison of units
derived from mathematical formula with the expected units.
The next elements of the list record the units of the
compartments and species established from either explicitly
declared or default units.
The next elements record the units of any parameters.
Subsequent elements of the list record the units derived for
each mathematical expression encountered within the model.
@note This function is utilised by the Unit Consistency Validator.
The list is populated prior to running the validation and thus
the consistency of units can be checked by accessing the members
of the list and comparing the appropriate data.
=item Model::isPopulatedListFormulaUnitsData
Predicate returning C<true> if
the list of FormulaUnitsData is populated.
@return C<true> if the list of FormulaUnitsData is populated,
C<false> otherwise.
=item Model::addFormulaUnitsData
@internal
Adds a copy of the given FormulaUnitsData object to this Model.
@param fud the FormulaUnitsData to add
=item Model::createFormulaUnitsData
@internal
Creates a new FormulaUnitsData inside this Model and returns it.
@return the FormulaUnitsData object created
=item Model::getFormulaUnitsData
@internal
Get the nth FormulaUnitsData object in this Model.
@return the nth FormulaUnitsData of this Model.
=item Model::getFormulaUnitsData
@internal
Get the nth FormulaUnitsData object in this Model.
@return the nth FormulaUnitsData of this Model.
=item Model::getFormulaUnitsData
@internal
Get a FormulaUnitsData object based on its unitReferenceId and typecode.
@return the FormulaUnitsData in this Model with the unitReferenceId C<sid>
and the typecode (int) C<typecode> or C<NULL>
if no such FormulaUnitsData exists.
@note The typecode (int) parameter is necessary as the unitReferenceId
of the FormulaUnitsData need not be unique. For example if a Species
with id 's' is assigned by an AssignmentRule there will be two
elements of the FormulaUnitsData list with the unitReferenceId 's';
one with
typecode 'SBML_SPECIES' referring to the units related to the species,
the other with typecode 'SBML_ASSIGNMENT_RULE' referring to the units
derived from the math element of the AssignmentRule.
=item Model::getFormulaUnitsData
@internal
Get a FormulaUnitsData object based on its unitReferenceId and typecode.
@return the FormulaUnitsData in this Model with the unitReferenceId C<sid>
and the typecode (int) C<typecode> or C<NULL>
if no such FormulaUnitsData exists.
@note The typecode (int) parameter is necessary as the unitReferenceId
of the FormulaUnitsData need not be unique. For example if a Species
with id 's' is assigned by an AssignmentRule there will be two
elements of the FormulaUnitsData list with the unitReferenceId 's';
one with
typecode 'SBML_SPECIES' referring to the units related to the species,
the other with typecode 'SBML_ASSIGNMENT_RULE' referring to the units
derived from the math element of the AssignmentRule.
=item Model::getFormulaUnitsDataForVariable
@internal
=item Model::getFormulaUnitsDataForAssignment
@internal
=item Model::getNumFormulaUnitsData
@internal
Get the number of FormulaUnitsData objects in this Model.
@return the number of FormulaUnitsData in this Model.
=item Model::getListFormulaUnitsData
@internal
Get the list of FormulaUnitsData object in this Model.
@return the list of FormulaUnitsData for this Model.
=item Model::getListFormulaUnitsData
@internal
Get the list of FormulaUnitsData object in this Model.
@return the list of FormulaUnitsData for this Model.
=item Model::hasRequiredElements
Predicate returning C<true> if
all the required elements for this Model object
have been set.
@note The required elements for a Model object are:
listOfCompartments (L1 only); listOfSpecies (L1V1 only);
listOfReactions(L1V1 only)
@return a boolean value indicating whether all the required
elements for this object have been defined.
=item Model::removeFunctionDefinition
Removes the nth FunctionDefinition object from this Model object and
returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
@param n the index of the FunctionDefinition object to remove
@return the FunctionDefinition object removed. As mentioned above,
the caller owns the returned item. C<NULL> is returned if the given index
is out of range.
=item Model::removeFunctionDefinition
Removes the FunctionDefinition object with the given identifier from this Model
object and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
If none of the FunctionDefinition objects in this Model object have the identifier
C<sid>, then C<NULL> is returned.
@param sid the identifier of the FunctionDefinition object to remove
@return the FunctionDefinition object removed. As mentioned above, the
caller owns the returned object. C<NULL> is returned if no FunctionDefinition
object with the identifier exists in this Model object.
=item Model::removeUnitDefinition
Removes the nth UnitDefinition object from this Model object and
returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
@param n the index of the UnitDefinition object to remove
@return the UnitDefinition object removed. As mentioned above,
the caller owns the returned item. C<NULL> is returned if the given index
is out of range.
=item Model::removeUnitDefinition
Removes the UnitDefinition object with the given identifier from this Model
object and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
If none of the UnitDefinition objects in this Model object have the identifier
C<sid>, then C<NULL> is returned.
@param sid the identifier of the UnitDefinition object to remove
@return the UnitDefinition object removed. As mentioned above, the
caller owns the returned object. C<NULL> is returned if no UnitDefinition
object with the identifier exists in this Model object.
=item Model::removeCompartmentType
Removes the nth CompartmentType object from this Model object and
returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
@param n the index of the CompartmentType object to remove
@return the ComapartmentType object removed. As mentioned above,
the caller owns the returned item. C<NULL> is returned if the given index
is out of range.
=item Model::removeCompartmentType
Removes the CompartmentType object with the given identifier from this Model
object and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
If none of the CompartmentType objects in this Model object have the identifier
C<sid>, then C<NULL> is returned.
@param sid the identifier of the object to remove
@return the CompartmentType object removed. As mentioned above, the
caller owns the returned object. C<NULL> is returned if no CompartmentType
object with the identifier exists in this Model object.
=item Model::removeSpeciesType
Removes the nth SpeciesType object from this Model object and
returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
@param n the index of the SpeciesType object to remove
@return the SpeciesType object removed. As mentioned above,
the caller owns the returned item. C<NULL> is returned if the given index
is out of range.
=item Model::removeSpeciesType
Removes the SpeciesType object with the given identifier from this Model
object and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
If none of the SpeciesType objects in this Model object have the identifier
C<sid>, then C<NULL> is returned.
@param sid the identifier of the SpeciesType object to remove
@return the SpeciesType object removed. As mentioned above, the
caller owns the returned object. C<NULL> is returned if no SpeciesType
object with the identifier exists in this Model object.
=item Model::removeCompartment
Removes the nth Compartment object from this Model object and
returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
@param n the index of the Compartment object to remove
@return the Compartment object removed. As mentioned above,
the caller owns the returned item. C<NULL> is returned if the given index
is out of range.
=item Model::removeCompartment
Removes the Compartment object with the given identifier from this Model
object and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
If none of the Compartment objects in this Model object have the identifier
C<sid>, then C<NULL> is returned.
@param sid the identifier of the Compartment object to remove
@return the Compartment object removed. As mentioned above, the
caller owns the returned object. C<NULL> is returned if no Compartment
object with the identifier exists in this Model object.
=item Model::removeSpecies
Removes the nth Species object from this Model object and
returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
@param n the index of the Species object to remove
@return the Species object removed. As mentioned above,
the caller owns the returned item. C<NULL> is returned if the given index
is out of range.
=item Model::removeSpecies
Removes the Species object with the given identifier from this Model
object and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
If none of the Species objects in this Model object have the identifier
C<sid>, then C<NULL> is returned.
@param sid the identifier of the Species object to remove
@return the Species object removed. As mentioned above, the
caller owns the returned object. C<NULL> is returned if no Species
object with the identifier exists in this Model object.
=item Model::removeParameter
Removes the nth Parameter object from this Model object and
returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
@param n the index of the Parameter object to remove
@return the Parameter object removed. As mentioned above,
the caller owns the returned item. C<NULL> is returned if the given index
is out of range.
=item Model::removeParameter
Removes the Parameter object with the given identifier from this Model
object and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
If none of the Parameter objects in this Model object have the identifier
C<sid>, then C<NULL> is returned.
@param sid the identifier of the Parameter object to remove
@return the Parameter object removed. As mentioned above, the
caller owns the returned object. C<NULL> is returned if no Parameter
object with the identifier exists in this Model object.
=item Model::removeInitialAssignment
Removes the nth InitialAssignment object from this Model object and
returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
@param n the index of the InitialAssignment object to remove
@return the InitialAssignment object removed. As mentioned above,
the caller owns the returned item. C<NULL> is returned if the given index
is out of range.
=item Model::removeInitialAssignment
Removes the InitialAssignment object with the given "symbol" attribute
from this Model object and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
If none of the InitialAssignment objects in this Model object have the
"symbol" attribute C<symbol>, then C<NULL> is returned.
@param symbol the "symbol" attribute of the InitialAssignment object to remove
@return the InitialAssignment object removed. As mentioned above, the
caller owns the returned object. C<NULL> is returned if no InitialAssignment
object with the "symbol" attribute exists in this Model object.
=item Model::removeRule
Removes the nth Rule object from this Model object and
returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
@param n the index of the Rule object to remove
@return the Rule object removed. As mentioned above,
the caller owns the returned item. C<NULL> is returned if the given index
is out of range.
=item Model::removeRule
Removes the Rule object with the given "variable" attribute from this Model
object and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
If none of the Rule objects in this Model object have the "variable" attribute
C<variable>, then C<NULL> is returned.
@param variable the "variable" attribute of the Rule object to remove
@return the Rule object removed. As mentioned above, the
caller owns the returned object. C<NULL> is returned if no Rule
object with the "variable" attribute exists in this Model object.
=item Model::removeConstraint
Removes the nth Constraint object from this Model object and
returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
@param n the index of the Constraint object to remove
@return the Constraint object removed. As mentioned above,
the caller owns the returned item. C<NULL> is returned if the given index
is out of range.
=item Model::removeReaction
Removes the nth Reaction object from this Model object and
returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
@param n the index of the Reaction object to remove
@return the Reaction object removed. As mentioned above,
the caller owns the returned item. C<NULL> is returned if the given index
is out of range.
=item Model::removeReaction
Removes the Reaction object with the given identifier from this Model
object and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
If none of the Reaction objects in this Model object have the identifier
C<sid>, then C<NULL> is returned.
@param sid the identifier of the Reaction object to remove
@return the Reaction object removed. As mentioned above, the
caller owns the returned object. C<NULL> is returned if no Reaction
object with the identifier exists in this Model object.
=item Model::removeEvent
Removes the nth Event object from this Model object and
returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
@param n the index of the Event object to remove
@return the Event object removed. As mentioned above,
the caller owns the returned item. C<NULL> is returned if the given index
is out of range.
=item Model::removeEvent
Removes the Event object with the given identifier from this Model
object and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
If none of the Event objects in this Model object have the identifier
C<sid>, then C<NULL> is returned.
@param sid the identifier of the Event object to remove
@return the Event object removed. As mentioned above, the
caller owns the returned object. C<NULL> is returned if no Event
object with the identifier exists in this Model object.
=item Model::appendFrom
Takes the contents of the passed-in Model, makes copies of everything,
and appends those copies to the appropriate places in this Model.
This method also calls the C<appendFrom> method on all libSBML
plug-in objects. C<opydetails> doc_what_are_plugins
@param model the Model to merge with this one.
=item Model::enablePackageInternal
@internal
Enables/Disables the given package with this element and child elements
(if any). (This is an internal implementation for enablePackage
function)
@note Subclasses of the SBML Core package in which one or more child
elements are defined must override this function.
=item Model::readOtherXML
@internal
Subclasses should override this method to read (and store) XHTML,
MathML, etc. directly from the XMLInputStream.
@return true if the subclass read from the stream, false otherwise.
=item Model::createObject
@internal
Create and return an SBML object of this class, if present.
@return the SBML object corresponding to next XMLToken in the
XMLInputStream or C<NULL> if the token was not recognized.
=item Model::addExpectedAttributes
@internal
Subclasses should override this method to get the list of
expected attributes.
This function is invoked from corresponding readAttributes()
function.
=item Model::readAttributes
@internal
Subclasses should override this method to read values from the given
XMLAttributes set into their specific fields. Be sure to call your
parents implementation of this method as well.
=item Model::readL1Attributes
@internal
=item Model::readL2Attributes
@internal
=item Model::readL3Attributes
@internal
=item Model::writeAttributes
@internal
Subclasses should override this method to write their XML attributes
to the XMLOutputStream. Be sure to call your parents implementation
of this method as well.
=item Model::syncAnnotation
@internal
Synchronizes the annotation of this SBML object.
Annotation element (XMLNode mAnnotation) is synchronized with the
current CVTerm objects (List mCVTerm), ModelHistory object
(ModelHistory mHistory) and ListOfLayouts object (ListOfLayouts mLayouts).
Currently, this method is called in getAnnotation, isSetAnnotation,
and writeElements methods.
=item Model::checkUnitDefinition
@internal
Internal function used in populateListFormulaUnitsData
=item Model::checkSpeciesReference
@internal
Internal function used in populateListFormulaUnitsData
=back
=head2 SBMLDocument
@sbmlpackage{core}
@htmlinclude pkg-marker-core.html Container for an SBML document and interface for global
operations on SBML documents.
@if clike LibSBML uses the class SBMLDocument as a
top-level container for storing SBML content and data associated with it
(such as warnings and error messages). The two primary means of reading
an SBML model, SBMLReader::readSBML() and
SBMLReader::readSBMLFromString(), both return a pointer to an
SBMLDocument object. From there, callers can inquire about any errors
encountered (e.g., using SBMLDocument::getNumErrors()), access the Model
object, and perform other actions such as consistency-checking and model
translation.
@endif@if python LibSBML uses the class SBMLDocument as a
top-level container for storing SBML content and data associated with it
(such as warnings and error messages). The two primary means of reading
an SBML model, SBMLReader::readSBML() and
SBMLReader::readSBMLFromString(), both return a pointer to an
SBMLDocument object. From there, callers can inquire about any errors
encountered (e.g., using SBMLDocument::getNumErrors()), access the Model
object, and perform other actions such as consistency-checking and model
translation.
@endif@if java LibSBML uses the class SBMLDocument as a top-level
container for storing SBML content and data associated with it (such as
warnings and error messages). The two primary means of reading an SBML
model, SBMLReader::readSBML(String filename) and
SBMLReader::readSBMLFromString(String xml), both return an SBMLDocument
object. From there, callers can inquire about any errors encountered
(e.g., using SBMLDocument::getNumErrors()), access the Model object, and
perform other actions such as consistency-checking and model
translation.
@endif@~
When creating fresh models programmatically, the starting point is
typically the creation of an SBMLDocument object instance. The
SBMLDocument constructor accepts arguments for the SBML Level and
Version of the model to be created. After creating the SBMLDocument
object, calling programs then typically call SBMLDocument::createModel()
almost immediately, and then proceed to call the methods on the Model
object to fill out the model's contents.
SBMLDocument corresponds roughly to the class <i>Sbml</i> defined in the
SBML Level 2 specification and <i>SBML</i> in the Level 3
specification. It does not have a direct correspondence in SBML
Level 1. (However, to make matters simpler for applications,
libSBML creates an SBMLDocument no matter whether the model is
Level 1, Level 2 or Level 3.) In its barest form, when written out in
XML format for (e.g.) SBML Level 2 Version 4, the corresponding
structure is the following:
@verbatim
<sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
...
</sbml>@endverbatim
SBMLDocument is derived from SBase, and therefore contains the usual SBase
attributes (in SBML Level 2 and Level 3) of "metaid" and "sboTerm", as
well as the subelements "notes" and "annotation". It also contains the
attributes "level" and "version" indicating the Level and Version of the
SBML data structure. These can be accessed using the methods defined by
the SBase class for that purpose.
@section checking Checking consistency and adherence to SBML specifications
One of the most important features of libSBML is its ability to perform
SBML validation to ensure that a model adheres to the SBML specification
for whatever Level+Version combination the model uses. SBMLDocument
provides the methods for running consistency-checking and validation
rules on the SBML content.
First, a brief explanation of the rationale is in order. In libSBML
versions up to and including the version 3.3.x series, the
individual methods for creating and setting attributes and other
components were quite lenient, and allowed a caller to compose SBML
entities that might not, in the end, represent valid SBML. This allowed
applications the freedom to do things such as save incomplete models
(which is useful when models are being developed over long periods of
time). In the version 4.x series, libSBML is somewhat stricter,
but still permits structures to be created independently and the results
to be combined in a separate step. In all these cases, it means that a
separate validation step is necessary when a calling program finally
wants to finish a complete SBML document.
The primary interface to this validation facility is SBMLDocument's
SBMLDocument::checkInternalConsistency() and
SBMLDocument::checkConsistency(). The former verifies the basic
internal consistency and syntax of an SBML document, and the latter
implements more elaborate validation rules (both those defined by the
SBML specifications, as well as additional rules offered by libSBML).
@if clike The checks performed by SBMLDocument::checkInternalConsistency() are
hardwired and cannot be changed by calling programs, but the validation
performed by SBMLDocument::checkConsistency() is under program control
using the method SBMLDocument::setConsistencyChecks(). Applications can
selectively disable specific kinds of checks that they may not be
interested in, by calling SBMLDocument::setConsistencyChecks() with
appropriate parameters.
@endif@if python The checks performed by SBMLDocument::checkInternalConsistency() are
hardwired and cannot be changed by calling programs, but the validation
performed by SBMLDocument::checkConsistency() is under program control
using the method SBMLDocument::setConsistencyChecks(). Applications can
selectively disable specific kinds of checks that they may not be
interested in, by calling SBMLDocument::setConsistencyChecks() with
appropriate parameters.
@endif@if java The checks performed by SBMLDocument::checkInternalConsistency() are
hardwired and cannot be changed by calling programs, but the validation
performed by SBMLDocument::checkConsistency() is under program control
using the method SBMLDocument::setConsistencyChecks(int categ, boolean
onoff). Applications can selectively disable specific kinds of checks
that they may not be interested by calling
SBMLDocument::setConsistencyChecks(int categ, boolean onoff) with
appropriate parameters.
@endif@~
These methods have slightly different relevance depending on whether a
model is created programmaticaly from scratch, or whether it is read in
from a file or data stream. The following list summarizes the possible
scenarios.
<em>Scenario 1: Creating a model from scratch</em>. Before writing out
the model,
@li Call SBMLDocument::checkInternalConsistency(), then inquire about
the results by calling SBMLDocument::getNumErrors()
@li Call @if java SBMLDocument::setConsistencyChecks(int categ, boolean
onoff) @else SBMLDocument::setConsistencyChecks() @endif@~ to configure
which checks will be performed by SBMLDocument::checkConsistency()
@li Call SBMLDocument::checkConsistency(), then inquire about the results by
calling SBMLDocument::getNumErrors()
<em>Scenario 2: Reading a model from a file or data stream.</em> After
reading the model,
@li Basic consistency checks will have been performed automatically by
libSBML upon reading the content, so you only need to inquire about the
results by using SBMLDocument::getNumErrors()
@li Call @if java SBMLDocument::setConsistencyChecks(int categ, boolean
onoff) @else SBMLDocument::setConsistencyChecks() @endif@~ to configure
which checks are performed by SBMLDocument::checkConsistency()
@li Call SBMLDocument::checkConsistency(), then inquire about the results
by calling SBMLDocument::getNumErrors()
@if clike An example of using the consistency-checking
and validation facilities is provided in this manual in the
section @ref libsbml-example. @endif@~
@section converting Converting documents between Levels and Versions of SBML
LibSBML provides facilities for limited translation of SBML between
Levels and Versions of the SBML specifications. The method for doing is
is @if java SBMLDocument::setLevelAndVersion(long lev, long ver, boolean strict) @else setLevelAndVersion() @endif. In
general, models can be converted upward without difficulty (e.g., from
SBML Level 1 to Level 2, or from an earlier Version of
Level 2 to the latest Version of Level 2). Sometimes models
can be translated downward as well, if they do not use constructs
specific to more advanced Levels of SBML.
Calling @if java SBMLDocument::setLevelAndVersion(long lev, long ver, boolean strict) @else SBMLDocument::setLevelAndVersion() @endif@~ will not I<necessarily> lead
to a successful conversion. The method will return a boolean value
to indicate success or failure. Callers must check the error log (see
next section) attached to the SBMLDocument object after calling
@if java SBMLDocument::setLevelAndVersion(long lev, long ver) @else SBMLDocument::setLevelAndVersion() @endif@~ in order to assess whether any
problems arose.
If an application is interested in translating to a lower Level and/or
Version of SBML within a Level, the following methods allow for prior
assessment of whether there is sufficient compatibility to make a
translation possible:
@li SBMLDocument::checkL1Compatibility(),
@li SBMLDocument::checkL2v1Compatibility(),
@li SBMLDocument::checkL2v2Compatibility(),
@li SBMLDocument::checkL2v3Compatibility(),
@li SBMLDocument::checkL2v4Compatibility(), and
@li SBMLDocument::checkL3v1Compatibility().
Some changes between Versions of SBML Level 2 may lead to
unexpected behaviors when attempting conversions in either direction.
For example, SBML Level 2 Version 4 relaxed the requirement
for consistency in units of measurement between expressions annd
quantities in a model. As a result, a model written in Version 4,
if converted to Version 3 with no other changes, may fail
validation as a Version 3 model because Version 3 imposed
stricter requirements on unit consistency.
Other changes between SBML Level 2 and Level 3 make downward conversions
challenging. In some cases, it means that a model converted to
Level 2 from Level 3 will contain attributes that were not
explicitly given in the Level 3 model, because in Level 2
these attributes may have been optional or have default values.
@section errors Error handling
Upon reading a model, SBMLDocument logs any problems encountered while
reading the model from the file or data stream. The log contains
objects that record diagnostic information about any notable issues that
arose. Whether the problems are warnings or errors, they are both
reported through a single common interface involving the object class
SBMLError.
The methods SBMLDocument::getNumErrors(), @if java SBMLDocument::getError(long n) @else SBMLDocument::getError() @endif@~ and
SBMLDocument::printErrors() allow callers to interact with the warnings
or errors logged. Alternatively, callers may retrieve the entire log as
an SBMLErrorLog object using the method SBMLDocument::getErrorLog().
The SBMLErrorLog object provides some alternative methods for
interacting with the set of errors and warnings. In either case,
applications typically should first call SBMLDocument::getNumErrors() to
find out if any issues have been logged after specific libSBML
operations such as the ones discussed in the sections above. If they
have, then an application will should proceed to inspect the individual
reports using either the direct interfaces on SBMLDocument or using the
methods on the SBMLErrorLog object.
@if clike An example of using the error facility is
provided in this manual in the
section @ref libsbml-example. @endif@~
=over
=item SBMLDocument::getDefaultLevel
The default SBML Level of new SBMLDocument objects.
C<opydetails> doc_sbmldocument_default_level
@return an integer indicating the most recent SBML specification Level
C<opydetails> doc_note_static_methods
@see @if clike getDefaultVersion() @else SBMLDocument::getDefaultVersion() @endif@~
=item SBMLDocument::getDefaultVersion
The default Version of new SBMLDocument objects.
C<opydetails> doc_sbmldocument_default_version
@return an integer indicating the most recent SBML specification
Version
C<opydetails> doc_note_static_methods
@see @if clike getDefaultLevel() @else SBMLDocument::getDefaultLevel() @endif@~
=item SBMLDocument::SBMLDocument
Creates a new SBMLDocument, optionally with given values for the SBML
Level and Version.
If <em>both</em> the SBML Level and Version attributes are not
specified, the SBML document is treated as having the latest Level and
Version of SBML as determined by SBMLDocument::getDefaultLevel() and
SBMLDocument::getDefaultVersion(); <em>however</em>, the SBMLDocument
object is otherwise left blank. In particular, the blank SBMLDocument
object has no associated XML attributes, including (but not limited
to) an XML namespace declaration. The XML namespace declaration is
not added until the model is written out, <em>or</em> the method
SBMLDocument::setLevelAndVersion(@if java long lev, long ver, boolean strict@endif)
is called. This may be important to keep in mind
if an application needs to add additional XML namespace declarations
on the C<<sbml>> element. Application writers should
either provide values for C<level> and C<version> on the call to this
constructor, or else call
SBMLDocument::setLevelAndVersion(@if java long lev, long ver, boolean strict@endif)
shortly after creating the SBMLDocument object.
@param level an integer for the SBML Level
@param version an integer for the Version within the SBML Level
@throws @if python ValueError @else SBMLConstructorException @endif@~
Thrown if the given C<level> and C<version> combination, or this kind
of SBML object, are either invalid or mismatched with respect to the
parent SBMLDocument object.
@if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
@see SBMLDocument::setLevelAndVersion(@if java long lev, long ver, boolean strict@endif)
@see getDefaultLevel()
@see getDefaultVersion()
=item SBMLDocument::SBMLDocument
Creates a new SBMLDocument using the given SBMLNamespaces object
C<sbmlns>.
C<opydetails> doc_what_are_sbmlnamespaces
@param sbmlns an SBMLNamespaces object.
@throws @if python ValueError @else SBMLConstructorException @endif@~
Thrown if the given C<level> and C<version> combination, or this kind
of SBML object, are either invalid or mismatched with respect to the
parent SBMLDocument object.
=item SBMLDocument::SBMLDocument
Copy constructor; creates a copy of this SBMLDocument.
@param orig the object to copy.
@throws @if python ValueError @else SBMLConstructorException @endif@~
Thrown if the argument C<orig> is C<NULL>.
=item SBMLDocument::accept
Accepts the given SBMLVisitor for this instance of SBMLDocument.
@param v the SBMLVisitor instance to be used.
@return the result of calling C<v.visit()>.
=item SBMLDocument::clone
Creates and returns a deep copy of this SBMLDocument.
@return a (deep) copy of this SBMLDocument.
=item SBMLDocument::getModel
Returns the Model object stored in this SBMLDocument.
It is important to note that this method <em>does not create</em> a
Model instance. The model in the SBMLDocument must have been created
at some prior time, for example using SBMLDocument::createModel()
or SBMLDocument::setModel(@if java Model m@endif).
This method returns C<NULL> if a model does not yet exist.
@return the Model contained in this SBMLDocument.
@see createModel()
=item SBMLDocument::getModel
Returns the Model object stored in this SBMLDocument.
It is important to note that this method <em>does not create</em> a
Model instance. The model in the SBMLDocument must have been created
at some prior time, for example using SBMLDocument::createModel()
or SBMLDocument::setModel(@if java Model m@endif).
This method returns C<NULL> if a model does not yet exist.
@return the Model contained in this SBMLDocument.
@see createModel()
=item SBMLDocument::getElementBySId
Returns the first child element found that has the given C<id> in the
model-wide SId namespace, or C<NULL> if no such object is found.
@param id string representing the id of objects to find
@return pointer to the first element found with the given C<id>.
=item SBMLDocument::getElementByMetaId
Returns the first child element it can find with the given C<metaid>, or
itself if it has the given C<metaid>, or C<NULL> if no such object is
found.
@param metaid string representing the metaid of objects to find
@return pointer to the first element found with the given C<metaid>.
=item SBMLDocument::getAllElements
Returns a List of all child SBase objects, including those nested to an
arbitrary depth
@return a List of pointers to all children objects.
=item SBMLDocument::expandFunctionDefinitions
Removes FunctionDefinition constructs from the document and expands
any instances of their use within C<<math>> elements.
For example, suppose a Model contains a FunctionDefinition with
identifier C<"f"> representing the math expression: <em>f(x, y) = x
y</em>. Suppose further that there is a reaction in which the
C<<math>> element of the KineticLaw object contains
C<f(s, p)>, where C<s> and C<p> are other identifiers
defined in the model. The outcome of invoking this method is that the
C<<math>> of the KineticLaw now represents the
expression <em>s p</em> and the model no longer contains any
FunctionDefinition objects.
@return bool C<true> if the transformation was successful,
C<false>, otherwise.
@note This function will check the consistency of a model before
attemptimg the transformation. If the model is not valid SBML, the
transformation will not be performed and the function will return @c
false.
=item SBMLDocument::expandInitialAssignments
Removes InitialAssignment constructs from the document and
replaces them with appropriate values.
For example, suppose a Model contains a InitialAssignment to a symbol
C<"k"> where C<"k"> is the identifier of a Parameter. The outcome of
invoking this method is that the "value" attribute of the Parameter
definition is set to the result calculated using the InitialAssignment
object's C<<math>> formula, and the corresponding
InitialAssignment is then removed from the Model.
@return bool C<true> if the transformation was successful,
C<false>, otherwise.
@note This function will check the consistency of a model before
attemptimg the transformation. If the model is not valid SBML, the
transformation will not be performed and the function will return @c
false. As part of that process, this method will check that it has
values for any components referred to by the C<<math>>
elements of InitialAssignment objects. In cases where not all of the
values have been declared (e.g., if the mathematical expression refers
to model entities that have no declared values), the InitialAssignment
in question will I<not> be removed and this method will return @c
false.
=item SBMLDocument::setLevelAndVersion
Sets the SBML Level and Version of this SBMLDocument instance,
attempting to convert the model as needed.
This method is the principal way in libSBML to convert models between
Levels and Versions of SBML. Generally, models can be converted
upward without difficulty (e.g., from SBML Level 1 to
Level 2, or from an earlier Version of Level 2 to the latest
Version of Level 2). Sometimes models can be translated downward
as well, if they do not use constructs specific to more advanced
Levels of SBML.
Before calling this method, callers may check compatibility directly
using the methods SBMLDocument::checkL1Compatibility(),
SBMLDocument::checkL2v1Compatibility(),
SBMLDocument::checkL2v2Compatibility(),
SBMLDocument::checkL2v3Compatibility(),
SBMLDocument::checkL2v4Compatibility(), and
SBMLDocument::checkL3v1Compatibility().
The valid combinations of SBML Level and Version as of this release
of libSBML are the following:
\n=over\n
\n=item\n\nLevel 1 Version 2
\n=item\n\nLevel 2 Version 1
\n=item\n\nLevel 2 Version 2
\n=item\n\nLevel 2 Version 3
\n=item\n\nLevel 2 Version 4
\n=item\n\nLevel 3 Version 1
\n=back\n
Strict conversion applies the additional criteria that both the
source and the target model must be consistent SBML. Users can
control the consistency checks that are applied using the
SBMLDocument::setConsistencyChecksForConversion(@if java int categ, boolean onoff@endif) method. If either
the source or the potential target model have validation errors, the
conversion is not performed. When a strict conversion is successful,
the underlying SBML object model is altered to reflect the new level
and version. Thus, information that cannot be converted
(e.g. sboTerms) will be lost.
@param level the desired SBML Level
@param version the desired Version within the SBML Level
@param strict boolean indicating whether to check consistency
of both the source and target model when performing
conversion (defaults to C< true >)
@param ignorePackages boolean indicating whether the presence of
packages should be ignored by the conversion routine
(defaults to C< false >)
@return C<true> if the level and version of the document were
successfully set to the requested values (which may have required
conversion of the model), C<false> otherwise.
@note Calling this method will not I<necessarily> lead to a successful
conversion. If the conversion fails, it will be logged in the error
list associated with this SBMLDocument. Callers should consult
getNumErrors() to find out if the conversion succeeded without
problems. For conversions from Level 2 to Level 1, callers
can also check the Level of the model after calling this method to
find out whether it is Level 1. (If the conversion to
Level 1 failed, the Level of this model will be left unchanged.)
@if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
@see checkL1Compatibility()
@see checkL2v1Compatibility()
@see checkL2v2Compatibility()
@see checkL2v3Compatibility()
@see checkL2v4Compatibility()
@see checkL3v1Compatibility()
@see checkL3v1Compatibility()
=item SBMLDocument::updateSBMLNamespace
@internal
@param package
@param level
@param version
=item SBMLDocument::setModel
Sets the Model for this SBMLDocument to a copy of the given Model.
@param m the new Model to use.
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif@~ The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_LEVEL_MISMATCH LIBSBML_LEVEL_MISMATCH @endlink
@li @link OperationReturnValues_t#LIBSBML_VERSION_MISMATCH LIBSBML_VERSION_MISMATCH @endlink
@see createModel()
@see getModel()
=item SBMLDocument::createModel
Creates a new Model inside this SBMLDocument, and returns a pointer to
it.
In SBML Level 2, the use of an identifier on a Model object is
optional. This method takes an optional argument, C<sid>, for setting
the identifier. If not supplied, the identifier attribute on the
Model instance is not set.
@param sid the identifier of the new Model to create.
@if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
@see getModel()
@see SBMLDocument::setModel(@if java Model m@endif)
=item SBMLDocument::setLocationURI
Sets the location of this SBMLDocument.
Called automatically when readSBMLFromFile is used, but may be set
manually as well.
=item SBMLDocument::getLocationURI
Get the location of this SBMLDocument.
If this document was read from a file or had its location set manually,
that filename or set location will be returned, otherwise, an empty
string is returned.
=item SBMLDocument::getLocationURI
Get the location of this SBMLDocument.
If this document was read from a file or had its location set manually,
that filename or set location will be returned, otherwise, an empty
string is returned.
=item SBMLDocument::setConsistencyChecks
Controls the consistency checks that are performed when
SBMLDocument::checkConsistency() is called.
This method works by adding or subtracting consistency checks from the
set of all possible checks that SBMLDocument::checkConsistency() knows
how to perform. This method may need to be called multiple times in
order to achieve the desired combination of checks. The first
argument (C<category>) in a call to this method indicates the category
of consistency/error checks that are to be turned on or off, and the
second argument (C<apply>, a boolean) indicates whether to turn it on
(value of C<true>) or off (value of C<false>).
@if clike
The possible categories (values to the argument C<category>) are the
set of values from the enumeration #SBMLErrorCategory_t.
The following are the possible choices:
@endif@if java
The possible categories (values to the argument C<category>) are the
set of constants whose names begin with the characters C<LIBSBML_CAT_>
in the interface class {@link libsbmlConstants}.
The following are the possible choices:
@endif@if python
The possible categories (values to the argument C<category>) are the
set of constants whose names begin with the characters C<LIBSBML_CAT_>
in the interface class @link libsbml libsbml@endlink.
The following are the possible choices:
@endif@~
\n=over\n
\n=item\n\n@link SBMLErrorCategory_t#LIBSBML_CAT_GENERAL_CONSISTENCY
LIBSBML_CAT_GENERAL_CONSISTENCY@endlink: Correctness and consistency
of specific SBML language constructs. Performing this set of checks
is highly recommended. With respect to the SBML specification, these
concern failures in applying the validation rules numbered 2xxxx in
the Level 2 Versions 2–4 and Level 3 Version 1
specifications.
\n=item\n\n@link SBMLErrorCategory_t#LIBSBML_CAT_IDENTIFIER_CONSISTENCY
LIBSBML_CAT_IDENTIFIER_CONSISTENCY@endlink: Correctness and
consistency of identifiers used for model entities. An example of
inconsistency would be using a species identifier in a reaction rate
formula without first having declared the species. With respect to
the SBML specification, these concern failures in applying the
validation rules numbered 103xx in the Level 2 Versions 2–4
and Level 3 Version 1 specifications.
\n=item\n\n@link SBMLErrorCategory_t#LIBSBML_CAT_UNITS_CONSISTENCY
LIBSBML_CAT_UNITS_CONSISTENCY@endlink: Consistency of measurement
units associated with quantities in a model. With respect to the SBML
specification, these concern failures in applying the validation rules
numbered 105xx in the Level 2 Versions 2–4 and Level 3
Version 1 specifications.
\n=item\n\n@link SBMLErrorCategory_t#LIBSBML_CAT_MATHML_CONSISTENCY
LIBSBML_CAT_MATHML_CONSISTENCY@endlink: Syntax of MathML constructs.
With respect to the SBML specification, these concern failures in
applying the validation rules numbered 102xx in the Level 2
Versions 2–4 and Level 3 Version 1 specifications.
\n=item\n\n@link SBMLErrorCategory_t#LIBSBML_CAT_SBO_CONSISTENCY
LIBSBML_CAT_SBO_CONSISTENCY@endlink: Consistency and validity of SBO
identifiers (if any) used in the model. With respect to the SBML
specification, these concern failures in applying the validation rules
numbered 107xx in the Level 2 Versions 2–4 and Level 3
Version 1 specifications.
\n=item\n\n@link SBMLErrorCategory_t#LIBSBML_CAT_OVERDETERMINED_MODEL
LIBSBML_CAT_OVERDETERMINED_MODEL@endlink: Static analysis of whether
the system of equations implied by a model is mathematically
overdetermined. With respect to the SBML specification, this is
validation rule #10601 in the Level 2 Versions 2–4 and
Level 3 Version 1 specifications.
\n=item\n\n@link SBMLErrorCategory_t#LIBSBML_CAT_MODELING_PRACTICE
LIBSBML_CAT_MODELING_PRACTICE@endlink: Additional checks for
recommended good modeling practice. (These are tests performed by
libSBML and do not have equivalent SBML validation rules.)
\n=back\n
<em>By default, all validation checks are applied</em> to the model in
an SBMLDocument object I<unless>
SBMLDocument::setConsistencyChecks(@if java int categ, boolean onoff@endif)
is called to indicate that only a subset should be applied. Further,
this default (i.e., performing all checks) applies separately to
<em>each new SBMLDocument object</em> created. In other words, each
time a model is read using SBMLReader::readSBML(@if java String filename@endif),
SBMLReader::readSBMLFromString(@if java String xml@endif),
or the global functions readSBML() and readSBMLFromString(), a new
SBMLDocument is created and for that document, a call to
SBMLDocument::checkConsistency() will default to applying all possible checks.
Calling programs must invoke
SBMLDocument::setConsistencyChecks(@if java int categ, boolean onoff@endif)
for each such new model if they wish to change the consistency checks
applied.
@param category a value drawn from @if clike #SBMLErrorCategory_t@else
the set of SBML error categories@endif@~ indicating the
consistency checking/validation to be turned on or off.
@param apply a boolean indicating whether the checks indicated by
C<category> should be applied or not.
@see SBMLDocument::checkConsistency()
=item SBMLDocument::setConsistencyChecksForConversion
Controls the consistency checks that are performed when
SBMLDocument::setLevelAndVersion(@if java long lev, long ver, boolean strict@endif) is called.
This method works by adding or subtracting consistency checks from the
set of all possible checks that may be performed to avoid conversion
to or from an invalid document. This method may need to be called
multiple times in
order to achieve the desired combination of checks. The first
argument (C<category>) in a call to this method indicates the category
of consistency/error checks that are to be turned on or off, and the
second argument (C<apply>, a boolean) indicates whether to turn it on
(value of C<true>) or off (value of C<false>).
@if clike
The possible categories (values to the argument C<category>) are the
set of values from the enumeration #SBMLErrorCategory_t.
The following are the possible choices:
@endif@if java
The possible categories (values to the argument C<category>) are the
set of constants whose names begin with the characters C<LIBSBML_CAT_>
in the interface class {@link libsbmlConstants}.
The following are the possible choices:
@endif@if python
The possible categories (values to the argument C<category>) are the
set of constants whose names begin with the characters C<LIBSBML_CAT_>
in the interface class @link libsbml libsbml@endlink.
The following are the possible choices:
@endif@~
\n=over\n
\n=item\n\n@link SBMLErrorCategory_t#LIBSBML_CAT_GENERAL_CONSISTENCY
LIBSBML_CAT_GENERAL_CONSISTENCY@endlink: Correctness and consistency
of specific SBML language constructs. Performing this set of checks
is highly recommended. With respect to the SBML specification, these
concern failures in applying the validation rules numbered 2xxxx in
the Level 2 Versions 2–4 and Level 3 Version 1
specifications.
\n=item\n\n@link SBMLErrorCategory_t#LIBSBML_CAT_IDENTIFIER_CONSISTENCY
LIBSBML_CAT_IDENTIFIER_CONSISTENCY@endlink: Correctness and
consistency of identifiers used for model entities. An example of
inconsistency would be using a species identifier in a reaction rate
formula without first having declared the species. With respect to
the SBML specification, these concern failures in applying the
validation rules numbered 103xx in the Level 2 Versions 2–4
and Level 3 Version 1 specifications.
\n=item\n\n@link SBMLErrorCategory_t#LIBSBML_CAT_UNITS_CONSISTENCY
LIBSBML_CAT_UNITS_CONSISTENCY@endlink: Consistency of measurement
units associated with quantities in a model. With respect to the SBML
specification, these concern failures in applying the validation rules
numbered 105xx in the Level 2 Versions 2–4 and Level 3
Version 1 specifications.
\n=item\n\n@link SBMLErrorCategory_t#LIBSBML_CAT_MATHML_CONSISTENCY
LIBSBML_CAT_MATHML_CONSISTENCY@endlink: Syntax of MathML constructs.
With respect to the SBML specification, these concern failures in
applying the validation rules numbered 102xx in the Level 2
Versions 2–4 and Level 3 Version 1 specifications.
\n=item\n\n@link SBMLErrorCategory_t#LIBSBML_CAT_SBO_CONSISTENCY
LIBSBML_CAT_SBO_CONSISTENCY@endlink: Consistency and validity of SBO
identifiers (if any) used in the model. With respect to the SBML
specification, these concern failures in applying the validation rules
numbered 107xx in the Level 2 Versions 2–4 and Level 3
Version 1 specifications.
\n=item\n\n@link SBMLErrorCategory_t#LIBSBML_CAT_OVERDETERMINED_MODEL
LIBSBML_CAT_OVERDETERMINED_MODEL@endlink: Static analysis of whether
the system of equations implied by a model is mathematically
overdetermined. With respect to the SBML specification, this is
validation rule #10601 in the Level 2 Versions 2–4 and
Level 3 Version 1 specifications.
\n=item\n\n@link SBMLErrorCategory_t#LIBSBML_CAT_MODELING_PRACTICE
LIBSBML_CAT_MODELING_PRACTICE@endlink: Additional checks for
recommended good modeling practice. (These are tests performed by
libSBML and do not have equivalent SBML validation rules.)
\n=back\n
<em>By default, all validation checks are applied</em> to the model in
an SBMLDocument object I<unless>
SBMLDocument::setConsistencyChecks(@if java int categ, boolean onoff@endif)
is called to indicate that only a subset should be applied. Further,
this default (i.e., performing all checks) applies separately to
<em>each new SBMLDocument object</em> created. In other words, each
time a model is read using SBMLReader::readSBML(@if java String filename@endif),
SBMLReader::readSBMLFromString(@if java String xml@endif),
or the global functions readSBML() and readSBMLFromString(), a new
SBMLDocument is created and for that document, a call to
SBMLDocument::checkConsistency() will default to applying all possible checks.
Calling programs must invoke
SBMLDocument::setConsistencyChecks(@if java int categ, boolean onoff@endif)
for each such new model if they wish to change the consistency checks
applied.
@param category a value drawn from @if clike #SBMLErrorCategory_t@else
the set of SBML error categories@endif@~ indicating the consistency
checking/validation to be turned on or off.
@param apply a boolean indicating whether the checks indicated by
C<category> should be applied or not.
@see SBMLDocument::setLevelAndVersion(@if java long lev, long ver, boolean strict@endif)
=item SBMLDocument::checkConsistency
Performs consistency checking and validation on this SBML document.
If this method returns a nonzero value (meaning, one or more
consistency checks have failed for SBML document), the failures may be
due to warnings I<or> errors. Callers should inspect the severity
flag in the individual SBMLError objects returned by
SBMLDocument::getError(@if java long n@endif) to determine the nature of the failures.
@return the number of failed checks (errors) encountered.
@see SBMLDocument::checkInternalConsistency()
=item SBMLDocument::validateSBML
Performs consistency checking and validation on this SBML document.
If this method returns a nonzero value (meaning, one or more
consistency checks have failed for SBML document), the failures may be
due to warnings I<or> errors. Callers should inspect the severity
flag in the individual SBMLError objects returned by
SBMLDocument::getError(@if java long n@endif) to determine the nature of the failures.
@note unlike checkConsistency this method will write the document
in order to determine all errors for the document. This will
also clear the error log.
@return the number of failed checks (errors) encountered.
@see SBMLDocument::checkConsistency()
=item SBMLDocument::checkInternalConsistency
Performs consistency checking on libSBML's internal representation of
an SBML Model.
Callers should query the results of the consistency check by calling
SBMLDocument::getError(@if java long n@endif).
@return the number of failed checks (errors) encountered.
The distinction between this method and
SBMLDocument::checkConsistency() is that this method reports on
fundamental syntactic and structural errors that violate the XML
Schema for SBML; by contrast, SBMLDocument::checkConsistency()
performs more elaborate model verifications and also validation
according to the validation rules written in the appendices of the
SBML Level 2 Versions 2–4 specification documents.
@see SBMLDocument::checkConsistency()
=item SBMLDocument::checkL1Compatibility
Performs a set of consistency checks on the document to establish
whether it is compatible with SBML Level 1 and can be converted
to Level 1.
Callers should query the results of the consistency check by calling
SBMLDocument::getError(@if java long n@endif).
@return the number of failed checks (errors) encountered.
=item SBMLDocument::checkL2v1Compatibility
Performs a set of consistency checks on the document to establish
whether it is compatible with SBML Level 2 Version 1 and can
be converted to Level 2 Version 1.
Callers should query the results of the consistency check by calling
SBMLDocument::getError(@if java long n@endif).
@return the number of failed checks (errors) encountered.
=item SBMLDocument::checkL2v2Compatibility
Performs a set of consistency checks on the document to establish
whether it is compatible with SBML Level 2 Version 2 and can
be converted to Level 2 Version 2.
Callers should query the results of the consistency check by calling
SBMLDocument::getError(@if java long n@endif).
@return the number of failed checks (errors) encountered.
=item SBMLDocument::checkL2v3Compatibility
Performs a set of consistency checks on the document to establish
whether it is compatible with SBML Level 2 Version 3 and can
be converted to Level 2 Version 3.
Callers should query the results of the consistency check by calling
SBMLDocument::getError(@if java long n@endif).
@return the number of failed checks (errors) encountered.
=item SBMLDocument::checkL2v4Compatibility
Performs a set of consistency checks on the document to establish
whether it is compatible with SBML Level 2 Version 4 and can
be converted to Level 2 Version 4.
Callers should query the results of the consistency check by calling
SBMLDocument::getError(@if java long n@endif).
@return the number of failed checks (errors) encountered.
=item SBMLDocument::checkL3v1Compatibility
Performs a set of consistency checks on the document to establish
whether it is compatible with SBML Level 3 Version 1 and can
be converted to Level 3 Version 1.
Callers should query the results of the consistency check by calling
SBMLDocument::getError(@if java long n@endif).
@return the number of failed checks (errors) encountered.
=item SBMLDocument::getError
Returns the nth error or warning encountered during parsing,
consistency checking, or attempted translation of this model.
Callers can use method XMLError::getSeverity() on the result to assess
the severity of the problem. The possible severity levels range from
informational messages to fatal errors.
@return the error or warning indexed by integer C<n>, or return @c
NULL if C<n > (getNumErrors() - 1)>.
@param n the integer index of the error sought.
@see SBMLDocument::getNumErrors()
=item SBMLDocument::getNumErrors
Returns the number of errors or warnings encountered during parsing,
consistency checking, or attempted translation of this model.
@return the number of errors or warnings encountered
@see SBMLDocument::getError(unsigned int n)
=item SBMLDocument::getNumErrors
Returns the number of errors or warnings encountered with the given
severity during parsing,
consistency checking, or attempted translation of this model.
@param severity the severity of the error sought.
@return the number of errors or warnings encountered
@see SBMLDocument::getError(unsigned int n)
=item SBMLDocument::printErrors
Prints all the errors or warnings encountered trying to parse,
check, or translate this SBML document.
It prints the text to the stream given by the optional parameter @p
stream. If no parameter is given, it prints the output to the
standard error stream.
If no errors have occurred, i.e., C<getNumErrors() == 0>, no
output will be sent to the stream.
The format of the output is:
@verbatim
N error(s):
line NNN: (id) message
@endverbatim
@param stream the ostream or ostringstream object indicating where
the output should be printed.
@if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
@see getNumErrors()
@see getErrorLog()
@see SBMLDocument::getError(unsigned int n)
=item SBMLDocument::setSBMLDocument
@internal
No-op; it is provided for consistency with the method available on
other libSBML object classes but has no effect on SBMLDocument.
=item SBMLDocument::connectToChild
@internal
Sets this SBML object to child SBML objects (if any).
(Creates a child-parent relationship by the parent)
Subclasses must override this function if they define
one ore more child elements.
Basically, this function needs to be called in
constructor, copy constructor and assignment operator.
@see setSBMLDocument
@see enablePackageInternal
=item SBMLDocument::convert
@internal
Converts this document using the converter that best matches
the given conversion properties.
@param props the conversion properties to use
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif@~ The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
@li @link OperationReturnValues_t#LIBSBML_CONV_CONVERSION_NOT_AVAILABLE LIBSBML_CONV_CONVERSION_NOT_AVAILABLE @endlink
=item SBMLDocument::enablePackageInternal
@internal
Enables/Disables the given package with this element and child
elements (if any).
(This is an internal implementation for enablePackage function)
@note Subclasses of the SBML Core package in which one or more child
elements are defined must override this function.
=item SBMLDocument::getTypeCode
Returns the libSBML type code for this SBML object.
C<opydetails> doc_what_are_typecodes
@return the SBML type code for this object:
@link SBMLTypeCode_t#SBML_DOCUMENT SBML_DOCUMENT@endlink (default).
C<opydetails> doc_warning_typecodes_not_unique
@see SBMLDocument::getElementName()
@see getPackageName()
=item SBMLDocument::getElementName
Returns the XML element name of this object, which for SBMLDocument,
is always C<"sbml">.
@return the name of this element, i.e., C<"sbml">.
=item SBMLDocument::getErrorLog
Returns the list of errors or warnings logged during parsing,
consistency checking, or attempted translation of this model.
@return the SBMLErrorLog used for this SBMLDocument
@see SBMLDocument::getNumErrors()
=item SBMLDocument::getErrorLog
Returns a constant pointer to the list of errors or warnings
logged during parsing, consistency checking, or attempted translation
of this model.
@return the SBMLErrorLog used for this SBMLDocument
@see SBMLDocument::getNumErrors()
=item SBMLDocument::getNamespaces
Returns a list of XML Namespaces associated with the XML content
of this SBML document.
@return the XML Namespaces associated with this SBML object
=item SBMLDocument::enableDefaultNS
Set/unset default namespace to each top-level element defined in the
given package extension.
This works by adding a C<xmlns="..."> attribute. No
prefix will be written when writing elements defined in the given
package extension if C<true> is given as second argument.
@param package the name or URI of the package extension.
@param flag boolean value to indicate whether to write a namespace
prefix.
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif@~ The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_PKG_UNKNOWN_VERSION LIBSBML_PKG_UNKNOWN_VERSION @endlink
=item SBMLDocument::isEnabledDefaultNS
Returns C<true> if a default namespace is added to each top-level
element defined in the given package extension, otherwise returns
C<false>.
This basically checks if the attribute
C<xmlns="..."> is present.
@param package the name or URI of the package extension.
@return a boolean
=item SBMLDocument::setPackageRequired
Sets the C<required> attribute value of the given package
extension.
@note The name of package must not be given if the package is not
enabled.
@param package the name or URI of the package extension.
@param flag Boolean value indicating whether the package is required.
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif@~ The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_PKG_UNKNOWN_VERSION LIBSBML_PKG_UNKNOWN_VERSION @endlink
=item SBMLDocument::getPackageRequired
Returns the C<required> attribute of the given package
extension.
@note The name of package must not be given if the package is not
enabled.
@param package the name or URI of the package extension.
@return Boolean flag indicating whether the package is flagged as
being required.
=item SBMLDocument::isSetPackageRequired
Returns C<true> if the required attribute of the given package extension
is defined, otherwise returns C<false>.
@note The name of package must not be given if the package is not
enabled.
@param package the name or URI of the package extension.
@return a Boolean
=item SBMLDocument::isIgnoredPackage
Returns C<true> if the given package extension is one of an ignored
packages, otherwise returns C<false>.
An ignored package is one that is defined to be used in this SBML
document, but the package is not enabled in this copy of libSBML.
@param pkgURI the URI of the package extension.
@return a Boolean, C<true> if the package is being ignored and
C<false> otherwise.
=item SBMLDocument::isDisabledIgnoredPackage
Returns C<true> if the given package extension is one of an ignored
packages that has been disabled, otherwise returns C<false>.
An ignored package is one that is defined to be used in this SBML
document, but the package is not enabled in this copy of libSBML.
It may have been disabled to avoid reproducing the package
information when writing out the file.
@param pkgURI the URI of the package extension.
@return a Boolean, C<true> if the package is being ignored and
C<false> otherwise.
=item SBMLDocument::setPkgRequired
Sets the value of the C<required> attribute for the given
package.
@note The name of package must not be given if the package is not
enabled.
@param package the name or URI of the package extension.
@param flag a Boolean value.
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif@~ The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_PKG_UNKNOWN_VERSION LIBSBML_PKG_UNKNOWN_VERSION @endlink
@deprecated Replaced in libSBML 5.2.0 by
setPackageRequired(@if java String package, boolean flag@endif)
=item SBMLDocument::getPkgRequired
Returns the C<required> attribute of the given package
extension.
@note The name of package must not be given if the package is not
enabled.
@param package the name or URI of the package extension.
@return a Boolean value indicating whether the package is flagged as
being required in this SBML document.
@deprecated Replaced in libSBML 5.2.0 by
getPackageRequired(@if java String package flag@endif)
=item SBMLDocument::isSetPkgRequired
Returns C<true> if the required attribute of the given package extension
is defined, otherwise returns C<false>.
@note The name of package must not be given if the package is not
enabled.
@param package the name or URI of the package extension.
@return a Boolean value.
@deprecated Replaced in libSBML 5.2.0 by
isSetPackageRequired(@if java String package flag@endif)
=item SBMLDocument::isIgnoredPkg
Returns C<true> if the given package extension is one of ignored
packages, otherwise returns C<false>.
An ignored package is one that is defined to be used in this SBML
document, but the package is not enabled in this copy of libSBML.
@param pkgURI the URI of the package extension.
@return a boolean
@deprecated Replaced in libSBML 5.2.0 by
isIgnoredPackage(@if java String pkgURI flag@endif)
=item SBMLDocument::getElementPosition
@internal
Return the position of this element.
@return the ordinal position of the element with respect to its
siblings or -1 (default) to indicate the position is not significant.
=item SBMLDocument::writeElements
@internal
Subclasses should override this method to write out their contained
SBML objects as XML elements. Be sure to call your parents
implementation of this method as well.
=item SBMLDocument::getApplicableValidators
@internal
Validation system.
=item SBMLDocument::getConversionValidators
@internal
Validation system.
=item SBMLDocument::setApplicableValidators
@internal
Validation system.
=item SBMLDocument::setConversionValidators
@internal
Validation system.
=item SBMLDocument::getNumValidators
@internal
Validation system.
=item SBMLDocument::clearValidators
@internal
Validation system.
=item SBMLDocument::addValidator
@internal
Validation system.
=item SBMLDocument::getValidator
@internal
Validation system.
=item SBMLDocument::createObject
@internal
Create and return an SBML object of this class, if present.
@return the SBML object corresponding to next XMLToken in the
XMLInputStream or C<NULL> if the token was not recognized.
=item SBMLDocument::addExpectedAttributes
@internal
Subclasses should override this method to get the list of
expected attributes.
This function is invoked from corresponding readAttributes()
function.
=item SBMLDocument::readAttributes
@internal
Subclasses should override this method to read values from the given
XMLAttributes set into their specific fields. Be sure to call your
parents implementation of this method as well.
=item SBMLDocument::writeAttributes
@internal
Subclasses should override this method to write their XML attributes
to the XMLOutputStream. Be sure to call your parents implementation
of this method as well.
=item SBMLDocument::writeXMLNS
@internal
Subclasses should override this method to write their xmlns attriubutes
(if any) to the XMLOutputStream. Be sure to call your parents implementation
of this method as well.
=back
=head2 FunctionDefinition
@sbmlpackage{core}
@htmlinclude pkg-marker-core.html Implementation of SBML's FunctionDefinition construct.
The FunctionDefinition structure associates an identifier with a
function definition. This identifier can then be used as the function
called in subsequent MathML content elsewhere in an SBML model.
FunctionDefinition has one required attribute, "id", to give the
function a unique identifier by which other parts of an SBML model
definition can refer to it. A FunctionDefinition instance can also have
an optional "name" attribute of type C<string>. Identifiers and names
must be used according to the guidelines described in the SBML
specification (e.g., Section 3.3 in the Level 2 Version 4
specification).
FunctionDefinition has a required "math" subelement containing a MathML
expression defining the function body. The content of this element can
only be a MathML "lambda" element. The "lambda" element must begin with
zero or more "bvar" elements, followed by any other of the elements in
the MathML subset allowed in SBML Level 2 I<except> "lambda" (i.e., a
"lambda" element cannot contain another "lambda" element). This is the
only place in SBML where a "lambda" element can be used. The function
defined by a FunctionDefinition is only available for use in other
MathML elements that I<follow> the FunctionDefinition definition in the
model. (These restrictions prevent recursive and mutually-recursive
functions from being expressed.)
A further restriction on the content of "math" is that it cannot contain
references to variables other than the variables declared to the
"lambda" itself. That is, the contents of MathML "ci" elements inside
the body of the "lambda" can only be the variables declared by its
"bvar" elements, or the identifiers of other FunctionDefinition
instances in the model. This means must be written so that all
variables or parameters used in the MathML content are passed to them
via their function parameters. In SBML Level 2, this restriction
applies also to the MathML C<csymbol> elements for I<time> and @em
delay; in SBML Level 3, it additionally applies to the C<csymbol>
element for I<avogadro>.
@note Function definitions (also informally known as user-defined
functions) were introduced in SBML Level 2. They have purposefully
limited capabilities. A function cannot reference parameters or other
model quantities outside of itself; values must be passed as parameters
to the function. Moreover, recursive and mutually-recursive functions
are not permitted. The purpose of these limitations is to balance power
against complexity of implementation. With the restrictions as they
are, function definitions could be implemented as textual
substitutions—they are simply macros. Software implementations
therefore do not need the full function-definition machinery typically
associated with programming languages.
<br><br>
Another important point to note is FunctionDefinition does not
have a separate attribute for defining the units of the value returned
by the function. The units associated with the function's return value,
when the function is called from within MathML expressions elsewhere in
SBML, are simply the overall units of the expression in
FunctionDefinition's "math" subelement when applied to the arguments
supplied in the call to the function. Ascertaining these units requires
performing dimensional analysis on the expression. (Readers may wonder
why there is no attribute. The reason is that having a separate
attribute for declaring the units would not only be redundant, but also
lead to the potential for having conflicting information. In the case
of a conflict between the declared units and those of the value actually
returned by the function, the only logical resolution rule would be to
assume that the correct units are those of the expression anyway.)
=over
=back
=head2 ListOfFunctionDefinitions
@sbmlpackage{core}
@htmlinclude pkg-marker-core.html Implementation of SBML's ListOfFunctionDefinitions
construct.
C<opydetails> doc_what_is_listof
=over
=item FunctionDefinition::FunctionDefinition
Creates a new FunctionDefinition using the given SBML C<level> and C<version>
values.
@param level an unsigned int, the SBML Level to assign to this FunctionDefinition
@param version an unsigned int, the SBML Version to assign to this
FunctionDefinition
@throws @if python ValueError @else SBMLConstructorException @endif@~
Thrown if the given C<level> and C<version> combination, or this kind
of SBML object, are either invalid or mismatched with respect to the
parent SBMLDocument object.
C<opydetails> doc_note_functiondefinition_setting_lv
=item FunctionDefinition::FunctionDefinition
Creates a new FunctionDefinition using the given SBMLNamespaces object
C<sbmlns>.
C<opydetails> doc_what_are_sbmlnamespaces
@param sbmlns an SBMLNamespaces object.
@throws @if python ValueError @else SBMLConstructorException @endif@~
Thrown if the given C<level> and C<version> combination, or this kind
of SBML object, are either invalid or mismatched with respect to the
parent SBMLDocument object.
C<opydetails> doc_note_functiondefinition_setting_lv
=item FunctionDefinition::FunctionDefinition
Copy constructor; creates a copy of this FunctionDefinition.
@param orig the object to copy.
@throws @if python ValueError @else SBMLConstructorException @endif@~
Thrown if the argument C<orig> is C<NULL>.
=item FunctionDefinition::accept
Accepts the given SBMLVisitor for this instance of FunctionDefinition.
@param v the SBMLVisitor instance to be used.
@return the result of calling C<v.visit()>, which indicates
whether the Visitor would like to visit the next FunctionDefinition in
the list of function definitions.
=item FunctionDefinition::clone
Creates and returns a deep copy of this FunctionDefinition.
@return a (deep) copy of this FunctionDefinition.
=item FunctionDefinition::getId
Returns the value of the "id" attribute of this FunctionDefinition.
@return the id of this FunctionDefinition.
=item FunctionDefinition::getName
Returns the value of the "name" attribute of this FunctionDefinition.
@return the name of this FunctionDefinition.
=item FunctionDefinition::getMath
Get the mathematical formula of this FunctionDefinition.
@return an ASTNode, the value of the "math" subelement of this
FunctionDefinition
=item FunctionDefinition::isSetId
Predicate returning C<true> if this
FunctionDefinition's "id" attribute is set.
@return C<true> if the "id" attribute of this FunctionDefinition is
set, C<false> otherwise.
=item FunctionDefinition::isSetName
Predicate returning C<true> if this
FunctionDefinition's "name" attribute is set.
@return C<true> if the "name" attribute of this FunctionDefinition is
set, C<false> otherwise.
=item FunctionDefinition::isSetMath
Predicate returning C<true> if this
FunctionDefinition's "math" subelement contains a value.
@return C<true> if the "math" for this FunctionDefinition is set,
C<false> otherwise.
=item FunctionDefinition::setId
Sets the value of the "id" attribute of this FunctionDefinition.
The string C<sid> is copied.
C<opydetails> doc_id_syntax
@param sid the string to use as the identifier of this FunctionDefinition
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif@~ The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item FunctionDefinition::setName
Sets the value of the "name" attribute of this FunctionDefinition.
The string in C<name> is copied.
@param name the new name for the FunctionDefinition
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif@~ The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item FunctionDefinition::setMath
Sets the "math" subelement of this FunctionDefinition to the Abstract
Syntax Tree given in C<math>.
@param math an AST containing the mathematical expression to
be used as the formula for this FunctionDefinition.
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif@~ The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT @endlink
=item FunctionDefinition::unsetName
Unsets the value of the "name" attribute of this FunctionDefinition.
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif@~ The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item FunctionDefinition::getArgument
Get the C<n>th argument to this function.
Callers should first find out the number of arguments to the function
by calling getNumArguments().
@param n an integer index for the argument sought.
@return the nth argument (bound variable) passed to this
FunctionDefinition.
@see getNumArguments()
=item FunctionDefinition::getArgument
Get the argument named C<name> to this FunctionDefinition.
@param name the exact name (case-sensitive) of the sought-after
argument
@return the argument (bound variable) having the given name, or C<NULL> if
no such argument exists.
=item FunctionDefinition::getBody
Get the mathematical expression that is the body of this
FunctionDefinition object.
@return the body of this FunctionDefinition as an Abstract Syntax
Tree, or C<NULL> if no body is defined.
=item FunctionDefinition::getBody
Get the mathematical expression that is the body of this
FunctionDefinition object.
@return the body of this FunctionDefinition as an Abstract Syntax
Tree, or C<NULL> if no body is defined.
=item FunctionDefinition::isSetBody
Predicate returning C<true> if the body of this
FunctionDefinition has set.
@return C<true> if the body of this FunctionDefinition is
set, C<false> otherwise.
=item FunctionDefinition::getNumArguments
Get the number of arguments (bound variables) taken by this
FunctionDefinition.
@return the number of arguments (bound variables) that must be passed
to this FunctionDefinition.
=item FunctionDefinition::getTypeCode
Returns the libSBML type code for this SBML object.
C<opydetails> doc_what_are_typecodes
@return the SBML type code for this object:
@link SBMLTypeCode_t#SBML_FUNCTION_DEFINITION SBML_FUNCTION_DEFINITION@endlink (default).
C<opydetails> doc_warning_typecodes_not_unique
@see getElementName()
@see getPackageName()
=item FunctionDefinition::getElementName
Returns the XML element name of this object, which for
FunctionDefinition, is always C<"functionDefinition">.
@return the name of this element, i.e., C<"functionDefinition">.
=item FunctionDefinition::writeElements
@internal
Subclasses should override this method to write out their contained
SBML objects as XML elements. Be sure to call your parents
implementation of this method as well.
=item FunctionDefinition::hasRequiredAttributes
Predicate returning C<true> if
all the required attributes for this FunctionDefinition object
have been set.
@note The required attributes for a FunctionDefinition object are:
@li "id"
@return a boolean value indicating whether all the required
attributes for this object have been defined.
=item FunctionDefinition::hasRequiredElements
Predicate returning C<true> if
all the required elements for this FunctionDefinition object
have been set.
@note The required elements for a FunctionDefinition object are:
@li "math"
@return a boolean value indicating whether all the required
elements for this object have been defined.
=item FunctionDefinition::renameUnitSIdRefs
Renames all the C<UnitSIdRef> attributes on this element.
C<opydetails> doc_what_is_unitsidref
This method works by looking at all unit identifier attribute values
(including, if appropriate, inside mathematical formulas), comparing the
unit identifiers to the value of C<oldid>. If any matches are found,
the matching identifiers are replaced with C<newid>. The method does
I<not> descend into child elements.
@param oldid the old identifier
@param newid the new identifier
=item FunctionDefinition::readOtherXML
@internal
Subclasses should override this method to read (and store) XHTML,
MathML, etc. directly from the XMLInputStream.
@return true if the subclass read from the stream, false otherwise.
=item FunctionDefinition::addExpectedAttributes
@internal
Subclasses should override this method to get the list of
expected attributes.
This function is invoked from corresponding readAttributes()
function.
=item FunctionDefinition::readAttributes
@internal
Subclasses should override this method to read values from the given
XMLAttributes set into their specific fields. Be sure to call your
parents implementation of this method as well.
=item FunctionDefinition::readL2Attributes
@internal
=item FunctionDefinition::readL3Attributes
@internal
=item FunctionDefinition::writeAttributes
@internal
Subclasses should override this method to write their XML attributes
to the XMLOutputStream. Be sure to call your parents implementation
of this method as well.
=item ListOfFunctionDefinitions::ListOfFunctionDefinitions
Creates a new ListOfFunctionDefinitions object.
The object is constructed such that it is valid for the given SBML
Level and Version combination.
@param level the SBML Level
@param version the Version within the SBML Level
=item ListOfFunctionDefinitions::ListOfFunctionDefinitions
Creates a new ListOfFunctionDefinitions object.
The object is constructed such that it is valid for the SBML Level and
Version combination determined by the SBMLNamespaces object in @p
sbmlns.
@param sbmlns an SBMLNamespaces object that is used to determine the
characteristics of the ListOfFunctionDefinitions object to be created.
=item ListOfFunctionDefinitions::clone
Creates and returns a deep copy of this ListOfFunctionDefinitions instance.
@return a (deep) copy of this ListOfFunctionDefinitions.
=item ListOfFunctionDefinitions::getItemTypeCode
Returns the libSBML type code for the objects contained in this ListOf
(i.e., FunctionDefinition objects, if the list is non-empty).
C<opydetails> doc_what_are_typecodes
@return the SBML type code for the objects contained in this ListOf:
@link SBMLTypeCode_t#SBML_FUNCTION_DEFINITION SBML_FUNCTION_DEFINITION@endlink (default).
@see getElementName()
@see getPackageName()
=item ListOfFunctionDefinitions::getElementName
Returns the XML element name of this object.
For ListOfFunctionDefinitions, the XML element name is @c
"listOfFunctionDefinitions".
@return the name of this element, i.e., C<"listOfFunctionDefinitions">.
=item ListOfFunctionDefinitions::get
Get a FunctionDefinition from the ListOfFunctionDefinitions.
@param n the index number of the FunctionDefinition to get.
@return the nth FunctionDefinition in this ListOfFunctionDefinitions.
@see size()
=item ListOfFunctionDefinitions::get
Get a FunctionDefinition from the ListOfFunctionDefinitions.
@param n the index number of the FunctionDefinition to get.
@return the nth FunctionDefinition in this ListOfFunctionDefinitions.
@see size()
=item ListOfFunctionDefinitions::get
Get a FunctionDefinition from the ListOfFunctionDefinitions
based on its identifier.
@param sid a string representing the identifier
of the FunctionDefinition to get.
@return FunctionDefinition in this ListOfFunctionDefinitions
with the given C<sid> or C<NULL> if no such
FunctionDefinition exists.
@see get(unsigned int n)
@see size()
=item ListOfFunctionDefinitions::get
Get a FunctionDefinition from the ListOfFunctionDefinitions
based on its identifier.
@param sid a string representing the identifier
of the FunctionDefinition to get.
@return FunctionDefinition in this ListOfFunctionDefinitions
with the given C<sid> or C<NULL> if no such
FunctionDefinition exists.
@see get(unsigned int n)
@see size()
=item ListOfFunctionDefinitions::remove
Removes the nth item from this ListOfFunctionDefinitions items and returns a pointer to
it.
The caller owns the returned item and is responsible for deleting it.
@param n the index of the item to remove
@see size()
=item ListOfFunctionDefinitions::remove
Removes item in this ListOfFunctionDefinitions items with the given identifier.
The caller owns the returned item and is responsible for deleting it.
If none of the items in this list have the identifier C<sid>, then @c
NULL is returned.
@param sid the identifier of the item to remove
@return the item removed. As mentioned above, the caller owns the
returned item.
=item ListOfFunctionDefinitions::getElementPosition
@internal
Get the ordinal position of this element in the containing object
(which in this case is the Model object).
The ordering of elements in the XML form of SBML is generally fixed
for most components in SBML. So, for example, the
ListOfFunctionDefinitions in a model is (in SBML Level 2 Version 4)
the first ListOf___. (However, it differs for different Levels and
Versions of SBML.)
@return the ordinal position of the element with respect to its
siblings, or C<-1> (default) to indicate the position is not significant.
=item ListOfFunctionDefinitions::createObject
@internal
Create and return an SBML object of this class, if present.
@return the SBML object corresponding to next XMLToken in the
XMLInputStream or C<NULL> if the token was not recognized.
=item UnitKind_equals
Tests for logical equality between two given C<UNIT_KIND_>
code values.
This function behaves exactly like C's C<==> operator, except
for the following two cases:
\n=over\n
<li>@link UnitKind_t#UNIT_KIND_LITER UNIT_KIND_LITER@endlink C<==> @link UnitKind_t#UNIT_KIND_LITRE UNIT_KIND_LITRE@endlink
<li>@link UnitKind_t#UNIT_KIND_METER UNIT_KIND_METER@endlink C<==> @link UnitKind_t#UNIT_KIND_METRE UNIT_KIND_METRE@endlink
\n=back\n
In the two cases above, C equality comparison would yield C<false>
(because each of the above is a distinct enumeration value), but
this function returns C<true>.
@param uk1 a C<UNIT_KIND_> value
@param uk2 a second C<UNIT_KIND_> value to compare to C<uk1>
@return nonzero (for C<true>) if C<uk1> is logically equivalent to @p
uk2, zero (for C<false>) otherwise.
@note For more information about the libSBML unit codes, please refer to
the class documentation for Unit.
@if conly
@memberof Unit_t
@endif
=item UnitKind_forName
Converts a text string naming a kind of unit to its corresponding
libSBML C<UNIT_KIND_> constant/enumeration value.
@param name a string, the name of a predefined base unit in SBML
@return @if clike a value from UnitKind_t corresponding to the given
string C<name> (determined in a case-insensitive manner).
@endif@if python a value the set of C<UNIT_KIND_> codes
defined in class @link libsbml libsbml@endlink, corresponding to the
string C<name> (determined in a case-insensitive
manner).@endif@if java a value the set of C<UNIT_KIND_> codes
defined in class {@link libsbmlConstants}, corresponding to the string
C<name> (determined in a case-insensitive manner).@endif@~
@note For more information about the libSBML unit codes, please refer to
the class documentation for Unit.
@if conly
@memberof Unit_t
@endif
=item UnitKind_toString
Converts a unit code to a text string equivalent.
@param uk @if clike a value from the UnitKind_t enumeration
@endif@if python a value from the set of C<UNIT_KIND_> codes
defined in the class @link libsbml libsbml@endlink
@endif@if java a value from the set of C<UNIT_KIND_> codes
defined in the class {@link libsbmlConstants}
@endif@~
@return the name corresponding to the given unit code.
@note For more information about the libSBML unit codes, please refer to
the class documentation for Unit.
@warning The string returned is a static data value. The caller does not
own the returned string and is therefore not allowed to modify it.
@if conly
@memberof Unit_t
@endif
=item UnitKind_isValidUnitKindString
Predicate for testing whether a given string corresponds to a
predefined libSBML unit code.
@param str a text string naming a base unit defined by SBML
@param level the Level of SBML
@param version the Version within the Level of SBML
@return nonzero (for C<true>) if string is the name of a valid
C<UNIT_KIND_> value, zero (for C<false>) otherwise.
@note For more information about the libSBML unit codes, please refer to
the class documentation for Unit.
@if conly
@memberof Unit_t
@endif
=back
=head2 Unit
@sbmlpackage{core}
@htmlinclude pkg-marker-core.html Implementation of SBML's Unit construct.
The SBML unit definition facility uses two classes of objects,
UnitDefinition and Unit. The approach to defining units in SBML is
compositional; for example, <em>meter second<sup> –2</sup></em> is
constructed by combining a Unit object representing <em>meter</em> with
another Unit object representing <em>second<sup> –2</sup></em>.
The combination is wrapped inside a UnitDefinition, which provides for
assigning an identifier and optional name to the combination. The
identifier can then be referenced from elsewhere in a model. Thus, the
UnitDefinition class is the container, and Unit instances are placed
inside UnitDefinition instances.
A Unit has four attributes named "kind", "exponent", "scale"
and "multiplier". It represents a (possibly transformed) reference to a
base unit. The attribute "kind" on Unit indicates the chosen base unit.
Its value must be one of the text strings listed below; this list
corresponds to SBML Level 3 Version 1 Core:
C<opydetails> doc_base_units
A few small differences exist between the Level 3 list of base
units and the list defined in other Level/Version combinations of SBML.
Specifically, Levels of SBML before Level 3 do not define @c
avogadro; conversely, Level 2 Version 1 defines C<Celsius>,
and Level 1 defines C<celsius>, C<meter>, and C<liter>, none of
which are available in Level 3. In libSBML, each of the predefined
base unit names is represented by an enumeration value @if clike in
#UnitKind_t@else whose name begins with the characters
C<UNIT_KIND_>@endif, discussed in a separate section below.
The attribute named "exponent" on Unit represents an exponent on the
unit. In SBML Level 2, the attribute is optional and has a default
value of C<1> (one); in SBML Level 3, the attribute is mandatory
and there is no default value. A Unit also has an attribute
called "scale"; its value must be an integer exponent for a power-of-ten
multiplier used to set the scale of the unit. For example, a unit
having a "kind" value of C<gram> and a "scale" value of C<-3> signifies
10<sup> –3</sup> \f$\times\f$ gram, or milligrams. In SBML
Level 2, the attribute is optional and has a default value of C<0>
(zero), because 10<sup> 0</sup> = 1; in SBML Level 3, the attribute
is mandatory and has no default value. Lastly, the attribute named
"multiplier" can be used to multiply the unit by a real-numbered factor;
this enables the definition of units that are not power-of-ten multiples
of SI units. For instance, a multiplier of 0.3048 could be used to
define C<foot> as a measure of length in terms of a C<metre>. The
"multiplier" attribute is optional in SBML Level 2, where it has a
default value of C<1> (one); in SBML Level 3, the attribute is
mandatory and has not default value.
@if clike
<h3><a class="anchor" name="UnitKind_t">UnitKind_t</a></h3>
@else
<h3><a class="anchor" name="UnitKind_t">%Unit identification codes</a></h3>
@endif@~
As discussed above, SBML defines a set of base units which serves as the
starting point for new unit definitions. This set of base units
consists of the SI units and a small number of additional convenience
units.
@if clike Until SBML Level 2 Version 3, there
existed a data type in the SBML specifications called C<UnitKind>,
enumerating the possible SBML base units. Although SBML Level 2
Version 3 removed this type from the language specification,
libSBML maintains the corresponding enumeration type #UnitKind_t as a
convenience and as a way to provide backward compatibility to previous
SBML Level/Version specifications. (The removal in SBML Level 2
Version 3 of the enumeration C<UnitKind> was also accompanied by
the redefinition of the data type C<UnitSId> to include the previous @c
UnitKind values as reserved symbols in the C<UnitSId> space. This
change has no net effect on permissible models, their representation or
their syntax. The purpose of the change in the SBML specification was
simply to clean up an inconsistency about the contexts in which these
values were usable.)
@endif@if java In SBML Level 2 Versions before
Version 3, there existed an enumeration of units called @c
UnitKind. In Version 3, this enumeration was removed and the
identifier class C<UnitSId> redefined to include the previous @c
UnitKind values as reserved symbols. This change has no net effect on
permissible models, their representation or their syntax. The purpose
of the change in the SBML specification was simply to clean up an
inconsistency about the contexts in which these values were usable.
However, libSBML maintains UnitKind in the form of of a set of static
integer constants whose names begin with the characters
C<UNIT_KIND_>. These constants are defined in the class
<code><a href="libsbmlConstants.html">libsbmlConstants</a></code>.
@endif@if python In SBML Level 2 Versions before
Version 3, there existed an enumeration of units called @c
UnitKind. In Version 3, this enumeration was removed and the
identifier class C<UnitSId> redefined to include the previous @c
UnitKind values as reserved symbols. This change has no net effect on
permissible models, their representation or their syntax. The purpose
of the change in the SBML specification was simply to clean up an
inconsistency about the contexts in which these values were usable.
However, libSBML maintains UnitKind in the form of of a set of static
integer constants whose names begin with the characters
C<UNIT_KIND_>. These constants are defined in the class
@link libsbml libsbml@endlink.
@endif@~
As a consequence of the fact that libSBML supports models in all Levels
and Versions of SBML, libSBML's set of C<UNIT_KIND_> values is a union
of all the possible base unit names defined in the different SBML
specifications. However, not every base unit is allowed in every
Level+Version combination of SBML. Note in particular the following
exceptions:
\n=over\n
\n=item\n\nThe alternate spelling C<"meter"> is included in
addition to the official SI spelling C<"metre">. This spelling is only
permitted in SBML Level 1 models.
\n=item\n\nThe alternate spelling C<"liter"> is included in addition to the
official SI spelling C<"litre">. This spelling is only permitted in
SBML Level 1 models.
\n=item\n\nThe unit C<"Celsius"> is included because of its presence in
specifications of SBML prior to SBML Level 2 Version 3.
\n=item\n\nThe unit C<avogadro> was introduced in SBML Level 3, and
is only permitted for use in SBML Level 3 models.
\n=back\n
@if clike The table below lists the symbols defined in the
C<UnitKind_t> enumeration, and their
meanings. @else The table below lists the unit
constants defined in libSBML, and their meanings. @endif@~
@htmlinclude unitkind-table.html
=over
=back
=head2 ListOfUnits
@sbmlpackage{core}
@htmlinclude pkg-marker-core.html Implementation of SBML's ListOfUnits construct.
ListOfUnits is entirely contained within UnitDefinition.
C<opydetails> doc_what_is_listof
=over
=item Unit::Unit
Creates a new Unit using the given SBML C<level> and C<version>
values.
@param level an unsigned int, the SBML Level to assign to this Unit
@param version an unsigned int, the SBML Version to assign to this
Unit
@throws @if python ValueError @else SBMLConstructorException @endif@~
Thrown if the given C<level> and C<version> combination, or this kind
of SBML object, are either invalid or mismatched with respect to the
parent SBMLDocument object.
C<opydetails> doc_note_unit_setting_lv
=item Unit::Unit
Creates a new Unit using the given SBMLNamespaces object
C<sbmlns>.
C<opydetails> doc_what_are_sbmlnamespaces
@param sbmlns an SBMLNamespaces object.
@throws @if python ValueError @else SBMLConstructorException @endif@~
Thrown if the given C<level> and C<version> combination, or this kind
of SBML object, are either invalid or mismatched with respect to the
parent SBMLDocument object.
C<opydetails> doc_note_unit_setting_lv
=item Unit::Unit
Copy constructor; creates a copy of this Unit.
@param orig the object to copy.
@throws @if python ValueError @else SBMLConstructorException @endif@~
Thrown if the argument C<orig> is C<NULL>.
=item Unit::accept
Accepts the given SBMLVisitor for this instance of Unit.
@param v the SBMLVisitor instance to be used.
@return the result of calling C<v.visit()>, which indicates
whether the Visitor would like to visit the next Unit in the list
of units within which this Unit is embedded (i.e., in the ListOfUnits
located in the enclosing UnitDefinition instance).
=item Unit::clone
Creates and returns a deep copy of this Unit.
@return a (deep) copy of this Unit.
=item Unit::initDefaults
Initializes the fields of this Unit object to "typical" default
values.
The SBML Unit component has slightly different aspects and default
attribute values in different SBML Levels and Versions. This method
sets the values to certain common defaults, based mostly on what they
are in SBML Level 2. Specifically:
\n=over\n
\n=item\n\nSets attribute "exponent" to C<1>
\n=item\n\nSets attribute "scale" to C<0>
\n=item\n\nSets attribute "multiplier" to C<1>.0
\n=back\n
The "kind" attribute is left unchanged.
=item Unit::getKind
Returns the "kind" of Unit this is.
@if clike
@return the value of the "kind" attribute of this Unit as a
value from the <a class="el" href="#UnitKind_t">UnitKind_t</a> enumeration.
@endif@if java
@return the value of the "kind" attribute of this Unit as a
value from the set of constants whose names begin
with C<UNIT_KIND_> defined in the class
<code><a href="libsbmlConstants.html">libsbmlConstants</a></code>.
@endif@if python
@return the value of the "kind" attribute of this Unit as a
value from the set of constants whose names begin
with C<UNIT_KIND_> defined in the class
@link libsbml libsbml@endlink.
@endif@~
=item Unit::getExponent
Returns the value of the "exponent" attribute of this unit.
@return the "exponent" value of this Unit, as an integer.
=item Unit::getExponentAsDouble
Returns the value of the "exponent" attribute of this unit.
@return the "exponent" value of this Unit, as a double.
=item Unit::getScale
Returns the value of the "scale" attribute of this unit.
@return the "scale" value of this Unit, as an integer.
=item Unit::getMultiplier
Returns the value of the "multiplier" attribute of this Unit.
@return the "multiplier" value of this Unit, as a double.
=item Unit::getOffset
Returns the value of the "offset" attribute of this Unit.
@return the "offset" value of this Unit, as a double.
C<opydetails> doc_warning_unit_offset_only_l2v1
=item Unit::isAmpere
Predicate for testing whether this Unit is of the kind C<ampere>.
@return C<true> if the kind of this Unit is C<ampere>, C<false>
otherwise.
=item Unit::isAvogadro
Predicate for testing whether this Unit is of the kind C<avogadro>.
@return C<true> if the kind of this Unit is C<avogadro>, C<false>
otherwise.
@note The unit C<avogadro> was introduced in SBML Level 3, and
is only permitted for use in SBML Level 3 models.
=item Unit::isBecquerel
Predicate for testing whether this Unit is of the kind C<becquerel>
@return C<true> if the kind of this Unit is C<becquerel>, C<false>
otherwise.
=item Unit::isCandela
Predicate for testing whether this Unit is of the kind C<candela>
@return C<true> if the kind of this Unit is C<candela>, C<false>
otherwise.
=item Unit::isCelsius
Predicate for testing whether this Unit is of the kind C<Celsius>
@return C<true> if the kind of this Unit is C<Celsius>, C<false>
otherwise.
@warning <span class="warning">The predefined unit C<Celsius> was
removed from the list of predefined units in SBML Level 2
Version 2 at the same time that the "offset" attribute was removed
from Unit definitions. LibSBML methods such as this one related to @c
Celsius are retained in order to support SBML Level 2
Version 1, but their use is strongly discouraged.</span>
=item Unit::isCoulomb
Predicate for testing whether this Unit is of the kind C<coulomb>
@return C<true> if the kind of this Unit is C<coulomb>, C<false>
otherwise.
=item Unit::isDimensionless
Predicate for testing whether this Unit is of the kind @c
dimensionless.
@return C<true> if the kind of this Unit is C<dimensionless>, C<false>
otherwise.
=item Unit::isFarad
Predicate for testing whether this Unit is of the kind C<farad>
@return C<true> if the kind of this Unit is C<farad>, C<false>
otherwise.
=item Unit::isGram
Predicate for testing whether this Unit is of the kind C<gram>
@return C<true> if the kind of this Unit is C<gram>, C<false>
otherwise.
=item Unit::isGray
Predicate for testing whether this Unit is of the kind C<gray>
@return C<true> if the kind of this Unit is C<gray>, C<false>
otherwise.
=item Unit::isHenry
Predicate for testing whether this Unit is of the kind C<henry>
@return C<true> if the kind of this Unit is C<henry>, C<false>
otherwise.
=item Unit::isHertz
Predicate for testing whether this Unit is of the kind C<hertz>
@return C<true> if the kind of this Unit is C<hertz>, C<false>
otherwise.
=item Unit::isItem
Predicate for testing whether this Unit is of the kind C<item>
@return C<true> if the kind of this Unit is C<item>, C<false>
otherwise.
=item Unit::isJoule
Predicate for testing whether this Unit is of the kind C<joule>
@return C<true> if the kind of this Unit is C<joule>, C<false>
otherwise.
=item Unit::isKatal
Predicate for testing whether this Unit is of the kind C<katal>
@return C<true> if the kind of this Unit is C<katal>, C<false>
otherwise.
=item Unit::isKelvin
Predicate for testing whether this Unit is of the kind C<kelvin>
@return C<true> if the kind of this Unit is C<kelvin>, C<false>
otherwise.
=item Unit::isKilogram
Predicate for testing whether this Unit is of the kind C<kilogram>
@return C<true> if the kind of this Unit is C<kilogram>, C<false>
otherwise.
=item Unit::isLitre
Predicate for testing whether this Unit is of the kind C<litre>
@return C<true> if the kind of this Unit is C<litre> or 'liter', @c
false
otherwise.
=item Unit::isLumen
Predicate for testing whether this Unit is of the kind C<lumen>
@return C<true> if the kind of this Unit is C<lumen>, C<false>
otherwise.
=item Unit::isLux
Predicate for testing whether this Unit is of the kind C<lux>
@return C<true> if the kind of this Unit is C<lux>, C<false>
otherwise.
=item Unit::isMetre
Predicate for testing whether this Unit is of the kind C<metre>
@return C<true> if the kind of this Unit is C<metre> or 'meter', @c
false
otherwise.
=item Unit::isMole
Predicate for testing whether this Unit is of the kind C<mole>
@return C<true> if the kind of this Unit is C<mole>, C<false>
otherwise.
=item Unit::isNewton
Predicate for testing whether this Unit is of the kind C<newton>
@return C<true> if the kind of this Unit is C<newton>, C<false>
otherwise.
=item Unit::isOhm
Predicate for testing whether this Unit is of the kind C<ohm>
@return C<true> if the kind of this Unit is C<ohm>, C<false>
otherwise.
=item Unit::isPascal
Predicate for testing whether this Unit is of the kind C<pascal>
@return C<true> if the kind of this Unit is C<pascal>, C<false>
otherwise.
=item Unit::isRadian
Predicate for testing whether this Unit is of the kind C<radian>
@return C<true> if the kind of this Unit is C<radian>, C<false>
otherwise.
=item Unit::isSecond
Predicate for testing whether this Unit is of the kind C<second>
@return C<true> if the kind of this Unit is C<second>, C<false>
otherwise.
=item Unit::isSiemens
Predicate for testing whether this Unit is of the kind C<siemens>
@return C<true> if the kind of this Unit is C<siemens>, C<false>
otherwise.
=item Unit::isSievert
Predicate for testing whether this Unit is of the kind C<sievert>
@return C<true> if the kind of this Unit is C<sievert>, C<false>
otherwise.
=item Unit::isSteradian
Predicate for testing whether this Unit is of the kind C<steradian>
@return C<true> if the kind of this Unit is C<steradian>, C<false>
otherwise.
=item Unit::isTesla
Predicate for testing whether this Unit is of the kind C<tesla>
@return C<true> if the kind of this Unit is C<tesla>, C<false>
otherwise.
=item Unit::isVolt
Predicate for testing whether this Unit is of the kind C<volt>
@return C<true> if the kind of this Unit is C<volt>, C<false>
otherwise.
=item Unit::isWatt
Predicate for testing whether this Unit is of the kind C<watt>
@return C<true> if the kind of this Unit is C<watt>, C<false>
otherwise.
=item Unit::isWeber
Predicate for testing whether this Unit is of the kind C<weber>
@return C<true> if the kind of this Unit is C<weber>, C<false>
otherwise.
=item Unit::isSetKind
Predicate to test whether the "kind" attribute of this Unit is set.
@return C<true> if the "kind" attribute of this Unit is set, @c
false otherwise.
=item Unit::isSetExponent
Predicate to test whether the "exponent" attribute of this Unit
is set.
@return C<true> if the "exponent" attribute of this Unit is set,
C<false> otherwise.
=item Unit::isSetScale
Predicate to test whether the "scale" attribute of this Unit
is set.
@return C<true> if the "scale" attribute of this Unit is set,
C<false> otherwise.
=item Unit::isSetMultiplier
Predicate to test whether the "multiplier" attribute of this Unit
is set.
@return C<true> if the "multiplier" attribute of this Unit is set,
C<false> otherwise.
=item Unit::setKind
Sets the "kind" attribute value of this Unit.
@if clike
@param kind a value from the <a class="el"
href="#UnitKind_t">UnitKind_t</a> enumeration.
@endif@if java
@param kind a unit identifier chosen from the set of constants whose
names begin with C<UNIT_KIND_> in <code><a
href="libsbmlConstants.html">libsbmlConstants</a></code>.
@endif@if python
@param kind a unit identifier chosen from the set of constants whose
names begin with C<UNIT_KIND_> in @link libsbml libsbml@endlink.
@endif@~
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item Unit::setExponent
Sets the "exponent" attribute value of this Unit.
@param value the integer to which the attribute "exponent" should be set
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item Unit::setExponent
Sets the "exponent" attribute value of this Unit.
@param value the double to which the attribute "exponent" should be set
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
=item Unit::setScale
Sets the "scale" attribute value of this Unit.
@param value the integer to which the attribute "scale" should be set
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
=item Unit::setMultiplier
Sets the "multipler" attribute value of this Unit.
@param value the floating-point value to which the attribute
"multiplier" should be set
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_UNEXPECTED_ATTRIBUTE LIBSBML_UNEXPECTED_ATTRIBUTE @endlink
=item Unit::setOffset
Sets the "offset" attribute value of this Unit.
@param value the float-point value to which the attribute "offset"
should set
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_UNEXPECTED_ATTRIBUTE LIBSBML_UNEXPECTED_ATTRIBUTE @endlink
C<opydetails> doc_warning_unit_offset_only_l2v1
=item Unit::getTypeCode
Returns the libSBML type code of this object instance.
C<opydetails> doc_what_are_typecodes
@return the SBML type code for this object:
@link SBMLTypeCode_t#SBML_UNIT SBML_UNIT@endlink (default).
C<opydetails> doc_warning_typecodes_not_unique
@see getPackageName()
@see getElementName()
=item Unit::getElementName
Returns the XML element name of this object, which for Unit, is
always C<"unit">.
@return the name of this element, i.e., C<"unit">.
=item Unit::writeElements
@internal
Subclasses should override this method to write out their contained
SBML objects as XML elements. Be sure to call your parents
implementation of this method as well.
=item Unit::isBuiltIn
Predicate to test whether a given string is the name of a
predefined SBML unit.
@param name a string to be tested against the predefined unit names
@param level the Level of SBML for which the determination should be
made. This is necessary because there are a few small differences
in allowed units between SBML Level 1 and Level 2.
@return C<true> if C<name> is one of the five SBML predefined unit
identifiers (C<"substance">, C<"volume">, C<"area">, C<"length"> or @c
"time"), C<false> otherwise.
@note The predefined unit identifiers C<"length"> and C<"area"> were
added in Level 2 Version 1.
C<opydetails> doc_note_static_methods
=item Unit::isUnitKind
Predicate to test whether a given string is the name of a valid
base unit in SBML (such as C<"gram"> or C<"mole">).
This method exists because prior to SBML Level 2 Version 3,
an enumeration called C<UnitKind> was defined by SBML. This enumeration
was removed in SBML Level 2 Version 3 and its values were
folded into the space of values of a type called C<UnitSId>. This method
therefore has less significance in SBML Level 2 Version 3
and Level 2 Version 4, but remains for backward
compatibility and support for reading models in older Versions of
Level 2.
@param name a string to be tested
@param level an unsigned int representing the SBML specification
Level
@param version an unsigned int representing the SBML specification
Version
@return C<true> if name is a valid SBML UnitKind, C<false> otherwise
@note The allowed unit names differ between SBML Levels 1
and 2 and again slightly between Level 2 Versions 1
and 2.
C<opydetails> doc_note_static_methods
=item Unit::areIdentical
Predicate returning C<true> if two
Unit objects are identical.
Two Unit objects are considered to be I<identical> if they match in
all attributes. (Contrast this to the method areEquivalent(@if java
Unit u1, Unit u2@endif), which compares Unit objects only with respect
to certain attributes.)
@param unit1 the first Unit object to compare
@param unit2 the second Unit object to compare
@return C<true> if all the attributes of unit1 are identical
to the attributes of unit2, C<false> otherwise.
C<opydetails> doc_note_static_methods
@see @if clike areEquivalent() @else Unit::areEquivalent(Unit u1, Unit u2) @endif@~
=item Unit::areEquivalent
Predicate returning C<true> if
Unit objects are equivalent.
Two Unit objects are considered to be I<equivalent> either if (1) both
have a "kind" attribute value of C<dimensionless>, or (2) their "kind",
"exponent" and (for SBML Level 2 Version 1) "offset"
attribute values are equal. (Contrast this to the method
areIdentical(@if java Unit u1, Unit u2@endif), which compares Unit objects with respect to all
attributes, not just the "kind" and "exponent".)
@param unit1 the first Unit object to compare
@param unit2 the second Unit object to compare
@return C<true> if the "kind" and "exponent" attributes of unit1 are
identical to the kind and exponent attributes of unit2, C<false>
otherwise.
C<opydetails> doc_note_static_methods
@see @if clike areIdentical() @else Unit::areIdentical(Unit u1, Unit u2) @endif@~
=item Unit::removeScale
Manipulates the attributes of the Unit to express the unit with the
value of the scale attribute reduced to zero.
For example, 1 millimetre can be expressed as a Unit with kind=@c
"metre" multiplier=C<"1"> scale=C<"-3"> exponent=C<"1">. It can also be
expressed as a Unit with kind=C<"metre">
multiplier=C<"0.001"> scale=C<"0"> exponent=C<"1">.
@param unit the Unit object to manipulate.
@return integer value indicating success/failure of the function. The
possible values returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
C<opydetails> doc_note_static_methods
@see @if clike convertToSI() @else Unit::convertToSI(Unit u) @endif@~
@see @if clike merge() @else Unit::merge(Unit u1, Unit u2) @endif@~
=item Unit::merge
Merges two Unit objects with the same "kind" attribute value into a
single Unit.
For example, the following,
@verbatim
<unit kind="metre" exponent="2"/>
<unit kind="metre" exponent="1"/>
@endverbatim
would be merged to become
@verbatim
<unit kind="metre" exponent="3"/>
@endverbatim
@param unit1 the first Unit object; the result of the operation is
left as a new version of this unit, modified in-place. Not modified if
the two units have different kinds.
@param unit2 the second Unit object to merge with the first
C<opydetails> doc_note_static_methods
@see @if clike convertToSI() @else Unit::convertToSI(Unit u) @endif@~
@see @if clike removeScale() @else Unit::removeScale(Unit u) @endif@~
=item Unit::convertToSI
Returns a UnitDefinition object containing the given C<unit> converted
to the appropriate SI unit.
This method exists because some units can be expressed in terms of
others when the same physical dimension is involved. For example, one
hertz is identical to 1 sec<sup>-1</sup>, one litre is equivalent
to 1 cubic decametre, and so on.
@param unit the Unit object to convert to SI
@return a UnitDefinition object containing the SI unit.
C<opydetails> doc_note_static_methods
@see @if clike merge() @else Unit::merge(Unit u1, Unit u2) @endif@~
=item Unit::hasRequiredAttributes
Predicate returning C<true> if
all the required attributes for this Unit object
have been set.
@note The required attributes for a Unit object are:
@li "kind"
@li "exponent" (required in SBML Level 3; optional in Level 2)
@li "multiplier" (required in SBML Level 3; optional in Level 2)
@li "scale" (required in SBML Level 3; optional in Level 2)
@return a boolean value indicating whether all the required
elements for this object have been defined.
=item Unit::setExponentUnitChecking
@internal
=item Unit::getExponentUnitChecking
@internal
=item Unit::getExponentUnitChecking
@internal
=item Unit::isUnitChecking
@internal
=item Unit::isUnitChecking
@internal
=item Unit::addExpectedAttributes
@internal
Subclasses should override this method to get the list of
expected attributes.
This function is invoked from corresponding readAttributes()
function.
=item Unit::readAttributes
@internal
Subclasses should override this method to read values from the given
XMLAttributes set into their specific fields. Be sure to call your
parents implementation of this method as well.
=item Unit::readL1Attributes
@internal
=item Unit::readL2Attributes
@internal
=item Unit::readL3Attributes
@internal
=item Unit::writeAttributes
@internal
Subclasses should override this method to write their XML attributes
to the XMLOutputStream. Be sure to call your parents implementation
of this method as well.
=item Unit::isL1UnitKind
@internal
Predicate to test whether a given string is the name of a valid
base unit in SBML Level 1 (such as C<"gram"> or C<"mole">)
@param name a string to be tested
@return C<true> if name is a valid SBML UnitKind, C<false> otherwise
=item Unit::isL2V1UnitKind
@internal
Predicate to test whether a given string is the name of a valid base
unit in SBML Level 2 Version 1 (such as C<"gram"> or @c
"mole")
@param name a string to be tested
@return C<true> if name is a valid SBML UnitKind, C<false> otherwise
=item Unit::isL2UnitKind
@internal
Predicate to test whether a given string is the name of a valid base
unit in SBML Level 2 Version 2, 3 or 4 (such as C<"gram"> or @c
"mole")
@param name a string to be tested
@return C<true> if name is a valid SBML UnitKind, C<false> otherwise
=item Unit::isL3UnitKind
@internal
Predicate to test whether a given string is the name of a valid base
unit in SBML Level 3 Version 1 (such as C<"gram"> or @c
"mole")
@param name a string to be tested
@return C<true> if name is a valid SBML UnitKind, C<false> otherwise
=item Unit::isExplicitlySetExponent
@internal
=item Unit::isExplicitlySetMultiplier
@internal
=item Unit::isExplicitlySetScale
@internal
=item Unit::isExplicitlySetOffset
@internal
=item ListOfUnits::ListOfUnits
Creates a new ListOfUnits object.
The object is constructed such that it is valid for the given SBML
Level and Version combination.
@param level the SBML Level
@param version the Version within the SBML Level
=item ListOfUnits::ListOfUnits
Creates a new ListOfUnits object.
The object is constructed such that it is valid for the SBML Level and
Version combination determined by the SBMLNamespaces object in @p
sbmlns.
@param sbmlns an SBMLNamespaces object that is used to determine the
characteristics of the ListOfUnits object to be created.
=item ListOfUnits::clone
Creates and returns a deep copy of this ListOfUnits.
@return a (deep) copy of this ListOfUnits.
=item ListOfUnits::getItemTypeCode
Returns the libSBML type code for the objects contained in this ListOf
(i.e., Unit objects, if the list is non-empty).
C<opydetails> doc_what_are_typecodes
@return the SBML type code for objects contained in this list:
@link SBMLTypeCode_t#SBML_UNIT SBML_UNIT@endlink (default).
@see getElementName()
@see getPackageName()
=item ListOfUnits::getElementName
Returns the XML element name of this object.
For ListOfUnits, the XML element name is C<"listOfUnits">.
@return the name of this element, i.e., C<"listOfUnits">.
=item ListOfUnits::get
Get a Unit from the ListOfUnits.
@param n the index number of the Unit to get.
@return the nth Unit in this ListOfUnits.
@see size()
=item ListOfUnits::get
Get a Unit from the ListOfUnits.
@param n the index number of the Unit to get.
@return the nth Unit in this ListOfUnits.
@see size()
=item ListOfUnits::remove
Removes the nth item from this ListOfUnits items and returns a pointer to
it.
The caller owns the returned item and is responsible for deleting it.
@param n the index of the item to remove
@see size()
=item ListOfUnits::getElementPosition
@internal
Get the ordinal position of this element in the containing object
(which in this case is the Model object).
@return the ordinal position of the element with respect to its
siblings, or C<-1> (default) to indicate the position is not significant.
=item ListOfUnits::createObject
@internal
Create a ListOfUnits object corresponding to the next token
in the XML input stream.
@return the SBML object corresponding to next XMLToken in the
XMLInputStream, or C<NULL> if the token was not recognized.
=back
=head2 UnitDefinition
@sbmlpackage{core}
@htmlinclude pkg-marker-core.html Implementation of SBML's UnitDefinition construct.
Units of measurement may be supplied in a number of contexts in an SBML
model. The SBML unit definition facility uses two classes of objects,
UnitDefinition and Unit. The approach to defining units in SBML is
compositional; for example, <em>meter second<sup> –2</sup></em> is
constructed by combining a Unit object representing <em>meter</em> with
another Unit object representing <em>second<sup> –2</sup></em>.
The combination is wrapped inside a UnitDefinition, which provides for
assigning an identifier and optional name to the combination. The
identifier can then be referenced from elsewhere in a model. Thus, the
UnitDefinition class is the container, and Unit instances are placed
inside UnitDefinition instances.
Two points are worth discussing in the context of SBML units. First,
unit declarations in SBML models are I<optional>. The consequence of
this is that a model must be numerically self-consistent independently
of unit declarations, for the benefit of software tools that cannot
interpret or manipulate units. Unit declarations in SBML are thus more
akin to a type of annotation; they can indicate intentions, and can be
used by model readers for checking the consistency of the model,
labeling simulation output, etc., but any transformations of values
implied by different units must be incorporated I<explicitly> into a
model.
Second, the vast majority of situations that require new SBML unit
definitions involve simple multiplicative combinations of base units and
factors. An example is <em>moles per litre per second</em>. What
distinguishes these sorts of unit definitions from more complex ones is
that they may be expressed without the use of an additive offset from a
zero point. The use of offsets complicates all unit definition systems,
yet in the domain of SBML, the real-life cases requiring offsets are few
(and in fact, to the best of our knowledge, only involve temperature).
Consequently, the SBML unit system has been consciously designed to
simplify implementation of unit support for the most common cases in
systems biology. The cost of this simplification is to require units
with offsets to be handled explicitly by the modeler.
@section unitdef-summary Summary of the UnitDefinition construct
UnitDefinition has two attributes and one subelement. The two
attributes are "id" and "name", and the subelement is ListOfUnits.
The required attribute "id" and optional attribute "name" are both
strings. The "id" attribute is used to give the defined unit a unique
identifier by which other parts of an SBML model definition can refer to
it. The "name" attribute is intended to be used for giving the unit
definition an optional human-readable name. Please see the <a
href="#unitdef-id">next section</a> for information about the values
permitted for "id".
A UnitDefinition must contain exactly one ListOfUnits, and this list
must contain one or more Unit definitions; see the definitions of these
other object classes for more information about them. The following
example illustrates a complete unit definition (when written in XML)
when they all the pieces are combined together. This defines "mmls"
to be millimoles per litre per second.
@verbatim
<listOfUnitDefinitions>
<unitDefinition id="mmls">
<listOfUnits>
<unit kind="mole" scale="-3"/>
<unit kind="litre" exponent="-1"/>
<unit kind="second" exponent="-1"/>
</listOfUnits>
</unitDefinition>
</listOfUnitDefinitions>
@endverbatim
@section unitdef-id Special considerations for Unit object identifiers
The attribute "id" in UnitDefinition cannot be given simply any value,
and the precise details of the values permitted differ slightly between
Levels of SBML:
\n=over\n
\n=item\n\nThe "id" of a UnitDefinition must I<not> contain a value from the
list of SBML's predefined base unit names (i.e., the strings C<gram>, @c
litre, etc.). In SBML Level 3, this list consists of the
following:
C<opydetails> doc_base_units
This list of predefined base units is nearly identical in SBML
Level 2 Version 4, the exception being that Level 2 does
not define C<avogadro>. SBML Level 2 Version 1 (and I<only>
this Level+Version combination) provides an additional predefined unit
name, C<Celsius>, not available in Level 3. Finally, SBML
Level 1 Versions 2–3 provide two more additional
predefined unit names, C<meter> and C<liter>. This is explained in
somewhat greater detail in the description of the Unit class.
\n=item\n\nIn SBML Level 2 (all Versions), there is an additional set of
reserved identifiers: C<substance>, C<volume>, C<area>, C<length>, and
C<time>. Using one of these values for the attribute "id" of a
UnitDefinition has the effect of redefining the model-wide default units
for the corresponding quantities. The list of special unit names in
SBML Level 2 is given in the table below:
@htmlinclude predefined-units.html
Also, SBML Level 2 imposes two limitations on redefining the
predefined unit C<substance>, C<volume>, C<area>, C<length>, and @c
time: (1) The UnitDefinition of a predefined SBML unit can only contain
a single Unit object within it. (2) The value of the "kind" attribute
in a Unit instance must be drawn from one of the values in the second
column of the table above.
The special unit names C<substance>, C<volume>, C<area>, C<length>, and
C<time> are not defined by SBML Level 3, which uses a different
approach to setting model-wide inherited units.
\n=back\n
@section sbml-units-limits Further comments about SBML's unit definition system
The vast majority of modeling situations requiring new SBML unit
definitions involve simple multiplicative combinations of base units and
factors. An example of this might be <em>moles per litre per
second</em>. What distinguishes these sorts of simpler unit definitions
from more complex ones is that they may be expressed without the use of
an additive offset from a zero point. The use of offsets complicates
all unit definition systems, yet in the domain of SBML the real-life
cases requiring offsets are few (and in fact, to the best of our
knowledge, only involve temperature). Consequently, the SBML unit
system has been consciously designed in a way that attempts to simplify
implementation of unit support for the most common cases in systems
biology.
As of SBML Level 2 Version 2, Unit no longer has the
attribute called "offset" introduced in SBML Level 2
Version 1. It turned out that the general case involving units
with offsets was incorrectly defined, and few (if any) developers even
attempted to support offset-based units in their software. In the
development of Level 2 Version 2, a consensus among SBML
developers emerged that a fully generalized unit scheme is I<so>
confusing and complicated that it actually I<impedes> interoperability.
SBML Level 2 Version 2, Version 3 and Version 4 acknowledge this
reality by reducing and simplifying the unit system, specifically by
removing the "offset" attribute on Unit and C<Celsius> as a pre-defined
unit.
The following guidelines suggest methods for handling units that do
require the use of zero offsets for their definitions:
\n=over\n
\n=item\n\n<em>Handling Celsius</em>. A model in which certain quantities are
temperatures measured in degrees Celsius can be converted
straightforwardly to a model in which those temperatures are in
kelvin. A software tool could do this by performing a straightforward
substitution using the following relationship: <em>T<sub> kelvin</sub> =
T<sub>Celsius</sub> + 273.15</em>. In every mathematical formula of the
model where a quantity (call it I<x>) in degrees Celsius appears,
replace I<x> with <em>x<sub>k</sub>+ 273.15</em>, where
<em>x<sub>k</sub></em> is now in kelvin. An alternative approach would
be to use a FunctionDefinition object to define a function encapsulating this
relationship above and then using that in the rest of the model as
needed. Since Celsius is a commonly-used unit, software tools could
help users by providing users with the ability to express temperatures
in Celsius in the tools' interfaces, and making substitutions
automatically when writing out the SBML.
\n=item\n\n<em>Other units requiring offsets</em>. One approach to handling
other kinds of units is to use a FunctionDefinition to define a function
encapsulating the necessary mathematical relationship, then
substituting a call to this function wherever the original quantity
appeared in the model. For example, here is a possible definition for
converting Fahrenheit to Celsius degrees:
@verbatim
<functionDefinition id="Fahrenheit_to_kelvin">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<lambda>
<bvar><ci> temp_in_fahrenheit </ci></bvar>
<apply>
<divide/>
<apply>
<plus/>
<ci> temp_in_fahrenheit </ci>
<cn> 459.67 </cn>
</apply>
<cn> 1.8 </cn>
</apply>
</lambda>
</math>
</functionDefinition>
@endverbatim
\n=item\n\nAn alternative approach not requiring the use of function definitions
is to use an AssignmentRule for each variable in Fahrenheit units.
The AssignmentRule could compute the conversion from Fahrenheit to
(say) kelvin, assign its value to a variable (in Kelvin units), and
then that variable could be used elsewhere in the model.
\n=item\n\nStill another approach is to rewrite the mathematical formulas of a
model to directly incorporate the conversion formula wherever the
original quantity appeared.
\n=back\n
Please consult the SBML specifications for more information about this
and other issues involving units.
=over
=back
=head2 ListOfUnitDefinitions
@sbmlpackage{core}
@htmlinclude pkg-marker-core.html Implementation of SBML's ListOfUnitDefinitions
construct.
C<opydetails> doc_what_is_listof
=over
=item UnitDefinition::UnitDefinition
Creates a new UnitDefinition using the given SBML C<level> and C<version>
values.
@param level an unsigned int, the SBML Level to assign to this UnitDefinition
@param version an unsigned int, the SBML Version to assign to this
UnitDefinition
@throws @if python ValueError @else SBMLConstructorException @endif@~
Thrown if the given C<level> and C<version> combination, or this kind
of SBML object, are either invalid or mismatched with respect to the
parent SBMLDocument object.
C<opydetails> doc_note_unitdefinition_setting_lv
=item UnitDefinition::UnitDefinition
Creates a new UnitDefinition using the given SBMLNamespaces object
C<sbmlns>.
C<opydetails> doc_what_are_sbmlnamespaces
@param sbmlns an SBMLNamespaces object.
@throws @if python ValueError @else SBMLConstructorException @endif@~
Thrown if the given C<level> and C<version> combination, or this kind
of SBML object, are either invalid or mismatched with respect to the
parent SBMLDocument object.
C<opydetails> doc_note_unitdefinition_setting_lv
=item UnitDefinition::UnitDefinition
Copy constructor; creates a copy of this UnitDefinition.
@param orig the object to copy.
@throws @if python ValueError @else SBMLConstructorException @endif@~
Thrown if the argument C<orig> is C<NULL>.
=item UnitDefinition::accept
Accepts the given SBMLVisitor for this instance of UnitDefinition.
@param v the SBMLVisitor instance to be used.
@return the result of calling C<v.visit()>, which indicates
whether the Visitor would like to visit the next UnitDefinition in the
list of units within which this UnitDefinition is embedded (i.e., in
the ListOfUnitDefinitions located in the enclosing Model instance).
=item UnitDefinition::clone
Creates and returns a deep copy of this UnitDefinition.
@return a (deep) copy of this UnitDefinition.
=item UnitDefinition::getElementBySId
Returns the first child element found that has the given C<id> in the
model-wide SId namespace, or C<NULL> if no such object is found.
@param id string representing the id of objects to find.
@return pointer to the first element found with the given C<id>.
=item UnitDefinition::getElementByMetaId
Returns the first child element it can find with the given C<metaid>, or
C<NULL> if no such object is found.
@param metaid string representing the metaid of objects to find
@return pointer to the first element found with the given C<metaid>.
=item UnitDefinition::getAllElements
Returns a List of all child SBase objects, including those nested to an
arbitrary depth
@return a List of pointers to all children objects.
=item UnitDefinition::getId
Returns the value of the "id" attribute of this UnitDefinition.
@return the id of this UnitDefinition.
=item UnitDefinition::getName
Returns the value of the "name" attribute of this UnitDefinition.
@return the name of this UnitDefinition.
=item UnitDefinition::isSetId
Predicate returning C<true> if this
UnitDefinition's "id" attribute is set.
@return C<true> if the "id" attribute of this UnitDefinition is
set, C<false> otherwise.
=item UnitDefinition::isSetName
Predicate returning C<true> if this
UnitDefinition's "name" attribute is set.
@return C<true> if the "name" attribute of this UnitDefinition is
set, C<false> otherwise.
=item UnitDefinition::setId
Sets the value of the "id" attribute of this UnitDefinition.
The string C<sid> is copied.
C<opydetails> doc_id_syntax
@param sid the string to use as the identifier of this UnitDefinition
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item UnitDefinition::setName
Sets the value of the "name" attribute of this UnitDefinition.
The string in C<name> is copied.
@param name the new name for the UnitDefinition
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item UnitDefinition::unsetName
Unsets the value of the "name" attribute of this UnitDefinition.
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item UnitDefinition::isVariantOfArea
Convenience function for testing if a given unit definition is a
variant of the predefined unit identifier C<"area">.
@return C<true> if this UnitDefinition is a variant of the predefined
unit C<area>, meaning square metres with only abritrary variations
in scale or multiplier values; C<false> otherwise.
=item UnitDefinition::isVariantOfLength
Convenience function for testing if a given unit definition is a
variant of the predefined unit identifier C<"length">.
@return C<true> if this UnitDefinition is a variant of the predefined
unit C<length>, meaning metres with only abritrary variations in scale
or multiplier values; C<false> otherwise.
=item UnitDefinition::isVariantOfSubstance
Convenience function for testing if a given unit definition is a
variant of the predefined unit identifier C<"substance">.
@return C<true> if this UnitDefinition is a variant of the predefined
unit C<substance>, meaning moles or items (and grams or kilograms from
SBML Level 2 Version 2 onwards) with only abritrary variations
in scale or multiplier values; C<false> otherwise.
=item UnitDefinition::isVariantOfTime
Convenience function for testing if a given unit definition is a
variant of the predefined unit identifier C<"time">.
@return C<true> if this UnitDefinition is a variant of the predefined
unit C<time>, meaning seconds with only abritrary variations in scale or
multiplier values; C<false> otherwise.
=item UnitDefinition::isVariantOfVolume
Convenience function for testing if a given unit definition is a
variant of the predefined unit identifier C<"volume">.
@return C<true> if this UnitDefinition is a variant of the predefined
unit C<volume>, meaning litre or cubic metre with only abritrary
variations in scale or multiplier values; C<false> otherwise.
=item UnitDefinition::isVariantOfDimensionless
Convenience function for testing if a given unit definition is a
variant of the unit C<"dimensionless">.
@return C<true> if this UnitDefinition is a variant of @c
dimensionless, meaning dimensionless with only abritrary variations in
scale or multiplier values; C<false> otherwise.
=item UnitDefinition::isVariantOfMass
Convenience function for testing if a given unit definition is a
variant of the predefined unit identifier C<"mass">.
@return C<true> if this UnitDefinition is a variant of mass units,
meaning gram or kilogram with only abritrary variations in scale or
multiplier values; C<false> otherwise.
=item UnitDefinition::isVariantOfSubstancePerTime
Convenience function for testing if a given unit definition is a
variant of the predefined unit C<"substance"> divided by the predefined
unit C<"time">.
@return C<true> if this UnitDefinition is a variant of the predefined
unit C<substance> per predefined unit C<time>, meaning it contains two
units one of which is a variant of substance and the other is a
variant of time which an exponent of -1; C<false> otherwise.
=item UnitDefinition::addUnit
Adds a copy of the given Unit to this UnitDefinition.
@param u the Unit instance to add to this UnitDefinition.
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_LEVEL_MISMATCH LIBSBML_LEVEL_MISMATCH @endlink
@li @link OperationReturnValues_t#LIBSBML_VERSION_MISMATCH LIBSBML_VERSION_MISMATCH @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
C<opydetails> doc_note_object_is_copied
@see createUnit()
=item UnitDefinition::createUnit
Creates a new and empty Unit, adds it to this UnitDefinition's list of
units, and returns it.
@return a newly constructed (and empty) Unit instance.
@note It is worth emphasizing that the attribute "kind" value of a
Unit is a required attribute for a valid Unit definition. The
createUnit() method does not assign a valid kind to the constructed
unit (instead, it sets the "kind" to @link UnitKind_t#UNIT_KIND_INVALID UNIT_KIND_INVALID@endlink).
Callers are cautioned to set the newly-constructed Unit's kind using
Unit::setKind(@if java int kind@endif) soon after calling this method.
@see addUnit(const Unit u)
=item UnitDefinition::getListOfUnits
Returns the list of Units for this UnitDefinition instance.
@return the ListOfUnits value for this UnitDefinition.
=item UnitDefinition::getListOfUnits
Returns the list of Units for this UnitDefinition instance.
@return the ListOfUnits value for this UnitDefinition.
=item UnitDefinition::getUnit
Returns a specific Unit instance belonging to this UnitDefinition.
@param n an integer, the index of the Unit to be returned.
@return the nth Unit of this UnitDefinition.
@see getNumUnits()
=item UnitDefinition::getUnit
Returns a specific Unit instance belonging to this UnitDefinition.
@param n an integer, the index of the Unit to be returned.
@return the nth Unit of this UnitDefinition.
=item UnitDefinition::getNumUnits
Returns the number of Unit objects contained within this
UnitDefinition.
@return an integer representing the number of Units in this
UnitDefinition.
=item UnitDefinition::removeUnit
Removes the nth Unit object from this UnitDefinition object and
returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
@param n the index of the Unit object to remove
@return the Unit object removed, or C<NULL> if the given index
is out of range.
=item UnitDefinition::setSBMLDocument
@internal
Sets the parent SBMLDocument of this SBML object.
@param d the SBMLDocument to use
=item UnitDefinition::connectToChild
@internal
Sets this SBML object to child SBML objects (if any).
(Creates a child-parent relationship by the parent)
Subclasses must override this function if they define
one ore more child elements.
Basically, this function needs to be called in
constructor, copy constructor and assignment operator.
@see setSBMLDocument
@see enablePackageInternal
=item UnitDefinition::enablePackageInternal
@internal
Enables/Disables the given package with this element and child
elements (if any).
(This is an internal implementation for enablePackage function)
@note Subclasses of the SBML Core package in which one or more child
elements are defined must override this function.
=item UnitDefinition::getTypeCode
Returns the libSBML type code for this object instance.
C<opydetails> doc_what_are_typecodes
@return the SBML type code for this object:
@link SBMLTypeCode_t#SBML_UNIT_DEFINITION SBML_UNIT_DEFINITION@endlink (default).
C<opydetails> doc_warning_typecodes_not_unique
@see getPackageName()
@see getElementName()
=item UnitDefinition::getElementName
Returns the XML element name of this object, which for UnitDefinition,
is always C<"unitDefinition">.
@return the name of this element, i.e., C<"unitDefinition">.
=item UnitDefinition::simplify
Simplifies the UnitDefinition such that any given kind of Unit object
occurs only once in the ListOfUnits.
For example, the following definition,
@verbatim
<unitDefinition>
<listOfUnits>
<unit kind="metre" exponent="1"/>
<unit kind="metre" exponent="2"/>
</listOfUnits>
<unitDefinition>
@endverbatim
will be simplified to
@verbatim
<unitDefinition>
<listOfUnits>
<unit kind="metre" exponent="3"/>
</listOfUnits>
<unitDefinition>
@endverbatim
@param ud the UnitDefinition object to be simplified.
C<opydetails> doc_note_static_methods
=item UnitDefinition::reorder
Alphabetically orders the Unit objects within the ListOfUnits of a
UnitDefinition.
@param ud the UnitDefinition object whose units are to be reordered.
C<opydetails> doc_note_static_methods
=item UnitDefinition::convertToSI
Convert a given UnitDefinition into a new UnitDefinition object
that uses SI units.
@param ud the UnitDefinition object to convert to SI
@return a new UnitDefinition object representing the results of the
conversion.
C<opydetails> doc_note_static_methods
=item UnitDefinition::areIdentical
Predicate returning C<true> if two
UnitDefinition objects are identical.
For the purposes of performing this comparison, two UnitDefinition
objects are considered identical when they contain identical lists of
Unit objects. Pairs of Unit objects in the lists are in turn
considered identical if they satisfy the predicate
Unit::areIdentical(@if java Unit u1, Unit u2@endif).
The predicate compares every attribute of the
Unit objects.
@param ud1 the first UnitDefinition object to compare
@param ud2 the second UnitDefinition object to compare
@return C<true> if all the Unit objects in ud1 are identical to the
Unit objects of ud2, C<false> otherwise.
C<opydetails> doc_note_static_methods
@see UnitDefinition::areEquivalent(const UnitDefinition ud1, const UnitDefinition ud2)
@see Unit::areIdentical(Unit unit1, Unit unit2)
=item UnitDefinition::areEquivalent
Predicate returning C<true> if two
UnitDefinition objects are equivalent.
For the purposes of performing this comparison, two UnitDefinition
objects are considered equivalent when they contain I<equivalent>
list of Unit objects. Unit objects are in turn considered equivalent
if they satisfy the predicate
Unit::areEquivalent(@if java Unit u1, Unit u2@endif).
The predicate tests a subset of the objects's attributes.
@param ud1 the first UnitDefinition object to compare
@param ud2 the second UnitDefinition object to compare
@return C<true> if all the Unit objects in ud1 are equivalent
to the Unit objects in ud2, C<false> otherwise.
C<opydetails> doc_note_static_methods
@see UnitDefinition::areIdentical(const UnitDefinition ud1, const UnitDefinition ud2)
@see Unit::areEquivalent(Unit unit1, Unit unit2)
=item UnitDefinition::areIdenticalSIUnits
@internal
=item UnitDefinition::combine
Combines two UnitDefinition objects into a single UnitDefinition.
This takes UnitDefinition objects C<ud1> and C<ud2>, and creates a
UnitDefinition object that expresses the product of the units of @p
ud1 and C<ud2>.
@param ud1 the first UnitDefinition object
@param ud2 the second UnitDefinition object
@return a UnitDefinition which represents the product of the
units of the two argument UnitDefinitions.
C<opydetails> doc_note_static_methods
=item UnitDefinition::divide
Combines two UnitDefinition objects into a single UnitDefinition as
a division.
This takes UnitDefinition objects C<ud1> and C<ud2>, and creates a
UnitDefinition object that expresses the division of the units of @p
ud1 and C<ud2>.
@param ud1 the first UnitDefinition object
@param ud2 the second UnitDefinition object
@return a UnitDefinition which represents the division of the
units of the two argument UnitDefinitions.
C<opydetails> doc_note_static_methods
=item UnitDefinition::printUnits
Expresses the given definition in a plain-text form.
For example,
UnitDefinition::printUnits(@if java UnitDefinition u@endif)
applied to
@verbatim
<unitDefinition>
<listOfUnits>
<unit kind="metre" exponent="1"/>
<unit kind="second" exponent="-2"/>
</listOfUnits>
<unitDefinition>
@endverbatim
will return the string C<"metre (exponent = 1, multiplier = 1,
scale = 0) second (exponent = -2, multiplier = 1, scale = 0)">
or, if the optional parameter C<compact> is given the value C<true>,
the string C<"(1 metre)^1 (1 second)^-2">. This method may
be useful for printing unit information to human users, or in
debugging software, or other situations.
@param ud the UnitDefinition object
@param compact boolean indicating whether the compact form
should be used (defaults to false)
@return a string expressing the unit definition defined by the given
UnitDefinition object C<ud>.
C<opydetails> doc_note_static_methods
=item UnitDefinition::writeElements
@internal
Subclasses should override this method to write out their contained
SBML objects as XML elements. Be sure to call your parents
implementation of this method as well.
=item UnitDefinition::hasRequiredAttributes
Predicate returning C<true> if
all the required attributes for this UnitDefinition object
have been set.
@note The required attributes for a UnitDefinition object are:
@li "id"
@return a boolean value indicating whether all the required
attributes for this object have been defined.
=item UnitDefinition::hasRequiredElements
Predicate returning C<true> if
all the required elements for this UnitDefinition object
have been set.
@note The required elements for a Constraint object are:
@li "listOfUnits" (required in SBML Level 2 only, optional in Level 3)
@return a boolean value indicating whether all the required
elements for this object have been defined.
=item UnitDefinition::createObject
@internal
Create and return a unitDefinition object, if present.
@return the SBML object corresponding to next XMLToken in the
XMLInputStream or C<NULL> if the token was not recognized.
=item UnitDefinition::addExpectedAttributes
@internal
Subclasses should override this method to get the list of
expected attributes.
This function is invoked from corresponding readAttributes()
function.
=item UnitDefinition::readAttributes
@internal
Subclasses should override this method to read values from the given
XMLAttributes set into their specific fields. Be sure to call your
parents implementation of this method as well.
=item UnitDefinition::readL1Attributes
@internal
=item UnitDefinition::readL2Attributes
@internal
=item UnitDefinition::readL3Attributes
@internal
=item UnitDefinition::writeAttributes
@internal
Subclasses should override this method to write their XML attributes
to the XMLOutputStream. Be sure to call your parents implementation
of this method as well.
=item ListOfUnitDefinitions::ListOfUnitDefinitions
Creates a new ListOfUnitDefinitions object.
The object is constructed such that it is valid for the given SBML
Level and Version combination.
@param level the SBML Level
@param version the Version within the SBML Level
=item ListOfUnitDefinitions::ListOfUnitDefinitions
Creates a new ListOfUnitDefinitions object.
The object is constructed such that it is valid for the SBML Level and
Version combination determined by the SBMLNamespaces object in @p
sbmlns.
@param sbmlns an SBMLNamespaces object that is used to determine the
characteristics of the ListOfUnitDefinitions object to be created.
=item ListOfUnitDefinitions::clone
Creates and returns a deep copy of this ListOfUnitDefinitions instance.
@return a (deep) copy of this ListOfUnitDefinitions.
=item ListOfUnitDefinitions::getItemTypeCode
Returns the libSBML type code for the objects contained in this ListOf
(i.e., UnitDefinition objects, if the list is non-empty).
C<opydetails> doc_what_are_typecodes
@return the SBML type code for objects contained in this list:
@link SBMLTypeCode_t#SBML_UNIT_DEFINITION SBML_UNIT_DEFINITION@endlink (default).
@see getElementName()
@see getPackageName()
=item ListOfUnitDefinitions::getElementName
Returns the XML element name of this object.
For ListOfUnitDefinitions, the XML element name is @c
"listOfUnitDefinitions".
@return the name of this element, i.e., C<"listOfUnitDefinitions">.
=item ListOfUnitDefinitions::get
Get a UnitDefinition from the ListOfUnitDefinitions.
@param n the index number of the UnitDefinition to get.
@return the nth UnitDefinition in this ListOfUnitDefinitions.
@see size()
=item ListOfUnitDefinitions::get
Get a UnitDefinition from the ListOfUnitDefinitions.
@param n the index number of the UnitDefinition to get.
@return the nth UnitDefinition in this ListOfUnitDefinitions.
@see size()
=item ListOfUnitDefinitions::get
Get a UnitDefinition from the ListOfUnitDefinitions
based on its identifier.
@param sid a string representing the identifier
of the UnitDefinition to get.
@return UnitDefinition in this ListOfUnitDefinitions
with the given C<sid> or C<NULL> if no such
UnitDefinition exists.
@see get(unsigned int n)
@see size()
=item ListOfUnitDefinitions::get
Get a UnitDefinition from the ListOfUnitDefinitions
based on its identifier.
@param sid a string representing the identifier
of the UnitDefinition to get.
@return UnitDefinition in this ListOfUnitDefinitions
with the given C<sid> or C<NULL> if no such
UnitDefinition exists.
@see get(unsigned int n)
@see size()
=item ListOfUnitDefinitions::getElementBySId
Returns the first child element found that has the given C<id> in the
model-wide SId namespace, or C<NULL> if no such object is found.
Note that UnitDefinitions themselves are in the UnitId namespace, not
the SId namespace, so no UnitDefinition object will be returned from
this function (and is the reason we override the base
ListOf::getElementBySId function here).
@param id string representing the id of objects to find
@return pointer to the first element found with the given C<id>.
=item ListOfUnitDefinitions::remove
Removes the nth item from this ListOfUnitDefinitions items and returns a pointer to
it.
The caller owns the returned item and is responsible for deleting it.
@param n the index of the item to remove
@see size()
=item ListOfUnitDefinitions::remove
Removes item in this ListOfUnitDefinitions items with the given identifier.
The caller owns the returned item and is responsible for deleting it.
If none of the items in this list have the identifier C<sid>, then @c
NULL is returned.
@param sid the identifier of the item to remove
@return the item removed. As mentioned above, the caller owns the
returned item.
=item ListOfUnitDefinitions::getElementPosition
@internal
Get the ordinal position of this element in the containing object
(which in this case is the Model object).
The ordering of elements in the XML form of SBML is generally fixed
for most components in SBML. So, for example, the
ListOfUnitDefinitions in a model is (in SBML Level 2
Version 4) the second ListOf___. (However, it differs for
different Levels and Versions of SBML.)
@return the ordinal position of the element with respect to its
siblings, or C<-1> (default) to indicate the position is not significant.
=item ListOfUnitDefinitions::createObject
@internal
Create and return a listOfUnitDefinitions object, if present.
@return the SBML object corresponding to next XMLToken in the
XMLInputStream or NULL if the token was not recognized.
=back
=head2 CompartmentType
@sbmlpackage{core}
@htmlinclude pkg-marker-core.html Implementation of SBML's Level 2's CompartmentType
construct.
SBML Level 2 Versions 2–4 provide the <em>compartment
type</em> as a grouping construct that can be used to establish a
relationship between multiple Compartment objects. A CompartmentType
object only has an identity, and this identity can only be used to
indicate that particular Compartment objects in the model belong to this
type. This may be useful for conveying a modeling intention, such as
when a model contains many similar compartments, either by their
biological function or the reactions they carry. Without a compartment
type construct, it would be impossible within SBML itself to indicate
that all of the compartments share an underlying conceptual relationship
because each SBML compartment must be given a unique and separate
identity. Compartment types have no mathematical meaning in
SBML—they have no effect on a model's mathematical interpretation.
Simulators and other numerical analysis software may ignore
CompartmentType definitions and references to them in a model.
There is no mechanism in SBML Level 2 for representing hierarchies of
compartment types. One CompartmentType instance cannot be the subtype
of another CompartmentType instance; SBML provides no means of defining
such relationships.
As with other major structures in SBML, CompartmentType has a mandatory
attribute, "id", used to give the compartment type an identifier. The
identifier must be a text string conforming to the identifer syntax
permitted in SBML. CompartmentType also has an optional "name"
attribute, of type C<string>. The "id" and "name" must be used
according to the guidelines described in the SBML specification (e.g.,
Section 3.3 in the Level 2 Version 4 specification).
CompartmentType was introduced in SBML Level 2 Version 2. It is not
available in SBML Level 1 nor in Level 3.
@see Compartment
@see ListOfCompartmentTypes
@see SpeciesType
@see ListOfSpeciesTypes
=over
=back
=head2 ListOfCompartmentTypes
@sbmlpackage{core}
@htmlinclude pkg-marker-core.html Implementation of SBML's ListOfCompartmentTypes
construct.
C<opydetails> doc_what_is_listof
=over
=item CompartmentType::CompartmentType
Creates a new CompartmentType using the given SBML C<level> and C<version>
values.
@param level an unsigned int, the SBML Level to assign to this
CompartmentType
@param version an unsigned int, the SBML Version to assign to this
CompartmentType
@throws @if python ValueError @else SBMLConstructorException @endif@~
Thrown if the given C<level> and C<version> combination, or this kind
of SBML object, are either invalid or mismatched with respect to the
parent SBMLDocument object.
C<opydetails> doc_compartmenttype_setting_lv
=item CompartmentType::CompartmentType
Creates a new CompartmentType using the given SBMLNamespaces object
C<sbmlns>.
C<opydetails> doc_what_are_sbmlnamespaces
It is worth emphasizing that although this constructor does not take an
identifier argument, in SBML Level 2 and beyond, the "id"
(identifier) attribute of a CompartmentType is required to have a value.
Thus, callers are cautioned to assign a value after calling this
constructor. Setting the identifier can be accomplished using the
method setId(@if java String id@endif).
@param sbmlns an SBMLNamespaces object.
@throws @if python ValueError @else SBMLConstructorException @endif@~
Thrown if the given C<level> and C<version> combination, or this kind
of SBML object, are either invalid or mismatched with respect to the
parent SBMLDocument object.
C<opydetails> doc_compartmenttype_setting_lv
=item CompartmentType::CompartmentType
Copy constructor; creates a copy of this CompartmentType.
@param orig the object to copy.
@throws @if python ValueError @else SBMLConstructorException @endif@~
Thrown if the argument C<orig> is C<NULL>.
=item CompartmentType::accept
Accepts the given SBMLVisitor for this instance of CompartmentType.
@param v the SBMLVisitor instance to be used.
@return the result of calling C<v.visit()>, which indicates
whether the Visitor would like to visit the next CompartmentType in
the list of compartment types.
=item CompartmentType::clone
Creates and returns a deep copy of this CompartmentType.
@return a (deep) copy of this CompartmentType.
=item CompartmentType::getId
Returns the value of the "id" attribute of this CompartmentType.
@return the id of this CompartmentType.
=item CompartmentType::getName
Returns the value of the "name" attribute of this CompartmentType.
@return the name of this CompartmentType.
=item CompartmentType::isSetId
Predicate returning C<true> if this
CompartmentType's "id" attribute is set.
@return C<true> if the "id" attribute of this CompartmentType is
set, C<false> otherwise.
=item CompartmentType::isSetName
Predicate returning C<true> if this
CompartmentType's "name" attribute is set.
@return C<true> if the "name" attribute of this CompartmentType is
set, C<false> otherwise.
=item CompartmentType::setId
Sets the value of the "id" attribute of this CompartmentType.
The string C<sid> is copied.
C<opydetails> doc_id_syntax
@param sid the string to use as the identifier of this CompartmentType
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif@~ The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item CompartmentType::setName
Sets the value of the "name" attribute of this CompartmentType.
The string in C<name> is copied.
@param name the new name for the CompartmentType
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif@~ The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item CompartmentType::unsetName
Unsets the value of the "name" attribute of this CompartmentType.
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif@~ The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item CompartmentType::getTypeCode
Returns the libSBML type code for this SBML object.
C<opydetails> doc_what_are_typecodes
@return the SBML type code for this object:
@link SBMLTypeCode_t#SBML_COMPARTMENT_TYPE SBML_COMPARTMENT_TYPE@endlink (default).
C<opydetails> doc_warning_typecodes_not_unique
@see getElementName()
@see getPackageName()
=item CompartmentType::getElementName
Returns the XML element name of this object, which for
CompartmentType, is always C<"compartmentType">.
@return the name of this element, i.e., C<"compartmentType">.
=item CompartmentType::writeElements
@internal
Subclasses should override this method to write out their contained
SBML objects as XML elements. Be sure to call your parents
implementation of this method as well.
=item CompartmentType::hasRequiredAttributes
Predicate returning C<true> if
all the required attributes for this CompartmentType object
have been set.
@note The required attributes for a CompartmentType object are:
@li "id"
@return a boolean value indicating whether all the required
attributes for this object have been defined.
=item CompartmentType::addExpectedAttributes
@internal
Subclasses should override this method to get the list of
expected attributes.
This function is invoked from corresponding readAttributes()
function.
=item CompartmentType::readAttributes
@internal
Subclasses should override this method to read values from the given
XMLAttributes set into their specific fields. Be sure to call your
parents implementation of this method as well.
@param attributes the XMLAttributes to use.
=item CompartmentType::readL2Attributes
@internal
=item CompartmentType::writeAttributes
@internal
Subclasses should override this method to write their XML attributes
to the XMLOutputStream. Be sure to call your parents implementation
of this method as well.
@param stream the XMLOutputStream to use.
=item ListOfCompartmentTypes::ListOfCompartmentTypes
Creates a new ListOfCompartmentTypes object.
The object is constructed such that it is valid for the given SBML
Level and Version combination.
@param level the SBML Level
@param version the Version within the SBML Level
=item ListOfCompartmentTypes::ListOfCompartmentTypes
Creates a new ListOfCompartmentTypes object.
The object is constructed such that it is valid for the SBML Level and
Version combination determined by the SBMLNamespaces object in @p
sbmlns.
@param sbmlns an SBMLNamespaces object that is used to determine the
characteristics of the ListOfCompartmentTypes object to be created.
=item ListOfCompartmentTypes::clone
Creates and returns a deep copy of this ListOfCompartmentTypes instance.
@return a (deep) copy of this ListOfCompartmentTypes.
=item ListOfCompartmentTypes::getItemTypeCode
Returns the libSBML type code for the objects contained in this ListOf
(i.e., CompartmentType objects, if the list is non-empty).
C<opydetails> doc_what_are_typecodes
@return the SBML type code for the objects contained in this ListOf
instance: @link SBMLTypeCode_t#SBML_COMPARTMENT_TYPE SBML_COMPARTMENT_TYPE@endlink (default).
@see getElementName()
@see getPackageName()
=item ListOfCompartmentTypes::getElementName
Returns the XML element name of this object.
For ListOfCompartmentTypes, the XML element name is @c
"listOfCompartmentTypes".
@return the name of this element, i.e., C<"listOfCompartmentTypes">.
=item ListOfCompartmentTypes::get
Get a CompartmentType from the ListOfCompartmentTypes.
@param n the index number of the CompartmentType to get.
@return the nth CompartmentType in this ListOfCompartmentTypes.
@see size()
=item ListOfCompartmentTypes::get
Get a CompartmentType from the ListOfCompartmentTypes.
@param n the index number of the CompartmentType to get.
@return the nth CompartmentType in this ListOfCompartmentTypes.
@see size()
=item ListOfCompartmentTypes::get
Get a CompartmentType from the ListOfCompartmentTypes
based on its identifier.
@param sid a string representing the identifier
of the CompartmentType to get.
@return CompartmentType in this ListOfCompartmentTypes
with the given C<sid> or C<NULL> if no such
CompartmentType exists.
@see get(unsigned int n)
@see size()
=item ListOfCompartmentTypes::get
Get a CompartmentType from the ListOfCompartmentTypes
based on its identifier.
@param sid a string representing the identifier
of the CompartmentType to get.
@return CompartmentType in this ListOfCompartmentTypes
with the given C<sid> or C<NULL> if no such
CompartmentType exists.
@see get(unsigned int n)
@see size()
=item ListOfCompartmentTypes::remove
Removes the nth item from this ListOfCompartmentTypes items
and returns a pointer to it.
The caller owns the returned item and is responsible for deleting it.
@param n the index of the item to remove
@see size()
=item ListOfCompartmentTypes::remove
Removes item in this ListOfCompartmentTypes items with the given identifier.
The caller owns the returned item and is responsible for deleting it.
If none of the items in this list have the identifier C<sid>, then @c
NULL is returned.
@param sid the identifier of the item to remove
@return the item removed. As mentioned above, the caller owns the
returned item.
=item ListOfCompartmentTypes::getElementPosition
@internal
Get the ordinal position of this element in the containing object
(which in this case is the Model object).
The ordering of elements in the XML form of SBML is generally fixed
for most components in SBML. For example, the
ListOfCompartmentTypes in a model (in SBML Level 2 Version 4) is the
third ListOf___. (However, it differs for different Levels and
Versions of SBML, so calling code should not hardwire this number.)
@return the ordinal position of the element with respect to its
siblings, or C<-1> (default) to indicate the position is not significant.
=item ListOfCompartmentTypes::createObject
@internal
Create a ListOfCompartmentTypes object corresponding to the next token
in the XML input stream.
@return the SBML object corresponding to next XMLToken in the
XMLInputStream, or C<NULL> if the token was not recognized.
=back
=head2 SpeciesType
@sbmlpackage{core}
@htmlinclude pkg-marker-core.html Implementation of SBML Level 2's SpeciesType
construct.
The term I<species> I<type> refers to reacting entities independent of
location. These include simple ions (e.g., protons, calcium), simple
molecules (e.g., glucose, ATP), large molecules (e.g., RNA,
polysaccharides, and proteins), and others.
SBML Level 2 Versions 2–4 provide an explicit
SpeciesType class of object to enable Species objects of the same type
to be related together. SpeciesType is a conceptual construct; the
existence of SpeciesType objects in a model has no effect on the model's
numerical interpretation. Except for the requirement for uniqueness of
species/species type combinations located in compartments, simulators
and other numerical analysis software may ignore SpeciesType definitions
and references to them in a model.
There is no mechanism in SBML Level 2 for representing hierarchies of
species types. One SpeciesType object cannot be the subtype of another
SpeciesType object; SBML provides no means of defining such
relationships.
As with other major structures in SBML, SpeciesType has a mandatory
attribute, "id", used to give the species type an identifier. The
identifier must be a text string conforming to the identifer syntax
permitted in SBML. SpeciesType also has an optional "name" attribute,
of type C<string>. The "id" and "name" must be used according to the
guidelines described in the SBML specification (e.g., Section 3.3 in
the Level 2 Version 4 specification).
SpeciesType was introduced in SBML Level 2 Version 2. It is not
available in SBML Level 1 nor in Level 3.
@see Species
@see ListOfSpeciesTypes
@see CompartmentType
@see ListOfCompartmentTypes
=over
=back
=head2 ListOfSpeciesTypes
@sbmlpackage{core}
@htmlinclude pkg-marker-core.html Implementation of SBML's ListOfSpeciesTypes construct.
C<opydetails> doc_what_is_listof
=over
=item SpeciesType::SpeciesType
Creates a new SpeciesType using the given SBML C<level> and C<version>
values.
@param level an unsigned int, the SBML Level to assign to this SpeciesType
@param version an unsigned int, the SBML Version to assign to this
SpeciesType
@throws @if python ValueError @else SBMLConstructorException @endif@~
Thrown if the given C<level> and C<version> combination, or this kind
of SBML object, are either invalid or mismatched with respect to the
parent SBMLDocument object.
C<opydetails> doc_note_speciestype_setting_lv
=item SpeciesType::SpeciesType
Creates a new SpeciesType using the given SBMLNamespaces object
C<sbmlns>.
C<opydetails> doc_what_are_sbmlnamespaces
It is worth emphasizing that although this constructor does not take
an identifier argument, in SBML Level 2 and beyond, the "id"
(identifier) attribute of a SpeciesType object is required to have a value.
Thus, callers are cautioned to assign a value after calling this
constructor. Setting the identifier can be accomplished using the
method SBase::setId(@if java String id@endif).
@param sbmlns an SBMLNamespaces object.
@throws @if python ValueError @else SBMLConstructorException @endif@~
Thrown if the given C<level> and C<version> combination, or this kind
of SBML object, are either invalid or mismatched with respect to the
parent SBMLDocument object.
C<opydetails> doc_note_speciestype_setting_lv
=item SpeciesType::SpeciesType
Copy constructor; creates a copy of this SpeciesType.
@param orig the object to copy.
@throws @if python ValueError @else SBMLConstructorException @endif@~
Thrown if the argument C<orig> is C<NULL>.
=item SpeciesType::accept
Accepts the given SBMLVisitor for this instance of SpeciesType.
@param v the SBMLVisitor instance to be used.
@return the result of calling C<v.visit()>, which indicates
whether the Visitor would like to visit the next SpeciesType in
the list of compartment types.
=item SpeciesType::clone
Creates and returns a deep copy of this SpeciesType.
@return a (deep) copy of this SpeciesType.
=item SpeciesType::getId
Returns the value of the "id" attribute of this SpeciesType.
@return the id of this SpeciesType.
=item SpeciesType::getName
Returns the value of the "name" attribute of this SpeciesType.
@return the name of this SpeciesType.
=item SpeciesType::isSetId
Predicate returning C<true> if this
SpeciesType's "id" attribute is set.
@return C<true> if the "id" attribute of this SpeciesType is
set, C<false> otherwise.
=item SpeciesType::isSetName
Predicate returning C<true> if this
SpeciesType's "name" attribute is set.
@return C<true> if the "name" attribute of this SpeciesType is
set, C<false> otherwise.
=item SpeciesType::setId
Sets the value of the "id" attribute of this SpeciesType.
The string C<sid> is copied.
C<opydetails> doc_id_syntax
@param sid the string to use as the identifier of this SpeciesType
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif@~ The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item SpeciesType::setName
Sets the value of the "name" attribute of this SpeciesType.
The string in C<name> is copied.
@param name the new name for the SpeciesType
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif@~ The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item SpeciesType::unsetName
Unsets the value of the "name" attribute of this SpeciesType.
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif@~ The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item SpeciesType::getTypeCode
Returns the libSBML type code for this SBML object.
C<opydetails> doc_what_are_typecodes
@return the SBML type code for this object:
@link SBMLTypeCode_t#SBML_SPECIES_TYPE SBML_SPECIES_TYPE@endlink (default).
C<opydetails> doc_warning_typecodes_not_unique
@see getElementName()
@see getPackageName()
=item SpeciesType::getElementName
Returns the XML element name of this object, which for
SpeciesType, is always C<"compartmentType">.
@return the name of this element, i.e., C<"compartmentType">.
=item SpeciesType::writeElements
@internal
Subclasses should override this method to write out their contained
SBML objects as XML elements. Be sure to call your parents
implementation of this method as well.
=item SpeciesType::hasRequiredAttributes
Predicate returning C<true> if
all the required attributes for this SpeciesType object
have been set.
@note The required attributes for a SpeciesType object are:
@li "id"
@return a boolean value indicating whether all the required
attributes for this object have been defined.
=item SpeciesType::addExpectedAttributes
@internal
Subclasses should override this method to get the list of
expected attributes.
This function is invoked from corresponding readAttributes()
function.
=item SpeciesType::readAttributes
@internal
Subclasses should override this method to read values from the given
XMLAttributes set into their specific fields. Be sure to call your
parents implementation of this method as well.
@param attributes the XMLAttributes to use.
=item SpeciesType::readL2Attributes
@internal
=item SpeciesType::writeAttributes
@internal
Subclasses should override this method to write their XML attributes
to the XMLOutputStream. Be sure to call your parents implementation
of this method as well.
@param stream the XMLOutputStream to use.
=item ListOfSpeciesTypes::ListOfSpeciesTypes
Creates a new ListOfSpeciesTypes object.
The object is constructed such that it is valid for the given SBML
Level and Version combination.
@param level the SBML Level
@param version the Version within the SBML Level
=item ListOfSpeciesTypes::ListOfSpeciesTypes
Creates a new ListOfSpeciesTypes object.
The object is constructed such that it is valid for the SBML Level and
Version combination determined by the SBMLNamespaces object in @p
sbmlns.
@param sbmlns an SBMLNamespaces object that is used to determine the
characteristics of the ListOfSpeciesTypes object to be created.
=item ListOfSpeciesTypes::clone
Creates and returns a deep copy of this ListOfSpeciesTypes instance.
@return a (deep) copy of this ListOfSpeciesTypes.
=item ListOfSpeciesTypes::getItemTypeCode
Returns the libSBML type code for the objects contained in this ListOf
(i.e., SpeciesType objects, if the list is non-empty).
C<opydetails> doc_what_are_typecodes
@return the SBML type code for objects contained in this list:
@link SBMLTypeCode_t#SBML_SPECIES_TYPE SBML_SPECIES_TYPE@endlink (default).
@see getElementName()
@see getPackageName()
=item ListOfSpeciesTypes::getElementName
Returns the XML element name of this object.
For ListOfSpeciesTypes, the XML element name is @c
"listOfSpeciesTypes".
@return the name of this element, i.e., C<"listOfSpeciesTypes">.
=item ListOfSpeciesTypes::get
Get a SpeciesType from the ListOfSpeciesTypes.
@param n the index number of the SpeciesType to get.
@return the nth SpeciesType in this ListOfSpeciesTypes.
@see size()
=item ListOfSpeciesTypes::get
Get a SpeciesType from the ListOfSpeciesTypes.
@param n the index number of the SpeciesType to get.
@return the nth SpeciesType in this ListOfSpeciesTypes.
@see size()
=item ListOfSpeciesTypes::get
Get a SpeciesType from the ListOfSpeciesTypes
based on its identifier.
@param sid a string representing the identifier
of the SpeciesType to get.
@return SpeciesType in this ListOfSpeciesTypes
with the given C<sid> or C<NULL> if no such
SpeciesType exists.
@see get(unsigned int n)
@see size()
=item ListOfSpeciesTypes::get
Get a SpeciesType from the ListOfSpeciesTypes
based on its identifier.
@param sid a string representing the identifier
of the SpeciesType to get.
@return SpeciesType in this ListOfSpeciesTypes
with the given C<sid> or C<NULL> if no such
SpeciesType exists.
@see get(unsigned int n)
@see size()
=item ListOfSpeciesTypes::remove
Removes the nth item from this ListOfSpeciesTypes items and returns a pointer to
it.
The caller owns the returned item and is responsible for deleting it.
@param n the index of the item to remove
@see size()
=item ListOfSpeciesTypes::remove
Removes item in this ListOfSpeciesTypes items with the given identifier.
The caller owns the returned item and is responsible for deleting it.
If none of the items in this list have the identifier C<sid>, then @c
NULL is returned.
@param sid the identifier of the item to remove
@return the item removed. As mentioned above, the caller owns the
returned item.
=item ListOfSpeciesTypes::getElementPosition
@internal
Get the ordinal position of this element in the containing object
(which in this case is the Model object).
The ordering of elements in the XML form of SBML is generally fixed
for most components in SBML. For example, the
ListOfSpeciesTypes in a model (in SBML Level 2 Version 4) is the
third ListOf___. (However, it differs for different Levels and
Versions of SBML, so calling code should not hardwire this number.)
@return the ordinal position of the element with respect to its
siblings, or C<-1> (default) to indicate the position is not significant.
=item ListOfSpeciesTypes::createObject
@internal
Create a ListOfSpeciesTypes object corresponding to the next token
in the XML input stream.
@return the SBML object corresponding to next XMLToken in the
XMLInputStream, or C<NULL> if the token was not recognized.
=back
=head2 Compartment
@sbmlpackage{core}
@htmlinclude pkg-marker-core.html Implementation of SBML's Compartment construct.
A compartment in SBML represents a bounded space in which species are
located. Compartments do not necessarily have to correspond to actual
structures inside or outside of a biological cell.
It is important to note that although compartments are optional in the
overall definition of Model, every species in an SBML model must be
located in a compartment. This in turn means that if a model defines
any species, the model must also define at least one compartment. The
reason is simply that species represent physical things, and therefore
must exist I<somewhere>. Compartments represent the I<somewhere>.
Compartment has one required attribute, "id", to give the compartment a
unique identifier by which other parts of an SBML model definition can
refer to it. A compartment can also have an optional "name" attribute
of type C<string>. Identifiers and names must be used according to the
guidelines described in the SBML specifications.
Compartment also has an optional attribute "spatialDimensions" that is
used to indicate the number of spatial dimensions possessed by the
compartment. Most modeling scenarios involve compartments with integer
values of "spatialDimensions" of C<3> (i.e., a three-dimensional
compartment, which is to say, a volume), or 2 (a two-dimensional
compartment, a surface), or C<1> (a one-dimensional compartment, a
line). In SBML Level 3, the type of this attribute is C<double>,
there are no restrictions on the permitted values of the
"spatialDimensions" attribute, and there are no default values. In SBML
Level 2, the value must be a positive C<integer>, and the default
value is C<3>; the permissible values in SBML Level 2 are C<3>, @c
2, C<1>, and C<0> (for a point).
Another optional attribute on Compartment is "size", representing the @em
initial total size of that compartment in the model. The "size" attribute
must be a floating-point value and may represent a volume (if the
compartment is a three-dimensional one), or an area (if the compartment is
two-dimensional), or a length (if the compartment is one-dimensional).
There is no default value of compartment size in SBML Level 2 or
Level 3. In particular, a missing "size" value <em>does not imply
that the compartment size is 1</em>. (This is unlike the definition of
compartment "volume" in SBML Level 1.) When the compartment's
"spatialDimensions" attribute does not have a value of C<0>, a missing
value of "size" for a given compartment signifies that the value either is
unknown, or to be obtained from an external source, or determined by an
InitialAssignment, AssignmentRule, AlgebraicRule or RateRule
@if conly structure @else object@endif@~ elsewhere in the model. In SBML
Level 2, there are additional special requirements on the values of
"size"; we discuss them in a <a href="#comp-l2">separate section
below</a>.
The units associated with a compartment's "size" attribute value may be
set using the optional attribute "units". The rules for setting and
using compartment size units differ between SBML Level 2 and
Level 3, and are discussed separately below.
Finally, the optional Compartment attribute named "constant" is used to
indicate whether the compartment's size stays constant after simulation
begins. A value of C<true> indicates the compartment's "size" cannot be
changed by any other construct except InitialAssignment; a value of @c
false indicates the compartment's "size" can be changed by other
constructs in SBML. In SBML Level 2, there is an additional
explicit restriction that if "spatialDimensions"=C<"0">, the value
cannot be changed by InitialAssignment either. Further, in
Level 2, "constant" has a default value of C<true>. In SBML
Level 3, there is no default value for the "constant" attribute.
@section comp-l2 Additional considerations in SBML Level 2
In SBML Level 2, the default units of compartment size, and the kinds
of units allowed as values of the attribute "units", interact with the
number of spatial dimensions of the compartment. The value of the "units"
attribute of a Compartment @if conly structure @else object@endif@~ must
be one of the base units (see Unit), or the predefined unit identifiers @c
volume, C<area>, C<length> or C<dimensionless>, or a new unit defined by a
UnitDefinition @if conly structure @else object@endif@~ in the enclosing
Model, subject to the restrictions detailed in the following table:
<table border="0" class="centered text-table width80 normal-font alt-row-colors"
style="padding-bottom: 0.5em">
<caption class="top-caption">Restrictions on values permitted for
compartment C<size> and C<units> attributes.</caption>
<tr>
<th align="left" valign="bottom">
Value of<br>C<spatialDimensions>
</th>
<th align="left" valign="bottom">
C<size><br>allowed?
</th>
<th align="left" valign="bottom">
C<units><br>allowed?
</th>
<th align="left" valign="bottom">
Allowable kinds of units
</th>
<th align="left" valign="bottom">
Default value of attribute C<units>
</th>
</tr>
<tr>
<td>C<3></td>
<td>yes</td>
<td>yes</td>
<td>units of volume, or C<dimensionless></td>
<td>C<volume></td>
</tr>
<tr>
<td>C<2></td>
<td>yes</td>
<td>yes</td>
<td>units of area, or C<dimensionless></td>
<td>C<area></td>
</tr>
<tr>
<td>C<1></td>
<td>yes</td>
<td>yes</td>
<td>units of length, or C<dimensionless></td>
<td>C<length></td>
</tr>
<tr>
<td>C<0></td>
<td>no</td>
<td>no</td>
<td>(no units allowed)</td>
<td></td>
</tr>
</tr>
</table>
In SBML Level 2, the units of the compartment size, as defined by the
"units" attribute or (if "units" is not set) the default value listed in
the table above, are used in the following ways when the compartment has
a "spatialDimensions" value greater than C<0>:
\n=over\n
\n=item\n\nThe value of the "units" attribute is used as the units of the
compartment identifier when the identifier appears as a numerical
quantity in a mathematical formula expressed in MathML.
\n=item\n\nThe C<math> element of an AssignmentRule or InitialAssignment
referring to this compartment must have identical units.
\n=item\n\nIn RateRule objects that set the rate of change of the compartment's
size, the units of the rule's C<math> element must be identical to the
compartment's "units" attribute divided by the default I<time> units.
(In other words, the units for the rate of change of compartment size
are <em>compartment size</em>/<em>time</em> units.
\n=item\n\nWhen a Species is to be treated in terms of concentrations or
density, the units of the spatial size portion of the concentration
value (i.e., the denominator in the units formula I<substance>/@em
size) are those indicated by the value of the "units" attribute on the
compartment in which the species is located.
\n=back\n
Compartments with "spatialDimensions"=C<0> require special treatment in
this framework. As implied above, the "size" attribute must not have a
value on an SBML Level 2 Compartment
@if conly structure @else object@endif@~ if the "spatialDimensions"
attribute has a value of C<0>. An additional related restriction is that
the "constant" attribute must default to or be set to C<true> if the value
of the "spatialDimensions" attribute is C<0>, because a zero-dimensional
compartment cannot ever have a size.
If a compartment has no size or dimensional units, how should such a
compartment's identifier be interpreted when it appears in mathematical
formulas? The answer is that such a compartment's identifier should not
appear in mathematical formulas in the first place—it has no
value, and its value cannot change. Note also that a zero-dimensional
compartment is a point, and species located at points can only be
described in terms of amounts, not spatially-dependent measures such as
concentration. Since SBML KineticLaw formulas are already in terms of
I<substance>/I<time> and not (say) I<concentration>/I<time>, volume
or other factors in principle are not needed for species located in
zero-dimensional compartments.
Finally, in SBML Level 2 Versions 2–4, each compartment in a
model may optionally be designated as belonging to a particular
compartment I<type>. The optional attribute "compartmentType" is used
identify the compartment type represented by the Compartment structure.
The "compartmentType" attribute's value must be the identifier of a
CompartmentType instance defined in the model. If the "compartmentType"
attribute is not present on a particular compartment definition, a
unique virtual compartment type is assumed for that compartment, and no
other compartment can belong to that compartment type. The values of
"compartmentType" attributes on compartments have no effect on the
numerical interpretation of a model. Simulators and other numerical
analysis software may ignore "compartmentType" attributes. The
"compartmentType" attribute and the CompartmentType
@if conly structures @else class of objects@endif@~ are
not present in SBML Level 3 Core nor in SBML Level 1.
@section comp-l3 Additional considerations in SBML Level 3
One difference between SBML Level 3 and lower Levels of SBML is
that there are no restrictions on the permissible values of the
"spatialDimensions" attribute, and there is no default value defined for
the attribute. The value of "spatialDimensions" does not have to be an
integer, either; this is to allow for the possibility of representing
structures with fractal dimensions.
The number of spatial dimensions possessed by a compartment cannot enter
into mathematical formulas, and therefore cannot directly alter the
numerical interpretation of a model. However, the value of
"spatialDimensions" I<does> affect the interpretation of the units
associated with a compartment's size. Specifically, the value of
"spatialDimensions" is used to select among the Model attributes
"volumeUnits", "areaUnits" and "lengthUnits" when a Compartment
@if conly object @else structure@endif@~ does not define a value for its
"units" attribute.
The "units" attribute may be left unspecified for a given compartment in a
model; in that case, the compartment inherits the unit of measurement
specified by one of the attributes on the enclosing Model
@if conly structure @else object@endif@~ instance. The applicable
attribute on Model depends on the value of the compartment's
"spatialDimensions" attribute; the relationship is shown in the table
below. If the Model @if conly structure @else object@endif@~ does not
define the relevant attribute ("volumeUnits", "areaUnits" or
"lengthUnits") for a given "spatialDimensions" value, the unit associated
with that Compartment @if conly structure @else object@endif's size is
undefined. If I<both> "spatialDimensions" and "units" are left unset on
a given Compartment @if conly structure @else object@endif@~ instance,
then no unit can be chosen from among the Model's "volumeUnits",
"areaUnits" or "lengthUnits" attributes (even if the Model instance
provides values for those attributes), because there is no basis to select
between them and there is no default value of "spatialDimensions".
Leaving the units of compartments' sizes undefined in an SBML model does
not render the model invalid; however, as a matter of best practice, we
strongly recommend that all models specify the units of measurement for
all compartment sizes.
<table border="0" class="centered text-table width80 normal-font alt-row-colors"
style="padding-bottom: 0.5em">
<caption class="top-caption">Interpretation of the Compartment "units" attribute.</caption>
<tr>
<th align="left" valign="bottom">
Value of attribute<br>"spatialDimensions"
</th>
<th align="left" valign="bottom">
Attribute of Model used<br>for inheriting the unit
</th>
<th align="left" valign="bottom">
Recommended candidate units
</th>
</tr>
<tr>
<td>C<3></td>
<td>"volumeUnits"</td>
<td>units of volume, or C<dimensionless></td>
</tr>
<tr>
<td>C<2></td>
<td>"areaUnits"</td>
<td>units of area, or C<dimensionless></td>
</tr>
<tr>
<td>C<1></td>
<td>"lengthUnits"</td>
<td>units of length, or C<dimensionless></td>
</tr>
<tr>
<td><em>other</em></td>
<td><em>no units inherited</em></td>
<td><em>no specific recommendations</em></td>
</tr>
</tr>
</table>
The unit of measurement associated with a compartment's size, as defined
by the "units" attribute or (if "units" is not set) the inherited value
from Model according to the table above, is used in the following ways:
\n=over\n
\n=item\n\nWhen the identifier of the compartment appears as a numerical
quantity in a mathematical formula expressed in MathML, it represents
the size of the compartment, and the unit associated with the size is
the value of the "units" attribute.
\n=item\n\nWhen a Species is to be treated in terms of concentrations or
density, the unit associated with the spatial size portion of the
concentration value (i.e., the denominator in the formula
<em>amount</em>/<em>size</em>) is specified by the value of the "units"
attribute on the compartment in which the species is located.
\n=item\n\nThe "math" elements of AssignmentRule, InitialAssignment and
EventAssignment @if conly structures @else objects@endif@~ setting the
value of the compartment size should all have the same units as the unit
associated with the compartment's size.
\n=item\n\nIn a RateRule @if conly structure @else object@endif@~ that defines a
rate of change for a compartment's size, the unit of the rule's "math"
element should be identical to the compartment's "units" attribute divided
by the model-wide unit of <em>time</em>. (In other words, {<em>unit of
compartment size</em>}/{<em>unit of time</em>}.)
\n=back\n
@section comp-other Other aspects of Compartment
In SBML Level 1 and Level 2, Compartment has an optional
attribute named "outside", whose value can be the identifier of another
Compartment @if conly structure @else object@endif@~ defined in the
enclosing Model @if conly structure @else object@endif@~. Doing so means
that the other compartment contains it or is outside of it. This enables
the representation of simple topological relationships between
compartments, for those simulation systems that can make use of the
information (e.g., for drawing simple diagrams of compartments). It is
worth noting that in SBML, there is no relationship between compartment
sizes when compartment positioning is expressed using the "outside"
attribute. The size of a given compartment does not in any sense include
the sizes of other compartments having it as the value of their "outside"
attributes. In other words, if a compartment I<B> has the identifier of
compartment I<A> as its "outside" attribute value, the size of I<A> does
not include the size of I<B>. The compartment sizes are separate.
In Level 2, there are two restrictions on the "outside" attribute.
First, because a compartment with "spatialDimensions" of C<0> has no
size, such a compartment cannot act as the container of any other
compartment I<except> compartments that I<also> have
"spatialDimensions" values of C<0>. Second, the directed graph formed
by representing Compartment structures as vertexes and the "outside"
attribute values as edges must be acyclic. The latter condition is
imposed to prevent a compartment from being contained inside itself. In
the absence of a value for "outside", compartment definitions in SBML
Level 2 do not have any implied spatial relationships between each
other.
=over
=back
=head2 ListOfCompartments
@sbmlpackage{core}
@htmlinclude pkg-marker-core.html Implementation of SBML Level 2's ListOfCompartments
construct.
C<opydetails> doc_what_is_listof
=over
=item Compartment::Compartment
Creates a new Compartment using the given SBML C<level> and C<version>
values.
@param level an unsigned int, the SBML Level to assign to this Compartment
@param version an unsigned int, the SBML Version to assign to this
Compartment
@throws @if python ValueError @else SBMLConstructorException @endif@~
Thrown if the given C<level> and C<version> combination, or this kind
of SBML object, are either invalid or mismatched with respect to the
parent SBMLDocument object.
C<opydetails> doc_note_compartment_setting_lv
=item Compartment::Compartment
Creates a new Compartment using the given SBMLNamespaces object
C<sbmlns>.
C<opydetails> doc_what_are_sbmlnamespaces
It is worth emphasizing that although this constructor does not take
an identifier argument, in SBML Level 2 and beyond, the "id"
(identifier) attribute of a Compartment is required to have a value.
Thus, callers are cautioned to assign a value after calling this
constructor. Setting the identifier can be accomplished using the
method @if java Compartment::setId(String id)@else setId()@endif.
@param sbmlns an SBMLNamespaces object.
@throws @if python ValueError @else SBMLConstructorException @endif@~
Thrown if the given C<level> and C<version> combination, or this kind
of SBML object, are either invalid or mismatched with respect to the
parent SBMLDocument object.
C<opydetails> doc_note_compartment_setting_lv
=item Compartment::Compartment
Copy constructor; creates a copy of a Compartment.
@param orig the Compartment instance to copy.
@throws @if python ValueError @else SBMLConstructorException @endif@~
Thrown if the argument C<orig> is C<NULL>.
=item Compartment::accept
Accepts the given SBMLVisitor for this instance of Compartment.
@param v the SBMLVisitor instance to be used.
@return the result of calling C<v.visit()>, which indicates
whether the Visitor would like to visit the next Compartment in the
list of compartments within which this Compartment is embedded (i.e.,
the ListOfCompartments in the parent Model).
=item Compartment::clone
Creates and returns a deep copy of this Compartment object.
@return a (deep) copy of this Compartment.
=item Compartment::initDefaults
Initializes the fields of this Compartment object to "typical" default
values.
The SBML Compartment component has slightly different aspects and
default attribute values in different SBML Levels and Versions.
This method sets the values to certain common defaults, based
mostly on what they are in SBML Level 2. Specifically:
@li Sets attribute "spatialDimensions" to C<3>
@li Sets attribute "constant" to C<true>
@li (Applies to Level 1 models only) Sets attribute "volume" to C<1>.0
@li (Applies to Level 3 models only) Sets attribute "units" to C<litre>
=item Compartment::getId
Returns the value of the "id" attribute of this Compartment object.
@return the id of this Compartment.
=item Compartment::getName
Returns the value of the "name" attribute of this Compartment object.
@return the name of this Compartment.
=item Compartment::getCompartmentType
Get the value of the "compartmentType" attribute of this Compartment
object.
@return the value of the "compartmentType" attribute of this
Compartment as a string.
@note The "compartmentType" attribute is only available in SBML
Level 2 Versions 2–4.
=item Compartment::getSpatialDimensions
Get the number of spatial dimensions of this Compartment object.
@return the value of the "spatialDimensions" attribute of this
Compartment as an unsigned integer
C<opydetails> doc_note_spatial_dimensions_as_double
@see getSpatialDimensionsAsDouble()
=item Compartment::getSpatialDimensionsAsDouble
Get the number of spatial dimensions of this Compartment object,
as a double.
@return the value of the "spatialDimensions" attribute of this
Compartment as a double, or C<NaN> if this model is not in SBML
Level 3 format.
C<opydetails> doc_note_spatial_dimensions_as_double
@see getSpatialDimensions()
=item Compartment::getSize
Get the size of this Compartment.
C<opydetails> doc_compartment_both_size_and_volume
@return the value of the "size" attribute ("volume" in Level 1) of
this Compartment as a floating-point number.
@note This method is identical to
@if java Compartment::getVolume()@else getVolume()@endif.
@see isSetSize()
@see getVolume()
=item Compartment::getVolume
Get the volume of this Compartment.
C<opydetails> doc_compartment_both_size_and_volume
@return the value of the "volume" attribute ("size" in Level 2) of
this Compartment, as a floating-point number.
C<opydetails> doc_note_compartment_volume
@note This method is identical to
@if java Compartment::getSize()@else getSize()@endif.
@see isSetVolume()
@see getSize()
=item Compartment::getUnits
Get the units of this compartment's size.
The value of an SBML compartment's "units" attribute establishes the
unit of measurement associated with the compartment's size.
@return the value of the "units" attribute of this Compartment, as a
string. An empty string indicates that no units have been assigned to
the value of the size.
C<opydetails> doc_note_unassigned_unit_are_not_a_default
@see isSetUnits()
@see @if java Compartment::setUnits(String sid)@else setUnits()@endif@~
@see getSize()
=item Compartment::getOutside
Get the identifier, if any, of the compartment that is designated
as being outside of this one.
@return the value of the "outside" attribute of this Compartment.
@note The "outside" attribute is defined in SBML Level 1 and
Level 2, but does not exist in SBML Level 3 Version 1
Core.
=item Compartment::getConstant
Get the value of the "constant" attribute of this Compartment.
@return C<true> if this Compartment's size is flagged as being
constant, C<false> otherwise.
=item Compartment::isSetId
Predicate returning C<true> if this
Compartment's "id" attribute is set.
@return C<true> if the "id" attribute of this Compartment is
set, C<false> otherwise.
=item Compartment::isSetName
Predicate returning C<true> if this
Compartment's "name" attribute is set.
@return C<true> if the "name" attribute of this Compartment is
set, C<false> otherwise.
=item Compartment::isSetCompartmentType
Predicate returning C<true> if this
Compartment's "compartmentType" attribute is set.
@return C<true> if the "compartmentType" attribute of this Compartment
is set, C<false> otherwise.
@note The "compartmentType" attribute is only available in SBML
Level 2 Versions 2–4.
=item Compartment::isSetSize
Predicate returning C<true> if this Compartment's "size" attribute is
set.
This method is similar but not identical to
@if java Compartment::isSetVolume()@else isSetVolume()@endif. The latter
should be used in the context of SBML Level 1 models instead of
@if java Compartment::isSetSize()@else isSetSize()@endif@~
because @if java Compartment::isSetVolume()@else isSetVolume()@endif@~
performs extra processing to take into account the difference in
default values between SBML Levels 1 and 2.
@return C<true> if the "size" attribute ("volume" in Level 2) of
this Compartment is set, C<false> otherwise.
@see isSetVolume()
@see @if java Compartment::setSize(double value)@else setSize()@endif@~
=item Compartment::isSetVolume
Predicate returning C<true> if this Compartment's "volume" attribute is
set.
This method is similar but not identical to
@if java Compartment::isSetSize()@else isSetSize()@endif. The latter
should not be used in the context of SBML Level 1 models because the
present method performs extra processing to take into account
the difference in default values between SBML Levels 1 and 2.
@return C<true> if the "volume" attribute ("size" in Level 2 and
above) of this Compartment is set, C<false> otherwise.
C<opydetails> doc_note_compartment_volume
@see isSetSize()
@see @if java Compartment::setVolume(double value)@else setVolume()@endif@~
=item Compartment::isSetUnits
Predicate returning C<true> if this
Compartment's "units" attribute is set.
@return C<true> if the "units" attribute of this Compartment is
set, C<false> otherwise.
C<opydetails> doc_note_unassigned_unit_are_not_a_default
=item Compartment::isSetOutside
Predicate returning C<true> if this
Compartment's "outside" attribute is set.
@return C<true> if the "outside" attribute of this Compartment is
set, C<false> otherwise.
@note The "outside" attribute is defined in SBML Level 1 and
Level 2, but does not exist in SBML Level 3 Version 1
Core.
=item Compartment::isSetSpatialDimensions
Predicate returning C<true> if this
Compartment's "spatialDimensions" attribute is set.
@return C<true> if the "spatialDimensions" attribute of this
Compartment is set, C<false> otherwise.
=item Compartment::isSetConstant
Predicate returning C<true> if this
Compartment's "constant" attribute is set.
@return C<true> if the "constant" attribute of this Compartment is
set, C<false> otherwise.
=item Compartment::setId
Sets the value of the "id" attribute of this Compartment.
The string C<sid> is copied.
C<opydetails> doc_id_syntax
@param sid the string to use as the identifier of this Compartment. If
the string is C<NULL>, this method will return
@link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink.
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item Compartment::setName
Sets the value of the "name" attribute of this Compartment.
The string in C<name> is copied.
@param name the new name for the Compartment. If the string is C<NULL>,
this method will return
@link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink.
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item Compartment::setCompartmentType
Sets the "compartmentType" attribute of this Compartment.
@param sid the identifier of a CompartmentType object defined elsewhere
in this Model. If the string is C<NULL>, this method will return
@link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink.
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
@li @link OperationReturnValues_t#LIBSBML_UNEXPECTED_ATTRIBUTE LIBSBML_UNEXPECTED_ATTRIBUTE @endlink
@note The "compartmentType" attribute is only available in SBML
Level 2 Versions 2–4.
=item Compartment::setSpatialDimensions
Sets the "spatialDimensions" attribute of this Compartment.
@param value an unsigned integer indicating the number of dimensions
of this compartment.
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
@li @link OperationReturnValues_t#LIBSBML_UNEXPECTED_ATTRIBUTE LIBSBML_UNEXPECTED_ATTRIBUTE @endlink
=item Compartment::setSpatialDimensions
Sets the "spatialDimensions" attribute of this Compartment as a double.
@param value a double indicating the number of dimensions
of this compartment.
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
@li @link OperationReturnValues_t#LIBSBML_UNEXPECTED_ATTRIBUTE LIBSBML_UNEXPECTED_ATTRIBUTE @endlink
=item Compartment::setSize
Sets the "size" attribute (or "volume" in SBML Level 1) of this
Compartment.
@param value a C<double> representing the size of this compartment
instance in whatever units are in effect for the compartment.
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@note This method is identical to
@if java Compartment::setVolume(double value)@else setVolume()@endif.
@see isSetSize()
@see @if java Compartment::setVolume(double value)@else setVolume()@endif
=item Compartment::setVolume
Sets the "volume" attribute (or "size" in SBML Level 2) of this
Compartment.
This method is identical to
@if java Compartment::setSize(double value)@else setSize()@endif@~
and is provided for compatibility between SBML Level 1 and
higher Levels of SBML.
@param value a C<double> representing the volume of this compartment
instance in whatever units are in effect for the compartment.
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
C<opydetails> doc_note_compartment_volume
@see isSetVolume()
@see @if java Compartment::setSize(double value)@else setSize()@endif@~
=item Compartment::setUnits
Sets the "units" attribute of this Compartment.
@param sid the identifier of the defined units to use. If C<sid> is @c
NULL, then this method will return
@link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink.
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item Compartment::setOutside
Sets the "outside" attribute of this Compartment.
@param sid the identifier of a compartment that encloses this one. If @p
sid is C<NULL>, then this method will return
@link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink.
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
@note The "outside" attribute is defined in SBML Level 1 and
Level 2, but does not exist in SBML Level 3 Version 1
Core.
=item Compartment::setConstant
Sets the value of the "constant" attribute of this Compartment.
@param value a boolean indicating whether the size/volume of this
compartment should be considered constant (C<true>) or variable
(C<false>).
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_UNEXPECTED_ATTRIBUTE LIBSBML_UNEXPECTED_ATTRIBUTE @endlink
=item Compartment::renameSIdRefs
Renames all the C<SIdRef> attributes on this element, including any
found in MathML.
C<opydetails> doc_what_is_sidref
This method works by looking at all attributes and (if appropriate)
mathematical formulas, comparing the identifiers to the value of @p
oldid. If any matches are found, the matching identifiers are replaced
with C<newid>. The method does I<not> descend into child elements.
@param oldid the old identifier
@param newid the new identifier
=item Compartment::renameUnitSIdRefs
Renames all the C<UnitSIdRef> attributes on this element.
C<opydetails> doc_what_is_unitsidref
This method works by looking at all unit identifier attribute values
(including, if appropriate, inside mathematical formulas), comparing the
unit identifiers to the value of C<oldid>. If any matches are found,
the matching identifiers are replaced with C<newid>. The method does
I<not> descend into child elements.
@param oldid the old identifier
@param newid the new identifier
=item Compartment::unsetName
Unsets the value of the "name" attribute of this Compartment.
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item Compartment::unsetCompartmentType
Unsets the value of the "compartmentType" attribute of this Compartment.
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
@li @link OperationReturnValues_t#LIBSBML_UNEXPECTED_ATTRIBUTE LIBSBML_UNEXPECTED_ATTRIBUTE @endlink
@note The "compartmentType" attribute is only available in SBML
Level 2 Versions 2–4.
@see setCompartmentType(const std::string& sid)
@see isSetCompartmentType()
=item Compartment::unsetSize
Unsets the value of the "size" attribute of this Compartment.
In SBML Level 1, a compartment's volume has a default value (@c
1.0) and therefore <em>should always be set</em>. Calling this method
on a Level 1 model resets the value to C<1>.0 rather than actually
unsetting it. In Level 2, a compartment's "size" is optional with
no default value, and unsetting it will result in the compartment having
no defined size.
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
@note This method is identical to
@if java Compartment::unsetVolume()@else unsetVolume()@endif.
=item Compartment::unsetVolume
Unsets the value of the "volume" attribute of this Compartment.
This method is identical to
@if java Compartment::unsetSize()@else unsetSize()@endif. Please refer
to that method's documentation for more information about its behavior.
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
C<opydetails> doc_note_compartment_volume
@see unsetSize()
=item Compartment::unsetUnits
Unsets the value of the "units" attribute of this Compartment.
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item Compartment::unsetOutside
Unsets the value of the "outside" attribute of this Compartment.
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
@note The "outside" attribute is defined in SBML Level 1 and
Level 2, but does not exist in SBML Level 3 Version 1
Core.
=item Compartment::unsetSpatialDimensions
Unsets the value of the "spatialDimensions" attribute of this
Compartment.
In SBML Levels prior to Level 3, compartments must always have a
value for the number of dimensions. Consequently, calling this method
on a model of SBML Level 1–2 will result in a return value of
@link OperationReturnValues_t#LIBSBML_UNEXPECTED_ATTRIBUTE LIBSBML_UNEXPECTED_ATTRIBUTE @endlink
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
@li @link OperationReturnValues_t#LIBSBML_UNEXPECTED_ATTRIBUTE LIBSBML_UNEXPECTED_ATTRIBUTE @endlink
@note This function is only valid for SBML Level 3.
=item Compartment::getDerivedUnitDefinition
Constructs and returns a UnitDefinition that corresponds to the units
of this Compartment's designated size.
C<opydetails> doc_compartment_units
@return a UnitDefinition that expresses the units of this
Compartment, or C<NULL> if one cannot be constructed.
C<opydetails> doc_note_unit_analysis_depends_on_model
@see isSetUnits()
@see getUnits()
=item Compartment::getDerivedUnitDefinition
Constructs and returns a UnitDefinition that corresponds to the units
of this Compartment's designated size.
C<opydetails> doc_compartment_units
@return a UnitDefinition that expresses the units of this
Compartment, or C<NULL> if one cannot be constructed.
C<opydetails> doc_note_unit_analysis_depends_on_model
@see isSetUnits()
@see getUnits()
=item Compartment::getTypeCode
Returns the libSBML type code for this SBML object.
C<opydetails> doc_what_are_typecodes
@return the SBML type code for this object:
@link SBMLTypeCode_t#SBML_COMPARTMENT SBML_COMPARTMENT@endlink (default).
C<opydetails> doc_warning_typecodes_not_unique
@see getElementName()
@see getPackageName()
=item Compartment::getElementName
Returns the XML element name of this object, which for Compartment, is
always C<"compartment">.
@return the name of this element, i.e., C<"compartment">.
=item Compartment::writeElements
@internal
Subclasses should override this method to write out their contained
SBML objects as XML elements. Be sure to call your parents
implementation of this method as well.
=item Compartment::hasRequiredAttributes
Predicate returning C<true> if all the required attributes for this
Compartment object have been set.
@note The required attributes for a Compartment object are:
@li "id" (or "name" in SBML Level 1)
@li "constant" (in SBML Level 3 only)
@return a boolean value indicating whether all the required
attributes for this object have been defined.
=item Compartment::addExpectedAttributes
@internal
Subclasses should override this method to get the list of
expected attributes.
This function is invoked from corresponding readAttributes()
function.
=item Compartment::readAttributes
@internal
Subclasses should override this method to read values from the given
XMLAttributes set into their specific fields. Be sure to call your
parents implementation of this method as well.
=item Compartment::readL1Attributes
@internal
=item Compartment::readL2Attributes
@internal
=item Compartment::readL3Attributes
@internal
=item Compartment::writeAttributes
@internal
Subclasses should override this method to write their XML attributes
to the XMLOutputStream. Be sure to call your parents implementation
of this method as well.
=item Compartment::isExplicitlySetSpatialDimensions
@internal
=item Compartment::isExplicitlySetConstant
@internal
=item ListOfCompartments::ListOfCompartments
Creates a new ListOfCompartments object.
The object is constructed such that it is valid for the given SBML
Level and Version combination.
@param level the SBML Level
@param version the Version within the SBML Level
=item ListOfCompartments::ListOfCompartments
Creates a new ListOfCompartments object.
The object is constructed such that it is valid for the SBML Level and
Version combination determined by the SBMLNamespaces object in @p
sbmlns.
@param sbmlns an SBMLNamespaces object that is used to determine the
characteristics of the ListOfCompartments object to be created.
=item ListOfCompartments::clone
Creates and returns a deep copy of this ListOfCompartments instance.
@return a (deep) copy of this ListOfCompartments.
=item ListOfCompartments::getItemTypeCode
Returns the libSBML type code for the objects contained in this ListOf
(i.e., Compartment objects, if the list is non-empty).
C<opydetails> doc_what_are_typecodes
@return the SBML type code for the objects contained in this ListOf
instance: @link SBMLTypeCode_t#SBML_COMPARTMENT SBML_COMPARTMENT@endlink (default).
@see getElementName()
@see getPackageName()
=item ListOfCompartments::getElementName
Returns the XML element name of this object.
For ListOfCompartments, the XML element name is C<"listOfCompartments">.
@return the name of this element, i.e., C<"listOfCompartments">.
=item ListOfCompartments::get
Get a Compartment from the ListOfCompartments.
@param n the index number of the Compartment to get.
@return the nth Compartment in this ListOfCompartments.
@see size()
=item ListOfCompartments::get
Get a Compartment from the ListOfCompartments.
@param n the index number of the Compartment to get.
@return the nth Compartment in this ListOfCompartments.
@see size()
=item ListOfCompartments::get
Get a Compartment from the ListOfCompartments
based on its identifier.
@param sid a string representing the identifier
of the Compartment to get.
@return Compartment in this ListOfCompartments
with the given C<sid> or C<NULL> if no such
Compartment exists.
@see get(unsigned int n)
@see size()
=item ListOfCompartments::get
Get a Compartment from the ListOfCompartments
based on its identifier.
@param sid a string representing the identifier
of the Compartment to get.
@return Compartment in this ListOfCompartments
with the given C<sid> or C<NULL> if no such
Compartment exists.
@see get(unsigned int n)
@see size()
=item ListOfCompartments::remove
Removes the nth item from this ListOfCompartments items and returns a pointer to
it.
The caller owns the returned item and is responsible for deleting it.
@param n the index of the item to remove
@see size()
=item ListOfCompartments::remove
Removes item in this ListOfCompartments items with the given identifier.
The caller owns the returned item and is responsible for deleting it.
If none of the items in this list have the identifier C<sid>, then
C<NULL> is returned.
@param sid the identifier of the item to remove
@return the item removed. As mentioned above, the caller owns the
returned item.
=item ListOfCompartments::getElementPosition
@internal
Get the ordinal position of this element in the containing object
(which in this case is the Model object).
The ordering of elements in the XML form of SBML is generally fixed
for most components in SBML. So, for example, the ListOfCompartments
in a model is (in SBML Level 2 Version 4) the fifth
ListOf___. (However, it differs for different Levels and Versions of
SBML.)
@return the ordinal position of the element with respect to its
siblings, or C<-1> (default) to indicate the position is not significant.
=item ListOfCompartments::createObject
@internal
Create and return an SBML object of this class, if present.
@return the SBML object corresponding to next XMLToken in the
XMLInputStream or C<NULL> if the token was not recognized.
=back
=head2 Species
@sbmlpackage{core}
@htmlinclude pkg-marker-core.html Implementation of SBML's Species construct.
A I<species> in SBML refers to a pool of entities that (a) are
considered indistinguishable from each other for the purposes of the
model, (b) participate in reactions, and (c) are located in a specific
I<compartment>. The SBML Species object class is intended to represent
these pools.
As with other major constructs in SBML, Species has a mandatory
attribute, "id", used to give the species type an identifier in the
model. The identifier must be a text string conforming to the identifer
syntax permitted in SBML. Species also has an optional "name"
attribute, of type C<string>. The "id" and "name" must be used
according to the guidelines described in the SBML specifications.
The required attribute "compartment" is used to identify the compartment
in which the species is located. The attribute's value must be the
identifier of an existing Compartment object. It is important to note
that there is no default value for the "compartment" attribute on
Species; every species in an SBML model must be assigned a compartment
I<explicitly>. (This also implies that every model with one or more
Species objects must define at least one Compartment object.)
@section species-amounts The initial amount and concentration of a species
The optional attributes "initialAmount" and "initialConcentration", both
having a data type of C<double>, can be used to set the I<initial>
quantity of the species in the compartment where the species is located.
These attributes are mutually exclusive; i.e., <em>only one</em> can
have a value on any given instance of a Species object. Missing
"initialAmount" and "initialConcentration" values implies that their
values either are unknown, or to be obtained from an external source, or
determined by an InitialAssignment or other SBML construct elsewhere in
the model.
A species' initial quantity in SBML is set by the "initialAmount" or
"initialConcentration" attribute exactly once. If the "constant"
attribute is C<true>, then the value of the species' quantity is fixed
and cannot be changed except by an InitialAssignment. These methods
differ in that the "initialAmount" and "initialConcentration" attributes
can only be used to set the species quantity to a literal floating-point
number, whereas the use of an InitialAssignment object allows the value
to be set using an arbitrary mathematical expression (which, thanks to
MathML's expressiveness, may evaluate to a rational number). If the
species' "constant" attribute is C<false>, the species' quantity value
may be overridden by an InitialAssignment or changed by AssignmentRule
or AlgebraicRule, and in addition, for <em>t > 0</em>, it may also be
changed by a RateRule, Event objects, and as a result of being a
reactant or product in one or more Reaction objects. (However, some
constructs are mutually exclusive; see the SBML specifications for the
precise details.) It is not an error to define "initialAmount" or
"initialConcentration" on a species and also redefine the value using an
InitialAssignment, but the "initialAmount" or "initialConcentration"
setting in that case is ignored. The SBML specifications provide
additional information about the semantics of assignments, rules and
values for simulation time <em>t</em> \f$\leq\f$ <em>0</em>.
SBML Level 2 additionally stipulates that in cases where a species'
compartment has a "spatialDimensions" value of C<0> (zero), the species
cannot have a value for "initialConcentration" because the concepts of
concentration and density break down when a container has zero
dimensions.
@section species-units The units of a species' amount or concentration
When the attribute "initialAmount" is set, the unit of measurement
associated with the value of "initialAmount" is specified by the Species
attribute "substanceUnits". When the "initialConcentration" attribute
is set, the unit of measurement associated with this concentration value
is {<em>unit of amount</em>} divided by {<em>unit of size</em>}, where
the {<em>unit of amount</em>} is specified by the Species
"substanceUnits" attribute, and the {<em>unit of size</em>} is specified
by the "units" attribute of the Compartment object in which the species
is located. Note that in either case, a unit of <em>amount</em> is
involved and determined by the "substanceUnits" attribute. Note
<strong>these two attributes alone do not determine the units of the
species when the species identifier appears in a mathematical
expression</strong>; <em>that</em> aspect is determined by the attribute
"hasOnlySubstanceUnits" discussed below.
In SBML Level 3, if the "substanceUnits" attribute is not set on a
given Species object instance, then the unit of <em>amount</em> for that
species is inherited from the "substanceUnits" attribute on the
enclosing Model object instance. If that attribute on Model is not set
either, then the unit associated with the species' quantity is
undefined.
In SBML Level 2, if the "substanceUnits" attribute is not set on a
given Species object instance, then the unit of <em>amount</em> for that
species is taken from the predefined SBML unit identifier @c
"substance". The value assigned to "substanceUnits" must be chosen from
one of the following possibilities: one of the base unit identifiers
defined in SBML, the built-in unit identifier C<"substance">, or the
identifier of a new unit defined in the list of unit definitions in the
enclosing Model object. The chosen units for "substanceUnits" must be
be C<"dimensionless">, C<"mole">, C<"item">, C<"kilogram">, C<"gram">,
or units derived from these.
As noted at the beginning of this section, simply setting
"initialAmount" or "initialConcentration" alone does I<not> determine
whether a species identifier represents an amount or a concentration
when it appears elsewhere in an SBML model. The role of the attribute
"hasOnlySubstanceUnits" is to indicate whether the units of the species,
when the species identifier appears in mathematical formulas, are
intended to be concentration or amount. The attribute takes on a
boolean value. In SBML Level 3, the attribute has no default value
and must always be set in a model; in SBML Level 2, it has a
default value of C<false>.
The <em>units of the species</em> are used in the following ways:
\n=over\n
\n=item\n\nWhen the species' identifier appears in a MathML formula, it
represents the species' quantity, and the unit of measurement associated
with the quantity is as described above.
\n=item\n\nThe "math" elements of AssignmentRule, InitialAssignment and
EventAssignment objects referring to this species should all have the
same units as the unit of measurement associated with the species
quantity.
\n=item\n\nIn a RateRule object that defines the rate of change of the
species' quantity, the unit associated with the rule's "math" element
should be equal to the unit of the species' quantity divided by the
model-wide unit of <em>time</em>; in other words, {<em>unit of species
quantity</em>}/{<em>unit of time</em>}.
\n=back\n
@section species-constant The "constant" and "boundaryCondition" attributes
The Species object class has two boolean attributes named "constant" and
"boundaryCondition", used to indicate whether and how the quantity of
that species can vary during a simulation. In SBML Level 2 they
are optional; in SBML Level 3 they are mandatory. The following
table shows how to interpret the combined values of these attributes.
@htmlinclude species-boundarycondition.html
By default, when a species is a product or reactant of one or more
reactions, its quantity is determined by those reactions. In SBML, it
is possible to indicate that a given species' quantity is <em>not</em>
determined by the set of reactions even when that species occurs as a
product or reactant; i.e., the species is on the <em>boundary</em> of
the reaction system, and its quantity is not determined by the
reactions. The boolean attribute "boundaryCondition" can be used to
indicate this. A value of C<false> indicates that the species I<is>
part of the reaction system. In SBML Level 2, the attribute has a
default value of C<false>, while in SBML Level 3, it has no
default.
The "constant" attribute indicates whether the species' quantity can be
changed at all, regardless of whether by reactions, rules, or constructs
other than InitialAssignment. A value of C<false> indicates that the
species' quantity can be changed. (This is also a common value because
the purpose of most simulations is precisely to calculate changes in
species quantities.) In SBML Level 2, the attribute has a default
value of C<false>, while in SBML Level 3, it has no default. Note
that the initial quantity of a species can be set by an
InitialAssignment irrespective of the value of the "constant" attribute.
In practice, a "boundaryCondition" value of C<true> means a differential
equation derived from the reaction definitions should not be generated
for the species. However, the species' quantity may still be changed by
AssignmentRule, RateRule, AlgebraicRule, Event, and InitialAssignment
constructs if its "constant" attribute is C<false>. Conversely, if the
species' "constant" attribute is C<true>, then its value cannot be
changed by anything except InitialAssignment.
A species having "boundaryCondition"=C<false> and "constant"=C<false>
can appear as a product and/or reactant of one or more reactions in the
model. If the species is a reactant or product of a reaction, it must
I<not> also appear as the target of any AssignmentRule or RateRule
object in the model. If instead the species has "boundaryCondition"=@c
false and "constant"=C<true>, then it cannot appear as a reactant or
product, or as the target of any AssignmentRule, RateRule or
EventAssignment object in the model.
@section species-l2-convfactor The conversionFactor attribute in SBML Level 3
In SBML Level 3, Species has an additional optional attribute,
"conversionFactor", that defines a conversion factor that applies to a
particular species. The value must be the identifier of a Parameter
object instance defined in the model. That Parameter object must be a
constant, meaning its "constant" attribute must be set to C<true>.
If a given Species object definition defines a value for its
"conversionFactor" attribute, it takes precedence over any factor
defined by the Model object's "conversionFactor" attribute.
The unit of measurement associated with a species' quantity can be
different from the unit of extent of reactions in the model. SBML
Level 3 avoids implicit unit conversions by providing an explicit
way to indicate any unit conversion that might be required. The use of
a conversion factor in computing the effects of reactions on a species'
quantity is explained in detail in the SBML Level 3 specification
document. Because the value of the "conversionFactor" attribute is the
identifier of a Parameter object, and because parameters can have units
attached to them, the transformation from reaction extent units to
species units can be completely specified using this approach.
Note that the unit conversion factor is <strong>only applied when
calculating the effect of a reaction on a species</strong>. It is not
used in any rules or other SBML constructs that affect the species, and
it is also not used when the value of the species is referenced in a
mathematical expression.
@section species-l2-type The speciesType attribute in SBML Level 2 Versions 2–4
In SBML Level 2 Versions 2–4, each species in a model
may optionally be designated as belonging to a particular species type.
The optional attribute "speciesType" is used to identify the species
type of the chemical entities that make up the pool represented by the
Species objects. The attribute's value must be the identifier of an
existing SpeciesType object in the model. If the "speciesType"
attribute is not present on a particular species definition, it means
the pool contains chemical entities of a type unique to that pool; in
effect, a virtual species type is assumed for that species, and no other
species can belong to that species type. The value of "speciesType"
attributes on species have no effect on the numerical interpretation of
a model; simulators and other numerical analysis software may ignore
"speciesType" attributes.
There can be only one species of a given species type in any given
compartment of a model. More specifically, for all Species objects
having a value for the "speciesType" attribute, the pair
<center>
("speciesType" attribute value, "compartment" attribute value)
</center>
must be unique across the set of all Species object in a model.
@section species-other The spatialSizeUnits attribute in SBML Level 2 Versions 1–2
In versions of SBML Level 2 before Version 3, the class
Species included an attribute called "spatialSizeUnits", which allowed
explicitly setting the units of size for initial concentration. LibSBML
retains this attribute for compatibility with older definitions of
Level 2, but its use is strongly discouraged because many software
tools do no properly interpret this unit declaration and it is
incompatible with all SBML specifications after Level 2
Version 3.
@section species-math Additional considerations for interpreting the numerical value of a species
Species are unique in SBML in that they have a kind of duality: a
species identifier may stand for either substance amount (meaning, a
count of the number of individual entities) or a concentration or
density (meaning, amount divided by a compartment size). The previous
sections explain the meaning of a species identifier when it is
referenced in a mathematical formula or in rules or other SBML
constructs; however, it remains to specify what happens to a species
when the compartment in which it is located changes in size.
When a species definition has a "hasOnlySubstanceUnits" attribute value
of C<false> and the size of the compartment in which the species is
located changes, the default in SBML is to assume that it is the
concentration that must be updated to account for the size change. This
follows from the principle that, all other things held constant, if a
compartment simply changes in size, the size change does not in itself
cause an increase or decrease in the number of entities of any species
in that compartment. In a sense, the default is that the I<amount> of
a species is preserved across compartment size changes. Upon such size
changes, the value of the concentration or density must be recalculated
from the simple relationship <em>concentration = amount / size</em> if
the value of the concentration is needed (for example, if the species
identifier appears in a mathematical formula or is otherwise referenced
in an SBML construct). There is one exception: if the species' quantity
is determined by an AssignmentRule, RateRule, AlgebraicRule, or an
EventAssignment and the species has a "hasOnlySubstanceUnits" attribute
value of C<false>, it means that the <em>concentration</em> is assigned
by the rule or event; in that case, the <em>amount</em> must be
calculated when the compartment size changes. (Events also require
additional care in this situation, because an event with multiple
assignments could conceivably reassign both a species quantity and a
compartment size simultaneously. Please refer to the SBML
specifications for the details.)
Note that the above only matters if a species has a
"hasOnlySubstanceUnits" attribute value of C<false>, meaning that the
species identifier refers to a concentration wherever the identifier
appears in a mathematical formula. If instead the attribute's value is
C<true>, then the identifier of the species <em>always</em> stands for
an amount wherever it appears in a mathematical formula or is referenced
by an SBML construct. In that case, there is never a question about
whether an assignment or event is meant to affect the amount or
concentration: it is always the amount.
A particularly confusing situation can occur when the species has
"constant" attribute value of C<true> in combination with a
"hasOnlySubstanceUnits" attribute value of C<false>. Suppose this
species is given a value for "initialConcentration". Does a "constant"
value of C<true> mean that the concentration is held constant if the
compartment size changes? No; it is still the amount that is kept
constant across a compartment size change. The fact that the species
was initialized using a concentration value is irrelevant.
=over
=back
=head2 ListOfSpecies
@sbmlpackage{core}
@htmlinclude pkg-marker-core.html Implementation of SBML Level 2's ListOfSpecies
construct.
C<opydetails> doc_what_is_listof
=over
=item Species::Species
Creates a new Species using the given SBML C<level> and C<version>
values.
@param level an unsigned int, the SBML Level to assign to this Species
@param version an unsigned int, the SBML Version to assign to this
Species
@throws @if python ValueError @else SBMLConstructorException @endif@~
Thrown if the given C<level> and C<version> combination, or this kind
of SBML object, are either invalid or mismatched with respect to the
parent SBMLDocument object.
C<opydetails> doc_note_species_setting_lv
=item Species::Species
Creates a new Species using the given SBMLNamespaces object
C<sbmlns>.
C<opydetails> doc_what_are_sbmlnamespaces
It is worth emphasizing that although this constructor does not take
an identifier argument, in SBML Level 2 and beyond, the "id"
(identifier) attribute of a Species is required to have a value.
Thus, callers are cautioned to assign a value after calling this
constructor. Setting the identifier can be accomplished using the
method Species::setId(@if java String id@endif).
@param sbmlns an SBMLNamespaces object.
@throws @if python ValueError @else SBMLConstructorException @endif@~
Thrown if the given C<level> and C<version> combination, or this kind
of SBML object, are either invalid or mismatched with respect to the
parent SBMLDocument object.
C<opydetails> doc_note_species_setting_lv
=item Species::Species
Copy constructor; creates a copy of this Species object.
@param orig the object to copy.
@throws @if python ValueError @else SBMLConstructorException @endif@~
Thrown if the argument C<orig> is C<NULL>.
=item Species::accept
Accepts the given SBMLVisitor for this instance of Species.
@param v the SBMLVisitor instance to be used.
@return the result of calling C<v.visit()>.
=item Species::clone
Creates and returns a deep copy of this Species object.
@return a (deep) copy of this Species object.
=item Species::initDefaults
Initializes the fields of this Species object to "typical" defaults
values.
The SBML Species component has slightly different aspects and
default attribute values in different SBML Levels and Versions.
This method sets the values to certain common defaults, based
mostly on what they are in SBML Level 2. Specifically:
\n=over\n
\n=item\n\nSets "boundaryCondition" to C<false>
\n=item\n\nSets "constant" to C<false>
\n=item\n\nsets "hasOnlySubstanceUnits" to C<false>
\n=item\n\n(Applies to Level 3 models only) Sets attribute "substanceUnits" to C<mole>
\n=back\n
=item Species::getId
Returns the value of the "id" attribute of this Species object.
@return the id of this Species object.
=item Species::getName
Returns the value of the "name" attribute of this Species object.
@return the name of this Species object.
=item Species::getSpeciesType
Get the type of this Species object object.
@return the value of the "speciesType" attribute of this
Species as a string.
@note The "speciesType" attribute is only available in SBML
Level 2 Versions 2–4.
=item Species::getCompartment
Get the compartment in which this species is located.
The compartment is designated by its identifier.
@return the value of the "compartment" attribute of this Species
object, as a string.
=item Species::getInitialAmount
Get the value of the "initialAmount" attribute.
@return the initialAmount of this Species, as a float-point number.
=item Species::getInitialConcentration
Get the value of the "initialConcentration" attribute.
@return the initialConcentration of this Species,, as a float-point
number.
@note The attribute "initialConcentration" is only available in SBML
Level 2 and 3. It does not exist on Species in Level 1.
=item Species::getSubstanceUnits
Get the value of the "substanceUnits" attribute.
@return the value of the "substanceUnits" attribute of this Species,
as a string. An empty string indicates that no units have been
assigned.
C<opydetails> doc_note_unassigned_unit_are_not_a_default
@see isSetSubstanceUnits()
@see setSubstanceUnits(const std::string& sid)
=item Species::getSpatialSizeUnits
Get the value of the "spatialSizeUnits" attribute.
@return the value of the "spatialSizeUnits" attribute of this Species
object, as a string.
C<opydetails> doc_warning_species_spatialSizeUnits
=item Species::getUnits
Get the value of the "units" attribute.
@return the units of this Species (L1 only).
C<opydetails> doc_note_species_units
=item Species::getHasOnlySubstanceUnits
Get the value of the "hasOnlySubstanceUnits" attribute.
@return C<true> if this Species' "hasOnlySubstanceUnits" attribute
value is nonzero, C<false> otherwise.
@note The "hasOnlySubstanceUnits" attribute does not exist in SBML
Level 1.
=item Species::getBoundaryCondition
Get the value of the "boundaryCondition" attribute.
@return C<true> if this Species' "boundaryCondition" attribute value
is nonzero, C<false> otherwise.
=item Species::getCharge
Get the value of the "charge" attribute.
@return the charge of this Species object.
C<opydetails> doc_note_charge_deprecated
=item Species::getConstant
Get the value of the "constant" attribute.
@return C<true> if this Species's "constant" attribute value is
nonzero, C<false> otherwise.
@note The attribute "constant" is only available in SBML Levels 2
and 3. It does not exist on Species in Level 1.
=item Species::getConversionFactor
Get the value of the "conversionFactor" attribute.
@return the conversionFactor of this Species, as a string.
@note The "conversionFactor" attribute was introduced in SBML
Level 3. It does not exist on Species in SBML Levels 1
and 2.
=item Species::isSetId
Predicate returning C<true> if this
Species object's "id" attribute is set.
@return C<true> if the "id" attribute of this Species is
set, C<false> otherwise.
=item Species::isSetName
Predicate returning C<true> if this
Species object's "name" attribute is set.
@return C<true> if the "name" attribute of this Species is
set, C<false> otherwise.
=item Species::isSetSpeciesType
Predicate returning C<true> if this Species object's
"speciesType" attribute is set.
@return C<true> if the "speciesType" attribute of this Species is
set, C<false> otherwise.
@note The "speciesType" attribute is only available in SBML
Level 2 Versions 2–4.
=item Species::isSetCompartment
Predicate returning C<true> if this
Species object's "compartment" attribute is set.
@return C<true> if the "compartment" attribute of this Species is
set, C<false> otherwise.
=item Species::isSetInitialAmount
Predicate returning C<true> if this
Species object's "initialAmount" attribute is set.
@return C<true> if the "initialAmount" attribute of this Species is
set, C<false> otherwise.
@note In SBML Level 1, Species' "initialAmount" is required and
therefore <em>should always be set</em>. (However, in Level 1, the
attribute has no default value either, so this method will not return
C<true> until a value has been assigned.) In SBML Level 2,
"initialAmount" is optional and as such may or may not be set.
=item Species::isSetInitialConcentration
Predicate returning C<true> if this
Species object's "initialConcentration" attribute is set.
@return C<true> if the "initialConcentration" attribute of this Species is
set, C<false> otherwise.
@note The attribute "initialConcentration" is only available in SBML
Level 2 and 3. It does not exist on Species in Level 1.
=item Species::isSetSubstanceUnits
Predicate returning C<true> if this
Species object's "substanceUnits" attribute is set.
@return C<true> if the "substanceUnits" attribute of this Species is
set, C<false> otherwise.
=item Species::isSetSpatialSizeUnits
Predicate returning C<true> if this
Species object's "spatialSizeUnits" attribute is set.
@return C<true> if the "spatialSizeUnits" attribute of this Species is
set, C<false> otherwise.
C<opydetails> doc_warning_species_spatialSizeUnits
=item Species::isSetUnits
Predicate returning C<true> if
this Species object's "units" attribute is set.
@return C<true> if the "units" attribute of this Species is
set, C<false> otherwise.
=item Species::isSetCharge
Predicate returning C<true> if this
Species object's "charge" attribute is set.
@return C<true> if the "charge" attribute of this Species is
set, C<false> otherwise.
C<opydetails> doc_note_charge_deprecated
=item Species::isSetConversionFactor
Predicate returning C<true> if this
Species object's "conversionFactor" attribute is set.
@return C<true> if the "conversionFactor" attribute of this Species is
set, C<false> otherwise.
@note The "conversionFactor" attribute was introduced in SBML
Level 3. It does not exist on Species in SBML Levels 1
and 2.
=item Species::isSetBoundaryCondition
Predicate returning C<true> if this
Species object's "boundaryCondition" attribute is set.
@return C<true> if the "boundaryCondition" attribute of this Species is
set, C<false> otherwise.
=item Species::isSetHasOnlySubstanceUnits
Predicate returning C<true> if this
Species object's "hasOnlySubstanceUnits" attribute is set.
@return C<true> if the "hasOnlySubstanceUnits" attribute of this Species is
set, C<false> otherwise.
@note The "hasOnlySubstanceUnits" attribute does not exist in SBML
Level 1.
=item Species::isSetConstant
Predicate returning C<true> if this
Species object's "constant" attribute is set.
@return C<true> if the "constant" attribute of this Species is
set, C<false> otherwise.
@note The attribute "constant" is only available in SBML Levels 2
and 3. It does not exist on Species in Level 1.
=item Species::setId
Sets the value of the "id" attribute of this Species object.
The string C<sid> is copied.
C<opydetails> doc_id_syntax
@param sid the string to use as the identifier of this Species
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item Species::setName
Sets the value of the "name" attribute of this Species object.
The string in C<name> is copied.
@param name the new name for the Species
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item Species::setSpeciesType
Sets the "speciesType" attribute of this Species object.
@param sid the identifier of a SpeciesType object defined elsewhere
in this Model.
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
@li @link OperationReturnValues_t#LIBSBML_UNEXPECTED_ATTRIBUTE LIBSBML_UNEXPECTED_ATTRIBUTE @endlink
@note The "speciesType" attribute is only available in SBML
Level 2 Versions 2–4.
=item Species::setCompartment
Sets the "compartment" attribute of this Species object.
@param sid the identifier of a Compartment object defined elsewhere
in this Model.
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item Species::setInitialAmount
Sets the "initialAmount" attribute of this Species and marks the field
as set.
This method also unsets the "initialConcentration" attribute.
@param value the value to which the "initialAmount" attribute should
be set.
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
=item Species::setInitialConcentration
Sets the "initialConcentration" attribute of this Species and marks
the field as set.
This method also unsets the "initialAmount" attribute.
@param value the value to which the "initialConcentration" attribute
should be set.
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_UNEXPECTED_ATTRIBUTE LIBSBML_UNEXPECTED_ATTRIBUTE @endlink
@note The attribute "initialConcentration" is only available in SBML
Level 2 and 3. It does not exist on Species in Level 1.
=item Species::setSubstanceUnits
Sets the "substanceUnits" attribute of this Species object.
@param sid the identifier of the unit to use.
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item Species::setSpatialSizeUnits
(SBML Level 2 Versions 1–2) Sets the "spatialSizeUnits" attribute of this Species object.
@param sid the identifier of the unit to use.
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
@li @link OperationReturnValues_t#LIBSBML_UNEXPECTED_ATTRIBUTE LIBSBML_UNEXPECTED_ATTRIBUTE @endlink
C<opydetails> doc_warning_species_spatialSizeUnits
=item Species::setUnits
(SBML Level 1 only) Sets the units of this Species object.
@param sname the identifier of the unit to use.
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item Species::setHasOnlySubstanceUnits
Sets the "hasOnlySubstanceUnits" attribute of this Species object.
@param value boolean value for the "hasOnlySubstanceUnits" attribute.
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_UNEXPECTED_ATTRIBUTE LIBSBML_UNEXPECTED_ATTRIBUTE @endlink
@note The "hasOnlySubstanceUnits" attribute does not exist in SBML
Level 1.
=item Species::setBoundaryCondition
Sets the "boundaryCondition" attribute of this Species object.
@param value boolean value for the "boundaryCondition" attribute.
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
=item Species::setCharge
Sets the "charge" attribute of this Species object.
@param value an integer to which to set the "charge" to.
C<opydetails> doc_note_charge_deprecated
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_UNEXPECTED_ATTRIBUTE LIBSBML_UNEXPECTED_ATTRIBUTE @endlink
=item Species::setConstant
Sets the "constant" attribute of this Species object.
@param value a boolean value for the "constant" attribute
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_UNEXPECTED_ATTRIBUTE LIBSBML_UNEXPECTED_ATTRIBUTE @endlink
@note The attribute "constant" is only available in SBML Levels 2
and 3. It does not exist on Species in Level 1.
=item Species::setConversionFactor
Sets the value of the "conversionFactor" attribute of this Species object.
The string in C<sid> is copied.
@param sid the new conversionFactor for the Species
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_UNEXPECTED_ATTRIBUTE LIBSBML_UNEXPECTED_ATTRIBUTE @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
@note The "conversionFactor" attribute was introduced in SBML
Level 3. It does not exist on Species in SBML Levels 1
and 2.
=item Species::unsetName
Unsets the value of the "name" attribute of this Species object.
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item Species::unsetSpeciesType
Unsets the "speciesType" attribute value of this Species object.
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
@note The attribute "speciesType" is only available in SBML
Level 2 Versions 2–4.
=item Species::unsetInitialAmount
Unsets the "initialAmount" attribute value of this Species object.
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item Species::unsetInitialConcentration
Unsets the "initialConcentration" attribute value of this Species object.
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
@note The attribute "initialConcentration" is only available in SBML
Level 2 and 3. It does not exist on Species in Level 1.
=item Species::unsetSubstanceUnits
Unsets the "substanceUnits" attribute value of this Species object.
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item Species::unsetSpatialSizeUnits
Unsets the "spatialSizeUnits" attribute value of this Species object.
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
C<opydetails> doc_warning_species_spatialSizeUnits
=item Species::unsetUnits
Unsets the "units" attribute value of this Species object.
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item Species::unsetCharge
Unsets the "charge" attribute
value of this Species object.
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_UNEXPECTED_ATTRIBUTE LIBSBML_UNEXPECTED_ATTRIBUTE @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
C<opydetails> doc_note_charge_deprecated
=item Species::unsetConversionFactor
Unsets the "conversionFactor" attribute value of this Species object.
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_UNEXPECTED_ATTRIBUTE LIBSBML_UNEXPECTED_ATTRIBUTE @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
@note The "conversionFactor" attribute was introduced in SBML
Level 3. It does not exist on Species in SBML Levels 1
and 2.
=item Species::getDerivedUnitDefinition
Constructs and returns a UnitDefinition that corresponds to the units
of this Species' amount or concentration.
Species in SBML have an attribute ("substanceUnits") for declaring the
units of measurement intended for the species' amount or concentration
(depending on which one applies). In the absence of a value given for
"substanceUnits", the units are taken from the enclosing Model's
definition of C<"substance"> or C<"substance">/<em>(size of the
compartment)</em> in which the species is located, or finally, if
these are not redefined by the Model, the relevant SBML default units
for those quantities. Following that procedure, the method
@if java Species::getDerivedUnitDefinition()@else getDerivedUnitDefinition()@endif@~
returns a UnitDefinition based on the
interpreted units of this species's amount or concentration.
Note that the functionality that facilitates unit analysis depends
on the model as a whole. Thus, in cases where the object has not
been added to a model or the model itself is incomplete,
unit analysis is not possible and this method will return C<NULL>.
Note also that unit declarations for Species are in terms of the @em
identifier of a unit, but this method returns a UnitDefinition object,
not a unit identifier. It does this by constructing an appropriate
UnitDefinition. Callers may find this particularly useful when used
in conjunction with the helper methods on UnitDefinition for comparing
different UnitDefinition objects.
In SBML Level 2 specifications prior to Version 3, Species
includes an additional attribute named "spatialSizeUnits", which
allows explicitly setting the units of size for initial concentration.
The @if java Species::getDerivedUnitDefinition()@else getDerivedUnitDefinition()@endif@~
takes this into account for models
expressed in SBML Level 2 Versions 1 and 2.
@return a UnitDefinition that expresses the units of this
Species, or C<NULL> if one cannot be constructed.
@see getSubstanceUnits()
=item Species::getDerivedUnitDefinition
Constructs and returns a UnitDefinition that corresponds to the units
of this Species' amount or concentration.
Species in SBML have an attribute ("substanceUnits") for declaring the
units of measurement intended for the species' amount or concentration
(depending on which one applies). In the absence of a value given for
"substanceUnits", the units are taken from the enclosing Model's
definition of C<"substance"> or C<"substance">/<em>(size of the
compartment)</em> in which the species is located, or finally, if
these are not redefined by the Model, the relevant SBML default units
for those quantities. Following that procedure, the method
@if java Species::getDerivedUnitDefinition()@else getDerivedUnitDefinition()@endif@~
returns a UnitDefinition based on the
interpreted units of this species's amount or concentration.
Note that the functionality that facilitates unit analysis depends
on the model as a whole. Thus, in cases where the object has not
been added to a model or the model itself is incomplete,
unit analysis is not possible and this method will return C<NULL>.
Note also that unit declarations for Species are in terms of the @em
identifier of a unit, but this method returns a UnitDefinition object,
not a unit identifier. It does this by constructing an appropriate
UnitDefinition. Callers may find this particularly useful when used
in conjunction with the helper methods on UnitDefinition for comparing
different UnitDefinition objects.
In SBML Level 2 specifications prior to Version 3, Species
includes an additional attribute named "spatialSizeUnits", which
allows explicitly setting the units of size for initial concentration.
The @if java Species::getDerivedUnitDefinition()@else getDerivedUnitDefinition()@endif@~
takes this into account for models
expressed in SBML Level 2 Versions 1 and 2.
@return a UnitDefinition that expresses the units of this
Species, or C<NULL> if one cannot be constructed.
@see getSubstanceUnits()
=item Species::getTypeCode
Returns the libSBML type code for this SBML object.
C<opydetails> doc_what_are_typecodes
@return the SBML type code for this object:
@link SBMLTypeCode_t#SBML_SPECIES SBML_SPECIES@endlink (default).
C<opydetails> doc_warning_typecodes_not_unique
@see getElementName()
@see getPackageName()
=item Species::getElementName
Returns the XML element name of this object, which for Species, is
always C<"species">.
@return the name of this element, i.e., C<"species">.
=item Species::writeElements
@internal
Subclasses should override this method to write out their contained
SBML objects as XML elements. Be sure to call your parents
implementation of this method as well.
=item Species::hasRequiredAttributes
Predicate returning C<true> if
all the required attributes for this Species object
have been set.
@note The required attributes for a Species object are:
@li "id" (or "name" in SBML Level 1)
@li "compartment"
@li "initialAmount" (required in SBML Level 1 only; optional otherwise)
@li "hasOnlySubstanceUnits" (required in SBML Level 3; optional in SBML Level 2)
@li "boundaryCondition" (required in SBML Level 3; optional in Levels 1 and 2)
@li "constant" (required in SBML Level 3; optional in SBML Level 2)
@return a boolean value indicating whether all the required
attributes for this object have been defined.
=item Species::renameSIdRefs
Renames all the C<SIdRef> attributes on this element, including any
found in MathML.
C<opydetails> doc_what_is_sidref
This method works by looking at all attributes and (if appropriate)
mathematical formulas, comparing the identifiers to the value of @p
oldid. If any matches are found, the matching identifiers are replaced
with C<newid>. The method does I<not> descend into child elements.
@param oldid the old identifier
@param newid the new identifier
=item Species::renameUnitSIdRefs
Renames all the C<UnitSIdRef> attributes on this element.
C<opydetails> doc_what_is_unitsidref
This method works by looking at all unit identifier attribute values
(including, if appropriate, inside mathematical formulas), comparing the
unit identifiers to the value of C<oldid>. If any matches are found,
the matching identifiers are replaced with C<newid>. The method does
I<not> descend into child elements.
@param oldid the old identifier
@param newid the new identifier
=item Species::addExpectedAttributes
@internal
Subclasses should override this method to get the list of
expected attributes.
This function is invoked from corresponding readAttributes()
function.
=item Species::readAttributes
@internal
Subclasses should override this method to read values from the given
XMLAttributes set into their specific fields. Be sure to call your
parents implementation of this method as well.
=item Species::readL1Attributes
@internal
=item Species::readL2Attributes
@internal
=item Species::readL3Attributes
@internal
=item Species::writeAttributes
@internal
Subclasses should override this method to write their XML attributes
to the XMLOutputStream. Be sure to call your parents implementation
of this method as well.
=item Species::isExplicitlySetBoundaryCondition
@internal
=item Species::isExplicitlySetConstant
@internal
=item Species::isExplicitlySetHasOnlySubsUnits
@internal
=item ListOfSpecies::ListOfSpecies
Creates a new ListOfSpecies object.
The object is constructed such that it is valid for the given SBML
Level and Version combination.
@param level the SBML Level
@param version the Version within the SBML Level
=item ListOfSpecies::ListOfSpecies
Creates a new ListOfSpecies object.
The object is constructed such that it is valid for the SBML Level and
Version combination determined by the SBMLNamespaces object in @p
sbmlns.
@param sbmlns an SBMLNamespaces object that is used to determine the
characteristics of the ListOfSpecies object to be created.
=item ListOfSpecies::clone
Creates and returns a deep copy of this ListOfSpeciess instance.
@return a (deep) copy of this ListOfSpeciess.
=item ListOfSpecies::getItemTypeCode
Returns the libSBML type code for the objects contained in this ListOf
(i.e., Species objects, if the list is non-empty).
C<opydetails> doc_what_are_typecodes
@return the SBML type code for objects contained in this list:
@link SBMLTypeCode_t#SBML_SPECIES SBML_SPECIES@endlink (default).
@see getElementName()
@see getPackageName()
=item ListOfSpecies::getElementName
Returns the XML element name of this object.
For ListOfSpeciess, the XML element name is C<"listOfSpeciess">.
@return the name of this element, i.e., C<"listOfSpeciess">.
=item ListOfSpecies::get
Get a Species from the ListOfSpecies.
@param n the index number of the Species to get.
@return the nth Species in this ListOfSpecies.
@see size()
=item ListOfSpecies::get
Get a Species from the ListOfSpecies.
@param n the index number of the Species to get.
@return the nth Species in this ListOfSpecies.
@see size()
=item ListOfSpecies::get
Get a Species from the ListOfSpecies
based on its identifier.
@param sid a string representing the identifier
of the Species to get.
@return Species in this ListOfSpecies
with the given C<sid> or C<NULL> if no such
Species exists.
@see get(unsigned int n)
@see size()
=item ListOfSpecies::get
Get a Species from the ListOfSpecies
based on its identifier.
@param sid a string representing the identifier
of the Species to get.
@return Species in this ListOfSpecies
with the given C<sid> or C<NULL> if no such
Species exists.
@see get(unsigned int n)
@see size()
=item ListOfSpecies::remove
Removes the nth item from this ListOfSpeciess items and returns a pointer to
it.
The caller owns the returned item and is responsible for deleting it.
@param n the index of the item to remove
@see size()
=item ListOfSpecies::remove
Removes item in this ListOfSpeciess items with the given identifier.
The caller owns the returned item and is responsible for deleting it.
If none of the items in this list have the identifier C<sid>, then @c
NULL is returned.
@param sid the identifier of the item to remove
@return the item removed. As mentioned above, the caller owns the
returned item.
=item ListOfSpecies::getElementPosition
@internal
Get the ordinal position of this element in the containing object
(which in this case is the Model object).
The ordering of elements in the XML form of SBML is generally fixed
for most components in SBML. So, for example, the ListOfSpeciess in
a model is (in SBML Level 2 Version 4) the sixth
ListOf___. (However, it differs for different Levels and Versions of
SBML.)
@return the ordinal position of the element with respect to its
siblings, or C<-1> (default) to indicate the position is not significant.
=item ListOfSpecies::createObject
@internal
Create and return an SBML object of this class, if present.
@return the SBML object corresponding to next XMLToken in the
XMLInputStream or C<NULL> if the token was not recognized.
=back
=head2 Parameter
@sbmlpackage{core}
@htmlinclude pkg-marker-core.html Implementation of SBML's Parameter construct.
A Parameter is used in SBML to define a symbol associated with a value;
this symbol can then be used in mathematical formulas in a model. By
default, parameters have constant value for the duration of a
simulation, and for this reason are called I<parameters> instead of @em
variables in SBML, although it is crucial to understand that <em>SBML
parameters represent both concepts</em>. Whether a given SBML
parameter is intended to be constant or variable is indicated by the
value of its "constant" attribute.
SBML's Parameter has a required attribute, "id", that gives the
parameter a unique identifier by which other parts of an SBML model
definition can refer to it. A parameter can also have an optional
"name" attribute of type C<string>. Identifiers and names must be used
according to the guidelines described in the SBML specifications.
The optional attribute "value" determines the value (of type C<double>)
assigned to the parameter. A missing value for "value" implies that
the value either is unknown, or to be obtained from an external source,
or determined by an initial assignment. The unit of measurement
associated with the value of the parameter can be specified using the
optional attribute "units". Here we only mention briefly some notable
points about the possible unit choices, but readers are urged to consult
the SBML specification documents for more information:
\n=over\n
\n=item\n\nIn SBML Level 3, there are no constraints on the units that
can be assigned to parameters in a model; there are also no units to
inherit from the enclosing Model object (unlike the case for, e.g.,
Species and Compartment).
\n=item\n\nIn SBML Level 2, the value assigned to the parameter's "units"
attribute must be chosen from one of the following possibilities: one of
the base unit identifiers defined in SBML; one of the built-in unit
identifiers C<"substance">, C<"time">, C<"volume">, C<"area"> or @c
"length"; or the identifier of a new unit defined in the list of unit
definitions in the enclosing Model structure. There are no constraints
on the units that can be chosen from these sets. There are no default
units for parameters.
\n=back\n
The Parameter structure has another boolean attribute named "constant"
that is used to indicate whether the parameter's value can vary during a
simulation. (In SBML Level 3, the attribute is mandatory and must
be given a value; in SBML Levels below Level 3, the attribute is
optional.) A value of C<true> indicates the parameter's value cannot be
changed by any construct except InitialAssignment. Conversely, if the
value of "constant" is C<false>, other constructs in SBML, such as rules
and events, can change the value of the parameter.
SBML Level 3 uses a separate object class, LocalParameter, for
parameters that are local to a Reaction's KineticLaw. In Levels prior
to SBML Level 3, the Parameter class is used both for definitions
of global parameters, as well as reaction-local parameters stored in a
list within KineticLaw objects. Parameter objects that are local to a
reaction (that is, those defined within the KineticLaw structure of a
Reaction) cannot be changed by rules and therefore are <em>implicitly
always constant</em>; consequently, in SBML Level 2, parameter
definitions within Reaction structures should I<not> have their
"constant" attribute set to C<false>.
What if a global parameter has its "constant" attribute set to C<false>,
but the model does not contain any rules, events or other constructs
that ever change its value over time? Although the model may be
suspect, this situation is not strictly an error. A value of C<false>
for "constant" only indicates that a parameter I<can> change value, not
that it I<must>.
As with all other major SBML components, Parameter is derived from
SBase, and the methods defined on SBase are available on Parameter.
@note The use of the term I<parameter> in SBML sometimes leads to
confusion among readers who have a particular notion of what something
called "parameter" should be. It has been the source of heated debate,
but despite this, no one has yet found an adequate replacement term that
does not have different connotations to different people and hence leads
to confusion among I<some> subset of users. Perhaps it would have been
better to have two constructs, one called I<constants> and the other
called I<variables>. The current approach in SBML is simply more
parsimonious, using a single Parameter construct with the boolean flag
"constant" indicating which flavor it is. In any case, readers are
implored to look past their particular definition of a I<parameter> and
simply view SBML's Parameter as a single mechanism for defining both
constants and (additional) variables in a model. (We write @em
additional because the species in a model are usually considered to be
the central variables.) After all, software tools are not required to
expose to users the actual names of particular SBML constructs, and
thus tools can present to their users whatever terms their designers
feel best matches their target audience.
@see ListOfParameters
=over
=back
=head2 ListOfParameters
@sbmlpackage{core}
@htmlinclude pkg-marker-core.html Implementation of SBML's ListOfParameters construct.
C<opydetails> doc_what_is_listof
=over
=item Parameter::Parameter
Creates a new Parameter using the given SBML C<level> and C<version>
values.
@param level an unsigned int, the SBML Level to assign to this Parameter
@param version an unsigned int, the SBML Version to assign to this
Parameter
@throws @if python ValueError @else SBMLConstructorException @endif@~
Thrown if the given C<level> and C<version> combination, or this kind
of SBML object, are either invalid or mismatched with respect to the
parent SBMLDocument object.
C<opydetails> doc_note_parameter_setting_lv
=item Parameter::Parameter
Creates a new Parameter using the given SBMLNamespaces object
C<sbmlns>.
C<opydetails> doc_what_are_sbmlnamespaces
It is worth emphasizing that although this constructor does not take
an identifier argument, in SBML Level 2 and beyond, the "id"
(identifier) attribute of a Parameter is required to have a value.
Thus, callers are cautioned to assign a value after calling this
constructor if no identifier is provided as an argument. Setting the
identifier can be accomplished using the method
@if java setId(String id)@else setId()@endif.
@param sbmlns an SBMLNamespaces object.
@throws @if python ValueError @else SBMLConstructorException @endif@~
Thrown if the given C<level> and C<version> combination, or this kind
of SBML object, are either invalid or mismatched with respect to the
parent SBMLDocument object.
C<opydetails> doc_note_parameter_setting_lv
=item Parameter::Parameter
Copy constructor; creates a copy of a Parameter.
@param orig the Parameter instance to copy.
@throws @if python ValueError @else SBMLConstructorException @endif@~
Thrown if the argument C<orig> is C<NULL>.
=item Parameter::accept
Accepts the given SBMLVisitor for this instance of Parameter.
@param v the SBMLVisitor instance to be used.
@return the result of calling C<v.visit()>, indicating
whether the Visitor would like to visit the next Parameter object in
the list of parameters within which I<the> present object is
embedded.
=item Parameter::clone
Creates and returns a deep copy of this Parameter.
@return a (deep) copy of this Parameter.
=item Parameter::initDefaults
Initializes the fields of this Parameter object to "typical" defaults
values.
The SBML Parameter component has slightly different aspects and
default attribute values in different SBML Levels and Versions. Many
SBML object classes defined by libSBML have an initDefaults() method
to set the values to certain common defaults, based mostly on what
they are in SBML Level 2. In the case of Parameter, this method
only sets the value of the "constant" attribute to C<true>.
@see getConstant()
@see isSetConstant()
@see setConstant(@if java boolean flag@endif)
=item Parameter::getId
Returns the value of the "id" attribute of this Parameter.
@return the id of this Parameter.
=item Parameter::getName
Returns the value of the "name" attribute of this Parameter.
@return the name of this Parameter.
=item Parameter::getValue
Gets the numerical value of this Parameter.
@return the value of the "value" attribute of this Parameter, as a
number of type C<double>.
@note B<It is crucial> that callers not blindly call
Parameter::getValue() without first using Parameter::isSetValue() to
determine whether a value has ever been set. Otherwise, the value
return by Parameter::getValue() may not actually represent a value
assigned to the parameter. The reason is simply that the data type
C<double> in a program always has I<some> value. A separate test is
needed to determine whether the value is a true model value, or
uninitialized data in a computer's memory location.
@see isSetValue()
@see setValue(double value)
@see getUnits()
=item Parameter::getUnits
Gets the units defined for this Parameter.
The value of an SBML parameter's "units" attribute establishes the
unit of measurement associated with the parameter's value.
@return the value of the "units" attribute of this Parameter, as a
string. An empty string indicates that no units have been assigned.
C<opydetails> doc_note_unassigned_unit_are_not_a_default
@see isSetUnits()
@see setUnits(@if java String units@endif)
@see getValue()
=item Parameter::getConstant
Gets the value of the "constant" attribute of this Parameter instance.
@return C<true> if this Parameter is declared as being constant,
C<false> otherwise.
C<opydetails> doc_note_parameter_about_constant
@see isSetConstant()
@see setConstant(@if java boolean flag@endif)
=item Parameter::isSetId
Predicate returning C<true> if this
Parameter's "id" attribute is set.
@return C<true> if the "id" attribute of this Parameter is
set, C<false> otherwise.
=item Parameter::isSetName
Predicate returning C<true> if this
Parameter's "name" attribute is set.
@return C<true> if the "name" attribute of this Parameter is
set, C<false> otherwise.
=item Parameter::isSetValue
Predicate returning C<true> if the
"value" attribute of this Parameter is set.
In SBML definitions after SBML Level 1 Version 1,
parameter values are optional and have no defaults. If a model read
from a file does not contain a setting for the "value" attribute of a
parameter, its value is considered unset; it does not default to any
particular value. Similarly, when a Parameter object is created in
libSBML, it has no value until given a value. The
Parameter::isSetValue() method allows calling applications to
determine whether a given parameter's value has ever been set.
In SBML Level 1 Version 1, parameters are required to have
values and therefore, the value of a Parameter B<should always be
set>. In Level 1 Version 2 and beyond, the value is
optional and as such, the "value" attribute may or may not be set.
@return C<true> if the value of this Parameter is set,
C<false> otherwise.
@see getValue()
@see setValue(double value)
=item Parameter::isSetUnits
Predicate returning C<true> if the
"units" attribute of this Parameter is set.
@return C<true> if the "units" attribute of this Parameter is
set, C<false> otherwise.
C<opydetails> doc_note_unassigned_unit_are_not_a_default
=item Parameter::isSetConstant
Predicate returning C<true> if the
"constant" attribute of this Parameter is set.
@return C<true> if the "constant" attribute of this Parameter is
set, C<false> otherwise.
C<opydetails> doc_note_parameter_about_constant
@see getConstant()
@see setConstant(@if java boolean flag@endif)
=item Parameter::setId
Sets the value of the "id" attribute of this Parameter.
The string C<sid> is copied.
C<opydetails> doc_id_syntax
@param sid the string to use as the identifier of this Parameter
@return integer value indicating success/failure of the
function. The possible values returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item Parameter::setName
Sets the value of the "name" attribute of this Parameter.
The string in C<name> is copied.
@param name the new name for the Parameter
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item Parameter::setValue
Sets the "value" attribute of this Parameter to the given C<double>
value and marks the attribute as set.
@param value a C<double>, the value to assign
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
=item Parameter::setUnits
Sets the "units" attribute of this Parameter to a copy of the given
units identifier C<units>.
@param units a string, the identifier of the units to assign to this
Parameter instance
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item Parameter::setConstant
Sets the "constant" attribute of this Parameter to the given boolean
C<flag>.
@param flag a boolean, the value for the "constant" attribute of this
Parameter instance
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_UNEXPECTED_ATTRIBUTE LIBSBML_UNEXPECTED_ATTRIBUTE @endlink
C<opydetails> doc_note_parameter_about_constant
@see getConstant()
@see isSetConstant()
=item Parameter::unsetName
Unsets the value of the "name" attribute of this Parameter.
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item Parameter::unsetValue
Unsets the "value" attribute of this Parameter instance.
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
In SBML Level 1 Version 1, parameters are required to have
values and therefore, the value of a Parameter B<should always be
set>. In SBML Level 1 Version 2 and beyond, the value
is optional and as such, the "value" attribute may or may not be set.
=item Parameter::unsetUnits
Unsets the "units" attribute of this Parameter instance.
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item Parameter::getDerivedUnitDefinition
Constructs and returns a UnitDefinition that corresponds to the units
of this Parameter's value.
Parameters in SBML have an attribute ("units") for declaring the units
of measurement intended for the parameter's value. B<No defaults are
defined> by SBML in the absence of a definition for "units". This
method returns a UnitDefinition object based on the units declared for
this Parameter using its "units" attribute, or it returns C<NULL> if
no units have been declared.
Note that unit declarations for Parameter objects are specified in
terms of the I<identifier> of a unit (e.g., using setUnits()), but
I<this> method returns a UnitDefinition object, not a unit
identifier. It does this by constructing an appropriate
UnitDefinition.For SBML Level 2 models, it will do this even when
the value of the "units" attribute is one of the special SBML
Level 2 unit identifiers C<"substance">, C<"volume">, C<"area">,
C<"length"> or C<"time">. Callers may find this useful in conjunction
with the helper methods provided by the UnitDefinition class for
comparing different UnitDefinition objects.
@return a UnitDefinition that expresses the units of this
Parameter, or C<NULL> if one cannot be constructed.
@note The libSBML system for unit analysis depends on the model as a
whole. In cases where the Parameter object has not yet been added to
a model, or the model itself is incomplete, unit analysis is not
possible, and consequently this method will return C<NULL>.
@see isSetUnits()
=item Parameter::getDerivedUnitDefinition
Constructs and returns a UnitDefinition that corresponds to the units
of this Parameter's value.
Parameters in SBML have an attribute ("units") for declaring the units
of measurement intended for the parameter's value. B<No defaults are
defined> by SBML in the absence of a definition for "units". This
method returns a UnitDefinition object based on the units declared for
this Parameter using its "units" attribute, or it returns C<NULL> if
no units have been declared.
Note that unit declarations for Parameter objects are specified in
terms of the I<identifier> of a unit (e.g., using setUnits()), but
I<this> method returns a UnitDefinition object, not a unit
identifier. It does this by constructing an appropriate
UnitDefinition. For SBML Level 2 models, it will do this even
when the value of the "units" attribute is one of the predefined SBML
units C<"substance">, C<"volume">, C<"area">, C<"length"> or @c
"time". Callers may find this useful in conjunction with the helper
methods provided by the UnitDefinition class for comparing different
UnitDefinition objects.
@return a UnitDefinition that expresses the units of this
Parameter, or C<NULL> if one cannot be constructed.
@note The libSBML system for unit analysis depends on the model as a
whole. In cases where the Parameter object has not yet been added to
a model, or the model itself is incomplete, unit analysis is not
possible, and consequently this method will return C<NULL>.
@see isSetUnits()
=item Parameter::getTypeCode
Returns the libSBML type code for this SBML object.
C<opydetails> doc_what_are_typecodes
@return the SBML type code for this object:
@link SBMLTypeCode_t#SBML_PARAMETER SBML_PARAMETER@endlink (default).
C<opydetails> doc_warning_typecodes_not_unique
@see getElementName()
@see getPackageName()
=item Parameter::getElementName
Returns the XML element name of this object, which for Parameter, is
always C<"parameter">.
@return the name of this element, i.e., C<"parameter">.
=item Parameter::writeElements
@internal
Subclasses should override this method to write out their contained
SBML objects as XML elements. Be sure to call your parents
implementation of this method as well.
=item Parameter::hasRequiredAttributes
Predicate returning C<true> if
all the required attributes for this Parameter object
have been set.
@note The required attributes for a Parameter object are:
@li "id" (or "name" in SBML Level 1)
@li "value" (required in Level 1, optional otherwise)
@return a boolean value indicating whether all the required
attributes for this object have been defined.
=item Parameter::renameUnitSIdRefs
Renames all the C<UnitSIdRef> attributes on this element.
C<opydetails> doc_what_is_unitsidref
This method works by looking at all unit identifier attribute values
(including, if appropriate, inside mathematical formulas), comparing the
unit identifiers to the value of C<oldid>. If any matches are found,
the matching identifiers are replaced with C<newid>. The method does
I<not> descend into child elements.
@param oldid the old identifier
@param newid the new identifier
=item Parameter::setCalculatingUnits
@internal
=item Parameter::addExpectedAttributes
@internal
Subclasses should override this method to get the list of
expected attributes.
This function is invoked from corresponding readAttributes()
function.
=item Parameter::readAttributes
@internal
Subclasses should override this method to read values from the given
XMLAttributes set into their specific fields. Be sure to call your
parents implementation of this method as well.
=item Parameter::readL1Attributes
@internal
=item Parameter::readL2Attributes
@internal
=item Parameter::readL3Attributes
@internal
=item Parameter::writeAttributes
@internal
Subclasses should override this method to write their XML attributes
to the XMLOutputStream. Be sure to call your parents implementation
of this method as well.
=item Parameter::isExplicitlySetConstant
@internal
=item Parameter::inferUnits
@internal
=item Parameter::inferUnitsFromAssignments
@internal
=item Parameter::inferUnitsFromRules
@internal
=item Parameter::inferUnitsFromReactions
@internal
=item Parameter::inferUnitsFromEvents
@internal
=item Parameter::inferUnitsFromEvent
@internal
=item Parameter::inferUnitsFromKineticLaw
@internal
=item Parameter::getCalculatingUnits
@internal
=item ListOfParameters::ListOfParameters
Creates a new ListOfParameters object.
The object is constructed such that it is valid for the given SBML
Level and Version combination.
@param level the SBML Level
@param version the Version within the SBML Level
=item ListOfParameters::ListOfParameters
Creates a new ListOfParameters object.
The object is constructed such that it is valid for the SBML Level and
Version combination determined by the SBMLNamespaces object in @p
sbmlns.
@param sbmlns an SBMLNamespaces object that is used to determine the
characteristics of the ListOfParameters object to be created.
=item ListOfParameters::clone
Creates and returns a deep copy of this ListOfParameters instance.
@return a (deep) copy of this ListOfParameters.
=item ListOfParameters::getItemTypeCode
Returns the libSBML type code for the objects contained in this ListOf
(i.e., Parameter objects, if the list is non-empty).
C<opydetails> doc_what_are_typecodes
@return the SBML type code for this objects contained in this list:
@link SBMLTypeCode_t#SBML_PARAMETER SBML_PARAMETER@endlink (default).
@see getElementName()
@see getPackageName()
=item ListOfParameters::getElementName
Returns the XML element name of this object.
For ListOfParameters, the XML element name is C<"listOfParameters">.
@return the name of this element, i.e., C<"listOfParameters">.
=item ListOfParameters::get
Returns the Parameter object located at position C<n> within this
ListOfParameters instance.
@param n the index number of the Parameter to get.
@return the nth Parameter in this ListOfParameters. If the index C<n>
is out of bounds for the length of the list, then C<NULL> is returned.
@see size()
@see get(const std::string& sid)
=item ListOfParameters::get
Returns the Parameter object located at position C<n> within this
ListOfParameters instance.
@param n the index number of the Parameter to get.
@return the nth Parameter in this ListOfParameters. If the index C<n>
is out of bounds for the length of the list, then C<NULL> is returned.
@see size()
@see get(const std::string& sid)
=item ListOfParameters::get
Returns the first Parameter object matching the given identifier.
@param sid a string, the identifier of the Parameter to get.
@return the Parameter object found. The caller owns the returned
object and is responsible for deleting it. If none of the items have
an identifier matching C<sid>, then C<NULL> is returned.
@see get(unsigned int n)
@see size()
=item ListOfParameters::get
Returns the first Parameter object matching the given identifier.
@param sid a string representing the identifier of the Parameter to
get.
@return the Parameter object found. The caller owns the returned
object and is responsible for deleting it. If none of the items have
an identifier matching C<sid>, then C<NULL> is returned.
@see get(unsigned int n)
@see size()
=item ListOfParameters::remove
Removes the nth item from this ListOfParameters, and returns a pointer
to it.
@param n the index of the item to remove
@return the item removed. The caller owns the returned object and is
responsible for deleting it. If the index number C<n> is out of
bounds for the length of the list, then C<NULL> is returned.
@see size()
=item ListOfParameters::remove
Removes the first Parameter object in this ListOfParameters
matching the given identifier, and returns a pointer to it.
@param sid the identifier of the item to remove.
@return the item removed. The caller owns the returned object and is
responsible for deleting it. If none of the items have an identifier
matching C<sid>, then C<NULL> is returned.
=item ListOfParameters::getElementPosition
@internal
Gets the ordinal position of this element in the containing object
(which in this case is the Model object).
The ordering of elements in the XML form of SBML is generally fixed
for most components in SBML. So, for example, the ListOfParameters
in a model is (in SBML Level 2 Version 4) the seventh
ListOf___. (However, it differs for different Levels and Versions of
SBML.)
@return the ordinal position of the element with respect to its
siblings, or C<-1> (default) to indicate the position is not significant.
=item ListOfParameters::createObject
@internal
Create a ListOfParameters object corresponding to the next token in
the XML input stream.
@return the SBML object corresponding to next XMLToken in the
XMLInputStream, or C<NULL> if the token was not recognized.
=back
=head2 LocalParameter
@sbmlpackage{core}
@htmlinclude pkg-marker-core.html Implementation of SBML Level 3's LocalParameter
construct.
LocalParameter has been introduced in SBML Level 3 to serve as the
object class for parameter definitions that are intended to be local to
a Reaction. Objects of class LocalParameter never appear at the Model
level; they are always contained within ListOfLocalParameters lists
which are in turn contained within KineticLaw objects.
Like its global Parameter counterpart, the LocalParameter object class
is used to define a symbol associated with a value; this symbol can then
be used in a model's mathematical formulas (and specifically, for
LocalParameter, reaction rate formulas). Unlike Parameter, the
LocalParameter class does not have a "constant" attribute: local
parameters within reactions are I<always> constant.
LocalParameter has one required attribute, "id", to give the
parameter a unique identifier by which other parts of an SBML model
definition can refer to it. A parameter can also have an optional
"name" attribute of type C<string>. Identifiers and names must be used
according to the guidelines described in the SBML specifications.
The optional attribute "value" determines the value (of type C<double>)
assigned to the parameter. A missing value for "value" implies that
the value either is unknown, or to be obtained from an external source,
or determined by an initial assignment. The unit of measurement
associated with the value of the parameter can be specified using the
optional attribute "units". Here we only mention briefly some notable
points about the possible unit choices, but readers are urged to consult
the SBML specification documents for more information:
\n=over\n
\n=item\n\nIn SBML Level 3, there are no constraints on the units that
can be assigned to parameters in a model; there are also no units to
inherit from the enclosing Model object.
\n=item\n\nIn SBML Level 2, the value assigned to the parameter's "units"
attribute must be chosen from one of the following possibilities: one of
the base unit identifiers defined in SBML; one of the built-in unit
identifiers C<"substance">, C<"time">, C<"volume">, C<"area"> or @c
"length"; or the identifier of a new unit defined in the list of unit
definitions in the enclosing Model structure. There are no constraints
on the units that can be chosen from these sets. There are no default
units for local parameters.
\n=back\n
As with all other major SBML components, LocalParameter is derived from
SBase, and the methods defined on SBase are available on LocalParameter.
@warning <span class="warning">LibSBML derives LocalParameter from
Parameter; however, this does not precisely match the object hierarchy
defined by SBML Level 3, where LocalParameter is derived directly
from SBase and not Parameter. We believe this arrangement makes it easier
for libSBML users to program applications that work with both SBML
Level 2 and SBML Level 3, but programmers should also keep in
mind this difference exists. A side-effect of libSBML's scheme is that
certain methods on LocalParameter that are inherited from Parameter do not
actually have relevance to LocalParameter objects. An example of this is
the methods pertaining to Parameter's attribute "constant" (i.e.,
isSetConstant(), setConstant(), and getConstant()).</span>
@see ListOfLocalParameters
@see KineticLaw
=over
=back
=head2 ListOfLocalParameters
@sbmlpackage{core}
@htmlinclude pkg-marker-core.html Implementation of SBML Level 3's
ListOfLocalParameters construct.
C<opydetails> doc_what_is_listof
=over
=item LocalParameter::LocalParameter
Creates a new LocalParameter object with the given SBML C<level> and
C<version> values.
@param level an unsigned int, the SBML Level to assign to this
LocalParameter.
@param version an unsigned int, the SBML Version to assign to this
LocalParameter.
@throws @if python ValueError @else SBMLConstructorException @endif@~
Thrown if the given C<level> and C<version> combination, or this kind
of SBML object, are either invalid or mismatched with respect to the
parent SBMLDocument object.
C<opydetails> doc_note_localparameter_setting_lv
=item LocalParameter::LocalParameter
Creates a new LocalParameter object with the given SBMLNamespaces
object C<sbmlns>.
C<opydetails> doc_what_are_sbmlnamespaces
It is worth emphasizing that although this constructor does not take
an identifier argument, in SBML Level 2 and beyond, the "id"
(identifier) attribute of a LocalParameter is required to have a value.
Thus, callers are cautioned to assign a value after calling this
constructor if no identifier is provided as an argument. Setting the
identifier can be accomplished using the method
@if java setId(String id)@else setId()@endif.
@param sbmlns an SBMLNamespaces object.
@throws @if python ValueError @else SBMLConstructorException @endif@~
Thrown if the given C<level> and C<version> combination, or this kind
of SBML object, are either invalid or mismatched with respect to the
parent SBMLDocument object.
C<opydetails> doc_note_compartment_setting_lv
=item LocalParameter::LocalParameter
Copy constructor; creates a copy of a given LocalParameter object.
@param orig the LocalParameter instance to copy.
@throws @if python ValueError @else SBMLConstructorException @endif@~
Thrown if the argument C<orig> is C<NULL>.
=item LocalParameter::LocalParameter
Copy constructor; creates a LocalParameter object by copying
the attributes of a given Parameter object.
@param orig the Parameter instance to copy.
@throws @if python ValueError @else SBMLConstructorException @endif@~
Thrown if the argument C<orig> is C<NULL>.
=item LocalParameter::accept
Accepts the given SBMLVisitor for this instance of LocalParameter.
@param v the SBMLVisitor instance to be used.
@return the result of calling C<v.visit()>, which indicates
whether the Visitor would like to visit the next LocalParameter in the list
of parameters within which this LocalParameter is embedded (i.e., either
the list of parameters in the parent Model or the list of parameters
in the enclosing KineticLaw).
=item LocalParameter::clone
Creates and returns a deep copy of this LocalParameter.
@return a (deep) copy of this LocalParameter.
=item LocalParameter::getDerivedUnitDefinition
Constructs and returns a UnitDefinition that corresponds to the units
of this LocalParameter's value.
C<opydetails> doc_localparameter_units
@return a UnitDefinition that expresses the units of this
LocalParameter, or C<NULL> if one cannot be constructed.
@note The libSBML system for unit analysis depends on the model as a
whole. In cases where the LocalParameter object has not yet been
added to a model, or the model itself is incomplete, unit analysis is
not possible, and consequently this method will return C<NULL>.
@see isSetUnits()
=item LocalParameter::getDerivedUnitDefinition
Constructs and returns a UnitDefinition that corresponds to the units
of this LocalParameter's value.
C<opydetails> doc_localparameter_units
@return a UnitDefinition that expresses the units of this
LocalParameter, or C<NULL> if one cannot be constructed.
@note The libSBML system for unit analysis depends on the model as a
whole. In cases where the LocalParameter object has not yet been
added to a model, or the model itself is incomplete, unit analysis is
not possible, and consequently this method will return C<NULL>.
@see isSetUnits()
=item LocalParameter::getTypeCode
Returns the libSBML type code for this SBML object.
C<opydetails> doc_what_are_typecodes
@return the SBML type code for this object:
@link SBMLTypeCode_t#SBML_LOCAL_PARAMETER SBML_LOCAL_PARAMETER@endlink (default).
C<opydetails> doc_warning_typecodes_not_unique
@see getElementName()
@see getPackageName()
=item LocalParameter::getElementName
Returns the XML element name of this object, which for LocalParameter,
is always C<"localParameter">.
@return the name of this element, i.e., C<"localParameter">.
=item LocalParameter::hasRequiredAttributes
Predicate returning C<true> if all the required attributes for this
LocalParameter object have been set.
@note The required attributes for a LocalParameter object are:
@li "id"
@li "value"
@return a boolean value indicating whether all the required
attributes for this object have been defined.
=item LocalParameter::getConstant
@internal
=item LocalParameter::isSetConstant
@internal
=item LocalParameter::setConstant
@internal
=item LocalParameter::addExpectedAttributes
@internal
Subclasses should override this method to get the list of
expected attributes.
This function is invoked from corresponding readAttributes()
function.
=item LocalParameter::readAttributes
@internal
Subclasses should override this method to read values from the given
XMLAttributes set into their specific fields. Be sure to call your
parents implementation of this method as well.
=item LocalParameter::readL3Attributes
@internal
=item LocalParameter::writeAttributes
@internal
Subclasses should override this method to write their XML attributes
to the XMLOutputStream. Be sure to call your parents implementation
of this method as well.
=item ListOfLocalParameters::ListOfLocalParameters
Creates a new ListOfLocalParameters object.
The object is constructed such that it is valid for the given SBML
Level and Version combination.
@param level the SBML Level
@param version the Version within the SBML Level
=item ListOfLocalParameters::ListOfLocalParameters
Creates a new ListOfLocalParameters object.
The object is constructed such that it is valid for the SBML Level and
Version combination determined by the SBMLNamespaces object in @p
sbmlns.
@param sbmlns an SBMLNamespaces object that is used to determine the
characteristics of the ListOfLocalParameters object to be created.
=item ListOfLocalParameters::clone
Creates and returns a deep copy of this ListOfLocalParameters object.
@return a (deep) copy of this ListOfLocalParameters.
=item ListOfLocalParameters::getItemTypeCode
Returns the libSBML type code for the objects contained in this ListOf
(i.e., LocalParameter objects, if the list is non-empty).
C<opydetails> doc_what_are_typecodes
@return the SBML type code for the objects contained in this ListOf:
@link SBMLTypeCode_t#SBML_LOCAL_PARAMETER SBML_LOCAL_PARAMETER@endlink (default).
@see getElementName()
@see getPackageName()
=item ListOfLocalParameters::getElementName
Returns the XML element name of this object.
For ListOfLocalParameters, the XML element name is C<"listOfLocalParameters">.
@return the name of this element, i.e., C<"listOfLocalParameters">.
=item ListOfLocalParameters::get
Returns the LocalParameter object located at position C<n> within this
ListOfLocalParameters instance.
@param n the index number of the LocalParameter to get.
@return the nth LocalParameter in this ListOfLocalParameters. If the
index C<n> is out of bounds for the length of the list, then C<NULL>
is returned.
@see size()
@see get(const std::string& sid)
=item ListOfLocalParameters::get
Returns the LocalParameter object located at position C<n> within this
ListOfLocalParameters instance.
@param n the index number of the LocalParameter to get.
@return the item at position C<n>. The caller owns the returned
object and is responsible for deleting it. If the index number C<n>
is out of bounds for the length of the list, then C<NULL> is returned.
@see size()
@see get(const std::string& sid)
=item ListOfLocalParameters::get
Returns the first LocalParameter object matching the given identifier.
@param sid a string, the identifier of the LocalParameter to get.
@return the LocalParameter object found. The caller owns the returned
object and is responsible for deleting it. If none of the items have
an identifier matching C<sid>, then C<NULL> is returned.
@see get(unsigned int n)
@see size()
=item ListOfLocalParameters::get
Returns the first LocalParameter object matching the given identifier.
@param sid a string representing the identifier of the LocalParameter
to get.
@return the LocalParameter object found. The caller owns the returned
object and is responsible for deleting it. If none of the items have
an identifier matching C<sid>, then C<NULL> is returned.
@see get(unsigned int n)
@see size()
=item ListOfLocalParameters::getElementBySId
Returns the first child element found that has the given C<id> in the
model-wide SId namespace, or C<NULL> if no such object is found.
Note that LocalParameters, while they use the SId namespace, are not in
the model-wide SId namespace, so no LocalParameter object will be
returned from this function (and is the reason we override the base
ListOf::getElementBySId function here).
@param id string representing the id of objects to find
@return pointer to the first element found with the given C<id>.
=item ListOfLocalParameters::remove
Removes the nth item from this ListOfLocalParameters, and returns a
pointer to it.
@param n the index of the item to remove.
@return the item removed. The caller owns the returned object and is
responsible for deleting it. If the index number C<n> is out of
bounds for the length of the list, then C<NULL> is returned.
@see size()
@see remove(const std::string& sid)
=item ListOfLocalParameters::remove
Removes the first LocalParameter object in this ListOfLocalParameters
matching the given identifier, and returns a pointer to it.
@param sid the identifier of the item to remove.
@return the item removed. The caller owns the returned object and is
responsible for deleting it. If none of the items have an identifier
matching C<sid>, then C<NULL> is returned.
=item ListOfLocalParameters::getElementPosition
@internal
Get the ordinal position of this element in the containing object
(which in this case is the Model object).
The ordering of elements in the XML form of SBML is generally fixed
for most components in SBML. So, for example, the ListOfLocalParameters
in a model is (in SBML Level 2 Version 4) the seventh
ListOf___. (However, it differs for different Levels and Versions of
SBML.)
@return the ordinal position of the element with respect to its
siblings, or C<-1> (default) to indicate the position is not significant.
=item ListOfLocalParameters::createObject
@internal
Create a ListOfLocalParameters object corresponding to the next token in
the XML input stream.
@return the SBML object corresponding to next XMLToken in the
XMLInputStream, or C<NULL> if the token was not recognized.
=back
=head2 InitialAssignment
@sbmlpackage{core}
@htmlinclude pkg-marker-core.html Implementation of SBML's InitialAssignment construct.
SBML Level 2 Versions 2–4 and SBML Level 3 provide two ways of assigning initial
values to entities in a model. The simplest and most basic is to set
the values of the appropriate attributes in the relevant components; for
example, the initial value of a model parameter (whether it is a
constant or a variable) can be assigned by setting its "value" attribute
directly in the model definition. However, this approach is not
suitable when the value must be calculated, because the initial value
attributes on different components such as species, compartments, and
parameters are single values and not mathematical expressions. In those
situations, the InitialAssignment construct can be used; it permits the
calculation of the value of a constant or the initial value of a
variable from the values of I<other> quantities in a model.
As explained below, the provision of InitialAssignment does not mean
that models necessarily must use this construct when defining initial
values of quantities in a model. If a value can be set directly using
the relevant attribute of a component in a model, then that
approach may be more efficient and more portable to other software
tools. InitialAssignment should be used when the other mechanism is
insufficient for the needs of a particular model.
The InitialAssignment construct has some similarities to AssignmentRule.
The main differences are: (a) an InitialAssignment can set the value of
a constant whereas an AssignmentRule cannot, and (b) unlike
AssignmentRule, an InitialAssignment definition only applies up to and
including the beginning of simulation time, i.e., <em>t \f$\leq\f$ 0</em>,
while an AssignmentRule applies at all times.
InitialAssignment has a required attribute, "symbol", whose value must
follow the guidelines for identifiers described in the SBML
specification (e.g., Section 3.3 in the Level 2 Version 4
specification). The value of this attribute in an InitialAssignment
object can be the identifier of a Compartment, Species or global
Parameter elsewhere in the model. The InitialAssignment defines the
initial value of the constant or variable referred to by the "symbol"
attribute. (The attribute's name is "symbol" rather than "variable"
because it may assign values to constants as well as variables in a
model.) Note that an initial assignment cannot be made to reaction
identifiers, that is, the "symbol" attribute value of an
InitialAssignment cannot be an identifier that is the "id" attribute
value of a Reaction object in the model. This is identical to a
restriction placed on rules.
InitialAssignment also has a required "math" subelement that contains a
MathML expression used to calculate the value of the constant or the
initial value of the variable. The units of the value computed by the
formula in the "math" subelement should (in SBML Level 2
Version 4 and in SBML Level 3) or must (in previous Versions) be identical to be the
units associated with the identifier given in the "symbol" attribute.
(That is, the units are the units of the species, compartment, or
parameter, as appropriate for the kind of object identified by the value
of "symbol".)
InitialAssignment was introduced in SBML Level 2 Version 2. It is not
available in SBML Level 2 Version 1 nor in any version of Level 1.
@section initassign-semantics Semantics of Initial Assignments
The value calculated by an InitialAssignment object overrides the value
assigned to the given symbol by the object defining that symbol. For
example, if a compartment's "size" attribute is set in its definition,
and the model also contains an InitialAssignment having that
compartment's identifier as its "symbol" attribute value, then the
interpretation is that the "size" assigned in the Compartment object
should be ignored and the value assigned based on the computation
defined in the InitialAssignment. Initial assignments can take place
for Compartment, Species and global Parameter objects regardless of the
value of their "constant" attribute.
The actions of all InitialAssignment objects are in general terms
the same, but differ in the precise details depending on the type
of variable being set:
\n=over\n
\n=item\n\n<em>In the case of a species</em>, an InitialAssignment sets the
referenced species' initial quantity (concentration or amount of
substance) to the value determined by the formula in the "math"
subelement. The overall units of the formula should (in SBML
Level 2 Version 4 and in SBML Level 3) or must (in previous Versions) be the same
as the units specified for the species.
\n=item\n\n<em>In the case of a compartment</em>, an InitialAssignment sets
the referenced compartment's initial size to the size determined by the
formula in "math". The overall units of the formula should (in SBML
Level 2 Version 4 and in SBML Level 3) or must (in previous Versions) be the same
as the units specified for the size of the compartment.
\n=item\n\n<em>In the case of a parameter</em>, an InitialAssignment sets the
referenced parameter's initial value to that determined by the formula
in "math". The overall units of the formula should (in SBML
Level 2 Version 4 and SBML Level 3) or must (in previous Versions) be the same
as the units defined for the parameter. \n=back\n
In the context of a simulation, initial assignments establish values
that are in effect prior to and including the start of simulation time,
i.e., <em>t \f$\leq\f$ 0</em>. Section 3.4.8 in the SBML Level 2
Version 4 and SBML Level 3 Version 1 Core specifications provides information about the interpretation of
assignments, rules, and entity values for simulation time up to and
including the start time <em>t = 0</em>; this is important for
establishing the initial conditions of a simulation if the model
involves expressions containing the <em>delay</em> "csymbol".
There cannot be two initial assignments for the same symbol in a model;
that is, a model must not contain two or more InitialAssignment objects
that both have the same identifier as their "symbol" attribute value. A
model must also not define initial assignments <em>and</em> assignment
rules for the same entity. That is, there cannot be <em>both</em> an
InitialAssignment and an AssignmentRule for the same symbol in a model,
because both kinds of constructs apply prior to and at the start of
simulated time—allowing both to exist for a given symbol would
result in indeterminism).
The ordering of InitialAssignment objects is not significant. The
combined set of InitialAssignment, AssignmentRule and KineticLaw
objects form a set of assignment statements that must be considered as a
whole. The combined set of assignment statements should not contain
algebraic loops: a chain of dependency between these statements should
terminate. (More formally, consider the directed graph of assignment
statements where nodes are a model's assignment statements and directed
arcs exist for each occurrence of a symbol in an assignment statement
"math" attribute. The directed arcs in this graph start from the
statement assigning the symbol and end at the statement that contains
the symbol in their math elements. Such a graph must be acyclic.)
Finally, it is worth being explicit about the expected behavior in the
following situation. Suppose (1) a given symbol has a value <em>x</em>
assigned to it in its definition, and (2) there is an initial assignment
having the identifier as its "symbol" value and reassigning the value to
<em>y</em>, <em>and</em> (3) the identifier is also used in the
mathematical formula of a second initial assignment. What value should
the second initial assignment use? It is <em>y</em>, the value assigned
to the symbol by the first initial assignment, not whatever value was
given in the symbol's definition. This follows directly from the
behavior described above: if an InitialAssignment object exists for a
given symbol, then the symbol's value is overridden by that initial
assignment.
=over
=back
=head2 ListOfInitialAssignments
@sbmlpackage{core}
@htmlinclude pkg-marker-core.html Implementation of SBML's ListOfInitialAssignments
construct.
C<opydetails> doc_what_is_listof
=over
=item InitialAssignment::InitialAssignment
Creates a new InitialAssignment using the given SBML C<level> and C<version>
values.
@param level an unsigned int, the SBML Level to assign to this InitialAssignment
@param version an unsigned int, the SBML Version to assign to this
InitialAssignment
@throws @if python ValueError @else SBMLConstructorException @endif@~
Thrown if the given C<level> and C<version> combination, or this kind
of SBML object, are either invalid or mismatched with respect to the
parent SBMLDocument object.
C<opydetails> doc_note_initialassignment_setting_lv
=item InitialAssignment::InitialAssignment
Creates a new InitialAssignment using the given SBMLNamespaces object
C<sbmlns>.
C<opydetails> doc_what_are_sbmlnamespaces
@param sbmlns an SBMLNamespaces object.
@throws @if python ValueError @else SBMLConstructorException @endif@~
Thrown if the given C<level> and C<version> combination, or this kind
of SBML object, are either invalid or mismatched with respect to the
parent SBMLDocument object.
C<opydetails> doc_note_initialassignment_setting_lv
=item InitialAssignment::InitialAssignment
Copy constructor; creates a copy of this InitialAssignment.
@param orig the object to copy.
@throws @if python ValueError @else SBMLConstructorException @endif@~
Thrown if the argument C<orig> is C<NULL>.
=item InitialAssignment::accept
Accepts the given SBMLVisitor for this instance of InitialAssignment.
@param v the SBMLVisitor instance to be used.
@return the result of calling C<v.visit()>, which indicates
whether the Visitor would like to visit the next InitialAssignment in
the list of compartment types.
=item InitialAssignment::clone
Creates and returns a deep copy of this InitialAssignment.
@return a (deep) copy of this InitialAssignment.
=item InitialAssignment::getSymbol
Get the value of the "symbol" attribute of this InitialAssignment.
@return the identifier string stored as the "symbol" attribute value
in this InitialAssignment.
=item InitialAssignment::getMath
Get the mathematical formula of this InitialAssignment.
@return an ASTNode, the value of the "math" subelement of this
InitialAssignment
=item InitialAssignment::isSetSymbol
Predicate returning C<true> if this
InitialAssignment's "symbol" attribute is set.
@return C<true> if the "symbol" attribute of this InitialAssignment
is set, C<false> otherwise.
=item InitialAssignment::isSetMath
Predicate returning C<true> if this
InitialAssignment's "math" subelement contains a value.
@return C<true> if the "math" for this InitialAssignment is set,
C<false> otherwise.
=item InitialAssignment::setSymbol
Sets the "symbol" attribute value of this InitialAssignment.
@param sid the identifier of a Species, Compartment or Parameter
object defined elsewhere in this Model.
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item InitialAssignment::setMath
Sets the "math" subelement of this InitialAssignment.
The AST passed in C<math> is copied.
@param math an AST containing the mathematical expression to
be used as the formula for this InitialAssignment.
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT @endlink
=item InitialAssignment::getDerivedUnitDefinition
Calculates and returns a UnitDefinition that expresses the units
of measurement assumed for the "math" expression of this
InitialAssignment.
C<opydetails> doc_initialassignment_units
C<opydetails> doc_note_unit_inference_depends_on_model
C<opydetails> doc_warning_initialassignment_math_literals
@return a UnitDefinition that expresses the units of the math
expression of this InitialAssignment, or C<NULL> if one cannot be constructed.
@see containsUndeclaredUnits()
=item InitialAssignment::getDerivedUnitDefinition
Calculates and returns a UnitDefinition that expresses the units
of measurement assumed for the "math" expression of this
InitialAssignment.
C<opydetails> doc_initialassignment_units
C<opydetails> doc_note_unit_inference_depends_on_model
C<opydetails> doc_warning_initialassignment_math_literals
@return a UnitDefinition that expresses the units of the math
expression of this InitialAssignment, or C<NULL> if one cannot be constructed.
@see containsUndeclaredUnits()
=item InitialAssignment::containsUndeclaredUnits
Predicate returning C<true> if the math expression of this
InitialAssignment contains parameters/numbers with undeclared units.
@return C<true> if the math expression of this InitialAssignment
includes parameters/numbers
with undeclared units, C<false> otherwise.
@note A return value of C<true> indicates that the UnitDefinition
returned by InitialAssignment::getDerivedUnitDefinition may not
accurately represent the units of the expression.
@see getDerivedUnitDefinition()
=item InitialAssignment::containsUndeclaredUnits
Predicate returning C<true> if the math expression of this
InitialAssignment contains parameters/numbers with undeclared units.
@return C<true> if the math expression of this InitialAssignment
includes parameters/numbers
with undeclared units, C<false> otherwise.
@note A return value of C<true> indicates that the UnitDefinition
returned by InitialAssignment::getDerivedUnitDefinition may not
accurately represent the units of the expression.
@see getDerivedUnitDefinition()
=item InitialAssignment::getTypeCode
Returns the libSBML type code for this SBML object.
C<opydetails> doc_what_are_typecodes
@return the SBML type code for this object:
@link SBMLTypeCode_t#SBML_INITIAL_ASSIGNMENT SBML_INITIAL_ASSIGNMENT@endlink (default).
C<opydetails> doc_warning_typecodes_not_unique
@see getElementName()
@see getPackageName()
=item InitialAssignment::getElementName
Returns the XML element name of this object, which for
InitialAssignment, is always C<"initialAssignment">.
@return the name of this element, i.e., C<"initialAssignment">.
=item InitialAssignment::writeElements
@internal
Subclasses should override this method to write out their contained
SBML objects as XML elements. Be sure to call your parents
implementation of this method as well.
=item InitialAssignment::hasRequiredAttributes
Predicate returning C<true> if all the required attributes for this
InitialAssignment object have been set.
@note The required attributes for an InitialAssignment object are:
@li "symbol"
@return a boolean value indicating whether all the required
attributes for this object have been defined.
=item InitialAssignment::hasRequiredElements
Predicate returning C<true> if all the required elements for this
InitialAssignment object have been set.
@note The required elements for a InitialAssignment object are:
@li "math"
@return a boolean value indicating whether all the required
elements for this object have been defined.
=item InitialAssignment::getId
@internal
=item InitialAssignment::renameSIdRefs
Renames all the C<SIdRef> attributes on this element, including any
found in MathML.
C<opydetails> doc_what_is_sidref
This method works by looking at all attributes and (if appropriate)
mathematical formulas, comparing the identifiers to the value of @p
oldid. If any matches are found, the matching identifiers are replaced
with C<newid>. The method does I<not> descend into child elements.
@param oldid the old identifier
@param newid the new identifier
=item InitialAssignment::renameUnitSIdRefs
Renames all the C<UnitSIdRef> attributes on this element.
C<opydetails> doc_what_is_unitsidref
This method works by looking at all unit identifier attribute values
(including, if appropriate, inside mathematical formulas), comparing the
unit identifiers to the value of C<oldid>. If any matches are found,
the matching identifiers are replaced with C<newid>. The method does
I<not> descend into child elements.
@param oldid the old identifier
@param newid the new identifier
=item InitialAssignment::replaceSIDWithFunction
@internal
Replace all nodes with the name 'id' from the child 'math' object with the provided function.
=item InitialAssignment::divideAssignmentsToSIdByFunction
@internal
If this assignment assigns a value to the 'id' element, replace the 'math' object with the function (existing/function).
=item InitialAssignment::multiplyAssignmentsToSIdByFunction
@internal
If this assignment assigns a value to the 'id' element, replace the 'math' object with the function (existing function).
=item InitialAssignment::readOtherXML
@internal
Subclasses should override this method to read (and store) XHTML,
MathML, etc. directly from the XMLInputStream.
@return true if the subclass read from the stream, false otherwise.
=item InitialAssignment::addExpectedAttributes
@internal
Subclasses should override this method to get the list of
expected attributes.
This function is invoked from corresponding readAttributes()
function.
=item InitialAssignment::readAttributes
@internal
Subclasses should override this method to read values from the given
XMLAttributes set into their specific fields. Be sure to call your
parents implementation of this method as well.
=item InitialAssignment::readL2Attributes
@internal
=item InitialAssignment::readL3Attributes
@internal
=item InitialAssignment::writeAttributes
@internal
Subclasses should override this method to write their XML attributes
to the XMLOutputStream. Be sure to call your parents implementation
of this method as well.
=item ListOfInitialAssignments::ListOfInitialAssignments
Creates a new ListOfInitialAssignments object.
The object is constructed such that it is valid for the given SBML
Level and Version combination.
@param level the SBML Level
@param version the Version within the SBML Level
=item ListOfInitialAssignments::ListOfInitialAssignments
Creates a new ListOfInitialAssignments object.
The object is constructed such that it is valid for the SBML Level and
Version combination determined by the SBMLNamespaces object in @p
sbmlns.
@param sbmlns an SBMLNamespaces object that is used to determine the
characteristics of the ListOfInitialAssignments object to be created.
=item ListOfInitialAssignments::clone
Creates and returns a deep copy of this ListOfInitialAssignments instance.
@return a (deep) copy of this ListOfInitialAssignments.
=item ListOfInitialAssignments::getItemTypeCode
Returns the libSBML type code for the objects contained in this ListOf
(i.e., InitialAssignment objects, if the list is non-empty).
C<opydetails> doc_what_are_typecodes
@return the SBML type code for the objects contained in this ListOf:
@link SBMLTypeCode_t#SBML_INITIAL_ASSIGNMENT SBML_INITIAL_ASSIGNMENT@endlink (default).
@see getElementName()
@see getPackageName()
=item ListOfInitialAssignments::getElementName
Returns the XML element name of this object.
For ListOfInitialAssignments, the XML element name is @c
"listOfInitialAssignments".
@return the name of this element, i.e., C<"listOfInitialAssignments">.
=item ListOfInitialAssignments::get
Get a InitialAssignment from the ListOfInitialAssignments.
@param n the index number of the InitialAssignment to get.
@return the nth InitialAssignment in this ListOfInitialAssignments.
@see size()
=item ListOfInitialAssignments::get
Get a InitialAssignment from the ListOfInitialAssignments.
@param n the index number of the InitialAssignment to get.
@return the nth InitialAssignment in this ListOfInitialAssignments.
@see size()
=item ListOfInitialAssignments::get
Get a InitialAssignment from the ListOfInitialAssignments
based on its identifier.
@param sid a string representing the identifier
of the InitialAssignment to get.
@return InitialAssignment in this ListOfInitialAssignments
with the given C<sid> or C<NULL> if no such
InitialAssignment exists.
@see get(unsigned int n)
@see size()
=item ListOfInitialAssignments::get
Get a InitialAssignment from the ListOfInitialAssignments
based on its identifier.
@param sid a string representing the identifier
of the InitialAssignment to get.
@return InitialAssignment in this ListOfInitialAssignments
with the given C<sid> or C<NULL> if no such
InitialAssignment exists.
@see get(unsigned int n)
@see size()
=item ListOfInitialAssignments::remove
Removes the nth item from this ListOfInitialAssignments items and returns a pointer to
it.
The caller owns the returned item and is responsible for deleting it.
@param n the index of the item to remove
@see size()
=item ListOfInitialAssignments::remove
Removes item in this ListOfInitialAssignments items with the given identifier.
The caller owns the returned item and is responsible for deleting it.
If none of the items in this list have the identifier C<sid>, then @c
NULL is returned.
@param sid the identifier of the item to remove
@return the item removed. As mentioned above, the caller owns the
returned item.
=item ListOfInitialAssignments::getElementBySId
Returns the first child element found that has the given C<id> in the
model-wide SId namespace, or C<NULL> if no such object is found.
Note that InitialAssignments do not actually have IDs, though the
libsbml interface pretends that they do: no initial assignment is
returned by this function.
@param id string representing the id of objects to find
@return pointer to the first element found with the given C<id>.
=item ListOfInitialAssignments::getElementPosition
@internal
Get the ordinal position of this element in the containing object
(which in this case is the Model object).
The ordering of elements in the XML form of SBML is generally fixed
for most components in SBML. So, for example, the
ListOfInitialAssignments in a model is (in SBML Level 2 Version 4)
the eighth ListOf___. (However, it differs for different Levels and
Versions of SBML.)
@return the ordinal position of the element with respect to its
siblings, or C<-1> (default) to indicate the position is not significant.
=item ListOfInitialAssignments::createObject
@internal
Create and return an SBML object of this class, if present.
@return the SBML object corresponding to next XMLToken in the
XMLInputStream or C<NULL> if the token was not recognized.
=back
=head2 Rule
@sbmlpackage{core}
@htmlinclude pkg-marker-core.html Implementation of SBML's Rule construct.
In SBML, I<rules> provide additional ways to define the values of
variables in a model, their relationships, and the dynamical behaviors
of those variables. They enable encoding relationships that cannot be
expressed using Reaction nor InitialAssignment objects alone.
The libSBML implementation of rules mirrors the SBML Level 3
Version 1 Core definition (which is in turn is very similar to the
Level 2 Version 4 definition), with Rule being the parent
class of three subclasses as explained below. The Rule class itself
cannot be instantiated by user programs and has no constructor; only the
subclasses AssignmentRule, AlgebraicRule and RateRule can be
instantiated directly.
C<opydetails> doc_rules_general_summary
=over
=back
=head2 ListOfRules
@sbmlpackage{core}
@htmlinclude pkg-marker-core.html Implementation of SBML's ListOfRules construct.
C<opydetails> doc_what_is_listof
=over
=item Rule::Rule
Copy constructor; creates a copy of this Rule.
@param orig the object to copy.
@throws @if python ValueError @else SBMLConstructorException @endif@~
Thrown if the argument C<orig> is C<NULL>.
=item Rule::accept
Accepts the given SBMLVisitor for this instance of Rule.
@param v the SBMLVisitor instance to be used.
@return the result of calling C<v.visit()>, which indicates
whether the Visitor would like to visit the next Rule object in the
list of rules within which I<the> present object is embedded.
=item Rule::clone
Creates and returns a deep copy of this Rule.
@return a (deep) copy of this Rule.
=item Rule::getFormula
Returns the mathematical expression of this Rule in text-string form.
The text string is produced by
@if java <code><a href="libsbml.html#formulaToString(org.sbml.libsbml.ASTNode)">libsbml.formulaToString()</a></code>@else SBML_formulaToString()@endif; please consult
the documentation for that function to find out more about the format
of the text-string formula.
@return the formula text string for this Rule.
@note The attribute "formula" is specific to SBML Level 1; in
higher Levels of SBML, it has been replaced with a subelement named
"math". However, libSBML provides a unified interface to the
underlying math expression and this method can be used for models
of all Levels of SBML.
@see getMath()
=item Rule::getMath
Get the mathematical formula of this Rule as an ASTNode tree.
@return an ASTNode, the value of the "math" subelement of this Rule.
@note The subelement "math" is present in SBML Levels 2
and 3. In SBML Level 1, the equivalent construct is the
attribute named "formula". LibSBML provides a unified interface to
the underlying math expression and this method can be used for models
of all Levels of SBML.
@see getFormula()
=item Rule::getVariable
Get the value of the "variable" attribute of this Rule object.
C<opydetails> doc_rule_level_1
@return the identifier string stored as the "variable" attribute value
in this Rule, or C<NULL> if this object is an AlgebraicRule object.
=item Rule::getUnits
Returns the units for the
mathematical formula of this Rule.
@return the identifier of the units for the expression of this Rule.
@note The attribute "units" exists on SBML Level 1 ParameterRule
objects only. It is not present in SBML Levels 2 and 3.
=item Rule::isSetFormula
Predicate returning C<true> if this Rule's mathematical expression is
set.
This method is equivalent to isSetMath(). This version is present for
easier compatibility with SBML Level 1, in which mathematical
formulas were written in text-string form.
@return C<true> if the mathematical formula for this Rule is
set, C<false> otherwise.
@note The attribute "formula" is specific to SBML Level 1; in
higher Levels of SBML, it has been replaced with a subelement named
"math". However, libSBML provides a unified interface to the
underlying math expression and this method can be used for models
of all Levels of SBML.
@see isSetMath()
=item Rule::isSetMath
Predicate returning C<true> if this Rule's mathematical expression is
set.
This method is equivalent to isSetFormula().
@return C<true> if the formula (or equivalently the math) for this
Rule is set, C<false> otherwise.
@note The subelement "math" is present in SBML Levels 2
and 3. In SBML Level 1, the equivalent construct is the
attribute named "formula". LibSBML provides a unified interface to
the underlying math expression and this method can be used for models
of all Levels of SBML.
@see isSetFormula()
=item Rule::isSetVariable
Predicate returning C<true> if this Rule's "variable" attribute is set.
C<opydetails> doc_rule_level_1
@return C<true> if the "variable" attribute value of this Rule is
set, C<false> otherwise.
=item Rule::isSetUnits
Predicate returning C<true> if this Rule's "units" attribute is set.
@return C<true> if the units for this Rule is set, C<false>
otherwise
@note The attribute "units" exists on SBML Level 1 ParameterRule
objects only. It is not present in SBML Levels 2 and 3.
=item Rule::setFormula
Sets the "math" subelement of this Rule to an expression in text-string
form.
This is equivalent to setMath(const ASTNode math). The provision of
using text-string formulas is retained for easier SBML Level 1
compatibility. The formula is converted to an ASTNode internally.
@param formula a mathematical formula in text-string form.
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT @endlink
@note The attribute "formula" is specific to SBML Level 1; in
higher Levels of SBML, it has been replaced with a subelement named
"math". However, libSBML provides a unified interface to the
underlying math expression and this method can be used for models
of all Levels of SBML.
@see setMath(const ASTNode math)
=item Rule::setMath
Sets the "math" subelement of this Rule to a copy of the given
ASTNode.
@param math the ASTNode_t structure of the mathematical formula.
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT @endlink
@note The subelement "math" is present in SBML Levels 2
and 3. In SBML Level 1, the equivalent construct is the
attribute named "formula". LibSBML provides a unified interface to
the underlying math expression and this method can be used for models
of all Levels of SBML.
@see setFormula(const std::string& formula)
=item Rule::setVariable
Sets the "variable" attribute value of this Rule object.
C<opydetails> doc_rule_level_1
@param sid the identifier of a Compartment, Species or Parameter
elsewhere in the enclosing Model object.
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
@li @link OperationReturnValues_t#LIBSBML_UNEXPECTED_ATTRIBUTE LIBSBML_UNEXPECTED_ATTRIBUTE @endlink
=item Rule::setUnits
Sets the units for this Rule.
@param sname the identifier of the units
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
@li @link OperationReturnValues_t#LIBSBML_UNEXPECTED_ATTRIBUTE LIBSBML_UNEXPECTED_ATTRIBUTE @endlink
@note The attribute "units" exists on SBML Level 1 ParameterRule
objects only. It is not present in SBML Levels 2 and 3.
=item Rule::unsetUnits
Unsets the "units" for this Rule.
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
@li @link OperationReturnValues_t#LIBSBML_UNEXPECTED_ATTRIBUTE LIBSBML_UNEXPECTED_ATTRIBUTE @endlink
@note The attribute "units" exists on SBML Level 1 ParameterRule
objects only. It is not present in SBML Levels 2 and 3.
=item Rule::getDerivedUnitDefinition
Calculates and returns a UnitDefinition that expresses the units of
measurement assumed for the "math" expression of this Rule.
C<opydetails> doc_rule_units
C<opydetails> doc_note_unit_inference_depends_on_model
C<opydetails> doc_warning_rule_math_literals
@return a UnitDefinition that expresses the units of the math
expression of this Rule, or C<NULL> if one cannot be constructed.
@see containsUndeclaredUnits()
=item Rule::getDerivedUnitDefinition
Calculates and returns a UnitDefinition that expresses the units of
measurement assumed for the "math" expression of this Rule.
C<opydetails> doc_rule_units
C<opydetails> doc_note_unit_inference_depends_on_model
C<opydetails> doc_warning_rule_math_literals
@return a UnitDefinition that expresses the units of the math
expression of this Rule, or C<NULL> if one cannot be constructed.
@see containsUndeclaredUnits()
=item Rule::containsUndeclaredUnits
Predicate returning C<true> if the math expression of this Rule contains
parameters/numbers with undeclared units.
@return C<true> if the math expression of this Rule includes
parameters/numbers with undeclared units, C<false> otherwise.
@note A return value of C<true> indicates that the UnitDefinition
returned by getDerivedUnitDefinition() may not accurately represent
the units of the expression.
@see getDerivedUnitDefinition()
=item Rule::containsUndeclaredUnits
Predicate returning C<true> if the math expression of this Rule contains
parameters/numbers with undeclared units.
@return C<true> if the math expression of this Rule includes
parameters/numbers with undeclared units, C<false> otherwise.
@note A return value of C<true> indicates that the UnitDefinition
returned by getDerivedUnitDefinition() may not accurately represent the
units of the expression.
@see getDerivedUnitDefinition()
=item Rule::getType
Returns a code representing the type of rule this is.
@return the rule type, which will be one of the following three possible
values:
@if clike
@li @link RuleType_t#RULE_TYPE_RATE RULE_TYPE_RATE@endlink
@li @link RuleType_t#RULE_TYPE_SCALAR RULE_TYPE_SCALAR@endlink
@li @link RuleType_t#RULE_TYPE_INVALID RULE_TYPE_INVALID@endlink
@endif@if python
@li @link libsbml.RULE_TYPE_RATE RULE_TYPE_RATE@endlink
@li @link libsbml.RULE_TYPE_SCALAR RULE_TYPE_SCALAR@endlink
@li @link libsbml.RULE_TYPE_INVALID RULE_TYPE_INVALID@endlink
@endif@if java
@li @link libsbmlConstants#RULE_TYPE_RATE RULE_TYPE_RATE@endlink
@li @link libsbmlConstants#RULE_TYPE_SCALAR RULE_TYPE_SCALAR@endlink
@li @link libsbmlConstants#RULE_TYPE_INVALID RULE_TYPE_INVALID@endlink
@endif@if csharp
@li @link libsbmlcs.libsbml.RULE_TYPE_RATE RULE_TYPE_RATE@endlink
@li @link libsbmlcs.libsbml.RULE_TYPE_SCALAR RULE_TYPE_SCALAR@endlink
@li @link libsbmlcs.libsbml.RULE_TYPE_INVALID RULE_TYPE_INVALID@endlink
@endif@~
@note The attribute "type" on Rule objects is present only in SBML
Level 1. In SBML Level 2 and later, the type has been
replaced by subclassing the Rule object.
=item Rule::isAlgebraic
Predicate returning C<true> if this Rule is an AlgebraicRule.
@return C<true> if this Rule is an AlgebraicRule, C<false> otherwise.
=item Rule::isAssignment
Predicate returning C<true> if this Rule is an AssignmentRule.
@return C<true> if this Rule is an AssignmentRule, C<false> otherwise.
=item Rule::isCompartmentVolume
Predicate returning C<true> if this Rule is an CompartmentVolumeRule
or equivalent.
This libSBML method works for SBML Level 1 models (where there is
such a thing as an explicit CompartmentVolumeRule), as well as other Levels of
SBML. For Levels above Level 1, this method checks the symbol
being affected by the rule, and returns C<true> if the symbol is the
identifier of a Compartment object defined in the model.
@return C<true> if this Rule is a CompartmentVolumeRule, C<false>
otherwise.
=item Rule::isParameter
Predicate returning C<true> if this Rule is an ParameterRule or
equivalent.
This libSBML method works for SBML Level 1 models (where there is
such a thing as an explicit ParameterRule), as well as other Levels of
SBML. For Levels above Level 1, this method checks the symbol
being affected by the rule, and returns C<true> if the symbol is the
identifier of a Parameter object defined in the model.
@return C<true> if this Rule is a ParameterRule, C<false>
otherwise.
=item Rule::isRate
Predicate returning C<true> if this Rule is a RateRule (SBML
Levels 2–3) or has a "type" attribute value of C<"rate">
(SBML Level 1).
@return C<true> if this Rule is a RateRule (Level 2) or has
type "rate" (Level 1), C<false> otherwise.
=item Rule::isScalar
Predicate returning C<true> if this Rule is an AssignmentRule (SBML
Levels 2–3) or has a "type" attribute value of C<"scalar">
(SBML Level 1).
@return C<true> if this Rule is an AssignmentRule (Level 2) or has
type "scalar" (Level 1), C<false> otherwise.
=item Rule::isSpeciesConcentration
Predicate returning C<true> if this Rule is a SpeciesConcentrationRule
or equivalent.
This libSBML method works for SBML Level 1 models (where there is
such a thing as an explicit SpeciesConcentrationRule), as well as
other Levels of SBML. For Levels above Level 1, this method
checks the symbol being affected by the rule, and returns C<true> if
the symbol is the identifier of a Species object defined in the model.
@return C<true> if this Rule is a SpeciesConcentrationRule, C<false>
otherwise.
=item Rule::getTypeCode
Returns the libSBML type code for this SBML object.
C<opydetails> doc_what_are_typecodes
@return the SBML type code for this object, either
@link SBMLTypeCode_t#SBML_ASSIGNMENT_RULE SBML_ASSIGNMENT_RULE@endlink,
@link SBMLTypeCode_t#SBML_RATE_RULE SBML_RATE_RULE@endlink, or
@link SBMLTypeCode_t#SBML_ALGEBRAIC_RULE SBML_ALGEBRAIC_RULE@endlink
for SBML Core.
C<opydetails> doc_warning_typecodes_not_unique
@see getElementName()
@see getPackageName()
=item Rule::getL1TypeCode
Returns the SBML Level 1 type code for this Rule object.
This method only applies to SBML Level 1 model objects. If this
is not an SBML Level 1 rule object, this method will return @link
SBMLTypeCode_t#SBML_UNKNOWN SBML_UNKNOWN@endlink.
@return the SBML Level 1 type code for this Rule (namely, @link
SBMLTypeCode_t#SBML_COMPARTMENT_VOLUME_RULE
SBML_COMPARTMENT_VOLUME_RULE@endlink, @link
SBMLTypeCode_t#SBML_PARAMETER_RULE SBML_PARAMETER_RULE@endlink, @link
SBMLTypeCode_t#SBML_SPECIES_CONCENTRATION_RULE
SBML_SPECIES_CONCENTRATION_RULE@endlink, or @link
SBMLTypeCode_t#SBML_UNKNOWN SBML_UNKNOWN@endlink).
=item Rule::getElementName
Returns the XML element name of this object
The returned value can be any of a number of different strings,
depending on the SBML Level in use and the kind of Rule object this
is. The rules as of libSBML version @htmlinclude libsbml-version.html
are the following:
\n=over\n
\n=item\n\n(Level 2 and 3) RateRule: returns C<"rateRule">
\n=item\n\n(Level 2 and 3) AssignmentRule: returns C<"assignmentRule">
\n=item\n\n(Level 2 and 3) AlgebraicRule: returns C<"algebraicRule">
\n=item\n\n(Level 1 Version 1) SpecieConcentrationRule: returns C<"specieConcentrationRule">
\n=item\n\n(Level 1 Version 2) SpeciesConcentrationRule: returns C<"speciesConcentrationRule">
\n=item\n\n(Level 1) CompartmentVolumeRule: returns C<"compartmentVolumeRule">
\n=item\n\n(Level 1) ParameterRule: returns C<"parameterRule">
\n=item\n\nUnknown rule type: returns C<"unknownRule">
\n=back\n
Beware that the last (C<"unknownRule">) is not a valid SBML element
name.
@return the name of this element
=item Rule::writeElements
@internal
Subclasses should override this method to write out their contained
SBML objects as XML elements. Be sure to call your parents
implementation of this method as well.
=item Rule::setL1TypeCode
Sets the SBML Level 1 type code for this Rule.
@param type the SBML Level 1 type code for this Rule. The
allowable values are @link SBMLTypeCode_t#SBML_COMPARTMENT_VOLUME_RULE
SBML_COMPARTMENT_VOLUME_RULE@endlink, @link
SBMLTypeCode_t#SBML_PARAMETER_RULE SBML_PARAMETER_RULE@endlink, and
@link SBMLTypeCode_t#SBML_SPECIES_CONCENTRATION_RULE
SBML_SPECIES_CONCENTRATION_RULE@endlink.
@return integer value indicating success/failure of the
function. The possible values returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS@endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE@endlink
if given C<type> value is not one of the above.
=item Rule::hasRequiredElements
Predicate returning C<true> if all the required elements for this Rule
object have been set.
The only required element for a Rule object is the "math" subelement.
@return a boolean value indicating whether all the required
elements for this object have been defined.
=item Rule::hasRequiredAttributes
Predicate returning C<true> if all the required attributes for this Rule
object have been set.
The required attributes for a Rule object depend on the type of Rule
it is. For AssignmentRule and RateRule objects (and SBML
Level 1's SpeciesConcentrationRule, CompartmentVolumeRule, and
ParameterRule objects), the required attribute is "variable"; for
AlgebraicRule objects, there is no required attribute.
@return a boolean value indicating whether all the required
elements for this object have been defined.
=item Rule::renameSIdRefs
Renames all the C<SIdRef> attributes on this element, including any
found in MathML.
C<opydetails> doc_what_is_sidref
This method works by looking at all attributes and (if appropriate)
mathematical formulas, comparing the identifiers to the value of @p
oldid. If any matches are found, the matching identifiers are replaced
with C<newid>. The method does I<not> descend into child elements.
@param oldid the old identifier
@param newid the new identifier
=item Rule::renameUnitSIdRefs
Renames all the C<UnitSIdRef> attributes on this element.
C<opydetails> doc_what_is_unitsidref
This method works by looking at all unit identifier attribute values
(including, if appropriate, inside mathematical formulas), comparing the
unit identifiers to the value of C<oldid>. If any matches are found,
the matching identifiers are replaced with C<newid>. The method does
I<not> descend into child elements.
@param oldid the old identifier
@param newid the new identifier
=item Rule::getInternalId
@internal
=item Rule::setInternalId
@internal
=item Rule::getId
@internal
=item Rule::replaceSIDWithFunction
@internal
Replace all nodes with the name 'id' from the child 'math' object with the provided function.
=item Rule::divideAssignmentsToSIdByFunction
@internal
If this rule assigns a value or a change to the 'id' element, replace the 'math' object with the function (existing/function).
=item Rule::multiplyAssignmentsToSIdByFunction
@internal
If this assignment assigns a value to the 'id' element, replace the 'math' object with the function (existing function).
=item Rule::Rule
@internal
Only subclasses may create Rules.
=item Rule::Rule
@internal
=item Rule::readOtherXML
@internal
Subclasses should override this method to read (and store) XHTML,
MathML, etc. directly from the XMLInputStream.
@return true if the subclass read from the stream, false otherwise.
=item Rule::addExpectedAttributes
@internal
Subclasses should override this method to get the list of
expected attributes.
This function is invoked from corresponding readAttributes()
function.
=item Rule::readAttributes
@internal
Subclasses should override this method to read values from the given
XMLAttributes set into their specific fields. Be sure to call your
parents implementation of this method as well.
=item Rule::readL1Attributes
@internal
=item Rule::readL2Attributes
@internal
=item Rule::readL3Attributes
@internal
=item Rule::writeAttributes
@internal
Subclasses should override this method to write their XML attributes
to the XMLOutputStream. Be sure to call your parents implementation
of this method as well.
=item ListOfRules::ListOfRules
Creates a new ListOfRules object.
The object is constructed such that it is valid for the given SBML
Level and Version combination.
@param level the SBML Level
@param version the Version within the SBML Level
=item ListOfRules::ListOfRules
Creates a new ListOfRules object.
The object is constructed such that it is valid for the SBML Level and
Version combination determined by the SBMLNamespaces object in @p
sbmlns.
@param sbmlns an SBMLNamespaces object that is used to determine the
characteristics of the ListOfRules object to be created.
=item ListOfRules::clone
Creates and returns a deep copy of this ListOfRules instance.
@return a (deep) copy of this ListOfRules.
=item ListOfRules::getItemTypeCode
Returns the libSBML type code for the objects contained in this ListOf
(i.e., Rule objects, if the list is non-empty).
C<opydetails> doc_what_are_typecodes
@return the SBML type code for objects contained in this list:
@link SBMLTypeCode_t#SBML_RULE SBML_RULE@endlink (default).
@see getElementName()
@see getPackageName()
=item ListOfRules::getElementName
Returns the XML element name of this object.
For ListOfRules, the XML element name is C<"listOfRules">.
@return the name of this element, i.e., C<"listOfRules">.
=item ListOfRules::get
Get a Rule from the ListOfRules.
@param n the index number of the Rule to get.
@return the nth Rule in this ListOfRules.
@see size()
=item ListOfRules::get
Get a Rule from the ListOfRules.
@param n the index number of the Rule to get.
@return the nth Rule in this ListOfRules.
@see size()
=item ListOfRules::get
Get a Rule from the ListOfRules based on its identifier.
@param sid a string representing the identifier of the Rule to get.
@return Rule in this ListOfRules with the given C<id> or C<NULL> if no
such Rule exists.
@see get(unsigned int n)
@see size()
=item ListOfRules::get
Get a Rule from the ListOfRules based on its identifier.
@param sid a string representing the identifier of the Rule to get.
@return Rule in this ListOfRules with the given C<sid> or C<NULL> if no
such Rule exists.
@see get(unsigned int n)
@see size()
=item ListOfRules::remove
Removes the nth item from this ListOfRules items and returns a pointer to
it.
The caller owns the returned item and is responsible for deleting it.
@param n the index of the item to remove
@see size()
=item ListOfRules::getElementBySId
Returns the first child element found that has the given C<id> in the
model-wide SId namespace, or C<NULL> if no such object is found.
Note that AssignmentRules and RateRules do not actually have IDs, but
the libsbml interface pretends that they do: no assignment rule or rate
rule is returned by this function.
@param id string representing the id of objects to find
@return pointer to the first element found with the given C<id>.
=item ListOfRules::remove
Removes item in this ListOfRules items with the given identifier.
The caller owns the returned item and is responsible for deleting it.
If none of the items in this list have the identifier C<sid>, then @c
NULL is returned.
@param sid the identifier of the item to remove
@return the item removed. As mentioned above, the caller owns the
returned item.
=item ListOfRules::getElementPosition
@internal
Get the ordinal position of this element in the containing object
(which in this case is the Model object).
The ordering of elements in the XML form of SBML is generally fixed
for most components in SBML.
@return the ordinal position of the element with respect to its
siblings, or C<-1> (default) to indicate the position is not significant.
=item ListOfRules::createObject
@internal
Create and return a listOfRules object, if present.
@return the SBML object corresponding to next XMLToken in the
XMLInputStream or C<NULL> if the token was not recognized.
=item ListOfRules::isValidTypeForList
@internal
=back
=head2 AlgebraicRule
@sbmlpackage{core}
@htmlinclude pkg-marker-core.html Implementation of SBML's AlgebraicRule construct.
The rule type AlgebraicRule is derived from the parent class Rule. It
is used to express equations that are neither assignments of model
variables nor rates of change. AlgebraicRule does not add any
attributes to the basic Rule; its role is simply to distinguish this
case from the other cases.
In the context of a simulation, algebraic rules are in effect at all
times, <em>t</em> \f$\geq\f$ <em>0</em>. For purposes of evaluating
expressions that involve the delay "csymbol" (see the SBML
specification), algebraic rules are considered to apply also at
<em>t</em> \f$\leq\f$ <em>0</em>. Please consult the relevant SBML
specification for additional information about the semantics of
assignments, rules, and entity values for simulation time <em>t</em>
\f$\leq\f$ <em>0</em>.
An SBML model must not be overdetermined. The ability to define
arbitrary algebraic expressions in an SBML model introduces the
possibility that a model is mathematically overdetermined by the overall
system of equations constructed from its rules, reactions and events.
Therefore, if an algebraic rule is introduced in a model, for at least
one of the entities referenced in the rule's "math" element the value of
that entity must not be completely determined by other constructs in the
model. This means that at least this entity must not have the attribute
"constant"=C<true> and there must also not be a rate rule or assignment
rule for it. Furthermore, if the entity is a Species object, its value
must not be determined by reactions, which means that it must either
have the attribute "boundaryCondition"=C<true> or else not be involved
in any reaction at all. These restrictions are explained in more detail
in the SBML specification documents.
In SBML Levels 2 and 3, Reaction object identifiers can be
referenced in the "math" expression of an algebraic rule, but reaction
rates can never be <em>determined</em> by algebraic rules. This is true
even when a reaction does not contain a KineticLaw
@if conly structure @else object@endif. (In such cases of missing
kinetic law definitions, the model is valid but incomplete; the rates of
reactions lacking kinetic laws are simply undefined, and not determined by
the algebraic rule.)
C<opydetails> doc_rules_general_summary
=over
=item AlgebraicRule::AlgebraicRule
Creates a new AlgebraicRule object using the given SBML C<level> and @p
version values.
@param level the SBML Level to assign to this AlgebraicRule object.
@param version the SBML Version to assign to this AlgebraicRule object.
@throws @if python ValueError @else SBMLConstructorException @endif
Thrown if the given C<level> and C<version> combination, or this kind
of SBML object, are either invalid or mismatched with respect to the
parent SBMLDocument object.
C<opydetails> doc_algebraicrule_setting_lv
=item AlgebraicRule::AlgebraicRule
Creates a new AlgebraicRule object using the given SBMLNamespaces object
C<sbmlns>.
The SBMLNamespaces object encapsulates SBML Level/Version/namespaces
information. It is used to communicate the SBML Level, Version, and
(in Level 3) packages used in addition to SBML Level 3 Core.
A common approach to using this class constructor is to create an
SBMLNamespaces object somewhere in a program, once, then pass it to
object constructors such as this one when needed.
@param sbmlns an SBMLNamespaces object.
@throws @if python ValueError @else SBMLConstructorException @endif
Thrown if the given C<level> and C<version> combination, or this kind
of SBML object, are either invalid or mismatched with respect to the
parent SBMLDocument object.
C<opydetails> doc_algebraicrule_setting_lv
=item AlgebraicRule::clone
Creates and returns a deep copy of this Rule.
@return a (deep) copy of this Rule.
=item AlgebraicRule::accept
Accepts the given SBMLVisitor for this instance of AlgebraicRule.
@param v the SBMLVisitor instance to be used.
@return the result of calling C<v.visit()>, which indicates
whether the Visitor would like to visit the next AlgebraicRule object
in the list of rules within which I<the> present object is embedded.
=item AlgebraicRule::setInternalIdOnly
@internal
sets the mInternalIdOnly flag
=item AlgebraicRule::getInternalIdOnly
@internal
=item AlgebraicRule::hasRequiredAttributes
Predicate returning C<true> if all the required attributes for this
AlgebraicRule object have been set.
@note In SBML Levels 2–3, there is no required attribute
for an AlgebraicRule object. For Level 1, the only required
attribute is "formula".
@return C<true> if the required attributes have been set, C<false>
otherwise.
=back
=head2 AssignmentRule
@sbmlpackage{core}
@htmlinclude pkg-marker-core.html Implementation of SBML's AssignmentRule construct.
The rule type AssignmentRule is derived from the parent class Rule. It
is used to express equations that set the values of variables. The
left-hand side (the attribute named "variable") of an assignment rule
can refer to the identifier of a Species, SpeciesReference (in SBML
Level 3), Compartment, or Parameter
@if conly structure @else object@endif@~ in the model (but not a
Reaction). The entity identified must have its "constant" attribute set
to C<false>. The effects of an assignment rule construct are in general
terms the same, but differ in the precise details depending on the type of
SBML component being set:
\n=over\n
\n=item\n\n<em>In the case of a species</em>, an SBML assignment rule sets the
referenced species' quantity (whether a "concentration" or "amount") to
the value determined by the formula in the MathML subelement "math".
The unit associated with the value produced by the "math" formula @em
should (in SBML Level 2 Version 4 and in SBML Level 3) or I<must> (in
SBML releases prior to Level 2 version 4) be equal to the unit
associated with the species' quantity. <em>Restrictions</em>: There
must not be both an AssignmentRule "variable" attribute and a
SpeciesReference "species" attribute having the same value in a model,
unless the referenced Species @if conly structure @else object@endif@~ has
its "boundaryCondition" attribute set to C<true>. In other words, an
assignment rule cannot be defined for a species that is created or
destroyed in a reaction unless that species is defined as a boundary
condition in the model.
\n=item\n\n(For SBML Level 3 only) <em>In the case of a species
reference</em>, an assignment rule sets the stoichiometry of the
referenced reactant or product to the value determined by the formula in
"math". The unit associated with the value produced by the "math"
formula should be consistent with the unit "dimensionless", because
reactant and product stoichiometries in reactions are dimensionless
quantities.
\n=item\n\n<em>In the case of a compartment</em>, an SBML assignment rule sets
the referenced compartment's size to the value determined by the formula
in the "math" subelement of the AssignmentRule
@if conly structure @else object@endif@~. The overall units of the
formula in "math" I<should> (in SBML Level 2 Version 4 and in
SBML Level 3) or I<must> (in SBML releases prior to Level 2
version 4) be the same as the units of the size of the compartment.
\n=item\n\n<em>In the case of a parameter</em>, an assignment rule sets the
referenced parameter's value to that determined by the formula in the
"math" subelement of the AssignmentRule
@if conly structure @else object@endif@~. The overall units of the
formula in the "math" subelement I<should> (in SBML Level 2
Version 4 and in SBML Level 3) or I<must> (in SBML releases
prior to Level 2 version 4) be the same as the units defined for
the parameter. \n=back\n
In the context of a simulation, assignment rules are in effect at all
times, <em>t</em> \f$\geq\f$ <em>0</em>. For purposes of evaluating
expressions that involve the <em>delay</em> "csymbol" (see the SBML
Level 2 specification), assignment rules are considered to apply
also at <em>t</em> \f$\leq\f$ <em>0</em>. Please consult the relevant
SBML specification for additional information about the semantics of
assignments, rules, and entity values for simulation time <em>t</em>
\f$\leq\f$ <em>0</em>.
A model must not contain more than one AssignmentRule or RateRule
@if conly structure @else object@endif@~ having the same value of
"variable"; in other words, in the set of all assignment rules and rate
rules in an SBML model, each variable appearing in the left-hand sides can
only appear once. This simply follows from the fact that an indeterminate
system would result if a model contained more than one assignment rule for
the same variable or both an assignment rule and a rate rule for the same
variable.
Similarly, a model must also not contain <em>both</em> an AssignmentRule
and an InitialAssignment definition for the same variable, because both
kinds of constructs apply prior to and at the start of simulation time,
i.e., <em>t</em> \f$\leq\f$ <em>0</em>. If a model contained both an
initial assignment and an assignment rule for the same variable, an
indeterminate system would result.
The value calculated by an AssignmentRule
@if conly structure @else object@endif@~ overrides the value assigned to
the given symbol by the model component defining that symbol. For
example, if a Compartment @if conly structure @else object@endif's
"size" attribute value is set in its definition, and the model also
contains an AssignmentRule @if conly structure @else object@endif@~
having that compartment's "id" as its "variable" value, then the "size"
assigned in the Compartment @if conly structure @else object@endif@~
definition is ignored and the value assigned based on the computation
defined in the AssignmentRule. This does <em>not</em> mean that a
definition for a given symbol can be omitted if there is an AssignmentRule
@if conly structure @else object@endif@~ involving it. For example,
there must be a Parameter @if conly structure @else object@endif@~
definition for a given parameter if there is an AssignmentRule definition
for that parameter. It is only a question of which value definition takes
precedence.
C<opydetails> doc_rules_general_summary
=over
=item AssignmentRule::AssignmentRule
Creates a new AssignmentRule using the given SBML C<level> and C<version>
values.
@param level an unsigned int, the SBML Level to assign to this AssignmentRule.
@param version an unsigned int, the SBML Version to assign to this
AssignmentRule.
@throws @if python ValueError @else SBMLConstructorException @endif@~
Thrown if the given C<level> and C<version> combination, or this kind
of SBML object, are either invalid or mismatched with respect to the
parent SBMLDocument object.
C<opydetails> doc_note_assignmentRule_setting_lv
=item AssignmentRule::AssignmentRule
Creates a new AssignmentRule using the given SBMLNamespaces object
C<sbmlns>.
C<opydetails> doc_what_are_sbmlnamespaces
@param sbmlns an SBMLNamespaces object.
@throws @if python ValueError @else SBMLConstructorException @endif@~
Thrown if the given C<level> and C<version> combination, or this kind
of SBML object, are either invalid or mismatched with respect to the
parent SBMLDocument object.
C<opydetails> doc_note_assignmentRule_setting_lv
=item AssignmentRule::clone
Creates and returns a deep copy of this Rule.
@return a (deep) copy of this Rule.
=item AssignmentRule::accept
Accepts the given SBMLVisitor for this instance of AssignmentRule.
@param v the SBMLVisitor instance to be used.
@return the result of calling C<v.visit()>, which indicates
whether the Visitor would like to visit the next AssignmentRule object
in the list of rules within which I<the> present object is embedded.
=item AssignmentRule::hasRequiredAttributes
Predicate returning C<true> if all the required attributes for this
AssignmentRule object have been set.
@note In SBML Levels 2–3, the only required attribute for
an AssignmentRule object is "variable". For Level 1, where the
equivalent attribute is known by different names ("compartment",
"species", or "name", depending on the type of object), there is an
additional required attribute called "formula".
@return C<true> if the required attributes have been set, C<false>
otherwise.
=item AssignmentRule::renameSIdRefs
Renames all the C<SIdRef> attributes on this element, including any
found in MathML.
C<opydetails> doc_what_is_sidref
This method works by looking at all attributes and (if appropriate)
mathematical formulas, comparing the identifiers to the value of @p
oldid. If any matches are found, the matching identifiers are replaced
with C<newid>. The method does I<not> descend into child elements.
@param oldid the old identifier
@param newid the new identifier
=back
=head2 RateRule
@sbmlpackage{core}
@htmlinclude pkg-marker-core.html Implementation of SBML's RateRule construct.
The rule type RateRule is derived from the parent class Rule. It is
used to express equations that determine the rates of change of
variables. The left-hand side (the "variable" attribute) can refer to
the identifier of a species, compartment, or parameter (but not a
reaction). The entity identified must have its "constant" attribute set
to C<false>. The effects of a RateRule are in general terms the same,
but differ in the precise details depending on which variable is being
set:
\n=over\n \n=item\n\n<em>In the case of a species</em>, a RateRule sets the rate of
change of the species' quantity (<em>concentration</em> or <em>amount of
substance</em>) to the value determined by the formula in the "math"
subelement of the RateRule object. The overall units of the formula in
"math" I<should> (in SBML Level 2 Version 4 and in SBML Level 3) or @em
must (in SBML releases prior to Level 2 version 4) be equal to
the unit of <em>species quantity</em> divided by the model-wide unit of
<em>time</em>. <em>Restrictions</em>: There must not be both a RateRule
"variable" attribute and a SpeciesReference "species" attribute having
the same value, unless that species has its "boundaryCondition"
attribute is set to C<true>. This means a rate rule cannot be defined
for a species that is created or destroyed in a reaction, unless that
species is defined as a boundary condition in the model.
\n=item\n\n(For SBML Level 3 only) <em>In the case of a species
reference</em>, a RateRule sets the rate of change of the stoichiometry
of the referenced reactant or product to the value determined by the
formula in "math". The unit associated with the value produced by the
"math" formula should be consistent with the unit "dimensionless"
divided by the model-wide unit of <em>time</em>.
\n=item\n\n<em>In the case of a compartment</em>, a RateRule sets the rate of
change of the compartment's size to the value determined by the formula
in the "math" subelement of the RateRule object. The overall units of
the formula I<should> (in SBML Level 2 Version 4 and in SBML
Level 3) or I<must> (in SBML releases prior to Level 2
version 4) be the units of the compartment's <em>size</em> divided
by the model-wide unit of <em>time</em>.
\n=item\n\n<em>In the case of a parameter</em>, a RateRule sets the rate of
change of the parameter's value to that determined by the formula in the
"math" subelement of the RateRule object. The overall units of the
formula I<should> (in SBML Level 2 Version 4 and in SBML
Level 3) or I<must> (in SBML releases prior to Level 2
version 4) be the Parameter object's "unit" attribute value divided
by the model-wide unit of <em>time</em>. \n=back\n
In the context of a simulation, rate rules are in effect for simulation
time <em>t</em> < <em>0</em>. Please consult the relevant SBML
specification for additional information about the semantics of
assignments, rules, and entity values for simulation time <em>t</em>
\f$\leq\f$ <em>0</em>.
As mentioned in the description of AssignmentRule, a model must not
contain more than one RateRule or AssignmentRule object having the same
value of "variable"; in other words, in the set of all assignment rules
and rate rules in an SBML model, each variable appearing in the
left-hand sides can only appear once. This simply follows from the fact
that an indeterminate system would result if a model contained more than
one assignment rule for the same variable or both an assignment rule and
a rate rule for the same variable.
C<opydetails> doc_rules_general_summary
=over
=item RateRule::RateRule
Creates a new RateRule using the given SBML C<level> and C<version>
values.
@param level an unsigned int, the SBML Level to assign to this RateRule
@param version an unsigned int, the SBML Version to assign to this
RateRule
@throws @if python ValueError @else SBMLConstructorException @endif@~
Thrown if the given C<level> and C<version> combination, or this kind
of SBML object, are either invalid or mismatched with respect to the
parent SBMLDocument object.
C<opydetails> doc_note_raterule_setting_lv
=item RateRule::RateRule
Creates a new RateRule using the given SBMLNamespaces object
C<sbmlns>.
C<opydetails> doc_what_are_sbmlnamespaces
@param sbmlns an SBMLNamespaces object.
@throws @if python ValueError @else SBMLConstructorException @endif@~
Thrown if the given C<level> and C<version> combination, or this kind
of SBML object, are either invalid or mismatched with respect to the
parent SBMLDocument object.
C<opydetails> doc_note_raterule_setting_lv
=item RateRule::clone
Creates and returns a deep copy of this Rule.
@return a (deep) copy of this Rule.
=item RateRule::accept
Accepts the given SBMLVisitor.
@param v the SBMLVisitor instance to be used.
@return the result of calling C<v.visit()>, which indicates
whether the Visitor would like to visit the next RateRule object
in the list of rules within which I<the> present object is embedded.
=item RateRule::hasRequiredAttributes
Predicate returning C<true> if
all the required attributes for this RateRule object
have been set.
@note In SBML Levels 2–3, the only required attribute for a
RateRule object is "variable". For Level 1, where the equivalent
attribute is known by different names ("compartment", "species", or
"name", depending on the type of object), there is an additional
required attribute called "formula".
@return C<true> if the required attributes have been set, C<false>
otherwise.
=item RateRule::renameSIdRefs
Renames all the C<SIdRef> attributes on this element, including any
found in MathML.
C<opydetails> doc_what_is_sidref
This method works by looking at all attributes and (if appropriate)
mathematical formulas, comparing the identifiers to the value of @p
oldid. If any matches are found, the matching identifiers are replaced
with C<newid>. The method does I<not> descend into child elements.
@param oldid the old identifier
@param newid the new identifier
=back
=head2 Constraint
@sbmlpackage{core}
@htmlinclude pkg-marker-core.html Implementation of SBML's Constraint construct.
The Constraint object class was introduced in SBML Level 2
Version 2 as a mechanism for stating the assumptions under which a
model is designed to operate. The <em>constraints</em> are statements
about permissible values of different quantities in a model.
Constraints are not used to compute dynamical values for simulation or
analysis, but rather, they serve an advisory role for
simulation/analysis tools.
SBML's Constraint object class has one required attribute, "id", to
give the parameter a unique identifier by which other parts of an SBML
model definition can refer to it. A Constraint object can also have an
optional "name" attribute of type C<string>. Identifiers and names must
be used according to the guidelines described in the SBML specification
(e.g., Section 3.3 in the Level 2 Version 4 specification).
Constraint has one required subelement, "math", containing a MathML
formula defining the condition of the constraint. This formula must
return a boolean value of C<true> when the model is a <em>valid</em>
state. The formula can be an arbitrary expression referencing the
variables and other entities in an SBML model. The evaluation of "math"
and behavior of constraints are described in more detail below.
A Constraint structure also has an optional subelement called "message".
This can contain a message in XHTML format that may be displayed to the
user when the condition of the formula in the "math" subelement
evaluates to a value of C<false>. Software tools are not required to
display the message, but it is recommended that they do so as a matter
of best practice. The XHTML content within a "message" subelement must
follow the same restrictions as for the "notes" element on SBase
described in in the SBML Level 2 specification; please consult the
<a target="_blank" href="http://sbml.org/Documents/Specifications">SBML
specification document</a> corresponding to the SBML Level and Version
of your model for more information about the requirements for "notes"
content.
Constraint was introduced in SBML Level 2 Version 2. It is
not available in earlier versions of Level 2 nor in any version of
Level 1.
@section constraint-semantics Semantics of Constraints
In the context of a simulation, a Constraint has effect at all times
<em>t \f$\geq\f$ 0</em>. Each Constraint's "math" subelement is first
evaluated after any InitialAssignment definitions in a model at <em>t =
0</em> and can conceivably trigger at that point. (In other words, a
simulation could fail a constraint immediately.)
Constraint structures <em>cannot and should not</em> be used to compute
the dynamical behavior of a model as part of, for example, simulation.
Constraints may be used as input to non-dynamical analysis, for instance
by expressing flux constraints for flux balance analysis.
The results of a simulation of a model containing a constraint are
invalid from any simulation time at and after a point when the function
given by the "math" subelement returns a value of C<false>. Invalid
simulation results do not make a prediction of the behavior of the
biochemical reaction network represented by the model. The precise
behavior of simulation tools is left undefined with respect to
constraints. If invalid results are detected with respect to a given
constraint, the "message" subelement may optionally be displayed to the
user. The simulation tool may also halt the simulation or clearly
delimit in output data the simulation time point at which the simulation
results become invalid.
SBML does not impose restrictions on duplicate Constraint definitions or
the order of evaluation of Constraint objects in a model. It is
possible for a model to define multiple constraints all with the same
mathematical expression. Since the failure of any constraint indicates
that the model simulation has entered an invalid state, a system is not
required to attempt to detect whether other constraints in the model
have failed once any one constraint has failed.
=over
=back
=head2 ListOfConstraints
@sbmlpackage{core}
@htmlinclude pkg-marker-core.html Implementation of SBML's ListOfConstraints construct.
C<opydetails> doc_what_is_listof
=over
=item Constraint::Constraint
Creates a new Constraint using the given SBML C<level> and C<version>
values.
@param level an unsigned int, the SBML Level to assign to this Constraint
@param version an unsigned int, the SBML Version to assign to this
Constraint
@throws @if python ValueError @else SBMLConstructorException @endif@~
Thrown if the given C<level> and C<version> combination, or this kind
of SBML object, are either invalid or mismatched with respect to the
parent SBMLDocument object.
C<opydetails> doc_constraint_setting_lv
=item Constraint::Constraint
Creates a new Constraint using the given SBMLNamespaces object
C<sbmlns>.
C<opydetails> doc_what_are_sbmlnamespaces
@param sbmlns an SBMLNamespaces object.
@throws @if python ValueError @else SBMLConstructorException @endif@~
Thrown if the given C<level> and C<version> combination, or this kind
of SBML object, are either invalid or mismatched with respect to the
parent SBMLDocument object.
C<opydetails> doc_constraint_setting_lv
=item Constraint::Constraint
Copy constructor; creates a copy of this Constraint.
@param orig the object to copy.
@throws @if python ValueError @else SBMLConstructorException @endif@~
Thrown if the argument C<orig> is C<NULL>.
=item Constraint::accept
Accepts the given SBMLVisitor for this instance of Constraint.
@param v the SBMLVisitor instance to be used.
@return the result of calling C<v.visit()>, which indicates
whether the Visitor would like to visit the next Constraint in the
list of constraints within which this Constraint is embedded (i.e., in
the ListOfConstraints located in the enclosing Model instance).
=item Constraint::clone
Creates and returns a deep copy of this Constraint.
@return a (deep) copy of this Constraint.
=item Constraint::getMessage
Get the message, if any, associated with this Constraint
@return the message for this Constraint, as an XMLNode.
=item Constraint::getMessageString
Get the message string, if any, associated with this Constraint
@return the message for this Constraint, as a string.
=item Constraint::getMath
Get the mathematical expression of this Constraint
@return the math for this Constraint, as an ASTNode.
=item Constraint::isSetMessage
Predicate returning C<true> if a
message is defined for this Constraint.
@return C<true> if the message of this Constraint is set,
C<false> otherwise.
=item Constraint::isSetMath
Predicate returning C<true> if a
mathematical formula is defined for this Constraint.
@return C<true> if the "math" subelement for this Constraint is
set, C<false> otherwise.
=item Constraint::setMessage
Sets the message of this Constraint.
The XMLNode tree passed in C<xhtml> is copied.
@param xhtml an XML tree containing XHTML content.
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif@~ The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT @endlink
=item Constraint::setMath
Sets the mathematical expression of this Constraint to a copy of the
AST given as C<math>.
@param math an ASTNode expression to be assigned as the "math"
subelement of this Constraint
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif@~ The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT @endlink
=item Constraint::unsetMessage
Unsets the "message" subelement of this Constraint.
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif@~ The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item Constraint::renameSIdRefs
Renames all the C<SIdRef> attributes on this element, including any
found in MathML.
C<opydetails> doc_what_is_sidref
This method works by looking at all attributes and (if appropriate)
mathematical formulas, comparing the identifiers to the value of @p
oldid. If any matches are found, the matching identifiers are replaced
with C<newid>. The method does I<not> descend into child elements.
@param oldid the old identifier
@param newid the new identifier
=item Constraint::renameUnitSIdRefs
Renames all the C<UnitSIdRef> attributes on this element.
C<opydetails> doc_what_is_unitsidref
This method works by looking at all unit identifier attribute values
(including, if appropriate, inside mathematical formulas), comparing the
unit identifiers to the value of C<oldid>. If any matches are found,
the matching identifiers are replaced with C<newid>. The method does
I<not> descend into child elements.
@param oldid the old identifier
@param newid the new identifier
=item Constraint::replaceSIDWithFunction
@internal
Replace all nodes with the name 'id' from the child 'math' object with the provided function.
=item Constraint::getTypeCode
Returns the libSBML type code for this SBML object.
C<opydetails> doc_what_are_typecodes
@return the SBML type code for this object:
@link SBMLTypeCode_t#SBML_CONSTRAINT SBML_CONSTRAINT@endlink (default).
C<opydetails> doc_warning_typecodes_not_unique
@see getElementName()
@see getPackageName()
=item Constraint::getElementName
Returns the XML element name of this object, which for Constraint, is
always C<"constraint">.
@return the name of this element, i.e., C<"constraint">.
=item Constraint::writeElements
@internal
Subclasses should override this method to write out their contained
SBML objects as XML elements. Be sure to call your parents
implementation of this method as well.
=item Constraint::hasRequiredElements
Predicate returning C<true> if
all the required elements for this Constraint object
have been set.
@note The required elements for a Constraint object are:
@li 'math'
@return a boolean value indicating whether all the required
elements for this object have been defined.
=item Constraint::readOtherXML
@internal
Subclasses should override this method to read (and store) XHTML,
MathML, etc. directly from the XMLInputStream.
@return true if the subclass read from the stream, false otherwise.
=item Constraint::addExpectedAttributes
@internal
Subclasses should override this method to get the list of
expected attributes.
This function is invoked from corresponding readAttributes()
function.
=item Constraint::readAttributes
@internal
Subclasses should override this method to read values from the given
XMLAttributes set into their specific fields. Be sure to call your
parents implementation of this method as well.
=item Constraint::readL2Attributes
@internal
=item Constraint::readL3Attributes
@internal
=item Constraint::writeAttributes
@internal
Subclasses should override this method to write their XML attributes
to the XMLOutputStream. Be sure to call your parents implementation
of this method as well.
=item ListOfConstraints::ListOfConstraints
Creates a new ListOfConstraints object.
The object is constructed such that it is valid for the given SBML
Level and Version combination.
@param level the SBML Level
@param version the Version within the SBML Level
=item ListOfConstraints::ListOfConstraints
Creates a new ListOfConstraints object.
The object is constructed such that it is valid for the SBML Level and
Version combination determined by the SBMLNamespaces object in @p
sbmlns.
@param sbmlns an SBMLNamespaces object that is used to determine the
characteristics of the ListOfConstraints object to be created.
=item ListOfConstraints::clone
Creates and returns a deep copy of this ListOfConstraints instance.
@return a (deep) copy of this ListOfConstraints.
=item ListOfConstraints::getItemTypeCode
Returns the libSBML type code for the objects contained in this ListOf
(i.e., Constraint objects, if the list is non-empty).
C<opydetails> doc_what_are_typecodes
@return the SBML type code for the objects contained in this ListOf
instance: @link SBMLTypeCode_t#SBML_CONSTRAINT SBML_CONSTRAINT@endlink (default).
@see getElementName()
@see getPackageName()
=item ListOfConstraints::getElementName
Returns the XML element name of this object.
For ListOfConstraints, the XML element name is C<"listOfConstraints">.
@return the name of this element, i.e., C<"listOfConstraints">.
=item ListOfConstraints::get
Get a Constraint from the ListOfConstraints.
@param n the index number of the Constraint to get.
@return the nth Constraint in this ListOfConstraints.
@see size()
=item ListOfConstraints::get
Get a Constraint from the ListOfConstraints.
@param n the index number of the Constraint to get.
@return the nth Constraint in this ListOfConstraints.
@see size()
=item ListOfConstraints::remove
Removes the nth item from this ListOfConstraints items and returns a
pointer to it.
The caller owns the returned item and is responsible for deleting it.
@param n the index of the item to remove
@see size()
=item ListOfConstraints::getElementPosition
@internal
Get the ordinal position of this element in the containing object
(which in this case is the Model object).
The ordering of elements in the XML form of SBML is generally fixed
for most components in SBML. So, for example, the ListOfConstraints
in a model is (in SBML Level 2 Version 4) the tenth ListOf___.
(However, it differs for different Levels and Versions of SBML.)
@return the ordinal position of the element with respect to its
siblings, or C<-1> (default) to indicate the position is not significant.
=item ListOfConstraints::createObject
@internal
Create and return an SBML object of this class, if present.
@return the SBML object corresponding to next XMLToken in the
XMLInputStream or C<NULL> if the token was not recognized.
=back
=head2 Reaction
@sbmlpackage{core}
@htmlinclude pkg-marker-core.html Implementation of SBML's Reaction construct.
A I<reaction> represents any transformation, transport or binding
process, typically a chemical reaction, that can change the quantity of
one or more species. In SBML, a reaction is defined primarily in terms
of the participating reactants and products (and their corresponding
stoichiometries), along with optional modifier species, an optional rate
at which the reaction takes place, and optional parameters.
As with other major objects in SBML, Reaction has a mandatory attribute,
"id", used to give the compartment type an identifier. The identifier
must be a text string conforming to the identifer syntax permitted in
SBML. In SBML Level 2 and Level 3, the reaction "id"
identifier can be used in mathematical formulas elsewhere in an SBML
model to represent the rate of that reaction; this usage is explained
below. Reaction also has an optional "name" attribute, of type @c
string. The "id" and "name" must be used according to the guidelines
described in the SBML specification.
The species participating as reactants, products, and/or modifiers in a
reaction are declared using lists of SpeciesReference and/or
ModifierSpeciesReference instances stored in subelements
"listOfReactants", "listOfProducts" and "listOfModifiers". Certain
restrictions are placed on the appearance of species in reaction
definitions:
\n=over\n
\n=item\n\nThe ability of a species to appear as a reactant or product of any
reaction in a model is governed by certain flags in that species'
definition; see the definition of Species for more information.
\n=item\n\nAny species appearing in the mathematical formula of the subelement
"kineticLaw" (described below) of a Reaction must be declared in at
least one of that Reaction's lists of reactants, products, and/or
modifiers. Put another way, it is an error for a reaction's kinetic law
formula to refer to species that have not been declared for that
reaction.
\n=item\n\nA reaction definition can contain an empty list of reactants
<em>or</em> an empty list of products, but it must have at least one
reactant or product; in other words, a reaction without any reactant or
product species is not permitted. (This restriction does not apply to
modifier species, which remain optional in all cases.)
\n=back\n
A reaction can contain up to one KineticLaw object in a subelement named
"kineticLaw". It defines the speed at which the process defined by the
reaction takes place. The description of KineticLaw provides more
details about its use. Note that although the inclusion of a KineticLaw
object in an instance of a Reaction component is optional, there is no
useful default that can be substituted in place of a missing rate
expression in a reaction. Moreover, a reaction's rate cannot be defined
in any other way in SBML—InitialAssignment, AssignmentRule,
RateRule, AlgebraicRule, Event, and other constructs in SBML cannot be
used to set the reaction rate separately. Nevertheless, for some
modeling applications, reactions without any defined rate can be
perfectly acceptable.
Reaction also has a boolean attribute named "reversible" for indicating
whether the reaction is reversible. This attribute is optional in SBML
Level 2, with a default of C<true>; it is mandatory in SBML
Level 3 (with no default value). To say that a reaction is @em
reversible is to say it can proceed in either the forward or the reverse
direction. Although the reversibility of a reaction can sometimes be
deduced by inspecting its rate expression, this is not always the case,
especially for complicated expressions. Moreover, the need in SBML to
allow rate expressions (i.e., KineticLaw) to be optional leads to the
need for a separate flag indicating reversibility. Note that labeling a
reaction as irreversible is an assertion that the reaction always
proceeds in the given forward direction. (Why else would it be flagged
as irreversible?) This implies the rate expression in the KineticLaw
always has a non-negative value during simulations. Software tools
could provide a means of optionally testing that this condition holds.
The presence of reversibility information in two places (i.e., the rate
expression and the "reversible" attribute on Reaction) leaves open the
possibility that a model could contain contradictory information, but
the creation of such a model would be an error on the part of the
software generating it.
The Reaction object class has another boolean attribute called "fast".
This attribute is optional in SBML Level 2, with a default of @c
false; it is mandatory in SBML Level 3 (with no default value). It
is used to indicate that a reaction occurs on a vastly faster time scale
thanothers in a system. Readers are directed to the SBML Level 2
Version 4 specification, which provides more detail about the
conditions under which a reaction can be considered to be fast in this
sense. The attribute's default value is C<false>. SBML Level 1
and Level 2 Version 1 incorrectly claimed that software tools
could ignore this attribute if they did not implement support for the
corresponding concept; however, further research in SBML has revealed
that this is not true, and "fast" <em>cannot be ignored</em> if it is
set to C<true>. SBML Level 2 Versions 2–4 therefore
stipulate that if a model has any reactions with "fast" set to C<true>,
a software tool must be able to respect the attribute or else indicate
to the user that it does not have the capacity to do so. Analysis
software cannot ignore the value of the "fast" attribute because doing
so may lead to different results as compared to a software system that
<em>does</em> make use of "fast".
In SBML Level 3 Version 1, the Reaction object has an
additional optional attribute named "compartment", whose value must be
the identifier of a compartment defined in the enclosing Model object.
The "compartment" attribute can be used to indicate the compartment in
which the reaction is assumed to take place. If the attribute is
present, its value must be the identifier of a Compartment object
defined in the enclosing Model object. Similar to the "reversible"
attribute, the value of the "compartment" attribute has no direct impact
on the construction of mathematical equations for the SBML model. When
a kinetic law is given for a reaction, the compartment location may
already be implicit in the kinetic law (although this cannot always be
guaranteed). Nevertheless, software tools may find the "compartment"
attribute value useful for such purposes as analyzing the structure of
the model, guiding the modeler in constructing correct rate formulas,
and visualization purposes.
Readers are urged to read the SBML specification for more details about
the proper use of Reaction.
=over
=back
=head2 ListOfReactions
@sbmlpackage{core}
@htmlinclude pkg-marker-core.html Implementation of SBML's ListOfReactions construct.
C<opydetails> doc_what_is_listof
=over
=item Reaction::Reaction
Creates a new Reaction using the given SBML C<level> and C<version>
values.
@param level an unsigned int, the SBML Level to assign to this Reaction
@param version an unsigned int, the SBML Version to assign to this
Reaction
@throws @if python ValueError @else SBMLConstructorException @endif@~
Thrown if the given C<level> and C<version> combination, or this kind
of SBML object, are either invalid or mismatched with respect to the
parent SBMLDocument object.
C<opydetails> doc_note_reaction_setting_lv
=item Reaction::Reaction
Creates a new Reaction using the given SBMLNamespaces object
C<sbmlns>.
C<opydetails> doc_what_are_sbmlnamespaces
@param sbmlns an SBMLNamespaces object.
@throws @if python ValueError @else SBMLConstructorException @endif@~
Thrown if the given C<level> and C<version> combination, or this kind
of SBML object, are either invalid or mismatched with respect to the
parent SBMLDocument object.
C<opydetails> doc_note_reaction_setting_lv
=item Reaction::Reaction
Copy constructor; creates a copy of this Reaction.
@param orig the object to copy.
@throws @if python ValueError @else SBMLConstructorException @endif@~
Thrown if the argument C<orig> is C<NULL>.
=item Reaction::accept
Accepts the given SBMLVisitor for this instance of Reaction.
@param v the SBMLVisitor instance to be used.
@return the result of calling C<v.visit()>.
=item Reaction::clone
Creates and returns a deep copy of this Reaction.
@return a (deep) copy of this Reaction.
=item Reaction::getElementBySId
Returns the first child element found that has the given C<id> in the
model-wide SId namespace, or C<NULL> if no such object is found.
@param id string representing the id of objects to find.
@return pointer to the first element found with the given C<id>.
=item Reaction::getElementByMetaId
Returns the first child element it can find with the given C<metaid>, or
C<NULL> if no such object is found.
@param metaid string representing the metaid of objects to find
@return pointer to the first element found with the given C<metaid>.
=item Reaction::getAllElements
Returns a List of all child SBase objects, including those nested to an
arbitrary depth
@return a List of pointers to all children objects.
=item Reaction::renameSIdRefs
Renames all the C<SIdRef> attributes on this element, including any
found in MathML.
C<opydetails> doc_what_is_sidref
This method works by looking at all attributes and (if appropriate)
mathematical formulas, comparing the identifiers to the value of @p
oldid. If any matches are found, the matching identifiers are replaced
with C<newid>. The method does I<not> descend into child elements.
@param oldid the old identifier
@param newid the new identifier
=item Reaction::initDefaults
Initializes the fields of this Reaction object to "typical" default
values.
The SBML Reaction component has slightly different aspects and
default attribute values in different SBML Levels and Versions.
This method sets the values to certain common defaults, based
mostly on what they are in SBML Level 2. Specifically:
@li Sets the "reversible" attribute to C<true>
@li Sets the "fast" attribute to C<false>
@li Marks the "fast" attribute as I<not> having been set
C<opydetails> doc_warning_reaction_cant_ignore_fast
=item Reaction::getId
Returns the value of the "id" attribute of this Reaction.
@return the id of this Reaction.
=item Reaction::getName
Returns the value of the "name" attribute of this Reaction.
@return the name of this Reaction.
=item Reaction::getKineticLaw
Returns the KineticLaw object contained in this Reaction.
@return the KineticLaw instance.
=item Reaction::getKineticLaw
Returns the KineticLaw object contained in this Reaction.
@return the KineticLaw instance.
=item Reaction::getReversible
Returns the value of the "reversible" attribute on the Reaction as a
boolean value.
@return the reversibility status of this Reaction.
=item Reaction::getFast
Returns the value of the "fast" attribute of this Reaction.
@return the "fast" status of this Reaction.
C<opydetails> doc_warning_reaction_cant_ignore_fast
=item Reaction::getCompartment
(SBML Level 3 only) Returns the value of the "compartment"
attribute on the Reaction.
@return the compartment of this Reaction.
@note The "compartment" attribute is available in SBML Level 3
Version 1 Core, but is not present on Reaction in lower Levels of
SBML.
=item Reaction::isSetId
Predicate returning C<true> if this
Reaction's "id" attribute is set.
@return C<true> if the "id" attribute of this Reaction is
set, C<false> otherwise.
=item Reaction::isSetName
Predicate returning C<true> if this
Reaction's "name" attribute is set.
@return C<true> if the "name" attribute of this Reaction is
set, C<false> otherwise.
=item Reaction::isSetKineticLaw
Predicate returning C<true> if this
Reaction contains a kinetic law object.
@return C<true> if a KineticLaw is present in this Reaction,, C<false>
otherwise.
=item Reaction::isSetFast
Predicate returning C<true> if the value of
the "fast" attribute on this Reaction.
@return C<true> if the "fast" attribute is true, C<false> otherwise.
C<opydetails> doc_warning_reaction_cant_ignore_fast
=item Reaction::isSetCompartment
Predicate returning C<true> if this
Reaction's "compartment" attribute is set.
@return C<true> if the "compartment" attribute of this Reaction is
set, C<false> otherwise.
@note The "compartment" attribute is available in SBML
Level 3 Version 1 Core, but is not present on Reaction in
lower Levels of SBML.
=item Reaction::isSetReversible
Predicate returning C<true> if this
Reaction's "reversible" attribute is set.
@return C<true> if the "reversible" attribute of this Reaction is
set, C<false> otherwise.
=item Reaction::setId
Sets the value of the "id" attribute of this Reaction.
The string C<sid> is copied.
C<opydetails> doc_id_syntax
@param sid the string to use as the identifier of this Reaction
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif@~ The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item Reaction::setName
Sets the value of the "name" attribute of this Reaction.
The string in C<name> is copied.
@param name the new name for the Reaction
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif@~ The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item Reaction::setKineticLaw
Sets the "kineticLaw" subelement of this Reaction to a copy of the
given KineticLaw object.
@param kl the KineticLaw object to use.
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif@~ The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_LEVEL_MISMATCH LIBSBML_LEVEL_MISMATCH @endlink
@li @link OperationReturnValues_t#LIBSBML_VERSION_MISMATCH LIBSBML_VERSION_MISMATCH @endlink
=item Reaction::setReversible
Sets the value of the "reversible" attribute of this Reaction.
@param value the value of the "reversible" attribute.
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif@~ The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
=item Reaction::setFast
Sets the value of the "fast" attribute of this Reaction.
@param value the value of the "fast" attribute.
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif@~ The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
C<opydetails> doc_warning_reaction_cant_ignore_fast
=item Reaction::setCompartment
Sets the value of the "compartment" attribute of this Reaction.
The string C<sid> is copied.
@param sid the string to use as the compartment of this Reaction
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif@~ The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_UNEXPECTED_ATTRIBUTE LIBSBML_UNEXPECTED_ATTRIBUTE @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
@note The "compartment" attribute is available in SBML
Level 3 Version 1 Core, but is not present on Reaction in
lower Levels of SBML.
=item Reaction::unsetName
Unsets the value of the "name" attribute of this Reaction.
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif@~ The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item Reaction::unsetKineticLaw
Unsets the "kineticLaw" subelement of this Reaction.
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif@~ The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item Reaction::unsetFast
Unsets the value of the "fast" attribute of this Reaction.
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif@~ The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
C<opydetails> doc_warning_reaction_cant_ignore_fast
=item Reaction::unsetCompartment
Unsets the value of the "compartment" attribute of this Reaction.
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif@~ The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_UNEXPECTED_ATTRIBUTE LIBSBML_UNEXPECTED_ATTRIBUTE @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
@note The "compartment" attribute is available in SBML
Level 3 Version 1 Core, but is not present on Reaction in
lower Levels of SBML.
=item Reaction::addReactant
Adds a given SpeciesReference object as a reactant in this Reaction.
The SpeciesReference instance in C<sr> is copied.
@param sr a SpeciesReference object referring to a Species in the
enclosing Model
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif@~ The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_LEVEL_MISMATCH LIBSBML_LEVEL_MISMATCH @endlink
@li @link OperationReturnValues_t#LIBSBML_VERSION_MISMATCH LIBSBML_VERSION_MISMATCH @endlink
@li @link OperationReturnValues_t#LIBSBML_DUPLICATE_OBJECT_ID LIBSBML_DUPLICATE_OBJECT_ID @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
C<opydetails> doc_note_object_is_copied
@see createReactant()
=item Reaction::addProduct
Adds a given SpeciesReference object as a product in this Reaction.
The SpeciesReference instance in C<sr> is copied.
@param sr a SpeciesReference object referring to a Species in the
enclosing Model
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif@~ The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_LEVEL_MISMATCH LIBSBML_LEVEL_MISMATCH @endlink
@li @link OperationReturnValues_t#LIBSBML_VERSION_MISMATCH LIBSBML_VERSION_MISMATCH @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
C<opydetails> doc_note_object_is_copied
@see createProduct()
=item Reaction::addModifier
Adds a given ModifierSpeciesReference object as a product in this
Reaction.
The ModifierSpeciesReference instance in C<msr> is copied.
@param msr a ModifierSpeciesReference object referring to a Species in
the enclosing Model
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif@~ The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_UNEXPECTED_ATTRIBUTE LIBSBML_UNEXPECTED_ATTRIBUTE @endlink
@li @link OperationReturnValues_t#LIBSBML_LEVEL_MISMATCH LIBSBML_LEVEL_MISMATCH @endlink
@li @link OperationReturnValues_t#LIBSBML_DUPLICATE_OBJECT_ID LIBSBML_DUPLICATE_OBJECT_ID @endlink
@li @link OperationReturnValues_t#LIBSBML_VERSION_MISMATCH LIBSBML_VERSION_MISMATCH @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
C<opydetails> doc_note_object_is_copied
@see createModifier()
=item Reaction::createReactant
Creates a new SpeciesReference, adds it to this Reaction's list of
reactants, and returns it.
@return a new SpeciesReference object.
=item Reaction::createProduct
Creates a new SpeciesReference, adds it to this Reaction's list of
products, and returns it.
@return a new SpeciesReference object.
=item Reaction::createModifier
Creates a new ModifierSpeciesReference, adds it to this Reaction's
list of modifiers and returns it.
@return a new ModifierSpeciesReference object.
=item Reaction::createKineticLaw
Creates a new KineticLaw object, installs it as this Reaction's
"kineticLaw" subelement, and returns it.
If this Reaction had a previous KineticLaw, it will be destroyed.
@return the new KineticLaw object
=item Reaction::getListOfReactants
Returns the list of reactants in this Reaction object.
@return the ListOfSpeciesReferences containing the references to the
species acting as reactants in this reaction
=item Reaction::getListOfReactants
Returns the list of reactants in this Reaction object.
@return the ListOfSpeciesReferences containing the references to the
species acting as reactants in this reaction
=item Reaction::getListOfProducts
Returns the list of products in this Reaction object.
@return the ListOfSpeciesReferences containing the references to the
species acting as products in this reaction
=item Reaction::getListOfProducts
Returns the list of products in this Reaction object.
@return the ListOfSpeciesReferences containing the references to the
species acting as products in this reaction
=item Reaction::getListOfModifiers
Returns the list of modifiers in this Reaction object.
@return the ListOfSpeciesReferences containing the references to the
species acting as modifiers in this reaction
=item Reaction::getListOfModifiers
Returns the list of modifiers in this Reaction object.
@return the ListOfSpeciesReferences containing the references to the
species acting as modifiers in this reaction
=item Reaction::getReactant
Returns the nth reactant species (as a SpeciesReference object) in
the list of reactants in this Reaction.
Callers should first call getNumReactants() to find out how many
reactants there are, to avoid using an invalid index number.
@param n the index of the reactant sought.
@return the nth reactant (as a SpeciesReference object) of this
Reaction.
=item Reaction::getReactant
Returns the nth reactant species (as a SpeciesReference object)
in the list of reactants in this Reaction.
Callers should first call getNumReactants() to find out how many
reactants there are, to avoid using an invalid index number.
@param n the index of the reactant sought.
@return the nth reactant (as a SpeciesReference object) of this
Reaction.
=item Reaction::getReactant
Returns the reactant species (as a SpeciesReference object) having
a specific identifier in this Reaction.
@param species the identifier of the reactant Species ("species"
attribute of the reactant SpeciesReference object)
@return a SpeciesReference object, or C<NULL> if no species with the
given identifier C<species> appears as a reactant in this Reaction.
=item Reaction::getReactant
Returns the reactant species (as a SpeciesReference object) having
a specific identifier in this Reaction.
@param species the identifier of the reactant Species ("species"
attribute of the reactant SpeciesReference object)
@return a SpeciesReference object, or C<NULL> if no species with the
given identifier C<species> appears as a reactant in this Reaction.
=item Reaction::getProduct
Returns the nth product species (as a SpeciesReference object) in
the list of products in this Reaction.
Callers should first call getNumProducts() to find out how many
products there are, to avoid using an invalid index number.
@param n the index of the product sought.
@return the nth product (as a SpeciesReference object) of this
Reaction.
=item Reaction::getProduct
Returns the nth product species (as a SpeciesReference object)
in the list of products in this Reaction.
Callers should first call getNumProducts() to find out how many
products there are, to avoid using an invalid index number.
@param n the index of the product sought.
@return the nth product (as a SpeciesReference object) of this
Reaction.
=item Reaction::getProduct
Returns the product species (as a SpeciesReference object) having
a specific identifier in this Reaction.
@param species the identifier of the product Species ("species"
attribute of the product SpeciesReference object)
@return a SpeciesReference object, or C<NULL> if no species with the
given identifier C<species> appears as a product in this Reaction.
=item Reaction::getProduct
Returns the product species (as a SpeciesReference object) having
a specific identifier in this Reaction.
@param species the identifier of the product Species ("species"
attribute of the product SpeciesReference object)
@return a SpeciesReference object, or C<NULL> if no species with the
given identifier C<species> appears as a product in this Reaction.
=item Reaction::getModifier
Returns the nth modifier species (as a ModifierSpeciesReference object)
in the list of modifiers of this Reaction.
Callers should first call getNumModifiers() to find out how many
modifiers there are, to avoid using an invalid index number.
@param n the index of the modifier species sought
@return the nth modifier (as a ModifierSpeciesReference object) of
this Reaction.
=item Reaction::getModifier
Returns the nth modifier species (as a ModifierSpeciesReference object)
in the list of modifiers of this Reaction.
Callers should first call getNumModifiers() to find out how many
modifiers there are, to avoid using an invalid index number.
@param n the index of the modifier species sought
@return the nth modifier (as a ModifierSpeciesReference object) of
this Reaction.
=item Reaction::getModifier
Returns the modifier species (as a ModifierSpeciesReference object)
having a specific identifier in this Reaction.
@param species the identifier of the modifier Species ("species"
attribute of the ModifierSpeciesReference object)
@return a ModifierSpeciesReference object, or C<NULL> if no species with
the given identifier C<species> appears as a modifier in this
Reaction.
=item Reaction::getModifier
Returns the modifier species (as a ModifierSpeciesReference object)
having a specific identifier in this Reaction.
@param species the identifier of the modifier Species ("species"
attribute of the ModifierSpeciesReference object)
@return a ModifierSpeciesReference object, or C<NULL> if no species with
the given identifier C<species> appears as a modifier in this
Reaction.
=item Reaction::getNumReactants
Returns the number of reactant species in this Reaction.
@return the number of reactants in this Reaction.
=item Reaction::getNumProducts
Returns the number of product species in this Reaction.
@return the number of products in this Reaction.
=item Reaction::getNumModifiers
Returns the number of modifier species in this Reaction.
@return the number of modifiers in this Reaction.
=item Reaction::removeReactant
Removes the nth reactant species (SpeciesReference object) in the list of
reactants in this Reaction and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
The caller should first call getNumReactants() to find out how many
reactants there are, to avoid using an invalid index number.
@param n the index of the reactant SpeciesReference object to remove
@return the removed reactant SpeciesReference object, or C<NULL> if the
given index is out of range.
=item Reaction::removeReactant
Removes the reactant species (SpeciesReference object) having the given
"species" attribute in this Reaction and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
@param species the "species" attribute of the reactant SpeciesReference
object
@return the removed reactant SpeciesReference object, or C<NULL> if no
reactant SpeciesReference object with the given "species" attribute
C<species> exists in this Reaction.
=item Reaction::removeProduct
Removes the nth product species (SpeciesReference object) in the list of
products in this Reaction and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
The caller should first call getNumProducts() to find out how many
products there are, to avoid using an invalid index number.
@param n the index of the product SpeciesReference object to remove
@return the removed product SpeciesReference object, or C<NULL> if the
given index is out of range.
=item Reaction::removeProduct
Removes the product species (SpeciesReference object) having the given
"species" attribute in this Reaction and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
@param species the "species" attribute of the product SpeciesReference
object
@return the removed product SpeciesReference object, or C<NULL> if no
product SpeciesReference object with the given "species" attribute
C<species> exists in this Reaction.
=item Reaction::removeModifier
Removes the nth modifier species (ModifierSpeciesReference object) in
the list of modifiers in this Reaction and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
The caller should first call getNumModifiers() to find out how many
modifiers there are, to avoid using an invalid index number.
@param n the index of the ModifierSpeciesReference object to remove
@return the removed ModifierSpeciesReference object, or C<NULL> if the
given index is out of range.
=item Reaction::removeModifier
Removes the modifier species (ModifierSpeciesReference object) having
the given "species" attribute in this Reaction and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
@param species the "species" attribute of the ModifierSpeciesReference
object
@return the removed ModifierSpeciesReference object, or C<NULL> if no
ModifierSpeciesReference object with the given "species" attribute @p
species exists in this Reaction.
=item Reaction::setSBMLDocument
@internal
Sets the parent SBMLDocument of this SBML object.
=item Reaction::connectToChild
@internal
Sets this SBML object to child SBML objects (if any).
(Creates a child-parent relationship by the parent)
Subclasses must override this function if they define
one ore more child elements.
Basically, this function needs to be called in
constructor, copy constructor and assignment operator.
@see setSBMLDocument
@see enablePackageInternal
=item Reaction::enablePackageInternal
@internal
Enables/Disables the given package with this element and child
elements (if any).
(This is an internal implementation for enablePackage function)
@note Subclasses of the SBML Core package in which one or more child
elements are defined must override this function.
=item Reaction::getTypeCode
Returns the libSBML type code for this SBML object.
C<opydetails> doc_what_are_typecodes
@return the SBML type code for this object:
@link SBMLTypeCode_t#SBML_REACTION SBML_REACTION@endlink (default).
C<opydetails> doc_warning_typecodes_not_unique
@see getElementName()
@see getPackageName()
=item Reaction::getElementName
Returns the XML element name of this object, which for Reaction, is
always C<"reaction">.
@return the name of this element, i.e., C<"reaction">.
=item Reaction::writeElements
@internal
Subclasses should override this method to write out their contained
SBML objects as XML elements. Be sure to call your parents
implementation of this method as well.
=item Reaction::hasRequiredAttributes
Predicate returning C<true> if all the required attributes for this
Reaction object have been set.
@note The required attributes for a Reaction object are:
@li "id" (or "name" in SBML Level 1)
@li "fast" (in Level 3 only, where it is defined as a required attribute)
@li "reversible" (in Level 3 only, where it is defined as a required attribute)
@return a boolean value indicating whether all the required
attributes for this object have been defined.
=item Reaction::createObject
@internal
Create and return an SBML object of this class, if present.
@return the SBML object corresponding to next XMLToken in the
XMLInputStream or C<NULL> if the token was not recognized.
=item Reaction::addExpectedAttributes
@internal
Subclasses should override this method to get the list of
expected attributes.
This function is invoked from corresponding readAttributes()
function.
=item Reaction::readAttributes
@internal
Subclasses should override this method to read values from the given
XMLAttributes set into their specific fields. Be sure to call your
parents implementation of this method as well.
=item Reaction::readL1Attributes
@internal
=item Reaction::readL2Attributes
@internal
=item Reaction::readL3Attributes
@internal
=item Reaction::writeAttributes
@internal
Subclasses should override this method to write their XML attributes
to the XMLOutputStream. Be sure to call your parents implementation
of this method as well.
=item Reaction::isExplicitlySetReversible
@internal
=item Reaction::isExplicitlySetFast
@internal
=item ListOfReactions::ListOfReactions
Creates a new ListOfReactions object.
The object is constructed such that it is valid for the given SBML
Level and Version combination.
@param level the SBML Level
@param version the Version within the SBML Level
=item ListOfReactions::ListOfReactions
Creates a new ListOfReactions object.
The object is constructed such that it is valid for the SBML Level and
Version combination determined by the SBMLNamespaces object in @p
sbmlns.
@param sbmlns an SBMLNamespaces object that is used to determine the
characteristics of the ListOfReactions object to be created.
=item ListOfReactions::clone
Creates and returns a deep copy of this ListOfReactions instance.
@return a (deep) copy of this ListOfReactions.
=item ListOfReactions::getItemTypeCode
Returns the libSBML type code for the objects contained in this ListOf
(i.e., Reaction objects, if the list is non-empty).
C<opydetails> doc_what_are_typecodes
@return the SBML type code for objects contained in this list:
@link SBMLTypeCode_t#SBML_REACTION SBML_REACTION@endlink (default).
@see getElementName()
@see getPackageName()
=item ListOfReactions::getElementName
Returns the XML element name of this object
For ListOfReactions, the XML element name is C<"listOfReactions">.
@return the name of this element, i.e., C<"listOfReactions">.
=item ListOfReactions::get
Get a Reaction from the ListOfReactions.
@param n the index number of the Reaction to get.
@return the nth Reaction in this ListOfReactions.
@see size()
=item ListOfReactions::get
Get a Reaction from the ListOfReactions.
@param n the index number of the Reaction to get.
@return the nth Reaction in this ListOfReactions.
@see size()
=item ListOfReactions::get
Get a Reaction from the ListOfReactions based on its identifier.
@param sid a string representing the identifier of the Reaction to get.
@return Reaction in this ListOfReactions with the given C<sid> or @c
NULL if no such Reaction exists.
@see get(unsigned int n)
@see size()
=item ListOfReactions::get
Get a Reaction from the ListOfReactions based on its identifier.
@param sid a string representing the identifier of the Reaction to get.
@return Reaction in this ListOfReactions with the given C<sid> or @c
NULL if no such Reaction exists.
@see get(unsigned int n)
@see size()
=item ListOfReactions::remove
Removes the nth item from this ListOfReactions items and returns a
pointer to it.
The caller owns the returned item and is responsible for deleting it.
@param n the index of the item to remove
@see size()
=item ListOfReactions::remove
Removes item in this ListOfReactions items with the given identifier.
The caller owns the returned item and is responsible for deleting it.
If none of the items in this list have the identifier C<sid>, then
NULL is returned.
@param sid the identifier of the item to remove
@return the item removed. As mentioned above, the caller owns the
returned item.
=item ListOfReactions::getElementPosition
@internal
Return the position of this element.
@return the ordinal position of the element with respect to its
siblings or -1 (default) to indicate the position is not significant.
=item ListOfReactions::createObject
@internal
Create and return an SBML object of this class, if present.
@return the SBML object corresponding to next XMLToken in the
XMLInputStream or C<NULL> if the token was not recognized.
=back
=head2 KineticLaw
@sbmlpackage{core}
@htmlinclude pkg-marker-core.html Implementation of SBML's KineticLaw construct.
An object of class KineticLaw is used to describe the rate at which the
process defined by a given Reaction takes place. KineticLaw has
subelements called "math" (for MathML content) and "listOfParameters"
(of class ListOfParameters), in addition to the attributes and
subelements it inherits from SBase.
KineticLaw's "math" subelement for holding a MathML formula defines the
rate of the reaction. The formula may refer to other entities in a
model as well as local parameter definitions within the scope of the
Reaction (see below). It is important to keep in mind, however, that
the only Species identifiers that can be used in this formula are those
declared in the lists of reactants, products and modifiers in the
Reaction structure. (In other words, before a species can be referenced
in the KineticLaw, it must be declared in one of those lists.)
KineticLaw provides a way to define I<local> parameters whose
identifiers can be used in the "math" formula of that KineticLaw
instance. Prior to SBML Level 3, these parameter definitions are
stored inside a "listOfParameters" subelement containing Parameter
objects; in SBML Level 3, this is achieved using a specialized
object class called LocalParameter and the containing subelement is
called "listOfLocalParameters". In both cases, the parameters so
defined are only visible within the KineticLaw; they cannot be accessed
outside. A local parameter within one reaction is not visible from
within another reaction, nor is it visible to any other construct
outside of the KineticLaw in which it is defined. In addition, another
important feature is that if such a Parameter (or in Level 3,
LocalParameter) object has the same identifier as another object in the
scope of the enclosing Model, the definition inside the KineticLaw takes
precedence. In other words, within the KineticLaw's "math" formula,
references to local parameter identifiers <strong>shadow any identical
global identifiers</strong>.
The values of local parameters defined within KineticLaw objects cannot
change. In SBML Level 3, this quality is built into the
LocalParameter construct. In Level 2, where the same kind of
Parameter object class is used as for global parameters, the Parameter
objects' "constant" attribute must always have a value of C<true>
(either explicitly or left to its default value).
@section shadowing-warning A warning about identifier shadowing
A common misconception is that different classes of objects (e.g.,
species, compartments, parameters) in SBML have different identifier
scopes. They do not. The implication is that if a KineticLaw's local
parameter definition uses an identifier identical to I<any> other
identifier defined in the model outside the KineticLaw, even if the
other identifier does I<not> belong to a parameter type of object, the
local parameter's identifier takes precedence within that KineticLaw's
"math" formula. It is not an error in SBML for identifiers to shadow
each other this way, but can lead to confusing and subtle errors.
@section version-diffs SBML Level/Version differences
In SBML Level 2 Version 1, the SBML specification
included two additional attributes on KineticLaw called "substanceUnits"
and "timeUnits". They were removed beginning with SBML Level 2
Version 2 because further research determined they introduced many
problems. The most significant problem was that their use could easily
lead to the creation of valid models whose reactions nevertheless could
not be integrated into a system of equations without outside knowledge
for converting the quantities used. Examination of real-life models
revealed that a common reason for using "substanceUnits" on KineticLaw
was to set the units of all reactions to the same set of substance
units, something that is better achieved by using UnitDefinition to
redefine C<"substance"> for the whole Model.
As mentioned above, in SBML Level 2 Versions 2–4, local
parameters are of class Parameter. In SBML Level 3, the class of
object is LocalParameter.
=over
=item KineticLaw::KineticLaw
Creates a new KineticLaw using the given SBML C<level> and C<version>
values.
@param level an unsigned int, the SBML Level to assign to this KineticLaw
@param version an unsigned int, the SBML Version to assign to this
KineticLaw
@throws @if python ValueError @else SBMLConstructorException @endif@~
Thrown if the given C<level> and C<version> combination, or this kind
of SBML object, are either invalid or mismatched with respect to the
parent SBMLDocument object.
C<opydetails> doc_note_kineticlaw_setting_lv
=item KineticLaw::KineticLaw
Creates a new KineticLaw using the given SBMLNamespaces object
C<sbmlns>.
C<opydetails> doc_what_are_sbmlnamespaces
@param sbmlns an SBMLNamespaces object.
@throws @if python ValueError @else SBMLConstructorException @endif@~
Thrown if the given C<level> and C<version> combination, or this kind
of SBML object, are either invalid or mismatched with respect to the
parent SBMLDocument object.
C<opydetails> doc_note_kineticlaw_setting_lv
=item KineticLaw::KineticLaw
Copy constructor; creates a copy of this KineticLaw.
@param orig the object to copy.
@throws @if python ValueError @else SBMLConstructorException @endif@~
Thrown if the argument C<orig> is C<NULL>.
=item KineticLaw::accept
Accepts the given SBMLVisitor for this instance of KineticLaw.
@param v the SBMLVisitor instance to be used.
@return the result of calling C<v.visit()>.
=item KineticLaw::clone
Creates and returns a deep copy of this KineticLaw object.
@return a (deep) copy of this KineticLaw.
=item KineticLaw::getElementBySId
Returns the first child element found that has the given C<id> in the
model-wide SId namespace, or C<NULL> if no such object is found.
@param id string representing the id of objects to find.
@return pointer to the first element found with the given C<id>.
=item KineticLaw::getElementByMetaId
Returns the first child element it can find with the given C<metaid>, or
C<NULL> if no such object is found.
@param metaid string representing the metaid of objects to find
@return pointer to the first element found with the given C<metaid>.
=item KineticLaw::getAllElements
Returns a List of all child SBase objects, including those nested to an
arbitrary depth
@return a List of pointers to all children objects.
=item KineticLaw::getFormula
Returns the mathematical formula for this KineticLaw object and return
it as as a text string.
This is fundamentally equivalent to
@if java KineticLaw::getMath()@else getMath()@endif.
This variant is provided principally for compatibility compatibility
with SBML Level 1.
@return a string representing the formula of this KineticLaw.
@note @htmlinclude level-1-uses-text-string-math.html
@see getMath()
=item KineticLaw::getMath
Returns the mathematical formula for this KineticLaw object and return
it as as an AST.
This is fundamentally equivalent to
@if java KineticLaw::getFormula()@else getFormula()@endif.
The latter is provided principally for compatibility compatibility
with SBML Level 1, which represented mathematical formulas in
text-string form.
@return the ASTNode representation of the mathematical formula.
@see getFormula()
=item KineticLaw::getTimeUnits
(SBML Level 2 Version 1 only) Returns the value of the
"timeUnits" attribute of this KineticLaw object.
@return the "timeUnits" attribute value.
C<opydetails> doc_note_timeunits_substanceunits
=item KineticLaw::getSubstanceUnits
(SBML Level 2 Version 1 only) Returns the value of the
"substanceUnits" attribute of this KineticLaw object.
@return the "substanceUnits" attribute value.
C<opydetails> doc_note_timeunits_substanceunits
=item KineticLaw::isSetFormula
Predicate returning C<true> if this KineticLaw's "formula" attribute is
set.
This is functionally identical to the method
@if java KineticLaw::isSetMath()@else isSetMath()@endif. It is
provided in order to mirror the parallel between
@if java KineticLaw::getFormula()@else getFormula()@endif@~ and
@if java KineticLaw::getMath()@else getMath()@endif.
@return C<true> if the formula (meaning the C<math> subelement) of
this KineticLaw is set, C<false> otherwise.
@note @htmlinclude level-1-uses-text-string-math.html
@see isSetMath()
=item KineticLaw::isSetMath
Predicate returning C<true> if this Kinetic's "math" subelement is set.
This is identical to the method
@if java KineticLaw::isSetFormula()@else isSetFormula()@endif.
It is provided in order to mirror the parallel between
@if java KineticLaw::getFormula()@else getFormula()@endif@~ and
@if java KineticLaw::getMath()@else getMath()@endif.
@return C<true> if the formula (meaning the C<math> subelement) of
this KineticLaw is set, C<false> otherwise.
@see isSetFormula()
=item KineticLaw::isSetTimeUnits
(SBML Level 2 Version 1 only) Predicate returning C<true> if
this SpeciesReference's "timeUnits" attribute is set.
@return C<true> if the "timeUnits" attribute of this KineticLaw object
is set, C<false> otherwise.
C<opydetails> doc_note_timeunits_substanceunits
=item KineticLaw::isSetSubstanceUnits
(SBML Level 2 Version 1 only) Predicate returning C<true> if
this SpeciesReference's "substanceUnits" attribute is set.
@return C<true> if the "substanceUnits" attribute of this KineticLaw
object is set, C<false> otherwise.
C<opydetails> doc_note_timeunits_substanceunits
=item KineticLaw::setFormula
Sets the mathematical expression of this KineticLaw instance to the
given C<formula>.
The given C<formula> string is copied. Internally, libSBML stores the
mathematical expression as an ASTNode.
@param formula the mathematical expression to use, represented in
text-string form.
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT @endlink
@note @htmlinclude level-1-uses-text-string-math.html
@see setMath(const ASTNode math)
=item KineticLaw::setMath
Sets the mathematical expression of this KineticLaw instance to a copy
of the given ASTNode.
This is fundamentally identical to
@if java KineticLaw::setFormula(String formula)@else getFormula()@endif.
The latter is provided principally for compatibility compatibility with
SBML Level 1, which represented mathematical formulas in text-string
form.
@param math an ASTNode representing a formula tree.
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT @endlink
@see setFormula(const std::string& formula)
=item KineticLaw::setTimeUnits
(SBML Level 2 Version 1 only) Sets the "timeUnits" attribute
of this KineticLaw object to a copy of the identifier in C<sid>.
@param sid the identifier of the units to use.
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
@li @link OperationReturnValues_t#LIBSBML_UNEXPECTED_ATTRIBUTE LIBSBML_UNEXPECTED_ATTRIBUTE @endlink
C<opydetails> doc_note_timeunits_substanceunits
=item KineticLaw::setSubstanceUnits
(SBML Level 2 Version 1 only) Sets the "substanceUnits"
attribute of this KineticLaw object to a copy of the identifier given
in C<sid>.
@param sid the identifier of the units to use.
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
@li @link OperationReturnValues_t#LIBSBML_UNEXPECTED_ATTRIBUTE LIBSBML_UNEXPECTED_ATTRIBUTE @endlink
C<opydetails> doc_note_timeunits_substanceunits
=item KineticLaw::unsetTimeUnits
(SBML Level 2 Version 1 only) Unsets the "timeUnits"
attribugte of this KineticLaw object.
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
@li @link OperationReturnValues_t#LIBSBML_UNEXPECTED_ATTRIBUTE LIBSBML_UNEXPECTED_ATTRIBUTE @endlink
C<opydetails> doc_note_timeunits_substanceunits
=item KineticLaw::unsetSubstanceUnits
(SBML Level 2 Version 1 only) Unsets the "substanceUnits"
attribute of this KineticLaw object.
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
@li @link OperationReturnValues_t#LIBSBML_UNEXPECTED_ATTRIBUTE LIBSBML_UNEXPECTED_ATTRIBUTE @endlink
C<opydetails> doc_note_timeunits_substanceunits
=item KineticLaw::addParameter
Adds a copy of the given Parameter object to the list of local
parameters in this KineticLaw.
@param p the Parameter to add
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_LEVEL_MISMATCH LIBSBML_LEVEL_MISMATCH @endlink
@li @link OperationReturnValues_t#LIBSBML_VERSION_MISMATCH LIBSBML_VERSION_MISMATCH @endlink
@li @link OperationReturnValues_t#LIBSBML_DUPLICATE_OBJECT_ID LIBSBML_DUPLICATE_OBJECT_ID @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
C<opydetails> doc_note_object_is_copied
@see createParameter()
=item KineticLaw::addLocalParameter
Adds a copy of the given LocalParameter object to the list of local
parameters in this KineticLaw.
@param p the LocalParameter to add
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_LEVEL_MISMATCH LIBSBML_LEVEL_MISMATCH @endlink
@li @link OperationReturnValues_t#LIBSBML_VERSION_MISMATCH LIBSBML_VERSION_MISMATCH @endlink
@li @link OperationReturnValues_t#LIBSBML_DUPLICATE_OBJECT_ID LIBSBML_DUPLICATE_OBJECT_ID @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
C<opydetails> doc_note_object_is_copied
@see createLocalParameter()
=item KineticLaw::createParameter
Creates a new Parameter object, adds it to this KineticLaw's list of
local parameters, and returns the Parameter object created.
@return a new Parameter object instance
@see addParameter(const Parameter p)
=item KineticLaw::createLocalParameter
Creates a new LocalParameter object, adds it to this KineticLaw's list
of local parameters, and returns the LocalParameter object created.
@return a new LocalParameter object instance
@see addLocalParameter(const LocalParameter p)
=item KineticLaw::getListOfParameters
Returns the list of local parameters in this KineticLaw object.
@return the list of Parameters for this KineticLaw.
=item KineticLaw::getListOfParameters
Returns the list of local parameters in this KineticLaw object.
@return the list of Parameters for this KineticLaw.
=item KineticLaw::getListOfLocalParameters
Returns the list of local parameters in this KineticLaw object.
@return the list of LocalParameters for this KineticLaw.
=item KineticLaw::getListOfLocalParameters
Returns the list of local parameters in this KineticLaw object.
@return the list of LocalParameters for this KineticLaw.
=item KineticLaw::getParameter
Returns the nth Parameter object in the list of local parameters in
this KineticLaw instance.
@param n the index of the Parameter object sought
@return the nth Parameter of this KineticLaw.
=item KineticLaw::getParameter
Returns the nth Parameter object in the list of local parameters in
this KineticLaw instance.
@param n the index of the Parameter object sought
@return the nth Parameter of this KineticLaw.
=item KineticLaw::getLocalParameter
Returns the nth LocalParameter object in the list of local parameters in
this KineticLaw instance.
@param n the index of the LocalParameter object sought
@return the nth LocalParameter of this KineticLaw.
=item KineticLaw::getLocalParameter
Returns the nth LocalParameter object in the list of local parameters in
this KineticLaw instance.
@param n the index of the LocalParameter object sought
@return the nth LocalParameter of this KineticLaw.
=item KineticLaw::getParameter
Returns a local parameter based on its identifier.
@param sid the identifier of the Parameter being sought.
@return the Parameter object in this KineticLaw instace having the
given "id", or C<NULL> if no such Parameter exists.
=item KineticLaw::getParameter
Returns a local parameter based on its identifier.
@param sid the identifier of the Parameter being sought.
@return the Parameter object in this KineticLaw instace having the
given "id", or C<NULL> if no such Parameter exists.
=item KineticLaw::getLocalParameter
Returns a local parameter based on its identifier.
@param sid the identifier of the LocalParameter being sought.
@return the LocalParameter object in this KineticLaw instace having the
given "id", or C<NULL> if no such LocalParameter exists.
=item KineticLaw::getLocalParameter
Returns a local parameter based on its identifier.
@param sid the identifier of the LocalParameter being sought.
@return the LocalParameter object in this KineticLaw instace having the
given "id", or C<NULL> if no such LocalParameter exists.
=item KineticLaw::getNumParameters
Returns the number of local parameters in this KineticLaw instance.
@return the number of Parameters in this KineticLaw.
=item KineticLaw::getNumLocalParameters
Returns the number of local parameters in this KineticLaw instance.
@return the number of LocalParameters in this KineticLaw.
=item KineticLaw::getDerivedUnitDefinition
Calculates and returns a UnitDefinition that expresses the units of
measurement assumed for the "math" expression of this KineticLaw.
C<opydetails> doc_kineticlaw_units
C<opydetails> doc_note_unit_inference_depends_on_model
C<opydetails> doc_warning_kineticlaw_math_literals
@return a UnitDefinition that expresses the units of the math
expression of this KineticLaw, or C<NULL> if one cannot be constructed.
@see containsUndeclaredUnits()
=item KineticLaw::getDerivedUnitDefinition
Calculates and returns a UnitDefinition that expresses the units of
measurement assumed for the "math" expression of this KineticLaw.
C<opydetails> doc_kineticlaw_units
C<opydetails> doc_note_unit_inference_depends_on_model
C<opydetails> doc_warning_kineticlaw_math_literals
@return a UnitDefinition that expresses the units of the math
expression of this KineticLaw, or C<NULL> if one cannot be constructed.
@see containsUndeclaredUnits()
=item KineticLaw::containsUndeclaredUnits
Predicate returning C<true> if the math expression of this KineticLaw
contains parameters/numbers with undeclared units.
@return C<true> if the math expression of this KineticLaw
includes parameters/numbers
with undeclared units, C<false> otherwise.
@note A return value of C<true> indicates that the UnitDefinition
returned by
@if java KineticLaw::getDerivedUnitDefinition()@else getDerivedUnitDefinition()@endif@~
may not accurately represent the units of the expression.
@see getDerivedUnitDefinition()
=item KineticLaw::containsUndeclaredUnits
Predicate returning C<true> if the math expression of this KineticLaw
contains parameters/numbers with undeclared units.
@return C<true> if the math expression of this KineticLaw
includes parameters/numbers
with undeclared units, C<false> otherwise.
@note A return value of C<true> indicates that the UnitDefinition
returned by
@if java KineticLaw::getDerivedUnitDefinition()@else getDerivedUnitDefinition()@endif@~
may not accurately represent the units of the expression.
@see getDerivedUnitDefinition()
=item KineticLaw::removeParameter
Removes the nth Parameter object in the list of local parameters
in this KineticLaw instance and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
@param n the index of the Parameter object to remove
@return the Parameter object removed. As mentioned above,
the caller owns the returned item. C<NULL> is returned if the given index
is out of range.
=item KineticLaw::removeLocalParameter
Removes the nth LocalParameter object in the list of local parameters
in this KineticLaw instance and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
@param n the index of the LocalParameter object to remove
@return the LocalParameter object removed. As mentioned above,
the caller owns the returned item. C<NULL> is returned if the given index
is out of range.
=item KineticLaw::removeParameter
Removes a Parameter object with the given identifier in the list of
local parameters in this KineticLaw instance and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
@param sid the identifier of the Parameter to remove
@return the Parameter object removed. As mentioned above, the
caller owns the returned object. C<NULL> is returned if no Parameter
object with the identifier exists in this KineticLaw instance.
=item KineticLaw::removeLocalParameter
Removes a LocalParameter object with the given identifier in the list of
local parameters in this KineticLaw instance and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
@param sid the identifier of the LocalParameter to remove
@return the LocalParameter object removed. As mentioned above, the
caller owns the returned object. C<NULL> is returned if no LocalParameter
object with the identifier exists in this KineticLaw instance.
=item KineticLaw::setSBMLDocument
@internal
Sets the parent SBMLDocument of this SBML object.
@param d the SBMLDocument to use.
=item KineticLaw::connectToChild
@internal
Sets this SBML object to child SBML objects (if any).
(Creates a child-parent relationship by the parent)
Subclasses must override this function if they define one ore more child
elements. Basically, this function needs to be called in constructor,
copy constructor and assignment operator.
@see setSBMLDocument
@see enablePackageInternal
=item KineticLaw::enablePackageInternal
@internal
Enables/Disables the given package with this element and child
elements (if any).
(This is an internal implementation for enablePackage function)
@note Subclasses of the SBML Core package in which one or more child
elements are defined must override this function.
=item KineticLaw::getTypeCode
Returns the libSBML type code for this SBML object.
C<opydetails> doc_what_are_typecodes
@return the SBML type code for this object:
@link SBMLTypeCode_t#SBML_KINETIC_LAW SBML_KINETIC_LAW@endlink (default).
C<opydetails> doc_warning_typecodes_not_unique
@see getElementName()
@see getPackageName()
=item KineticLaw::getElementName
Returns the XML element name of this object, which for Species, is
always C<"kineticLaw">.
@return the name of this element, i.e., C<"kineticLaw">.
=item KineticLaw::getElementPosition
@internal
Return the position of this element.
@return the ordinal position of the element with respect to its
siblings or -1 (default) to indicate the position is not significant.
=item KineticLaw::writeElements
@internal
Subclasses should override this method to write out their contained
SBML objects as XML elements. Be sure to call your parents
implementation of this method as well.
=item KineticLaw::hasRequiredAttributes
Predicate returning C<true> if all the required attributes for this
KineticLaw object have been set.
@note The required attributes for a KineticLaw object are:
@li "formula" (SBML Level 1 only)
@return a boolean value indicating whether all the required
attributes for this object have been defined.
=item KineticLaw::hasRequiredElements
Predicate returning C<true> if all the required elements for this
KineticLaw object have been set.
@note The required elements for a KineticLaw object are:
@li "math"
@return a boolean value indicating whether all the required
elements for this object have been defined.
=item KineticLaw::removeFromParentAndDelete
Finds this KineticLaw's Reaction parent and calls unsetKineticLaw() on
it, indirectly deleting itself.
Overridden from the SBase function since the parent is not a ListOf.
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif@~ The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item KineticLaw::renameSIdRefs
Renames all the C<SIdRef> attributes on this element, including any
found in MathML.
C<opydetails> doc_what_is_sidref
This method works by looking at all attributes and (if appropriate)
mathematical formulas, comparing the identifiers to the value of @p
oldid. If any matches are found, the matching identifiers are replaced
with C<newid>. The method does I<not> descend into child elements.
@param oldid the old identifier
@param newid the new identifier
=item KineticLaw::renameUnitSIdRefs
Renames all the C<UnitSIdRef> attributes on this element
C<opydetails> doc_what_is_unitsidref
This method works by looking at all unit identifier attribute values
(including, if appropriate, inside mathematical formulas), comparing the
unit identifiers to the value of C<oldid>. If any matches are found,
the matching identifiers are replaced with C<newid>. The method does
I<not> descend into child elements.
@param oldid the old identifier
@param newid the new identifier
=item KineticLaw::getInternalId
@internal
=item KineticLaw::setInternalId
@internal
=item KineticLaw::replaceSIDWithFunction
@internal
Replace all nodes with the name 'id' from the child 'math' object with the provided function.
=item KineticLaw::divideAssignmentsToSIdByFunction
@internal
If this reaction id matches the provided 'id' string, replace the 'math' object with the function (existing/function).
=item KineticLaw::multiplyAssignmentsToSIdByFunction
@internal
If this assignment assigns a value to the 'id' element, replace the 'math' object with the function (existing function).
=item KineticLaw::createObject
@internal
Create and return an SBML object of this class, if present.
@return the SBML object corresponding to next XMLToken in the
XMLInputStream or C<NULL> if the token was not recognized.
=item KineticLaw::readOtherXML
@internal
Subclasses should override this method to read (and store) XHTML,
MathML, etc. directly from the XMLInputStream.
@return true if the subclass read from the stream, false otherwise.
=item KineticLaw::addExpectedAttributes
@internal
Subclasses should override this method to get the list of
expected attributes.
This function is invoked from corresponding readAttributes()
function.
=item KineticLaw::readAttributes
@internal
Subclasses should override this method to read values from the given
XMLAttributes set into their specific fields. Be sure to call your
parents implementation of this method as well.
=item KineticLaw::readL1Attributes
@internal
=item KineticLaw::readL2Attributes
@internal
=item KineticLaw::readL3Attributes
@internal
=item KineticLaw::writeAttributes
@internal
Subclasses should override this method to write their XML attributes
to the XMLOutputStream. Be sure to call your parents implementation
of this method as well.
=back
=head2 SimpleSpeciesReference
@sbmlpackage{core}
@htmlinclude pkg-marker-core.html Implementation of SBML's SimpleSpeciesReference
construct.
As mentioned in the description of Reaction, every species that enters
into a given reaction must appear in that reaction's lists of reactants,
products and/or modifiers. In an SBML model, all species that may
participate in any reaction are listed in the "listOfSpecies" element of
the top-level Model object. Lists of products, reactants and modifiers
in Reaction objects do not introduce new species, but rather, they refer
back to those listed in the model's top-level "listOfSpecies". For
reactants and products, the connection is made using SpeciesReference
objects; for modifiers, it is made using ModifierSpeciesReference
objects. SimpleSpeciesReference is an abstract type that serves as the
parent class of both SpeciesReference and ModifierSpeciesReference. It
is used simply to hold the attributes and elements that are common to
the latter two structures.
The SimpleSpeciesReference structure has a mandatory attribute,
"species", which must be a text string conforming to the identifer
syntax permitted in SBML. This attribute is inherited by the
SpeciesReference and ModifierSpeciesReference subclasses derived from
SimpleSpeciesReference. The value of the "species" attribute must be
the identifier of a species defined in the enclosing Model. The species
is thereby declared as participating in the reaction being defined. The
precise role of that species as a reactant, product, or modifier in the
reaction is determined by the subclass of SimpleSpeciesReference (i.e.,
either SpeciesReference or ModifierSpeciesReference) in which the
identifier appears.
SimpleSpeciesReference also contains an optional attribute, "id",
allowing instances to be referenced from other structures. No SBML
structures currently do this; however, such structures are anticipated
in future SBML Levels.
=over
=item SimpleSpeciesReference::SimpleSpeciesReference
Creates a new SimpleSpeciesReference using the given SBML C<level> and C<version>
values.
@param level an unsigned int, the SBML Level to assign to this SimpleSpeciesReference
@param version an unsigned int, the SBML Version to assign to this
SimpleSpeciesReference
@throws @if python ValueError @else SBMLConstructorException @endif@~
Thrown if the given C<level> and C<version> combination, or this kind
of SBML object, are either invalid or mismatched with respect to the
parent SBMLDocument object.
=item SimpleSpeciesReference::SimpleSpeciesReference
Copy constructor; creates a copy of this SimpleSpeciesReference.
@param orig the object to copy.
@throws @if python ValueError @else SBMLConstructorException @endif@~
Thrown if the argument C<orig> is C<NULL>.
=item SimpleSpeciesReference::accept
Accepts the given SBMLVisitor.
@param v the SBMLVisitor instance to be used.
@return the result of calling C<v.visit()>.
=item SimpleSpeciesReference::getId
Returns the value of the "id" attribute of this SimpleSpeciesReference.
@return the id of this SimpleSpeciesReference.
=item SimpleSpeciesReference::getName
Returns the value of the "name" attribute of this SimpleSpeciesReference.
@return the name of this SimpleSpeciesReference.
=item SimpleSpeciesReference::getSpecies
Get the value of the "species" attribute.
@return the value of the attribute "species" for this
SimpleSpeciesReference.
=item SimpleSpeciesReference::isSetId
Predicate returning C<true> if this
SimpleSpeciesReference's "id" attribute is set.
@return C<true> if the "id" attribute of this SimpleSpeciesReference is
set, C<false> otherwise.
=item SimpleSpeciesReference::isSetName
Predicate returning C<true> if this
SimpleSpeciesReference's "name" attribute is set.
@return C<true> if the "name" attribute of this SimpleSpeciesReference is
set, C<false> otherwise.
=item SimpleSpeciesReference::isSetSpecies
Predicate returning C<true> if this
SimpleSpeciesReference's "species" attribute is set.
@return C<true> if the "species" attribute of this
SimpleSpeciesReference is set, C<false> otherwise.
=item SimpleSpeciesReference::setSpecies
Sets the "species" attribute of this SimpleSpeciesReference.
The identifier string passed in C<sid> is copied.
@param sid the identifier of a species defined in the enclosing
Model's ListOfSpecies.
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item SimpleSpeciesReference::setId
Sets the value of the "id" attribute of this SimpleSpeciesReference.
The string C<sid> is copied.
C<opydetails> doc_id_syntax
@param sid the string to use as the identifier of this SimpleSpeciesReference
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
@li @link OperationReturnValues_t#LIBSBML_UNEXPECTED_ATTRIBUTE LIBSBML_UNEXPECTED_ATTRIBUTE @endlink
=item SimpleSpeciesReference::setName
Sets the value of the "name" attribute of this SimpleSpeciesReference.
The string in C<name> is copied.
@param name the new name for the SimpleSpeciesReference
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
@li @link OperationReturnValues_t#LIBSBML_UNEXPECTED_ATTRIBUTE LIBSBML_UNEXPECTED_ATTRIBUTE @endlink
=item SimpleSpeciesReference::unsetId
Unsets the value of the "id" attribute of this SimpleSpeciesReference.
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item SimpleSpeciesReference::unsetName
Unsets the value of the "name" attribute of this SimpleSpeciesReference.
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item SimpleSpeciesReference::isModifier
Predicate returning C<true> if this
is a ModifierSpeciesReference.
@return C<true> if this SimpleSpeciesReference's subclass is
ModiferSpeciesReference, C<false> if it is a plain SpeciesReference.
=item SimpleSpeciesReference::renameSIdRefs
Renames all the C<SIdRef> attributes on this element, including any
found in MathML.
C<opydetails> doc_what_is_sidref
This method works by looking at all attributes and (if appropriate)
mathematical formulas, comparing the identifiers to the value of @p
oldid. If any matches are found, the matching identifiers are replaced
with C<newid>. The method does I<not> descend into child elements.
@param oldid the old identifier
@param newid the new identifier
=item SimpleSpeciesReference::hasRequiredAttributes
@internal
=item SimpleSpeciesReference::SimpleSpeciesReference
@internal
Creates a new SimpleSpeciesReference using the given SBMLNamespaces object
C<sbmlns>.
C<opydetails> doc_what_are_sbmlnamespaces
@param sbmlns an SBMLNamespaces object.
@note Upon the addition of a SimpleSpeciesReference object to an
SBMLDocument (e.g., using Model::addSimpleSpeciesReference()), the
SBML XML namespace of the document I<overrides> the value used when
creating the SimpleSpeciesReference object via this constructor. This
is necessary to ensure that an SBML document is a consistent
structure. Nevertheless, the ability to supply the values at the time
of creation of a SimpleSpeciesReference is an important aid to
producing valid SBML. Knowledge of the intented SBML Level and
Version determine whether it is valid to assign a particular value to
an attribute, or whether it is valid to add an object to an existing
SBMLDocument.
=item SimpleSpeciesReference::addExpectedAttributes
@internal
Subclasses should override this method to get the list of
expected attributes.
This function is invoked from corresponding readAttributes()
function.
=item SimpleSpeciesReference::readAttributes
@internal
Subclasses should override this method to read values from the given
XMLAttributes set into their specific fields. Be sure to call your
parents implementation of this method as well.
=item SimpleSpeciesReference::readL1Attributes
@internal
=item SimpleSpeciesReference::readL2Attributes
@internal
=item SimpleSpeciesReference::readL3Attributes
@internal
=item SimpleSpeciesReference::writeAttributes
@internal
Subclasses should override this method to write their XML attributes
to the XMLOutputStream. Be sure to call your parents implementation
of this method as well.
=back
=head2 SpeciesReference
@sbmlpackage{core}
@htmlinclude pkg-marker-core.html Implementation of SBML's SpeciesReference construct.
The Reaction structure provides a way to express which species act as
reactants and which species act as products in a reaction. In a given
reaction, references to those species acting as reactants and/or
products are made using instances of SpeciesReference structures in a
Reaction object's lists of reactants and products.
A species can occur more than once in the lists of reactants and
products of a given Reaction instance. The effective stoichiometry for
a species in a reaction is the sum of the stoichiometry values given on
the SpeciesReference object in the list of products minus the sum of
stoichiometry values given on the SpeciesReference objects in the list
of reactants. A positive value indicates the species is effectively a
product and a negative value indicates the species is effectively a
reactant. SBML places no restrictions on the effective stoichiometry of
a species in a reaction; for example, it can be zero. In the following
SBML fragment, the two reactions have the same effective stoichiometry
for all their species:
@verbatim
<reaction id="x">
<listOfReactants>
<speciesReference species="a"/>
<speciesReference species="a"/>
<speciesReference species="b"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="c"/>
<speciesReference species="b"/>
</listProducts>
</reaction>
<reaction id="y">
<listOfReactants>
<speciesReference species="a" stoichiometry="2"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="c"/>
</listProducts>
</reaction>
@endverbatim
The precise structure of SpeciesReference differs between SBML
Level 2 and Level 3. We discuss the two variants in separate
sections below.
@section spr-l2 SpeciesReference in SBML Level 2
The mandatory "species" attribute of SpeciesReference must have as its
value the identifier of an existing species defined in the enclosing
Model. The species is thereby designated as a reactant or product in
the reaction. Which one it is (i.e., reactant or product) is indicated
by whether the SpeciesReference appears in the Reaction's "reactant" or
"product" lists.
Product and reactant stoichiometries can be specified using
<em>either</em> "stoichiometry" or "stoichiometryMath" in a
SpeciesReference object. The "stoichiometry" attribute is of type
double and should contain values greater than zero (0). The
"stoichiometryMath" element is implemented as an element containing a
MathML expression. These two are mutually exclusive; only one of
"stoichiometry" or "stoichiometryMath" should be defined in a given
SpeciesReference instance. When neither the attribute nor the element
is present, the value of "stoichiometry" in the SpeciesReference
instance defaults to C<1>.
For maximum interoperability, the "stoichiometry" attribute should be
used in preference to "stoichiometryMath" when a species' stoichiometry
is a simple scalar number (integer or decimal). When the stoichiometry
is a rational number, or when it is a more complicated formula,
"stoichiometryMath" must be used. The MathML expression in
"stoichiometryMath" may also refer to identifiers of entities in a model
(except reaction identifiers). However, the only species identifiers
that can be used in "stoichiometryMath" are those referenced in the
Reaction list of reactants, products and modifiers.
The following is a simple example of a species reference for species @c
X0, with stoichiometry C<2>, in a list of reactants within a reaction
having the identifier C<J1>:
@verbatim
<model>
...
<listOfReactions>
<reaction id="J1">
<listOfReactants>
<speciesReference species="X0" stoichiometry="2">
</listOfReactants>
...
</reaction>
...
</listOfReactions>
...
</model>
@endverbatim
The following is a more complex example of a species reference for
species X0, with a stoichiometry formula consisting of the parameter
C<x>:
@verbatim
<model>
...
<listOfReactions>
<reaction id="J1">
<listOfReactants>
<speciesReference species="X0">
<stoichiometryMath>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci>x</ci>
</math>
</stoichiometryMath>
</speciesReference>
</listOfReactants>
...
</reaction>
...
</listOfReactions>
...
</model>
@endverbatim
@section spr-l3 SpeciesReference in SBML Level 3
In Level 2's definition of a reaction, the stoichiometry attribute of a
SpeciesReference is actually a combination of two factors, the standard
biochemical stoichiometry and a conversion factor that may be needed to
translate the units of the species quantity to the units of the reaction
rate. Unfortunately, Level 2 offers no direct way of decoupling
these two factors, or for explicitly indicating the units. The only way
to do it in Level 2 is to use the StoichiometryMath object
associated with SpeciesReferences, and to reference SBML Parameter
objects from within the StoichiometryMath formula. This works because
Parameter offers a way to attach units to a numerical value, but the
solution is indirect and awkward for something that should be a simple
matter. Moreover, the question of how to properly encode
stoichiometries in SBML reactions has caused much confusion among
implementors of SBML software.
SBML Level 3 approaches this problem differently. It (1) extends
the the use of the SpeciesReference identifier to represent the value of
the "stoichiometry" attribute, (2) makes the "stoichiometry" attribute
optional, (3) removes StoichiometryMath, and (4) adds a new "constant"
boolean attribute on SpeciesReference.
As in Level 2, the "stoichiometry" attribute is of type
C<double> and should contain values greater than zero (C<0>). A
missing "stoichiometry" implies that the stoichiometry is either
unknown, or to be obtained from an external source, or determined by an
InitialAssignment object or other SBML construct elsewhere in the model.
A species reference's stoichiometry is set by its "stoichiometry"
attribute exactly once. If the SpeciesReference object's "constant"
attribute has the value C<true>, then the stoichiometry is fixed and
cannot be changed except by an InitialAssignment object. These two
methods of setting the stoichiometry (i.e., using "stoichiometry"
directly, or using InitialAssignment) differ in that the "stoichiometry"
attribute can only be set to a literal floating-point number, whereas
InitialAssignment allows the value to be set using an arbitrary
mathematical expression. (As an example, the approach could be used to
set the stoichiometry to a rational number of the form I<p>/I<q>,
where I<p> and I<q> are integers, something that is occasionally
useful in the context of biochemical reaction networks.) If the species
reference's "constant" attribute has the value C<false>, the species
reference's value may be overridden by an InitialAssignment or changed
by AssignmentRule or AlgebraicRule, and in addition, for simulation time
<em>t > 0</em>, it may also be changed by a RateRule or Event
objects. (However, some of these constructs are mutually exclusive; see
the SBML Level 3 Version 1 Core specifiation for more
details.) It is not an error to define "stoichiometry" on a species
reference and also redefine the stoichiometry using an
InitialAssignment, but the "stoichiometry" attribute in that case is
ignored.
The value of the "id" attribute of a SpeciesReference can be used as the
content of a C<<ci>> element in MathML formulas
elsewhere in the model. When the identifier appears in a MathML
C<<ci>> element, it represents the stoichiometry of the
corresponding species in the reaction where the SpeciesReference object
instance appears. More specifically, it represents the value of the
"stoichiometry" attribute on the SpeciesReference object.
In SBML Level 3, the unit of measurement associated with the value of a
species' stoichiometry is always considered to be C<dimensionless>.
This has the following implications:
\n=over\n
\n=item\n\nWhen a species reference's identifier appears in mathematical
formulas elsewhere in the model, the unit associated with that value is
C<dimensionless>.
\n=item\n\nThe units of the "math" elements of AssignmentRule,
InitialAssignment and EventAssignment objects setting the stoichiometry
of the species reference should be C<dimensionless>.
\n=item\n\nIf a species reference's identifier is the subject of a RateRule,
the unit associated with the RateRule object's value should be
C<dimensionless>/<em>time</em>, where <em>time</em> is the
model-wide unit of time set on the Model object.
\n=back\n
=over
=back
=head2 ListOfSpeciesReferences
@sbmlpackage{core}
@htmlinclude pkg-marker-core.html Implementation of SBML's ListOfSpeciesReferences
construct.
C<opydetails> doc_what_is_listof
=over
=item SpeciesReference::SpeciesReference
Creates a new SpeciesReference using the given SBML C<level> and C<version>
values.
@param level an unsigned int, the SBML Level to assign to this SpeciesReference
@param version an unsigned int, the SBML Version to assign to this
SpeciesReference
C<opydetails> doc_note_speciesreference_setting_lv
=item SpeciesReference::SpeciesReference
Creates a new SpeciesReference using the given SBMLNamespaces object
C<sbmlns>.
@param sbmlns an SBMLNamespaces object.
C<opydetails> doc_note_speciesreference_setting_lv
=item SpeciesReference::SpeciesReference
Copy constructor; creates a copy of this SpeciesReference.
@param orig the SpeciesReference instance to copy.
@throws @if python ValueError @else SBMLConstructorException @endif@~
Thrown if the argument C<orig> is C<NULL>.
=item SpeciesReference::accept
Accepts the given SBMLVisitor.
@param v the SBMLVisitor instance to be used.
@return the result of calling C<v.visit()>.
=item SpeciesReference::clone
Creates and returns a deep copy of this SpeciesReference instance.
@return a (deep) copy of this SpeciesReference.
=item SpeciesReference::initDefaults
Initializes the fields of this SpeciesReference object to "typical"
default values.
The SBML SpeciesReference component has slightly different aspects and
default attribute values in different SBML Levels and Versions.
This method sets the values to certain common defaults, based
mostly on what they are in SBML Level 2. Specifically:
\n=over\n
\n=item\n\nSets attribute "stoichiometry" to C<1>.0
\n=item\n\n(Applies to Level 1 models only) Sets attribute "denominator" to C<1>
\n=back\n
@see getDenominator()
@see setDenominator(int value)
@see getStoichiometry()
@see setStoichiometry(double value)
@see getStoichiometryMath()
@see setStoichiometryMath(const StoichiometryMath math)
=item SpeciesReference::getStoichiometry
Get the value of the "stoichiometry" attribute.
In SBML Level 2, product and reactant stoichiometries can be specified
using <em>either</em> "stoichiometry" or "stoichiometryMath" in a
SpeciesReference object. The former is to be used when a
stoichiometry is simply a scalar number, while the latter is for
occasions when it needs to be a rational number or it needs to
reference other mathematical expressions. The "stoichiometry"
attribute is of type C<double> and should contain values greater than
zero (C<0>). The "stoichiometryMath" element is implemented as an
element containing a MathML expression. These two are mutually
exclusive; only one of "stoichiometry" or "stoichiometryMath" should
be defined in a given SpeciesReference instance. When neither the
attribute nor the element is present, the value of "stoichiometry" in
the SpeciesReference instance defaults to C<1>. For maximum
interoperability between different software tools, the "stoichiometry"
attribute should be used in preference to "stoichiometryMath" when a
species' stoichiometry is a simple scalar number (integer or
decimal).
In SBML Level 3, there is no StoichiometryMath, and SpeciesReference
objects have only the "stoichiometry" attribute.
@return the value of the (scalar) "stoichiometry" attribute of this
SpeciesReference.
@see getStoichiometryMath()
=item SpeciesReference::getStoichiometryMath
Get the content of the "stoichiometryMath" subelement as an ASTNode
tree.
The "stoichiometryMath" element exists only in SBML Level 2. There,
product and reactant stoichiometries can be specified using
<em>either</em> "stoichiometry" or "stoichiometryMath" in a
SpeciesReference object. The former is to be used when a
stoichiometry is simply a scalar number, while the latter is for
occasions when it needs to be a rational number or it needs to
reference other mathematical expressions. The "stoichiometry"
attribute is of type C<double> and should contain values greater than
zero (C<0>). The "stoichiometryMath" element is implemented as an
element containing a MathML expression. These two are mutually
exclusive; only one of "stoichiometry" or "stoichiometryMath" should
be defined in a given SpeciesReference instance. When neither the
attribute nor the element is present, the value of "stoichiometry" in
the SpeciesReference instance defaults to C<1>. For maximum
interoperability between different software tools, the "stoichiometry"
attribute should be used in preference to "stoichiometryMath" when a
species' stoichiometry is a simple scalar number (integer or decimal).
@return the content of the "stoichiometryMath" subelement of this
SpeciesReference.
=item SpeciesReference::getStoichiometryMath
Get the content of the "stoichiometryMath" subelement as an ASTNode
tree.
The "stoichiometryMath" element exists only in SBML Level 2. There,
product and reactant stoichiometries can be specified using
<em>either</em> "stoichiometry" or "stoichiometryMath" in a
SpeciesReference object. The former is to be used when a
stoichiometry is simply a scalar number, while the latter is for
occasions when it needs to be a rational number or it needs to
reference other mathematical expressions. The "stoichiometry"
attribute is of type C<double> and should contain values greater than
zero (C<0>). The "stoichiometryMath" element is implemented as an
element containing a MathML expression. These two are mutually
exclusive; only one of "stoichiometry" or "stoichiometryMath" should
be defined in a given SpeciesReference instance. When neither the
attribute nor the element is present, the value of "stoichiometry" in
the SpeciesReference instance defaults to C<1>. For maximum
interoperability between different software tools, the "stoichiometry"
attribute should be used in preference to "stoichiometryMath" when a
species' stoichiometry is a simple scalar number (integer or decimal).
@return the content of the "stoichiometryMath" subelement of this
SpeciesReference.
@see getStoichiometry()
=item SpeciesReference::getDenominator
Get the value of the "denominator" attribute, for the case of a
rational-numbered stoichiometry or a model in SBML Level 1.
The "denominator" attribute is only actually written out in the case
of an SBML Level 1 model. In SBML Level 2, rational-number
stoichiometries are written as MathML elements in the
"stoichiometryMath" subelement. However, as a convenience to users,
libSBML allows the creation and manipulation of rational-number
stoichiometries by supplying the numerator and denominator directly
rather than having to manually create an ASTNode object. LibSBML
will write out the appropriate constructs (either a combination of
"stoichiometry" and "denominator" in the case of SBML Level 1, or a
"stoichiometryMath" subelement in the case of SBML Level 2).
@return the value of the "denominator" attribute of this
SpeciesReference.
=item SpeciesReference::getConstant
Get the value of the "constant" attribute.
@return the value of the "constant" attribute of this
SpeciesReference.
=item SpeciesReference::isSetStoichiometryMath
Predicate returning C<true> if this
SpeciesReference's "stoichiometryMath" subelement is set
@return C<true> if the "stoichiometryMath" subelement of this
SpeciesReference is set, C<false> otherwise.
=item SpeciesReference::isSetConstant
Predicate returning C<true> if this
SpeciesReference's "constant" attribute is set
@return C<true> if the "constant" attribute of this
SpeciesReference is set, C<false> otherwise.
=item SpeciesReference::isSetStoichiometry
Predicate returning C<true> if this
SpeciesReference's "stoichiometry" attribute is set.
@return C<true> if the "stoichiometry" attribute of this
SpeciesReference is set, C<false> otherwise.
=item SpeciesReference::setStoichiometry
Sets the value of the "stoichiometry" attribute of this
SpeciesReference.
In SBML Level 2, product and reactant stoichiometries can be specified
using <em>either</em> "stoichiometry" or "stoichiometryMath" in a
SpeciesReference object. The former is to be used when a
stoichiometry is simply a scalar number, while the latter is for
occasions when it needs to be a rational number or it needs to
reference other mathematical expressions. The "stoichiometry"
attribute is of type C<double> and should contain values greater than
zero (C<0>). The "stoichiometryMath" element is implemented as an
element containing a MathML expression. These two are mutually
exclusive; only one of "stoichiometry" or "stoichiometryMath" should
be defined in a given SpeciesReference instance. When neither the
attribute nor the element is present, the value of "stoichiometry" in
the SpeciesReference instance defaults to C<1>. For maximum
interoperability between different software tools, the "stoichiometry"
attribute should be used in preference to "stoichiometryMath" when a
species' stoichiometry is a simple scalar number (integer or
decimal).
In SBML Level 3, there is no StoichiometryMath, and SpeciesReference
objects have only the "stoichiometry" attribute.
@param value the new value of the "stoichiometry" attribute
@note In SBML Level 2, the "stoichiometryMath" subelement of this
SpeciesReference object will be unset because the "stoichiometry"
attribute and the stoichiometryMath" subelement are mutually
exclusive.
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
=item SpeciesReference::setStoichiometryMath
Sets the "stoichiometryMath" subelement of this SpeciesReference.
The Abstract Syntax Tree in C<math> is copied.
In SBML Level 2, product and reactant stoichiometries can be specified
using <em>either</em> "stoichiometry" or "stoichiometryMath" in a
SpeciesReference object. The former is to be used when a
stoichiometry is simply a scalar number, while the latter is for
occasions when it needs to be a rational number or it needs to
reference other mathematical expressions. The "stoichiometry"
attribute is of type C<double> and should contain values greater than
zero (C<0>). The "stoichiometryMath" element is implemented as an
element containing a MathML expression. These two are mutually
exclusive; only one of "stoichiometry" or "stoichiometryMath" should
be defined in a given SpeciesReference instance. When neither the
attribute nor the element is present, the value of "stoichiometry" in
the SpeciesReference instance defaults to C<1>. For maximum
interoperability between different software tools, the "stoichiometry"
attribute should be used in preference to "stoichiometryMath" when a
species' stoichiometry is a simple scalar number (integer or
decimal).
In SBML Level 3, there is no StoichiometryMath, and SpeciesReference
objects have only the "stoichiometry" attribute.
@param math the StoichiometryMath expression that is to be copied as the
content of the "stoichiometryMath" subelement.
@note In SBML Level 2, the "stoichiometry" attribute of this
SpeciesReference object will be unset (isSetStoichiometry() will
return C<false> although getStoichiometry() will return C<1>.0) if the
given math is not null because the "stoichiometry" attribute and the
stoichiometryMath" subelement are mutually exclusive.
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_UNEXPECTED_ATTRIBUTE LIBSBML_UNEXPECTED_ATTRIBUTE @endlink
@li @link OperationReturnValues_t#LIBSBML_LEVEL_MISMATCH LIBSBML_LEVEL_MISMATCH @endlink
@li @link OperationReturnValues_t#LIBSBML_VERSION_MISMATCH LIBSBML_VERSION_MISMATCH @endlink
=item SpeciesReference::setDenominator
Set the value of the "denominator" attribute, for the case of a
rational-numbered stoichiometry or a model in SBML Level 1.
The "denominator" attribute is only actually written out in the case
of an SBML Level 1 model. In SBML Level 2, rational-number
stoichiometries are written as MathML elements in the
"stoichiometryMath" subelement. However, as a convenience to users,
libSBML allows the creation and manipulation of rational-number
stoichiometries by supplying the numerator and denominator directly
rather than having to manually create an ASTNode object. LibSBML
will write out the appropriate constructs (either a combination of
"stoichiometry" and "denominator" in the case of SBML Level 1, or
a "stoichiometryMath" subelement in the case of SBML Level 2).
@param value the scalar value
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
=item SpeciesReference::setConstant
Sets the "constant" attribute of this SpeciesReference to the given boolean
C<flag>.
@param flag a boolean, the value for the "constant" attribute of this
SpeciesReference instance
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_UNEXPECTED_ATTRIBUTE LIBSBML_UNEXPECTED_ATTRIBUTE @endlink
=item SpeciesReference::unsetStoichiometryMath
Unsets the "stoichiometryMath" subelement of this SpeciesReference.
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_UNEXPECTED_ATTRIBUTE LIBSBML_UNEXPECTED_ATTRIBUTE @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
In SBML Level 2, product and reactant stoichiometries can be specified
using <em>either</em> "stoichiometry" or "stoichiometryMath" in a
SpeciesReference object. The former is to be used when a
stoichiometry is simply a scalar number, while the latter is for
occasions when it needs to be a rational number or it needs to
reference other mathematical expressions. The "stoichiometry"
attribute is of type C<double> and should contain values greater than
zero (C<0>). The "stoichiometryMath" element is implemented as an
element containing a MathML expression. These two are mutually
exclusive; only one of "stoichiometry" or "stoichiometryMath" should
be defined in a given SpeciesReference instance. When neither the
attribute nor the element is present, the value of "stoichiometry" in
the SpeciesReference instance defaults to C<1>. For maximum
interoperability between different software tools, the "stoichiometry"
attribute should be used in preference to "stoichiometryMath" when a
species' stoichiometry is a simple scalar number (integer or
decimal).
In SBML Level 3, there is no StoichiometryMath, and SpeciesReference
objects have only the "stoichiometry" attribute.
@note In SBML Level 2, the "stoichiometry" attribute of this
SpeciesReference object will be reset to a default value (C<1>.0) if
the "stoichiometry" attribute has not been set.
=item SpeciesReference::unsetStoichiometry
Unsets the "stoichiometry" attribute of this SpeciesReference.
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
@note In SBML Level 1, the "stoichiometry" attribute of this
SpeciesReference object will be just reset to a default value (C<1>.0)
and isSetStoichiometry() will still return C<true>. In SBML
Level 2, the "stoichiometry" attribute of this object will be
unset (which will result in isSetStoichiometry() returning C<false>,
although getStoichiometry() will return C<1>.0) if the
"stoichiometryMath" subelement is set, otherwise the attribute
will be just reset to the default value (C<1>.0) (and
isSetStoichiometry() will still return C<true>). In SBML
Level 3, the "stoichiometry" attribute of this object will be set
to C<NaN> and isSetStoichiometry() will return C<false>.
=item SpeciesReference::createStoichiometryMath
Creates a new, empty StoichiometryMath object, adds it to this
SpeciesReference, and returns it.
@return the newly created StoichiometryMath object instance
@see Reaction::addReactant(const SpeciesReference sr)
@see Reaction::addProduct(const SpeciesReference sr)
=item SpeciesReference::setAnnotation
Sets the value of the "annotation" subelement of this SBML object to a
copy of C<annotation>.
Any existing content of the "annotation" subelement is discarded.
Unless you have taken steps to first copy and reconstitute any
existing annotations into the C<annotation> that is about to be
assigned, it is likely that performing such wholesale replacement is
unfriendly towards other software applications whose annotations are
discarded. An alternative may be to use appendAnnotation().
@param annotation an XML structure that is to be used as the content
of the "annotation" subelement of this object
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@see appendAnnotation(const XMLNode annotation)
@see appendAnnotation(const std::string& annotation)
=item SpeciesReference::setAnnotation
Sets the value of the "annotation" subelement of this SBML object to a
copy of C<annotation>.
Any existing content of the "annotation" subelement is discarded.
Unless you have taken steps to first copy and reconstitute any
existing annotations into the C<annotation> that is about to be
assigned, it is likely that performing such wholesale replacement is
unfriendly towards other software applications whose annotations are
discarded. An alternative may be to use appendAnnotation().
@param annotation an XML string that is to be used as the content
of the "annotation" subelement of this object
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
@see appendAnnotation(const XMLNode annotation)
@see appendAnnotation(const std::string& annotation)
=item SpeciesReference::appendAnnotation
Appends annotation content to any existing content in the "annotation"
subelement of this object.
The content in C<annotation> is copied. Unlike
SpeciesReference::setAnnotation(@if java String annotation@endif),
this method allows other annotations to be preserved when an application
adds its own data.
@param annotation an XML structure that is to be copied and appended
to the content of the "annotation" subelement of this object
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
@see setAnnotation(const std::string& annotation)
@see setAnnotation(const XMLNode annotation)
=item SpeciesReference::appendAnnotation
Appends annotation content to any existing content in the "annotation"
subelement of this object.
The content in C<annotation> is copied. Unlike
SpeciesReference::setAnnotation(@if java String annotation@endif), this
method allows other annotations to be preserved when an application
adds its own data.
@param annotation an XML string that is to be copied and appended
to the content of the "annotation" subelement of this object
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
@see setAnnotation(const std::string& annotation)
@see setAnnotation(const XMLNode annotation)
=item SpeciesReference::getTypeCode
Returns the libSBML type code for this SBML object.
C<opydetails> doc_what_are_typecodes
@return the SBML type code for this object:
@link SBMLTypeCode_t#SBML_SPECIES_REFERENCE SBML_SPECIES_REFERENCE@endlink (default).
@see getElementName()
@see getPackageName()
=item SpeciesReference::getElementName
Returns the XML element name of this object, which for
SpeciesReference, is always C<"speciesReference">.
@return the name of this element, i.e., C<"speciesReference">.
=item SpeciesReference::writeElements
@internal
Subclasses should override this method to write out their contained
SBML objects as XML elements. Be sure to call your parents
implementation of this method as well.
=item SpeciesReference::sortMath
@internal
=item SpeciesReference::hasRequiredAttributes
Predicate returning C<true> if
all the required attributes for this SpeciesReference object
have been set.
@note The required attributes for a SpeciesReference object are:
@li "species"
@li "constant" (only available SBML Level 3)
@return a boolean value indicating whether all the required
attributes for this object have been defined.
=item SpeciesReference::createObject
@internal
Create and return a speciesReference object, if present.
@return the SBML object corresponding to next XMLToken in the
XMLInputStream or C<NULL> if the token was not recognized.
=item SpeciesReference::readOtherXML
@internal
Subclasses should override this method to read (and store) XHTML,
MathML, etc. directly from the XMLInputStream.
@return true if the subclass read from the stream, false otherwise.
=item SpeciesReference::addExpectedAttributes
@internal
Subclasses should override this method to get the list of
expected attributes.
This function is invoked from corresponding readAttributes()
function.
=item SpeciesReference::readAttributes
@internal
Subclasses should override this method to read values from the given
XMLAttributes set into their specific fields. Be sure to call your
parents implementation of this method as well.
=item SpeciesReference::readL1Attributes
@internal
=item SpeciesReference::readL2Attributes
@internal
=item SpeciesReference::readL3Attributes
@internal
=item SpeciesReference::writeAttributes
@internal
Subclasses should override this method to write their XML attributes
to the XMLOutputStream. Be sure to call your parents implementation
of this method as well.
=item SpeciesReference::syncAnnotation
@internal
Synchronizes the annotation of this SBML object.
Annotation element (XMLNode mAnnotation) is synchronized with the
current CVTerm objects (List mCVTerm) and id string (std::string mId)
Currently, this method is called in getAnnotation(), isSetAnnotation(),
and writeElements() methods.
=item SpeciesReference::isExplicitlySetStoichiometry
@internal
=item SpeciesReference::isExplicitlySetDenominator
@internal
=item ListOfSpeciesReferences::ListOfSpeciesReferences
Creates a new, empty ListOfSpeciesReferences object.
The object is constructed such that it is valid for the given SBML
Level and Version combination.
@param level the SBML Level
@param version the Version within the SBML Level
=item ListOfSpeciesReferences::ListOfSpeciesReferences
Creates a new ListOfSpeciesReferences object.
The object is constructed such that it is valid for the SBML Level and
Version combination determined by the SBMLNamespaces object in @p
sbmlns.
@param sbmlns an SBMLNamespaces object that is used to determine the
characteristics of the ListOfSpeciesReferences object to be created.
=item ListOfSpeciesReferences::clone
Creates and returns a deep copy of this ListOfSpeciesReferences
instance.
@return a (deep) copy of this ListOfSpeciesReferences.
=item ListOfSpeciesReferences::getItemTypeCode
Returns the libSBML type code for the objects contained in this ListOf
(i.e., SpeciesReference objects, if the list is non-empty).
C<opydetails> doc_what_are_typecodes
@return the SBML type code for objects contained in this list:
@link SBMLTypeCode_t#SBML_SPECIES_REFERENCE SBML_SPECIES_REFERENCE@endlink (default).
@see getElementName()
@see getPackageName()
=item ListOfSpeciesReferences::getElementName
Returns the XML element name of this object.
For ListOfSpeciesReferences, the XML element name is @c
"listOfSpeciesReferences".
@return the name of this element, i.e., C<"listOfSpeciesReferences">.
=item ListOfSpeciesReferences::get
Get a SpeciesReference from the ListOfSpeciesReferences.
@param n the index number of the SpeciesReference to get.
@return the nth SpeciesReference in this ListOfSpeciesReferences.
@see size()
=item ListOfSpeciesReferences::get
Get a SpeciesReference from the ListOfSpeciesReferences.
@param n the index number of the SpeciesReference to get.
@return the nth SpeciesReference in this ListOfSpeciesReferences.
@see size()
=item ListOfSpeciesReferences::get
Get a SpeciesReference from the ListOfSpeciesReferences
based on its identifier.
@param sid a string representing the identifier
of the SpeciesReference to get.
@return SpeciesReference in this ListOfSpeciesReferences
with the given C<sid> or C<NULL> if no such
SpeciesReference exists.
@see get(unsigned int n)
@see size()
=item ListOfSpeciesReferences::get
Get a SpeciesReference from the ListOfSpeciesReferences
based on its identifier.
@param sid a string representing the identifier
of the SpeciesReference to get.
@return SpeciesReference in this ListOfSpeciesReferences
with the given C<sid> or C<NULL> if no such
SpeciesReference exists.
@see get(unsigned int n)
@see size()
=item ListOfSpeciesReferences::remove
Removes the nth item from this ListOfSpeciesReferences items and returns a pointer to
it.
The caller owns the returned item and is responsible for deleting it.
@param n the index of the item to remove
@see size()
=item ListOfSpeciesReferences::remove
Removes item in this ListOfSpeciesReferences items with the given identifier.
The caller owns the returned item and is responsible for deleting it.
If none of the items in this list have the identifier C<sid>, then @c
NULL is returned.
@param sid the identifier of the item to remove
@return the item removed. As mentioned above, the caller owns the
returned item.
=item ListOfSpeciesReferences::getElementPosition
@internal
Get the ordinal position of this element in the containing object
(which in this case is the Model object).
@return the ordinal position of the element with respect to its
siblings, or C<-1> (default) to indicate the position is not significant.
=item ListOfSpeciesReferences::setType
@internal
Sets type of this ListOfSpeciesReferences.
=item ListOfSpeciesReferences::createObject
@internal
Create and return a listOfSpeciesReferences object, if present.
@return the SBML object corresponding to next XMLToken in the
XMLInputStream or C<NULL> if the token was not recognized.
=back
=head2 ModifierSpeciesReference
@sbmlpackage{core}
@htmlinclude pkg-marker-core.html Implementation of SBML's ModifierSpeciesReference
construct.
Sometimes a species appears in the kinetic rate formula of a reaction
but is itself neither created nor destroyed in that reaction (for
example, because it acts as a catalyst or inhibitor). In SBML, all such
species are simply called I<modifiers> without regard to the detailed
role of those species in the model. The Reaction structure provides a
way to express which species act as modifiers in a given reaction. This
is the purpose of the list of modifiers available in Reaction. The list
contains instances of ModifierSpeciesReference structures.
The ModifierSpeciesReference structure inherits the mandatory attribute
"species" and optional attributes "id" and "name" from the parent class
SimpleSpeciesReference. See the description of SimpleSpeciesReference
for more information about these.
The value of the "species" attribute must be the identifier of a species
defined in the enclosing Model; this species is designated as a modifier
for the current reaction. A reaction may have any number of modifiers.
It is permissible for a modifier species to appear simultaneously in the
list of reactants and products of the same reaction where it is
designated as a modifier, as well as to appear in the list of reactants,
products and modifiers of other reactions in the model.
=over
=item ModifierSpeciesReference::ModifierSpeciesReference
Creates a new ModifierSpeciesReference using the given SBML C<level> and
C<version> values.
@param level an unsigned int, the SBML Level to assign to this
ModifierSpeciesReference
@param version an unsigned int, the SBML Version to assign to this
ModifierSpeciesReference
C<opydetails> doc_note_modifierspeciesreference_setting_lv
=item ModifierSpeciesReference::ModifierSpeciesReference
Creates a new ModifierSpeciesReference using the given SBMLNamespaces
object C<sbmlns>.
@param sbmlns an SBMLNamespaces object.
C<opydetails> doc_note_modifierspeciesreference_setting_lv
=item ModifierSpeciesReference::accept
Accepts the given SBMLVisitor.
@param v the SBMLVisitor instance to be used.
@return the result of calling C<v.visit()>.
=item ModifierSpeciesReference::clone
Creates and returns a deep copy of this ModifierSpeciesReference
instance.
@return a (deep) copy of this ModifierSpeciesReference.
=item ModifierSpeciesReference::getTypeCode
Returns the libSBML type code for this SBML object.
C<opydetails> doc_what_are_typecodes
@return the SBML type code for this object:
@link SBMLTypeCode_t#SBML_MODIFIER_SPECIES_REFERENCE SBML_MODIFIER_SPECIES_REFERENCE@endlink (default).
C<opydetails> doc_warning_typecodes_not_unique
@see getElementName()
@see getPackageName()
=item ModifierSpeciesReference::getElementName
Returns the XML element name of this object, which for Species, is
always C<"modifierSpeciesReference">.
@return the name of this element, i.e., C<"modifierSpeciesReference">.
=item ModifierSpeciesReference::hasRequiredAttributes
Predicate returning C<true> if
all the required attributes for this ModifierSpeciesReference object
have been set.
@note The required attributes for a ModifierSpeciesReference object are:
species
=back
=head2 Event
@sbmlpackage{core}
@htmlinclude pkg-marker-core.html Implementation of SBML's Event construct.
An SBML Event object defines when the event can occur, the variables
that are affected by it, how the variables are affected, and the event's
relationship to other events. The effect of the event can optionally be
delayed after the occurrence of the condition which invokes it.
The operation of Event is divided into two phases (even when the event
is not delayed): one when the event is I<triggered>, and the other when
the event is I<executed>. Trigger objects define the conditions for
triggering an event, Delay objects define when the event is actually
executed, EventAssignment objects define the effects of executing the
event, and (in SBML Level 3) Priority objects influence the order
of EventAssignment performance in cases of simultaneous events. Please
consult the descriptions of Trigger, Delay, EventAssignment and Priority
for more information.
@section version-diffs SBML Level/Version differences
@subsection sbml-l3 SBML Level 3
SBML Level 3 introduces several changes to the structure and components
of Events compared to SBML Level 2. These changes fall into two
main categories: changes to what is optional or required, and additions
of new attributes and elements.
\n=over\n
\n=item\n\nThe attribute "useValuesFromTriggerTime" on Event is mandatory (it
was optional in Level 2);
\n=item\n\nEvent's "listOfEventAssignments" element (of class
ListOfEventAssignments) is optional (it was mandatory in Level 2);
\n=item\n\nEvent's "priority" element (of class Priority) is new in
Level 3; and
\n=item\n\nThe Trigger object gains new mandatory attributes (described as part
of the definition of Trigger).
\n=back\n
The changes to the attributes of Event are described below; the changes
to Trigger and Priority are described in their respective sections.
@subsection sbml-l2 SBML Level 2
In SBML Level 2 versions before Version 4, the semantics of
Event time delays were defined such that the expressions in the event's
assignments were always evaluated at the time the event was
<em>triggered</em>. This definition made it difficult to define an event
whose assignment formulas were meant to be evaluated at the time the
event was <em>executed</em> (i.e., after the time period defined by the
value of the Delay element). In SBML Level 2 Version 4 and in
Level 3, the attribute "useValuesFromTriggerTime" on Event allows a
model to indicate the time at which the event's assignments are intended
the values of the assignment formulas are computed at the moment the
event is triggered, not after the delay. If "useValuesFromTriggerTime"=@c
false, it means that the formulas in the event's assignments are to be
computed I<after> the delay, at the time the event is executed.
The definition of Event in SBML Level 2 Versions 1 and 2 includes
an additional attribute called "timeUnits", which allowed the time units
of the Delay to be set explicitly. Later Versions of SBML Level 2
as well as SBML Level 3 do not define this attribute. LibSBML
supports this attribute for compatibility with previous versions of SBML
Level 2; however, if a model in SBML Level 3 or Level 2
Versions 3–4 format sets the attribute, the
consistency-checking method SBMLDocument::checkConsistency() will report
an error.
The attribute "useValuesFromTriggerTime" was introduced in SBML
Level 2 Version 4. Models defined in prior Versions of SBML
Level 2 cannot use this attribute, and
SBMLDocument::checkConsistency() will report an error if they do.
@section semantics Semantics of events in SBML Level 3 Version 1
The detailed semantics of events are described in the specification
documents for each SBML Level/Version. Here we include the description
from the SBML Level 1 Version 1.
Any transition of a Trigger object's "math" formula from the value @c
false to C<true> will cause the enclosing Event object to
<em>trigger</em>. Such a transition is not possible at the very start
of a simulation (i.e., at time <em>t = 0</em>) unless the Trigger
object's "initialValue" attribute has a value of C<false>; this defines
the value of the trigger formula to be C<false> immediately prior to the
start of simulation, thereby giving it the potential to change in value
from C<false> to C<true> when the formula is evaluated at <em>t =
0</em>. If "initialValue"=C<true>, then the trigger expression cannot
transition from C<false> to C<true> at <em>t = 0</em> but may do so at
some time <em>t E<gt> 0</em>.
Consider an Event object definition <EM>E</EM> with delay <em>d</em> in
which the Trigger object's "math" formula makes a transition in value
from C<false> to C<true> at times <em>t<sub>1</sub></em> and
<em>t<sub>2</sub></em>. The EventAssignment within the Event object
will have effect at <em>t<sub>1</sub> + d</em> and
<em>t<sub>2</sub> + d</em> irrespective of the relative times of
<em>t<sub>1</sub></em> and <em>t<sub>2</sub></em>. For example, events
can "overlap" so that <em>t<sub>1</sub> E<lt> t<sub>2</sub> <
t<sub>1</sub> + d</em> still causes an event assignments to occur at
<em>t<sub>1</sub> + d</em> and <em>t<sub>2</sub> + d</em>.
It is entirely possible for two events to be executed simultaneously,
and it is possible for events to trigger other events (i.e., an event
assignment can cause an event to trigger). This leads to several
points:
\n=over\n
\n=item\n\nA software package should retest all event triggers after executing
an event assignment in order to account for the possibility that the
assignment causes another event trigger to transition from C<false> to
C<true>. This check should be made after each individual Event object's
execution, even when several events are to be executed simultaneously.
\n=item\n\nAny Event object whose Trigger "persistent" attribute has the value
C<false> must have its trigger expression reevaluated continuously
between when the event is triggered and when it is executed. If
its trigger expression ever evaluates to C<false>, it must be removed
from the queue of events pending execution and treated as any other
event whose trigger expression evaluates to C<false>.
\n=item\n\nAlthough the precise time at which events are executed is not
resolved beyond the given execution point in simulated time, it is
assumed that the order in which the events occur <em>is</em> resolved.
This order can be significant in determining the overall outcome of a
given simulation. When an event <EM>X</EM> <em>triggers</em> another
event <EM>Y</EM> and event <EM>Y</EM> has zero delay, then event
<EM>Y</EM> is added to the existing set of simultaneous events that are
pending <em>execution</em>. Events <EM>X</EM> and <EM>Y</EM> form a
cascade of events at the same point in simulation time. An event such
as <EM>Y</EM> may have a special priority if it contains a Priority
subobject.
\n=item\n\nAll events in a model are open to being in a cascade. The position
of an event in the event queue does not affect whether it can be in the
cascade: event <EM>Y</EM> can be triggered whether it is before or after
<EM>X</EM> in the queue of events pending execution. A cascade of
events can be potentially infinite (never terminate); when this occurs a
simulator should indicate this has occurred—it is incorrect for a
simulator to break a cascade arbitrarily and continue the simulation
without at least indicating that the infinite cascade occurred.
\n=item\n\nSimultaneous events having no defined priorities are executed in an
undefined order. This does not mean that the behavior of the simulation
is completely undefined; merely that the <em>order</em> of execution of
these particular events is undefined. A given simulator may use any
algorithm to choose an order as long as every event is executed exactly
once.
\n=item\n\nEvents with defined priorities are executed in the order implied by
their Priority "math" formula values, with events having higher
priorities being executed ahead of events with lower priorities, and
events with identical priorities being executed in a random order with
respect to one another (as determined at run-time by some random
algorithm equivalent to coin-flipping). Newly-triggered events that are
to be executed immediately (i.e., if they define no delays) should be
inserted into the queue of events pending execution according to their
priorities: events with higher priority values value must be inserted
ahead of events with lower priority values and after any pending events
with even higher priorities, and inserted randomly among pending events
with the same priority values. Events without Priority objects must be
inserted into the queue in some fashion, but the algorithm used to place
it in the queue is undefined. Similarly, there is no restriction on the
order of a newly-inserted event with a defined Priority with respect to
any other pending Event without a defined Priority.
\n=item\n\nA model variable that is the target of one or more event
assignments can change more than once when simultaneous events are
processed at some time point <em>t</em>. The model's behavior (output)
for such a variable is the value of the variable at the end of
processing all the simultaneous events at time <em>t</em>.
\n=back\n
@see Trigger
@see Priority
@see Delay
@see EventAssignment
=over
=back
=head2 ListOfEvents
@sbmlpackage{core}
@htmlinclude pkg-marker-core.html Implementation of SBML's ListOfEvents construct.
C<opydetails> doc_what_is_listof
=over
=item Event::Event
Creates a new Event using the given SBML C<level> and C<version>
values.
@param level an unsigned int, the SBML Level to assign to this Event
@param version an unsigned int, the SBML Version to assign to this
Event
@throws @if python ValueError @else SBMLConstructorException @endif@~
Thrown if the given C<level> and C<version> combination, or this kind
of SBML object, are either invalid or mismatched with respect to the
parent SBMLDocument object.
C<opydetails> doc_event_setting_lv
=item Event::Event
Creates a new Event using the given SBMLNamespaces object
C<sbmlns>.
C<opydetails> doc_what_are_sbmlnamespaces
@param sbmlns an SBMLNamespaces object.
@throws @if python ValueError @else SBMLConstructorException @endif@~
Thrown if the given C<level> and C<version> combination, or this kind
of SBML object, are either invalid or mismatched with respect to the
parent SBMLDocument object.
C<opydetails> doc_event_setting_lv
=item Event::Event
Copy constructor; creates a copy of this Event.
@param orig the object to copy.
@throws @if python ValueError @else SBMLConstructorException @endif@~
Thrown if the argument C<orig> is C<NULL>.
=item Event::accept
Accepts the given SBMLVisitor for this instance of Event.
@param v the SBMLVisitor instance to be used.
@return the result of calling C<v.visit()>, which indicates
whether the Visitor would like to visit the next Event in the list
of events within which this Event is embedded.
=item Event::clone
Creates and returns a deep copy of this Event.
@return a (deep) copy of this Event.
=item Event::getElementBySId
Returns the first child element found that has the given C<id> in the
model-wide SId namespace, or C<NULL> if no such object is found.
@param id string representing the id of objects to find
@return pointer to the first element found with the given C<id>.
=item Event::getElementByMetaId
Returns the first child element it can find with the given C<metaid>, or
C<NULL> if no such object is found.
@param metaid string representing the metaid of objects to find
@return pointer to the first element found with the given C<metaid>.
=item Event::getAllElements
Returns a List of all child SBase objects, including those nested to an
arbitrary depth.
@return a List of pointers to all children objects.
=item Event::getId
Returns the value of the "id" attribute of this Event.
@return the id of this Event.
=item Event::getName
Returns the value of the "name" attribute of this Event.
@return the name of this Event.
=item Event::getTrigger
Get the event trigger portion of this Event.
@return the Trigger object of this Event.
=item Event::getTrigger
Get the event trigger portion of this Event.
@return the Trigger object of this Event.
=item Event::getDelay
Get the assignment delay portion of this Event, if there is one.
@return the delay of this Event if one is defined, or C<NULL> if none
is defined.
=item Event::getDelay
Get the assignment delay portion of this Event, if there is one.
@return the delay of this Event if one is defined, or C<NULL> if none
is defined.
=item Event::getPriority
(SBML Level 3 only) Get the event priority portion of this
Event.
@return the Priority object of this Event.
@note The element "priority" is available in SBML Level 3
Version 1 Core, but is not present in lower Levels of SBML.
=item Event::getPriority
(SBML Level 3 only) Get the event priority portion of this
Event.
@return the Priority object of this Event.
@note The element "priority" is available in SBML Level 3
Version 1 Core, but is not present in lower Levels of SBML.
=item Event::getTimeUnits
Get the value of the "timeUnits" attribute of this Event, if it has one.
@return the value of the attribute "timeUnits" as a string.
C<opydetails> doc_warning_event_timeUnits
=item Event::getUseValuesFromTriggerTime
Get the value of the "useValuesFromTriggerTime" attribute of this Event.
C<opydetails> doc_event_using_useValuesFromTriggerTime
@return the value of the attribute "useValuesFromTriggerTime" as a boolean.
C<opydetails> doc_warning_useValuesFromTriggerTime
=item Event::isSetId
Predicate returning C<true> if this
Event's "id" attribute is set.
@return C<true> if the "id" attribute of this Event is
set, C<false> otherwise.
=item Event::isSetName
Predicate returning C<true> if this
Event's "name" attribute is set.
@return C<true> if the "name" attribute of this Event is
set, C<false> otherwise.
=item Event::isSetTrigger
Predicate for testing whether the trigger for this Event is set.
@return C<true> if the trigger of this Event is set, C<false>
otherwise.
=item Event::isSetDelay
Predicate for testing whether the delay for this Event is set.
@return C<true> if the delay of this Event is set, C<false>
otherwise.
=item Event::isSetPriority
(SBML Level 3 only) Predicate for testing whether the priority
for this Event is set.
@return C<true> if the priority of this Event is set, C<false>
otherwise.
@note The element "priority" is available in SBML Level 3
Version 1 Core, but is not present in lower Levels of SBML.
=item Event::isSetTimeUnits
Predicate for testing whether the "timeUnits" attribute of this Event
is set.
@return C<true> if the "timeUnits" attribute of this Event is
set, C<false> otherwise.
C<opydetails> doc_warning_event_timeUnits
=item Event::isSetUseValuesFromTriggerTime
Predicate for testing whether the "useValuesFromTriggerTime" attribute of this Event
is set.
@return C<true> if the "useValuesFromTriggerTime" attribute of this Event is
set, C<false> otherwise.
@note In SBML Level 2, this attribute is optional and has a default value of
C<true>, whereas in Level 3 Version 1, this optional is mandatory and
has no default value.
=item Event::setId
Sets the value of the "id" attribute of this Event.
The string C<sid> is copied.
C<opydetails> doc_id_syntax
@param sid the string to use as the identifier of this Event
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif@~ The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item Event::setName
Sets the value of the "name" attribute of this Event.
The string in C<name> is copied.
@param name the new name for the Event
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif@~ The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item Event::setTrigger
Sets the trigger definition of this Event to a copy of the given
Trigger object instance.
@param trigger the Trigger object instance to use.
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif@~ The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_LEVEL_MISMATCH LIBSBML_LEVEL_MISMATCH @endlink
@li @link OperationReturnValues_t#LIBSBML_VERSION_MISMATCH LIBSBML_VERSION_MISMATCH @endlink
=item Event::setDelay
Sets the delay definition of this Event to a copy of the given Delay
object instance.
@param delay the Delay object instance to use
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif@~ The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_LEVEL_MISMATCH LIBSBML_LEVEL_MISMATCH @endlink
@li @link OperationReturnValues_t#LIBSBML_VERSION_MISMATCH LIBSBML_VERSION_MISMATCH @endlink
=item Event::setPriority
(SBML Level 3 only) Sets the priority definition of this Event
to a copy of the given Priority object instance.
@param priority the Priority object instance to use
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif@~ The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_LEVEL_MISMATCH LIBSBML_LEVEL_MISMATCH @endlink
@li @link OperationReturnValues_t#LIBSBML_VERSION_MISMATCH LIBSBML_VERSION_MISMATCH @endlink
@li @link OperationReturnValues_t#LIBSBML_UNEXPECTED_ATTRIBUTE LIBSBML_UNEXPECTED_ATTRIBUTE @endlink
@note The element "priority" is available in SBML Level 3
Version 1 Core, but is not present in lower Levels of SBML.
=item Event::setTimeUnits
Sets the "timeUnits" attribute of this Event to a copy of C<sid>.
@param sid the identifier of the time units to use.
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif@~ The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
@li @link OperationReturnValues_t#LIBSBML_UNEXPECTED_ATTRIBUTE LIBSBML_UNEXPECTED_ATTRIBUTE @endlink
C<opydetails> doc_warning_event_timeUnits
=item Event::setUseValuesFromTriggerTime
Sets the "useValuesFromTriggerTime" attribute of this Event to a C<value>.
C<opydetails> doc_event_using_useValuesFromTriggerTime
@param value the value of useValuesFromTriggerTime to use.
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif@~ The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_UNEXPECTED_ATTRIBUTE LIBSBML_UNEXPECTED_ATTRIBUTE @endlink
C<opydetails> doc_warning_useValuesFromTriggerTime
=item Event::unsetId
Unsets the value of the "id" attribute of this Event.
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif@~ The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item Event::unsetName
Unsets the value of the "name" attribute of this Event.
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif@~ The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item Event::unsetDelay
Unsets the Delay of this Event.
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif@~ The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item Event::unsetPriority
(SBML Level 3 only) Unsets the Priority of this Event.
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif@~ The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
@note The element "priority" is available in SBML Level 3
Version 1 Core, but is not present in lower Levels of SBML.
=item Event::unsetTrigger
Unsets the Trigger of this Event.
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif@~ The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
@note The element "priority" is available in SBML Level 3
Version 1 Core, but is not present in lower Levels of SBML.
=item Event::unsetTimeUnits
Unsets the "timeUnits" attribute of this Event.
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif@~ The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_UNEXPECTED_ATTRIBUTE LIBSBML_UNEXPECTED_ATTRIBUTE @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
C<opydetails> doc_warning_event_timeUnits
=item Event::addEventAssignment
Appends a copy of the given EventAssignment to this Event.
@param ea the EventAssignment object to add.
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif@~ The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_LEVEL_MISMATCH LIBSBML_LEVEL_MISMATCH @endlink
@li @link OperationReturnValues_t#LIBSBML_VERSION_MISMATCH LIBSBML_VERSION_MISMATCH @endlink
@li @link OperationReturnValues_t#LIBSBML_DUPLICATE_OBJECT_ID LIBSBML_DUPLICATE_OBJECT_ID @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
C<opydetails> doc_note_object_is_copied
@see createEventAssignment()
=item Event::createEventAssignment
Creates a new, empty EventAssignment, adds it to this Event's list of
event assignments and returns the EventAssignment.
@return the newly created EventAssignment object instance
@see addEventAssignment(const EventAssignment ea)
=item Event::createTrigger
Creates a new, empty Trigger, adds it to this Event and
returns the Trigger.
@return the newly created Trigger object instance
=item Event::createDelay
Creates a new, empty Delay, adds it to this Event and
returns the Delay.
@return the newly created Delay object instance
=item Event::createPriority
(SBML Level 3 only) Creates a new, empty Priority, adds it to this
Event and returns the Priority.
@return the newly created Priority object instance
@note The element "priority" is available in SBML Level 3
Version 1 Core, but is not present in lower Levels of SBML.
=item Event::getListOfEventAssignments
Returns the list of event assignments for this Event.
@return the list of EventAssignments for this Event.
=item Event::getListOfEventAssignments
Returns the list of event assignments for this Event.
@return the list of EventAssignments for this Event.
=item Event::getEventAssignment
Return a specific EventAssignment object of this Event.
@param n an integer, the index of the EventAssignment object to return
@return the C<n>th EventAssignment of this Event.
=item Event::getEventAssignment
Return a specific EventAssignment object of this Event.
@param n an integer, the index of the EventAssignment object to return
@return the C<n>th EventAssignment of this Event.
=item Event::getEventAssignment
Return the event assignment indicated by the given C<variable>.
@param variable a string, the identifier of the variable whose
EventAssignment is being sought.
@return the EventAssignment for the given C<variable>, or C<NULL> if
no such EventAssignment exits.
=item Event::getEventAssignment
Return the event assignment indicated by the given C<variable>.
@param variable a string, the identifier of the variable whose
EventAssignment is being sought.
@return the EventAssignment for the given C<variable>, or C<NULL> if
no such EventAssignment exits.
=item Event::getNumEventAssignments
Returns the number of EventAssignment objects attached to this
Event.
@return the number of EventAssignments in this Event.
=item Event::removeEventAssignment
Removes the nth EventAssignment object from this Event object and
returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
@param n the index of the EventAssignment object to remove
@return the EventAssignment object removed. As mentioned above,
the caller owns the returned item. C<NULL> is returned if the given index
is out of range.
=item Event::removeEventAssignment
Removes the EventAssignment object with the given "variable" attribute
from this Event object and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
If none of the EventAssignment objects in this Event object have the
"variable" attribute C<variable>, then C<NULL> is returned.
@param variable the "variable" attribute of the EventAssignment object
to remove
@return the EventAssignment object removed. As mentioned above, the
caller owns the returned object. C<NULL> is returned if no EventAssignment
object with the "variable" attribute exists in this Event object.
=item Event::setSBMLDocument
@internal
Sets the parent SBMLDocument of this SBML object.
@param d the SBMLDocument to use
=item Event::connectToChild
@internal
Sets this SBML object to child SBML objects (if any).
(Creates a child-parent relationship by the parent)
Subclasses must override this function if they define
one ore more child elements.
Basically, this function needs to be called in
constructor, copy constructor and assignment operator.
@see setSBMLDocument
@see enablePackageInternal
=item Event::enablePackageInternal
@internal
Enables/Disables the given package with this element and child
elements (if any).
(This is an internal implementation for enablePackage function)
@note Subclasses of the SBML Core package in which one or more child
elements are defined must override this function.
=item Event::getTypeCode
Returns the libSBML type code of this object instance.
C<opydetails> doc_what_are_typecodes
@return the SBML type code for this object:
@link SBMLTypeCode_t#SBML_EVENT SBML_EVENT@endlink (default).
C<opydetails> doc_warning_typecodes_not_unique
@see getElementName()
@see getPackageName()
=item Event::getElementName
Returns the XML element name of this object, which for Event, is
always C<"event">.
@return the name of this element, i.e., C<"event">.
=item Event::writeElements
@internal
Subclasses should override this method to write out their contained
SBML objects as XML elements. Be sure to call your parents
implementation of this method as well.
=item Event::setInternalIdOnly
@internal
sets the mInternalIdOnly flag
=item Event::hasRequiredAttributes
Predicate returning C<true> if all the required attributes for this
Event object have been set.
@note The required attributes for an Event object are:
@li "useValuesfromTriggerTime" (required in SBML Level 3)
=item Event::hasRequiredElements
Predicate returning C<true> if
all the required elements for the given Event_t structure
have been set.
@note The required elements for an Event object are:
@li "trigger"
@li "listOfEventAssignments" (required in SBML Level 2, optional in Level 3)
=item Event::createObject
@internal
Create and return an SBML object of this class, if present.
@return the SBML object corresponding to next XMLToken in the
XMLInputStream or C<NULL> if the token was not recognized.
=item Event::addExpectedAttributes
@internal
Subclasses should override this method to get the list of
expected attributes.
This function is invoked from corresponding readAttributes()
function.
=item Event::readAttributes
@internal
Subclasses should override this method to read values from the given
XMLAttributes set into their specific fields. Be sure to call your
parents implementation of this method as well.
=item Event::readL2Attributes
@internal
=item Event::readL3Attributes
@internal
=item Event::writeAttributes
@internal
Subclasses should override this method to write their XML attributes
to the XMLOutputStream. Be sure to call your parents implementation
of this method as well.
=item Event::isExplicitlySetUVFTT
@internal
=item ListOfEvents::ListOfEvents
Creates a new ListOfEvents object.
The object is constructed such that it is valid for the given SBML
Level and Version combination.
@param level the SBML Level
@param version the Version within the SBML Level
=item ListOfEvents::ListOfEvents
Creates a new ListOfEvents object.
The object is constructed such that it is valid for the SBML Level and
Version combination determined by the SBMLNamespaces object in @p
sbmlns.
@param sbmlns an SBMLNamespaces object that is used to determine the
characteristics of the ListOfEvents object to be created.
=item ListOfEvents::clone
Creates and returns a deep copy of this ListOfEvents.
@return a (deep) copy of this ListOfEvents.
=item ListOfEvents::getItemTypeCode
Returns the libSBML type code for the objects contained in this ListOf
(i.e., Event objects, if the list is non-empty).
C<opydetails> doc_what_are_typecodes
@return the SBML type code for the objects contained in this ListOf:
@link SBMLTypeCode_t#SBML_EVENT SBML_EVENT@endlink (default).
@see getElementName()
@see getPackageName()
=item ListOfEvents::getElementName
Returns the XML element name of this object.
For ListOfEvents, the XML element name is C<"listOfEvents">.
@return the name of this element, i.e., C<"listOfEvents">.
=item ListOfEvents::get
Get an Event from the ListOfEvents.
@param n the index number of the Event to get.
@return the C<n>th Event in this ListOfEvents.
@see size()
=item ListOfEvents::get
Get an Event from the ListOfEvents.
@param n the index number of the Event to get.
@return the C<n>th Event in this ListOfEvents.
@see size()
=item ListOfEvents::get
Get an Event from the ListOfEvents
based on its identifier.
@param sid a string representing the identifier
of the Event to get.
@return Event in this ListOfEvents
with the given C<sid> or C<NULL> if no such
Event exists.
@see get(unsigned int n)
@see size()
=item ListOfEvents::get
Get an Event from the ListOfEvents
based on its identifier.
@param sid a string representing the identifier
of the Event to get.
@return Event in this ListOfEvents
with the given C<sid> or C<NULL> if no such
Event exists.
@see get(unsigned int n)
@see size()
=item ListOfEvents::remove
Removes the nth item from this ListOfEvents items and returns a pointer to
it.
The caller owns the returned item and is responsible for deleting it.
@param n the index of the item to remove
@see size()
=item ListOfEvents::remove
Removes item in this ListOfEvents items with the given identifier.
The caller owns the returned item and is responsible for deleting it.
If none of the items in this list have the identifier C<sid>, then
C<NULL> is returned.
@param sid the identifier of the item to remove
@return the item removed. As mentioned above, the caller owns the
returned item.
=item ListOfEvents::getElementPosition
@internal
Get the ordinal position of this element in the containing object
(which in this case is the Model object).
The ordering of elements in the XML form of SBML is generally fixed
for most components in SBML. So, for example, the ListOfEvents in a
model is (in SBML Level 2 Version 4) the twelfth ListOf___.
(However, it differs for different Levels and Versions of SBML, so
calling code should not hardwire this number.)
@return the ordinal position of the element with respect to its
siblings, or C<-1> (default) to indicate the position is not significant.
=item ListOfEvents::createObject
@internal
Create and return an SBML object of this class, if present.
@return the SBML object corresponding to next XMLToken in the
XMLInputStream or C<NULL> if the token was not recognized.
=back
=head2 EventAssignment
@sbmlpackage{core}
@htmlinclude pkg-marker-core.html Implementation of SBML's EventAssignment construct for
Event.
Event contains an optional element called "listOfEventAssignments", of
class ListOfEventAssignments. In every instance of an event definition
in a model, the object's "listOfEventAssignments" element must have a
non-empty list of one or more "eventAssignment" elements of class
EventAssignment. The object class EventAssignment has one required
attribute, "variable", and a required element, "math". Being derived
from SBase, it also has all the usual attributes and elements of its
parent class.
An Event object defines when the event can occur, the variables that are
affected by the event, and how the variables are affected. The purpose
of the EventAssignment object class is to define how variables are
affected by an Event. In SBML Level 2, every Event object instance
must have a nonempty list of event assignments; in SBML Level 3,
the list of assignments is optional.
The operation of an Event is divided into two phases (regardless of
whether a delay is involved): one phase when the event is I<triggered>,
and the other when the event is I<executed>. EventAssignment objects
are interpreted when an event is executed. The effects are described
below.
@section event-variable The attribute "variable"
The EventAssignment attribute "variable" must be the identifier of an
existing Compartment, Species, SpeciesReference, or Parameter
instance defined in the model. When the event is executed, the value of
the model component identified by "variable" is changed by the
EventAssignment to the value computed by the "math" element; that is, a
species' quantity, species reference's stoichiometry, compartment's size
or parameter's value are reset to the value computed by "math".
Certain restrictions are placed on what can appear in "variable":
\n=over\n
\n=item\n\nThe object identified by the value of the EventAssignment attribute
"variable" must not have its "constant" attribute set to or default to
C<true>. (Constants cannot be affected by events.)
\n=item\n\nThe "variable" attribute must not contain the identifier of a
reaction; only species, species references, compartment and parameter
values may be set by an Event.
\n=item\n\nThe value of every "variable" attribute must be unique among the set
of EventAssignment structures within a given Event structure. In other
words, a single event cannot have multiple EventAssignment objects
assigning the same variable. (All of them would be performed at the
same time when that particular Event triggers, resulting in
indeterminacy.) However, I<separate> Event instances can refer to the
same variable.
\n=item\n\nA variable cannot be assigned a value in an EventAssignment object
instance and also be assigned a value by an AssignmentRule; i.e., the
value of an EventAssignment's "variable" attribute cannot be the same as
the value of a AssignmentRule' "variable" attribute. (Assignment rules
hold at all times, therefore it would be inconsistent to also define an
event that reassigns the value of the same variable.)
\n=back\n
Note that the time of assignment of the object identified by the
value of the "variable" attribute is always the time at which the Event
is <em>executed</em>, not when it is <em>triggered</em>. The timing is
controlled by the optional Delay in an Event. The time of
assignment is not affected by the "useValuesFromTriggerTime"
attribute on Event—that attribute affects the time at which the
EventAssignment's "math" expression is I<evaluated>. In other
words, SBML allows decoupling the time at which the
"variable" is assigned from the time at which its value
expression is calculated.
@section event-math The "math" subelement in an EventAssignment
The MathML expression contained in an EventAssignment defines the new
value of the variable being assigned by the Event.
As mentioned above, the time at which the expression in "math" is
evaluated is determined by the attribute "useValuesFromTriggerTime" on
Event. If the attribute value is C<true>, the expression must be
evaluated when the event is I<triggered>; more precisely, the values of
identifiers occurring in MathML C<<ci>> elements in the
EventAssignment's "math" expression are the values they have at the
point when the event I<triggered>. If, instead,
"useValuesFromTriggerTime"'s value is C<false>, it means the values at
I<execution> time should be used; that is, the values of identifiers
occurring in MathML C<<ci>> elements in the
EventAssignment's "math" expression are the values they have at the
point when the event I<executed>.
@section version-diffs SBML Level/Version differences
Between Version 4 and previous versions of SBML Level 2, the
requirements regarding the matching of units between an
EvengAssignment's formula and the units of the object identified by the
"variable" attribute changed. Previous versions required consistency,
but in SBML Level 2 Version 4 and in SBML Level 3, unit
consistency is only I<recommended>. More precisely:
\n=over\n
\n=item\n\nIn the case of a species, an EventAssignment sets the referenced
species' quantity (concentration or amount of substance) to the value
determined by the formula in the EventAssignment's "math" subelement.
The units of the "math" formula should (in SBML Level 2
Version 4 and in Level 3) or must (in previous Versions of
Level 2) be identical to the units of the species.
\n=item\n\n(SBML Level 3 only.) In the case of a species reference, an
EventAssignment sets the stoichiometry of the reactant or product
referenced by the SpeciesReference object to the value determined by the
formula in the "math" element. The unit associated with the value
produced by the "math" formula should be C<dimensionless>, because
reactant and product stoichiometries in reactions are dimensionless
quantities.
\n=item\n\nIn the case of a compartment, an EventAssignment sets the
referenced compartment's size to the size determined by the formula in
the "math" subelement of the EventAssignment. The overall units of the
formula should (in SBML Level 2 Version 4 and in Level 3)
or must (in previous Versions of Level 2) be identical to the units
specified for the size of the compartment identified by the
EventAssignment's "variable" attribute.
\n=item\n\nIn the case of a parameter, an EventAssignment sets the referenced
parameter's value to that determined by the formula in "math". The
overall units of the formula should (in SBML Level 2 Version 4
and Level 3) or must (in previous Versions of Level 2) be
identical to the units defined for the parameter.
\n=back\n
Note that the formula placed in the "math" element <em>has no assumed
units</em>. The consistency of the units of the formula, and the units
of the entity which the assignment affects, must be explicitly
established just as in the case of the value of the Delay subelement.
An approach similar to the one discussed in the context of Delay may be
used for the formula of an EventAssignment.
@see Event
=over
=back
=head2 ListOfEventAssignments
@sbmlpackage{core}
@htmlinclude pkg-marker-core.html Implementation of SBML's ListOfEventAssignments
construct.
C<opydetails> doc_what_is_listof
=over
=item EventAssignment::EventAssignment
Creates a new EventAssignment using the given SBML C<level> and C<version>
values.
@param level an unsigned int, the SBML Level to assign to this EventAssignment
@param version an unsigned int, the SBML Version to assign to this
EventAssignment
@throws @if python ValueError @else SBMLConstructorException @endif@~
Thrown if the given C<level> and C<version> combination, or this kind
of SBML object, are either invalid or mismatched with respect to the
parent SBMLDocument object.
C<opydetails> doc_note_eventassignment_setting_lv
=item EventAssignment::EventAssignment
Creates a new EventAssignment using the given SBMLNamespaces object
C<sbmlns>.
C<opydetails> doc_what_are_sbmlnamespaces
@param sbmlns an SBMLNamespaces object.
@throws @if python ValueError @else SBMLConstructorException @endif@~
Thrown if the given C<level> and C<version> combination, or this kind
of SBML object, are either invalid or mismatched with respect to the
parent SBMLDocument object.
C<opydetails> doc_note_eventassignment_setting_lv
=item EventAssignment::EventAssignment
Copy constructor; creates a copy of this EventAssignment.
@param orig the object to copy.
@throws @if python ValueError @else SBMLConstructorException @endif@~
Thrown if the argument C<orig> is C<NULL>.
=item EventAssignment::accept
Accepts the given SBMLVisitor for this instance of EventAssignment.
@param v the SBMLVisitor instance to be used.
@return the result of calling C<v.visit()>, which indicates
whether the Visitor would like to visit the next EventAssignment in
the list within which this EventAssignment is embedded (i.e., in the
ListOfEventAssignments located in the enclosing Event instance).
=item EventAssignment::clone
Creates and returns a deep copy of this EventAssignment.
@return a (deep) copy of this EventAssignment.
=item EventAssignment::getVariable
Get the value of this EventAssignment's "variable" attribute.
@return the identifier stored in the "variable" attribute of this
EventAssignment.
=item EventAssignment::getMath
Get the mathematical expression in this EventAssignment's "math"
subelement.
@return the top ASTNode of an abstract syntax tree representing the
mathematical formula in this EventAssignment.
=item EventAssignment::isSetVariable
Predicate for testing whether the attribute "variable" of this
EventAssignment is set.
@return C<true> if the "variable" attribute of this EventAssignment
is set, C<false> otherwise.
=item EventAssignment::isSetMath
Predicate for testing whether the "math" subelement of this
EventAssignment is set.
@return C<true> if this EventAssignment has a "math" subelement,
C<false> otherwise.
=item EventAssignment::setVariable
Sets the attribute "variable" of this EventAssignment to a copy of
the given identifier string.
@param sid the identifier of a Compartment, Species or (global)
Parameter defined in this model.
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif@~ The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item EventAssignment::setMath
Sets the "math" subelement of this EventAssignment to a copy of the
given ASTNode.
@param math an ASTNode that will be copied and stored as the
mathematical formula for this EventAssignment.
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif@~ The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT @endlink
=item EventAssignment::getDerivedUnitDefinition
Calculates and returns a UnitDefinition that expresses the units of
measurement assumed for the "math" expression of this EventAssignment.
C<opydetails> doc_eventassignment_units
C<opydetails> doc_note_unit_inference_depends_on_model
C<opydetails> doc_warning_eventassignment_math_literals
@return a UnitDefinition that expresses the units of the math
expression of this EventAssignment, or C<NULL> if one cannot be constructed.
@see containsUndeclaredUnits()
=item EventAssignment::getDerivedUnitDefinition
Calculates and returns a UnitDefinition that expresses the units of
measurement assumed for the "math" expression of this EventAssignment.
C<opydetails> doc_eventassignment_units
C<opydetails> doc_note_unit_inference_depends_on_model
C<opydetails> doc_warning_eventassignment_math_literals
@return a UnitDefinition that expresses the units of the math
expression of this EventAssignment, or C<NULL> if one cannot be constructed.
@see containsUndeclaredUnits()
=item EventAssignment::containsUndeclaredUnits
Predicate returning C<true> if the math expression of this
EventAssignment contains literal numbers or parameters with undeclared
units.
C<opydetails> doc_eventassignment_units
If the expression contains literal numbers or parameters with undeclared
units, libSBML may not be able to compute the full units of the
expression and will only return what it can compute. Callers should
always use EventAssignment::containsUndeclaredUnits() when using
EventAssignment::getDerivedUnitDefinition() to decide whether the
returned units may be incomplete.
@return C<true> if the math expression of this EventAssignment
includes parameters/numbers
with undeclared units, C<false> otherwise.
@note A return value of C<true> indicates that the UnitDefinition
returned by EventAssignment::getDerivedUnitDefinition() may not
accurately represent the units of the expression.
@see getDerivedUnitDefinition()
=item EventAssignment::containsUndeclaredUnits
Predicate returning C<true> if the math expression of this
EventAssignment contains literal numbers or parameters with undeclared
units.
C<opydetails> doc_eventassignment_units
If the expression contains literal numbers or parameters with undeclared
units, libSBML may not be able to compute the full units of the
expression and will only return what it can compute. Callers should
always use EventAssignment::containsUndeclaredUnits() when using
EventAssignment::getDerivedUnitDefinition() to decide whether the
returned units may be incomplete.
@return C<true> if the math expression of this EventAssignment
includes parameters/numbers
with undeclared units, C<false> otherwise.
@note A return value of C<true> indicates that the UnitDefinition
returned by EventAssignment::getDerivedUnitDefinition() may not
accurately represent the units of the expression.
@see getDerivedUnitDefinition()
=item EventAssignment::getTypeCode
Returns the libSBML type code of this object instance.
C<opydetails> doc_what_are_typecodes
@return the SBML type code for this object:
@link SBMLTypeCode_t#SBML_EVENT_ASSIGNMENT SBML_EVENT_ASSIGNMENT@endlink (default).
C<opydetails> doc_warning_typecodes_not_unique
@see getElementName()
@see getPackageName()
=item EventAssignment::getElementName
Returns the XML element name of this object, which for
EventAssignment, is always C<"eventAssignment">.
@return the name of this element, i.e., C<"eventAssignment">.
=item EventAssignment::writeElements
@internal
Subclasses should override this method to write out their contained
SBML objects as XML elements. Be sure to call your parents
implementation of this method as well.
=item EventAssignment::hasRequiredAttributes
Predicate returning C<true> if all the required attributes for this
EventAssignment object have been set.
@note The required attributes for a EventAssignment object are:
@li "variable"
@return a boolean value indicating whether all the required
attributes for this object have been defined.
=item EventAssignment::hasRequiredElements
Predicate returning C<true> if all the required elements for this
EventAssignment object have been set.
@note The required elements for a EventAssignment object are:
@li "math"
@return a boolean value indicating whether all the required
elements for this object have been defined.
=item EventAssignment::getId
@internal
=item EventAssignment::renameSIdRefs
Renames all the C<SIdRef> attributes on this element, including any
found in MathML.
C<opydetails> doc_what_is_sidref
This method works by looking at all attributes and (if appropriate)
mathematical formulas, comparing the identifiers to the value of @p
oldid. If any matches are found, the matching identifiers are replaced
with C<newid>. The method does I<not> descend into child elements.
@param oldid the old identifier
@param newid the new identifier
=item EventAssignment::renameUnitSIdRefs
Renames all the C<UnitSIdRef> attributes on this element.
C<opydetails> doc_what_is_unitsidref
This method works by looking at all unit identifier attribute values
(including, if appropriate, inside mathematical formulas), comparing the
unit identifiers to the value of C<oldid>. If any matches are found,
the matching identifiers are replaced with C<newid>. The method does
I<not> descend into child elements.
@param oldid the old identifier
@param newid the new identifier
=item EventAssignment::replaceSIDWithFunction
@internal
Replace all nodes with the name 'id' from the child 'math' object with the provided function.
=item EventAssignment::divideAssignmentsToSIdByFunction
@internal
If this assignment assigns a value to the 'id' element, replace the 'math' object with the function (existing/function).
=item EventAssignment::multiplyAssignmentsToSIdByFunction
@internal
If this assignment assigns a value to the 'id' element, replace the 'math' object with the function (existing function).
=item EventAssignment::readOtherXML
@internal
Subclasses should override this method to read (and store) XHTML,
MathML, etc. directly from the XMLInputStream.
@return true if the subclass read from the stream, false otherwise.
=item EventAssignment::addExpectedAttributes
@internal
Subclasses should override this method to get the list of
expected attributes.
This function is invoked from corresponding readAttributes()
function.
=item EventAssignment::readAttributes
@internal
Subclasses should override this method to read values from the given
XMLAttributes set into their specific fields. Be sure to call your
parents implementation of this method as well.
=item EventAssignment::readL2Attributes
@internal
=item EventAssignment::readL3Attributes
@internal
=item EventAssignment::writeAttributes
@internal
Subclasses should override this method to write their XML attributes
to the XMLOutputStream. Be sure to call your parents implementation
of this method as well.
=item ListOfEventAssignments::ListOfEventAssignments
Creates a new ListOfEventAssignments object.
The object is constructed such that it is valid for the given SBML
Level and Version combination.
@param level the SBML Level
@param version the Version within the SBML Level
=item ListOfEventAssignments::ListOfEventAssignments
Creates a new ListOfEventAssignments object.
The object is constructed such that it is valid for the SBML Level and
Version combination determined by the SBMLNamespaces object in @p
sbmlns.
@param sbmlns an SBMLNamespaces object that is used to determine the
characteristics of the ListOfEventAssignments object to be created.
=item ListOfEventAssignments::clone
Creates and returns a deep copy of this ListOfEventAssignments.
@return a (deep) copy of this ListOfEventAssignments.
=item ListOfEventAssignments::getItemTypeCode
Returns the libSBML type code for the objects contained in this ListOf
(i.e., EventAssignment objects, if the list is non-empty).
C<opydetails> doc_what_are_typecodes
@return the SBML type code for the objects contained in this ListOf:
@link SBMLTypeCode_t#SBML_EVENT_ASSIGNMENT SBML_EVENT_ASSIGNMENT@endlink (default).
@see getElementName()
@see getPackageName()
=item ListOfEventAssignments::getElementName
Returns the XML element name of this object.
For ListOfEventAssignments, the XML element name is @c
"listOfEventAssignments".
@return the name of this element, i.e., C<"listOfEventAssignments">.
=item ListOfEventAssignments::get
Get a EventAssignment from the ListOfEventAssignments.
@param n the index number of the EventAssignment to get.
@return the nth EventAssignment in this ListOfEventAssignments.
@see size()
=item ListOfEventAssignments::get
Get a EventAssignment from the ListOfEventAssignments.
@param n the index number of the EventAssignment to get.
@return the nth EventAssignment in this ListOfEventAssignments.
@see size()
=item ListOfEventAssignments::get
Get a EventAssignment from the ListOfEventAssignments
based on its identifier.
@param sid a string representing the identifier
of the EventAssignment to get.
@return EventAssignment in this ListOfEventAssignments
with the given C<sid> or C<NULL> if no such
EventAssignment exists.
@see get(unsigned int n)
@see size()
=item ListOfEventAssignments::get
Get a EventAssignment from the ListOfEventAssignments
based on its identifier.
@param sid a string representing the identifier
of the EventAssignment to get.
@return EventAssignment in this ListOfEventAssignments
with the given C<sid> or C<NULL> if no such
EventAssignment exists.
@see get(unsigned int n)
@see size()
=item ListOfEventAssignments::remove
Removes the nth item from this ListOfEventAssignments items and returns
a pointer to it.
The caller owns the returned item and is responsible for deleting it.
@param n the index of the item to remove
@see size()
=item ListOfEventAssignments::remove
Removes item in this ListOfEventAssignments items with the given
identifier.
The caller owns the returned item and is responsible for deleting it.
If none of the items in this list have the identifier C<sid>, then @c
NULL is returned.
@param sid the identifier of the item to remove
@return the item removed. As mentioned above, the caller owns the
returned item.
=item ListOfEventAssignments::getElementBySId
Returns the first child element found that has the given C<id> in the
model-wide SId namespace, or C<NULL> if no such object is found.
Note that EventAssignments do not actually have IDs, but the libsbml
interface pretends that they do: no event assignment is returned by this
function.
@param id string representing the id of objects to find
@return pointer to the first element found with the given C<id>.
=item ListOfEventAssignments::getElementPosition
@internal
Get the ordinal position of this element in the containing object
(which in this case is the Model object).
@return the ordinal position of the element with respect to its
siblings, or C<-1> (default) to indicate the position is not significant.
=item ListOfEventAssignments::createObject
@internal
Create and return an SBML object of this class, if present.
@return the SBML object corresponding to next XMLToken in the
XMLInputStream or C<NULL> if the token was not recognized.
=back
=head2 Trigger
@sbmlpackage{core}
@htmlinclude pkg-marker-core.html Implementation of SBML's Trigger construct for Event.
An Event object defines when the event can occur, the variables that are
affected by the event, and how the variables are affected. The Trigger
construct in SBML is used to define a mathematical expression that
determines when an Event is I<triggered>.
A Trigger object in SBML Level 2 and Level 3 contains one
subelement named "math" containing a MathML expression. The expression
must evaluate to a value of type C<boolean>. The exact moment at which
the expression evaluates to C<true> is the time point when the Event is
I<triggered>. In SBML Level 3, Trigger has additional attributes
that must be assigned values; they are discussed in a separate section
below.
An event only I<triggers> when its Trigger expression makes the
transition in value from C<false> to C<true>. The event will also
trigger at any subsequent time points when the trigger makes this
transition; in other words, an event can be triggered multiple times
during a simulation if its trigger condition makes the transition from
C<false> to C<true> more than once. In SBML Level 3, the behavior
at the very start of simulation (i.e., at <em>t = 0</em>, where
<em>t</em> stands for time) is determined in part by the boolean flag
"initialValue". This and other additional features introduced in SBML
Level 3 are discussed further below.
@section version-diffs Version differences
SBML Level 3 Version 1 introduces two required attributes
on the Trigger object: "persistent" and "initialValue". The rest of
this introduction describes these two attributes.
@subsection trigger-persistent The "persistent" attribute on Trigger
In the interval between when an Event object <em>triggers</em> (i.e.,
its Trigger object expression transitions in value from C<false> to
C<true>) and when its assignments are to be <em>executed</em>, conditions
in the model may change such that the trigger expression transitions
back from C<true> to C<false>. Should the event's assignments still be
made if this happens? Answering this question is the purpose of the
"persistent" attribute on Trigger.
If the boolean attribute "persistent" has a value of C<true>, then once
the event is triggered, all of its assignments are always performed when
the time of execution is reached. The name I<persistent> is meant to
evoke the idea that the trigger expression does not have to be
re-checked after it triggers if "persistent"=C<true>. Conversely, if
the attribute value is C<false>, then the trigger expression is not
assumed to persist: if the expression transitions in value back to @c
false at any time between when the event triggered and when it is to be
executed, the event is no longer considered to have triggered and its
assignments are not executed. (If the trigger expression transitions
once more to C<true> after that point, then the event is triggered, but
this then constitutes a whole new event trigger-and-execute sequence.)
The "persistent" attribute can be especially useful when Event objects
contain Delay objects, but it is relevant even in a model without delays
if the model contains two or more events. As explained in the
introduction to this section, the operation of all events in SBML
(delayed or not) is conceptually divided into two phases,
<em>triggering</em> and <em>execution</em>; however, unless events have
priorities associated with them, SBML does not mandate a particular
ordering of event execution in the case of simultaneous events. Models
with multiple events can lead to situations where the execution of one
event affects another event's trigger expression value. If that other
event has "persistent"=C<false>, and its trigger expression evaluates to
C<false> before it is to be executed, the event must not be executed
after all.
@subsection trigger-initialvalue The "initialValue" attribute on Trigger
As mentioned above, an event <em>triggers</em> when the mathematical
expression in its Trigger object transitions in value from C<false> to
C<true>. An unanswered question concerns what happens at the start of a
simulation: can event triggers make this transition at <em>t = 0</em>,
where <em>t</em> stands for time?
In order to determine whether an event may trigger at <em>t = 0</em>, it
is necessary to know what value the Trigger object's "math" expression
had immediately prior to <em>t = 0</em>. This starting value of the
trigger expression is determined by the value of the boolean attribute
"initialValue". A value of C<true> means the trigger expression is
taken to have the value C<true> immediately prior to <em>t = 0</em>. In
that case, the trigger cannot transition in value from C<false> to @c
true at the moment simulation begins (because it has the value C<true>
both before and after <em>t = 0</em>), and can only make the transition
from C<false> to C<true> sometime <em>after</em> <em>t = 0</em>. (To do
that, it would also first have to transition to C<false> before it could
make the transition from C<false> back to C<true>.) Conversely, if
"initialValue"=C<false>, then the trigger expression is assumed to start
with the value C<false>, and therefore may trigger at <em>t = 0</em> if
the expression evaluates to C<true> at that moment.
@see Event
@see Delay
@see EventAssignment
=over
=item Trigger::Trigger
Creates a new Trigger using the given SBML C<level> and C<version>
values.
@param level an unsigned int, the SBML Level to assign to this Trigger
@param version an unsigned int, the SBML Version to assign to this
Trigger
@throws @if python ValueError @else SBMLConstructorException @endif@~
Thrown if the given C<level> and C<version> combination, or this kind
of SBML object, are either invalid or mismatched with respect to the
parent SBMLDocument object.
=item Trigger::Trigger
Creates a new Trigger using the given SBMLNamespaces object
C<sbmlns>.
C<opydetails> doc_what_are_sbmlnamespaces
@param sbmlns an SBMLNamespaces object.
@throws @if python ValueError @else SBMLConstructorException @endif@~
Thrown if the given C<level> and C<version> combination, or this kind
of SBML object, are either invalid or mismatched with respect to the
parent SBMLDocument object.
=item Trigger::Trigger
Copy constructor; creates a copy of this Trigger.
@param orig the object to copy.
@throws @if python ValueError @else SBMLConstructorException @endif@~
Thrown if the argument C<orig> is C<NULL>.
=item Trigger::accept
Accepts the given SBMLVisitor for this instance of Trigger.
@param v the SBMLVisitor instance to be used.
@return the result of calling C<v.visit()>.
=item Trigger::clone
Creates and returns a deep copy of this Trigger.
@return a (deep) copy of this Trigger.
=item Trigger::getMath
Get the mathematical formula for the trigger and return it
as an AST.
@return the math of this Trigger.
=item Trigger::getInitialValue
(SBML Level 3 only) Get the value of the "initialValue" attribute
of this Trigger.
@return the boolean value stored as the "initialValue" attribute value
in this Trigger.
@note The attribute "initialValue" is available in SBML Level 3
Version 1 Core, but is not present in lower Levels of SBML.
=item Trigger::getPersistent
(SBML Level 3 only) Get the value of the "persistent" attribute
of this Trigger.
@return the boolean value stored as the "persistent" attribute value
in this Trigger.
@note The attribute "persistent" is available in SBML Level 3
Version 1 Core, but is not present in lower Levels of SBML.
=item Trigger::isSetMath
Predicate to test whether the math for this trigger is set.
@return C<true> if the formula (meaning the "math" subelement) of
this Trigger is set, C<false> otherwise.
=item Trigger::isSetInitialValue
(SBML Level 3 only) Predicate to test whether the "initialValue"
attribute for this trigger is set.
@return C<true> if the initialValue attribute of
this Trigger is set, C<false> otherwise.
@note The attribute "initialValue" is available in SBML Level 3
Version 1 Core, but is not present in lower Levels of SBML.
=item Trigger::isSetPersistent
(SBML Level 3 only) Predicate to test whether the "persistent"
attribute for this trigger is set.
@return C<true> if the persistent attribute of
this Trigger is set, C<false> otherwise.
@note The attribute "persistent" is available in SBML Level 3
Version 1 Core, but is not present in lower Levels of SBML.
=item Trigger::setMath
Sets the trigger expression of this Trigger instance to a copy of the given
ASTNode.
@param math an ASTNode representing a formula tree.
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif@~ The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT @endlink
=item Trigger::setInitialValue
(SBML Level 3 only) Sets the "initialValue" attribute of this Trigger instance.
@param initialValue a boolean representing the initialValue to be set.
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif@~ The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_UNEXPECTED_ATTRIBUTE LIBSBML_UNEXPECTED_ATTRIBUTE @endlink
@note The attribute "initialValue" is available in SBML Level 3
Version 1 Core, but is not present in lower Levels of SBML.
=item Trigger::setPersistent
(SBML Level 3 only) Sets the "persistent" attribute of this Trigger instance.
@param persistent a boolean representing the persistent value to be set.
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif@~ The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_UNEXPECTED_ATTRIBUTE LIBSBML_UNEXPECTED_ATTRIBUTE @endlink
@note The attribute "persistent" is available in SBML Level 3
Version 1 Core, but is not present in lower Levels of SBML.
=item Trigger::getTypeCode
Returns the libSBML type code of this object instance.
C<opydetails> doc_what_are_typecodes
@return the SBML type code for this object:
@link SBMLTypeCode_t#SBML_TRIGGER SBML_TRIGGER@endlink (default).
C<opydetails> doc_warning_typecodes_not_unique
@see getElementName()
@see getPackageName()
=item Trigger::getElementName
Returns the XML element name of this object, which for Trigger, is
always C<"trigger">.
@return the name of this element, i.e., C<"trigger">.
=item Trigger::renameSIdRefs
Renames all the C<SIdRef> attributes on this element, including any
found in MathML.
C<opydetails> doc_what_is_sidref
This method works by looking at all attributes and (if appropriate)
mathematical formulas, comparing the identifiers to the value of @p
oldid. If any matches are found, the matching identifiers are replaced
with C<newid>. The method does I<not> descend into child elements.
@param oldid the old identifier
@param newid the new identifier
=item Trigger::renameUnitSIdRefs
Renames all the C<UnitSIdRef> attributes on this element.
C<opydetails> doc_what_is_unitsidref
This method works by looking at all unit identifier attribute values
(including, if appropriate, inside mathematical formulas), comparing the
unit identifiers to the value of C<oldid>. If any matches are found,
the matching identifiers are replaced with C<newid>. The method does
I<not> descend into child elements.
@param oldid the old identifier
@param newid the new identifier
=item Trigger::replaceSIDWithFunction
@internal
Replace all nodes with the name 'id' from the child 'math' object with the provided function.
=item Trigger::getElementPosition
@internal
Returns the position of this element.
@return the ordinal position of the element with respect to its
siblings or -1 (default) to indicate the position is not significant.
=item Trigger::writeElements
@internal
Subclasses should override this method to write out their contained
SBML objects as XML elements. Be sure to call your parents
implementation of this method as well.
=item Trigger::hasRequiredElements
Predicate returning C<true> if
all the required elements for this Trigger object
have been set.
@note The required elements for a Trigger object are:
@li "math"
@return a boolean value indicating whether all the required
elements for this object have been defined.
=item Trigger::hasRequiredAttributes
Predicate returning C<true> if
all the required attributes for this Trigger object
have been set.
@note The required attributes for a Trigger object are:
@li "persistent" (required in SBML Level 3)
@li "initialValue" (required in SBML Level 3)
@return a boolean value indicating whether all the required
attributes for this object have been defined.
=item Trigger::removeFromParentAndDelete
Finds this Trigger's Event parent and calls unsetTrigger() on it, indirectly deleting itself. Overridden from the SBase function since the parent is not a ListOf.
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif@~ The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item Trigger::readOtherXML
@internal
Subclasses should override this method to read (and store) XHTML,
MathML, etc. directly from the XMLInputStream.
@return true if the subclass read from the stream, false otherwise.
=item Trigger::addExpectedAttributes
@internal
Subclasses should override this method to get the list of
expected attributes.
This function is invoked from corresponding readAttributes()
function.
=item Trigger::readAttributes
@internal
Subclasses should override this method to read values from the given
XMLAttributes set into their specific fields. Be sure to call your
parents implementation of this method as well.
=item Trigger::readL2Attributes
@internal
=item Trigger::readL3Attributes
@internal
=item Trigger::writeAttributes
@internal
Subclasses should override this method to write their XML attributes
to the XMLOutputStream. Be sure to call your parents implementation
of this method as well.
=back
=head2 Delay
@sbmlpackage{core}
@htmlinclude pkg-marker-core.html Implementation of SBML's Delay construct for Event.
An Event object defines when the event can occur, the variables that
are affected by the event, and how the variables are affected. The
effect of the event can optionally be delayed after the occurrence of
the condition which invokes it. An event delay is defined using an
object of class Delay.
The object class Delay is derived from SBase and adds a single
subelement called "math". This subelement is used to hold MathML
content. The mathematical formula represented by "math" must evaluate
to a numerical value. It is used as the length of time between when the
event is I<triggered> and when the event's assignments are
actually I<executed>. If no delay is present on a given Event, a time
delay of zero is assumed.
The expression in "math" must be evaluated at the time the event is @em
triggered. The expression must always evaluate to a nonnegative number
(otherwise, a nonsensical situation could arise where an event is
defined to execute before it is triggered!).
@section delay-units The units of the mathematical expression in a Delay
In SBML Level 2 versions before Version 4, the units of the
numerical value computed by the Delay's "math" expression are @em
required to be in units of time, or the model is considered to have a
unit consistency error. In Level 2 Version 4 as well as SBML
Level 3 Version 1 Core, this requirement is relaxed; these
specifications only stipulate that the units of the numerical value
computed by a Delay instance's "math" expression I<should> match the
model's units of time (meaning the definition of the C<time> units in
the model). LibSBML respects these requirements, and depending on
whether an earlier Version of SBML Level 2 is in use, libSBML may
or may not flag unit inconsistencies as errors or merely warnings.
Note that <em>units are not predefined or assumed</em> for the contents
of "math" in a Delay object; rather, they must be defined explicitly for
each instance of a Delay object in a model. This is an important point
to bear in mind when literal numbers are used in delay expressions. For
example, the following Event instance would result in a warning logged
by SBMLDocument::checkConsistency() about the fact that libSBML cannot
verify the consistency of the units of the expression. The reason is
that the formula inside the "math" element does not have any declared
units, whereas what is expected in this context is units of time:
@verbatim
<model>
...
<listOfEvents>
<event useValuesFromTriggerTime="true">
...
<delay>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<cn> 1 </cn>
</math>
</delay>
...
</event>
</listOfEvents>
...
</model>
@endverbatim
The C<<cn> 1 </cn>> within the mathematical formula
of the C<delay> above has <em>no units declared</em>. To make the
expression have the needed units of time, literal numbers should be
avoided in favor of defining Parameter objects for each quantity, and
declaring units for the Parameter values. The following fragment of
SBML illustrates this approach:
@verbatim
<model>
...
<listOfParameters>
<parameter id="transcriptionDelay" value="10" units="second"/>
</listOfParameters>
...
<listOfEvents>
<event useValuesFromTriggerTime="true">
...
<delay>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> transcriptionDelay </ci>
</math>
</delay>
...
</event>
</listOfEvents>
...
</model>
@endverbatim
In SBML Level 3, an alternative approach is available in the form
of the C<units> attribute, which SBML Level 3 allows to appear on
MathML C<cn> elements. The value of this attribute can be used to
indicate the unit of measurement to be associated with the number in the
content of a C<cn> element. The attribute is named C<units> but,
because it appears inside MathML element (which is in the XML namespace
for MathML and not the namespace for SBML), it must always be prefixed
with an XML namespace prefix for the SBML Level 3 Version 1
namespace. The following is an example of this approach:
@verbatim
<model timeUnits="second" ...>
...
<listOfEvents>
<event useValuesFromTriggerTime="true">
...
<delay>
<math xmlns="http://www.w3.org/1998/Math/MathML"
xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
<cn sbml:units="second"> 10 </cn>
</math>
</delay>
...
</event>
</listOfEvents>
...
</model>
@endverbatim
=over
=item Delay::Delay
Creates a new Delay using the given SBML C<level> and C<version>
values.
@param level an unsigned int, the SBML Level to assign to this Delay
@param version an unsigned int, the SBML Version to assign to this
Delay
@throws @if python ValueError @else SBMLConstructorException @endif@~
Thrown if the given C<level> and C<version> combination, or this kind
of SBML object, are either invalid or mismatched with respect to the
parent SBMLDocument object.
C<opydetails> doc_delay_setting_lv
=item Delay::Delay
Creates a new Delay using the given SBMLNamespaces object
C<sbmlns>.
C<opydetails> doc_what_are_sbmlnamespaces
@param sbmlns an SBMLNamespaces object.
@throws @if python ValueError @else SBMLConstructorException @endif@~
Thrown if the given C<level> and C<version> combination, or this kind
of SBML object, are either invalid or mismatched with respect to the
parent SBMLDocument object.
C<opydetails> doc_delay_setting_lv
=item Delay::Delay
Copy constructor; creates a copy of this Delay.
@param orig the object to copy.
@throws @if python ValueError @else SBMLConstructorException @endif@~
Thrown if the argument C<orig> is C<NULL>.
=item Delay::accept
Accepts the given SBMLVisitor for this instance of Delay.
@param v the SBMLVisitor instance to be used.
@return the result of calling C<v.visit()>.
=item Delay::clone
Creates and returns a deep copy of this Delay.
@return a (deep) copy of this Delay.
=item Delay::getMath
Get the mathematical formula for the delay and return it
as an AST.
@return the math of this Delay.
=item Delay::isSetMath
Predicate to test whether the formula for this delay is set.
@return C<true> if the formula (meaning the C<math> subelement) of
this Delay is set, C<false> otherwise.
=item Delay::setMath
Sets the delay expression of this Delay instance to a copy of the given
ASTNode.
@param math an ASTNode representing a formula tree.
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif@~ The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT @endlink
=item Delay::getDerivedUnitDefinition
Calculates and returns a UnitDefinition that expresses the units
of measurement assumed for the "math" expression of this Delay.
C<opydetails> doc_delay_units
C<opydetails> doc_note_unit_inference_depends_on_model
C<opydetails> doc_warning_delay_math_literals
@return a UnitDefinition that expresses the units of the math
expression of this Delay, or C<NULL> if one cannot be constructed.
@see containsUndeclaredUnits()
=item Delay::getDerivedUnitDefinition
Calculates and returns a UnitDefinition that expresses the units
of measurement assumed for the "math" expression of this Delay.
C<opydetails> doc_delay_units
C<opydetails> doc_note_unit_inference_depends_on_model
C<opydetails> doc_warning_delay_math_literals
@return a UnitDefinition that expresses the units of the math
expression of this Delay, or C<NULL> if one cannot be constructed.
@see containsUndeclaredUnits()
=item Delay::containsUndeclaredUnits
Predicate returning C<true> if the "math" expression in this Delay
instance contains parameters with undeclared units or literal numbers.
C<opydetails> doc_delay_units
If the expression contains literal numbers or parameters with undeclared
units, <strong>libSBML may not be able to compute the full units of the
expression</strong> and will only return what it can compute. Callers
should always use Delay::containsUndeclaredUnits() when using
Delay::getDerivedUnitDefinition() to decide whether the returned units
may be incomplete.
@return C<true> if the math expression of this Delay includes
numbers/parameters with undeclared units, C<false> otherwise.
@note A return value of C<true> indicates that the UnitDefinition
returned by Delay::getDerivedUnitDefinition() may not accurately
represent the units of the expression.
@see getDerivedUnitDefinition()
=item Delay::containsUndeclaredUnits
Predicate returning C<true> if the "math" expression in this Delay
instance contains parameters with undeclared units or literal numbers.
C<opydetails> doc_delay_units
If the expression contains literal numbers or parameters with undeclared
units, <strong>libSBML may not be able to compute the full units of the
expression</strong> and will only return what it can compute. Callers
should always use Delay::containsUndeclaredUnits() when using
Delay::getDerivedUnitDefinition() to decide whether the returned units
may be incomplete.
@return C<true> if the math expression of this Delay includes
numbers/parameters with undeclared units, C<false> otherwise.
@note A return value of C<true> indicates that the UnitDefinition
returned by Delay::getDerivedUnitDefinition() may not accurately
represent the units of the expression.
@see getDerivedUnitDefinition()
=item Delay::getTypeCode
Returns the libSBML type code of this object instance.
C<opydetails> doc_what_are_typecodes
@return the SBML type code for this object:
@link SBMLTypeCode_t#SBML_DELAY SBML_DELAY@endlink (default).
C<opydetails> doc_warning_typecodes_not_unique
@see getElementName()
@see getPackageName()
=item Delay::getElementName
Returns the XML element name of this object, which for Delay, is
always C<"delay">.
@return the name of this element, i.e., C<"delay">.
@see getTypeCode()
=item Delay::getElementPosition
@internal
Returns the position of this element.
@return the ordinal position of the element with respect to its
siblings or -1 (default) to indicate the position is not significant.
=item Delay::writeElements
@internal
Subclasses should override this method to write out their contained
SBML objects as XML elements. Be sure to call your parents
implementation of this method as well.
=item Delay::hasRequiredElements
Predicate returning C<true> if
all the required elements for this Delay object
have been set.
@note The required elements for a Delay object are:
@li "math"
@return a boolean value indicating whether all the required
elements for this object have been defined.
=item Delay::removeFromParentAndDelete
Finds this Delay's Event parent and calls unsetDelay() on it, indirectly
deleting itself.
Overridden from the SBase function since the parent is not a ListOf.
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif@~ The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item Delay::renameSIdRefs
Renames all the C<SIdRef> attributes on this element, including any
found in MathML.
C<opydetails> doc_what_is_sidref
This method works by looking at all attributes and (if appropriate)
mathematical formulas, comparing the identifiers to the value of @p
oldid. If any matches are found, the matching identifiers are replaced
with C<newid>. The method does I<not> descend into child elements.
@param oldid the old identifier
@param newid the new identifier
=item Delay::renameUnitSIdRefs
Renames all the C<UnitSIdRef> attributes on this element
C<opydetails> doc_what_is_unitsidref
This method works by looking at all unit identifier attribute values
(including, if appropriate, inside mathematical formulas), comparing the
unit identifiers to the value of C<oldid>. If any matches are found,
the matching identifiers are replaced with C<newid>. The method does
I<not> descend into child elements.
@param oldid the old identifier
@param newid the new identifier
=item Delay::replaceSIDWithFunction
@internal
Replace all nodes with the name 'id' from the child 'math' object with the provided function.
=item Delay::getInternalId
@internal
=item Delay::setInternalId
@internal
=item Delay::readOtherXML
@internal
Subclasses should override this method to read (and store) XHTML,
MathML, etc. directly from the XMLInputStream.
@return true if the subclass read from the stream, false otherwise.
=item Delay::addExpectedAttributes
@internal
Subclasses should override this method to get the list of
expected attributes.
This function is invoked from corresponding readAttributes()
function.
=item Delay::readAttributes
@internal
Subclasses should override this method to read values from the given
XMLAttributes set into their specific fields. Be sure to call your
parents implementation of this method as well.
=item Delay::readL2Attributes
@internal
=item Delay::readL3Attributes
@internal
=item Delay::writeAttributes
@internal
Subclasses should override this method to write their XML attributes
to the XMLOutputStream. Be sure to call your parents implementation
of this method as well.
=back
=head2 Priority
@sbmlpackage{core}
@htmlinclude pkg-marker-core.html Implementation of SBML Level 3's Priority construct for
Event.
The Priority object class (which was introduced in SBML Level 3
Version 1), like Delay, is derived from SBase and contains a MathML
formula stored in the element "math". This formula is used to compute a
dimensionless numerical value that influences the order in which a
simulator is to perform the assignments of two or more events that
happen to be executed simultaneously. The formula may evaluate to any
C<double> value (and thus may be a positive or negative number, or
zero), with positive numbers taken to signifying a higher priority than
zero or negative numbers. If no Priority object is present on a given
Event object, no priority is defined for that event.
@section priority-interp The interpretation of priorities on events in a model
For the purposes of SBML, <em>simultaneous event execution</em> is
defined as the situation in which multiple events have identical
times of execution. The time of execution is calculated as the
sum of the time at which a given event's Trigger is <em>triggered</em>
plus its Delay duration, if any. Here, <em>identical times</em> means
<em>mathematically equal</em> instants in time. (In practice,
simulation software adhering to this specification may have to
rely on numerical equality instead of strict mathematical
equality; robust models will ensure that this difference will not
cause significant discrepancies from expected behavior.)
If no Priority subobjects are defined for two or more Event objects,
then those events are still executed simultaneously but their order of
execution is <em>undefined by the SBML Level 3 Version 1
specification</em>. A software implementation may choose to execute
such simultaneous events in any order, as long as each event is executed
only once and the requirements of checking the "persistent" attribute
(and acting accordingly) are satisfied.
If Priority subobjects are defined for two or more
simultaneously-triggered events, the order in which those particular
events must be executed is dictated by their Priority objects,
as follows. If the values calculated using the two Priority
objects' "math" expressions differ, then the event having
the higher priority value must be executed before the event with
the lower value. If, instead, the two priority values are
mathematically equal, then the two events must be triggered in a
<em>random</em> order. It is important to note that a <em>random
order is not the same as an undefined order</em>: given multiple
runs of the same model with identical conditions, an undefined
ordering would permit a system to execute the events in (for
example) the same order every time (according to whatever scheme
may have been implemented by the system), whereas the explicit
requirement for random ordering means that the order of execution
in different simulation runs depends on random chance. In other
words, given two events <em>A</em> and <em>B</em>, a randomly-determined
order must lead to an equal chance of executing <em>A</em> first or
<em>B</em> first, every time those two events are executed
simultaneously.
A model may contain a mixture of events, some of which have
Priority subobjects and some do not. Should a combination of
simultaneous events arise in which some events have priorities
defined and others do not, the set of events with defined
priorities must trigger in the order determined by their Priority
objects, and the set of events without Priority objects must be
executed in an <em>undefined</em> order with respect to each other
and with respect to the events with Priority subobjects. (Note
that <em>undefined order</em> does not necessarily mean random
order, although a random ordering would be a valid implementation
of this requirement.)
The following example may help further clarify these points.
Suppose a model contains four events that should be executed
simultaneously, with two of the events having Priority objects
with the same value and the other two events having Priority
objects with the same, but different, value. The two events with
the higher priorities must be executed first, in a random order
with respect to each other, and the remaining two events must be
executed after them, again in a random order, for a total of four
possible and equally-likely event executions: A-B-C-D, A-B-D-C,
B-A-C-D, and B-A-D-C. If, instead, the model contains four events
all having the same Priority values, there are 4! or 24
possible orderings, each of which must be equally likely to be
chosen. Finally, if none of the four events has a Priority
subobject defined, or even if exactly one of the four events has a
defined Priority, there are again 24 possible orderings, but the
likelihood of choosing any particular ordering is undefined; the
simulator can choose between events as it wishes. (The SBML
specification only defines the effects of priorities on Event
objects with respect to <em>other</em> Event objects with
priorities. Putting a priority on a <em>single</em> Event object
in a model does not cause it to fall within that scope.)
@section priority-eval Evaluation of Priority expressions
An event's Priority object "math" expression must be
evaluated at the time the Event is to be <em>executed</em>. During
a simulation, all simultaneous events have their Priority values
calculated, and the event with the highest priority is selected for
next execution. Note that it is possible for the execution of one
Event object to cause the Priority value of another
simultaneously-executing Event object to change (as well as to
trigger other events, as already noted). Thus, after executing
one event, and checking whether any other events in the model have
been triggered, all remaining simultaneous events that
<em>either</em> (i) have Trigger objects with attributes
"persistent"=C<false> <em>or</em> (ii) have Trigger
expressions that did not transition from C<true> to
C<false>, must have their Priority expression reevaluated.
The highest-priority remaining event must then be selected for
execution next.
@section priority-units Units of Priority object's mathematical expressions
The unit associated with the value of a Priority object's
"math" expression should be C<dimensionless>. This is
because the priority expression only serves to provide a relative
ordering between different events, and only has meaning with
respect to other Priority object expressions. The value of
Priority objects is not comparable to any other kind of object in
an SBML model.
@note The Priority construct exists only in SBML Level 3; it cannot
be used in SBML Level 2 or Level 1 models.
@see Event
@see Delay
@see EventAssignment
=over
=item Priority::Priority
Creates a new Priority object using the given SBML C<level> and @p
version values.
@param level an unsigned int, the SBML Level to assign to this Priority
@param version an unsigned int, the SBML Version to assign to this
Priority
@throws @if python ValueError @else SBMLConstructorException @endif@~
Thrown if the given C<level> and C<version> combination, or this kind
of SBML object, are either invalid or mismatched with respect to the
parent SBMLDocument object.
C<opydetails> doc_note_priority_setting_lv
C<opydetails> doc_note_priority_only_l3
=item Priority::Priority
Creates a new Priority object using the given SBMLNamespaces object
C<sbmlns>.
C<opydetails> doc_what_are_sbmlnamespaces
@param sbmlns an SBMLNamespaces object.
@throws @if python ValueError @else SBMLConstructorException @endif@~
Thrown if the given C<level> and C<version> combination, or this kind
of SBML object, are either invalid or mismatched with respect to the
parent SBMLDocument object.
C<opydetails> doc_note_priority_setting_lv
C<opydetails> doc_note_priority_only_l3
=item Priority::Priority
Copy constructor; creates a copy of this Priority.
@param orig the object to copy.
@throws @if python ValueError @else SBMLConstructorException @endif@~
Thrown if the argument C<orig> is C<NULL>.
=item Priority::accept
Accepts the given SBMLVisitor for this instance of Priority.
@param v the SBMLVisitor instance to be used.
@return the result of calling C<v.visit()>.
=item Priority::clone
Creates and returns a deep copy of this Priority.
@return a (deep) copy of this Priority.
=item Priority::getMath
Get the mathematical formula for the priority and return it
as an AST.
@return the math of this Priority.
=item Priority::isSetMath
Predicate to test whether the formula for this delay is set.
@return C<true> if the formula (meaning the C<math> subelement) of
this Priority is set, C<false> otherwise.
=item Priority::setMath
Sets the math expression of this Priority instance to a copy of the given
ASTNode.
@param math an ASTNode representing a formula tree.
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif@~ The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT @endlink
=item Priority::getTypeCode
Returns the libSBML type code of this object instance.
C<opydetails> doc_what_are_typecodes
@return the SBML type code for this object:
@link SBMLTypeCode_t#SBML_PRIORITY SBML_PRIORITY@endlink (default).\
C<opydetails> doc_warning_typecodes_not_unique
@see getElementName()
@see getPackageName()
=item Priority::getElementName
Returns the XML element name of this object, which for Priority, is
always C<"priority">.
@return the name of this element, i.e., C<"priority">.
@see getTypeCode()
=item Priority::getElementPosition
@internal
Returns the position of this element.
@return the ordinal position of the element with respect to its
siblings or -1 (default) to indicate the position is not significant.
=item Priority::writeElements
@internal
Subclasses should override this method to write out their contained
SBML objects as XML elements. Be sure to call your parents
implementation of this method as well.
=item Priority::hasRequiredElements
Predicate returning C<true> if all the required elements for this
Priority object have been set.
@note The required elements for a Priority object are:
@li "math"
@return a boolean value indicating whether all the required
elements for this object have been defined.
=item Priority::removeFromParentAndDelete
Finds this Priority's Event parent and calls unsetPriority() on it,
indirectly deleting itself.
Overridden from the SBase function since the parent is not a ListOf.
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif@~ The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item Priority::renameSIdRefs
Renames all the C<SIdRef> attributes on this element, including any
found in MathML.
C<opydetails> doc_what_is_sidref
This method works by looking at all attributes and (if appropriate)
mathematical formulas, comparing the identifiers to the value of @p
oldid. If any matches are found, the matching identifiers are replaced
with C<newid>. The method does I<not> descend into child elements.
@param oldid the old identifier
@param newid the new identifier
=item Priority::renameUnitSIdRefs
Renames all the C<UnitSIdRef> attributes on this element.
C<opydetails> doc_what_is_unitsidref
This method works by looking at all unit identifier attribute values
(including, if appropriate, inside mathematical formulas), comparing the
unit identifiers to the value of C<oldid>. If any matches are found,
the matching identifiers are replaced with C<newid>. The method does
I<not> descend into child elements.
@param oldid the old identifier
@param newid the new identifier
=item Priority::replaceSIDWithFunction
@internal
Replace all nodes with the name 'id' from the child 'math' object with the provided function.
=item Priority::getInternalId
@internal
=item Priority::setInternalId
@internal
=item Priority::readOtherXML
@internal
Subclasses should override this method to read (and store) XHTML,
MathML, etc. directly from the XMLInputStream.
@return true if the subclass read from the stream, false otherwise.
=item Priority::addExpectedAttributes
@internal
Subclasses should override this method to get the list of
expected attributes.
This function is invoked from corresponding readAttributes()
function.
=item Priority::readAttributes
@internal
Subclasses should override this method to read values from the given
XMLAttributes set into their specific fields. Be sure to call your
parents implementation of this method as well.
=item Priority::readL3Attributes
@internal
=item Priority::writeAttributes
@internal
Subclasses should override this method to write their XML attributes
to the XMLOutputStream. Be sure to call your parents implementation
of this method as well.
=back
=head2 SBO
@sbmlpackage{core}
@htmlinclude pkg-marker-core.html Methods for interacting with Systems Biology Ontology
terms.
@htmlinclude not-sbml-warning.html
The values of "id" attributes on SBML components allow the components to
be cross-referenced within a model. The values of "name" attributes on
SBML components provide the opportunity to assign them meaningful labels
suitable for display to humans. The specific identifiers and labels
used in a model necessarily must be unrestricted by SBML, so that
software and users are free to pick whatever they need. However, this
freedom makes it more difficult for software tools to determine, without
additional human intervention, the semantics of models more precisely
than the semantics provided by the SBML object classes defined in other
sections of this document. For example, there is nothing inherent in a
parameter with identifier C<k> that would indicate to a
software tool it is a first-order rate constant (if that's what
C<k> happened to be in some given model). However, one may
need to convert a model between different representations (e.g.,
Henri-Michaelis-Menten versus elementary steps), or to use it with
different modeling approaches (discrete or continuous). One may also
need to relate the model components with other description formats such
as SBGN (<a target="_blank"
href="http://www.sbgn.org/">http://www.sbgn.org/</a>) using deeper
semantics. Although an advanced software tool <em>might</em> be able to
deduce the semantics of some model components through detailed analysis
of the kinetic rate expressions and other parts of the model, this
quickly becomes infeasible for any but the simplest of models.
An approach to solving this problem is to associate model components
with terms from carefully curated controlled vocabularies (CVs). This
is the purpose of the optional "sboTerm" attribute provided on the SBML
class SBase. The "sboTerm" attribute always refers to terms belonging
to the Systems Biology Ontology (SBO).
@section use Use of SBO
Labeling model components with terms from shared controlled vocabularies
allows a software tool to identify each component using identifiers that
are not tool-specific. An example of where this is useful is the desire
by many software developers to provide users with meaningful names for
reaction rate equations. Software tools with editing interfaces
frequently provide these names in menus or lists of choices for users.
However, without a standardized set of names or identifiers shared
between developers, a given software package cannot reliably interpret
the names or identifiers of reactions used in models written by other
tools.
The first solution that might come to mind is to stipulate that certain
common reactions always have the same name (e.g., "Michaelis-Menten"), but
this is simply impossible to do: not only do humans often disagree on
the names themselves, but it would not allow for correction of errors or
updates to the list of predefined names except by issuing new releases
of the SBML specification—to say nothing of many other limitations
with this approach. Moreover, the parameters and variables that appear
in rate expressions also need to be identified in a way that software
tools can interpret mechanically, implying that the names of these
entities would also need to be regulated.
The Systems Biology Ontology (SBO) provides terms for identifying most
elements of SBML. The relationship implied by an "sboTerm" on an SBML
model component is <em>is-a</em> between the characteristic of the
component meant to be described by SBO on this element and the SBO
term identified by the value of the "sboTerm". By adding SBO term
references on the components of a model, a software tool can provide
additional details using independent, shared vocabularies that can
enable <em>other</em> software tools to recognize precisely what the
component is meant to be. Those tools can then act on that information.
For example, if the SBO identifier C<"SBO>:0000049" is assigned
to the concept of "first-order irreversible mass-action kinetics,
continuous framework", and a given KineticLaw object in a model has an
"sboTerm" attribute with this value, then regardless of the identifier
and name given to the reaction itself, a software tool could use this to
inform users that the reaction is a first-order irreversible mass-action
reaction. This kind of reverse engineering of the meaning of reactions
in a model would be difficult to do otherwise, especially for more
complex reaction types.
The presence of SBO labels on Compartment, Species, and Reaction
objects in SBML can help map those entities to equivalent concepts in
other standards, such as (but not limited to) BioPAX (<a target="_blank"
href="http://www.biopax.org/">http://www.biopax.org/</a>), PSI-MI (<a
target="_blank"
href="http://www.psidev.info/index.php?q=node/60">http://www.psidev.info</a>),
or the Systems Biology Graphical Notation (SBGN, <a target="_blank"
href="http://www.sbgn.org/">http://www.sbgn.org/</a>). Such mappings
can be used in conversion procedures, or to build interfaces, with SBO
becoming a kind of "glue" between standards of representation.
The presence of the label on a kinetic expression can also allow
software tools to make more intelligent decisions about reaction rate
expressions. For example, an application could recognize certain types
of reaction formulas as being ones it knows how to solve with optimized
procedures. The application could then use internal, optimized code
implementing the rate formula indexed by identifiers such as
C<"SBO>:0000049" appearing in SBML models.
Finally, SBO labels may be very valuable when it comes to model
integration, by helping identify interfaces, convert mathematical
expressions and parameters etc.
Although the use of SBO can be beneficial, it is critical to keep in
mind that the presence of an "sboTerm" value on an object <em>must not
change the fundamental mathematical meaning</em> of the model. An SBML
model must be defined such that it stands on its own and does not depend
on additional information added by SBO terms for a correct mathematical
interpretation. SBO term definitions will not imply any alternative
mathematical semantics for any SBML object labeled with that term. Two
important reasons motivate this principle. First, it would be too
limiting to require all software tools to be able to understand the SBO
vocabularies in addition to understanding SBML. Supporting SBO is not
only additional work for the software developer; for some kinds of
applications, it may not make sense. If SBO terms on a model are
optional, it follows that the SBML model <em>must</em> remain
unambiguous and fully interpretable without them, because an application
reading the model may ignore the terms. Second, we believe allowing the
use of "sboTerm" to alter the mathematical meaning of a model would
allow too much leeway to shoehorn inconsistent concepts into SBML
objects, ultimately reducing the interoperability of the models.
@section relationship Relationships between SBO and SBML
The goal of SBO labeling for SBML is to clarify to the fullest extent
possible the nature of each element in a model. The approach taken in
SBO begins with a hierarchically-structured set of controlled
vocabularies with six main divisions: (1) entity, (2) participant role,
(3) quantitative parameter, (4) modeling framework, (5) mathematical
expression, and (6) interaction. The web site for SBO (<a
target="_blank"
href="http://biomodels.net/sbo">http://biomodels.net</a>) should be
consulted for the current version of the ontology.
The Systems Biology Ontology (SBO) is not part of SBML; it is being
developed separately, to allow the modeling community to evolve the
ontology independently of SBML. However, the terms in the ontology are
being designed keeping SBML components in mind, and are classified into
subsets that can be directly related with SBML components such as
reaction rate expressions, parameters, and others. The use of "sboTerm"
attributes is optional, and the presence of "sboTerm" on an element does
not change the way the model is <em>interpreted</em>. Annotating SBML
elements with SBO terms adds additional semantic information that may
be used to <em>convert</em> the model into another model, or another
format. Although SBO support provides an important source of
information to understand the meaning of a model, software does not need
to support "sboTerm" to be considered SBML-compliant.
=over
=item SBO::readTerm
@internal
Reads (and checks) sboTerm from the given XMLAttributes set.
@return the sboTerm as an integer or -1 if the sboTerm was not in the
correct format or not found.
=item SBO::writeTerm
@internal
Writes sboTerm as an XMLAttribute with the given prefix to the given XMLOutputStream.
=item SBO::isQuantitativeParameter
Returns C<true> if the given term identifier comes from the stated branch of SBO.
@return C<true> if C<term> is-a SBO <em>"quantiative parameter"</em>, C<false>
otherwise.
C<opydetails> doc_note_static_methods
=item SBO::isParticipantRole
Returns C<true> if the given term identifier comes from the stated branch of SBO.
@return C<true> if C<term> is-a SBO <em>"participant role"</em>, C<false> otherwise.
C<opydetails> doc_note_static_methods
=item SBO::isModellingFramework
Returns C<true> if the given term identifier comes from the stated branch of SBO.
@return C<true> if C<term> is-a SBO <em>"modeling framework"</em>, C<false> otherwise.
C<opydetails> doc_note_static_methods
=item SBO::isMathematicalExpression
Returns C<true> if the given term identifier comes from the stated branch of SBO.
@return C<true> if C<term> is-a SBO <em>"mathematical expression"</em>, C<false> otherwise.
C<opydetails> doc_note_static_methods
=item SBO::isKineticConstant
Returns C<true> if the given term identifier comes from the stated branch of SBO.
@return C<true> if C<term> is-a SBO <em>"kinetic constant"</em>, C<false> otherwise.
C<opydetails> doc_note_static_methods
=item SBO::isReactant
Returns C<true> if the given term identifier comes from the stated branch of SBO.
@return C<true> if C<term> is-a SBO <em>"reactant"</em>, C<false> otherwise.
C<opydetails> doc_note_static_methods
=item SBO::isProduct
Returns C<true> if the given term identifier comes from the stated branch of SBO.
@return C<true> if C<term> is-a SBO <em>"product"</em>, C<false> otherwise.
C<opydetails> doc_note_static_methods
=item SBO::isModifier
Returns C<true> if the given term identifier comes from the stated branch of SBO.
@return C<true> if C<term> is-a SBO <em>"modifier"</em>, C<false> otherwise.
C<opydetails> doc_note_static_methods
=item SBO::isRateLaw
Returns C<true> if the given term identifier comes from the stated branch of SBO.
@return C<true> if C<term> is-a SBO <em>"rate law"</em>, C<false> otherwise.
C<opydetails> doc_note_static_methods
=item SBO::isEvent
Returns C<true> if the given term identifier comes from the stated branch of SBO.
@return C<true> if C<term> is-a SBO <em>"event"</em>, C<false> otherwise.
C<opydetails> doc_note_static_methods
=item SBO::isPhysicalParticipant
Returns C<true> if the given term identifier comes from the stated branch of SBO.
@return C<true> if C<term> is-a SBO <em>"physical participant</em>, C<false> otherwise.
C<opydetails> doc_note_static_methods
=item SBO::isParticipant
Returns C<true> if the given term identifier comes from the stated branch of SBO.
@return C<true> if C<term> is-a SBO <em>"participant"</em>, C<false> otherwise.
C<opydetails> doc_note_static_methods
=item SBO::isInteraction
Returns C<true> if the given term identifier comes from the stated branch of SBO.
@return C<true> if C<term> is-a SBO <em>"interaction"</em>, C<false> otherwise.
C<opydetails> doc_note_static_methods
=item SBO::isEntity
Returns C<true> if the given term identifier comes from the stated branch of SBO.
@return C<true> if C<term> is-a SBO <em>"entity"</em>, C<false> otherwise.
C<opydetails> doc_note_static_methods
=item SBO::isFunctionalEntity
Returns C<true> if the given term identifier comes from the stated branch of SBO.
@return C<true> if C<term> is-a SBO <em>"functional entity"</em>, C<false> otherwise.
C<opydetails> doc_note_static_methods
=item SBO::isMaterialEntity
Returns C<true> if the given term identifier comes from the stated branch of SBO.
@return C<true> if C<term> is-a SBO <em>"material entity"</em>, C<false> otherwise.
C<opydetails> doc_note_static_methods
=item SBO::isConservationLaw
Returns C<true> if the given term identifier comes from the stated branch of SBO.
@return C<true> if C<term> is-a SBO <em>"conservation law"</em>, C<false> otherwise.
C<opydetails> doc_note_static_methods
=item SBO::isSteadyStateExpression
Returns C<true> if the given term identifier comes from the stated branch of SBO.
@return C<true> if C<term> is-a SBO <em>"steady state expression"</em>, C<false> otherwise.
C<opydetails> doc_note_static_methods
=item SBO::isFunctionalCompartment
Returns C<true> if the given term identifier comes from the stated branch of SBO.
@return C<true> if C<term> is-a SBO <em>"functional compartment"</em>, C<false> otherwise.
C<opydetails> doc_note_static_methods
=item SBO::isContinuousFramework
Returns C<true> if the given term identifier comes from the stated branch of SBO.
@return C<true> if C<term> is-a SBO <em>"continuous framework"</em>, C<false> otherwise.
C<opydetails> doc_note_static_methods
=item SBO::isDiscreteFramework
Returns C<true> if the given term identifier comes from the stated branch of SBO.
@return C<true> if C<term> is-a SBO <em>"discrete framework"</em>, C<false> otherwise.
C<opydetails> doc_note_static_methods
=item SBO::isLogicalFramework
Returns C<true> if the given term identifier comes from the stated branch of SBO.
@return C<true> if C<term> is-a SBO <em>"logical framework"</em>, C<false> otherwise.
C<opydetails> doc_note_static_methods
=item SBO::isMetadataRepresentation
Returns C<true> if the given term identifier comes from the stated branch of SBO.
@return C<true> if C<term> is-a SBO <em>"metadata representation"</em>, C<false> otherwise.
C<opydetails> doc_note_static_methods
=item SBO::isOccurringEntityRepresentation
Returns C<true> if the given term identifier comes from the stated branch of SBO.
@return C<true> if C<term> is-a SBO <em>"occurring entity representation"</em>, C<false> otherwise.
C<opydetails> doc_note_static_methods
=item SBO::isPhysicalEntityRepresentation
Returns C<true> if the given term identifier comes from the stated branch of SBO.
@return C<true> if C<term> is-a SBO <em>"physical entity representation"</em>, C<false> otherwise.
C<opydetails> doc_note_static_methods
=item SBO::isSystemsDescriptionParameter
Returns C<true> if the given term identifier comes from the stated branch of SBO.
@return C<true> if C<term> is-a SBO <em>"systems description parameter"</em>, C<false> otherwise.
C<opydetails> doc_note_static_methods
=item SBO::isObselete
Predicate for checking whether the given term is obsolete.
@return C<true> if C<term> is-a SBO <em>"obsolete"</em> term, C<false> otherwise.
C<opydetails> doc_note_static_methods
=item SBO::intToString
Returns the integer as a correctly formatted SBO identifier string.
@return the given integer sboTerm as a zero-padded seven digit string.
@note If the sboTerm is not in the correct range
(0000000–9999999), an empty string is returned.
C<opydetails> doc_note_static_methods
=item SBO::stringToInt
Returns the string as a correctly formatted SBO integer portion.
@return the given string sboTerm as an integer. If the sboTerm is not
in the correct format (a zero-padded, seven digit string), C<-1> is
returned.
C<opydetails> doc_note_static_methods
=item SBO::checkTerm
Checks the format of the given SBO identifier string.
@return C<true> if sboTerm is in the correct format (a zero-padded, seven
digit string), C<false> otherwise.
C<opydetails> doc_note_static_methods
=item SBO::checkTerm
Checks the format of the given SBO identifier, given in the form of
the integer portion alone.
@return C<true> if sboTerm is in the range (0000000–9999999), C<false>
otherwise.
C<opydetails> doc_note_static_methods
=item SBO::isChildOf
@internal
Returns C<true> if the given term identifier comes from the stated branch of SBO.
@return true if the term is-a parent, false otherwise
=item SBO::populateSBOTree
@internal
Returns C<true> if the given term identifier comes from the stated branch of SBO.
populates the parent-child map
=back
=head2 SyntaxChecker
@sbmlpackage{core}
@htmlinclude pkg-marker-core.html Methods for checking syntax of SBML identifiers and other
strings.
@htmlinclude not-sbml-warning.html
This utility class provides static methods for checking the syntax of
identifiers and other text used in an SBML model. The methods allow
callers to verify that strings such as SBML identifiers and XHTML notes
text conform to the SBML specifications.
=over
=item SyntaxChecker::isValidSBMLSId
Returns true C<true> or C<false> depending on whether the argument
string conforms to the syntax of SBML identifiers.
C<opydetails> doc_what_is_sid
This method provides programs with the ability to test explicitly that
the identifier strings they create conform to the SBML identifier
syntax.
@param sid string to be checked for conformance to SBML identifier
syntax.
@return C<true> if the string conforms to type SBML data type
C<SId>, C<false> otherwise.
C<opydetails> doc_id_syntax
C<opydetails> doc_note_static_methods
@see @if clike isValidUnitSId(std::string sid) @else SyntaxChecker::isValidUnitSId(std::string sid) @endif@~
@see @if clike isValidXMLID(std::string sid) @else SyntaxChecker::isValidXMLID(std::string sid) @endif@~
=item SyntaxChecker::isValidXMLID
Returns C<true> or C<false> depending on whether the argument string
conforms to the XML data type C<ID>.
C<opydetails> doc_what_is_metaid
This method provides programs with the ability to test explicitly that
the identifier strings they create conform to the SBML identifier
syntax.
@param id string to be checked for conformance to the syntax of
<a target="_blank" href="http://www.w3.org/TR/REC-xml/#id">XML ID</a>.
@return C<true> if the string is a syntactically-valid value for the
XML type <a target="_blank"
href="http://www.w3.org/TR/REC-xml/#id">ID</a>, C<false> otherwise.
@note @htmlinclude xmlid-syntax.html
C<opydetails> doc_note_static_methods
@see @if clike isValidSBMLSId(std::string sid) @else SyntaxChecker::isValidSBMLSId(std::string sid) @endif@~
@see @if clike isValidUnitSId(std::string sid) @else SyntaxChecker::isValidUnitSId(std::string sid) @endif@~
=item SyntaxChecker::isValidXMLanyURI
Returns C<true> or C<false> depending on whether the C<uri> argument string
conforms to the XML data type C<anyURI>.
Type anyURI is defined by XML Schema 1.0. It is a character string
data type whose values are interpretable as URIs (Universal Resource
Identifiers) as described by the W3C document RFC 3986. LibSBML
does not provide an explicit XML C<anyURI> data type; it uses
ordinary character strings, which is easier for applications to
support. LibSBML does, however, test for anyURI validity at
various times, such as when reading in models from files and data
streams.
This method provides programs with the ability to test explicitly that
the strings they create conform to the XML anyURI syntax.
@param uri string to be checked for conformance to the syntax of
<a target="_blank"
href="http://www.w3.org/TR/xmlschema-2/#anyURI">anyURI</a>.
@return C<true> if the string is a syntactically-valid value for the
XML type <a target="_blank"
href="http://www.w3.org/TR/xmlschema-2/#anyURI">anyURI</a>,
C<false> otherwise.
C<opydetails> doc_note_static_methods
=item SyntaxChecker::isValidUnitSId
Returns C<true> or C<false> depending on whether the argument string
conforms to the syntax of SBML unit identifiers.
In SBML, the identifiers of units (of both the predefined units and
user-defined units) must conform to a data type called
C<UnitSId> in the SBML specifications. LibSBML does not
provide an explicit C<UnitSId> data type; it uses ordinary
character strings, which is easier for applications to support.
LibSBML does, however, test for identifier validity at various times,
such as when reading in models from files and data streams.
This method provides programs with the ability to test explicitly that
the identifier strings they create conform to the SBML identifier
syntax.
@param units string to be checked for conformance to SBML unit
identifier syntax.
@return C<true> if the string conforms to type SBML data type
C<UnitSId>, C<false> otherwise.
@note @htmlinclude unitid-syntax.html
C<opydetails> doc_note_static_methods
@see @if clike isValidSBMLSId(std::string sid) @else SyntaxChecker::isValidSBMLSId(std::string sid) @endif@~
@see @if clike isValidXMLID(std::string sid) @else SyntaxChecker::isValidXMLID(std::string sid) @endif@~
=item SyntaxChecker::hasExpectedXHTMLSyntax
Returns C<true> or C<false> depending on whether the given XMLNode
object contains valid XHTML content.
C<opydetails> doc_what_are_notes
An aspect of XHTML validity is that the content is declared to be in
the XML namespace for XHTML 1.0. There is more than one way in
which this can be done in XML. In particular, a model might not
contain the declaration within the "notes" or "message" subelement
itself, but might instead place the declaration on an enclosing
element and use an XML namespace prefix within the "notes" element to
refer to it. In other words, the following is valid:
@verbatim
<sbml xmlns="http://www.sbml.org/sbml/level2/version3" level="2" version="3"
xmlns:xhtml="http://www.w3.org/1999/xhtml">
<model>
<notes>
<xhtml:body>
<xhtml:center><xhtml:h2>A Simple Mitotic Oscillator</xhtml:h2></xhtml:center>
<xhtml:p>A minimal cascade model for the mitotic oscillator.</xhtml:p>
</xhtml:body>
</notes>
... rest of model ...
</sbml>
@endverbatim
Contrast the above with the following, self-contained version, which
places the XML namespace declaration within the C<<notes>>
element itself:
@verbatim
<sbml xmlns="http://www.sbml.org/sbml/level2/version3" level="2" version="3">
<model>
<notes>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<title/>
</head>
<body>
<center><h2>A Simple Mitotic Oscillator</h2></center>
<p>A minimal cascade model for the mitotic oscillator.</p>
</body>
</html>
</notes>
... rest of model ...
</sbml>
@endverbatim
Both of the above are valid XML. The purpose of the C<sbmlns>
argument to this method is to allow callers to check the validity of
"notes" and "message" subelements whose XML namespace declarations
have been put elsewhere in the manner illustrated above. Callers can
can pass in the SBMLNamespaces object of a higher-level model
component if the XMLNode object does not itself have the XML namespace
declaration for XHTML 1.0.
@param xhtml the XMLNode to be checked for conformance.
@param sbmlns the SBMLNamespaces associated with the object.
@return C<true> if the XMLNode content conforms, C<false> otherwise.
C<opydetails> doc_note_static_methods
@if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
=item SyntaxChecker::isValidInternalSId
@internal
Returns true C<true> or C<false> depending on whether the argument
string conforms to the syntax of SBML identifiers or is empty.
=item SyntaxChecker::isValidInternalUnitSId
@internal
=item SyntaxChecker::isAllowedElement
@internal
=item SyntaxChecker::hasDeclaredNS
@internal
=item SyntaxChecker::isCorrectHTMLNode
@internal
=item SyntaxChecker::isUnicodeLetter
@internal
Checks if a character is part of the Unicode Letter set.
@return true if the character is a part of the set, false otherwise.
=item SyntaxChecker::isUnicodeDigit
@internal
Checks if a character is part of the Unicode Digit set.
@return true if the character is a part of the set, false otherwise.
=item SyntaxChecker::isCombiningChar
@internal
Checks if a character is part of the Unicode CombiningChar set.
@return true if the character is a part of the set, false otherwise.
=item SyntaxChecker::isExtender
@internal
Checks if a character is part of the Unicode Extender set.
@return true if the character is a part of the set, false otherwise.
=back
=head2 StoichiometryMath
@sbmlpackage{core}
@htmlinclude pkg-marker-core.html Implementation of SBML Level 2's StoichiometryMath
construct.
@section l2-stoichiometries Stoichiometries in SBML Level 2
In SBML Level 2, product and reactant stoichiometries can be specified
using I<either> the "stoichiometry" attribute or a "stoichiometryMath"
element in a SpeciesReference object. The "stoichiometry" attribute is
of type C<double> and should contain values greater than zero (0). The
"stoichiometryMath" element is implemented as an element containing a
MathML expression. These two are mutually exclusive; only one of
"stoichiometry" or "stoichiometryMath" should be defined in a given
SpeciesReference instance. When neither the attribute nor the element
is present, the value of "stoichiometry" in the enclosing
SpeciesReference instance defaults to C<1>.
For maximum interoperability, SpeciesReference's "stoichiometry"
attribute should be used in preference to "stoichiometryMath" when a
species' stoichiometry is a simple scalar number (integer or decimal).
When the stoichiometry is a rational number, or when it is a more
complicated formula, "stoichiometryMath" must be used. The MathML
expression in "stoichiometryMath" may also refer to identifiers of
entities in a model (except reaction identifiers). However, the only
species identifiers that can be used in "stoichiometryMath" are those
referenced in the enclosing Reaction's list of reactants, products and
modifiers.
The "stoichiometry" attribute and the "stoichiometryMath" element, when
either is used, is each interpreted as a factor applied to the reaction
rate to produce the rate of change of the species identified by the
"species" attribute in the enclosing SpeciesReference. This is the
normal interpretation of a stoichiometry, but in SBML, one additional
consideration has to be taken into account. The reaction rate, which is
the result of the KineticLaw's "math" element, is always in the model's
I<substance> per I<time> units. However, the rate of change of the
species will involve the species' I<substance> units (i.e., the units
identified by the Species object's "substanceUnits" attribute), and
these units may be different from the model's default I<substance>
units. If the units I<are> different, the stoichiometry must
incorporate a conversion factor for converting the model's I<substance>
units to the species' I<substance> units. The conversion factor is
assumed to be included in the scalar value of the "stoichiometry"
attribute if "stoichiometry" is used. If instead "stoichiometryMath" is
used, then the product of the model's "substance" units times the
"stoichiometryMath" units must match the I<substance> units of the
species. Note that in either case, if the species' units and the
model's default I<substance> units are the same, the stoichiometry ends
up being a dimensionless number and equivalent to the standard chemical
stoichiometry found in textbooks. Examples and more explanations of
this are given in the SBML specification.
The following is a simple example of a species reference for species @c
"X0", with stoichiometry C<2>, in a list of reactants within a reaction
having the identifier C<"J1">:
@verbatim
<model>
...
<listOfReactions>
<reaction id="J1">
<listOfReactants>
<speciesReference species="X0" stoichiometry="2">
</listOfReactants>
...
</reaction>
...
</listOfReactions>
...
</model>
@endverbatim
The following is a more complex example of a species reference for
species C<"X0">, with a stoichiometry formula consisting of
a rational number:
@verbatim
<model>
...
<listOfReactions>
<reaction id="J1">
<listOfReactants>
<speciesReference species="X0">
<stoichiometryMath>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<cn type="rational"> 3 <sep/> 2 </cn>
</math>
</stoichiometryMath>
</speciesReference>
</listOfReactants>
...
</reaction>
...
</listOfReactions>
...
</model>
@endverbatim
Additional discussions of stoichiometries and implications for species
and reactions are included in the documentation of SpeciesReference
class.
@section l3-stoichiometries Stoichiometries in SBML Level 3
The StoichiometryMath construct is not defined in SBML Level 3
Version 1 Core. Instead, Level 3 defines the identifier of
SpeciesReference objects as a stand-in for the stoichiometry of the
reactant or product being referenced, and allows that identifier to be
used elsewhere in SBML models, including (for example) InitialAssignment
objects. This makes it possible to achieve the same effect as
StoichiometryMath, but with other SBML objects. For instance, to
produce a stoichiometry value that is a rational number, a model can use
InitialAssignment to assign the identifier of a SpeciesReference object
to a MathML expression evaluating to a rational number. This is
analogous to the same way that, in Level 2, the model would use
StoichiometryMath with a MathML expression evaluating to a rational
number.
In SBML Level 2, the stoichiometry of a reactant or product is a
combination of both a <em>biochemical stoichiometry</em> (meaning, the
standard stoichiometry of a species in a reaction) and any necessary
unit conversion factors. The introduction of an explicit attribute on
the Species object for a conversion factor allows Level 3 to avoid
having to overload the meaning of stoichiometry. In Level 3, the
stoichiometry given by a SpeciesReference object in a reaction is a
"proper" biochemical stoichiometry, meaning a dimensionless number free
of unit conversions.
@see SpeciesReference
@see Reaction
=over
=item StoichiometryMath::StoichiometryMath
Creates a new StoichiometryMath object using the given SBML C<level>
values.
@param level an unsigned int, the SBML Level to assign to this StoichiometryMath
@param version an unsigned int, the SBML Version to assign to this
StoichiometryMath
@throws @if python ValueError @else SBMLConstructorException @endif@~
Thrown if the given C<level> and C<version> combination, or this kind
of SBML object, are either invalid or mismatched with respect to the
parent SBMLDocument object.
C<opydetails> doc_note_stoichiometrymath_availability
C<opydetails> doc_note_stoichiometrymath_setting_lv
=item StoichiometryMath::StoichiometryMath
Creates a new StoichiometryMath object using the given SBMLNamespaces object
C<sbmlns>.
C<opydetails> doc_what_are_sbmlnamespaces
@param sbmlns an SBMLNamespaces object.
@throws @if python ValueError @else SBMLConstructorException @endif@~
Thrown if the given C<level> and C<version> combination, or this kind
of SBML object, are either invalid or mismatched with respect to the
parent SBMLDocument object.
C<opydetails> doc_note_stoichiometrymath_availability
C<opydetails> doc_note_stoichiometrymath_setting_lv
=item StoichiometryMath::StoichiometryMath
Copy constructor; creates a copy of this StoichiometryMath.
@param orig the object to copy.
@throws @if python ValueError @else SBMLConstructorException @endif@~
Thrown if the argument C<orig> is C<NULL>.
=item StoichiometryMath::accept
Accepts the given SBMLVisitor for this instance of StoichiometryMath.
@param v the SBMLVisitor instance to be used.
@return the result of calling C<v.visit()>.
=item StoichiometryMath::clone
Creates and returns a deep copy of this StoichiometryMath object.
@return a (deep) copy of this StoichiometryMath.
=item StoichiometryMath::getMath
Retrieves the mathematical formula within this StoichiometryMath and
return it as an AST.
@return the math of this StoichiometryMath.
C<opydetails> doc_note_stoichiometrymath_availability
=item StoichiometryMath::isSetMath
Predicate to test whether the math for this StoichiometryMath object
is set.
@return C<true> if the formula (meaning the C<math> subelement) of
this StoichiometryMath is set, C<false> otherwise.
C<opydetails> doc_note_stoichiometrymath_availability
=item StoichiometryMath::setMath
Sets the 'math' expression of this StoichiometryMath instance to a
copy of the given ASTNode.
@param math an ASTNode representing a formula tree.
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT @endlink
C<opydetails> doc_note_stoichiometrymath_availability
=item StoichiometryMath::getDerivedUnitDefinition
Calculates and returns a UnitDefinition object that expresses the
units returned by the math expression in this StoichiometryMath
object.
The units are calculated based on the mathematical expression in the
StoichiometryMath and the model quantities referenced by
C<<ci>> elements used within that expression. The
StoichiometryMath::getDerivedUnitDefinition() method returns the
calculated units.
Note that the functionality that facilitates unit analysis depends
on the model as a whole. Thus, in cases where the object has not
been added to a model or the model itself is incomplete,
unit analysis is not possible and this method will return C<NULL>.
@return a UnitDefinition that expresses the units of the math,
or C<NULL> if one cannot be constructed.
@warning <span class="warning">Note that it is possible the "math"
expression in the StoichiometryMath instance contains literal numbers or
parameters with undeclared units. In those cases, it is not possible to
calculate the units of the overall expression without making
assumptions. LibSBML does not make assumptions about the units, and
StoichiometryMath::getDerivedUnitDefinition() only returns the units as
far as it is able to determine them. For example, in an expression
<em>X + Y</em>, if <em>X</em> has unambiguously-defined units and
<em>Y</em> does not, it will return the units of <em>X</em>. When using
this method, <strong>it is critical that callers also invoke the
method</strong> StoichiometryMath::containsUndeclaredUnits() <strong>to
determine whether this situation holds</strong>. Callers should take
suitable action in those situations.</span>
@see containsUndeclaredUnits()
=item StoichiometryMath::getDerivedUnitDefinition
Calculates and returns a UnitDefinition object that expresses the
units returned by the math expression in this StoichiometryMath
object.
The units are calculated based on the mathematical expression in the
StoichiometryMath and the model quantities referenced by
C<<ci>> elements used within that expression. The
StoichiometryMath::getDerivedUnitDefinition() method returns the
calculated units.
Note that the functionality that facilitates unit analysis depends
on the model as a whole. Thus, in cases where the object has not
been added to a model or the model itself is incomplete,
unit analysis is not possible and this method will return C<NULL>.
@return a UnitDefinition that expresses the units of the math,
or C<NULL> if one cannot be constructed.
@warning <span class="warning">Note that it is possible the "math"
expression in the StoichiometryMath instance contains literal numbers or
parameters with undeclared units. In those cases, it is not possible to
calculate the units of the overall expression without making
assumptions. LibSBML does not make assumptions about the units, and
StoichiometryMath::getDerivedUnitDefinition() only returns the units as
far as it is able to determine them. For example, in an expression
<em>X + Y</em>, if <em>X</em> has unambiguously-defined units and
<em>Y</em> does not, it will return the units of <em>X</em>. When using
this method, <strong>it is critical that callers also invoke the
method</strong> StoichiometryMath::containsUndeclaredUnits() <strong>to
determine whether this situation holds</strong>. Callers should take
suitable action in those situations.</span>
@see containsUndeclaredUnits()
=item StoichiometryMath::containsUndeclaredUnits
Predicate returning C<true> if the math
expression of this StoichiometryMath object contains literal numbers
or parameters with undeclared units.
The StoichiometryMath::getDerivedUnitDefinition() method returns what
libSBML computes the units of the Stoichiometry to be, to the extent
that libSBML can compute them. However, if the expression contains
literal numbers or parameters with undeclared units, libSBML may not
be able to compute the full units of the expression and will only
return what it can compute. Callers should always use
StoichiometryMath::containsUndeclaredUnits() when using
StoichiometryMath::getDerivedUnitDefinition() to decide whether the
returned units may be incomplete.
@return C<true> if the math expression of this StoichiometryMath
includes numbers/parameters with undeclared units, C<false> otherwise.
@note A return value of C<true> indicates that the UnitDefinition
returned by StoichiometryMath::getDerivedUnitDefinition() may not
accurately represent the units of the expression.
@see getDerivedUnitDefinition()
=item StoichiometryMath::containsUndeclaredUnits
Predicate returning C<true> if the math
expression of this StoichiometryMath object contains literal numbers
or parameters with undeclared units.
The StoichiometryMath::getDerivedUnitDefinition() method returns what
libSBML computes the units of the Stoichiometry to be, to the extent
that libSBML can compute them. However, if the expression contains
literal numbers or parameters with undeclared units, libSBML may not
be able to compute the full units of the expression and will only
return what it can compute. Callers should always use
StoichiometryMath::containsUndeclaredUnits() when using
StoichiometryMath::getDerivedUnitDefinition() to decide whether the
returned units may be incomplete.
@return C<true> if the math expression of this StoichiometryMath
includes numbers/parameters with undeclared units, C<false> otherwise.
@note A return value of C<true> indicates that the UnitDefinition
returned by StoichiometryMath::getDerivedUnitDefinition() may not
accurately represent the units of the expression.
@see getDerivedUnitDefinition()
=item StoichiometryMath::getTypeCode
Returns the libSBML type code of this object instance.
C<opydetails> doc_what_are_typecodes
@return the SBML type code for this object:
@link SBMLTypeCode_t#SBML_STOICHIOMETRY_MATH SBML_STOICHIOMETRY_MATH@endlink (default).
C<opydetails> doc_warning_typecodes_not_unique
@see getElementName()
@see getPackageName()
=item StoichiometryMath::getElementName
Returns the XML element name of this object, which for StoichiometryMath, is
always C<"stoichiometryMath">.
@return the name of this element, i.e., C<"stoichiometryMath">.
=item StoichiometryMath::getElementPosition
@internal
Returns the position of this element.
@return the ordinal position of the element with respect to its
siblings or C<-1> (default) to indicate the position is not significant.
=item StoichiometryMath::writeElements
@internal
Subclasses should override this method to write out their contained
SBML objects as XML elements. Be sure to call your parents
implementation of this method as well.
=item StoichiometryMath::hasRequiredElements
Predicate returning C<true> if
all the required elements for this StoichiometryMath object
have been set.
@note The required elements for a StoichiometryMath object are:
@li "math"
@return a boolean value indicating whether all the required
elements for this object have been defined.
=item StoichiometryMath::removeFromParentAndDelete
Finds this StoichiometryMath's SpeciesReference parent and calls
unsetStoichiometryMath() on it, indirectly deleting itself.
Overridden from the SBase function since the parent is not a ListOf.
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif@~ The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item StoichiometryMath::renameSIdRefs
Renames all the C<SIdRef> attributes on this element, including any
found in MathML.
C<opydetails> doc_what_is_sidref
This method works by looking at all attributes and (if appropriate)
mathematical formulas, comparing the identifiers to the value of @p
oldid. If any matches are found, the matching identifiers are replaced
with C<newid>. The method does I<not> descend into child elements.
@param oldid the old identifier
@param newid the new identifier
=item StoichiometryMath::renameUnitSIdRefs
Renames all the C<UnitSIdRef> attributes on this element.
C<opydetails> doc_what_is_unitsidref
This method works by looking at all unit identifier attribute values
(including, if appropriate, inside mathematical formulas), comparing the
unit identifiers to the value of C<oldid>. If any matches are found,
the matching identifiers are replaced with C<newid>. The method does
I<not> descend into child elements.
@param oldid the old identifier
@param newid the new identifier
=item StoichiometryMath::replaceSIDWithFunction
@internal
Replace all nodes with the name 'id' from the child 'math' object with the provided function.
=item StoichiometryMath::getInternalId
@internal
=item StoichiometryMath::setInternalId
@internal
=item StoichiometryMath::readOtherXML
@internal
Subclasses should override this method to read (and store) XHTML,
MathML, etc. directly from the XMLInputStream.
@return true if the subclass read from the stream, false otherwise.
=item StoichiometryMath::addExpectedAttributes
@internal
Subclasses should override this method to get the list of
expected attributes.
This function is invoked from corresponding readAttributes()
function.
=item StoichiometryMath::readAttributes
@internal
Subclasses should override this method to read values from the given
XMLAttributes set into their specific fields. Be sure to call your
parents implementation of this method as well.
=item StoichiometryMath::readL2Attributes
@internal
=item StoichiometryMath::writeAttributes
@internal
Subclasses should override this method to write their XML attributes
to the XMLOutputStream. Be sure to call your parents implementation
of this method as well.
=back
=head2 SBMLNamespaces
@sbmlpackage{core}
@htmlinclude pkg-marker-core.html Class to store SBML Level, Version and namespace
information.
@htmlinclude not-sbml-warning.html
There are differences in the definitions of components between different
SBML Levels, as well as Versions within Levels. For example, the
"sboTerm" attribute was not introduced until Level 2
Version 2, and then only on certain component classes; the SBML
Level 2 Version 3 specification moved the "sboTerm" attribute
to the SBase class, thereby allowing nearly all components to have SBO
annotations. As a result of differences such as those, libSBML needs to
track the SBML Level and Version of every object created.
The purpose of the SBMLNamespaces object class is to make it easier to
communicate SBML Level and Version data between libSBML constructors and
other methods. The SBMLNamespaces object class tracks 3-tuples
(triples) consisting of SBML Level, Version, and the corresponding SBML
XML namespace.
The plural name (SBMLNamespaces) is not a mistake, because in SBML
Level 3, objects may have extensions added by Level 3 packages
used by a given model and therefore may have multiple namespaces
associated with them; however, until the introduction of SBML
Level 3, the SBMLNamespaces object only records one SBML
Level/Version/namespace combination at a time. Most constructors for
SBML objects in libSBML take a SBMLNamespaces object as an argument,
thereby allowing the constructor to produce the proper combination of
attributes and other internal data structures for the given SBML Level
and Version.
=over
=item SBMLNamespaces::SBMLNamespaces
Creates a new SBMLNamespaces object corresponding to the given SBML
C<level> and C<version>.
C<opydetails> doc_sbmlnamespaces_what_is_it
@param level the SBML level
@param version the SBML version
@if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
=item SBMLNamespaces::SBMLNamespaces
(For extensions) Creates a new SBMLNamespaces object corresponding to
the combination of (1) the given SBML C<level> and C<version>, and (2)
the given C<package> with the C<package> C<version>.
C<opydetails> doc_sbmlnamespaces_what_is_it
@param level the SBML Level
@param version the SBML Version
@param pkgName the string of package name (e.g. "layout", "multi")
@param pkgVersion the package version
@param pkgPrefix the prefix of the package namespace (e.g. "layout", "multi") to be added.
The package's name will be used if the given string is empty (default).
@throws SBMLExtensionException if the extension module that supports the
combination of the given SBML Level, SBML Version, package name, and
package version has not been registered with libSBML.
=item SBMLNamespaces::SBMLNamespaces
Copy constructor; creates a copy of a SBMLNamespaces.
@param orig the SBMLNamespaces instance to copy.
@throws @if python ValueError @else SBMLConstructorException @endif@~
Thrown if the argument C<orig> is C<NULL>.
=item SBMLNamespaces::clone
Creates and returns a deep copy of this SBMLNamespaces.
@return a (deep) copy of this SBMLNamespaces.
=item SBMLNamespaces::getSBMLNamespaceURI
Returns a string representing the SBML XML namespace for the
given C<level> and C<version> of SBML.
@param level the SBML level
@param version the SBML version
@return a string representing the SBML namespace that reflects the
SBML Level and Version specified.
C<opydetails> doc_note_static_methods
=item SBMLNamespaces::getSupportedNamespaces
Returns a list of all supported SBMLNamespaces in this version of
libsbml.
@return a list with supported SBML namespaces.
C<opydetails> doc_note_static_methods
=item SBMLNamespaces::freeSBMLNamespaces
Frees the list of supported namespaces as generated by
getSupportedNamespaces().
@param supportedNS the list to be freed.
C<opydetails> doc_note_static_methods
=item SBMLNamespaces::getURI
Returns a string representing the SBML XML namespace of this
object.
@return a string representing the SBML namespace that reflects the
SBML Level and Version of this object.
=item SBMLNamespaces::getLevel
Get the SBML Level of this SBMLNamespaces object.
@return the SBML Level of this SBMLNamespaces object.
=item SBMLNamespaces::getLevel
Get the SBML Level of this SBMLNamespaces object.
@return the SBML Level of this SBMLNamespaces object.
=item SBMLNamespaces::getVersion
Get the SBML Version of this SBMLNamespaces object.
@return the SBML Version of this SBMLNamespaces object.
=item SBMLNamespaces::getVersion
Get the SBML Version of this SBMLNamespaces object.
@return the SBML Version of this SBMLNamespaces object.
=item SBMLNamespaces::getNamespaces
Get the XML namespaces list for this SBMLNamespaces object.
C<opydetails> doc_sbmlnamespaces_what_is_it
@return the XML namespaces of this SBMLNamespaces object.
=item SBMLNamespaces::getNamespaces
Get the XML namespaces list for this SBMLNamespaces object.
C<opydetails> doc_sbmlnamespaces_what_is_it
@return the XML namespaces of this SBMLNamespaces object.
=item SBMLNamespaces::addNamespaces
Add the given XML namespaces list to the set of namespaces within this
SBMLNamespaces object.
The following code gives an example of how one could add the XHTML
namespace to the list of namespaces recorded by the top-level
C<<sbml>> element of a model. It gives the new
namespace a prefix of C<html>. @if clike
@verbatim
SBMLDocument sd;
try
{
sd = new SBMLDocument(3, 1);
}
catch (SBMLConstructorException e)
{
// Here, have code to handle a truly exceptional situation. Candidate
// causes include invalid combinations of SBML Level and Version
// (impossible if hardwired as given here), running out of memory, and
// unknown system exceptions.
}
SBMLNamespaces sn = sd->getNamespaces();
if (sn != NULL)
{
sn->add("http://www.w3.org/1999/xhtml", "html");
}
else
{
// Handle another truly exceptional situation.
}
@endverbatim
@endif@if java
@verbatim
SBMLDocument sd;
try
{
sd = new SBMLDocument(3, 1);
}
catch (SBMLConstructorException e)
{
// Here, have code to handle a truly exceptional situation. Candidate
// causes include invalid combinations of SBML Level and Version
// (impossible if hardwired as given here), running out of memory, and
// unknown system exceptions.
}
SBMLNamespaces sn = sd.getNamespaces();
if (sn != null)
{
sn.add("http://www.w3.org/1999/xhtml", "html");
}
else
{
// Handle another truly exceptional situation.
}
@endverbatim
@endif@if python
@verbatim
sbmlDoc = None
try:
sbmlDoc = SBMLDocument(3, 1)
except ValueError:
# Do something to handle exceptional situation. Candidate
# causes include invalid combinations of SBML Level and Version
# (impossible if hardwired as given here), running out of memory, and
# unknown system exceptions.
namespaces = sbmlDoc.getNamespaces()
if namespaces == None:
# Do something to handle case of no namespaces.
status = namespaces.add("http://www.w3.org/1999/xhtml", "html")
if status != LIBSBML_OPERATION_SUCCESS:
# Do something to handle failure.
@endverbatim
@endif@if csharp
@verbatim
SBMLDocument sd = null;
try
{
sd = new SBMLDocument(3, 1);
}
catch (SBMLConstructorException e)
{
// Here, have code to handle a truly exceptional situation.
// Candidate causes include invalid combinations of SBML
// Level and Version (impossible if hardwired as given here),
// running out of memory, and unknown system exceptions.
}
XMLNamespaces sn = sd.getNamespaces();
if (sn != null)
{
sn.add("http://www.w3.org/1999/xhtml", "html");
}
else
{
// Handle another truly exceptional situation.
}
@endverbatim
@endif@~
@param xmlns the XML namespaces to be added.
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif@~ The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT @endlink
=item SBMLNamespaces::addNamespace
Add an XML namespace (a pair of URI and prefix) to the set of namespaces
within this SBMLNamespaces object.
@param uri the XML namespace to be added.
@param prefix the prefix of the namespace to be added.
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif@~ The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT @endlink
=item SBMLNamespaces::removeNamespace
Removes an XML namespace from the set of namespaces within this
SBMLNamespaces object.
@param uri the XML namespace to be added.
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif@~ The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INDEX_EXCEEDS_SIZE LIBSBML_INDEX_EXCEEDS_SIZE @endlink
=item SBMLNamespaces::addPackageNamespace
Add an XML namespace (a pair of URI and prefix) of a package extension
to the set of namespaces within this SBMLNamespaces object.
The SBML Level and SBML Version of this object is used.
@param pkgName the string of package name (e.g. "layout", "multi")
@param pkgVersion the package version
@param prefix the prefix of the package namespace to be added.
The package's name will be used if the given string is empty (default).
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif@~ The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
@note An XML namespace of a non-registered package extension can't be
added by this function (@link
OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE@endlink
will be returned).
@see addNamespace(@if java String uri, String prefix@endif)
=item SBMLNamespaces::addPackageNamespaces
Add the XML namespaces of package extensions in the given XMLNamespace
object to the set of namespaces within this SBMLNamespaces object
(Non-package XML namespaces are not added by this function).
@param xmlns the XML namespaces to be added.
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif@~ The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
@note XML namespaces of a non-registered package extensions are not
added (just ignored) by this function. @link
OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE
LIBSBML_INVALID_ATTRIBUTE_VALUE@endlink will be returned if the given
xmlns is null.
=item SBMLNamespaces::removePackageNamespace
Removes an XML namespace of a package extension from the set of namespaces
within this SBMLNamespaces object.
@param level the SBML level
@param version the SBML version
@param pkgName the string of package name (e.g. "layout", "multi")
@param pkgVersion the package version
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif@~ The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
@li @link OperationReturnValues_t#LIBSBML_INDEX_EXCEEDS_SIZE LIBSBML_INDEX_EXCEEDS_SIZE @endlink
=item SBMLNamespaces::addPkgNamespace
@internal
Add an XML namespace (a pair of URI and prefix) of a package extension
to the set of namespaces within this SBMLNamespaces object.
The SBML Level and SBML Version of this object is used.
@param pkgName the string of package name (e.g. "layout", "multi")
@param pkgVersion the package version
@param prefix the prefix of the package namespace to be added.
The package's name will be used if the given string is empty (default).
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif@~ The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
@note An XML namespace of a non-registered package extension can't be
added by this function (@link
OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE@endlink
will be returned).
@see addNamespace(@if java String uri, String prefix@endif)
=item SBMLNamespaces::addPkgNamespaces
@internal
Add the XML namespaces of package extensions in the given XMLNamespace
object to the set of namespaces within this SBMLNamespaces object.
Non-package XML namespaces are not added by this function.
@param xmlns the XML namespaces to be added.
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif@~ The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
@note XML namespaces of a non-registered package extensions are not
added (just ignored) by this function. @link
OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE
LIBSBML_INVALID_ATTRIBUTE_VALUE@endlink will be returned if the given
xmlns is null.
=item SBMLNamespaces::removePkgNamespace
@internal
Removes an XML namespace of a package extension from the set of
namespaces within this SBMLNamespaces object.
@param level the SBML level
@param version the SBML version
@param pkgName the string of package name (e.g. "layout", "multi")
@param pkgVersion the package version
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif@~ The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
@li @link OperationReturnValues_t#LIBSBML_INDEX_EXCEEDS_SIZE LIBSBML_INDEX_EXCEEDS_SIZE @endlink
=item SBMLNamespaces::isSBMLNamespace
Predicate returning C<true> if the given URL is one of SBML XML
namespaces.
@param uri the URI of namespace
@return C<true> if the "uri" is one of SBML namespaces, C<false> otherwise.
C<opydetails> doc_note_static_methods
=item SBMLNamespaces::isValidCombination
Predicate returning C<true> if the given set of namespaces represent a
valid set
@return C<true> if the set of namespaces is valid, C<false> otherwise.
=item SBMLNamespaces::setLevel
@internal
=item SBMLNamespaces::setVersion
@internal
=item SBMLNamespaces::setNamespaces
@internal
=item SBMLNamespaces::getPackageName
Returns the name of the main package for this namespace.
@return the name of the main package for this namespace.
"core" will be returned if this namespace is defined in the SBML
core.
=item SBMLNamespaces::initSBMLNamespace
@internal
=back
=head2 SBMLTransforms
@sbmlpackage{core}
@htmlinclude pkg-marker-core.html Methods for transform elements of SBML
@internal
=over
=item SBMLTransforms::replaceFD
@internal
Expands the math represented by the ASTNode to implement the functionality
of the FunctionDefinition, if it occurs within the original
math.
For example, an ASTNode represents the math expression: f(s, p) where
f is the id of a FunctionDefinition representing f(x, y) = x y.
The outcome of the function is that the ASTNode now represents
the math expression: s p
@param math ASTNode representing the math to be transformed
@param fd the FunctionDefinition to be expanded
@param idsToExclude an optional list of function definition ids to exclude.
C<opydetails> doc_note_static_methods
=item SBMLTransforms::replaceFD
@internal
Expands the math represented by the ASTNode to implement the functionality
of all the FunctionDefinitions in the list, if they occur within the
original math.
For example, an ASTNode represents the math expression: f(s, g(p, q)) where
f is the id of a FunctionDefinition representing f(x, y) = x y
and g is the id of a FunctionDefinition representing f(x, y) = x/y
The outcome of the function is that the ASTNode now represents
the math expression: s p/q
@param math ASTNode representing the math to be transformed
@param lofd the ListOfFunctionDefinitions to be expanded
@param idsToExclude an optional list of function definition ids to exclude.
C<opydetails> doc_note_static_methods
=item SBMLTransforms::expandInitialAssignments
@internal
=item SBMLTransforms::evaluateASTNode
@internal
=back
=head2 SBMLConstructorException
@sbmlpackage{core}
@htmlinclude pkg-marker-core.html Class of exceptions thrown by constructors of some
libSBML objects.
In some situations, constructors for SBML objects may need to indicate to
callers that the creation of the object failed. The failure may be for
different reasons, such as an attempt to use invalid parameters or a
system condition such as a memory error. To communicate this to callers,
those classes will throw an SBMLConstructorException.
In languages that don't have an exception mechanism (e.g., C), the
constructors generally try to return an error code instead of throwing
an exception.
=over
=item SBMLConstructorException::getSBMLErrMsg
Returns the message associated with this SBML exception.
@return the message string.
=back
=head2 ConversionOption
@sbmlpackage{core}
@htmlinclude pkg-marker-core.html Class of object that encapsulates a conversion option.
@htmlinclude libsbml-facility-only-warning.html
LibSBML provides a number of converters that can perform transformations
on SBML documents. These converters allow their behaviors to be
controlled by setting property values. Converter properties are
communicated using objects of class ConversionProperties, and within
such objects, individual options are encapsulated using ConversionOption
objects.
A ConversionOption object consists of four parts:
@li A I<key>, acting as the name of the option;
@li A I<value> of this option;
@li A I<type> for the value; this is chosen from the enumeration type
<a class="el" href="#ConversionOptionType_t">ConversionOptionType_t</a>; and
@li A I<description> consisting of a text string that describes the
option in some way.
There are no constraints on the values of keys or descriptions;
authors of SBML converters are free to choose them as they see fit.
@section ConversionOptionType_t Conversion option data types
An option in ConversionOption must have a data type declared, to
indicate whether it is a string value, an integer, and so forth. The
possible types of values are taken from the enumeration <a
class="el" href="#ConversionOptionType_t">ConversionOptionType_t</a>.
The following are the possible values:
<p>
<center>
<table width="90%" cellspacing="1" cellpadding="1" border="0" class="normal-font">
<tr style="background: lightgray" class="normal-font">
<td><strong>Enumerator</strong></td>
<td><strong>Meaning</strong></td>
</tr>
<tr>
<td>C<@link ConversionOptionType_t#CNV_TYPE_BOOL CNV_TYPE_BOOL@endlink></td>
<td>Indicates the value type is a Boolean.</td>
</tr>
<tr>
<td>C<@link ConversionOptionType_t#CNV_TYPE_DOUBLE CNV_TYPE_DOUBLE@endlink></td>
<td>Indicates the value type is a double-sized float.</td>
</tr>
<tr>
<td>C<@link ConversionOptionType_t#CNV_TYPE_INT CNV_TYPE_INT@endlink></td>
<td>Indicates the value type is an integer.</td>
</tr>
<tr>
<td>C<@link ConversionOptionType_t#CNV_TYPE_SINGLE CNV_TYPE_SINGLE@endlink></td>
<td>Indicates the value type is a float.</td>
</tr>
<tr>
<td>C<@link ConversionOptionType_t#CNV_TYPE_STRING CNV_TYPE_STRING@endlink></td>
<td>Indicates the value type is a string.</td>
</tr>
</table>
</center>
@see ConversionProperties
=over
=item ConversionOption::ConversionOption
Creates a new ConversionOption.
This is the general constructor, taking arguments for all aspects of
an option. Other constructors exist with different arguments.
@param key the key for this option
@param value an optional value for this option
@param type the type of this option
@param description the description for this option
=item ConversionOption::ConversionOption
Creates a new ConversionOption specialized for string-type options.
@param key the key for this option
@param value the value for this option
@param description an optional description
=item ConversionOption::ConversionOption
Creates a new ConversionOption specialized for Boolean-type options.
@param key the key for this option
@param value the value for this option
@param description an optional description
=item ConversionOption::ConversionOption
Creates a new ConversionOption specialized for double-type options.
@param key the key for this option
@param value the value for this option
@param description an optional description
=item ConversionOption::ConversionOption
Creates a new ConversionOption specialized for float-type options.
@param key the key for this option
@param value the value for this option
@param description an optional description
=item ConversionOption::ConversionOption
Creates a new ConversionOption specialized for integer-type options.
@param key the key for this option
@param value the value for this option
@param description an optional description
=item ConversionOption::ConversionOption
Copy constructor; creates a copy of an ConversionOption object.
@param orig the ConversionOption object to copy.
@throws @if python ValueError @else SBMLConstructorException @endif@~
Thrown if the argument C<orig> is C<NULL>.
=item ConversionOption::clone
Creates and returns a deep copy of this ConversionOption object.
@return a (deep) copy of this ConversionOption object.
=item ConversionOption::getKey
Returns the key for this option.
@return the key, as a string.
=item ConversionOption::setKey
Sets the key for this option.
@param key a string representing the key to set.
=item ConversionOption::getValue
Returns the value of this option.
@return the value of this option, as a string.
=item ConversionOption::setValue
Sets the value for this option.
@param value the value to set, as a string.
=item ConversionOption::getDescription
Returns the description string for this option.
@return the description of this option.
=item ConversionOption::setDescription
Sets the description text for this option.
@param description the description to set for this option.
=item ConversionOption::getType
Returns the type of this option
@return the type of this option.
=item ConversionOption::setType
Sets the type of this option.
@param type the type value to use.
=item ConversionOption::getBoolValue
Returns the value of this option as a Boolean.
@return the value of this option.
=item ConversionOption::setBoolValue
Set the value of this option to a given Boolean value.
Invoking this method will also set the type of the option to
@link ConversionOptionType_t#CNV_TYPE_BOOL CNV_TYPE_BOOL@endlink.
@param value the Boolean value to set
=item ConversionOption::getDoubleValue
Returns the value of this option as a C<double>.
@return the value of this option.
=item ConversionOption::setDoubleValue
Set the value of this option to a given C<double> value.
Invoking this method will also set the type of the option to
@link ConversionOptionType_t#CNV_TYPE_DOUBLE CNV_TYPE_DOUBLE@endlink.
@param value the value to set
=item ConversionOption::getFloatValue
Returns the value of this option as a C<float>.
@return the value of this option as a float
=item ConversionOption::setFloatValue
Set the value of this option to a given C<float> value.
Invoking this method will also set the type of the option to
@link ConversionOptionType_t#CNV_TYPE_SINGLE CNV_TYPE_SINGLE@endlink.
@param value the value to set
=item ConversionOption::getIntValue
Returns the value of this option as an C<integer>.
@return the value of this option, as an int
=item ConversionOption::setIntValue
Set the value of this option to a given C<int> value.
Invoking this method will also set the type of the option to
@link ConversionOptionType_t#CNV_TYPE_INT CNV_TYPE_INT@endlink.
@param value the value to set
=back
=head2 ConversionProperties
@sbmlpackage{core}
@htmlinclude pkg-marker-core.html Class of object that encapsulates the properties of an
SBML converter.
@htmlinclude libsbml-facility-only-warning.html
The properties of SBML converters are communicated using objects of
class ConversionProperties, and within such objects, individual options
are encapsulated using ConversionOption objects. The ConversionProperties
class provides numerous methods for setting and getting options.
ConversionProperties objects are also used to determine the target SBML
namespace when an SBML converter's behavior depends on the intended
Level+Version combination of SBML. In addition, it is conceivable that
conversions may be affected by SBML Level 3 packages being used
by an SBML document. These, too, are communicated by the values of
the SBML namespaces set on a ConversionProperties object.
@see ConversionOption
@see SBMLNamespaces
=over
=item ConversionProperties::ConversionProperties
Constructor that initializes the conversion properties
with a specific SBML target namespace.
@param targetNS the target namespace to convert to
=item ConversionProperties::ConversionProperties
Copy constructor.
@param orig the object to copy.
@throws @if python ValueError @else SBMLConstructorException @endif@~
Thrown if the argument C<orig> is C<NULL>.
=item ConversionProperties::clone
Creates and returns a deep copy of this ConversionProperties object.
@return a (deep) copy of this ConversionProperties object.
=item ConversionProperties::getTargetNamespaces
Returns the current target SBML namespace.
@return the SBMLNamepaces object expressing the target namespace.
=item ConversionProperties::hasTargetNamespaces
Returns C<true> if the target SBML namespace has been set.
@return C<true> if the target namespace has been set, C<false>
otherwise.
=item ConversionProperties::setTargetNamespaces
Sets the target namespace.
@param targetNS the target namespace to use.
=item ConversionProperties::getDescription
Returns the description string for a given option in this properties
object.
@param key the key for the option.
@return the description text of the option with the given key.
=item ConversionProperties::getType
Returns the type of a given option in this properties object.
@param key the key for the option.
@return the type of the option with the given key.
=item ConversionProperties::getOption
Returns the ConversionOption object for a given key.
@param key the key for the option.
@return the option with the given key.
=item ConversionProperties::addOption
Adds a copy of the given option to this properties object.
@param option the option to add
=item ConversionProperties::addOption
Adds a new ConversionOption object with the given parameters.
@param key the key for the new option
@param value (optional) the value of that option
@param type (optional) the type of the option
@param description (optional) the description for the option
=item ConversionProperties::addOption
Adds a new ConversionOption object with the given parameters.
@param key the key for the new option
@param value the string value of that option
@param description (optional) the description for the option
=item ConversionProperties::addOption
Adds a new ConversionOption object with the given parameters.
@param key the key for the new option
@param value the boolean value of that option
@param description (optional) the description for the option
=item ConversionProperties::addOption
Adds a new ConversionOption object with the given parameters.
@param key the key for the new option
@param value the double value of that option
@param description (optional) the description for the option
=item ConversionProperties::addOption
Adds a new ConversionOption object with the given parameters.
@param key the key for the new option
@param value the float value of that option
@param description (optional) the description for the option
=item ConversionProperties::addOption
Adds a new ConversionOption object with the given parameters.
@param key the key for the new option
@param value the integer value of that option
@param description (optional) the description for the option
=item ConversionProperties::removeOption
Removes the option with the given key from this properties object.
@param key the key for the new option to remove
@return the removed option
=item ConversionProperties::hasOption
Returns C<true> if this properties object contains an option with
the given key.
@param key the key of the option to find.
@return C<true> if an option with the given C<key> exists in
this properties object, C<false> otherwise.
=item ConversionProperties::getValue
Returns the value of the given option as a string.
@param key the key for the option.
@return the string value of the option with the given key.
=item ConversionProperties::setValue
Sets the value of the given option to a string.
@param key the key for the option
@param value the new value
=item ConversionProperties::getBoolValue
Returns the value of the given option as a Boolean.
@param key the key for the option.
@return the boolean value of the option with the given key.
=item ConversionProperties::setBoolValue
Sets the value of the given option to a Boolean.
@param key the key for the option.
@param value the new Boolean value.
=item ConversionProperties::getDoubleValue
Returns the value of the given option as a C<double>.
@param key the key for the option.
@return the double value of the option with the given key.
=item ConversionProperties::setDoubleValue
Sets the value of the given option to a C<double>.
@param key the key for the option.
@param value the new double value.
=item ConversionProperties::getFloatValue
Returns the value of the given option as a C<float>.
@param key the key for the option.
@return the float value of the option with the given key.
=item ConversionProperties::setFloatValue
Sets the value of the given option to a C<float>.
@param key the key for the option.
@param value the new float value.
=item ConversionProperties::getIntValue
Returns the value of the given option as an integer.
@param key the key for the option.
@return the int value of the option with the given key.
=item ConversionProperties::setIntValue
Sets the value of the given option to an integer.
@param key the key for the option.
@param value the new integer value.
=back
=head2 SBMLConverter
@sbmlpackage{core}
@htmlinclude pkg-marker-core.html Base class for SBML converters.
@htmlinclude libsbml-facility-only-warning.html
The SBMLConverter class is the base class for the various SBML @em
converters: classes of objects that transform or convert SBML documents.
These transformations can involve essentially anything that can be
written algorithmically; examples include converting the units of
measurement in a model, or converting from one Level+Version combination
of SBML to another.
LibSBML provides a number of built-in converters, and applications can
create their own by subclassing SBMLConverter and following the examples
of the existing converters. The following are the built-in converters
in libSBML @htmlinclude libsbml-version.html:
@li SBMLFunctionDefinitionConverter
@li SBMLInitialAssignmentConverter
@li SBMLLevelVersionConverter
@li SBMLRuleConverter
@li SBMLStripPackageConverter
@li SBMLUnitsConverter
Many converters provide the ability to configure their behavior to some
extent. This is realized through the use of I<properties> that offer
different I<options>. Two related classes implement these features:
ConversionProperties and ConversionOptions. The default property values
for each converter can be interrogated using the method
SBMLConverter::getDefaultProperties() on the converter class.
=over
=item SBMLConverter::SBMLConverter
Creates a new SBMLConverter object.
=item SBMLConverter::SBMLConverter
Copy constructor; creates a copy of an SBMLConverter object.
@param c the SBMLConverter object to copy.
@throws @if python ValueError @else SBMLConstructorException @endif@~
Thrown if the argument C<orig> is C<NULL>.
=item SBMLConverter::clone
Creates and returns a deep copy of this SBMLConverter object.
@return a (deep) copy of this SBMLConverter object.
=item SBMLConverter::getDocument
Returns the SBML document that is the subject of the conversions.
@return the current SBMLDocument object.
=item SBMLConverter::getDocument
Returns the SBML document that is the subject of the conversions.
@return the current SBMLDocument object, as a const reference.
=item SBMLConverter::getDefaultProperties
Returns the default properties of this converter.
A given converter exposes one or more properties that can be adjusted
in order to influence the behavior of the converter. This method
returns the I<default> property settings for this converter. It is
meant to be called in order to discover all the settings for the
converter object. The run-time properties of the converter object can
be adjusted by using the method
SBMLConverter::setProperties(const ConversionProperties props).
@return the default properties for the converter.
@see setProperties(@if java ConversionProperties props@endif)
@see matchesProperties(@if java ConversionProperties props@endif)
=item SBMLConverter::getTargetNamespaces
Returns the target SBML namespaces of the currently set properties.
SBML namespaces are used by libSBML to express the Level+Version of
the SBML document (and, possibly, any SBML Level 3 packages in
use). Some converters' behavior is affected by the SBML namespace
configured in the converter. For example, the actions of
SBMLLevelVersionConverter, the converter for converting SBML documents
from one Level+Version combination to another, are fundamentally
dependent on the SBML namespaces being targeted.
@return the SBMLNamespaces object that describes the SBML namespaces
in effect.
=item SBMLConverter::matchesProperties
Predicate returning C<true> if this converter's properties matches a
given set of configuration properties.
@param props the configuration properties to match.
@return C<true> if this converter's properties match, C<false>
otherwise.
=item SBMLConverter::setDocument
Sets the current SBML document to the given SBMLDocument object.
@param doc the document to use for this conversion.
@warning Even though the C<doc> is 'const', it is immediately cast
to a non-const version, which is then usually changed by the
converter upon a successful conversion. This function is here
solely to preserve backwards compatibility.
@return integer value indicating the success/failure of the operation.
@if clike The value is drawn from the enumeration
#OperationReturnValues_t. @endif@~ The set of possible values that may
be returned ultimately depends on the specific subclass of
SBMLConverter being used, but the default method can return the
following values:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
=item SBMLConverter::setDocument
Sets the current SBML document to the given SBMLDocument object.
@param doc the document to use for this conversion.
@return integer value indicating the success/failure of the operation.
@if clike The value is drawn from the enumeration
#OperationReturnValues_t. @endif@~ The set of possible values that may
be returned ultimately depends on the specific subclass of
SBMLConverter being used, but the default method can return the
following values:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
=item SBMLConverter::setProperties
Sets the configuration properties to be used by this converter.
A given converter exposes one or more properties that can be adjusted
in order to influence the behavior of the converter. This method sets
the current properties for this converter.
@param props the ConversionProperties object defining the properties
to set.
@return integer value indicating the success/failure of the operation.
@if clike The value is drawn from the enumeration
#OperationReturnValues_t. @endif@~ The set of possible values that may
be returned ultimately depends on the specific subclass of
SBMLConverter being used, but the default method can return the
following values:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
@see getProperties()
@see matchesProperties(@if java ConversionProperties props@endif)
=item SBMLConverter::getProperties
Returns the current properties in effect for this converter.
A given converter exposes one or more properties that can be adjusted
in order to influence the behavior of the converter. This method
returns the current properties for this converter; in other words, the
settings in effect at this moment. To change the property values, you
can use SBMLConverter::setProperties(const ConversionProperties props).
@return the currently set configuration properties.
@see setProperties(@if java ConversionProperties props@endif)
@see matchesProperties(@if java ConversionProperties props@endif)
=item SBMLConverter::convert
Perform the conversion.
This method causes the converter to do the actual conversion work,
that is, to convert the SBMLDocument object set by
SBMLConverter::setDocument(@if java const SBMLDocument doc@endif) and
with the configuration options set by
SBMLConverter::setProperties(@if java const ConversionProperties props@endif).
@return integer value indicating the success/failure of the operation.
@if clike The value is drawn from the enumeration
#OperationReturnValues_t. @endif@~ The set of possible values that may
be returned depends on the converter subclass; please consult
the documentation for the relevant class to find out what the
possibilities are.
=back
=head2 SBMLConverterRegistry
@sbmlpackage{core}
@htmlinclude pkg-marker-core.html Registry of all SBML converters.
@htmlinclude libsbml-facility-only-warning.html
LibSBML provides facilities for transforming and converting SBML
documents in various ways. These transformations can involve
essentially anything that can be written algorithmically; examples
include converting the units of measurement in a model, or converting
from one Level+Version combination of SBML to another. Converters are
implemented as objects derived from the class SBMLConverter.
The converter registry, implemented as a singleton object of class
SBMLConverterRegistry, maintains a list of known converters and provides
methods for discovering them. Callers can use the method
SBMLConverterRegistry::getNumConverters() to find out how many
converters are registered, then use
SBMLConverterRegistry::getConverterByIndex(@if java int index@endif) to
iterate over each one; alternatively, callers can use
SBMLConverterRegistry::getConverterFor(@if java const ConversionProperties& props@endif)
to search for a converter having specific properties.
=over
=item SBMLConverterRegistry::getInstance
Returns the singleton instance for the converter registry.
Prior to using the registry, callers have to obtain a copy of the
registry. This static method provides the means for doing that.
@return the singleton for the converter registry.
=item SBMLConverterRegistry::addConverter
Adds the given converter to the registry of SBML converters.
@param converter the converter to add to the registry.
@return integer value indicating the success/failure of the operation.
@if clike The value is drawn from the enumeration
#OperationReturnValues_t. @endif@~ The possible values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT @endlink
=item SBMLConverterRegistry::getConverterByIndex
Returns the converter with the given index number.
Converters are given arbitrary index numbers by the registry. Callers
can use the method SBMLConverterRegistry::getNumConverters() to find
out how many converters are registered, then use this method to
iterate over the list and obtain each one in turn.
@param index the zero-based index of the converter to fetch.
@return the converter with the given index number, or C<NULL> if the
number is less than C<0> or there is no converter at the given index
position.
=item SBMLConverterRegistry::getConverterFor
Returns the converter that best matches the given configuration
properties.
Many converters provide the ability to configure their behavior. This
is realized through the use of I<properties> that offer different @em
options. The present method allows callers to search for converters
that have specific property values. Callers can do this by creating a
ConversionProperties object, adding the desired option(s) to the
object, then passing the object to this method.
@param props a ConversionProperties object defining the properties
to match against.
@return the converter matching the properties, or C<NULL> if no
suitable converter is found.
@see getConverterByIndex(@if java int index@endif)
=item SBMLConverterRegistry::getNumConverters
Returns the number of converters known by the registry.
@return the number of registered converters.
@see getConverterByIndex(@if java int index@endif)
=item SBMLConverterRegistry::SBMLConverterRegistry
@internal
protected constructor, use the getInstance() method to access the registry.
=back
=head2 SBMLFunctionDefinitionConverter
@sbmlpackage{core}
@htmlinclude pkg-marker-core.html SBML converter for replacing function definitions.
@htmlinclude libsbml-facility-only-warning.html
This is an SBML converter for manipulating user-defined functions in an
SBML file. When invoked on the current model, it performs the following
operation:
<ol>
<li>Read the list of user-defined functions in the model (i.e., the
list of FunctionDefinition objects);
<li>Look for invocations of the function in mathematical expressions
throughout the model; and
<li>For each invocation found, replaces the invocation with a
in-line copy of the function's body, similar to how macro expansions
might be performed in scripting and programming languages.
</ol>
For example, suppose the model contains a function definition
representing the function <i>f(x, y) = x y</i>. Further
suppose this functions invoked somewhere else in the model, in
a mathematical formula, as <i>f(s, p)</i>. The outcome of running
SBMLFunctionDefinitionConverter on the model will be to replace
the call to <i>f</i> with the expression <i>s p</i>.
@see SBMLInitialAssignmentConverter
@see SBMLLevelVersionConverter
@see SBMLRuleConverter
@see SBMLStripPackageConverter
@see SBMLUnitsConverter
=over
=item SBMLFunctionDefinitionConverter::SBMLFunctionDefinitionConverter
Creates a new SBMLFunctionDefinitionConverter object.
=item SBMLFunctionDefinitionConverter::SBMLFunctionDefinitionConverter
Copy constructor; creates a copy of an SBMLFunctionDefinitionConverter
object.
@param obj the SBMLFunctionDefinitionConverter object to copy.
=item SBMLFunctionDefinitionConverter::clone
Creates and returns a deep copy of this SBMLFunctionDefinitionConverter
object.
@return a (deep) copy of this converter.
=item SBMLFunctionDefinitionConverter::matchesProperties
Returns C<true> if this converter object's properties match the given
properties.
A typical use of this method involves creating a ConversionProperties
object, setting the options desired, and then calling this method on
an SBMLFunctionDefinitionConverter object to find out if the object's
property values match the given ones. This method is also used by
SBMLConverterRegistry::getConverterFor(@if java const ConversionProperties& props@endif)
to search across all registered converters for one matching particular
properties.
@param props the properties to match.
@return C<true> if this converter's properties match, C<false>
otherwise.
=item SBMLFunctionDefinitionConverter::convert
Replaces invocations of each user-defined function with an in-line
copy, similar to macro expansion.
@return integer value indicating the success/failure of the operation.
@if clike The value is drawn from the enumeration
#OperationReturnValues_t. @endif@~ The possible values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT @endlink
@li @link OperationReturnValues_t#LIBSBML_CONV_INVALID_SRC_DOCUMENT LIBSBML_CONV_INVALID_SRC_DOCUMENT @endlink
=item SBMLFunctionDefinitionConverter::getDefaultProperties
Returns the default properties of this converter.
A given converter exposes one or more properties that can be adjusted
in order to influence the behavior of the converter. This method
returns the I<default> property settings for this converter. It is
meant to be called in order to discover all the settings for the
converter object.
@return the ConversionProperties object describing the default properties
for this converter.
=item SBMLFunctionDefinitionConverter::expandFD_errors
@internal
=back
=head2 SBMLInitialAssignmentConverter
@sbmlpackage{core}
@htmlinclude pkg-marker-core.html SBML converter for replacing initial assignments.
@htmlinclude libsbml-facility-only-warning.html
This is an SBML converter for replacing InitialAssignment objects
(when possible) by setting the initial value attributes on the model
objects being assigned. In other words, for every object that is
the target of an initial assignment in the model, it evaluates the
mathematical expression of the assignment to get a numerical value,
and then sets the corresponding attribute of the object to the
value. The effects for different kinds of SBML components are
as follows:
<center>
<table border="0" class="text-table width80 normal-font alt-row-colors">
<tr style="background: lightgray; font-size: 14px;">
<th align="left" width="200">Component</th>
<th align="left">Effect</th>
</tr>
<tr>
<td>Compartment</td>
<td>Sets the value of the C<size> attribute.</td>
</tr>
<tr>
<td>Species</td>
<td>Sets the value of either the C<initialAmount>
or the C<initialConcentration> attributes, depending
on the value of the Species object's
C<hasOnlySubstanceUnits> attribute.</td>
</tr>
<tr>
<td>Parameter</td>
<td>Sets the value of the C<value> attribute.</td>
</tr>
<tr>
<td>SpeciesReference</td>
<td>Sets the value of the C<stoichiometry> attribute
in the Reaction object where the SpeciesReference object appears.</td>
</tr>
</table>
</center>
@see SBMLFunctionDefinitionConverter
@see SBMLLevelVersionConverter
@see SBMLRuleConverter
@see SBMLStripPackageConverter
@see SBMLUnitsConverter
=over
=item SBMLInitialAssignmentConverter::SBMLInitialAssignmentConverter
Creates a new SBMLInitialAssignmentConverter object.
=item SBMLInitialAssignmentConverter::SBMLInitialAssignmentConverter
Copy constructor; creates a copy of an SBMLInitialAssignmentConverter
object.
@param obj the SBMLInitialAssignmentConverter object to copy.
=item SBMLInitialAssignmentConverter::clone
Creates and returns a deep copy of this SBMLInitialAssignmentConverter
object.
@return a (deep) copy of this converter.
=item SBMLInitialAssignmentConverter::matchesProperties
Returns C<true> if this converter object's properties match the given
properties.
A typical use of this method involves creating a ConversionProperties
object, setting the options desired, and then calling this method on
an SBMLInitialAssignmentConverter object to find out if the object's
property values match the given ones. This method is also used by
SBMLConverterRegistry::getConverterFor(@if java const ConversionProperties& props@endif)
to search across all registered converters for one matching particular
properties.
@param props the properties to match.
@return C<true> if this converter's properties match, C<false>
otherwise.
=item SBMLInitialAssignmentConverter::convert
Perform the conversion.
This method causes the converter to do the actual conversion work,
that is, to convert the SBMLDocument object set by
SBMLConverter::setDocument(@if java const SBMLDocument doc@endif) and
with the configuration options set by
SBMLConverter::setProperties(@if java const ConversionProperties props@endif).
@return integer value indicating the success/failure of the operation.
@if clike The value is drawn from the enumeration
#OperationReturnValues_t. @endif@~ The possible values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT @endlink
=item SBMLInitialAssignmentConverter::getDefaultProperties
Returns the default properties of this converter.
A given converter exposes one or more properties that can be adjusted
in order to influence the behavior of the converter. This method
returns the I<default> property settings for this converter. It is
meant to be called in order to discover all the settings for the
converter object.
@return the ConversionProperties object describing the default properties
for this converter.
=back
=head2 SBMLLevelVersionConverter
@sbmlpackage{core}
@htmlinclude pkg-marker-core.html SBML converter for transforming documents from one
Level+Version to another.
@htmlinclude libsbml-facility-only-warning.html
This SBML converter takes an SBML document of one SBML Level+Version
combination and attempts to convert it to another Level+Version combination.
The target Level+Version is set using an SBMLNamespace object in the
ConversionProperties object that controls this converter.
This class is the basis for
SBMLDocument::setLevelAndVersion(@if java long lev, long ver, boolean strict@endif).
@see SBMLFunctionDefinitionConverter
@see SBMLInitialAssignmentConverter
@see SBMLRuleConverter
@see SBMLStripPackageConverter
@see SBMLUnitsConverter
=over
=item SBMLLevelVersionConverter
Creates a new SBMLLevelVersionConverter object.
=item SBMLLevelVersionConverter
Copy constructor; creates a copy of an SBMLLevelVersionConverter
object.
@param obj the SBMLLevelVersionConverter object to copy.
=item clone
Creates and returns a deep copy of this SBMLLevelVersionConverter
object.
@return a (deep) copy of this converter.
=item matchesProperties
Returns C<true> if this converter object's properties match the given
properties.
A typical use of this method involves creating a ConversionProperties
object, setting the options desired, and then calling this method on
an SBMLLevelVersionConverter object to find out if the object's
property values match the given ones. This method is also used by
SBMLConverterRegistry::getConverterFor(@if java const ConversionProperties& props@endif)
to search across all registered converters for one matching particular
properties.
@param props the properties to match.
@return C<true> if this converter's properties match, C<false>
otherwise.
=item convert
Perform the conversion.
This method causes the converter to do the actual conversion work,
that is, to convert the SBMLDocument object set by
SBMLConverter::setDocument(@if java const SBMLDocument doc@endif) and
with the configuration options set by
SBMLConverter::setProperties(@if java const ConversionProperties props@endif).
SBMLConverter::setProperties(@if java const ConversionProperties props@endif).
@return integer value indicating the success/failure of the operation.
@if clike The value is drawn from the enumeration
#OperationReturnValues_t. @endif@~ The possible values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT @endlink
=item getDefaultProperties
Returns the default properties of this converter.
A given converter exposes one or more properties that can be adjusted
in order to influence the behavior of the converter. This method
returns the I<default> property settings for this converter. It is
meant to be called in order to discover all the settings for the
converter object.
@return the ConversionProperties object describing the default properties
for this converter.
=item getTargetLevel
Returns the target SBML Level for the conversion.
@return an integer indicating the SBML Level.
=item getTargetVersion
Returns the target SBML Version for the conversion.
@return an integer indicating the Version within the SBML Level.
=item getValidityFlag
Returns the flag indicating whether the conversion has been set to "strict".
@return C<true> if strict validity has been requested, C<false>
otherwise.
=back
=head2 SBMLRuleConverter
@sbmlpackage{core}
@htmlinclude pkg-marker-core.html SBML converter for reordering rules and assignments in a
model.
@htmlinclude libsbml-facility-only-warning.html
This converter reorders assignments in a model. Specifically, it sorts
the list of assignment rules (i.e., the AssignmentRule objects contained
in the ListOfAssignmentRules within the Model object) and the initial
assignments (i.e., the InitialAssignment objects contained in the
ListOfInitialAssignments) such that, within each set, assignments that
depend on prior values are placed after the values are set. For
example, if there is an assignment rule stating <i>a = b + 1</i>, and
another rule stating <i>b = 3</i>, the list of rules is sorted and the
rules are arranged so that the rule for <i>b = 3</i> appears I<before>
the rule for <i>a = b + 1</i>. Similarly, if dependencies of this
sort exist in the list of initial assignments in the model, the initial
assignments are sorted as well.
Beginning with SBML Level 2, assignment rules have no ordering
required—the order in which the rules appear in an SBML file has
no significance. Software tools, however, may need to reorder
assignments for purposes of evaluating them. For example, for
simulators that use time integration methods, it would be a good idea to
reorder assignment rules such as the following,
<i>b = a + 10 seconds</i><br>
<i>a = time</i>
so that the evaluation of the rules is independent of integrator
step sizes. (This is due to the fact that, in this case, the order in
which the rules are evaluated changes the result.) This converter
can be used to reorder the SBML objects regardless of whether the
input file contained them in the desired order. Here is a code
fragment to illustrate how to do that:
@verbatim
ConversionProperties props;
props.addOption("sortRules", true, "sort rules");
SBMLConverter converter;
converter.setProperties(&props);
converter.setDocument(&doc);
converter.convert();
@endverbatim
@note The two sets of assignments (list of assignment rules on the one
hand, and list of initial assignments on the other hand) are handled @em
independently. In an SBML model, these entities are treated differently
and no amount of sorting can deal with inter-dependencies between
assignments of the two kinds.
@see SBMLFunctionDefinitionConverter
@see SBMLInitialAssignmentConverter
@see SBMLLevelVersionConverter
@see SBMLStripPackageConverter
@see SBMLUnitsConverter
=over
=item SBMLRuleConverter::SBMLRuleConverter
Creates a new SBMLLevelVersionConverter object.
=item SBMLRuleConverter::SBMLRuleConverter
Copy constructor; creates a copy of an SBMLLevelVersionConverter
object.
@param obj the SBMLLevelVersionConverter object to copy.
=item SBMLRuleConverter::clone
Creates and returns a deep copy of this SBMLLevelVersionConverter
object.
@return a (deep) copy of this converter.
=item SBMLRuleConverter::matchesProperties
Returns C<true> if this converter object's properties match the given
properties.
A typical use of this method involves creating a ConversionProperties
object, setting the options desired, and then calling this method on
an SBMLLevelVersionConverter object to find out if the object's
property values match the given ones. This method is also used by
SBMLConverterRegistry::getConverterFor(@if java const ConversionProperties& props@endif)
to search across all registered converters for one matching particular
properties.
@param props the properties to match.
@return C<true> if this converter's properties match, C<false>
otherwise.
=item SBMLRuleConverter::convert
Perform the conversion.
This method causes the converter to do the actual conversion work,
that is, to convert the SBMLDocument object set by
SBMLConverter::setDocument(@if java const SBMLDocument doc@endif) and
with the configuration options set by
SBMLConverter::setProperties(@if java const ConversionProperties props@endif).
@return integer value indicating the success/failure of the operation.
@if clike The value is drawn from the enumeration
#OperationReturnValues_t. @endif@~ The possible values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT @endlink
@li @link OperationReturnValues_t#LIBSBML_CONV_INVALID_SRC_DOCUMENT LIBSBML_CONV_INVALID_SRC_DOCUMENT @endlink
=item SBMLRuleConverter::getDefaultProperties
Returns the default properties of this converter.
A given converter exposes one or more properties that can be adjusted
in order to influence the behavior of the converter. This method
returns the I<default> property settings for this converter. It is
meant to be called in order to discover all the settings for the
converter object.
@return the ConversionProperties object describing the default properties
for this converter.
=back
=head2 SBMLStripPackageConverter
@sbmlpackage{core}
@htmlinclude pkg-marker-core.html SBML converter for removing packages.
@htmlinclude libsbml-facility-only-warning.html
This SBML converter takes an SBML document and removes (strips) a package
from it. No conversion is performed; the package constructs are simply
removed from the SBML document. The package to be stripped is determined
by the value of the option "package" on the conversion properties.
@see SBMLFunctionDefinitionConverter
@see SBMLLevelVersionConverter
@see SBMLRuleConverter
@see SBMLLevelVersionConverter
@see SBMLUnitsConverter
=over
=item SBMLStripPackageConverter::SBMLStripPackageConverter
Creates a new SBMLStripPackageConverter object.
=item SBMLStripPackageConverter::SBMLStripPackageConverter
Copy constructor; creates a copy of an SBMLStripPackageConverter
object.
@param obj the SBMLStripPackageConverter object to copy.
=item SBMLStripPackageConverter::clone
Creates and returns a deep copy of this SBMLStripPackageConverter
object.
@return a (deep) copy of this converter.
=item SBMLStripPackageConverter::matchesProperties
Returns C<true> if this converter object's properties match the given
properties.
A typical use of this method involves creating a ConversionProperties
object, setting the options desired, and then calling this method on
an SBMLStripPackageConverter object to find out if the object's
property values match the given ones. This method is also used by
SBMLConverterRegistry::getConverterFor(@if java const ConversionProperties& props@endif)
to search across all registered converters for one matching particular
properties.
@param props the properties to match.
@return C<true> if this converter's properties match, C<false>
otherwise.
=item SBMLStripPackageConverter::convert
Perform the conversion.
This method causes the converter to do the actual conversion work,
that is, to convert the SBMLDocument object set by
SBMLConverter::setDocument(@if java const SBMLDocument doc@endif) and
with the configuration options set by
SBMLConverter::setProperties(@if java const ConversionProperties props@endif).
@return integer value indicating the success/failure of the operation.
@if clike The value is drawn from the enumeration
#OperationReturnValues_t. @endif@~ The possible values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item SBMLStripPackageConverter::getDefaultProperties
Returns the default properties of this converter.
A given converter exposes one or more properties that can be adjusted
in order to influence the behavior of the converter. This method
returns the I<default> property settings for this converter. It is
meant to be called in order to discover all the settings for the
converter object.
@return the ConversionProperties object describing the default properties
for this converter.
=back
=head2 SBMLUnitsConverter
@sbmlpackage{core}
@htmlinclude pkg-marker-core.html SBML converter to convert a model's units to SI units.
@htmlinclude libsbml-facility-only-warning.html
This SBML converter converts the units in a model to base SI units,
namely metre, kilogram, second, Ampere, Kelvin, mole and candela.
Unit conversion will only be performed on models that are fully unit
consistent; that is, all objects have associated units, and there are no
literal numbers with no units specified. In the case of an SBML
Level 3 model involving math expressions, this means that the @c
timeUnits attribute on the Model object must be set, and if there are
any reactions in the model, the C<extentUnits> attribute on the Model
object must also be set.
This converter has the additional Boolean property "removeUnusedUnits"
that can be used to tell the converter whether to remove any
UnitDefinition objects that are not referred to, after conversion is
complete. You can set this value by adding the property using
@verbatim
prop.addOption("removeUnusedUnits", false);
@endverbatim
The converter's default behavior is to remove the unused
UnitDefinition objects in the model.
@see SBMLFunctionDefinitionConverter
@see SBMLLevelVersionConverter
@see SBMLRuleConverter
@see SBMLStripPackageConverter
@see SBMLUnitsConverter
=over
=item SBMLUnitsConverter::SBMLUnitsConverter
Creates a new SBMLUnitsConverter object.
=item SBMLUnitsConverter::SBMLUnitsConverter
Copy constructor; creates a copy of an SBMLUnitsConverter
object.
@param obj the SBMLUnitsConverter object to copy.
=item SBMLUnitsConverter::clone
Creates and returns a deep copy of this SBMLUnitsConverter
object.
@return a (deep) copy of this converter.
=item SBMLUnitsConverter::matchesProperties
Returns C<true> if this converter object's properties match the given
properties.
A typical use of this method involves creating a ConversionProperties
object, setting the options desired, and then calling this method on
an SBMLUnitsConverter object to find out if the object's
property values match the given ones. This method is also used by
SBMLConverterRegistry::getConverterFor(@if java const ConversionProperties& props@endif)
to search across all registered converters for one matching particular
properties.
@param props the properties to match.
@return C<true> if this converter's properties match, C<false>
otherwise.
=item SBMLUnitsConverter::convert
Convers the units in the model to base SI units; namely metre,
kilogram, second, Ampere, Kelvin, mole and candela.
@return integer value indicating the success/failure of the operation.
@if clike The value is drawn from the enumeration
#OperationReturnValues_t. @endif@~ The possible values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT @endlink
@li @link OperationReturnValues_t#LIBSBML_CONV_CONVERSION_NOT_AVAILABLE LIBSBML_CONV_CONVERSION_NOT_AVAILABLE @endlink
@li @link OperationReturnValues_t#LIBSBML_CONV_INVALID_SRC_DOCUMENT LIBSBML_CONV_INVALID_SRC_DOCUMENT @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item SBMLUnitsConverter::getDefaultProperties
Returns the default properties of this converter.
A given converter exposes one or more properties that can be adjusted
in order to influence the behavior of the converter. This method
returns the I<default> property settings for this converter. It is
meant to be called in order to discover all the settings for the
converter object.
@return the ConversionProperties object describing the default properties
for this converter.
=back
=head2 SBMLValidator
@sbmlpackage{core}
@htmlinclude pkg-marker-core.html Base class for SBML validators
@htmlinclude not-sbml-warning.html
LibSBML implements facilities for verifying that a given SBML document
is valid according to the SBML specifications; it also exposes the
validation interface so that user programs and SBML Level 3 package
authors may use the facilities to implement new validators. There are
two main interfaces to libSBML's validation facilities, based on the
classes Validator and SBMLValidator.
The Validator class is the basis of the system for validating an SBML
document against the validation rules defined in the SBML
specifications. The scheme used by Validator relies is compact and uses
the I<visitor> programming pattern, but it relies on C/C++ features and
is not directly accessible from language bindings. SBMLValidator offers
a framework for straightforward class-based extensibility, so that user
code can subclass SBMLValidator to implement new validation systems,
different validators can be introduced or turned off at run-time, and
interfaces can be provided in the libSBML language bindings.
SBMLValidator can call Validator functionality internally (as is the
case in the current implementation of SBMLInternalValidator) or use
entirely different implementation approaches, as necessary.
Users of libSBML may already be familiar with the facilities encompassed
by the validation system, in the form of the consistency-checking methods
defined on SBMLDocument. The methods SBMLDocument::setConsistencyChecks(@if java int categ, boolean onoff@endif),
SBMLDocument::checkConsistency(), SBMLDocument::checkInternalConsistency()
and other method of that sort are in fact implemented via SBMLValidator,
specifically as methods on the class SBMLInternalValidator.
Authors may use SBMLValidator as the base class for their own validator
extensions to libSBML. The class SBMLInternalValidator may serve as a
code example for how to implement such things.
=over
=item SBMLValidator::SBMLValidator
Creates a new SBMLValidator.
=item SBMLValidator::SBMLValidator
Copy constructor; creates a copy of an SBMLValidator object.
@param orig the object to copy.
@throws @if python ValueError @else SBMLConstructorException @endif@~
Thrown if the argument C<orig> is C<NULL>.
=item SBMLValidator::clone
Creates and returns a deep copy of this SBMLValidator.
@return a (deep) copy of this SBMLValidator.
=item SBMLValidator::getDocument
Returns the current SBML document in use by this validator.
@return the current SBML document
@see setDocument(@if java SBMLDocument doc@endif)
=item SBMLValidator::getDocument
Returns the current SBML document in use by this validator.
@return a const reference to the current SBML document
@see setDocument(@if java SBMLDocument doc@endif)
=item SBMLValidator::setDocument
Sets the current SBML document to the given SBMLDocument object.
@param doc the document to use for this validation
@return an integer value indicating the success/failure of the
validation. @if clike The value is drawn from the enumeration
#OperationReturnValues_t. @endif@~ The possible values returned by this
function are
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@see getDocument()
=item SBMLValidator::validate
Runs this validator on the current SBML document.
@return an integer value indicating the success/failure of the
validation. @if clike The value is drawn from the enumeration
#OperationReturnValues_t. @endif@~ The possible values returned by this
function are determined by the specific subclasses of this class.
=item SBMLValidator::clearFailures
Clears this validator's list of failures.
If you are validating multiple SBML documents with the same validator,
call this method after you have processed the list of failures from
the last validation run and before validating the next document.
@if clike @see getFailures() @endif@~
=item SBMLValidator::getFailures
Returns a list of SBMLError objects (if any) that were logged by the
last run of this validator.
@return a list of errors, warnings and other diagnostics logged during
validation.
@see clearFailures()
=item SBMLValidator::logFailure
Adds the given failure to this list of Validators failures.
@param err an SBMLError object representing an error or warning
@if clike @see getFailures() @endif@~
=item SBMLValidator::validate
Validates the given SBMLDocument object.
This is identical to calling setDocument(@if java SBMLDocument d @endif)
followed by validate().
@param d the SBML document to validate
@return the number of validation failures that occurred. The objects
describing the actual failures can be retrieved using getFailures().
=item SBMLValidator::validate
Validates the SBML document located at the given C<filename>.
This is a convenience method that saves callers the trouble of
using SBMLReader to read the document first.
@param filename the path to the file to be read and validated.
@return the number of validation failures that occurred. The objects
describing the actual failures can be retrieved using getFailures().
=item SBMLValidator::getErrorLog
Returns the list of errors or warnings logged during parsing,
consistency checking, or attempted translation of this model.
Note that this refers to the SBMLDocument object's error log (i.e.,
the list returned by SBMLDocument::getErrorLog()). I<That> list of
errors and warnings is I<separate> from the validation failures
tracked by this validator (i.e., the list returned by getFailures()).
@return the SBMLErrorLog used for the SBMLDocument
@if clike @see getFailures() @endif@~
=item SBMLValidator::getModel
Returns the Model object stored in the SBMLDocument.
It is important to note that this method <em>does not create</em> a
Model instance. The model in the SBMLDocument must have been created
at some prior time, for example using SBMLDocument::createModel()
or SBMLDocument::setModel(@if java Model m@endif).
This method returns C<NULL> if a model does not yet exist.
@return the Model contained in this validator's SBMLDocument object.
@see SBMLDocument::setModel(@if java Model m@endif)
@see SBMLDocument::createModel()
=item SBMLValidator::getModel
Returns the Model object stored in the SBMLDocument.
It is important to note that this method <em>does not create</em> a
Model instance. The model in the SBMLDocument must have been created
at some prior time, for example using SBMLDocument::createModel()
or SBMLDocument::setModel(@if java Model m@endif).
This method returns C<NULL> if a model does not yet exist.
@return the Model contained in this validator's SBMLDocument object.
@see SBMLDocument::setModel(@if java Model m@endif)
@see SBMLDocument::createModel()
=item SBMLValidator::getNumFailures
Returns the number of failures encountered in the last validation run.
This method returns the number of failures logged by this validator.
This number only reflects I<this> validator's actions; the number may
not be the same as the number of errors and warnings logged on the
SBMLDocument object's error log (i.e., the object returned by
SBMLDocument::getErrorLog()), because other parts of libSBML may log
errors and warnings beyond those found by this validator.
@return the number of errors logged by this validator.
=item SBMLValidator::getFailure
Returns the failure object at index n in this validator's list of
failures logged during the last run.
Callers should use getNumFailures() first, to find out the number
of entries in this validator's list of failures.
@param n an integer indicating the index of the object to return from
the failures list; index values start at 0.
@return the failure at the given index number.
@see getNumFailures()
=back
=head2 SBMLExternalValidator
@sbmlpackage{core}
@htmlinclude pkg-marker-core.html
@internal
=over
=item SBMLExternalValidator::SBMLExternalValidator
@internal
Constructor.
=item SBMLExternalValidator::SBMLExternalValidator
@internal
Copy constructor.
=item SBMLExternalValidator::clone
@internal
Creates and returns a deep copy of this converter.
@return a (deep) copy of this converter.
=item SBMLExternalValidator::validate
@internal
the actual conversion
@return status code represeting success/failure/conversion impossible
=item SBMLExternalValidator::getProgram
@internal
Returns the program name of the validator to be run
@return the program name of the validator to be run
=item SBMLExternalValidator::setProgram
@internal
Sets the name of the program to run
@param program the program to be started
=item SBMLExternalValidator::getOutputFileName
@internal
Returns the output file name (this is the file the external program will write)
@return the output file name
=item SBMLExternalValidator::setOutputFileName
@internal
Sets the output file name
@param outputFileName the name of the output XML file
=item SBMLExternalValidator::getSBMLFileName
@internal
@return the name of the SBML file (the document of this validator will be written to it)
=item SBMLExternalValidator::setSBMLFileName
@internal
Sets the filename for the temporary file to be created
@param sbmlFileName the temporary name
=item SBMLExternalValidator::clearArguments
@internal
Clear all additional arguments
=item SBMLExternalValidator::addArgument
@internal
Adds the given argument to the list of additional arguments
@param arg the argument
=item SBMLExternalValidator::getNumArguments
@internal
@return the number of arguments.
=item SBMLExternalValidator::getArgument
@internal
Returns the argument for the given index.
@param n the zero based index of the argument.
@return the argument at the given index.
=item SBMLExternalValidator::getArguments
@internal
@return all arguments
=item SBMLExternalValidator::setArguments
@internal
Sets the additional arguments
@param args teh additional arguments
=back
=head2 XMLAttributes
@sbmlpackage{core}
@htmlinclude pkg-marker-core.html Representation of attributes on an XML node.
@htmlinclude not-sbml-warning.html
=over
=item XMLAttributes::XMLAttributes
Creates a new empty XMLAttributes set.
=item XMLAttributes::XMLAttributes
Copy constructor; creates a copy of this XMLAttributes set.
C<orig> the XMLAttributes object to copy.
@throws @if python ValueError @else XMLConstructorException @endif@~
Thrown if the argument C<orig> is C<NULL>.
=item XMLAttributes::clone
Creates and returns a deep copy of this XMLAttributes set.
@return a (deep) copy of this XMLAttributes set.
=item XMLAttributes::add
Adds an attribute (a name/value pair) to this XMLAttributes object,
optionally with a prefix and URI defining a namespace.
@param name a string, the local name of the attribute.
@param value a string, the value of the attribute.
@param namespaceURI a string, the namespace URI of the attribute.
@param prefix a string, the prefix of the namespace
@return an integer code indicating the success or failure of the
function. The possible values returned by this
function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@note if local name with the same namespace URI already exists in this
attribute set, its value and prefix will be replaced.
@if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
=item XMLAttributes::add
Adds an attribute with the given XMLTriple/value pair to this XMLAttributes set.
@note if local name with the same namespace URI already exists in this attribute set,
its value and prefix will be replaced.
@param triple an XMLTriple, the XML triple of the attribute.
@param value a string, the value of the attribute.
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
=item XMLAttributes::addResource
@internal
Adds an name/value pair to this XMLAttributes set.
This method is similar to the add method but an attribute with same name wont
be overwritten. This facilitates the addition of multiple resource attributes
in CVTerm class.
@param name a string, the name of the attribute.
@param value a string, the value of the attribute.
@note This function is only internally used to store multiple rdf:resource
attributes in CVTerm class, and thus should not be used for other purposes.
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
=item XMLAttributes::removeResource
Removes an attribute with the given index from this XMLAttributes set.
@param n an integer the index of the resource to be deleted
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INDEX_EXCEEDS_SIZE LIBSBML_INDEX_EXCEEDS_SIZE @endlink
=item XMLAttributes::remove
Removes an attribute with the given index from this XMLAttributes set.
(This function is an alias of XMLAttributes::removeResource(@if java int n@endif) ).
@param n an integer the index of the resource to be deleted
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INDEX_EXCEEDS_SIZE LIBSBML_INDEX_EXCEEDS_SIZE @endlink
=item XMLAttributes::remove
Removes an attribute with the given local name and namespace URI from
this XMLAttributes set.
@param name a string, the local name of the attribute.
@param uri a string, the namespace URI of the attribute.
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INDEX_EXCEEDS_SIZE LIBSBML_INDEX_EXCEEDS_SIZE @endlink
=item XMLAttributes::remove
Removes an attribute with the given XMLTriple from this XMLAttributes set.
@param triple an XMLTriple, the XML triple of the attribute.
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INDEX_EXCEEDS_SIZE LIBSBML_INDEX_EXCEEDS_SIZE @endlink
=item XMLAttributes::clear
Clears (deletes) all attributes in this XMLAttributes object.
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
=item XMLAttributes::getIndex
Return the index of an attribute with the given name.
@note A namespace bound to the name is not checked by this function.
Thus, if there are multiple attributes with the given local name and
different namespaces, the smallest index among those attributes will
be returned. XMLAttributes::getIndex(const std::string& name, const std::string& uri) const or
XMLAttributes::getIndex(const XMLTriple& triple) const should be used to get an index of an
attribute with the given local name and namespace.
@param name a string, the local name of the attribute for which the
index is required.
@return the index of an attribute with the given local name, or -1 if not present.
=item XMLAttributes::getIndex
Return the index of an attribute with the given local name and namespace URI.
@param name a string, the local name of the attribute.
@param uri a string, the namespace URI of the attribute.
@return the index of an attribute with the given local name and namespace URI,
or -1 if not present.
=item XMLAttributes::getIndex
Return the index of an attribute with the given XMLTriple.
@param triple an XMLTriple, the XML triple of the attribute for which
the index is required.
@return the index of an attribute with the given XMLTriple, or -1 if not present.
=item XMLAttributes::getLength
Return the number of attributes in the set.
@return the number of attributes in this XMLAttributes set.
=item XMLAttributes::getNumAttributes
Return the number of attributes in the set.
@return the number of attributes in this XMLAttributes set.
This function is an alias for getLength introduced for consistency
with other XML classes.
=item XMLAttributes::getName
Return the local name of an attribute in this XMLAttributes set (by position).
@param index an integer, the position of the attribute whose local name is
required.
@return the local name of an attribute in this list (by position).
@note If index is out of range, an empty string will be returned. Use
XMLAttributes::hasAttribute(int index) const to test for the attribute
existence.
=item XMLAttributes::getPrefix
Return the prefix of an attribute in this XMLAttributes set (by position).
@param index an integer, the position of the attribute whose prefix is
required.
@return the namespace prefix of an attribute in this list (by
position).
@note If index is out of range, an empty string will be returned. Use
XMLAttributes::hasAttribute(int index) const to test for the attribute
existence.
=item XMLAttributes::getPrefixedName
Return the prefixed name of an attribute in this XMLAttributes set (by position).
@param index an integer, the position of the attribute whose prefixed
name is required.
@return the prefixed name of an attribute in this list (by
position).
@note If index is out of range, an empty string will be returned. Use
XMLAttributes::hasAttribute(int index) const to test for attribute existence.
=item XMLAttributes::getURI
Return the namespace URI of an attribute in this XMLAttributes set (by position).
@param index an integer, the position of the attribute whose namespace URI is
required.
@return the namespace URI of an attribute in this list (by position).
@note If index is out of range, an empty string will be returned. Use
XMLAttributes::hasAttribute(int index) const to test for attribute existence.
=item XMLAttributes::getValue
Return the value of an attribute in this XMLAttributes set (by position).
@param index an integer, the position of the attribute whose value is
required.
@return the value of an attribute in the list (by position).
@note If index is out of range, an empty string will be returned. Use
XMLAttributes::hasAttribute(int index) const to test for attribute existence.
=item XMLAttributes::getValue
Return an attribute's value by name.
@param name a string, the local name of the attribute whose value is required.
@return The attribute value as a string.
@note If an attribute with the given local name does not exist, an
empty string will be returned. Use
XMLAttributes::hasAttribute(const std::string name, const std::string uri) const
to test for attribute existence. A namespace bound to the local name
is not checked by this function. Thus, if there are multiple
attributes with the given local name and different namespaces, the
value of an attribute with the smallest index among those attributes
will be returned. XMLAttributes::getValue(const std::string name) const or
XMLAttributes::getValue(const XMLTriple& triple) const should be used to get a value of an
attribute with the given local name and namespace.
=item XMLAttributes::getValue
Return a value of an attribute with the given local name and namespace URI.
@param name a string, the local name of the attribute whose value is required.
@param uri a string, the namespace URI of the attribute.
@return The attribute value as a string.
@note If an attribute with the given local name and namespace URI does
not exist, an empty string will be returned. Use
XMLAttributes::hasAttribute(const std::string name, const std::string uri) const
to test for attribute existence.
=item XMLAttributes::getValue
Return a value of an attribute with the given XMLTriple.
@param triple an XMLTriple, the XML triple of the attribute whose
value is required.
@return The attribute value as a string.
@note If an attribute with the given XMLTriple does not exist, an
empty string will be returned. Use
XMLAttributes::hasAttribute(const XMLTriple& triple) const to test for attribute existence.
=item XMLAttributes::hasAttribute
Predicate returning C<true> or C<false> depending on whether
an attribute with the given index exists in this XMLAttributes.
@param index an integer, the position of the attribute.
@return C<true> if an attribute with the given index exists in this
XMLAttributes, C<false> otherwise.
=item XMLAttributes::hasAttribute
Predicate returning C<true> or C<false> depending on whether
an attribute with the given local name and namespace URI exists in this
XMLAttributes.
@param name a string, the local name of the attribute.
@param uri a string, the namespace URI of the attribute.
@return C<true> if an attribute with the given local name and namespace
URI exists in this XMLAttributes, C<false> otherwise.
=item XMLAttributes::hasAttribute
Predicate returning C<true> or C<false> depending on whether
an attribute with the given XML triple exists in this XMLAttributes.
@param triple an XMLTriple, the XML triple of the attribute
@return C<true> if an attribute with the given XML triple exists in this
XMLAttributes, C<false> otherwise.
=item XMLAttributes::isEmpty
Predicate returning C<true> or C<false> depending on whether
this XMLAttributes set is empty.
@return C<true> if this XMLAttributes set is empty, C<false> otherwise.
=item XMLAttributes::readInto
Reads the value for the attribute name into value. If the given local
name was not found or value could be interpreted as a boolean, value
is not modified.
According to the W3C XML Schema, valid boolean values are: "true",
"false", "1", and "0" (case-insensitive). For more information, see:
http://www.w3.org/TR/xmlschema-2/#boolean
If an XMLErrorLog is passed in datatype format errors are logged. If
required is true, missing attributes are also logged.
@param name a string, the local name of the attribute.
@param value a boolean, the value of the attribute.
@param log an XMLErrorLog, the error log.
@param required a boolean, indicating whether the attribute is required.
@param line an unsigned int, the line number at which the error occured.
@param column an unsigned int, the column number at which the error occured.
@returns C<true> if the attribute was read into value, C<false> otherwise.
@note A namespace bound to the given local name is not checked by this
function. XMLAttributes::readInto(const XMLTriple, bool&, ...) const should
be used to read a value for an attribute name with a prefix and
namespace.
@if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
=item XMLAttributes::readInto
Reads the value for the attribute with the given XMLTriple into value.
If the XMLTriple was not found or value could be interpreted as a boolean,
value is not modified.
According to the W3C XML Schema, valid boolean values are: "true",
"false", "1", and "0" (case-insensitive). For more information, see:
http://www.w3.org/TR/xmlschema-2/#boolean
If an XMLErrorLog is passed in datatype format errors are logged. If
required is true, missing attributes are also logged.
@param triple an XMLTriple, the XML triple of the attribute.
@param value a boolean, the value of the attribute.
@param log an XMLErrorLog, the error log.
@param required a boolean, indicating whether the attribute is required.
@param line an unsigned int, the line number at which the error occured.
@param column an unsigned int, the column number at which the error occured.
@returns C<true> if the attribute was read into value, C<false> otherwise.
@if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
=item XMLAttributes::readInto
Reads the value for the attribute name into value. If the given local
name was not found or value could be interpreted as a double, value is
not modified.
According to the W3C XML Schema, valid doubles are the same as valid
doubles for C and the special values "INF", "-INF", and "NaN"
(case-sensitive). For more information, see:
http://www.w3.org/TR/xmlschema-2/#double
If an XMLErrorLog is passed in datatype format errors are logged. If
required is true, missing attributes are also logged.
@param name a string, the local name of the attribute.
@param value a double, the value of the attribute.
@param log an XMLErrorLog, the error log.
@param required a boolean, indicating whether the attribute is required.
@param line an unsigned int, the line number at which the error occured.
@param column an unsigned int, the column number at which the error occured.
@returns C<true> if the attribute was read into value, C<false> otherwise.
@note A namespace bound to the given local name is not checked by this
function. XMLAttributes::readInto(const XMLTriple, double&, ...) const
should be used to read a value for an attribute name with a prefix and
namespace.
@if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
=item XMLAttributes::readInto
Reads the value for the attribute with the given XMLTriple into value.
If the triple was not found or value could be interpreted as a double,
value is not modified.
According to the W3C XML Schema, valid doubles are the same as valid
doubles for C and the special values "INF", "-INF", and "NaN"
(case-sensitive). For more information, see:
http://www.w3.org/TR/xmlschema-2/#double
If an XMLErrorLog is passed in datatype format errors are logged. If
required is true, missing attributes are also logged.
@param triple an XMLTriple, the XML triple of the attribute.
@param value a double, the value of the attribute.
@param log an XMLErrorLog, the error log.
@param required a boolean, indicating whether the attribute is required.
@param line an unsigned int, the line number at which the error occured.
@param column an unsigned int, the column number at which the error occured.
@returns C<true> if the attribute was read into value, C<false> otherwise.
@if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
=item XMLAttributes::readInto
Reads the value for the attribute name into value. If the given local
name was not found or value could be interpreted as an long, value is
not modified.
According to the W3C XML Schema valid integers include zero, all
positive and all negative whole numbers. For practical purposes, we
limit values to what can be stored in a long. For more information,
see: http://www.w3.org/TR/xmlschema-2/#integer
If an XMLErrorLog is passed in datatype format errors are logged. If
required is true, missing attributes are also logged.
@param name a string, the local name of the attribute.
@param value a long, the value of the attribute.
@param log an XMLErrorLog, the error log.
@param required a boolean, indicating whether the attribute is required.
@param line an unsigned int, the line number at which the error occured.
@param column an unsigned int, the column number at which the error occured.
@returns C<true> if the attribute was read into value, C<false> otherwise.
@note A namespace bound to the given local name is not checked by this
function. XMLAttributes::readInto(const XMLTriple, long&, ...) const should
be used to read a value for an attribute name with a prefix and
namespace.
@if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
=item XMLAttributes::readInto
Reads the value for the attribute XMLTriple into value.
If the XMLTriple was not found or value could be interpreted as a long,
value is not modified.
According to the W3C XML Schema valid integers include zero, all
positive and all negative whole numbers. For practical purposes, we
limit values to what can be stored in a long. For more information,
see: http://www.w3.org/TR/xmlschema-2/#integer
If an XMLErrorLog is passed in datatype format errors are logged. If
required is true, missing attributes are also logged.
@param triple an XMLTriple, the XML triple of the attribute.
@param value a long, the value of the attribute.
@param log an XMLErrorLog, the error log.
@param required a boolean, indicating whether the attribute is required.
@param line an unsigned int, the line number at which the error occured.
@param column an unsigned int, the column number at which the error occured.
@returns C<true> if the attribute was read into value, C<false> otherwise.
@if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
=item XMLAttributes::readInto
Reads the value for the attribute name into value. If the given local
name was not found or value could be interpreted as an int, value is
not modified.
According to the W3C XML Schema valid integers include zero, all
positive and all negative whole numbers. For practical purposes, we
limit values to what can be stored in a int. For more information,
see: http://www.w3.org/TR/xmlschema-2/#integer
If an XMLErrorLog is passed in datatype format errors are logged. If
required is true, missing attributes are also logged.
@param name a string, the local name of the attribute.
@param value an integer, the value of the attribute.
@param log an XMLErrorLog, the error log.
@param required a boolean, indicating whether the attribute is required.
@param line an unsigned int, the line number at which the error occured.
@param column an unsigned int, the column number at which the error occured.
@returns C<true> if the attribute was read into value, C<false> otherwise.
@note A namespace bound to the given local name is not checked by this
function. XMLAttributes::readInto(const XMLTriple, int&, ...) const should
be used to read a value for an attribute name with a prefix and
namespace.
@if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
=item XMLAttributes::readInto
Reads the value for the attribute with the given XMLTriple into value.
If the XMLTriple was not found or value could be interpreted as an int,
value is not modified.
According to the W3C XML Schema valid integers include zero, all
positive and all negative whole numbers. For practical purposes, we
limit values to what can be stored in a int. For more information,
see: http://www.w3.org/TR/xmlschema-2/#integer
If an XMLErrorLog is passed in datatype format errors are logged. If
required is true, missing attributes are also logged.
@param triple an XMLTriple, the XML triple of the attribute.
@param value an integer, the value of the attribute.
@param log an XMLErrorLog, the error log.
@param required a boolean, indicating whether the attribute is required.
@param line an unsigned int, the line number at which the error occured.
@param column an unsigned int, the column number at which the error occured.
@returns C<true> if the attribute was read into value, C<false> otherwise.
@if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
=item XMLAttributes::readInto
Reads the value for the attribute name into value. If the given local
name was not found or value could be interpreted as an unsigned int,
value is not modified.
According to the W3C XML Schema valid integers include zero, all
positive and all negative whole numbers. For practical purposes, we
limit values to what can be stored in a unsigned int. For more
information, see: http://www.w3.org/TR/xmlschema-2/#integer
If an XMLErrorLog is passed in datatype format errors are logged. If
required is true, missing attributes are also logged.
@param name a string, the local name of the attribute.
@param value an unsigned integer, the value of the attribute.
@param log an XMLErrorLog, the error log.
@param required a boolean, indicating whether the attribute is required.
@param line an unsigned int, the line number at which the error occured.
@param column an unsigned int, the column number at which the error occured.
@returns C<true> if the attribute was read into value, C<false> otherwise.
@note A namespace bound to the given local name is not checked by this
function. XMLAttributes::readInto(const XMLTriple, unsigned int&,
...) const should be used to read a value for an attribute name with a
prefix and namespace.
@if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
=item XMLAttributes::readInto
Reads the value for the attribute with the given XMLTriple into value.
If the XMLTriple was not found or value could be interpreted as an unsigned int,
value is not modified.
According to the W3C XML Schema valid integers include zero, all
positive and all negative whole numbers. For practical purposes, we
limit values to what can be stored in a unsigned int. For more
information, see: http://www.w3.org/TR/xmlschema-2/#integer
If an XMLErrorLog is passed in datatype format errors are logged. If
required is true, missing attributes are also logged.
@param triple an XMLTriple, the XML triple of the attribute.
@param value an unsigned integer, the value of the attribute.
@param log an XMLErrorLog, the error log.
@param required a boolean, indicating whether the attribute is required.
@param line an unsigned int, the line number at which the error occured.
@param column an unsigned int, the column number at which the error occured.
@returns C<true> if the attribute was read into value, C<false> otherwise.
@if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
=item XMLAttributes::readInto
Reads the value for the attribute name into value. If the given local
name was not found, value is not modified.
If an XMLErrorLog is passed in and required is true, missing
attributes are logged.
@param name a string, the local name of the attribute.
@param value a string, the value of the attribute.
@param log an XMLErrorLog, the error log.
@param required a boolean, indicating whether the attribute is required.
@param line an unsigned int, the line number at which the error occured.
@param column an unsigned int, the column number at which the error occured.
@returns C<true> if the attribute was read into value, C<false> otherwise.
@note A namespace bound to the given local name is not checked by this
function. XMLAttributes::readInto(const XMLTriple, std::string&, ...) const
should be used to read a value for an attribute name with a prefix and
namespace.
@if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
=item XMLAttributes::readInto
Reads the value for the attribute with the given XMLTriple into value.
If the XMLTriple was not found, value is not modified.
If an XMLErrorLog is passed in and required is true, missing
attributes are logged.
@param triple an XMLTriple, the XML triple of the attribute.
@param value a string, the value of the attribute.
@param log an XMLErrorLog, the error log.
@param required a boolean, indicating whether the attribute is required.
@param line an unsigned int, the line number at which the error occured.
@param column an unsigned int, the column number at which the error occured.
@returns C<true> if the attribute was read into value, C<false> otherwise.
@if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
=item XMLAttributes::write
@internal
Writes this XMLAttributes set to stream.
@param stream XMLOutputStream, stream to which this XMLAttributes
set is to be written.
=item XMLAttributes::setErrorLog
@internal
(Optional) Sets the log used when logging attributeTypeError() and
attributeRequired() errors.
@param log the log to use
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
=item XMLAttributes::attributeTypeError
@internal
Logs an attribute datatype error.
@param name name of the attribute
@param type the datatype of the attribute value.
@param log the XMLErrorLog where the error should be logged
@param line an unsigned int, the line number at which the error occured.
@param column an unsigned int, the column number at which the error occured.
=item XMLAttributes::attributeRequiredError
@internal
Logs an error indicating a required attribute was missing.
Used internally.
@param name name of the attribute
@param log the XMLErrorLog where the error should be logged
@param line an unsigned int, the line number at which the error occured.
@param column an unsigned int, the column number at which the error occured.
=item XMLAttributes::readInto
@internal
Reads the value for the attribute with the given index into value.
If the attribute was not found or value could be interpreted as a boolean,
value is not modified.
According to the W3C XML Schema, valid boolean values are: "true",
"false", "1", and "0" (case-insensitive). For more information, see:
http://www.w3.org/TR/xmlschema-2/#boolean
If an XMLErrorLog is passed in datatype format errors are logged. If
required is true, missing attributes are also logged.
@param index a int, the index of the attribute.
@param name a string, the name of the attribute
(only used for an error message (if error detected))
@param value a boolean, the value of the attribute.
@param log an XMLErrorLog, the error log.
@param required a boolean, indicating whether the attribute is required.
@param line an unsigned int, the line number at which the error occured.
@param column an unsigned int, the column number at which the error occured.
@returns C<true> if the attribute was read into value, C<false> otherwise.
=item XMLAttributes::readInto
@internal
Reads the value for the attribute with the given index into value.
If name was not found or value could be interpreted as a double, value
is not modified.
According to the W3C XML Schema, valid doubles are the same as valid
doubles for C and the special values "INF", "-INF", and "NaN"
(case-sensitive). For more information, see:
http://www.w3.org/TR/xmlschema-2/#double
If an XMLErrorLog is passed in datatype format errors are logged. If
required is true, missing attributes are also logged.
@param index a int, the index of the attribute.
@param name a string, the name of the attribute
(only used for an error message (if error detected))
@param value a double, the value of the attribute.
@param log an XMLErrorLog, the error log.
@param required a boolean, indicating whether the attribute is required.
@param line an unsigned int, the line number at which the error occured.
@param column an unsigned int, the column number at which the error occured.
@returns C<true> if the attribute was read into value, C<false> otherwise.
=item XMLAttributes::readInto
@internal
Reads the value for the attribute with the given index into value.
If the attribute was not found or value could be interpreted as a long,
value is not modified.
According to the W3C XML Schema valid integers include zero, all
positive and all negative whole numbers. For practical purposes, we
limit values to what can be stored in a long. For more information,
see: http://www.w3.org/TR/xmlschema-2/#integer
If an XMLErrorLog is passed in datatype format errors are logged. If
required is true, missing attributes are also logged.
@param index a int, the index of the attribute.
@param name a string, the name of the attribute
(only used for an error message (if error detected))
@param value a long, the value of the attribute.
@param log an XMLErrorLog, the error log.
@param required a boolean, indicating whether the attribute is required.
@param line an unsigned int, the line number at which the error occured.
@param column an unsigned int, the column number at which the error occured.
@returns C<true> if the attribute was read into value, C<false> otherwise.
=item XMLAttributes::readInto
@internal
Reads the value for the attribute with the given index into value.
If the attribute was not found or value could be interpreted as an integer,
value is not modified.
According to the W3C XML Schema valid integers include zero, all
positive and all negative whole numbers. For practical purposes, we
limit values to what can be stored in a int. For more information,
see: http://www.w3.org/TR/xmlschema-2/#integer
If an XMLErrorLog is passed in datatype format errors are logged. If
required is true, missing attributes are also logged.
@param index a int, the index of the attribute.
@param name a string, the name of the attribute
(only used for an error message (if error detected))
@param value an integer, the value of the attribute.
@param log an XMLErrorLog, the error log.
@param required a boolean, indicating whether the attribute is required.
@param line an unsigned int, the line number at which the error occured.
@param column an unsigned int, the column number at which the error occured.
@returns C<true> if the attribute was read into value, C<false> otherwise.
=item XMLAttributes::readInto
@internal
Reads the value for the attribute with the given index into value.
If the attribute was not found or value could be interpreted as an
unsigned int, value is not modified.
According to the W3C XML Schema valid integers include zero, all
positive and all negative whole numbers. For practical purposes, we
limit values to what can be stored in a unsigned int. For more
information, see: http://www.w3.org/TR/xmlschema-2/#integer
If an XMLErrorLog is passed in datatype format errors are logged. If
required is true, missing attributes are also logged.
@param index a int, the index of the attribute.
@param name a string, the name of the attribute
(only used for an error message (if error detected))
@param value an unsigned integer, the value of the attribute.
@param log an XMLErrorLog, the error log.
@param required a boolean, indicating whether the attribute is required.
@param line an unsigned int, the line number at which the error occured.
@param column an unsigned int, the column number at which the error occured.
@returns C<true> if the attribute was read into value, C<false> otherwise.
=item XMLAttributes::readInto
@internal
Reads the value for the attribute with the given index into value.
If the attribute was not found, value is not modified.
If an XMLErrorLog is passed in and required is true, missing
attributes are logged.
@param index a int, the index of the attribute.
@param name a string, the name of the attribute
(only used for an error message (if error detected))
@param value a string, the value of the attribute.
@param log an XMLErrorLog, the error log.
@param required a boolean, indicating whether the attribute is required.
@param line an unsigned int, the line number at which the error occured.
@param column an unsigned int, the column number at which the error occured.
@returns C<true> if the attribute was read into value, C<false> otherwise.
=back
=head2 XMLConstructorException
@sbmlpackage{core}
@htmlinclude pkg-marker-core.html Class of exceptions thrown by constructors of some
libSBML objects.
@htmlinclude not-sbml-warning.html
In some situations, constructors for SBML objects may need to indicate
to callers that the creation of the object failed. The failure may be
for different reasons, such as an attempt to use invalid parameters or a
system condition such as a memory error. To communicate this to
callers, those classes will throw an XMLConstructorException. @if cpp
Callers can use the standard C++ C<std::exception> method
C<what()> to extract the diagnostic message stored with the
exception.@endif@~
<p>
In languages that don't have an exception mechanism (e.g., C), the
constructors generally try to return an error code instead of throwing
an exception.
@see SBMLConstructorException
=over
=back
=head2 XMLNamespaces
@sbmlpackage{core}
@htmlinclude pkg-marker-core.html Representation of XML Namespaces.
@htmlinclude not-sbml-warning.html
This class serves to organize functionality for tracking XML namespaces
in a document or data stream. The namespace declarations are stored as
a list of pairs of XML namespace URIs and prefix strings. These
correspond to the parts of a namespace declaration on an XML element.
For example, in the following XML fragment,
@verbatim
<annotation>
<mysim:nodecolors xmlns:mysim="urn:lsid:mysim.org"
mysim:bgcolor="green" mysim:fgcolor="white"/>
</annotation>
@endverbatim
there is one namespace declaration. Its URI is
C<urn:lsid:mysim.org> and its prefix is C<mysim>.
This pair could be stored as one item in an XMLNamespaces list.
XMLNamespaces provides various methods for manipulating the list of
prefix-URI pairs. Individual namespaces stored in a given XMLNamespace
object instance can be retrieved based on their index using
XMLNamespaces::getPrefix(int index), or by their characteristics such as
their URI or position in the list.
=over
=item XMLNamespaces::XMLNamespaces
Creates a new empty list of XML namespace declarations.
=item XMLNamespaces::XMLNamespaces
Copy constructor; creates a copy of this XMLNamespaces list.
@param orig the XMLNamespaces object to copy
@throws @if python ValueError @else XMLConstructorException @endif@~
Thrown if the argument C<orig> is C<NULL>.
=item XMLNamespaces::clone
Creates and returns a deep copy of this XMLNamespaces list.
@return a (deep) copy of this XMLNamespaces list.
=item XMLNamespaces::add
Appends an XML namespace prefix and URI pair to this list of namespace
declarations.
An XMLNamespaces object stores a list of pairs of namespaces and their
prefixes. If there is an XML namespace with the given C<uri> prefix
in this list, then its corresponding URI will be overwritten by the
new C<uri> unless the uri represents the core sbml namespace.
Calling programs could use one of the other XMLNamespaces
methods, such as
XMLNamespaces::hasPrefix(@if java String@endif) and
XMLNamespaces::hasURI(@if java String@endif) to
inquire whether a given prefix and/or URI
is already present in this XMLNamespaces object.
If the C<uri> represents the sbml namespaces then it will not be
overwritten, as this has potentially serious consequences. If it
is necessary to replace the sbml namespace the namespace should be removed
prior to adding the new namespace.
@param uri a string, the uri for the namespace
@param prefix a string, the prefix for the namespace
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
@if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
=item XMLNamespaces::remove
Removes an XML Namespace stored in the given position of this list.
@param index an integer, position of the namespace to remove.
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INDEX_EXCEEDS_SIZE LIBSBML_INDEX_EXCEEDS_SIZE @endlink
=item XMLNamespaces::remove
Removes an XML Namespace with the given prefix.
@param prefix a string, prefix of the required namespace.
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INDEX_EXCEEDS_SIZE LIBSBML_INDEX_EXCEEDS_SIZE @endlink
@see remove(int index)
=item XMLNamespaces::clear
Clears (deletes) all XML namespace declarations in this XMLNamespaces
object.
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED@endlink
@see remove(int index)
=item XMLNamespaces::getIndex
Look up the index of an XML namespace declaration by URI.
An XMLNamespaces object stores a list of pairs of namespaces and their
prefixes. If this XMLNamespaces object contains a pair with the given
URI C<uri>, this method returns its index in the list.
@param uri a string, the URI of the sought-after namespace.
@return the index of the given declaration, or C<-1> if not
present.
=item XMLNamespaces::containsUri
Tests whether the given uri is contained in this set of namespaces.
=item XMLNamespaces::getIndexByPrefix
Look up the index of an XML namespace declaration by prefix.
An XMLNamespaces object stores a list of pairs of namespaces and their
prefixes. If this XMLNamespaces object contains a pair with the given
prefix C<prefix>, this method returns its index in the list.
@param prefix a string, the prefix string of the sought-after
namespace
@return the index of the given declaration, or C<-1> if not
present.
=item XMLNamespaces::getLength
Returns the total number of URI-and-prefix pairs stored in this
particular XMLNamespaces instance.
@return the number of namespaces in this list.
=item XMLNamespaces::getNumNamespaces
Returns the total number of URI-and-prefix pairs stored in this
particular XMLNamespaces instance.
@return the number of namespaces in this list.
This function is an alias for getLength introduced for consistency
with other XML classes.
=item XMLNamespaces::getPrefix
Look up the prefix of an XML namespace declaration by its position.
An XMLNamespaces object stores a list of pairs of namespaces and their
prefixes. This method returns the prefix of the C<n>th
element in that list (if it exists). Callers should use
XMLAttributes::getLength() first to find out how many namespaces are
stored in the list.
@param index an integer, position of the sought-after prefix
@return the prefix of an XML namespace declaration in this list (by
position), or an empty string if the C<index> is out of range
@see getLength()
=item XMLNamespaces::getPrefix
Look up the prefix of an XML namespace declaration by its URI.
An XMLNamespaces object stores a list of pairs of namespaces and their
prefixes. This method returns the prefix for a pair that has the
given C<uri>.
@param uri a string, the URI of the prefix being sought
@return the prefix of an XML namespace declaration given its URI, or
an empty string if no such C<uri> exists in this XMLNamespaces object
=item XMLNamespaces::getURI
Look up the URI of an XML namespace declaration by its position.
An XMLNamespaces object stores a list of pairs of namespaces and their
prefixes. This method returns the URI of the C<n>th element
in that list (if it exists). Callers should use
XMLAttributes::getLength() first to find out how many namespaces are
stored in the list.
@param index an integer, position of the required URI.
@return the URI of an XML namespace declaration in this list (by
position), or an empty string if the C<index> is out of range.
@see getLength()
=item XMLNamespaces::getURI
Look up the URI of an XML namespace declaration by its prefix.
An XMLNamespaces object stores a list of pairs of namespaces and their
prefixes. This method returns the namespace URI for a pair that has
the given C<prefix>.
@param prefix a string, the prefix of the required URI
@return the URI of an XML namespace declaration having the given @p
prefix, or an empty string if no such prefix-and-URI pair exists
in this XMLNamespaces object
@if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
@see getURI()
=item XMLNamespaces::isEmpty
Predicate returning C<true> or C<false> depending on whether this
XMLNamespaces list is empty.
@return C<true> if this XMLNamespaces list is empty, C<false> otherwise.
=item XMLNamespaces::hasURI
Predicate returning C<true> or C<false> depending on whether an XML
Namespace with the given URI is contained in this XMLNamespaces list.
@param uri a string, the uri for the namespace
@return C<true> if an XML Namespace with the given URI is contained in
this XMLNamespaces list, C<false> otherwise.
=item XMLNamespaces::hasPrefix
Predicate returning C<true> or C<false> depending on whether an XML
Namespace with the given prefix is contained in this XMLNamespaces
list.
@param prefix a string, the prefix for the namespace
@return C<true> if an XML Namespace with the given URI is contained in
this XMLNamespaces list, C<false> otherwise.
=item XMLNamespaces::hasNS
Predicate returning C<true> or C<false> depending on whether an XML
Namespace with the given URI and prefix pair is contained in this
XMLNamespaces list.
@param uri a string, the URI for the namespace
@param prefix a string, the prefix for the namespace
@return C<true> if an XML Namespace with the given uri/prefix pair is
contained in this XMLNamespaces list, C<false> otherwise.
=item XMLNamespaces::removeDefault
@internal
Removes the default XML namespace.
=item XMLNamespaces::containIdenticalSetNS
@internal
=back
=head2 XMLToken
@sbmlpackage{core}
@htmlinclude pkg-marker-core.html Representation of a token in an XML stream.
@htmlinclude not-sbml-warning.html
=over
=item XMLToken::XMLToken
Creates a new empty XMLToken.
=item XMLToken::XMLToken
Creates a start element XMLToken with the given set of attributes and
namespace declarations.
@param triple XMLTriple.
@param attributes XMLAttributes, the attributes to set.
@param namespaces XMLNamespaces, the namespaces to set.
@param line an unsigned int, the line number (default = 0).
@param column an unsigned int, the column number (default = 0).
@if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
=item XMLToken::XMLToken
Creates a start element XMLToken with the given set of attributes.
@param triple XMLTriple.
@param attributes XMLAttributes, the attributes to set.
@param line an unsigned int, the line number (default = 0).
@param column an unsigned int, the column number (default = 0).
@if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
=item XMLToken::XMLToken
Creates an end element XMLToken.
@param triple XMLTriple.
@param line an unsigned int, the line number (default = 0).
@param column an unsigned int, the column number (default = 0).
@if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
=item XMLToken::XMLToken
Creates a text XMLToken.
@param chars a string, the text to be added to the XMLToken
@param line an unsigned int, the line number (default = 0).
@param column an unsigned int, the column number (default = 0).
@throws @if python ValueError @else XMLConstructorException @endif@~
Thrown if the argument C<orig> is C<NULL>.
@if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
=item XMLToken::XMLToken
Copy constructor; creates a copy of this XMLToken.
@param orig the XMLToken object to copy.
@throws @if python ValueError @else XMLConstructorException @endif@~
Thrown if the argument C<orig> is C<NULL>.
=item XMLToken::clone
Creates and returns a deep copy of this XMLToken.
@return a (deep) copy of this XMLToken set.
=item XMLToken::getAttributes
Returns the attributes of this element.
@return the XMLAttributes of this XML element.
=item XMLToken::setAttributes
Sets an XMLAttributes to this XMLToken.
Nothing will be done if this XMLToken is not a start element.
@param attributes XMLAttributes to be set to this XMLToken.
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_XML_OPERATION LIBSBML_INVALID_XML_OPERATION @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT @endlink
@note This function replaces the existing XMLAttributes with the new one.
=item XMLToken::addAttr
Adds an attribute to the attribute set in this XMLToken optionally
with a prefix and URI defining a namespace.
Nothing will be done if this XMLToken is not a start element.
@param name a string, the local name of the attribute.
@param value a string, the value of the attribute.
@param namespaceURI a string, the namespace URI of the attribute.
@param prefix a string, the prefix of the namespace
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_XML_OPERATION LIBSBML_INVALID_XML_OPERATION @endlink
@note if local name with the same namespace URI already exists in the
attribute set, its value and prefix will be replaced.
@if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
=item XMLToken::addAttr
Adds an attribute with the given XMLTriple/value pair to the attribute set
in this XMLToken.
Nothing will be done if this XMLToken is not a start element.
@note if local name with the same namespace URI already exists in the
attribute set, its value and prefix will be replaced.
@param triple an XMLTriple, the XML triple of the attribute.
@param value a string, the value of the attribute.
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_XML_OPERATION LIBSBML_INVALID_XML_OPERATION @endlink
=item XMLToken::removeAttr
Removes an attribute with the given index from the attribute set in
this XMLToken.
Nothing will be done if this XMLToken is not a start element.
@param n an integer the index of the resource to be deleted
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_XML_OPERATION LIBSBML_INVALID_XML_OPERATION @endlink
@li @link OperationReturnValues_t#LIBSBML_INDEX_EXCEEDS_SIZE LIBSBML_INDEX_EXCEEDS_SIZE @endlink
=item XMLToken::removeAttr
Removes an attribute with the given local name and namespace URI from
the attribute set in this XMLToken.
Nothing will be done if this XMLToken is not a start element.
@param name a string, the local name of the attribute.
@param uri a string, the namespace URI of the attribute.
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_XML_OPERATION LIBSBML_INVALID_XML_OPERATION @endlink
@li @link OperationReturnValues_t#LIBSBML_INDEX_EXCEEDS_SIZE LIBSBML_INDEX_EXCEEDS_SIZE @endlink
=item XMLToken::removeAttr
Removes an attribute with the given XMLTriple from the attribute set
in this XMLToken.
Nothing will be done if this XMLToken is not a start element.
@param triple an XMLTriple, the XML triple of the attribute.
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_XML_OPERATION LIBSBML_INVALID_XML_OPERATION @endlink
@li @link OperationReturnValues_t#LIBSBML_INDEX_EXCEEDS_SIZE LIBSBML_INDEX_EXCEEDS_SIZE @endlink
=item XMLToken::clearAttributes
Clears (deletes) all attributes in this XMLToken.
Nothing will be done if this XMLToken is not a start element.
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_XML_OPERATION LIBSBML_INVALID_XML_OPERATION @endlink
=item XMLToken::getAttrIndex
Return the index of an attribute with the given local name and namespace URI.
@param name a string, the local name of the attribute.
@param uri a string, the namespace URI of the attribute.
@return the index of an attribute with the given local name and namespace URI,
or C<-1> if not present.
@if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
=item XMLToken::getAttrIndex
Return the index of an attribute with the given XMLTriple.
@param triple an XMLTriple, the XML triple of the attribute for which
the index is required.
@return the index of an attribute with the given XMLTriple, or C<-1> if not present.
=item XMLToken::getAttributesLength
Return the number of attributes in the attributes set.
@return the number of attributes in the attributes set in this XMLToken.
=item XMLToken::getAttrName
Return the local name of an attribute in the attributes set in this
XMLToken (by position).
@param index an integer, the position of the attribute whose local name
is required.
@return the local name of an attribute in this list (by position).
@note If index
is out of range, an empty string will be returned. Use
XMLToken::hasAttr(@if java int index@endif)
to test for the attribute existence.
=item XMLToken::getAttrPrefix
Return the prefix of an attribute in the attribute set in this
XMLToken (by position).
@param index an integer, the position of the attribute whose prefix is
required.
@return the namespace prefix of an attribute in the attribute set
(by position).
@note If index is out of range, an empty string will be returned. Use
XMLToken::hasAttr(@if java int index@endif) to test
for the attribute existence.
=item XMLToken::getAttrPrefixedName
Return the prefixed name of an attribute in the attribute set in this
XMLToken (by position).
@param index an integer, the position of the attribute whose prefixed
name is required.
@return the prefixed name of an attribute in the attribute set
(by position).
@note If index is out of range, an empty string will be returned. Use
XMLToken::hasAttr(@if java int index@endif) to test
for attribute existence.
=item XMLToken::getAttrURI
Return the namespace URI of an attribute in the attribute set in this
XMLToken (by position).
@param index an integer, the position of the attribute whose namespace
URI is required.
@return the namespace URI of an attribute in the attribute set (by position).
@note If index is out of range, an empty string will be returned. Use
XMLToken::hasAttr(@if java int index@endif) to test
for attribute existence.
=item XMLToken::getAttrValue
Return the value of an attribute in the attribute set in this XMLToken
(by position).
@param index an integer, the position of the attribute whose value is
required.
@return the value of an attribute in the attribute set (by position).
@note If index is out of range, an empty string will be returned. Use
XMLToken::hasAttr(@if java int index@endif) to test
for attribute existence.
=item XMLToken::getAttrValue
Return a value of an attribute with the given local name and namespace URI.
@param name a string, the local name of the attribute whose value is required.
@param uri a string, the namespace URI of the attribute.
@return The attribute value as a string.
@note If an attribute with the
given local name and namespace URI does not exist, an empty string will be
returned.
Use XMLToken::hasAttr(@if java String name, String uri@endif)
to test for attribute existence.
@if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
=item XMLToken::getAttrValue
Return a value of an attribute with the given XMLTriple.
@param triple an XMLTriple, the XML triple of the attribute whose
value is required.
@return The attribute value as a string.
@note If an attribute with the
given XMLTriple does not exist, an empty string will be returned.
Use XMLToken::hasAttr(@if java XMLTriple triple@endif)
to test for attribute existence.
=item XMLToken::hasAttr
Predicate returning C<true> or C<false> depending on whether
an attribute with the given index exists in the attribute set in this
XMLToken.
@param index an integer, the position of the attribute.
@return C<true> if an attribute with the given index exists in the attribute
set in this XMLToken, C<false> otherwise.
=item XMLToken::hasAttr
Predicate returning C<true> or C<false> depending on whether
an attribute with the given local name and namespace URI exists
in the attribute set in this XMLToken.
@param name a string, the local name of the attribute.
@param uri a string, the namespace URI of the attribute.
@return C<true> if an attribute with the given local name and namespace
URI exists in the attribute set in this XMLToken, C<false> otherwise.
@if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
=item XMLToken::hasAttr
Predicate returning C<true> or C<false> depending on whether
an attribute with the given XML triple exists in the attribute set in
this XMLToken
@param triple an XMLTriple, the XML triple of the attribute
@return C<true> if an attribute with the given XML triple exists
in the attribute set in this XMLToken, C<false> otherwise.
=item XMLToken::isAttributesEmpty
Predicate returning C<true> or C<false> depending on whether
the attribute set in this XMLToken set is empty.
@return C<true> if the attribute set in this XMLToken is empty,
C<false> otherwise.
=item XMLToken::getNamespaces
Returns the XML namespace declarations for this XML element.
@return the XML namespace declarations for this XML element.
=item XMLToken::setNamespaces
Sets an XMLnamespaces to this XML element.
Nothing will be done if this XMLToken is not a start element.
@param namespaces XMLNamespaces to be set to this XMLToken.
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_XML_OPERATION LIBSBML_INVALID_XML_OPERATION @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT @endlink
@note This function replaces the existing XMLNamespaces with the new one.
=item XMLToken::addNamespace
Appends an XML namespace prefix and URI pair to this XMLToken.
If there is an XML namespace with the given prefix in this XMLToken,
then the existing XML namespace will be overwritten by the new one.
Nothing will be done if this XMLToken is not a start element.
@param uri a string, the uri for the namespace
@param prefix a string, the prefix for the namespace
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_XML_OPERATION LIBSBML_INVALID_XML_OPERATION @endlink
@if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
=item XMLToken::removeNamespace
Removes an XML Namespace stored in the given position of the XMLNamespaces
of this XMLToken.
Nothing will be done if this XMLToken is not a start element.
@param index an integer, position of the removed namespace.
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_XML_OPERATION LIBSBML_INVALID_XML_OPERATION @endlink
@li @link OperationReturnValues_t#LIBSBML_INDEX_EXCEEDS_SIZE LIBSBML_INDEX_EXCEEDS_SIZE @endlink
=item XMLToken::removeNamespace
Removes an XML Namespace with the given prefix.
Nothing will be done if this XMLToken is not a start element.
@param prefix a string, prefix of the required namespace.
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_XML_OPERATION LIBSBML_INVALID_XML_OPERATION @endlink
@li @link OperationReturnValues_t#LIBSBML_INDEX_EXCEEDS_SIZE LIBSBML_INDEX_EXCEEDS_SIZE @endlink
=item XMLToken::clearNamespaces
Clears (deletes) all XML namespace declarations in the XMLNamespaces of
this XMLToken.
Nothing will be done if this XMLToken is not a start element.
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_XML_OPERATION LIBSBML_INVALID_XML_OPERATION @endlink
=item XMLToken::getNamespaceIndex
Look up the index of an XML namespace declaration by URI.
@param uri a string, uri of the required namespace.
@return the index of the given declaration, or C<-1> if not present.
=item XMLToken::getNamespaceIndexByPrefix
Look up the index of an XML namespace declaration by prefix.
@param prefix a string, prefix of the required namespace.
@return the index of the given declaration, or C<-1> if not present.
=item XMLToken::getNamespacesLength
Returns the number of XML namespaces stored in the XMLNamespaces
of this XMLToken.
@return the number of namespaces in this list.
=item XMLToken::getNamespacePrefix
Look up the prefix of an XML namespace declaration by position.
Callers should use getNamespacesLength() to find out how many
namespaces are stored in the XMLNamespaces.
@param index an integer, position of the required prefix.
@return the prefix of an XML namespace declaration in the XMLNamespaces
(by position).
@note If index is out of range, an empty string will be
returned.
@see getNamespacesLength()
=item XMLToken::getNamespacePrefix
Look up the prefix of an XML namespace declaration by its URI.
@param uri a string, the URI of the prefix being sought
@return the prefix of an XML namespace declaration given its URI.
@note If C<uri> does not exist, an empty string will be returned.
=item XMLToken::getNamespaceURI
Look up the URI of an XML namespace declaration by its position.
@param index an integer, position of the required URI.
@return the URI of an XML namespace declaration in the XMLNamespaces
(by position).
@note If C<index> is out of range, an empty string will be
returned.
@see getNamespacesLength()
=item XMLToken::getNamespaceURI
Look up the URI of an XML namespace declaration by its prefix.
@param prefix a string, the prefix of the required URI
@return the URI of an XML namespace declaration given its prefix.
@note If C<prefix> does not exist, an empty string will be returned.
@if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
=item XMLToken::isNamespacesEmpty
Predicate returning C<true> or C<false> depending on whether
the XMLNamespaces of this XMLToken is empty.
@return C<true> if the XMLNamespaces of this XMLToken is empty,
C<false> otherwise.
=item XMLToken::hasNamespaceURI
Predicate returning C<true> or C<false> depending on whether
an XML Namespace with the given URI is contained in the XMLNamespaces of
this XMLToken.
@param uri a string, the uri for the namespace
@return C<true> if an XML Namespace with the given URI is contained in the
XMLNamespaces of this XMLToken, C<false> otherwise.
=item XMLToken::hasNamespacePrefix
Predicate returning C<true> or C<false> depending on whether
an XML Namespace with the given prefix is contained in the XMLNamespaces of
this XMLToken.
@param prefix a string, the prefix for the namespace
@return C<true> if an XML Namespace with the given URI is contained in the
XMLNamespaces of this XMLToken, C<false> otherwise.
=item XMLToken::hasNamespaceNS
Predicate returning C<true> or C<false> depending on whether
an XML Namespace with the given uri/prefix pair is contained in the
XMLNamespaces ofthis XMLToken.
@param uri a string, the uri for the namespace
@param prefix a string, the prefix for the namespace
@return C<true> if an XML Namespace with the given uri/prefix pair is
contained in the XMLNamespaces of this XMLToken, C<false> otherwise.
=item XMLToken::setTriple
Sets the XMLTripe (name, uri and prefix) of this XML element.
Nothing will be done if this XML element is a text node.
@param triple XMLTriple to be added to this XML element.
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_XML_OPERATION LIBSBML_INVALID_XML_OPERATION @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT @endlink
=item XMLToken::getName
Returns the (unqualified) name of this XML element.
@return the (unqualified) name of this XML element.
=item XMLToken::getPrefix
Returns the namespace prefix of this XML element.
@return the namespace prefix of this XML element.
@note If no prefix
exists, an empty string will be return.
=item XMLToken::getURI
Returns the namespace URI of this XML element.
@return the namespace URI of this XML element.
=item XMLToken::getCharacters
Returns the text of this element.
@return the characters of this XML text.
=item XMLToken::append
Appends characters to this XML text content.
@param chars string, characters to append
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED@endlink
=item XMLToken::getColumn
Returns the column at which this XMLToken occurred in the input
document or data stream.
@return the column at which this XMLToken occurred.
=item XMLToken::getLine
Returns the line at which this XMLToken occurred in the input document
or data stream.
@return the line at which this XMLToken occurred.
=item XMLToken::isElement
Predicate returning C<true> or C<false> depending on whether
this XMLToken is an XML element.
@return C<true> if this XMLToken is an XML element, C<false> otherwise.
=item XMLToken::isEnd
Predicate returning C<true> or C<false> depending on whether
this XMLToken is an XML end element.
@return C<true> if this XMLToken is an XML end element, C<false> otherwise.
=item XMLToken::isEndFor
Predicate returning C<true> or C<false> depending on whether
this XMLToken is an XML end element for the given start element.
@param element XMLToken, element for which query is made.
@return C<true> if this XMLToken is an XML end element for the given
XMLToken start element, C<false> otherwise.
=item XMLToken::isEOF
Predicate returning C<true> or C<false> depending on whether
this XMLToken is an end of file marker.
@return C<true> if this XMLToken is an end of file (input) marker, C<false>
otherwise.
=item XMLToken::isStart
Predicate returning C<true> or C<false> depending on whether
this XMLToken is an XML start element.
@return C<true> if this XMLToken is an XML start element, C<false> otherwise.
=item XMLToken::isText
Predicate returning C<true> or C<false> depending on whether
this XMLToken is an XML text element.
@return C<true> if this XMLToken is an XML text element, C<false> otherwise.
=item XMLToken::setEnd
Declares this XML start element is also an end element.
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED@endlink
=item XMLToken::setEOF
Declares this XMLToken is an end-of-file (input) marker.
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED@endlink
=item XMLToken::unsetEnd
Declares this XML start/end element is no longer an end element.
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED@endlink
=item XMLToken::write
@internal
Writes this XMLToken to stream.
@param stream XMLOutputStream, stream to which this XMLToken
is to be written.
=item XMLToken::toString
Prints a string representation of the underlying token stream, for
debugging purposes.
=back
=head2 XMLNode
@sbmlpackage{core}
@htmlinclude pkg-marker-core.html Representation of a node in an XML document tree.
Beginning with version 3.0.0, libSBML implements an XML abstraction
layer. This layer presents a uniform XML interface to calling programs
regardless of which underlying XML parser libSBML has actually been
configured to use. The basic data object in the XML abstraction is a
I<node>, represented by XMLNode.
An XMLNode can contain any number of children. Each child is another
XMLNode, thereby forming a tree. The methods XMLNode::getNumChildren()
and XMLNode::getChild(@if java long n@endif) can be used to access the tree
structure starting from a given node.
Each XMLNode is subclassed from XMLToken, and thus has the same methods
available as XMLToken. These methods include XMLToken::getNamespaces(),
XMLToken::getPrefix(), XMLToken::getName(), XMLToken::getURI(), and
XMLToken::getAttributes().
@section xmlnode-str2xmlnode Conversion between an XML string and an XMLNode
LibSBML provides the following utility functions for converting an XML
string (e.g., C<<annotation>...</annotation>>)
to/from an XMLNode object.
\n=over\n
\n=item\n\nXMLNode::toXMLString() returns a string representation of the XMLNode object.
\n=item\n\nXMLNode::convertXMLNodeToString(@if java XMLNode node@endif)
(static function) returns a string representation
of the given XMLNode object.
\n=item\n\nXMLNode::convertStringToXMLNode(@if java String xml@endif)
(static function) returns an XMLNode object converted
from the given XML string.
\n=back\n
The returned XMLNode object by XMLNode::convertStringToXMLNode(@if java String xml@endif)
is a dummy root (container) XMLNode if the given XML string has two or
more top-level elements (e.g.,
"C<<p>...</p><p>...</p>>"). In the
dummy root node, each top-level element in the given XML string is
contained as a child XMLNode. XMLToken::isEOF() can be used to identify
if the returned XMLNode object is a dummy node or not. Here is an
example: @if clike
@verbatim
// Checks if the XMLNode object returned by XMLNode::convertStringToXMLNode() is a dummy root node:
std::string str = "...";
XMLNode xn = XMLNode::convertStringToXMLNode(str);
if ( xn == NULL )
{
// returned value is null (error)
...
}
else if ( xn->isEOF() )
{
// root node is a dummy node
for ( int i = 0; i E<lt> xn->getNumChildren(); i++ )
{
// access to each child node of the dummy node.
XMLNode& xnChild = xn->getChild(i);
...
}
}
else
{
// root node is NOT a dummy node
...
}
@endverbatim
@endif@if java
@verbatim
// Checks if the returned XMLNode object is a dummy root node:
String str = "...";
XMLNode xn = XMLNode.convertStringToXMLNode(str);
if ( xn == null )
{
// returned value is null (error)
...
}
else if ( xn.isEOF() )
{
// root node is a dummy node
for ( int i = 0; i E<lt> xn.getNumChildren(); i++ )
{
// access to each child node of the dummy node.
XMLNode xnChild = xn.getChild(i);
...
}
}
else
{
// root node is NOT a dummy node
...
}
@endverbatim
@endif@if python
@verbatim
xn = XMLNode.convertStringToXMLNode("<p></p>")
if xn == None:
# Do something to handle exceptional situation.
elif xn.isEOF():
# Node is a dummy node.
else:
# None is not a dummy node.
@endverbatim
@endif@~
=over
=item XMLNode::XMLNode
Creates a new empty XMLNode with no children.
=item XMLNode::XMLNode
Creates a new XMLNode by copying token.
@param token XMLToken to be copied to XMLNode
=item XMLNode::XMLNode
Creates a new start element XMLNode with the given set of attributes and
namespace declarations.
@param triple XMLTriple.
@param attributes XMLAttributes, the attributes to set.
@param namespaces XMLNamespaces, the namespaces to set.
@param line an unsigned int, the line number (default = 0).
@param column an unsigned int, the column number (default = 0).
@if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
=item XMLNode::XMLNode
Creates a start element XMLNode with the given set of attributes.
@param triple XMLTriple.
@param attributes XMLAttributes, the attributes to set.
@param line an unsigned int, the line number (default = 0).
@param column an unsigned int, the column number (default = 0).
@if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
=item XMLNode::XMLNode
Creates an end element XMLNode.
@param triple XMLTriple.
@param line an unsigned int, the line number (default = 0).
@param column an unsigned int, the column number (default = 0).
@if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
=item XMLNode::XMLNode
Creates a text XMLNode.
@param chars a string, the text to be added to the XMLToken
@param line an unsigned int, the line number (default = 0).
@param column an unsigned int, the column number (default = 0).
@if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
=item XMLNode::XMLNode
@internal
Creates a new XMLNode by reading XMLTokens from stream.
The stream must be positioned on a start element
(C<stream.peek().isStart() == true>) and will be read until
the matching end element is found.
@param stream XMLInputStream from which XMLNode is to be created.
=item XMLNode::XMLNode
Copy constructor; creates a copy of this XMLNode.
@param orig the XMLNode instance to copy.
@throws @if python ValueError @else XMLConstructorException @endif@~
Thrown if the argument C<orig> is C<NULL>.
=item XMLNode::clone
Creates and returns a deep copy of this XMLNode.
@return a (deep) copy of this XMLNode.
=item XMLNode::addChild
Adds a copy of C<node> as a child of this XMLNode.
The given C<node> is added at the end of the list of children.
@param node the XMLNode to be added as child.
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_XML_OPERATION LIBSBML_INVALID_XML_OPERATION @endlink
@note The given node is added at the end of the children list.
=item XMLNode::insertChild
Inserts a copy of the given node as the C<n>th child of this
XMLNode.
If the given index C<n> is out of range for this XMLNode instance,
the C<node> is added at the end of the list of children. Even in
that situation, this method does not throw an error.
@param n an integer, the index at which the given node is inserted
@param node an XMLNode to be inserted as C<n>th child.
@return a reference to the newly-inserted child C<node>
=item XMLNode::removeChild
Removes the C<n>th child of this XMLNode and returns the
removed node.
It is important to keep in mind that a given XMLNode may have more
than one child. Calling this method erases all existing references to
child nodes I<after> the given position C<n>. If the index C<n> is
greater than the number of child nodes in this XMLNode, this method
takes no action (and returns C<NULL>).
@param n an integer, the index of the node to be removed
@return the removed child, or C<NULL> if C<n> is greater than the number
of children in this node
@note The caller owns the returned node and is responsible for deleting it.
=item XMLNode::removeChildren
Removes all children from this node.
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
=item XMLNode::getChild
Returns the C<n>th child of this XMLNode.
If the index C<n> is greater than the number of child nodes,
this method returns an empty node.
@param n an unsigned integer, the index of the node to return
@return the C<n>th child of this XMLNode.
=item XMLNode::getChild
Returns the C<n>th child of this XMLNode.
If the index C<n> is greater than the number of child nodes,
this method returns an empty node.
@param n an unsigned integer, the index of the node to return
@return the C<n>th child of this XMLNode.
=item XMLNode::getChild
Returns the first child of this XMLNode with the corresponding name.
If no child with corrsponding name can be found,
this method returns an empty node.
@param name the name of the node to return
@return the first child of this XMLNode with given name.
=item XMLNode::getChild
Returns the first child of this XMLNode with the corresponding name.
If no child with corrsponding name can be found,
this method returns an empty node.
@param name the name of the node to return
@return the first child of this XMLNode with given name.
=item XMLNode::getIndex
Return the index of the first child of this XMLNode with the given name.
@param name a string, the name of the child for which the
index is required.
@return the index of the first child of this XMLNode with the given
name, or -1 if not present.
=item XMLNode::hasChild
Return a boolean indicating whether this XMLNode has a child with the
given name.
@param name a string, the name of the child to be checked.
@return boolean indicating whether this XMLNode has a child with the
given name.
=item XMLNode::equals
Compare this XMLNode against another XMLNode returning true if both
nodes represent the same XML tree, or false otherwise.
@param other another XMLNode to compare against.
@param ignoreURI whether to ignore the namespace URI when doing the
comparison.
@return boolean indicating whether this XMLNode represents the same XML
tree as another.
=item XMLNode::getNumChildren
Returns the number of children for this XMLNode.
@return the number of children for this XMLNode.
=item XMLNode::write
@internal
Writes this XMLNode and its children to stream.
@param stream XMLOutputStream, stream to which this XMLNode
is to be written.
=item XMLNode::toXMLString
Returns a string representation of this XMLNode.
@return a string derived from this XMLNode.
=item XMLNode::convertXMLNodeToString
Returns a string representation of a given XMLNode.
@param node the XMLNode to be represented as a string
@return a string-form representation of C<node>
=item XMLNode::convertStringToXMLNode
Returns an XMLNode which is derived from a string containing XML
content.
The XML namespace must be defined using argument C<xmlns> if the
corresponding XML namespace attribute is not part of the string of the
first argument.
@param xmlstr string to be converted to a XML node.
@param xmlns XMLNamespaces the namespaces to set (default value is C<NULL>).
@note The caller owns the returned XMLNode and is reponsible for
deleting it. The returned XMLNode object is a dummy root (container)
XMLNode if the top-level element in the given XML string is NOT
C<<html>>, C<<body>>,
C<<annotation>>, or C<<notes>>. In
the dummy root node, each top-level element in the given XML string is
contained as a child XMLNode. XMLToken::isEOF() can be used to
identify if the returned XMLNode object is a dummy node.
@return a XMLNode which is converted from string C<xmlstr>. If the
conversion failed, this method returns C<NULL>.
@if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
=back
=head2 XMLTriple
@sbmlpackage{core}
@htmlinclude pkg-marker-core.html Representation of a qualified XML name.
@htmlinclude not-sbml-warning.html
A "triple" in the libSBML XML layer encapsulates the notion of qualified
name, meaning an element name or an attribute name with an optional
namespace qualifier. An XMLTriple instance carries up to three data items:
\n=over\n
\n=item\n\nThe name of the attribute or element; that is, the attribute name
as it appears in an XML document or data stream;
\n=item\n\nThe XML namespace prefix (if any) of the attribute. For example,
in the following fragment of XML, the namespace prefix is the string
C<mysim> and it appears on both the element
C<someelement> and the attribute C<attribA>. When
both the element and the attribute are stored as XMLTriple objects,
their <i>prefix</i> is C<mysim>.
@verbatim
<mysim:someelement mysim:attribA="value" />
@endverbatim
\n=item\n\nThe XML namespace URI with which the prefix is associated. In
XML, every namespace used must be declared and mapped to a URI.
\n=back\n
XMLTriple objects are the lowest-level data item in the XML layer
of libSBML. Other objects such as XMLToken make use of XMLTriple
objects.
=over
=item XMLTriple::XMLTriple
Creates a new, empty XMLTriple.
=item XMLTriple::XMLTriple
Creates a new XMLTriple with the given C<name>, C<uri> and and @p
prefix.
@param name a string, name for the XMLTriple.
@param uri a string, URI of the XMLTriple.
@param prefix a string, prefix for the URI of the XMLTriple,
@throws @if python ValueError @else XMLConstructorException @endif@~
Thrown if the argument C<orig> is C<NULL>.
=item XMLTriple::XMLTriple
Creates a new XMLTriple by splitting the given C<triplet> on the
separator character C<sepchar>.
Triplet may be in one of the following formats:
\n=over\n
\n=item\n\nname
\n=item\n\nURI sepchar name
\n=item\n\nURI sepchar name sepchar prefix
\n=back\n
@param triplet a string representing the triplet as above
@param sepchar a character, the sepchar used in the triplet
@throws @if python ValueError @else XMLConstructorException @endif@~
Thrown if the argument C<orig> is C<NULL>.
@if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
=item XMLTriple::XMLTriple
Copy constructor; creates a copy of this XMLTriple set.
@param orig the XMLTriple object to copy.
@throws @if python ValueError @else XMLConstructorException @endif@~
Thrown if the argument C<orig> is C<NULL>.
=item XMLTriple::clone
Creates and returns a deep copy of this XMLTriple set.
@return a (deep) copy of this XMLTriple set.
=item XMLTriple::getName
Returns the I<name> portion of this XMLTriple.
@return a string, the name from this XMLTriple.
=item XMLTriple::getPrefix
Returns the I<prefix> portion of this XMLTriple.
@return a string, the I<prefix> portion of this XMLTriple.
=item XMLTriple::getURI
Returns the I<URI> portion of this XMLTriple.
@return URI a string, the I<prefix> portion of this XMLTriple.
=item XMLTriple::getPrefixedName
Returns the prefixed name from this XMLTriple.
@return a string, the prefixed name from this XMLTriple.
=item XMLTriple::isEmpty
Predicate returning C<true> or C<false> depending on whether
this XMLTriple is empty.
@return C<true> if this XMLTriple is empty, C<false> otherwise.
=back
=head2 XMLOutputStream
@sbmlpackage{core}
@htmlinclude pkg-marker-core.html Interface to an XML output stream.
=over
=item XMLOutputStream::XMLOutputStream
Creates a new XMLOutputStream that wraps stream.
@if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
=item XMLOutputStream::endElement
Writes the given XML end element name to this XMLOutputStream.
=item XMLOutputStream::endElement
Writes the given XML end element 'prefix:name' to this
XMLOutputStream.
=item XMLOutputStream::setAutoIndent
Turns automatic indentation on or off for this XMLOutputStream.
=item XMLOutputStream::startElement
Writes the given XML start element name to this XMLOutputStream.
=item XMLOutputStream::startElement
Writes the given XML start element 'prefix:name' to this
XMLOutputStream.
=item XMLOutputStream::startEndElement
Writes the given XML start and end element name to this XMLOutputStream.
=item XMLOutputStream::startEndElement
Writes the given XML start and end element 'prefix:name' to this
XMLOutputStream.
=item XMLOutputStream::writeAttribute
Writes the given attribute, name="value" to this XMLOutputStream.
=item XMLOutputStream::writeAttribute
Writes the given attribute, prefix:name="value" to this XMLOutputStream.
=item XMLOutputStream::writeAttribute
Writes the given attribute, prefix:name="value" to this
XMLOutputStream.
=item XMLOutputStream::writeAttribute
Writes the given attribute, name="value" to this XMLOutputStream.
=item XMLOutputStream::writeAttribute
Writes the given attribute, prefix:name="value" to this XMLOutputStream.
=item XMLOutputStream::writeAttribute
Writes the given attribute, prefix:name="value" to this
XMLOutputStream.
=item XMLOutputStream::writeAttribute
Writes the given attribute, name="true" or name="false" to this
XMLOutputStream.
=item XMLOutputStream::writeAttribute
Writes the given attribute, prefix:name="true" or prefix:name="false" to this
XMLOutputStream.
=item XMLOutputStream::writeAttribute
Writes the given attribute, prefix:name="true" or prefix:name="false"
to this XMLOutputStream.
=item XMLOutputStream::writeAttribute
Writes the given attribute, name="value" to this XMLOutputStream.
=item XMLOutputStream::writeAttribute
Writes the given attribute, prefix:name="value" to this XMLOutputStream.
=item XMLOutputStream::writeAttribute
Writes the given attribute, prefix:name="value" to this
XMLOutputStream.
=item XMLOutputStream::writeAttribute
Writes the given attribute, name="value" to this XMLOutputStream.
=item XMLOutputStream::writeAttribute
Writes the given attribute, prefix:name="value" to this XMLOutputStream.
=item XMLOutputStream::writeAttribute
Writes the given attribute, prefix:name="value" to this
XMLOutputStream.
=item XMLOutputStream::writeAttribute
Writes the given attribute, name="value" to this XMLOutputStream.
=item XMLOutputStream::writeAttribute
Writes the given attribute, prefix:name="value" to this XMLOutputStream.
=item XMLOutputStream::writeAttribute
Writes the given attribute, prefix:name="value" to this
XMLOutputStream.
=item XMLOutputStream::writeAttribute
Writes the given attribute, name="value" to this XMLOutputStream.
=item XMLOutputStream::writeAttribute
Writes the given attribute, prefix:name="value" to this XMLOutputStream.
=item XMLOutputStream::writeAttribute
Writes the given attribute, prefix:name="value" to this
XMLOutputStream.
=item XMLOutputStream::writeXMLDecl
Writes the XML declaration:
<?xml version="1.0" encoding="..."?>
=item XMLOutputStream::writeComment
Writes an XML comment:
<?xml version="1.0" encoding="..."?>
=item XMLOutputStream::downIndent
Decreases the indentation level for this XMLOutputStream.
=item XMLOutputStream::upIndent
Increases the indentation level for this XMLOutputStream.
=item XMLOutputStream::getStringStream
=item XMLOutputStream::getSBMLNamespaces
Returns the SBMLNamespaces object attached to this XMLInputStream
if it has been set, NULL otherwise.
@return the SBMLNamespaces object or NULL if none has been set.
=item XMLOutputStream::setSBMLNamespaces
Sets the SBMLNamespaces object to allow this stream to reference
the available SBML namespaces being read.
=item XMLOutputStream::XMLOutputStream
Copy Constructor, made private so as to notify users, that copying an input stream is not supported.
=item XMLOutputStream::XMLOutputStream
Unitialized XMLOutputStreams may only be created by subclasses.
=item XMLOutputStream::writeChars
Outputs the given characters to the underlying stream.
=item XMLOutputStream::writeIndent
Outputs indentation whitespace.
@if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
=item XMLOutputStream::writeName
Outputs name.
=item XMLOutputStream::writeName
Outputs prefix:name.
=item XMLOutputStream::writeValue
Outputs value in quotes.
=item XMLOutputStream::writeValue
Outputs value in quotes.
=item XMLOutputStream::writeValue
Outputs "true" or "false" in quotes.
=item XMLOutputStream::writeValue
Outputs the double value in quotes, or "INF", "-INF", or "NaN".
=item XMLOutputStream::writeValue
Outputs the long value in quotes.
=item XMLOutputStream::writeValue
Outputs the int value in quotes.
=item XMLOutputStream::writeValue
Outputs the int value in quotes.
=item XMLOutputStream::setStringStream
=item XMLOutputStream::unsetStringStream
=item XMLOutputStringStream::XMLOutputStringStream
Creates a new XMLOutputStream that wraps stream.
@if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
=item XMLOutputStringStream::getString
=item XMLOutputFileStream::XMLOutputFileStream
Creates a new XMLOutputStream that wraps stream.
@if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
=back
=head2 XMLInputStream
@sbmlpackage{core}
@htmlinclude pkg-marker-core.html An interface to an XML input stream.
=over
=item XMLInputStream::XMLInputStream
Creates a new XMLInputStream.
C<content> the source of the stream.
C<isFile> boolean flag to indicate whether C<content> is a file name.
If C<true>, C<content> is assumed to be the file from which the XML
content is to be read. If C<false>, C<content> is taken to be a
string that I<is> the content to be read.
C<library> the name of the parser library to use.
C<errorLog> the XMLErrorLog object to use.
@if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
=item XMLInputStream::getEncoding
Returns the encoding of the XML stream.
@return the encoding of the XML stream.
=item XMLInputStream::getVersion
Returns the version of the XML stream.
@return the version of the XML stream.
=item XMLInputStream::getErrorLog
Returns an XMLErrorLog which can be used to log XML parse errors and
other validation errors (and messages).
@return an XMLErrorLog which can be used to log XML parse errors and
other validation errors (and messages).
=item XMLInputStream::isEOF
Returns true if end of file (stream) has been reached, false
otherwise.
@return true if end of file (stream) has been reached, false
otherwise.
=item XMLInputStream::isError
Returns true if a fatal error occurred while reading from this stream.
@return true if a fatal error occurred while reading from this stream.
=item XMLInputStream::isGood
Returns true if the stream is in a good state (i.e. isEOF() and
isError() are both false), false otherwise.
@return true if the stream is in a good state (i.e. isEOF() and
isError() are both false), false otherwise.
=item XMLInputStream::next
Consumes the next XMLToken and return it.
@return the next XMLToken or EOF (XMLToken.isEOF() == true).
=item XMLInputStream::peek
Returns the next XMLToken without consuming it. A subsequent call to
either peek() or next() will return the same token.
@return the next XMLToken or EOF (XMLToken.isEOF() == true).
=item XMLInputStream::skipPastEnd
Consume zero or more XMLTokens up to and including the corresponding
end XML element or EOF.
=item XMLInputStream::skipText
Consume zero or more XMLTokens up to but not including the next XML
element or EOF.
=item XMLInputStream::setErrorLog
Sets the XMLErrorLog this stream will use to log errors.
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif@~ The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item XMLInputStream::toString
Prints a string representation of the underlying token stream, for
debugging purposes.
=item XMLInputStream::getSBMLNamespaces
Returns the SBMLNamespaces object attached to this XMLInputStream
if it has been set, NULL otherwise.
@return the SBMLNamespaces object or NULL if none has been set.
=item XMLInputStream::setSBMLNamespaces
Sets the SBMLNamespaces object to allow this stream to reference
the available SBML namespaces being read.
=item XMLInputStream::determineNumberChildren
Analyses the tokens in the stream and returns the number of
child tokens of the given element.
@param elementName a string representing the name of the element
for which the number of children are to be determined.
This function allows information from the input stream to be determined
without the need to actually read and consume the tokens in
the stream. This functionality
is particularly utilized when reading MathML.
The function will return the number of child elements of the
element represented by the elementName supplied, i.e. the number
of child elements encountered before the closing tag for the
elementname supplied. If the elementName
has not been supplied then the function assumes that it is reading
an apply element followed by a function element.
@note This function assumes the stream has been read up to and
including the element elementName.
@return an unsigned int giving the number of children of the
element specified.
=item XMLInputStream::determineNumSpecificChildren
Analyses the tokens in the stream and returns the number of
child tokens of the specified type within the given element.
@param childName a string representing the name of the child
element whose number is to be determined.
@param container a string representing the name of the element
for which the number of children are to be determined.
This function allows information from the input stream to be determined
without the need to actually read and consume the tokens in
the stream. This functionality
is particularly utilized when reading MathML.
The function will return the number of child elements of the
element represented by the childName supplied within the element
specified by the container, i.e. the number
of child elements encountered before the closing tag for the
container supplied.
@note This function assumes the stream has been read up to and
including the element container.
@return an unsigned int giving the number of children of type childName
within the container element specified.
=item XMLInputStream::XMLInputStream
Copy Constructor, made private so as to notify users, that copying an input stream is not supported.
=item XMLInputStream::XMLInputStream
Unitialized XMLInputStreams may only be created by subclasses.
=item XMLInputStream::queueToken
Runs mParser until mTokenizer is ready to deliver at least one
XMLToken or a fatal error occurs.
=item XMLInputStream::requeueToken
=back
=head2 XMLError
@sbmlpackage{core}
@htmlinclude pkg-marker-core.html Representation of errors, warnings and other diagnostics
@htmlinclude not-sbml-warning.html
LibSBML can be configured to use any of a number of XML parsers; at the
time of this writing, libSBML supports Xerces versions 2.4 through 3.1,
Expat version 1.95.x and higher, and libxml2 version 2.6.16 and higher.
These parsers each report different status codes for the various
exceptions that can occur during XML processing. The XMLError object
class abstracts away from the particular diagnostics reported by the
different parsers and presents a single uniform interface and set of
status codes, along with operations for manipulating the error objects.
When the libSBML XML parser layer encounters an error in the XML content
being processed, or when there is something else wrong (such as an
out-of-memory condition), the problems are reported as XMLError objects.
Each XMLError object instance has an identification number that
identifies the nature of the problem.
@if clike This error identifier will be up to five digits
long and drawn from the enumeration <a class="el"
href="#error-codes">XMLErrorCode_t</a>. Applications can use the
error identifiers as a means of recognizing the error encountered and
changing their behavior if desired. @else This
error identifier is one of the constants listed in the next section below.
Applications can use the error identifiers as a means of recognizing the
error encountered and changing their behavior if desired. @endif@~
Integer error codes are useful for software, but not so much for telling
humans what happened. For this reason, XMLError also provides two text
messages describing the nature of the error. These messages are
accessible by means of the methods XMLError::getShortMessage() and
XMLError::getMessage(). The method XMLError::getShortMessage() returns
a very brief synopsis of the warning or error condition, whereas
XMLError::getMessage() returns a longer explanation. These text strings
are suitable for displaying to human users.
Each XMLError object also contains a category code; its value may be
retrieved using the method XMLError::getCategory(). Category values
are drawn from @if clike the enumeration <a class="el" href="#XMLErrorCategory_t">XMLErrorCategory_t</a> described below.@else a
set of constants whose names begin with the characters C<LIBSBML_CAT_>, described below.@endif@~ Categories
are used by libSBML to provide more information to calling programs about
the nature of a given error.
In addition to category codes, each XMLError object also has a severity
code; its value may be retrieved using the method
XMLError::getSeverity(). Severity code values are drawn from
@if clike the enumeration <a class="el" href="#XMLErrorSeverity_t">XMLErrorSeverity_t</a>@else a
set of constants whose names begin with the characters C<LIBSBML_SEV_@endif>,
described below. Severity levels range from informational
(@link XMLErrorSeverity_t#LIBSBML_SEV_INFO LIBSBML_SEV_INFO@endlink) to
fatal errors (@link XMLErrorSeverity_t#LIBSBML_SEV_FATAL LIBSBML_SEV_FATAL@endlink).
Finally, XMLError objects record the line and column near where the
problem occurred in the XML content. The values can be retrieved using
the methods XMLError::getLine() and XMLError::getColumn(). We say "near
where the problem occurred", because many factors affect how accurate
the line/column information ultimately is. For example, sometimes, the
underlying XML parsers can only report such information for the parent
XML element where an error occurs, and not for the specific point where
the problem occurs. In other situations, some parsers report invalid
line and/or column numbers altogether. If this occurs, libSBML sets the
line and/or column number in the XMLError object to either
C<0> or the value of the maximum unsigned long integer
representable on the platform where libSBML is running. The probability
that a true line or column number in an SBML model would equal this
value is vanishingly small; thus, if an application encounters these
values in an XMLError object, it can assume no valid line/column number
could be provided by libSBML in that situation.
@if clike
<h3><a class="anchor" name="error-codes">XMLErrorCode_t</a></h3>
This is an enumeration of all the error and warning codes returned by
the XML layer in libSBML. Each code is an integer with a 4-digit value
less than 10000. The following table lists each possible value and a
brief description of its meaning.
@endif@if java <h3><a class="anchor"
name="error-codes">Error codes associated with XMLError objects</a></h3>
The error and warning codes returned by the XML layer in libSBML are
listed in the table below. In the libSBML Java language interface,
these error identifiers are currently implemented as static integer
constants defined in the interface class <code><a
href="libsbmlConstants.html">libsbmlConstants</a></code>. This is
admittedly not an ideal approach from the standpoint of modern Java
programming, but it was necessary to work around the lack of
enumerations in Java prior to JDK 1.5. Future versions of libSBML may
use a proper Java enumeration type to define the error
identifiers. @endif@if csharp <h3><a class="anchor"
name="error-codes">Error codes associated with XMLError objects</a></h3>
The error and warning codes returned by the XML layer in libSBML are
listed in the table below. In the libSBML C# language interface,
these error identifiers are currently implemented as static integer
constants defined in the interface class @link libsbmlcs.libsbml@endlink.@endif@~
<center>
<table cellspacing="1" cellpadding="1" border="0" class="text-table width80 normal-font alt-row-colors">
<caption>Possible XMLError error codes. Depending on the programming
language in use, the <em>Enumerator</em> values will be defined either
as a value from the enumeration XMLErrorCode_t or as integer constants.
To make this table more compact, we have shortened the identifiers for
the category and severity codes to their essential parts. To get the
actual names of the constants, prepend C<LIBSBML_CAT_> to the
category names and C<LIBSBML_SEV_> to the severity names
shown in the two right-hand columns.
</caption>
<tr style="background: lightgray" class="normal-font">
<th>Enumerator</th>
<th>Meaning</th>
<th width="90">Category</th>
<th width="90">Severity</th>
</tr>
<tr><td>@link XMLErrorCode_t#XMLUnknownError XMLUnknownError@endlink</td><td>Unrecognized error encountered internally</td><td>INTERNAL</td><td>FATAL</td></tr>
<tr><td>@link XMLErrorCode_t#XMLOutOfMemory XMLOutOfMemory@endlink</td> <td>Out of memory</td><td>SYSTEM</td><td>FATAL</td></tr>
<tr><td>@link XMLErrorCode_t#XMLFileUnreadable XMLFileUnreadable@endlink</td> <td>File unreadable</td><td>SYSTEM</td><td>ERROR</td></tr>
<tr><td>@link XMLErrorCode_t#XMLFileUnwritable XMLFileUnwritable@endlink</td> <td>File unwritable</td><td>SYSTEM</td><td>ERROR</td></tr>
<tr><td>@link XMLErrorCode_t#XMLFileOperationError XMLFileOperationError@endlink</td><td>Error encountered while attempting file operation</td><td>SYSTEM</td><td>ERROR</td></tr>
<tr><td>@link XMLErrorCode_t#XMLNetworkAccessError XMLNetworkAccessError@endlink</td><td>Network access error</td><td>SYSTEM</td><td>ERROR</td></tr>
<tr><td>@link XMLErrorCode_t#InternalXMLParserError InternalXMLParserError@endlink</td><td>Internal XML parser state error</td><td>INTERNAL</td><td>FATAL</td></tr>
<tr><td>@link XMLErrorCode_t#UnrecognizedXMLParserCode UnrecognizedXMLParserCode@endlink</td><td>XML parser returned an unrecognized error code</td><td>INTERNAL</td><td>FATAL</td></tr>
<tr><td>@link XMLErrorCode_t#XMLTranscoderError XMLTranscoderError@endlink</td><td>Character transcoder error</td><td>INTERNAL</td><td>FATAL</td></tr>
<tr><td>@link XMLErrorCode_t#MissingXMLDecl MissingXMLDecl@endlink</td><td>Missing XML declaration at beginning of XML input</td><td>XML</td><td>ERROR</td></tr>
<tr><td>@link XMLErrorCode_t#MissingXMLEncoding MissingXMLEncoding@endlink</td><td>Missing encoding attribute in XML declaration</td><td>XML</td><td>ERROR</td></tr>
<tr><td>@link XMLErrorCode_t#BadXMLDecl BadXMLDecl@endlink</td><td>Invalid or unrecognized XML declaration or XML encoding</td><td>XML</td><td>ERROR</td></tr>
<tr><td>@link XMLErrorCode_t#BadXMLDOCTYPE BadXMLDOCTYPE@endlink</td><td>Invalid, malformed or unrecognized XML DOCTYPE declaration</td><td>XML</td><td>ERROR</td></tr>
<tr><td>@link XMLErrorCode_t#InvalidCharInXML InvalidCharInXML@endlink</td><td>Invalid character in XML content</td><td>XML</td><td>ERROR</td></tr>
<tr><td>@link XMLErrorCode_t#BadlyFormedXML BadlyFormedXML@endlink</td><td>XML content is not well-formed</td><td>XML</td><td>ERROR</td></tr>
<tr><td>@link XMLErrorCode_t#UnclosedXMLToken UnclosedXMLToken@endlink</td><td>Unclosed XML token</td><td>XML</td><td>ERROR</td></tr>
<tr><td>@link XMLErrorCode_t#InvalidXMLConstruct InvalidXMLConstruct@endlink</td><td>XML construct is invalid or not permitted</td><td>XML</td><td>ERROR</td></tr>
<tr><td>@link XMLErrorCode_t#XMLTagMismatch XMLTagMismatch@endlink</td><td>Element tag mismatch or missing tag</td><td>XML</td><td>ERROR</td></tr>
<tr><td>@link XMLErrorCode_t#DuplicateXMLAttribute DuplicateXMLAttribute@endlink</td><td>Duplicate XML attribute</td><td>XML</td><td>ERROR</td></tr>
<tr><td>@link XMLErrorCode_t#UndefinedXMLEntity UndefinedXMLEntity@endlink</td><td>Undefined XML entity</td><td>XML</td><td>ERROR</td></tr>
<tr><td>@link XMLErrorCode_t#BadProcessingInstruction BadProcessingInstruction@endlink</td><td>Invalid, malformed or unrecognized XML processing instruction</td><td>XML</td><td>ERROR</td></tr>
<tr><td>@link XMLErrorCode_t#BadXMLPrefix BadXMLPrefix@endlink</td><td>Invalid or undefined XML namespace prefix</td><td>XML</td><td>ERROR</td></tr>
<tr><td>@link XMLErrorCode_t#BadXMLPrefixValue BadXMLPrefixValue@endlink</td><td>Invalid XML namespace prefix value</td><td>XML</td><td>ERROR</td></tr>
<tr><td>@link XMLErrorCode_t#MissingXMLRequiredAttribute MissingXMLRequiredAttribute@endlink</td><td>Missing a required XML attribute</td><td>XML</td><td>ERROR</td></tr>
<tr><td>@link XMLErrorCode_t#XMLAttributeTypeMismatch XMLAttributeTypeMismatch@endlink</td><td>Data type mismatch for the value of an attribute</td><td>XML</td><td>ERROR</td></tr>
<tr><td>@link XMLErrorCode_t#XMLBadUTF8Content XMLBadUTF8Content@endlink</td><td>Invalid UTF8 content</td><td>XML</td><td>ERROR</td></tr>
<tr><td>@link XMLErrorCode_t#MissingXMLAttributeValue MissingXMLAttributeValue@endlink</td><td>Missing or improperly formed attribute value</td><td>XML</td><td>ERROR</td></tr>
<tr><td>@link XMLErrorCode_t#BadXMLAttributeValue BadXMLAttributeValue@endlink</td><td>Invalid or unrecognizable attribute value</td><td>XML</td><td>ERROR</td></tr>
<tr><td>@link XMLErrorCode_t#BadXMLAttribute BadXMLAttribute@endlink</td><td>Invalid, unrecognized or malformed attribute</td><td>XML</td><td>ERROR</td></tr>
<tr><td>@link XMLErrorCode_t#UnrecognizedXMLElement UnrecognizedXMLElement@endlink</td><td>Element either not recognized or not permitted</td><td>XML</td><td>ERROR</td></tr>
<tr><td>@link XMLErrorCode_t#BadXMLComment BadXMLComment@endlink</td><td>Badly formed XML comment</td><td>XML</td><td>ERROR</td></tr>
<tr><td>@link XMLErrorCode_t#BadXMLDeclLocation BadXMLDeclLocation@endlink</td><td>XML declaration not permitted in this location</td><td>XML</td><td>ERROR</td></tr>
<tr><td>@link XMLErrorCode_t#XMLUnexpectedEOF XMLUnexpectedEOF@endlink</td><td>Reached end of input unexpectedly</td><td>XML</td><td>ERROR</td></tr>
<tr><td>@link XMLErrorCode_t#BadXMLIDValue BadXMLIDValue@endlink</td><td>Value is invalid for XML ID, or has already been used</td><td>XML</td><td>ERROR</td></tr>
<tr><td>@link XMLErrorCode_t#BadXMLIDRef BadXMLIDRef@endlink</td><td>XML ID value was never declared</td><td>XML</td><td>ERROR</td></tr>
<tr><td>@link XMLErrorCode_t#UninterpretableXMLContent UninterpretableXMLContent@endlink</td><td>Unable to interpret content</td><td>XML</td><td>ERROR</td></tr>
<tr><td>@link XMLErrorCode_t#BadXMLDocumentStructure BadXMLDocumentStructure@endlink</td><td>Bad XML document structure</td><td>XML</td><td>ERROR</td></tr>
<tr><td>@link XMLErrorCode_t#InvalidAfterXMLContent InvalidAfterXMLContent@endlink</td><td>Encountered invalid content after expected content</td><td>XML</td><td>ERROR</td></tr>
<tr><td>@link XMLErrorCode_t#XMLExpectedQuotedString XMLExpectedQuotedString@endlink</td><td>Expected to find a quoted string</td><td>XML</td><td>ERROR</td></tr>
<tr><td>@link XMLErrorCode_t#XMLEmptyValueNotPermitted XMLEmptyValueNotPermitted@endlink</td><td>An empty value is not permitted in this context</td><td>XML</td><td>ERROR</td></tr>
<tr><td>@link XMLErrorCode_t#XMLBadNumber XMLBadNumber@endlink</td><td>Invalid or unrecognized number</td><td>XML</td><td>ERROR</td></tr>
<tr><td>@link XMLErrorCode_t#XMLBadColon XMLBadColon@endlink</td><td>Colon characters are invalid in this context</td><td>XML</td><td>ERROR</td></tr>
<tr><td>@link XMLErrorCode_t#MissingXMLElements MissingXMLElements@endlink</td><td>One or more expected elements are missing</td><td>XML</td><td>ERROR</td></tr>
<tr><td>@link XMLErrorCode_t#XMLContentEmpty XMLContentEmpty@endlink</td><td>Main XML content is empty</td><td>XML</td><td>ERROR</td></tr>
</table>
</center>
@if clike
<h3><a class="anchor" name="error-categories">XMLErrorCategory_t</a></h3>
As discussed above, each XMLError object contains a value for a category
identifier, describing the type of issue that the XMLError object
represents. The category can be retrieved from an XMLError object using
the method XMLError::getCategory(). The value is chosen from the
enumeration of category codes <a class="el" href="#XMLErrorCategory_t">
XMLErrorCategory_t</a>. The following table
lists each possible value and a brief description of its meaning.
@endif@if java <h3><a class="anchor"
name="error-categories">Category codes associated with XMLError objects</a></h3>
As discussed above, each XMLError object contains a value for a category
identifier, describing the type of issue that the XMLError object represents.
The category can be retrieved from an XMLError object using the method
XMLError::getCategory(). The following table lists each possible value
and a brief description of its meaning.
As is the case with the error codes, in the libSBML Java language
interface, the category identifiers are currently implemented as static
integer constants defined in the interface class
C<libsbmlConstants> in the file "<a
href="libsbmlConstants.html">libsbmlConstants.java</a>".
@endif@if csharp <h3><a class="anchor"
name="error-categories">Category codes associated with XMLError objects</a></h3>
As discussed above, each XMLError object contains a value for a category
identifier, describing the type of issue that the XMLError object represents.
The category can be retrieved from an XMLError object using the method
XMLError::getCategory(). The following table lists each possible value
and a brief description of its meaning.
As is the case with the error codes, in the libSBML C# language
interface, the category identifiers are currently implemented as static
integer constants defined in the interface
class @link libsbmlcs.libsbml@endlink. @endif@~
<center>
<table width="90%" cellspacing="1" cellpadding="1" border="0" class="text-table width80 normal-font alt-row-colors">
<tr style="background: lightgray" class="normal-font">
<th>Enumerator</th>
<th>Meaning</th>
</tr>
<tr><td>@link XMLErrorCategory_t#LIBSBML_CAT_INTERNAL LIBSBML_CAT_INTERNAL@endlink</td>
<td>A problem involving the libSBML
software itself or the underlying XML parser. This almost certainly
indicates a software defect (i.e., bug) in libSBML. Please report
instances of this to the libSBML developers.</td></tr>
<tr><td>@link XMLErrorCategory_t#LIBSBML_CAT_SYSTEM LIBSBML_CAT_SYSTEM@endlink</td>
<td>A problem reported by the operating
system, such as an inability to read or write a file. This indicates
something that is not a program error but is outside of the control of
libSBML.</td></tr>
<tr><td>@link XMLErrorCategory_t#LIBSBML_CAT_XML LIBSBML_CAT_XML@endlink</td>
<td>A problem in the XML content itself. This
usually arises from malformed XML or the use of
constructs not permitted in SBML.</td></tr>
</table>
</center>
@if clike
<h3><a class="anchor" name="error-severities">XMLErrorSeverity_t</a></h3>
As described above, each XMLError object contains a value for a severity
code, describing how critical is the issue that the XMLError object
represents. The severity can be retrieved from an XMLError object using
the method XMLError::getSeverity(). The value is chosen from the
enumeration of category codes <a class="el" href="#XMLErrorSeverity_t">
XMLErrorSeverity_t</a>. The following table
lists each possible value and a brief description of its meaning.
@endif@if java <h3><a class="anchor"
name="error-severities">Severity codes associated with XMLError objects</a></h3>
As described above, each XMLError object contains a value for a severity
code, describing how severe is the issue that the XMLError object
represents. The severity be retrieved from an XMLError object using the
method XMLError::getSeverity(). The following table lists each possible
value and a brief description of its meaning.
As is the case with the category codes, in the libSBML Java language
interface, these severity codes are currently
implemented as static integer constants defined in the interface class
C<libsbmlConstants> in the file "<a
href="libsbmlConstants.html">libsbmlConstants.java</a>". This
is admittedly not an ideal approach from the standpoint of modern Java
programming, but it was necessary to work around the lack of
enumerations in Java prior to JDK 1.5. Future versions of libSBML may
use a proper Java enumeration type to define the severity
codes. @endif@if csharp <h3><a class="anchor"
name="error-severities">Severity codes associated with XMLError objects</a></h3>
As described above, each XMLError object contains a value for a severity
code, describing how severe is the issue that the XMLError object
represents. The severity be retrieved from an XMLError object using the
method XMLError::getSeverity(). The following table lists each possible
value and a brief description of its meaning.
As is the case with the category codes, in the libSBML C# language
interface, these severity codes are currently
implemented as static integer constants defined in the interface class
@link libsbmlcs.libsbml@endlink.@endif@~
<center>
<table width="90%" cellspacing="1" cellpadding="1" border="0" class="text-table width80 normal-font alt-row-colors">
<tr style="background: lightgray" class="normal-font">
<th>Enumerator</th>
<th>Meaning</th>
</tr>
<tr><td>@link XMLErrorSeverity_t#LIBSBML_SEV_INFO LIBSBML_SEV_INFO@endlink</td>
<td>The error is actually informational and
not necessarily a serious problem.</td></tr>
<tr><td>@link XMLErrorSeverity_t#LIBSBML_SEV_WARNING LIBSBML_SEV_WARNING@endlink</td>
<td>The error object represents a problem
that is not serious enough to necessarily stop the problem, but
applications should take note of the problem and evaluate what its
implications may be.</td></tr>
<tr><td>@link XMLErrorSeverity_t#LIBSBML_SEV_ERROR LIBSBML_SEV_ERROR@endlink</td>
<td>The error object represents a serious
error. The application may continue running but it is unlikely to be
able to continue processing the same XML file or data stream.</td></tr>
<tr><td>@link XMLErrorSeverity_t#LIBSBML_SEV_FATAL LIBSBML_SEV_FATAL@endlink</td>
<td>A serious error occurred, such as an
out-of-memory condition, and the software should terminate
immediately.</td></tr>
</table>
</center>
=over
=item XMLError::XMLError
Creates a new XMLError to report that something occurred during XML
processing.
XMLError objects have identification numbers to indicate the nature of
the exception. @if clike These numbers are drawn from
the enumeration <a class="el"
href="#error-codes">XMLErrorCode_t</a>.
@else These numbers are defined as unsigned
integer constants in the file
"libsbmlConstants.java". See the <a class="el"
href="#error-codes">top of this documentation</a> for a table
listing the possible values and their meanings. @endif@~ The argument @p
errorId to this constructor I<can> be (but does not have to be) a
value from this @if clike enumeration. If it is a value
from <a class="el" href="#error-codes">XMLErrorCode_t</a>, the
XMLError class assumes the error is a low-level system or XML layer
error and <em>prepends</em> a built-in, predefined error message to
any string passed in the argument C<details> to this constructor. In
addition, all <a class="el" href="#error-codes">XMLErrorCode_t</a>
errors have associated values for the C<severity> and C<category>
codes, and these fields are filled-in as well from the enumerations <a
class="el" href="#error-severities">XMLErrorSeverity_t</a> and <a
class="el" href="#error-categories">XMLErrorCategory_t</a>,
respectively. @else set of constants. If it is
one of the predefined error identifiers, the XMLError class assumes
the error is a low-level system or XML layer error and
<em>prepends</em> a built-in, predefined error message to any string
passed in the argument C<details> to this constructor. In addition,
all the predefined error identifiers have associated values for the @p
severity and C<category> codes, and these fields are filled-in as
well. @endif@~
If the error identifier C<errorId> is a number greater than 9999, this
constructor assumes that the error was generated from another part of
the software, and does not do additional filling in of values beyond
the defaults in the constructor itself. This allows XMLError to serve
as a base class for other errors (and is used in this way elsewhere in
libSBML). Callers should fill in all the parameters with suitable
values if generating errors with codes greater than 9999 to make
maximum use of the XMLError facilities.
@if clike As mentioned above, there are two other
enumerations, <a class="el"
href="#error-severities">XMLErrorSeverity_t</a> and <a class="el"
href="#error-categories">XMLErrorCategory_t</a>, used for indicating
the severity and category of error for the predefined XMLError codes.
The values passed in C<severity> and C<category> override the defaults
assigned based on the error code. If the value of C<errorId> is a
value from <a class="el" href="#error-codes">XMLErrorCode_t</a>,
callers do not need to fill in C<severity> and C<category>.
Conversely, if C<errorId> is not a value from <a class="el"
href="#error-codes">XMLErrorCode_t</a>, callers can use other
values (not just those from <a class="el"
href="#error-severities">XMLErrorSeverity_t</a> and <a class="el"
href="#error-categories">XMLErrorCategory_t</a>, but their own
special values) for C<severity> and @p
category. @else As mentioned above,
there are additional constants defined for <a class="el"
href="#error-severities">standard severity</a> and <a class="el"
href="#error-categories">standard category</a> codes, and every predefined
error in libSBML has an associated value for severity and category taken
from these predefined sets. These constants have symbol names
prefixed with C<LIBSBML_SEV_> and C<LIBSBML_CAT_>,
respectively. If the value of C<errorId> is one of the standard error
codes, callers do not need to fill in C<severity> and C<category> in a
call to this constructor. Conversely, if C<errorId> is not an existing
XML-level error code, callers can use other values for C<severity> and
C<category>. @endif@~
@param errorId an unsigned int, the identification number of the error.
@param details a string containing additional details about the error.
If the error code in C<errorId> is one that is recognized by XMLError,
the given message is I<appended> to a predefined message associated
with the given code. If the error code is not recognized, the message
is stored as-is as the text of the error.
@param line an unsigned int, the line number at which the error occured.
@param column an unsigned int, the column number at which the error occured.
@param severity an integer indicating severity of the error.
@param category an integer indicating the category to which the error
belongs.
@if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
=item XMLError::XMLError
Copy constructor; creates a copy of this XMLError.
C<orig> the XMLError object to copy.
@throws @if python ValueError @else XMLConstructorException @endif@~
Thrown if the argument C<orig> is C<NULL>.
=item XMLError::getErrorId
Returns the identifier of this error.
@return the error code for this error.
@see getMessage()
@see getShortMessage()
@see getCategory()
@see getSeverity()
=item XMLError::getMessage
Returns the message text of this error.
The message associated with an error object describes the nature of
the problem. The message returned by this method is generally longer
and clearer than the message returned by XMLError::getShortMessage(),
but not in all cases.
Callers may use XMLError::getCategory() and XMLError::getSeverity() to
obtain additional information about the nature and severity of the
problem.
@return the message text
@see getErrorId()
@see getShortMessage()
@see getCategory()
@see getSeverity()
=item XMLError::getShortMessage
Returns a brief message for this error.
This is an alternative error message that, in general, is as short as
the authors could make it. However, brevity is often inversely
proportional to clarity, so this short message may not be sufficiently
informative to understand the nature of the error. Calling
applications may wish to check XMLError::getMessage() in addition or
instead.
@return the short error message text
@see getErrorId()
@see getMessage()
@see getCategory()
@see getSeverity()
=item XMLError::getLine
Returns the line number in the XML input near where the error, warning
or other diagnostic occurred.
We say "near where the problem occurred", because many factors affect
how accurate the line/column information ultimately is. For example,
sometimes, the underlying XML parsers can only report such information
for the parent XML element where an error occurs, and not for the
specific point where the problem occurs. In other situations, some
parsers report invalid line and/or column numbers altogether. If this
occurs, libSBML sets the line and/or column number in the XMLError
object to either C<0> or the value of the maximum unsigned
long integer representable on the platform where libSBML is running.
The probability that a true line or column number in an SBML model
would equal this value is vanishingly small; thus, if an application
encounters these values in an XMLError object, it can assume no valid
line/column number could be provided by libSBML in that situation.
@return the line number
@see getColumn()
=item XMLError::getColumn
Returns the column number in the XML input near where the error,
warning or other diagnostic occurred.
We say "near where the problem occurred", because many factors affect
how accurate the line/column information ultimately is. For example,
sometimes, the underlying XML parsers can only report such information
for the parent XML element where an error occurs, and not for the
specific point where the problem occurs. In other situations, some
parsers report invalid line and/or column numbers altogether. If this
occurs, libSBML sets the line and/or column number in the XMLError
object to either C<0> or the value of the maximum unsigned
long integer representable on the platform where libSBML is running.
The probability that a true line or column number in an SBML model
would equal this value is vanishingly small; thus, if an application
encounters these values in an XMLError object, it can assume no valid
line/column number could be provided by libSBML in that situation.
@return the column number
@see getLine()
=item XMLError::getSeverity
Returns the severity of this error.
XMLError defines an enumeration of severity codes for the XML layer.
Applications that build on XMLError by subclassing it may add their
own severity codes with numbers higher than those in the predefined
set of severity codes.
@return the severity of this XMLError.
@see getSeverityAsString()
@see getCategory()
=item XMLError::getSeverityAsString
Returns a string describing the severity level of this error.
XMLError defines an enumeration of severity codes for the XML layer.
Applications that build on XMLError by subclassing it may add their
own severity codes with numbers higher than those in the predefined
set of severity codes.
@return string representing the severity of this XMLError.
@see getSeverity()
@see getCategoryAsString()
=item XMLError::getCategory
Returns the category of this error.
XMLError defines an enumeration of category codes for the XML layer.
Applications that build on XMLError by subclassing it may add their
own categories with numbers higher than those in the predefined
set of category codes.
Categories can be used to partition errors into distinct groups.
Among other things, this can be used to prevent id conflicts by
uniquely identifying an XMLError by both id and category.
@return the category of this XMLError.
@see getSeverity()
@see getCategoryAsString()
=item XMLError::getCategoryAsString
Returns a string describing the category of this error.
XMLError defines an enumeration of category codes for the XML layer.
Applications that build on XMLError by subclassing it may add their
own categories with numbers higher than those in the predefined
set of category codes.
Categories can be used to partition errors into distinct groups.
Among other things, this can be used to prevent id conflicts by
uniquely identifying an XMLError by both id and category.
@return string representing the category of this XMLError.
@see getCategory()
@see getSeverityAsString()
=item XMLError::isInfo
Predicate returning C<true> or C<false> depending on whether this
error object is for information purposes only.
This is equivalent to obtaining the severity code from an XMLError
object (via XMLError::getSeverity()) and then comparing it to the
value @link XMLErrorSeverity_t#LIBSBML_SEV_INFO LIBSBML_SEV_INFO@endlink from the
@if clike enumeration #XMLErrorSeverity_t. @else set of predefined
severity codes.@endif@~
@return C<true> if this XMLError is for informational purposes only,
C<false> otherwise.
@see isWarning()
@see isError()
@see isFatal()
=item XMLError::isWarning
Predicate returning C<true> or C<false> depending on whether
this error object is a warning.
This is equivalent to obtaining the severity code from an XMLError
object (via XMLError::getSeverity()) and then comparing it to the
value @link XMLErrorSeverity_t#LIBSBML_SEV_WARNING LIBSBML_SEV_WARNING@endlink from the
@if clike enumeration #XMLErrorSeverity_t. @else set of predefined
severity codes.@endif@~
@return C<true> if this error is a warning, C<false> otherwise.
@see isInfo()
@see isError()
@see isFatal()
=item XMLError::isError
Predicate returning C<true> or C<false> depending on whether this
error is a significant error.
This is equivalent to obtaining the severity code from an XMLError
object (via XMLError::getSeverity()) and then comparing it to the
value @link XMLErrorSeverity_t#LIBSBML_SEV_ERROR LIBSBML_SEV_ERROR@endlink from the
@if clike enumeration #XMLErrorSeverity_t. @else set of predefined
severity codes.@endif@~
@return C<true> if this error is an error, C<false> otherwise.
@see isInfo()
@see isWarning()
@see isFatal()
=item XMLError::isFatal
Predicate returning C<true> or C<false> depending on whether this
error is a fatal run-time error.
This is equivalent to obtaining the severity code from an XMLError
object (via XMLError::getSeverity()) and then comparing it to the
value @link XMLErrorSeverity_t#LIBSBML_SEV_FATAL LIBSBML_SEV_FATAL@endlink from the
@if clike enumeration #XMLErrorSeverity_t. @else set of predefined severity codes.@endif@~
@return C<true> if this error is a fatal error, C<false> otherwise.
@see isInfo()
@see isWarning()
@see isError()
=item XMLError::isInternal
Predicate returning C<true> or C<false> depending on whether this
error resulted from an internal program error.
This is equivalent to obtaining the category identifier from an
XMLError object (via XMLError::getCategory()) and then comparing it to
the value @link XMLErrorCategory_t#LIBSBML_CAT_INTERNAL LIBSBML_CAT_INTERNAL@endlink from the
@if clike enumeration #XMLErrorCategory_t. @else set of predefined category codes.@endif@~
@return C<true> or C<false>
@see isSystem()
@see isXML()
=item XMLError::isSystem
Predicate returning C<true> or C<false> depending on whether this
error was generated by the operating system.
This is equivalent to obtaining the category identifier from an
XMLError object (via XMLError::getCategory()) and then comparing it to
the value @link XMLErrorCategory_t#LIBSBML_CAT_SYSTEM LIBSBML_CAT_SYSTEM@endlink from the
@if clike enumeration #XMLErrorCategory_t. @else set of predefined category codes.@endif@~
@return C<true> or C<false>
@see isInternal()
@see isXML()
=item XMLError::isXML
Predicate returning C<true> or C<false> depending on whether this
error resulted from a problem in the XML input (e.g., an XML syntax
error).
This is equivalent to obtaining the category identifier from an
XMLError object (via XMLError::getCategory()) and then comparing it to
the value @link XMLErrorCategory_t#LIBSBML_CAT_XML LIBSBML_CAT_XML@endlink from the
@if clike enumeration #XMLErrorCategory_t. @else set of predefined category codes.@endif@~
@return C<true> or C<false>
@see isInternal()
@see isSystem()
=item XMLError::isValid
Predicate returning C<true> or C<false> depending on whether this
error resulted from a problem or whether it was logged as an unknown
error.
This is equivalent to obtaining the error identifier from an
XMLError object (via XMLError::getErrorId()) and then comparing it to
the value XMLUnknownError or UnknownError from the
@if clike enumeration #XMLErrorCode_t. @else set of predefined error codes.@endif@~
@return C<true> or C<false>
=item XMLError::setLine
Sets the line number where this error occurred.
@param line an unsigned int, the line number to set.
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@see setColumn(unsigned int column)
=item XMLError::setColumn
Sets the column number where this error occurred.
@param column an unsigned int, the column number to set.
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@see setLine(unsigned int line)
=item XMLError::getStandardMessage
Returns a copy of the message string associated with the given
predefined XMLError code.
@param code the error code whose message is sought; it must be a
predefined value from @if clike <a class="el" href="#error-codes">
XMLErrorCode_t</a>. @else <a class="el" href="#error-codes">the set
of predefined error identifiers</a>.@endif@~
=item XMLError::getPackage
Returns the SBML Level 3 package extension (if any) that logged
this error.
Each error logged by an libSBML extension for SBML Level 3 packages
includes a record of the package that logged it. The field is a simple
text string. If the string is empty or has the value C<"core">, then
the error came from libSBML core; otherwise, the string will be the
short-form name of the package (e.g., C<"comp"> for the Hierarchical
Model Composition package).
@return a string representing the name of the package that logged this
error. If the error did not come from a package extension, the value
will be the empty string or C<"core">.
=item XMLError::getErrorIdOffset
Returns libSBML's internal numerical offset for the error code
associated with this error.
In the SBML Level 3 package specifications, package validation
rules are identified by 5-digit numbers prefixed with the nickname of
the package itself—e.g., “comp-10101”,
“fbc-20301”, etc. Historically, libSBML reported error
codes as pure integers, and some application software systems make
decisions based on the numerical values of the error codes. To permit
these applications to continue to function in this fashion, libSBML
internally continues to maintain error identifiers as pure integers. To
handle the possibility that errors may come from package extensions,
libSBML uses numerical offsets added to the internal error codes. These
offsets add two leading digits to the regular 5-digit error codes; for
example, “comp” error codes are stored as 1010101, 1020102,
etc. The offset in this case is 1000000. Another package will have the
offset 2000000, yet another will have 3000000, etc.
This method returns the integer offset in this error's error code.
Calling applications can get the 5-digit package-specific number for a
given error code by subtracting the offset from the value reported by
getErrorId():
@verbatim
getErrorId() - getErrorIdOffset()
@endverbatim
When libSBML produces error messages, it combines the text string
returned by getPackage() with the subtracted value of the error code,
to produce a text string of the form “comp-10101”.
@see getErrorId()
@see getPackage()
=back
=head2 XMLErrorLog
@sbmlpackage{core}
@htmlinclude pkg-marker-core.html Log of errors and other events encountered while
processing an XML file or data stream.
@htmlinclude not-sbml-warning.html
The error log is a list. The XML layer of libSBML maintains an error
log associated with a given XML document or data stream. When an
operation results in an error, or when there is something wrong with the
XML content, the problem is reported as an XMLError object stored in the
XMLErrorLog list. Potential problems range from low-level issues (such
as the inability to open a file) to XML syntax errors (such as
mismatched tags or other problems).
A typical approach for using this error log is to first use
@if java XMLErrorLog::getNumErrors()@else getNumErrors()@endif@~
to inquire how many XMLError object instances it contains, and then to
iterate over the list of objects one at a time using
getError(unsigned int n) const. Indexing in the list begins at 0.
In normal circumstances, programs using libSBML will actually obtain an
SBMLErrorLog rather than an XMLErrorLog. The former is subclassed from
XMLErrorLog and simply wraps commands for working with SBMLError objects
rather than the low-level XMLError objects. Classes such as
SBMLDocument use the higher-level SBMLErrorLog.
=over
=item XMLErrorLog::getNumErrors
Returns the number of errors that have been logged.
To retrieve individual errors from the log, callers may use
@if clike getError() @else XMLErrorLog::getError(unsigned int n) @endif.
@return the number of errors that have been logged.
=item XMLErrorLog::getError
Returns the <i>n</i>th XMLError object in this log.
Index C<n> is counted from 0. Callers should first inquire about the
number of items in the log by using the method
@if java XMLErrorLog::getNumErrors()@else getNumErrors()@endif.
Attempts to use an error index number that exceeds the actual number
of errors in the log will result in a C<NULL> being returned.
@param n the index number of the error to retrieve (with 0 being the
first error).
@return the <i>n</i>th XMLError in this log, or C<NULL> if C<n> is
greater than or equal to
@if java XMLErrorLog::getNumErrors()@else getNumErrors()@endif.
@see getNumErrors()
=item XMLErrorLog::clearLog
Deletes all errors from this log.
=item XMLErrorLog::XMLErrorLog
@internal
Creates a new empty XMLErrorLog.
=item XMLErrorLog::XMLErrorLog
@internal
Copy Constructor
=item XMLErrorLog::add
@internal
Logs the given XMLError.
@param error XMLError, the error to be logged.
=item XMLErrorLog::add
@internal
Logs (copies) the XMLErrors in the given XMLError list to this
XMLErrorLog.
@param errors list, a list of XMLError to be added to the log.
=item XMLErrorLog::add
@internal
Logs (copies) the XMLErrors in the given XMLError list to this
XMLErrorLog.
@param errors list, a list of XMLError to be added to the log.
=item XMLErrorLog::setParser
@internal
Sets the XMLParser associated with this XMLErrorLog.
The XMLParser will be used to obtain the current line and column
number for XMLError objects that lack line and column numbers when
they are logged. This method is used by libSBML's internal XML
parsing code and probably has no useful reason to be called from
application programs.
@param p XMLParser, the parser to use
@return integer value indicating success/failure of the
function. The possible values returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item XMLErrorLog::toString
Writes all errors contained in this log to a string and returns it.
This method uses printErrors() to format the diagnostic messages.
Please consult that method for information about the organization
of the messages in the string returned by this method.
@return a string containing all logged errors and warnings.
@see printErrors()
=item XMLErrorLog::printErrors
Prints all the errors or warnings stored in this error log.
This method prints the text to the stream given by the optional
parameter C<stream>. If no stream is given, the method prints the
output to the standard error stream.
The format of the output is:
@verbatim
N error(s):
line NNN: (id) message
@endverbatim
If no errors have occurred, i.e.,
C<getNumErrors() == 0>, then no output will be produced.
@param stream the ostream or ostringstream object indicating where
the output should be printed.
@if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
=item XMLErrorLog::isSeverityOverridden
Returns a boolean indicating whether or not the severity has been
overridden.
@return C<true> if an error severity override has been set, C<false>
otherwise.
@see setSeverityOverride(@if java int severity@endif)
=item XMLErrorLog::unsetSeverityOverride
Usets an existing override.
@see setSeverityOverride(@if java int severity@endif)
=item XMLErrorLog::getSeverityOverride
Returns the current override.
@return a severity override code. The possible values are @if clike drawn
from the enumeration #XMLErrorSeverityOverride_t@endif:
@li @link XMLErrorSeverityOverride_t#LIBSBML_OVERRIDE_DISABLED LIBSBML_OVERRIDE_DISABLED@endlink
@li @link XMLErrorSeverityOverride_t#LIBSBML_OVERRIDE_DONT_LOG LIBSBML_OVERRIDE_DONT_LOG@endlink
@li @link XMLErrorSeverityOverride_t#LIBSBML_OVERRIDE_WARNING LIBSBML_OVERRIDE_WARNING@endlink
@see setSeverityOverride(@if java int severity@endif)
=item XMLErrorLog::setSeverityOverride
Set the severity override.
@param severity an override code indicating what to do. If the value is
@link XMLErrorSeverityOverride_t#LIBSBML_OVERRIDE_DISABLED LIBSBML_OVERRIDE_DISABLED@endlink
(the default setting) all errors logged will be given the severity
specified in their usual definition. If the value is
@link XMLErrorSeverityOverride_t#LIBSBML_OVERRIDE_WARNING LIBSBML_OVERRIDE_WARNING@endlink,
then all errors will be logged as warnings. If the value is
@link XMLErrorSeverityOverride_t#LIBSBML_OVERRIDE_DONT_LOG LIBSBML_OVERRIDE_DONT_LOG@endlink,
no error will be logged, regardless of their severity.
@see getSeverityOverride()
=item XMLErrorLog::changeErrorSeverity
Changes the severity override for errors in the log that have a given
severity.
This searches through the list of errors in the log, comparing each
one's severity to the value of C<originalSeverity>. For each error
encountered with that severity logged by the named C<package>, the
severity of the error is reset to C<targetSeverity>.
@param originalSeverity the severity code to match
@param targetSeverity the severity code to use as the new severity
@param package a string, the name of an SBML Level 3 package
extension to use to narrow the search for errors. A value of C<"all">
signifies to match against errors logged from any package; a value of a
package nickname such as C<"comp"> signifies to limit consideration to
errors from just that package.
@if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
@see getSeverityOverride()
=back
=head2 SBMLErrorLog
@sbmlpackage{core}
@htmlinclude pkg-marker-core.html Log of errors and other events encountered during SBML
processing.
@htmlinclude not-sbml-warning.html
The error log is a list. Each SBMLDocument maintains its own
SBMLErrorLog. When a libSBML operation on SBML content results in an
error, or when there is something worth noting about the SBML content,
the issue is reported as an SBMLError object stored in the SBMLErrorLog
list.
SBMLErrorLog is derived from XMLErrorLog, an object class that serves
exactly the same purpose but for the XML parsing layer. XMLErrorLog
provides crucial methods such as
@if java XMLErrorLog::getNumErrors()@else getNumErrors()@endif@~
for determining how many SBMLError or XMLError objects are in the log.
SBMLErrorLog inherits these methods.
The general approach to working with SBMLErrorLog in user programs
involves first obtaining a pointer to a log from a libSBML object such
as SBMLDocument. Callers should then use
@if java XMLErrorLog::getNumErrors()@else getNumErrors() @endif@~ to inquire how
many objects there are in the list. (The answer may be 0.) If there is
at least one SBMLError object in the SBMLErrorLog instance, callers can
then iterate over the list using
SBMLErrorLog::getError(@if java long n@endif)@if clike const@endif,
using methods provided by the SBMLError class to find out the error code
and associated information such as the error severity, the message, and
the line number in the input.
If you wish to simply print the error strings for a human to read, an
easier and more direct way might be to use SBMLDocument::printErrors().
@see SBMLError
@see XMLErrorLog
@see XMLError
=over
=item SBMLErrorLog::getError
Returns the <i>n</i>th SBMLError object in this log.
Index C<n> is counted from 0. Callers should first inquire about the
number of items in the log by using the
@if java XMLErrorLog::getNumErrors()@else getNumErrors()@endif@~ method.
Attempts to use an error index number that exceeds the actual number
of errors in the log will result in a C<NULL> being returned.
@param n the index number of the error to retrieve (with 0 being the
first error).
@return the <i>n</i>th SBMLError in this log, or C<NULL> if C<n> is
greater than or equal to
@if java XMLErrorLog::getNumErrors()@else getNumErrors()@endif.
@see getNumErrors()
=item SBMLErrorLog::getNumFailsWithSeverity
Returns the number of errors that have been logged with the given
severity code.
C<opydetails> doc_errorlog_what_are_severities
@if clike @param severity a value from
#SBMLErrorSeverity_t @endif@if java @param severity a
value from the set of C<LIBSBML_SEV_> constants defined by
the interface class <code><a
href="libsbmlConstants.html">libsbmlConstants</a></code> @endif@if python @param severity a
value from the set of C<LIBSBML_SEV_> constants defined by
the interface class @link libsbml libsbml@endlink. @endif@~
@return a count of the number of errors with the given severity code.
@see getNumErrors()
=item SBMLErrorLog::getNumFailsWithSeverity
Returns the number of errors that have been logged with the given
severity code.
C<opydetails> doc_errorlog_what_are_severities
@if clike @param severity a value from
#SBMLErrorSeverity_t @endif@if java @param severity a
value from the set of C<LIBSBML_SEV_> constants defined by
the interface class <code><a
href="libsbmlConstants.html">libsbmlConstants</a></code> @endif@if python @param severity a
value from the set of C<LIBSBML_SEV_> constants defined by
the interface class @link libsbml libsbml@endlink. @endif@~
@return a count of the number of errors with the given severity code.
@see getNumErrors()
=item SBMLErrorLog::SBMLErrorLog
@internal
Creates a new, empty SBMLErrorLog.
=item SBMLErrorLog::SBMLErrorLog
@internal
Copy Constructor
=item SBMLErrorLog::logError
@internal
Convenience function that combines creating an SBMLError object and
adding it to the log.
@param errorId an unsigned int, the identification number of the error.
@param level an unsigned int, the SBML Level
@param version an unsigned int, the SBML Level's Version
@param details a string containing additional details about the error.
If the error code in C<errorId> is one that is recognized by SBMLError,
the given message is I<appended> to a predefined message associated
with the given code. If the error code is not recognized, the message
is stored as-is as the text of the error.
@param line an unsigned int, the line number at which the error occured.
@param column an unsigned int, the column number at which the error occured.
@param severity an integer indicating severity of the error.
@param category an integer indicating the category to which the error
belongs.
@if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
=item SBMLErrorLog::logPackageError
@internal
=item SBMLErrorLog::add
@internal
Adds the given SBMLError to the log.
@param error SBMLError, the error to be logged.
=item SBMLErrorLog::add
@internal
Adds (copies) the SBMLErrors in the given SBMLError list to this
SBMLErrorLog.
@param errors list, a list of SBMLError to be added to the log.
=item SBMLErrorLog::add
@internal
Adds (copies) the SBMLErrors in the given SBMLError vector to this
SBMLErrorLog.
@param errors vector, a vector of SBMLError to be added to the log.
=item SBMLErrorLog::remove
Removes an error having errorId from the SBMLError list.
Only the first item will be removed if there are multiple errors
with the given errorId.
@param errorId the error identifier of the error to be removed.
=item SBMLErrorLog::contains
Returns true if SBMLErrorLog contains an errorId
@param errorId the error identifier of the error to be found.
=back
=head2 SBMLError
@sbmlpackage{core}
@htmlinclude pkg-marker-core.html Representation of errors, warnings and other diagnostics
@htmlinclude not-sbml-warning.html
When a libSBML operation on SBML content results in an error, or when
there is something wrong with the SBML content, the problems are
reported as SBMLError objects. These are generally stored in an
SBMLErrorLog object; this log object, in turn, is kept in the
SBMLDocument object containing the SBML content. Applications can
obtain the list of logged errors using SBMLDocument::getErrorLog() and
then use the methods provided by SBMLErrorLog to access individual
SBMLError objects. (Note that despite the word "error" in the name,
SBMLError objects are used to represent not only "true" errors, but also
warnings and some informational diagnostics. The name is a historical
hold-over from early versions of libSBML, in which the object really was
only used to report errors.)
@if clike
Each SBMLError object instance has an identification number that
identifies the nature of the problem. This "error id" number will be up
to five digits long, and it will be listed in one of two enumerations:
<a class="el" href="#SBMLErrorCode_t"> SBMLErrorCode_t</a> (described <a
class="el" href="#SBMLErrorCode_t"> below</a>) or @link
XMLError::XMLErrorCode_t XMLErrorCode_t @endlink (described in the
documentation for the class XMLError). The former enumeration contains
all the SBML validation rule numbers listed in the appendices of the
SBML specification documents, as well as some additional
libSBML-specific error codes.
@endif@if java
Each SBMLError object instance has an identification number that
identifies the nature of the problem. This "error id" number will be up
to five digits long, and it will come from one of two sets of static
integer constants defined in the interface class <code><a
href="libsbmlConstants.html"> libsbmlConstants</a></code>: either the
SBML error identifiers <a class="el" href="#SBMLErrorCode_t"> (described
below)</a> or the XML error identifiers (described in the documentation
for the class <code><a href="XMLError.html"> XMLError</a></code>). The
former set of constants includes all the SBML validation rule numbers
listed in the appendices of the SBML specification documents, as well as
some additional libSBML-specific error codes.
@endif@if python
Each SBMLError object instance has an identification number that
identifies the nature of the problem. This "error id" number will be up
to five digits long, and it will come from one
of two sets of static integer constants defined in
the interface class @link libsbml libsbml@endlink: either the SBML
error identifiers <a
class="el" href="#SBMLErrorCode_t"> (described below)</a> or the XML
error identifiers (described in the documentation for the class XMLError).
The former set of constants
includes all the SBML validation rule numbers listed in the appendices
of the SBML specification documents, as well as some additional
libSBML-specific error codes.
@endif@~
Error codes are useful mainly for software. For human readers,
SBMLError also includes text messages that describe the nature of a
given problem. The messages can be accessed using
SBMLError::getShortMessage() and SBMLError::getMessage(). The former
provides a brief one-line description of the issue, while
SBMLError::getMessage() provides a more detailed text, including (if
appropriate) references to sections of the SBML specifications where
relevant topics are discussed. These text strings are suitable for
displaying to human users.
@if clike
An SBMLError object also contains a category code; its value may be
retrieved using the method SBMLError::getCategory(). Category values
are drawn from the enumeration <a class="el"
href="#SBMLErrorCategory_t">SBMLErrorCategory_t</a> described below.
Categories are used to partition errors into distinct conceptual groups.
This is principally used by the libSBML validation system to group
classes of validation checks. For example,
@link SBMLErrorCategory_t#LIBSBML_CAT_IDENTIFIER_CONSISTENCY LIBSBML_CAT_IDENTIFIER_CONSISTENCY@endlink
is the category for tests that check identifier consistency;
@link SBMLErrorCategory_t#LIBSBML_CAT_MATHML_CONSISTENCY LIBSBML_CAT_MATHML_CONSISTENCY@endlink
is the category for MathML consistency checking; and
so on.
@endif@if java
An SBMLError object also contains a category code; its value may be
retrieved using the method SBMLError::getCategory(). Category values
are drawn from a set of static integer constants
defined in <code><a href="libsbmlConstants.html">libsbmlConstants</a></code>,
and having names beginning with the characters
C<LIBSBML_CAT_>. The list of possible codes is described in a
separate section below. Categories are used to partition errors into
distinct conceptual groups. This is principally used by the libSBML
validation system to group classes of validation checks. For example,
@link SBMLErrorCategory_t#LIBSBML_CAT_IDENTIFIER_CONSISTENCY LIBSBML_CAT_IDENTIFIER_CONSISTENCY@endlink
is the category for tests that check identifier consistency;
@link SBMLErrorCategory_t#LIBSBML_CAT_MATHML_CONSISTENCY LIBSBML_CAT_MATHML_CONSISTENCY@endlink
is the category for MathML consistency checking; and
so on.
@endif@if python
An SBMLError object also contains a category code; its value may be
retrieved using the method SBMLError::getCategory(). Category values
are drawn from a set of static integer constants
defined in @link libsbml libsbml@endlink and having names beginning with the characters
C<LIBSBML_CAT_>. The list of possible codes is described in a
separate section below. Categories are used to partition errors into
distinct conceptual groups. This is principally used by the libSBML
validation system to group classes of validation checks. For example,
@link SBMLErrorCategory_t#LIBSBML_CAT_IDENTIFIER_CONSISTENCY LIBSBML_CAT_IDENTIFIER_CONSISTENCY@endlink
is the category for tests that check identifier consistency;
@link SBMLErrorCategory_t#LIBSBML_CAT_MATHML_CONSISTENCY LIBSBML_CAT_MATHML_CONSISTENCY@endlink
is the category for MathML consistency checking; and
so on.
@endif@~
In addition, SBMLError also has a severity code. Its value may be
retrieved using the method SBMLError::getSeverity(). The possible
severity values are the same as those reported by @if clike XMLError.@endif@if python XMLError.@endif@if java <code><a href="XMLError.html">XMLError</a></code>.@endif@~
Severity levels currently range from informational
(@link XMLErrorSeverity_t#LIBSBML_SEV_INFO LIBSBML_SEV_INFO@endlink)
to fatal errors
(@link XMLErrorSeverity_t#LIBSBML_SEV_FATAL LIBSBML_SEV_FATAL@endlink).
They can be
used by an application to evaluate how serious a given problem
is.
Finally, SBMLError records the line and column near where the problem
occurred in the SBML content. The values may be retrieved using the
methods SBMLError::getLine() and SBMLError::getColumn(). We say "near",
because a lot of factors affect how accurate the line/column information
ultimately is. For example, different XML parsers have different
conventions for which line and column number they report for a
particular problem (which makes a difference when a problem involves an
opening XML tag on one line and a closing tag on another line). In some
situations, some parsers report invalid line and/or column numbers
altogether. If this occurs, libSBML sets the line and/or column number
in the SBMLError object to the the value of the maximum unsigned long
integer representable on the platform where libSBML is running. (This
is equal to the constant named C<ULONG_MAX> in C and C++.)
The probability that a true line or column number in an SBML model would
equal this value is vanishingly small; thus, if an application
encounters these values in an XMLError object, it can assume no valid
line/column number could be provided by libSBML in that situation.
@if clike
<h3><a class="anchor" name="SBMLErrorCode_t">SBMLErrorCode_t</a></h3>
SBMLErrorCode_t is an enumeration of all SBML-level error, warning and
informational diagnostic codes. Every SBMLError object has an error
code value that can be either a value from this enumeration, or a value
from the @link XMLError::XMLErrorCode_t XMLErrorCode_t @endlink
enumeration (see the documentation for XMLError). The latter values
apply when the error or warning signifies a basic XML issue rather than
an SBML issue per se. The values of SBMLErrorCode_t are distinguished
from those of @link XMLError::XMLErrorCode_t XMLErrorCode_t @endlink by
being numbered 10000 and higher, while the XML layer's codes are 9999 and
lower. The method SBMLError::getErrorId() returns the error code of a
given SBMLError object instance.
The following is a table of the symbolic names of SBMLErrorCode_t values
and the meaning of each code. In this table, the right-hand columns
titled "L1V1", "L1V2", etc. refer to Levels and Versions of the SBML
specifications, and the entries in each column refer to whether the
severity of the condition in that particular Level+Version of SBML.
The codes stand for the following:
@endif@if java <h3><a class="anchor"
name="SBMLErrorCode_t">Error codes associated with SBMLError objects</a></h3>
The error and warning codes returned by libSBML are listed in the table
below. The method SBMLError::getErrorId() returns the error code of a
given SBMLError object instance. In the libSBML Java language
interface, these error identifiers are currently
implemented as static integer constants defined in the interface class
<code><a href="libsbmlConstants.html">libsbmlConstants</a></code>. This
is admittedly not an ideal approach from the standpoint of modern Java
programming, but it was necessary to work around the lack of
enumerations in Java prior to JDK 1.5. Future versions of libSBML may
use a proper Java enumeration type to define the error identifiers.
In this table, the right-hand columns titled "L1V1", "L1V2", etc. refer
to Levels and Versions of the SBML specifications, and the entries in
each column refer to whether the severity of the condition in that
particular Level+Version of SBML. The codes stand for the following:
@endif@if python <h3><a class="anchor"
name="SBMLErrorCode_t">Error codes associated with SBMLError objects</a></h3>
The error and warning codes returned by libSBML are listed in the table
below. The method SBMLError::getErrorId() returns the error code of a
given SBMLError object instance. In the libSBML Python language
interface, these error identifiers are currently
implemented as static integer constants defined in the interface class
@link libsbml libsbml@endlink.
In this table, the right-hand columns titled "L1V1", "L1V2", etc. refer
to Levels and Versions of the SBML specifications, and the entries in
each column refer to whether the severity of the condition in that
particular Level+Version of SBML. The codes stand for the following:
@endif@~
<table cellspacing="1" cellpadding="2" border="0" class="normal-font">
<tr><td class="s-na">N</td><td>= Not applicable</td></tr>
<tr><td class="s-info">I</td><td>= Informational</td></tr>
<tr><td class="s-warning">W</td><td>= Warning</td></tr>
<tr><td class="s-error">E</td><td>= Error</td></tr>
<tr><td class="s-fatal">F</td><td>= Fatal</td></tr>
</table>
The text shown in the "Meaning" is the text returned by the
SBMLError::getShortMessage() method on a given SBMLError object. A
longer and (hopefully) clearer explanation of the issue is returned by
SBMLError::getMessage().
The error codes come from different lists depending on whether they're
from libSBML core or from an SBML Level 3 package extension.
@if clike The errors below come from #XMLErrorCode_t and #SBMLErrorCode_t
(for core), and #CompSBMLErrorCode_t, #FbcSBMLErrorCode_t,
#LayoutSBMLErrorCode_t, and #QualSBMLErrorCode_t (for packages).@endif
@if notclike However, in the language interfaces other than C++, all
libSBML error codes are ultimately represented as integer constants rather
than separate enumerations lists, and they are all stored in a single
interface class. Codes from different libSBML extensions have names that
begin with the package's nickname, such as C<Qual> for
the Qualitative Models package, C<Layout> for the Layout
package, and so on. If the name of a code does not begin with one of
the package nicknames (C<%Layout>, C<Fbc>,
C<Comp>, C<Qual>, etc.), then it is a code
from libSBML core.@endif
C<opydetails> doc_sbml_error_table
@if clike <h3><a class="anchor" name="SBMLErrorCategory_t">SBMLErrorCategory_t</a></h3>
SBMLErrorCategory_t is an enumeration of category codes for SBMLError
diagnostics. The category can be retrieved from an SBMLError object
using the method SBMLError::getCategory(). These enumeration values are
distinct from (and in addition to) the @link
XMLError::XMLErrorCategory_t XMLErrorCategory_t @endlink codes used by
the parent XMLError object. User programs receiving an SBMLError object
can use this distinction to check whether the error represents a
low-level XML problem or an SBML problem.
The following table lists each possible value and a brief description of
its meaning.
@endif@if python <h3><a class="anchor" name="SBMLErrorCategory_t">Category codes associated with SBMLError objects</a></h3>
As discussed above, each SBMLError object contains a value for a
category identifier, describing the type of issue that the SBMLError
object represents. The category can be retrieved from an SBMLError
object using the method SBMLError::getCategory(). The following table
lists each possible value and a brief description of its meaning.
As is the case with the error codes, in the libSBML Python language
interface, the category identifiers are currently implemented as static
integer constants defined in the interface class
@link libsbml libsbml@endlink.
The following table lists each possible value and a brief description of
its meaning.
@endif@if java <h3><a class="anchor"
name="SBMLErrorCategory_t">Category codes associated with SBMLError objects</a></h3>
As discussed above, each SBMLError object contains a value for a
category identifier, describing the type of issue that the SBMLError
object represents. The category can be retrieved from an SBMLError
object using the method SBMLError::getCategory(). The following table
lists each possible value and a brief description of its meaning.
As is the case with the error codes, in the libSBML Java language
interface, the category identifiers are currently implemented as static
integer constants defined in the interface class
{@link libsbmlConstants}.
The following table lists each possible value and a brief description of
its meaning.
@endif@if csharp <h3><a class="anchor"
name="SBMLErrorCategory_t">Category codes associated with SBMLError objects</a></h3>
As discussed above, each SBMLError object contains a value for a
category identifier, describing the type of issue that the SBMLError
object represents. The category can be retrieved from an SBMLError
object using the method SBMLError::getCategory(). The following table
lists each possible value and a brief description of its meaning.
As is the case with the error codes, in the libSBML C# language
interface, the category identifiers are currently implemented as static
integer constants defined in the interface class
{@link libsbmlcs.libsbml}.
The following table lists each possible value and a brief description of
its meaning.
@endif@~
<center>
<table width="90%" cellspacing="1" cellpadding="4" border="0" class="text-table normal-font alt-row-colors">
<tr style="background: lightgray" class="normal-font">
<th>Enumerator</td>
<th>Meaning</td>
</tr>
<tr><td>@link XMLErrorCategory_t#LIBSBML_CAT_SBML LIBSBML_CAT_SBML@endlink</td><td>General error not falling into
another category below.</td></tr>
<tr><td>@link XMLErrorCategory_t#LIBSBML_CAT_SBML_L1_COMPAT LIBSBML_CAT_SBML_L1_COMPAT@endlink</td><td>Category of errors
that can only occur during attempted translation from one Level/Version
of SBML to another. This particular category applies to errors
encountered while trying to convert a model from SBML Level 2 to SBML
Level 1.</td></tr>
<tr><td>@link XMLErrorCategory_t#LIBSBML_CAT_SBML_L2V1_COMPAT LIBSBML_CAT_SBML_L2V1_COMPAT@endlink</td><td>Category of errors
that can only occur during attempted translation from one Level/Version
of SBML to another. This particular category applies to errors
encountered while trying to convert a model to SBML Level 2
Version 1.</td></tr>
<tr><td>@link XMLErrorCategory_t#LIBSBML_CAT_SBML_L2V2_COMPAT LIBSBML_CAT_SBML_L2V2_COMPAT@endlink</td><td>Category of errors
that can only occur during attempted translation from one Level/Version
of SBML to another. This particular category applies to errors
encountered while trying to convert a model to SBML Level 2
Version 2.</td></tr>
<tr><td>@link XMLErrorCategory_t#LIBSBML_CAT_GENERAL_CONSISTENCY LIBSBML_CAT_GENERAL_CONSISTENCY@endlink</td><td>Category of
errors that can occur while validating general SBML constructs. With
respect to the SBML specification, these concern failures in applying
the validation rules numbered 2xxxx in the Level 2 Versions 2–4
and Level 3 Version 1 specifications.</td></tr>
<tr><td>@link XMLErrorCategory_t#LIBSBML_CAT_IDENTIFIER_CONSISTENCY LIBSBML_CAT_IDENTIFIER_CONSISTENCY@endlink</td><td>Category of
errors that can occur while validating symbol identifiers in a model.
With respect to the SBML specification, these concern failures in
applying the validation rules numbered 103xx in the Level 2 Versions 2–4
and Level 3 Version 1 specifications.</td></tr>
<tr><td>@link XMLErrorCategory_t#LIBSBML_CAT_UNITS_CONSISTENCY LIBSBML_CAT_UNITS_CONSISTENCY@endlink</td><td>Category of
errors that can occur while validating the units of measurement on
quantities in a model. With respect to the SBML specification, these
concern failures in applying the validation rules numbered 105xx in the
Level 2 Versions 2–4
and Level 3 Version 1 specifications.</td></tr>
<tr><td>@link XMLErrorCategory_t#LIBSBML_CAT_MATHML_CONSISTENCY LIBSBML_CAT_MATHML_CONSISTENCY@endlink</td><td>Category of
errors that can occur while validating MathML formulas in a model. With
respect to the SBML specification, these concern failures in applying
the validation rules numbered 102xx in the Level 2 Versions 2–4
and Level 3 Version 1 specifications.</td></tr>
<tr><td>@link XMLErrorCategory_t#LIBSBML_CAT_SBO_CONSISTENCY LIBSBML_CAT_SBO_CONSISTENCY@endlink</td><td>Category of errors
that can occur while validating SBO identifiers in a model. With
respect to the SBML specification, these concern failures in applying
the validation rules numbered 107xx in the Level 2 Versions 2–4
and Level 3 Version 1 specifications.</td></tr>
<tr><td>@link XMLErrorCategory_t#LIBSBML_CAT_OVERDETERMINED_MODEL LIBSBML_CAT_OVERDETERMINED_MODEL@endlink</td><td>Error in the
system of equations in the model: the system is overdetermined,
therefore violating a tenet of proper SBML. With respect to the SBML
specification, this is validation rule #10601 in the SBML Level 2 Versions 2–4
and Level 3 Version 1 specifications.</td></tr>
<tr><td>@link XMLErrorCategory_t#LIBSBML_CAT_SBML_L2V3_COMPAT LIBSBML_CAT_SBML_L2V3_COMPAT@endlink</td><td>Category of errors
that can only occur during attempted translation from one Level/Version
of SBML to another. This particular category applies to errors
encountered while trying to convert a model to SBML Level 2
Version 3.</td></tr>
<tr><td>@link XMLErrorCategory_t#LIBSBML_CAT_MODELING_PRACTICE LIBSBML_CAT_MODELING_PRACTICE@endlink</td><td>Category of
warnings about recommended good practices involving SBML and
computational modeling. (These are tests performed by libSBML and do
not have equivalent SBML validation rules.)</td></tr>
<tr><td>@link XMLErrorCategory_t#LIBSBML_CAT_INTERNAL_CONSISTENCY LIBSBML_CAT_INTERNAL_CONSISTENCY@endlink</td><td>Category of
errors that can occur while validating libSBML's internal representation
of SBML constructs. (These are tests performed by libSBML and do
not have equivalent SBML validation rules.)</td></tr>
<tr><td>@link XMLErrorCategory_t#LIBSBML_CAT_SBML_L2V4_COMPAT LIBSBML_CAT_SBML_L2V4_COMPAT@endlink</td><td>Category of errors
that can only occur during attempted translation from one Level/Version
of SBML to another. This particular category applies to errors
encountered while trying to convert a model to SBML Level 2
Version 4.</td></tr>
<tr><td>@link XMLErrorCategory_t#LIBSBML_CAT_SBML_L3V1_COMPAT LIBSBML_CAT_SBML_L3V1_COMPAT@endlink</td><td>Category of errors
that can only occur during attempted translation from one Level/Version
of SBML to another. This particular category applies to errors
encountered while trying to convert a model to SBML Level 3
Version 1.</td></tr>
</table>
</center>
@if clike
<h3><a class="anchor" name="SBMLErrorSeverity_t">SBMLErrorSeverity_t</a></h3>
This is an enumeration of severity codes for SBMLError diagnostics.
User programs receiving an SBMLError object can use this distinction to
check whether the error represents a low-level XML problem or an SBML
problem.
In libSBML version @htmlinclude libsbml-version.html
there are no additional severity codes in SBMLErrorSeverity_t beyond
those defined in @link XMLError::XMLErrorSeverity_t XMLErrorSeverity_t@endlink.
<hr>
@endif@if java <h3><a class="anchor"
name="SBMLErrorSeverity_t">Severity codes associated with SBMLError
objects</h3>
In libSBML version @htmlinclude libsbml-version.html
there are no additional severity codes beyond those defined by XMLError.
They are implemented as static integer constants defined in the interface
class <code><a href="libsbmlConstants.html">libsbmlConstants</a></code>,
and have names beginning with C<LIBSBML_SEV_>.
@endif@if python <h3><a class="anchor"
name="SBMLErrorSeverity_t">Severity codes associated with SBMLError
objects</h3>
In libSBML version @htmlinclude libsbml-version.html
there are no additional severity codes beyond those defined by XMLError.
They are implemented as static integer constants defined in the
interface class @link libsbml libsbml@endlink, and have names beginning
with C<LIBSBML_SEV_>.
@endif@~
=over
=item SBMLError::SBMLError
Creates a new SBMLError to report that something occurred during SBML
processing.
When a libSBML operation on SBML content results in a warning, error
or other diagnostic, the issue is reported as an SBMLError object.
SBMLError objects have identification numbers to indicate the nature
of the exception. @if clike These numbers are drawn from
the enumeration <a class="el"
href="#SBMLErrorCode_t">
SBMLErrorCode_t</a>. @endif@if java These numbers are
defined as unsigned integer constants in the file
"libsbmlConstants.html". See the <a class="el"
href="#SBMLErrorCode_t">top of this documentation page</a> for a table
listing the possible values and their meanings. @endif@if python These
numbers are defined as unsigned integer constants in the interface
class @link libsbml libsbml@endlink. See the <a class="el"
href="#SBMLErrorCode_t">top of this documentation page</a> for a table
listing the possible values and their meanings. @endif@~ The argument
C<errorId> to this constructor I<can> be (but does not have to be) a
value from this @if clike enumeration. If it I<is> a value
from <a class="el" href="#SBMLErrorCode_t">SBMLErrorCode_t</a>, the
SBMLError class assumes the error is a low-level system or SBML layer
error and <em>prepends</em> a built-in, predefined error message to
any string passed in the argument C<details> to this constructor. In
addition, all <a class="el"
href="#SBMLErrorCode_t">SBMLErrorCode_t</a> errors have associated
values for the C<severity> and C<category> codes, and these fields are
filled-in as well from the enumerations <a class="el"
href="#SBMLErrorSeverity_t">SBMLErrorSeverity_t</a> and <a class="el"
href="#SBMLErrorCategory_t">SBMLErrorCategory_t</a>,
respectively. @else set of constants. If it @em
is one of the predefined error identifiers, the SBMLError class
assumes the error is a low-level system or SBML layer error and
<em>prepends</em> a built-in, predefined error message to any string
passed in the argument C<details> to this constructor. In addition,
all the predefined error identifiers have associated values for the
C<severity> and C<category> codes, and these fields are filled-in using
the libSBML defaults for each different error identifier. @endif@~
If the error identifier C<errorId> is a number greater than 99999, the
SBMLError class assumes the error was generated from another part of
the software and does not do additional filling in of values beyond
the default in the constructor itself. This allows SBMLError to serve
as a base class for other errors, such as for user-defined validation
rules (see Validator). Callers should fill in all the parameters with
suitable values if generating errors with codes greater than 99999 to
make maximum use of the SBMLError facilities.
@if clike As mentioned above, there are two other
enumerations, <a class="el"
href="#SBMLErrorSeverity_t">SBMLErrorSeverity_t</a> and <a class="el"
href="#SBMLErrorCategory_t">SBMLErrorCategory_t</a>, used for indicating
the severity and category of error for the predefined SBMLError codes.
The values passed in C<severity> and C<category> override the defaults
assigned based on the error code. If the value of C<errorId> is a
value from <a class="el" href="#SBMLErrorCode_t">SBMLErrorCode_t</a>,
callers do not need to fill in C<severity> and C<category>.
Conversely, if C<errorId> is not a value from <a class="el"
href="#SBMLErrorCode_t">SBMLErrorCode_t</a>, callers can use other
values (not just those from <a class="el"
href="#SBMLErrorSeverity_t">SBMLErrorSeverity_t</a> and <a class="el"
href="#SBMLErrorCategory_t">SBMLErrorCategory_t</a>, but their own
special values) for C<severity> and
C<category>. @else As mentioned above,
there are additional constants defined for <a class="el"
href="#SBMLErrorSeverity_t">standard severity</a> and <a class="el"
href="#SBMLErrorCategory_t">standard category</a> codes, and every predefined
error in libSBML has an associated value for severity and category taken
from these predefined sets. These constants have symbol names
prefixed with C<LIBSBML_SEV_> and C<LIBSBML_CAT_>,
respectively. If the value of C<errorId> is one of the standard error
codes, callers do not need to fill in C<severity> and C<category> in a
call to this constructor. Conversely, if C<errorId> is not an existing
SBML-level error code, callers can use other values for C<severity> and
C<category>. @endif@~
Please see the top of the documentation for SBMLError for a longer
discussion of the possible error codes, their meanings, and their
applicability to different combinations of Level+Version of SBML.
@param errorId an unsigned int, the identification number of the error.
@param level the SBML Level of the SBML model
@param version the SBML Version within the Level of the SBML model
@param details a string containing additional details about the error.
If the error code in C<errorId> is one that is recognized by SBMLError,
the given message is I<appended> to a predefined message associated
with the given code. If the error code is not recognized, the message
is stored as-is as the text of the error.
@param line an unsigned int, the line number at which the error occured.
@param column an unsigned int, the column number at which the error occured.
@param severity an integer indicating severity of the error.
@param category an integer indicating the category to which the error
belongs.
@param package the SBML Level package involved.
@param pkgVersion the version of the C<package>.
@if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
=item SBMLError::SBMLError
Copy constructor; creates a copy of this SBMLError.
=back
=head2 CVTerm
@sbmlpackage{core}
@htmlinclude pkg-marker-core.html Representation of MIRIAM-compliant controlled vocabulary
annotation.
@htmlinclude not-sbml-warning.html
The SBML Level 2 and Level 3 specifications define a simple
format for annotating models when (a) referring to controlled vocabulary
terms and database identifiers that define and describe biological and
biochemical entities, and (b) describing the creator of a model and the
model's modification history. This SBML format is a concrete syntax that
conforms to the guidelines of MIRIAM (<a target="_blank"
href="http://www.nature.com/nbt/journal/v23/n12/abs/nbt1156.html">"Minimum
Information Requested in the Annotation of biochemical Models"</a>,
<i>Nature Biotechnology</i>, vol. 23, no. 12, Dec. 2005). The format uses
a subset of W3C RDF (<a target="_blank"
href="http://www.w3.org/RDF/">Resource Description Format</a>). In order
to help application developers work with annotations in this format,
libSBML provides several helper classes that provide higher-level
interfaces to the data elements; these classes include CVTerm,
ModelCreator, ModelHistory, RDFAnnotationParser, and Date.
@section annotation-parts Components of an SBML annotation
The SBML annotation format consists of RDF-based content placed inside
an C<<annotation>> element attached to an SBML component
such as Species, Compartment, etc. The following template illustrates
the different parts of SBML annotations in XML form:
<pre class="fragment">
<<span style="background-color: #bbb">SBML_ELEMENT</span> <span style="background-color: #d0eed0">+++</span> metaid="<span style="border-bottom: 1px solid black">meta id</span>" <span style="background-color: #d0eed0">+++</span>>
<span style="background-color: #d0eed0">+++</span>
<annotation>
<span style="background-color: #d0eed0">+++</span>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:dc="http://purl.org/dc/elements/1.1/"
xmlns:dcterm="http://purl.org/dc/terms/"
xmlns:vcard="http://www.w3.org/2001/vcard-rdf/3.0#"
xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"
xmlns:bqmodel="http://biomodels.net/model-qualifiers/" >
<rdf:Description rdf:about="#<span style="border-bottom: 1px solid black">meta id</span>">
<span style="background-color: #e0e0e0; border-bottom: 2px dotted #888">HISTORY</span>
<<span style="background-color: #bbb">RELATION_ELEMENT</span>>
<rdf:Bag>
<rdf:li rdf:resource="<span style="background-color: #d0d0ee">URI</span>" />
<span style="background-color: #edd">...</span>
</rdf:Bag>
</<span style="background-color: #bbb">RELATION_ELEMENT</span>>
<span style="background-color: #edd">...</span>
</rdf:Description>
<span style="background-color: #d0eed0">+++</span>
</rdf:RDF>
<span style="background-color: #d0eed0">+++</span>
</annotation>
<span style="background-color: #d0eed0">+++</span>
</<span style="background-color: #bbb">SBML_ELEMENT</span>>
</pre>
In the template above, the placeholder
<span class="code" style="background-color: #bbb">SBML_ELEMENT</span> stands for
the XML tag name of an SBML model component (e.g., C<model>,
C<reaction>, etc.) and the placeholder
<span class="code" style="border-bottom: 1px solid black">meta id</span>
stands for the element's meta identifier, which is a field available
on all SBML components derived from the SBase base object class.
The <span style="border-bottom: 2px dotted #888">dotted</span>
portions are optional, the symbol
<span class="code" style="background-color: #d0eed0">+++</span> is a placeholder
for either no content or valid XML content that is not defined by
this annotation scheme, and the ellipses
<span class="code" style="background-color: #edd">...</span>
are placeholders for zero or more elements of the same form as the
immediately preceding element. The optional content
<span class="code" style="background-color: #e0e0e0; border-bottom: 2px dotted #888">HISTORY</span>
is a creation and modification history; in libSBML, this is stored
using ModelHistory objects.
The placeholder <span class="code" style="background-color:
#bbb">RELATION_ELEMENT</span> refers to a BioModels.net qualifier element
name. This is an element in either the XML namespace
C<"http://biomodels.net/model-qualifiers"> (for model
qualifiers) or C<"http://biomodels.net/biology-qualifiers"> (for
biological qualifier). Note that these namespace URIs are only labels,
and not actual Web locations, which means you cannot visit an address such
as C<"http://biomodels.net/model-qualifiers"> in your browser or
try to have your application access it. @if Refer instead to the enumerations
#ModelQualifierType_t and #BiolQualifierType_t for a list of the available
relationship elements that can be used for <span class="code"
style="background-color: #bbb">RELATION_ELEMENT</span>.@endif@~
The <span class="code" style="background-color: #d0d0ee">URI</span> is a
required data value that uniquely identifies a resource and data within
that resource to which the annotation refers. Again, being URIs, these do
not refer to physical Web locations; nevertheless, applications will often
want a means of finding the resource to which a given <span class="code"
style="background-color: #d0d0ee">URI</span> refers. Providing the
facilities for this task is the purpose of MIRIAM Resources, described in
detail online at <a target="_blank"
href="http://biomodels.net/miriam">http://biomodels.net/miriam</a>) and
also in the paper <a target="_blank"
href="http://www.biomedcentral.com/1752-0509/1/58">"MIRIAM Resources: tools to generate and
resolve robust cross-references in Systems Biology"</a>, <i>BMC Systems
Biology</i>, 58(1), 2007.
The relation-resource pairs above are the "controlled vocabulary" terms
that which CVTerm is designed to store and manipulate. The next section
describes these parts in more detail. For more information about
SBML annotations in general, please refer to Section 6 in the
SBML Level 2 (Versions 2–4) or Level 3 specification
documents.
@section cvterm-parts The parts of a CVTerm
Annotations that refer to controlled vocabularies are managed in libSBML
using CVTerm objects. A set of RDF-based annotations attached to a
given SBML C<<annotation>> element are read by
RDFAnnotationParser and converted into a list of these CVTerm objects.
Each CVTerm object instance stores the following components of an
annotation:
\n=over\n
<li>The I<qualifier>, which can be a BioModels.net "biological
qualifier", a BioModels.net "model qualifier", or an unknown qualifier
(as far as the CVTerm class is concerned). Qualifiers are used in
MIRIAM to indicate the nature of the relationship between the object
being annotated and the resource. In CVTerm, the qualifiers can be
manipulated using the methods CVTerm::getQualifierType(),
CVTerm::setQualifierType(@if java int type@endif), and related methods.
<li>The I<resource>, represented by a URI (which, we must remind
developers, is not the same as a URL). In the CVTerm class, the
resource component can be manipulated using the methods
CVTerm::addResource(@if java String resource@endif) and
CVTerm::removeResource(@if java String resource@endif).
\n=back\n
Note that a CVTerm contains a single qualifier, but possibly more than
one resource. This corresponds to the possibility of an annotation that
points to multiple resources, all of which are qualified by the same
BioModels.net qualifier. The CVTerm object class supports this by
supporting a list of resources.
Detailed explanations of the qualifiers defined by BioModels.net can be
found at <a target="_blank"
href="http://biomodels.net/qualifiers">http://biomodels.net/qualifiers</a>.
=over
=item CVTerm::CVTerm
Creates an empty CVTerm, optionally with the given
@if clike #QualifierType_t value@else qualifier@endif@~ C<type>.
C<opydetails> doc_what_are_cvterms
This method creates an empty CVTerm object. The possible qualifier
types usable as values of C<type> are @link
QualifierType_t#MODEL_QUALIFIER MODEL_QUALIFIER@endlink and @link
QualifierType_t#BIOLOGICAL_QUALIFIER BIOLOGICAL_QUALIFIER@endlink. If
an explicit value for C<type> is not given, this method defaults to
using @link QualifierType_t#UNKNOWN_QUALIFIER
UNKNOWN_QUALIFIER@endlink. The @if clike #QualifierType_t value@else qualifier type@endif@~
can be set later using the
CVTerm::setQualifierType(@if java int type@endif) method.
Different BioModels.net qualifier elements encode different types of
relationships. Please refer to the SBML specification or the <a
target="_blank" href="http://biomodels.net/qualifiers/">BioModels.net
qualifiers web page</a> for an explanation of the meaning of these
different qualifiers.
@param type a @if clike #QualifierType_t value@else qualifier type@endif@~
@if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
=item CVTerm::CVTerm
Creates a new CVTerm from the given XMLNode.
C<opydetails> doc_what_are_cvterms
This method creates a CVTerm object from the given XMLNode object @p
node. XMLNode is libSBML's representation of a node in an XML tree of
elements, and each such element can be placed in a namespace. This
constructor looks for the element to be in the XML namespaces
C<"http://biomodels.net/model-qualifiers"> (for
model qualifiers) and
C<"http://biomodels.net/biology-qualifiers"> (for
biological qualifier), and if they are, creates CVTerm objects for
the result.
@param node an XMLNode representing a CVTerm.
@note This method assumes that the given XMLNode object C<node> is of
the correct structural form.
=item CVTerm::CVTerm
Copy constructor; creates a copy of a CVTerm object.
@param orig the CVTerm instance to copy.
@throws @if python ValueError @else SBMLConstructorException @endif@~
Thrown if the argument C<orig> is C<NULL>.
=item CVTerm::clone
Creates and returns a deep copy of this CVTerm object.
@return a (deep) copy of this CVTerm.
=item CVTerm::getQualifierType
Returns the qualifier type of this CVTerm object.
C<opydetails> doc_cvterm_common_description
The placeholder <span class="code" style="background-color: #bbb">
RELATION_ELEMENT</span> refers to a BioModels.net qualifier
element name. This is an element in either the XML namespace
C<"http://biomodels.net/model-qualifiers"> (for model
qualifiers) or C<"http://biomodels.net/biology-qualifiers">
(for biological qualifier). The present method returns a code
identifying which one of these two relationship namespaces is being
used; any other qualifier in libSBML is considered unknown (as far as
the CVTerm class is concerned). Consequently, this method will return
one of the following values:
@li @link QualifierType_t#MODEL_QUALIFIER MODEL_QUALIFIER@endlink
@li @link QualifierType_t#BIOLOGICAL_QUALIFIER BIOLOGICAL_QUALIFIER@endlink
@li @link QualifierType_t#UNKNOWN_QUALIFIER UNKNOWN_QUALIFIER@endlink
The specific relationship of this CVTerm to the enclosing SBML object
can be determined using the CVTerm methods such as
getModelQualifierType() and getBiologicalQualifierType(). Callers
will typically want to use the present method to find out which one of
the I<other> two methods to call to find out the specific
relationship.
@return the @if clike #QualifierType_t value@else qualifier type@endif@~
of this object or @link QualifierType_t#UNKNOWN_QUALIFIER UNKNOWN_QUALIFIER@endlink
(the default).
@see getResources()
@see getModelQualifierType()
@see getBiologicalQualifierType()
=item CVTerm::getModelQualifierType
Returns the model qualifier type of this CVTerm object.
C<opydetails> doc_cvterm_common_description
The placeholder <span class="code" style="background-color: #bbb">
RELATION_ELEMENT</span> refers to a BioModels.net qualifier
element name. This is an element in either the XML namespace
C<"http://biomodels.net/model-qualifiers"> (for model
qualifiers) or C<"http://biomodels.net/biology-qualifiers">
(for biological qualifier). Callers will typically use
getQualifierType() to find out the type of qualifier relevant to this
particular CVTerm object, then if it is a I<model> qualifier, use the
present method to determine the specific qualifier.
Annotations with model qualifiers express a relationship between an
annotation resource and the <em>modeling concept</em> represented by a
given object in the model. The diagram below illustrates the
relationship in this case:
@image html model-qualifiers.png "Relationship expressed by model qualifiers"
@image latex model-qualifiers.png "Relationship expressed by model qualifiers"
<br> The set of known model qualifiers is, at the time of this libSBML
release, the following:
@li @link ModelQualifierType_t#BQM_IS BQM_IS@endlink
@li @link ModelQualifierType_t#BQM_IS_DESCRIBED_BY BQM_IS_DESCRIBED_BY@endlink
@li @link ModelQualifierType_t#BQM_IS_DERIVED_FROM BQM_IS_DERIVED_FROM@endlink
Any other BioModels.net qualifier found in the model is considered
unknown by libSBML and reported as
@link ModelQualifierType_t#BQM_UNKNOWN BQM_UNKNOWN@endlink.
@return the @if clike #ModelQualifierType_t value@else model qualifier type@endif@~
of this object or @link ModelQualifierType_t#BQM_UNKNOWN BQM_UNKNOWN@endlink
(the default).
=item CVTerm::getBiologicalQualifierType
Returns the biological qualifier type of this CVTerm object.
C<opydetails> doc_cvterm_common_description
The placeholder <span class="code" style="background-color: #bbb">
RELATION_ELEMENT</span> refers to a BioModels.net qualifier
element name. This is an element in either the XML namespace
C<"http://biomodels.net/model-qualifiers"> (for model
qualifiers) or C<"http://biomodels.net/biology-qualifiers">
(for biological qualifier). Callers will typically use
getQualifierType() to find out the type of qualifier relevant to this
particular CVTerm object, then if it is a I<biological> qualifier,
use the present method to determine the specific qualifier.
Annotations with biological qualifiers express a relationship between an
annotation resource and the <em>biological concept</em> represented by a
given object in the model. The diagram
below illustrates the relationship in this case:
@image html biology-qualifiers.png "Relationship expressed by biological qualifiers"
@image latex biology-qualifiers.png "Relationship expressed by biological qualifiers"
<br> The set of known biological qualifiers is, at the time of this
libSBML release, the following:
@li @link BiolQualifierType_t#BQB_IS BQB_IS@endlink
@li @link BiolQualifierType_t#BQB_HAS_PART BQB_HAS_PART@endlink
@li @link BiolQualifierType_t#BQB_IS_PART_OF BQB_IS_PART_OF@endlink
@li @link BiolQualifierType_t#BQB_IS_VERSION_OF BQB_IS_VERSION_OF@endlink
@li @link BiolQualifierType_t#BQB_HAS_VERSION BQB_HAS_VERSION@endlink
@li @link BiolQualifierType_t#BQB_IS_HOMOLOG_TO BQB_IS_HOMOLOG_TO@endlink
@li @link BiolQualifierType_t#BQB_IS_DESCRIBED_BY BQB_IS_DESCRIBED_BY@endlink
@li @link BiolQualifierType_t#BQB_IS_ENCODED_BY BQB_IS_ENCODED_BY@endlink
@li @link BiolQualifierType_t#BQB_ENCODES BQB_ENCODES@endlink
@li @link BiolQualifierType_t#BQB_OCCURS_IN BQB_OCCURS_IN@endlink
@li @link BiolQualifierType_t#BQB_HAS_PROPERTY BQB_HAS_PROPERTY@endlink
@li @link BiolQualifierType_t#BQB_IS_PROPERTY_OF BQB_IS_PROPERTY_OF@endlink
Any other BioModels.net qualifier found in the model is considered
unknown by libSBML and reported as
@link BiolQualifierType_t#BQB_UNKNOWN BQB_UNKNOWN@endlink.
@return the @if clike #BiolQualifierType_t value@else biology qualifier type@endif@~
of this object or @link BiolQualifierType_t#BQB_UNKNOWN BQB_UNKNOWN@endlink
(the default).
=item CVTerm::getResources
Returns the resource references for this CVTerm object.
C<opydetails> doc_cvterm_common_description
The <span class="code" style="background-color: #d0d0ee">resource
URI</span> values shown in the template above are stored internally in
CVTerm objects using an XMLAttributes object. Each attribute stored
inside the XMLAttributes will have the same name (specifically,
"C<rdf:resource>") but a different value, and the
value will be a <span class="code" style="background-color: #d0d0ee">
resource URI</span> shown in the XML template above.
A valid CVTerm entity must always have at least one resource and
a value for the relationship qualifier.
@return the XMLAttributes that store the resources of this CVTerm.
@see getQualifierType()
@see addResource(const std::string& resource)
@see getResourceURI(unsigned int n)
=item CVTerm::getResources
Returns the resources for this CVTerm object.
C<opydetails> doc_cvterm_common_description
The <span class="code" style="background-color: #d0d0ee">resource
URI</span> values shown in the template above are stored internally in
CVTerm objects using an XMLAttributes object. Each attribute stored
inside the XMLAttributes will have the same name (specifically,
"C<rdf:resource>") but a different value, and the
value will be a <span class="code" style="background-color: #d0d0ee">
resource URI</span> shown in the XML template above.
A valid CVTerm entity must always have at least one resource and
a value for the relationship qualifier.
@return the XMLAttributes that store the resources of this CVTerm.
@see getQualifierType()
@see addResource(const std::string& resource)
@see getResourceURI(unsigned int n)
=item CVTerm::getNumResources
Returns the number of resources for this CVTerm object.
C<opydetails> doc_cvterm_common_description
The fragment above illustrates that there can be more than one
resource referenced by a given relationship annotation (i.e., the
<span class="code" style="background-color: #d0d0ee">resource
URI</span> values associated with a particular <span class="code"
style="background-color: #bbb">RELATION_ELEMENT</span>). The present
method returns a count of the resources stored in this CVTerm object.
@return the number of resources in the set of XMLAttributes
of this CVTerm.
@see getResources()
@see getResourceURI(unsigned int n)
=item CVTerm::getResourceURI
Returns the value of the <em>n</em>th resource for this CVTerm object.
C<opydetails> doc_cvterm_common_description
The fragment above illustrates that there can be more than one
resource referenced by a given relationship annotation (i.e., the
<span class="code" style="background-color: #d0d0ee">resource
URI</span> values associated with a particular <span class="code"
style="background-color: #bbb">RELATION_ELEMENT</span>). LibSBML
stores all resource URIs in a single CVTerm object for a given
relationship. Callers can use getNumResources() to find out how many
resources are stored in this CVTerm object, then call this method to
retrieve the <em>n</em>th resource URI.
@param n the index of the resource to query
@return string representing the value of the nth resource
in the set of XMLAttributes of this CVTerm.
@see getNumResources()
@see getQualifierType()
=item CVTerm::setQualifierType
Sets the @if clike #QualifierType_t@else qualifier code@endif@~ of this
CVTerm object.
@param type the @if clike #QualifierType_t value@else qualifier type@endif.
The possible values returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS@endlink
@see getQualifierType()
=item CVTerm::setModelQualifierType
Sets the @if clike #ModelQualifierType_t value@else model qualifier type@endif@~
of this CVTerm object.
@param type the @if clike #ModelQualifierType_t value@else model qualifier type@endif@~
@return integer value indicating success/failure of the
function. The possible values returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS@endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE@endlink
@note If the Qualifier Type of this object is not
@link QualifierType_t#MODEL_QUALIFIER MODEL_QUALIFIER@endlink,
then the ModelQualifierType_t value will default to
@link QualifierType_t#BQM_UNKNOWN BQM_UNKNOWN@endlink.
@see getQualifierType()
@see setQualifierType(@if java int type@endif)
=item CVTerm::setBiologicalQualifierType
Sets the @if clike #BiolQualifierType_t value@else biology qualifier type@endif@~
of this CVTerm object.
@param type the @if clike #BiolQualifierType_t value@else biology qualifier type@endif.
@return integer value indicating success/failure of the
function. The possible values returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS@endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE@endlink
@note If the Qualifier Type of this object is not
@link QualifierType_t#BIOLOGICAL_QUALIFIER BIOLOGICAL_QUALIFIER@endlink,
then the @if clike #BiolQualifierType_t value@else biology qualifier type@endif@~ will default
to @link BiolQualifierType_t#BQB_UNKNOWN BQB_UNKNOWN@endlink.
@see getQualifierType()
@see setQualifierType(@if java int type@endif)
=item CVTerm::setModelQualifierType
Sets the @if clike #ModelQualifierType_t@endif@if java model qualifier type code@endif@~ value of this CVTerm object.
@param qualifier the string representing a model qualifier
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS@endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE@endlink
@note If the Qualifier Type of this object is not
@link QualifierType_t#MODEL_QUALIFIER MODEL_QUALIFIER@endlink,
then the ModelQualifierType_t value will default to
@link QualifierType_t#BQM_UNKNOWN BQM_UNKNOWN@endlink.
@see getQualifierType()
@see setQualifierType(@if java int type@endif)
=item CVTerm::setBiologicalQualifierType
Sets the @if clike #BiolQualifierType_t@endif@if java biology qualifier
type code@endif@~ of this CVTerm object.
@param qualifier the string representing a biology qualifier
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS@endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE@endlink
@note If the Qualifier Type of this object is not
@link QualifierType_t#BIOLOGICAL_QUALIFIER BIOLOGICAL_QUALIFIER@endlink,
then the @if clike #BiolQualifierType_t@endif@if java biology qualifier type code@endif@~ value will default
to @link BiolQualifierType_t#BQB_UNKNOWN BQB_UNKNOWN@endlink.
@see getQualifierType()
@see setQualifierType(@if java int type@endif)
=item CVTerm::addResource
Adds a resource reference to this CVTerm object.
C<opydetails> doc_what_are_cvterms
The specific RDF element used in this SBML format for referring to
external entities is C<<rdf:Description>>, with a
C<<rdf:Bag>> element containing one or more
C<<rdf:li>> elements. Each such element refers to a
data item in an external resource; the resource and data item are
together identified uniquely using a URI. The following template
illustrates the structure:
<pre class="fragment">
<rdf:Description rdf:about="#<span style="border-bottom: 1px solid black">meta id</span>">
<span style="background-color: #e0e0e0; border-bottom: 2px dotted #888">HISTORY</span>
<<span style="background-color: #bbb">RELATION_ELEMENT</span>>
<rdf:Bag>
<rdf:li rdf:resource="<span style="background-color: #d0d0ee">resource URI</span>" />
<span style="background-color: #edd">...</span>
</rdf:Bag>
</<span style="background-color: #bbb">RELATION_ELEMENT</span>>
<span style="background-color: #edd">...</span>
</rdf:Description>
</pre>
In the template above, the placeholder <span class="code"
style="border-bottom: 1px solid black">meta id</span> stands for the
element's meta identifier, which is a field available on all SBML
components derived from the SBase base object class. The <span
style="border-bottom: 2px dotted #888">dotted</span> portions are
optional, and the ellipses <span class="code"
style="background-color: #edd">...</span> are placeholders for zero or
more elements of the same form as the immediately preceding element.
The placeholder <span class="code" style="background-color: #bbb">
RELATION_ELEMENT</span> refers to a BioModels.net qualifier element
name. This is an element in either the XML namespace
C<"http://biomodels.net/model-qualifiers"> (for model
qualifiers) or C<"http://biomodels.net/biology-qualifiers">
(for biological qualifier).
The <span class="code" style="background-color: #d0d0ee">resource
URI</span> is a required data value that uniquely identifies a
resource and data within that resource to which the annotation refers.
The present method allows callers to add a reference to a resource URI
with the same relationship to the enclosing SBML object. (In other
words, the argument to this method is a <span class="code"
style="background-color: #d0d0ee">resource URI</span> as shown in the
XML fragment above.) Resources are stored in this CVTerm object
within an XMLAttributes object.
The relationship of this CVTerm to the enclosing SBML object can be
determined using the CVTerm methods such as getModelQualifierType()
and getBiologicalQualifierType().
@param resource a string representing the URI of the resource and data
item being referenced; e.g.,
C<"http://www.geneontology.org/#GO:0005892">.
@return integer value indicating success/failure of the call. The
possible values returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS@endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED@endlink
@see getResources()
@see removeResource(std::string resource)
@see getQualifierType()
@see getModelQualifierType()
@see getBiologicalQualifierType()
=item CVTerm::removeResource
Removes a resource URI from the set of resources stored in this CVTerm
object.
@param resource a string representing the resource URI to remove;
e.g., C<"http://www.geneontology.org/#GO:0005892">.
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS@endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE@endlink
@see addResource(const std::string& resource)
=item CVTerm::hasRequiredAttributes
Predicate returning C<true> if all the required elements for this
CVTerm object have been set.
@note The required attributes for a CVTerm are:
@li a <em>qualifier type</em>, which can be either a model qualifier or a biological qualifier
@li at least one resource
=item CVTerm::hasBeenModified
@internal
=item CVTerm::resetModifiedFlags
@internal
=back
=head2 Date
@sbmlpackage{core}
@htmlinclude pkg-marker-core.html Representation of MIRIAM-compliant dates used in
ModelHistory.
@htmlinclude not-sbml-warning.html
A Date object stores a reasonably complete representation of date and
time. Its purpose is to serve as a way to store dates to be read and
written in the <a target="_blank"
href="http://www.w3.org/TR/NOTE-datetime">W3C date format</a> used in
RDF Dublin Core annotations within SBML. The W3C date format is a
restricted form of <a target="_blank"
href="http://en.wikipedia.org/wiki/ISO_8601">ISO 8601</a>, the
international standard for the representation of dates and times. A
time and date value in this W3C format takes the form
YYYY-MM-DDThh:mm:ssXHH:ZZ (e.g., C<1997-07-16T19:20:30+01:00>)
where XHH:ZZ is the time zone offset. The libSBML Date object contains
the following fields to represent these values:
@li I<year>: an unsigned int representing the year. This should be a
four-digit number such as C<2011>.
@li I<month>: an unsigned int representing the month, with a range of
values of 1–12. The value C<1> represents January, and so on.
@li I<day>: an unsigned int representing the day of the month, with a
range of values of 1–31.
@li I<hour>: an unsigned int representing the hour on a 24-hour clock,
with a range of values of 0–23.
@li I<minute>: an unsigned int representing the minute, with a range
of 0–59.
@li I<second>: an unsigned int representing the second, with a range
of 0–59.
@li I<sign>: an unsigned int representing the sign of the offset (C<0>
signifying C<+> and C<1> signifying C<->). See the paragraph below for
further explanations.
@li I<hours> offset: an unsigned int representing the time zone's hour
offset from GMT.
@li I<minute> offset: an unsigned int representing the time zone's
minute offset from GMT.
To illustrate the time zone offset, a value of C<-05:00> would
correspond to USA Eastern Standard Time. In the Date object, this would
require a value of C<1> for the sign field, C<5> for the hour offset and
C<0> for the minutes offset.
In the restricted RDF annotations used in SBML, described in
Section 6 of the SBML Level 2 and Level 3 specification
documents, date/time stamps can be used to indicate the time of
creation and modification of a model. The following SBML model fragment
illustrates this:
@verbatim
<model metaid="_180340" id="GMO" name="Goldbeter1991_MinMitOscil">
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:dc="http://purl.org/dc/elements/1.1/"
xmlns:dcterms="http://purl.org/dc/terms/"
xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" >
<rdf:Description rdf:about="#_180340">
<dc:creator>
<rdf:Bag>
<rdf:li rdf:parseType="Resource">
<vCard:N rdf:parseType="Resource">
<vCard:Family>Shapiro</vCard:Family>
<vCard:Given>Bruce</vCard:Given>
</vCard:N>
<vCard:EMAIL>bshapiro@jpl.nasa.gov</vCard:EMAIL>
<vCard:ORG rdf:parseType="Resource">
<vCard:Orgname>NASA Jet Propulsion Laboratory</vCard:Orgname>
</vCard:ORG>
</rdf:li>
</rdf:Bag>
</dc:creator>
<dcterms:created rdf:parseType="Resource">
<dcterms:W3CDTF>2005-02-06T23:39:40+00:00</dcterms:W3CDTF>
</dcterms:created>
<dcterms:modified rdf:parseType="Resource">
<dcterms:W3CDTF>2005-09-13T13:24:56+00:00</dcterms:W3CDTF>
</dcterms:modified>
</rdf:Description>
</rdf:RDF>
</annotation>
</model>
@endverbatim
=over
=item Date::Date
Creates a time and date representation for use in model annotations
and elsewhere.
The following is the complete set of possible arguments to this
constructor, with default values as indicated:
@param year an unsigned integer representing the year. This should be
a four-digit number such as C<2011>. (Default value used if this
argument is not given: C<2000>.)
@param month an unsigned integer representing the month, with a range
of values of 1–12. The value C<1> represents January, and so
on. (Default value used if this argument is not given: C<1>.)
@param day an unsigned integer representing the day of the month, with
a range of values of 1–31. (Default value used if this argument
is not given: C<1>.)
@param hour an unsigned integer representing the hour on a 24-hour
clock, with a range of values of 0–23. (Default value used if
this argument is not given: C<0>.)
@param minute an unsigned integer representing the minute, with a
range of 0–59. (Default value used if this argument is not
given: C<0>.)
@param second an unsigned integer representing the second, with a
range of 0–59. (Default value used if this argument is not
given: C<0>.)
@param sign an unsigned integer representing the sign of the offset
(C<0> signifying C<+> and C<1> signifying C<->). See the paragraph
below for further explanations. (Default value used if this argument
is not given: C<0>.)
@param hoursOffset an unsigned integer representing the time zone's
hour offset from GMT. (Default value used if this argument is not
given: C<0>.)
@param minutesOffset an unsigned integer representing the time zone's
minute offset from GMT. (Default value used if this argument is not
given: C<0>.)
To illustrate the time zone offset, a value of C<-05:00>
would correspond to USA Eastern Standard Time. In the Date object,
this would require a value of C<1> for the sign field, C<5> for the
hour offset and C<0> for the minutes offset.
@if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
=item Date::Date
Creates a Date object from a string expressing a date and time value.
This constructor expects its argument to be in the <a target="_blank"
href="http://www.w3.org/TR/NOTE-datetime">W3C date format with time
zone offset</a>, used in RDF Dublin Core annotations within SBML.
C<opydetails> doc_date_string_format
If this constructor is given a C<NULL> argument or a string of length
zero, it constructs a Date object with the value of January 1, 2000,
at time 00:00 UTC. Otherwise, the argument I<must> be in the
complete format described above, or unpredictable results will happen.
@param date a string representing the date.
=item Date::Date
Copy constructor; creates a copy of this Date.
@param orig the object to copy.
@throws @if python ValueError @else SBMLConstructorException @endif@~
Thrown if the argument C<orig> is C<NULL>.
=item Date::clone
Returns a copy of this Date.
@return a (deep) copy of this Date.
=item Date::getYear
Returns the year from this Date.
@return the year from this Date.
=item Date::getMonth
Returns the month from this Date.
@return the month from this Date.
=item Date::getDay
Returns the day from this Date.
@return the day from this Date.
=item Date::getHour
Returns the hour from this Date.
@return the hour from this Date.
=item Date::getMinute
Returns the minute from this Date.
@return the minute from this Date.
=item Date::getSecond
Returns the seconds from this Date.
@return the seconds from this Date.
=item Date::getSignOffset
Returns the sign of the time zone offset from this Date.
@return the sign of the offset from this Date.
=item Date::getHoursOffset
Returns the hours of the time zone offset from this Date.
@return the hours of the offset from this Date.
=item Date::getMinutesOffset
Returns the minutes of the time zone offset from this Date.
@return the minutes of the offset from this Date.
=item Date::getDateAsString
Returns the current Date value in text-string form.
The string returned will be in the <a target="_blank"
href="http://www.w3.org/TR/NOTE-datetime">W3C date format with time
zone offset</a>, used in RDF Dublin Core annotations within SBML.
C<opydetails> doc_date_string_format
@return the date as a string.
=item Date::setYear
Sets the value of the year of this Date object.
The value given as argument must be between 1000 and 9999 inclusive.
(In the millennium during which this libSBML documentation is being
written, a typical value is C<2011>, but we hope that SBML will
continue to be used for a long time.)
@param year an unsigned int representing the year.
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif@~ The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item Date::setMonth
Sets the value of the month of this Date object.
@param month an unsigned int representing the month; it must be in the
range 1–12 or an error will be signaled.
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif@~ The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item Date::setDay
Sets the value of the day of this Date object.
@param day an unsigned int representing the day; it must be in the
range 0–31 or an error will be signaled.
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif@~ The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item Date::setHour
Sets the value of the hour of this Date object.
@param hour an unsigned int representing the hour to set; it must be
in the range 0–23 or an error will be signaled.
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif@~ The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item Date::setMinute
Sets the value of the minute of this Date object.
@param minute an unsigned int representing the minute to set; it must
be in the range 0–59 or an error will be signaled.
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif@~ The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item Date::setSecond
Sets the value of the second of the Date object.
@param second an unsigned int representing the seconds; it must
be in the range 0–59 or an error will be signaled.
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif@~ The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item Date::setSignOffset
Sets the value of the sign of the time zone offset of this Date object.
The only permissible values are C<0> and C<1>.
@param sign an unsigned int representing the sign of the offset, with
C<0> signifying C<+> and C<1> signifying C<->.
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif@~ The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item Date::setHoursOffset
Sets the value of this Date object's time zone hour offset.
@param hoursOffset an unsigned int representing the hours of the
offset; it must be in the range 0–23 or an error will be
signaled.
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif@~ The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item Date::setMinutesOffset
Sets the value of this Date object's time zone minutes offset.
@param minutesOffset an unsigned int representing the minutes of the
offset; it must be in the range 0–59 or an error will be
signaled.
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif@~ The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item Date::setDateAsString
Sets the value of this Date object using a date and time value
expressed as a text string.
This method expects its argument to be in the <a target="_blank"
href="http://www.w3.org/TR/NOTE-datetime">W3C date format with time
zone offset</a>, used in RDF Dublin Core annotations within SBML.
C<opydetails> doc_date_string_format
If this method is given a C<NULL> argument or a string of length zero,
it constructs a Date object with the value of January 1, 2000, at time
00:00 UTC. Otherwise, the argument I<must> be in the complete format
described above, or unpredictable results will happen.
@param date a string representing the date.
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif@~ The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item Date::representsValidDate
Returns true or false depending on whether this date object represents
a valid date and time value.
This method verifies that the date/time value stored in this object is
well-formed and represents plausible values. A time and date value in
the W3C format takes the form YYYY-MM-DDThh:mm:ssXHH:ZZ (e.g.,
C<1997-07-16T19:20:30+01:00>) where XHH:ZZ is the time zone
offset. This method checks such things as whether the value of the
month number is less than or equal to 12, whether the value of the
minutes number is less than or equal to 59, whether a time zone offset
is set, etc.
@return C<true> if the date is valid, C<false> otherwise.
=item Date::hasBeenModified
@internal
=item Date::resetModifiedFlags
@internal
=item Date::parseDateStringToNumbers
@internal
Sets the value of the individual numbers from the date
as a string.
=item Date::parseDateNumbersToString
@internal
Sets the value of the date as a string from the individual numbers.
=back
=head2 ModelCreator
@sbmlpackage{core}
@htmlinclude pkg-marker-core.html Representation of MIRIAM-compliant model creator data
used in ModelHistory.
@htmlinclude not-sbml-warning.html
The SBML specification beginning with Level 2 Version 2
defines a standard approach to recording model history and model creator
information in a form that complies with MIRIAM ("Minimum Information
Requested in the Annotation of biochemical Models", <i>Nature
Biotechnology</i>, vol. 23, no. 12, Dec. 2005). For the model creator,
this form involves the use of parts of the <a target="_blank"
href="http://en.wikipedia.org/wiki/VCard">vCard</a> representation.
LibSBML provides the ModelCreator class as a convenience high-level
interface for working with model creator data. Objects of class
ModelCreator can be used to store and carry around creator data within a
program, and the various methods in this object class let callers
manipulate the different parts of the model creator representation.
@section parts The different parts of a model creator definition
The ModelCreator class mirrors the structure of the MIRIAM model creator
annotations in SBML. The following template illustrates these different
fields when they are written in XML form:
<pre class="fragment">
<vCard:N rdf:parseType="Resource">
<vCard:Family><span style="background-color: #bbb">family name</span></vCard:Family>
<vCard:Given><span style="background-color: #bbb">given name</span></vCard:Given>
</vCard:N>
...
<vCard:EMAIL><span style="background-color: #bbb">email address</span></vCard:EMAIL>
...
<vCard:ORG rdf:parseType="Resource">
<vCard:Orgname><span style="background-color: #bbb">organization</span></vCard:Orgname>
</vCard:ORG>
</pre>
Each of the separate data values
<span class="code" style="background-color: #bbb">family name</span>,
<span class="code" style="background-color: #bbb">given name</span>,
<span class="code" style="background-color: #bbb">email address</span>, and
<span class="code" style="background-color: #bbb">organization</span> can
be set and retrieved via corresponding methods in the ModelCreator
class. These methods are documented in more detail below.
=over
=item ModelCreator::ModelCreator
Creates a new ModelCreator object.
=item ModelCreator::ModelCreator
Creates a new ModelCreator from an XMLNode.
@param creator the XMLNode from which to create the ModelCreator.
=item ModelCreator::ModelCreator
Copy constructor; creates a copy of the ModelCreator.
@param orig the object to copy.
@throws @if python ValueError @else SBMLConstructorException @endif@~
Thrown if the argument C<orig> is C<NULL>.
=item ModelCreator::clone
Creates and returns a copy of this ModelCreator.
@return a (deep) copy of this ModelCreator.
=item ModelCreator::getFamilyName
Returns the "family name" stored in this ModelCreator object.
@return the "family name" portion of the ModelCreator object.
=item ModelCreator::getGivenName
Returns the "given name" stored in this ModelCreator object.
@return the "given name" portion of the ModelCreator object.
=item ModelCreator::getEmail
Returns the "email" stored in this ModelCreator object.
@return email from the ModelCreator.
=item ModelCreator::getOrganization
Returns the "organization" stored in this ModelCreator object.
@return organization from the ModelCreator.
=item ModelCreator::getOrganisation
(Alternate spelling) Returns the "organization" stored in this
ModelCreator object.
@note This function is an alias of getOrganization().
@return organization from the ModelCreator.
@see getOrganization()
=item ModelCreator::isSetFamilyName
Predicate returning C<true> or C<false> depending on whether this
ModelCreator's "family name" part is set.
@return C<true> if the familyName of this ModelCreator is set, C<false> otherwise.
=item ModelCreator::isSetGivenName
Predicate returning C<true> or C<false> depending on whether this
ModelCreator's "given name" part is set.
@return C<true> if the givenName of this ModelCreator is set, C<false> otherwise.
=item ModelCreator::isSetEmail
Predicate returning C<true> or C<false> depending on whether this
ModelCreator's "email" part is set.
@return C<true> if the email of this ModelCreator is set, C<false> otherwise.
=item ModelCreator::isSetOrganization
Predicate returning C<true> or C<false> depending on whether this
ModelCreator's "organization" part is set.
@return C<true> if the organization of this ModelCreator is set, C<false> otherwise.
=item ModelCreator::isSetOrganisation
(Alternate spelling) Predicate returning C<true> or C<false> depending
on whether this ModelCreator's "organization" part is set.
@note This function is an alias of isSetOrganization().
@return C<true> if the organization of this ModelCreator is set, C<false> otherwise.
@see isSetOrganization()
=item ModelCreator::setFamilyName
Sets the "family name" portion of this ModelCreator object.
@param familyName a string representing the familyName of the ModelCreator.
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif@~ The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
=item ModelCreator::setGivenName
Sets the "given name" portion of this ModelCreator object.
@param givenName a string representing the givenName of the ModelCreator.
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif@~ The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
=item ModelCreator::setEmail
Sets the "email" portion of this ModelCreator object.
@param email a string representing the email of the ModelCreator.
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif@~ The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
=item ModelCreator::setOrganization
Sets the "organization" portion of this ModelCreator object.
@param organization a string representing the organization of the
ModelCreator.
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif@~ The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
=item ModelCreator::setOrganisation
(Alternate spelling) Sets the "organization" portion of this
ModelCreator object.
@param organization a string representing the organization of the
ModelCreator.
@note This function is an alias of setOrganization(const std::string& organization).
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif@~ The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@see setOrganization(std::string organization)
=item ModelCreator::unsetFamilyName
Unsets the "family name" portion of this ModelCreator object.
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif@~ The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item ModelCreator::unsetGivenName
Unsets the "given name" portion of this ModelCreator object.
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif@~ The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item ModelCreator::unsetEmail
Unsets the "email" portion of this ModelCreator object.
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif@~ The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item ModelCreator::unsetOrganization
Unsets the "organization" portion of this ModelCreator object.
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif@~ The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item ModelCreator::unsetOrganisation
(Alternate spelling) Unsets the "organization" portion of this ModelCreator object.
@note This function is an alias of unsetOrganization().
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif@~ The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
@see unsetOrganization()
=item ModelCreator::getAdditionalRDF
@internal
=item ModelCreator::hasRequiredAttributes
Predicate returning C<true> if all the required elements for this
ModelCreator object have been set.
The only required elements for a ModelCreator object are the "family
name" and "given name".
@return a boolean value indicating whether all the required
elements for this object have been defined.
=item ModelCreator::hasBeenModified
@internal
=item ModelCreator::resetModifiedFlags
@internal
=back
=head2 ModelHistory
@sbmlpackage{core}
@htmlinclude pkg-marker-core.html Representation of MIRIAM-compliant model history data.
@htmlinclude not-sbml-warning.html
The SBML specification beginning with Level 2 Version 2 defines
a standard approach to recording optional model history and model creator
information in a form that complies with MIRIAM (<a target="_blank"
href="http://www.nature.com/nbt/journal/v23/n12/abs/nbt1156.html">"Minimum
Information Requested in the Annotation of biochemical Models"</a>,
<i>Nature Biotechnology</i>, vol. 23, no. 12, Dec. 2005). LibSBML
provides the ModelHistory class as a convenient high-level interface for
working with model history data.
Model histories in SBML consist of one or more <em>model creators</em>,
a single date of I<creation>, and one or more I<modification> dates.
The overall XML form of this data takes the following form:
<pre class="fragment">
<dc:creator>
<rdf:Bag>
<rdf:li rdf:parseType="Resource">
<span style="background-color: #d0eed0">+++</span>
<vCard:N rdf:parseType="Resource">
<vCard:Family><span style="background-color: #bbb">family name</span></vCard:Family>
<vCard:Given><span style="background-color: #bbb">given name</span></vCard:Given>
</vCard:N>
<span style="background-color: #d0eed0">+++</span>
<span style="border-bottom: 2px dotted #888"><vCard:EMAIL><span style="background-color: #bbb">email address</span></vCard:EMAIL></span>
<span style="background-color: #d0eed0">+++</span>
<span style="border-bottom: 2px dotted #888"><vCard:ORG rdf:parseType="Resource"></span>
<span style="border-bottom: 2px dotted #888"><vCard:Orgname><span style="background-color: #bbb">organization name</span></vCard:Orgname></span>
<span style="border-bottom: 2px dotted #888"></vCard:ORG></span>
<span style="background-color: #d0eed0">+++</span>
</rdf:li>
<span style="background-color: #edd">...</span>
</rdf:Bag>
</dc:creator>
<dcterms:created rdf:parseType="Resource">
<dcterms:W3CDTF><span style="background-color: #bbb">creation date</span></dcterms:W3CDTF>
</dcterms:created>
<dcterms:modified rdf:parseType="Resource">
<dcterms:W3CDTF><span style="background-color: #bbb">modification date</span></dcterms:W3CDTF>
</dcterms:modified>
<span style="background-color: #edd">...</span>
</pre>
In the template above, the <span style="border-bottom: 2px dotted #888">underlined</span>
portions are optional, the symbol
<span class="code" style="background-color: #d0eed0">+++</span> is a placeholder
for either no content or valid XML content that is not defined by
the annotation scheme, and the ellipses
<span class="code" style="background-color: #edd">...</span>
are placeholders for zero or more elements of the same form as the
immediately preceding element. The various placeholders for content, namely
<span class="code" style="background-color: #bbb">family name</span>,
<span class="code" style="background-color: #bbb">given name</span>,
<span class="code" style="background-color: #bbb">email address</span>,
<span class="code" style="background-color: #bbb">organization</span>,
<span class="code" style="background-color: #bbb">creation date</span>, and
<span class="code" style="background-color: #bbb">modification date</span>
are data that can be filled in using the various methods on
the ModelHistory class described below.
@see ModelCreator
@see Date
=over
=item ModelHistory::ModelHistory
Creates a new ModelHistory object.
=item ModelHistory::ModelHistory
Copy constructor; creates a copy of this ModelHistory object.
@param orig the object to copy.
@throws @if python ValueError @else SBMLConstructorException @endif@~
Thrown if the argument C<orig> is C<NULL>.
=item ModelHistory::clone
Creates and returns a copy of this ModelHistory object
@return a (deep) copy of this ModelHistory object.
=item ModelHistory::getCreatedDate
Returns the "creation date" portion of this ModelHistory object.
@return a Date object representing the creation date stored in
this ModelHistory object.
=item ModelHistory::getModifiedDate
Returns the "modified date" portion of this ModelHistory object.
Note that in the MIRIAM format for annotations, there can be multiple
modification dates. The libSBML ModelHistory class supports this by
storing a list of "modified date" values. If this ModelHistory object
contains more than one "modified date" value in the list, this method
will return the first one in the list.
@return a Date object representing the date of modification
stored in this ModelHistory object.
=item ModelHistory::isSetCreatedDate
Predicate returning C<true> or C<false> depending on whether this
ModelHistory's "creation date" is set.
@return C<true> if the creation date value of this ModelHistory is
set, C<false> otherwise.
=item ModelHistory::isSetModifiedDate
Predicate returning C<true> or C<false> depending on whether this
ModelHistory's "modified date" is set.
@return C<true> if the modification date value of this ModelHistory
object is set, C<false> otherwise.
=item ModelHistory::setCreatedDate
Sets the creation date of this ModelHistory object.
@param date a Date object representing the date to which the "created
date" portion of this ModelHistory should be set.
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif@~ The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT @endlink
=item ModelHistory::setModifiedDate
Sets the modification date of this ModelHistory object.
@param date a Date object representing the date to which the "modified
date" portion of this ModelHistory should be set.
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif@~ The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT @endlink
=item ModelHistory::addModifiedDate
Adds a copy of a Date object to the list of "modified date" values
stored in this ModelHistory object.
In the MIRIAM format for annotations, there can be multiple
modification dates. The libSBML ModelHistory class supports this by
storing a list of "modified date" values.
@param date a Date object representing the "modified date" that should
be added to this ModelHistory object.
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif@~ The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT @endlink
=item ModelHistory::getListModifiedDates
Returns the list of "modified date" values (as Date objects) stored in
this ModelHistory object.
In the MIRIAM format for annotations, there can be multiple
modification dates. The libSBML ModelHistory class supports this by
storing a list of "modified date" values.
@return the list of modification dates for this ModelHistory object.
=item ModelHistory::getModifiedDate
Get the nth Date object in the list of "modified date" values stored
in this ModelHistory object.
In the MIRIAM format for annotations, there can be multiple
modification dates. The libSBML ModelHistory class supports this by
storing a list of "modified date" values.
@return the nth Date in the list of ModifiedDates of this
ModelHistory.
=item ModelHistory::getNumModifiedDates
Get the number of Date objects in this ModelHistory object's list of
"modified dates".
In the MIRIAM format for annotations, there can be multiple
modification dates. The libSBML ModelHistory class supports this by
storing a list of "modified date" values.
@return the number of ModifiedDates in this ModelHistory.
=item ModelHistory::addCreator
Adds a copy of a ModelCreator object to the list of "model creator"
values stored in this ModelHistory object.
In the MIRIAM format for annotations, there can be multiple model
creators. The libSBML ModelHistory class supports this by storing a
list of "model creator" values.
@param mc the ModelCreator to add
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif@~ The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item ModelHistory::getListCreators
Returns the list of ModelCreator objects stored in this ModelHistory
object.
In the MIRIAM format for annotations, there can be multiple model
creators. The libSBML ModelHistory class supports this by storing a
list of "model creator" values.
@return the list of ModelCreator objects.
=item ModelHistory::getCreator
Get the nth ModelCreator object stored in this ModelHistory object.
In the MIRIAM format for annotations, there can be multiple model
creators. The libSBML ModelHistory class supports this by storing a
list of "model creator" values.
@return the nth ModelCreator object.
=item ModelHistory::getNumCreators
Get the number of ModelCreator objects stored in this ModelHistory
object.
In the MIRIAM format for annotations, there can be multiple model
creators. The libSBML ModelHistory class supports this by storing a
list of "model creator" values.
@return the number of ModelCreators objects.
=item ModelHistory::hasRequiredAttributes
Predicate returning C<true> if all the required elements for this
ModelHistory object have been set.
The required elements for a ModelHistory object are "created
name", "modified date", and at least one "model creator".
@return a boolean value indicating whether all the required
elements for this object have been defined.
=item ModelHistory::hasBeenModified
@internal
=item ModelHistory::resetModifiedFlags
@internal
=back
=head2 RDFAnnotationParser
@sbmlpackage{core}
@htmlinclude pkg-marker-core.html Read/write/manipulate RDF annotations stored in SBML
annotation elements.
@htmlinclude not-sbml-warning.html
RDFAnnotationParser is a libSBML construct used as part of the libSBML
support for annotations conforming to the guidelines specified by MIRIAM
(<a target="_blank"
href="http://www.nature.com/nbt/journal/v23/n12/abs/nbt1156.html">"Minimum
Information Requested in the Annotation of biochemical Models"</a>,
<i>Nature Biotechnology</i>, vol. 23, no. 12, Dec. 2005). Section 6 of
the SBML Level 2 and Level 3 specification documents defines a
recommended way of encoding MIRIAM information using a subset of RDF (<a
target="_blank" href="http://www.w3.org/RDF/">Resource Description
Format</a>). The general scheme is as follows. A set of RDF-based
annotations attached to a given SBML C<<annotation>>
element are read by RDFAnnotationParser and converted into a list of
CVTerm objects. There are different versions of the main method, @if clike RDFAnnotationParser::parseRDFAnnotation(const XMLNode annotation, List CVTerms) @endif@if java RDFAnnotationParser::parseRDFAnnotation(const XMLNode annotation, CVTermList CVTerms) @endif@~ and
RDFAnnotationParser::parseRDFAnnotation(const XMLNode annotation), used
depending on whether the annotation in question concerns the MIRIAM model
history or other MIRIAM resource annotations. A special object class,
ModelHistory, is used to make it easier to manipulate model history
annotations.
All of the methods on RDFAnnotationParser are static; the class exists
only to encapsulate the annotation and CVTerm parsing and manipulation
functionality.
=over
=item RDFAnnotationParser::parseRDFAnnotation
Parses an annotation (given as an XMLNode tree) into a list of
CVTerm objects.
This is used to take an annotation that has been read into an SBML
model, identify the RDF elements within it, and create a list of
corresponding CVTerm (controlled vocabulary term) objects.
@param annotation XMLNode containing the annotation.
@param CVTerms list of CVTerm objects to be created.
@param metaId optional metaId, if set only the RDF annotation for this metaId will be returned.
@param stream optional XMLInputStream that facilitates error logging.
C<opydetails> doc_note_static_methods
=item RDFAnnotationParser::parseRDFAnnotation
Parses an annotation into a ModelHistory class instance.
This is used to take an annotation that has been read into an SBML
model, identify the RDF elements representing model history
information, and create a list of corresponding CVTerm objects.
@param annotation XMLNode containing the annotation.
@param stream optional XMLInputStream that facilitates error logging
@param metaId optional metaId, if set only the RDF annotation for this metaId will be returned.
C<opydetails> doc_note_static_methods
@return a pointer to the ModelHistory created.
=item RDFAnnotationParser::createAnnotation
Creates a blank annotation and returns its root XMLNode object.
This creates a completely empty SBML C<<annotation>>
element. It is not attached to any SBML element. An example of how
this might be used is illustrated in the following code fragment. In
this example, suppose that C<content> is an XMLNode object previously
created, containing MIRIAM-style annotations, and that C<sbmlObject>
is an SBML object derived from SBase (e.g., a Model, or a Species, or
a Compartment, etc.). Then:@if clike
@verbatim
int success; // Status code variable, used below.
XMLNode RDF = createRDFAnnotation(); // Create RDF annotation XML structure.
success = RDF->addChild(...content...); // Put some content into it.
... // Check "success" return code value.
XMLNode ann = createAnnotation(); // Create <annotation> container.
success = ann->addChild(RDF); // Put the RDF annotation into it.
... // Check "success" return code value.
success = sbmlObject->setAnnotation(ann); // Set object's annotation to what we built.
... // Check "success" return code value.
@endverbatim
@endif@if java
@verbatim
int success; // Status code variable, used below.
XMLNode RDF = createRDFAnnotation(); // Create RDF annotation XML structure.
success = RDF.addChild(...content...); // Put some content into it.
... // Check "success" return code value.
XMLNode ann = createAnnotation(); // Create <annotation> container.
success = ann.addChild(RDF); // Put the RDF annotation into it.
... // Check "success" return code value.
success = sbmlObject.setAnnotation(ann); // Set object's annotation to what we built.
... // Check "success" return code value.
@endverbatim
@endif@if python
@verbatim
RDF = RDFAnnotationParser.createRDFAnnotation() # Create RDF annotation XML structure.
success = RDF.addChild(...content...) # Put some content into it.
... # Check "success" return code value.
annot = RDFAnnotationParser.createAnnotation() # Create <annotation> container.
success = annot.addChild(RDF) # Put the RDF annotation into it.
... # Check "success" return code value.
success = sbmlObject.setAnnotation(annot) # Set object's annotation to what we built.
... # Check "success" return code value.
@endverbatim
@endif@~
The SBML specification contains more information about the format of
annotations. We urge readers to consult Section 6 of the SBML
Level 2 (Versions 2–4) and SBML Level 3 specification
documents.
@return a pointer to an XMLNode for the annotation
C<opydetails> doc_note_static_methods
@see @if clike createRDFAnnotation() @else RDFAnnotationParser::createRDFAnnotation() @endif@~
=item RDFAnnotationParser::createRDFAnnotation
Creates a blank RDF element suitable for use in SBML annotations.
The annotation created by this method has namespace declarations for
all the relevant XML namespaces used in RDF annotations and also has
an empty RDF element. The result is the following XML:
@verbatim
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:dc="http://purl.org/dc/elements/1.1/"
xmlns:dcterms="http://purl.org/dc/terms/"
xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#"
xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"
xmlns:bqmodel="http://biomodels.net/model-qualifiers/" >
</rdf:RDF>
@endverbatim
Note that this does not create the containing SBML
C<<annotation>> element; the method
@if clike createAnnotation()@else RDFAnnotationParser::createAnnotation()@endif@~
is available for creating the container.
@return a pointer to an XMLNode
C<opydetails> doc_note_static_methods
@see @if clike createAnnotation() @else RDFAnnotationParser::createAnnotation() @endif@~
=item RDFAnnotationParser::createRDFDescription
Takes an SBML object and creates an empty XMLNode corresponding to an
RDF "Description" element.
This method is a handy way of creating RDF description objects linked
by the appropriate "metaid" field to the given C<object>, for
insertion into RDF annotations in a model. The method retrieves the
"metaid" attribute from the C<object> passed in as argument, then
creates an empty element having the following form
(where <span class="code" style="background-color: #eed0d0">metaid</span>
the value of the "metaid" attribute of the argument):
<pre class="fragment">
<rdf:Description rdf:about="#<span style="background-color: #eed0d0">metaid</span>" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
...
</rdf:Description>
</pre>
Note that this method does I<not> create a complete annotation or
even an RDF element; it only creates the "Description" portion. Callers
will need to use other methods such as
@if clike createRDFAnnotation()@else RDFAnnotationParser::createRDFAnnotation()@endif@~
to create the rest of the structure for an annotation.
@param obj the object to which the "Description" refers
@return a new XMLNode containing the "rdf:Description" element with
its "about" attribute value set to the C<object> meta identifier.
C<opydetails> doc_note_static_methods
@see @if clike createRDFAnnotation() @else RDFAnnotationParser::createRDFAnnotation() @endif@~
=item RDFAnnotationParser::createCVTerms
Takes a list of CVTerm objects and creates a the RDF "Description"
element.
This essentially takes the given SBML object, reads out the CVTerm
objects attached to it, creates an RDF "Description" element to hold
the terms, and adds each term with appropriate qualifiers.
@param obj the SBML object to start from
@return the XMLNode tree corresponding to the Description element of
an RDF annotation.
C<opydetails> doc_note_static_methods
=item RDFAnnotationParser::parseCVTerms
Takes a list of CVTerm objects and creates a complete SBML annotation
around it.
This essentially takes the given SBML object, reads out the CVTerm
objects attached to it, calls @if clike createRDFAnnotation()@else
RDFAnnotationParser::createRDFAnnotation()@endif@~ to create an RDF
annotation to hold the terms, and finally calls @if clike
createAnnotation()@else
RDFAnnotationParser::createAnnotation()@endif@~ to wrap the result as
an SBML C<<annotation>> element.
@param obj the SBML object to start from
@return the XMLNode tree corresponding to the annotation.
C<opydetails> doc_note_static_methods
=item RDFAnnotationParser::parseModelHistory
Reads the model history and cvTerms stored in C<obj> and creates the
XML structure for an SBML annotation representing that metadata if
there is a model history stored in C<obj>.
@param obj any SBase object
@return the XMLNode corresponding to an annotation containing
MIRIAM-compliant model history and CV term information in RDF format.
@note If the object does not have a history element stored then
C<NULL> is returned even if CVTerms are present.
C<opydetails> doc_note_static_methods
=item RDFAnnotationParser::parseOnlyModelHistory
Reads the model history stored in C<obj> and creates the
XML structure for an SBML annotation representing that history.
@param obj any SBase object
@return the XMLNode corresponding to an annotation containing
MIRIAM-compliant model history information in RDF format.
C<opydetails> doc_note_static_methods
=item RDFAnnotationParser::deleteRDFAnnotation
Deletes any SBML MIRIAM RDF annotation found in the given XMLNode
tree and returns
any remaining annotation content.
The name of the XMLNode given as parameter C<annotation> must be
"annotation", or else this method returns C<NULL>. The method will
walk down the XML structure looking for elements that are in the
RDF XML namespace, and remove them if they conform to the syntax
of a History or CVTerm element.
@param annotation the XMLNode tree within which the RDF annotation is
to be found and deleted
@return the XMLNode structure that is left after RDF annotations are
deleted.
C<opydetails> doc_note_static_methods
=item RDFAnnotationParser::deleteRDFHistoryAnnotation
Deletes any SBML MIRIAM RDF 'History' annotation found in the given
XMLNode tree and returns
any remaining annotation content.
The name of the XMLNode given as parameter C<annotation> must be
"annotation", or else this method returns C<NULL>. The method will
walk down the XML structure looking for elements that are in the
RDF XML namespace, and remove any that conform to the syntax of a
History element.
@param annotation the XMLNode tree within which the RDF annotation is
to be found and deleted
@return the XMLNode structure that is left after RDF annotations are
deleted.
C<opydetails> doc_note_static_methods
=item RDFAnnotationParser::deleteRDFCVTermAnnotation
Deletes any SBML MIRIAM RDF 'CVTerm' annotation found in the given
XMLNode tree and returns
any remaining annotation content.
The name of the XMLNode given as parameter C<annotation> must be
"annotation", or else this method returns C<NULL>. The method will
walk down the XML structure looking for elements that are in the
RDF XML namespace, and remove any that conform to the syntax of a
CVTerm element.
@param annotation the XMLNode tree within which the RDF annotation is
to be found and deleted
@return the XMLNode structure that is left after RDF annotations are
deleted.
C<opydetails> doc_note_static_methods
=item RDFAnnotationParser::hasRDFAnnotation
@internal
=item RDFAnnotationParser::hasAdditionalRDFAnnotation
@internal
=item RDFAnnotationParser::hasCVTermRDFAnnotation
@internal
=item RDFAnnotationParser::hasHistoryRDFAnnotation
@internal
=item RDFAnnotationParser::createRDFDescription
@internal
=item RDFAnnotationParser::createRDFDescriptionWithCVTerms
@internal
=item RDFAnnotationParser::createRDFDescriptionWithHistory
@internal
=item RDFAnnotationParser::deriveCVTermsFromAnnotation
@internal
=item RDFAnnotationParser::deriveHistoryFromAnnotation
@internal
=back
=head2 ISBMLExtensionNamespaces
@sbmlpackage{core}
@internal
=over
=back
=head2 SBaseExtensionPoint
@sbmlpackage{core}
@htmlinclude pkg-marker-core.html Representation of an extension point of SBML's package
extension.
@if notclike @internal @endif@~
SBaseExtensionPoint represents an element to be extended (extension point) and the
extension point is identified by a combination of a package name and a typecode of the
element.
<p>
For example, an SBaseExtensionPoint object which represents an extension point of the model
element defined in the <em>core</em> package can be created as follows:
@verbatim
SBaseExtensionPoint modelextp("core", SBML_MODEL);
@endverbatim
Similarly, an SBaseExtensionPoint object which represents an extension point of
the layout element defined in the layout extension can be created as follows:
@verbatim
SBaseExtensionPoint layoutextp("layout", SBML_LAYOUT_LAYOUT);
@endverbatim
SBaseExtensionPoint object is required as one of arguments of the constructor
of SBasePluginCreator<class SBasePluginType, class SBMLExtensionType>
template class to identify an extension poitnt to which the plugin object created
by the creator class is plugged in.
For example, the SBasePluginCreator class which creates a LayoutModelPlugin object
of the layout extension which is plugged in to the model element of the <em>core</em>
package can be created with the corresponding SBaseExtensionPoint object as follows:
@verbatim
// std::vector object that contains a list of URI (package versions) supported
// by the plugin object.
std::vector<std::string> packageURIs;
packageURIs.push_back(getXmlnsL3V1V1());
packageURIs.push_back(getXmlnsL2());
// creates an extension point (model element of the "core" package)
SBaseExtensionPoint modelExtPoint("core",SBML_MODEL);
// creates an SBasePluginCreator object
SBasePluginCreator<LayoutModelPlugin, LayoutExtension> modelPluginCreator(modelExtPoint,packageURIs);
@endverbatim
This kind of code is implemented in init() function of each SBMLExtension derived classes.
=over
=item SBaseExtensionPoint::SBaseExtensionPoint
constructor
=item SBaseExtensionPoint::SBaseExtensionPoint
copy constructor
=item SBaseExtensionPoint::clone
Creates and returns a deep copy of this SBaseExtensionPoint.
@return a (deep) copy of this SBaseExtensionPoint.
=item SBaseExtensionPoint::getPackageName
Returns the package name of this extension point.
=item SBaseExtensionPoint::getTypeCode
Returns the typecode of this extension point.
=back
=head2 SBasePlugin
@sbmlpackage{core}
@htmlinclude pkg-marker-core.html Representation of a plug-in object of SBML's package
extension.
Additional attributes and/or elements of a package extension which are directly
contained by some pre-defined element are contained/accessed by <a href="#SBasePlugin">
SBasePlugin </a> class which is extended by package developers for each extension point.
The extension point, which represents an element to be extended, is identified by a
combination of a Package name and a typecode of the element, and is represented by
SBaseExtensionPoint class.
</p>
<p>
For example, the layout extension defines <em><listOfLayouts></em> element which is
directly contained in <em><model></em> element of the core package.
In the layout package (provided as one of example packages in libSBML-5), the additional
element for the model element is implemented as ListOfLayouts class (an SBase derived class) and
the object is contained/accessed by a LayoutModelPlugin class (an SBasePlugin derived class).
</p>
<p>
SBasePlugin class defines basic virtual functions for reading/writing/checking
additional attributes and/or top-level elements which should or must be overridden by
subclasses like SBase class and its derived classes.
</p>
<p>
Package developers must implement an SBasePlugin exntended class for
each element to be extended (e.g. SBMLDocument, Model, ...) in which additional
attributes and/or top-level elements of the package extension are directly contained.
</p>
To implement reading/writing functions for attributes and/or top-level
elements of the SBsaePlugin extended class, package developers should or must
override the corresponding virtual functions below provided in the SBasePlugin class:
\n=over\n
\n=item\n\n<p>reading elements : </p>
<ol>
\n=item\n\nC<virtual SBase createObject (XMLInputStream& stream) >
<p>This function must be overridden if one or more additional elements are defined.</p>
</li>
\n=item\n\nC<virtual bool readOtherXML (SBase parentObject, XMLInputStream& stream)>
<p>This function should be overridden if elements of annotation, notes, MathML, etc. need
to be directly parsed from the given XMLInputStream object @if clike instead of the
SBase::readAnnotation(XMLInputStream& stream)
and/or SBase::readNotes(XMLInputStream& stream) functions@endif.
</p>
</li>
</ol>
</li>
\n=item\n\n<p>reading attributes (must be overridden if additional attributes are defined) :</p>
<ol>
<li>C<virtual void addExpectedAttributes(ExpectedAttributes& attributes) ></li>
<li>C<virtual void readAttributes (const XMLAttributes& attributes, const ExpectedAttributes& expectedAttributes)></li>
</ol>
</li>
\n=item\n\n<p>writing elements (must be overridden if additional elements are defined) :</p>
<ol>
<li>C<virtual void writeElements (XMLOutputStream& stream) const ></li>
</ol>
</li>
\n=item\n\n<p>writing attributes : </p>
<ol>
<li>C<virtual void writeAttributes (XMLOutputStream& stream) const >
<p>This function must be overridden if one or more additional attributes are defined.</p>
</li>
<li>C<virtual void writeXMLNS (XMLOutputStream& stream) const >
<p>This function must be overridden if one or more additional xmlns attributes are defined.</p>
</li>
</ol>
</li>
\n=item\n\n<p>checking elements (should be overridden) :</p>
<ol>
<li>C<virtual bool hasRequiredElements() const ></li>
</ol>
</li>
\n=item\n\n<p>checking attributes (should be overridden) :</p>
<ol>
<li>C<virtual bool hasRequiredAttributes() const ></li>
</ol>
</li>
\n=back\n
<p>
To implement package-specific creating/getting/manipulating functions of the
SBasePlugin derived class (e.g., getListOfLayouts(), createLyout(), getLayout(),
and etc are implemented in LayoutModelPlugin class of the layout package), package
developers must newly implement such functions (as they like) in the derived class.
</p>
<p>
SBasePlugin class defines other virtual functions of internal implementations
such as:
\n=over\n
<li>C< virtual void setSBMLDocument(SBMLDocument d) >
<li>C< virtual void connectToParent(SBase sbase) >
<li>C< virtual void enablePackageInternal(const std::string& pkgURI, const std::string& pkgPrefix, bool flag) >
\n=back\n
These functions must be overridden by subclasses in which one or more top-level elements are defined.
</p>
<p>
For example, the following three SBasePlugin extended classes are implemented in
the layout extension:
</p>
<ol>
\n=item\n\n<p><a href="class_s_b_m_l_document_plugin.html"> SBMLDocumentPlugin </a> class for SBMLDocument element</p>
\n=over\n
\n=item\n\n<em> required </em> attribute is added to SBMLDocument object.
</li>
\n=back\n
<p>
(<a href="class_s_b_m_l_document_plugin.html"> SBMLDocumentPlugin </a> class is a common SBasePlugin
extended class for SBMLDocument class. Package developers can use this class as-is if no additional
elements/attributes (except for <em> required </em> attribute) is needed for the SBMLDocument class
in their packages, otherwise package developers must implement a new SBMLDocumentPlugin derived class.)
</p>
\n=item\n\n<p>LayoutModelPlugin class for Model element</p>
\n=over\n
\n=item\n\n<listOfLayouts> element is added to Model object.
</li>
\n=item\n\n<p>
The following virtual functions for reading/writing/checking
are overridden: (type of arguments and return values are omitted)
</p>
\n=over\n
\n=item\n\nC< createObject() > : (read elements)
</li>
\n=item\n\nC< readOtherXML() > : (read elements in annotation of SBML L2)
</li>
\n=item\n\nC< writeElements() > : (write elements)
</li>
\n=back\n
</li>
\n=item\n\n<p>
The following virtual functions of internal implementations
are overridden: (type of arguments and return values are omitted)
</p>
\n=over\n
\n=item\n\nC< setSBMLDocument() >
</li>
\n=item\n\nC< connectToParent() >
</li>
\n=item\n\nC< enablePackageInternal() >
</li>
\n=back\n
</li>
\n=item\n\n<p>
The following creating/getting/manipulating functions are newly
implemented: (type of arguments and return values are omitted)
</p>
\n=over\n
\n=item\n\nC< getListOfLayouts() >
</li>
\n=item\n\nC< getLayout () >
</li>
\n=item\n\nC< addLayout() >
</li>
\n=item\n\nC< createLayout() >
</li>
\n=item\n\nC< removeLayout() >
</li>
\n=item\n\nC< getNumLayouts() >
</li>
\n=back\n
</li>
\n=back\n
</li>
\n=item\n\n<p>LayoutSpeciesReferencePlugin class for SpeciesReference element (used only for SBML L2V1) </p>
\n=over\n
<li>
<em> id </em> attribute is internally added to SpeciesReference object
only for SBML L2V1
</li>
<li>
The following virtual functions for reading/writing/checking
are overridden: (type of arguments and return values are omitted)
</li>
\n=over\n
<li>
C< readOtherXML() >
</li>
<li>
C< writeAttributes() >
</li>
\n=back\n
\n=back\n
</li>
</ol>
=over
=item SBasePlugin::getElementNamespace
Returns the XML namespace (URI) of the package extension
of this plugin object.
@return the URI of the package extension of this plugin object.
=item SBasePlugin::getPrefix
Returns the prefix of the package extension of this plugin object.
@return the prefix of the package extension of this plugin object.
=item SBasePlugin::getPackageName
Returns the package name of this plugin object.
@return the package name of this plugin object.
=item SBasePlugin::clone
Creates and returns a deep copy of this SBasePlugin object.
@return a (deep) copy of this SBase object
=item SBasePlugin::getElementBySId
Returns the first child element found that has the given C<id> in the model-wide SId namespace, or C<NULL> if no such object is found.
@param id string representing the id of objects to find
@return pointer to the first element found with the given C<id>.
=item SBasePlugin::getElementByMetaId
Returns the first child element it can find with the given C<metaid>, or C<NULL> if no such object is found.
@param metaid string representing the metaid of objects to find
@return pointer to the first element found with the given C<metaid>.
=item SBasePlugin::getAllElements
Returns a List of all child SBase objects, including those nested to an arbitrary depth
@return a List of pointers to all children objects.
=item SBasePlugin::setSBMLDocument
@internal
Sets the parent SBMLDocument of this plugin object.
Subclasses which contain one or more SBase derived elements must
override this function.
@param d the SBMLDocument object to use
@see connectToParent()
@see enablePackageInternal()
=item SBasePlugin::connectToParent
@internal
Sets the parent SBML object of this plugin object to
this object and child elements (if any).
(Creates a child-parent relationship by this plugin object)
This function is called when this object is created by
the parent element.
Subclasses must override this this function if they have one
or more child elements. Also, SBasePlugin::connectToParent(@if java SBase sbase@endif)
must be called in the overridden function.
@param sbase the SBase object to use
@if cpp
@see setSBMLDocument()
@see enablePackageInternal()
@endif
=item SBasePlugin::enablePackageInternal
@internal
Enables/Disables the given package with child elements in this plugin
object (if any).
(This is an internal implementation invoked from
SBase::enablePackageInternal() function)
Subclasses which contain one or more SBase derived elements should
override this function if elements defined in them can be extended by
some other package extension.
@if cpp
@see setSBMLDocument()
@see connectToParent()
@endif
=item SBasePlugin::stripPackage
@internal
=item SBasePlugin::getSBMLDocument
Returns the parent SBMLDocument of this plugin object.
@return the parent SBMLDocument object of this plugin object.
=item SBasePlugin::getSBMLDocument
Returns the parent SBMLDocument of this plugin object.
@return the parent SBMLDocument object of this plugin object.
=item SBasePlugin::getURI
Gets the URI to which this element belongs to.
For example, all elements that belong to SBML Level 3 Version 1 Core
must would have the URI "http://www.sbml.org/sbml/level3/version1/core";
all elements that belong to Layout Extension Version 1 for SBML Level 3
Version 1 Core must would have the URI
"http://www.sbml.org/sbml/level3/version1/layout/version1/"
Unlike getElementNamespace, this function first returns the URI for this
element by looking into the SBMLNamespaces object of the document with
the its package name. if not found it will return the result of
getElementNamespace
@return the URI this elements
@see getPackageName()
@see getElementNamespace()
@see SBMLDocument::getSBMLNamespaces()
@see getSBMLDocument()
=item SBasePlugin::getParentSBMLObject
Returns the parent SBase object to which this plugin
object connected.
@return the parent SBase object to which this plugin
object connected.
=item SBasePlugin::getParentSBMLObject
Returns the parent SBase object to which this plugin
object connected.
@return the parent SBase object to which this plugin
object connected.
=item SBasePlugin::setElementNamespace
Sets the XML namespace to which this element belongs to.
For example, all elements that belong to SBML Level 3 Version 1 Core
must set the namespace to "http://www.sbml.org/sbml/level3/version1/core";
all elements that belong to Layout Extension Version 1 for SBML Level 3
Version 1 Core must set the namespace to
"http://www.sbml.org/sbml/level3/version1/layout/version1/"
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif@~ The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item SBasePlugin::getLevel
Returns the SBML level of the package extension of
this plugin object.
@return the SBML level of the package extension of
this plugin object.
=item SBasePlugin::getVersion
Returns the SBML version of the package extension of
this plugin object.
@return the SBML version of the package extension of
this plugin object.
=item SBasePlugin::getPackageVersion
Returns the package version of the package extension of
this plugin object.
@return the package version of the package extension of
this plugin object.
=item SBasePlugin::replaceSIDWithFunction
@internal
If this object has a child 'math' object (or anything with ASTNodes in general), replace all nodes with the name 'id' with the provided function.
@note This function does nothing itself--subclasses with ASTNode subelements must override this function.
=item SBasePlugin::divideAssignmentsToSIdByFunction
@internal
If the function of this object is to assign a value has a child 'math' object (or anything with ASTNodes in general), replace the 'math' object with the function (existing/function).
@note This function does nothing itself--subclasses with ASTNode subelements must override this function.
=item SBasePlugin::multiplyAssignmentsToSIdByFunction
@internal
If this assignment assigns a value to the 'id' element, replace the 'math' object with the function (existing function).
=item SBasePlugin::hasIdentifierBeginningWith
@internal
Check to see if the given prefix is used by any of the IDs defined by extension elements. A package that defines its own 'id' attribute for a core element would check that attribute here.
=item SBasePlugin::prependStringToAllIdentifiers
@internal
Add the given string to all identifiers in the object. If the string is added to anything other than an id or a metaid, this code is responsible for tracking down and renaming all idRefs in the package extention that identifier comes from.
=item SBasePlugin::transformIdentifiers
@internal
=item SBasePlugin::getLine
@internal
Returns the line number on which this object first appears in the XML
representation of the SBML document.
@return the line number of the underlying SBML object.
@note The line number for each construct in an SBML model is set upon
reading the model. The accuracy of the line number depends on the
correctness of the XML representation of the model, and on the
particular XML parser library being used. The former limitation
relates to the following problem: if the model is actually invalid
XML, then the parser may not be able to interpret the data correctly
and consequently may not be able to establish the real line number.
The latter limitation is simply that different parsers seem to have
their own accuracy limitations, and out of all the parsers supported
by libSBML, none have been 100% accurate in all situations. (At this
time, libSBML supports the use of <a target="_blank"
href="http://xmlsoft.org">libxml2</a>, <a target="_blank"
href="http://expat.sourceforge.net/">Expat</a> and <a target="_blank"
href="http://xerces.apache.org/xerces-c/">Xerces</a>.)
@see getColumn()
=item SBasePlugin::getColumn
@internal
Returns the column number on which this object first appears in the XML
representation of the SBML document.
@return the column number of the underlying SBML object.
@note The column number for each construct in an SBML model is set
upon reading the model. The accuracy of the column number depends on
the correctness of the XML representation of the model, and on the
particular XML parser library being used. The former limitation
relates to the following problem: if the model is actually invalid
XML, then the parser may not be able to interpret the data correctly
and consequently may not be able to establish the real column number.
The latter limitation is simply that different parsers seem to have
their own accuracy limitations, and out of all the parsers supported
by libSBML, none have been 100% accurate in all situations. (At this
time, libSBML supports the use of <a target="_blank"
href="http://xmlsoft.org">libxml2</a>, <a target="_blank"
href="http://expat.sourceforge.net/">Expat</a> and <a target="_blank"
href="http://xerces.apache.org/xerces-c/">Xerces</a>.)
@see getLine()
=item SBasePlugin::getSBMLNamespaces
@internal
=item SBasePlugin::logUnknownElement
@internal
Helper to log a common type of error for elements.
=item SBasePlugin::SBasePlugin
@internal
Constructor. Creates an SBasePlugin object with the URI and
prefix of an package extension.
=item SBasePlugin::SBasePlugin
@internal
Copy constructor. Creates a copy of this SBase object.
=item SBasePlugin::getErrorLog
@internal
Returns the SBMLErrorLog used to log errors while reading and
validating SBML.
@return the SBMLErrorLog used to log errors while reading and
validating SBML.
=item SBasePlugin::logUnknownAttribute
@internal
Helper to log a common type of error.
=item SBasePlugin::logEmptyString
@internal
Helper to log a common type of error.
=back
=head2 SBMLDocumentPlugin
@sbmlpackage{core}
@htmlinclude pkg-marker-core.html Template class for the SBMLDocument Plugin class needed
by all packages.
Plugin objects for the SBMLDocument element must be this class or a
derived class of this class. Package developers should use this class
as-is if only "required" attribute is added in the SBMLDocument element by
their packages. Otherwise, developers must implement a derived class of
this class and use that class as the plugin object for the SBMLDocument
element.
=over
=item SBMLDocumentPlugin::SBMLDocumentPlugin
Constructor
@param uri the URI of package
@param prefix the prefix for the given package
@param sbmlns the SBMLNamespaces object for the package
=item SBMLDocumentPlugin::SBMLDocumentPlugin
Copy constructor. Creates a copy of this object.
=item SBMLDocumentPlugin::clone
Creates and returns a deep copy of this SBMLDocumentPlugin object.
@return a (deep) copy of this object
=item SBMLDocumentPlugin::setRequired
Sets the bool value of "required" attribute of corresponding package
in SBMLDocument element.
@param value the bool value of "required" attribute of corresponding
package in SBMLDocument element.
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_UNEXPECTED_ATTRIBUTE LIBSBML_UNEXPECTED_ATTRIBUTE @endlink
=item SBMLDocumentPlugin::getRequired
Returns the bool value of "required" attribute of corresponding
package in SBMLDocument element.
@return the bool value of "required" attribute of corresponding
package in SBMLDocument element.
=item SBMLDocumentPlugin::isSetRequired
Predicate returning C<true> or C<false> depending on whether this
SBMLDocumentPlugin's "required" attribute has been set.
@return C<true> if the "required" attribute of this SBMLDocument has been
set, C<false> otherwise.
=item SBMLDocumentPlugin::unsetRequired
Unsets the value of the "required" attribute of this SBMLDocumentPlugin.
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif@~ The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item SBMLDocumentPlugin::isCompFlatteningImplemented
@internal
=item SBMLDocumentPlugin::checkConsistency
@internal
Check consistency function.
=back
=head2 SBMLExtension
@sbmlpackage{core}
@htmlinclude pkg-marker-core.html The core component of SBML's package extension.
@if notclike @internal @endif@~
SBMLExtension class (abstract class) is a core component of package extension
which needs to be extended by package developers.
The class provides functions for getting common attributes of package extension
(e.g., package name, package version, and etc.), functions for adding (registering)
each instantiated SBasePluginCreator object, and a static function (defined in each
SBMLExtension extended class) for initializing/registering the package extension
when the library of the package is loaded.
@section howto How to implement an SBMLExtension extended class for each package extension
Package developers must implement an SBMLExtension extended class for
their packages (e.g. GroupsExtension class is implemented for groups extension).
The extended class is implemented based on the following steps:
(NOTE:
"src/packages/groups/extension/GroupsExtension.{h,cpp}" and
"src/packages/layout/extension/LayoutExtension.{h,cpp}" are
example files in which SBMLExtension derived classes are implemented)
<ol>
\n=item\n\nDefine the following static functions in the extended class:
(examples of groups extension are shown respectively)
<ol>
\n=item\n\n<p>A string of package name (label) (The function name must be "getPackageName".)</p>
@verbatim
const std::string& GroupsExtension::getPackageName ()
{
static const std::string pkgName = "groups";
return pkgName;
}
@endverbatim
</li>
\n=item\n\n<p>
Methods returning an integer of Default SBML level, version, and package version
(The method names must be "getDefaultLevel()", "getDefaultVersion()", and
"getDefaultPackageVersion()" respectively.)
</p>
@verbatim
unsigned int GroupsExtension::getDefaultLevel()
{
return 3;
}
unsigned int GroupsExtension::getDefaultVersion()
{
return 1;
}
unsigned int GroupsExtension::getDefaultPackageVersion()
{
return 1;
}
@endverbatim
</li>
\n=item\n\n<p> Methods returning Strings that represent the URI of packages </p>
@verbatim
const std::string& GroupsExtension::getXmlnsL3V1V1 ()
{
static const std::string xmlns = "http://www.sbml.org/sbml/level3/version1/groups/version1";
return xmlns;
}
@endverbatim
</li>
\n=item\n\n<p>Strings that represent the other URI needed in this package (if any) </p>
</li>
</ol>
</li>
\n=item\n\nOverride the following pure virtual functions
\n=over\n
\n=item\n\nC<virtual const std::string& getName () const =0>. This function returns the name of the package (e.g., "layout", "groups"). </li>
\n=item\n\nC<virtual unsigned int getLevel (const std::string &uri) const =0>. This function returns the SBML level with the given URI of this package. </li>
\n=item\n\nC<virtual unsigned int getVersion (const std::string &uri) const =0>. This function returns the SBML version with the given URI of this package. </li>
\n=item\n\nC<virtual unsigned int getPackageVersion (const std::string &uri) const =0>. This function returns the package version with the given URI of this package.</li>
\n=item\n\nC<virtual unsigned int getURI (unsigned int sbmlLevel, unsigned int sbmlVersion, unsigned int pkgVersion) const =0>.
This function returns the URI (namespace) of the package corresponding to the combination of the given sbml level, sbml version, and pacakege version</li>
\n=item\n\nC<virtual SBMLExtension clone () const = 0>. This function creates and returns a deep copy of this derived object.</li>
\n=back\n
<p>For example, the above functions are overridden in the groups
package ("src/packages/groups/extension/GroupsExtension.cpp") as follows:</p>
@verbatim
const std::string&
GroupsExtension::getName() const
{
return getPackageName();
}
unsigned int
GroupsExtension::getLevel(const std::string &uri) const
{
if (uri == getXmlnsL3V1V1())
{
return 3;
}
return 0;
}
unsigned int
GroupsExtension::getVersion(const std::string &uri) const
{
if (uri == getXmlnsL3V1V1())
{
return 1;
}
return 0;
}
unsigned int
GroupsExtension::getPackageVersion(const std::string &uri) const
{
if (uri == getXmlnsL3V1V1())
{
return 1;
}
return 0;
}
const std::string&
GroupsExtension::getURI(unsigned int sbmlLevel, unsigned int sbmlVersion, unsigned int pkgVersion) const
{
if (sbmlLevel == 3)
{
if (sbmlVersion == 1)
{
if (pkgVersion == 1)
{
return getXmlnsL3V1V1();
}
}
}
static std::string empty = "";
return empty;
}
GroupsExtension
GroupsExtension::clone () const
{
return new GroupsExtension( this);
}
@endverbatim
Constructor, copy Constructor, and destructor also must be overridden
if additional data members are defined in the derived class.
</li>
\n=item\n\n<p>
Define typedef and template instantiation code for the package specific SBMLExtensionNamespaces template class
</p>
<ol>
\n=item\n\ntypedef for the package specific SBMLExtensionNamespaces template class
<p> For example, the typedef for GroupsExtension (defined in the groups package) is implemented in GroupsExtension.h as follows:</p>
@verbatim
// GroupsPkgNamespaces is derived from the SBMLNamespaces class and used when creating an object of
// SBase derived classes defined in groups package.
typedef SBMLExtensionNamespaces<GroupsExtension> GroupsPkgNamespaces;
@endverbatim
</li>
\n=item\n\ntemplate instantiation code for the above typedef definition in the implementation file (i.e., .cpp file).
<p> For example, the template instantiation code for GroupsExtension is implemented in GroupsExtension.cpp
as follows:
</p>
@verbatim
// Instantiate SBMLExtensionNamespaces<GroupsExtension> (GroupsPkgNamespaces) for DLL.
template class LIBSBML_EXTERN SBMLExtensionNamespaces<GroupsExtension>;
@endverbatim
</li>
</ol>
<p> The SBMLExtensionNamespaces template class is a derived class of
SBMLNamespaces and can be used as an argument of constructors
of SBase derived classes defined in the package extensions.
For example, a GroupsPkgNamespaces object can be used when creating a group
object as follows:
</P>
@verbatim
GroupPkgNamespaces gpns(3,1,1); // The arguments are SBML Level, SBML Version, and Groups Package Version.
Group g = new Group(&gpns); // Creates a group object of L3V1 Groups V1.
@endverbatim
<p>
Also, the GroupsPkgNamespaces object can be used when creating an
SBMLDocument object with the groups package as follows:
</p>
@verbatim
GroupsPkgNamespaces gpns(3,1,1);
SBMLDocument doc;
doc = new SBMLDocument(&gnps); // Creates an SBMLDocument of L3V1 with Groups V1.
@endverbatim
</li>
\n=item\n\nOverride the following pure virtual function which returns the SBMLNamespaces derived object
@verbatim
virtual SBMLNamespaces getSBMLExtensionNamespaces (const std::string &uri) const =0
@endverbatim
<p> For example, the function is overridden in GroupsExtension
class as follows:</p>
@verbatim
SBMLNamespaces
GroupsExtension::getSBMLExtensionNamespaces(const std::string &uri) const
{
GroupsPkgNamespaces pkgns = NULL;
if ( uri == getXmlnsL3V1V1())
{
pkgns = new GroupsPkgNamespaces(3,1,1);
}
return pkgns;
}
@endverbatim
</li>
\n=item\n\nDefine an enum type for representing the typecode of elements (SBase extended classes) defined in the package extension
<p> For example, SBMLGroupsTypeCode_t for groups package is
defined in GroupsExtension.h as follows: </p>
@verbatim
typedef enum
{
SBML_GROUPS_GROUP = 200
, SBML_GROUPS_MEMBER = 201
} SBMLGroupsTypeCode_t;
@endverbatim
<p> <em>SBML_GROUPS_GROUP</em> corresponds to the Group class (<group>)
and <em>SBML_GROUPS_MEMBER</em> corresponds to the Member (<member>) class, respectively.
<p> Similarly, SBMLLayoutTypeCode_t
for layout package is defined in LayoutExtension.h as follows: </p>
@verbatim
typedef enum
{
SBML_LAYOUT_BOUNDINGBOX = 100
, SBML_LAYOUT_COMPARTMENTGLYPH = 101
, SBML_LAYOUT_CUBICBEZIER = 102
, SBML_LAYOUT_CURVE = 103
, SBML_LAYOUT_DIMENSIONS = 104
, SBML_LAYOUT_GRAPHICALOBJECT = 105
, SBML_LAYOUT_LAYOUT = 106
, SBML_LAYOUT_LINESEGMENT = 107
, SBML_LAYOUT_POINT = 108
, SBML_LAYOUT_REACTIONGLYPH = 109
, SBML_LAYOUT_SPECIESGLYPH = 110
, SBML_LAYOUT_SPECIESREFERENCEGLYPH = 111
, SBML_LAYOUT_TEXTGLYPH = 112
} SBMLLayoutTypeCode_t;
@endverbatim
<p>
These enum values are returned by corresponding getTypeCode() functions.
(e.g. SBML_GROUPS_GROUP is returned in Group::getTypeCode())
</p>
<p>
The value of each typecode can be duplicated between those of different
packages (In the above SBMLLayoutTypeCode_t and SBMLGroupsTypeCode_t types,
unique values are assigned to enum values, but this is not mandatory.)
</p>
<p>
Thus, to distinguish the typecodes of different packages, not only the return
value of getTypeCode() function but also that of getPackageName()
function should be checked as follows:
</p>
@verbatim
void example (const SBase sb)
{
const std::string pkgName = sb->getPackageName();
if (pkgName == "core") {
switch (sb->getTypeCode()) {
case SBML_MODEL:
....
break;
case SBML_REACTION:
....
}
}
else if (pkgName == "layout") {
switch (sb->getTypeCode()) {
case SBML_LAYOUT_LAYOUT:
....
break;
case SBML_LAYOUT_REACTIONGLYPH:
....
}
}
else if (pkgName == "groups") {
switch (sb->getTypeCode()) {
case SBML_GROUPS_GROUP:
....
break;
case SBML_GROUPS_MEMBER:
....
}
}
...
}
@endverbatim
</li>
\n=item\n\nOverride the following pure virtual function which returns a string corresponding to the given typecode:
@verbatim
virtual const char SBMLExtension::getStringFromTypeCode(int typeCode) const;
@endverbatim
<p> For example, the function for groups extension is implemented as follows: </p>
@verbatim
static
const char SBML_GROUPS_TYPECODE_STRINGS[] =
{
"Group"
, "Member"
};
const char
GroupsExtension::getStringFromTypeCode(int typeCode) const
{
int min = SBML_GROUPS_GROUP;
int max = SBML_GROUPS_MEMBER;
if ( typeCode E<lt> min || typeCode E<gt> max)
{
return "(Unknown SBML Groups Type)";
}
return SBML_GROUPS_TYPECODE_STRINGS[typeCode - min];
}
@endverbatim
</li>
\n=item\n\nImplements a "static void init()" function in the derived class
<p> In the init() function, initialization code which creates an instance of
the derived class and registering code which registers the instance to
SBMLExtensionRegistry class are implemented.
</p>
For example, the init() function for groups package is implemented as follows:
@verbatim
void
GroupsExtension::init()
{
//-------------------------------------------------------------------------
//
// 1. Checks if the groups package has already been registered.
//
//-------------------------------------------------------------------------
if ( SBMLExtensionRegistry::getInstance().isRegistered(getPackageName()) )
{
// do nothing;
return;
}
//-------------------------------------------------------------------------
//
// 2. Creates an SBMLExtension derived object.
//
//-------------------------------------------------------------------------
GroupsExtension groupsExtension;
//-------------------------------------------------------------------------------------
//
// 3. Creates SBasePluginCreatorBase derived objects required for this
// extension. The derived classes can be instantiated by using the following
// template class.
//
// temaplate<class SBasePluginType> class SBasePluginCreator
//
// The constructor of the creator class has two arguments:
//
// (1) SBaseExtensionPoint : extension point to which the plugin object connected
// (2) std::vector<std::string> : a std::vector object that contains a list of URI
// (package versions) supported by the plugin object.
//
// For example, two plugin objects (plugged in SBMLDocument and Model elements) are
// required for the groups extension.
//
// Since only 'required' attribute is used in SBMLDocument by the groups package, and
// the 'required' flag must always be 'false', the existing
// SBMLDocumentPluginNotRequired class can be used as-is for the plugin.
//
// Since the lists of supported package versions (currently only L3V1-groups-V1 supported )
// are equal in the both plugin objects, the same vector object is given to each
// constructor.
//
//---------------------------------------------------------------------------------------
std::vector<std::string> packageURIs;
packageURIs.push_back(getXmlnsL3V1V1());
SBaseExtensionPoint sbmldocExtPoint("core",SBML_DOCUMENT);
SBaseExtensionPoint modelExtPoint("core",SBML_MODEL);
SBasePluginCreator<SBMLDocumentPluginNotRequired, GroupsExtension> sbmldocPluginCreator(sbmldocExtPoint,packageURIs);
SBasePluginCreator<GroupsModelPlugin, GroupsExtension> modelPluginCreator(modelExtPoint,packageURIs);
//--------------------------------------------------------------------------------------
//
// 3. Adds the above SBasePluginCreatorBase derived objects to the SBMLExtension derived object.
//
//--------------------------------------------------------------------------------------
groupsExtension.addSBasePluginCreator(&sbmldocPluginCreator);
groupsExtension.addSBasePluginCreator(&modelPluginCreator);
//-------------------------------------------------------------------------
//
// 4. Registers the SBMLExtension derived object to SBMLExtensionRegistry
//
//-------------------------------------------------------------------------
int result = SBMLExtensionRegistry::getInstance().addExtension(&groupsExtension);
if (result != LIBSBML_OPERATION_SUCCESS)
{
std::cerr << "[Error] GroupsExtension::init() failed." << std::endl;
}
}
@endverbatim
</p>
</li>
\n=item\n\nInstantiate a global SBMLExtensionRegister variable in appropriate
implementation file
<p> For example, the global variable for the groups extension is instantiated in GroupsExtension.cpp as follows: </p>
@verbatim
static SBMLExtensionRegister<GroupsExtension> groupsExtensionRegister;
@endverbatim
The init() function is invoked when the global variable is instantiated,
by which initialization and registering the package extension are performed.
</li>
</ol>
=over
=item SBMLExtension::SBMLExtension
Constructor.
=item SBMLExtension::SBMLExtension
Copy constructor.
=item SBMLExtension::getNumOfSBasePlugins
Returns the number of SBasePlugin objects stored in this object.
@return the number of SBasePlugin objects stored in this object.
=item SBMLExtension::getNumOfSupportedPackageURI
Returns the number of supported package Namespace (package versions) of this
package extension.
@return the number of supported package Namespace (package versions) of this
package extension.
=item SBMLExtension::isSupported
Returns a flag indicating, whether the given URI (package version) is
supported by this package extension.
@return true if the given URI (package version) is supported by this
package extension, otherwise false is returned.
=item SBMLExtension::getSupportedPackageURI
Returns the ith URI (the supported package version)
@param i the index of the list of URI (the list of supporeted package versions)
@return the URI of supported package version with the given index.
=item SBMLExtension::clone
(NOTICE) Package developers MUST OVERRIDE this pure virtual function
in their derived class.
Creates and returns a deep copy of this SBMLExtension object.
@return a (deep) copy of this SBase object
=item SBMLExtension::getName
(NOTICE) Package developers MUST OVERRIDE this pure virtual function
in their derived class.
Returns the name of this package (e.g. "layout", "multi").
@return the name of package extension
=item SBMLExtension::getURI
(NOTICE) Package developers MUST OVERRIDE this pure virtual function
in their derived class.
Returns the uri corresponding to the given SBML level, SBML version, and package version.
@param sbmlLevel the level of SBML
@param sbmlVersion the version of SBML
@param pkgVersion the version of package
@return a string of the package URI
=item SBMLExtension::getLevel
(NOTICE) Package developers MUST OVERRIDE this pure virtual function
in their derived class.
Returns the SBML level associated with the given URI of this package.
@param uri the string of URI that represents a versions of the package
@return the SBML level associated with the given URI of this package.
=item SBMLExtension::getVersion
(NOTICE) Package developers MUST OVERRIDE this pure virtual function
in their derived class.
Returns the SBML version associated with the given URI of this package.
@param uri the string of URI that represents a versions of the package
@return the SBML version associated with the given URI of this package.
=item SBMLExtension::getPackageVersion
(NOTICE) Package developers MUST OVERRIDE this pure virtual function
in their derived class.
Returns the package version associated with the given URI of this package.
@param uri the string of URI that represents a versions of this package
@return the package version associated with the given URI of this package.
=item SBMLExtension::getStringFromTypeCode
(NOTICE) Package developers MUST OVERRIDE this pure virtual function
in their derived class.
This method takes a type code of this package and returns a string
representing the code.
=item SBMLExtension::getSBMLExtensionNamespaces
(NOTICE) Package developers MUST OVERRIDE this pure virtual function in
their derived class.
Returns an SBMLExtensionNamespaces<class SBMLExtensionType> object
(e.g. SBMLExtensionNamespaces<LayoutExtension> whose alias type is
LayoutPkgNamespaces) corresponding to the given uri.
Null will be returned if the given uri is not defined in the corresponding
package.
@param uri the string of URI that represents one of versions of the package
@return an SBMLExtensionNamespaces<class SBMLExtensionType> object. NULL
will be returned if the given uri is not defined in the corresponding
package.
=item SBMLExtension::setEnabled
enable/disable this package.
Returned value is the result of this function.
@param isEnabled the bool value: true (enabled) or false (disabled)
@return true if this function call succeeded, otherwise false is returned.
=item SBMLExtension::isEnabled
Check if this package is enabled (true) or disabled (false).
@return true if this package is enabled, otherwise false is returned.
=item SBMLExtension::removeL2Namespaces
Removes the L2 Namespaces.
This method should be overridden by all extensions that want to serialize
to an L2 annotation.
=item SBMLExtension::addL2Namespaces
Adds all L2 Extension namespaces to the namespace list.
This method should be overridden by all extensions that want to serialize
to an L2 annotation.
=item SBMLExtension::enableL2NamespaceForDocument
Adds the L2 Namespace to the document and enables the extension.
If the extension supports serialization to SBML L2 Annotations, this
method should be overrridden, so it will be activated.
=item SBMLExtension::isInUse
Indicates whether this extension is being used by the given SBMLDocument.
The default implementation returns true. This means that when a document
had this extension enabled, it will not be possible to convert it to L2
as we cannot make sure that the extension can be converted.
@param doc the SBML document to test.
@return a boolean indicating whether the extension is actually being used
by the document.
=item SBMLExtension::getErrorTableIndex
@internal
=back
=head2 SBMLExtensionException
@sbmlpackage{core}
@htmlinclude pkg-marker-core.html Exceptions for libSBML extensions for SBML Level 3 packages.
=over
=item SBMLExtensionException::SBMLExtensionException
constructor
=back
=head2 SBMLExtensionNamespaces
@sbmlpackage{core}
@htmlinclude pkg-marker-core.html Class to store the Level, Version and XML namespace
information of an SBML extension package.
=over
=item SBMLExtensionNamespaces::SBMLExtensionNamespaces
Creates a new SBMLExtensionNamespaces object corresponding to the given SBML
C<level>, C<version> and C<package> version.
@note SBMLExtensionException will be thrown if the extension module
that supports the combination of the given sbml level, sbml version,
package name, and package version has not been registered.
@param level the SBML level
@param version the SBML version
@param pkgVersion the package version
@param prefix the prefix of the package namespace (e.g. "layout", "multi")
to be added. The package's name will be used if the given string is empty
(default).
=item SBMLExtensionNamespaces::SBMLExtensionNamespaces
Copy constructor; creates a copy of a SBMLExtensionNamespaces.
@param orig the SBMLExtensionNamespaces instance to copy.
=back
=head2 SBMLExtensionRegistry
@sbmlpackage{core}
@htmlinclude pkg-marker-core.html Registry class in which extension packages are registered.
=over
=item SBMLExtensionRegistry::getInstance
Returns an instance (singleton) of the SBMLExtensionRegistry class.
This function needs to be invoked when manipulating the SBMLExtensionRegistry class.
@return the instance of the SBMLExtensionRegistry object.
=item SBMLExtensionRegistry::addExtension
Add the given SBMLExtension to this SBMLExtensionRegistry.
@param ext the SBMLExtension object to be added.
@return integer value indicating success/failure of the
function. The possible values returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_PKG_CONFLICT LIBSBML_PKG_CONFLICT @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item SBMLExtensionRegistry::getExtension
Returns an SBMLExtension object with the given package URI or package name (string).
@param package the URI or name of the package extension
@return a clone of the SBMLExtension object with the given package URI or name. The returned
extension is to be freed (i.e.: deleted) by the caller!
=item SBMLExtensionRegistry::removeL2Namespaces
Remove all L2 Extension namespaces from the namespace list. This will call all
overriden SBMLExtension::removeL2Namespaces methods.
=item SBMLExtensionRegistry::addL2Namespaces
adds all L2 Extension namespaces to the namespace list. This will call all
overriden SBMLExtension::addL2Namespaces methods.
=item SBMLExtensionRegistry::enableL2NamespaceForDocument
Enables all extensions that support serialization / deserialization with
SBML Annotations.
=item SBMLExtensionRegistry::disableUnusedPackages
Goes through all extensions in the list of plugins of the given document
and disables all plugins that are not being used.
=item SBMLExtensionRegistry::disablePackage
Disables the package with the given URI / name.
=item SBMLExtensionRegistry::isPackageEnabled
If the given C<package> is enabled, returns C<true>; otherwise,
returns C<false>.
@return the status (enabled = B<true>, disabled = B<false> of the given package.
=item SBMLExtensionRegistry::enablePackage
Enables the package with the given URI / name.
=item SBMLExtensionRegistry::getExtensionInternal
Returns an SBMLExtension object with the given package URI or package name (string).
@param package the URI or name of the package extension
@return the SBMLExtension object with the given package URI or name. The returned
extension is NOT ALLOWED to be freed (i.e.: deleted)!
=item SBMLExtensionRegistry::getNumExtension
Returns the number of SBMLExtension with the given extension point.
@param extPoint the SBaseExtensionPoint
@return the number of SBMLExtension with the given extension point.
=item SBMLExtensionRegistry::setEnabled
Enable/disable the package with the given uri.
@param uri the URI of the target package.
@param isEnabled the bool value corresponding to enabled (true) or
disabled (false)
@return false will be returned if the given bool value is false
or the given package is not registered, otherwise true will be
returned.
=item SBMLExtensionRegistry::isEnabled
Checks if the extension with the given URI is enabled (true) or
disabled (false)
@param uri the URI of the target package.
@return false will be returned if the given package is disabled
or not registered, otherwise true will be returned.
=item SBMLExtensionRegistry::isRegistered
Checks if the extension with the given URI is registered (true)
or not (false)
@param uri the URI of the target package.
@return true will be returned if the package with the given URI
is registered, otherwise false will be returned.
=item SBMLExtensionRegistry::getRegisteredPackageNames
Returns a list of registered packages (such as 'layout', 'fbc' or 'comp')
the list contains char strings and has to be freed by the caller.
@return the names of the registered packages in a list
=item SBMLExtensionRegistry::getNumRegisteredPackages
Returns the number of registered packages.
@return the number of registered packages.
=item SBMLExtensionRegistry::getRegisteredPackageName
Returns the registered package name at the given index
@param index zero based index of the package name to return
@return the package name with the given index or NULL
=item SBMLExtensionRegistry::SBMLExtensionRegistry
=item SBMLExtensionRegistry::SBMLExtensionRegistry
=back
=head2 ASTBase
@sbmlpackage{core}
@htmlinclude pkg-marker-core.html Base node for AST classes.
@internal
=over
=item ASTBase::ASTBase
@internal
Copy constructor
=item ASTBase::deepCopy
@internal
Creates a copy (clone).
=item ASTBase::loadASTPlugins
@internal
=item ASTBase::getType
@internal
Get the type of this ASTNode. The value returned is one of the
enumeration values such as @link ASTNodeType_t#AST_LAMBDA
AST_LAMBDA@endlink, @link ASTNodeType_t#AST_PLUS AST_PLUS@endlink,
etc.
@return the type of this ASTNode.
=item ASTBase::getExtendedType
@internal
=item ASTBase::isSetType
@internal
=item ASTBase::setType
@internal
Sets the type of this ASTNode to the given type code. A side-effect
of doing this is that any numerical values previously stored in this
node are reset to zero.
@param type the type to which this node should be set
@return integer value indicating success/failure of the
function. The possible values returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item ASTBase::setType
@internal
=item ASTBase::isAvogadro
@internal
=item ASTBase::isBoolean
@internal
=item ASTBase::isBinaryFunction
@internal
=item ASTBase::isConstant
@internal
=item ASTBase::isExponential
@internal
=item ASTBase::isCiNumber
@internal
=item ASTBase::isConstantNumber
@internal
=item ASTBase::isCSymbolFunction
@internal
=item ASTBase::isCSymbolNumber
@internal
=item ASTBase::isFunction
@internal
=item ASTBase::isInteger
@internal
=item ASTBase::isLambda
@internal
=item ASTBase::isLogical
@internal
=item ASTBase::isName
@internal
=item ASTBase::isNaryFunction
@internal
=item ASTBase::isNumber
@internal
=item ASTBase::isOperator
@internal
=item ASTBase::isPiecewise
@internal
=item ASTBase::isQualifier
@internal
=item ASTBase::isRational
@internal
=item ASTBase::isReal
@internal
=item ASTBase::isRelational
@internal
=item ASTBase::isSemantics
@internal
=item ASTBase::isUnaryFunction
@internal
=item ASTBase::isUnknown
@internal
=item ASTBase::isUserFunction
@internal
=item ASTBase::isNumberNode
@internal
=item ASTBase::isFunctionNode
@internal
=item ASTBase::isTopLevelMathMLFunctionNodeTag
@internal
=item ASTBase::isTopLevelMathMLNumberNodeTag
@internal
=item ASTBase::write
@internal
=item ASTBase::read
@internal
=item ASTBase::addExpectedAttributes
@internal
=item ASTBase::readAttributes
@internal
=item ASTBase::logError
@internal
=item ASTBase::isChild
@internal
=item ASTBase::setIsChildFlag
@internal
=item ASTBase::getClass
@internal
=item ASTBase::getId
@internal
=item ASTBase::getStyle
@internal
=item ASTBase::getParentSBMLObject
@internal
=item ASTBase::isSetClass
@internal
=item ASTBase::isSetId
@internal
=item ASTBase::isSetStyle
@internal
=item ASTBase::isSetParentSBMLObject
@internal
=item ASTBase::setClass
@internal
=item ASTBase::setId
@internal
=item ASTBase::setStyle
@internal
=item ASTBase::setParentSBMLObject
@internal
=item ASTBase::unsetClass
@internal
=item ASTBase::unsetId
@internal
=item ASTBase::unsetStyle
@internal
=item ASTBase::unsetParentSBMLObject
@internal
=item ASTBase::getFunction
@internal
=item ASTBase::addPlugin
@internal
=item ASTBase::getPlugin
@internal
Returns a plug-in object (extension interface) for an SBML Level 3
package extension with the given package name or URI.
@param package the name or URI of the package
@return the plug-in object (the libSBML extension interface) of
a package extension with the given package name or URI.
=item ASTBase::getPlugin
@internal
Returns a plug-in object (extension interface) for an SBML Level 3
package extension with the given package name or URI.
@param package the name or URI of the package
@return the plug-in object (the libSBML extension interface) of a
package extension with the given package name or URI.
=item ASTBase::getPlugin
@internal
Returns the nth plug-in object (extension interface) for an SBML Level 3
package extension.
@param n the index of the plug-in to return
@return the plug-in object (the libSBML extension interface) of
a package extension with the given package name or URI.
=item ASTBase::getPlugin
@internal
Returns the nth plug-in object (extension interface) for an SBML Level 3
package extension.
@param n the index of the plug-in to return
@return the plug-in object (the libSBML extension interface) of a
package extension with the given package name or URI.
=item ASTBase::getNumPlugins
@internal
Returns the number of plug-in objects (extenstion interfaces) for SBML
Level 3 package extensions known.
@return the number of plug-in objects (extension interfaces) of
package extensions known by this instance of libSBML.
=item ASTBase::getTypeFromName
@internal
=item ASTBase::getNameFromType
@internal
=item ASTBase::setUserData
@internal
=item ASTBase::*getUserData
@internal
=item ASTBase::isSetUserData
@internal
=item ASTBase::unsetUserData
@internal
=item ASTBase::writeNodeOfType
@internal
=item ASTBase::isWellFormedNode
@internal
=item ASTBase::hasCorrectNumberArguments
@internal
=item ASTBase::getTypeCode
@internal
=item ASTBase::getPackageName
@internal
=item ASTBase::setPackageName
@internal
=item ASTBase::hasCnUnits
@internal
=item ASTBase::getUnitsPrefix
@internal
=item ASTBase::resetPackageName
@internal
=item ASTBase::checkPrefix
@internal
=item ASTBase::writeStartEndElement
@internal
=item ASTBase::writeConstant
@internal
=item ASTBase::writeStartElement
@internal
=item ASTBase::writeAttributes
@internal
=item ASTBase::writeENotation
@internal
=item ASTBase::writeENotation
@internal
=item ASTBase::writeNegInfinity
@internal
=item ASTBase::syncMembersFrom
@internal
=item ASTBase::syncMembersAndResetParentsFrom
@internal
=item ASTBase::syncPluginsFrom
@internal
=item ASTBase::getValue
@internal
=item ASTBase::getNumChildren
@internal
=back
=head2 ASTNode
@sbmlpackage{core}
@htmlinclude pkg-marker-core.html Abstract Syntax Tree (AST) representation of a
mathematical expression.
@htmlinclude not-sbml-warning.html
Abstract Syntax Trees (ASTs) are a simple kind of data structure used in
libSBML for storing mathematical expressions. The ASTNode is the
cornerstone of libSBML's AST representation. An AST "node" represents the
most basic, indivisible part of a mathematical formula and come in many
types. For instance, there are node types to represent numbers (with
subtypes to distinguish integer, real, and rational numbers), names
(e.g., constants or variables), simple mathematical operators, logical
or relational operators and functions. LibSBML ASTs provide a canonical,
in-memory representation for all mathematical formulas regardless of
their original format (which might be MathML or might be text strings).
C<opydetails> doc_what_is_astnode
@if clike <h3><a class="anchor" name="ASTNodeType_t">
ASTNodeType_t</a></h3> @else <h3><a class="anchor"
name="ASTNodeType_t">The set of possible ASTNode types</a></h3> @endif@~
C<opydetails> doc_astnode_types
<h3><a class="anchor" name="math-convert">Converting between ASTs and text strings</a></h3>
The text-string form of mathematical formulas produced by @if clike SBML_formulaToString()@endif@if csharp SBML_formulaToString()@endif@if python libsbml.formulaToString()@endif@if java <code><a href="libsbml.html#formulaToString(org.sbml.libsbml.ASTNode)">libsbml.formulaToString()</a></code>@endif@~ and
read by @if clike SBML_parseFormula()@endif@if csharp SBML_parseFormula()@endif@if python libsbml.parseFormula()@endif@if java <code><a href="libsbml.html#parseFormula(java.lang.String)">libsbml.parseFormula(String formula)</a></code>@endif@~
and
@if clike SBML_parseL3Formula()@endif@if csharp SBML_parseL3Formula()@endif@if python libsbml.parseL3Formula()@endif@if java <code><a href="libsbml.html#parseL3Formula(java.lang.String)">libsbml.parseL3Formula(String formula)</a></code>@endif@~
are in a simple C-inspired infix notation. A
formula in one of these two text-string formats can be handed to a program
that understands SBML mathematical expressions, or used as part of a
translation system. The libSBML distribution comes with example
programs in the C<"examples"> subdirectory that demonstrate such things
as translating infix formulas into MathML and vice-versa.
Please see the documentation for the functions
@if clike SBML_parseFormula()@endif@if csharp SBML_parseFormula()@endif@if python libsbml.parseFormula()@endif@if java <code><a href="libsbml.html#parseFormula(java.lang.String)">libsbml.parseFormula(String formula)</a></code>@endif@~
and
@if clike SBML_parseL3Formula()@endif@if csharp SBML_parseL3Formula()@endif@if python libsbml.parseL3Formula()@endif@if java <code><a href="libsbml.html#parseL3Formula(java.lang.String)">libsbml.parseL3Formula(String formula)</a></code>@endif@~
for detailed explanations of the infix syntax they accept.
@if clike @see SBML_parseL3Formula()@endif@~
@if csharp @see SBML_parseL3Formula()@endif@~
@if python @see libsbml.parseL3Formula()@endif@~
@if java @see <code><a href="libsbml.html#parseL3Formula(String formula)">libsbml.parseL3Formula(String formula)</a></code>@endif@~
@if clike @see SBML_parseFormula()@endif@~
@if csharp @see SBML_parseFormula()@endif@~
@if python @see libsbml.parseFormula()@endif@~
@if java @see <code><a href="libsbml.html#parseFormula(String formula)">libsbml.parseFormula(String formula)</a></code>@endif@~
@if clike @see SBML_formulaToString()@endif@~
@if csharp @see SBML_formulaToString()@endif@~
@if python @see libsbml.formulaToString()@endif@~
@if java @see <code><a href="libsbml.html#formulaToString(org.sbml.libsbml.ASTNode)">libsbml.formulaToString()</a></code>@endif@~
=over
=item ASTNode::ASTNode
Creates a new ASTNode.
Unless the argument C<type> is given, the returned node will by
default have a type of @link ASTNodeType_t#AST_UNKNOWN
AST_UNKNOWN@endlink. If the type isn't supplied when caling this
constructor, the caller should set the node type to something else as
soon as possible using
@if clike setType()@else ASTNode::setType(int)@endif.
@param type an optional
@if clike @link #ASTNodeType_t ASTNodeType_t@endlink@else type@endif@~
code indicating the type of node to create.
@if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
=item ASTNode::ASTNode
@internal
=item ASTNode::ASTNode
@internal
=item ASTNode::ASTNode
@internal
=item ASTNode::ASTNode
Creates a new ASTNode from the given Token.
The resulting ASTNode will contain the same data as the given C<token>.
@param token the token to use as a starting point for creating the
ASTNode object.
=item ASTNode::ASTNode
Copy constructor; creates a deep copy of the given ASTNode.
@param orig the ASTNode to be copied.
=item ASTNode::freeName
Frees the name of this ASTNode and sets it to C<NULL>.
This operation is only applicable to ASTNode objects corresponding to
operators, numbers, or @link ASTNodeType_t#AST_UNKNOWN
AST_UNKNOWN@endlink. This method has no effect on other types of
nodes.
@return integer value indicating success/failure of the
function. The possible values returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_UNEXPECTED_ATTRIBUTE LIBSBML_UNEXPECTED_ATTRIBUTE @endlink
=item ASTNode::canonicalize
Converts this ASTNode to a canonical form.
The rules determining the canonical form conversion are as follows:
@li If the node type is @link ASTNodeType_t#AST_NAME AST_NAME@endlink
and the node name matches C<"ExponentialE">, C<"Pi">, C<"True"> or @c
"False" the node type is converted to the corresponding
C<AST_CONSTANT_><em><span class="placeholder">X</span></em> type.
@li If the node type is an @link ASTNodeType_t#AST_FUNCTION
AST_FUNCTION@endlink and the node name matches an SBML (MathML) function name, logical operator name, or
relational operator name, the node is converted to the corresponding
C<AST_FUNCTION_><em><span class="placeholder">X</span></em> or
C<AST_LOGICAL_><em><span class="placeholder">X</span></em> type.
SBML Level 1 function names are searched first; thus, for
example, canonicalizing C<log> will result in a node type of @link
ASTNodeType_t#AST_FUNCTION_LN AST_FUNCTION_LN@endlink. (See the SBML
Level 1 Version 2 Specification, Appendix C.)
Sometimes, canonicalization of a node results in a structural
conversion of the node as a result of adding a child. For example, a
node with the SBML Level 1 function name C<sqr> and a single
child node (the argument) will be transformed to a node of type
@link ASTNodeType_t#AST_FUNCTION_POWER AST_FUNCTION_POWER@endlink with
two children. The first child will remain unchanged, but the second
child will be an ASTNode of type @link ASTNodeType_t#AST_INTEGER
AST_INTEGER@endlink and a value of 2. The function names that result
in structural changes are: C<log10>, C<sqr>, and C<sqrt>.
@return C<true> if this node was successfully converted to
canonical form, C<false> otherwise.
=item ASTNode::addChild
Adds the given node as a child of this ASTNode.
Child nodes are added in-order, from left to right.
@param child the ASTNode instance to add
@return integer value indicating success/failure of the
function. The possible values returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
C<opydetails> doc_warning_modifying_structure
@see prependChild(ASTNode child)
@see replaceChild(unsigned int n, ASTNode child)
@see insertChild(unsigned int n, ASTNode child)
@see removeChild(unsigned int n)
@see isWellFormedASTNode()
=item ASTNode::prependChild
Adds the given node as a child of this ASTNode.
This method adds child nodes from right to left.
@param child the ASTNode instance to add
@return integer value indicating success/failure of the
function. The possible values returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
C<opydetails> doc_warning_modifying_structure
@see addChild(ASTNode child)
@see replaceChild(unsigned int n, ASTNode child)
@see insertChild(unsigned int n, ASTNode child)
@see removeChild(unsigned int n)
=item ASTNode::removeChild
Removes the nth child of this ASTNode object.
@param n unsigned int the index of the child to remove
@return integer value indicating success/failure of the
function. The possible values returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INDEX_EXCEEDS_SIZE LIBSBML_INDEX_EXCEEDS_SIZE @endlink
C<opydetails> doc_warning_modifying_structure
@see addChild(ASTNode child)
@see prependChild(ASTNode child)
@see replaceChild(unsigned int n, ASTNode child)
@see insertChild(unsigned int n, ASTNode child)
=item ASTNode::replaceChild
Replaces the nth child of this ASTNode with the given ASTNode.
@param n unsigned int the index of the child to replace
@param newChild ASTNode to replace the nth child
@return integer value indicating success/failure of the
function. The possible values returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INDEX_EXCEEDS_SIZE LIBSBML_INDEX_EXCEEDS_SIZE @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT @endlink
C<opydetails> doc_warning_modifying_structure
@see addChild(ASTNode child)
@see prependChild(ASTNode child)
@see insertChild(unsigned int n, ASTNode child)
@see removeChild(unsigned int n)
=item ASTNode::insertChild
Inserts the given ASTNode node at a given point in the current ASTNode's
list of children.
@param n unsigned int the index of the ASTNode being added
@param newChild ASTNode to insert as the nth child
@return integer value indicating success/failure of the
function. The possible values returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INDEX_EXCEEDS_SIZE LIBSBML_INDEX_EXCEEDS_SIZE @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT @endlink
C<opydetails> doc_warning_modifying_structure
@see addChild(ASTNode child)
@see prependChild(ASTNode child)
@see replaceChild(unsigned int n, ASTNode child)
@see removeChild(unsigned int n)
=item ASTNode::deepCopy
Creates a recursive copy of this node and all its children.
@return a copy of this ASTNode and all its children. The caller owns
the returned ASTNode and is responsible for deleting it.
=item ASTNode::getChild
Returns the child at index n of this node.
@param n the index of the child to get
@return the nth child of this ASTNode or C<NULL> if this node has no nth
child (C<n > >
@if clike getNumChildren()@else ASTNode::getNumChildren()@endif@~
C<- 1>).
@see getNumChildren()
@see getLeftChild()
@see getRightChild()
=item ASTNode::getLeftChild
Returns the left child of this node.
@return the left child of this ASTNode. This is equivalent to calling
@if clike getChild()@else ASTNode::getChild(unsigned int)@endif@~
with an argument of C<0>.
@see getNumChildren()
@see getChild(@if java unsigned int n@endif)
@see getRightChild()
=item ASTNode::getRightChild
Returns the right child of this node.
@return the right child of this ASTNode, or C<NULL> if this node has no
right child. If
@if clike getNumChildren()@else ASTNode::getNumChildren()@endif@~
C<> 1>, then this is equivalent to:
@verbatim
getChild( getNumChildren() - 1 );
@endverbatim
@see getNumChildren()
@see getLeftChild()
@see getChild(@if java unsigned int n@endif)
=item ASTNode::getNumChildren
Returns the number of children of this node.
@return the number of children of this ASTNode, or 0 is this node has
no children.
=item ASTNode::addSemanticsAnnotation
Adds the given XMLNode as a MathML C<<semantics>>
element to this ASTNode.
C<opydetails> doc_about_mathml_semantic_annotations
@param sAnnotation the annotation to add.
@return integer value indicating success/failure of the
function. The possible values returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
C<opydetails> doc_note_mathml_semantic_annotations_uncommon
@see ASTNode::getNumSemanticsAnnotations()
@see ASTNode::getSemanticsAnnotation(@if java unsigned int n@endif)
=item ASTNode::getNumSemanticsAnnotations
Returns the number of MathML C<<semantics>> element
elements on this node.
C<opydetails> doc_about_mathml_semantic_annotations
@return the number of annotations of this ASTNode.
C<opydetails> doc_note_mathml_semantic_annotations_uncommon
@see ASTNode::addSemanticsAnnotation(@if java XMLNode sAnnotation@endif)
@see ASTNode::getSemanticsAnnotation(@if java unsigned int n@endif)
=item ASTNode::getSemanticsAnnotation
Returns the nth MathML C<<semantics>> element on this
ASTNode.
C<opydetails> doc_about_mathml_semantic_annotations
@param n the index of the annotation to return. Callers should
use ASTNode::getNumSemanticsAnnotations() to first find out how
many annotations there are.
@return the nth annotation inside this ASTNode, or C<NULL> if this node has
no nth annotation (C<n >>
@if clike getNumSemanticsAnnotations()@else ASTNode::getNumSemanticsAnnotations()@endif@~
C<- 1>).
C<opydetails> doc_note_mathml_semantic_annotations_uncommon
@see ASTNode::addSemanticsAnnotation(@if java XMLNode sAnnotation@endif)
@see ASTNode::getNumSemanticsAnnotations()
=item ASTNode::getListOfNodes
Returns a list of nodes satisfying a given predicate.
This performs a depth-first search of the tree rooted at this ASTNode
object, and returns a List of nodes for which the given function
C<predicate(node)> returns C<true>.
For portability between different programming languages, the predicate
is passed in as a pointer to a function. @if clike The function
definition must have the type @link ASTNode.h::ASTNodePredicate
ASTNodePredicate@endlink, which is defined as
@verbatim
int ( ASTNodePredicate) (const ASTNode node);
@endverbatim
where a return value of nonzero represents C<true> and zero
represents C<false>. @endif
@param predicate the predicate to use
@return the list of nodes for which the predicate returned C<true>
. The List returned is owned by the caller and should be
deleted after the caller is done using it. The ASTNode objects in the
list; however, are not owned by the caller (as they still belong to
the tree itself), and therefore should not be deleted.
@see ASTNode::fillListOfNodes(@if java ASTNodePredicate predicate, List lst@endif)
=item ASTNode::fillListOfNodes
Returns a list of nodes rooted at a given node and satisfying a given
predicate.
This method is identical to calling
ASTNode::getListOfNodes(@if java ASTNodePredicate predicate@endif), except
that instead of creating a new List object, it uses the one passed in as
argument C<lst>. This method a depth-first search of the tree rooted at
this ASTNode object, and adds to the list C<lst> the nodes for which the
given function C<predicate(node)> returns C<true>.
For portability between different programming languages, the predicate
is passed in as a pointer to a function. The function definition must
have the type @link ASTNode.h::ASTNodePredicate
ASTNodePredicate@endlink, which is defined as
@verbatim
int ( ASTNodePredicate) (const ASTNode_t node);
@endverbatim
where a return value of nonzero represents C<true> and zero
represents C<false>.
@param predicate the predicate to use.
@param lst the List to which ASTNode objects should be added.
@see getListOfNodes(@if java ASTNodePredicate predicate@endif)
=item ASTNode::getCharacter
Returns the value of this node as a single character.
This function should be called only when
@if clike getType()@else ASTNode::getType()@endif@~ returns
@link ASTNodeType_t#AST_PLUS AST_PLUS@endlink,
@link ASTNodeType_t#AST_MINUS AST_MINUS@endlink,
@link ASTNodeType_t#AST_TIMES AST_TIMES@endlink,
@link ASTNodeType_t#AST_DIVIDE AST_DIVIDE@endlink or
@link ASTNodeType_t#AST_POWER AST_POWER@endlink.
@return the value of this ASTNode as a single character
=item ASTNode::getId
Returns the MathML C<id> attribute value of this ASTNode.
@return the MathML id of this ASTNode.
@see isSetId()
@see setId(@if java const std::string& id@endif)
@see unsetId()
=item ASTNode::getClass
Returns the MathML C<class> attribute value of this ASTNode.
@return the MathML class of this ASTNode, if any exists.
@see isSetClass()
@see @if java setClassName(const std::string& id)@else setClass()@endif@~
@see unsetClass()
=item ASTNode::getStyle
Returns the MathML C<style> attribute value of this ASTNode.
@return the MathML style of this ASTNode, if any exists.
@see isSetStyle()
@see setStyle(@if java const std::string& id@endif)
@see unsetStyle()
=item ASTNode::getInteger
Returns the value of this node as an integer.
If this node type is @link ASTNodeType_t#AST_RATIONAL
AST_RATIONAL@endlink, this method returns the value of the numerator.
@return the value of this ASTNode as a (C<long>) integer.
@note This function should be called only when
@if clike getType()@else ASTNode::getType()@endif@~ returns
@link ASTNodeType_t#AST_INTEGER AST_INTEGER@endlink or
@link ASTNodeType_t#AST_RATIONAL AST_RATIONAL@endlink.
It will return C<0> if the node type is I<not> one of these, but since
C<0> may be a valid value for integer, it is important to be sure that
the node type is one of the expected types in order to understand if @c
0 is the actual value.
=item ASTNode::getName
Returns the value of this node as a string.
This function may be called on nodes that (1) are not operators, i.e.,
nodes for which @if clike isOperator()@else ASTNode::isOperator()@endif@~
returns C<false>, and (2) are not numbers, i.e.,
@if clike isNumber()@else ASTNode::isNumber()@endif@~ returns C<false>.
@return the value of this ASTNode as a string, or C<NULL> if it is
a node that does not have a name equivalent (e.g., if it is a number).
=item ASTNode::getOperatorName
Returns the value of this operator node as a string.
This function may be called on nodes that are operators, i.e., nodes for
which @if clike isOperator()@else ASTNode::isOperator()@endif@~ returns
C<true>.
@return the name of this operator ASTNode as a string (or C<NULL> if not
an operator).
=item ASTNode::getNumerator
Returns the value of the numerator of this node.
This function should be called only when
@if clike getType()@else ASTNode::getType()@endif@~ returns
@link ASTNodeType_t#AST_RATIONAL AST_RATIONAL@endlink or
@link ASTNodeType_t#AST_INTEGER AST_INTEGER@endlink.
@return the value of the numerator of this ASTNode.
=item ASTNode::getDenominator
Returns the value of the denominator of this node.
@return the value of the denominator of this ASTNode, or C<1> if
this node has no numerical value.
@note This function should be called only when
@if clike getType()@else ASTNode::getType()@endif@~ returns
@link ASTNodeType_t#AST_RATIONAL AST_RATIONAL@endlink.
It will return C<1> if the node type is another type, but since C<1> may
be a valid value for the denominator of a rational number, it is
important to be sure that the node type is the correct type in order to
correctly interpret the returned value.
=item ASTNode::getReal
Returns the real-numbered value of this node.
This function performs the necessary arithmetic if the node type is
@link ASTNodeType_t#AST_REAL_E AST_REAL_E@endlink (<em>mantissa
10<sup> exponent</sup></em>) or
@link ASTNodeType_t#AST_RATIONAL AST_RATIONAL@endlink
(<em>numerator / denominator</em>).
@return the value of this ASTNode as a real (double), or C<0>
if this is not a node that holds a number.
@note This function should be called only when this ASTNode has a
numerical value type. It will return C<0> if the node type is another
type, but since C<0> may be a valid value, it is important to be sure
that the node type is the correct type in order to correctly interpret
the returned value.
=item ASTNode::getMantissa
Returns the mantissa value of this node.
If @if clike getType()@else ASTNode::getType()@endif@~ returns
@link ASTNodeType_t#AST_REAL AST_REAL@endlink, this method is
identical to ASTNode::getReal().
@return the value of the mantissa of this ASTNode, or C<0> if this
node is not a type that has a real-numbered value.
@note This function should be called only when
@if clike getType()@else ASTNode::getType()@endif@~ returns
@link ASTNodeType_t#AST_REAL_E AST_REAL_E@endlink,
@link ASTNodeType_t#AST_REAL AST_REAL@endlink or
@link ASTNodeType_t#AST_NAME_AVOGADRO AST_NAME_AVOGADRO@endlink. It
will return C<0> if the node type is another type, but since C<0> may be
a valid value, it is important to be sure that the node type is the
correct type in order to correctly interpret the returned value.
=item ASTNode::getExponent
Returns the exponent value of this ASTNode.
@return the value of the exponent of this ASTNode, or C<0> if this
is not a type of node that has an exponent.
@note This function should be called only when
@if clike getType()@else ASTNode::getType()@endif@~
returns @link ASTNodeType_t#AST_REAL_E AST_REAL_E@endlink.
It will return C<0> if the node type is another type, but since C<0> may
be a valid value, it is important to be sure that the node type is the
correct type in order to correctly interpret the returned value.
=item ASTNode::getPrecedence
Returns the precedence of this node in the infix math syntax of SBML
Level 1.
For more information about the infix syntax, see the discussion about <a
href="#math-convert">text string formulas</a> at the top of the
documentation for ASTNode.
@return an integer indicating the precedence of this ASTNode
=item ASTNode::getType
Returns the type of this ASTNode.
The value returned is one of the Core AST type codes such as
@link ASTNodeType_t#AST_LAMBDA AST_LAMBDA@endlink,
@link ASTNodeType_t#AST_PLUS AST_PLUS@endlink, etc.
@return the type of this ASTNode.
@note The introduction of extensibility in SBML Level 3 brings with
it a need to allow for the possibility of node types that are defined by
plug-ins implementing SBML Level 3 packages. If a given ASTNode is
a construct created by a package rather than libSBML Core, then
getType() will return @link ASTNodeType_t#AST_ORIGINATES_IN_PACKAGE
AST_ORIGINATES_IN_PACKAGE@endlink. Callers can then obtain the
package-specific type by calling getExtendedType().
@see getExtendedType()
=item ASTNode::getExtendedType
Returns the extended type of this ASTNode.
The type may be either a core
@if notclike integer type code@else ASTNodeType_t value@endif
or a value of a type code defined by an SBML Level 3 package.
@return the type of this ASTNode.
@note When the ASTNode is of a type from a package, the
value returned by ASTNode::getType() will be @link
ASTNodeType_t#AST_ORIGINATES_IN_PACKAGE AST_ORIGINATES_IN_PACKAGE@endlink
and getExtendedType() will return a package-specific type code.
To find out the possible package-specific types (if any), please
consult the documentation for the particular package.
@see getType()
=item ASTNode::getUnits
Returns the units of this ASTNode.
@htmlinclude about-sbml-units-attrib.html
@return the units of this ASTNode.
@note The C<sbml:units> attribute is only available in SBML
Level 3. It may not be used in Levels 1–2 of SBML.
@if clike @see SBML_parseL3Formula()@endif@~
@if csharp @see SBML_parseL3Formula()@endif@~
@if python @see libsbml.parseL3Formula()@endif@~
@if java @see <code><a href="libsbml.html#parseL3Formula(String formula)">libsbml.parseL3Formula(String formula)</a></code>@endif@~
=item ASTNode::isAvogadro
Returns C<true> if this node represents the predefined
value for Avogadro's constant.
SBML Level 3 introduced a predefined MathML C<<csymbol>>
for the value of Avogadro's constant. LibSBML stores this internally as
a node of type @link ASTNodeType_t#AST_NAME_AVOGADRO AST_NAME_AVOGADRO@endlink.
This method returns C<true> if this node has that type.
@return C<true> if this ASTNode is the special symbol avogadro,
C<false> otherwise.
@if clike @see SBML_parseL3Formula()@endif@~
@if csharp @see SBML_parseL3Formula()@endif@~
@if python @see libsbml.parseL3Formula()@endif@~
@if java @see <code><a href="libsbml.html#parseL3Formula(String formula)">libsbml.parseL3Formula(String formula)</a></code>@endif@~
=item ASTNode::isBoolean
Returns C<true> if this node has a Boolean type.
The ASTNode objects that have Boolean types are the logical operators,
relational operators, and the constants C<true> or C<false>.
@return C<true> if this ASTNode has a Boolean type, C<false> otherwise.
=item ASTNode::returnsBoolean
Returns C<true> if this node returns a Boolean value.
This function looks at the whole ASTNode rather than just the top level
of the ASTNode. Thus, it will consider return values from piecewise
statements. In addition, if this ASTNode uses a function call to a
user-defined function, the return value of the corresponding
FunctionDefinition object will be determined. Note that this is only
possible where the ASTNode can trace its parent Model; that is, the
ASTNode must represent the C<<math>> element of some
SBML object that has already been added to an instance of an
SBMLDocument.
@param model the Model to use as context
@see isBoolean()
@return true if this ASTNode returns a boolean, C<false> otherwise.
=item ASTNode::isConstant
Returns C<true> if this node represents a MathML
constant.
Examples of MathML constants include such things as pi.
@return C<true> if this ASTNode is a MathML constant, C<false>
otherwise.
@note This function will also return C<true> for nodes of type @link
ASTNodeType_t#AST_NAME_AVOGADRO AST_NAME_AVOGADRO@endlink in SBML Level 3.
=item ASTNode::isFunction
Returns C<true> if this node represents a function.
The three types of functions in SBML are MathML functions (e.g.,
C<abs()>), SBML Level 1 functions (in the SBML
Level 1 math syntax), and user-defined functions (using
FunctionDefinition in SBML Level 2 and 3).
@return C<true> if this ASTNode is a function, C<false> otherwise.
=item ASTNode::isInfinity
Returns C<true> if this node represents the special IEEE 754
value for infinity.
@return C<true> if this ASTNode is the special IEEE 754 value infinity,
C<false> otherwise.
=item ASTNode::isInteger
Returns C<true> if this node contains an integer value.
@return C<true> if this ASTNode is of type @link
ASTNodeType_t#AST_INTEGER AST_INTEGER@endlink, C<false> otherwise.
=item ASTNode::isLambda
Returns C<true> if this node is a MathML
C<<lambda>>.
@return C<true> if this ASTNode is of type @link ASTNodeType_t#AST_LAMBDA
AST_LAMBDA@endlink, C<false> otherwise.
=item ASTNode::isLog10
Returns C<true> if this node represents a C<log10> function.
More precisely, this predicate returns C<true> if the node type is @link
ASTNodeType_t#AST_FUNCTION_LOG AST_FUNCTION_LOG@endlink with two
children, the first of which is an @link ASTNodeType_t#AST_INTEGER
AST_INTEGER@endlink equal to 10.
@return C<true> if the given ASTNode represents a C<log10>() function, @c
false otherwise.
@if clike @see SBML_parseL3Formula()@endif@~
@if csharp @see SBML_parseL3Formula()@endif@~
@if python @see libsbml.parseL3Formula()@endif@~
@if java @see <code><a href="libsbml.html#parseL3Formula(String formula)">libsbml.parseL3Formula(String formula)</a></code>@endif@~
=item ASTNode::isLogical
Returns C<true> if this node is a MathML logical operator.
The possible MathML logical operators are C<and>, C<or>, C<not>, and @c
xor.
@return C<true> if this ASTNode is a MathML logical operator, C<false>
otherwise.
=item ASTNode::isName
Returns C<true> if this node is a user-defined variable name
or the symbols for time or Avogadro's constant.
SBML Levels 2 and 3 provides C<<csymbol>>
definitions for "time" and "avogadro", which can be used to represent
simulation time and Avogadro's constant in MathML.
@return C<true> if this ASTNode is a user-defined variable name in SBML
or the special symbols for time or Avogadro's constant. It returns @c
false otherwise.
=item ASTNode::isNaN
Returns C<true> if this node represents the special IEEE 754
value "not a number" (NaN).
@return C<true> if this ASTNode is the special IEEE 754 NaN, C<false>
otherwise.
=item ASTNode::isNegInfinity
Returns C<true> if this node represents the special IEEE 754
value "negative infinity".
@return C<true> if this ASTNode is the special IEEE 754 value negative
infinity, C<false> otherwise.
=item ASTNode::isNumber
Returns C<true> if this node contains a number.
@return C<true> if this ASTNode is a number, C<false> otherwise.
=item ASTNode::isOperator
Returns C<true> if this node is a mathematical
operator.
The possible mathematical operators in the MathML syntax supported by
SBML are C<+>, C<->, C< >, C</>
and C<^> (power).
@return C<true> if this ASTNode is an operator, C<false> otherwise.
=item ASTNode::isPiecewise
Returns C<true> if this node is the MathML
C<<piecewise>> construct.
@return C<true> if this ASTNode is a MathML C<piecewise> function,
C<false> otherwise.
=item ASTNode::isQualifier
Predicate returning C<true> if this node is a MathML
qualifier.
The MathML qualifier node types are C<bvar>, C<degree>, C<base>, @c
piece, and C<otherwise>.
@return C<true> if this ASTNode is a MathML qualifier, C<false>
otherwise.
=item ASTNode::isRational
Returns C<true> if this node represents a rational number.
@return C<true> if this ASTNode is of type @link
ASTNodeType_t#AST_RATIONAL AST_RATIONAL@endlink, @c
false otherwise.
=item ASTNode::isReal
Returns C<true> if this node can represent a real number.
More precisely, this node must be of one of the following types: @link
ASTNodeType_t#AST_REAL AST_REAL@endlink, @link ASTNodeType_t#AST_REAL_E
AST_REAL_E@endlink or @link ASTNodeType_t#AST_RATIONAL
AST_RATIONAL@endlink.
@return C<true> if the value of this ASTNode can represented as a real
number, C<false> otherwise.
=item ASTNode::isRelational
Returns C<true> if this node is a MathML
relational operator.
The MathML relational operators are C<==>, C<>=>,
C<>>, C<<>, and C<!=>.
@return C<true> if this ASTNode is a MathML relational operator, @c
false otherwise.
=item ASTNode::isSemantics
Predicate returning C<true> if this node is a MathML
semantics node.
@return C<true> if this ASTNode is a MathML semantics node, C<false>
otherwise.
=item ASTNode::isSqrt
Returns C<true> if this node represents a square root
function.
More precisely, the node type must be @link
ASTNodeType_t#AST_FUNCTION_ROOT AST_FUNCTION_ROOT@endlink with two
children, the first of which is an @link ASTNodeType_t#AST_INTEGER
AST_INTEGER@endlink node having value equal to 2.
@return C<true> if the given ASTNode represents a C<sqrt()>
function, C<false> otherwise.
=item ASTNode::isUMinus
Returns C<true> if this node is a unary minus operator.
A node is defined as a unary minus node if it is of type @link
ASTNodeType_t#AST_MINUS AST_MINUS@endlink and has exactly one child.
For numbers, unary minus nodes can be "collapsed" by negating the
number. In fact,
@if clike SBML_parseFormula()@endif@if csharp SBML_parseFormula()@endif@if python libsbml.parseFormula()@endif@if java <code><a href="libsbml.html#parseFormula(java.lang.String)">libsbml.parseFormula(String formula)</a></code>@endif@~
does this during its parsing process, and
@if clike SBML_parseL3Formula()@endif@if csharp SBML_parseL3Formula()@endif@if python libsbml.parseL3Formula()@endif@if java <code><a href="libsbml.html#parseL3Formula(java.lang.String)">libsbml.parseL3Formula(String formula)</a></code>@endif@~
has a configuration option that allows this behavior to be turned
on or off. However, unary minus nodes for symbols
(@link ASTNodeType_t#AST_NAME AST_NAME@endlink) cannot
be "collapsed", so this predicate function is necessary.
@return C<true> if this ASTNode is a unary minus, C<false>
otherwise.
@if clike @see SBML_parseL3Formula()@endif@~
@if csharp @see SBML_parseL3Formula()@endif@~
@if python @see libsbml.parseL3Formula()@endif@~
@if java @see <code><a href="libsbml.html#parseL3Formula(String formula)">libsbml.parseL3Formula(String formula)</a></code>@endif@~
=item ASTNode::isUPlus
Returns C<true> if this node is a unary plus operator.
A node is defined as a unary plus node if it is of type @link
ASTNodeType_t#AST_PLUS AST_PLUS@endlink and has exactly one child.
@return C<true> if this ASTNode is a unary plus, C<false> otherwise.
=item ASTNode::hasTypeAndNumChildren
Returns C<true> if this node is of a certain type with a specific number
of children.
Designed for use in cases where it is useful to discover if the node is a
unary not or unary minus, or a times node with no children, etc.
@param type the type of ASTNode sought.
@param numchildren the number of child nodes sought.
@return C<true> if this ASTNode is has the specified type and number of
children, C<false> otherwise.
=item ASTNode::isUnknown
Returns C<true> if this node has an unknown type.
"Unknown" nodes have the type @link ASTNodeType_t#AST_UNKNOWN
AST_UNKNOWN@endlink. Nodes with unknown types will not appear in an
ASTNode tree returned by libSBML based upon valid SBML input; the only
situation in which a node with type @link ASTNodeType_t#AST_UNKNOWN
AST_UNKNOWN@endlink may appear is immediately after having create a
new, untyped node using the ASTNode constructor. Callers creating
nodes should endeavor to set the type to a valid node type as soon as
possible after creating new nodes.
@return C<true> if this ASTNode is of type @link
ASTNodeType_t#AST_UNKNOWN AST_UNKNOWN@endlink, C<false> otherwise.
=item ASTNode::isSetId
Returns C<true> if this node has a value for the MathML
attribute C<id>.
@return true if this ASTNode has an attribute id, C<false>
otherwise.
@see isSetClass()
@see isSetStyle()
@see setId(@if java const std::string& id@endif)
@see unsetId()
=item ASTNode::isSetClass
Returns C<true> if this node has a value for the MathML
attribute C<class>.
@return true if this ASTNode has an attribute class, C<false>
otherwise.
@see isSetId()
@see isSetStyle()
@see @if java setClassName(const std::string& id)@else setClass()@endif@~
@see unsetClass()
=item ASTNode::isSetStyle
Returns C<true> if this node has a value for the MathML
attribute C<style>.
@return true if this ASTNode has an attribute style, C<false>
otherwise.
@see isSetClass()
@see isSetId()
@see setStyle(@if java const std::string& id@endif)
@see unsetStyle()
=item ASTNode::isSetUnits
Returns C<true> if this node has the attribute
C<sbml:units>.
@htmlinclude about-sbml-units-attrib.html
@return C<true> if this ASTNode has units associated with it, C<false>
otherwise.
@note The C<sbml:units> attribute is only available in SBML
Level 3. It may not be used in Levels 1–2 of SBML.
@see hasUnits()
@see setUnits(@if java const std::string& units@endif)
=item ASTNode::hasUnits
Returns C<true> if this node or any of its
children nodes have the attribute C<sbml:units>.
@htmlinclude about-sbml-units-attrib.html
@return C<true> if this ASTNode or its children has units associated
with it, C<false> otherwise.
@note The C<sbml:units> attribute is only available in SBML
Level 3. It may not be used in Levels 1–2 of SBML.
@see isSetUnits()
@see setUnits(@if java const std::string& units@endif)
=item ASTNode::setCharacter
Sets the value of this ASTNode to the given character. If character
is one of C<+>, C<->, C< >, C</> or C<^>, the node
type will be set accordingly. For all other characters, the node type
will be set to @link ASTNodeType_t#AST_UNKNOWN AST_UNKNOWN@endlink.
@param value the character value to which the node's value should be
set.
@return integer value indicating success/failure of the function. The
possible values returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
=item ASTNode::setId
Sets the MathML attribute C<id> of this ASTNode.
@param id C<string> representing the identifier.
@return integer value indicating success/failure of the
function. The possible values returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@see isSetId()
@see getId()
@see unsetId()
=item ASTNode::setClass
Sets the MathML attribute C<class> of this ASTNode.
@param className C<string> representing the MathML class for this node.
@return integer value indicating success/failure of the
function. The possible values returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@if java
@note In the API interfaces for languages other than Java, this method
is named C<setClass()>, but in Java it is renamed
C<setClassName()> to avoid a name collision with Java's
standard object method of the same name.
@endif@~
@see isSetClass()
@see getClass()
@see unsetClass()
=item ASTNode::setStyle
Sets the MathML attribute C<style> of this ASTNode.
@param style C<string> representing the identifier.
@return integer value indicating success/failure of the
function. The possible values returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@see isSetStyle()
@see getStyle()
@see unsetStyle()
=item ASTNode::setName
Sets the value of this ASTNode to the given name.
As a side effect, this ASTNode object's type will be reset to
@link ASTNodeType_t#AST_NAME AST_NAME@endlink if (and <em>only
if</em>) the ASTNode was previously an operator (i.e.,
@if clike isOperator()@else ASTNode::isOperator()@endif@~
returns C<true>), number
(i.e., @if clike isNumber()@else ASTNode::isNumber()@endif@~
returns C<true>), or unknown.
This allows names to be set for @link ASTNodeType_t#AST_FUNCTION
AST_FUNCTION@endlink nodes and the like.
@param name the string containing the name to which this node's value
should be set.
@return integer value indicating success/failure of the function. The
possible values returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
=item ASTNode::setValue
Sets the value of this ASTNode to the given integer
As a side effect, this operation sets the node type to @link
ASTNodeType_t#AST_INTEGER AST_INTEGER@endlink.
@param value the integer to which this node's value should be set.
@return integer value indicating success/failure of the function. The
possible values returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
=item ASTNode::setValue
Sets the value of this ASTNode to the given (C<long>) integer
As a side effect, this operation sets the node type to @link
ASTNodeType_t#AST_INTEGER AST_INTEGER@endlink.
@param value the integer to which this node's value should be set.
@return integer value indicating success/failure of the function. The
possible values returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
=item ASTNode::setValue
Sets the value of this ASTNode to the given rational.
As a side effect, this operation sets the node type to @link
ASTNodeType_t#AST_RATIONAL AST_RATIONAL@endlink.
@param numerator the numerator value of the rational.
@param denominator the denominator value of the rational.
@return integer value indicating success/failure of the function. The
possible values returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
=item ASTNode::setValue
Sets the value of this ASTNode to the given real (C<double>).
As a side effect, this operation sets the node type to @link
ASTNodeType_t#AST_REAL AST_REAL@endlink.
This is functionally equivalent to:
@verbatim
setValue(value, 0);
@endverbatim
@param value the C<double> format number to which this node's value
should be set.
@return integer value indicating success/failure of the function. The
possible values returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
=item ASTNode::setValue
Sets the value of this ASTNode to the given real (C<double>)
As a side effet, this operation sets the node type to
@link ASTNodeType_t#AST_REAL_E AST_REAL_E@endlink.
@param mantissa the mantissa of this node's real-numbered value.
@param exponent the exponent of this node's real-numbered value.
@return integer value indicating success/failure of the
function. The possible values returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
=item ASTNode::setType
Sets the type of this ASTNode to the given type code.
@param type the type to which this node should be set.
@return integer value indicating success/failure of the
function. The possible values returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
@note A side-effect of doing this is that any numerical values
previously stored in this node are reset to zero.
@see getType()
@see setType(int Type)
=item ASTNode::setType
Sets the type of this ASTNode.
This uses integer type codes, which may come from ASTNodeType_t or an
enumeration of AST types in an SBML Level 3 package.
@param type the integer representing the type to which this node should
be set.
@return integer value indicating success/failure of the
function. The possible values returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
@note A side-effect of doing this is that any numerical values
previously stored in this node are reset to zero.
@see getType()
@see setType(ASTNodeType_t type)
=item ASTNode::setUnits
Sets the units of this ASTNode to units.
The units will be set I<only> if this ASTNode object represents a
MathML C<<cn>> element, i.e., represents a number.
Callers may use
@if clike isNumber()@else ASTNode::isNumber()@endif@~
to inquire whether the node is of that type.
@htmlinclude about-sbml-units-attrib.html
@param units C<string> representing the unit identifier.
@return integer value indicating success/failure of the
function. The possible values returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_UNEXPECTED_ATTRIBUTE LIBSBML_UNEXPECTED_ATTRIBUTE @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
@note The C<sbml:units> attribute is only available in SBML
Level 3. It may not be used in Levels 1–2 of SBML.
@see isSetUnits()
@see hasUnits()
=item ASTNode::swapChildren
Swaps the children of this node with the children of another node.
@param that the other node whose children should be used to replace
<em>this</em> node's children.
@return integer value indicating success/failure of the
function. The possible values returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item ASTNode::renameSIdRefs
Renames all the SIdRef attributes on this node and its child nodes.
@param oldid the old identifier.
@param newid the new identifier.
=item ASTNode::renameUnitSIdRefs
Renames all the UnitSIdRef attributes on this node and its child nodes.
The only place UnitSIDRefs appear in MathML C<<cn>>
elements, so the effects of this method are limited to that.
@param oldid the old identifier.
@param newid the new identifier.
=item ASTNode::replaceIDWithFunction
@internal
Replace any nodes of type AST_NAME with the name 'id' from the child 'math' object with the provided ASTNode.
=item ASTNode::unsetUnits
Unsets the units of this ASTNode.
@return integer value indicating success/failure of the
function. The possible values returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_UNEXPECTED_ATTRIBUTE LIBSBML_UNEXPECTED_ATTRIBUTE @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item ASTNode::unsetId
Unsets the MathML C<id> attribute of this ASTNode.
@return integer value indicating success/failure of the
function. The possible values returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item ASTNode::unsetClass
Unsets the MathML C<class> attribute of this ASTNode.
@return integer value indicating success/failure of the
function. The possible values returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item ASTNode::unsetStyle
Unsets the MathML C<style> attribute of this ASTNode.
@return integer value indicating success/failure of the
function. The possible values returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item ASTNode::setDefinitionURL
Sets the MathML attribute C<definitionURL>.
@param url the URL value for the C<definitionURL> attribute.
@return integer value indicating success/failure of the
function. The possible values returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT @endlink
@see setDefinitionURL(const std::string& url)
@see getDefinitionURL()
@see getDefinitionURLString()
=item ASTNode::setDefinitionURL
Sets the MathML attribute C<definitionURL>.
@param url the URL value for the C<definitionURL> attribute.
@return integer value indicating success/failure of the
function. The possible values returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT @endlink
@see setDefinitionURL(XMLAttributes url)
@see getDefinitionURL()
@see getDefinitionURLString()
=item ASTNode::getDefinitionURL
Returns the MathML C<definitionURL> attribute value.
@return the value of the C<definitionURL> attribute, in the form of
a libSBML XMLAttributes object.
@see setDefinitionURL(XMLAttributes url)
@see setDefinitionURL(const std::string& url)
@see getDefinitionURLString()
=item ASTNode::replaceArgument
Replaces occurrences of a given name with a given ASTNode.
For example, if the formula in this ASTNode is C<x + y>,
then the C<<bvar>> is C<x> and C<arg> is an ASTNode
representing the real value C<3>. This method substitutes C<3> for @c
x within this ASTNode object.
@param bvar a string representing the variable name to be substituted.
@param arg an ASTNode representing the name/value/formula to use as
a replacement.
=item ASTNode::setParentSBMLObject
Sets the parent SBML object.
@param sb the parent SBML object of this ASTNode.
@return integer value indicating success/failure of the
function. The possible values returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
@see isSetParentSBMLObject()
@see getParentSBMLObject()
=item ASTNode::getParentSBMLObject
Returns the parent SBML object.
@return the parent SBML object of this ASTNode.
@see isSetParentSBMLObject()
@see setParentSBMLObject(@if java SBase sb@endif)
=item ASTNode::unsetParentSBMLObject
Unsets the parent SBML object.
@return integer value indicating success/failure of the
function. The possible values returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item ASTNode::isSetParentSBMLObject
Returns C<true> if this node has a value for the parent SBML
object.
@return true if this ASTNode has an parent SBML object set, C<false> otherwise.
@see getParentSBMLObject()
@see setParentSBMLObject(@if java SBase sb@endif)
=item ASTNode::reduceToBinary
Reduces this ASTNode to a binary tree.
Example: if this ASTNode is C<and(x, y, z)>, then the
formula of the reduced node is C<and(and(x, y), z)>. The
operation replaces the formula stored in the current ASTNode object.
=item ASTNode::setUserData
Sets the user data of this node.
The user data can be used by the application developer to attach custom
information to the node. In case of a deep copy, this attribute will
passed as it is. The attribute will be never interpreted by this class.
@param userData specifies the new user data.
@return integer value indicating success/failure of the
function. The possible values returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
@if clike
@see ASTNode::isSetUserData()
@see ASTNode::getUserData()
@see ASTNode::unsetUserData()
@endif
=item ASTNode::*getUserData
Returns the user data that has been previously set via setUserData().
@return the user data of this node, or C<NULL> if no user data has been
set.
@if clike
@see ASTNode::isSetUserData()
@see ASTNode::setUserData()
@see ASTNode::unsetUserData()
@endif@~
=item ASTNode::unsetUserData
Unsets the user data of this node.
The user data can be used by the application developer to attach custom
information to the node. In case of a deep copy, this attribute will
passed as it is. The attribute will be never interpreted by this class.
@return integer value indicating success/failure of the
function. The possible values returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
@if clike
@see ASTNode::setUserData()
@see ASTNode::getUserData()
@see ASTNode::isSetUserData()
@endif@~
=item ASTNode::isSetUserData
Returns C<true> if this node has a user data object.
@return true if this ASTNode has a user data object set, C<false>
otherwise.
@if clike
@see ASTNode::setUserData()
@see ASTNode::getUserData()
@see ASTNode::unsetUserData()
@endif@~
=item ASTNode::isWellFormedASTNode
Returns C<true> or C<false> depending on whether this
ASTNode is well-formed.
@note An ASTNode may be well-formed, with each node and its children
having the appropriate number of children for the given type, but may
still be invalid in the context of its use within an SBML model.
@return C<true> if this ASTNode is well-formed, C<false> otherwise.
@see hasCorrectNumberArguments()
=item ASTNode::hasCorrectNumberArguments
Returns C<true> if this ASTNode has the correct number of children for
its type.
For example, an ASTNode with type @link ASTNodeType_t#AST_PLUS
AST_PLUS@endlink expects 2 child nodes.
@return C<true> if this ASTNode has the appropriate number of children
for its type, C<false> otherwise.
@note This function performs a check on the top-level node only. Child
nodes are not checked.
@see isWellFormedASTNode()
=item ASTNode::getDefinitionURLString
Returns the MathML C<definitionURL> attribute value as a string.
@return the value of the C<definitionURL> attribute, as a string.
@see getDefinitionURL()
@see setDefinitionURL(const std::string& url)
@see setDefinitionURL(XMLAttributes url)
=item ASTNode::write
@internal
=item ASTNode::read
@internal
=item ASTNode::writeNodeOfType
@internal
=item ASTNode::getNumBvars
@internal
=item ASTNode::getTypeCode
@internal
=item ASTNode::getPackageName
@internal
=item ASTNode::containsVariable
@internal
=item ASTNode::getNumVariablesWithUndeclaredUnits
@internal
=item ASTNode::canonicalizeConstant
@internal
Internal helper function for canonicalize().
=item ASTNode::canonicalizeFunction
@internal
=item ASTNode::canonicalizeFunctionL1
@internal
=item ASTNode::canonicalizeLogical
@internal
=item ASTNode::canonicalizeRelational
@internal
=item ASTNode::hasCnUnits
@internal
=item ASTNode::getUnitsPrefix
@internal
=item ASTNode::ASTNode
@internal
=item ASTNode::ASTNode
@internal
=item ASTNode::reset
@internal
=item ASTNode::connectPlugins
@internal
=item ASTNode::getNumber
@internal
=item ASTNode::getFunction
@internal
=item readMathML
@internal
Reads the MathML from the given XMLInputStream, constructs a corresponding
abstract syntax tree and returns a pointer to the root of the tree.
=item writeMathML
@internal
Writes the given ASTNode (and its children) to the XMLOutputStream_t as
MathML.
=item readMathMLFromString
Reads the MathML from the given XML string, constructs a corresponding
abstract syntax tree, and returns a pointer to the root of the tree.
@param xml a string containing a full MathML expression
@return the root of an AST corresponding to the given mathematical
expression, otherwise C<NULL> is returned if the given string is C<NULL>
or invalid.
@if conly
@memberof ASTNode_t
@endif
=item readMathMLFromStringWithNamespaces
Reads the MathML from the given XML string, constructs a corresponding
abstract syntax tree, and returns a pointer to the root of the tree.
@param xml a string containing a full MathML expression
@param xmlns a XMLNamespaces_t object containing namespaces that
are considered active during the read e.g. an L3 package namespace
@return the root of an AST corresponding to the given mathematical
expression, otherwise C<NULL> is returned if the given string is C<NULL>
or invalid.
@if conly
@memberof ASTNode_t
@endif
=item writeMathMLToString
Writes the given ASTNode_t (and its children) to a string as MathML, and
returns the string.
@param node the root of an AST to write out to the stream.
@return a string containing the written-out MathML representation
of the given AST.
@note The string is owned by the caller and should be freed (with
free()) when no longer needed. C<NULL> is returned if the given
argument is C<NULL>.
@if conly
@memberof ASTNode_t
@endif
=item SBML_parseFormula
Parses the given SBML formula and returns a representation of it as an
Abstract Syntax Tree (AST).
C<opydetails> doc_summary_of_string_math
C<opydetails> doc_warning_L1_math_string_syntax
@param formula the text-string formula expression to be parsed
@return the root node of the AST corresponding to the C<formula>, or @c
NULL if an error occurred in parsing the formula
@if clike @see SBML_formulaToString()
@see SBML_parseL3FormulaWithSettings()
@see SBML_parseL3Formula()
@see SBML_parseL3FormulaWithModel()
@see SBML_getLastParseL3Error()
@see SBML_getDefaultL3ParserSettings()
@endif@~
@if csharp @see SBML_formulaToString()
@see SBML_parseL3FormulaWithSettings()
@see SBML_parseL3Formula()
@see SBML_parseL3FormulaWithModel()
@see SBML_getLastParseL3Error()
@see SBML_getDefaultL3ParserSettings()
@endif@~
@if python @see libsbml.formulaToString()
@see libsbml.parseL3FormulaWithSettings()
@see libsbml.parseL3Formula()
@see libsbml.parseL3FormulaWithModel()
@see libsbml.getLastParseL3Error()
@see libsbml.getDefaultL3ParserSettings()
@endif@~
@if java @see <code><a href="libsbml.html#formulaToString(org.sbml.libsbml.ASTNode tree)">libsbml.formulaToString(ASTNode tree)</a></code>
@see <code><a href="libsbml.html#parseL3FormulaWithSettings(java.lang.String, org.sbml.libsbml.L3ParserSettings)">libsbml.parseL3FormulaWithSettings(String formula, L3ParserSettings settings)</a></code>
@see <code><a href="libsbml.html#parseL3Formula(java.lang.String)">libsbml.parseL3Formula(String formula)</a></code>
@see <code><a href="libsbml.html#parseL3FormulaWithModel(java.lang.String, org.sbml.libsbml.Model)">parseL3FormulaWithModel(String formula, Model model)</a></code>
@see <code><a href="libsbml.html#getLastParseL3Error()">getLastParseL3Error()</a></code>
@see <code><a href="libsbml.html#getDefaultL3ParserSettings()">getDefaultL3ParserSettings()</a></code>
@endif@~
@if conly
@memberof ASTNode_t
@endif
=item SBML_formulaToString
Converts an AST to a string representation of a formula using a syntax
basically derived from SBML Level 1.
C<opydetails> doc_summary_of_string_math
C<opydetails> doc_warning_L1_math_string_syntax
@param tree the AST to be converted.
@return the formula from the given AST as an SBML Level 1 text-string
mathematical formula. The caller owns the returned string and is
responsible for freeing it when it is no longer needed.
@if clike @see SBML_formulaToString()
@see SBML_parseL3FormulaWithSettings()
@see SBML_parseL3Formula()
@see SBML_parseL3FormulaWithModel()
@see SBML_getLastParseL3Error()
@see SBML_getDefaultL3ParserSettings()
@endif@~
@if csharp @see SBML_formulaToString()
@see SBML_parseL3FormulaWithSettings()
@see SBML_parseL3Formula()
@see SBML_parseL3FormulaWithModel()
@see SBML_getLastParseL3Error()
@see SBML_getDefaultL3ParserSettings()
@endif@~
@if python @see libsbml.formulaToString()
@see libsbml.parseL3FormulaWithSettings()
@see libsbml.parseL3Formula()
@see libsbml.parseL3FormulaWithModel()
@see libsbml.getLastParseL3Error()
@see libsbml.getDefaultL3ParserSettings()
@endif@~
@if java @see <code><a href="libsbml.html#formulaToString(org.sbml.libsbml.ASTNode tree)">libsbml.formulaToString(ASTNode tree)</a></code>
@see <code><a href="libsbml.html#parseL3FormulaWithSettings(java.lang.String, org.sbml.libsbml.L3ParserSettings)">libsbml.parseL3FormulaWithSettings(String formula, L3ParserSettings settings)</a></code>
@see <code><a href="libsbml.html#parseL3Formula(java.lang.String)">libsbml.parseL3Formula(String formula)</a></code>
@see <code><a href="libsbml.html#parseL3FormulaWithModel(java.lang.String, org.sbml.libsbml.Model)">parseL3FormulaWithModel(String formula, Model model)</a></code>
@see <code><a href="libsbml.html#getLastParseL3Error()">getLastParseL3Error()</a></code>
@see <code><a href="libsbml.html#getDefaultL3ParserSettings()">getDefaultL3ParserSettings()</a></code>
@endif@~
@if conly
@memberof ASTNode_t
@endif
=item SBML_parseL3Formula
Parses the given mathematical formula and returns a representation of it
as an Abstract Syntax Tree (AST).
C<opydetails> doc_summary_of_string_math_l3
@param formula the text-string formula expression to be parsed
@return the root node of an AST representing the mathematical formula,
or C<NULL> if an error occurred while parsing the formula. When C<NULL>
is returned, an error is recorded internally; information about the
error can be retrieved using
@if clike SBML_getLastParseL3Error()@endif@if csharp SBML_getLastParseL3Error()@endif@if python libsbml.getLastParseL3Error()@endif@if java <code><a href="libsbml.html#getLastParseL3Error()">libsbml.getLastParseL3Error()</a></code>@endif@~.
@if clike @see SBML_formulaToString()
@see SBML_formulaToL3String()
@see SBML_parseL3FormulaWithSettings()
@see SBML_parseL3Formula()
@see SBML_parseL3FormulaWithModel()
@see SBML_getLastParseL3Error()
@see SBML_getDefaultL3ParserSettings()
@endif@~
@if csharp @see SBML_formulaToString()
@see SBML_formulaToL3String()
@see SBML_parseL3FormulaWithSettings()
@see SBML_parseL3Formula()
@see SBML_parseL3FormulaWithModel()
@see SBML_getLastParseL3Error()
@see SBML_getDefaultL3ParserSettings()
@endif@~
@if python @see libsbml.formulaToString()
@see libsbml.formulaToL3String()
@see libsbml.parseL3FormulaWithSettings()
@see libsbml.parseL3Formula()
@see libsbml.parseL3FormulaWithModel()
@see libsbml.getLastParseL3Error()
@see libsbml.getDefaultL3ParserSettings()
@endif@~
@if java @see <code><a href="libsbml.html#formulaToString(org.sbml.libsbml.ASTNode tree)">libsbml.formulaToString(ASTNode tree)</a></code>
@see <code><a href="libsbml.html#parseL3FormulaWithSettings(java.lang.String, org.sbml.libsbml.L3ParserSettings)">libsbml.parseL3FormulaWithSettings(String formula, L3ParserSettings settings)</a></code>
@see <code><a href="libsbml.html#parseL3Formula(java.lang.String)">libsbml.parseL3Formula(String formula)</a></code>
@see <code><a href="libsbml.html#parseL3FormulaWithModel(java.lang.String, org.sbml.libsbml.Model)">parseL3FormulaWithModel(String formula, Model model)</a></code>
@see <code><a href="libsbml.html#getLastParseL3Error()">getLastParseL3Error()</a></code>
@see <code><a href="libsbml.html#getDefaultL3ParserSettings()">getDefaultL3ParserSettings()</a></code>
@endif@~
@if conly
@memberof ASTNode_t
@endif
=item SBML_parseL3FormulaWithModel
Parses the given mathematical formula using specific a specific Model to
resolve symbols, and returns an Abstract Syntax Tree (AST)
representation of the result.
This is identical to
@if clike SBML_parseL3Formula()@endif@if csharp SBML_parseL3Formula()@endif@if python libsbml.parseL3Formula()@endif@if java <code><a href="libsbml.html#parseL3Formula(java.lang.String)">libsbml.parseL3Formula(String formula)</a></code>@endif@~,
except that this function uses the given model in the argument C<model>
to check against identifiers that appear in the C<formula>.
For more details about the parser, please see the definition of
the function @if clike SBML_parseL3Formula()@endif@if csharp SBML_parseL3Formula()@endif@if python libsbml.parseL3Formula()@endif@if java <code><a href="libsbml.html#parseL3Formula(java.lang.String)">libsbml.parseL3Formula(String formula)</a></code>@endif@~.
@param formula the mathematical formula expression to be parsed
@param model the Model object to use for checking identifiers
@return the root node of an AST representing the mathematical formula,
or C<NULL> if an error occurred while parsing the formula. When C<NULL>
is returned, an error is recorded internally; information about the
error can be retrieved using
@if clike SBML_getLastParseL3Error()@endif@if csharp SBML_getLastParseL3Error()@endif@if python libsbml.getLastParseL3Error()@endif@if java <code><a href="libsbml.html#getLastParseL3Error()">libsbml.getLastParseL3Error()</a></code>@endif@~.
@if clike @see SBML_formulaToString()
@see SBML_parseL3FormulaWithSettings()
@see SBML_parseL3Formula()
@see SBML_getLastParseL3Error()
@see SBML_getDefaultL3ParserSettings()
@endif@~
@if csharp @see SBML_formulaToString()
@see SBML_parseL3FormulaWithSettings()
@see SBML_parseL3Formula()
@see SBML_getLastParseL3Error()
@see SBML_getDefaultL3ParserSettings()
@endif@~
@if python @see libsbml.formulaToString()
@see libsbml.parseL3FormulaWithSettings()
@see libsbml.parseL3Formula()
@see libsbml.getLastParseL3Error()
@see libsbml.getDefaultL3ParserSettings()
@endif@~
@if java @see <code><a href="libsbml.html#formulaToString(org.sbml.libsbml.ASTNode tree)">libsbml.formulaToString(ASTNode tree)</a></code>
@see <code><a href="libsbml.html#parseL3FormulaWithSettings(java.lang.String, org.sbml.libsbml.L3ParserSettings)">libsbml.parseL3FormulaWithSettings(String formula, L3ParserSettings settings)</a></code>
@see <code><a href="libsbml.html#parseL3Formula(java.lang.String)">libsbml.parseL3Formula(String formula)</a></code>
@see <code><a href="libsbml.html#getLastParseL3Error()">getLastParseL3Error()</a></code>
@see <code><a href="libsbml.html#getDefaultL3ParserSettings()">getDefaultL3ParserSettings()</a></code>
@endif@~
@if conly
@memberof ASTNode_t
@endif
=item SBML_parseL3FormulaWithSettings
Parses the given mathematical formula using specific parser settings and
returns an Abstract Syntax Tree (AST) representation of the result.
This is identical to
@if clike SBML_parseL3Formula()@endif@if csharp SBML_parseL3Formula()@endif@if python libsbml.parseL3Formula()@endif@if java <code><a href="libsbml.html#parseL3Formula(java.lang.String)">libsbml.parseL3Formula(String formula)</a></code>@endif@~,
except that this function uses the parser settings given in the argument
C<settings>. The settings override the default parsing behavior.
The parameter C<settings> allows callers to change the following parsing
behaviors:
@li Use a specific Model object against which identifiers to compare
identifiers. This causes the parser to search the Model for identifiers
that the parser encounters in the formula. If a given symbol in the
formula matches the identifier of a Species, Compartment, Parameter,
Reaction, SpeciesReference or FunctionDefinition in the Model, then the
symbol is assumed to refer to that model entity instead of any possible
mathematical terms with the same symbol. For example, if the parser is
given a Model containing a Species with the identifier
"C<pi>", and the formula to be parsed is
"C<3 pi>", the MathML produced will contain the
construct C<<ci> pi </ci>> instead of the
construct C<<pi/>>.
@li Whether to parse "C<log(x)>" with a single
argument as the base 10
logarithm of x, the natural logarithm of x, or treat the case as an
error.
@li Whether to parse "C<number id>" by interpreting
C<id> as the identifier of a unit of measurement associated with the
number, or whether to treat the case as an error.
@li Whether to parse "C<avogadro>" as an ASTNode of
type @link ASTNodeType_t#AST_NAME_AVOGADRO AST_NAME_AVOGADRO@endlink or
as type @link ASTNodeType_t#AST_NAME AST_NAME@endlink.
@li Whether to always create explicit ASTNodes of type @link
ASTNodeType_t#AST_MINUS AST_MINUS@endlink for all unary minuses, or
collapse and remove minuses where possible.
For more details about the parser, please see the definition of
L3ParserSettings and
@if clike SBML_parseL3Formula()@endif@if csharp SBML_parseL3Formula()@endif@if python libsbml.parseL3Formula()@endif@if java <code><a href="libsbml.html#parseL3Formula(java.lang.String)">libsbml.parseL3Formula(String formula)</a></code>@endif@~.
@param formula the mathematical formula expression to be parsed
@param settings the settings to be used for this parser invocation
@return the root node of an AST representing the mathematical formula,
or C<NULL> if an error occurred while parsing the formula. When C<NULL>
is returned, an error is recorded internally; information about the
error can be retrieved using
@if clike SBML_getLastParseL3Error()@endif@if csharp SBML_getLastParseL3Error()@endif@if python libsbml.getLastParseL3Error()@endif@if java <code><a href="libsbml.html#getLastParseL3Error()">libsbml.getLastParseL3Error()</a></code>@endif@~.
@if clike @see SBML_formulaToString()
@see SBML_parseL3Formula()
@see SBML_parseL3FormulaWithModel()
@see SBML_getLastParseL3Error()
@see SBML_getDefaultL3ParserSettings()
@endif@~
@if csharp @see SBML_formulaToString()
@see SBML_parseL3Formula()
@see SBML_parseL3FormulaWithModel()
@see SBML_getLastParseL3Error()
@see SBML_getDefaultL3ParserSettings()
@endif@~
@if python @see libsbml.formulaToString()
@see libsbml.parseL3Formula()
@see libsbml.parseL3FormulaWithModel()
@see libsbml.getLastParseL3Error()
@see libsbml.getDefaultL3ParserSettings()
@endif@~
@if java @see <code><a href="libsbml.html#formulaToString(org.sbml.libsbml.ASTNode tree)">libsbml.formulaToString(ASTNode tree)</a></code>
@see <code><a href="libsbml.html#parseL3Formula(java.lang.String)">libsbml.parseL3Formula(String formula)</a></code>
@see <code><a href="libsbml.html#parseL3FormulaWithModel(java.lang.String, org.sbml.libsbml.Model)">parseL3FormulaWithModel(String formula, Model model)</a></code>
@see <code><a href="libsbml.html#getLastParseL3Error()">getLastParseL3Error()</a></code>
@see <code><a href="libsbml.html#getDefaultL3ParserSettings()">getDefaultL3ParserSettings()</a></code>
@endif@~
@if conly
@memberof ASTNode_t
@endif
=item SBML_getDefaultL3ParserSettings
Returns a copy of the default parser settings used by @if clike SBML_parseL3Formula()@endif@if csharp SBML_parseL3Formula()@endif@if python libsbml.parseL3Formula()@endif@if java <code><a href="libsbml.html#parseL3Formula(java.lang.String)">libsbml.parseL3Formula(String formula)</a></code>@endif@~.
The settings structure allows callers to change the following parsing
behaviors:
@li Use a specific Model object against which identifiers to compare
identifiers. This causes the parser to search the Model for identifiers
that the parser encounters in the formula. If a given symbol in the
formula matches the identifier of a Species, Compartment, Parameter,
Reaction, SpeciesReference or FunctionDefinition in the Model, then the
symbol is assumed to refer to that model entity instead of any possible
mathematical terms with the same symbol. For example, if the parser is
given a Model containing a Species with the identifier
"C<pi>", and the formula to be parsed is
"C<3 pi>", the MathML produced will contain the
construct C<<ci> pi </ci>> instead of the
construct C<<pi/>>.
@li Whether to parse "C<log(x)>" with a single
argument as the base 10
logarithm of x, the natural logarithm of x, or treat the case as an
error.
@li Whether to parse "C<number id>" by interpreting
C<id> as the identifier of a unit of measurement associated with the
number, or whether to treat the case as an error.
@li Whether to parse "C<avogadro>" as an ASTNode of
type @link ASTNodeType_t#AST_NAME_AVOGADRO AST_NAME_AVOGADRO@endlink or
as type @link ASTNodeType_t#AST_NAME AST_NAME@endlink.
@li Whether to always create explicit ASTNodes of type @link
ASTNodeType_t#AST_MINUS AST_MINUS@endlink for all unary minuses, or
collapse and remove minuses where possible.
For more details about the parser, please see the definition of
L3ParserSettings and
@if clike SBML_parseL3Formula()@endif@if csharp SBML_parseL3Formula()@endif@if python libsbml.parseL3Formula()@endif@if java <code><a href="libsbml.html#parseL3Formula(java.lang.String)">libsbml.parseL3Formula(String formula)</a></code>@endif@~.
@if clike @see SBML_formulaToString()
@see SBML_parseL3FormulaWithSettings()
@see SBML_parseL3Formula()
@see SBML_parseL3FormulaWithModel()
@see SBML_getLastParseL3Error()
@endif@~
@if csharp @see SBML_formulaToString()
@see SBML_parseL3FormulaWithSettings()
@see SBML_parseL3Formula()
@see SBML_parseL3FormulaWithModel()
@see SBML_getLastParseL3Error()
@endif@~
@if python @see libsbml.formulaToString()
@see libsbml.parseL3FormulaWithSettings()
@see libsbml.parseL3Formula()
@see libsbml.parseL3FormulaWithModel()
@see libsbml.getLastParseL3Error()
@endif@~
@if java @see <code><a href="libsbml.html#formulaToString(org.sbml.libsbml.ASTNode tree)">libsbml.formulaToString(ASTNode tree)</a></code>
@see <code><a href="libsbml.html#parseL3FormulaWithSettings(java.lang.String, org.sbml.libsbml.L3ParserSettings)">libsbml.parseL3FormulaWithSettings(String formula, L3ParserSettings settings)</a></code>
@see <code><a href="libsbml.html#parseL3Formula(java.lang.String)">libsbml.parseL3Formula(String formula)</a></code>
@see <code><a href="libsbml.html#parseL3FormulaWithModel(java.lang.String, org.sbml.libsbml.Model)">parseL3FormulaWithModel(String formula, Model model)</a></code>
@see <code><a href="libsbml.html#getLastParseL3Error()">getLastParseL3Error()</a></code>
@endif@~
@if conly
@memberof L3ParserSettings_t
@endif
=item SBML_getLastParseL3Error
Returns the last error reported by the parser.
If @if clike SBML_parseL3Formula()@endif@if csharp SBML_parseL3Formula()@endif@if python libsbml.parseL3Formula()@endif@if java <code><a href="libsbml.html#parseL3Formula(java.lang.String)">libsbml.parseL3Formula(String formula)</a></code>@endif@~,
@if clike SBML_parseL3FormulaWithSettings()@endif@if csharp SBML_parseL3FormulaWithSettings()@endif@if python libsbml.parseL3FormulaWithSettings()@endif@if java <code><a href="libsbml.html#parseL3FormulaWithSettings(java.lang.String, org.sbml.libsbml.L3ParserSettings)">libsbml.parseL3FormulaWithSettings(String formula, L3ParserSettings settings)</a></code>@endif@~, or
@if clike SBML_parseL3FormulaWithModel()@endif@if csharp SBML_parseL3FormulaWithModel()@endif@if python libsbml.parseL3FormulaWithModel()@endif@if java <code><a href="libsbml.html#parseL3FormulaWithModel(java.lang.String, org.sbml.libsbml.Model)">libsbml.parseL3FormulaWithModel(String formula, Model model)</a></code>@endif@~ return C<NULL>, an error is set internally which is accessible
via this function.
@return a string describing the error that occurred. This will contain
the string the parser was trying to parse, which character it had parsed
when it encountered the error, and a description of the error.
@if clike @see SBML_formulaToString()
@see SBML_parseL3FormulaWithSettings()
@see SBML_parseL3Formula()
@see SBML_parseL3FormulaWithModel()
@see SBML_getDefaultL3ParserSettings()
@endif@~
@if csharp @see SBML_formulaToString()
@see SBML_parseL3FormulaWithSettings()
@see SBML_parseL3Formula()
@see SBML_parseL3FormulaWithModel()
@see SBML_getDefaultL3ParserSettings()
@endif@~
@if python @see libsbml.formulaToString()
@see libsbml.parseL3FormulaWithSettings()
@see libsbml.parseL3Formula()
@see libsbml.parseL3FormulaWithModel()
@see libsbml.getDefaultL3ParserSettings()
@endif@~
@if java @see <code><a href="libsbml.html#formulaToString(org.sbml.libsbml.ASTNode tree)">libsbml.formulaToString(ASTNode tree)</a></code>
@see <code><a href="libsbml.html#parseL3FormulaWithSettings(java.lang.String, org.sbml.libsbml.L3ParserSettings)">libsbml.parseL3FormulaWithSettings(String formula, L3ParserSettings settings)</a></code>
@see <code><a href="libsbml.html#parseL3Formula(java.lang.String)">libsbml.parseL3Formula(String formula)</a></code>
@see <code><a href="libsbml.html#parseL3FormulaWithModel(java.lang.String, org.sbml.libsbml.Model)">parseL3FormulaWithModel(String formula, Model model)</a></code>
@see <code><a href="libsbml.html#getDefaultL3ParserSettings()">getDefaultL3ParserSettings()</a></code>
@endif@~
@if conly
@memberof ASTNode_t
@endif
=back
=head2 L3ParserSettings
@sbmlpackage{core}
@htmlinclude pkg-marker-core.html A helper class for controlling the behavior of the
text-string formula parser.
@htmlinclude not-sbml-warning.html
The function
@if clike SBML_parseL3FormulaWithSettings()@endif@if csharp SBML_parseL3FormulaWithSettings()@endif@if python libsbml.parseL3FormulaWithSettings()@endif@if java <code><a href="libsbml.html#parseL3FormulaWithSettings(java.lang.String, org.sbml.libsbml.L3ParserSettings)">libsbml.parseL3FormulaWithSettings(String formula, L3ParserSettings settings)</a></code>@endif@~,
along with its variants
@if clike SBML_parseFormula()@endif@if csharp SBML_parseFormula()@endif@if python libsbml.parseFormula()@endif@if java <code><a href="libsbml.html#parseFormula(java.lang.String)">libsbml.parseFormula(java.lang.String formula)</a></code>@endif@~
and
@if clike SBML_parseL3FormulaWithModel()@endif@if csharp SBML_parseL3FormulaWithModel()@endif@if python libsbml.parseL3FormulaWithModel()@endif@if java <code><a href="libsbml.html#parseL3FormulaWithModel(java.lang.String, org.sbml.libsbml.Model)">libsbml.parseL3FormulaWithModel(String formula, Model model)</a></code>@endif@~,
are the interfaces to a parser for mathematical formulas expressed as
text strings. The parser converts the text-string formulas into
Abstract Syntax Trees (ASTs), represented in libSBML using ASTNode
objects. Compared to the parser implemented by the function
@if clike SBML_parseFormula()@endif@if csharp SBML_parseFormula()@endif@if python libsbml.parseFormula()@endif@if java <code><a href="libsbml.html#parseFormula(java.lang.String)">libsbml.parseFormula(java.lang.String formula)</a></code>@endif@~,
which was designed primarily for converting the mathematical formula
strings in SBML Level 1, the "L3" variant of the parser accepts an
extended formula syntax. It also has a number of configurable behaviors.
This class (L3ParserSettings) is an object used to communicate the
configuration settings with callers.
The following aspects of the parser are configurable:
\n=over\n
\n=item\n\nThe function C<log> with a single argument ("C<log(x)>")
can be parsed as C<log10(x)>, C<ln(x)>, or treated
as an error, as desired.
\n=item\n\nUnary minus signs can be collapsed or preserved; that is,
sequential pairs of unary minuses (e.g., "C<- -3>")
can be removed from the input entirely and single unary minuses can be
incorporated into the number node, or all minuses can be preserved in
the AST node structure.
\n=item\n\nParsing of units embedded in the input string can be turned on and
off.
\n=item\n\nThe string C<avogadro> can be parsed as a MathML I<csymbol> or
as an identifier.
\n=item\n\nA Model object may optionally be provided to the parser using
the variant function call @if clike SBML_parseL3FormulaWithModel()@endif@if csharp SBML_parseL3FormulaWithModel()@endif@if python libsbml.SBML_parseL3FormulaWithModel()@endif@if java <code><a href="libsbml.html#parseL3FormulaWithModel(java.lang.String, org.sbml.libsbml.Model)">libsbml.parseL3FormulaWithModel(String formula, Model model)</a></code>@endif@~.
or stored in a L3ParserSettings object passed to the variant function
@if clike SBML_parseL3FormulaWithSettings()@endif@if csharp SBML_parseL3FormulaWithSettings()@endif@if python libsbml.parseL3FormulaWithSettings()@endif@if java <code><a href="libsbml.html#parseL3FormulaWithSettings(java.lang.String, org.sbml.libsbml.L3ParserSettings)">libsbml.parseL3FormulaWithSettings(String formula, org.sbml.libsbml.L3ParserSettings settings)</a></code>@endif@~.
When a Model object is provided, identifiers (values of type C<SId>)
from that model are used in preference to pre-defined MathML
definitions. More precisely, the Model entities whose identifiers will
shadow identical symbols in the mathematical formula are: Species,
Compartment, Parameter, Reaction, and SpeciesReference. For instance,
if the parser is given a Model containing a Species with the identifier
"C<pi>", and the formula to be parsed is
"C<3 pi>", the MathML produced will contain the
construct C<<ci> pi </ci>> instead of the
construct C<<pi/>>.
\n=item\n\nSimilarly, when a Model object is provided, C<SId> values of
user-defined functions present in the Model will be used preferentially
over pre-defined MathML functions. For example, if the passed-in Model
contains a FunctionDefinition with the identifier
"C<sin>", that function will be used instead of the
predefined MathML function C<<sin/>>.
\n=back\n
To obtain the default configuration values, callers can use the function
@if clike SBML_getDefaultL3ParserSettings()@endif@if csharp SBML_getDefaultL3ParserSettings()@endif@if python libsbml.SBML_getDefaultL3ParserSettings()@endif@if java <code><a href="libsbml.html#getDefaultL3ParserSettings()">libsbml.getDefaultL3ParserSettings()</a></code>@endif@~.
To change the configuration, callers can create an L3ParserSettings
object, set the desired characteristics using the methods
provided, and pass that object to
@if clike SBML_parseL3FormulaWithSettings()@endif@if csharp SBML_parseL3FormulaWithSettings()@endif@if python libsbml.parseL3FormulaWithSettings()@endif@if java <a href="libsbml.html#parseL3FormulaWithSettings(java.lang.String, org.sbml.libsbml.L3ParserSettings)">C<libsbml.parseL3FormulaWithSettings(String formula, L3ParserSettings settings)></a>@endif@~.
@if clike @see SBML_parseL3FormulaWithSettings()
@see SBML_parseL3Formula()
@see SBML_parseL3FormulaWithModel()
@endif@~
@if csharp @see SBML_parseL3FormulaWithSettings()
@see SBML_parseL3Formula()
@see SBML_parseL3FormulaWithModel()
@endif@~
@if python @see libsbml.parseL3FormulaWithSettings()
@see libsbml.parseL3Formula()
@see libsbml.parseL3FormulaWithModel()
@endif@~
@if java @see <code><a href="libsbml.html#parseL3FormulaWithSettings(java.lang.String, org.sbml.libsbml.L3ParserSettings)">libsbml.parseL3FormulaWithSettings(String formula, L3ParserSettings settings)</a></code>
@see <code><a href="libsbml.html#parseL3Formula(java.lang.String)">libsbml.parseL3Formula(String formula)</a></code>
@see <code><a href="libsbml.html#parseL3FormulaWithModel(java.lang.String, org.sbml.libsbml.Model)">parseL3FormulaWithModel(String formula, Model model)</a></code>
@endif@~
=over
=item L3ParserSettings::L3ParserSettings
Creates a new L3ParserSettings object with default values.
This is the default constructor for the L3ParserSettings object. It
sets the Model to C<NULL> and other settings to @c
L3P_PARSE_LOG_AS_LOG10, C<L3P_EXPAND_UNARY_MINUS>, C<L3P_PARSE_UNITS>,
and C<L3P_AVOGADRO_IS_CSYMBOL>.
=item L3ParserSettings::L3ParserSettings
Creates a new L3ParserSettings object with specific values for all
possible settings.
@param model a Model object to be used for disambiguating identifiers
@param parselog a flag that controls how the parser will handle
the symbol C<log> in formulas
@param collapseminus a flag that controls how the parser will handle
minus signs
@param parseunits a flag that controls how the parser will handle
apparent references to units of measurement associated with raw
numbers in a formula
@param avocsymbol a flag that controls how the parser will handle
the appearance of the symbol C<avogadro> in a formula
@see getModel()
@see setModel(@if java Model model@endif)
@see unsetModel()
@see getParseLog()
@see setParseLog(@if java int type@endif)
@see getParseUnits()
@see setParseUnits(@if java boolean units@endif)
@see getParseCollapseMinus()
@see setParseCollapseMinus(@if java boolean collapseminus@endif)
@see getParseAvogadroCsymbol()
@see setParseAvogadroCsymbol(@if java boolean l2only@endif)
=item L3ParserSettings::setModel
Sets the model reference in this L3ParserSettings object.
When a Model object is provided, identifiers (values of type C<SId>)
from that model are used in preference to pre-defined MathML
definitions. More precisely, the Model entities whose identifiers will
shadow identical symbols in the mathematical formula are: Species,
Compartment, Parameter, Reaction, and SpeciesReference. For instance,
if the parser is given a Model containing a Species with the identifier
"C<pi>", and the formula to be parsed is
"C<3 pi>", the MathML produced will contain the
construct C<<ci> pi </ci>> instead of the
construct C<<pi/>>.
Similarly, when a Model object is provided, C<SId> values of
user-defined functions present in the Model will be used preferentially
over pre-defined MathML functions. For example, if the passed-in Model
contains a FunctionDefinition with the identifier
"C<sin>", that function will be used instead of the
predefined MathML function C<<sin/>>.
@param model a Model object to be used for disambiguating identifiers
@warning <span class="warning">This does I<not> copy the Model object.
This means that modifications made to the object after invoking this
method may affect parsing behavior.</span>
@see getModel()
@see unsetModel()
=item L3ParserSettings::getModel
Returns the Model object referenced by this L3ParserSettings object.
@see setModel(@if java Model model@endif)
@see unsetModel()
=item L3ParserSettings::unsetModel
Sets the Model reference in this L3ParserSettings object to C<NULL>.
@see setModel(@if java Model model@endif)
@see getModel()
=item L3ParserSettings::setParseLog
Sets the behavior for handling C<log> in mathematical formulas.
The function C<log> with a single argument
("C<log(x)>") can be parsed as
C<log10(x)>, C<ln(x)>, or treated as an error, as
desired.
@param type a constant, one of following three possibilities:
@li @link ParseLogType_t#L3P_PARSE_LOG_AS_LOG10 L3P_PARSE_LOG_AS_LOG10@endlink
@li @link ParseLogType_t#L3P_PARSE_LOG_AS_LN L3P_PARSE_LOG_AS_LN@endlink
@li @link ParseLogType_t#L3P_PARSE_LOG_AS_ERROR L3P_PARSE_LOG_AS_ERROR@endlink
@see getParseLog()
=item L3ParserSettings::getParseLog
Returns the current setting indicating what to do with formulas
containing the function C<log> with one argument.
The function C<log> with a single argument
("C<log(x)>") can be parsed as
C<log10(x)>, C<ln(x)>, or treated as an error, as
desired.
@return One of following three constants:
@li @link ParseLogType_t#L3P_PARSE_LOG_AS_LOG10 L3P_PARSE_LOG_AS_LOG10@endlink
@li @link ParseLogType_t#L3P_PARSE_LOG_AS_LN L3P_PARSE_LOG_AS_LN@endlink
@li @link ParseLogType_t#L3P_PARSE_LOG_AS_ERROR L3P_PARSE_LOG_AS_ERROR@endlink
@see setParseLog(@if java int type@endif)
=item L3ParserSettings::setParseCollapseMinus
Sets the behavior for handling unary minuses appearing in mathematical
formulas.
This setting affects two behaviors. First, pairs of multiple unary
minuses in a row (e.g., "C<- -3>") can be
collapsed and ignored in the input, or the multiple minuses can be
preserved in the AST node tree that is generated by the parser.
Second, minus signs in front of numbers can be collapsed into the
number node itself; for example, a "C<- 4.1>" can
be turned into a single ASTNode of type @link ASTNodeType_t#AST_REAL
AST_REAL@endlink with a value of C<-4.1>, or it can be
turned into a node of type @link ASTNodeType_t#AST_MINUS
AST_MINUS@endlink having a child node of type @link
ASTNodeType_t#AST_REAL AST_REAL@endlink. This method lets you tell
the parser which behavior to use—either collapse minuses or
always preserve them. The two possibilities are represented using the
following constants:
@li @link ParseLogType_t#L3P_COLLAPSE_UNARY_MINUS
L3P_COLLAPSE_UNARY_MINUS@endlink (value = C<true>): collapse unary
minuses where possible.
@li @link ParseLogType_t#L3P_EXPAND_UNARY_MINUS
L3P_EXPAND_UNARY_MINUS@endlink (value = C<false>): do not collapse
unary minuses, and instead translate each one into an AST node of type
@link ASTNodeType_t#AST_MINUS AST_MINUS@endlink.
@param collapseminus a boolean value (one of the constants
@link ParseLogType_t#L3P_COLLAPSE_UNARY_MINUS
L3P_COLLAPSE_UNARY_MINUS@endlink or
@link ParseLogType_t#L3P_EXPAND_UNARY_MINUS
L3P_EXPAND_UNARY_MINUS@endlink) indicating how unary minus signs in
the input should be handled.
@see getParseCollapseMinus()
=item L3ParserSettings::getParseCollapseMinus
Returns a flag indicating the current behavior set for handling
multiple unary minuses in formulas.
This setting affects two behaviors. First, pairs of multiple unary
minuses in a row (e.g., "C<- -3>") can be
collapsed and ignored in the input, or the multiple minuses can be
preserved in the AST node tree that is generated by the parser.
Second, minus signs in front of numbers can be collapsed into the
number node itself; for example, a "C<- 4.1>" can
be turned into a single ASTNode of type @link ASTNodeType_t#AST_REAL
AST_REAL@endlink with a value of C<-4.1>, or it can be
turned into a node of type @link ASTNodeType_t#AST_MINUS
AST_MINUS@endlink having a child node of type @link
ASTNodeType_t#AST_REAL AST_REAL@endlink. This method lets you tell
the parser which behavior to use—either collapse minuses or
always preserve them. The two possibilities are represented using the
following constants:
@li @link ParseLogType_t#L3P_COLLAPSE_UNARY_MINUS
L3P_COLLAPSE_UNARY_MINUS@endlink (value = C<true>): collapse unary
minuses where possible.
@li @link ParseLogType_t#L3P_EXPAND_UNARY_MINUS
L3P_EXPAND_UNARY_MINUS@endlink (value = C<false>): do not collapse
unary minuses, and instead translate each one into an AST node of type
@link ASTNodeType_t#AST_MINUS AST_MINUS@endlink.
@return A boolean, one of @link
ParseLogType_t#L3P_COLLAPSE_UNARY_MINUS
L3P_COLLAPSE_UNARY_MINUS@endlink or @link
ParseLogType_t#L3P_EXPAND_UNARY_MINUS L3P_EXPAND_UNARY_MINUS@endlink.
@see setParseCollapseMinus(@if java boolean collapseminus@endif)
=item L3ParserSettings::setParseUnits
Sets the parser's behavior in handling units associated with numbers
in a mathematical formula.
In SBML Level 2, there is no means of associating a unit of
measurement with a pure number in a formula, while SBML Level 3
does define a syntax for this. In Level 3, MathML
C<<cn>> elements can have an attribute named C<units>
placed in the SBML namespace, which can be used to indicate the units
to be associated with the number. The text-string infix formula
parser allows units to be placed after raw numbers; they are
interpreted as unit identifiers for units defined by the SBML
specification or in the containing Model object. Some examples
include: "C<4 mL>", "C<2.01
Hz>", "C<3.1e-6 M>", and
"C<(5/8) inches>". To produce a valid SBML model,
there must either exist a UnitDefinition corresponding to the
identifier of the unit, or the unit must be defined in Table 2 of
the SBML specification.
@param units A boolean indicating whether to parse units:
@li @link ParseLogType_t#L3P_PARSE_UNITS L3P_PARSE_UNITS@endlink
(value = C<true>): parse units in the text-string formula.
@li @link ParseLogType_t#L3P_NO_UNITS L3P_NO_UNITS@endlink (value = @c
false): treat units in the text-string formula as errors.
@see getParseUnits()
=item L3ParserSettings::getParseUnits
Returns C<if> the current settings allow units in text-string
mathematical formulas.
In SBML Level 2, there is no means of associating a unit of
measurement with a pure number in a formula, while SBML Level 3
does define a syntax for this. In Level 3, MathML
C<<cn>> elements can have an attribute named C<units>
placed in the SBML namespace, which can be used to indicate the units
to be associated with the number. The text-string infix formula
parser allows units to be placed after raw numbers; they are
interpreted as unit identifiers for units defined by the SBML
specification or in the containing Model object. Some examples
include: "C<4 mL>", "C<2.01
Hz>", "C<3.1e-6 M>", and
"C<(5/8) inches>". To produce a valid SBML model,
there must either exist a UnitDefinition corresponding to the
identifier of the unit, or the unit must be defined in Table 2 of
the SBML specification.
Since SBML Level 2 does not have the ability to associate units with
pure numbers, the value should be set to C<false> when parsing text-string
formulas intended for use in SBML Level 2 documents.
@return A boolean indicating whether to parse units:
@li @link ParseLogType_t#L3P_PARSE_UNITS L3P_PARSE_UNITS@endlink
(value = C<true>): parse units in the text-string formula.
@li @link ParseLogType_t#L3P_NO_UNITS L3P_NO_UNITS@endlink (value = @c
false): treat units in the text-string formula as errors.
@see setParseUnits(@if java boolean units@endif)
=item L3ParserSettings::setParseAvogadroCsymbol
Sets the parser's behavior in handling the string C<avogadro> in
mathematical formulas.
SBML Level 3 defines a symbol for representing the value of
Avogadro's constant, but it is not defined in SBML Level 2. As a
result, the text-string formula parser must behave differently
depending on which SBML Level is being targeted. The argument to this
method can be one of two values:
@li @link ParseLogType_t#L3P_AVOGADRO_IS_CSYMBOL
L3P_AVOGADRO_IS_CSYMBOL@endlink (value = C<true>): tells the parser to
translate the string C<avogadro> (in any capitalization) into an AST
node of type @link ASTNodeType_t#AST_NAME_AVOGADRO
AST_NAME_AVOGADRO@endlink.
@li @link ParseLogType_t#L3P_AVOGADRO_IS_NAME
L3P_AVOGADRO_IS_NAME@endlink (value = C<false>): tells the parser to
translate the string C<avogadro> into an AST of type @link
ASTNodeType_t#AST_NAME AST_NAME@endlink.
Since SBML Level 2 does not define a symbol for Avogadro's
constant, the value should be set to C<false> when parsing text-string
formulas intended for use in SBML Level 2 documents.
@param l2only a boolean value (one of the constants
@link ParseLogType_t#L3P_AVOGADRO_IS_CSYMBOL
L3P_AVOGADRO_IS_CSYMBOL@endlink or
@link ParseLogType_t#L3P_AVOGADRO_IS_NAME
L3P_AVOGADRO_IS_NAME@endlink) indicating how the string C<avogadro>
should be treated when encountered in a formula.
@see getParseAvogadroCsymbol()
=item L3ParserSettings::getParseAvogadroCsymbol
Returns C<true> if the current settings are oriented towards handling
C<avogadro> for SBML Level 3.
SBML Level 3 defines a symbol for representing the value of
Avogadro's constant, but it is not defined in SBML Level 2. As a
result, the text-string formula parser must behave differently
depending on which SBML Level is being targeted.
@return A boolean indicating which mode is currently set; the value is
one of the following possibilities:
@li @link ParseLogType_t#L3P_AVOGADRO_IS_CSYMBOL
L3P_AVOGADRO_IS_CSYMBOL@endlink (value = C<true>): tells the parser to
translate the string C<avogadro> (in any capitalization) into an AST
node of type @link ASTNodeType_t#AST_NAME_AVOGADRO
AST_NAME_AVOGADRO@endlink.
@li @link ParseLogType_t#L3P_AVOGADRO_IS_NAME
L3P_AVOGADRO_IS_NAME@endlink (value = C<false>): tells the parser to
translate the string C<avogadro> into an AST of type @link
ASTNodeType_t#AST_NAME AST_NAME@endlink.
@see setParseAvogadroCsymbol(@if java boolean l2only@endif)
=back
=head2 ASTBasePlugin
@sbmlpackage{core}
@htmlinclude pkg-marker-core.html Base class for extensions that plug into AST classes.
@internal
=over
=item ASTBasePlugin::clone
@internal
Creates and returns a deep copy of this ASTBasePlugin object.
@return a (deep) copy of this SBase object
=item ASTBasePlugin::getElementNamespace
@internal
Returns the XML namespace (URI) of the package extension
of this plugin object.
@return the URI of the package extension of this plugin object.
=item ASTBasePlugin::getPrefix
@internal
Returns the prefix of the package extension of this plugin object.
@return the prefix of the package extension of this plugin object.
=item ASTBasePlugin::getPackageName
@internal
Returns the package name of this plugin object.
@return the package name of this plugin object.
=item ASTBasePlugin::setSBMLExtension
@internal
=item ASTBasePlugin::setPrefix
@internal
=item ASTBasePlugin::connectToParent
@internal
Sets the parent SBML object of this plugin object to
this object and child elements (if any).
(Creates a child-parent relationship by this plugin object)
This function is called when this object is created by
the parent element.
Subclasses must override this this function if they have one
or more child elements. Also, ASTBasePlugin::connectToParent(@if java SBase sbase@endif)
must be called in the overridden function.
@param sbase the SBase object to use
@see setSBMLDocument
@see enablePackageInternal
=item ASTBasePlugin::enablePackageInternal
@internal
Enables/Disables the given package with child elements in this plugin
object (if any).
(This is an internal implementation invoked from
SBase::enablePackageInternal() function)
Subclasses which contain one or more SBase derived elements should
override this function if elements defined in them can be extended by
some other package extension.
@see setSBMLDocument
@see connectToParent
=item ASTBasePlugin::stripPackage
@internal
=item ASTBasePlugin::getURI
@internal
Gets the URI to which this element belongs to.
For example, all elements that belong to SBML Level 3 Version 1 Core
must would have the URI "http://www.sbml.org/sbml/level3/version1/core";
all elements that belong to Layout Extension Version 1 for SBML Level 3
Version 1 Core must would have the URI
"http://www.sbml.org/sbml/level3/version1/layout/version1/"
Unlike getElementNamespace, this function first returns the URI for this
element by looking into the SBMLNamespaces object of the document with
the its package name. if not found it will return the result of
getElementNamespace
@return the URI this elements
@see getPackageName
@see getElementNamespace
@see SBMLDocument::getSBMLNamespaces
@see getSBMLDocument
=item ASTBasePlugin::getParentASTObject
@internal
Returns the parent ASTNode object to which this plugin
object connected.
@return the parent ASTNode object to which this plugin
object connected.
=item ASTBasePlugin::getParentASTObject
@internal
Returns the parent ASTNode object to which this plugin
object connected.
@return the parent ASTNode object to which this plugin
object connected.
=item ASTBasePlugin::setElementNamespace
@internal
Sets the XML namespace to which this element belongs to.
For example, all elements that belong to SBML Level 3 Version 1 Core
must set the namespace to "http://www.sbml.org/sbml/level3/version1/core";
all elements that belong to Layout Extension Version 1 for SBML Level 3
Version 1 Core must set the namespace to
"http://www.sbml.org/sbml/level3/version1/layout/version1/"
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif@~ The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item ASTBasePlugin::getLevel
@internal
Returns the SBML level of the package extension of
this plugin object.
@return the SBML level of the package extension of
this plugin object.
=item ASTBasePlugin::getVersion
@internal
Returns the SBML version of the package extension of
this plugin object.
@return the SBML version of the package extension of
this plugin object.
=item ASTBasePlugin::getPackageVersion
@internal
Returns the package version of the package extension of
this plugin object.
@return the package version of the package extension of
this plugin object.
=item ASTBasePlugin::getSBMLNamespaces
@internal
=item ASTBasePlugin::isSetMath
@internal
=item ASTBasePlugin::getMath
@internal
=item ASTBasePlugin::createMath
@internal
=item ASTBasePlugin::addChild
@internal
=item ASTBasePlugin::getChild
@internal
=item ASTBasePlugin::getNumChildren
@internal
=item ASTBasePlugin::insertChild
@internal
=item ASTBasePlugin::prependChild
@internal
=item ASTBasePlugin::removeChild
@internal
=item ASTBasePlugin::replaceChild
@internal
=item ASTBasePlugin::swapChildren
@internal
=item ASTBasePlugin::read
@internal
=item ASTBasePlugin::addExpectedAttributes
@internal
=item ASTBasePlugin::readAttributes
@internal
=item ASTBasePlugin::writeAttributes
@internal
=item ASTBasePlugin::writeXMLNS
@internal
=item ASTBasePlugin::isNumberNode
@internal
=item ASTBasePlugin::isFunctionNode
@internal
=item ASTBasePlugin::isLogical
@internal
=item ASTBasePlugin::isConstantNumber
@internal
=item ASTBasePlugin::isCSymbolFunction
@internal
=item ASTBasePlugin::isCSymbolNumber
@internal
=item ASTBasePlugin::isName
@internal
=item ASTBasePlugin::isNumber
@internal
=item ASTBasePlugin::isOperator
@internal
=item ASTBasePlugin::isRelational
@internal
=item ASTBasePlugin::representsQualifier
@internal
=item ASTBasePlugin::isFunction
@internal
=item ASTBasePlugin::representsUnaryFunction
@internal
=item ASTBasePlugin::representsBinaryFunction
@internal
=item ASTBasePlugin::representsNaryFunction
@internal
=item ASTBasePlugin::isTopLevelMathMLFunctionNodeTag
@internal
=item ASTBasePlugin::isTopLevelMathMLNumberNodeTag
@internal
=item ASTBasePlugin::getTypeFromName
@internal
=item ASTBasePlugin::getNameFromType
@internal
=item ASTBasePlugin::ASTBasePlugin
@internal
Constructor. Creates an ASTBasePlugin object with the URI and
prefix of an package extension.
=item ASTBasePlugin::ASTBasePlugin
@internal
=item ASTBasePlugin::ASTBasePlugin
@internal
Copy constructor. Creates a copy of this SBase object.
=item GroupsExtension::getPackageName
Returns the package name of this extension.
=item GroupsExtension::getDefaultLevel
Returns the default SBML Level this extension.
=item GroupsExtension::getDefaultVersion
Returns the default SBML Version this extension.
=item GroupsExtension::getDefaultPackageVersion
Returns the default SBML version this extension.
=item GroupsExtension::getXmlnsL3V1V1
Returns URI of supported versions of this package.
=item GroupsExtension::GroupsExtension
Constructor
=item GroupsExtension::GroupsExtension
Copy constructor.
=item GroupsExtension::clone
Creates and returns a deep copy of this GroupsExtension object.
@return a (deep) copy of this SBase object
=item GroupsExtension::getName
Returns the name of this package ("groups")
@pram the name of this package ("groups")
=item GroupsExtension::getURI
Returns the URI (namespace) of the package corresponding to the combination of
the given sbml level, sbml version, and package version.
Empty string will be returned if no corresponding URI exists.
@param sbmlLevel the level of SBML
@param sbmlVersion the version of SBML
@param pkgVersion the version of package
@return a string of the package URI
=item GroupsExtension::getLevel
Returns the SBML level with the given URI of this package.
@param uri the string of URI that represents one of versions of groups package
@return the SBML level with the given URI of this package. 0 will be returned
if the given URI is invalid.
=item GroupsExtension::getVersion
Returns the SBML version with the given URI of this package.
@param uri the string of URI that represents one of versions of groups package
@return the SBML version with the given URI of this package. 0 will be returned
if the given URI is invalid.
=item GroupsExtension::getPackageVersion
Returns the package version with the given URI of this package.
@param uri the string of URI that represents one of versions of groups package
@return the package version with the given URI of this package. 0 will be returned
if the given URI is invalid.
=item GroupsExtension::getSBMLExtensionNamespaces
Returns an SBMLExtensionNamespaces<GroupsExtension> object whose alias type is
GroupsPkgNamespace.
Null will be returned if the given uri is not defined in the groups package.
@param uri the string of URI that represents one of versions of groups package
@return an GroupsPkgNamespace object corresponding to the given uri. NULL will
be returned if the given URI is not defined in groups package.
=item GroupsExtension::getStringFromTypeCode
This method takes a type code from the Groups package and returns a string representing
the code.
=item GroupsExtension::init
@internal
Initializes groups extension by creating an object of this class with
required SBasePlugin derived objects and registering the object
to the SBMLExtensionRegistry class.
(NOTE) This function is automatically invoked when creating the following
global object in GroupsExtension.cpp
static SBMLExtensionRegister<GroupsExtension> groupsExtensionRegistry;
=item GroupsExtension::getErrorTable
@internal
Return the entry in the error table at this index.
@param index an unsigned intgere representing the index of the error in the GroupsSBMLErrorTable
@return packageErrorTableEntry object in the GroupsSBMLErrorTable corresponding to the index given.
=item GroupsExtension::getErrorTableIndex
@internal
Return the index in the error table with the given errorId.
@param errorId an unsigned intgere representing the errorId of the error in the GroupsSBMLErrorTable
@return unsigned integer representing the index in the GroupsSBMLErrorTable corresponding to the errorId given.
=item GroupsExtension::getErrorIdOffset
@internal
Return the offset for the errorId range for the groups L3 package.
@return unsigned intege representing the offset for errors GroupsSBMLErrorTable.
=item GroupsModelPlugin::GroupsModelPlugin
Creates a new GroupsModelPlugin
=item GroupsModelPlugin::GroupsModelPlugin
Copy constructor for GroupsModelPlugin.
@param orig; the GroupsModelPlugin instance to copy.
=item GroupsModelPlugin::clone
Creates and returns a deep copy of this GroupsModelPlugin object.
@return a (deep) copy of this SBase object
=item GroupsModelPlugin::createObject
@internal
Subclasses must override this method to create, store, and then
return an SBML object corresponding to the next XMLToken in the
XMLInputStream if they have their specific elements.
@return the SBML object corresponding to next XMLToken in the
XMLInputStream or NULL if the token was not recognized.
=item GroupsModelPlugin::writeElements
@internal
Subclasses must override this method to write out their contained
SBML objects as XML elements if they have their specific elements.
=item GroupsModelPlugin::hasRequiredElements
@internal
Checks if this plugin object has all the required elements.
Subclasses should override this function if they have their specific
elements.
@return true if this pugin object has all the required elements,
otherwise false will be returned.
=item GroupsModelPlugin::getListOfGroups
@internal
Returns the ListOfGroups in this plugin object.
@return ListOfGroups object in this plugin object.
=item GroupsModelPlugin::getListOfGroups
@internal
Returns the ListOfGroups in this plugin object.
@return ListOfGroups object in this plugin object.
=item GroupsModelPlugin::getGroup
@internal
Returns the Group object that belongs to the given index. If the
index is invalid, NULL is returned.
@param n the index number of the Group to get.
@return the nth Group in the ListOfGroups.
=item GroupsModelPlugin::getGroup
@internal
Returns the Group object that belongs to the given index. If the
index is invalid, NULL is returned.
@param n the index number of the Group to get.
@return the nth Group in the ListOfGroups.
=item GroupsModelPlugin::getGroup
@internal
Returns the group object based on its identifier.
@param sid a string representing the identifier
of the Group to get.
@return Group in the ListOfGroups with the given id
or NULL if no such Group exists.
@see get(unsigned int n)
@see size()
=item GroupsModelPlugin::getGroup
@internal
Returns the group object based on its identifier.
@param sid a string representing the identifier
of the Group to get.
@return Group in the ListOfGroups with the given id
or NULL if no such Group exists.
@see get(unsigned int n)
@see size()
=item GroupsModelPlugin::addGroup
@internal
Adds a copy of the given Group object to the list of groups.
@param group the Group object to be added to the list of groups.
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif The possible values
returned by this function are:
@li LIBSBML_OPERATION_SUCCESS
=item GroupsModelPlugin::createGroup
@internal
Creates a new groups object and adds it to the list of groups objects
and returns it.
@return a newly created Group object
=item GroupsModelPlugin::removeGroup
@internal
Removes the nth Group object from this plugin object and
returns a pointer to it.
The caller owns the returned object and is responsible for
deleting it.
@param n the index of the Group object to remove
@return the Group object removed. As mentioned above, the
caller owns the returned object. NULL is returned if the
given index is out of range.
=item GroupsModelPlugin::removeGroup
@internal
Removes the Group object with the given id attribute from
this plugin object and returns a pointer to it.
The caller owns the returned object and is responsible for
deleting it.
@param sid the id attribute of the Group object to remove
@return the Group object removed. As mentioned above, the
caller owns the returned object. NULL is returned if the
given index is out of range.
=item GroupsModelPlugin::getNumGroups
@internal
Returns the number of Group object in this plugin object.
@return the number of Group object in this plugin object.
=item GroupsModelPlugin::setSBMLDocument
@internal
Sets the parent SBMLDocument of this plugin object.
Subclasses which contain one or more SBase derived elements must
override this function.
@param d the SBMLDocument object to use
@see connectToParent
@see enablePackageInternal
=item GroupsModelPlugin::connectToParent
@internal
Sets the parent SBML object of this plugin object to
this object and child elements (if any).
(Creates a child-parent relationship by this plugin object)
This function is called when this object is created by
the parent element.
Subclasses must override this this function if they have one
or more child elements.Also, SBasePlugin::connectToParent()
must be called in the overridden function.
@param sbase the SBase object to use
@see setSBMLDocument
@see enablePackageInternal
=item GroupsModelPlugin::enablePackageInternal
@internal
Enables/Disables the given package with child elements in this plugin
object (if any).
(This is an internal implementation invoked from
SBase::enablePakcageInternal() function)
@note Subclasses in which one or more SBase derived elements are
defined must override this function.
@see setSBMLDocument
@see connectToParent
=item GroupsModelPlugin::accept
@internal
=item Member::Member
Creates a new Member with the given level, version, and package version.
@param level an unsigned int, the SBML Level to assign to this Member
@param version an unsigned int, the SBML Version to assign to this Member
@param pkgVersion an unsigned int, the SBML Groups Version to assign to this Member
=item Member::Member
Creates a new Member with the given GroupsPkgNamespaces object.
@param groupsns the GroupsPkgNamespaces object
=item Member::Member
Copy constructor for Member.
@param orig; the Member instance to copy.
=item Member::clone
Creates and returns a deep copy of this Member object.
@return a (deep) copy of this Member object.
=item Member::getId
Returns the value of the "id" attribute of this Member.
@return the value of the "id" attribute of this Member as a string.
=item Member::isSetId
Predicate returning C<true> or C<false> depending on whether this
Member's "id" attribute has been set.
@return C<true> if this Member's "id" attribute has been set,
otherwise C<false> is returned.
=item Member::setId
Sets the value of the "id" attribute of this Member.
@param id; const std::string& value of the "id" attribute to be set
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif The possible values
returned by this function are:
@li LIBSBML_OPERATION_SUCCESS
@li LIBSBML_INVALID_ATTRIBUTE_VALUE
=item Member::unsetId
Unsets the value of the "id" attribute of this Member.
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif The possible values
returned by this function are:
@li LIBSBML_OPERATION_SUCCESS
@li LIBSBML_OPERATION_FAILED
=item Member::getName
Returns the value of the "name" attribute of this Member.
@return the value of the "name" attribute of this Member as a string.
=item Member::isSetName
Predicate returning C<true> or C<false> depending on whether this
Member's "name" attribute has been set.
@return C<true> if this Member's "name" attribute has been set,
otherwise C<false> is returned.
=item Member::setName
Sets the value of the "name" attribute of this Member.
@param name; const std::string& value of the "name" attribute to be set
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif The possible values
returned by this function are:
@li LIBSBML_OPERATION_SUCCESS
@li LIBSBML_INVALID_ATTRIBUTE_VALUE
=item Member::unsetName
Unsets the value of the "name" attribute of this Member.
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif The possible values
returned by this function are:
@li LIBSBML_OPERATION_SUCCESS
@li LIBSBML_OPERATION_FAILED
=item Member::getIdRef
Returns the value of the "idRef" attribute of this Member.
@return the value of the "idRef" attribute of this Member as a string.
=item Member::isSetIdRef
Predicate returning C<true> or C<false> depending on whether this
Member's "idRef" attribute has been set.
@return C<true> if this Member's "idRef" attribute has been set,
otherwise C<false> is returned.
=item Member::setIdRef
Sets the value of the "idRef" attribute of this Member.
@param idRef; const std::string& value of the "idRef" attribute to be set
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif The possible values
returned by this function are:
@li LIBSBML_OPERATION_SUCCESS
@li LIBSBML_INVALID_ATTRIBUTE_VALUE
=item Member::unsetIdRef
Unsets the value of the "idRef" attribute of this Member.
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif The possible values
returned by this function are:
@li LIBSBML_OPERATION_SUCCESS
@li LIBSBML_OPERATION_FAILED
=item Member::getMetaIdRef
Returns the value of the "metaIdRef" attribute of this Member.
@return the value of the "metaIdRef" attribute of this Member as a string.
=item Member::isSetMetaIdRef
Predicate returning C<true> or C<false> depending on whether this
Member's "metaIdRef" attribute has been set.
@return C<true> if this Member's "metaIdRef" attribute has been set,
otherwise C<false> is returned.
=item Member::setMetaIdRef
Sets the value of the "metaIdRef" attribute of this Member.
@param metaIdRef; const std::string& value of the "metaIdRef" attribute to be set
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif The possible values
returned by this function are:
@li LIBSBML_OPERATION_SUCCESS
@li LIBSBML_INVALID_ATTRIBUTE_VALUE
=item Member::unsetMetaIdRef
Unsets the value of the "metaIdRef" attribute of this Member.
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif The possible values
returned by this function are:
@li LIBSBML_OPERATION_SUCCESS
@li LIBSBML_OPERATION_FAILED
=item Member::getElementName
Returns the XML element name of this object, which for Member, is
always C<"member">.
@return the name of this element, i.e. C<"member">.
=item Member::getTypeCode
Returns the libSBML type code for this SBML object.
@if clike LibSBML attaches an identifying code to every kind of SBML
object. These are known as <em>SBML type codes</em>. The set of
possible type codes is defined in the enumeration #SBMLTypeCode_t.
The names of the type codes all begin with the characters C<
>
SBML_. @endif@if java LibSBML attaches an identifying code to every
kind of SBML object. These are known as <em>SBML type codes</em>. In
other languages, the set of type codes is stored in an enumeration; in
the Java language interface for libSBML, the type codes are defined as
static integer constants in the interface class {@link
libsbmlConstants}. The names of the type codes all begin with the
characters C<SBML_>. @endif@if python LibSBML attaches an identifying
code to every kind of SBML object. These are known as <em>SBML type
codes</em>. In the Python language interface for libSBML, the type
codes are defined as static integer constants in the interface class
@link libsbml@endlink. The names of the type codes all begin with the
characters C<SBML_>. @endif@if csharp LibSBML attaches an identifying
code to every kind of SBML object. These are known as <em>SBML type
codes</em>. In the C# language interface for libSBML, the type codes
are defined as static integer constants in the interface class @link
libsbmlcs.libsbml@endlink. The names of the type codes all begin with
the characters C<SBML_>. @endif
@return the SBML type code for this object, or
@link SBMLTypeCode_t#SBML_UNKNOWN SBML_UNKNOWN@endlink (default).
@see getElementName()
=item Member::hasRequiredAttributes
Predicate returning C<true> if all the required attributes
for this Member object have been set.
@note The required attributes for a Member object are:
@return a boolean value indicating whether all the required
attributes for this object have been defined.
=item Member::writeElements
@internal
Subclasses should override this method to write out their contained
SBML objects as XML elements. Be sure to call your parents
implementation of this method as well.
=item Member::accept
@internal
Accepts the given SBMLVisitor.
=item Member::setSBMLDocument
@internal
Sets the parent SBMLDocument.
=item Member::enablePackageInternal
@internal
Enables/Disables the given package with this element.
=item Member::addExpectedAttributes
@internal
Get the list of expected attributes for this element.
=item Member::readAttributes
@internal
Read values from the given XMLAttributes set into their specific fields.
=item Member::writeAttributes
@internal
Write values of XMLAttributes to the output stream.
=item ListOfMembers::ListOfMembers
Creates a new ListOfMembers with the given level, version, and package version.
@param level an unsigned int, the SBML Level to assign to this ListOfMembers
@param version an unsigned int, the SBML Version to assign to this ListOfMembers
@param pkgVersion an unsigned int, the SBML Groups Version to assign to this ListOfMembers
=item ListOfMembers::ListOfMembers
Creates a new ListOfMembers with the given GroupsPkgNamespaces object.
@param groupsns the GroupsPkgNamespaces object
=item ListOfMembers::clone
Creates and returns a deep copy of this ListOfMembers object.
@return a (deep) copy of this ListOfMembers object.
=item ListOfMembers::get
Get a Member from the ListOfMembers.
@param n the index number of the Member to get.
@return the nth Member in this ListOfMembers.
@see size()
=item ListOfMembers::get
Get a Member from the ListOfMembers.
@param n the index number of the Member to get.
@return the nth Member in this ListOfMembers.
@see size()
=item ListOfMembers::get
Get a Member from the ListOfMembers
based on its identifier.
@param sid a string representing the identifier
of the Member to get.
@return Member in this ListOfMembers
with the given id or NULL if no such
Member exists.
@see get(unsigned int n)
@see size()
=item ListOfMembers::get
Get a Member from the ListOfMembers
based on its identifier.
@param sid a string representing the identifier
of the Member to get.
@return Member in this ListOfMembers
with the given id or NULL if no such
Member exists.
@see get(unsigned int n)
@see size()
=item ListOfMembers::remove
Removes the nth Member from this ListOfMembers
and returns a pointer to it.
The caller owns the returned item and is responsible for deleting it.
@param n the index of the Member to remove.
@see size()
=item ListOfMembers::remove
Removes the Member from this ListOfMembers with the given identifier
and returns a pointer to it.
The caller owns the returned item and is responsible for deleting it.
If none of the items in this list have the identifier C<sid>, then
C<NULL> is returned.
@param sid the identifier of the Member to remove.
@return the Member removed. As mentioned above, the caller owns the
returned item.
=item ListOfMembers::getElementName
Returns the XML element name of this object, which for ListOfMembers, is
always C<"listOfMembers">.
@return the name of this element, i.e. C<"listOfMembers">.
=item ListOfMembers::getTypeCode
Returns the libSBML type code for this SBML object.
@if clike LibSBML attaches an identifying code to every kind of SBML
object. These are known as <em>SBML type codes</em>. The set of
possible type codes is defined in the enumeration #SBMLTypeCode_t.
The names of the type codes all begin with the characters C<
>
SBML_. @endif@if java LibSBML attaches an identifying code to every
kind of SBML object. These are known as <em>SBML type codes</em>. In
other languages, the set of type codes is stored in an enumeration; in
the Java language interface for libSBML, the type codes are defined as
static integer constants in the interface class {@link
libsbmlConstants}. The names of the type codes all begin with the
characters C<SBML_>. @endif@if python LibSBML attaches an identifying
code to every kind of SBML object. These are known as <em>SBML type
codes</em>. In the Python language interface for libSBML, the type
codes are defined as static integer constants in the interface class
@link libsbml@endlink. The names of the type codes all begin with the
characters C<SBML_>. @endif@if csharp LibSBML attaches an identifying
code to every kind of SBML object. These are known as <em>SBML type
codes</em>. In the C# language interface for libSBML, the type codes
are defined as static integer constants in the interface class @link
libsbmlcs.libsbml@endlink. The names of the type codes all begin with
the characters C<SBML_>. @endif
@return the SBML type code for this object, or
@link SBMLTypeCode_t#SBML_UNKNOWN SBML_UNKNOWN@endlink (default).
@see getElementName()
=item ListOfMembers::getItemTypeCode
Returns the libSBML type code for the SBML objects
contained in this ListOf object
@if clike LibSBML attaches an identifying code to every kind of SBML
object. These are known as <em>SBML type codes</em>. The set of
possible type codes is defined in the enumeration #SBMLTypeCode_t.
The names of the type codes all begin with the characters C<
>
SBML_. @endif@if java LibSBML attaches an identifying code to every
kind of SBML object. These are known as <em>SBML type codes</em>. In
other languages, the set of type codes is stored in an enumeration; in
the Java language interface for libSBML, the type codes are defined as
static integer constants in the interface class {@link
libsbmlConstants}. The names of the type codes all begin with the
characters C<SBML_>. @endif@if python LibSBML attaches an identifying
code to every kind of SBML object. These are known as <em>SBML type
codes</em>. In the Python language interface for libSBML, the type
codes are defined as static integer constants in the interface class
@link libsbml@endlink. The names of the type codes all begin with the
characters C<SBML_>. @endif@if csharp LibSBML attaches an identifying
code to every kind of SBML object. These are known as <em>SBML type
codes</em>. In the C# language interface for libSBML, the type codes
are defined as static integer constants in the interface class @link
libsbmlcs.libsbml@endlink. The names of the type codes all begin with
the characters C<SBML_>. @endif
@return the SBML type code for the objects in this ListOf instance, or
@link SBMLTypeCode_t#SBML_UNKNOWN SBML_UNKNOWN@endlink (default).
@see getElementName()
=item ListOfMembers::createObject
@internal
Creates a new Member in this ListOfMembers
=item ListOfMembers::writeXMLNS
@internal
Write the namespace for the Groups package.
=item MemberConstraint::MemberConstraint
Creates a new MemberConstraint with the given level, version, and package version.
@param level an unsigned int, the SBML Level to assign to this MemberConstraint
@param version an unsigned int, the SBML Version to assign to this MemberConstraint
@param pkgVersion an unsigned int, the SBML Groups Version to assign to this MemberConstraint
=item MemberConstraint::MemberConstraint
Creates a new MemberConstraint with the given GroupsPkgNamespaces object.
@param groupsns the GroupsPkgNamespaces object
=item MemberConstraint::MemberConstraint
Copy constructor for MemberConstraint.
@param orig; the MemberConstraint instance to copy.
=item MemberConstraint::clone
Creates and returns a deep copy of this MemberConstraint object.
@return a (deep) copy of this MemberConstraint object.
=item MemberConstraint::getId
Returns the value of the "id" attribute of this MemberConstraint.
@return the value of the "id" attribute of this MemberConstraint as a string.
=item MemberConstraint::isSetId
Predicate returning C<true> or C<false> depending on whether this
MemberConstraint's "id" attribute has been set.
@return C<true> if this MemberConstraint's "id" attribute has been set,
otherwise C<false> is returned.
=item MemberConstraint::setId
Sets the value of the "id" attribute of this MemberConstraint.
@param id; const std::string& value of the "id" attribute to be set
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif The possible values
returned by this function are:
@li LIBSBML_OPERATION_SUCCESS
@li LIBSBML_INVALID_ATTRIBUTE_VALUE
=item MemberConstraint::unsetId
Unsets the value of the "id" attribute of this MemberConstraint.
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif The possible values
returned by this function are:
@li LIBSBML_OPERATION_SUCCESS
@li LIBSBML_OPERATION_FAILED
=item MemberConstraint::getName
Returns the value of the "name" attribute of this MemberConstraint.
@return the value of the "name" attribute of this MemberConstraint as a string.
=item MemberConstraint::isSetName
Predicate returning C<true> or C<false> depending on whether this
MemberConstraint's "name" attribute has been set.
@return C<true> if this MemberConstraint's "name" attribute has been set,
otherwise C<false> is returned.
=item MemberConstraint::setName
Sets the value of the "name" attribute of this MemberConstraint.
@param name; const std::string& value of the "name" attribute to be set
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif The possible values
returned by this function are:
@li LIBSBML_OPERATION_SUCCESS
@li LIBSBML_INVALID_ATTRIBUTE_VALUE
=item MemberConstraint::unsetName
Unsets the value of the "name" attribute of this MemberConstraint.
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif The possible values
returned by this function are:
@li LIBSBML_OPERATION_SUCCESS
@li LIBSBML_OPERATION_FAILED
=item MemberConstraint::getDistinctAttribute
Returns the value of the "distinctAttribute" attribute of this MemberConstraint.
@return the value of the "distinctAttribute" attribute of this MemberConstraint as a string.
=item MemberConstraint::isSetDistinctAttribute
Predicate returning C<true> or C<false> depending on whether this
MemberConstraint's "distinctAttribute" attribute has been set.
@return C<true> if this MemberConstraint's "distinctAttribute" attribute has been set,
otherwise C<false> is returned.
=item MemberConstraint::setDistinctAttribute
Sets the value of the "distinctAttribute" attribute of this MemberConstraint.
@param distinctAttribute; const std::string& value of the "distinctAttribute" attribute to be set
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif The possible values
returned by this function are:
@li LIBSBML_OPERATION_SUCCESS
@li LIBSBML_INVALID_ATTRIBUTE_VALUE
=item MemberConstraint::unsetDistinctAttribute
Unsets the value of the "distinctAttribute" attribute of this MemberConstraint.
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif The possible values
returned by this function are:
@li LIBSBML_OPERATION_SUCCESS
@li LIBSBML_OPERATION_FAILED
=item MemberConstraint::getIdenticalAttribute
Returns the value of the "identicalAttribute" attribute of this MemberConstraint.
@return the value of the "identicalAttribute" attribute of this MemberConstraint as a string.
=item MemberConstraint::isSetIdenticalAttribute
Predicate returning C<true> or C<false> depending on whether this
MemberConstraint's "identicalAttribute" attribute has been set.
@return C<true> if this MemberConstraint's "identicalAttribute" attribute has been set,
otherwise C<false> is returned.
=item MemberConstraint::setIdenticalAttribute
Sets the value of the "identicalAttribute" attribute of this MemberConstraint.
@param identicalAttribute; const std::string& value of the "identicalAttribute" attribute to be set
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif The possible values
returned by this function are:
@li LIBSBML_OPERATION_SUCCESS
@li LIBSBML_INVALID_ATTRIBUTE_VALUE
=item MemberConstraint::unsetIdenticalAttribute
Unsets the value of the "identicalAttribute" attribute of this MemberConstraint.
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif The possible values
returned by this function are:
@li LIBSBML_OPERATION_SUCCESS
@li LIBSBML_OPERATION_FAILED
=item MemberConstraint::getElementName
Returns the XML element name of this object, which for MemberConstraint, is
always C<"memberConstraint">.
@return the name of this element, i.e. C<"memberConstraint">.
=item MemberConstraint::getTypeCode
Returns the libSBML type code for this SBML object.
@if clike LibSBML attaches an identifying code to every kind of SBML
object. These are known as <em>SBML type codes</em>. The set of
possible type codes is defined in the enumeration #SBMLTypeCode_t.
The names of the type codes all begin with the characters C<
>
SBML_. @endif@if java LibSBML attaches an identifying code to every
kind of SBML object. These are known as <em>SBML type codes</em>. In
other languages, the set of type codes is stored in an enumeration; in
the Java language interface for libSBML, the type codes are defined as
static integer constants in the interface class {@link
libsbmlConstants}. The names of the type codes all begin with the
characters C<SBML_>. @endif@if python LibSBML attaches an identifying
code to every kind of SBML object. These are known as <em>SBML type
codes</em>. In the Python language interface for libSBML, the type
codes are defined as static integer constants in the interface class
@link libsbml@endlink. The names of the type codes all begin with the
characters C<SBML_>. @endif@if csharp LibSBML attaches an identifying
code to every kind of SBML object. These are known as <em>SBML type
codes</em>. In the C# language interface for libSBML, the type codes
are defined as static integer constants in the interface class @link
libsbmlcs.libsbml@endlink. The names of the type codes all begin with
the characters C<SBML_>. @endif
@return the SBML type code for this object, or
@link SBMLTypeCode_t#SBML_UNKNOWN SBML_UNKNOWN@endlink (default).
@see getElementName()
=item MemberConstraint::hasRequiredAttributes
Predicate returning C<true> if all the required attributes
for this MemberConstraint object have been set.
@note The required attributes for a MemberConstraint object are:
@return a boolean value indicating whether all the required
attributes for this object have been defined.
=item MemberConstraint::writeElements
@internal
Subclasses should override this method to write out their contained
SBML objects as XML elements. Be sure to call your parents
implementation of this method as well.
=item MemberConstraint::accept
@internal
Accepts the given SBMLVisitor.
=item MemberConstraint::setSBMLDocument
@internal
Sets the parent SBMLDocument.
=item MemberConstraint::enablePackageInternal
@internal
Enables/Disables the given package with this element.
=item MemberConstraint::addExpectedAttributes
@internal
Get the list of expected attributes for this element.
=item MemberConstraint::readAttributes
@internal
Read values from the given XMLAttributes set into their specific fields.
=item MemberConstraint::writeAttributes
@internal
Write values of XMLAttributes to the output stream.
=item ListOfMemberConstraints::ListOfMemberConstraints
Creates a new ListOfMemberConstraints with the given level, version, and package version.
@param level an unsigned int, the SBML Level to assign to this ListOfMemberConstraints
@param version an unsigned int, the SBML Version to assign to this ListOfMemberConstraints
@param pkgVersion an unsigned int, the SBML Groups Version to assign to this ListOfMemberConstraints
=item ListOfMemberConstraints::ListOfMemberConstraints
Creates a new ListOfMemberConstraints with the given GroupsPkgNamespaces object.
@param groupsns the GroupsPkgNamespaces object
=item ListOfMemberConstraints::clone
Creates and returns a deep copy of this ListOfMemberConstraints object.
@return a (deep) copy of this ListOfMemberConstraints object.
=item ListOfMemberConstraints::get
Get a MemberConstraint from the ListOfMemberConstraints.
@param n the index number of the MemberConstraint to get.
@return the nth MemberConstraint in this ListOfMemberConstraints.
@see size()
=item ListOfMemberConstraints::get
Get a MemberConstraint from the ListOfMemberConstraints.
@param n the index number of the MemberConstraint to get.
@return the nth MemberConstraint in this ListOfMemberConstraints.
@see size()
=item ListOfMemberConstraints::get
Get a MemberConstraint from the ListOfMemberConstraints
based on its identifier.
@param sid a string representing the identifier
of the MemberConstraint to get.
@return MemberConstraint in this ListOfMemberConstraints
with the given id or NULL if no such
MemberConstraint exists.
@see get(unsigned int n)
@see size()
=item ListOfMemberConstraints::get
Get a MemberConstraint from the ListOfMemberConstraints
based on its identifier.
@param sid a string representing the identifier
of the MemberConstraint to get.
@return MemberConstraint in this ListOfMemberConstraints
with the given id or NULL if no such
MemberConstraint exists.
@see get(unsigned int n)
@see size()
=item ListOfMemberConstraints::remove
Removes the nth MemberConstraint from this ListOfMemberConstraints
and returns a pointer to it.
The caller owns the returned item and is responsible for deleting it.
@param n the index of the MemberConstraint to remove.
@see size()
=item ListOfMemberConstraints::remove
Removes the MemberConstraint from this ListOfMemberConstraints with the given identifier
and returns a pointer to it.
The caller owns the returned item and is responsible for deleting it.
If none of the items in this list have the identifier C<sid>, then
C<NULL> is returned.
@param sid the identifier of the MemberConstraint to remove.
@return the MemberConstraint removed. As mentioned above, the caller owns the
returned item.
=item ListOfMemberConstraints::getId
Returns the value of the "id" attribute of this ListOfMemberConstraints.
@return the value of the "id" attribute of this ListOfMemberConstraints as a string.
=item ListOfMemberConstraints::isSetId
Predicate returning C<true> or C<false> depending on whether this
ListOfMemberConstraints' "id" attribute has been set.
@return C<true> if this ListOfMemberConstraints' "id" attribute has been set,
otherwise C<false> is returned.
=item ListOfMemberConstraints::setId
Sets the value of the "id" attribute of this ListOfMemberConstraints.
@param id; const std::string& value of the "id" attribute to be set
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif The possible values
returned by this function are:
@li LIBSBML_OPERATION_SUCCESS
@li LIBSBML_INVALID_ATTRIBUTE_VALUE
=item ListOfMemberConstraints::unsetId
Unsets the value of the "id" attribute of this ListOfMemberConstraints.
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif The possible values
returned by this function are:
@li LIBSBML_OPERATION_SUCCESS
@li LIBSBML_OPERATION_FAILED
=item ListOfMemberConstraints::getName
Returns the value of the "name" attribute of this ListOfMemberConstraints.
@return the value of the "name" attribute of this ListOfMemberConstraints as a string.
=item ListOfMemberConstraints::isSetName
Predicate returning C<true> or C<false> depending on whether this
ListOfMemberConstraints' "name" attribute has been set.
@return C<true> if this ListOfMemberConstraints' "name" attribute has been set,
otherwise C<false> is returned.
=item ListOfMemberConstraints::setName
Sets the value of the "name" attribute of this ListOfMemberConstraints.
@param name; const std::string& value of the "name" attribute to be set
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif The possible values
returned by this function are:
@li LIBSBML_OPERATION_SUCCESS
@li LIBSBML_INVALID_ATTRIBUTE_VALUE
=item ListOfMemberConstraints::unsetName
Unsets the value of the "name" attribute of this ListOfMemberConstraints.
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif The possible values
returned by this function are:
@li LIBSBML_OPERATION_SUCCESS
@li LIBSBML_OPERATION_FAILED
=item ListOfMemberConstraints::getMembersShareType
Returns the value of the "membersShareType" attribute of this ListOfMemberConstraints.
@return the value of the "membersShareType" attribute of this ListOfMemberConstraints as a string.
=item ListOfMemberConstraints::isSetMembersShareType
Predicate returning C<true> or C<false> depending on whether this
ListOfMemberConstraints's "membersShareType" attribute has been set.
@return C<true> if this ListOfMemberConstraints's "membersShareType" attribute has been set,
otherwise C<false> is returned.
=item ListOfMemberConstraints::setMembersShareType
Sets the value of the "membersShareType" attribute of this ListOfMemberConstraints.
@param membersShareType; const std::string& value of the "membersShareType" attribute to be set
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif The possible values
returned by this function are:
@li LIBSBML_OPERATION_SUCCESS
@li LIBSBML_INVALID_ATTRIBUTE_VALUE
=item ListOfMemberConstraints::unsetMembersShareType
Unsets the value of the "membersShareType" attribute of this ListOfMemberConstraints.
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif The possible values
returned by this function are:
@li LIBSBML_OPERATION_SUCCESS
@li LIBSBML_OPERATION_FAILED
=item ListOfMemberConstraints::getElementName
Returns the XML element name of this object, which for ListOfMemberConstraints, is
always C<"listOfMemberConstraints">.
@return the name of this element, i.e. C<"listOfMemberConstraints">.
=item ListOfMemberConstraints::getTypeCode
Returns the libSBML type code for this SBML object.
@if clike LibSBML attaches an identifying code to every kind of SBML
object. These are known as <em>SBML type codes</em>. The set of
possible type codes is defined in the enumeration #SBMLTypeCode_t.
The names of the type codes all begin with the characters C<
>
SBML_. @endif@if java LibSBML attaches an identifying code to every
kind of SBML object. These are known as <em>SBML type codes</em>. In
other languages, the set of type codes is stored in an enumeration; in
the Java language interface for libSBML, the type codes are defined as
static integer constants in the interface class {@link
libsbmlConstants}. The names of the type codes all begin with the
characters C<SBML_>. @endif@if python LibSBML attaches an identifying
code to every kind of SBML object. These are known as <em>SBML type
codes</em>. In the Python language interface for libSBML, the type
codes are defined as static integer constants in the interface class
@link libsbml@endlink. The names of the type codes all begin with the
characters C<SBML_>. @endif@if csharp LibSBML attaches an identifying
code to every kind of SBML object. These are known as <em>SBML type
codes</em>. In the C# language interface for libSBML, the type codes
are defined as static integer constants in the interface class @link
libsbmlcs.libsbml@endlink. The names of the type codes all begin with
the characters C<SBML_>. @endif
@return the SBML type code for this object, or
@link SBMLTypeCode_t#SBML_UNKNOWN SBML_UNKNOWN@endlink (default).
@see getElementName()
=item ListOfMemberConstraints::getItemTypeCode
Returns the libSBML type code for the SBML objects
contained in this ListOf object
@if clike LibSBML attaches an identifying code to every kind of SBML
object. These are known as <em>SBML type codes</em>. The set of
possible type codes is defined in the enumeration #SBMLTypeCode_t.
The names of the type codes all begin with the characters C<
>
SBML_. @endif@if java LibSBML attaches an identifying code to every
kind of SBML object. These are known as <em>SBML type codes</em>. In
other languages, the set of type codes is stored in an enumeration; in
the Java language interface for libSBML, the type codes are defined as
static integer constants in the interface class {@link
libsbmlConstants}. The names of the type codes all begin with the
characters C<SBML_>. @endif@if python LibSBML attaches an identifying
code to every kind of SBML object. These are known as <em>SBML type
codes</em>. In the Python language interface for libSBML, the type
codes are defined as static integer constants in the interface class
@link libsbml@endlink. The names of the type codes all begin with the
characters C<SBML_>. @endif@if csharp LibSBML attaches an identifying
code to every kind of SBML object. These are known as <em>SBML type
codes</em>. In the C# language interface for libSBML, the type codes
are defined as static integer constants in the interface class @link
libsbmlcs.libsbml@endlink. The names of the type codes all begin with
the characters C<SBML_>. @endif
@return the SBML type code for the objects in this ListOf instance, or
@link SBMLTypeCode_t#SBML_UNKNOWN SBML_UNKNOWN@endlink (default).
@see getElementName()
=item ListOfMemberConstraints::createObject
@internal
Creates a new MemberConstraint in this ListOfMemberConstraints
=item ListOfMemberConstraints::writeXMLNS
@internal
Write the namespace for the Groups package.
=item ListOfMemberConstraints::addExpectedAttributes
@internal
Subclasses should override this method to get the list of
expected attributes.
This function is invoked from corresponding readAttributes()
function.
=item ListOfMemberConstraints::readAttributes
@internal
Reads the attributes of corresponding package in SBMLDocument element.
=item ListOfMemberConstraints::writeAttributes
@internal
Writes the attributes of corresponding package in SBMLDocument element.
=item Group::Group
Creates a new Group with the given level, version, and package version.
@param level an unsigned int, the SBML Level to assign to this Group
@param version an unsigned int, the SBML Version to assign to this Group
@param pkgVersion an unsigned int, the SBML Groups Version to assign to this Group
=item Group::Group
Creates a new Group with the given GroupsPkgNamespaces object.
@param groupsns the GroupsPkgNamespaces object
=item Group::Group
Copy constructor for Group.
@param orig; the Group instance to copy.
=item Group::clone
Creates and returns a deep copy of this Group object.
@return a (deep) copy of this Group object.
=item Group::getId
Returns the value of the "id" attribute of this Group.
@return the value of the "id" attribute of this Group as a string.
=item Group::isSetId
Predicate returning C<true> or C<false> depending on whether this
Group's "id" attribute has been set.
@return C<true> if this Group's "id" attribute has been set,
otherwise C<false> is returned.
=item Group::setId
Sets the value of the "id" attribute of this Group.
@param id; const std::string& value of the "id" attribute to be set
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif The possible values
returned by this function are:
@li LIBSBML_OPERATION_SUCCESS
@li LIBSBML_INVALID_ATTRIBUTE_VALUE
=item Group::unsetId
Unsets the value of the "id" attribute of this Group.
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif The possible values
returned by this function are:
@li LIBSBML_OPERATION_SUCCESS
@li LIBSBML_OPERATION_FAILED
=item Group::getName
Returns the value of the "name" attribute of this Group.
@return the value of the "name" attribute of this Group as a string.
=item Group::isSetName
Predicate returning C<true> or C<false> depending on whether this
Group's "name" attribute has been set.
@htmlinclude comment-set-methods.html
@return C<true> if this Group's "name" attribute has been set,
otherwise C<false> is returned.
=item Group::setName
Sets the value of the "name" attribute of this Group.
The string in C<name> is copied.
@htmlinclude comment-set-methods.html
@param name; const std::string& value of the "name" attribute to be set
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif The possible values
returned by this function are:
@li LIBSBML_OPERATION_SUCCESS
@li LIBSBML_INVALID_ATTRIBUTE_VALUE
=item Group::unsetName
Unsets the value of the "name" attribute of this Group.
@htmlinclude comment-set-methods.html
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif The possible values
returned by this function are:
@li LIBSBML_OPERATION_SUCCESS
@li LIBSBML_OPERATION_FAILED
=item Group::getKind
Returns the value of the "kind" attribute of this Group.
@return the kind of this Group.
=item Group::isSetKind
Predicate returning C<true> or C<false> depending on whether this
Group's "kind" attribute has been set.
@htmlinclude comment-set-methods.html
@return C<true> if this Group's "kind" attribute has been set,
otherwise C<false> is returned.
=item Group::setKind
Sets the value of the "kind" attribute of this Group.
The string in C<kind> is copied.
@htmlinclude comment-set-methods.html
@param kind the new kind for the Group
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif The possible values
returned by this function are:
@li LIBSBML_OPERATION_SUCCESS
@li LIBSBML_INVALID_ATTRIBUTE_VALUE
=item Group::unsetKind
Unsets the value of the "kind" attribute of this Group.
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif The possible values
returned by this function are:
@li LIBSBML_OPERATION_SUCCESS
@li LIBSBML_OPERATION_FAILED
=item Group::getListOfMembers
Returns the ListOf object that holds all members.
@return the ListOf object that holds all members.
=item Group::getMember
Returns the member with the given index.
If the index is invalid, NULL is returned.
@param n the index number of the Member to get.
@return the nth Member in the ListOfMembers.
=item Group::getMember
Returns the member with the given index.
If the index is invalid, NULL is returned.
@param n the index number of the Member to get.
@return the nth Member in the ListOfMembers.
=item Group::getMember
Returns the member with the given symbol.
If the index is invalid, NULL is returned.
@param symbol a string representing the symbol attribute
of the Member to get.
@return Member in the ListOfMembers with the given symbol
or NULL if no such Member exists.
=item Group::getMember
Returns the member with the given symbol.
If the index is invalid, NULL is returned.
@param symbol a string representing the symbol attribute
of the Member to get.
@return Member in the ListOfMembers with the given symbol
or NULL if no such Member exists.
=item Group::addMember
Adds a copy of the given Member objcect to the list of members.
@param member the Member object to be added to the list of
members.
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif The possible values
returned by this function are:
@li LIBSBML_OPERATION_SUCCESS
=item Group::getNumMembers
Returns the number of members for this group.
@return the number of members for this group.
=item Group::createMember
Creates a Member object, adds it to the end of the
member objects list and returns a pointer to the newly
created object.
@return a newly created Member object
=item Group::removeMember
Removes the member with the given index from the group.
A pointer to the member that was removed is returned.
If no member has been removed, NULL is returned.
@param n the index of the Member object to remove
@return the Member object removed. As mentioned above,
the caller owns the returned object. NULL is returned if
the given index is out of range.
=item Group::removeMember
Removes the member with the given symbol from the group.
A pointer to the member that was removed is returned.
If no member has been removed, NULL is returned.
@param symbol the symbol attribute of the Member object to remove
@return the Member object removed. As mentioned above,
the caller owns the returned object. NULL is returned if
the given index is out of range.
=item Group::getListOfMemberConstraints
Returns the "ListOfMemberConstraints" in this Group object.
@return the "ListOfMemberConstraints" attribute of this Group.
=item Group::getListOfMemberConstraints
Returns the "ListOfMemberConstraints" in this Group object.
@return the "ListOfMemberConstraints" attribute of this Group.
=item Group::getMemberConstraint
Get a MemberConstraint from the ListOfMemberConstraints.
@param n the index number of the MemberConstraint to get.
@return the nth MemberConstraint in the ListOfMemberConstraints within this Group.
@see getNumMemberConstraints()
=item Group::getMemberConstraint
Get a MemberConstraint from the ListOfMemberConstraints.
@param n the index number of the MemberConstraint to get.
@return the nth MemberConstraint in the ListOfMemberConstraints within this Group.
@see getNumMemberConstraints()
=item Group::getMemberConstraint
Get a MemberConstraint from the ListOfMemberConstraints
based on its identifier.
@param sid a string representing the identifier
of the MemberConstraint to get.
@return the MemberConstraint in the ListOfMemberConstraints
with the given id or NULL if no such
MemberConstraint exists.
@see getMemberConstraint(unsigned int n)
@see getNumMemberConstraints()
=item Group::getMemberConstraint
Get a MemberConstraint from the ListOfMemberConstraints
based on its identifier.
@param sid a string representing the identifier
of the MemberConstraint to get.
@return the MemberConstraint in the ListOfMemberConstraints
with the given id or NULL if no such
MemberConstraint exists.
@see getMemberConstraint(unsigned int n)
@see getNumMemberConstraints()
=item Group::addMemberConstraint
Adds a copy the given "MemberConstraint" to this Group.
@param mc; the MemberConstraint object to add
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif The possible values
returned by this function are:
@li LIBSBML_OPERATION_SUCCESS
@li LIBSBML_INVALID_ATTRIBUTE_VALUE
=item Group::getNumMemberConstraints
Get the number of MemberConstraint objects in this Group.
@return the number of MemberConstraint objects in this Group
=item Group::createMemberConstraint
Creates a new MemberConstraint object, adds it to this Groups
ListOfMemberConstraints and returns the MemberConstraint object created.
@return a new MemberConstraint object instance
@see addMemberConstraint(const MemberConstraint mc)
=item Group::removeMemberConstraint
Removes the nth MemberConstraint from the ListOfMemberConstraints within this Group.
and returns a pointer to it.
The caller owns the returned item and is responsible for deleting it.
@param n the index of the MemberConstraint to remove.
@see getNumMemberConstraints()
=item Group::removeMemberConstraint
Removes the MemberConstraint with the given identifier from the ListOfMemberConstraints within this Group
and returns a pointer to it.
The caller owns the returned item and is responsible for deleting it.
If none of the items in this list have the identifier C<sid>, then
C<NULL> is returned.
@param sid the identifier of the MemberConstraint to remove.
@return the MemberConstraint removed. As mentioned above, the caller owns the
returned item.
=item Group::getElementName
Subclasses should override this method to return XML element name of
this SBML object.
@return the string of the name of this element.
=item Group::getTypeCode
@return the typecode (int) of this SBML object or SBML_UNKNOWN
(default).
@see getElementName()
=item Group::writeElements
@internal
Subclasses should override this method to write out their contained
SBML objects as XML elements. Be sure to call your parents
implementation of this method as well. For example:
SBase::writeElements(stream);
mReactans.write(stream);
mProducts.write(stream);
...
=item Group::accept
@internal
Accepts the given SBMLVisitor.
@return the result of calling C<v.visit()>, which indicates
whether or not the Visitor would like to visit the SBML object's next
sibling object (if available).
=item Group::setSBMLDocument
@internal
Sets the parent SBMLDocument of this SBML object.
@param d the SBMLDocument object to use
=item Group::connectToChild
@internal
Sets this SBML object to child SBML objects (if any).
(Creates a child-parent relationship by the parent)
Subclasses must override this function if they define
one ore more child elements.
Basically, this function needs to be called in
constructor, copy constructor, assignment operator.
@see setSBMLDocument
@see enablePackageInternal
=item Group::enablePackageInternal
@internal
Enables/Disables the given package with this element and child
elements (if any).
(This is an internal implementation for enablePakcage function)
@note Subclasses in which one or more child elements are defined
must override this function.
=item Group::hasRequiredAttributes
@internal
=item Group::hasRequiredElements
@internal
=item Group::createObject
@return the SBML object corresponding to next XMLToken in the
XMLInputStream or NULL if the token was not recognized.
=item Group::addExpectedAttributes
Subclasses should override this method to get the list of
expected attributes.
This function is invoked from corresponding readAttributes()
function.
=item Group::readAttributes
Subclasses should override this method to read values from the given
XMLAttributes set into their specific fields. Be sure to call your
parents implementation of this method as well.
=item Group::writeAttributes
Subclasses should override this method to write their XML attributes
to the XMLOutputStream. Be sure to call your parents implementation
of this method as well. For example:
SBase::writeAttributes(stream);
stream.writeAttribute( "id" , mId );
stream.writeAttribute( "name", mName );
...
=item ListOfGroups::clone
@return a (deep) copy of this ListOfGroups.
=item ListOfGroups::ListOfGroups
Creates a new ListOfGroups with the given level, version, and package version.
=item ListOfGroups::ListOfGroups
Creates a new ListOfGroups with the given GroupsPkgNamespaces object.
=item ListOfGroups::get
Get a Group from the ListOfGroups.
@param n the index number of the Group to get.
@return the nth Group in this ListOfGroups.
@see size()
=item ListOfGroups::get
Get a Group from the ListOfGroups.
@param n the index number of the Group to get.
@return the nth Group in this ListOfGroups.
@see size()
=item ListOfGroups::get
Get a Group from the ListOfGroups
based on its identifier.
@param sid a string representing the identifier
of the Group to get.
@return Group in this ListOfGroups
with the given id or NULL if no such
Group exists.
@see get(unsigned int n)
@see size()
=item ListOfGroups::get
Get a Group from the ListOfGroups
based on its identifier.
@param sid a string representing the identifier
of the Group to get.
@return Group in this ListOfGroups
with the given id or NULL if no such
Group exists.
@see get(unsigned int n)
@see size()
=item ListOfGroups::remove
Removes the nth item from this ListOfGroups items and returns a pointer to
it.
The caller owns the returned item and is responsible for deleting it.
@param n the index of the item to remove
@see size()
=item ListOfGroups::remove
Removes item in this ListOfGroups items with the given identifier.
The caller owns the returned item and is responsible for deleting it.
If none of the items in this list have the identifier C<sid>, then C<
>
NULL is returned.
@param sid the identifier of the item to remove
@return the item removed. As mentioned above, the caller owns the
returned item.
=item ListOfGroups::getItemTypeCode
@return the typecode (int) of SBML objects contained in this ListOf or
SBML_UNKNOWN (default).
=item ListOfGroups::getElementName
Subclasses should override this method to return XML element name of
this SBML object.
@return the string of the name of this element.
=item ListOfGroups::createObject
@return the SBML object corresponding to next XMLToken in the
XMLInputStream or NULL if the token was not recognized.
=item ListOfGroups::writeXMLNS
=item RenderExtension::getPackageName
Returns the package name of this extension.
=item RenderExtension::getDefaultLevel
Returns the default SBML Level this extension.
=item RenderExtension::getDefaultVersion
Returns the default SBML Version this extension.
=item RenderExtension::getDefaultPackageVersion
Returns the default SBML version this extension.
=item RenderExtension::getXmlnsL3V1V1
Returns URI of supported versions of this package.
=item RenderExtension::getXmlnsL2
=item RenderExtension::RenderExtension
Constructor
=item RenderExtension::RenderExtension
Copy constructor.
=item RenderExtension::clone
Creates and returns a deep copy of this RenderExtension object.
@return a (deep) copy of this RenderExtension object
=item RenderExtension::getName
Returns the name of this package ("fbc")
@pram the name of this package ("fbc")
=item RenderExtension::getURI
Returns the URI (namespace) of the package corresponding to the combination of
the given sbml level, sbml version, and package version.
Empty string will be returned if no corresponding URI exists.
@param sbmlLevel the level of SBML
@param sbmlVersion the version of SBML
@param pkgVersion the version of package
@return a string of the package URI
=item RenderExtension::getLevel
Returns the SBML level with the given URI of this package.
@param uri the string of URI that represents one of versions of layout package
@return the SBML level with the given URI of this package. 0 will be returned
if the given URI is invalid.
=item RenderExtension::getVersion
Returns the SBML version with the given URI of this package.
@param uri the string of URI that represents one of versions of layout package
@return the SBML version with the given URI of this package. 0 will be returned
if the given URI is invalid.
=item RenderExtension::getPackageVersion
Returns the package version with the given URI of this package.
@param uri the string of URI that represents one of versions of layout package
@return the package version with the given URI of this package. 0 will be returned
if the given URI is invalid.
=item RenderExtension::getSBMLExtensionNamespaces
Returns an SBMLExtensionNamespaces<GroupsExtension> object whose alias type is
LayoutPkgNamespace.
Null will be returned if the given uri is not defined in the layout package.
@param uri the string of URI that represents one of versions of layout package
@return an LayoutPkgNamespace object corresponding to the given uri. NULL will
be returned if the given URI is not defined in layout package.
=item RenderExtension::getStringFromTypeCode
This method takes a type code of groups package and returns a string representing
the code.
=item RenderExtension::init
@internal
Initializes layout extension by creating an object of this class with
required SBasePlugin derived objects and registering the object
to the SBMLExtensionRegistry class.
(NOTE) This function is automatically invoked when creating the following
global object in GroupsExtension.cpp
static SBMLExtensionRegister<GroupsExtension> groupsExtensionRegistry;
=item RenderExtension::removeL2Namespaces
Removes the L2 Namespace from a document.
This method should be overridden by all extensions that want to serialize
to an L2 annotation.
=item RenderExtension::addL2Namespaces
adds all L2 Extension namespaces to the namespace list.
This method should be overridden by all extensions that want to serialize
to an L2 annotation.
=item RenderExtension::enableL2NamespaceForDocument
Adds the L2 Namespace to the document and enables the extension.
If the extension supports serialization to SBML L2 Annotations, this
method should be overrridden, so it will be activated.
=item RenderExtension::isInUse
Determines whether this extension is being used by the given SBMLDocument
The implementation returns true if the list of layouts contains a global render information,
or a layout object contains a local render information object.
@param doc the sbml document to test.
@return a boolean indicating whether the extension is actually being used
byy the document.
=item RenderListOfLayoutsPlugin::RenderListOfLayoutsPlugin
Constructor
=item RenderListOfLayoutsPlugin::RenderListOfLayoutsPlugin
Copy constructor. Creates a copy of this SBase object.
=item RenderListOfLayoutsPlugin::clone
Creates and returns a deep copy of this RenderListOfLayoutsPlugin object.
@return a (deep) copy of this RenderListOfLayoutsPlugin object
=item RenderListOfLayoutsPlugin::hasRequiredElements
@internal
Checks if this plugin object has all the required elements.
Subclasses should override this function if they have their specific
elements.
@return true if this pugin object has all the required elements,
otherwise false will be returned.
=item RenderListOfLayoutsPlugin::appendFrom
@internal
=item RenderListOfLayoutsPlugin::getListOfGlobalRenderInformation
Returns a pointer to the list object that contains local render information.
=item RenderListOfLayoutsPlugin::getListOfGlobalRenderInformation
Returns a const pointer to the list object that contains local render information.
=item RenderListOfLayoutsPlugin::getNumGlobalRenderInformationObjects
Returns the number of local render information objects.
=item RenderListOfLayoutsPlugin::getRenderInformation
Returns a pointer to the local render information object with the given
index.
If the index is invalid, C<NULL> is returned.
=item RenderListOfLayoutsPlugin::getRenderInformation
Returns a const pointer to the local render information object with the given
index.
If the index is invalid, C<NULL> is returned.
=item RenderListOfLayoutsPlugin::getRenderInformation
Returns a pointer to the local render information object with the given
id.
If no object with the given C<id> exists, C<NULL> is returned.
=item RenderListOfLayoutsPlugin::getRenderInformation
Returns a const pointer to the local render information object with the given
id.
If no object with the given C<id> exists, C<NULL> is returned.
=item RenderListOfLayoutsPlugin::addGlobalRenderInformation
Adds a copy of the given local render information object to the list of
local render information objects.
If an object with the same id exists, it is replaced.
=item RenderListOfLayoutsPlugin::createGlobalRenderInformation
Creates a new local render information object and adds it to the list.
The created object does not have a id and it is the responsibility of
the calling code to ensure that it gets one.
For constraints on the id, please consult the render information document.
=item RenderListOfLayoutsPlugin::removeGlobalRenderInformation
Removed the render information with the given index from the list.
The removed object is returned. It is the responsibility of the calling
code to delete the object.
If the index is not valid, C<NULL> is returned.
=item RenderListOfLayoutsPlugin::removeGlobalRenderInformation
Removed the render information with the given C<id> from the list.
The removed object is returned. It is the responsibility of the calling
code to delete the object.
If an object with the given C<id> does not exist, C<NULL> is returned.
=item RenderListOfLayoutsPlugin::getAllElements
Returns a List of all child SBase objects, including those nested to an
arbitrary depth
@return a List of pointers to all children objects.
=item RenderListOfLayoutsPlugin::setSBMLDocument
@internal
Sets the parent SBMLDocument of this plugin object.
Subclasses which contain one or more SBase derived elements must
override this function.
@param d the SBMLDocument object to use
@see connectToParent
@see enablePackageInternal
=item RenderListOfLayoutsPlugin::connectToParent
@internal
Sets the parent SBML object of this plugin object to
this object and child elements (if any).
(Creates a child-parent relationship by this plugin object)
This function is called when this object is created by
the parent element.
Subclasses must override this this function if they have one
or more child elements.Also, SBasePlugin::connectToParent()
must be called in the overridden function.
@param sbase the SBase object to use
@see setSBMLDocument
@see enablePackageInternal
=item RenderListOfLayoutsPlugin::enablePackageInternal
@internal
Enables/Disables the given package with child elements in this plugin
object (if any).
(This is an internal implementation invoked from
SBase::enablePakcageInternal() function)
@note Subclasses in which one or more SBase derived elements are
defined must override this function.
@see setSBMLDocument
@see connectToParent
=item RenderListOfLayoutsPlugin::parseAnnotation
=item RenderListOfLayoutsPlugin::syncAnnotation
@internal
Synchronizes the annotation of this SBML object.
Annotation element (XMLNode mAnnotation) is synchronized with the
current CVTerm objects (List mCVTerm), ModelHistory object
(ModelHistory mHistory) and ListOfLayouts object (ListOfLayouts mLayouts).
Currently, this method is called in getAnnotation, isSetAnnotation,
and writeElements methods.
=item RenderListOfLayoutsPlugin::parseAnnotation
@internal
Parse L2 annotation if supported
=item RenderListOfLayoutsPlugin::readOtherXML
@internal
Subclasses should override this method to read (and store) XHTML,
MathML, etc. directly from the XMLInputStream.
@return true if the subclass read from the stream, false otherwise.
=item RenderListOfLayoutsPlugin::createObject
@internal
Subclasses must override this method to create, store, and then
return an SBML object corresponding to the next XMLToken in the
XMLInputStream if they have their specific elements.
@return the SBML object corresponding to next XMLToken in the
XMLInputStream or NULL if the token was not recognized.
=item RenderListOfLayoutsPlugin::writeElements
@internal
Subclasses must override this method to write out their contained
SBML objects as XML elements if they have their specific elements.
=item RenderListOfLayoutsPlugin::writeAttributes
@internal
Serialize the render information as L2 annotation
=item RenderLayoutPlugin::RenderLayoutPlugin
Constructor
=item RenderLayoutPlugin::RenderLayoutPlugin
Copy constructor. Creates a copy of this SBase object.
=item RenderLayoutPlugin::clone
Creates and returns a deep copy of this RenderLayoutPlugin object.
@return a (deep) copy of this RenderLayoutPlugin object
=item RenderLayoutPlugin::getListOfLocalRenderInformation
Returns a pointer to the list object that contains local render information.
=item RenderLayoutPlugin::getListOfLocalRenderInformation
Returns a const pointer to the list object that contains local render information.
=item RenderLayoutPlugin::getNumLocalRenderInformationObjects
Returns the number of local render information objects.
=item RenderLayoutPlugin::getRenderInformation
Returns a pointer to the local render information object with the given
index.
If the index is invalid, C<NULL> is returned.
=item RenderLayoutPlugin::getRenderInformation
Returns a const pointer to the local render information object with the given
index.
If the index is invalid, C<NULL> is returned.
=item RenderLayoutPlugin::getRenderInformation
Returns a pointer to the local render information object with the given
id.
If no object with the given C<id> exists, C<NULL> is returned.
=item RenderLayoutPlugin::getRenderInformation
Returns a const pointer to the local render information object with the given
id.
If no object with the given C<id> exists, C<NULL> is returned.
=item RenderLayoutPlugin::addLocalRenderInformation
Adds a copy of the given local render information object to the list of
local render information objects.
If an object with the same id exists, it is replaced.
=item RenderLayoutPlugin::createLocalRenderInformation
Creates a new local render information object and adds it to the list.
The created object does not have a id and it is the responsibility of
the calling code to ensure that it gets one.
For constraints on the id, please consult the render information document.
=item RenderLayoutPlugin::removeLocalRenderInformation
Removed the render information with the given index from the list.
The removed object is returned. It is the responsibility of the calling
code to delete the object.
If the index is not valid, C<NULL> is returned.
=item RenderLayoutPlugin::removeLocalRenderInformation
Removed the render information with the given C<id> from the list.
The removed object is returned. It is the responsibility of the calling
code to delete the object.
If an object with the given C<id> does not exist, C<NULL> is returned.
=item RenderLayoutPlugin::getAllElements
Returns a List of all child SBase objects, including those nested to an
arbitrary depth
@return a List of pointers to all children objects.
=item RenderLayoutPlugin::createObject
@internal
Subclasses must override this method to create, store, and then
return an SBML object corresponding to the next XMLToken in the
XMLInputStream if they have their specific elements.
@return the SBML object corresponding to next XMLToken in the
XMLInputStream or NULL if the token was not recognized.
=item RenderLayoutPlugin::writeElements
@internal
Subclasses must override this method to write out their contained
SBML objects as XML elements if they have their specific elements.
=item RenderLayoutPlugin::writeAttributes
@internal
Serialize the render information as L2 annotation
=item RenderLayoutPlugin::hasRequiredElements
@internal
Checks if this plugin object has all the required elements.
Subclasses should override this function if they have their specific
elements.
@return true if this pugin object has all the required elements,
otherwise false will be returned.
=item RenderLayoutPlugin::setSBMLDocument
@internal
Sets the parent SBMLDocument of this plugin object.
Subclasses which contain one or more SBase derived elements must
override this function.
@param d the SBMLDocument object to use
@see connectToParent
@see enablePackageInternal
=item RenderLayoutPlugin::connectToParent
@internal
Sets the parent SBML object of this plugin object to
this object and child elements (if any).
(Creates a child-parent relationship by this plugin object)
This function is called when this object is created by
the parent element.
Subclasses must override this this function if they have one
or more child elements.Also, SBasePlugin::connectToParent()
must be called in the overridden function.
@param sbase the SBase object to use
@see setSBMLDocument
@see enablePackageInternal
=item RenderLayoutPlugin::enablePackageInternal
@internal
Enables/Disables the given package with child elements in this plugin
object (if any).
(This is an internal implementation invoked from
SBase::enablePakcageInternal() function)
@note Subclasses in which one or more SBase derived elements are
defined must override this function.
@see setSBMLDocument
@see connectToParent
=item RenderLayoutPlugin::syncAnnotation
@internal
Synchronizes the annotation of this SBML object.
Annotation element (XMLNode mAnnotation) is synchronized with the
current CVTerm objects (List mCVTerm), ModelHistory object
(ModelHistory mHistory) and ListOfLayouts object (ListOfLayouts mLayouts).
Currently, this method is called in getAnnotation, isSetAnnotation,
and writeElements methods.
=item RenderLayoutPlugin::parseAnnotation
@internal
Parse L2 annotation if supported
=item RenderLayoutPlugin::readOtherXML
@internal
Subclasses should override this method to read (and store) XHTML,
MathML, etc. directly from the XMLInputStream.
@return true if the subclass read from the stream, false otherwise.
=item RenderGraphicalObjectPlugin::RenderGraphicalObjectPlugin
Constructor
=item RenderGraphicalObjectPlugin::RenderGraphicalObjectPlugin
Copy constructor. Creates a copy of this SBase object.
=item RenderGraphicalObjectPlugin::clone
Creates and returns a deep copy of this RenderGraphicalObjectPlugin object.
@return a (deep) copy of this RenderGraphicalObjectPlugin object
=item RenderGraphicalObjectPlugin::addExpectedAttributes
@internal
Subclasses should override this method to get the list of
expected attributes.
This function is invoked from corresponding readAttributes()
function.
=item RenderGraphicalObjectPlugin::readAttributes
@internal
Reads the attributes of corresponding package in SBMLDocument element.
=item RenderGraphicalObjectPlugin::writeAttributes
@internal
Writes the attributes of corresponding package in SBMLDocument element.
=item RenderGraphicalObjectPlugin::getObjectRole
Returns the object role string for the object.
=item RenderGraphicalObjectPlugin::setObjectRole
Sets the object role string for the object.
=item RenderGraphicalObjectPlugin::isSetObjectRole
Returns whether the object role has been set or not.
=back
=head2 Transformation
implementation of a 3D transformation matrix.
The Transformation class represents a 3D transformation which normally is a 4x4 matrix.
Since the last row is always 0 0 0 1 for affine transformations, we leave out those values
and store the matrix as an array of 4x3 columns
=over
=item Transformation::Transformation
Creates a new Transformation object from the given XMLNode object.
The XMLNode object has to contain a valid XML representation of a
Transformation object as defined in the render extension specification.
This method is normally called when render information is read from a file and
should normally not have to be called explicitely.
@param node the XMLNode object reference that describes the Transformation
object to be instantiated.
=item Transformation::getIdentityMatrix
Returns a 3D identity matrix.
The matrix contains 12 double values.
=item Transformation::Transformation
Creates a new Transformation object with the given SBML level
and SBML version.
@param level SBML level of the new object
@param level SBML version of the new object
=item Transformation::Transformation
Creates a new Transformation object with the given SBMLNamespaces.
@param sbmlns The SBML namespace for the object.
=item Transformation::Transformation
Copy constructor.
=item Transformation::setMatrix
Sets the matrix to the values given in the array.
@param m array with new values to be set for this Transformation object.
=item Transformation::getMatrix
Returns the matrix which is an array of double values of length 12.
@return a pointer to the array of numbers for the transformation.
=item Transformation::isSetMatrix
Returns true if the matrix has been set or false otherwise.
The matrix is considered as set if none of the values in the matrix is NaN.
@return true or false depending on whether a NaN was found.
=back
=head2 Transformation2D
implementation of a 2D transformation matrix.
The Transformation2D class represents a 2D transformation. it is derived from Transformation
and inherits all the attributes of a 3D transformation. In addition is provides new methods to
explicitly get and set 2D transformation properties.
A 2D transformation normally consists of a 3x3 matrix, but since the last row is always 0 0 1,
this is reduced to a 6 value array.
Using one of the new 2D specific functions to set the matrix always updates the 3D matrix
automatically and vice versa, so the 2D data and the 3D data inherited from Transformation should
always be consistent.
=over
=item Transformation2D::Contributor
=item Transformation2D::getIdentityMatrix2D
Returns a 2D identity matrix.
The matrix contains 6 double values.
=item Transformation2D::Transformation2D
Creates a new Transformation2D object with the given SBML level
and SBML version.
@param level SBML level of the new object
@param level SBML version of the new object
=item Transformation2D::Transformation2D
Creates a new Transformation2D object with the given SBMLNamespaces.
@param sbmlns The SBML namespace for the object.
=item Transformation2D::Transformation2D
Copy constructor.
=item Transformation2D::Transformation2D
Creates a new Transformation2D object from the given XMLNode object.
The XMLNode object has to contain a valid XML representation of a
Transformation2D object as defined in the render extension specification.
This method is normally called when render information is read from a file and
should normally not have to be called explicitely.
@param node the XMLNode object reference that describes the Transformation2D
object to be instantiated.
=item Transformation2D::Transformation2D
Instantiates a Transformation with all numerical values set to
the values in the given array.
This constructor is deprecated. The new libsbml API only has
constructors which take the SBML level and version or one that takes
an SBMLNamespaces object.
=item Transformation2D::setMatrix2D
Sets the 2D matrix to the values given in the array.
The 3D matrix is updated accordingly.
@param m array with new values to be set for this Transformation object.
=item Transformation2D::setMatrix
Sets the 2D matrix to the values given in the array.
The 2D matrix is updated accordingly.
@param m array with new values to be set for this Transformation object.
=item Transformation2D::getMatrix2D
Returns the 2D matrix which is an array of double values of length 6.
@return a pointer to the array of numbers for the 2D transformation.
=item Transformation2D::toXML
Creates an XMLNode object from this Transformation2D object.
@return the XMLNode with the XML representation for the
Transformation2D object.
This method is purely virtual and has to be overwritten by derived classes.
=item Transformation2D::readAttributes
@internal
Subclasses should override this method to read values from the given
XMLAttributes set into their specific fields. Be sure to call your
parents implementation of this method as well.
=item Transformation2D::addExpectedAttributes
@internal
Subclasses should override this method to get the list of
expected attributes.
This function is invoked from corresponding readAttributes()
function.
=item Transformation2D::parseTransformation
@internal
Tries to parse the numerical values from the given string
and fill the matrix with them. The method will accept strings
representing 6 or 12 numerical values and fill the 2D or 3D matrix
accordingly.
The other matrix is updated automatically.
@param transformationString string representing 6 or 12 numerical values.
=item Transformation2D::addTransformation2DAttributes
@internal
Adds the transformation attribute to the given XMLAttributes object.
@param transformation the transformation to add as attribute.
@param att XMLAttributes where the attribute needs to be added to
=item Transformation2D::getElementName
Returns the XML element name of this object.
This is overridden by subclasses to return a string appropriate to the
SBML component. For example, Model defines it as returning "model",
CompartmentType defines it as returning "compartmentType", etc.
NOTE: this function is only ever going to be called from the constructor
=item Transformation2D::get2DTransformationString
@internal
Returns the transformation array as a string for storage in an XML
attribute.
=item Transformation2D::updateMatrix3D
@internal
Sets the 3D matrix from the 2D matrix.
=item Transformation2D::updateMatrix2D
@internal
Fills the 2D matrix with data from the 3D matrix.
=item Transformation2D::writeAttributes
@internal
Subclasses should override this method to write their XML attributes
to the XMLOutputStream. Be sure to call your parents implementation
of this method as well. For example:
SBase::writeAttributes(stream);
stream.writeAttribute( "id" , mId );
stream.writeAttribute( "name", mName );
...
=back
=head2 GraphicalPrimitive1D
base class for all graphical primitives which implements all 1D attributes
The GraphicalPrimitive1D class implements attributes and methods necessary for 1D objects
like lines. The attributes that are implemented are a stroke color, a stroke width and
a stroke dasharray for dashed line drawing.
Additionally this class adds an id attribute with which all graphical primitives can be
referenced.
The GraphicalPrimitive1D class is derived from Transformation2D and inherits all its methods
and attributes.
=over
=item GraphicalPrimitive1D::GraphicalPrimitive1D
Creates a new GraphicalPrimitive1D object with the given SBML level
and SBML version.
@param level SBML level of the new object
@param level SBML version of the new object
=item GraphicalPrimitive1D::GraphicalPrimitive1D
Creates a new GraphicalPrimitive1D object with the given SBMLNamespaces.
@param sbmlns The SBML namespace for the object.
=item GraphicalPrimitive1D::GraphicalPrimitive1D
Copy constructor.
=item GraphicalPrimitive1D::GraphicalPrimitive1D
Creates a new GraphicalPrimitive1D object from the given XMLNode object.
The XMLNode object has to contain a valid XML representation of a
GraphicalPrimitive1D object as defined in the render extension specification.
This method is normally called when render information is read from a file and
should normally not have to be called explicitely.
@param node the XMLNode object reference that describes the GraphicalPrimitive1D
object to be instantiated.
=item GraphicalPrimitive1D::GraphicalPrimitive1D
Constructor which creates a GraphicalPrimitive1D.
The transformation properties are not set, neither is the stroke or the stroke width.
The id is set to the given string.
@param id The id for the GraphicalPrimitive1D object
This constructor is deprecated. The new libsbml API only has
constructors which take the SBML level and version or one that takes
an SBMLNamespaces object.
=item GraphicalPrimitive1D::setStroke
Sets the stroke color to the given color definition id or color value string.
(@see ColorDefinition)
@param stroke id of a ColorDefinition object or a valid color value string.
=item GraphicalPrimitive1D::setStrokeWidth
Sets the stroke width.
@param width New width for strokes. Should be a positive value.
=item GraphicalPrimitive1D::setDashArray
Sets the dasharray to the values in the given array.
@param array Array of alternating stroke and gap length values.
=item GraphicalPrimitive1D::setDashArray
Sets the dasharray from the given string.
If the string is not a valid dasharray string, false
is returned and the dasharray remains in the state is was
before the call.
The individual numerical values in the string have to be separated by kommas.
@param arrayString a string with number representing a dash array.
@return true is setting the dasharray from the string succeed or false otherwise.
=item GraphicalPrimitive1D::getStroke
Returns the stroke color.
@return the id of the color definition or a color value string.
=item GraphicalPrimitive1D::getStrokeWidth
Returns the stroke width.
@return the stroke width
=item GraphicalPrimitive1D::getDashArray
Returns a const reference to the stroke dasharray.
@return const reference to stroke dash array
=item GraphicalPrimitive1D::getDashArray
Returns a reference to the stroke dasharray.
@return reference to stroke dash array
=item GraphicalPrimitive1D::isSetStrokeWidth
Returns true is the stroke width has been set or false otherwise.
The stroke width is considered set if it is not NaN.
@return true is the stroke width is set.
=item GraphicalPrimitive1D::isSetStroke
Returns true is the stroke has been set or false otherwise.
The stroke color is considered set if the string is not empty.
@return true if the stroke color is set.
=item GraphicalPrimitive1D::isSetDashArray
Returns true is the dash array has been set or false otherwise.
The array is considered set if it is not empty and if the first entry is
not NaN.
@true if the dasharray is set.
=item GraphicalPrimitive1D::getNumDashes
Returns the number of defined dashes.
=item GraphicalPrimitive1D::getDashByIndex
Returns the dash at the given index.
=item GraphicalPrimitive1D::addDash
Adds a dash at the end of the current list
=item GraphicalPrimitive1D::clearDashes
Clears all defined dashes.
=item GraphicalPrimitive1D::setDashByIndex
Sets the dash at the given position.
=item GraphicalPrimitive1D::insertDash
Inserts the dash at the given position.
=item GraphicalPrimitive1D::removeDash
Removes the dash at the given index
=item GraphicalPrimitive1D::toXML
Creates an XMLNode object from this GraphicalPrimitive1D object.
@return the XMLNode with the XML representation for the
GraphicalPrimitive1D object.
This method is purely virtual and has to be implemented by subclasses.
=item GraphicalPrimitive1D::getId
Returns the value of the "id" attribute of this GraphicalPrimitive.
@return the id of the GraphicalPrimitive
=item GraphicalPrimitive1D::isSetId
Predicate returning C<true> or C<false> depending on whether this
GraphicalPrimitive's "id" attribute has been set.
@return returns true or false depending on whether the id on the
GraphicalPrimitive has been set.
=item GraphicalPrimitive1D::setId
Sets the value of the "id" attribute of this GraphicalPrimitive.
@param id the new id for the GraphicalPrimitive
@return status if the operation succeeded
=item GraphicalPrimitive1D::unsetId
Unsets the value of the "id" attribute of this GraphicalPrimitive.
=item GraphicalPrimitive1D::readAttributes
@internal
Subclasses should override this method to read values from the given
XMLAttributes set into their specific fields. Be sure to call your
parents implementation of this method as well.
=item GraphicalPrimitive1D::addExpectedAttributes
@internal
Subclasses should override this method to get the list of
expected attributes.
This function is invoked from corresponding readAttributes()
function.
=item GraphicalPrimitive1D::addGraphicalPrimitive1DAttributes
@internal
Adds all set attributes specific to the given GraphicalPrimitive1D objects to the given
XMLAttributes object.
=item GraphicalPrimitive1D::parseDashArray
@internal
This method parses a dasharray string into the given vector.
The vector is first cleared.
If the dasharray is invalid, false is returned.
=item GraphicalPrimitive1D::writeAttributes
@internal
Subclasses should override this method to write their XML attributes
to the XMLOutputStream. Be sure to call your parents implementation
of this method as well. For example:
SBase::writeAttributes(stream);
stream.writeAttribute( "id" , mId );
stream.writeAttribute( "name", mName );
...
=back
=head2 GraphicalPrimitive2D
base class for all graphical primitives which implements all 2D attributes
The GraphicalPrimitive2D class implements attributes and methods necessary for 2D objects
like rectangles, polygons or ellipses. The attributes that are implemented are a fill color
and a fill rule that specifies how the fill color is applied.
The GraphicalPrimitive2D class is derived from GraphicalPrimitive1D and inherits all its methods
and attributes.
=over
=item Contributor
=item GraphicalPrimitive2D
Creates a new GraphicalPrimitive2D object with the given SBML level
and SBML version.
@param level SBML level of the new object
@param level SBML version of the new object
=item GraphicalPrimitive2D
Creates a new GraphicalPrimitive2D object with the given SBMLNamespaces.
@param sbmlns The SBML namespace for the object.
=item GraphicalPrimitive2D
Copy constructor.
=item GraphicalPrimitive2D
Creates a new GraphicalPrimitive2D object from the given XMLNode object.
The XMLNode object has to contain a valid XML representation of a
GraphicalPrimitive2D object as defined in the render extension specification.
This method is normally called when render information is read from a file and
should normally not have to be called explicitely.
@param node the XMLNode object reference that describes the GraphicalPrimitive2D
object to be instantiated.
=item ~GraphicalPrimitive2D
Destroy this GraphicalPrimitive2D object.
=item GraphicalPrimitive2D
Constructor which creates a GraphicalPrimitive2D.
The attributes inherited from GraphicalPrimitive1D are set as described
in the corresponding constructor for GraphicalPrimitive1D (@see GraphicalPrimitive1D).
The fill and the fill rule are unset.
This constructor is deprecated. The new libsbml API only has
constructors which take the SBML level and version or one that takes
an SBMLNamespaces object.
=item setFillColor
Set fill color to the id of a color definition, the id of a gradient
definition or a color value string.
@param color the id of a color deifnition or a gradient or a color value string.
=item setFillRule
Sets the fill rule. Possible values are GraphicalPrimitive2D::NONZERO,
GraphicalPrimitive2D::EVENODD, GraphicalPrimitive::INHERIT or
GraphicalPrimitive2D::UNSET.
If the fill rule for an object is unset, it default to INHERIT,
which means that it inherits the attribute from it's parent group.
The topmost group in an object hierarchy has a default value for this
attribute which is GraphicalPrimitive2D::NONZERO.
For more details please consult the render extension specification.
@param rule the fill rule to be set.
=item getFillColor
Returns the fill color.
@return this id of the fill color or the fill gradient or the fill color value string.
=item getFillRule
Returns the fill rule.
@return this fill rule enum
=item isSetFill
Returns true if the fill attribute is set or false otherwise.
The fill attribute is considered set if the string is not empty.
This function is deprecated, please use isSetFillColor instead.
@return true is the fill color is set.
=item isSetFillColor
Returns true if the fill attribute is set or false otherwise.
The fill attribute is considered set if the string is not empty.
@return true is the fill color is set.
=item isSetFillRule
Returns true if the fill rule attribute is set or false otherwise.
The fill rule is considered as set if it is not GraphicalPrimitive2D::UNSET.
@return true is the fill color is set.
=item addGraphicalPrimitive2DAttributes
@internal
Adds all set attributes specific to the given GraphicalPrimitive2D objects to the given
XMLAttributes object.
=item readAttributes
@internal
Subclasses should override this method to read values from the given
XMLAttributes set into their specific fields. Be sure to call your
parents implementation of this method as well.
=item addExpectedAttributes
@internal
Subclasses should override this method to get the list of
expected attributes.
This function is invoked from corresponding readAttributes()
function.
=item writeAttributes
@internal
Subclasses should override this method to write their XML attributes
to the XMLOutputStream. Be sure to call your parents implementation
of this method as well. For example:
SBase::writeAttributes(stream);
stream.writeAttribute( "id" , mId );
stream.writeAttribute( "name", mName );
...
=back
=head2 RenderInformationBase
abstract base class for local and global render information.
In the SBML render extension, local and global render information representations
share many attributes. These are implemented in this abstract base class.
GlobalRenderInformation and LocalRenderInformation are the classes that are derived
from this base class.
All render information objects have the following things in common:
a) a set of color definitions
b) a set of gradient definitions
c) a set of line endings
In addition to those, they share attributes for background color and some meta information
as to which program created the render information etc.
=over
=item RenderInformationBase::RenderInformationBase
Creates a new RenderInformationBase object with the given SBML level
and SBML version.
@param level SBML level of the new object
@param level SBML version of the new object
=item RenderInformationBase::RenderInformationBase
Creates a new RenderInformationBase object with the given SBMLNamespaces.
@param sbmlns The SBML namespace for the object.
=item RenderInformationBase::parseXML
Parses the xml information in the given node and sets the attributes.
This method should never be called by the user. It is only used to read render
information from annotations.
@param node the XMLNode object reference that describes the RenderInfromationBase
object to be instantiated.
=item RenderInformationBase::RenderInformationBase
Constructor which creates a RenderInformationBase object
empty color definition, gradient definition
and line endings set.
For the object to be valid a valid background color value.
This constructor is deprecated. The new libsbml API only has
constructors which take the SBML level and version or one that takes
an SBMLNamespaces object.
=item RenderInformationBase::getProgramName
Returns the program name that created the render information.
@return the name string of the program
=item RenderInformationBase::setProgramName
Sets the name of the program that created the render information.
@param name the name of the programm
=item RenderInformationBase::getProgramVersion
Returns the version of the program that created the render information.
@return the version of the program as a string.
=item RenderInformationBase::setProgramVersion
Sets the version string of the program that created the render information.
@param version version string of the program
=item RenderInformationBase::getReferenceRenderInformationId
Returns the id of the referenced render information object.
RenderInfromation objects can reference other render information objects
and information that is not found in the current render information is then
expected to be in the referenced render information object.
Global render information objects can only reference other global
render information objects, local render information objects can reference other local
render information objects from the same list of local render information or other
global render infromation.
@return the id of the referenced render infromation object.
=item RenderInformationBase::setReferenceRenderInformationId
Sets the id of the referenced render information object.
The user has to make sure that render infromation referencing
does not create loops.
@param id the id of the referenced render infromation
=item RenderInformationBase::getNumColorDefinitions
Returns the number of color definitions.
@return the number of color definitions in the render information.
=item RenderInformationBase::getListOfColorDefinitions
Returns a pointer to the list of color definitions.
@return pointer to the list of color definitions.
=item RenderInformationBase::getListOfColorDefinitions
Returns a const pointer to the list of color definitions.
@return const pointer to the list of color definitions.
=item RenderInformationBase::getColorDefinition
Returns a pointer to the color definition with the given index, or C<NULL
>
if the index is invalid.
@param index of the ColorDefinition object to be returned
@return pointer to the ColorDefinition object at the given index or NULL
=item RenderInformationBase::getColorDefinition
Returns a const pointer to the color definition with the given index, or C<NULL
>
if the index is invalid.
@param index of the ColorDefinition object to be returned
@return const pointer to the ColorDefinition object at the given index or NULL
=item RenderInformationBase::getColorDefinition
Returns a pointer to the color definition with the given C<id>, or C<NULL
>
if there is no color definition with that id.
@param id of the color definition object to be returned.
@return a pointer to the color definition object with the given C<id>
or NULL if there is no color definition with given C<id
>
=item RenderInformationBase::getColorDefinition
Returns a const pointer to the color definition with the given C<id>, or C<NULL
>
if there is no color definition with that id.
@param id of the color definition object to be returned.
@return a const pointer to the color definition object with the given C<id>
or NULL if there is no color definition with given C<id
>
=item RenderInformationBase::createColorDefinition
Creates a new color definition object without an id.
For the object to be valid an id has to be set that is unique
within the list of color definitions and the list of gradients within
the render information.
The created ColorDefinition object is added to and owned by the render information.
@return pointer to new ColorDefinition object
=item RenderInformationBase::removeColorDefinition
Removes the color definition with the given index from the list of color definitions.
If the index is valid, the object is removed and a pointer to the removed object
is returned.
The caller is responsible for deleting thew object.
If the index is invalid, C<NULL> is returned.
@param index index of the color definition to be removed.
@ return pointer to the removed object
=item RenderInformationBase::addColorDefinition
Adds a copy of the given color definition to the end of the list of
color definitions.
The color definition has to be valid, i.e. have a unique id and a valid color value.
Otherwise it is not added.
@param cd const pointer to ColorDefinition object to be added
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif The possible values
returned by this function are:
@li LIBSBML_OPERATION_SUCCESS
@li LIBSBML_LEVEL_MISMATCH
@li LIBSBML_VERSION_MISMATCH
@li LIBSBML_OPERATION_FAILED
@note This method should be used with some caution. The fact that
this method I<copies> the object passed to it means that the caller
will be left holding a physically different object instance than the
one contained in this Reaction. Changes made to the original object
instance (such as resetting attribute values) will <em>not affect the
instance in the Reaction</em>. In addition, the caller should make
sure to free the original object if it is no longer being used, or
else a memory leak will result. Please see RenderInformationBase::createColorDefinition()
for a method that does not lead to these issues.
@see createColorDefinition()
=item RenderInformationBase::getNumGradientDefinitions
Returns the number of gradient definitions in the render information.
@return number of gradient definitions
=item RenderInformationBase::getListOfGradientDefinitions
Returns a pointer to the list of gradient definitions.
@return pointer to ListOfGradientDefinitions
=item RenderInformationBase::getListOfGradientDefinitions
Returns a const pointer to the list of gradient definitions.
@return const pointer to ListOfGradientDefinitions
=item RenderInformationBase::getGradientDefinition
Returns a pointer to the gradient definition with the given index, or C<NULL
>
if the index is invalid.
@param index index of the GradientDefinition object to be returned
@return pointer to the GradientDefinition object with the given index or NULL
if the index was invalid.
=item RenderInformationBase::getGradientDefinition
Returns a const pointer to the gradient definition with the given index, or C<NULL
>
if the index is invalid.
@param index index of the GradientDefinition object to be returned
@return const pointer to the GradientDefinition object with the given index or NULL
if the index was invalid.
=item RenderInformationBase::getGradientDefinition
Returns a pointer to the gradient definition with the given C<id>, or C<NULL
>
if there is no gradient definition with that id.
@param id of the gradient definition object to be returned.
@return a pointer to the gradient definition object with the given C<id>
or NULL if there is no gradient definition with given C<id
>
=item RenderInformationBase::getGradientDefinition
Returns a const pointer to the gradient definition with the given C<id>, or C<NULL
>
if there is no gradient definition with that id.
@param id of the gradient definition object to be returned.
@return a const pointer to the gradient definition object with the given C<id>
or NULL if there is no gradient definition with given C<id
>
=item RenderInformationBase::createLinearGradientDefinition
Creates a new linear gradient definition.
The newly created object is added to the render
information and also owned by it.
Since the newly created object has no id and no gradient stops,
it is invalid until those things have been added.
@return pointer to newly created LinearGradient object.
=item RenderInformationBase::createRadialGradientDefinition
Creates a new radial gradient definition.
The newly created object is added to the render
information and also owned by it.
Since the newly created object has no id and no gradient stops,
it is invalid until those things have been added.
@return pointer to newly created RadialGradient object.
=item RenderInformationBase::removeGradientDefinition
Removes the gradient definition with the given index.
If the index is valid, the object is removed and a pointer to the removed object
is returned.
The caller is responsible for deleting thew object.
If the index is invalid, C<NULL> is returned.
@param index index of the gradient definition object to be removed.
@ return pointer to the removed object
=item RenderInformationBase::addGradientDefinition
Adds a copy of the given gradient definition to the end of the list of
gradient definitions.
The Gradient definition has to be valid, so is has to have at least two
gradient stops and an id.
@param gradient GradientDefinition object to be added
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif The possible values
returned by this function are:
@li LIBSBML_OPERATION_SUCCESS
@li LIBSBML_LEVEL_MISMATCH
@li LIBSBML_VERSION_MISMATCH
@li LIBSBML_OPERATION_FAILED
@note This method should be used with some caution. The fact that
this method I<copies> the object passed to it means that the caller
will be left holding a physically different object instance than the
one contained in this RenderInformationBase. Changes made to the original object
instance (such as resetting attribute values) will <em>not affect the
instance in the RenderInformationBase</em>. In addition, the caller should make
sure to free the original object if it is no longer being used, or
else a memory leak will result. Please see
RenderInformationBase::createLinearGradientDefinition() or
RenderInformationBase::createRadialGradientDefinition()
for methods that does not lead to these issues.
@see createRadialGradientDefinition()
@see createLinearGradientDefinition()
=item RenderInformationBase::getNumLineEndings
Returns the number of line endings for the render information.
@return number of line endings in the render information.
=item RenderInformationBase::getListOfLineEndings
Returns a pointer to the list of line endings.
@return pointer to the list of line endings.
=item RenderInformationBase::getListOfLineEndings
Returns a const pointer to the list of line endings.
@return const pointer to the list of line endings.
=item RenderInformationBase::getLineEnding
Returns a pointer to the line ending with the given index, or C<NULL
>
if the index is invalid.
@param index of the line ending object to be returned.
@return a pointer to the line ending object with the given index
or NULL if the index was out of bounds.
=item RenderInformationBase::getLineEnding
Returns a const pointer to the line ending with the given index, or C<NULL
>
if the index is invalid.
@param index of the line ending object to be returned.
@return a const pointer to the line ending object with the given index
or NULL if the index was out of bounds.
=item RenderInformationBase::getLineEnding
Returns a pointer to the line ending with the given C<id>, or C<NULL
>
if there is no line ending with that id.
@param id of the line ending object to be returned.
@return a pointer to the line ending object with the given C<id>
or NULL if there is no line ending with given C<id
>
=item RenderInformationBase::getLineEnding
Returns a const pointer to the line ending with the given C<id>, or C<NULL
>
if there is no line ending with that id.
@param id of the line ending object to be returned.
@return a const pointer to the line ending object with the given C<id>
or NULL if there is no line ending with given C<id
>
=item RenderInformationBase::createLineEnding
Creates a new line ending.
The new line ending object is added to and owned by the
render information. Since it does not have an id or a valid group
or a valid viewport, it should be considered invalid until those
things have been set.
@return pointer to the newlyy created LineEnding object
=item RenderInformationBase::removeLineEnding
Removes the line ending with the given index.
If the index is valid, the object is removed and a pointer to the removed object
is returned.
The caller is responsible for deleting thew object.
If the index is invalid, C<NULL> is returned.
@param index index of the object to be removed.
@ return pointer to the removed object
=item RenderInformationBase::addLineEnding
Adds a copy of the given line ending to the end of the list of line
endings.
The new LineEnding is only added if it is valid.
@param le const pointer to LineEnding to be added
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif The possible values
returned by this function are:
@li LIBSBML_OPERATION_SUCCESS
@li LIBSBML_LEVEL_MISMATCH
@li LIBSBML_VERSION_MISMATCH
@li LIBSBML_OPERATION_FAILED
@note This method should be used with some caution. The fact that
this method I<copies> the object passed to it means that the caller
will be left holding a physically different object instance than the
one contained in this RenderInformationBase. Changes made to the original object
instance (such as resetting attribute values) will <em>not affect the
instance in the RenderInformationBase</em>. In addition, the caller should make
sure to free the original object if it is no longer being used, or
else a memory leak will result. Please see RenderInformationBase::createLineEnding()
for a method that does not lead to these issues.
@see createLineEnding()
=item RenderInformationBase::getBackgroundColor
Returns the background color which is either the id of a color in the
list of color definitions, or a color value.
@return background color id or value string
=item RenderInformationBase::setBackgroundColor
Sets the background color to either the id of a color in the list of
color definitions, or a color value.
@param bg id of a color definition or a valid color value to be used as background color.
=item RenderInformationBase::getId
Returns the value of the "id" attribute of this RenderInformationBase.
@return the id of the RenderInformationBase
=item RenderInformationBase::isSetId
Predicate returning C<true> or C<false> depending on whether this
RenderInformationBase's "id" attribute has been set.
@return returns true or false depending on whether the id on the
RenderInformationBase has been set.
=item RenderInformationBase::setId
Sets the value of the "id" attribute of this RenderInformationBase.
@param id the new id for the RenderInformationBase
@return status if the operation succeeded
=item RenderInformationBase::unsetId
Unsets the value of the "id" attribute of this RenderInformationBase.
=item RenderInformationBase::getName
Returns the value of the "name" attribute of this RenderInformationBase.
@return the name of the RenderInformationBase
=item RenderInformationBase::isSetName
Predicate returning C<true> or C<false> depending on whether this
RenderInformationBase's "name" attribute has been set.
@return returns true or false depending on whether the name on the
RenderInformationBase has been set.
=item RenderInformationBase::setName
Sets the value of the "name" attribute of this RenderInformationBase.
@param name the new name for the RenderInformationBase
@return status if the operation succeeded
=item RenderInformationBase::unsetName
Unsets the value of the "name" attribute of this RenderInformationBase.
=item RenderInformationBase::getAllElements
Returns a List of all child SBase objects, including those nested to an
arbitrary depth
@return a List of pointers to all children objects.
=item RenderInformationBase::setSBMLDocument
@internal
Sets the parent SBMLDocument of this SBML object.
@param d the SBMLDocument object to use
=item RenderInformationBase::connectToChild
@internal
Sets this SBML object to child SBML objects (if any).
(Creates a child-parent relationship by the parent)
Subclasses must override this function if they define
one ore more child elements.
Basically, this function needs to be called in
constructor, copy constructor, assignment operator.
@see setSBMLDocument
@see enablePackageInternal
=item RenderInformationBase::enablePackageInternal
@internal
Enables/Disables the given package with this element and child
elements (if any).
(This is an internal implementation for enablePakcage function)
@note Subclasses in which one or more child elements are defined
must override this function.
=item RenderInformationBase::setParentSBMLObject
Sets the parent SBML object of this SBML object.
@param sb the SBML object to use
=item RenderInformationBase::addRenderInformationBaseAttributes
@internal
Adds the RenderInformationBase specific attributes to the given XMLAttributes object.
=item RenderInformationBase::readAttributes
@internal
Reads in RenderInfromationBase specific attributes from the given XMLAttributes object.
=item RenderInformationBase::addExpectedAttributes
@internal
Subclasses should override this method to get the list of
expected attributes.
This function is invoked from corresponding readAttributes()
function.
=item RenderInformationBase::createObject
@internal
@return the SBML object corresponding to next XMLToken in the
XMLInputStream or NULL if the token was not recognized.
=item RenderInformationBase::writeAttributes
@internal
Subclasses should override this method to write their XML attributes
to the XMLOutputStream. Be sure to call your parents implementation
of this method as well. For example:
SBase::writeAttributes(stream);
stream.writeAttribute( "id" , mId );
stream.writeAttribute( "name", mName );
...
=item RenderInformationBase::writeElements
@internal
Subclasses should override this method to write out their contained
SBML objects as XML elements. Be sure to call your parents
implementation of this method as well. For example:
SBase::writeElements(stream);
mReactants.write(stream);
mProducts.write(stream);
...
=back
=head2 GradientBase
abstract base class for linear and radial gradients
The base class implements common structures to both gradient classes.
Both gradients have an id attribute which is used to reference a gradient
within other render extension constructs. The id of a gradient can be used
to define the fill style of 2D objects like e.g. rectangles.
Further both gradient classes have a ListOfGradientStop objects which holds
the GradientStop objects that define the gradient and bothe classes have an
attribute called spreadMethod which defines how a gradient is applied to an
object.
=over
=back
=head2 ListOfGradientDefinitions
a container class that holds a list of gradient definitions.
There are two types of gradient definitions: LinearGradient and
RadialGradient
Each RenderInformation object can have it's own list of gradient definitions.
=over
=item ListOfGradientDefinitions::ListOfGradientDefinitions
Creates a new ListOfGradientDefinitions object from the given XMLNode object.
The XMLNode object has to contain a valid XML representation of a
ListOfGradientDefinitions object as defined in the render extension specification.
This method is normally called when render information is read from a file and
should normally not have to be called explicitely.
@param node the XMLNode object reference that describes the ListOfGradientDefinitions
object to be instantiated.
=item ListOfGradientDefinitions::clone
Creates and returns a deep copy of the ListOfGradientDefinitions object.
@return a (deep) copy of this ListOfGradientDefinitions
=item ListOfGradientDefinitions::ListOfGradientDefinitions
Constructor which instantiates an empty ListOfGradientDefinitions object.
=item ListOfGradientDefinitions::ListOfGradientDefinitions
Ctor.
=item ListOfGradientDefinitions::ListOfGradientDefinitions
Copy constructor. Creates a copy of this ListOfGradientDefinitions object.
=item ListOfGradientDefinitions::getItemTypeCode
Get the type code of the objects contained in this ListOf.
@if clike LibSBML attaches an identifying code to every kind of SBML
object. These are known as <em>SBML type codes</em>. The set of
possible type codes is defined in the enumeration #SBMLTypeCode_t.
The names of the type codes all begin with the characters C<
>
SBML_. @endif@if java LibSBML attaches an identifying code to every
kind of SBML object. These are known as <em>SBML type codes</em>. In
other languages, the set of type codes is stored in an enumeration; in
the Java language interface for libSBML, the type codes are defined as
static integer constants in the interface class {@link
libsbmlConstants}. The names of the type codes all begin with the
characters C<SBML_>. @endif@if python LibSBML attaches an identifying
code to every kind of SBML object. These are known as <em>SBML type
codes</em>. In the Python language interface for libSBML, the type
codes are defined as static integer constants in the interface class
@link libsbml@endlink. The names of the type codes all begin with the
characters C<SBML_>. @endif@if csharp LibSBML attaches an identifying
code to every kind of SBML object. These are known as <em>SBML type
codes</em>. In the C# language interface for libSBML, the type codes
are defined as static integer constants in the interface class @link
libsbmlcs.libsbml@endlink. The names of the type codes all begin with
the characters C<SBML_>. @endif
@return the SBML type code for the objects contained in this ListOf
instance, or @link SBMLTypeCode_t#SBML_UNKNOWN SBML_UNKNOWN@endlink (default).
=item ListOfGradientDefinitions::isValidTypeForList
=item ListOfGradientDefinitions::toXML
Creates an XMLNode object from this ListOfGradientDefinitions object.
@return the XMLNode with the XML representation for the
ListOfGradientDefinitions object.
=item ListOfGradientDefinitions::getElementName
Returns the XML element name of this object, which for
ListOfGradientDefinitions, is always C<"listOfGradientDefinitions">.
@return the name of this element, i.e., C<"listOfGradientDefinitions">.
=item ListOfGradientDefinitions::get
Returns a pointer to the GradientBase with the given index or NULL if
the index is invalid.
@param i index of the GradientBase object to be returned
@return pointer to the GradientBase at the given index or NULL.
=item ListOfGradientDefinitions::get
Returns a const pointer to the GradientBase with the given index or NULL if
the index is invalid.
@param i index of the GradientBase object to be returned
@return const pointer to the GradientBase at the given index or NULL.
=item ListOfGradientDefinitions::get
Returns a pointer to the GradientBase with the given C<id> or C<NULL> if
the id is invalid.
@param id id of the GradientBase object to be returned
@return pointer to the GradientBase at the given C<id> or C<NULL>.
=item ListOfGradientDefinitions::get
Returns a const pointer to the GradientBase with the given C<id> or C<NULL> if
the id is invalid.
@param id id of the GradientBase object to be returned
@return const pointer to the GradientBase at the given C<id> or C<NULL>.
=item ListOfGradientDefinitions::remove
Removes the nth item from this ListOfGradientDefinitions items and returns a pointer to
it.
The caller owns the returned item and is responsible for deleting it.
@param n the index of the item to remove
@see size()
=item ListOfGradientDefinitions::remove
Removes item in this ListOfGradientDefinitions items with the given identifier.
The caller owns the returned item and is responsible for deleting it.
If none of the items in this list have the identifier C<sid>, then C<
>
NULL is returned.
@param sid the identifier of the item to remove
@return the item removed. As mentioned above, the caller owns the
returned item.
=item ListOfGradientDefinitions::createObject
@internal
@return the SBML object corresponding to next XMLToken in the
XMLInputStream or NULL if the token was not recognized.
=item GradientBase
Creates a new GradientBase object with the given SBML level
and SBML version.
@param level SBML level of the new object
@param level SBML version of the new object
=item GradientBase
Creates a new GradientBase object with the given SBMLNamespaces.
@param sbmlns The SBML namespace for the object.
=item GradientBase
Creates a new GradientBase object from the given XMLNode object.
The XMLNode object has to contain a valid XML representation of a
GradientBase object as defined in the render extension specification.
This method is normally called when render information is read from a file and
should normally not have to be called explicitely.
@param node the XMLNode object reference that describes the GradientBase
object to be instantiated.
=item GradientBase
Constructor which creates a GradientBase with no gradient stops.
The spreadMethod attribute is set to GradientBase::PAD and the id is
set to the given value.
This object is not valid until it gets at least two gradient stops.
@param id The id for the gradient definition object
This constructor is deprecated. The new libsbml API only has
constructors which take the SBML level and version or one that takes
an SBMLNamespaces object.
=item ~GradientBase
Destroy this GradientBase object.
=item getSpreadMethod
Returns the spreadmethod of the gradient.
Valid values are GradientBase::PAD, GradientBase::REFLECT
and GradientBase::REPEAT.
@return the spread method for the gradient object.
=item setSpreadMethod
Sets the spread method.
Valid values are GradientBase::PAD, GradientBase::REFLECT
and GradientBase::REPEAT.
@param method The new spread method for the gradient.
=item getNumGradientStops
Returns the number of gradient stops.
A valid gradient needs at least two gradient stops
@return the number of gradient stops in the gradient.
=item getListOfGradientStops
Returns a pointer to the gradient stop vector.
@return a pointer to the ListOfGradientStops object
for the gradient.
=item getListOfGradientStops
Returns a const pointer to the gradient stop vector.
@return a const pointer to the ListOfGradientStops object
for the gradient.
=item getGradientStop
Returns a pointer to the gradient stop with the given index or NULL
if the index is invalid.
@param i index of the gradient stop to be returned. The index has to be between 0 and
getNumGradientStops() - 1.
@return a pointer to the gradient stop with the given index
or NULL if the index was out of bounds.
=item getGradientStop
Returns a const pointer to the gradient stop with the given index or NULL
if the index is invalid.
@param i index of the gradient stop to be returned. The index has to be between 0 and
getNumGradientStops() - 1.
@return a const pointer to the gradient stop with the given index
or NULL if the index was out of bounds.
=item createGradientStop
Creates a new GradientStop. The new GradientStop object is automatically
added to the gradient and the gradient own the object-
@return a pointer to the newly created GradientStop.
=item addGradientStop
Adds a copy of the given GradientStop object to the end
of the list of gradient stops.
@param pStop a const pointer to the new gradient stop
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif The possible values
returned by this function are:
@li LIBSBML_OPERATION_SUCCESS
@li LIBSBML_LEVEL_MISMATCH
@li LIBSBML_VERSION_MISMATCH
@li LIBSBML_OPERATION_FAILED
@note This method should be used with some caution. The fact that
this method I<copies> the object passed to it means that the caller
will be left holding a physically different object instance than the
one contained in this GradientBase. Changes made to the original object
instance (such as resetting attribute values) will <em>not affect the
instance in the GradientBase</em>. In addition, the caller should make
sure to free the original object if it is no longer being used, or
else a memory leak will result. Please see GradientBase::createGradientStop()
for a method that does not lead to these issues.
@see createGradientStop()
=item getAllElements
Returns a List of all child SBase objects, including those nested to an
arbitrary depth
@return a List of pointers to all children objects.
=item writeElements
@internal
Subclasses should override this method to write out their contained
SBML objects as XML elements. Be sure to call your parents
implementation of this method as well. For example:
SBase::writeElements(stream);
mReactants.write(stream);
mProducts.write(stream);
...
=item clone
Creates and returns a deep copy of this GradientBase object.
This method is purely abstract and has to be implemented by derived
classes.
@return a (deep) copy of this GradientBase.
=item getElementName
Returns the XML element name of this object.
This is overridden by subclasses to return a string appropriate to the
SBML component. For example, Model defines it as returning "model",
CompartmentType defines it as returning "compartmentType", etc.
NOTE: this function is only ever going to be called from the constructor
=item accept
Accepts the given SBMLVisitor.
@return the result of calling C<v.visit()>, which indicates
whether or not the Visitor would like to visit the SBML object's next
sibling object (if available).
=item toXML
Creates an XMLNode object from this GradientBase object.
@return the XMLNode with the XML representation for the
GradientBase object.
This method is purely abstract and needs to be implemented
by derived classes.
=item setSBMLDocument
@internal
Sets the parent SBMLDocument of this SBML object.
@param d the SBMLDocument object to use
=item connectToChild
@internal
Sets this SBML object to child SBML objects (if any).
(Creates a child-parent relationship by the parent)
Subclasses must override this function if they define
one ore more child elements.
Basically, this function needs to be called in
constructor, copy constructor, assignment operator.
@see setSBMLDocument
@see enablePackageInternal
=item enablePackageInternal
@internal
Enables/Disables the given package with this element and child
elements (if any).
(This is an internal implementation for enablePakcage function)
@note Subclasses in which one or more child elements are defined
must override this function.
=item getId
Returns the value of the "id" attribute of this GradientBase object.
@return the id of the gradient
=item isSetId
Predicate returning C<true> or C<false> depending on whether this
GradientBase's "id" attribute has been set.
@return returns true or false depending on whether the id on the
GradientBase has been set.
=item setId
Sets the value of the "id" attribute of this GradientBase.
@param id the new id for the GradientBase
@return status if the operation succeeded
=item unsetId
Unsets the value of the "id" attribute of this GradientBase.
=item setParentSBMLObject
Sets the parent SBML object of this SBML object.
@param sb the SBML object to use
=item hasRequiredAttributes
@internal
=item hasRequiredElements
@internal
=item readAttributes
@internal
Subclasses should override this method to read values from the given
XMLAttributes set into their specific fields. Be sure to call your
parents implementation of this method as well.
=item addExpectedAttributes
@internal
Subclasses should override this method to get the list of
expected attributes.
This function is invoked from corresponding readAttributes()
function.
=item writeAttributes
@internal
Subclasses should override this method to write their XML attributes
to the XMLOutputStream. Be sure to call your parents implementation
of this method as well. For example:
SBase::writeAttributes(stream);
stream.writeAttribute( "id" , mId );
stream.writeAttribute( "name", mName );
...
=item getSpreadMethodString
@internal
Returns the attribute string for the spread method set on the
gradient.
=item getSpreadMethodForString
@internal
Converts the given string into a spread method.
If the string does not represnt a valid spread method, PAD is
returned.
=item addGradientAttributesAndChildren
@internal
This method is used when writing out gradietns to XML.
I writes out the attributes and children that re common to linear and radial gradient.
=item createObject
@internal
@return the SBML object corresponding to next XMLToken in the
XMLInputStream or NULL if the token was not recognized.
=back
=head2 Style
abstract base class for local and global styles
Local and global styles in the SBML render extension have many attributes and methods in common.
These have been implemented in the abstract base class Style.
A style is a graphical representation for certain layout objects. The assignment of styles to
individual layout objects can either be done through layout object ids (local styles only),
layout object types (SPECIES, COMPARTMENT, etc.) or layout object roles.
=over
=item Style::Style
Creates a new Style object with the given SBML level
and SBML version.
@param level SBML level of the new object
@param level SBML version of the new object
=item Style::Style
Creates a new Style object with the given SBMLNamespaces.
@param sbmlns The SBML namespace for the object.
=item Style::Style
Creates a new Style object from the given XMLNode object.
The XMLNode object has to contain a valid XML representation of a
Style object as defined in the render extension specification.
This method is normally called when render information is read from a file and
should normally not have to be called explicitely.
@param node the XMLNode object reference that describes the Style
object to be instantiated.
=item Style::Style
Constructor which creates a Style with an empty group
and empty role and type list.
The group has to be filled before the object is valid.
This constructor is deprecated. The new libsbml API only has
constructors which take the SBML level and version or one that takes
an SBMLNamespaces object.
=item Style::setGroup
Sets the group of the Style.
@param group New group to be set on the style.
The group is copied.
=item Style::getGroup
Returns a const pointer to the group of the Style.
@return const pointer to the group.
=item Style::getGroup
Returns a pointer to the group of the Style.
@return pointer to the group.
=item Style::getNumRoles
Returns the number of ids in the role list.
@return the number of roles in the role list.
=item Style::createRoleString
@return the string of all roles
=item Style::createTypeString
@return the string of all types
=item Style::addRole
Adds an id to the role list.
@param role New role to be added to the role list.
=item Style::isInRoleList
Checks whether a given role is in the role list.
@param role role string to check for in the role list.
=item Style::removeRole
Removes the given role from the role list.
@param role role string to be removed from the role list.
=item Style::setRoleList
Sets the complete role list to a copy of the given list.
@param roleList New list of role strings to be set on the style.
=item Style::getRoleList
Returns a const reference to the role list.
@return reference to the role list.
=item Style::getTypeList
Returns the type list.
@return reference to the type list.
=item Style::getRoleList
Returns a const reference to the role list.
@return const reference to the role list.
=item Style::getTypeList
Returns the type list.
@return const reference to the type list.
=item Style::setTypeList
Sets the complete type list to a copy of the given list.
@param typeList the list of types to be set for the style.
=item Style::getNumTypes
Returns the number of types in the type list.
@return number of types in type list.
=item Style::addType
Adds a type string to the type list.
@param type new type string to be added to the type list
=item Style::isInTypeList
Checks whether a given type string is in the type list.
@param type string to be searched for in the type list
@return true or false depending on whether the given string was
found in the type list.
=item Style::removeType
Removes a type string from the type list.
@param type type string to be removed from the type list.
=item Style::getAllElements
Returns a List of all child SBase objects, including those nested to an
arbitrary depth
@return a List of pointers to all children objects.
=item Style::accept
Accepts the given SBMLVisitor for this instance of Style.
@param v the SBMLVisitor instance to be used.
@return the result of calling C<v.visit()>.
=item Style::clone
Creates and returns a deep copy of this Style object.
This method is purely abstract and has to be implemented in derived classes.
@return a (deep) copy of this Style object
=item Style::getElementName
Returns the XML element name of this object.
This is overridden by subclasses to return a string appropriate to the
SBML component. For example, Model defines it as returning "model",
CompartmentType defines it as returning "compartmentType", etc.
NOTE: this function is only ever going to be called from the constructor
=item Style::writeElements
@internal
Subclasses should override this method to write out their contained
SBML objects as XML elements. Be sure to call your parents
implementation of this method as well. For example:
SBase::writeElements(stream);
mReactants.write(stream);
mProducts.write(stream);
...
=item Style::toXML
Creates an XMLNode object from this Style object.
@return the XMLNode with the XML representation for the
Style object.
=item Style::setSBMLDocument
@internal
Sets the parent SBMLDocument of this SBML object.
@param d the SBMLDocument object to use
=item Style::connectToChild
@internal
Sets this SBML object to child SBML objects (if any).
(Creates a child-parent relationship by the parent)
Subclasses must override this function if they define
one ore more child elements.
Basically, this function needs to be called in
constructor, copy constructor, assignment operator.
@see setSBMLDocument
@see enablePackageInternal
=item Style::enablePackageInternal
@internal
Enables/Disables the given package with this element and child
elements (if any).
(This is an internal implementation for enablePakcage function)
@note Subclasses in which one or more child elements are defined
must override this function.
=item Style::getId
Returns the value of the "id" attribute of this Style.
@return the id of the Style
=item Style::isSetId
Predicate returning C<true> or C<false> depending on whether this
Style's "id" attribute has been set.
@return returns true or false depending on whether the id on the
Style has been set.
=item Style::setId
Sets the value of the "id" attribute of this Style.
@param id the new id for the Style
@return status if the operation succeeded
=item Style::unsetId
Unsets the value of the "id" attribute of this Style.
=item Style::getName
Returns the value of the "name" attribute of this Style.
@return the name of the Style
=item Style::isSetName
Predicate returning C<true> or C<false> depending on whether this
Style's "name" attribute has been set.
@return returns true or false depending on whether the name on the
Style has been set.
=item Style::setName
Sets the value of the "name" attribute of this Style.
@param name the new name for the Style
@return status if the operation succeeded
=item Style::unsetName
Unsets the value of the "name" attribute of this Style.
=item Style::setParentSBMLObject
Sets the parent SBML object of this SBML object.
@param sb the SBML object to use
=item Style::hasRequiredAttributes
@internal
=item Style::hasRequiredElements
@internal
=item Style::createObject
@internal
@return the SBML object corresponding to next XMLToken in the
XMLInputStream or NULL if the token was not recognized.
=item Style::readAttributes
@internal
Subclasses should override this method to read values from the given
XMLAttributes set into their specific fields. Be sure to call your
parents implementation of this method as well.
=item Style::addExpectedAttributes
@internal
Subclasses should override this method to get the list of
expected attributes.
This function is invoked from corresponding readAttributes()
function.
=item Style::writeAttributes
@internal
Subclasses should override this method to write their XML attributes
to the XMLOutputStream. Be sure to call your parents implementation
of this method as well. For example:
SBase::writeAttributes(stream);
stream.writeAttribute( "id" , mId );
stream.writeAttribute( "name", mName );
...
=item Style::readListOfRoles
@internal
Parse the list of roles into the role list.
=item Style::readListOfTypes
@internal
Parse the list of types into the type list.
=item Style::addListOfRoles
@internal
Adds the typeList attribute to an XMLAttributes object.
=item Style::addListOfTypes
@internal
Adds the roleList attribute to an XMLAttributes object.
=item Style::writeTypeList
@internal
Writes the type list to an XML stream.
=item Style::writeRolesList
@internal
Writes the role list to an XML stream.
=item Style::readIntoSet
@internal
Devides a string into individual elements and stores them in the given set.
=item Style::createStringFromSet
@internal
Concatenates individual elements from a set to a string.
The string is returned.
=back
=head2 ColorDefinition
LibSBML implementation for the ColorDefinition construct from
the SBML render extension.
A I<ColorDefinition> specifies an id for a certain RGBA value which can
then be referenced by this id in other render extension constructs.
The use of ids like e.g. "lightyellow" might be more descriptive than the
corresponding RGBA value.
A ColorDefinition has two mandatory attributes which are the id for the
color definition and the corresponding RGBA value. The RGBA value has the
same notation as in HTML files or CSS style sheets. It starts with the '#'
character followed by 8 digit hexadecimal string. Optionally the alpha part
can be omited in which case it defaults to FF.
Valid value string are e.g. "#000000" or "#000000FF" for fully opaque black
or "#FF000010" for an almost completly transparent red.
Internally the RGBA components are stored as integer values in the range of 0 to 255
and most methods use integer values instead of the hexadecimal value string.
=over
=back
=head2 ListOfColorDefinitions
LibSBML implementation for a container which holds zero or more ColorDefinition
objects.
=over
=item ColorDefinition::ColorDefinition
Creates a new ColorDefinition object with the given SBML level
and SBML version.
@param level SBML level of the new object
@param level SBML version of the new object
=item ColorDefinition::ColorDefinition
Creates a new ColorDefinition object with the given SBMLNamespaces.
@param sbmlns The SBML namespace for the object.
=item ColorDefinition::ColorDefinition
Creates a new ColorDefinition object from the given XMLNode object.
The XMLNode object has to contain a valid XML representation of a
ColorDefinition object as defined in the render extension specification.
This method is normally called when render information is read from a file and
should normally not have to be called explicitely.
(FOR BACKWARD COMPATIBILITY)
@param node the XMLNode object reference that describes the ColorDefinition
object to be instantiated.
=item ColorDefinition::ColorDefinition
Constructor which sets the ColorDefinition to the given RGBA values.
@param r Red component value. Has to be in the range of 0 to 255.
@param g Green component value. Has to be in the range of 0 to 255.
@param b Blue component value. Has to be in the range of 0 to 255.
@param a Alpha component value. Has to be in the range of 0 to 255.
The alpha component can be omitted. In that case it has a default value of 255.
This constructor is deprecated. The new libsbml API only has
constructors which take the SBML level and version or one that takes
an SBMLNamespaces object.
=item ColorDefinition::ColorDefinition
Constructor which sets the ColorDefinition to completely opaque
black and sets the id to the given string.
@param id the id of the color definition. The user has to make sure
that the id is unique within the given set of color definitions.
This constructor is deprecated. The new libsbml API only has
constructors which take the SBML level and version or one that takes
an SBMLNamespaces object.
=item ColorDefinition::ColorDefinition
Constructor which sets the ColorDefinition to the given RGBA values
and sets the id.
@param id the id of the color definition. The user has to make sure
that the id is unique within the given set of color definitions.
@param r Red component value. Has to be in the range of 0 to 255.
@param g Green component value. Has to be in the range of 0 to 255.
@param b Blue component value. Has to be in the range of 0 to 255.
@param a Alpha component value. Has to be in the range of 0 to 255.
The alpha component can be omitted. In that case it has a default value of 255.
This constructor is deprecated. The new libsbml API only has
constructors which take the SBML level and version or one that takes
an SBMLNamespaces object.
=item ColorDefinition::getRed
Returns the red color component.
@return the red color component for the ColorDefinition.
=item ColorDefinition::getGreen
Returns the green color component.
@return the green color component for the ColorDefinition.
=item ColorDefinition::getBlue
Returns the blue color component.
@return the blue color component for the ColorDefinition.
=item ColorDefinition::getAlpha
Returns the alpha color component.
@return the alpha color component for the ColorDefinition.
=item ColorDefinition::setRed
Sets the red color component.
@param c the new red component value for the color definition.
=item ColorDefinition::setGreen
Sets the green color component.
@param c the new green component value for the color definition.
=item ColorDefinition::setBlue
Sets the blue color component.
@param c the new blue component value for the color definition.
=item ColorDefinition::setAlpha
Sets alpha red color component.
@param c the new alpha component value for the color definition.
=item ColorDefinition::setRGBA
Sets the red green, blue and alpha color component.
The alpha value is optional and defaults to 255 if not given.
@param r Red component value. Has to be in the range of 0 to 255.
@param g Green component value. Has to be in the range of 0 to 255.
@param b Blue component value. Has to be in the range of 0 to 255.
@param a Alpha component value. Has to be in the range of 0 to 255.
The alpha component can be omitted. In that case it has a default value of 255.
=item ColorDefinition::setColorValue
Sets the color value from a given value string.
If the string is not a valid value string, the color value is set to
black and false is returned.
@param valueString A const reference to a string that represents a valid color value,
e.g. "#FFFFFFFF" for fully opaque white.
@return true or false depending on whether setting the color value from the string
was successfull.
=item ColorDefinition::createValueString
Creates a string the represents the current color value.
@return The string representation of the color value.
=item ColorDefinition::accept
Accepts the given SBMLVisitor for this instance of ColorDefinition.
@param v the SBMLVisitor instance to be used.
@return the result of calling C<v.visit()>.
=item ColorDefinition::clone
Creates and returns a deep copy of this ColorDefinition object.
@return a (deep) copy of this ColorDefinition object
=item ColorDefinition::getElementName
Returns the XML element name of this object.
This is overridden by subclasses to return a string appropriate to the
SBML component. For example, Model defines it as returning "model",
CompartmentType defines it as returning "compartmentType", etc.
=item ColorDefinition::writeElements
@internal
Subclasses should override this method to write out their contained
SBML objects as XML elements. Be sure to call your parents
implementation of this method as well. For example:
SBase::writeElements(stream);
mReactants.write(stream);
mProducts.write(stream);
...
=item ColorDefinition::getTypeCode
Returns the libSBML type code for this SBML object.
@if clike LibSBML attaches an identifying code to every
kind of SBML object. These are known as <em>SBML type codes</em>.
The set of possible type codes is defined in the enumeration
#SBMLTypeCode_t. The names of the type codes all begin with the
characters C<SBML_>. @endif@if java LibSBML attaches an
identifying code to every kind of SBML object. These are known as
<em>SBML type codes</em>. In other languages, the set of type codes
is stored in an enumeration; in the Java language interface for
libSBML, the type codes are defined as static integer constants in
interface class {@link libsbmlConstants}. The names of the type codes
all begin with the characters C<SBML_>. @endif
@return the SBML type code for this object, or C<SBML_UNKNOWN> (default).
@see getElementName()
=item ColorDefinition::toXML
Creates an XMLNode object from this ColorDefinition object.
@return the XMLNode with the XML representation for the
ColorDefinition object.
=item ColorDefinition::getId
Returns the value of the "id" attribute of this ColorDefinition.
@return the id of the ColorDefinition
=item ColorDefinition::isSetId
Predicate returning C<true> or C<false> depending on whether this
GraphicalPrimitive's "id" attribute has been set.
@return returns true or false depending on whether the id on the
GraphicalPrimitive has been set.
=item ColorDefinition::setId
Sets the value of the "id" attribute of this GraphicalPrimitive.
@param id the new id for the GraphicalPrimitive
@return status if the operation succeeded
=item ColorDefinition::unsetId
Unsets the value of the "id" attribute of this ColorDefinition.
=item ColorDefinition::hasRequiredAttributes
@internal
=item ColorDefinition::hasRequiredElements
@internal
=item ColorDefinition::createObject
@internal
@return the SBML object corresponding to next XMLToken in the
XMLInputStream or NULL if the token was not recognized.
=item ColorDefinition::readAttributes
@internal
Subclasses should override this method to read values from the given
XMLAttributes set into their specific fields. Be sure to call your
parents implementation of this method as well.
=item ColorDefinition::addExpectedAttributes
@internal
Subclasses should override this method to get the list of
expected attributes.
This function is invoked from corresponding readAttributes()
function.
=item ColorDefinition::writeAttributes
@internal
Subclasses should override this method to write their XML attributes
to the XMLOutputStream. Be sure to call your parents implementation
of this method as well. For example:
SBase::writeAttributes(stream);
stream.writeAttribute( "id" , mId );
stream.writeAttribute( "name", mName );
...
=item ListOfColorDefinitions::ListOfColorDefinitions
Creates a new ListOfColorDefinitions object from the given XMLNode object.
The XMLNode object has to contain a valid XML representation of a
ListOfColorDefinitions object as defined in the render extension specification.
This method is normally called when render information is read from a file and
should normally not have to be called explicitely.
@param node the XMLNode object reference that describes the ListOfColorDefinitions
object to be instantiated.
=item ListOfColorDefinitions::clone
Creates and returns a deep copy of the ListOfColorDefinitions object.
@return a (deep) copy of this ListOfColorDefinitions
=item ListOfColorDefinitions::ListOfColorDefinitions
Constructor which instantiates an empty ListOfColorDefinitions object.
=item ListOfColorDefinitions::ListOfColorDefinitions
Ctor.
=item ListOfColorDefinitions::ListOfColorDefinitions
Copy constructor. Creates a copy of this ListOfColorDefinitions object.
=item ListOfColorDefinitions::getElementName
Returns the XML element name of this object, which for
ListOfColorDefinitions, is always C<"listOfColorDefinitions">.
@return the name of this element, i.e., C<"listOfColorDefinitions">.
=item ListOfColorDefinitions::toXML
Creates an XMLNode object from this ListOfColorDefinitions object.
@return the XMLNode with the XML representation for the
ListOfColorDefinitions object.
=item ListOfColorDefinitions::get
Returns a pointer to the ColorDefinition with the given index or NULL if
the index is invalid.
@param i index of the ColorDefinition object to be returned
@return pointer to the ColorDefinition at the given index or NULL.
=item ListOfColorDefinitions::get
Returns a const pointer to the ColorDefinition with the given index or NULL if
the index is invalid.
@param i index of the ColorDefinition object to be returned
@return const pointer to the ColorDefinition at the given index or NULL.
=item ListOfColorDefinitions::get
Returns a pointer to the ColorDefinition with the given C<id> or C<NULL> if
the id is invalid.
@param id id of the ColorDefinition object to be returned
@return pointer to the ColorDefinition at the given C<id> or C<NULL>.
=item ListOfColorDefinitions::get
Returns a const pointer to the ColorDefinition with the given C<id> or C<NULL> if
the id is invalid.
@param id id of the ColorDefinition object to be returned
@return const pointer to the ColorDefinition at the given C<id> or C<NULL>.
=item ListOfColorDefinitions::remove
Removes the nth item from this ListOfColorDefinitions items and returns a pointer to
it.
The caller owns the returned item and is responsible for deleting it.
@param n the index of the item to remove
@see size()
=item ListOfColorDefinitions::remove
Removes item in this ListOfColorDefinition items with the given identifier.
The caller owns the returned item and is responsible for deleting it.
If none of the items in this list have the identifier C<sid>, then C<
>
NULL is returned.
@param sid the identifier of the item to remove
@return the item removed. As mentioned above, the caller owns the
returned item.
=item ListOfColorDefinitions::getItemTypeCode
Get the type code of the objects contained in this ListOf.
@if clike LibSBML attaches an identifying code to every kind of SBML
object. These are known as <em>SBML type codes</em>. The set of
possible type codes is defined in the enumeration #SBMLTypeCode_t.
The names of the type codes all begin with the characters C<
>
SBML_. @endif@if java LibSBML attaches an identifying code to every
kind of SBML object. These are known as <em>SBML type codes</em>. In
other languages, the set of type codes is stored in an enumeration; in
the Java language interface for libSBML, the type codes are defined as
static integer constants in the interface class {@link
libsbmlConstants}. The names of the type codes all begin with the
characters C<SBML_>. @endif@if python LibSBML attaches an identifying
code to every kind of SBML object. These are known as <em>SBML type
codes</em>. In the Python language interface for libSBML, the type
codes are defined as static integer constants in the interface class
@link libsbml@endlink. The names of the type codes all begin with the
characters C<SBML_>. @endif@if csharp LibSBML attaches an identifying
code to every kind of SBML object. These are known as <em>SBML type
codes</em>. In the C# language interface for libSBML, the type codes
are defined as static integer constants in the interface class @link
libsbmlcs.libsbml@endlink. The names of the type codes all begin with
the characters C<SBML_>. @endif
@return the SBML type code for the objects contained in this ListOf
instance, or @link SBMLTypeCode_t#SBML_UNKNOWN SBML_UNKNOWN@endlink (default).
=item ListOfColorDefinitions::createObject
@internal
@return the SBML object corresponding to next XMLToken in the
XMLInputStream or NULL if the token was not recognized.
=back
=head2 RelAbsVector
This class represents a pair of numerical values where one value represents an absolute
value and the other value is a relative value in percent.
For many elements in the render extension, it is necessary to specify coordinates not in terms
of absolute values, but rather in terms of relative values or even a combination of absolute
and relative values.
Such a pair of values where one represents an absolute value and the other represents a relative
value can be expressed by a RelAbsVector.
The relative and absolute values to initialize a RelAbsVector object can either be given as
numerical datatypes (double) or as a valid value string.
A value string is a combination of an absolute value and a relative value and the absolute
value if given has to come first. So valid value strings would be: "5.0e3+20%", or "100%" or "4".
=over
=item RelAbsVector::RelAbsVector
Constructor with two values.
First value sets the absolute value, second sets the relative value (%).
@param a absolute value
@param a relative value in % (50 -> 50%)
=item RelAbsVector::RelAbsVector
Constructor with a value string.
If the string does not represent a valid value, the relative and the
absolute component of the RelAbsVector are set to NaN.
=item RelAbsVector::setCoordinate
Sets the relative and absolute value.
@param abs absolute value
@param rel relative value. If the relative value is omitted, it is set to 0.
=item RelAbsVector::setCoordinate
Sets the coordinatees from the given string.
If the string does not represent a valid value, the relative and the
absolute component of the RelAbsVector are set to NaN.
@param coordString value string
=item RelAbsVector::setAbsoluteValue
Sets the absolute coordinate value.
@param abs absolute value to be set
=item RelAbsVector::setRelativeValue
Sets the relative coordinate value.
@param rel relative value to be set
=item RelAbsVector::getAbsoluteValue
Returns the absolute coordinate value.
@return absolute value
=item RelAbsVector::getRelativeValue
Returns the relative coordinate value.
@return absolute value
=back
=head2 Ellipse
graphical representation of an ellipse from the SBML render extension
The ellipse class is derived from GraphicalPrimitive2D, so it inherits all its attributes
and methods. Therefore ellipses can have a transformation, a stroke and a stroke with to draw the edge
as well as a fill style and fill style related settings.
Besides those inherited attributes, an ellipse if defined by its center point which can be specified
as a combination of absolute and relative values and its radii for the two axes. The radii can also be
specified in terms absolute and/or relative values.
=over
=item Ellipse::Ellipse
Creates a new Ellipse object with the given SBML level
and SBML version.
@param level SBML level of the new object
@param level SBML version of the new object
=item Ellipse::Ellipse
Creates a new Ellipse object with the given SBMLNamespaces.
@param sbmlns The SBML namespace for the object.
=item Ellipse::Ellipse
Creates a new RadialGradient object from the given XMLNode object.
The XMLNode object has to contain a valid XML representation of a
RadialGradient object as defined in the render extension specification.
This method is normally called when render information is read from a file and
should normally not have to be called explicitely.
@param node the XMLNode object reference that describes the RadialGradient
object to be instantiated.
This constructor is deprecated. The new libsbml API only has
constructors which take the SBML level and version or one that takes
an SBMLNamespaces object.
=item Ellipse::Ellipse
Instantiates a new ellipse object with the center set to 0,0,0
and the radii also set to 0.
The id is set to the given string.
@param id the id of the ellipse.
This constructor is deprecated. The new libsbml API only has
constructors which take the SBML level and version or one that takes
an SBMLNamespaces object.
=item Ellipse::Ellipse
Constructor with 2D center and radius.
instantiates a new ellipse object with the center.
The z coordinate of the center is set to 0.
The id is unset and both radii are set to the given radius.
@param cx x value of the center point
@param cy y value of the center point
@param r radius along both axis
This constructor is deprecated. The new libsbml API only has
constructors which take the SBML level and version or one that takes
an SBMLNamespaces object.
=item Ellipse::Ellipse
Constructor with 2D center and radii.
This constructor is deprecated. The new libsbml API only has
constructors which take the SBML level and version or one that takes
an SBMLNamespaces object.
=item Ellipse::Ellipse
Constructor with 3D center and radii.
instantiates a new ellipse object with the center and radii.
The id is unset.
@param cx x value of the center point
@param cy y value of the center point
@param cz z value of the center point
@param rx radius along the x axis
@param ry radius along the y axis
This constructor is deprecated. The new libsbml API only has
constructors which take the SBML level and version or one that takes
an SBMLNamespaces object.
=item Ellipse::Ellipse
Constructor with id, 2D center and radius.
instantiates a new ellipse object with the given C<id> and center.
Both radii are set to the given radius r. This actually yields a circle.
@param id id for the ellipse
@param cx x value of the center point
@param cy y value of the center point
@param r radius along both axis
This constructor is deprecated. The new libsbml API only has
constructors which take the SBML level and version or one that takes
an SBMLNamespaces object.
=item Ellipse::Ellipse
Constructor with id, 2D center and radii.
instantiates a new ellipse object with the given C<id>, center and radii.
@param id id for the ellipse
@param cx x value of the center point
@param cy y value of the center point
@param rx radius along the x axis
@param ry radius along the y axis
This constructor is deprecated. The new libsbml API only has
constructors which take the SBML level and version or one that takes
an SBMLNamespaces object.
=item Ellipse::Ellipse
Constructor with id, 3D center and radii.
instantiates a new ellipse object with the given C<id>, center and radii.
@param id id for the ellipse
@param cx x value of the center point
@param cy y value of the center point
@param cz z value of the center point
@param rx radius along the x axis
@param ry radius along the y axis
This constructor is deprecated. The new libsbml API only has
constructors which take the SBML level and version or one that takes
an SBMLNamespaces object.
=item Ellipse::getCX
Returns the x coordinate for the center point as a const reference.
@return const reference to the x coordinatee of the center point.
=item Ellipse::getCY
Returns the y coordinate for the center point as a const reference.
@return const reference to the y coordinatee of the center point.
=item Ellipse::getCZ
Returns the z coordinate for the center point as a const reference.
@return const reference to the z coordinatee of the center point.
=item Ellipse::getRX
Returns the radius along the x axis as a const reference.
@return const reference to the radius along the x axis
=item Ellipse::getRY
Returns the radius along the y axis as a const reference.
@return const reference to the radius along the y axis
=item Ellipse::getCX
Returns the x coordinate for the center point as a reference.
@return reference to the x coordinatee of the center point.
=item Ellipse::getCY
Returns the y coordinate for the center point as a reference.
@return reference to the y coordinatee of the center point.
=item Ellipse::getCZ
Returns the z coordinate for the center point as a reference.
@return reference to the z coordinatee of the center point.
=item Ellipse::getRX
Returns the radius along the x axis as a reference.
@return reference to the radius along the x axis
=item Ellipse::getRY
Returns the radius along the y axis as a reference.
@return reference to the radius along the y axis
=item Ellipse::setCX
Sets the x coordinates for the center point.
@param cx x value of the center point
=item Ellipse::setCY
Sets the y coordinates for the center point.
@param cy y value of the center point
=item Ellipse::setCZ
Sets the z coordinates for the center point.
@param cz z value of the center point
=item Ellipse::setRX
Sets the radius along the x axis
@param rx radius along the x axis
=item Ellipse::setRY
Sets the radius along the y axis
@param ry radius along the y axis
=item Ellipse::setCenter2D
Sets the 2D coordinates for the center point.
The z coodintate is set to 50%
@param cx x value of the center point
@param cy y value of the center point
=item Ellipse::setCenter3D
Sets the 3D coordinates for the center point.
@param cx x value of the center point
@param cy y value of the center point
@param cz z value of the center point
=item Ellipse::setRadii
Sets the radii of the ellipse
@param rx radius along the x axis
@param ry radius along the y axis
=item Ellipse::writeElements
@internal
Subclasses should override this method to write out their contained
SBML objects as XML elements. Be sure to call your parents
implementation of this method as well. For example:
SBase::writeElements(stream);
mReactants.write(stream);
mProducts.write(stream);
...
=item Ellipse::getElementName
Returns the XML element name of this object.
This is overridden by subclasses to return a string appropriate to the
SBML component. For example, Ellipse defines it as returning "ellipse",
=item Ellipse::clone
Creates and returns a deep copy of this Ellipse object.
@return a (deep) copy of this Ellipse object
=item Ellipse::getTypeCode
Returns the libSBML type code for this SBML object.
@if clike LibSBML attaches an identifying code to every
kind of SBML object. These are known as <em>SBML type codes</em>.
The set of possible type codes is defined in the enumeration
#SBMLTypeCode_t. The names of the type codes all begin with the
characters C<SBML_>. @endif@if java LibSBML attaches an
identifying code to every kind of SBML object. These are known as
<em>SBML type codes</em>. In other languages, the set of type codes
is stored in an enumeration; in the Java language interface for
libSBML, the type codes are defined as static integer constants in
interface class {@link libsbmlConstants}. The names of the type codes
all begin with the characters C<SBML_>. @endif
@return the SBML type code for this object, or C<SBML_UNKNOWN> (default).
@see getElementName()
=item Ellipse::accept
Accepts the given SBMLVisitor.
@return the result of calling C<v.visit()>, which indicates
whether or not the Visitor would like to visit the SBML object's next
sibling object (if available).
=item Ellipse::toXML
Creates an XMLNode object from this Ellipse object.
@return the XMLNode with the XML representation for the
Ellipse object.
=item Ellipse::hasRequiredAttributes
@internal
=item Ellipse::hasRequiredElements
@internal
=item Ellipse::createObject
@internal
@return the SBML object corresponding to next XMLToken in the
XMLInputStream or NULL if the token was not recognized.
=item Ellipse::readAttributes
@internal
Subclasses should override this method to read values from the given
XMLAttributes set into their specific fields. Be sure to call your
parents implementation of this method as well.
=item Ellipse::addExpectedAttributes
@internal
Subclasses should override this method to get the list of
expected attributes.
This function is invoked from corresponding readAttributes()
function.
=item Ellipse::writeAttributes
@internal
Subclasses should override this method to write their XML attributes
to the XMLOutputStream. Be sure to call your parents implementation
of this method as well. For example:
SBase::writeAttributes(stream);
stream.writeAttribute( "id" , mId );
stream.writeAttribute( "name", mName );
...
=back
=head2 GlobalRenderInformation
GlobalRenderInformation is the render information stored in the ListOfLayouts. GlobalRenderInformation can be
applied to all layouts.
GlobalRenderInformation is one of the subclasses of RenderInformationBase. A global render information object
contains color definitions, gradient definitions and line endings as defined in RenderInformationBase.
Additionally it has a list of global styles which specifies type and role based render information.
Global render information can not specify id based render information because it does not belong to a certain layout
but it belongs to all layouts.
=over
=back
=head2 ListOfGlobalRenderInformation
container class that stores GlobalRenderInformation objects.
The ListOfLayouts in the SBML model contains a ListOfGlobalRenderInformation which holds all GlobalRenderInformation
objects.
=over
=item GlobalRenderInformation::GlobalRenderInformation
Creates a new GlobalRenderInformation object with the given SBML level
and SBML version.
@param level SBML level of the new object
@param level SBML version of the new object
=item GlobalRenderInformation::GlobalRenderInformation
Creates a new GlobalRenderInformation object with the given SBMLNamespaces.
@param sbmlns The SBML namespace for the object.
=item GlobalRenderInformation::parseXML
Parses the xml information in the given node and sets the attributes.
This method should never be called by the user. It is only used to read render
information from annotations.
@param node the XMLNode object reference that describes the GlobalRenderInformation
object to be instantiated.
=item GlobalRenderInformation::GlobalRenderInformation
Constructor which creates a GlobalRenderInformation with the given C<id
>
and all lists empty.
@param id the new id for the GlobalRenderInformation.
This constructor is deprecated. The new libsbml API only has
constructors which take the SBML level and version or one that takes
an SBMLNamespaces object.
=item GlobalRenderInformation::getNumStyles
Returns the number of styles.
@return the number of global styles in the global render information object
=item GlobalRenderInformation::getListOfStyles
Returns a pointer to the ListOfGlobalStyles object.
@return pointer to the list of global styles.
=item GlobalRenderInformation::getListOfStyles
Returns a const pointer to the ListOfGlobalStyles object.
@return const pointer to the list of global styles.
=item GlobalRenderInformation::getStyle
Returns a pointer to the style with the given index.
If the index is invalid, C<NULL> is returned.
@param i index of the GlobalStyle to be returned.
@return pointer to the style with the given index or NULL
=item GlobalRenderInformation::getStyle
Returns a const pointer to the style with the given index.
If the index is invalid, C<NULL> is returned.
@param i index of the GlobalStyle to be returned.
@return const pointer to the style with the given index or NULL
=item GlobalRenderInformation::getStyle
Returns a pointer to the style with the given C<id>.
If the id is invalid, C<NULL> is returned.
@param id id of the GlobalStyle to be returned.
@return pointer to the style with the given C<id> or C<NULL
>
=item GlobalRenderInformation::getStyle
Returns a pointer to the style with the given C<id>.
If the id is invalid, C<NULL> is returned.
@param id id of the GlobalStyle to be returned.
@return const pointer to the style with the given C<id> or C<NULL
>
=item GlobalRenderInformation::createStyle
Creates a new GlobalStyle object. The object is added to and owned
by the GlobalRenderInformation object.
@param id for the new style.
@ return a pointer to the newly created GlobalStyle object.
=item GlobalRenderInformation::addStyle
Adds a copy of a GlobalStyle to the GlobalRenderInformation object.
The style is only added if it is valid, i.e. it has to have an id and
a valid group.
@param pointer to the global style object to be added.
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif The possible values
returned by this function are:
@li LIBSBML_OPERATION_SUCCESS
@li LIBSBML_LEVEL_MISMATCH
@li LIBSBML_VERSION_MISMATCH
@li LIBSBML_OPERATION_FAILED
@note This method should be used with some caution. The fact that
this method I<copies> the object passed to it means that the caller
will be left holding a physically different object instance than the
one contained in this GlobalRenderInformation. Changes made to the original object
instance (such as resetting attribute values) will <em>not affect the
instance in the GlobalRenderInformation</em>. In addition, the caller should make
sure to free the original object if it is no longer being used, or
else a memory leak will result. Please see GlobalRenderInformation::createStyle()
for a method that does not lead to these issues.
@see createStyle()
=item GlobalRenderInformation::getAllElements
Returns a List of all child SBase objects, including those nested to an
arbitrary depth
@return a List of pointers to all children objects.
=item GlobalRenderInformation::writeElements
@internal
Subclasses should override this method to write out their contained
SBML objects as XML elements. Be sure to call your parents
implementation of this method as well. For example:
SBase::writeElements(stream);
mReactants.write(stream);
mProducts.write(stream);
...
=item GlobalRenderInformation::getElementName
Returns the XML element name of this object, which for
GlobalRenderInformation, is always C<"renderInformation">.
@return the name of this element, i.e., C<"renderInformation">.
=item GlobalRenderInformation::clone
Creates and returns a deep copy of this GlobalRenderInformation object.
@return a (deep) copy of this GlobalRenderInformation.
=item GlobalRenderInformation::getTypeCode
Returns the libSBML type code for this SBML object.
@if clike LibSBML attaches an identifying code to every
kind of SBML object. These are known as <em>SBML type codes</em>.
The set of possible type codes is defined in the enumeration
#SBMLTypeCode_t. The names of the type codes all begin with the
characters C<SBML_>. @endif@if java LibSBML attaches an
identifying code to every kind of SBML object. These are known as
<em>SBML type codes</em>. In other languages, the set of type codes
is stored in an enumeration; in the Java language interface for
libSBML, the type codes are defined as static integer constants in
interface class {@link libsbmlConstants}. The names of the type codes
all begin with the characters C<SBML_>. @endif
@return the SBML type code for this object, or C<SBML_UNKNOWN> (default).
@see getElementName()
=item GlobalRenderInformation::accept
Accepts the given SBMLVisitor.
@return the result of calling C<v.visit()>, which indicates
whether or not the Visitor would like to visit the SBML object's next
sibling object (if available).
=item GlobalRenderInformation::toXML
Creates an XMLNode object from this GlobalRenderInformation object.
@return the XMLNode with the XML representation for the
GlobalRenderInformation object.
=item GlobalRenderInformation::setSBMLDocument
@internal
Sets the parent SBMLDocument of this SBML object.
@param d the SBMLDocument object to use
=item GlobalRenderInformation::connectToChild
@internal
Sets this SBML object to child SBML objects (if any).
(Creates a child-parent relationship by the parent)
Subclasses must override this function if they define
one ore more child elements.
Basically, this function needs to be called in
constructor, copy constructor, assignment operator.
@see setSBMLDocument
@see enablePackageInternal
=item GlobalRenderInformation::enablePackageInternal
@internal
Enables/Disables the given package with this element and child
elements (if any).
(This is an internal implementation for enablePakcage function)
@note Subclasses in which one or more child elements are defined
must override this function.
=item GlobalRenderInformation::createObject
@internal
@return the SBML object corresponding to next XMLToken in the
XMLInputStream or NULL if the token was not recognized.
=item GlobalRenderInformation::readAttributes
@internal
Subclasses should override this method to read values from the given
XMLAttributes set into their specific fields. Be sure to call your
parents implementation of this method as well.
=item GlobalRenderInformation::addExpectedAttributes
@internal
Subclasses should override this method to get the list of
expected attributes.
This function is invoked from corresponding readAttributes()
function.
=item GlobalRenderInformation::writeAttributes
@internal
Subclasses should override this method to write their XML attributes
to the XMLOutputStream. Be sure to call your parents implementation
of this method as well. For example:
SBase::writeAttributes(stream);
stream.writeAttribute( "id" , mId );
stream.writeAttribute( "name", mName );
...
=item ListOfGlobalRenderInformation::clone
Creates and returns a deep copy of the ListOfGlobalRenderInformation object.
@return a (deep) copy of this ListOfGlobalRenderInformation
=item ListOfGlobalRenderInformation::parseXML
Parses the xml information in the given node and sets the attributes.
This method should never be called by the user. It is only used to read render
information from annotations.
@param node the XMLNode object reference that describes the ListOfGlobalRenderInformation
object to be instantiated.
=item ListOfGlobalRenderInformation::ListOfGlobalRenderInformation
Constructor which instantiates an empty ListOfGlobalRenderInformation object.
=item ListOfGlobalRenderInformation::ListOfGlobalRenderInformation
Ctor.
=item ListOfGlobalRenderInformation::ListOfGlobalRenderInformation
Copy constructor for ListOfGlobalRenderInformation objects.
=item ListOfGlobalRenderInformation::getItemTypeCode
Get the type code of the objects contained in this ListOf.
@if clike LibSBML attaches an identifying code to every kind of SBML
object. These are known as <em>SBML type codes</em>. The set of
possible type codes is defined in the enumeration #SBMLTypeCode_t.
The names of the type codes all begin with the characters C<
>
SBML_. @endif@if java LibSBML attaches an identifying code to every
kind of SBML object. These are known as <em>SBML type codes</em>. In
other languages, the set of type codes is stored in an enumeration; in
the Java language interface for libSBML, the type codes are defined as
static integer constants in the interface class {@link
libsbmlConstants}. The names of the type codes all begin with the
characters C<SBML_>. @endif@if python LibSBML attaches an identifying
code to every kind of SBML object. These are known as <em>SBML type
codes</em>. In the Python language interface for libSBML, the type
codes are defined as static integer constants in the interface class
@link libsbml@endlink. The names of the type codes all begin with the
characters C<SBML_>. @endif@if csharp LibSBML attaches an identifying
code to every kind of SBML object. These are known as <em>SBML type
codes</em>. In the C# language interface for libSBML, the type codes
are defined as static integer constants in the interface class @link
libsbmlcs.libsbml@endlink. The names of the type codes all begin with
the characters C<SBML_>. @endif
@return the SBML type code for the objects contained in this ListOf
instance, or @link SBMLTypeCode_t#SBML_UNKNOWN SBML_UNKNOWN@endlink (default).
=item ListOfGlobalRenderInformation::isValidTypeForList
=item ListOfGlobalRenderInformation::getElementName
Returns the XML element name of this object, which for
ListOfGlobalRenderInformation, is always C<"listOfGlobalRenderInformation">.
@return the name of this element, i.e., C<"listOfGlobalRenderInformation">.
=item ListOfGlobalRenderInformation::toXML
Creates an XMLNode object from this ListOfGlobalRenderInformation object.
@return the XMLNode with the XML representation for the
ListOfGlobalRenderInformation object.
=item ListOfGlobalRenderInformation::setVersion
Sets the version of the render information list.
The version consists of a major and a minor version number.
@param major major version number
@param minor minor version number
=item ListOfGlobalRenderInformation::getMajorVersion
Returns the major version of the render information list.
@return the major version number of the global render information list
=item ListOfGlobalRenderInformation::getMinorVersion
Returns the minor version of the render information list.
@return the minor version number of the global render information list
=item ListOfGlobalRenderInformation::getVersionString
Returns the version as a string.
@return the version of the GlobalRenderInformation object
as a string
=item ListOfGlobalRenderInformation::get
Returns a pointer to the GlobalRenderInformation with the given index or NULL if
the index is invalid.
@param i index of the GlobalRenderInformation object to be returned
@return pointer to the GlobalRenderInformation at the given index or NULL.
=item ListOfGlobalRenderInformation::get
Returns a const pointer to the GlobalRenderInformation with the given index or NULL if
the index is invalid.
@param i index of the GlobalRenderInformation object to be returned
@return const pointer to the GlobalRenderInformation at the given index or NULL.
=item ListOfGlobalRenderInformation::get
Returns a pointer to the GlobalRenderInformation with the given C<id> or C<NULL> if
the id is invalid.
@param id id of the GlobalRenderInformation object to be returned
@return pointer to the GlobalRenderInformation at the given C<id> or C<NULL>.
=item ListOfGlobalRenderInformation::get
Returns a const pointer to the GlobalRenderInformation with the given C<id> or C<NULL> if
the id is invalid.
@param id id of the GlobalRenderInformation object to be returned
@return const pointer to the GlobalRenderInformation at the given C<id> or C<NULL>.
=item ListOfGlobalRenderInformation::remove
Removes the nth item from this ListOfGlobalRenderInformation items and returns a pointer to
it.
The caller owns the returned item and is responsible for deleting it.
@param n the index of the item to remove
@see size()
=item ListOfGlobalRenderInformation::remove
Removes item in this ListOfGlobalRenderInformation items with the given identifier.
The caller owns the returned item and is responsible for deleting it.
If none of the items in this list have the identifier C<sid>, then C<
>
NULL is returned.
@param sid the identifier of the item to remove
@return the item removed. As mentioned above, the caller owns the
returned item.
=item ListOfGlobalRenderInformation::createObject
@internal
@return the SBML object corresponding to next XMLToken in the
XMLInputStream or NULL if the token was not recognized.
=item ListOfGlobalRenderInformation::addExpectedAttributes
@internal
=item ListOfGlobalRenderInformation::writeAttributes
@internal
Subclasses should override this method to write their XML attributes
to the XMLOutputStream. Be sure to call your parents implementation
of this method as well. For example:
SBase::writeAttributes(stream);
stream.writeAttribute( "id" , mId );
stream.writeAttribute( "name", mName );
...
=item ListOfGlobalRenderInformation::writeXMLNS
@internal
Subclasses should override this method to write their xmlns attriubutes
(if any) to the XMLOutputStream.
=back
=head2 GlobalStyle
implementation of the GlobalStyle concept of the SBML render extension.
Global styles are the style information objects used in GlobalRenderInformation (@see GlobalRenderInformation).
Global styles can be associated with layout objects by role and type, but not by id, otherwise global
styles and local styles are equivalent.
Since GlobalStyle is derived from Styles, it inherits all of the methods and attributes from Style. (@see Style)
=over
=back
=head2 ListOfGlobalStyles
ListOfGlobalStyles is the container class that stores GlobalStyles in GlobalRenderInformation objects.
Each GlobalRenderInformation object contains a ListOfGlobalStyles which contains zero or
more global style objects.
=over
=item GlobalStyle::GlobalStyle
Creates a new GlobalStyle object with the given SBML level
and SBML version.
@param level SBML level of the new object
@param level SBML version of the new object
=item GlobalStyle::GlobalStyle
Creates a new GlobalStyle object with the given SBMLNamespaces.
@param sbmlns The SBML namespace for the object.
=item GlobalStyle::GlobalStyle
Creates a new GlobalStyle object from the given XMLNode object.
The XMLNode object has to contain a valid XML representation of a
GlobalStyle object as defined in the render extension specification.
This method is normally called when render information is read from a file and
should normally not have to be called explicitely.
@param node the XMLNode object reference that describes the GlobalStyle
object to be instantiated.
=item GlobalStyle::GlobalStyle
Constructor which creates a GlobalStyle with the given C<id
>
and all lists empty.
@param id the new id for the GlobalStyle.
This constructor is deprecated. The new libsbml API only has
constructors which take the SBML level and version or one that takes
an SBMLNamespaces object.
=item GlobalStyle::getTypeCode
Returns the libSBML type code for this SBML object.
@if clike LibSBML attaches an identifying code to every
kind of SBML object. These are known as <em>SBML type codes</em>.
The set of possible type codes is defined in the enumeration
#SBMLTypeCode_t. The names of the type codes all begin with the
characters C<SBML_>. @endif@if java LibSBML attaches an
identifying code to every kind of SBML object. These are known as
<em>SBML type codes</em>. In other languages, the set of type codes
is stored in an enumeration; in the Java language interface for
libSBML, the type codes are defined as static integer constants in
interface class {@link libsbmlConstants}. The names of the type codes
all begin with the characters C<SBML_>. @endif
@return the SBML type code for this object, or C<SBML_UNKNOWN> (default).
This method is purely abstract and has to be implemented by derived
classes.
@see getElementName()
=item GlobalStyle::getElementName
Returns the XML element name of this object, which for
GlobalStyle, is always C<"renderInformation">.
@return the name of this element, i.e., C<"renderInformation">.
=item GlobalStyle::clone
Creates and returns a deep copy of this GlobalStyle object.
@return a (deep) copy of this GlobalStyle.
=item ListOfGlobalStyles::clone
Creates and returns a deep copy of the ListOfGlobalStyles object.
@return a (deep) copy of this ListOfGlobalStyles
=item ListOfGlobalStyles::ListOfGlobalStyles
Creates a new ListOfGlobalStyles object from the given XMLNode object.
The XMLNode object has to contain a valid XML representation of a
ListOfGlobalStyles object as defined in the render extension specification.
This method is normally called when render information is read from a file and
should normally not have to be called explicitely.
@param node the XMLNode object reference that describes the ListOfGlobalStyles
object to be instantiated.
=item ListOfGlobalStyles::ListOfGlobalStyles
Constructor which instantiates an empty ListOfGlobalStyles object.
=item ListOfGlobalStyles::ListOfGlobalStyles
Ctor.
=item ListOfGlobalStyles::ListOfGlobalStyles
Copy constructor for ListOfGlobalStyles objects.
=item ListOfGlobalStyles::getTypeCode
Returns the libSBML type code for the objects contained in this ListOf
(i.e., GradientDefinition objects, if the list is non-empty).
@if clike LibSBML attaches an identifying code to every
kind of SBML object. These are known as <em>SBML type codes</em>.
The set of possible type codes is defined in the enumeration
#SBMLTypeCode_t. The names of the type codes all begin with the
characters C<SBML_>. @endif@if java LibSBML attaches an
identifying code to every kind of SBML object. These are known as
<em>SBML type codes</em>. In other languages, the set of type codes
is stored in an enumeration; in the Java language interface for
libSBML, the type codes are defined as static integer constants in
interface class {@link libsbmlConstants}. The names of the type codes
all begin with the characters C<SBML_>. @endif
@return the SBML type code for the objects contained in this ListOf
instance, or C<SBML_UNKNOWN> (default).
@see getElementName()
=item ListOfGlobalStyles::getItemTypeCode
Get the type code of the objects contained in this ListOf.
@if clike LibSBML attaches an identifying code to every kind of SBML
object. These are known as <em>SBML type codes</em>. The set of
possible type codes is defined in the enumeration #SBMLTypeCode_t.
The names of the type codes all begin with the characters C<
>
SBML_. @endif@if java LibSBML attaches an identifying code to every
kind of SBML object. These are known as <em>SBML type codes</em>. In
other languages, the set of type codes is stored in an enumeration; in
the Java language interface for libSBML, the type codes are defined as
static integer constants in the interface class {@link
libsbmlConstants}. The names of the type codes all begin with the
characters C<SBML_>. @endif@if python LibSBML attaches an identifying
code to every kind of SBML object. These are known as <em>SBML type
codes</em>. In the Python language interface for libSBML, the type
codes are defined as static integer constants in the interface class
@link libsbml@endlink. The names of the type codes all begin with the
characters C<SBML_>. @endif@if csharp LibSBML attaches an identifying
code to every kind of SBML object. These are known as <em>SBML type
codes</em>. In the C# language interface for libSBML, the type codes
are defined as static integer constants in the interface class @link
libsbmlcs.libsbml@endlink. The names of the type codes all begin with
the characters C<SBML_>. @endif
@return the SBML type code for the objects contained in this ListOf
instance, or @link SBMLTypeCode_t#SBML_UNKNOWN SBML_UNKNOWN@endlink (default).
=item ListOfGlobalStyles::getElementName
Returns the XML element name of this object, which for
ListOfGlobalStyles, is always C<"listOfStyles">.
@return the name of this element, i.e., C<"listOfStyles">.
=item ListOfGlobalStyles::toXML
Creates an XMLNode object from this ListOfGlobalStyles object.
@return the XMLNode with the XML representation for the
ListOfGlobalStyles object.
=item ListOfGlobalStyles::get
Returns a pointer to the GlobalStyle with the given index or NULL if
the index is invalid.
@param i index of the GlobalStyle object to be returned
@return pointer to the GlobalStyle at the given index or NULL.
=item ListOfGlobalStyles::get
Returns a const pointer to the GlobalStyle with the given index or NULL if
the index is invalid.
@param i index of the GlobalStyle object to be returned
@return const pointer to the GlobalStyle at the given index or NULL.
=item ListOfGlobalStyles::get
Returns a pointer to the GlobalStyle with the given C<id> or C<NULL> if
the id is invalid.
@param id id of the GlobalStyle object to be returned
@return pointer to the GlobalStyle at the given C<id> or C<NULL>.
=item ListOfGlobalStyles::get
Returns a const pointer to the GlobalStyle with the given C<id> or C<NULL> if
the id is invalid.
@param id id of the GlobalStyle object to be returned
@return const pointer to the GlobalStyle at the given C<id> or C<NULL>.
=item ListOfGlobalStyles::remove
Removes the nth item from this ListOfGlobalStyles items and returns a pointer to
it.
The caller owns the returned item and is responsible for deleting it.
@param n the index of the item to remove
@see size()
=item ListOfGlobalStyles::remove
Removes item in this ListOfGlobalStyles items with the given identifier.
The caller owns the returned item and is responsible for deleting it.
If none of the items in this list have the identifier C<sid>, then C<
>
NULL is returned.
@param sid the identifier of the item to remove
@return the item removed. As mentioned above, the caller owns the
returned item.
=item ListOfGlobalStyles::createObject
@internal
@return the SBML object corresponding to next XMLToken in the
XMLInputStream or NULL if the token was not recognized.
=back
=head2 GradientStop
LibSBML implementation of the gradient stop concept from the
SBML render extension. The gradient stop concept was more or less taken from
the corresponding concept in SVG.
A GradientStop object represents the color at a certain location in a linear or
radial gradient.
Each gradient should contain two or more gradient stops which mark the edges of a region
within this region color are interpolated based on the distance of the location to the
edges of the region.
A gradient stop has two attributes. The first attribute is an offset which determines the
location for the gradient stop within the object the gradient is appllied to.
The offset can either be ab absolute value or a relative value or a combination of absolute
and relative value. E.g. a value of "50%" for the offset means that the gradient stop is located
at 50% of the gradient vector. For more information and examples, see the render extension
specification or the SVG specification.
The second attribute defines the color for the gradient stop. The color can either be defined
be a color value string or by the id of a ColorDefinition object. (@see ColorDefinition)
=over
=back
=head2 ListOfGradientStops
a container that holds zero or more GradientStop objects.
The ListOfGradientStops is used in linear and radial gradient objects to store the
GradientStop objects that define the gradient. A valid gradient should have two or more
gradient stops.
=over
=item GradientStop::GradientStop
Creates a new GradientStop object with the given SBML level
and SBML version.
@param level SBML level of the new object
@param level SBML version of the new object
=item GradientStop::GradientStop
Creates a new GradientStop object with the given SBMLNamespaces.
@param sbmlns The SBML namespace for the object.
=item GradientStop::GradientStop
Creates a new GradientStop object from the given XMLNode object.
The XMLNode object has to contain a valid XML representation of a
GradientStop object as defined in the render extension specification.
This method is normally called when render information is read from a file and
should normally not have to be called explicitely.
@param node the XMLNode object reference that describes the GradientStop
object to be instantiated.
=item GradientStop::getOffset
Returns the offset of the gradient.
@return a const reference to the offset of the gradient stop.
=item GradientStop::getOffset
Returns the offset of the gradient.
@return a reference to the offset of the gradient stop.
=item GradientStop::setOffset
Sets the offset for the gradient stop.
@param abs the absolute value of the offset.
@param rel the relative value of the offset.
=item GradientStop::setOffset
Sets the offset to the value specified by the given string.
The string has to represent a combination of an absolute
and relative value.
Valid value string would e.g. be "45.0", "30%" or
"10+5%". If the value is a combination of both relative and
absolute value, the absolute value has to come before the relative
value. Number can be given as integer values or floating point values
and the two components can be combined by '+' or '-'. Depending on
whethr the relative value should be added or subtracted from the
absolute value.
If the given string is not valid, the offset will have an absolute
and a relative value of NaN.
@param a string representing a valid offset value.
=item GradientStop::setOffset
Sets the offset to the given vector object.
@param offset The RelAbsVector object that specifies the
offset of the gradient stop.
=item GradientStop::getStopColor
Returns the stop color id or the value string.
Since ids can not start with the '#' character,
this is the way to determine if the gradient stop
uses a color value or a color id.
@return the color id or value string
=item GradientStop::setStopColor
Sets the stop color id or the stop color value.
@param color Either the id of a ColorDefinition object, or a color
value string.
=item GradientStop::accept
Accepts the given SBMLVisitor for this instance of Group.
@param v the SBMLVisitor instance to be used.
@return the result of calling C<v.visit()>.
=item GradientStop::clone
Creates and returns a deep copy of this GradientStop object.
@return a (deep) copy of this GradientStop object
=item GradientStop::getElementName
Returns the XML element name of this object.
This is overridden by subclasses to return a string appropriate to the
SBML component. For example, Model defines it as returning "model",
CompartmentType defines it as returning "compartmentType", etc.
=item GradientStop::toXML
Creates an XMLNode object from this GradientStop object.
@return the XMLNode with the XML representation for the
GradientStop object.
=item GradientStop::getTypeCode
Returns the libSBML type code for this SBML object.
@if clike LibSBML attaches an identifying code to every
kind of SBML object. These are known as <em>SBML type codes</em>.
The set of possible type codes is defined in the enumeration
#SBMLTypeCode_t. The names of the type codes all begin with the
characters C<SBML_>. @endif@if java LibSBML attaches an
identifying code to every kind of SBML object. These are known as
<em>SBML type codes</em>. In other languages, the set of type codes
is stored in an enumeration; in the Java language interface for
libSBML, the type codes are defined as static integer constants in
interface class {@link libsbmlConstants}. The names of the type codes
all begin with the characters C<SBML_>. @endif
@return the SBML type code for this object, or C<SBML_UNKNOWN> (default).
@see getElementName()
=item GradientStop::hasRequiredAttributes
@internal
=item GradientStop::hasRequiredElements
@internal
=item GradientStop::readAttributes
@internal
Subclasses should override this method to read values from the given
XMLAttributes set into their specific fields. Be sure to call your
parents implementation of this method as well.
=item GradientStop::addExpectedAttributes
@internal
Subclasses should override this method to get the list of
expected attributes.
This function is invoked from corresponding readAttributes()
function.
=item GradientStop::writeAttributes
@internal
Subclasses should override this method to write their XML attributes
to the XMLOutputStream. Be sure to call your parents implementation
of this method as well. For example:
SBase::writeAttributes(stream);
stream.writeAttribute( "id" , mId );
stream.writeAttribute( "name", mName );
...
=item ListOfGradientStops::clone
Creates a deep copy of the ListOfGradientStops object.
@return a (deep) copy of this ListOfGradientStops
=item ListOfGradientStops::ListOfGradientStops
Creates a new ListOfGradientStops object from the given XMLNode object.
The XMLNode object has to contain a valid XML representation of a
ListOfGradientStops object as defined in the render extension specification.
This method is normally called when render information is read from a file and
should normally not have to be called explicitely.
@param node the XMLNode object reference that describes the ListOfGradientStops
object to be instantiated.
=item ListOfGradientStops::ListOfGradientStops
Constructor which instantiated an empty ListOfGradientStops object.
=item ListOfGradientStops::ListOfGradientStops
Ctor.
=item ListOfGradientStops::ListOfGradientStops
Copy constructor; creates a copy of the given ListOfGradientStops object.
@param the ListOfGradientStops object to be copied.
=item ListOfGradientStops::getElementName
Returns the XML element name of this object, which for
ListOfGradientStops, is always C<"listOfGradientStops">.
@return the name of this element, i.e., C<"listOfGradientStops">.
=item ListOfGradientStops::toXML
Creates an XMLNode object from this ListOfGradientStops object.
@return the XMLNode with the XML representation for the
ListOfGradientStops object.
=item ListOfGradientStops::get
Returns a pointer to the GradientStop with the given index or NULL if
the index is invalid.
@param i index of the GradientStop object to be returned
@return pointer to the GradientStop at the given index or NULL.
=item ListOfGradientStops::get
Returns a const pointer to the GradientStop with the given index or NULL if
the index is invalid.
@param i index of the GradientStop object to be returned
@return const pointer to the GradientStop at the given index or NULL.
=item ListOfGradientStops::remove
Removes the nth item from this ListOfGradientStops items and returns a pointer to
it.
The caller owns the returned item and is responsible for deleting it.
@param n the index of the item to remove
@see size()
=item ListOfGradientStops::getItemTypeCode
Get the type code of the objects contained in this ListOf.
@if clike LibSBML attaches an identifying code to every kind of SBML
object. These are known as <em>SBML type codes</em>. The set of
possible type codes is defined in the enumeration #SBMLTypeCode_t.
The names of the type codes all begin with the characters C<
>
SBML_. @endif@if java LibSBML attaches an identifying code to every
kind of SBML object. These are known as <em>SBML type codes</em>. In
other languages, the set of type codes is stored in an enumeration; in
the Java language interface for libSBML, the type codes are defined as
static integer constants in the interface class {@link
libsbmlConstants}. The names of the type codes all begin with the
characters C<SBML_>. @endif@if python LibSBML attaches an identifying
code to every kind of SBML object. These are known as <em>SBML type
codes</em>. In the Python language interface for libSBML, the type
codes are defined as static integer constants in the interface class
@link libsbml@endlink. The names of the type codes all begin with the
characters C<SBML_>. @endif@if csharp LibSBML attaches an identifying
code to every kind of SBML object. These are known as <em>SBML type
codes</em>. In the C# language interface for libSBML, the type codes
are defined as static integer constants in the interface class @link
libsbmlcs.libsbml@endlink. The names of the type codes all begin with
the characters C<SBML_>. @endif
@return the SBML type code for the objects contained in this ListOf
instance, or @link SBMLTypeCode_t#SBML_UNKNOWN SBML_UNKNOWN@endlink (default).
=item ListOfGradientStops::createObject
@internal
@return the SBML object corresponding to next XMLToken in the
XMLInputStream or NULL if the token was not recognized.
=back
=head2 Image
implementation of the Image concept from the SBML
render extension
The image class represents a bitmap image representation. It is derived from Transformation2D
and inherits all its attributes.
There is an attribute that can be used to specify a file URL where that specifies where the image
data can be found. If the URL is a relative path, it is considered to be relative to
the document that contains the render extension info.
The path should be the location of a JPEG or PNG image, other image formats are currently not supported
by the SBML render extension.
Additionally it provides an id attribute as well as attributes that determine the dimensions
and the position of the image relative to its viewport.
=over
=item Image::Image
Creates a new Image object with the given SBML level
and SBML version.
@param level SBML level of the new object
@param level SBML version of the new object
=item Image::Image
Creates a new Image object with the given SBMLNamespaces.
@param sbmlns The SBML namespace for the object.
=item Image::Image
Creates a new Image object from the given XMLNode object.
The XMLNode object has to contain a valid XML representation of a
Image object as defined in the render extension specification.
This method is normally called when render information is read from a file and
should normally not have to be called explicitely.
@param node the XMLNode object reference that describes the Image
object to be instantiated.
=item Image::Image
Instantiates an Image object with the given C<id>.
The image reference is unset, the position and the dimensions
values of the image are set to 0.
For the image to be valid, the reference has to be set and it has to
have dimensions different from and larger than 0.
This constructor is deprecated. The new libsbml API only has
constructors which take the SBML level and version or one that takes
an SBMLNamespaces object.
=item Image::setCoordinates
Sets the position of the image relative to its viewport.
The position can either be specified in relative or in absolut coordinates
or a combination of both.
The z coordinatee can be omitted. In that case it is set to 0.
@param x x coordinate of the image position
@param y y coordinate of the image position
@param z z coordinate of the image position
=item Image::setX
Sets the x coordinate of the image position.
The position can either be specified in relative or in absolut coordinates
or a combination of both.
@param x x coordinate of the image position
=item Image::setY
Sets the y coordinate of the image position.
The position can either be specified in relative or in absolut coordinates
or a combination of both.
@param y y coordinate of the image position
=item Image::setZ
Sets the z coordinate of the image position.
The position can either be specified in relative or in absolut coordinates
or a combination of both.
@param z z coordinate of the image position
=item Image::getX
Returns a reference to the x coordinate of the image position.
@return reference to the x coordinate of the image position.
=item Image::getY
Returns a reference to the y coordinate of the image position.
@return reference to the y coordinate of the image position.
=item Image::getZ
Returns a reference to the z coordinate of the image position.
@return reference to the z coordinate of the image position.
=item Image::getX
Returns a const reference to the x coordinate of the image position.
@return const reference to the x coordinate of the image position.
=item Image::getY
Returns a const reference to the y coordinate of the image position.
@return const reference to the y coordinate of the image position.
=item Image::getZ
Returns a const reference to the z coordinate of the image position.
@return const reference to the z coordinate of the image position.
=item Image::setDimensions
Sets the dimensions of the image.
The dimensions can be set as relative values or absolute values, or
a combination of both.
@param width the width of the image when rendered
@param height the height of the image when rendered
=item Image::setWidth
Sets the width of the image when rendered.
The width can be set as relative values or absolute values, or
a combination of both.
@param width the width of the image when rendered
=item Image::setHeight
Sets the height of the image when rendered.
The height can be set as relative values or absolute values, or
a combination of both.
@param height the height of the image when rendered
=item Image::getWidth
Returns a reference to the width of the image.
@return reference to the width
=item Image::getHeight
Returns a reference to the height of the image.
@return reference to the height
=item Image::getWidth
Returns a const reference to the width of the image.
@return const reference to the width
=item Image::getHeight
Returns a const reference to the height of the image.
@return const reference to the height
=item Image::setImageReference
Sets the reference to the image location.
Relative paths are relative to the document that contains the render information.
The path should be the location to a JPEG or PNG bitmap image, other formats are
currently not supported.
@param ref A URL string that specifies where the image is located on the disk.
=item Image::getImageReference
Returns the image reference URL string.
@return THe path to the image data as a string.
=item Image::isSetImageReference
Returns true if the image reference has been set.
The image reference is considered set if the string does not
only contain whitespace characters.
@return true if the image reference has been set.
=item Image::accept
Accepts the given SBMLVisitor.
@return the result of calling C<v.visit()>, which indicates
whether or not the Visitor would like to visit the SBML object's next
sibling object (if available).
=item Image::clone
Creates and returns a deep copy of this Image object.
@return a (deep) copy of this Image.
=item Image::getElementName
Returns the XML element name of this object, which for
Image, is always C<"image">.
@return the name of this element, i.e., C<"image">.
=item Image::getTypeCode
Returns the libSBML type code for this SBML object.
@if clike LibSBML attaches an identifying code to every
kind of SBML object. These are known as <em>SBML type codes</em>.
The set of possible type codes is defined in the enumeration
#SBMLTypeCode_t. The names of the type codes all begin with the
characters C<SBML_>. @endif@if java LibSBML attaches an
identifying code to every kind of SBML object. These are known as
<em>SBML type codes</em>. In other languages, the set of type codes
is stored in an enumeration; in the Java language interface for
libSBML, the type codes are defined as static integer constants in
interface class {@link libsbmlConstants}. The names of the type codes
all begin with the characters C<SBML_>. @endif
@return the SBML type code for this object, or C<SBML_UNKNOWN> (default).
@see getElementName()
=item Image::toXML
Creates an XMLNode object from this Image object.
@return the XMLNode with the XML representation for the
Image object.
=item Image::getId
Returns the value of the "id" attribute of this Image.
@return the id of the Image
=item Image::isSetId
Predicate returning C<true> or C<false> depending on whether this
Image's "id" attribute has been set.
@return returns true or false depending on whether the id on the
Image has been set.
=item Image::setId
Sets the value of the "id" attribute of this Image.
@param id the new id for the Image
@return status if the operation succeeded
=item Image::unsetId
Unsets the value of the "id" attribute of this Image.
=item Image::hasRequiredAttributes
@internal
=item Image::hasRequiredElements
@internal
=item Image::readAttributes
@internal
Subclasses should override this method to read values from the given
XMLAttributes set into their specific fields. Be sure to call your
parents implementation of this method as well.
=item Image::addExpectedAttributes
@internal
Subclasses should override this method to get the list of
expected attributes.
This function is invoked from corresponding readAttributes()
function.
=item Image::writeAttributes
@internal
Subclasses should override this method to write their XML attributes
to the XMLOutputStream. Be sure to call your parents implementation
of this method as well. For example:
SBase::writeAttributes(stream);
stream.writeAttribute( "id" , mId );
stream.writeAttribute( "name", mName );
...
=back
=head2 Text
Text element from the SBML render extension. Is used to represent text render information.
The Text class represents text to be rendered in the context of a style.
The Text class inherits all attributes and methods from its base class GraphicalPrimitive1D.
The text also holds a string for the actual text that is to be rendered for the Text object.
Additional attributes specify how the text is to be rendered, e.g. which font family is to be used
and how the text is to be aligned within the viewport.
=over
=item Text
Creates a new Text object with the given SBML level
and SBML version.
@param level SBML level of the new object
@param level SBML version of the new object
=item Text
Creates a new Text object with the given SBMLNamespaces.
@param sbmlns The SBML namespace for the object.
=item Text
Creates a new Text object from the given XMLNode object.
The XMLNode object has to contain a valid XML representation of a
Text object as defined in the render extension specification.
This method is normally called when render information is read from a file and
should normally not have to be called explicitely.
@param node the XMLNode object reference that describes the Text
object to be instantiated.
=item ~Text
Destroy this Text object.
=item Text
Instantiates a new Text object with the given C<id> and position offset.
The position offset coordinates can be omitted and will be set to 0 in
that case.
All attributes are set as described for the default constructor
of GraphicalPrimitive1D.
All the font rendering attributes as well
as the text to be rendered are unset.
@param id id string for the Text object
@param x x coordinate of the position offset
@param y y coordinate of the position offset
@param z z coordinate of the position offset
This constructor is deprecated. The new libsbml API only has
constructors which take the SBML level and version or one that takes
an SBMLNamespaces object.
=item setCoordinates
Sets the position of the text within the viewport.
This is like an offset that is applied after alignment.
If the z coordinate is omitted, it is set to 0.
@param x x coordinate of the position offset
@param y y coordinate of the position offset
@param z z coordinate of the position offset
=item setX
Sets the x position of the text within the viewport.
This is like an offset that is applied after alignment.
@param x x coordinate of the position offset
=item setY
Sets the y position of the text within the viewport.
This is like an offset that is applied after alignment.
@param y y coordinate of the position offset
=item setZ
Sets the z position of the text within the viewport.
This is like an offset that is applied after alignment.
@param z z coordinate of the position offset
=item getX
Returns the x position offset as a const reference.
This offset is applied after alignment.
@return const reference of x position offset
=item getY
Returns the y position offset as a const reference.
This offset is applied after alignment.
@return const reference of y position offset
=item getZ
Returns the z position offset as a const reference.
This offset is applied after alignment.
@return const reference of z position offset
=item getX
Returns the x position offset as a reference.
This offset is applied after alignment.
@return reference of x position offset
=item getY
Returns the y position offset as a reference.
This offset is applied after alignment.
@return reference of y position offset
=item getZ
Returns the z position offset as a reference.
This offset is applied after alignment.
@return reference of z position offset
=item setFontFamily
Sets the font family.
@param family The name of the font family, e.g. Helvetica
=item setFontSize
Sets the font size.
Normally this is an absolute value, e.g. 18 for a 18pt font.
It is however allowed the specify the font size in terms of relative values
in relation to the current viewport. In most cases the viewport will be the
dimensions of a bounding box of a layout object.
@param size the new font size.
=item setFontWeight
Sets the font weight.
Valid values are Text::WEIGHT_UNSET, Text::WEIGHT_NORMAL or
Text::WEIGHT_BOLD.
@param weight The new text weight to be set.
=item setFontStyle
Sets the font style.
Valid values are Text::STYLE_UNSET, Text::STYLE_NORMAL or
Text::STYLE_ITALIC
@param style The new font style to be set.
=item setTextAnchor
Sets the text anchor.
This is defines the horizontal text position.
Valid values are Text::ANCHOR_UNSET, Text::ANCHOR_START,
Text::ANCHOR_MIDDLE and Text_ANCHOR_END.
Text::ANCHOR_BASELINE is not a valid value
for the text-anchor attribute. If you set the text anchor to
Text::ANCHOR_BASELINE, it will be set to Text::ANCHOR_UNSET.
@param anchor The new horizontal alignment flag.
=item setVTextAnchor
Sets the vertical text anchor.
This is defines the vertical text position.
Valid values are Text::ANCHOR_UNSET, Text::ANCHOR_TOP,
Text::ANCHOR_MIDDLE and Text_ANCHOR_BOTTOM.
@param anchor The new vertical alignment flag.
=item getFontFamily
Returns the font family.
@return The name of the font family to be used for text rendering.
=item getFontSize
Returns the font size as a const reference.
@return const reference to the size to be used for rendering text.
=item getFontSize
Returns the font size as a reference.
@return A reference to the size to be used for rendering text.
=item getFontWeight
Returns the font weight.
@return font weight used to render text children
=item getFontStyle
Returns the font style.
@return font style used to render text children
=item getTextAnchor
Returns the text anchor.
@return the horizontal text alignment flag
=item getVTextAnchor
Returns the vertical text anchor.
@return the vertical text alignment flag
=item isSetTextAnchor
Returns true if the horizonal alignment attribute has been set.
@return true is flag is not Text::ANCHOR_UNSET
=item isSetVTextAnchor
Returns true if the vertical alignment attribute has been set.
@return true is flag is not Text::ANCHOR_UNSET
=item getText
Returns the text for the Text object.
@return the text string to be rendered for the Text object.
=item setText
Sets the text for the text element.
@param text The text to be rendered for the Text object.
=item isSetText
Returns true if the text is set to something else than the empty string.
@return true if the text is not empty.
=item accept
Accepts the given SBMLVisitor for this instance of Group.
@param v the SBMLVisitor instance to be used.
@return the result of calling C<v.visit()>.
=item clone
Creates and returns a deep copy of this Text object.
@return a (deep) copy of this Text object
=item getElementName
Returns the XML element name of this object, which for
Text, is always C<"text">.
@return the name of this element, i.e., C<"text">.
=item getTypeCode
Returns the libSBML type code for this SBML object.
@if clike LibSBML attaches an identifying code to every
kind of SBML object. These are known as <em>SBML type codes</em>.
The set of possible type codes is defined in the enumeration
#SBMLTypeCode_t. The names of the type codes all begin with the
characters C<SBML_>. @endif@if java LibSBML attaches an
identifying code to every kind of SBML object. These are known as
<em>SBML type codes</em>. In other languages, the set of type codes
is stored in an enumeration; in the Java language interface for
libSBML, the type codes are defined as static integer constants in
interface class {@link libsbmlConstants}. The names of the type codes
all begin with the characters C<SBML_>. @endif
@return the SBML type code for this object, or C<SBML_UNKNOWN> (default).
This method is purely abstract and has to be implemented by derived
classes.
@see getElementName()
=item isSetFontFamily
Returns true if the font family has been set or false otherwise.
@return true if the font family string is not empty
=item isSetFontSize
Returns true if the font size has been set or false otherwise.
@return true if the RelAbsVector specifying the font size does not
contain NaN either as the absolute or the relative value.
=item isSetFontWeight
Returns true if the font weight has been set or false otherwise.
@return true is the flag is not Text::WEIGHT_UNSET
=item isSetFontStyle
Returns true if the font style has been set or false otherwise.
@return true is the flag is not Text::STYLE_UNSET
=item toXML
Creates an Text object from this Group object.
@return the XMLNode with the XML representation for the
Text object.
=item hasRequiredAttributes
@internal
=item hasRequiredElements
@internal
=item setElementText
When overridden allows SBase elements to use the text included in between
the elements tags. The default implementation does nothing.
@param text the text string found between the element tags.
=item write
@internal
=item readAttributes
@internal
Subclasses should override this method to read values from the given
XMLAttributes set into their specific fields. Be sure to call your
parents implementation of this method as well.
=item addExpectedAttributes
@internal
Subclasses should override this method to get the list of
expected attributes.
This function is invoked from corresponding readAttributes()
function.
=item addTextAttributes
@internal
Adds the text rendering attributes of the given Text object
to the given XMLAttributes object.
=item writeAttributes
@internal
Subclasses should override this method to write their XML attributes
to the XMLOutputStream. Be sure to call your parents implementation
of this method as well. For example:
SBase::writeAttributes(stream);
stream.writeAttribute( "id" , mId );
stream.writeAttribute( "name", mName );
...
=item writeElements
@internal
Subclasses should override this method to write out their contained
SBML objects as XML elements. Be sure to call your parents
implementation of this method as well. For example:
SBase::writeElements(stream);
mReactants.write(stream);
mProducts.write(stream);
...
=item Rectangle::Rectangle
Creates a new Rectangle object with the given SBML level
and SBML version.
@param level SBML level of the new object
@param level SBML version of the new object
=item Rectangle::Rectangle
Creates a new Rectangle object with the given SBMLNamespaces.
@param sbmlns The SBML namespace for the object.
=item Rectangle::Rectangle
Creates a new Rectangle object from the given XMLNode object.
The XMLNode object has to contain a valid XML representation of a
Rectangle object as defined in the render extension specification.
This method is normally called when render information is read from a file and
should normally not have to be called explicitely.
@param node the XMLNode object reference that describes the Rectangle
object to be instantiated.
=item Rectangle::Rectangle
Instantiates a new Rectangle object.
All attributes are set as described for the default constructor
of GraphicalPrimitive2D.
The id is set to the given string and all rectangle specific attributes are set to 0.
@param id id string for the rectangle
This constructor is deprecated. The new libsbml API only has
constructors which take the SBML level and version or one that takes
an SBMLNamespaces object.
=item Rectangle::Rectangle
Instantiates a new Rectangle object.
All attributes are set as described for the default constructor
of GraphicalPrimitive2D.
The id is set to the given string and all rectangle specific attributes
are set to the given values.
@param id id string for the rectangle
@param x x coordinate of the position
@param y y coordinate of the position
@param z z coordinate of the position
@param w w width
@param h h height
This constructor is deprecated. The new libsbml API only has
constructors which take the SBML level and version or one that takes
an SBMLNamespaces object.
=item Rectangle::Rectangle
Instantiates a new Rectangle object.
All attributes are set as described for the default constructor
of GraphicalPrimitive2D.
The id is set to the given string and all rectangle specific attributes
are set to the given values. The z coordinate of the position is set to 0.
@param id id string for the rectangle
@param x x coordinate of the position
@param y y coordinate of the position
@param w w width
@param h h height
This constructor is deprecated. The new libsbml API only has
constructors which take the SBML level and version or one that takes
an SBMLNamespaces object.
=item Rectangle::setCoordinatesAndSize
Sets the position and the size of the Rectangle within the viewport.
@param x x coordinate of the position
@param y y coordinate of the position
@param z z coordinate of the position
@param w w width
@param h h height
=item Rectangle::setCoordinates
Sets the position of the Rectangle within the viewport.
@param x x coordinate of the position
@param y y coordinate of the position
@param z z coordinate of the position
=item Rectangle::setSize
Sets the size of the Rectangle
@param w w width
@param h h height
=item Rectangle::setWidth
Sets the siwidth of the Rectangle
@param w w width
=item Rectangle::setHeight
Sets the height of the Rectangle
@param h h height
=item Rectangle::setRadii
Sets the two corner radii of the rectangle
@param rx corner radius along the x axis
@param ry corner radius along the y axis
=item Rectangle::setRadiusX
Sets the corner radius along the x axis
@param rx corner radius along the x axis
=item Rectangle::setRadiusY
Sets the corner radius along the y axis
@param ry corner radius along the y axis
=item Rectangle::setX
Sets the x position of the Rectangle within the viewport.
@param x x coordinate of the position
=item Rectangle::setY
Sets the y position of the Rectangle within the viewport.
@param y y coordinate of the position
=item Rectangle::setZ
Sets the z position of the Rectangle within the viewport.
@param z z coordinate of the position
=item Rectangle::getX
Returns the x coordinate of the rectangles position
@return const reference to RelAbsVector that represents the x position
=item Rectangle::getY
Returns the y coordinate of the rectangles position
@return const reference to RelAbsVector that represents the y position
=item Rectangle::getZ
Returns the z coordinate of the rectangles position
@return const reference to RelAbsVector that represents the z position
=item Rectangle::getWidth
Returns the with of the rectangle
@return const reference to the RelAbsVector that represents the width
=item Rectangle::getHeight
Returns the height of the rectangle
@return const reference to the RelAbsVector that represents the height
=item Rectangle::getRadiusX
Returns the corner radius along the x axis
@return const reference to the RelAbsVector that corner radius along the x axis
=item Rectangle::getRadiusY
Returns the corner radius along the y axis
@return const reference to the RelAbsVector that corner radius along the y axis
=item Rectangle::getX
Returns the x coordinate of the rectangles position
@return reference to RelAbsVector that represents the x position
=item Rectangle::getY
Returns the y coordinate of the rectangles position
@return reference to RelAbsVector that represents the y position
=item Rectangle::getZ
Returns the z coordinate of the rectangles position
@return reference to RelAbsVector that represents the z position
=item Rectangle::getWidth
Returns the with of the rectangle
@return reference to the RelAbsVector that represents the width
=item Rectangle::getHeight
Returns the height of the rectangle
@return reference to the RelAbsVector that represents the height
=item Rectangle::getRadiusX
Returns the corner radius along the x axis
@return reference to the RelAbsVector that corner radius along the x axis
=item Rectangle::getRadiusY
Returns the corner radius along the y axis
@return reference to the RelAbsVector that corner radius along the y axis
=item Rectangle::accept
Accepts the given SBMLVisitor for this instance of Rectangle.
@param v the SBMLVisitor instance to be used.
@return the result of calling C<v.visit()>.
=item Rectangle::clone
Creates and returns a deep copy of this Rectangle object.
@return a (deep) copy of this Rectangle object
=item Rectangle::getElementName
Returns the XML element name of this object.
This is overridden by subclasses to return a string appropriate to the
SBML component. For example, Model defines it as returning "model",
CompartmentType defines it as returning "compartmentType", etc.
=item Rectangle::getTypeCode
Returns the libSBML type code for this SBML object.
@if clike LibSBML attaches an identifying code to every
kind of SBML object. These are known as <em>SBML type codes</em>.
The set of possible type codes is defined in the enumeration
#SBMLTypeCode_t. The names of the type codes all begin with the
characters C<SBML_>. @endif@if java LibSBML attaches an
identifying code to every kind of SBML object. These are known as
<em>SBML type codes</em>. In other languages, the set of type codes
is stored in an enumeration; in the Java language interface for
libSBML, the type codes are defined as static integer constants in
interface class {@link libsbmlConstants}. The names of the type codes
all begin with the characters C<SBML_>. @endif
@return the SBML type code for this object, or C<SBML_UNKNOWN> (default).
@see getElementName()
=item Rectangle::toXML
Creates an XMLNode object from this Rectangle object.
@return the XMLNode with the XML representation for the
Rectangle object.
=item Rectangle::hasRequiredAttributes
@internal
=item Rectangle::hasRequiredElements
@internal
=item Rectangle::readAttributes
@internal
Subclasses should override this method to read values from the given
XMLAttributes set into their specific fields. Be sure to call your
parents implementation of this method as well.
=item Rectangle::addExpectedAttributes
@internal
Subclasses should override this method to get the list of
expected attributes.
This function is invoked from corresponding readAttributes()
function.
=item Rectangle::writeAttributes
@internal
Subclasses should override this method to write their XML attributes
to the XMLOutputStream. Be sure to call your parents implementation
of this method as well. For example:
SBase::writeAttributes(stream);
stream.writeAttribute( "id" , mId );
stream.writeAttribute( "name", mName );
...
=back
=head2 RenderPoint
Represents a point where the coordinates can be made up of absolute
as well as relative values (@see RelAbsVector)
Render objects are often specified relative to the current viewport, i.e. we need
a way to specify relative coordinate values in curves. For this we introduced the RenderPoint
and the RenderCubicBezier class in the render extension.
Those two classes are used to specify curve and polygon elements (@see RenderCurve or @see Polygon).
=over
=item RenderPoint::RenderPoint
Creates a new RenderPoint object with the given SBML level
and SBML version.
@param level SBML level of the new object
@param level SBML version of the new object
=item RenderPoint::RenderPoint
Creates a new RenderPoint object with the given SBMLNamespaces.
@param sbmlns The SBML namespace for the object.
=item RenderPoint::RenderPoint
Copy constructor for RenderPoint objects.
=item RenderPoint::RenderPoint
Creates a new point with the given ccordinates.
@param x x coordinate of the RenderPoint object
@param y y coordinate of the RenderPoint object
@param z z coordinate of the RenderPoint object
If the z value is omitted, it is set to 0.
=item RenderPoint::RenderPoint
Creates a new RenderPoint object from the given XMLNode object.
The XMLNode object has to contain a valid XML representation of a
RenderPoint object as defined in the render extension specification.
This method is normally called when render information is read from a file and
should normally not have to be called explicitely.
@param node the XMLNode object reference that describes the RenderPoint
object to be instantiated.
=item RenderPoint::x
Returns the x coordinate of the RenderPoint as a const reference.
@return const reference to x coordinate.
=item RenderPoint::y
Returns the y coordinate of the RenderPoint as a const reference.
@return const reference to y coordinate.
=item RenderPoint::z
Returns the z coordinate of the RenderPoint as a const reference.
@return const reference to z coordinate.
=item RenderPoint::x
Returns the x coordinate of the RenderPoint as a reference.
@return reference to x coordinate.
=item RenderPoint::y
Returns the y coordinate of the RenderPoint as a reference.
@return reference to y coordinate.
=item RenderPoint::z
Returns the z coordinate of the RenderPoint as a reference.
@return reference to z coordinate.
=item RenderPoint::setX
Sets the x ccordiante of the RenderPoint object.
@param x x coordinate to be set.
=item RenderPoint::setY
Sets the y ccordiante of the RenderPoint object.
@param y y coordinate to be set.
=item RenderPoint::setZ
Sets the z ccordiante of the RenderPoint object.
@param z z coordinate to be set.
=item RenderPoint::setCoordinates
Sets the coordinates of the RenderPoint to the given values.
@param x x coordinate to be set.
@param y y coordinate to be set.
@param z z coordinate to be set. If the z coordinate is omitted, it is set to 0.
=item RenderPoint::setOffsets
Sets the coordinates of the RenderPoint to the given values.
This method is deprecated, please use setCoordinates.
@param x x coordinate to be set.
@param y y coordinate to be set.
@param z z coordinate to be set. If the z coordinate is omitted, it is set to 0.
=item RenderPoint::initDefaults
Sets the Z offset to 0.0.
=item RenderPoint::writeElements
@internal
Subclasses should override this method to write out their contained
SBML objects as XML elements. Be sure to call your parents
implementation of this method as well. For example:
SBase::writeElements(stream);
mReactants.write(stream);
mProducts.write(stream);
...
=item RenderPoint::setElementName
Sets the element name which is returned by getElementName.
RenderPoint objects can have different element names depending on context.
@param name the string with the element name to be set.
=item RenderPoint::getElementName
Returns the XML element name of this object, which for
RenderPoint, depends on the context.
The name that is returned has to be set with
setElementName.
@return the name of this element (@see setElementName)
=item RenderPoint::clone
Creates and returns a deep copy of this RenderPoint object.
@return a (deep) copy of this RenderPoint object
=item RenderPoint::getTypeCode
Returns the libSBML type code for this SBML object.
@if clike LibSBML attaches an identifying code to every
kind of SBML object. These are known as <em>SBML type codes</em>.
The set of possible type codes is defined in the enumeration
#int. The names of the type codes all begin with the
characters C<SBML_>. @endif@if java LibSBML attaches an
identifying code to every kind of SBML object. These are known as
<em>SBML type codes</em>. In other languages, the set of type codes
is stored in an enumeration; in the Java language interface for
libSBML, the type codes are defined as static integer constants in
interface class {@link libsbmlConstants}. The names of the type codes
all begin with the characters C<SBML_>. @endif
@return the SBML type code for this object, or C<SBML_UNKNOWN> (default).
@see getElementName()
=item RenderPoint::accept
Accepts the given SBMLVisitor.
@return the result of calling C<v.visit()>, which indicates
whether or not the Visitor would like to visit the SBML object's next
sibling object (if available).
=item RenderPoint::toXML
Creates an XMLNode object from this ColorDefinition object.
@return the XMLNode with the XML representation for the
ColorDefinition object.
=item RenderPoint::hasRequiredAttributes
@internal
=item RenderPoint::hasRequiredElements
@internal
=item RenderPoint::createObject
@internal
@return the SBML object corresponding to next XMLToken in the
XMLInputStream or NULL if the token was not recognized.
=item RenderPoint::readAttributes
@internal
Subclasses should override this method to read values from the given
XMLAttributes set into their specific fields. Be sure to call your
parents implementation of this method as well.
=item RenderPoint::addExpectedAttributes
@internal
Subclasses should override this method to get the list of
expected attributes.
This function is invoked from corresponding readAttributes()
function.
=item RenderPoint::writeAttributes
@internal
Subclasses should override this method to write their XML attributes
to the XMLOutputStream. Be sure to call your parents implementation
of this method as well. For example:
SBase::writeAttributes(stream);
stream.writeAttribute( "id" , mId );
stream.writeAttribute( "name", mName );
...
=item RenderPoint::writeXMLNS
Subclasses should override this method to write their xmlns attriubutes
(if any) to the XMLOutputStream.
=back
=head2 RenderCubicBezier
CubicBezier representation for RenderCurve objects and Polygon objects.
The RenderCubicBezier is derived from RenderPoint and is the second element needed to
represent arbitrary curves with relative coordinates as they can appear in RenderCurves
and Polygon objects.
In addition to the attributes inherited from RenderPoint, RenderCubicBezier has two additional
attributes for the two base points that define a cubic bezier curve.
Segments in a RenderCurve or a Polygon are always defined by two consecutive RenderPoint or
RenderCubicBezier elements. The first element in a list of RenderPoints has to be a RenderPoint
object, all following elements can either be RenderPoints or RenderCubicBezier elements.
If the second element is a RenderPoint, the two elements represent a straight line segement,
if the second element if a RenderCubicBezier, the two elements represent a cubic bezier curve
segment.
For further details please have a look at the SBML render extension specification.
=over
=item RenderCubicBezier::RenderCubicBezier
Creates a new RenderCubicBezier object with the given SBML level
and SBML version.
@param level SBML level of the new object
@param level SBML version of the new object
=item RenderCubicBezier::RenderCubicBezier
Creates a new RenderCubicBezier object with the given SBMLNamespaces.
@param sbmlns The SBML namespace for the object.
=item RenderCubicBezier::RenderCubicBezier
Copy constructor for RenderCubicBezier objects.
=item RenderCubicBezier::RenderCubicBezier
Creates a CubicBezier with the given points.
@param bp1_x x coordinatee of the first base point.
@param bp1_y y coordinatee of the first base point.
@param bp1_z z coordinatee of the first base point.
@param bp1_x x coordinatee of the second base point.
@param bp1_y y coordinatee of the second base point.
@param bp1_z z coordinatee of the second base point.
@param bp1_x x coordinatee of the end point.
@param bp1_y y coordinatee of the end point.
@param bp1_z z coordinatee of the end point.
=item RenderCubicBezier::RenderCubicBezier
Creates a new RenderCubicBezier object from the given XMLNode object.
The XMLNode object has to contain a valid XML representation of a
RenderCubicBezier object as defined in the render extension specification.
This method is normally called when render information is read from a file and
should normally not have to be called explicitely.
@param node the XMLNode object reference that describes the RenderCubicBezier
object to be instantiated.
=item RenderCubicBezier::basePoint1_X
Returns the x value of the first base point of the curve (the one closer to the
starting point) as a const reference.
@return const reference to x value of first base point
=item RenderCubicBezier::basePoint1_Y
Returns the y value of the first base point of the curve (the one closer to the
starting point) as a const reference.
@return const reference to y value of first base point
=item RenderCubicBezier::basePoint1_Z
Returns the z value of the first base point of the curve (the one closer to the
starting point) as a const reference.
@return const reference to z value of first base point
=item RenderCubicBezier::basePoint2_X
Returns the x value of the second base point of the curve (the one further from the
starting point) as a const reference.
@return const reference to x value of second base point
=item RenderCubicBezier::basePoint2_Y
Returns the y value of the second base point of the curve (the one further from the
starting point) as a const reference.
@return const reference to y value of second base point
=item RenderCubicBezier::basePoint2_Z
Returns the z value of the second base point of the curve (the one further from the
starting point) as a const reference.
@return const reference to z value of second base point
=item RenderCubicBezier::basePoint1_X
Returns the x value of the first base point of the curve (the one closer to the
starting point) as a reference.
@return reference to x value of first base point
=item RenderCubicBezier::basePoint1_Y
Returns the y value of the first base point of the curve (the one closer to the
starting point) as a reference.
@return reference to y value of first base point
=item RenderCubicBezier::basePoint1_Z
Returns the z value of the first base point of the curve (the one closer to the
starting point) as a reference.
@return reference to z value of first base point
=item RenderCubicBezier::basePoint2_X
Returns the x value of the second base point of the curve (the one further from the
starting point) as a reference.
@return reference to x value of second base point
=item RenderCubicBezier::basePoint2_Y
Returns the y value of the second base point of the curve (the one further from the
starting point) as a reference.
@return reference to y value of second base point
=item RenderCubicBezier::basePoint2_Z
Returns the z value of the second base point of the curve (the one further from the
starting point) as a reference.
@return reference to z value of second base point
=item RenderCubicBezier::setBasePoint1_X
Sets the x value of the first base point of the curve (the one closer to the
starting point).
@param x x coordinate of first base point.
=item RenderCubicBezier::setBasePoint1_Y
Sets the y value of the first base point of the curve (the one closer to the
starting point).
@param y y coordinate of first base point.
=item RenderCubicBezier::setBasePoint1_Z
Sets the z value of the first base point of the curve (the one closer to the
starting point).
@param z z coordinate of first base point.
=item RenderCubicBezier::setBasePoint2_X
Sets the x value of the second base point of the curve (the one further from the
starting point).
@param x value of second base point.
=item RenderCubicBezier::setBasePoint2_Y
Sets the y value of the second base point of the curve (the one further from the
starting point).
@param y value of second base point.
=item RenderCubicBezier::setBasePoint2_Z
Sets the z value of the second base point of the curve (the one further from the
starting point).
@param z value of second base point.
=item RenderCubicBezier::setBasePoint1
Sets the first basepoint to the given coordinatees.
@param x coordinate of second base point.
@param y coordinate of second base point.
@param z coordinate of second base point.
If the z coodinate is omitted, it is set to 0.
=item RenderCubicBezier::setBasePoint2
Sets the second basepoint to the given coordinatees.
@param x coordinate of second base point.
@param y coordinate of second base point.
@param z coordinate of second base point.
If the z coodinate is omitted, it is set to 0.
=item RenderCubicBezier::getElementName
Returns the XML element name of this object, which for
RenderCubicBezier, is always C<"element">.
@return the name of this element, i.e., C<"element">.
=item RenderCubicBezier::clone
Creates and returns a deep copy of the RenderCubicBezier object.
@return a (deep) copy of this RenderCubicBezier
=item RenderCubicBezier::getTypeCode
Returns the libSBML type code for the objects contained in this ListOf
(i.e., ColorDefinition objects, if the list is non-empty).
@if clike LibSBML attaches an identifying code to every
kind of SBML object. These are known as <em>SBML type codes</em>.
The set of possible type codes is defined in the enumeration
#int. The names of the type codes all begin with the
characters C<SBML_>. @endif@if java LibSBML attaches an
identifying code to every kind of SBML object. These are known as
<em>SBML type codes</em>. In other languages, the set of type codes
is stored in an enumeration; in the Java language interface for
libSBML, the type codes are defined as static integer constants in
interface class {@link libsbmlConstants}. The names of the type codes
all begin with the characters C<SBML_>. @endif
@return the SBML type code for the objects contained in this ListOf
instance, or C<SBML_UNKNOWN> (default).
@see getElementName()
=item RenderCubicBezier::toXML
Creates an XMLNode object from this RenderCubicBezier object.
@return the XMLNode with the XML representation for the
RenderCubicBezier object.
=item RenderCubicBezier::hasRequiredAttributes
@internal
=item RenderCubicBezier::hasRequiredElements
@internal
=item RenderCubicBezier::readAttributes
@internal
Subclasses should override this method to read values from the given
XMLAttributes set into their specific fields. Be sure to call your
parents implementation of this method as well.
=item RenderCubicBezier::addExpectedAttributes
@internal
Subclasses should override this method to get the list of
expected attributes.
This function is invoked from corresponding readAttributes()
function.
=item RenderCubicBezier::writeAttributes
@internal
Subclasses should override this method to write their XML attributes
to the XMLOutputStream. Be sure to call your parents implementation
of this method as well. For example:
SBase::writeAttributes(stream);
stream.writeAttribute( "id" , mId );
stream.writeAttribute( "name", mName );
...
=item RenderCubicBezier::writeXMLNS
Subclasses should override this method to write their xmlns attriubutes
(if any) to the XMLOutputStream.
=back
=head2 RenderCurve
implementation of the Curve concept from the SBML render extension
The curve concept in the SBML render extension is similar to the curves in the SBML layout.
Each curve consists of a number of either straight line segments or cubic bezier elements.
The two element types can also by mixed in a single curve object.
In contrast to layout curves, render curves can not have gaps and the individual coordinates of the
curve elements can be specified as a combination of absolute and relative values.
Another difference to layout curves is the fact that render curves can specify decorations to be applied
to the start and/or the end of the curve (@see LineEnding).
Since RenderCurve is derived from GraphicalPrimitive1D, it inherits all its attributes and methods.
=over
=item RenderCurve::RenderCurve
Creates a new RenderCurve object with the given SBML level
and SBML version.
@param level SBML level of the new object
@param level SBML version of the new object
=item RenderCurve::RenderCurve
Creates a new RenderCurve object with the given SBMLNamespaces.
@param sbmlns The SBML namespace for the object.
=item RenderCurve::RenderCurve
Creates a new RenderCurve object from the given XMLNode object.
The XMLNode object has to contain a valid XML representation of a
RenderCurve object as defined in the render extension specification.
This method is normally called when render information is read from a file and
should normally not have to be called explicitely.
@param node the XMLNode object reference that describes the RenderCurve
object to be instantiated.
=item RenderCurve::RenderCurve
Instantiates an empty curve object with the given C<id>.
The decorations are unset and there are no curve elements.
This constructor is deprecated. The new libsbml API only has
constructors which take the SBML level and version or one that takes
an SBMLNamespaces object.
=item RenderCurve::setStartHead
Sets the id of the start head.
@param The id of a LineEnding object to be applied to the start of the curve.
=item RenderCurve::setEndHead
Sets the id of the end head.
@param The id of a LineEnding object to be applied to the end of the curve.
=item RenderCurve::getStartHead
Returns the id of the LineEnding object to be applied to the start of the curve.
@return id of the LineEnding for the start of the curve.
=item RenderCurve::getEndHead
Returns the id of the LineEnding object to be applied to the end of the curve.
@return id of the LineEnding for the end of the curve.
=item RenderCurve::getNumElements
Returns the number of curve segments.
@return number of elements in the curve.
=item RenderCurve::createCubicBezier
Creates a new bezier element.
The element is added to and owned by the curve.
@return The newly created RenderCubicBezier object.
=item RenderCurve::createPoint
Creates a new point element.
The element is added to and owned by the curve.
@return The newly created RenderCubicBezier object.
=item RenderCurve::getElement
Returns a const pointer to the curve segment with the given index or NULL if
the id is invalid.
@param index the index of the curve element to be returned
@return a const pointer to the curve element with the given index or NULL
if the index was out of bounds.
=item RenderCurve::getCurveElement
Returns a pointer to the curve segment with the given index or NULL if
the id is invalid.
This method call is deprecated, please use getElement instead.
@param index the index of the curve element to be returned
@return a pointer to the curve element with the given index or NULL
if the index was out of bounds.
=item RenderCurve::getCurveElement
Returns a const pointer to the curve segment with the given index or NULL if
the id is invalid.
This method call is deprecated, please use getElement instead.
@param index the index of the curve element to be returned
@return a const pointer to the curve element with the given index or NULL
if the index was out of bounds.
=item RenderCurve::getElement
Returns a pointer to the curve segment with the given index or NULL if
the id is invalid.
@param index the index of the curve element to be returned
@return a pointer to the curve element with the given index or NULL
if the index was out of bounds.
=item RenderCurve::addElement
Adds a copy of the given curve segment to the end of the list of
curve segments.
@param cs pointer to the RenderPoint object to be added to the end of the curve elements list.
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif The possible values
returned by this function are:
@li LIBSBML_OPERATION_SUCCESS
@li LIBSBML_LEVEL_MISMATCH
@li LIBSBML_VERSION_MISMATCH
@li LIBSBML_OPERATION_FAILED
@note This method should be used with some caution. The fact that
this method I<copies> the object passed to it means that the caller
will be left holding a physically different object instance than the
one contained in this RenderCurve. Changes made to the original object
instance (such as resetting attribute values) will <em>not affect the
instance in the RenderCurve</em>. In addition, the caller should make
sure to free the original object if it is no longer being used, or
else a memory leak will result. Please see RenderCurve::createPoint()
or RenderCurve::createCubicBezier()
for methods that do not lead to these issues.
@see createPoint()
@see createCubicBezier()
=item RenderCurve::removeElement
Removes the curve segment with the given index.
If the index is valid, a pointer to the removed element is returned
and the caller is responsible for deleting the object.
If the index is not valid, C<NULL> is returned.
@param i index of element to be removed.
@return pointer to removed element.
=item RenderCurve::getListOfElements
Returns a const pointer to the list of curve segments.
@return const pointer to the ListOfCurveElements object for the RenderCurve.
=item RenderCurve::getListOfElements
Returns a pointer to the list of curve segments.
@return pointer to the ListOfCurveElements object for the RenderCurve.
=item RenderCurve::getAllElements
Returns a List of all child SBase objects, including those nested to an
arbitrary depth
@return a List of pointers to all children objects.
=item RenderCurve::renameSIdRefs
Renames all the C<SIdRef> attributes on this element, including any
found in MathML content (if such exists).
This method works by looking at all attributes and (if appropriate)
mathematical formulas, comparing the identifiers to the value of @p
oldid. If any matches are found, the matching identifiers are replaced
with C<newid>. The method does I<not> descend into child elements.
@param oldid the old identifier
@param newid the new identifier
=item RenderCurve::accept
Accepts the given SBMLVisitor.
@return the result of calling C<v.visit()>, which indicates
whether or not the Visitor would like to visit the SBML object's next
sibling object (if available).
=item RenderCurve::clone
Creates and returns a deep copy of the RenderCurve object.
@return a (deep) copy of this RenderCurve
=item RenderCurve::getElementName
Returns the XML element name of this object, which for
RenderCurve, is always C<"curve">.
@return the name of this element, i.e., C<"curve">.
=item RenderCurve::getTypeCode
Returns the libSBML type code for this SBML object.
@if clike LibSBML attaches an identifying code to every
kind of SBML object. These are known as <em>SBML type codes</em>.
The set of possible type codes is defined in the enumeration
#SBMLTypeCode_t. The names of the type codes all begin with the
characters C<SBML_>. @endif@if java LibSBML attaches an
identifying code to every kind of SBML object. These are known as
<em>SBML type codes</em>. In other languages, the set of type codes
is stored in an enumeration; in the Java language interface for
libSBML, the type codes are defined as static integer constants in
interface class {@link libsbmlConstants}. The names of the type codes
all begin with the characters C<SBML_>. @endif
@return the SBML type code for this object, or C<SBML_UNKNOWN> (default).
@see getElementName()
=item RenderCurve::isSetStartHead
Returns true if the start head is set or false otherwise.
The start decoration is considered set if the string is not empty and if
it is not the string "none"
@return true is the start decoration id is set
=item RenderCurve::isSetEndHead
Returns true if the end head is set or false otherwise.
The end decoration is considered set if the string is not empty and if
it is not the string "none"
@return true is the end decoration id is set
=item RenderCurve::toXML
Creates an XMLNode object from this RenderCurve object.
@return the XMLNode with the XML representation for the
RenderCurve object.
=item RenderCurve::setSBMLDocument
@internal
Sets the parent SBMLDocument of this SBML object.
@param d the SBMLDocument object to use
=item RenderCurve::connectToChild
@internal
Sets this SBML object to child SBML objects (if any).
(Creates a child-parent relationship by the parent)
Subclasses must override this function if they define
one ore more child elements.
Basically, this function needs to be called in
constructor, copy constructor, assignment operator.
@see setSBMLDocument
@see enablePackageInternal
=item RenderCurve::enablePackageInternal
@internal
Enables/Disables the given package with this element and child
elements (if any).
(This is an internal implementation for enablePakcage function)
@note Subclasses in which one or more child elements are defined
must override this function.
=item RenderCurve::setParentSBMLObject
Sets the parent SBML object of this SBML object.
@param sb the SBML object to use
=item RenderCurve::readAttributes
@internal
Subclasses should override this method to read values from the given
XMLAttributes set into their specific fields. Be sure to call your
parents implementation of this method as well.
=item RenderCurve::addExpectedAttributes
@internal
Subclasses should override this method to get the list of
expected attributes.
This function is invoked from corresponding readAttributes()
function.
=item RenderCurve::writeAttributes
@internal
Subclasses should override this method to write their XML attributes
to the XMLOutputStream. Be sure to call your parents implementation
of this method as well. For example:
SBase::writeAttributes(stream);
stream.writeAttribute( "id" , mId );
stream.writeAttribute( "name", mName );
...
=item RenderCurve::createObject
@internal
@return the SBML object corresponding to next XMLToken in the
XMLInputStream or NULL if the token was not recognized.
=item RenderCurve::writeElements
@internal
Subclasses should override this method to write out their contained
SBML objects as XML elements. Be sure to call your parents
implementation of this method as well. For example:
SBase::writeElements(stream);
mReactants.write(stream);
mProducts.write(stream);
...
=back
=head2 Polygon
class representing a polygon from the SBML render extension
The Polygon is very similar to the RenderCurve class. The only difference is that in the
polygon the end point of the last element in the curve segment list is
automatically connected to the start point of the first element.
Since a polygon is a closed shape and doesn't really have a start or an end, it does not get
decorations as the RenderCurve does.
So a polygon is always closed and can therefor have a fill style and fill style related attributes.
Those attributes are inherited from Polygons base class GraphicalPrimitive2D.
=over
=item Polygon::Polygon
Creates a new Polygon object with the given SBML level
and SBML version.
@param level SBML level of the new object
@param level SBML version of the new object
=item Polygon::Polygon
Creates a new Polygon object with the given SBMLNamespaces.
@param sbmlns The SBML namespace for the object.
=item Polygon::Polygon
Creates a new Polygon object from the given XMLNode object.
The XMLNode object has to contain a valid XML representation of a
Polygon object as defined in the render extension specification.
This method is normally called when render information is read from a file and
should normally not have to be called explicitely.
@param node the XMLNode object reference that describes the Polygon
object to be instantiated.
=item Polygon::Polygon
Instanciates a polygon with the given C<id> and no elements.
All attributes inherited from GraphicalPrimitive are set as described
in the corresponding constructor of that class (@see GraphicalPrimitive2D)
@param id id string for the polygon
This constructor is deprecated. The new libsbml API only has
constructors which take the SBML level and version or one that takes
an SBMLNamespaces object.
=item Polygon::getNumElements
Returns the number of segments.
@return number of elements in the polygon.
=item Polygon::getListOfElements
Returns a const pointer to the list of segments.
@return const pointer to the ListOfCurveElements object for the Polygon.
=item Polygon::getListOfElements
Returns a pointer to the list of segments.
@return pointer to the ListOfCurveElements object for the Polygon.
=item Polygon::createPoint
Creates a new point element.
The element is added to and owned by the polygon.
@return The newly created RenderCubicBezier object.
=item Polygon::createCubicBezier
Creates a new bezier element.
The element is added to and owned by the polygon.
@return The newly created RenderCubicBezier object.
=item Polygon::getElement
Returns a pointer to the segment with the given index or NULL if
the id is invalid.
@param index the index of the element to be returned
@return a pointer to the element with the given index or NULL
if the index was out of bounds.
=item Polygon::getElement
Returns a const pointer to the segment with the given index or NULL if
the id is invalid.
@param index the index of the element to be returned
@return a const pointer to the element with the given index or NULL
if the index was out of bounds.
=item Polygon::addElement
Adds a copy of the given segment to the end of the list of
segments.
@param cs pointer to the RenderPoint object to be added to the end of the elements list.
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif The possible values
returned by this function are:
@li LIBSBML_OPERATION_SUCCESS
@li LIBSBML_LEVEL_MISMATCH
@li LIBSBML_VERSION_MISMATCH
@li LIBSBML_OPERATION_FAILED
@note This method should be used with some caution. The fact that
this method I<copies> the object passed to it means that the caller
will be left holding a physically different object instance than the
one contained in this Polygon. Changes made to the original object
instance (such as resetting attribute values) will <em>not affect the
instance in the Polygon</em>. In addition, the caller should make
sure to free the original object if it is no longer being used, or
else a memory leak will result. Please see Polygon::createPoint()
or Polygon::createCubicBezier()
for methods that do not lead to these issues.
@see createPoint()
@see createCubicBezier()
=item Polygon::getAllElements
Returns a List of all child SBase objects, including those nested to an
arbitrary depth
@return a List of pointers to all children objects.
=item Polygon::accept
Accepts the given SBMLVisitor.
@return the result of calling C<v.visit()>, which indicates
whether or not the Visitor would like to visit the SBML object's next
sibling object (if available).
=item Polygon::clone
Creates and returns a deep copy of the Polygon object.
@return a (deep) copy of this Polygon
=item Polygon::getElementName
Returns the XML element name of this object, which for
Polygon, is always C<"polygon">.
@return the name of this element, i.e., C<"polygon">.
=item Polygon::getTypeCode
Returns the libSBML type code for this SBML object.
@if clike LibSBML attaches an identifying code to every
kind of SBML object. These are known as <em>SBML type codes</em>.
The set of possible type codes is defined in the enumeration
#SBMLTypeCode_t. The names of the type codes all begin with the
characters C<SBML_>. @endif@if java LibSBML attaches an
identifying code to every kind of SBML object. These are known as
<em>SBML type codes</em>. In other languages, the set of type codes
is stored in an enumeration; in the Java language interface for
libSBML, the type codes are defined as static integer constants in
interface class {@link libsbmlConstants}. The names of the type codes
all begin with the characters C<SBML_>. @endif
@return the SBML type code for this object, or C<SBML_UNKNOWN> (default).
@see getElementName()
=item Polygon::toXML
Creates an XMLNode object from this Polygon object.
@return the XMLNode with the XML representation for the
Polygon object.
=item Polygon::setSBMLDocument
@internal
Sets the parent SBMLDocument of this SBML object.
@param d the SBMLDocument object to use
=item Polygon::connectToChild
@internal
Sets this SBML object to child SBML objects (if any).
(Creates a child-parent relationship by the parent)
Subclasses must override this function if they define
one ore more child elements.
Basically, this function needs to be called in
constructor, copy constructor, assignment operator.
@see setSBMLDocument
@see enablePackageInternal
=item Polygon::enablePackageInternal
@internal
Enables/Disables the given package with this element and child
elements (if any).
(This is an internal implementation for enablePakcage function)
@note Subclasses in which one or more child elements are defined
must override this function.
=item Polygon::setParentSBMLObject
Sets the parent SBML object of this SBML object.
@param sb the SBML object to use
=item Polygon::readAttributes
@internal
Subclasses should override this method to read values from the given
XMLAttributes set into their specific fields. Be sure to call your
parents implementation of this method as well.
=item Polygon::addExpectedAttributes
@internal
Subclasses should override this method to get the list of
expected attributes.
This function is invoked from corresponding readAttributes()
function.
=item Polygon::writeAttributes
@internal
Subclasses should override this method to write their XML attributes
to the XMLOutputStream. Be sure to call your parents implementation
of this method as well. For example:
SBase::writeAttributes(stream);
stream.writeAttribute( "id" , mId );
stream.writeAttribute( "name", mName );
...
=item Polygon::createObject
@internal
@return the SBML object corresponding to next XMLToken in the
XMLInputStream or NULL if the token was not recognized.
=item Polygon::writeElements
@internal
Subclasses should override this method to write out their contained
SBML objects as XML elements. Be sure to call your parents
implementation of this method as well. For example:
SBase::writeElements(stream);
mReactants.write(stream);
mProducts.write(stream);
...
=back
=head2 RenderGroup
The RenderGroup concept from the SBML render extension is used to group graphical primitives together
to create composite representations from simple primitives.
The RenderGroup class is derived from GrphicalPrimitive2D and inherits all its methods and attributes.
In addition to those, the class defines attributes to specify text render properties (@see Text),
curve decorations (@see RenderCurve) an id and a list of child elements which can be any
graphical primitive or other groups.
The attributes of a group are inherited by all children of the group unless they specify
the attribute themselves.
=over
=back
=head2 ListOfDrawables
container class that stores objects derived from Transformation2D.
Layouts can contain ListOfDrawables which holds all
Transformation2D objects for a certain group.
=over
=item ListOfDrawables::clone
Creates and returns a deep copy of the ListOfDrawables object.
@return a (deep) copy of this ListOfDrawables
=item ListOfDrawables::ListOfDrawables
Constructor which instantiates an empty ListOfDrawables object.
=item ListOfDrawables::ListOfDrawables
Ctor.
=item ListOfDrawables::ListOfDrawables
Copy constructor. Creates a copy of this ListOfDrawables object.
=item ListOfDrawables::get
Returns a pointer to the Transformation2D with the given index or NULL if
the index is invalid.
@param i index of the Transformation2D object to be returned
@return pointer to the Transformation2D at the given index or NULL.
=item ListOfDrawables::get
Returns a const pointer to the Transformation2D with the given index or NULL if
the index is invalid.
@param i index of the Transformation2D object to be returned
@return const pointer to the Transformation2D at the given index or NULL.
=item ListOfDrawables::get
Returns a pointer to the Transformation2D with the given C<id> or C<NULL> if
the id is invalid.
@param id id of the Transformation2D object to be returned
@return pointer to the Transformation2D at the given C<id> or C<NULL>.
=item ListOfDrawables::get
Returns a const pointer to the Transformation2D with the given C<id> or C<NULL> if
the id is invalid.
@param id id of the Transformation2D object to be returned
@return const pointer to the Transformation2D at the given C<id> or C<NULL>.
=item ListOfDrawables::remove
Removes the nth item from this ListOfDrawables items and returns a pointer to
it.
The caller owns the returned item and is responsible for deleting it.
@param n the index of the item to remove
@see size()
=item ListOfDrawables::remove
Removes item in this ListOfDrawables items with the given identifier.
The caller owns the returned item and is responsible for deleting it.
If none of the items in this list have the identifier C<sid>, then C<
>
NULL is returned.
@param sid the identifier of the item to remove
@return the item removed. As mentioned above, the caller owns the
returned item.
=item ListOfDrawables::getElementName
Returns the name of this element.
@return the name of the element, in this case "listOfDrawables"
=item ListOfDrawables::getItemTypeCode
Get the type code of the objects contained in this ListOf.
@if clike LibSBML attaches an identifying code to every kind of SBML
object. These are known as <em>SBML type codes</em>. The set of
possible type codes is defined in the enumeration #SBMLTypeCode_t.
The names of the type codes all begin with the characters C<
>
SBML_. @endif@if java LibSBML attaches an identifying code to every
kind of SBML object. These are known as <em>SBML type codes</em>. In
other languages, the set of type codes is stored in an enumeration; in
the Java language interface for libSBML, the type codes are defined as
static integer constants in the interface class {@link
libsbmlConstants}. The names of the type codes all begin with the
characters C<SBML_>. @endif@if python LibSBML attaches an identifying
code to every kind of SBML object. These are known as <em>SBML type
codes</em>. In the Python language interface for libSBML, the type
codes are defined as static integer constants in the interface class
@link libsbml@endlink. The names of the type codes all begin with the
characters C<SBML_>. @endif@if csharp LibSBML attaches an identifying
code to every kind of SBML object. These are known as <em>SBML type
codes</em>. In the C# language interface for libSBML, the type codes
are defined as static integer constants in the interface class @link
libsbmlcs.libsbml@endlink. The names of the type codes all begin with
the characters C<SBML_>. @endif
@return the SBML type code for the objects contained in this ListOf
instance, or @link SBMLTypeCode_t#SBML_UNKNOWN SBML_UNKNOWN@endlink (default).
=item ListOfDrawables::isValidTypeForList
=item ListOfDrawables::createObject
@internal
@return the SBML object corresponding to next XMLToken in the
XMLInputStream or NULL if the token was not recognized.
=item RenderGroup::readAttributes
@internal
Subclasses should override this method to read values from the given
XMLAttributes set into their specific fields. Be sure to call your
parents implementation of this method as well.
=item RenderGroup::addExpectedAttributes
@internal
Subclasses should override this method to get the list of
expected attributes.
This function is invoked from corresponding readAttributes()
function.
=item RenderGroup::RenderGroup
Creates a new RenderGroup object with the given SBML level
and SBML version.
@param level SBML level of the new object
@param level SBML version of the new object
=item RenderGroup::RenderGroup
Creates a new RenderGroup object with the given SBMLNamespaces.
@param sbmlns The SBML namespace for the object.
=item RenderGroup::RenderGroup
Creates a new RenderGroup object from the given XMLNode object.
The XMLNode object has to contain a valid XML representation of a
RenderGroup object as defined in the render extension specification.
This method is normally called when render information is read from a file and
should normally not have to be called explicitely.
@param node the XMLNode object reference that describes the RenderGroup
object to be instantiated.
=item RenderGroup::RenderGroup
Instantiates a new RenderGroup object.
All attributes are set as described for the default constructor
of GraphicalPrimitive2D.
All the font rendering attributes and the curve decorations
are unset. The id is set to the given string.
@param id the id for the RenderGroup object.
This constructor is deprecated. The new libsbml API only has
constructors which take the SBML level and version or one that takes
an SBMLNamespaces object.
=item RenderGroup::setFontFamily
Sets the font family.
@param family The name of the font family, e.g. Helvetica
=item RenderGroup::setFontSize
Sets the font size.
Normally this is an absolute value, e.g. 18 for a 18pt font.
It is however allowed the specify the font size in terms of relative values
in relation to the current viewport. In most cases the viewport will be the
dimensions of a bounding box of a layout object.
@param size the new font size.
=item RenderGroup::setFontWeight
Sets the font weight.
Valid values are Text::WEIGHT_UNSET, Text::WEIGHT_NORMAL or
Text::WEIGHT_BOLD.
@param weight The new text weight to be set.
=item RenderGroup::setFontStyle
Sets the font style.
Valid values are Text::STYLE_UNSET, Text::STYLE_NORMAL or
Text::STYLE_ITALIC
@param style The new font style to be set.
=item RenderGroup::setTextAnchor
Sets the text anchor.
This is defines the horizontal text position.
Valid values are Text::ANCHOR_UNSET, Text::ANCHOR_START,
Text::ANCHOR_MIDDLE and Text_ANCHOR_END.
Text::ANCHOR_BASELINE is not a valid value
for the text-anchor attribute. If you set the text anchor to
Text::ANCHOR_BASELINE, it will be set to Text::ANCHOR_UNSET.
@param anchor The new horizontal alignment flag.
=item RenderGroup::setVTextAnchor
Sets the vertical text anchor.
This is defines the vertical text position.
Valid values are Text::ANCHOR_UNSET, Text::ANCHOR_TOP,
Text::ANCHOR_MIDDLE and Text_ANCHOR_BOTTOM.
@param anchor The new vertical alignment flag.
=item RenderGroup::setStartHead
Sets the id of the start head.
@param The id of a LineEnding object to be applied to the start of curve children.
=item RenderGroup::setEndHead
Sets the id of the end head.
@param The id of a LineEnding object to be applied to the end of curve children.
=item RenderGroup::getFontFamily
Returns the font family.
@return The name of the font family to be used for text rendering.
=item RenderGroup::getFontSize
Returns the font size as a reference.
@return A reference to the size to be used for rendering text.
=item RenderGroup::getFontSize
Returns the font size as a const reference.
@return A const reference to the size to be used for rendering text.
=item RenderGroup::getFontWeight
Returns the font weight.
@return font weight used to render text children
=item RenderGroup::getFontStyle
Returns the font style.
@return font style used to render text children
=item RenderGroup::getTextAnchor
Returns the text anchor.
@return the horizontal text alignment flag
=item RenderGroup::getVTextAnchor
Returns the vertical text anchor.
@return the vertical text alignment flag
=item RenderGroup::getStartHead
Returns the id of the LineEnding object to be applied to the start of the curve.
@return id of the LineEnding for the start of curves.
=item RenderGroup::getEndHead
Returns the id of the LineEnding object to be applied to the end of the curve.
@return id of the LineEnding for the end of curves.
=item RenderGroup::getNumElements
Returns the number of children in the group.
@return The number of child elements in the group.
=item RenderGroup::getListOfElements
Returns a const pointer to the list of elements.
@return const pointer to the list of children
=item RenderGroup::getListOfElements
Returns the list of elements.
@return pointer to the list of children
=item RenderGroup::getElement
Returns pointer to the element with index n.
If there is no such element, C<NULL> is returned.
@param index index of element to be returned
@return pointer to element with index index or NULL if
index is out of bounds.
=item RenderGroup::getElement
Returns const pointer to the element with index n.
If there is no such element, C<NULL> is returned.
@param index index of element to be returned
@return pointer to element with index index or NULL if
index is out of bounds.
=item RenderGroup::getElement
Returns pointer to the element with the given C<id>.
If there is no such element, C<NULL> is returned.
Since the id on all those object is optional, this routine
might not be as helpful as similar routines in other classes.
@param id id of element to be returned
@return pointer to element with id or NULL if
there is no object with that id
=item RenderGroup::getElement
Returns const pointer to the element with given index.
If there is no such element, C<NULL> is returned.
Since the id on all those object is optional, this routine
might not be as helpful as similar routines in other classes.
@param id id of element to be returned
@return pointer to element with the given C<id> or C<NULL> if
there is no object with that id
=item RenderGroup::getAllElements
Returns a List of all child SBase objects, including those nested to an
arbitrary depth
@return a List of pointers to all children objects.
=item RenderGroup::accept
Accepts the given SBMLVisitor for this instance of RenderGroup.
@param v the SBMLVisitor instance to be used.
@return the result of calling C<v.visit()>.
=item RenderGroup::isSetTextAnchor
Returns true if the horizonal alignment attribute has been set.
@return true is flag is not Text::ANCHOR_UNSET
=item RenderGroup::isSetVTextAnchor
Returns true if the vertical alignment attribute has been set.
@return true is flag is not Text::ANCHOR_UNSET
=item RenderGroup::clone
Creates and returns a deep copy of this RenderGroup object.
@return a (deep) copy of this RenderGroup object
=item RenderGroup::getElementName
Returns the XML element name of this object, which for
RenderGroup, is always C<"g">.
@return the name of this element, i.e., C<"g">.
=item RenderGroup::createImage
Creates an image object and adds it to the end of the list of child
elements. The new element is owned by the group.
@return pointer to the new Image child.
=item RenderGroup::createGroup
Creates an group object and adds it to the end of the list of child
elements The new element is owned by the group..
@return pointer to the new RenderGroup child.
=item RenderGroup::createRectangle
Creates a rectangle object and adds it to the end of the list of child
elements The new element is owned by the group..
@return pointer to the new Rectangle child.
=item RenderGroup::createEllipse
Creates an ellipse object and adds it to the end of the list of child
elements The new element is owned by the group..
@return pointer to the new Ellipse child.
=item RenderGroup::createCurve
Creates a curve object and adds it to the end of the list of child
elements The new element is owned by the group..
@return pointer to the new RenderCurve child.
=item RenderGroup::createPolygon
Creates a polygon object and adds it to the end of the list of child
elements The new element is owned by the group..
@return pointer to the new Polygon child.
=item RenderGroup::createText
Creates a text object and adds it to the end of the list of child
elements The new element is owned by the group..
@return pointer to the new Text child.
=item RenderGroup::addChildElement
Adds a copy of the given element to the end of the list of children elements.
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif The possible values
returned by this function are:
@li LIBSBML_OPERATION_SUCCESS
@li LIBSBML_LEVEL_MISMATCH
@li LIBSBML_VERSION_MISMATCH
@li LIBSBML_OPERATION_FAILED
@note This method should be used with some caution. The fact that
this method I<copies> the object passed to it means that the caller
will be left holding a physically different object instance than the
one contained in this RenderGroup. Changes made to the original object
instance (such as resetting attribute values) will <em>not affect the
instance in the RenderGroup</em>. In addition, the caller should make
sure to free the original object if it is no longer being used, or
else a memory leak will result. Please see RenderGroup::createXXX()
for methods that do not lead to these issues.
@see createEllipse()
@see createRectangle()
@see createPolygon()
@see createText()
@see createCurve()
@see createRenderGroup()
@see createImage()
=item RenderGroup::isSetStartHead
Returns true if the start head is set or false otherwise.
The start decoration is considered set if the string is not empty and if
it is not the string "none"
@return true is the start decoration id is set
=item RenderGroup::isSetEndHead
Returns true if the end head is set or false otherwise.
The end decoration is considered set if the string is not empty and if
it is not the string "none"
@return true is the end decoration id is set
=item RenderGroup::isSetFontFamily
Returns true if the font family has been set or false otherwise.
@return true if the font family string is not empty
=item RenderGroup::isSetFontSize
Returns true if the font size has been set or false otherwise.
@return true if the RelAbsVector specifying the font size does not
contain NaN either as the absolute or the relative value.
=item RenderGroup::isSetFontWeight
Returns true if the font weight has been set or false otherwise.
@return true is the flag is not Text::WEIGHT_UNSET
=item RenderGroup::isSetFontStyle
Returns true if the font style has been set or false otherwise.
@return true is the flag is not Text::STYLE_UNSET
=item RenderGroup::toXML
Creates an XMLNode object from this RenderGroup object.
@return the XMLNode with the XML representation for the
RenderGroup object.
=item RenderGroup::setSBMLDocument
@internal
Sets the parent SBMLDocument of this SBML object.
@param d the SBMLDocument object to use
=item RenderGroup::connectToChild
@internal
Sets this SBML object to child SBML objects (if any).
(Creates a child-parent relationship by the parent)
Subclasses must override this function if they define
one ore more child elements.
Basically, this function needs to be called in
constructor, copy constructor, assignment operator.
@see setSBMLDocument
@see enablePackageInternal
=item RenderGroup::enablePackageInternal
@internal
Enables/Disables the given package with this element and child
elements (if any).
(This is an internal implementation for enablePakcage function)
@note Subclasses in which one or more child elements are defined
must override this function.
=item RenderGroup::setParentSBMLObject
Sets the parent SBML object of this SBML object.
@param sb the SBML object to use
=item RenderGroup::getTypeCode
Returns the libSBML type code for this SBML object.
@if clike LibSBML attaches an identifying code to every
kind of SBML object. These are known as <em>SBML type codes</em>.
The set of possible type codes is defined in the enumeration
#SBMLTypeCode_t. The names of the type codes all begin with the
characters C<SBML_>. @endif@if java LibSBML attaches an
identifying code to every kind of SBML object. These are known as
<em>SBML type codes</em>. In other languages, the set of type codes
is stored in an enumeration; in the Java language interface for
libSBML, the type codes are defined as static integer constants in
interface class {@link libsbmlConstants}. The names of the type codes
all begin with the characters C<SBML_>. @endif
@return the SBML type code for this object, or C<SBML_UNKNOWN> (default).
@see getElementName()
=item RenderGroup::importOldCurve
@internal
Imports curves that follow the older curve specification from an XMLNode object.
=item RenderGroup::addTextAttributes
@internal
Adds the text rendering attributes of the given RenderGroup object
to the given XMLAttributes object.
=item RenderGroup::writeAttributes
@internal
Subclasses should override this method to write their XML attributes
to the XMLOutputStream. Be sure to call your parents implementation
of this method as well. For example:
SBase::writeAttributes(stream);
stream.writeAttribute( "id" , mId );
stream.writeAttribute( "name", mName );
...
=item RenderGroup::createObject
@internal
@return the SBML object corresponding to next XMLToken in the
XMLInputStream or NULL if the token was not recognized.
=item RenderGroup::writeElements
@internal
Subclasses should override this method to write out their contained
SBML objects as XML elements. Be sure to call your parents
implementation of this method as well. For example:
SBase::writeElements(stream);
mReactants.write(stream);
mProducts.write(stream);
...
=back
=head2 LinearGradient
Representation of a linear gradient object from the SBML render extension.
The concept of a linear gradient is more or or less taken from SVG.
A linear gradient is defined by a vector which determines the direction and the length
of the gradient. So for a valid gradient this vector should have a length different from 0.
Otherwise all restrictions for the GradientBase class apply. (@see GradientBase)
The vector for a linear gradient is defined by a start and an endpoint and each point consists
of three absolute-relative value pairs (@see RelAbsVector)
For examples of LinearGradients see the render extension specification and/or
the SVG specification.
=over
=item LinearGradient::LinearGradient
Creates a new LinearGradient object with the given SBML level
and SBML version.
@param level SBML level of the new object
@param level SBML version of the new object
=item LinearGradient::LinearGradient
Creates a new LinearGradient object with the given SBMLNamespaces.
@param sbmlns The SBML namespace for the object.
=item LinearGradient::LinearGradient
Creates a new LinearGradient object from the given XMLNode object.
The XMLNode object has to contain a valid XML representation of a
LinearGradient object as defined in the render extension specification.
This method is normally called when render information is read from a file and
should normally not have to be called explicitely.
@param node the XMLNode object reference that describes the LinearGradient
object to be instantiated.
=item LinearGradient::LinearGradient
Constructor which creates a LinearGradient with no gradient stops.
The id is set to the given value.
The LinearGradient object is invalid until it has an id and at least two
gradient stops.
The start and the end of the linear gradient vector are set to (0,0,0).
A linear gradient with a vector of length zero should also be considered invalid.
@param id the new id for the LinearGradient.
This constructor is deprecated. The new libsbml API only has
constructors which take the SBML level and version or one that takes
an SBMLNamespaces object.
=item LinearGradient::setCoordinates
Sets the 3D coordinates for the start and the end point of the linear gradient vector.
Each value can be a combination of absolute and relative value and is represented by
a RelAbsVector object.
@param x1 x value of the start point of the linear gradient vector
@param y1 y value of the start point of the linear gradient vector
@param z1 z value of the start point of the linear gradient vector
@param x2 x value of the end point of the linear gradient vector
@param y2 y value of the end point of the linear gradient vector
@param z2 z value of the end point of the linear gradient vector
=item LinearGradient::setCoordinates
Sets the 2D coordinates for the start and the end point of the linear gradient vector.
The z values are automatically set to 0.
Each value can be a combination of absolute and relative value and is represented by
a RelAbsVector object.
@param x1 x value of the start point of the linear gradient vector
@param y1 y value of the start point of the linear gradient vector
@param x2 x value of the end point of the linear gradient vector
@param y2 y value of the end point of the linear gradient vector
=item LinearGradient::setPoint1
Sets the coordinates for the start point of the linear gradient vector.
Each value can be a combination of absolute and relative value and is represented by
a RelAbsVector object.
The z value can be omitted. In that case it is set to 0.
@param x x value of the start point of the linear gradient vector
@param y y value of the start point of the linear gradient vector
@param z z value of the start point of the linear gradient vector
=item LinearGradient::setPoint2
Sets the coordinates for the end point of the linear gradient vector.
Each value can be a combination of absolute and relative value and is represented by
a RelAbsVector object.
The z value can be omitted. In that case it is set to 0.
@param x x value of the end point of the linear gradient vector
@param y y value of the end point of the linear gradient vector
@param z z value of the end point of the linear gradient vector
=item LinearGradient::getXPoint1
Returns the x coordinate for the start point as a const reference.
@return RelAbsVector that represents the x value of the start point.
=item LinearGradient::getYPoint1
Returns the y coordinate for the start point as a const reference.
@return RelAbsVector that represents the y value of the start point.
=item LinearGradient::getZPoint1
Returns the z coordinate for the start point as a const reference.
@return RelAbsVector that represents the z value of the start point.
=item LinearGradient::getXPoint2
Returns the x coordinate for the end point as a const reference.
@return RelAbsVector that represents the x value of the start point.
=item LinearGradient::getYPoint2
Returns the y coordinate for the end point as a const reference.
@return RelAbsVector that represents the y value of the start point.
=item LinearGradient::getZPoint2
Returns the z coordinate for the end point as a const reference.
@return RelAbsVector that represents the z value of the start point.
=item LinearGradient::getXPoint1
Returns the x coordinate for the start point as a reference.
@return RelAbsVector that represents the x value of the start point.
=item LinearGradient::getYPoint1
Returns the y coordinate for the start point as a reference.
@return RelAbsVector that represents the y value of the start point.
=item LinearGradient::getZPoint1
Returns the z coordinate for the start point as a reference.
@return RelAbsVector that represents the z value of the start point.
=item LinearGradient::getXPoint2
Returns the x coordinate for the end point as a reference.
@return RelAbsVector that represents the x value of the start point.
=item LinearGradient::getYPoint2
Returns the y coordinate for the end point as a reference.
@return RelAbsVector that represents the y value of the start point.
=item LinearGradient::getZPoint2
Returns the z coordinate for the end point as a reference.
@return RelAbsVector that represents the z value of the start point.
=item LinearGradient::accept
Accepts the given SBMLVisitor for this instance of LinearGradient.
@param v the SBMLVisitor instance to be used.
@return the result of calling C<v.visit()>.
=item LinearGradient::clone
Creates and returns a deep copy of this LinearGradient object.
@return a (deep) copy of this LinearGradient object
=item LinearGradient::getElementName
Returns the XML element name of this object.
This is overridden by subclasses to return a string appropriate to the
SBML component. For example, Model defines it as returning "model",
CompartmentType defines it as returning "compartmentType", etc.
=item LinearGradient::getTypeCode
Returns the libSBML type code for this SBML object.
@if clike LibSBML attaches an identifying code to every
kind of SBML object. These are known as <em>SBML type codes</em>.
The set of possible type codes is defined in the enumeration
#SBMLTypeCode_t. The names of the type codes all begin with the
characters C<SBML_>. @endif@if java LibSBML attaches an
identifying code to every kind of SBML object. These are known as
<em>SBML type codes</em>. In other languages, the set of type codes
is stored in an enumeration; in the Java language interface for
libSBML, the type codes are defined as static integer constants in
interface class {@link libsbmlConstants}. The names of the type codes
all begin with the characters C<SBML_>. @endif
@return the SBML type code for this object, or C<SBML_UNKNOWN> (default).
@see getElementName()
=item LinearGradient::toXML
Creates an XMLNode object from this LinearGradient object.
@return the XMLNode with the XML representation for the
LinearGradient object.
=item LinearGradient::readAttributes
@internal
Subclasses should override this method to read values from the given
XMLAttributes set into their specific fields. Be sure to call your
parents implementation of this method as well.
=item LinearGradient::addExpectedAttributes
@internal
Subclasses should override this method to get the list of
expected attributes.
This function is invoked from corresponding readAttributes()
function.
=item LinearGradient::writeAttributes
@internal
Subclasses should override this method to write their XML attributes
to the XMLOutputStream. Be sure to call your parents implementation
of this method as well. For example:
SBase::writeAttributes(stream);
stream.writeAttribute( "id" , mId );
stream.writeAttribute( "name", mName );
...
=back
=head2 LineEnding
a LineEnding is a decoration element for the start and/or end
of curves in the SBML render extension, e.g. arrow heads
LineEndings in the SBML render extension are used to apply certain decorations
to the end of curves. Since many curves in layout diagrams use the same decoration
for the beginnings and start of a line, it would be highly redundant to encode
those decorations with each line. Therefor LineEnding objects can be defined which are
then applied to the beginning or the ends of several curve objects.
A LineEnding contains an id by which it can be referenced from curve styles, it contains
a visual representation of the decoration in the form of a render extension Group object
and it has some attributes that define the viewport and how the LineEnding is to be applied
to a curve.
A LineEnding object is only valid if it has an id, a viewport that has an area which is not 0
and a valid group object.
=over
=back
=head2 ListOfLineEndings
container class to store LineEnding objects
Each RenderInformation object can contain its own ListOfLineEndings object.
=over
=item LineEnding::LineEnding
Creates a new LineEnding object with the given SBML level
and SBML version.
@param level SBML level of the new object
@param level SBML version of the new object
=item LineEnding::LineEnding
Creates a new LineEnding object with the given SBMLNamespaces.
@param sbmlns The SBML namespace for the object.
=item LineEnding::LineEnding
Creates a new LineEnding object from the given XMLNode object.
The XMLNode object has to contain a valid XML representation of a
LineEnding object as defined in the render extension specification.
This method is normally called when render information is read from a file and
should normally not have to be called explicitely.
@param node the XMLNode object reference that describes the LineEnding
object to be instantiated.
=item LineEnding::LineEnding
Copy constructor.
=item LineEnding::LineEnding
Constructor which creates a LineEnding with an empty group object,
and a viewport with a size of 0.
The id is set to the given value.
In order to get a valid object, the group object has to be valid,
the group object has to have descendants other than groups and
the viewport has to have a positive size.
@param id The id for the LineEnding.
This constructor is deprecated. The new libsbml API only has
constructors which take the SBML level and version or one that takes
an SBMLNamespaces object.
=item LineEnding::setEnableRotationalMapping
Sets whether rotational mapping is to be done or not.
This flag determines whether the LineEnding is rotated
according to the direction of the curve when it is applied.
For details on this, see the render extension specification.
@param enable Boolean flag that specifies whether rotational mapping
for the line ending is to be enabled or not.
=item LineEnding::getIsEnabledRotationalMapping
Returns whether rotational mapping is enabled or not.
@return bool value that specifies if rotational mapping is
enabled for the LineEnding or not.
=item LineEnding::setBoundingBox
Sets the viewport for the LineEnding.
@param box The viewport bounding box for the LineEnding.
=item LineEnding::getBoundingBox
Returns a pointer to the viewport bounding box.
@return pointer to the viewport bounding box.
=item LineEnding::getBoundingBox
Returns a const pointer to the viewport bounding box.
@return const pointer to the viewport bounding box.
=item LineEnding::setGroup
Sets the group of the LineEnding to a copy of the given group.
@param group const pointer to the group to be set for the bounding box.
The group object is copied.
=item LineEnding::getGroup
Returns a const pointer to the group object.
@return const pointer to the group object
=item LineEnding::getGroup
Returns a pointer to the group object.
@return pointer to the group object
=item LineEnding::getAllElements
Returns a List of all child SBase objects, including those nested to an
arbitrary depth
@return a List of pointers to all children objects.
=item LineEnding::accept
Accepts the given SBMLVisitor for this instance of LineEnding.
@param v the SBMLVisitor instance to be used.
@return the result of calling C<v.visit()>.
=item LineEnding::clone
Creates and returns a deep copy of this LineEnding object.
@return a (deep) copy of this LineEnding object
=item LineEnding::getElementName
Returns the XML element name of this object.
This is overridden by subclasses to return a string appropriate to the
SBML component. For example, Model defines it as returning "model",
CompartmentType defines it as returning "compartmentType", etc.
=item LineEnding::toXML
Creates an XMLNode object from this LineEnding object.
@return the XMLNode with the XML representation for the
LineEnding object.
=item LineEnding::setSBMLDocument
@internal
Sets the parent SBMLDocument of this SBML object.
@param d the SBMLDocument object to use
=item LineEnding::connectToChild
@internal
Sets this SBML object to child SBML objects (if any).
(Creates a child-parent relationship by the parent)
Subclasses must override this function if they define
one ore more child elements.
Basically, this function needs to be called in
constructor, copy constructor, assignment operator.
@see setSBMLDocument
@see enablePackageInternal
=item LineEnding::enablePackageInternal
@internal
Enables/Disables the given package with this element and child
elements (if any).
(This is an internal implementation for enablePakcage function)
@note Subclasses in which one or more child elements are defined
must override this function.
=item LineEnding::getTypeCode
Returns the libSBML type code for this SBML object.
@if clike LibSBML attaches an identifying code to every
kind of SBML object. These are known as <em>SBML type codes</em>.
The set of possible type codes is defined in the enumeration
#SBMLTypeCode_t. The names of the type codes all begin with the
characters C<SBML_>. @endif@if java LibSBML attaches an
identifying code to every kind of SBML object. These are known as
<em>SBML type codes</em>. In other languages, the set of type codes
is stored in an enumeration; in the Java language interface for
libSBML, the type codes are defined as static integer constants in
interface class {@link libsbmlConstants}. The names of the type codes
all begin with the characters C<SBML_>. @endif
@return the SBML type code for this object, or C<SBML_UNKNOWN> (default).
@see getElementName()
=item LineEnding::getId
Returns the value of the "id" attribute of this GraphicalPrimitive.
@return the id of the GraphicalPrimitive
=item LineEnding::isSetId
Predicate returning C<true> or C<false> depending on whether this
GraphicalPrimitive's "id" attribute has been set.
@return returns true or false depending on whether the id on the
GraphicalPrimitive has been set.
=item LineEnding::setId
Sets the value of the "id" attribute of this GraphicalPrimitive.
@param id the new id for the GraphicalPrimitive
@return status if the operation succeeded
=item LineEnding::unsetId
Unsets the value of the "id" attribute of this GraphicalPrimitive.
=item LineEnding::setParentSBMLObject
Sets the parent SBML object of this SBML object.
@param sb the SBML object to use
=item LineEnding::hasRequiredAttributes
@internal
=item LineEnding::hasRequiredElements
@internal
=item LineEnding::readAttributes
@internal
When reading SBML render extension, this method takes care of
getting the attributes to the LineEnding object.
@param const reference to XMLAttributes object which contains
the attributes to be set on the LineEnding.
=item LineEnding::addExpectedAttributes
@internal
Subclasses should override this method to get the list of
expected attributes.
This function is invoked from corresponding readAttributes()
function.
=item LineEnding::createObject
@internal
@return the SBML object corresponding to next XMLToken in the
XMLInputStream or NULL if the token was not recognized.
=item LineEnding::writeAttributes
@internal
Subclasses should override this method to write their XML attributes
to the XMLOutputStream. Be sure to call your parents implementation
of this method as well. For example:
SBase::writeAttributes(stream);
stream.writeAttribute( "id" , mId );
stream.writeAttribute( "name", mName );
...
=item LineEnding::writeElements
@internal
Subclasses should override this method to write out their contained
SBML objects as XML elements. Be sure to call your parents
implementation of this method as well. For example:
SBase::writeElements(stream);
mReactants.write(stream);
mProducts.write(stream);
...
=item LineEnding::writeXMLNS
@internal
Subclasses should override this method to write their xmlns attriubutes
(if any) to the XMLOutputStream.
=item ListOfLineEndings::clone
Creates and returns a deep copy of the ListOfLineEndings object.
@return a (deep) copy of this ListOfLineEndings
=item ListOfLineEndings::ListOfLineEndings
Creates a new ListOfLineEndings object from the given XMLNode object.
The XMLNode object has to contain a valid XML representation of a
ListOfLineEndings object as defined in the render extension specification.
This method is normally called when render information is read from a file and
should normally not have to be called explicitely.
@param node the XMLNode object reference that describes the ListOfLineEndings
object to be instantiated.
=item ListOfLineEndings::ListOfLineEndings
Constructor which instantiates an empty ListOfLineEndings object.
=item ListOfLineEndings::ListOfLineEndings
Ctor.
=item ListOfLineEndings::ListOfLineEndings
Copy constructor. Creates a copy of this ListOfLineEndings object.
=item ListOfLineEndings::getElementName
Returns the XML element name of this object, which for
ListOfLineEndings, is always C<"listOfLineEndings">.
@return the name of this element, i.e., C<"listOfLineEndings">.
=item ListOfLineEndings::toXML
Creates an XMLNode object from this ListOfLineEndings object.
@return the XMLNode with the XML representation for the
ListOfLineEndings object.
=item ListOfLineEndings::get
Returns a pointer to the LineEnding with the given index or NULL if
the index is invalid.
@param i index of the LineEnding object to be returned
@return pointer to the LineEnding at the given index or NULL.
=item ListOfLineEndings::get
Returns a const pointer to the LineEnding with the given index or NULL if
the index is invalid.
@param i index of the LineEnding object to be returned
@return const pointer to the LineEnding at the given index or NULL.
=item ListOfLineEndings::get
Returns a pointer to the LineEnding with the given C<id> or C<NULL> if
the id is invalid.
@param id id of the LineEnding object to be returned
@return pointer to the LineEnding at the given C<id> or C<NULL>.
=item ListOfLineEndings::get
Returns a const pointer to the LineEnding with the given C<id> or C<NULL> if
the id is invalid.
@param id id of the LineEnding object to be returned
@return const pointer to the LineEnding at the given C<id> or C<NULL>.
=item ListOfLineEndings::remove
Removes the nth item from this ListOfLineEndings items and returns a pointer to
it.
The caller owns the returned item and is responsible for deleting it.
@param n the index of the item to remove
@see size()
=item ListOfLineEndings::remove
Removes item in this ListOfLineEndings items with the given identifier.
The caller owns the returned item and is responsible for deleting it.
If none of the items in this list have the identifier C<sid>, then C<
>
NULL is returned.
@param sid the identifier of the item to remove
@return the item removed. As mentioned above, the caller owns the
returned item.
=item ListOfLineEndings::getItemTypeCode
Get the type code of the objects contained in this ListOf.
@if clike LibSBML attaches an identifying code to every kind of SBML
object. These are known as <em>SBML type codes</em>. The set of
possible type codes is defined in the enumeration #SBMLTypeCode_t.
The names of the type codes all begin with the characters C<
>
SBML_. @endif@if java LibSBML attaches an identifying code to every
kind of SBML object. These are known as <em>SBML type codes</em>. In
other languages, the set of type codes is stored in an enumeration; in
the Java language interface for libSBML, the type codes are defined as
static integer constants in the interface class {@link
libsbmlConstants}. The names of the type codes all begin with the
characters C<SBML_>. @endif@if python LibSBML attaches an identifying
code to every kind of SBML object. These are known as <em>SBML type
codes</em>. In the Python language interface for libSBML, the type
codes are defined as static integer constants in the interface class
@link libsbml@endlink. The names of the type codes all begin with the
characters C<SBML_>. @endif@if csharp LibSBML attaches an identifying
code to every kind of SBML object. These are known as <em>SBML type
codes</em>. In the C# language interface for libSBML, the type codes
are defined as static integer constants in the interface class @link
libsbmlcs.libsbml@endlink. The names of the type codes all begin with
the characters C<SBML_>. @endif
@return the SBML type code for the objects contained in this ListOf
instance, or @link SBMLTypeCode_t#SBML_UNKNOWN SBML_UNKNOWN@endlink (default).
=item ListOfLineEndings::createObject
@internal
@return the SBML object corresponding to next XMLToken in the
XMLInputStream or NULL if the token was not recognized.
=back
=head2 ListOfCurveElements
A container to store curve elements (RenderPoint and RenderCubicBezier). Use in RenderCurve and Polygon
The ListOfCurveElements is a container class to store the curve elements of RenderCurve
objects and Polygon objects.
=over
=item ListOfCurveElements::ListOfCurveElements
Creates a new ListOfCurveElements object from the given XMLNode object.
The XMLNode object has to contain a valid XML representation of a
ListOfCurveElements object as defined in the render extension specification.
This method is normally called when render information is read from a file and
should normally not have to be called explicitely.
@param node the XMLNode object reference that describes the ListOfCurveElements
object to be instantiated.
=item ListOfCurveElements::clone
Creates and returns a deep copy of the ListOfCurveElements object.
@return a (deep) copy of this ListOfCurveElements
=item ListOfCurveElements::ListOfCurveElements
Constructor which instantiates an empty ListOfCurveElements object.
=item ListOfCurveElements::ListOfCurveElements
Ctor.
=item ListOfCurveElements::ListOfCurveElements
Copy constructor for ListOfCurveElements objects.
=item ListOfCurveElements::get
Returns a pointer to the RenderPoint with the given index or NULL if
the index is invalid.
@param i index of the RenderPoint object to be returned
@return pointer to the RenderPoint at the given index or NULL.
=item ListOfCurveElements::get
Returns a const pointer to the RenderPoint with the given index or NULL if
the index is invalid.
@param i index of the RenderPoint object to be returned
@return const pointer to the RenderPoint at the given index or NULL.
=item ListOfCurveElements::remove
Removes the RenderPoint with the given index and returns a pointer to the
removed object. The caller is responsible for freeing the associated memory.
@param i index of the RenderPoint object to be removed
@return pointer to the removed RenderPoint or NULL if the index
was not valid.
=item ListOfCurveElements::getElementName
Returns the XML element name of this object, which for
ListOfCurveElements, is always C<"listOfCurveElements">.
@return the name of this element, i.e., C<"listOfCurveElements">.
=item ListOfCurveElements::toXML
Creates an XMLNode object from this ListOfCurveElements object.
@return the XMLNode with the XML representation for the
ListOfCurveElements object.
=item ListOfCurveElements::getItemTypeCode
Get the type code of the objects contained in this ListOf.
@if clike LibSBML attaches an identifying code to every kind of SBML
object. These are known as <em>SBML type codes</em>. The set of
possible type codes is defined in the enumeration #SBMLTypeCode_t.
The names of the type codes all begin with the characters C<
>
SBML_. @endif@if java LibSBML attaches an identifying code to every
kind of SBML object. These are known as <em>SBML type codes</em>. In
other languages, the set of type codes is stored in an enumeration; in
the Java language interface for libSBML, the type codes are defined as
static integer constants in the interface class {@link
libsbmlConstants}. The names of the type codes all begin with the
characters C<SBML_>. @endif@if python LibSBML attaches an identifying
code to every kind of SBML object. These are known as <em>SBML type
codes</em>. In the Python language interface for libSBML, the type
codes are defined as static integer constants in the interface class
@link libsbml@endlink. The names of the type codes all begin with the
characters C<SBML_>. @endif@if csharp LibSBML attaches an identifying
code to every kind of SBML object. These are known as <em>SBML type
codes</em>. In the C# language interface for libSBML, the type codes
are defined as static integer constants in the interface class @link
libsbmlcs.libsbml@endlink. The names of the type codes all begin with
the characters C<SBML_>. @endif
@return the SBML type code for the objects contained in this ListOf
instance, or @link SBMLTypeCode_t#SBML_UNKNOWN SBML_UNKNOWN@endlink (default).
=item ListOfCurveElements::isValidTypeForList
=item ListOfCurveElements::createObject
@internal
@return the SBML object corresponding to next XMLToken in the
XMLInputStream or NULL if the token was not recognized.
=back
=head2 LocalRenderInformation
LocalRenderInformation is the render information stored in Layouts.
LocalRenderInformation can be applied to all layouts.
LocalRenderInformation is one of the subclasses of RenderInformationBase. A local render information object
contains color definitions, gradient definitions and line endings as defined in RenderInformationBase.
Additionally it has a list of local styles which specifies type, role and id based render information.
Local render information can specify id based render information because it does belong to a certain layout and it can reference ids of object in that layout.
=over
=back
=head2 ListOfLocalRenderInformation
container class that stores LocalRenderInformation objects.
Layouts can contain ListOfLocalRenderInformation which holds all
LocalRenderInformation objects for a certain layout.
=over
=item LocalRenderInformation::LocalRenderInformation
Creates a new LocalRenderInformation object with the given SBML level
and SBML version.
@param level SBML level of the new object
@param level SBML version of the new object
=item LocalRenderInformation::LocalRenderInformation
Creates a new LocalRenderInformation object with the given SBMLNamespaces.
@param sbmlns The SBML namespace for the object.
=item LocalRenderInformation::parseXML
Parses the xml information in the given node and sets the attributes.
This method should never be called by the user. It is only used to read render
information from annotations.
@param node the XMLNode object reference that describes the LocalRenderInformation
object to be instantiated.
=item LocalRenderInformation::LocalRenderInformation
Constructor which creates a LocalRenderInformation with the given C<id
>
and all lists empty.
@param id the new id for the LocalRenderInformation.
This constructor is deprecated. The new libsbml API only has
constructors which take the SBML level and version or one that takes
an SBMLNamespaces object.
=item LocalRenderInformation::getNumStyles
Returns the number of styles.
@return the number of local styles in the global render information object
=item LocalRenderInformation::clone
Creates and returns a deep copy of this LocalRenderInformation object.
@return a (deep) copy of this LocalRenderInformation.
=item LocalRenderInformation::getAllElements
Returns a List of all child SBase objects, including those nested to an
arbitrary depth
@return a List of pointers to all children objects.
=item LocalRenderInformation::accept
Accepts the given SBMLVisitor.
@return the result of calling C<v.visit()>, which indicates
whether or not the Visitor would like to visit the SBML object's next
sibling object (if available).
=item LocalRenderInformation::getListOfStyles
Returns a pointer to the ListOfLocalStyles object.
@return pointer to the list of local styles.
=item LocalRenderInformation::getListOfStyles
Returns a const pointer to the ListOfLocalStyles object.
@return const pointer to the list of local styles.
=item LocalRenderInformation::getStyle
Returns a pointer to the style with the given index.
If the index is invalid, C<NULL> is returned.
@param i index of the LocalStyle to be returned.
@return pointer to the style with the given index or NULL
=item LocalRenderInformation::getStyle
Returns a pointer to the style with the given index.
If the index is invalid, C<NULL> is returned.
@param i index of the LocalStyle to be returned.
@return const pointer to the style with the given index or NULL
=item LocalRenderInformation::getStyle
Returns a pointer to the style with the given C<id>.
If the id is invalid, C<NULL> is returned.
@param id id of the LocalStyle to be returned.
@return pointer to the style with the given C<id> or C<NULL
>
=item LocalRenderInformation::getStyle
Returns a pointer to the style with the given C<id>.
If the id is invalid, C<NULL> is returned.
@param id id of the LocalStyle to be returned.
@return const pointer to the style with the given C<id> or C<NULL
>
=item LocalRenderInformation::createStyle
Creates a new LocalStyle object. The object is added to and owned
by the LocalRenderInformation object.
@param id for the new style.
@ return a pointer to the newly created LocalStyle object.
=item LocalRenderInformation::addStyle
Adds a copy of a LocalStyle to the GlobalRenderInformation object.
The style is only added if it is valid, i.e. it has to have an id and
a valid group.
@param pointer to the local style object to be added.
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif The possible values
returned by this function are:
@li LIBSBML_OPERATION_SUCCESS
@li LIBSBML_LEVEL_MISMATCH
@li LIBSBML_VERSION_MISMATCH
@li LIBSBML_OPERATION_FAILED
@note This method should be used with some caution. The fact that
this method I<copies> the object passed to it means that the caller
will be left holding a physically different object instance than the
one contained in this LocalRenderInformation. Changes made to the original object
instance (such as resetting attribute values) will <em>not affect the
instance in the LocalRenderInformation</em>. In addition, the caller should make
sure to free the original object if it is no longer being used, or
else a memory leak will result. Please see LocalRenderInformation::createStyle()
for a method that does not lead to these issues.
@see createStyle()
=item LocalRenderInformation::toXML
Creates an XMLNode object from this LocalRenderInformation object.
@return the XMLNode with the XML representation for the
LocalRenderInformation object.
=item LocalRenderInformation::getElementName
Returns the XML element name of this object, which for
LocalRenderInformation, is always C<"renderInformation">.
@return the name of this element, i.e., C<"renderInformation">.
=item LocalRenderInformation::getTypeCode
Returns the libSBML type code for this SBML object.
@if clike LibSBML attaches an identifying code to every
kind of SBML object. These are known as <em>SBML type codes</em>.
The set of possible type codes is defined in the enumeration
#SBMLTypeCode_t. The names of the type codes all begin with the
characters C<SBML_>. @endif@if java LibSBML attaches an
identifying code to every kind of SBML object. These are known as
<em>SBML type codes</em>. In other languages, the set of type codes
is stored in an enumeration; in the Java language interface for
libSBML, the type codes are defined as static integer constants in
interface class {@link libsbmlConstants}. The names of the type codes
all begin with the characters C<SBML_>. @endif
@return the SBML type code for this object, or C<SBML_UNKNOWN> (default).
@see getElementName()
=item LocalRenderInformation::setSBMLDocument
@internal
Sets the parent SBMLDocument of this SBML object.
@param d the SBMLDocument object to use
=item LocalRenderInformation::connectToChild
@internal
Sets this SBML object to child SBML objects (if any).
(Creates a child-parent relationship by the parent)
Subclasses must override this function if they define
one ore more child elements.
Basically, this function needs to be called in
constructor, copy constructor, assignment operator.
@see setSBMLDocument
@see enablePackageInternal
=item LocalRenderInformation::enablePackageInternal
@internal
Enables/Disables the given package with this element and child
elements (if any).
(This is an internal implementation for enablePakcage function)
@note Subclasses in which one or more child elements are defined
must override this function.
=item LocalRenderInformation::readAttributes
@internal
Subclasses should override this method to read values from the given
XMLAttributes set into their specific fields. Be sure to call your
parents implementation of this method as well.
=item LocalRenderInformation::addExpectedAttributes
@internal
Subclasses should override this method to get the list of
expected attributes.
This function is invoked from corresponding readAttributes()
function.
=item LocalRenderInformation::createObject
@internal
@return the SBML object corresponding to next XMLToken in the
XMLInputStream or NULL if the token was not recognized.
=item LocalRenderInformation::writeAttributes
@internal
Subclasses should override this method to write their XML attributes
to the XMLOutputStream. Be sure to call your parents implementation
of this method as well. For example:
SBase::writeAttributes(stream);
stream.writeAttribute( "id" , mId );
stream.writeAttribute( "name", mName );
...
=item LocalRenderInformation::writeElements
@internal
Subclasses should override this method to write out their contained
SBML objects as XML elements. Be sure to call your parents
implementation of this method as well. For example:
SBase::writeElements(stream);
mReactants.write(stream);
mProducts.write(stream);
...
=item ListOfLocalRenderInformation::clone
Creates and returns a deep copy of the ListOfLocalRenderInformation object.
@return a (deep) copy of this ListOfLocalRenderInformation
=item ListOfLocalRenderInformation::ListOfLocalRenderInformation
Constructor which instantiates an empty ListOfLocalRenderInformation object.
=item ListOfLocalRenderInformation::ListOfLocalRenderInformation
Ctor.
=item ListOfLocalRenderInformation::ListOfLocalRenderInformation
Copy constructor for ListOfLocalRenderInformation objects.
=item ListOfLocalRenderInformation::getElementName
Returns the XML element name of this object, which for
ListOfLocalRenderInformation, is always C<"listOfRenderInformation">.
@return the name of this element, i.e., C<"listOfRenderInformation">.
=item ListOfLocalRenderInformation::toXML
Creates an XMLNode object from this ListOfGradientDefinitions object.
@return the XMLNode with the XML representation for the
ListOfGradientDefinitions object.
=item ListOfLocalRenderInformation::setVersion
Sets the version of the render information list.
The version consists of a major and a minor version number.
@param major major version number
@param minor minor version number
=item ListOfLocalRenderInformation::getMajorVersion
Returns the major version of the render information list.
@return the major version number of the local render information list
=item ListOfLocalRenderInformation::getMinorVersion
Returns the minor version of the render information list.
@return the minor version number of the local render information list
=item ListOfLocalRenderInformation::getVersionString
Returns the version as a string.
@return the version of the LocalRenderInformation object
as a string
=item ListOfLocalRenderInformation::get
Returns a pointer to the LocalRenderInformation with the given index or NULL if
the index is invalid.
@param i index of the LocalRenderInformation object to be returned
@return pointer to the LocalRenderInformation at the given index or NULL.
=item ListOfLocalRenderInformation::get
Returns a const pointer to the LocalRenderInformation with the given index or NULL if
the index is invalid.
@param i index of the LocalRenderInformation object to be returned
@return const pointer to the LocalRenderInformation at the given index or NULL.
=item ListOfLocalRenderInformation::get
Returns a pointer to the LocalRenderInformation with the given C<id> or C<NULL> if
the id is invalid.
@param id id of the LocalRenderInformation object to be returned
@return pointer to the LocalRenderInformation at the given C<id> or C<NULL>.
=item ListOfLocalRenderInformation::get
Returns a const pointer to the LocalRenderInformation with the given C<id> or C<NULL> if
the id is invalid.
@param id id of the LocalRenderInformation object to be returned
@return const pointer to the LocalRenderInformation at the given C<id> or C<NULL>.
=item ListOfLocalRenderInformation::remove
Removes the nth item from this ListOfLocalRenderInformation items and returns a pointer to
it.
The caller owns the returned item and is responsible for deleting it.
@param n the index of the item to remove
@see size()
=item ListOfLocalRenderInformation::remove
Removes item in this ListOfLocalRenderInformation items with the given identifier.
The caller owns the returned item and is responsible for deleting it.
If none of the items in this list have the identifier C<sid>, then C<
>
NULL is returned.
@param sid the identifier of the item to remove
@return the item removed. As mentioned above, the caller owns the
returned item.
=item ListOfLocalRenderInformation::getItemTypeCode
Get the type code of the objects contained in this ListOf.
@if clike LibSBML attaches an identifying code to every kind of SBML
object. These are known as <em>SBML type codes</em>. The set of
possible type codes is defined in the enumeration #SBMLTypeCode_t.
The names of the type codes all begin with the characters C<
>
SBML_. @endif@if java LibSBML attaches an identifying code to every
kind of SBML object. These are known as <em>SBML type codes</em>. In
other languages, the set of type codes is stored in an enumeration; in
the Java language interface for libSBML, the type codes are defined as
static integer constants in the interface class {@link
libsbmlConstants}. The names of the type codes all begin with the
characters C<SBML_>. @endif@if python LibSBML attaches an identifying
code to every kind of SBML object. These are known as <em>SBML type
codes</em>. In the Python language interface for libSBML, the type
codes are defined as static integer constants in the interface class
@link libsbml@endlink. The names of the type codes all begin with the
characters C<SBML_>. @endif@if csharp LibSBML attaches an identifying
code to every kind of SBML object. These are known as <em>SBML type
codes</em>. In the C# language interface for libSBML, the type codes
are defined as static integer constants in the interface class @link
libsbmlcs.libsbml@endlink. The names of the type codes all begin with
the characters C<SBML_>. @endif
@return the SBML type code for the objects contained in this ListOf
instance, or @link SBMLTypeCode_t#SBML_UNKNOWN SBML_UNKNOWN@endlink (default).
=item ListOfLocalRenderInformation::isValidTypeForList
=item ListOfLocalRenderInformation::createObject
@internal
@return the SBML object corresponding to next XMLToken in the
XMLInputStream or NULL if the token was not recognized.
=item ListOfLocalRenderInformation::addExpectedAttributes
@internal
=item ListOfLocalRenderInformation::writeAttributes
@internal
Subclasses should override this method to write their XML attributes
to the XMLOutputStream. Be sure to call your parents implementation
of this method as well. For example:
SBase::writeAttributes(stream);
stream.writeAttribute( "id" , mId );
stream.writeAttribute( "name", mName );
...
=item ListOfLocalRenderInformation::writeXMLNS
@internal
Subclasses should override this method to write their xmlns attriubutes
(if any) to the XMLOutputStream.
=back
=head2 LocalStyle
implementation of the LocalStyle concept of the SBML render extension.
Local styles are the style information objects used in LocalRenderInformation (@see LocalRenderInformation).
Local styles can be associated with layout objects by role and type as well as by
id of layout objects from the layout the local style belongs to.
Since LocalStyle is derived from Styles, it inherits all of the methods and attributes from Style. (@see Style)
=over
=back
=head2 ListOfLocalStyles
ListOfLocalStyles is the container class that stores LocalStyles in LocalRenderInformation objects.
Each LocalRenderInformation object contains a ListOfLocalStyles which contains zero or
more local style objects.
=over
=item LocalStyle::LocalStyle
Creates a new LocalStyle object with the given SBML level
and SBML version.
@param level SBML level of the new object
@param level SBML version of the new object
=item LocalStyle::LocalStyle
Creates a new LocalStyle object with the given SBMLNamespaces.
@param sbmlns The SBML namespace for the object.
=item LocalStyle::LocalStyle
Creates a new LocalStyle object from the given XMLNode object.
The XMLNode object has to contain a valid XML representation of a
LocalStyle object as defined in the render extension specification.
This method is normally called when render information is read from a file and
should normally not have to be called explicitely.
@param node the XMLNode object reference that describes the LocalStyle
object to be instantiated.
=item LocalStyle::LocalStyle
Constructor which creates a LocalStyle with an empty group
and empty id, role and type list.
The group has to be filled before the
object is valid.
This constructor is deprecated. The new libsbml API only has
constructors which take the SBML level and version or one that takes
an SBMLNamespaces object.
=item LocalStyle::getNumIds
Returns the number of ids in the id set.
@return the number of ids in the id set
=item LocalStyle::getIdList
Returns the id list.
@return the reference to the list of ids for the local style.
=item LocalStyle::getIdList
Returns the id list.
@return the const reference to the list of ids for the local style.
=item LocalStyle::setIdList
Sets the id list.
@param idList The list of ids to be set on the local style.
=item LocalStyle::addId
Adds another id to the set.
@param id the id string to be added to the id list.
=item LocalStyle::createIdString
@return the string of all roles
=item LocalStyle::isInIdList
Checks whether a given C<id> is in the id list.
@param id the id to be searched for
@return true or false depending on whether the given C<id> is in the id list or not.
=item LocalStyle::removeId
Removes an id from the set.
@param the id to be removed from the id list.
=item LocalStyle::getTypeCode
Returns the libSBML type code for this SBML object.
@if clike LibSBML attaches an identifying code to every
kind of SBML object. These are known as <em>SBML type codes</em>.
The set of possible type codes is defined in the enumeration
#SBMLTypeCode_t. The names of the type codes all begin with the
characters C<SBML_>. @endif@if java LibSBML attaches an
identifying code to every kind of SBML object. These are known as
<em>SBML type codes</em>. In other languages, the set of type codes
is stored in an enumeration; in the Java language interface for
libSBML, the type codes are defined as static integer constants in
interface class {@link libsbmlConstants}. The names of the type codes
all begin with the characters C<SBML_>. @endif
@return the SBML type code for this object, or C<SBML_UNKNOWN> (default).
@see getElementName()
=item LocalStyle::clone
Creates and returns a deep copy of this LocalStyle object.
@return a (deep) copy of this LocalStyle object
=item LocalStyle::getElementName
Returns the XML element name of this object.
This is overridden by subclasses to return a string appropriate to the
SBML component. For example, Model defines it as returning "model",
CompartmentType defines it as returning "compartmentType", etc.
=item LocalStyle::toXML
Creates an XMLNode object from this LocalStyle object.
@return the XMLNode with the XML representation for the
LocalStyle object.
=item LocalStyle::readAttributes
@internal
Subclasses should override this method to read values from the given
XMLAttributes set into their specific fields. Be sure to call your
parents implementation of this method as well.
=item LocalStyle::addExpectedAttributes
@internal
Subclasses should override this method to get the list of
expected attributes.
This function is invoked from corresponding readAttributes()
function.
=item LocalStyle::addListOfIds
@internal
This method adds the attribute for the list of ids to
the given XMLnode.
@param node the node where the attribute needs to be added
=item LocalStyle::writeAttributes
@internal
Subclasses should override this method to write their XML attributes
to the XMLOutputStream. Be sure to call your parents implementation
of this method as well. For example:
SBase::writeAttributes(stream);
stream.writeAttribute( "id" , mId );
stream.writeAttribute( "name", mName );
...
=item LocalStyle::writeIdList
@internal
Writes the id list to an XML stream.
=item ListOfLocalStyles::clone
Creates and returns a deep copy of the ListOfLocalStyles object.
@return a (deep) copy of this ListOfLocalStyles
=item ListOfLocalStyles::ListOfLocalStyles
Creates a new ListOfLocalStyles object from the given XMLNode object.
The XMLNode object has to contain a valid XML representation of a
ListOfLocalStyles object as defined in the render extension specification.
This method is normally called when render information is read from a file and
should normally not have to be called explicitely.
@param node the XMLNode object reference that describes the ListOfLocalStyles
object to be instantiated.
=item ListOfLocalStyles::ListOfLocalStyles
Constructor which instantiates an empty ListOfLocalStyles object.
=item ListOfLocalStyles::ListOfLocalStyles
Ctor.
=item ListOfLocalStyles::ListOfLocalStyles
Copy constructor for ListOfLocalStyles objects.
=item ListOfLocalStyles::getTypeCode
Returns the libSBML type code for the objects contained in this ListOf
(i.e., GradientDefinition objects, if the list is non-empty).
@if clike LibSBML attaches an identifying code to every
kind of SBML object. These are known as <em>SBML type codes</em>.
The set of possible type codes is defined in the enumeration
#SBMLTypeCode_t. The names of the type codes all begin with the
characters C<SBML_>. @endif@if java LibSBML attaches an
identifying code to every kind of SBML object. These are known as
<em>SBML type codes</em>. In other languages, the set of type codes
is stored in an enumeration; in the Java language interface for
libSBML, the type codes are defined as static integer constants in
interface class {@link libsbmlConstants}. The names of the type codes
all begin with the characters C<SBML_>. @endif
@return the SBML type code for the objects contained in this ListOf
instance, or C<SBML_UNKNOWN> (default).
@see getElementName()
=item ListOfLocalStyles::getElementName
Returns the XML element name of this object, which for
ListOfLocalStyles, is always C<"listOfLocalStyles">.
@return the name of this element, i.e., C<"listOfLocalStyles">.
=item ListOfLocalStyles::toXML
Creates an XMLNode object from this ListOfLocalStyles object.
@return the XMLNode with the XML representation for the
ListOfLocalStyles object.
=item ListOfLocalStyles::get
Returns a pointer to the LocalStyle with the given index or NULL if
the index is invalid.
@param i index of the LocalStyle object to be returned
@return pointer to the LocalStyle at the given index or NULL.
=item ListOfLocalStyles::get
Returns a const pointer to the LocalStyle with the given index or NULL if
the index is invalid.
@param i index of the LocalStyle object to be returned
@return const pointer to the LocalStyle at the given index or NULL.
=item ListOfLocalStyles::get
Returns a pointer to the LocalStyle with the given C<id> or C<NULL> if
the id is invalid.
@param id id of the LocalStyle object to be returned
@return pointer to the LocalStyle at the given C<id> or C<NULL>.
=item ListOfLocalStyles::get
Returns a const pointer to the LocalStyle with the given C<id> or C<NULL> if
the id is invalid.
@param id id of the LocalStyle object to be returned
@return const pointer to the LocalStyle at the given C<id> or C<NULL>.
=item ListOfLocalStyles::remove
Removes the nth item from this ListOfLocalStyles items and returns a pointer to
it.
The caller owns the returned item and is responsible for deleting it.
@param n the index of the item to remove
@see size()
=item ListOfLocalStyles::remove
Removes item in this ListOfLocalStyles items with the given identifier.
The caller owns the returned item and is responsible for deleting it.
If none of the items in this list have the identifier C<sid>, then C<
>
NULL is returned.
@param sid the identifier of the item to remove
@return the item removed. As mentioned above, the caller owns the
returned item.
=item ListOfLocalStyles::getItemTypeCode
Returns the libSBML type code for this SBML object.
@if clike LibSBML attaches an identifying code to every
kind of SBML object. These are known as <em>SBML type codes</em>.
The set of possible type codes is defined in the enumeration
#SBMLTypeCode_t. The names of the type codes all begin with the
characters C<SBML_>. @endif@if java LibSBML attaches an
identifying code to every kind of SBML object. These are known as
<em>SBML type codes</em>. In other languages, the set of type codes
is stored in an enumeration; in the Java language interface for
libSBML, the type codes are defined as static integer constants in
interface class {@link libsbmlConstants}. The names of the type codes
all begin with the characters C<SBML_>. @endif
@return the SBML type code for this object, or C<SBML_UNKNOWN> (default).
@see getElementName()
=item ListOfLocalStyles::createObject
@internal
@return the SBML object corresponding to next XMLToken in the
XMLInputStream or NULL if the token was not recognized.
=back
=head2 RadialGradient
Representation of a radial gradient object from the SBML render extension.
The concept of a radial gradient is more or or less taken from SVG.
A radial gradient is defined by a center point, a radius and an optional focal point.
So for a valid gradient the radius should have a positive length different from 0 and
the focal point should be within the circle defined by the center point and the radius.
Otherwise all restrictions for the GradientBase class apply. (@see GradientBase)
The center and the focal point of a radial gradient are defined by three pairs of
absolute-relative value. (@see RelAbsVector)
The radius is also defined asn an absolute-relative value pair.
For examples of RadialGradients see the render extension specification and/or
the SVG specification.
=over
=item RadialGradient::RadialGradient
Creates a new RadialGradient object with the given SBML level
and SBML version.
@param level SBML level of the new object
@param level SBML version of the new object
=item RadialGradient::RadialGradient
Creates a new RadialGradient object with the given SBMLNamespaces.
@param sbmlns The SBML namespace for the object.
=item RadialGradient::RadialGradient
Creates a new RadialGradient object from the given XMLNode object.
The XMLNode object has to contain a valid XML representation of a
RadialGradient object as defined in the render extension specification.
This method is normally called when render information is read from a file and
should normally not have to be called explicitely.
@param node the XMLNode object reference that describes the RadialGradient
object to be instantiated.
=item RadialGradient::RadialGradient
Constructor which creates a RadialGradient with no gradient stops.
The id is set to the given value.
The RadialGradient object is invalid until it has an id and at least two
gradient stops.
The start and the end of the linear gradient vector are set to (0,0,0).
A linear gradient with a vector of length zero should also be considered invalid.
@param id the new id for the RadialGradient.
This constructor is deprecated. The new libsbml API only has
constructors which take the SBML level and version or one that takes
an SBMLNamespaces object.
=item RadialGradient::setCoordinates
Sets the 3D coordinates for the center and the focal
point as well as the radius.
Each value can be a combination of absolute and relative value and is represented by
a RelAbsVector object.
@param x x value of the center point of the radial gradient vector
@param y y value of the center point of the radial gradient vector
@param z z value of the center point of the radial gradient vector
@param r x value of the radius of the radial gradient vector
@param fx x value of the focal point of the radial gradient vector
@param fy y value of the focal point of the radial gradient vector
@param fz z value of the focal point of the radial gradient vector
=item RadialGradient::setCoordinates
Sets the 2D coordinates for the center and the focal
point as well as the radius.
The z values are automatically set to 0.
Each value can be a combination of absolute and relative value and is represented by
a RelAbsVector object.
@param x x value of the center point of the radial gradient vector
@param y y value of the center point of the radial gradient vector
@param r x value of the radius of the radial gradient vector
@param fx x value of the focal point of the radial gradient vector
@param fy y value of the focal point of the radial gradient vector
=item RadialGradient::setCenter
Sets the coordinates for the center point.
@param x x value of the center point of the radial gradient vector
@param y y value of the center point of the radial gradient vector
@param z z value of the center point of the radial gradient vector
The z argument can be omitted. In that case it is set to 0.
=item RadialGradient::setFocalPoint
Sets the coordinates for the focal point.
@param x x value of the focal point of the radial gradient vector
@param y y value of the focal point of the radial gradient vector
@param z z value of the focal point of the radial gradient vector.
The z argument can be omitted. In that case it is set to 0.
=item RadialGradient::setRadius
Sets the radius of the radial gradient.
@param r radius of the radial gradient vector.
=item RadialGradient::getCenterX
Returns the x coordinate for the center point as a const reference.
@return const reference to the x coordinatee of the center point.
=item RadialGradient::getCenterY
Returns the y coordinate for the center point as a const reference.
@return const reference to the y coordinatee of the center point.
=item RadialGradient::getCenterZ
Returns the z coordinate for the center point as a const reference.
@return const reference to the z coordinatee of the center point.
=item RadialGradient::getFocalPointX
Returns the x coordinate for the focal point as a const reference.
@return const reference to the x coordinatee of the focal point.
=item RadialGradient::getFocalPointY
Returns the y coordinate for the focal point as a const reference.
@return const reference to the y coordinatee of the focal point.
=item RadialGradient::getFocalPointZ
Returns the z coordinate for the focal point as a const reference.
@return const reference to the z coordinatee of the focal point.
=item RadialGradient::getRadius
Returns the radius as a const reference.
@return const reference to the radius
=item RadialGradient::getCenterX
Returns the x coordinate for the center point as a reference.
@return reference to the x coordinatee of the center point.
=item RadialGradient::getCenterY
Returns the y coordinate for the center point as a reference.
@return reference to the y coordinatee of the center point.
=item RadialGradient::getCenterZ
Returns the z coordinate for the center point as a reference.
@return reference to the z coordinatee of the center point.
=item RadialGradient::getFocalPointX
Returns the x coordinate for the focal point as a reference.
@return reference to the x coordinatee of the focal point.
=item RadialGradient::getFocalPointY
Returns the y coordinate for the focal point as a reference.
@return reference to the y coordinatee of the focal point.
=item RadialGradient::getFocalPointZ
Returns the z coordinate for the focal point as a reference.
@return reference to the z coordinatee of the focal point.
=item RadialGradient::getRadius
Returns the radius as a reference.
@return reference to the radius
=item RadialGradient::accept
Accepts the given SBMLVisitor for this instance of RadialGradient.
@param v the SBMLVisitor instance to be used.
@return the result of calling C<v.visit()>.
=item RadialGradient::clone
Creates and returns a deep copy of this RadialGradient object.
@return a (deep) copy of this RadialGradient object
=item RadialGradient::getElementName
Returns the XML element name of this object.
This is overridden by subclasses to return a string appropriate to the
SBML component. For example, Model defines it as returning "model",
CompartmentType defines it as returning "compartmentType", etc.
=item RadialGradient::getTypeCode
Returns the libSBML type code for this SBML object.
@if clike LibSBML attaches an identifying code to every
kind of SBML object. These are known as <em>SBML type codes</em>.
The set of possible type codes is defined in the enumeration
#SBMLTypeCode_t. The names of the type codes all begin with the
characters C<SBML_>. @endif@if java LibSBML attaches an
identifying code to every kind of SBML object. These are known as
<em>SBML type codes</em>. In other languages, the set of type codes
is stored in an enumeration; in the Java language interface for
libSBML, the type codes are defined as static integer constants in
interface class {@link libsbmlConstants}. The names of the type codes
all begin with the characters C<SBML_>. @endif
@return the SBML type code for this object, or C<SBML_UNKNOWN> (default).
@see getElementName()
=item RadialGradient::toXML
Creates an XMLNode object from this RadialGradient object.
@return the XMLNode with the XML representation for the
RadialGradient object.
=item RadialGradient::readAttributes
@internal
Subclasses should override this method to read values from the given
XMLAttributes set into their specific fields. Be sure to call your
parents implementation of this method as well.
=item RadialGradient::addExpectedAttributes
@internal
Subclasses should override this method to get the list of
expected attributes.
This function is invoked from corresponding readAttributes()
function.
=item RadialGradient::writeAttributes
@internal
Subclasses should override this method to write their XML attributes
to the XMLOutputStream. Be sure to call your parents implementation
of this method as well. For example:
SBase::writeAttributes(stream);
stream.writeAttribute( "id" , mId );
stream.writeAttribute( "name", mName );
...
=back
=head2 Point
@sbmlpackage{layout}
@htmlinclude pkg-marker-layout.html The representation of a point in the
“layout” package.
A point is specified via the required attributes 'x', 'y' and an optional
attribute 'z', all of which are of type double. If the attribute z is not
specified, the object is a two dimensional object. The Point class also
has an optional attribute id of type SId. While not used in the
“layout” package, it can be used by programs to refer to the
elements.
=over
=item Point::Point
Creates a new point with x,y and z set to 0.0.
=item Point::Point
Ctor.
=item Point::Point
Copy constructor.
=item Point::Point
Creates a new point with the given ccordinates.
=item Point::Point
Creates a new Point from the given XMLNode
=item Point::x
Returns the x offset.
=item Point::y
Returns the y offset.
=item Point::z
Returns the z offset.
=item Point::getXOffset
Returns the x offset.
=item Point::getYOffset
Returns the y offset.
=item Point::getZOffset
Returns the z offset.
=item Point::setX
Sets the x offset.
=item Point::setY
Sets the y offset.
=item Point::setZ
Sets the z offset.
=item Point::setXOffset
Sets the x offset.
=item Point::setYOffset
Sets the y offset.
=item Point::setZOffset
Sets the z offset.
=item Point::setOffsets
Sets the coordinates to the given values.
=item Point::getZOffsetExplicitlySet
=item Point::initDefaults
Sets the Z offset to 0.0.
=item Point::getId
Returns the value of the "id" attribute of this Point.
=item Point::isSetId
Predicate returning C<true> or C<false> depending on whether this
Point's "id" attribute has been set.
=item Point::setId
Sets the value of the "id" attribute of this Point.
=item Point::unsetId
Unsets the value of the "id" attribute of this Point.
=item Point::writeElements
@internal
Subclasses should override this method to write out their contained
SBML objects as XML elements. Be sure to call your parents
implementation of this method as well. For example:
SBase::writeElements(stream);
mReactants.write(stream);
mProducts.write(stream);
...
=item Point::setElementName
Sets the element name to be returned by getElementName.
=item Point::getElementName
Returns the XML element name of
this SBML object.
=item Point::clone
Creates and returns a deep copy of this Point.
@return a (deep) copy of this Point.
=item Point::getTypeCode
Returns the libSBML type code of this object instance.
C<opydetails> doc_what_are_typecodes
@return the SBML type code for this object:
@link SBMLLayoutTypeCode_t#SBML_LAYOUT_POINT SBML_LAYOUT_POINT@endlink
C<opydetails> doc_warning_typecodes_not_unique
@see getElementName()
@see getPackageName()
=item Point::accept
Accepts the given SBMLVisitor.
@return the result of calling C<v.visit()>, which indicates
whether or not the Visitor would like to visit the SBML object's next
sibling object (if available).
=item Point::toXML
Creates an XMLNode object from this.
=item Point::createObject
@internal
Create and return an SBML object of this class, if present.
@return the SBML object corresponding to next XMLToken in the
XMLInputStream or NULL if the token was not recognized.
=item Point::addExpectedAttributes
@internal
Subclasses should override this method to get the list of
expected attributes.
This function is invoked from corresponding readAttributes()
function.
=item Point::readAttributes
@internal
Subclasses should override this method to read values from the given
XMLAttributes set into their specific fields. Be sure to call your
parents implementation of this method as well.
=item Point::writeAttributes
@internal
Subclasses should override this method to write their XML attributes
to the XMLOutputStream. Be sure to call your parents implementation
of this method as well. For example:
SBase::writeAttributes(stream);
stream.writeAttribute( "id" , mId );
stream.writeAttribute( "name", mName );
...
=back
=head2 Dimensions
@sbmlpackage{layout}
@htmlinclude pkg-marker-layout.html The Dimensions class describes the overall 2D or 3D
shape of a “layout” package object.
A dimension is specified via the required attributes width, height and an
optional attribute depth, all of which are of type double. If the
attribute depth is not specified, the object is a two dimensional object.
The width attribute of Dimensions specifies the size of the object in the
direction of the positive x axis, the height attribute specifies the size
of the object along the positive y axis and the depth attribute specifies
the size of the object along the positive z axis. All sizes for Dimensions
objects are positive values, and so the attributes are not allowed to take
negative values. The Dimensions class also has an optional attribute id
of type SId. While not used in the “layout” package, it can be
used by programs to refer to the elements.
=over
=item Dimensions::Dimensions
Creates a new Dimensions object with the given level, version, and package version
and with all sizes set to 0.0.
=item Dimensions::Dimensions
Creates a new Dimensions object with the given LayoutPkgNamespaces object.
=item Dimensions::Dimensions
Copy constructor.
=item Dimensions::Dimensions
Creates a new Dimensions object with the given sizes.
=item Dimensions::Dimensions
Creates a new Dimensions object from the given XMLNode
=item Dimensions::width
Returns the width.
=item Dimensions::height
Returns the height.
=item Dimensions::depth
Returns the depth.
=item Dimensions::getWidth
Returns the width.
=item Dimensions::getHeight
Returns the height.
=item Dimensions::getDepth
Returns the depth.
=item Dimensions::setWidth
Sets the width to the given value.
=item Dimensions::setHeight
Sets the height to the given value.
=item Dimensions::setDepth
Sets the depth to the given value.
=item Dimensions::setBounds
Sets all sizes of the Dimensions object to the given values.
=item Dimensions::getDExplicitlySet
=item Dimensions::initDefaults
Sets the depth to 0.0
=item Dimensions::getId
Returns the value of the "id" attribute of this Dimensions.
=item Dimensions::isSetId
Predicate returning C<true> or C<false> depending on whether this
Dimensions's "id" attribute has been set.
=item Dimensions::setId
Sets the value of the "id" attribute of this Dimensions.
=item Dimensions::unsetId
Unsets the value of the "id" attribute of this Dimensions.
=item Dimensions::writeElements
@internal
Subclasses should override this method to write out their contained
SBML objects as XML elements. Be sure to call your parents
implementation of this method as well. For example:
SBase::writeElements(stream);
mReactants.write(stream);
mProducts.write(stream);
...
=item Dimensions::getElementName
Returns the XML element name of
this SBML object.
=item Dimensions::clone
Creates and returns a deep copy of this Dimensions.
@return a (deep) copy of this Dimensions object.
=item Dimensions::getTypeCode
Returns the libSBML type code of this object instance.
C<opydetails> doc_what_are_typecodes
@return the SBML type code for this object:
@link SBMLLayoutTypeCode_t#SBML_LAYOUT_DIMENSIONS SBML_LAYOUT_DIMENSIONS@endlink
C<opydetails> doc_warning_typecodes_not_unique
@see getElementName()
@see getPackageName()
=item Dimensions::accept
Accepts the given SBMLVisitor.
@return the result of calling C<v.visit()>, which indicates
whether or not the Visitor would like to visit the SBML object's next
sibling object (if available).
=item Dimensions::toXML
Creates an XMLNode object from this.
=item Dimensions::createObject
@internal
Create and return an SBML object of this class, if present.
@return the SBML object corresponding to next XMLToken in the
XMLInputStream or NULL if the token was not recognized.
=item Dimensions::addExpectedAttributes
@internal
Subclasses should override this method to get the list of
expected attributes.
This function is invoked from corresponding readAttributes()
function.
=item Dimensions::readAttributes
@internal
Subclasses should override this method to read values from the given
XMLAttributes set into their specific fields. Be sure to call your
parents implementation of this method as well.
=item Dimensions::writeAttributes
@internal
Subclasses should override this method to write their XML attributes
to the XMLOutputStream. Be sure to call your parents implementation
of this method as well. For example:
SBase::writeAttributes(stream);
stream.writeAttribute( "id" , mId );
stream.writeAttribute( "name", mName );
...
=back
=head2 BoundingBox
@sbmlpackage{layout}
@htmlinclude pkg-marker-layout.html Representation of a bounding box.
=over
=item BoundingBox::BoundingBox
Default Constructor set position and dimensions to (0.0,0.0,0.0) and
the id to an empty string.
=item BoundingBox::BoundingBox
Creates a new BoundingBox object with the given LayoutPkgNamespaces object.
=item BoundingBox::BoundingBox
Copy constructor.
=item BoundingBox::BoundingBox
Constructor set position and dimensions to (0.0,0.0,0.0) and the id to
a copy of the given string.
(FOR BACKWARD COMPATIBILITY)
=item BoundingBox::BoundingBox
Constructor which sets the id, the coordinates and the dimensions to
the given 2D values.
(FOR BACKWARD COMPATIBILITY)
=item BoundingBox::BoundingBox
Constructor which sets the id, the coordinates and the dimensions to
the given 3D values.
(FOR BACKWARD COMPATIBILITY)
=item BoundingBox::BoundingBox
Constructor which sets the id, the coordinates and the dimensions to
the given values.
(FOR BACKWARD COMPATIBILITY)
=item BoundingBox::BoundingBox
Creates a new BoundingBox from the given XMLNode
(FOR BACKWARD COMPATIBILITY)
=item BoundingBox::getId
Returns the value of the "id" attribute of this BoundingBox.
=item BoundingBox::isSetId
Predicate returning C<true> or C<false> depending on whether this
BoundingBox's "id" attribute has been set.
=item BoundingBox::setId
Sets the value of the "id" attribute of this BoundingBox.
=item BoundingBox::unsetId
Unsets the value of the "id" attribute of this BoundingBox.
=item BoundingBox::getPosition
Returns the position of the BoundingBox as const referece to a Point
object.
=item BoundingBox::getDimensions
Returns the dimensions of the BoundingBox as const referece to a
Dimensions object.
=item BoundingBox::getAllElements
Returns a List of all child SBase objects, including those nested to an
arbitrary depth
@return a List of pointers to all children objects.
=item BoundingBox::getPosition
Returns the position of the BoundingBox as referece to a Point object.
=item BoundingBox::getDimensions
Returns the dimensions of the BoundingBox as referece to a Dimensions
object.
=item BoundingBox::setPosition
Sets the position to a copy of the Point object given.
=item BoundingBox::setDimensions
Sets the dimensions to a copy of the Dimensions object given.
=item BoundingBox::getDimensionsExplicitlySet
Return true or false based on whether Dimensions have been set
=item BoundingBox::getPositionExplicitlySet
Return true or false based on whether Dimensions have been set
=item BoundingBox::initDefaults
Does nothing yet since there are no defaults fo a BoundingBox.
=item BoundingBox::x
Get the x offset of the bounding box.
=item BoundingBox::y
Get the y offset of the bounding box.
=item BoundingBox::z
Get the z offset of the bounding box.
=item BoundingBox::width
Get the width of the bounding box.
=item BoundingBox::height
Get the height of the bounding box.
=item BoundingBox::depth
Get the depth of the bounding box.
=item BoundingBox::setX
Set x offset of the bounding box
=item BoundingBox::setY
Set y offset of the bounding box
=item BoundingBox::setZ
Set z offset of the bounding box
=item BoundingBox::setWidth
Set width of the bounding box
=item BoundingBox::setHeight
Set height of the bounding box
=item BoundingBox::setDepth
Set depth of the bounding box
=item BoundingBox::writeElements
@internal
Subclasses should override this method to write out their contained
SBML objects as XML elements. Be sure to call your parents
implementation of this method as well. For example:
SBase::writeElements(stream);
mReactants.write(stream);
mProducts.write(stream);
...
=item BoundingBox::getElementName
Returns the XML element name of
this SBML object.
=item BoundingBox::clone
Creates and returns a deep copy of this BoundingBox.
@return a (deep) copy of this BoundingBox.
=item BoundingBox::getTypeCode
Returns the libSBML type code of this object instance.
C<opydetails> doc_what_are_typecodes
@return the SBML type code for this object:
@link SBMLLayoutTypeCode_t#SBML_LAYOUT_BOUNDINGBOX SBML_LAYOUT_BOUNDINGBOX@endlink
C<opydetails> doc_warning_typecodes_not_unique
@see getElementName()
@see getPackageName()
=item BoundingBox::accept
Accepts the given SBMLVisitor.
@return the result of calling C<v.visit()>, which indicates
whether or not the Visitor would like to visit the SBML object's next
sibling object (if available).
=item BoundingBox::toXML
Creates an XMLNode object from this.
=item BoundingBox::setSBMLDocument
@internal
Sets the parent SBMLDocument of this SBML object.
@param d the SBMLDocument object to use
=item BoundingBox::connectToChild
@internal
Sets this SBML object to child SBML objects (if any).
(Creates a child-parent relationship by the parent)
Subclasses must override this function if they define
one ore more child elements.
Basically, this function needs to be called in
constructor, copy constructor, assignment operator.
@see setSBMLDocument
@see enablePackageInternal
=item BoundingBox::enablePackageInternal
@internal
Enables/Disables the given package with this element and child
elements (if any).
(This is an internal implementation for enablePakcage function)
@note Subclasses in which one or more child elements are defined
must override this function.
=item BoundingBox::createObject
@internal
Create and return an SBML object of this class, if present.
@return the SBML object corresponding to next XMLToken in the
XMLInputStream or NULL if the token was not recognized.
=item BoundingBox::addExpectedAttributes
@internal
Subclasses should override this method to get the list of
expected attributes.
This function is invoked from corresponding readAttributes()
function.
=item BoundingBox::readAttributes
@internal
Subclasses should override this method to read values from the given
XMLAttributes set into their specific fields. Be sure to call your
parents implementation of this method as well.
=item BoundingBox::writeAttributes
@internal
Subclasses should override this method to write their XML attributes
to the XMLOutputStream. Be sure to call your parents implementation
of this method as well. For example:
SBase::writeAttributes(stream);
stream.writeAttribute( "id" , mId );
stream.writeAttribute( "name", mName );
...
=back
=head2 GraphicalObject
@sbmlpackage{layout}
@htmlinclude pkg-marker-layout.html The basic “layout” package element for
storing layout information.
All the more specific layout elements (CompartmentGlyph, GeneralGlyph,
SpeciesGlyph, ReactionGlyph, ReferenceGlyph, TextGlyph, and
SpeciesReferenceGlyph) are derived from the class GraphicalObject. Each
object of class GraphicalObject has a mandatory BoundingBox, which
specifies the position and the size of the object. While GraphicalObject
is the base class for most elements in the “layout” package,
it is not an abstract class. It can be instantiated when used in the
listOfAdditionalGraphicalObjects to describe additional elements and
relationships. Since it only describes a BoundingBox, programs are
encouraged to add Annotation objects that describe program-specific
graphical information.
=over
=back
=head2 ListOfGraphicalObjects
@sbmlpackage{layout}
@htmlinclude pkg-marker-layout.html Implementation of the ListOfAdditionalGraphicalObjects
construct from the “layout” package.
The ListOfGraphicalObjects class in libSBML actually represents the
ListOfAdditionalGraphicalObjects class in the “layout”
package, and is a container for the additional GraphicalObject elements of
a Layout.
C<opydetails> doc_what_is_listof
@see GraphicalObject
=over
=item GraphicalObject::GraphicalObject
Creates a new GraphicalObject.
=item GraphicalObject::GraphicalObject
Creates a new GraphicalObject with the given LayoutPkgNamespaces
=item GraphicalObject::GraphicalObject
Creates a new GraphicalObject with the given C<id>.
(FOR BACKWARD COMPATIBILITY)
=item GraphicalObject::GraphicalObject
Creates a new GraphicalObject with the given C<id> and 2D coordinates for
the bounding box.
(FOR BACKWARD COMPATIBILITY)
=item GraphicalObject::GraphicalObject
Creates a new GraphicalObject with the given C<id> and 3D coordinates for
the bounding box.
(FOR BACKWARD COMPATIBILITY)
=item GraphicalObject::GraphicalObject
Creates a new GraphicalObject with the given C<id> and 3D coordinates for
the bounding box.
(FOR BACKWARD COMPATIBILITY)
=item GraphicalObject::GraphicalObject
Creates a new GraphicalObject with the given C<id> and 3D coordinates for
the bounding box.
(FOR BACKWARD COMPATIBILITY)
=item GraphicalObject::GraphicalObject
Creates a new GraphicalObject from the given XMLNode
(FOR BACKWARD COMPATIBILITY)
=item GraphicalObject::GraphicalObject
Copy constructor.
=item GraphicalObject::initDefaults
Does nothing. No defaults are defined for GraphicalObject.
=item GraphicalObject::getAllElements
Returns a List of all child SBase objects, including those nested to an
arbitrary depth
@return a List of pointers to all children objects.
=item GraphicalObject::renameMetaIdRefs
Renames all the C<MetaIdRef> attributes on this element.
This method works by looking at all meta-attribute values, comparing
the identifiers to the value of C<oldid>. If any matches are found,
the matching identifiers are replaced with C<newid>. The method does
I<not> descend into child elements.
@param oldid the old identifier
@param newid the new identifier
=item GraphicalObject::getId
Returns the value of the "id" attribute of this GraphicalObject.
=item GraphicalObject::isSetId
Predicate returning C<true> or C<false> depending on whether this
GraphicalObject's "id" attribute has been set.
=item GraphicalObject::setId
Sets the value of the "id" attribute of this GraphicalObject.
=item GraphicalObject::unsetId
Unsets the value of the "id" attribute of this GraphicalObject.
=item GraphicalObject::getMetaIdRef
Returns the value of the "metaidRef" attribute of this GraphicalObject.
=item GraphicalObject::isSetMetaIdRef
Predicate returning C<true> or C<false> depending on whether this
GraphicalObject's "metaidRef" attribute has been set.
=item GraphicalObject::setMetaIdRef
Sets the value of the "metaidRef" attribute of this GraphicalObject.
=item GraphicalObject::unsetMetaIdRef
Unsets the value of the "metaidRef" attribute of this GraphicalObject.
=item GraphicalObject::setBoundingBox
Sets the boundingbox for the GraphicalObject.
=item GraphicalObject::getBoundingBox
Returns the bounding box for the GraphicalObject.
=item GraphicalObject::getBoundingBox
Returns the bounding box for the GraphicalObject.
=item GraphicalObject::getBoundingBoxExplicitlySet
=item GraphicalObject::writeElements
@internal
Subclasses should override this method to write out their contained
SBML objects as XML elements. Be sure to call your parents
implementation of this method as well. For example:
SBase::writeElements(stream);
mReactants.write(stream);
mProducts.write(stream);
...
=item GraphicalObject::getElementName
Returns the XML element name of
this SBML object.
=item GraphicalObject::clone
Creates and returns a deep copy of this GraphicalObject.
@return a (deep) copy of this GraphicalObject.
=item GraphicalObject::getTypeCode
Returns the libSBML type code of this object instance.
C<opydetails> doc_what_are_typecodes
@return the SBML type code for this object:
@link SBMLLayoutTypeCode_t#SBML_LAYOUT_GRAPHICALOBJECT SBML_LAYOUT_GRAPHICALOBJECT@endlink
C<opydetails> doc_warning_typecodes_not_unique
@see getElementName()
@see getPackageName()
=item GraphicalObject::accept
Accepts the given SBMLVisitor.
@return the result of calling C<v.visit()>, which indicates
whether or not the Visitor would like to visit the SBML object's next
sibling object (if available).
=item GraphicalObject::toXML
Creates an XMLNode object from this.
=item GraphicalObject::setSBMLDocument
@internal
Sets the parent SBMLDocument of this SBML object.
@param d the SBMLDocument object to use
=item GraphicalObject::connectToChild
@internal
Sets this SBML object to child SBML objects (if any).
(Creates a child-parent relationship by the parent)
Subclasses must override this function if they define
one ore more child elements.
Basically, this function needs to be called in
constructor, copy constructor, assignment operator.
@see setSBMLDocument
@see enablePackageInternal
=item GraphicalObject::enablePackageInternal
@internal
Enables/Disables the given package with this element and child
elements (if any).
(This is an internal implementation for enablePakcage function)
@note Subclasses in which one or more child elements are defined
must override this function.
=item GraphicalObject::createObject
@internal
Create and return an SBML object of this class, if present.
@return the SBML object corresponding to next XMLToken in the
XMLInputStream or NULL if the token was not recognized.
=item GraphicalObject::addExpectedAttributes
@internal
Subclasses should override this method to get the list of
expected attributes.
This function is invoked from corresponding readAttributes()
function.
=item GraphicalObject::readAttributes
@internal
Subclasses should override this method to read values from the given
XMLAttributes set into their specific fields. Be sure to call your
parents implementation of this method as well.
=item GraphicalObject::writeAttributes
@internal
Subclasses should override this method to write their XML attributes
to the XMLOutputStream. Be sure to call your parents implementation
of this method as well. For example:
SBase::writeAttributes(stream);
stream.writeAttribute( "id" , mId );
stream.writeAttribute( "name", mName );
...
=item GraphicalObject::writeXMLNS
@internal
Subclasses should override this method to write their xmlns attriubutes
(if any) to the XMLOutputStream.
=item ListOfGraphicalObjects::clone
Creates and returns a deep copy of this ListOfGraphicalObjects.
@return a (deep) copy of this ListOfGraphicalObjects.
=item ListOfGraphicalObjects::ListOfGraphicalObjects
Ctor.
=item ListOfGraphicalObjects::ListOfGraphicalObjects
Ctor.
=item ListOfGraphicalObjects::getItemTypeCode
Returns the libSBML type code for the SBML objects
contained in this ListOf object.
C<opydetails> doc_what_are_typecodes
@return the SBML type code for objects contained in this list:
@link SBMLTypeCode_t#SBML_LAYOUT_GRAPHICALOBJECT SBML_LAYOUT_GRAPHICALOBJECT@endlink (default).
@see getElementName()
@see getPackageName()
=item ListOfGraphicalObjects::getElementName
Returns the XML element name of
this SBML object.
=item ListOfGraphicalObjects::setElementName
@internal
=item ListOfGraphicalObjects::get
Get a GraphicalObject from the ListOfGraphicalObjects.
@param n the index number of the GraphicalObject to get.
@return the nth GraphicalObject in this ListOfGraphicalObjects.
@see size()
=item ListOfGraphicalObjects::get
Get a GraphicalObject from the ListOfGraphicalObjects.
@param n the index number of the GraphicalObject to get.
@return the nth GraphicalObject in this ListOfGraphicalObjects.
@see size()
=item ListOfGraphicalObjects::get
Get a GraphicalObject from the ListOfGraphicalObjects
based on its identifier.
@param sid a string representing the identifier
of the GraphicalObject to get.
@return GraphicalObject in this ListOfGraphicalObjects
with the given C<sid> or C<NULL> if no such
GraphicalObject exists.
@see get(unsigned int n)
@see size()
=item ListOfGraphicalObjects::get
Get a GraphicalObject from the ListOfGraphicalObjects
based on its identifier.
@param sid a string representing the identifier
of the GraphicalObject to get.
@return GraphicalObject in this ListOfGraphicalObjects
with the given C<sid> or C<NULL> if no such
GraphicalObject exists.
@see get(unsigned int n)
@see size()
=item ListOfGraphicalObjects::remove
Removes the nth item from this ListOfGraphicalObjects items and returns a pointer to
it.
The caller owns the returned item and is responsible for deleting it.
@param n the index of the item to remove
@see size()
=item ListOfGraphicalObjects::remove
Removes item in this ListOfGraphicalObjects items with the given identifier.
The caller owns the returned item and is responsible for deleting it.
If none of the items in this list have the identifier C<sid>, then @c
NULL is returned.
@param sid the identifier of the item to remove
@return the item removed. As mentioned above, the caller owns the
returned item.
=item ListOfGraphicalObjects::toXML
Creates an XMLNode object from this.
=item ListOfGraphicalObjects::createObject
@internal
Create and return an SBML object of this class, if present.
@return the SBML object corresponding to next XMLToken in the
XMLInputStream or NULL if the token was not recognized.
=item ListOfGraphicalObjects::isValidTypeForList
@internal
=back
=head2 CompartmentGlyph
@sbmlpackage{layout}
@htmlinclude pkg-marker-layout.html Representation of a compartment glyph.
=over
=item CompartmentGlyph::CompartmentGlyph
Default Constructor which creates a new CompartmentGlyph. Id and
associated compartment id are unset.
=item CompartmentGlyph::CompartmentGlyph
Ctor.
=item CompartmentGlyph::CompartmentGlyph
Constructor which creates a new CompartmentGlyph with the given C<id>.
(FOR BACKWARD COMPATIBILITY)
=item CompartmentGlyph::CompartmentGlyph
Constructor which creates a new CompartmentGlyph. Id and associated
compartment id are set to copies of the values given as arguments.
(FOR BACKWARD COMPATIBILITY)
=item CompartmentGlyph::CompartmentGlyph
Creates a new CompartmentGlyph from the given XMLNode
(FOR BACKWARD COMPATIBILITY)
=item CompartmentGlyph::CompartmentGlyph
Copy constructor.
=item CompartmentGlyph::getCompartmentId
Returns the id of the associated compartment.
=item CompartmentGlyph::setCompartmentId
Sets the id of the associated compartment.
=item CompartmentGlyph::isSetCompartmentId
Returns true if the id of the associated compartment is not the empty
string.
=item CompartmentGlyph::getOrder
Returns the compartment order.
=item CompartmentGlyph::setOrder
Sets the compartment order
=item CompartmentGlyph::unsetOrder
Sets the compartment order
=item CompartmentGlyph::isSetOrder
Returns true if the compartment order has been set
=item CompartmentGlyph::renameSIdRefs
Renames all the C<SIdRef> attributes on this element, including any
found in MathML content (if such exists).
This method works by looking at all attributes and (if appropriate)
mathematical formulas, comparing the identifiers to the value of @p
oldid. If any matches are found, the matching identifiers are replaced
with C<newid>. The method does I<not> descend into child elements.
@param oldid the old identifier
@param newid the new identifier
=item CompartmentGlyph::initDefaults
Calls initDefaults from GraphicalObject.
=item CompartmentGlyph::writeElements
@internal
Subclasses should override this method to write out their contained
SBML objects as XML elements. Be sure to call your parents
implementation of this method as well. For example:
SBase::writeElements(stream);
mReactants.write(stream);
mProducts.write(stream);
...
=item CompartmentGlyph::getElementName
Returns the XML element name of
this SBML object.
=item CompartmentGlyph::clone
Creates and returns a deep copy of this CompartmentGlyph.
@return a (deep) copy of this CompartmentGlyph.
=item CompartmentGlyph::getTypeCode
Returns the libSBML type code of this object instance.
C<opydetails> doc_what_are_typecodes
@return the SBML type code for this object:
@link SBMLLayoutTypeCode_t#SBML_LAYOUT_COMPARTMENTGLYPH SBML_LAYOUT_COMPARTMENTGLYPH@endlink
C<opydetails> doc_warning_typecodes_not_unique
@see getElementName()
@see getPackageName()
=item CompartmentGlyph::toXML
Creates an XMLNode object from this.
=item CompartmentGlyph::createObject
@internal
Create and return an SBML object of this class, if present.
@return the SBML object corresponding to next XMLToken in the
XMLInputStream or NULL if the token was not recognized.
=item CompartmentGlyph::addExpectedAttributes
@internal
Subclasses should override this method to get the list of
expected attributes.
This function is invoked from corresponding readAttributes()
function.
=item CompartmentGlyph::readAttributes
@internal
Subclasses should override this method to read values from the given
XMLAttributes set into their specific fields. Be sure to call your
parents implementation of this method as well.
=item CompartmentGlyph::writeAttributes
@internal
Subclasses should override this method to write their XML attributes
to the XMLOutputStream. Be sure to call your parents implementation
of this method as well. For example:
SBase::writeAttributes(stream);
stream.writeAttribute( "id" , mId );
stream.writeAttribute( "name", mName );
...
=back
=head2 LineSegment
@sbmlpackage{layout}
@htmlinclude pkg-marker-layout.html The representation of a line in the
“layout” package.
The LineSegment class consists of the mandatory attribute xsi:type and two
child elements of type Point. One is called 'start' and represents the
starting point of the line, the other is called 'end' and represents the
endpoint of the line. The LineSegment class is also the base class for
CubicBezier, which represent curved lines instead of straight ones.
=over
=item LineSegment::LineSegment
Creates a line segment with the given SBML level, version, and package version
and both points set to (0.0,0.0,0.0)
=item LineSegment::LineSegment
Creates a line segment with the LayoutPkgNamespaces and both points set to (0.0,0.0,0.0)
=item LineSegment::LineSegment
Creates a new line segment with the given 2D coordinates.
=item LineSegment::LineSegment
Copy constructor.
=item LineSegment::LineSegment
Creates a new line segment with the given 3D coordinates.
=item LineSegment::LineSegment
Creates a new line segment with the two given points.
=item LineSegment::LineSegment
Creates a new LineSegment from the given XMLNode
=item LineSegment::getAllElements
Returns a List of all child SBase objects, including those nested to an
arbitrary depth
@return a List of pointers to all children objects.
=item LineSegment::getStart
Returns the start point of the line.
=item LineSegment::getStart
Returns the start point of the line.
=item LineSegment::setStart
Initializes the start point with a copy of the given Point object.
=item LineSegment::setStart
Initializes the start point with the given coordinates.
=item LineSegment::getEnd
Returns the end point of the line.
=item LineSegment::getEnd
Returns the end point of the line.
=item LineSegment::setEnd
Initializes the end point with a copy of the given Point object.
=item LineSegment::setEnd
Initializes the end point with the given coordinates.
=item LineSegment::getStartExplicitlySet
@internal
=item LineSegment::getEndExplicitlySet
@internal
=item LineSegment::initDefaults
Does noting since no defaults are defined for LineSegment.
=item LineSegment::writeElements
@internal
Subclasses should override this method to write out their contained
SBML objects as XML elements. Be sure to call your parents
implementation of this method as well. For example:
SBase::writeElements(stream);
mReactants.write(stream);
mProducts.write(stream);
...
=item LineSegment::getElementName
Returns the XML element name of
this SBML object.
=item LineSegment::clone
Creates and returns a deep copy of this LineSegment.
@return a (deep) copy of this LineSegment.
=item LineSegment::getTypeCode
Returns the libSBML type code of this object instance.
C<opydetails> doc_what_are_typecodes
@return the SBML type code for this object:
@link SBMLLayoutTypeCode_t#SBML_LAYOUT_LINESEGMENT SBML_LAYOUT_LINESEGMENT@endlink
C<opydetails> doc_warning_typecodes_not_unique
@see getElementName()
@see getPackageName()
=item LineSegment::accept
Accepts the given SBMLVisitor.
@return the result of calling C<v.visit()>, which indicates
whether or not the Visitor would like to visit the SBML object's next
sibling object (if available).
=item LineSegment::toXML
Creates an XMLNode object from this.
=item LineSegment::setSBMLDocument
@internal
Sets the parent SBMLDocument of this SBML object.
@param d the SBMLDocument object to use
=item LineSegment::connectToChild
@internal
Sets this SBML object to child SBML objects (if any).
(Creates a child-parent relationship by the parent)
Subclasses must override this function if they define
one ore more child elements.
Basically, this function needs to be called in
constructor, copy constructor, assignment operator.
@see setSBMLDocument
@see enablePackageInternal
=item LineSegment::enablePackageInternal
@internal
Enables/Disables the given package with this element and child
elements (if any).
(This is an internal implementation for enablePakcage function)
@note Subclasses in which one or more child elements are defined
must override this function.
=item LineSegment::createObject
@internal
Create and return an SBML object of this class, if present.
@return the SBML object corresponding to next XMLToken in the
XMLInputStream or NULL if the token was not recognized.
=item LineSegment::addExpectedAttributes
@internal
Subclasses should override this method to get the list of
expected attributes.
This function is invoked from corresponding readAttributes()
function.
=item LineSegment::readAttributes
@internal
Subclasses should override this method to read values from the given
XMLAttributes set into their specific fields. Be sure to call your
parents implementation of this method as well.
=item LineSegment::writeAttributes
@internal
Subclasses should override this method to write their XML attributes
to the XMLOutputStream. Be sure to call your parents implementation
of this method as well. For example:
SBase::writeAttributes(stream);
stream.writeAttribute( "id" , mId );
stream.writeAttribute( "name", mName );
...
=item LineSegment::writeXMLNS
@internal
Subclasses should override this method to write their xmlns attriubutes
(if any) to the XMLOutputStream.
=back
=head2 CubicBezier
@sbmlpackage{layout}
@htmlinclude pkg-marker-layout.html A CubicBezier represents a smooth curve in the
“layout” package.
In order to be able to represent smooth curves the “layout”
package defines the class CubicBezier. It represents a Bezier curve, and
is readily available in most graphics APIs. The class CubicBezier is
derived from LineSegment. It consists of four elements: the two inherited
elements 'start' and 'end', which specify the starting point and the
endpoint of the cubic bezier curve, and two elements 'basePoint1' and
'basePoint2', which specify the two additional base points that are needed
to describe a cubic bezier curve.
=over
=item CubicBezier::CubicBezier
Creates a CubicBezier and returns the pointer.
=item CubicBezier::CubicBezier
Ctor.
=item CubicBezier::CubicBezier
Creates a CubicBezier with the given 2D coordinates and returns the
pointer.
(FOR BACKWARD COMPATIBILITY)
=item CubicBezier::CubicBezier
Creates a CubicBezier with the given 3D coordinates and returns the
pointer.
(FOR BACKWARD COMPATIBILITY)
=item CubicBezier::CubicBezier
Copy constructor.
(FOR BACKWARD COMPATIBILITY)
=item CubicBezier::CubicBezier
Creates a CubicBezier with the given points and returns the pointer.
(FOR BACKWARD COMPATIBILITY)
=item CubicBezier::CubicBezier
Creates a CubicBezier with the given points and returns the pointer.
(FOR BACKWARD COMPATIBILITY)
=item CubicBezier::CubicBezier
Creates a new Layout from the given XMLNode
(FOR BACKWARD COMPATIBILITY)
=item CubicBezier::getAllElements
Returns a List of all child SBase objects, including those nested to an
arbitrary depth
@return a List of pointers to all children objects.
=item CubicBezier::getBasePoint1
Returns the first base point of the curve (the one closer to the
starting point).
=item CubicBezier::getBasePoint1
Returns the first base point of the curve (the one closer to the
starting point).
=item CubicBezier::setBasePoint1
Initializes first base point with a copy of the given point.
=item CubicBezier::setBasePoint1
Initializes first base point with the given coordinates.
=item CubicBezier::getBasePoint2
Returns the second base point of the curve (the one closer to the end
point).
=item CubicBezier::getBasePoint2
Returns the second base point of the curve (the one closer to the end
point).
=item CubicBezier::setBasePoint2
Initializes second base point with a copy of the given point.
=item CubicBezier::setBasePoint2
Initializes second base point with the given coordinates.
=item CubicBezier::getBasePt1ExplicitlySet
@internal
=item CubicBezier::getBasePt2ExplicitlySet
@internal
=item CubicBezier::initDefaults
Calls initDefaults from LineSegment.
=item CubicBezier::straighten
Makes a line from a CubicBezier by setting both base points into the
middle between the start and the end point.
=item CubicBezier::writeElements
@internal
Subclasses should override this method to write out their contained
SBML objects as XML elements. Be sure to call your parents
implementation of this method as well. For example:
SBase::writeElements(stream);
mReactants.write(stream);
mProducts.write(stream);
...
=item CubicBezier::getElementName
Returns the XML element name of
this SBML object.
=item CubicBezier::clone
Creates and returns a deep copy of this CubicBezier.
@return a (deep) copy of this CubicBezier.
=item CubicBezier::getTypeCode
Returns the libSBML type code of this object instance.
C<opydetails> doc_what_are_typecodes
@return the SBML type code for this object:
@link SBMLLayoutTypeCode_t#SBML_LAYOUT_CUBICBEZIER SBML_LAYOUT_CUBICBEZIER@endlink
C<opydetails> doc_warning_typecodes_not_unique
@see getElementName()
@see getPackageName()
=item CubicBezier::accept
Accepts the given SBMLVisitor.
@return the result of calling C<v.visit()>, which indicates
whether or not the Visitor would like to visit the SBML object's next
sibling object (if available).
=item CubicBezier::toXML
Creates an XMLNode object from this.
=item CubicBezier::setSBMLDocument
@internal
Sets the parent SBMLDocument of this SBML object.
@param d the SBMLDocument object to use
=item CubicBezier::connectToChild
@internal
Sets this SBML object to child SBML objects (if any).
(Creates a child-parent relationship by the parent)
Subclasses must override this function if they define
one ore more child elements.
Basically, this function needs to be called in
constructor, copy constructor, assignment operator.
@see setSBMLDocument
@see enablePackageInternal
=item CubicBezier::enablePackageInternal
@internal
Enables/Disables the given package with this element and child
elements (if any).
(This is an internal implementation for enablePakcage function)
@note Subclasses in which one or more child elements are defined
must override this function.
=item CubicBezier::createObject
@internal
Create and return an SBML object of this class, if present.
@return the SBML object corresponding to next XMLToken in the
XMLInputStream or NULL if the token was not recognized.
=item CubicBezier::addExpectedAttributes
@internal
Subclasses should override this method to get the list of
expected attributes.
This function is invoked from corresponding readAttributes()
function.
=item CubicBezier::readAttributes
@internal
Subclasses should override this method to read values from the given
XMLAttributes set into their specific fields. Be sure to call your
parents implementation of this method as well.
=item CubicBezier::writeAttributes
@internal
Subclasses should override this method to write their XML attributes
to the XMLOutputStream. Be sure to call your parents implementation
of this method as well. For example:
SBase::writeAttributes(stream);
stream.writeAttribute( "id" , mId );
stream.writeAttribute( "name", mName );
...
=item CubicBezier::writeXMLNS
@internal
Subclasses should override this method to write their xmlns attriubutes
(if any) to the XMLOutputStream.
=back
=head2 Curve
@sbmlpackage{layout}
@htmlinclude pkg-marker-layout.html The Curve class describes how to connect elements in a
diagram defined with the use of the “layout” package. A curve
is fully specified by a mandatory listOfCurveSegments element and is used
in four places in the “layout” package:
@li SpeciesReferenceGlyph: Here it describes a curve from/to the center
piece of the parent ReactionGlyph to/from the SpeciesGlyph it represents.
@li ReactionGlyph: Here it describes a curve for the center piece of a
reaction.
@li ReferenceGlyph: Here it describes a curve from/to the center piece of
the parent GeneralGlyph to/from the glyph it represents.
@li GeneralGlyph: Here it describes a curve for the center piece of an
additional relationship.
In the text above, the term 'center piece' refers to either the Curve
element of a ReactionGlyph, or its BoundingBox.
=over
=back
=head2 ListOfLineSegments
@sbmlpackage{layout}
@htmlinclude pkg-marker-layout.html Implementation of the ListOfLineSegments construct
from the 'layout' package.
The ListOfLineSegments is a container for the LineSegment elements of a Curve.
C<opydetails> doc_what_is_listof
@see Input
=over
=item ListOfLineSegments::clone
Creates and returns a deep copy of this ListOfLineSegments.
@return a (deep) copy of this ListOfLineSegments.
=item ListOfLineSegments::ListOfLineSegments
Ctor.
=item ListOfLineSegments::ListOfLineSegments
Ctor.
=item ListOfLineSegments::getItemTypeCode
Returns the libSBML type code for the SBML objects
contained in this ListOf object.
C<opydetails> doc_what_are_typecodes
@return the SBML type code for objects contained in this list:
@link SBMLTypeCode_t#SBML_LAYOUT_LINESEGMENT SBML_LAYOUT_LINESEGMENT@endlink (default).
@see getElementName()
@see getPackageName()
=item ListOfLineSegments::getElementName
Returns the XML element name of
this SBML object.
=item ListOfLineSegments::get
Get a LineSegment from the ListOfLineSegments.
@param n the index number of the LineSegment to get.
@return the nth LineSegment in this ListOfLineSegments.
@see size()
=item ListOfLineSegments::get
Get a LineSegment from the ListOfLineSegments.
@param n the index number of the LineSegment to get.
@return the nth LineSegment in this ListOfLineSegments.
@see size()
=item ListOfLineSegments::remove
Removes the nth item from this ListOfLineSegments items and returns a pointer to
it.
The caller owns the returned item and is responsible for deleting it.
@param n the index of the item to remove
@see size()
=item ListOfLineSegments::toXML
Creates an XMLNode object from this.
=item ListOfLineSegments::createObject
@internal
Create and return an SBML object of this class, if present.
@return the SBML object corresponding to next XMLToken in the
XMLInputStream or NULL if the token was not recognized.
=item ListOfLineSegments::isValidTypeForList
=item Curve::Curve
Creates a curve with an empty list of segments.
=item Curve::Curve
Creates a new Curve with the given LayoutPkgNamespaces object.
=item Curve::Curve
Creates a new Curve from the given XMLNode
=item Curve::Curve
Copy constructor.
=item Curve::initDefaults
Does nothing since no defaults are defined for Curve.
=item Curve::getAllElements
Returns a List of all child SBase objects, including those nested to an
arbitrary depth
@return a List of pointers to all children objects.
=item Curve::getListOfCurveSegments
Returns a reference to the ListOf object that holds all the curve
segments.
=item Curve::getListOfCurveSegments
Returns a refernce to the ListOf object That holds all the curve
segments.
=item Curve::getCurveSegment
Returns a pointer to the curve segment with the given index.
If the index is invalid, C<NULL> is returned.
=item Curve::getCurveSegment
Returns a pointer to the curve segment with the given index.
If the index is invalid, C<NULL> is returned.
=item Curve::addCurveSegment
Adds a new CurveSegment to the end of the list.
=item Curve::getNumCurveSegments
Returns the number of curve segments.
=item Curve::createLineSegment
Creates a new LineSegment and adds it to the end of the list. A
reference to the new LineSegment object is returned.
=item Curve::createCubicBezier
Creates a new CubicBezier and adds it to the end of the list. A
reference to the new CubicBezier object is returned.
=item Curve::writeElements
@internal
Subclasses should override this method to write out their contained
SBML objects as XML elements. Be sure to call your parents
implementation of this method as well. For example:
SBase::writeElements(stream);
mReactants.write(stream);
mProducts.write(stream);
...
=item Curve::getElementName
Returns the XML element name of
this SBML object.
=item Curve::clone
Creates and returns a deep copy of this Curve.
@return a (deep) copy of this Curve.
=item Curve::getTypeCode
Returns the libSBML type code of this object instance.
C<opydetails> doc_what_are_typecodes
@return the SBML type code for this object:
@link SBMLLayoutTypeCode_t#SBML_LAYOUT_CURVE SBML_LAYOUT_CURVE@endlink
C<opydetails> doc_warning_typecodes_not_unique
@see getElementName()
@see getPackageName()
=item Curve::accept
Accepts the given SBMLVisitor.
@return the result of calling C<v.visit()>, which indicates
whether or not the Visitor would like to visit the SBML object's next
sibling object (if available).
=item Curve::toXML
Creates an XMLNode object from this.
=item Curve::setSBMLDocument
@internal
Sets the parent SBMLDocument of this SBML object.
@param d the SBMLDocument object to use
=item Curve::connectToChild
@internal
Sets this SBML object to child SBML objects (if any).
(Creates a child-parent relationship by the parent)
Subclasses must override this function if they define
one ore more child elements.
Basically, this function needs to be called in
constructor, copy constructor, assignment operator.
@see setSBMLDocument
@see enablePackageInternal
=item Curve::enablePackageInternal
@internal
Enables/Disables the given package with this element and child
elements (if any).
(This is an internal implementation for enablePakcage function)
@note Subclasses in which one or more child elements are defined
must override this function.
=item Curve::createObject
@internal
Create and return an SBML object of this class, if present.
@return the SBML object corresponding to next XMLToken in the
XMLInputStream or NULL if the token was not recognized.
=item Curve::addExpectedAttributes
@internal
Subclasses should override this method to get the list of
expected attributes.
This function is invoked from corresponding readAttributes()
function.
=item Curve::readAttributes
@internal
Subclasses should override this method to read values from the given
XMLAttributes set into their specific fields. Be sure to call your
parents implementation of this method as well.
=item Curve::writeAttributes
@internal
Subclasses should override this method to write their XML attributes
to the XMLOutputStream. Be sure to call your parents implementation
of this method as well. For example:
SBase::writeAttributes(stream);
stream.writeAttribute( "id" , mId );
stream.writeAttribute( "name", mName );
...
=back
=head2 SpeciesReferenceGlyph
@sbmlpackage{layout}
@htmlinclude pkg-marker-layout.html A SpeciesReferenceGlyph represents a reactant or
product from a Reaction in the “layout” package.
The SpeciesReferenceGlyph element describes the graphical connection
between a SpeciesGlyph and a ReactionGlyph (which would be an arrow or
some curve in most cases). A SpeciesReferenceGlyph inherits from
GraphicalObject, and adds a mandatory attribute 'speciesGlyph' and two
optional attributes 'speciesReference' and 'role'. Optionally, the
SpeciesReferenceGlyph also has a child element 'curve'.
If the curve is specified, it overrides the inherited bounding box.
=over
=item SpeciesReferenceGlyph::SpeciesReferenceGlyph
Creates a new SpeciesReferenceGlyph with the given SBML level, version and
package version. The id if the associated species
reference and the id of the associated species glyph are set to the
empty string. The role is set to SPECIES_ROLE_UNDEFINED.
=item SpeciesReferenceGlyph::SpeciesReferenceGlyph
Ctor.
=item SpeciesReferenceGlyph::SpeciesReferenceGlyph
Creates a new SpeciesReferenceGlyph. The id is given as the first
argument, the id of the associated species glyph is given as the
second argument. The third argument is the id of the associated
species reference and the fourth argument is the role.
=item SpeciesReferenceGlyph::SpeciesReferenceGlyph
Creates a new SpeciesReferenceGlyph from the given XMLNode
=item SpeciesReferenceGlyph::SpeciesReferenceGlyph
Copy constructor.
=item SpeciesReferenceGlyph::getSpeciesGlyphId
Returns the id of the associated SpeciesGlyph.
=item SpeciesReferenceGlyph::setSpeciesGlyphId
Sets the id of the associated species glyph.
=item SpeciesReferenceGlyph::getSpeciesReferenceId
Returns the id of the associated species reference.
=item SpeciesReferenceGlyph::setSpeciesReferenceId
Sets the id of the associated species reference.
=item SpeciesReferenceGlyph::getRoleString
Returns a string representation of the role.
=item SpeciesReferenceGlyph::getRole
Returns the role.
=item SpeciesReferenceGlyph::setRole
Sets the role based on a string.
The String can be one of:
SUBSTRATE
PRODUCT
SIDESUBSTRATE
SIDEPRODUCT
MODIFIER
ACTIVATOR
INHIBITOR
=item SpeciesReferenceGlyph::setRole
Sets the role.
=item SpeciesReferenceGlyph::getAllElements
Returns a List of all child SBase objects, including those nested to an
arbitrary depth
@return a List of pointers to all children objects.
=item SpeciesReferenceGlyph::renameSIdRefs
Renames all the C<SIdRef> attributes on this element, including any
found in MathML content (if such exists).
This method works by looking at all attributes and (if appropriate)
mathematical formulas, comparing the identifiers to the value of @p
oldid. If any matches are found, the matching identifiers are replaced
with C<newid>. The method does I<not> descend into child elements.
@param oldid the old identifier
@param newid the new identifier
=item SpeciesReferenceGlyph::getCurve
Returns the curve object for the species reference glyph
=item SpeciesReferenceGlyph::getCurve
Returns the curve object for the species reference glyph
=item SpeciesReferenceGlyph::setCurve
Sets the curve object for the species reference glyph.
=item SpeciesReferenceGlyph::isSetCurve
Returns true if the curve consists of one or more segments.
=item SpeciesReferenceGlyph::getCurveExplicitlySet
=item SpeciesReferenceGlyph::isSetSpeciesGlyphId
Returns true if the id of the associated species glyph is not the
empty string.
=item SpeciesReferenceGlyph::isSetSpeciesReferenceId
Returns true if the id of the associated species reference is not the
empty string.
=item SpeciesReferenceGlyph::isSetRole
Returns true of role is different from SPECIES_ROLE_UNDEFINED.
=item SpeciesReferenceGlyph::initDefaults
Calls initDefaults on GraphicalObject and sets role to
SPECIES_ROLE_UNDEFINED.
=item SpeciesReferenceGlyph::createLineSegment
Creates a new LineSegment object, adds it to the end of the list of
curve segment objects of the curve and returns a reference to the
newly created object.
=item SpeciesReferenceGlyph::createCubicBezier
Creates a new CubicBezier object, adds it to the end of the list of
curve segment objects of the curve and returns a reference to the
newly created object.
=item SpeciesReferenceGlyph::writeElements
@internal
Subclasses should override this method to write out their contained
SBML objects as XML elements. Be sure to call your parents
implementation of this method as well. For example:
SBase::writeElements(stream);
mReactants.write(stream);
mProducts.write(stream);
...
=item SpeciesReferenceGlyph::getElementName
Returns the XML element name of
this SBML object.
=item SpeciesReferenceGlyph::clone
Creates and returns a deep copy of this SpeciesReferenceGlyph.
@return a (deep) copy of this SpeciesReferenceGlyph.
=item SpeciesReferenceGlyph::getTypeCode
Returns the libSBML type code of this object instance.
C<opydetails> doc_what_are_typecodes
@return the SBML type code for this object:
@link SBMLLayoutTypeCode_t#SBML_LAYOUT_SPECIESREFERENCEGLYPH SBML_LAYOUT_SPECIESREFERENCEGLYPH@endlink
C<opydetails> doc_warning_typecodes_not_unique
@see getElementName()
@see getPackageName()
=item SpeciesReferenceGlyph::accept
Accepts the given SBMLVisitor.
@return the result of calling C<v.visit()>, which indicates
whether or not the Visitor would like to visit the SBML object's next
sibling object (if available).
=item SpeciesReferenceGlyph::toXML
Creates an XMLNode object from this.
=item SpeciesReferenceGlyph::setSBMLDocument
@internal
Sets the parent SBMLDocument of this SBML object.
@param d the SBMLDocument object to use
=item SpeciesReferenceGlyph::connectToChild
@internal
Sets this SBML object to child SBML objects (if any).
(Creates a child-parent relationship by the parent)
Subclasses must override this function if they define
one ore more child elements.
Basically, this function needs to be called in
constructor, copy constructor, assignment operator.
@see setSBMLDocument
@see enablePackageInternal
=item SpeciesReferenceGlyph::enablePackageInternal
@internal
Enables/Disables the given package with this element and child
elements (if any).
(This is an internal implementation for enablePakcage function)
@note Subclasses in which one or more child elements are defined
must override this function.
=item SpeciesReferenceGlyph::createObject
@internal
Create and return an SBML object of this class, if present.
@return the SBML object corresponding to next XMLToken in the
XMLInputStream or NULL if the token was not recognized.
=item SpeciesReferenceGlyph::addExpectedAttributes
@internal
Subclasses should override this method to get the list of
expected attributes.
This function is invoked from corresponding readAttributes()
function.
=item SpeciesReferenceGlyph::readAttributes
@internal
Subclasses should override this method to read values from the given
XMLAttributes set into their specific fields. Be sure to call your
parents implementation of this method as well.
=item SpeciesReferenceGlyph::writeAttributes
@internal
Subclasses should override this method to write their XML attributes
to the XMLOutputStream. Be sure to call your parents implementation
of this method as well. For example:
SBase::writeAttributes(stream);
stream.writeAttribute( "id" , mId );
stream.writeAttribute( "name", mName );
...
=back
=head2 ReferenceGlyph
@sbmlpackage{layout}
@htmlinclude pkg-marker-layout.html The ReferenceGlyph is used by the “layout”
package to connect a GraphicalObject and a GeneralGlyph.
The ReferenceGlyph element describes the graphical connection between an
arbitrary GraphicalObject (or derived element) and a GeneralGlyph (which
would be an arrow or some curve in most cases). A ReferenceGlyph inherits
from GraphicalObject. Additionally it has a mandatory attribute 'glyph'
and two optional attributes 'reference' and 'role'. Optionally, the
ReferenceGlyph also has an element 'curve'. The ReferenceGlyph should
either contain a bounding box or a curve specification. If both are
given, the bounding box should be ignored.
=over
=item ReferenceGlyph::ReferenceGlyph
Creates a new ReferenceGlyph with the given SBML level, version and
package version. The id if the associated
reference and the id of the associated glyph are set to the
empty string. The role is set to empty.
=item ReferenceGlyph::ReferenceGlyph
Ctor.
=item ReferenceGlyph::ReferenceGlyph
Creates a new ReferenceGlyph. The id is given as the first
argument, the id of the associated glyph is given as the
second argument. The third argument is the id of the associated
reference and the fourth argument is the role.
=item ReferenceGlyph::ReferenceGlyph
Creates a new ReferenceGlyph from the given XMLNode
=item ReferenceGlyph::ReferenceGlyph
Copy constructor.
=item ReferenceGlyph::getAllElements
Returns a List of all child SBase objects, including those nested to an
arbitrary depth
@return a List of pointers to all children structures.
=item ReferenceGlyph::renameSIdRefs
Renames all the C<SIdRef> attributes on this element, including any
found in MathML content (if such exists).
This method works by looking at all attributes and (if appropriate)
mathematical formulas, comparing the identifiers to the value of @p
oldid. If any matches are found, the matching identifiers are replaced
with C<newid>. The method does I<not> descend into child elements.
@param oldid the old identifier
@param newid the new identifier
=item ReferenceGlyph::getGlyphId
Returns the id of the associated glyph.
=item ReferenceGlyph::setGlyphId
Sets the id of the associated glyph.
=item ReferenceGlyph::getReferenceId
Returns the id of the associated sbml reference.
=item ReferenceGlyph::setReferenceId
Sets the id of the associated sbml reference.
=item ReferenceGlyph::getRole
Returns a string representation of the role.
=item ReferenceGlyph::setRole
Sets the role.
=item ReferenceGlyph::getCurve
Returns the curve object for the reference glyph
=item ReferenceGlyph::getCurve
Returns the curve object for the reference glyph
=item ReferenceGlyph::setCurve
Sets the curve object for the reference glyph.
=item ReferenceGlyph::isSetCurve
Returns true if the curve consists of one or more segments.
=item ReferenceGlyph::getCurveExplicitlySet
=item ReferenceGlyph::isSetGlyphId
Returns true if the id of the associated glyph is not the
empty string.
=item ReferenceGlyph::isSetReferenceId
Returns true if the id of the associated reference is not the
empty string.
=item ReferenceGlyph::isSetRole
Returns true of role is different from the empty string.
=item ReferenceGlyph::initDefaults
Calls initDefaults on GraphicalObject
=item ReferenceGlyph::createLineSegment
Creates a new LineSegment object, adds it to the end of the list of
curve segment objects of the curve and returns a reference to the
newly created object.
=item ReferenceGlyph::createCubicBezier
Creates a new CubicBezier object, adds it to the end of the list of
curve segment objects of the curve and returns a reference to the
newly created object.
=item ReferenceGlyph::writeElements
@internal
Subclasses should override this method to write out their contained
SBML objects as XML elements. Be sure to call your parents
implementation of this method as well. For example:
SBase::writeElements(stream);
mReactants.write(stream);
mProducts.write(stream);
...
=item ReferenceGlyph::getElementName
Returns the XML element name of
this SBML object.
=item ReferenceGlyph::clone
Creates and returns a deep copy of this ReferenceGlyph.
@return a (deep) copy of this ReferenceGlyph.
=item ReferenceGlyph::getTypeCode
Returns the libSBML type code of this object instance.
C<opydetails> doc_what_are_typecodes
@return the SBML type code for this object:
@link SBMLLayoutTypeCode_t#SBML_LAYOUT_REFERENCEGLYPH SBML_LAYOUT_REFERENCEGLYPH@endlink
C<opydetails> doc_warning_typecodes_not_unique
@see getElementName()
@see getPackageName()
=item ReferenceGlyph::accept
Accepts the given SBMLVisitor.
@return the result of calling C<v.visit()>, which indicates
whether or not the Visitor would like to visit the SBML object's next
sibling object (if available).
=item ReferenceGlyph::toXML
Creates an XMLNode object from this.
=item ReferenceGlyph::setSBMLDocument
@internal
Sets the parent SBMLDocument of this SBML object.
@param d the SBMLDocument object to use
=item ReferenceGlyph::connectToChild
@internal
Sets this SBML object to child SBML objects (if any).
(Creates a child-parent relationship by the parent)
Subclasses must override this function if they define
one ore more child elements.
Basically, this function needs to be called in
constructor, copy constructor, assignment operator.
@see setSBMLDocument
@see enablePackageInternal
=item ReferenceGlyph::enablePackageInternal
@internal
Enables/Disables the given package with this element and child
elements (if any).
(This is an internal implementation for enablePakcage function)
@note Subclasses in which one or more child elements are defined
must override this function.
=item ReferenceGlyph::createObject
@internal
Create and return an SBML object of this class, if present.
@return the SBML object corresponding to next XMLToken in the
XMLInputStream or NULL if the token was not recognized.
=item ReferenceGlyph::addExpectedAttributes
@internal
Subclasses should override this method to get the list of
expected attributes.
This function is invoked from corresponding readAttributes()
function.
=item ReferenceGlyph::readAttributes
@internal
Subclasses should override this method to read values from the given
XMLAttributes set into their specific fields. Be sure to call your
parents implementation of this method as well.
=item ReferenceGlyph::writeAttributes
@internal
Subclasses should override this method to write their XML attributes
to the XMLOutputStream. Be sure to call your parents implementation
of this method as well. For example:
SBase::writeAttributes(stream);
stream.writeAttribute( "id" , mId );
stream.writeAttribute( "name", mName );
...
=back
=head2 GeneralGlyph
@sbmlpackage{layout}
@htmlinclude pkg-marker-layout.html The GeneralGlyph is used by the “layout”
package to represent any SBML object.
The GeneralGlyph is used to facilitate the representation of elements
other than Compartment, Species and Reaction and thus can be used for the
display of relationships of Rule or elements defined by other SBML
packages. It closely follows the structure of the ReactionGlyph.
GeneralGlyph is defined to have an optional attribute reference as well as
the elements curve, listOfReferenceGlyphs and listOfSubGlyphs.
=over
=back
=head2 ListOfReferenceGlyphs
@sbmlpackage{layout}
@htmlinclude pkg-marker-layout.html Implementation of the ListOfReferenceGlyphs construct
from the “layout” package.
The ListOfReferenceGlyphs is a container for the ReferenceGlyph elements of a GeneralGlyph.
C<opydetails> doc_what_is_listof
@see ReferenceGlyph
=over
=item ListOfReferenceGlyphs::clone
Creates and returns a deep copy of this ListOfReferenceGlyphs.
@return a (deep) copy of this ListOfReferenceGlyphs.
=item ListOfReferenceGlyphs::ListOfReferenceGlyphs
Ctor.
=item ListOfReferenceGlyphs::ListOfReferenceGlyphs
Ctor.
=item ListOfReferenceGlyphs::getItemTypeCode
Returns the libSBML type code for the SBML objects
contained in this ListOf object.
C<opydetails> doc_what_are_typecodes
@return the SBML type code for objects contained in this list:
@link SBMLTypeCode_t#SBML_LAYOUT_REFERENCEGLYPH SBML_LAYOUT_REFERENCEGLYPH@endlink (default).
@see getElementName()
@see getPackageName()
=item ListOfReferenceGlyphs::getElementName
Returns the XML element name of
this SBML object.
=item ListOfReferenceGlyphs::get
Get a ReferenceGlyph from the ListOfReferenceGlyphs.
@param n the index number of the ReferenceGlyph to get.
@return the nth ReferenceGlyph in this ListOfReferenceGlyphs.
@see size()
=item ListOfReferenceGlyphs::get
Get a ReferenceGlyph from the ListOfReferenceGlyphs.
@param n the index number of the ReferenceGlyph to get.
@return the nth ReferenceGlyph in this ListOfReferenceGlyphs.
@see size()
=item ListOfReferenceGlyphs::get
Get a ReferenceGlyph from the ListOfReferenceGlyphs
based on its identifier.
@param sid a string representing the identifier
of the ReferenceGlyph to get.
@return ReferenceGlyph in this ListOfReferenceGlyphs
with the given C<sid> or C<NULL> if no such
ReferenceGlyph exists.
@see get(unsigned int n)
@see size()
=item ListOfReferenceGlyphs::get
Get a ReferenceGlyph from the ListOfReferenceGlyphs
based on its identifier.
@param sid a string representing the identifier
of the ReferenceGlyph to get.
@return ReferenceGlyph in this ListOfReferenceGlyphs
with the given C<sid> or C<NULL> if no such
ReferenceGlyph exists.
@see get(unsigned int n)
@see size()
=item ListOfReferenceGlyphs::remove
Removes the nth item from this ListOfReferenceGlyphs items and returns a pointer to
it.
The caller owns the returned item and is responsible for deleting it.
@param n the index of the item to remove
@see size()
=item ListOfReferenceGlyphs::remove
Removes item in this ListOfReferenceGlyphs items with the given identifier.
The caller owns the returned item and is responsible for deleting it.
If none of the items in this list have the identifier C<sid>, then @c
NULL is returned.
@param sid the identifier of the item to remove
@return the item removed. As mentioned above, the caller owns the
returned item.
=item ListOfReferenceGlyphs::toXML
Creates an XMLNode object from this.
=item ListOfReferenceGlyphs::createObject
@internal
Create and return an SBML object of this class, if present.
@return the SBML object corresponding to next XMLToken in the
XMLInputStream or NULL if the token was not recognized.
=item GeneralGlyph::GeneralGlyph
Creates a new GeneralGlyph. The list of reference glyph and subglyphs is
empty and the id of the associated element is set to the empty
string.
=item GeneralGlyph::GeneralGlyph
Creates a new GeneralGlyph with the given LayoutPkgNamespaces object.
=item GeneralGlyph::GeneralGlyph
Creates a glyph with the given LayoutPkgNamespaces and id.
(FOR BACKWARD COMPATIBILITY)
=item GeneralGlyph::GeneralGlyph
Creates a glyph with the given LayoutPkgNamespaces, id and set the id of the
associated element to the second argument.
(FOR BACKWARD COMPATIBILITY)
=item GeneralGlyph::GeneralGlyph
Creates a new GeneralGlyph from the given XMLNode
(FOR BACKWARD COMPATIBILITY)
=item GeneralGlyph::GeneralGlyph
Copy constructor.
=item GeneralGlyph::getAllElements
Returns a List of all child SBase objects, including those nested to an
arbitrary depth
@return a List of pointers to all children objects.
=item GeneralGlyph::renameSIdRefs
Renames all the C<SIdRef> attributes on this element, including any
found in MathML content (if such exists).
This method works by looking at all attributes and (if appropriate)
mathematical formulas, comparing the identifiers to the value of @p
oldid. If any matches are found, the matching identifiers are replaced
with C<newid>. The method does I<not> descend into child elements.
@param oldid the old identifier
@param newid the new identifier
=item GeneralGlyph::getReferenceId
Returns the id of the associated element.
=item GeneralGlyph::setReferenceId
Sets the id of the associated element.
=item GeneralGlyph::isSetReferenceId
Returns true if the id of the associated element is not the empty
string.
=item GeneralGlyph::getListOfReferenceGlyphs
Returns the ListOf object that hold the reference glyphs.
=item GeneralGlyph::getListOfReferenceGlyphs
Returns the ListOf object that hold the reference glyphs.
=item GeneralGlyph::getListOfSubGlyphs
Returns the ListOf object that hold the sub glyphs.
=item GeneralGlyph::getListOfSubGlyphs
Returns the ListOf object that hold the sub glyphs.
=item GeneralGlyph::getReferenceGlyph
Returns the reference glyph with the given index.
If the index is invalid, C<NULL> is returned.
=item GeneralGlyph::getReferenceGlyph
Returns the reference glyph with the given index.
If the index is invalid, C<NULL> is returned.
=item GeneralGlyph::getSubGlyph
Returns the sub glyph with the given index.
If the index is invalid, C<NULL> is returned.
=item GeneralGlyph::getSubGlyph
Returns the sub glyph with the given index.
If the index is invalid, C<NULL> is returned.
=item GeneralGlyph::addReferenceGlyph
Adds a new reference glyph to the list.
=item GeneralGlyph::addSubGlyph
Adds a new subglyph to the list.
=item GeneralGlyph::getNumReferenceGlyphs
Returns the number of reference glyph objects.
=item GeneralGlyph::getNumSubGlyphs
Returns the number of subglyph objects.
=item GeneralGlyph::initDefaults
Calls initDefaults from GraphicalObject.
=item GeneralGlyph::getCurve
Returns the curve object for the reaction glyph
=item GeneralGlyph::getCurve
Returns the curve object for the reaction glyph
=item GeneralGlyph::setCurve
Sets the curve object for the reaction glyph.
=item GeneralGlyph::isSetCurve
Returns true if the curve consists of one or more segments.
=item GeneralGlyph::getCurveExplicitlySet
=item GeneralGlyph::createReferenceGlyph
Creates a new ReferenceGlyph object, adds it to the end of the
list of reference objects and returns a reference to the newly
created object.
=item GeneralGlyph::createLineSegment
Creates a new LineSegment object, adds it to the end of the list of
curve segment objects of the curve and returns a reference to the
newly created object.
=item GeneralGlyph::createCubicBezier
Creates a new CubicBezier object, adds it to the end of the list of
curve segment objects of the curve and returns a reference to the
newly created object.
=item GeneralGlyph::removeReferenceGlyph
Remove the reference glyph with the given index.
A pointer to the object is returned. If no object has been removed, NULL
is returned.
=item GeneralGlyph::removeSubGlyph
Remove the subglyph with the given index.
A pointer to the object is returned. If no object has been removed, NULL
is returned.
=item GeneralGlyph::removeReferenceGlyph
Remove the reference glyph with the given C<id>.
A pointer to the object is returned. If no object has been removed, NULL
is returned.
=item GeneralGlyph::removeSubGlyph
Remove the subglyph with the given C<id>.
A pointer to the object is returned. If no object has been removed, NULL
is returned.
=item GeneralGlyph::getIndexForReferenceGlyph
Returns the index of the reference glyph with the given C<id>.
If the glyph does not contain a reference glyph with this
id, @if cpp numeric_limits<unsigned int>::max() @endif@if notcpp the
value of the maximum long integer@endif@~ is returned as an indicator.
=item GeneralGlyph::getIndexForSubGlyph
Returns the index of the subglyph with the given C<id>.
If the glyph does not contain a subglyph with this
id, @if cpp numeric_limits<unsigned int>::max() @endif@if notcpp the
value of the maximum long integer@endif@~ is returned as an indicator.
=item GeneralGlyph::writeElements
@internal
Subclasses should override this method to write out their contained
SBML objects as XML elements. Be sure to call your parents
implementation of this method as well. For example:
SBase::writeElements(stream);
mReactants.write(stream);
mProducts.write(stream);
...
=item GeneralGlyph::getElementName
Returns the XML element name of
this SBML object.
=item GeneralGlyph::clone
Creates and returns a deep copy of this GeneralGlyph.
@return a (deep) copy of this GeneralGlyph.
=item GeneralGlyph::getTypeCode
Returns the libSBML type code of this object instance.
C<opydetails> doc_what_are_typecodes
@return the SBML type code for this object:
@link SBMLLayoutTypeCode_t#SBML_LAYOUT_GENERALGLYPH SBML_LAYOUT_GENERALGLYPH@endlink
C<opydetails> doc_warning_typecodes_not_unique
@see getElementName()
@see getPackageName()
=item GeneralGlyph::accept
Accepts the given SBMLVisitor.
@return the result of calling C<v.visit()>, which indicates
whether or not the Visitor would like to visit the SBML object's next
sibling object (if available).
=item GeneralGlyph::toXML
Creates an XMLNode object from this.
=item GeneralGlyph::setSBMLDocument
@internal
Sets the parent SBMLDocument of this SBML object.
@param d the SBMLDocument object to use
=item GeneralGlyph::connectToChild
@internal
Sets this SBML object to child SBML objects (if any).
(Creates a child-parent relationship by the parent)
Subclasses must override this function if they define
one ore more child elements.
Basically, this function needs to be called in
constructor, copy constructor, assignment operator.
@see setSBMLDocument
@see enablePackageInternal
=item GeneralGlyph::enablePackageInternal
@internal
Enables/Disables the given package with this element and child
elements (if any).
(This is an internal implementation for enablePakcage function)
@note Subclasses in which one or more child elements are defined
must override this function.
=item GeneralGlyph::createObject
@internal
Create and return an SBML object of this class, if present.
@return the SBML object corresponding to next XMLToken in the
XMLInputStream or NULL if the token was not recognized.
=item GeneralGlyph::addExpectedAttributes
@internal
Subclasses should override this method to get the list of
expected attributes.
This function is invoked from corresponding readAttributes()
function.
=item GeneralGlyph::readAttributes
@internal
Subclasses should override this method to read values from the given
XMLAttributes set into their specific fields. Be sure to call your
parents implementation of this method as well.
=item GeneralGlyph::writeAttributes
@internal
Subclasses should override this method to write their XML attributes
to the XMLOutputStream. Be sure to call your parents implementation
of this method as well. For example:
SBase::writeAttributes(stream);
stream.writeAttribute( "id" , mId );
stream.writeAttribute( "name", mName );
...
=back
=head2 ReactionGlyph
@sbmlpackage{layout}
@htmlinclude pkg-marker-layout.html The ReactionGlyph is used to represent Reaction
elements in the layout.
Analogous to how a Reaction object has to at least have one reactant or
product, the ReactionGlyph has to at least have one SpeciesReferenceGlyph
stored in the ListOfSpeciesReferenceGlyphs. Figure 12 on the following
page provides the UML diagram for the class definition. The ReactionGlyph
inherits from GraphicalObject. In addition to the attributes inherited
from GraphicalObject, the ReactionGlyph is described by an attribute
reaction, a Curve element and a listOfSpeciesReferenceGlyphs element. The
Curve describes the center section of a ReactionGlyph. The center section
is frequently used by tools to separate the point where substrates arcs
come together, from the point where product arcs split off. The Curve is
optional, and when not present the dimensions of the inherited BoundingBox
describes the center section, by storing its position and dimension.
=over
=back
=head2 ListOfSpeciesReferenceGlyphs
@sbmlpackage{layout}
@htmlinclude pkg-marker-layout.html Implementation of the ListOfSpeciesReferenceGlyphs
construct from the “layout” package.
The ListOfSpeciesReferenceGlyphs is a container for the SpeciesReferenceGlyphs elements of a ReactionGlyph.
C<opydetails> doc_what_is_listof
@see SpeciesReferenceGlyph
=over
=item ListOfSpeciesReferenceGlyphs::clone
Creates and returns a deep copy of this ListOfSpeciesReferenceGlyphs.
@return a (deep) copy of this ListOfSpeciesReferenceGlyphs.
=item ListOfSpeciesReferenceGlyphs::ListOfSpeciesReferenceGlyphs
Ctor.
=item ListOfSpeciesReferenceGlyphs::ListOfSpeciesReferenceGlyphs
Ctor.
=item ListOfSpeciesReferenceGlyphs::getItemTypeCode
Returns the libSBML type code for the SBML objects
contained in this ListOf object.
C<opydetails> doc_what_are_typecodes
@return the SBML type code for objects contained in this list:
@link SBMLTypeCode_t#SBML_LAYOUT_SPECIESREFERENCEGLYPH SBML_LAYOUT_SPECIESREFERENCEGLYPH@endlink (default).
@see getElementName()
@see getPackageName()
=item ListOfSpeciesReferenceGlyphs::getElementName
Returns the XML element name of
this SBML object.
=item ListOfSpeciesReferenceGlyphs::get
Get a SpeciesReferenceGlyph from the ListOfSpeciesReferenceGlyphs.
@param n the index number of the SpeciesReferenceGlyph to get.
@return the nth SpeciesReferenceGlyph in this ListOfSpeciesReferenceGlyphs.
@see size()
=item ListOfSpeciesReferenceGlyphs::get
Get a SpeciesReferenceGlyph from the ListOfSpeciesReferenceGlyphs.
@param n the index number of the SpeciesReferenceGlyph to get.
@return the nth SpeciesReferenceGlyph in this ListOfSpeciesReferenceGlyphs.
@see size()
=item ListOfSpeciesReferenceGlyphs::get
Get a SpeciesReferenceGlyph from the ListOfSpeciesReferenceGlyphs
based on its identifier.
@param sid a string representing the identifier
of the SpeciesReferenceGlyph to get.
@return SpeciesReferenceGlyph in this ListOfSpeciesReferenceGlyphs
with the given C<sid> or C<NULL> if no such
SpeciesReferenceGlyph exists.
@see get(unsigned int n)
@see size()
=item ListOfSpeciesReferenceGlyphs::get
Get a SpeciesReferenceGlyph from the ListOfSpeciesReferenceGlyphs
based on its identifier.
@param sid a string representing the identifier
of the SpeciesReferenceGlyph to get.
@return SpeciesReferenceGlyph in this ListOfSpeciesReferenceGlyphs
with the given C<sid> or C<NULL> if no such
SpeciesReferenceGlyph exists.
@see get(unsigned int n)
@see size()
=item ListOfSpeciesReferenceGlyphs::remove
Removes the nth item from this ListOfSpeciesReferenceGlyphs items and returns a pointer to
it.
The caller owns the returned item and is responsible for deleting it.
@param n the index of the item to remove
@see size()
=item ListOfSpeciesReferenceGlyphs::remove
Removes item in this ListOfSpeciesReferenceGlyphs items with the given identifier.
The caller owns the returned item and is responsible for deleting it.
If none of the items in this list have the identifier C<sid>, then @c
NULL is returned.
@param sid the identifier of the item to remove
@return the item removed. As mentioned above, the caller owns the
returned item.
=item ListOfSpeciesReferenceGlyphs::toXML
Creates an XMLNode object from this.
=item ListOfSpeciesReferenceGlyphs::createObject
@internal
Create and return an SBML object of this class, if present.
@return the SBML object corresponding to next XMLToken in the
XMLInputStream or NULL if the token was not recognized.
=item ReactionGlyph::ReactionGlyph
Creates a new ReactionGlyph. The list of species reference glyph is
empty and the id of the associated reaction is set to the empty
string.
=item ReactionGlyph::ReactionGlyph
Creates a new ReactionGlyph with the given LayoutPkgNamespaces object.
=item ReactionGlyph::ReactionGlyph
Creates a ResctionGlyph with the given LayoutPkgNamespaces and id.
(FOR BACKWARD COMPATIBILITY)
=item ReactionGlyph::ReactionGlyph
Creates a ResctionGlyph with the given LayoutPkgNamespaces, id and set the id of the
associated reaction to the second argument.
(FOR BACKWARD COMPATIBILITY)
=item ReactionGlyph::ReactionGlyph
Creates a new ReactionGlyph from the given XMLNode
(FOR BACKWARD COMPATIBILITY)
=item ReactionGlyph::ReactionGlyph
Copy constructor.
=item ReactionGlyph::getReactionId
Returns the id of the associated reaction.
=item ReactionGlyph::setReactionId
Sets the id of the associated reaction.
=item ReactionGlyph::isSetReactionId
Returns true if the id of the associated reaction is not the empty
string.
=item ReactionGlyph::getListOfSpeciesReferenceGlyphs
Returns the ListOf object that hold the species reference glyphs.
=item ReactionGlyph::getListOfSpeciesReferenceGlyphs
Returns the ListOf object that hold the species reference glyphs.
=item ReactionGlyph::getSpeciesReferenceGlyph
Returns the species reference glyph with the given index.
If the index is invalid, C<NULL> is returned.
=item ReactionGlyph::getSpeciesReferenceGlyph
Returns the species reference glyph with the given index.
If the index is invalid, C<NULL> is returned.
=item ReactionGlyph::addSpeciesReferenceGlyph
Adds a new species reference glyph to the list.
=item ReactionGlyph::getNumSpeciesReferenceGlyphs
Returns the number of species reference glyph objects.
=item ReactionGlyph::initDefaults
Calls initDefaults from GraphicalObject.
=item ReactionGlyph::getAllElements
Returns a List of all child SBase objects, including those nested to an
arbitrary depth
@return a List of pointers to all children objects.
=item ReactionGlyph::renameSIdRefs
Renames all the C<SIdRef> attributes on this element, including any
found in MathML content (if such exists).
This method works by looking at all attributes and (if appropriate)
mathematical formulas, comparing the identifiers to the value of @p
oldid. If any matches are found, the matching identifiers are replaced
with C<newid>. The method does I<not> descend into child elements.
@param oldid the old identifier
@param newid the new identifier
=item ReactionGlyph::getCurve
Returns the curve object for the reaction glyph
=item ReactionGlyph::getCurve
Returns the curve object for the reaction glyph
=item ReactionGlyph::setCurve
Sets the curve object for the reaction glyph.
=item ReactionGlyph::isSetCurve
Returns true if the curve consists of one or more segments.
=item ReactionGlyph::getCurveExplicitlySet
=item ReactionGlyph::createSpeciesReferenceGlyph
Creates a new SpeciesReferenceGlyph object, adds it to the end of the
list of species reference objects and returns a reference to the newly
created object.
=item ReactionGlyph::createLineSegment
Creates a new LineSegment object, adds it to the end of the list of
curve segment objects of the curve and returns a reference to the
newly created object.
=item ReactionGlyph::createCubicBezier
Creates a new CubicBezier object, adds it to the end of the list of
curve segment objects of the curve and returns a reference to the
newly created object.
=item ReactionGlyph::removeSpeciesReferenceGlyph
Remove the species reference glyph with the given index.
A pointer to the object is returned. If no object has been removed, NULL
is returned.
=item ReactionGlyph::removeSpeciesReferenceGlyph
Remove the species reference glyph with the given C<id>.
A pointer to the object is returned. If no object has been removed, NULL
is returned.
=item ReactionGlyph::getIndexForSpeciesReferenceGlyph
Returns the index of the species reference glyph with the given C<id>.
If the reaction glyph does not contain a species reference glyph with this
id, @if cpp numeric_limits<unsigned int>::max() @endif@if notcpp the
value of the maximum long integer@endif@~ is returned as an indicator.
=item ReactionGlyph::writeElements
@internal
Subclasses should override this method to write out their contained
SBML objects as XML elements. Be sure to call your parents
implementation of this method as well. For example:
SBase::writeElements(stream);
mReactants.write(stream);
mProducts.write(stream);
...
=item ReactionGlyph::getElementName
Returns the XML element name of
this SBML object.
=item ReactionGlyph::clone
Creates and returns a deep copy of this ReactionGlyph object.
@return a (deep) copy of this ReactionGlyph.
=item ReactionGlyph::getTypeCode
Returns the libSBML type code of this object instance.
C<opydetails> doc_what_are_typecodes
@return the SBML type code for this object:
@link SBMLLayoutTypeCode_t#SBML_LAYOUT_REACTIONGLYPH SBML_LAYOUT_REACTIONGLYPH@endlink
C<opydetails> doc_warning_typecodes_not_unique
@see getElementName()
@see getPackageName()
=item ReactionGlyph::accept
Accepts the given SBMLVisitor.
@return the result of calling C<v.visit()>, which indicates
whether or not the Visitor would like to visit the SBML object's next
sibling object (if available).
=item ReactionGlyph::toXML
Creates an XMLNode object from this.
=item ReactionGlyph::setSBMLDocument
@internal
Sets the parent SBMLDocument of this SBML object.
@param d the SBMLDocument object to use
=item ReactionGlyph::connectToChild
@internal
Sets this SBML object to child SBML objects (if any).
(Creates a child-parent relationship by the parent)
Subclasses must override this function if they define
one ore more child elements.
Basically, this function needs to be called in
constructor, copy constructor, assignment operator.
@see setSBMLDocument
@see enablePackageInternal
=item ReactionGlyph::enablePackageInternal
@internal
Enables/Disables the given package with this element and child
elements (if any).
(This is an internal implementation for enablePakcage function)
@note Subclasses in which one or more child elements are defined
must override this function.
=item ReactionGlyph::createObject
@internal
Create and return an SBML object of this class, if present.
@return the SBML object corresponding to next XMLToken in the
XMLInputStream or NULL if the token was not recognized.
=item ReactionGlyph::addExpectedAttributes
@internal
Subclasses should override this method to get the list of
expected attributes.
This function is invoked from corresponding readAttributes()
function.
=item ReactionGlyph::readAttributes
@internal
Subclasses should override this method to read values from the given
XMLAttributes set into their specific fields. Be sure to call your
parents implementation of this method as well.
=item ReactionGlyph::writeAttributes
@internal
Subclasses should override this method to write their XML attributes
to the XMLOutputStream. Be sure to call your parents implementation
of this method as well. For example:
SBase::writeAttributes(stream);
stream.writeAttribute( "id" , mId );
stream.writeAttribute( "name", mName );
...
=back
=head2 SpeciesGlyph
@sbmlpackage{layout}
@htmlinclude pkg-marker-layout.html The SpeciesGlyph represents a Species in the
“layout” package.
In addition to the attributes it inherits from GraphicalObject, the
SpeciesGlyph object has an optional 'species' attribute.
=over
=item SpeciesGlyph::SpeciesGlyph
Creates a new SpeciesGlyph with the given SBML level, version, and package version
and the id of the associated species set to the empty string.
=item SpeciesGlyph::SpeciesGlyph
Ctor.
=item SpeciesGlyph::SpeciesGlyph
Creates a new SpeciesGlyph with the given C<id>.
(FOR BACKWARD COMPATIBILITY)
=item SpeciesGlyph::SpeciesGlyph
Creates a new SpeciesGlyph with the given C<id> and the id of the
associated species object set to the second argument.
(FOR BACKWARD COMPATIBILITY)
=item SpeciesGlyph::SpeciesGlyph
Creates a new SpeciesGlyph from the given XMLNode
=item SpeciesGlyph::SpeciesGlyph
Copy constructor.
=item SpeciesGlyph::renameSIdRefs
Renames all the C<SIdRef> attributes on this element, including any
found in MathML content (if such exists).
This method works by looking at all attributes and (if appropriate)
mathematical formulas, comparing the identifiers to the value of @p
oldid. If any matches are found, the matching identifiers are replaced
with C<newid>. The method does I<not> descend into child elements.
@param oldid the old identifier
@param newid the new identifier
=item SpeciesGlyph::getSpeciesId
Returns the id of the associated species object.
=item SpeciesGlyph::setSpeciesId
Sets the id of the associated species object.
=item SpeciesGlyph::isSetSpeciesId
Returns true if the id of the associated species object is not the
empty string.
=item SpeciesGlyph::initDefaults
Calls initDefaults from GraphicalObject.
=item SpeciesGlyph::writeElements
@internal
Subclasses should override this method to write out their contained
SBML objects as XML elements. Be sure to call your parents
implementation of this method as well. For example:
SBase::writeElements(stream);
mReactants.write(stream);
mProducts.write(stream);
...
=item SpeciesGlyph::getElementName
Returns the XML element name of
this SBML object.
=item SpeciesGlyph::clone
Creates and returns a deep copy of this SpeciesGlyph.
@return a (deep) copy of this SpeciesGlyph.
=item SpeciesGlyph::getTypeCode
Returns the libSBML type code of this object instance.
C<opydetails> doc_what_are_typecodes
@return the SBML type code for this object:
@link SBMLLayoutTypeCode_t#SBML_LAYOUT_SPECIESGLYPH SBML_LAYOUT_SPECIESGLYPH@endlink
C<opydetails> doc_warning_typecodes_not_unique
@see getElementName()
@see getPackageName()
=item SpeciesGlyph::toXML
Creates an XMLNode object from this.
=item SpeciesGlyph::createObject
@internal
Create and return an SBML object of this class, if present.
@return the SBML object corresponding to next XMLToken in the
XMLInputStream or NULL if the token was not recognized.
=item SpeciesGlyph::addExpectedAttributes
@internal
Subclasses should override this method to get the list of
expected attributes.
This function is invoked from corresponding readAttributes()
function.
=item SpeciesGlyph::readAttributes
@internal
Subclasses should override this method to read values from the given
XMLAttributes set into their specific fields. Be sure to call your
parents implementation of this method as well.
=item SpeciesGlyph::writeAttributes
@internal
Subclasses should override this method to write their XML attributes
to the XMLOutputStream. Be sure to call your parents implementation
of this method as well. For example:
SBase::writeAttributes(stream);
stream.writeAttribute( "id" , mId );
stream.writeAttribute( "name", mName );
...
=back
=head2 TextGlyph
@sbmlpackage{layout}
@htmlinclude pkg-marker-layout.html The TextGlyph class describes the position and
dimension of text labels in the “layout” package.
It inherits from GraphicalObject and adds the attributes graphicalObject,
text and originOfText.
=over
=item TextGlyph::TextGlyph
Creates a new TextGlyph with the given SBML level, versin and package
version. The ids of the associated GraphicalObject and
the originOfText are set to the empty string. The actual text is set
to the empty string as well.
=item TextGlyph::TextGlyph
Ctor.
=item TextGlyph::TextGlyph
Creates a new TextGlyph. The id is given as the first argument.
(FOR BACKWARD COMPATIBILITY)
=item TextGlyph::TextGlyph
Creates a new TextGlyph. The id is given as the first argument, the
text to be displayed as the second. All other attirbutes are set to
the empty string.
(FOR BACKWARD COMPATIBILITY)
=item TextGlyph::TextGlyph
Creates a new TextGlyph from the given XMLNode
(FOR BACKWARD COMPATIBILITY)
=item TextGlyph::TextGlyph
Copy constructor.
=item TextGlyph::renameSIdRefs
Renames all the C<SIdRef> attributes on this element, including any
found in MathML content (if such exists).
This method works by looking at all attributes and (if appropriate)
mathematical formulas, comparing the identifiers to the value of @p
oldid. If any matches are found, the matching identifiers are replaced
with C<newid>. The method does I<not> descend into child elements.
@param oldid the old identifier
@param newid the new identifier
=item TextGlyph::getText
Returns the text to be displayed by the text glyph.
=item TextGlyph::setText
Sets the text to be displayed by the text glyph.
=item TextGlyph::getGraphicalObjectId
Returns the id of the associated graphical object.
=item TextGlyph::setGraphicalObjectId
Sets the id of the associated graphical object.
=item TextGlyph::getOriginOfTextId
Returns the id of the origin of text.
=item TextGlyph::setOriginOfTextId
Sets the id of the origin of text.
=item TextGlyph::isSetText
Returns true if the text is not the empty string.
=item TextGlyph::isSetOriginOfTextId
Returns true if the id of the origin of text is not the empty string.
=item TextGlyph::isSetGraphicalObjectId
Returns true if the id of the associated graphical object is not the
empty string.
=item TextGlyph::initDefaults
Calls initDefaults from GraphicalObject.
=item TextGlyph::writeElements
@internal
Subclasses should override this method to write out their contained
SBML objects as XML elements. Be sure to call your parents
implementation of this method as well. For example:
SBase::writeElements(stream);
mReactants.write(stream);
mProducts.write(stream);
...
=item TextGlyph::getElementName
Returns the XML element name of
this SBML object.
=item TextGlyph::clone
Creates and returns a deep copy of this TextGlyph.
@return a (deep) copy of this TextGlyph.
=item TextGlyph::getTypeCode
Returns the libSBML type code of this object instance.
C<opydetails> doc_what_are_typecodes
@return the SBML type code for this object:
@link SBMLLayoutTypeCode_t#SBML_LAYOUT_TEXTGLYPH SBML_LAYOUT_TEXTGLYPH@endlink
C<opydetails> doc_warning_typecodes_not_unique
@see getElementName()
@see getPackageName()
=item TextGlyph::toXML
Creates an XMLNode object from this.
=item TextGlyph::createObject
@internal
Create and return an SBML object of this class, if present.
@return the SBML object corresponding to next XMLToken in the
XMLInputStream or NULL if the token was not recognized.
=item TextGlyph::addExpectedAttributes
@internal
Subclasses should override this method to get the list of
expected attributes.
This function is invoked from corresponding readAttributes()
function.
=item TextGlyph::readAttributes
@internal
Subclasses should override this method to read values from the given
XMLAttributes set into their specific fields. Be sure to call your
parents implementation of this method as well.
=item TextGlyph::writeAttributes
@internal
Subclasses should override this method to write their XML attributes
to the XMLOutputStream. Be sure to call your parents implementation
of this method as well. For example:
SBase::writeAttributes(stream);
stream.writeAttribute( "id" , mId );
stream.writeAttribute( "name", mName );
...
=back
=head2 Layout
@sbmlpackage{layout}
@htmlinclude pkg-marker-layout.html Each Layout object stores a set of layout information
for objects in the Model.
The Layout class stores layout information for some or all elements of the
SBML model as well as additional objects that need not be connected to the
model. The Layout has two attributes: id and name. Additionally, a
Dimensions element specifies the size of the layout. The actual layout
elements are contained in several lists, namely: a
ListOfCompartmentGlyphs, a ListOfSpeciesGlyphs, a ListOfReactionGlyphs, a
ListOfTextGlyphs, and a ListOfAdditionalGraphicalObjects. Each of these
lists can only occur once, and, if present, are not allowed to be empty.
=over
=back
=head2 ListOfCompartmentGlyphs
@sbmlpackage{layout}
@htmlinclude pkg-marker-layout.html Implementation of the ListOfCompartmentGlyphs
construct from the “layout” package.
The ListOfCompartmentGlyphs is a container for the CompartmentGlyph elements of a Layout.
C<opydetails> doc_what_is_listof
@see CompartmentGlyph
=over
=back
=head2 ListOfSpeciesGlyphs
@sbmlpackage{layout}
@htmlinclude pkg-marker-layout.html Implementation of the ListOfSpeciesGlyphs construct
from the “layout” package.
The ListOfSpeciesGlyphs is a container for the SpeciesGlyph elements of a Layout.
C<opydetails> doc_what_is_listof
@see SpeciesGlyph
=over
=back
=head2 ListOfReactionGlyphs
@sbmlpackage{layout}
@htmlinclude pkg-marker-layout.html Implementation of the ListOfReactionGlyphs construct
from the “layout” package.
The ListOfReactionGlyphs is a container for the ReactionGlyph elements of a Layout.
C<opydetails> doc_what_is_listof
@see ReactionGlyph
=over
=back
=head2 ListOfTextGlyphs
@sbmlpackage{layout}
@htmlinclude pkg-marker-layout.html Implementation of the ListOfTextGlyphs construct from
the “layout” package.
The ListOfTextGlyphs is a container for the TextGlyph elements of a Layout.
C<opydetails> doc_what_is_listof
@see TextGlyph
=over
=back
=head2 ListOfLayouts
@sbmlpackage{layout}
@htmlinclude pkg-marker-layout.html Implementation of the ListOfLayouts construct from
the “layout” package.
The ListOfLayouts is a container for the Layout elements of an extended Model element.
C<opydetails> doc_what_is_listof
@see Layout
=over
=item ListOfCompartmentGlyphs::clone
Creates and returns a deep copy of this ListOfCompartmentGlyphs.
@return a (deep) copy of this ListOfCompartmentGlyphs.
=item ListOfCompartmentGlyphs::ListOfCompartmentGlyphs
Ctor.
=item ListOfCompartmentGlyphs::ListOfCompartmentGlyphs
Ctor.
=item ListOfCompartmentGlyphs::getItemTypeCode
Returns the libSBML type code for the SBML objects
contained in this ListOf object.
C<opydetails> doc_what_are_typecodes
@return the SBML type code for objects contained in this list:
@link SBMLTypeCode_t#SBML_LAYOUT_COMPARTMENTGLYPH SBML_LAYOUT_COMPARTMENTGLYPH@endlink (default).
@see getElementName()
@see getPackageName()
=item ListOfCompartmentGlyphs::getElementName
Returns the XML element name of
this SBML object.
=item ListOfCompartmentGlyphs::toXML
Creates an XMLNode object from this.
=item ListOfCompartmentGlyphs::get
Get a CompartmentGlyph from the ListOfCompartmentGlyphs.
@param n the index number of the CompartmentGlyph to get.
@return the nth CompartmentGlyph in this ListOfCompartmentGlyphs.
@see size()
=item ListOfCompartmentGlyphs::get
Get a CompartmentGlyph from the ListOfCompartmentGlyphs.
@param n the index number of the CompartmentGlyph to get.
@return the nth CompartmentGlyph in this ListOfCompartmentGlyphs.
@see size()
=item ListOfCompartmentGlyphs::get
Get a CompartmentGlyph from the ListOfCompartmentGlyphs
based on its identifier.
@param sid a string representing the identifier
of the CompartmentGlyph to get.
@return CompartmentGlyph in this ListOfCompartmentGlyphs
with the given C<sid> or C<NULL> if no such
CompartmentGlyph exists.
@see get(unsigned int n)
@see size()
=item ListOfCompartmentGlyphs::get
Get a CompartmentGlyph from the ListOfCompartmentGlyphs
based on its identifier.
@param sid a string representing the identifier
of the CompartmentGlyph to get.
@return CompartmentGlyph in this ListOfCompartmentGlyphs
with the given C<sid> or C<NULL> if no such
CompartmentGlyph exists.
@see get(unsigned int n)
@see size()
=item ListOfCompartmentGlyphs::remove
Removes the nth item from this ListOfCompartmentGlyphs items and returns a pointer to
it.
The caller owns the returned item and is responsible for deleting it.
@param n the index of the item to remove
@see size()
=item ListOfCompartmentGlyphs::remove
Removes item in this ListOfCompartmentGlyphs items with the given identifier.
The caller owns the returned item and is responsible for deleting it.
If none of the items in this list have the identifier C<sid>, then @c
NULL is returned.
@param sid the identifier of the item to remove
@return the item removed. As mentioned above, the caller owns the
returned item.
=item ListOfCompartmentGlyphs::createObject
@internal
Create and return an SBML object of this class, if present.
@return the SBML object corresponding to next XMLToken in the
XMLInputStream or NULL if the token was not recognized.
=item ListOfSpeciesGlyphs::clone
Creates and returns a deep copy of this ListOfSpeciesGlyphs.
@return a (deep) copy of this ListOfSpeciesGlyphs.
=item ListOfSpeciesGlyphs::ListOfSpeciesGlyphs
Ctor.
=item ListOfSpeciesGlyphs::ListOfSpeciesGlyphs
Ctor.
=item ListOfSpeciesGlyphs::getItemTypeCode
Returns the libSBML type code for the SBML objects
contained in this ListOf object.
C<opydetails> doc_what_are_typecodes
@return the SBML type code for objects contained in this list:
@link SBMLTypeCode_t#SBML_LAYOUT_SPECIESGLYPH SBML_LAYOUT_SPECIESGLYPH@endlink (default).
@see getElementName()
@see getPackageName()
=item ListOfSpeciesGlyphs::getElementName
Returns the XML element name of
this SBML object.
=item ListOfSpeciesGlyphs::get
Get a SpeciesGlyph from the ListOfSpeciesGlyphs.
@param n the index number of the SpeciesGlyph to get.
@return the nth SpeciesGlyph in this ListOfSpeciesGlyphs.
@see size()
=item ListOfSpeciesGlyphs::get
Get a SpeciesGlyph from the ListOfSpeciesGlyphs.
@param n the index number of the SpeciesGlyph to get.
@return the nth SpeciesGlyph in this ListOfSpeciesGlyphs.
@see size()
=item ListOfSpeciesGlyphs::get
Get a SpeciesGlyph from the ListOfSpeciesGlyphs
based on its identifier.
@param sid a string representing the identifier
of the SpeciesGlyph to get.
@return SpeciesGlyph in this ListOfSpeciesGlyphs
with the given C<sid> or C<NULL> if no such
SpeciesGlyph exists.
@see get(unsigned int n)
@see size()
=item ListOfSpeciesGlyphs::get
Get a SpeciesGlyph from the ListOfSpeciesGlyphs
based on its identifier.
@param sid a string representing the identifier
of the SpeciesGlyph to get.
@return SpeciesGlyph in this ListOfSpeciesGlyphs
with the given C<sid> or C<NULL> if no such
SpeciesGlyph exists.
@see get(unsigned int n)
@see size()
=item ListOfSpeciesGlyphs::remove
Removes the nth item from this ListOfSpeciesGlyphs items and returns a pointer to
it.
The caller owns the returned item and is responsible for deleting it.
@param n the index of the item to remove
@see size()
=item ListOfSpeciesGlyphs::remove
Removes item in this ListOfSpeciesGlyphs items with the given identifier.
The caller owns the returned item and is responsible for deleting it.
If none of the items in this list have the identifier C<sid>, then @c
NULL is returned.
@param sid the identifier of the item to remove
@return the item removed. As mentioned above, the caller owns the
returned item.
=item ListOfSpeciesGlyphs::toXML
Creates an XMLNode object from this.
=item ListOfSpeciesGlyphs::createObject
@internal
Create and return an SBML object of this class, if present.
@return the SBML object corresponding to next XMLToken in the
XMLInputStream or NULL if the token was not recognized.
=item ListOfReactionGlyphs::clone
Creates and returns a deep copy of this ListOfReactionGlyphs.
@return a (deep) copy of this ListOfReactionGlyphs.
=item ListOfReactionGlyphs::ListOfReactionGlyphs
Ctor.
=item ListOfReactionGlyphs::ListOfReactionGlyphs
Ctor.
=item ListOfReactionGlyphs::getItemTypeCode
Returns the libSBML type code for the SBML objects
contained in this ListOf object.
C<opydetails> doc_what_are_typecodes
@return the SBML type code for objects contained in this list:
@link SBMLTypeCode_t#SBML_LAYOUT_REACTIONGLYPH SBML_LAYOUT_REACTIONGLYPH@endlink (default).
@see getElementName()
@see getPackageName()
=item ListOfReactionGlyphs::getElementName
Returns the XML element name of
this SBML object.
=item ListOfReactionGlyphs::get
Get a ReactionGlyph from the ListOfReactionGlyphs.
@param n the index number of the ReactionGlyph to get.
@return the nth ReactionGlyph in this ListOfReactionGlyphs.
@see size()
=item ListOfReactionGlyphs::get
Get a ReactionGlyph from the ListOfReactionGlyphs.
@param n the index number of the ReactionGlyph to get.
@return the nth ReactionGlyph in this ListOfReactionGlyphs.
@see size()
=item ListOfReactionGlyphs::get
Get a ReactionGlyph from the ListOfReactionGlyphs
based on its identifier.
@param sid a string representing the identifier
of the ReactionGlyph to get.
@return ReactionGlyph in this ListOfReactionGlyphs
with the given C<sid> or C<NULL> if no such
ReactionGlyph exists.
@see get(unsigned int n)
@see size()
=item ListOfReactionGlyphs::get
Get a ReactionGlyph from the ListOfReactionGlyphs
based on its identifier.
@param sid a string representing the identifier
of the ReactionGlyph to get.
@return ReactionGlyph in this ListOfReactionGlyphs
with the given C<sid> or C<NULL> if no such
ReactionGlyph exists.
@see get(unsigned int n)
@see size()
=item ListOfReactionGlyphs::remove
Removes the nth item from this ListOfReactionGlyphs items and returns a pointer to
it.
The caller owns the returned item and is responsible for deleting it.
@param n the index of the item to remove
@see size()
=item ListOfReactionGlyphs::remove
Removes item in this ListOfReactionGlyphs items with the given identifier.
The caller owns the returned item and is responsible for deleting it.
If none of the items in this list have the identifier C<sid>, then @c
NULL is returned.
@param sid the identifier of the item to remove
@return the item removed. As mentioned above, the caller owns the
returned item.
=item ListOfReactionGlyphs::toXML
Creates an XMLNode object from this.
=item ListOfReactionGlyphs::createObject
@internal
Create and return an SBML object of this class, if present.
@return the SBML object corresponding to next XMLToken in the
XMLInputStream or NULL if the token was not recognized.
=item ListOfTextGlyphs::clone
Creates and returns a deep copy of this ListOfTextGlyphs.
@return a (deep) copy of this ListOfTextGlyphs.
=item ListOfTextGlyphs::ListOfTextGlyphs
Ctor.
=item ListOfTextGlyphs::ListOfTextGlyphs
Ctor.
=item ListOfTextGlyphs::getItemTypeCode
Returns the libSBML type code for the SBML objects
contained in this ListOf object.
C<opydetails> doc_what_are_typecodes
@return the SBML type code for objects contained in this list:
@link SBMLTypeCode_t#SBML_LAYOUT_TEXTGLYPH SBML_LAYOUT_TEXTGLYPH@endlink (default).
@see getElementName()
@see getPackageName()
=item ListOfTextGlyphs::getElementName
Returns the XML element name of
this SBML object.
=item ListOfTextGlyphs::get
Get a TextGlyph from the ListOfTextGlyphs.
@param n the index number of the TextGlyph to get.
@return the nth TextGlyph in this ListOfTextGlyphs.
@see size()
=item ListOfTextGlyphs::get
Get a TextGlyph from the ListOfTextGlyphs.
@param n the index number of the TextGlyph to get.
@return the nth TextGlyph in this ListOfTextGlyphs.
@see size()
=item ListOfTextGlyphs::get
Get a TextGlyph from the ListOfTextGlyphs
based on its identifier.
@param sid a string representing the identifier
of the TextGlyph to get.
@return TextGlyph in this ListOfTextGlyphs
with the given C<sid> or C<NULL> if no such
TextGlyph exists.
@see get(unsigned int n)
@see size()
=item ListOfTextGlyphs::get
Get a TextGlyph from the ListOfTextGlyphs
based on its identifier.
@param sid a string representing the identifier
of the TextGlyph to get.
@return TextGlyph in this ListOfTextGlyphs
with the given C<sid> or C<NULL> if no such
TextGlyph exists.
@see get(unsigned int n)
@see size()
=item ListOfTextGlyphs::remove
Removes the nth item from this ListOfTextGlyphs items and returns a pointer to
it.
The caller owns the returned item and is responsible for deleting it.
@param n the index of the item to remove
@see size()
=item ListOfTextGlyphs::remove
Removes item in this ListOfTextGlyphs items with the given identifier.
The caller owns the returned item and is responsible for deleting it.
If none of the items in this list have the identifier C<sid>, then @c
NULL is returned.
@param sid the identifier of the item to remove
@return the item removed. As mentioned above, the caller owns the
returned item.
=item ListOfTextGlyphs::toXML
Creates an XMLNode object from this.
=item ListOfTextGlyphs::createObject
@internal
Create and return an SBML object of this class, if present.
@return the SBML object corresponding to next XMLToken in the
XMLInputStream or NULL if the token was not recognized.
=item Layout::removeObjectWithId
@internal
=item Layout::getObjectWithId
@internal
=item Layout::getObjectWithId
@internal
=item Layout::Layout
Creates a new Layout with the given level, version, and package version.
=item Layout::Layout
Creates a new Layout with the given LayoutPkgNamespaces object.
=item Layout::Layout
Creates a new Layout with the given C<id> and dimensions.
(FOR BACKWARD COMPATIBILITY)
=item Layout::Layout
Creates a new Layout from the given XMLNode
(only for SBML Level2)
(FOR BACKWARD COMPATIBILITY)
=item Layout::Layout
Copy constructor.
=item Layout::initDefaults
Does nothing since no defaults are defined for Layout.
=item Layout::getId
Returns the value of the "id" attribute of this Layout.
=item Layout::isSetId
Predicate returning C<true> or C<false> depending on whether this
Layout's "id" attribute has been set.
=item Layout::setId
Sets the value of the "id" attribute of this Layout.
=item Layout::unsetId
Unsets the value of the "id" attribute of this Layout.
=item Layout::getName
Returns the value of the "name" attribute of this Layout.
=item Layout::isSetName
Predicate returning C<true> or C<false> depending on whether this
Layout's "name" attribute has been set.
=item Layout::setName
Sets the value of the "name" attribute of this Layout.
=item Layout::unsetName
Unsets the value of the "name" attribute of this Layout.
=item Layout::getDimensions
Returns the dimensions of the layout.
=item Layout::getDimensions
Returns the dimensions of the layout.
=item Layout::setDimensions
Sets the dimensions of the layout.
=item Layout::getDimensionsExplicitlySet
Predicate returning true if the dimensions has been set
=item Layout::getListOfCompartmentGlyphs
Returns the ListOf object that holds all compartment glyphs.
=item Layout::getListOfSpeciesGlyphs
Returns the ListOf object that holds all species glyphs.
=item Layout::getListOfReactionGlyphs
Returns the ListOf object that holds all reaction glyphs.
=item Layout::getListOfTextGlyphs
Returns the ListOf object that holds all text glyphs.
=item Layout::getListOfAdditionalGraphicalObjects
Returns the ListOf object that holds all additonal graphical objects.
=item Layout::getListOfCompartmentGlyphs
Returns the ListOf object that holds all compartment glyphs.
=item Layout::getListOfSpeciesGlyphs
Returns the ListOf object that holds all species glyphs.
=item Layout::getListOfReactionGlyphs
Returns the ListOf object that holds all reaction glyphs.
=item Layout::getListOfTextGlyphs
Returns the ListOf object that holds all text glyphs.
=item Layout::getListOfAdditionalGraphicalObjects
Returns the ListOf object that holds all additional graphical objects.
=item Layout::getAllElements
Returns a List of all child SBase objects, including those nested to an
arbitrary depth
@return a List of pointers to all children objects.
=item Layout::getCompartmentGlyph
Returns the compartment glyph with the given index.
If the index is invalid, C<NULL> is returned.
=item Layout::getCompartmentGlyph
Returns the compartment glyph with the given index.
If the index is invalid, C<NULL> is returned.
=item Layout::getSpeciesGlyph
Returns the species glyph with the given index.
If the index is invalid, C<NULL> is returned.
=item Layout::getSpeciesGlyph
Returns the species glyph with the given index.
If the index is invalid, C<NULL> is returned.
=item Layout::getReactionGlyph
Returns the reaction glyph with the given index.
If the index is invalid, C<NULL> is returned.
=item Layout::getReactionGlyph
Returns the reaction glyph with the given index.
If the index is invalid, C<NULL> is returned.
=item Layout::getTextGlyph
Returns the text glyph with the given index.
If the index is invalid, C<NULL> is returned.
=item Layout::getTextGlyph
Returns the text glyph with the given index.
If the index is invalid, C<NULL> is returned.
=item Layout::getAdditionalGraphicalObject
Returns the additional graphical object with the given index.
If the index is invalid, C<NULL> is returned.
=item Layout::getAdditionalGraphicalObject
Returns the additional graphical object with the given index.
If the index is invalid, C<NULL> is returned.
=item Layout::getGeneralGlyph
Returns the general glyph with the given index.
If the index is invalid, C<NULL> is returned.
=item Layout::getGeneralGlyph
Returns the general glyph with the given index.
If the index is invalid, C<NULL> is returned.
=item Layout::getCompartmentGlyph
Returns the compartment glyph that has the given C<id>, or C<NULL> if no
compartment glyph has the id.
=item Layout::getSpeciesGlyph
Returns the species glyph that has the given C<id>, or C<NULL> if no species
glyph has the id.
=item Layout::getReactionGlyph
Returns the reaction glyph that has the given C<id>, or C<NULL> if no
reaction glyph has the id.
=item Layout::getTextGlyph
Returns the text glyph that has the given C<id>, or C<NULL> if no text glyph
has the id.
=item Layout::getAdditionalGraphicalObject
Returns the additional graphical object that has the given C<id>, or C<NULL>
if no graphical object has the id.
=item Layout::getGeneralGlyph
Returns the general glyph that has the given C<id>, or C<NULL>
if no graphical object has the id.
=item Layout::getCompartmentGlyph
Returns the compartment glyph that has the given C<id>, or C<NULL> if no
compartment glyph has the id.
=item Layout::getSpeciesGlyph
Returns the species glyph that has the given C<id>, or C<NULL> if no species
glyph has the id.
=item Layout::getReactionGlyph
Returns the reaction glyph that has the given C<id>, or C<NULL> if no
reaction glyph has the id.
=item Layout::getTextGlyph
Returns the text glyph that has the given C<id>, or C<NULL> if no text glyph
has the id.
=item Layout::getAdditionalGraphicalObject
Returns the additional graphical object that has the given C<id>, or C<NULL>
if no graphical object has the id.
=item Layout::getGeneralGlyph
Returns the general glyph that has the given C<id>, or C<NULL>
if no graphical object has the id.
=item Layout::addCompartmentGlyph
Adds a new compartment glyph.
=item Layout::addSpeciesGlyph
Adds a new species glyph.
=item Layout::addReactionGlyph
Adds a new reaction glyph.
=item Layout::addTextGlyph
Adds a new text glyph.
=item Layout::addAdditionalGraphicalObject
Adds a new additional graphical object glyph.
=item Layout::addGeneralGlyph
Adds a new general glyph.
=item Layout::getNumCompartmentGlyphs
Returns the number of compartment glyphs for the layout.
=item Layout::getNumSpeciesGlyphs
Returns the number of species glyphs for the layout.
=item Layout::getNumReactionGlyphs
Returns the number of reaction glyphs for the layout.
=item Layout::getNumTextGlyphs
Returns the number of text glyphs for the layout.
=item Layout::getNumAdditionalGraphicalObjects
Returns the number of additional graphical objects for the layout.
=item Layout::getNumGeneralGlyphs
Returns the number of general glyphs for the layout.
=item Layout::createCompartmentGlyph
Creates a CompartmentGlyph object, adds it to the end of the
compartment glyph objects list and returns a pointer to the newly
created object.
=item Layout::createSpeciesGlyph
Creates a SpeciesGlyph object, adds it to the end of the species glyph
objects list and returns a pointer to the newly created object.
=item Layout::createReactionGlyph
Creates a ReactionGlyph object, adds it to the end of the reaction
glyph objects list and returns a pointer to the newly created
object.
=item Layout::createGeneralGlyph
Creates a GeneralGlyph object, adds it to the end of the additional
objects list and returns a reference to the newly created object.
=item Layout::createTextGlyph
Creates a TextGlyph object, adds it to the end of the text glyph
objects list and returns a pointer to the newly created object.
=item Layout::createAdditionalGraphicalObject
Creates a GraphicalObject object, adds it to the end of the additional
graphical objects list and returns a pointer to the newly created
object.
=item Layout::createSpeciesReferenceGlyph
Creates a new SpeciesReferenceGlyph for the last ReactionGlyph and
adds it to its list of SpeciesReferenceGlyph objects. A pointer to
the newly created object is returned.
=item Layout::createLineSegment
Creates a new LineSegment for the Curve object of the last
ReactionGlyph or the last SpeciesReferenceGlyph in the last
ReactionGlyph and adds it to its list of SpeciesReferenceGlyph
objects. A pointer to the newly created object is returned.
=item Layout::createCubicBezier
Creates a new CubicBezier for the Curve object of the last
ReactionGlyph or the last SpeciesReferenceGlyph in the last
ReactionGlyph and adds it to its list of SpeciesReferenceGlyph
objects. A pointer to the newly created object is returned.
=item Layout::removeCompartmentGlyph
Removes the compartment glyph with the given index from the layout.
A pointer to the compartment glyph that was removed is returned.
If no compartment glyph has been removed, C<NULL> is returned.
=item Layout::removeSpeciesGlyph
Removes the species glyph with the given index from the layout.
A pointer to the species glyph that was removed is returned.
If no species glyph has been removed, C<NULL> is returned.
=item Layout::removeReactionGlyph
Removes the reaction glyph with the given index from the layout.
A pointer to the reaction glyph that was removed is returned.
If no reaction glyph has been removed, C<NULL> is returned.
=item Layout::removeTextGlyph
Removes the text glyph with the given index from the layout.
A pointer to the text glyph that was removed is returned.
If no text glyph has been removed, C<NULL> is returned.
=item Layout::removeAdditionalGraphicalObject
Removes the graphical object with the given index from the layout.
A pointer to the graphical object that was removed is returned.
If no graphical object has been removed, C<NULL> is returned.
=item Layout::removeCompartmentGlyph
Remove the compartment glyph with the given C<id>.
A pointer to the removed compartment glyph is returned.
If no compartment glyph has been removed, C<NULL> is returned.
=item Layout::removeSpeciesGlyph
Remove the species glyph with the given C<id>.
A pointer to the removed species glyph is returned.
If no species glyph has been removed, C<NULL> is returned.
=item Layout::removeReactionGlyph
Remove the reaction glyph with the given C<id>.
A pointer to the removed reaction glyph is returned.
If no reaction glyph has been removed, C<NULL> is returned.
=item Layout::removeSpeciesReferenceGlyph
Remove the species reference glyph with the given C<id>.
A pointer to the removed species reference glyph is returned.
If no species reference glyph has been removed, C<NULL> is returned.
=item Layout::removeTextGlyph
Remove the text glyph with the given C<id>.
A pointer to the removed text glyph is returned.
If no text glyph has been removed, C<NULL> is returned.
=item Layout::removeAdditionalGraphicalObject
Remove the graphical object with the given C<id>.
A pointer to the removed graphical object is returned.
If no graphical object has been removed, C<NULL> is returned.
=item Layout::writeElements
@internal
Subclasses should override this method to write out their contained
SBML objects as XML elements. Be sure to call your parents
implementation of this method as well. For example:
SBase::writeElements(stream);
mReactants.write(stream);
mProducts.write(stream);
...
=item Layout::getElementName
Returns the XML element name of
this SBML object.
=item Layout::clone
Creates and returns a deep copy of this Layout.
@return a (deep) copy of this Layout.
=item Layout::getTypeCode
Returns the libSBML type code of this object instance.
C<opydetails> doc_what_are_typecodes
@return the SBML type code for this object:
@link SBMLLayoutTypeCode_t#SBML_LAYOUT_LAYOUT SBML_LAYOUT_LAYOUT@endlink
C<opydetails> doc_warning_typecodes_not_unique
@see getElementName()
@see getPackageName()
=item Layout::accept
Accepts the given SBMLVisitor.
@return the result of calling C<v.visit()>, which indicates
whether or not the Visitor would like to visit the SBML object's next
sibling object (if available).
=item Layout::toXML
Creates an XMLNode object from this.
=item Layout::setSBMLDocument
@internal
Sets the parent SBMLDocument of this SBML object.
@param d the SBMLDocument object to use
=item Layout::connectToChild
@internal
Sets this SBML object to child SBML objects (if any).
(Creates a child-parent relationship by the parent)
Subclasses must override this function if they define
one ore more child elements.
Basically, this function needs to be called in
constructor, copy constructor, assignment operator.
@see setSBMLDocument
@see enablePackageInternal
=item Layout::enablePackageInternal
@internal
Enables/Disables the given package with this element and child
elements (if any).
(This is an internal implementation for enablePakcage function)
@note Subclasses in which one or more child elements are defined
must override this function.
=item Layout::createObject
@internal
Create and return an SBML object of this class, if present.
@return the SBML object corresponding to next XMLToken in the
XMLInputStream or NULL if the token was not recognized.
=item Layout::addExpectedAttributes
@internal
Subclasses should override this method to get the list of
expected attributes.
This function is invoked from corresponding readAttributes()
function.
=item Layout::readAttributes
@internal
Subclasses should override this method to read values from the given
XMLAttributes set into their specific fields. Be sure to call your
parents implementation of this method as well.
=item Layout::writeAttributes
@internal
Subclasses should override this method to write their XML attributes
to the XMLOutputStream. Be sure to call your parents implementation
of this method as well. For example:
SBase::writeAttributes(stream);
stream.writeAttribute( "id" , mId );
stream.writeAttribute( "name", mName );
...
=item ListOfLayouts::clone
Creates and returns a deep copy of this ListOfLayouts.
@return a (deep) copy of this ListOfLayouts.
=item ListOfLayouts::ListOfLayouts
Ctor.
=item ListOfLayouts::ListOfLayouts
Ctor.
=item ListOfLayouts::getItemTypeCode
Returns the libSBML type code for the SBML objects
contained in this ListOf object.
C<opydetails> doc_what_are_typecodes
@return the SBML type code for objects contained in this list:
@link SBMLTypeCode_t#SBML_LAYOUT_LAYOUT SBML_LAYOUT_LAYOUT@endlink (default).
@see getElementName()
@see getPackageName()
=item ListOfLayouts::getElementName
Returns the XML element name of
this SBML object.
=item ListOfLayouts::get
Get a Layout from the ListOfLayouts.
@param n the index number of the Layout to get.
@return the nth Layout in this ListOfLayouts.
@see size()
=item ListOfLayouts::get
Get a Layout from the ListOfLayouts.
@param n the index number of the Layout to get.
@return the nth Layout in this ListOfLayouts.
@see size()
=item ListOfLayouts::get
Get a Layout from the ListOfLayouts
based on its identifier.
@param sid a string representing the identifier
of the Layout to get.
@return Layout in this ListOfLayouts
with the given C<id> or C<NULL> if no such
Layout exists.
@see get(unsigned int n)
@see size()
=item ListOfLayouts::get
Get a Layout from the ListOfLayouts
based on its identifier.
@param sid a string representing the identifier
of the Layout to get.
@return Layout in this ListOfLayouts
with the given C<sid> or C<NULL> if no such
Layout exists.
@see get(unsigned int n)
@see size()
=item ListOfLayouts::remove
Removes the nth item from this ListOfLayouts items and returns a pointer to
it.
The caller owns the returned item and is responsible for deleting it.
@param n the index of the item to remove
@see size()
=item ListOfLayouts::remove
Removes item in this ListOfLayouts items with the given identifier.
The caller owns the returned item and is responsible for deleting it.
If none of the items in this list have the identifier C<sid>, then @c
NULL is returned.
@param sid the identifier of the item to remove
@return the item removed. As mentioned above, the caller owns the
returned item.
=item ListOfLayouts::toXML
Creates an XMLNode object from this.
=item ListOfLayouts::resetElementNamespace
=item ListOfLayouts::createObject
@internal
Create and return an SBML object of this class, if present.
@return the SBML object corresponding to next XMLToken in the
XMLInputStream or NULL if the token was not recognized.
=item ListOfLayouts::writeXMLNS
@internal
=back
=head2 LayoutExtension
@sbmlpackage{layout}
@htmlinclude pkg-marker-layout.html The core module of the 'layout' package extension.
=over
=back
=head2 LayoutPkgNamespaces
@sbmlpackage{layout}
@htmlinclude pkg-marker-layout.html Extension of SBMLNamespaces for the SBML Level 3
'layout' package.
=over
=item LayoutExtension::getPackageName
Returns the package name of this extension.
=item LayoutExtension::getDefaultLevel
Returns the default SBML Level this extension.
=item LayoutExtension::getDefaultVersion
Returns the default SBML Version this extension.
=item LayoutExtension::getDefaultPackageVersion
Returns the default SBML version this extension.
=item LayoutExtension::getXmlnsL3V1V1
Returns URI of supported versions of this package.
=item LayoutExtension::getXmlnsL2
=item LayoutExtension::getXmlnsXSI
=item LayoutExtension::LayoutExtension
Constructor
=item LayoutExtension::LayoutExtension
Copy constructor.
=item LayoutExtension::clone
Creates and returns a deep copy of this LayoutExtension object.
@return a (deep) copy of this LayoutExtension object
=item LayoutExtension::getName
Returns the name of this package ("layout")
@return the name of this package ("layout")
=item LayoutExtension::getURI
Returns the namespace URI corresponding to the combination of the given
SBML Level, Version, and package version.
@param sbmlLevel the level of SBML
@param sbmlVersion the version of SBML
@param pkgVersion the version of package
@return a string of the package URI, or an empty string if no
corresponding URI exists.
=item LayoutExtension::getLevel
Returns the SBML Level for the given URI of this package.
@param uri the string of URI that represents one of versions of the
“layout” package
@return the SBML Level with the given URI of this package, or C<0> if
the given URI is invalid.
=item LayoutExtension::getVersion
Returns the SBML Version for the given URI of this package.
@param uri the string of URI that represents one of versions of the
“layout” package
@return the SBML version with the given URI of this package, or C<0> if
the given URI is invalid.
=item LayoutExtension::getPackageVersion
Returns the package version for the given URI of this package.
@param uri the string of URI that represents one of versions of the
“layout” package
@return the package version with the given URI of this package, or C<0>
if the given URI is invalid.
=item LayoutExtension::getStringFromTypeCode
Takes a type code of the “layout” package and returns a string
describing the code.
=item LayoutExtension::getSBMLExtensionNamespaces
Returns an LayoutPkgNamespaces object.
@param uri the string of URI that represents one of versions of the
“layout” package
@return an LayoutPkgNamespace object corresponding to the given C<uri>,
or C<NULL> if the URI is not defined in the Layout package.
=item LayoutExtension::init
@internal
Initializes layout extension by creating an object of this class with
required SBasePlugin derived objects and registering the object
to the SBMLExtensionRegistry class.
(NOTE) This function is automatically invoked when creating the following
global object in LayoutExtension.cpp
static SBMLExtensionRegister<LayoutExtension> layoutExtensionRegistry;
=item LayoutExtension::removeL2Namespaces
Removes the L2 Namespace from a document.
This method should be overridden by all extensions that want to serialize
to an L2 annotation.
=item LayoutExtension::addL2Namespaces
adds all L2 Extension namespaces to the namespace list.
This method should be overridden by all extensions that want to serialize
to an L2 annotation.
=item LayoutExtension::enableL2NamespaceForDocument
Adds the L2 Namespace to the document and enables the extension.
If the extension supports serialization to SBML L2 Annotations, this
method should be overrridden, so it will be activated.
=item LayoutExtension::isInUse
Determines whether this extension is being used by the given SBMLDocument
The implementation returns true if the model object contains one
or more layouts.
@param doc the sbml document to test.
@return a boolean indicating whether the extension is actually being used
byy the document.
=item LayoutExtension::getErrorTable
@internal
Return the entry in the error table at this index.
@param index an unsigned intgere representing the index of the error in the LayoutSBMLErrorTable
@return packageErrorTableEntry object in the LayoutSBMLErrorTable corresponding to the index given.
=item LayoutExtension::getErrorTableIndex
@internal
Return the index in the error table with the given errorId.
@param errorId an unsigned intgere representing the errorId of the error in the LayoutSBMLErrorTable
@return unsigned integer representing the index in the LayoutSBMLErrorTable corresponding to the errorId given.
=item LayoutExtension::getErrorIdOffset
@internal
Return the offset for the errorId range for the layout L3 package.
@return unsigned intege representing the offset for errors LayoutSBMLErrorTable.
=back
=head2 LayoutModelPlugin
@sbmlpackage{layout}
@htmlinclude pkg-marker-layout.html Implementation of the 'layout' package extention to the
Model construct.
=over
=item LayoutModelPlugin::LayoutModelPlugin
Constructor
=item LayoutModelPlugin::LayoutModelPlugin
Copy constructor. Creates a copy of this SBase object.
=item LayoutModelPlugin::clone
Creates and returns a deep copy of this LayoutModelPlugin object.
@return a (deep) copy of this LayoutModelPlugin object
=item LayoutModelPlugin::getAllElements
Returns a List of all child SBase objects, including those nested to an
arbitrary depth
@return a List of pointers to all children objects.
=item LayoutModelPlugin::getListOfLayouts
Returns the ListOfLayouts object for this Model.
@return the ListOfLayouts object for this Model.
=item LayoutModelPlugin::getListOfLayouts
Returns the ListOfLayouts object for this Model.
@return the ListOfLayouts object for this Model.
=item LayoutModelPlugin::getLayout
Returns the layout object that belongs to the given index. If the
index is invalid, C<NULL> is returned.
@param index the index of list of layout objects.
@return the Layout object that belongs to the given index. NULL
is returned if the index is invalid.
=item LayoutModelPlugin::getLayout
Returns the layout object that belongs to the given index. If the
index is invalid, C<NULL> is returned.
@param index the index of list of layout objects.
@return the Layout object that belongs to the given index. NULL
is returned if the index is invalid.
=item LayoutModelPlugin::getLayout
Returns the layout object with the given C<sid> attribute. If the
id is invalid, C<NULL> is returned.
@param sid the id attribute of the layout object.
@return the Layout object with the given C<sid> attribute. NULL
is returned if the given C<sid> is invalid.
=item LayoutModelPlugin::getLayout
Returns the layout object with the given C<sid> attribute. If the
id is invalid, C<NULL> is returned.
@param sid the id attribute of the layout object.
@return the Layout object with the given C<sid> attribute. NULL
is returned if the given C<sid> is invalid.
=item LayoutModelPlugin::addLayout
Adds a copy of the layout object to the list of layouts.
@param layout the layout object to be added.
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif@~ The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
=item LayoutModelPlugin::createLayout
Creates a new layout object and adds it to the list of layout objects
and returns it.
@return a new layout object.
=item LayoutModelPlugin::removeLayout
Removes the nth Layout object from this Model object and
returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
@param n the index of the Layout object to remove
@return the Layout object removed. As mentioned above, the caller owns the
returned object. C<NULL> is returned if the given index is out of range.
=item LayoutModelPlugin::getNumLayouts
Returns the number of layout objects.
@return the number of layout objects.
=item LayoutModelPlugin::appendFrom
@internal
=item LayoutModelPlugin::setSBMLDocument
@internal
Sets the parent SBMLDocument of this plugin object.
Subclasses which contain one or more SBase derived elements must
override this function.
@param d the SBMLDocument object to use
@see connectToParent
@see enablePackageInternal
=item LayoutModelPlugin::connectToParent
@internal
Sets the parent SBML object of this plugin object to
this object and child elements (if any).
(Creates a child-parent relationship by this plugin object)
This function is called when this object is created by
the parent element.
Subclasses must override this this function if they have one
or more child elements. Also, SBasePlugin::connectToParent()
must be called in the overridden function.
@param sbase the SBase object to use
@if cpp
@see setSBMLDocument
@see enablePackageInternal
@endif
=item LayoutModelPlugin::enablePackageInternal
@internal
Enables/Disables the given package with child elements in this plugin
object (if any).
(This is an internal implementation invoked from
SBase::enablePakcageInternal() function)
@note Subclasses in which one or more SBase derived elements are
defined must override this function.
@if cpp
@see setSBMLDocument
@see connectToParent
@endif
=item LayoutModelPlugin::accept
@internal
=back
=head2 LayoutSpeciesReferencePlugin
@sbmlpackage{layout}
@htmlinclude pkg-marker-layout.html Implementation of the 'layout' package extention to the
SpeciesReference construct.
=over
=item LayoutSpeciesReferencePlugin::LayoutSpeciesReferencePlugin
Constructor
=item LayoutSpeciesReferencePlugin::LayoutSpeciesReferencePlugin
Copy constructor. Creates a copy of this SBase object.
=item LayoutSpeciesReferencePlugin::clone
Creates and returns a deep copy of this LayoutSpeciesReferencePlugin object.
@return a (deep) copy of this LayoutSpeciesReferencePlugin object
=item parseLayoutAnnotation
takes an annotation that has been read into the model
identifies the RDF elements
and creates a List of Layouts from the annotation
=item deleteLayoutAnnotation
Takes an XMLNode and tries to find the layout annotation node and deletes it if it was found.
=item parseLayouts
Creates an XMLNode that represents the layouts of the model from the given Model object.
=item parseSpeciesReferenceAnnotation
takes an annotation that has been read into the species reference
identifies the id elements and set the id of the species reference
=item deleteLayoutIdAnnotation
Takes an XMLNode and tries to find the layoutId annotation node and deletes it if it was found.
=item parseLayoutId
Creates an XMLNode that represents the layoutId annotation of the species reference from the given SpeciesReference object.
=back
=head2 CompExtension
@sbmlpackage{comp}
@htmlinclude pkg-marker-comp.html The core module of the “comp” package
extension.
=over
=back
=head2 CompPkgNamespaces
@sbmlpackage{comp}
@htmlinclude pkg-marker-comp.html Extension of SBMLNamespaces for the SBML Level 3
'comp' package.
=over
=item CompExtension::getPackageName
Returns the package name of this extension.
=item CompExtension::getDefaultLevel
Returns the default SBML Level this extension.
=item CompExtension::getDefaultVersion
Returns the default SBML Version this extension.
=item CompExtension::getDefaultPackageVersion
Returns the default SBML version this extension.
=item CompExtension::getXmlnsL3V1V1
Returns URI of supported versions of this package.
=item CompExtension::CompExtension
Constructor
=item CompExtension::CompExtension
Copy constructor.
=item CompExtension::clone
Creates and returns a deep copy of this CompExtension object.
@return a (deep) copy of this CompExtension object
=item CompExtension::getName
Returns the name of this package as a short-form label
("C<comp>").
@return the name of this package.
=item CompExtension::getURI
Returns the namespace URI corresponding to the combination of the given
SBML Level, Version, and package version.
@param sbmlLevel the level of SBML
@param sbmlVersion the version of SBML
@param pkgVersion the version of package
@return a string of the package URI, or an empty string if no
corresponding URI exists.
=item CompExtension::getLevel
Returns the SBML Level for the given URI of this package.
@param uri the string of URI that represents one of versions of the
“comp” package
@return the SBML Level with the given URI of this package, or C<0> if
the given URI is invalid.
=item CompExtension::getVersion
Returns the SBML Version for the given URI of this package.
@param uri the string of URI that represents one of versions of the
“comp” package
@return the SBML version with the given URI of this package, or C<0> if
the given URI is invalid.
=item CompExtension::getPackageVersion
Returns the package version for the given URI of this package.
@param uri the string of URI that represents one of versions of the
“comp” package
@return the package version with the given URI of this package, or C<0
>
if the given URI is invalid.
=item CompExtension::getSBMLExtensionNamespaces
Returns an CompPkgNamespaces object.
@param uri the string of URI that represents one of versions of the
“comp” package
@return an CompPkgNamespace object corresponding to the given C<uri>, or
C<NULL> if the URI is not defined in the Hierarchical Model Composition
package.
=item CompExtension::getStringFromTypeCode
Takes a type code of the “comp” package and returns a string
describing the code.
=item CompExtension::init
@internal
Initializes comp extension by creating an object of this class with
required SBasePlugin derived objects and registering the object
to the SBMLExtensionRegistry class.
(NOTE) This function is automatically invoked when creating the following
global object in CompExtension.cpp
static SBMLExtensionRegister<CompExtension> compExtensionRegistry;
=item CompExtension::getErrorTable
@internal
=item CompExtension::getErrorTableIndex
@internal
=item CompExtension::getErrorIdOffset
@internal
=back
=head2 CompSBasePlugin
@sbmlpackage{comp}
@htmlinclude pkg-marker-comp.html Implementation of the “comp” package
extention to the SBase construct.
The CompSBasePlugin class inherits from the SBasePlugin class,
and codifies the extentions to the SBase class defined in the
@ref comp @if java "Hierarchical Model Composition"@endif@~
package (“comp”). This extention allows the modeler to define
one or more submodel elements which the parent SBase object replaces,
and/or a single submodel element which replaces the parent SBase object.
This is accomplished through the addition of an optional ListOfReplacedElements
child, which may contain one or more ReplacedElement objects, each of which
references a submodel object to be replaced by the containing SBase object,
and through the addition of a single optional ReplacedBy child, which
references a submodel object which is to replace the containing SBase object.
If a single SBase element both contains a ListOfReplacedElements and has a ReplacedBy
child, it and all the referenced ReplacedElement objects are to be replaced
by the object referenced by the ReplacedBy element.
@see ReplacedElement
@see ReplacedBy
=over
=item CompSBasePlugin::CompSBasePlugin
Constructor.
=item CompSBasePlugin::CompSBasePlugin
Copy constructor. Creates a copy of this CompSBasePlugin object.
=item CompSBasePlugin::clone
Creates and returns a deep copy of this CompSBasePlugin object.
@return a (deep) copy of this CompSBasePlugin object
=item CompSBasePlugin::createObject
@internal
Create and return an SBML object of this class, if present.
@return the SBML object corresponding to next XMLToken in the
XMLInputStream or C<NULL> if the token was not recognized.
=item CompSBasePlugin::writeElements
@internal
Subclasses must override this method to write out their contained
SBML objects as XML elements if they have their specific elements.
=item CompSBasePlugin::getElementBySId
Returns the first child element found that has the given C<id> in the
model-wide SId namespace, or C<NULL> if no such object is found.
@param id string representing the id of objects to find
@return a pointer to the SBase element with the given C<id>.
=item CompSBasePlugin::getElementByMetaId
Returns the first child element it can find with the given C<metaid>, or
itself if it has the given C<metaid>, or C<NULL> if no such object is
found.
@param metaid string representing the metaid of objects to find
@return a pointer to the SBase element with the given C<metaid>.
=item CompSBasePlugin::getAllElements
Returns a List of all child SBase objects, including those nested to an
arbitrary depth.
@return a List of pointers to all children objects.
=item CompSBasePlugin::getListOfReplacedElements
Returns the ListOf object that holds all replacedElements.
@return the ListOf object that holds all replacedElements.
=item CompSBasePlugin::getReplacedElement
Returns the ReplacedElement with the given index.
@param n the index number of the ReplacedElement to get.
@return the nth ReplacedElement in the ListOfReplacedElements. If the
index is invalid, C<NULL> is returned.
=item CompSBasePlugin::getReplacedElement
Returns the ReplacedElement with the given index.
@param n the index number of the ReplacedElement to get.
@return the nth ReplacedElement in the ListOfReplacedElements. If the
index is invalid, C<NULL> is returned.
=item CompSBasePlugin::addReplacedElement
Adds a copy of the given ReplacedElement object to the list of ReplacedElements.
@param replacedElement the ReplacedElement object to be added to the
list of ReplacedElements. Fails if the added ReplacedElement is C<NULL>,
does not match the level/version/package of the parent object, or cannot
be added to the list of replaced elements.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT @endlink
@li @link OperationReturnValues_t#LIBSBML_LEVEL_MISMATCH LIBSBML_LEVEL_MISMATCH @endlink
@li @link OperationReturnValues_t#LIBSBML_VERSION_MISMATCH LIBSBML_VERSION_MISMATCH @endlink
@li @link OperationReturnValues_t#LIBSBML_PKG_VERSION_MISMATCH LIBSBML_VERSION_MISMATCH @endlink
=item CompSBasePlugin::getNumReplacedElements
Returns the number of ReplacedElements for this CompSBasePlugin.
@return the number of ReplacedElements for this CompSBasePlugin.
=item CompSBasePlugin::clearReplacedElements
Remove all ReplacedElements, if any exist.
=item CompSBasePlugin::createReplacedElement
Creates a ReplacedElement object, adds it to the end of the
ReplacedElement objects list and returns a pointer to the newly
created object.
@return a newly created ReplacedElement object
=item CompSBasePlugin::removeReplacedElement
Removes the ReplacedElement with the given index.
A pointer to the ReplacedElement that was removed is returned.
If no ReplacedElement has been removed, C<NULL> is returned.
@param index the index of the ReplacedElement object to remove
@return the ReplacedElement object removed. As mentioned above,
the caller owns the returned object. C<NULL> is returned if
the given index is out of range.
=item CompSBasePlugin::getReplacedBy
Get the child ReplacedBy of this SBase.
@return the const ReplacedBy child of this SBase
=item CompSBasePlugin::getReplacedBy
Get the child ReplacedBy of this SBase.
@return the ReplacedBy child of this SBase.
=item CompSBasePlugin::isSetReplacedBy
Predicate for testing whether the ReplacedBy for this SBase is set.
@return C<true> if the ReplacedBy of this SBase is set, C<false
>
otherwise.
=item CompSBasePlugin::setReplacedBy
Sets the ReplacedBy definition of this SBase to a copy of the given
ReplacedBy object instance.
This method fails if the added ReplacedBy does not match the
level/version/package of the parent object or if the added ReplacedBy
cannot be copied.
@param replacedBy the ReplacedBy object instance to use.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
@li @link OperationReturnValues_t#LIBSBML_LEVEL_MISMATCH LIBSBML_LEVEL_MISMATCH @endlink
@li @link OperationReturnValues_t#LIBSBML_VERSION_MISMATCH LIBSBML_VERSION_MISMATCH @endlink
@li @link OperationReturnValues_t#LIBSBML_PKG_VERSION_MISMATCH LIBSBML_VERSION_MISMATCH @endlink
=item CompSBasePlugin::createReplacedBy
Creates a new, empty ReplacedBy, adds it to this CompSBasePlugin and
returns the created ReplacedBy.
@return the newly created ReplacedBy object instance
=item CompSBasePlugin::unsetReplacedBy
Unsets the child ReplacedBy of this SBase.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item CompSBasePlugin::logInvalidId
Helper to log a common type of error.
=item CompSBasePlugin::setSBMLDocument
@internal
Sets the parent SBMLDocument of this plugin object.
Subclasses which contain one or more SBase derived elements must
override this function.
@param d the SBMLDocument object to use
@see connectToParent
@see enablePackageInternal
=item CompSBasePlugin::connectToChild
@internal
Sets the parent of this SBML object to child SBML objects (if any).
(Creates a child-parent relationship by the parent)
@see setSBMLDocument
@see enablePackageInternal
=item CompSBasePlugin::connectToParent
@internal
Sets the parent SBML object of this SBML object.
(Creates a child-parent relationship by the child)
This function is called when a child element is
set/added/created by its parent element (e.g. by setXXX,
addXXX, createXXX, and connectToChild functions of the
parent element).
@param parent the SBML object to use
=item CompSBasePlugin::enablePackageInternal
@internal
Enables/Disables the given package with child elements in this plugin
object (if any).
(This is an internal implementation invoked from
SBase::enablePackageInternal() function)
@note Subclasses in which one or more SBase derived elements are
defined must override this function.
@see setSBMLDocument
@see connectToParent
=item CompSBasePlugin::accept
@internal
=item CompSBasePlugin::createListOfReplacedElements
=back
=head2 CompModelPlugin
@sbmlpackage{comp}
@htmlinclude pkg-marker-comp.html Implementation of the “comp” package
extention to the Model construct.
The CompModelPlugin class inherits from the SBMLSBasePlugin class, and
codifies the extentions to the Model class defined in the SBML
Level 3 @ref comp @if java "Hierarchical Model Composition"@endif@~
package (“comp”). This extention allows a Model to define
Submodels (other Models that are instantiated as new parts of the parent
Model), and Ports, a defined interface for including the given Model as a
Submodel of a different Model.
Submodels are stored in an optional child ListOfSubmodels object, which,
if present, must contain one or more Submodel objects. All of the Submodels
present in the ListOfSubmodels are defined to be instantiated in the
'complete' Model.
Ports are stored in an optional child ListOfPorts object, which,
if present, must contain one or more Port objects. All of the Ports
present in the ListOfPorts collectively define the 'port interface'
of the Model.
=over
=item CompModelPlugin::CompModelPlugin
Constructor.
=item CompModelPlugin::CompModelPlugin
Copy constructor. Creates a copy of this CompModelPlugin object.
=item CompModelPlugin::clone
Creates and returns a deep copy of this CompModelPlugin object.
@return a (deep) copy of this CompModelPlugin object
=item CompModelPlugin::createObject
@internal
Create and return an SBML object of this class, if present.
@return the SBML object corresponding to next XMLToken in the
XMLInputStream or NULL if the token was not recognized.
=item CompModelPlugin::writeElements
@internal
=item CompModelPlugin::getElementBySId
Returns the first child element found that has the given C<id> in the
model-wide SId namespace, or C<NULL> if no such object is found.
@param id a string representing the id of objects to find.
@return a pointer to the SBase element with the given C<id>.
=item CompModelPlugin::getElementByMetaId
Returns the first child element it can find with the given meta
identifier, or itself if it has the given C<metaid>, or C<NULL> if no
such object is found.
@param metaid a string representing the metaid of objects to find.
@return a pointer to the SBase element with the given C<metaid>.
=item CompModelPlugin::getAllElements
Returns a List of all child SBase objects, including those nested to an
arbitrary depth.
@return a List of pointers to all children objects.
=item CompModelPlugin::getListOfSubmodels
Returns the ListOf object that holds all submodels.
@return the ListOf object that holds all submodels.
=item CompModelPlugin::getSubmodel
Returns the submodel with the given index.
If the index is invalid, C<NULL> is returned.
@param n the index number of the Submodel to get.
@return the nth Submodel in the ListOfSubmodels.
=item CompModelPlugin::getSubmodel
Returns the submodel with the given index.
@param n the index number of the Submodel to get.
@return the nth Submodel in the ListOfSubmodels. If the index C<n> is
invalid, C<NULL> is returned.
=item CompModelPlugin::getSubmodel
Returns the submodel with the given identifier.
@param id the identifier of the Submodel to get.
@return the Submodel in the ListOfSubmodels with the given identifier.
If no such submodel with identifier C<id> exists, C<NULL> is returned.
=item CompModelPlugin::getSubmodel
Returns the submodel with the given identifier.
@param id the identifier of the Submodel to get.
@return the Submodel in the ListOfSubmodels with the given
identifier. If no submodel with identifier C<id> exists, C<NULL> is
returned.
=item CompModelPlugin::addSubmodel
Adds a copy of the given Submodel object to the list of submodels.
Fails if the added submodel is C<NULL>, does not match the
level/version/package of the parent object, or cannot be added to the
list of submodels.
@param submodel the Submodel object to be added to the list of
submodels.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT @endlink
@li @link OperationReturnValues_t#LIBSBML_LEVEL_MISMATCH LIBSBML_LEVEL_MISMATCH @endlink
@li @link OperationReturnValues_t#LIBSBML_VERSION_MISMATCH LIBSBML_VERSION_MISMATCH @endlink
@li @link OperationReturnValues_t#LIBSBML_PKG_VERSION_MISMATCH LIBSBML_VERSION_MISMATCH @endlink
=item CompModelPlugin::getNumSubmodels
Returns the number of submodels for this CompModelPlugin.
@return the number of submodels for this CompModelPlugin.
=item CompModelPlugin::createSubmodel
Creates a Submodel object, adds it to the end of the
submodel objects list and returns a pointer to the newly
created object.
@return a newly created Submodel object
=item CompModelPlugin::removeSubmodel
Removes the submodel with the given index.
A pointer to the submodel that was removed is returned.
@param index the index of the Submodel object to remove
@return the Submodel object removed. As mentioned above, the caller
owns the returned object. C<NULL> is returned if the given C<index> is
out of range and no submodel has been removed, C<NULL> is returned.
=item CompModelPlugin::getListOfPorts
Returns the ListOf object that holds all ports.
@return the ListOf object that holds all ports.
=item CompModelPlugin::getPort
Returns the port with the given index.
@param n the index number of the Port to get.
@return the nth Port in the ListOfPorts. If the index C<n> is invalid,
C<NULL> is returned.
=item CompModelPlugin::getPort
Returns the port with the given index.
@param n the index number of the Port to get.
@return the nth Port in the ListOfPorts. If the index C<n> is invalid,
C<NULL> is returned.
=item CompModelPlugin::getPort
Returns the port with the given identifier.
@param id the id of the Port to get.
@return the Port in the ListOfPorts with the given identifier. If the
identifier is invalid, C<NULL> is returned.
=item CompModelPlugin::getPort
Returns the port with the given identifier.
@param id the id of the Port to get.
@return the Port in the ListOfPorts with the given identifier. If the
identifier is invalid, C<NULL> is returned.
=item CompModelPlugin::addPort
Adds a copy of the given Port object to the list of ports.
@param port the Port object to be added to the list of ports. Fails if
the added port is C<NULL>, does not match the level/version/package of the
parent object, or cannot be added to the list of ports.
@return integer value indicating success/failure of the
operation. The possible return values:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT @endlink
@li @link OperationReturnValues_t#LIBSBML_LEVEL_MISMATCH LIBSBML_LEVEL_MISMATCH @endlink
@li @link OperationReturnValues_t#LIBSBML_VERSION_MISMATCH LIBSBML_VERSION_MISMATCH @endlink
@li @link OperationReturnValues_t#LIBSBML_PKG_VERSION_MISMATCH LIBSBML_VERSION_MISMATCH @endlink
=item CompModelPlugin::getNumPorts
Returns the number of ports for this CompModelPlugin.
@return the number of ports for this CompModelPlugin.
=item CompModelPlugin::createPort
Creates a Port object, adds it to the end of the
port objects list and returns a pointer to the newly
created object.
@return a newly created Port object
=item CompModelPlugin::removePort
Removes the port with the given index.
@param index the index of the Port object to remove
@return the Port object removed. As mentioned above,
the caller owns the returned object. C<NULL> is returned if
the given index is out of range.
=item CompModelPlugin::setDivider
Set the string used as the divider between names when renaming and
flattening models.
The divider string consists of two underscore characters
("C<__>") by default. This method will fail if called
with an empty C<divider>, or a C<divider> that cannot be used internally as part
of a valid SBML SId.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item CompModelPlugin::getDivider
Get the string used as the divider between names when renaming and
flattening models.
The divider string consists of two underscore characters
("C<__>") by default, and can be overridden
with the setDivider() function.
@see setDivider(const std::string& divider)
=item CompModelPlugin::setSBMLDocument
@internal
Sets the parent SBMLDocument of this plugin object.
Subclasses which contain one or more SBase derived elements must
override this function.
@param d the SBMLDocument object to use
@see connectToParent
@see enablePackageInternal
=item CompModelPlugin::connectToChild
@internal
Sets the parent of this SBML object to child SBML objects (if any).
(Creates a child-parent relationship by the parent)
@see setSBMLDocument
@see enablePackageInternal
=item CompModelPlugin::connectToParent
@internal
Sets the parent SBML object of this SBML object.
(Creates a child-parent relationship by the child)
This function is called when a child element is
set/added/created by its parent element (e.g. by setXXX,
addXXX, createXXX, and connectToChild functions of the
parent element).
@param parent the SBML object to use
=item CompModelPlugin::enablePackageInternal
@internal
Enables/Disables the given package with child elements in this plugin
object (if any).
(This is an internal implementation invoked from
SBase::enablePackageInternal() function)
@note Subclasses in which one or more SBase derived elements are
defined must override this function.
@see setSBMLDocument
@see connectToParent
=item CompModelPlugin::accept
@internal
=item CompModelPlugin::setTransformer
Sets the custom transformer that is to be used, instead of the standard
prefixing with the given divider. This makes it possible to finely control
how elements are altered.
If not set, only ids and meta ids will be prefixed.
NOTE: the model plugin only holds the pointer to the element it does not
take ownership of it. Thus the calling program is responsible of
freeing the transformer when no longer needed (i.e after the
SBML document has been deleted)
=item CompModelPlugin::getTransformer
@return any custom transformer set for prefix operations, will be NULL by default.
=item CompModelPlugin::isSetTransformer
@return an indicator, whether a custom transformer has been set.
=item CompModelPlugin::unsetTransformer
Unsets any custom prefix transformers.
=item CompModelPlugin::flattenModel
Flatten and return a copy of this hierarchical model.
Follows all the rules of the hierarchical model composition package and
returns a version with all submodels copied into the main model, with all
deletions removed and all replaced elements replaced, following any and
all rules of conversion factors. Only the ports created for this model
will remain.
@return a Model object with no submodels. On failure, return C<NULL>.
=item CompModelPlugin::removeCollectedElements
Deletes any elements in 'toremove' that do not already exist in 'removed',
while taking care to not double-delete any element. Intended for use with
collectDeletionsAndDeleteCompConstructs and
collectRenameAndConvertReplacements.
=item CompModelPlugin::instantiateSubmodels
Loop through all Submodels in this Model, instantiate all of them,
perform all deletions, and synchronize all replacements, including using
any conversion factors that may exist. The resulting models are stored
in the Submodel objects, and available from
'Submodel::getInstantiation()'
@return an integer value indicating success/failure of the operation.
Possible return values from this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
In this case, 'invalid object' means that this Submodel itself is invalid, and no Model can be instantiated from it.
=item CompModelPlugin::getRemovedSet
@internal
=item CompModelPlugin::appendFrom
=item CompModelPlugin::saveAllReferencedElements
=item CompModelPlugin::renameAllIDsAndPrepend
=item CompModelPlugin::performDeletions
@internal
=item CompModelPlugin::collectDeletionsAndDeleteSome
Collects all elements from instantiated submodels slated to be deleted,
and stores them in 'toremove', and also actually deletes the comp constructs
Deletions, ReplacedElements, and ReplacedBy's. This is so that
it is possible to delete a deletion or replacement, and end up with a model
that still has the element that would have otherwise been deleted.
Also, actually deletes local parameters, because this potentially affects
the naming conventions when replacing.
Any comp elements or local parameters that have been removed will be added to 'removed', and
any elements that are to be removed will be added to 'toremove'.
=item CompModelPlugin::performReplacementsAndConversions
@internal
=item CompModelPlugin::collectRenameAndConvertReplacements
Removes all elements from instantiated submodels slated to be replaced,
and points all old references to that element to the replacement
element. Also takes any 'replacedBy' construct, deleting the original
object, renaming the replacement object with the replaced object's
identifiers, and points all old references to the replacement object's
old identifiers to the new identifiers.
=item CompModelPlugin::findUniqueSubmodPrefixes
@internal
=item CompModelPlugin::renameIDs
@internal
=item CompModelPlugin::resetPorts
@internal
=item CompModelPlugin::saveAllReferencedElements
@internal
=back
=head2 CompSBMLDocumentPlugin
@sbmlpackage{comp}
@htmlinclude pkg-marker-comp.html Implementation of the “comp” package
extention to the SBMLDocument construct.
The CompSBMLDocumentPlugin class inherits from the SBMLDocumentPlugin
class, and codifies the extentions to the SBMLDocument class defined in
the SBML Level 3 @ref comp
@if java "Hierarchical Model Composition"@endif@~
package (“comp”). This extention allows multiple Model
objects to be defined in a single SBMLDocument, stored in an optional
child ListOfModelDefinitions object, as well as define references to Model
objects in other files, stored in the optional child
ListOfExternalModelDefinitions object. These model definitions, if
present, allow Submodel objects to reference other Models to instantiate.
The presence of ModelDefinitions and ExternalModelDefinitions in an
SBMLDocument does not change the default Model in the file. If a
SBMLDocument is submitted somewhere to be simulated, it is still the
C<<model>> child of the C<<sbml>> element
that should be simulated.
In addition, as all packages do, the CompSBMLDocumentPlugin defines a
required flag named C<required>, which indicates whether
“comp” constructs can be used to change the core mathematics of the
C<<model>> child of the C<<sbml>> element.
Because they can, this attribute must be set C<true>.
=over
=item CompSBMLDocumentPlugin::CompSBMLDocumentPlugin
Constructor.
=item CompSBMLDocumentPlugin::CompSBMLDocumentPlugin
Copy constructor. Creates a copy of this CompSBMLDocumentPlugin object.
=item CompSBMLDocumentPlugin::clone
Creates and returns a deep copy of this CompSBMLDocumentPlugin object.
@return a (deep) copy of this CompSBMLDocumentPlugin object
=item CompSBMLDocumentPlugin::getElementBySId
Returns the first child element found that has the given C<id> in the
model-wide SId namespace, or C<NULL> if no such object is found.
@param id string representing the identifier of objects to find
@return a pointer to the SBase element with the given C<id>.
@note The comp SBML document plugin has multiple model-wide SId
namespaces, so a valid document may well contain multiple elements with
the same SId that reside in separate models. It is not recommended to
ever call this function—instead, call the function on the child
ModelDefinition objects.
=item CompSBMLDocumentPlugin::getElementByMetaId
Returns the first child element it can find with the given C<metaid>, or
itself if it has the given C<metaid>, or C<NULL> if no such object is
found.
@param metaid string representing the meta identifier of objects to find
@return a pointer to the SBase element with the given C<metaid>.
=item CompSBMLDocumentPlugin::getAllElements
Returns a List of all child SBase objects, including those nested to an
arbitrary depth
@return a List of pointers to all children objects.
=item CompSBMLDocumentPlugin::createObject
@internal
Create and return an SBML object of this class, if present.
@return the SBML object corresponding to next XMLToken in the
XMLInputStream or C<NULL> if the token was not recognized.
=item CompSBMLDocumentPlugin::writeElements
@internal
Subclasses must override this method to write out their contained
SBML objects as XML elements if they have their specific elements.
=item CompSBMLDocumentPlugin::checkConsistency
@internal
Check consistency function.
=item CompSBMLDocumentPlugin::accept
@internal
=item CompSBMLDocumentPlugin::getListOfModelDefinitions
Returns the ListOf object that holds all ModelDefinitions.
@return the ListOf object that holds all ModelDefinitions.
=item CompSBMLDocumentPlugin::getModelDefinition
Returns the ModelDefinition with the given index.
@param n the index number of the ModelDefinition to get.
@return the nth ModelDefinition in the ListOfModelDefinitions. If the
index is invalid, C<NULL> is returned.
=item CompSBMLDocumentPlugin::getModelDefinition
Returns the ModelDefinition with the given index.
@param n the index number of the ModelDefinition to get.
@return the nth ModelDefinition in the ListOfModelDefinitions. If the
index C<n> is invalid, C<NULL> is returned.
=item CompSBMLDocumentPlugin::getModelDefinition
Returns the model definition object based on its identifier.
@param sid a string representing the identifier
of the model definition to get.
@return ModelDefinition in the ListOfModelDefinitions with the given C<sid
>
or C<NULL> if no such ModelDefinition exists.
@see getModelDefinition(unsigned int n)
@see getListOfModelDefinitions()
=item CompSBMLDocumentPlugin::getModelDefinition
Returns the model definition object based on its identifier.
@param sid a string representing the identifier
of the model definition to get.
@return ModelDefinition in the ListOfModelDefinitions with the given C<sid
>
or C<NULL> if no such ModelDefinition exists.
@see getModelDefinition(unsigned int n)
@see getListOfModelDefinitions()
=item CompSBMLDocumentPlugin::addModelDefinition
Adds a copy of the given ModelDefinition object to the list of
ModelDefinitions.
@param modelDefinition the ModelDefinition object to be added to the
list of ModelDefinitions. Fails if the added ModelDefinition is C<NULL>,
does not match the level/version/package of the parent object, or cannot
be added to the list of replaced elements.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT @endlink
@li @link OperationReturnValues_t#LIBSBML_LEVEL_MISMATCH LIBSBML_LEVEL_MISMATCH @endlink
@li @link OperationReturnValues_t#LIBSBML_VERSION_MISMATCH LIBSBML_VERSION_MISMATCH @endlink
@li @link OperationReturnValues_t#LIBSBML_PKG_VERSION_MISMATCH LIBSBML_VERSION_MISMATCH @endlink
=item CompSBMLDocumentPlugin::getNumModelDefinitions
Returns the number of ModelDefinitions for this SBMLDocumentPlugin.
@return the number of ModelDefinitions.
=item CompSBMLDocumentPlugin::createModelDefinition
Creates a ModelDefinition object, adds it to the end of the
ModelDefinition objects list and returns a pointer to the newly
created object.
@return a newly created ModelDefinition object
=item CompSBMLDocumentPlugin::removeModelDefinition
Removes the ModelDefinition with the given index from the CompSBMLDocumentPlugin.
A pointer to the ModelDefinition that was removed is returned.
If no ModelDefinition has been removed, C<NULL> is returned.
@param index the index of the ModelDefinition object to remove
@return the ModelDefinition object removed. As mentioned above,
the caller owns the returned object. C<NULL> is returned if
the given index is out of range.
=item CompSBMLDocumentPlugin::removeModelDefinition
Removes the ModelDefinition with the given C<id> from the CompSBMLDocumentPlugin.
A pointer to the ModelDefinition that was removed is returned.
If no ModelDefinition has been removed, C<NULL> is returned.
@param id the id of the ModelDefinition object to remove
@return the ModelDefinition object removed. As mentioned above,
the caller owns the returned object. C<NULL> is returned if
the given index is out of range.
=item CompSBMLDocumentPlugin::getListOfExternalModelDefinitions
Returns the ListOf object that holds all ExternalModelDefinitions.
@return the ListOf object that holds all ExternalModelDefinitions.
=item CompSBMLDocumentPlugin::getExternalModelDefinition
Returns the ExternalModelDefinition with the given index.
@param n the index number of the ExternalModelDefinition to get.
@return the nth ExternalModelDefinition in the
ListOfExternalModelDefinitions. If the index is invalid, C<NULL> is
returned.
=item CompSBMLDocumentPlugin::getExternalModelDefinition
Returns the ExternalModelDefinition with the given index.
@param n the index number of the ExternalModelDefinition to get.
@return the nth ExternalModelDefinition in the
ListOfExternalModelDefinitions. If the index is invalid, C<NULL> is
returned.
=item CompSBMLDocumentPlugin::getExternalModelDefinition
Returns the model definition object based on its identifier.
@param sid a string representing the identifier
of the model definition to get.
@return ExternalModelDefinition in the ListOfExternalModelDefinitions with the given C<sid
>
or C<NULL> if no such ExternalModelDefinition exists.
@see getExternalModelDefinition(unsigned int n)
@see getListOfExternalModelDefinitions()
=item CompSBMLDocumentPlugin::getExternalModelDefinition
Returns the model definition object based on its identifier.
@param sid a string representing the identifier
of the model definition to get.
@return ExternalModelDefinition in the ListOfExternalModelDefinitions with the given C<sid
>
or C<NULL> if no such ExternalModelDefinition exists.
@see getExternalModelDefinition(unsigned int n)
@see getListOfExternalModelDefinitions()
=item CompSBMLDocumentPlugin::getModel
Searches the model namespace of the document and returns the Model,
ModelDefinition, or ExternalModelDefintion object with the given
identifier.
@param sid a string representing the identifier of the model definition to get.
@return The SBase corresponding to the given C<sid> or C<NULL> if no such
model exists. If no such model exists, this will return C<NULL>.
=item CompSBMLDocumentPlugin::getModel
Searches the model namespace of the document and returns the Model,
ModelDefinition, or ExternalModelDefintion object with the given
identifier.
@param sid a string representing the identifier of the model definition to get.
@return The SBase corresponding to the given C<sid> or C<NULL> if no such
model exists. If no such model exists, this will return C<NULL>.
=item CompSBMLDocumentPlugin::setRequired
Sets the bool value of "required" attribute of corresponding package
in SBMLDocument element. The only legal value is 'true' for the
Hierarchical Model Composition package.
@param value the bool value of "required" attribute of corresponding
package in SBMLDocument element.
@return integer value indicating success/failure of the
function. The possible values
returned by this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_UNEXPECTED_ATTRIBUTE LIBSBML_UNEXPECTED_ATTRIBUTE @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item CompSBMLDocumentPlugin::addExternalModelDefinition
Adds a copy of the given ExternalModelDefinition object to the list of
ExternalModelDefinitions.
@param externalModelDefinition the ExternalModelDefinition object to be
added to the list of ExternalModelDefinitions. Fails if the added
ExternalModelDefinition is C<NULL>, does not match the
level/version/package of the parent object, or cannot be added to the
list of external model definitions.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT @endlink
@li @link OperationReturnValues_t#LIBSBML_LEVEL_MISMATCH LIBSBML_LEVEL_MISMATCH @endlink
@li @link OperationReturnValues_t#LIBSBML_VERSION_MISMATCH LIBSBML_VERSION_MISMATCH @endlink
@li @link OperationReturnValues_t#LIBSBML_PKG_VERSION_MISMATCH LIBSBML_VERSION_MISMATCH @endlink
=item CompSBMLDocumentPlugin::getNumExternalModelDefinitions
Returns the number of ExternalModelDefinitions for this SBMLDocumentPlugin.
@return the number of ExternalModelDefinitions for this SBMLDocumentPlugin.
=item CompSBMLDocumentPlugin::createExternalModelDefinition
Creates a ExternalModelDefinition object, adds it to the end of the
ExternalModelDefinition objects list and returns a pointer to the newly
created object.
@return a newly created ExternalModelDefinition object
=item CompSBMLDocumentPlugin::removeExternalModelDefinition
Removes the ExternalModelDefinition with the given index.
A pointer to the ExternalModelDefinition that was removed is returned.
If no ExternalModelDefinition has been removed, C<NULL> is returned.
@param index the index of the ExternalModelDefinition object to remove
@return the ExternalModelDefinition object removed. As mentioned above,
the caller owns the returned object. C<NULL> is returned if
the given index is out of range.
=item CompSBMLDocumentPlugin::removeExternalModelDefinition
Removes the ExternalModelDefinition with the given C<id>.
A pointer to the ExternalModelDefinition that was removed is returned.
If no ExternalModelDefinition has been removed, C<NULL> is returned.
@param id the id of the ExternalModelDefinition object to remove
@return the ExternalModelDefinition object removed. As mentioned above,
the caller owns the returned object. C<NULL> is returned if
the given index is out of range.
=item CompSBMLDocumentPlugin::setSBMLDocument
@internal
Sets the parent SBMLDocument of this plugin object.
Subclasses which contain one or more SBase derived elements must
override this function.
@param d the SBMLDocument object to use
@see connectToParent
@see enablePackageInternal
=item CompSBMLDocumentPlugin::connectToChild
@internal
Sets the parent of this SBML object to child SBML objects (if any).
(Creates a child-parent relationship by the parent)
@see setSBMLDocument
@see enablePackageInternal
=item CompSBMLDocumentPlugin::connectToParent
@internal
Sets the parent SBML object of this SBML object.
(Creates a child-parent relationship by the child)
This function is called when a child element is
set/added/created by its parent element (e.g. by setXXX,
addXXX, createXXX, and connectToChild functions of the
parent element).
@param parent the SBML object to use
=item CompSBMLDocumentPlugin::enablePackageInternal
@internal
Enables/Disables the given package with child elements in this plugin
object (if any).
(This is an internal implementation invoked from
SBase::enablePackageInternal() function)
@note Subclasses in which one or more SBase derived elements are
defined must override this function.
@see setSBMLDocument
@see connectToParent
=item CompSBMLDocumentPlugin::getOverrideCompFlattening
@internal
=item CompSBMLDocumentPlugin::setOverrideCompFlattening
@internal
=item CompSBMLDocumentPlugin::getSBMLDocumentFromURI
Uses the suite of URI resolvers to find the document referenced by the
URI, or C<NULL> if no document can be found. The pointer returned is a
non-owning pointer: this CompSBMLDocumentPlugin owns the document in
question, and will return the same pointer if the same URI is requested
later. This is so that when Model objects are returned by
ExternalModelDefinition functions, the document the model is from will
persist. The public interface for this function is therefore to use
ExternalModelDefinition::getReferencedModel() function.
=item CompSBMLDocumentPlugin::getResolvedURI
Used by getSBMDocumentFromURI to first resolve the URI into its
canonical form, for example, from 'model.xml" to
"file:/path/to/model.xml".
=item CompSBMLDocumentPlugin::clearStoredURIDocuments
Clears the internal list of SBMLDocuments kept when resolving URIs. May
invalidate distributed pointers, and therefore should only be used if a
call to getSBMLDocumentFromURI has returned an incorrect document, and
the URI resolvers have since been tweaked so as to no longer return the
same result.
=back
=head2 SBMLUri
@sbmlpackage{comp}
@htmlinclude pkg-marker-comp.html utility class for handling URIs.
@htmlinclude libsbml-facility-only-warning.html
This class implements functionality for parsing URIs and extracting
information about them.
@see SBMLResolver
@see SBMLFileResolver
=over
=item SBMLUri::SBMLUri
Creates a new SBMLUri from the given string URI.
=item SBMLUri::SBMLUri
Copy constructor. Creates a copy of an SBMLUri object.
@param orig the SBMLUri object to copy.
@throws @if python ValueError @else SBMLConstructorException @endif@~
Thrown if the argument C<orig> is C<NULL>.
=item SBMLUri::clone
Creates and returns a deep copy of this SBMLUri object.
@return a (deep) copy of this SBMLFileResolver object.
=item SBMLUri::getScheme
Returns the scheme of the stored URI.
The I<scheme> of the URI is the text before the first colon character.
Typical examples of what this might return are the strings C<"file"> or
C<"http">. If the current URI does not have a scheme, this method
returns an empty string.
@return the parsed scheme, such as C<"http">, or an empty string if no
scheme exists for the current URI.
=item SBMLUri::getHost
Returns the host portion of the stored URI.
For a scheme such as C<"http">, this method returns the part of the URI
after C<"http>://" and before the next C<">/" character. URIs with file
or URN schemes have no host; in that case, this method returns an empty
string.
@return the host of the URI, or an empty string in the case of files
or URNs schemes that do not possess a host portion.
=item SBMLUri::getPath
Returns the path and filename portion of the stored URI.
This method returns the text after the scheme, colon, and host (if
present), and before the next C<"?"> character. The result may be an
empty string for some URIs.
@return the path of the URI (i.e., the full filename with path)
=item SBMLUri::getQuery
Returns the query portion of the stored URI.
The equery portion of a URI is the text after a filename, starting with
the character C<"?">. For many URIs, this is an empty string.
@return the query of the URI (i.e., the part after the full filename
with path)
=item SBMLUri::getUri
Returns the full stored URI, after replacing backslashes with slashes.
@return the original URI, with backslashes replaced with slashes.
=item SBMLUri::relativeTo
Constructs a new URI relative to this object and the given URI.
For example,
@verbatim
SBMLUri("c:\\test").relativeTo("test.xml")
@endverbatim
would construct a new file URI, with path
C<c:/test/test.xml>.
@param uri a URI to be added to this object
@return the resulting new URI
=item SBMLUri::parse
=back
=head2 SBMLResolver
@sbmlpackage{comp}
@htmlinclude pkg-marker-comp.html Base class for SBML resolvers.
@htmlinclude libsbml-facility-only-warning.html
The SBMLResolver class is the base class for the various SBML I<
>
resolvers: facilities that take a unique identifier as input and return
the document associated with that identifier. In SBML, resolvers come
into play with the SBML Level 3 Hierarchical Model Composition
package; this package includes features that allow a model to be composed
from pieces that are external to a given SBML document, which implies the
need to be able to identify and locate those external pieces. The
SBMLResolver class and its subclasses provide facilities for software
applications to be able to do these tasks.
LibSBML provides a number of built-in resolvers, and applications can
create their own by subclassing SBMLResolver and following the examples
of the existing resolvers. The following are the built-in resolvers
in libSBML @htmlinclude libsbml-version.html:
@li SBMLFileResolver
More resolvers may be provided by libSBML in the future. Application
authors may also write their own. @if cpp An example of how to create
an HTTP resolver is included with the libSBML distribution in the file
@ref SBMLHttpResolverExample.cpp "SBMLHttpResolverExample.cpp".@endif
@see SBMLUri
=over
=item SBMLResolver::SBMLResolver
Creates a new SBMLResolver object.
=item SBMLResolver::SBMLResolver
Copy constructor. Creates a copy of an SBMLResolver object.
@param c the SBMLResolver object to copy.
@throws @if python ValueError @else SBMLConstructorException @endif@~
Thrown if the argument C<orig> is C<NULL>.
=item SBMLResolver::clone
Creates and returns a deep copy of this SBMLResolver object.
@return a (deep) copy of this SBMLResolver object.
=item SBMLResolver::resolve
Resolves the document for the given URI.
@param uri the URI to the target document
@param baseUri base URI, in case the URI is a relative one
@return the document, if this resolver can resolve the document or NULL.
=item SBMLResolver::resolveUri
Resolves the full URI for the given URI without actually reading the
document.
@param uri the URI to the target document
@param baseUri base URI, in case the URI is a relative one
@return the full URI to the document, if this resolver can resolve the document or NULL.
=back
=head2 SBMLFileResolver
@sbmlpackage{comp}
@htmlinclude pkg-marker-comp.html A resolver for documents stored on a file system.
@htmlinclude libsbml-facility-only-warning.html
In SBML, I<resolvers> come into play with the SBML Level 3
Hierarchical Model Composition package (“comp”); this package
includes features that allow a model to be composed from pieces that are
external to a given SBML document, which implies the need to be able to
identify and locate those external pieces. The identifiers used in
“comp” are URIs (<a target="_blank"
href="http://en.wikipedia.org/wiki/Uniform_resource_identifier">Uniform
Resource Identifiers</a>).
SBMLFileResolver is a class implementing the ability to resolve URIs to
files. It works on the local file system only. It can resolve relative
and absolute paths, and directories to be searched can be specified using
the methods @if clike SBMLFileResolver::setAdditionalDirs(), @endif
SBMLFileResolver::addAdditionalDir(@if java String dir@endif) and
SBMLFileResolver::clearAdditionalDirs().
@see SBMLResolver
@see SBMLUri
=over
=item SBMLFileResolver::SBMLFileResolver
Creates a new SBMLFileResolver object.
=item SBMLFileResolver::SBMLFileResolver
Copy constructor. Creates a copy of an SBMLFileResolver object.
@param c the SBMLFileResolver object to copy.
@throws @if python ValueError @else SBMLConstructorException @endif@~
Thrown if the argument C<orig> is C<NULL>.
=item SBMLFileResolver::clone
Creates and returns a deep copy of this SBMLFileResolver object.
@return a (deep) copy of this SBMLFileResolver object.
=item SBMLFileResolver::resolve
Resolves the document for the given URI.
@param uri the URI to the target document
@param baseUri base URI, in case the URI is a relative one
@return the document, if this resolver can resolve the document or NULL.
=item SBMLFileResolver::resolveUri
Resolves the full URI for a given URI without actually reading the
document.
@param uri the URI to the target document
@param baseUri base URI, in case the URI is a relative one
@return the full URI to the document, if this resolver can resolve the
document or NULL.
=item SBMLFileResolver::setAdditionalDirs
Sets the list of directories in which to search for files to resolve.
Unlike the similar
SBMLFileResolver::addAdditionalDir(@if java String dir@endif), this
method replaces any current list of search directories with the given
list of C<dirs>.
@param dirs A vector of strings which contain directories
@see addAdditionalDir(@if java String dir@endif)
@see clearAdditionalDirs()
=item SBMLFileResolver::clearAdditionalDirs
Removes the list of directories to search for files to resolve.
After this method is called,
SBMLFileResolver::resolve(const std::string &uri, const std::string& baseUri)
will only search absolute or relative directories. New directories can
be added using SBMLFileResolver::addAdditionalDir(@if java String
dir@endif) @if clike or setAdditionalDirs()@endif.
@see addAdditionalDir(@if java String dir@endif)
@if clike @see setAdditionalDirs()@endif
=item SBMLFileResolver::addAdditionalDir
Adds a directory to the list of directories to search for files to
resolve.
@param dir the directory to add.
@see clearAdditionalDirs()
@if clike @see setAdditionalDirs()@endif
=back
=head2 SBMLResolverRegistry
@sbmlpackage{comp}
@htmlinclude pkg-marker-comp.html Registry of all SBML resolvers.
@htmlinclude libsbml-facility-only-warning.html
LibSBML provides facilities for resolving SBML documents in various ways
from a given URI. Resolvers are implemented as objects derived from the
class SBMLResolver.
The resolver registry maintains a list of known resolvers and provides
methods for discovering them. It is implemented as a singleton object of
class SBMLResolverRegistry. Callers can use the method
SBMLResolverRegistry::getNumResolvers() to find out how many resolvers are
registered, then use SBMLResolverRegistry::getResolverByIndex(@if java int
index@endif) to iterate over each one;
@see SBMLFileResolver
=over
=item SBMLResolverRegistry::getInstance
Returns the singleton instance for the resolver registry.
Prior to using the registry, callers have to obtain a copy of the
registry. This static method provides the means for doing that.
@return the singleton for the resolver registry.
=item SBMLResolverRegistry::addResolver
Adds the given resolver to the registry of SBML resolvers.
@param resolver the resolver to add to the registry.
@return integer value indicating the success/failure of the operation.
@if clike The value is drawn from the enumeration
#OperationReturnValues_t. @endif@~ The possible values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT @endlink
=item SBMLResolverRegistry::removeResolver
Removes the resolver with the given index.
@param index the index of the resolver to be removed
@return integer value indicating the success/failure of the operation.
@if clike The value is drawn from the enumeration
#OperationReturnValues_t. @endif@~ The possible values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT @endlink
=item SBMLResolverRegistry::getResolverByIndex
Returns the resolver with the given index number.
Resolvers are given arbitrary index numbers by the registry. Callers
can use the method SBMLResolverRegistry::getNumResolvers() to find
out how many resolvers are registered, then use this method to
iterate over the list and obtain each one in turn.
@param index the zero-based index of the resolver to fetch.
@return the resolver with the given index number, or C<NULL> if the
number is less than C<0> or there is no resolver at the given index
position.
=item SBMLResolverRegistry::getNumResolvers
Returns the number of resolvers known by the registry.
@return the number of registered resolvers.
@see getResolverByIndex(@if java int index@endif)
=item SBMLResolverRegistry::resolve
Resolves the document for the given URI.
@param uri the URI to the target document
@param baseUri base URI, in case the URI is a relative one
@return the document, if this resolver can resolve the document or NULL.
=item SBMLResolverRegistry::resolveUri
Resolves the full URI for the given URI without actually reading the
document.
@param uri the URI to the target document
@param baseUri base URI, in case the URI is a relative one
@return the full URI to the document, if this resolver can resolve the document or NULL.
=item SBMLResolverRegistry::SBMLResolverRegistry
@internal
protected constructor, use the getInstance() method to access the registry.
=back
=head2 CompBase
@sbmlpackage{comp}
@htmlinclude pkg-marker-comp.html A convenience subclass of “comp” package
SBase-derived classes
The CompBase class derives from SBase, and defines a few functions
and features common to all SBase-derived classes in the SBML Level 3
@ref comp @if java "Hierarchical Model Composition"@endif@~ package
(“comp”).
=over
=item CompBase::CompBase
Creates a new CompBase with the given level, version, and package version.
@param level the SBML Level
@param version the Version within the SBML Level
@param pkgVersion the version of the package
=item CompBase::CompBase
Creates a new CompBase with the given SBMLExtensionNamespaces object.
@param compns the namespace object.
=item CompBase::CompBase
Copy constructor.
@param source the object to copy.
=item CompBase::getPackageURI
Returns the XML namespace (URI) of the package extension
of this object.
@return the URI of the package extension of this plugin object.
=item CompBase::getPackageName
Returns the package name of this plugin object.
@return the package name of this plugin object.
=item CompBase::getPackageVersion
Returns the package version of the package extension of
this plugin object.
@return the package version of the package extension of
this plugin object.
=item CompBase::getParentModel
Returns the Model object to which the referenced child object belongs.
=item CompBase::readAttributes
@internal
Subclasses should override this method to read values from the given
XMLAttributes set into their specific fields. Be sure to call your
parents implementation of this method as well.
=item CompBase::writeAttributes
@internal
Subclasses should override this method to write their XML attributes
to the XMLOutputStream. Be sure to call your parents implementation
of this method as well. For example:
SBase::writeAttributes(stream);
stream.writeAttribute( "submodel" , mSubmodel );
...
=item CompBase::logUnknownElement
@internal
Helper to log a common type of error for elements.
=item CompBase::logUnknownAttribute
@internal
Helper to log a common type of error.
=item CompBase::logEmptyString
@internal
Helper to log a common type of error.
=item CompBase::logInvalidId
@internal
Helper to log a common type of error.
=item CompBase::logMissingAttribute
@internal
Helper to log a common type of error.
=item CompBase::hasValidLevelVersionNamespaceCombination
@internal
Predicate returning C<true> if this
object's level/version and namespace values correspond to a valid
SBML specification.
The valid combination of SBML Level and Version, “comp” package version, and Namespace as of this
release of libSBML is the following:
\n=over\n
\n=item\n\nLevel 3 Version 1 Package Version 1: C<"http://www.sbml.org/sbml/level3/version1/comp/version1">
\n=back\n
@param typecode the typecode for this element
@param xmlns the namespaces used by this element.
@note This function is provided as convenience method to be called from constructors. This
allows to use it in scenarios where the namespaces or typecode have not yet been initialized.
@return C<true> if the level, version and namespace values of this
SBML object correspond to a valid set of values, C<false> otherwise.
=item CompBase::removeFromParentAndPorts
@internal
Remove the given SBase object, and any Ports that point to it.
A static function for removing elements--it is illegal to reference
an element from a port that has been deleted or replaced, but if
it happens, we need to not actually crash. This function finds and
deletes all such invalid ports before deleting the object.
=item CompBase::removeFromParentAndPorts
@internal
DEPRECATED FUNCTION: DO NOT USE
Remove the given SBase object, and any Ports that point to it. Unsafe,
because the program might later attempt to delete any removed Port.
=back
=head2 SBaseRef
@sbmlpackage{comp}
@htmlinclude pkg-marker-comp.html Implementation of the SBaseRef construct from the
“comp” package.
The SBaseRef class was introduced by the SBML Level 3 @ref comp
@if java "Hierarchical Model Composition"@endif@~ package
(“comp”) as the principle way by which submodel elements may
be referenced. The SBaseRef class is usually found as the base class of a
Port, Deletion, ReplacedElement, or ReplacedBy class, but may appear as an
child of one of the above classes if the parent object references a
Submodel.
An SBaseRef object must reference an element using exactly one of the
optional attributes of the class. Subclasses of SBaseRef may define
additional optional attributes that are legal ways to reference an element.
SBaseRef objects may reference elements that do not live in the Model parent
of the SBaseRef object. However, the SBaseRef class itself does not
provide a method of determining which Model or Submodel is being referenced.
The subclasses of SBaseRef provide methods for this instead.
Once the Model to which the SBaseRef object is referencing has been established,
there are four optional attributes defined in the SBaseRef class that
are each methods of referencing an element:
@li "portRef" (type PortSIdRef): As its name implies, this attribute is used to
refer to a port identifier, in the case when the reference being
constructed with the SBaseRef is intended to refer to a port on a
submodel. The namespace of the PortSIdRef value is the set
of identifiers of type PortSId defined in the submodel, not
the parent model.
@li "idRef" (type SIdRef): As its name implies, this attribute is used to
refer to a regular identifier (i.e., the value of an "id"
attribute on some other object), in the case when the reference being
constructed with the SBaseRef is intended to refer to an object that
does not have a port identifier. The namespace of the SIdRef
value is the set of identifiers of type SId defined in the
submodel, not the parent model.
@li "unitRef" (type UnitSIdRef): This attribute is used to refer to the identifier
of a UnitDefinition object. The namespace of the UnitSIdRef
value is the set of unit identifiers defined in the submodel, not the
parent model. (Note that even though this attribute is of type UnitSIdRef,
the reserved unit identifiers that are defined by SBML Level 3 (see
Section 3.1.10 of the core specification) are
not permitted as values of "unitRef". Reserved unit
identifiers may not be replaced or deleted.)
@li "metaIdRef" (type IDREF): This attribute is used to refer to a "metaid"
attribute value on some other object, in the case when the reference
being constructed with the SBaseRef is intended to refer to an object
that does not have a port identifier. The namespace of the "metaIdRef"
value is the entire document in which the referenced model resides, but
must refer to a subelement of the referenced model. Since meta identifiers are
optional attributes of SBase, all SBML objects have the potential to
have a meta identifier value.
An SBaseRef object may have up to one subcomponent named "sBaseRef", of
type SBaseRef. This permits recursive structures to be constructed so
that objects inside submodels can be referenced.
The form of such recursive references must be as follows. The
highest-level SBaseRef object of such a chain (which will necessarily
be an object of class Port, Deletion, ReplacedElement or ReplacedBy,
because they are the only classes derived from the class SBaseRef) must
refer to a Submodel object in the containing model. All child
SBaseRef objects in the chain must refer to components inside the
Model instance to which the Submodel refers.
=over
=item SBaseRef::SBaseRef
Creates a new SBaseRef with the given level, version, and package version.
@param level the SBML Level
@param version the Version within the SBML Level
@param pkgVersion the version of the package
=item SBaseRef::SBaseRef
Creates a new SBaseRef with the given CompPkgNamespaces object.
@param compns the namespace to use
=item SBaseRef::SBaseRef
Copy constructor.
=item SBaseRef::clone
Creates and returns a deep copy of this SBaseRef object.
@return a (deep) copy of this SBaseRef object
=item SBaseRef::getElementBySId
Returns the first child element found that has the given C<id> in the
model-wide SId namespace, or C<NULL> if no such object is found.
@param id string representing the id of objects to find
@return a pointer to the SBase element with the given C<id>.
=item SBaseRef::getElementByMetaId
Returns the first child element it can find with the given C<metaid>, or
itself if it has the given C<metaid>, or C<NULL> if no such object is found.
@param metaid string representing the metaid of objects to find
@return a pointer to the SBase element with the given C<metaid>.
=item SBaseRef::getAllElements
Returns a List of all child SBase objects, including those nested to an
arbitrary depth.
@return a List of pointers to all children objects.
=item SBaseRef::getMetaIdRef
Returns the value of the "metaIdRef" attribute of this SBaseRef.
@return the value of the "metaIdRef" attribute of this SBaseRef.
=item SBaseRef::isSetMetaIdRef
Predicate returning C<true> or C<false> depending on whether this
SBaseRef's "metaIdRef" attribute has been set.
@return C<true> if this SBaseRef's "metaIdRef" attribute has been set,
otherwise C<false> is returned.
=item SBaseRef::setMetaIdRef
Sets the value of the "metaIdRef" attribute of this SBaseRef.
This method fails if the id is not a valid syntax for an IDREF (@link
OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE
LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink), or if the SBaseRef already
points to an element of the submodel using a different interface (@link
OperationReturnValues_t#LIBSBML_OPERATION_FAILED
LIBSBML_OPERATION_FAILED @endlink). An sBaseRef must use exactly one
method to point to a submodel element.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item SBaseRef::unsetMetaIdRef
Unsets the value of the "metaIdRef" attribute of this SBaseRef.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item SBaseRef::getPortRef
Returns the value of the "portRef" attribute of this SBaseRef.
@return the value of the "portRef" attribute of this SBaseRef.
=item SBaseRef::isSetPortRef
Predicate returning C<true> or C<false> depending on whether this
SBaseRef's "portRef" attribute has been set.
@return C<true> if this SBaseRef's "portRef" attribute has been set,
otherwise C<false> is returned.
=item SBaseRef::setPortRef
Sets the value of the "portRef" attribute of this SBaseRef. Fails if
the id is not a valid syntax for a PortSIdRef (@link
OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE
LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink), or if the SBaseRef already
points to an element of the submodel using a different interface (@link
OperationReturnValues_t#LIBSBML_OPERATION_FAILED
LIBSBML_OPERATION_FAILED @endlink). An SBaseRef must use exactly one
method to point to a submodel element.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item SBaseRef::unsetPortRef
Unsets the value of the "portRef" attribute of this SBaseRef.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item SBaseRef::getIdRef
Returns the value of the "idRef" attribute of this SBaseRef.
@return the value of the "idRef" attribute of this SBaseRef.
=item SBaseRef::isSetIdRef
Predicate returning C<true> or C<false> depending on whether this
SBaseRef's "idRef" attribute has been set.
@return C<true> if this SBaseRef's "idRef" attribute has been set,
otherwise C<false> is returned.
=item SBaseRef::setIdRef
Sets the value of the "idRef" attribute of this SBaseRef.
This method fails if the id is not a valid syntax for an SIdRef (@link
OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE
LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink), or if the SBaseRef already
points to an element of the submodel using a different interface (@link
OperationReturnValues_t#LIBSBML_OPERATION_FAILED
LIBSBML_OPERATION_FAILED @endlink). A sBaseRef must use exactly one
method to point to a submodel element.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item SBaseRef::unsetIdRef
Unsets the value of the "idRef" attribute of this SBaseRef.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item SBaseRef::getUnitRef
Returns the value of the "unitRef" attribute of this SBaseRef.
@return the value of the "unitRef" attribute of this SBaseRef.
=item SBaseRef::isSetUnitRef
Predicate returning C<true> or C<false> depending on whether this
SBaseRef's "unitRef" attribute has been set.
@return C<true> if this SBaseRef's "unitRef" attribute has been set,
otherwise C<false> is returned.
=item SBaseRef::setUnitRef
Sets the value of the "unitRef" attribute of this SBaseRef.
This method fails if the id is not a valid syntax for a UnitSIdRef (@link
OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE
LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink), or if the SBaseRef already
points to an element of the submodel using a different interface (@link
OperationReturnValues_t#LIBSBML_OPERATION_FAILED
LIBSBML_OPERATION_FAILED @endlink). A sBaseRef must use exactly one
method to point to a submodel element.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item SBaseRef::unsetUnitRef
Unsets the value of the "unitRef" attribute of this SBaseRef.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item SBaseRef::getSBaseRef
Get the child sBaseRef of this sBaseRef.
@return the const SBaseRef child of this SBaseRef, or NULL if none exists.
=item SBaseRef::getSBaseRef
Get the child sBaseRef of this SBaseRef.
@return the SBaseRef child of this SBaseRef, or NULL if none exists.
=item SBaseRef::isSetSBaseRef
Predicate for testing whether the sBaseRef for this SBaseRef is set.
@return C<true> if the sBaseRef of this SBaseRef is set, C<false
>
otherwise.
=item SBaseRef::setSBaseRef
Sets the sBaseRef definition of this SBaseRef to a copy of the given
SBaseRef object instance.
This method fails if the added sBaseRef does not match the
level/version/package of the parent object or if the added sBaseRef cannot
be copied.
@param sBaseRef the SBaseRef object instance to use.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
@li @link OperationReturnValues_t#LIBSBML_LEVEL_MISMATCH LIBSBML_LEVEL_MISMATCH @endlink
@li @link OperationReturnValues_t#LIBSBML_VERSION_MISMATCH LIBSBML_VERSION_MISMATCH @endlink
@li @link OperationReturnValues_t#LIBSBML_PKG_VERSION_MISMATCH LIBSBML_VERSION_MISMATCH @endlink
=item SBaseRef::createSBaseRef
Creates a new, empty SBaseRef, adds it to this SBaseRef and
returns the created SBaseRef.
@return the newly created SBaseRef object instance.
=item SBaseRef::unsetSBaseRef
Unsets the child SBaseRef of this SBaseRef. Deletes the former SBaseRef child,
if one existed.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item SBaseRef::getNumReferents
Returns how many elements are being referred to by this SBaseRef. A
valid SBaseRef will have exactly one. Possible referents are portRef,
idRef, unitRef, and metaIdRef.
@return integer value between 0 and 4: the number of different ways this element points to its referent.
=item SBaseRef::hasRequiredAttributes
Returns true if getNumReferents() is exactly 1.
@return boolean: 'true' if the attributes are correctly set; 'false' if not.
=item SBaseRef::renameSIdRefs
Renames all the SIdRef attributes on this element if they match
C<oldid>, but not any found in child or plugin elements.
=item SBaseRef::getElementName
Returns the XML element name of
this SBML object.
@return the string of the name of this element.
=item SBaseRef::getTypeCode
Returns the libSBML type code of this object instance.
C<opydetails> doc_what_are_typecodes
@return the SBML type code for this object:
@link SBMLCompTypeCode_t#SBML_COMP_SBASEREF SBML_COMP_SBASEREF@endlink
C<opydetails> doc_warning_typecodes_not_unique
@see getElementName()
@see getPackageName()
=item SBaseRef::writeElements
@internal
Subclasses should override this method to write out their contained
SBML objects as XML elements. Be sure to call your parents
implementation of this method as well. For example:
SBase::writeElements(stream);
mReactants.write(stream);
mProducts.write(stream);
...
=item SBaseRef::accept
Accepts the given SBMLVisitor.
@return the result of calling C<v.visit()>, which indicates
whether or not the Visitor would like to visit the SBML object's next
sibling object (if available).
=item SBaseRef::setSBMLDocument
@internal
Sets the parent SBMLDocument of this SBML object.
@param d the SBMLDocument object to use
=item SBaseRef::connectToChild
@internal
Sets this SBML object to child SBML objects (if any).
(Creates a child-parent relationship by the parent)
Subclasses must override this function if they define
one ore more child elements.
Basically, this function needs to be called in
constructor, copy constructor, assignment operator.
@see setSBMLDocument
@see enablePackageInternal
=item SBaseRef::getReferencedElementFrom
Examines the referenced Model for the referenced object, and returns it, if found.
@param model the Model in which to look for the object referenced by
this SBaseRef.
@return the element in the referenced Model to which this SBaseRef
refers. If this object references an object in a Submodel, the returned
object will be in the instantiated Model in that Submodel.
=item SBaseRef::saveReferencedElement
Finds and stores the referenced object by finding the Model it needs to
point to, calling 'saveReferencedElement' on its parent (which will also
be a SBaseRef or one of its subclasses), and the storing the result.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item SBaseRef::getReferencedElement
Returns the object pointed to by this element. If that element was
previously found and set with 'saveReferencedElement', that element is
returned; otherwise, 'saveReferencedElement' is called first, and the
found element is returned.
=item SBaseRef::clearReferencedElement
Removes the saved referenced element, if it had been saved earlier.
=item SBaseRef::performDeletion
DEPRECATED FUNCTION: DO NOT USE
Deletes the referenced object,
plus any other elements that element points to through ReplacedElement
or ReplacedBy children. Instead of calling this function directly, use
'CompModelPlugin::instantiateSubmodels' instead, which deals with all the
intricacies of replacements and deletions, and gives you access to the
non-flattened hierarchical form of the model.
=item SBaseRef::removeFromParentAndDelete
Finds this SBaseRef's parent, which can either be a List or can be
another SBaseRef, and tells it to remove this.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item SBaseRef::addExpectedAttributes
@internal
Subclasses should override this method to get the list of
expected attributes.
This function is invoked from corresponding readAttributes()
function.
=item SBaseRef::readAttributes
@internal
Subclasses should override this method to read values from the given
XMLAttributes set into their specific fields. Be sure to call your
parents implementation of this method as well.
=item SBaseRef::createObject
@internal
Create and return an SBML object of this class, if present.
@return the SBML object corresponding to next XMLToken in the
XMLInputStream or C<NULL> if the token was not recognized.
=item SBaseRef::writeAttributes
@internal
Subclasses should override this method to write their XML attributes
to the XMLOutputStream. Be sure to call your parents implementation
of this method as well. For example:
SBase::writeAttributes(stream);
stream.writeAttribute( "metaIdRef", mMetaIdRef );
...
=item SBaseRef::getDirectReference
@internal
Get the direct referenced object, which might be a Port.
=item SBaseRef::collectDeletions
Collects (in 'toremove') the referenced object,
plus any other elements that element points to through ReplacedElement
or ReplacedBy children. Does not delete the object directly; this should
be done carefully to avoid double-deletions or misinterpretation of
nested replacements/deletions. Any element already in 'removed' will
not be added to 'toremove', nor will its children be checked.
=back
=head2 Replacing
@sbmlpackage{comp}
@htmlinclude pkg-marker-comp.html A convenience subclass of the ReplacedElement and
ReplacedBy constructs from the “comp” package.
The Replacing class does not exist officialy in the the @ref comp
@if java "Hierarchical Model Composition"@endif@~ package
(“comp”), but is implemented here as a convenience subclass of
the ReplacedElement and ReplacedBy classes, since both of those classes
define a 'submodelRef' attribute.
The required attribute "submodelRef" takes a value of type
SIdRef, which must be the identifier of a Submodel object in
the containing model. The model referenced by the
Submodel object establishes the object namespaces for the
"portRef", "idRef", "unitRef" and "metaIdRef"
attributes: only objects within the Model object may be referenced by
those attributes.
=over
=item Replacing::Replacing
Creates a new Replacing with the given level, version, and package
version.
@param level the SBML Level
@param version the Version within the SBML Level
@param pkgVersion the version of the package
=item Replacing::Replacing
Creates a new Replacing with the given CompPkgNamespaces object.
@param compns the namespace to use
=item Replacing::Replacing
Copy constructor.
=item Replacing::getSubmodelRef
Returns the value of the "submodelRef" attribute of this SBaseRef.
@return the value of the "submodelRef" attribute of this SBaseRef.
=item Replacing::isSetSubmodelRef
Predicate returning C<true> or C<false> depending on whether this
SBaseRef's "submodelRef" attribute has been set.
@return C<true> if this SBaseRef's "submodelRef" attribute has been set,
otherwise C<false> is returned.
=item Replacing::setSubmodelRef
Sets the value of the "submodelRef" attribute of this SBaseRef. Fails
if the id is not a valid syntax for an SIdRef.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item Replacing::unsetSubmodelRef
Unsets the value of the "SubmodelRef" attribute of this SBaseRef.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item Replacing::hasRequiredAttributes
Returns true if getNumReferents() is exactly 1 and if the submodelRef is set.
@return boolean: 'true' if the attributes are correctly set; 'false' if not.
=item Replacing::saveReferencedElement
Finds and stores the referenced object. Finds the Submodel to which
it refers, getting the instantiated Model inside that Submodel, calling
'getReferencedElementFrom' on that model, and storing the result.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item Replacing::renameSIdRefs
Renames all the SIdRef attributes on this element if they match
C<oldid>, but not any found in child or plugin elements.
=item Replacing::performReplacement
DEPRECATED FUNCTION: DO NOT USE
To retain old functionality, this function calls performReplacementAndCollect,
and then actually removes the now-redundant element. However, this can lead
to doubly-deleted elements, as well as the incorrect interpretation of some
models. The replacement function performReplacementAndCollect
has been marked protected, in the hopes that people will instead simply
use CompModelPlugin::instantiateSubmodels, which hides all the complexity while
still allowing access to a non-flattened version of a hierarchical model.
=item Replacing::writeElements
@internal
Subclasses should override this method to write out their contained
SBML objects as XML elements. Be sure to call your parents
implementation of this method as well. For example:
SBase::writeElements(stream);
mReactants.write(stream);
mProducts.write(stream);
...
=item Replacing::accept
Accepts the given SBMLVisitor.
@return the result of calling C<v.visit()>, which indicates
whether or not the Visitor would like to visit the SBML object's next
sibling object (if available).
=item Replacing::setSBMLDocument
@internal
Sets the parent SBMLDocument of this SBML object.
@param d the SBMLDocument object to use
=item Replacing::replaceWithAndMaybeDelete
@internal
=item Replacing::addExpectedAttributes
@internal
Subclasses should override this method to get the list of
expected attributes.
This function is invoked from corresponding readAttributes()
function.
=item Replacing::readAttributes
@internal
Subclasses should override this method to read values from the given
XMLAttributes set into their specific fields. Be sure to call your
parents implementation of this method as well.
=item Replacing::writeAttributes
@internal
Subclasses should override this method to write their XML attributes
to the XMLOutputStream. Be sure to call your parents implementation
of this method as well. For example:
SBase::writeAttributes(stream);
stream.writeAttribute( "conversionFactor", mConversionFactor );
...
=item Replacing::updateIDs
@internal
Searches the model that C<oldnames> came from for references to any of its ids,
and replaces them with references to C<newnames>.
@param oldnames the object being replaced, and whose parent Model contains
the references that need to be updated.
@param newnames the object that should now be referenced instead, to which
any references to C<oldnames> should now point.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT @endlink
=item Replacing::performConversions
@internal
Modify mathematical references to the referenced object according to the C<conversionFactor>.
Find all idrefs in the Model that have mathematical meaning, and convert
them to instead reference the C<replacement>, modified according to the
C<conversionFactor>. Will modify the referenced object's use in MathML
nodes according to replacementID/conversionFactor, and will multiply the
MathML of elements that assign to the referenced object by the C<conversionFactor>.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item Replacing::convertConversionFactor
@internal
Multiply this element's conversion factor (if present) to the C<conversionFactor>.
=item Replacing::performReplacementAndCollect
An internal flattening routine, necessarily overridden by any subclass, to
rename the necessary elements, perform any conversions, and add the now-redundant
element to the 'toremove' list.
=back
=head2 Deletion
@sbmlpackage{comp}
@htmlinclude pkg-marker-comp.html Implementation of the Deletion construct from the
“comp” package.
The Deletion class was introduced by the SBML Level 3 @ref comp
@if java "Hierarchical Model Composition"@endif@~ package
(“comp”) to allow elements of submodels to be removed before
instantiation.
The Deletion object class is used to define a deletion operation
to be applied when a submodel instantiates a model definition.
Deletions may be useful in hierarchical model composition scenarios for
various reasons. For example, some components in a submodel may be
redundant in the composed model, perhaps because the same features are
implemented in a different way in the new model.
Deletions function as follows. When the Model to which the Submodel
object refers (via the "modelRef" attribute) is read and processed for
inclusion into the composed model, each Deletion object identifies an
object to remove from that Model instance. The resulting submodel
instance consists of everything in the Model object instance minus the
entities referenced by the list of Deletion objects.
As might be expected, deletions can have wide-ranging implications,
especially when the object deleted has substantial substructure, as in
the case of reactions. The following are rules regarding deletions and
their effects.
@li An object that has been deleted is considered inaccessible.
Any element that has been deleted (or replaced)
may not be referenced by an SBaseRef object.
@li If the deleted object has child objects and other structures, the
child objects and substructure are also considered to be deleted.
@li It is not an error to delete explicitly an object that is already
deleted by implication (for example as a result of the second point
above). The resulting model is the same.
@li If the deleted object is from an SBML namespace that is not
understood by the interpreter, the deletion must be ignored—the
object will not need to be deleted, as the interpreter could not
understand the package. If an interpreter cannot tell whether
a referenced object does not exist or if exists in an unparsed namespace
it may produce a warning.
The Deletion object class is subclassed from SBaseRef, and reuses all the
machinery provided by SBaseRef. In addition, it defines two optional
attributes, "id" and "name". The "id" attribute can be used to give an
identifier to a given deletion operation. The identifier has no
mathematical meaning, but it may be useful for creating submodels that
can be manipulated more directly by other submodels. (Indeed, it is
legitimate for an enclosing model definition to delete a deletion!)
The optional "name" attribute is provided on Deletion for the
same reason it is provided on other elements that have identifiers;
viz., to provide for the possibility of giving a human-readable name to
the object. The name may be useful in situations when deletions are
displayed to modelers.
=over
=item Deletion::Deletion
Creates a new Deletion with the given level, version, and package version.
@param level the SBML Level
@param version the Version within the SBML Level
@param pkgVersion the version of the package
=item Deletion::Deletion
Creates a new Deletion with the given CompPkgNamespaces object.
=item Deletion::Deletion
Copy constructor.
=item Deletion::clone
Creates and returns a deep copy of this Deletion object.
@return a (deep) copy of this Deletion object
=item Deletion::setId
Sets the value of the "id" attribute of this Deletion.
This method fails if the C<id> is not a valid syntax for an SId.
@param id the identifier to use
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item Deletion::getId
Returns the value of the "id" attribute of this Deletion.
@return the name of this Deletion.
=item Deletion::isSetId
Predicate returning C<true> or C<false> depending on whether this
object's "id" attribute has been set.
@htmlinclude comment-set-methods.html
@return C<true> if the "id" attribute of this object has been
set, C<false> otherwise.
=item Deletion::unsetId
Unsets the value of the "id" attribute of this Deletion.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item Deletion::setName
Sets the value of the "name" attribute of this Deletion.
The string in C<name> is copied.
@param name the new name for the Deletion
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item Deletion::getName
Returns the value of the "name" attribute of this Deletion.
@return the name of this Deletion.
=item Deletion::isSetName
Predicate returning C<true> or C<false> depending on whether this
object's "name" attribute has been set.
@htmlinclude comment-set-methods.html
@return C<true> if the "name" attribute of this object has been set, C<
>
false otherwise.
=item Deletion::unsetName
Unsets the value of the "name" attribute of this Deletion.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item Deletion::getElementName
Returns the XML element name of this SBML object.
@return the string of the name of this element.
=item Deletion::getTypeCode
Returns the libSBML type code of this object instance.
C<opydetails> doc_what_are_typecodes
@return the SBML type code for this object:
@link SBMLCompTypeCode_t#SBML_COMP_DELETION SBML_COMP_DELETION@endlink
C<opydetails> doc_warning_typecodes_not_unique
@see getElementName()
@see getPackageName()
=item Deletion::saveReferencedElement
Finds and stores the referenced object. It finds its Submodel parent,
gets its instantiated Model object, calls
'getReferencedElementFrom' on that model, and stores the result.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item Deletion::accept
@internal
Accepts the given SBMLVisitor.
@return the result of calling C<v.visit()>, which indicates
whether or not the Visitor would like to visit the SBML object's next
sibling object (if available).
=item Deletion::addExpectedAttributes
@internal
Subclasses should override this method to get the list of
expected attributes.
This function is invoked from corresponding readAttributes()
function.
=item Deletion::readAttributes
@internal
Subclasses should override this method to read values from the given
XMLAttributes set into their specific fields. Be sure to call your
parents implementation of this method as well.
=item Deletion::writeAttributes
@internal
Subclasses should override this method to write their XML attributes
to the XMLOutputStream. Be sure to call your parents implementation
of this method as well. For example:
SBase::writeAttributes(stream);
stream.writeAttribute( "id" , mId );
...
=back
=head2 ExternalModelDefinition
@sbmlpackage{comp}
@htmlinclude pkg-marker-comp.html Implementation of the ExternalModelDefinition construct
from the “comp” package.
The ExternalModelDefinition class was introduced by the SBML Level 3
@ref comp @if java "Hierarchical Model Composition"@endif@~
package (“comp”) to define references to Model
objects defined in other files.
ExternalModelDefinition objects are model definitions—in and of
themselves, they are definitions of models but not uses of those models.
The class provides a way to declare and identify them so that Model
objects in the present SBML document can use them in Submodel objects.
ExternalModelDefinition contains two required attributes
("source" and "id") and three optional attributes
("modelRef", "md5" and "name").
The "id" attribute serves to provide a handle for the external
model reference so that Submodel objects can refer to it. Crucially,
it is not the identifier of the model being referenced; rather,
it is an identifier for this ExternalModelDefinition object within the
current SBML document. The "id" attribute takes a required value
of type SId, and must be unique across all Model and ExternalModelDefinition
objects present in the document.
ExternalModelDefinition also has an optional "name" attribute, of
type 'string'. The "name" attribute may be used to provide
a human-readable description of the ExternalModelDefintion object.
The required attribute "source" is used to locate the SBML document
containing an external model definition. The value of this attribute must
be of type anyURI. Since URIs may be either URLs, URNs, or relative or
absolute file locations, this offers flexibility in referencing SBML
documents. In all cases, the "source" attribute value must refer
specifically to an SBML Level 3 Version 1 document; prior
Levels/Versions of SBML are not supported by this package. The entire
file at the given location is referenced. The "source" attribute must
have a value for every ExternalModelDefinition instance.
ExternalModelDefinition's optional attribute "modelRef", of type
SIdRef, is used to identify a Model or
ExternalModelDefinition object within the SBML document located at
"source". The object referenced may be the main model in the
document, or it may be a model definition contained in the SBML
document's ListOfModelDefinitions or
ListOfExternalModelDefinitions lists. Loops are not allowed: it
must be possible to follow a chain of ExternalModelDefinition objects
to its end in a Model object.
In core SBML, the "id" on Model is an optional attribute, and therefore,
it is possible that the Model object in a given SBML document does not
have an identifier. In that case, there is no value to give to the
"modelRef" attribute in ExternalModelDefinition. If "modelRef" does not
have a value, then the main model (i.e., the C<<model>>
element within the C<<sbml>> element) in the referenced
file is interpreted as being the model referenced by this
ExternalModelDefinition instance.
Finally, the optional "md5" attribute takes a string value. If
set, it must be an MD5 checksum value computed over the document
referenced by "source". This checksum can serve as a data
integrity check over the contents of the "source". Applications
may use this to verify that the contents have not changed since the time
that the ExternalModelDefinition reference was constructed.
=over
=item ExternalModelDefinition::ExternalModelDefinition
Creates a new ExternalModelDefinition with the given level, version, and
package version.
@param level the SBML Level
@param version the Version within the SBML Level
@param pkgVersion the version of the package
=item ExternalModelDefinition::ExternalModelDefinition
Creates a new ExternalModelDefinition with the given CompPkgNamespaces
object.
@param compns the namespace to use.
=item ExternalModelDefinition::ExternalModelDefinition
Copy constructor.
@param source the object to copy.
=item ExternalModelDefinition::clone
Creates and returns a deep copy of this ExternalModelDefinition object.
@return a (deep) copy of this ExternalModelDefinition object
=item ExternalModelDefinition::setId
Sets the value of the "id" attribute of this ExternalModelDefinition.
This method fails if the C<id> is not a valid syntax for an SId.
@param id the identifier to use
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item ExternalModelDefinition::getId
Returns the value of the "id" attribute of this ExternalModelDefinition.
@return the name of this ExternalModelDefinition.
=item ExternalModelDefinition::isSetId
Predicate returning C<true> or C<false> depending on whether this
object's "id" attribute has been set.
@htmlinclude comment-set-methods.html
@return C<true> if the "id" attribute of this object has been
set, C<false> otherwise.
=item ExternalModelDefinition::unsetId
Unsets the value of the "id" attribute of this ExternalModelDefinition.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item ExternalModelDefinition::setName
Sets the value of the "name" attribute of this ExternalModelDefinition.
The string in C<name> is copied.
@param name the new name for the ExternalModelDefinition
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item ExternalModelDefinition::getName
Returns the value of the "name" attribute of this
ExternalModelDefinition.
@return the name of this ExternalModelDefinition.
=item ExternalModelDefinition::isSetName
Predicate returning C<true> or C<false> depending on whether this
object's "name" attribute has been set.
@htmlinclude comment-set-methods.html
@return C<true> if the "name" attribute of this object has been
set, C<false> otherwise.
=item ExternalModelDefinition::unsetName
Unsets the value of the "name" attribute of this
ExternalModelDefinition.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item ExternalModelDefinition::getModelRef
Returns the value of the "modelRef" attribute of this
ExternalModelDefinition.
@return the value of the "modelRef" attribute of this
ExternalModelDefinition.
=item ExternalModelDefinition::isSetModelRef
Predicate returning C<true> or C<false> depending on whether this
ExternalModelDefinition's "modelRef" attribute has been set.
@return C<true> if this ExternalModelDefinition's "modelRef" attribute
has been set, otherwise C<false> is returned.
=item ExternalModelDefinition::setModelRef
Sets the value of the "modelRef" attribute of this
ExternalModelDefinition. Fails if the C<id> is not a valid syntax for an
SIdRef.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item ExternalModelDefinition::unsetModelRef
Unsets the value of the "modelRef" attribute of this
ExternalModelDefinition.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item ExternalModelDefinition::getMd5
Returns the value of the "md5" attribute of this
ExternalModelDefinition.
@return the value of the "md5" attribute of this
ExternalModelDefinition.
=item ExternalModelDefinition::isSetMd5
Predicate returning C<true> or C<false> depending on whether this
ExternalModelDefinition's "md5" attribute has been set.
@return C<true> if this ExternalModelDefinition's "md5" attribute has
been set, otherwise C<false> is returned.
=item ExternalModelDefinition::setMd5
Sets the value of the "md5" attribute of this ExternalModelDefinition.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item ExternalModelDefinition::unsetMd5
Unsets the value of the "md5" attribute of this ExternalModelDefinition.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item ExternalModelDefinition::getSource
Returns the value of the "source" attribute of this
ExternalModelDefinition.
@return the value of the "source" attribute of this
ExternalModelDefinition.
=item ExternalModelDefinition::isSetSource
Predicate returning C<true> or C<false> depending on whether this
ExternalModelDefinition's "source" attribute has been set.
@return C<true> if this ExternalModelDefinition's "source" attribute has
been set, otherwise C<false> is returned.
=item ExternalModelDefinition::setSource
Sets the value of the "source" attribute of this
ExternalModelDefinition.
@param source the value to use for the "source" attribute.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item ExternalModelDefinition::unsetSource
Unsets the value of the "source" attribute of this
ExternalModelDefinition.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item ExternalModelDefinition::hasRequiredAttributes
Returns true if the "modelRef" and "id" attributes are set, and false if not.
This method does not check to see if the referred-to model actually
exists.
@return boolean: C<true> if the attributes are correctly set; C<false
>
if not.
=item ExternalModelDefinition::getElementName
Returns the XML element name of this SBML object.
@return the string of the name of this element.
=item ExternalModelDefinition::getTypeCode
Returns the libSBML type code of this object instance.
C<opydetails> doc_what_are_typecodes
@return the SBML type code for this object:
@link SBMLCompTypeCode_t#SBML_COMP_EXTERNALMODELDEFINITION SBML_COMP_EXTERNALMODELDEFINITION@endlink
C<opydetails> doc_warning_typecodes_not_unique
@see getElementName()
@see getPackageName()
=item ExternalModelDefinition::writeElements
@internal
Subclasses should override this method to write out their contained
SBML objects as XML elements. Be sure to call your parents
implementation of this method as well. For example:
<pre>
SBase::writeElements(stream);
mReactants.write(stream);
mProducts.write(stream);
...
<pre>
=item ExternalModelDefinition::accept
@internal
Accepts the given SBMLVisitor.
@return the result of calling C<v.visit()>, which indicates
whether or not the Visitor would like to visit the SBML object's next
sibling object (if available).
=item ExternalModelDefinition::getReferencedModel
Resolves and returns the referenced Model object of this ExternalModelDefinition.
If none can be found, an error is set and NULL is returned. The
returned Model is a non-owning pointer to the model; the original
Model is saved (along with the SBMLDocument from which it comes) as
a child of the CompSBMLDocumentPlugin of the SBMLDocument to which this
Model belongs. If this ExternalModelDefinition is not part of any
SBMLDocument, NULL will be returned.
=item ExternalModelDefinition::addExpectedAttributes
@internal
Subclasses should override this method to get the list of
expected attributes.
This function is invoked from corresponding readAttributes()
function.
=item ExternalModelDefinition::readAttributes
@internal
Subclasses should override this method to read values from the given
XMLAttributes set into their specific fields. Be sure to call your
parents implementation of this method as well.
=item ExternalModelDefinition::writeAttributes
@internal
Subclasses should override this method to write their XML attributes
to the XMLOutputStream. Be sure to call your parents implementation
of this method as well. For example:
SBase::writeAttributes(stream);
stream.writeAttribute( "submodel" , mSubmodel );
...
=item ExternalModelDefinition::getReferencedModel
@internal
=back
=head2 ListOfDeletions
@sbmlpackage{comp}
@htmlinclude pkg-marker-comp.html Implementation of the ListOfDeletions construct from the
“comp” package.
The ListOfDeletions is a container for the “comp”
Submodel that defines elements to be removed before instantiation.
C<opydetails> doc_what_is_listof
@see Deletion
@see ListOfExternalModelDefinitions
@see ListOfModelDefinitions
@see ListOfPorts
@see ListOfReplacedElements
@see ListOfSubmodels
=over
=item ListOfDeletions::clone
Creates and returns a deep copy of this ListOfDeletions object.
@return a (deep) copy of this ListOfDeletions.
=item ListOfDeletions::ListOfDeletions
Creates a new ListOfDeletions with the given level, version, and package
version.
@param level the SBML Level
@param version the Version within the SBML Level
@param pkgVersion the version of the package
=item ListOfDeletions::ListOfDeletions
Creates a new ListOfDeletions with the given CompPkgNamespaces object.
@param compns the namespace to use
=item ListOfDeletions::get
Get a Deletion from the ListOfDeletions.
@param n the index number of the Deletion to get.
@return the nth Deletion in this ListOfDeletions.
@see size()
=item ListOfDeletions::get
Get a Deletion from the ListOfDeletions.
@param n the index number of the Deletion to get.
@return the nth Deletion in this ListOfDeletions.
@see size()
=item ListOfDeletions::get
Get a Deletion from the ListOfDeletions
based on its identifier.
@param sid a string representing the identifier
of the Deletion to get.
@return Deletion in this ListOfDeletions
with the given C<sid> or C<NULL> if no such
Member exists.
@see get(unsigned int n)
@see size()
=item ListOfDeletions::get
Get a Deletion from the ListOfDeletions
based on its identifier.
@param sid a string representing the identifier
of the Deletion to get.
@return Deletion in this ListOfDeletions
with the given C<sid> or C<NULL> if no such
Deletion exists.
@see get(unsigned int n)
@see size()
=item ListOfDeletions::remove
Removes the nth item from this ListOfDeletions items and returns a
pointer to it.
The caller owns the returned item and is responsible for deleting it.
@param n the index of the item to remove
@see size()
=item ListOfDeletions::remove
Removes an item from this ListOfDeletions items based on its identifier
and returns a pointer to it.
The caller owns the returned item and is responsible for deleting it.
@param sid string representing the id of the item to remove
@see size()
=item ListOfDeletions::getItemTypeCode
Returns the libSBML type code for the objects contained in this ListOf
(i.e., Deletion objects, if the list is non-empty).
C<opydetails> doc_what_are_typecodes
@return the SBML type code for objects contained in this list:
@link SBMLTypeCode_t#SBML_COMP_DELETION SBML_COMP_DELETION@endlink (default).
@see getElementName()
@see getPackageName()
=item ListOfDeletions::getElementName
Returns the XML element name of this SBML object.
@return the string of the name of this element.
=item ListOfDeletions::createObject
@internal
Create and return an SBML object of this class, if present.
@return the SBML object corresponding to next XMLToken in the
XMLInputStream or C<NULL> if the token was not recognized.
=item ListOfDeletions::writeXMLNS
@internal
=back
=head2 ListOfExternalModelDefinitions
@sbmlpackage{comp}
@htmlinclude pkg-marker-comp.html Implementation of the ListOfExternalModelDefinitions
construct from the “comp” package.
The ListOfExternalModelDefinitions is a container for the extended
SBMLDocument that defines references to Models defined in external
files.
C<opydetails> doc_what_is_listof
@see ExternalModelDefinition
@see ListOfDeletions
@see ListOfModelDefinitions
@see ListOfPorts
@see ListOfReplacedElements
@see ListOfSubmodels
=over
=item ListOfExternalModelDefinitions::clone
Creates and returns a deep copy of this ListOfExternalModelDefinitions object.
@return a (deep) copy of this ListOfExternalModelDefinitions.
=item ListOfExternalModelDefinitions::ListOfExternalModelDefinitions
Creates a new ListOfExternalModelDefinitions with the given level,
version, and package version.
@param level the SBML Level
@param version the Version within the SBML Level
@param pkgVersion the version of the package
=item ListOfExternalModelDefinitions::ListOfExternalModelDefinitions
Creates a new ListOfExternalModelDefinitions with the given
CompPkgNamespaces object.
@param compns the namespace to use
=item ListOfExternalModelDefinitions::get
Get a ExternalModelDefinition from the ListOfExternalModelDefinitions.
@param n the index number of the ExternalModelDefinition to get.
@return the nth ExternalModelDefinition in this
ListOfExternalModelDefinitions.
@see size()
=item ListOfExternalModelDefinitions::get
Get a ExternalModelDefinition from the ListOfExternalModelDefinitions.
@param n the index number of the ExternalModelDefinition to get.
@return the nth ExternalModelDefinition in this
ListOfExternalModelDefinitions.
@see size()
=item ListOfExternalModelDefinitions::get
Get a Model from the ListOfExternalModelDefinitions
based on its identifier.
@param sid a string representing the identifier
of the Model to get.
@return Model in this ListOfExternalModelDefinitions
with the given C<sid> or C<NULL> if no such
Member exists.
@see get(unsigned int n)
@see size()
=item ListOfExternalModelDefinitions::get
Get a Model from the ListOfExternalModelDefinitions
based on its identifier.
@param sid a string representing the identifier
of the Model to get.
@return Model in this ListOfExternalModelDefinitions
with the given C<sid> or C<NULL> if no such
Model exists.
@see get(unsigned int n)
@see size()
=item ListOfExternalModelDefinitions::remove
Removes the nth item from this ListOfExternalModelDefinitions items and
returns a pointer to it.
The caller owns the returned item and is responsible for deleting it.
@param n the index of the item to remove
@see size()
=item ListOfExternalModelDefinitions::remove
Removes the item with given C<sid> from this ListOfModelDefinitions items
and returns a pointer to it.
The caller owns the returned item and is responsible for deleting it.
@param sid the id of the item to remove
@see size()
=item ListOfExternalModelDefinitions::getItemTypeCode
Returns the libSBML type code for the objects contained in this ListOf
(i.e., Model objects, if the list is non-empty).
C<opydetails> doc_what_are_typecodes
@return the SBML type code for objects contained in this list:
@link SBMLTypeCode_t#SBML_COMP_EXTERNALMODELDEFINITION SBML_COMP_EXTERNALMODELDEFINITION@endlink (default).
@see getElementName()
@see getPackageName()
=item ListOfExternalModelDefinitions::getElementName
Returns the XML element name of
this SBML object.
@return the string of the name of this element.
=item ListOfExternalModelDefinitions::accept
@internal
Accepts the given SBMLVisitor.
@param v the SBMLVisitor instance to be used.
@return the result of calling C<v.visit()>, which indicates
whether the Visitor would like to visit the next item in the
list.
=item ListOfExternalModelDefinitions::createObject
@internal
Create and return an SBML object of this class, if present.
@return the SBML object corresponding to next XMLToken in the
XMLInputStream or NULL if the token was not recognized.
=item ListOfExternalModelDefinitions::writeXMLNS
@internal
=back
=head2 ListOfModelDefinitions
@sbmlpackage{comp}
@htmlinclude pkg-marker-comp.html Implementation of the ListOfModelDefinitions construct
from the “comp” package.
The ListOfModelDefinitions is a container for the extended
SBMLDocument that allows one to define multiple Models in a single file
for use in Submodel objects.
C<opydetails> doc_what_is_listof
@see ModelDefinition
@see ListOfDeletions
@see ListOfExternalModelDefinitions
@see ListOfPorts
@see ListOfReplacedElements
@see ListOfSubmodels
=over
=item ListOfModelDefinitions::clone
Creates and returns a deep copy of this ListOfModelDefinitions object.
@return a (deep) copy of this ListOfModelDefinitions.
=item ListOfModelDefinitions::ListOfModelDefinitions
Creates a new ListOfModelDefinitions with the given level, version, and
package version.
@param level the SBML Level
@param version the Version within the SBML Level
@param pkgVersion the version of the package
=item ListOfModelDefinitions::ListOfModelDefinitions
Creates a new ListOfModelDefinitions with the given CompPkgNamespaces
object.
=item ListOfModelDefinitions::get
Get a ModelDefinition from the ListOfModelDefinitions.
@param n the index number of the ModelDefinition to get.
@return the nth ModelDefinition in this ListOfModelDefinitions.
@see size()
=item ListOfModelDefinitions::get
Get a ModelDefinition from the ListOfModelDefinitions.
@param n the index number of the ModelDefinition to get.
@return the nth ModelDefinition in this ListOfModelDefinitions.
@see size()
=item ListOfModelDefinitions::get
Get a Model from the ListOfModelDefinitions
based on its identifier.
@param sid a string representing the identifier
of the Model to get.
@return Model in this ListOfModelDefinitions
with the given C<sid> or C<NULL> if no such
Member exists.
@see get(unsigned int n)
@see size()
=item ListOfModelDefinitions::get
Get a Model from the ListOfModelDefinitions
based on its identifier.
@param sid a string representing the identifier
of the Model to get.
@return Model in this ListOfModelDefinitions
with the given C<sid> or C<NULL> if no such
Model exists.
@see get(unsigned int n)
@see size()
=item ListOfModelDefinitions::remove
Removes the nth item from this ListOfModelDefinitions items and returns
a pointer to it.
The caller owns the returned item and is responsible for deleting it.
@param n the index of the item to remove
@see size()
=item ListOfModelDefinitions::*remove
Removes the item with given identifer from this ListOfModelDefinitions
items and returns a pointer to it.
The caller owns the returned item and is responsible for deleting it.
@param sid the id of the item to remove
@see size()
=item ListOfModelDefinitions::getItemTypeCode
Returns the libSBML type code for the objects contained in this ListOf
(i.e., ModelDefinition objects, if the list is non-empty).
C<opydetails> doc_what_are_typecodes
@return the SBML type code for objects contained in this list:
@link SBMLTypeCode_t#SBML_COMP_MODELDEFINITION SBML_COMP_MODELDEFINITION@endlink (default).
@see getElementName()
@see getPackageName()
=item ListOfModelDefinitions::getElementName
Returns the XML element name of
this SBML object.
@return the string of the name of this element.
=item ListOfModelDefinitions::createObject
@internal
Create and return an SBML object of this class, if present.
@return the SBML object corresponding to next XMLToken in the
XMLInputStream or NULL if the token was not recognized.
=item ListOfModelDefinitions::writeXMLNS
@internal
=back
=head2 ListOfPorts
@sbmlpackage{comp}
@htmlinclude pkg-marker-comp.html Implementation of the ListOfPorts construct from the
“comp” package.
The ListOfPorts is a container for the extended
Model for Port objects for that Model.
C<opydetails> doc_what_is_listof
@see Port
@see ListOfDeletions
@see ListOfExternalModelDefinitions
@see ListOfModelDefinitions
@see ListOfReplacedElements
@see ListOfSubmodels
=over
=item ListOfPorts::clone
Creates and returns a deep copy of this ListOfPorts object.
@return a (deep) copy of this ListOfPorts.
=item ListOfPorts::ListOfPorts
Creates a new ListOfPorts with the given level, version, and package version.
@param level the SBML Level
@param version the Version within the SBML Level
@param pkgVersion the version of the package
=item ListOfPorts::ListOfPorts
Creates a new ListOfPorts with the given CompPkgNamespaces object.
@param compns the namespace to use
=item ListOfPorts::get
Get a Port from the ListOfPorts.
@param n the index number of the Port to get.
@return the nth Port in this ListOfPorts.
@see size()
=item ListOfPorts::get
Get a Port from the ListOfPorts.
@param n the index number of the Port to get.
@return the nth Port in this ListOfPorts.
@see size()
=item ListOfPorts::get
Get a Port from the ListOfPorts
based on its identifier.
@param sid a string representing the identifier
of the Port to get.
@return Port in this ListOfPorts
with the given C<sid> or C<NULL> if no such
Member exists.
@see get(unsigned int n)
@see size()
=item ListOfPorts::get
Get a Port from the ListOfPorts
based on its identifier.
@param sid a string representing the identifier
of the Port to get.
@return Port in this ListOfPorts
with the given C<sid> or C<NULL> if no such
Port exists.
@see get(unsigned int n)
@see size()
=item ListOfPorts::remove
Removes an item from this ListOfPorts items based on the identifier and
returns a pointer to it.
The caller owns the returned item and is responsible for deleting it.
@param sid string representing the id of the Port to remove
@see size()
=item ListOfPorts::remove
Removes the nth item from this ListOfPorts items and returns a pointer
to it.
The caller owns the returned item and is responsible for deleting it.
@param n the index of the item to remove
@see size()
=item ListOfPorts::getItemTypeCode
Returns the libSBML type code for the objects contained in this ListOf
(i.e., Port objects, if the list is non-empty).
C<opydetails> doc_what_are_typecodes
@return the SBML type code for objects contained in this list:
@link SBMLTypeCode_t#SBML_COMP_PORT SBML_COMP_PORT@endlink (default).
@see getElementName()
@see getPackageName()
=item ListOfPorts::getElementName
Returns the XML element name of
this SBML object.
@return the string of the name of this element.
=item ListOfPorts::getElementBySId
Returns the first child element found that has the given C<id> in the
model-wide SId namespace, or C<NULL> if no such object is found. Since the
id of Port objects are in the PortSId namespace, no Port object is
returned by this function.
@param id string representing the id of objects to find
@return a pointer to the SBase element with the given C<id>.
=item ListOfPorts::createObject
@internal
Create and return an SBML object of this class, if present.
@return the SBML object corresponding to next XMLToken in the
XMLInputStream or NULL if the token was not recognized.
=item ListOfPorts::writeXMLNS
@internal
=back
=head2 ListOfReplacedElements
@sbmlpackage{comp}
@htmlinclude pkg-marker-comp.html Implementation of the ListOfReplacedElements construct
from the “comp” package.
The ListOfReplacedElements is a container for any SBase object. It
contains ReplacedElement objects, which point to elements the parent
SBase object is to replace.
C<opydetails> doc_what_is_listof
@see ReplacedElement
@see ListOfDeletions
@see ListOfExternalModelDefinitions
@see ListOfModelDefinitions
@see ListOfPorts
@see ListOfSubmodels
=over
=item ListOfReplacedElements::clone
Creates and returns a deep copy of this ListOfReplacedElements object.
@return a (deep) copy of this ListOfReplacedElements.
=item ListOfReplacedElements::ListOfReplacedElements
Creates a new ListOfReplacedElements with the given level, version, and
package version.
@param level the SBML Level
@param version the Version within the SBML Level
@param pkgVersion the version of the package
=item ListOfReplacedElements::ListOfReplacedElements
Creates a new ListOfReplacedElements with the given CompPkgNamespaces
object.
@param compns the namespace to use
=item ListOfReplacedElements::get
Get a ReplacedElement from the ListOfReplacedElements.
@param n the index number of the ReplacedElement to get.
@return the nth ReplacedElement in this ListOfReplacedElements.
@see size()
=item ListOfReplacedElements::get
Get a ReplacedElement from the ListOfReplacedElements.
@param n the index number of the ReplacedElement to get.
@return the nth ReplacedElement in this ListOfReplacedElements.
@see size()
=item ListOfReplacedElements::remove
Removes the nth item from this ListOfReplacedElements items and returns
a pointer to it.
The caller owns the returned item and is responsible for deleting it.
@param n the index of the item to remove
@see size()
=item ListOfReplacedElements::getItemTypeCode
Returns the libSBML type code for the objects contained in this ListOf
(i.e., ReplacedElements objects, if the list is non-empty).
C<opydetails> doc_what_are_typecodes
@return the SBML type code for objects contained in this list:
@link SBMLTypeCode_t#SBML_COMP_REPLACEDELEMENT SBML_COMP_REPLACEDELEMENT@endlink (default).
@see getElementName()
@see getPackageName()
=item ListOfReplacedElements::getElementName
Returns the XML element name of
this SBML object.
@return the string of the name of this element.
=item ListOfReplacedElements::createObject
@internal
Create and return an SBML object of this class, if present.
@return the SBML object corresponding to next XMLToken in the
XMLInputStream or NULL if the token was not recognized.
=item ListOfReplacedElements::writeXMLNS
@internal
=back
=head2 ListOfSubmodels
@sbmlpackage{comp}
@htmlinclude pkg-marker-comp.html Implementation of the ListOfSubmodels construct from the
“comp” package.
The ListOfSubmodels is a container for the extended
Model that contains Submodel objects to be instantiated in that Model.
C<opydetails> doc_what_is_listof
@see Submodel
@see ListOfDeletions
@see ListOfExternalModelDefinitions
@see ListOfModelDefinitions
@see ListOfPorts
@see ListOfReplacedElements
=over
=item ListOfSubmodels::clone
Creates and returns a deep copy of this ListOfSubmodels object.
@return a (deep) copy of this ListOfSubmodels.
=item ListOfSubmodels::ListOfSubmodels
Creates a new ListOfSubmodels with the given level, version, and package
version.
@param level the SBML Level
@param version the Version within the SBML Level
@param pkgVersion the version of the package
=item ListOfSubmodels::ListOfSubmodels
Creates a new ListOfSubmodels with the given CompPkgNamespaces object.
@param compns the namespace to use
=item ListOfSubmodels::get
Get a Submodel from the ListOfSubmodels.
@param n the index number of the Submodel to get.
@return the nth Submodel in this ListOfSubmodels.
@see size()
=item ListOfSubmodels::get
Get a Submodel from the ListOfSubmodels.
@param n the index number of the Submodel to get.
@return the nth Submodel in this ListOfSubmodels.
@see size()
=item ListOfSubmodels::get
Get a Model from the ListOfSubmodels
based on its identifier.
@param sid a string representing the identifier
of the Model to get.
@return Model in this ListOfSubmodels
with the given C<sid> or C<NULL> if no such
Member exists.
@see get(unsigned int n)
@see size()
=item ListOfSubmodels::get
Get a Model from the ListOfSubmodels
based on its identifier.
@param sid a string representing the identifier
of the Model to get.
@return Model in this ListOfSubmodels
with the given C<sid> or C<NULL> if no such
Model exists.
@see get(unsigned int n)
@see size()
=item ListOfSubmodels::remove
Removes the nth item from this ListOfSubmodels items and returns a
pointer to it.
The caller owns the returned item and is responsible for deleting it.
@param n the index of the item to remove
@see size()
=item ListOfSubmodels::remove
Removes an item from this ListOfSubmodels items based on its identifier
and returns a pointer to it.
The caller owns the returned item and is responsible for deleting it.
@param sid string representing the identifier of the item to remove
@see size()
=item ListOfSubmodels::getItemTypeCode
Returns the libSBML type code for the objects contained in this ListOf
(i.e., Submodel objects, if the list is non-empty).
C<opydetails> doc_what_are_typecodes
@return the SBML type code for objects contained in this list:
@link SBMLTypeCode_t#SBML_COMP_SUBMODEL SBML_COMP_SUBMODEL@endlink (default).
@see getElementName()
@see getPackageName()
=item ListOfSubmodels::getElementName
Returns the XML element name of
this SBML object.
@return the string of the name of this element.
=item ListOfSubmodels::createObject
@internal
Create and return an SBML object of this class, if present.
@return the SBML object corresponding to next XMLToken in the
XMLInputStream or NULL if the token was not recognized.
=item ListOfSubmodels::writeXMLNS
@internal
=back
=head2 ModelDefinition
@sbmlpackage{comp}
@htmlinclude pkg-marker-comp.html Implementation of the ModelDefinition construct from the
“comp” package.
The @ref comp @if java "Hierarchical Model Composition"@endif@~
package (“comp”) allows multiple Model objects
to be defined in a single SBMLDocument. While these new Model objects are
not new SBML classes, they are given a new name,
C<<modelDefinition>>, and reside in ListOfModelDefinition
objects. In libSBML, this class inherits from the Model class, changing
only the expected parent of the object, and the XML name.
An additional restriction is placed on the "id" attribute of ModelDefinition
objects: not only must it be unique across all such attributes of type SId
within the ModelDefintion, it must also be unique across all Model,
ModelDefinition, and ExternalModelDefinition objects in the same SBMLDocument.
=over
=item ModelDefinition::ModelDefinition
Creates a new ModelDefinition with the given level, version, and package
version.
@param level the SBML Level
@param version the Version within the SBML Level
@param pkgVersion the version of the package
=item ModelDefinition::ModelDefinition
Creates a new ModelDefinition with the given CompPkgNamespaces object.
@param compns the namespace to use
=item ModelDefinition::ModelDefinition
Copy constructor from base Model object.
=item ModelDefinition::clone
Creates and returns a deep copy of this ModelDefinition object.
@return a (deep) copy of this ModelDefinition object
=item ModelDefinition::getElementName
The only difference between a Model and a ModelDefinition is the
element name ('modelDefinition')
@return the string of the name of this element ("modelDefintion").
@see getTypeCode()
=item ModelDefinition::getTypeCode
Returns the libSBML type code of this object instance.
C<opydetails> doc_what_are_typecodes
@return the SBML type code for this object:
@link SBMLCompTypeCode_t#SBML_COMP_MODELDEFINITION SBML_COMP_MODELDEFINITION@endlink
C<opydetails> doc_warning_typecodes_not_unique
@see getElementName()
@see getPackageName()
=item ModelDefinition::removeFromParentAndDelete
Finds this Model's parent ListOfModelDefinitions and removes itself from
it and deletes itself.
This method actually just calls the SBase function, since the Model
class overrides it, but that's actually what we want to happen here.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item ModelDefinition::accept
@internal
Accepts the given SBMLVisitor.
@return the result of calling C<v.visit()>, which indicates
whether or not the Visitor would like to visit the SBML object's next
sibling object (if available).
=item ModelDefinition::addExpectedAttributes
@internal
Subclasses should override this method to get the list of
expected attributes.
This function is invoked from corresponding readAttributes()
function.
=item ModelDefinition::readAttributes
@internal
Subclasses should override this method to read values from the given
XMLAttributes set into their specific fields. Be sure to call your
parents implementation of this method as well.
=back
=head2 Port
@sbmlpackage{comp}
@htmlinclude pkg-marker-comp.html Implementation of the Port construct from the
“comp” package.
The Port class was introduced by the SBML Level 3 @ref comp
@if java "Hierarchical Model Composition"@endif@~ package
(“comp”) to allow a Model to define a standard interface
between it and other models that might use it as a submodel. It derives
from the SBaseRef class, and the elements defined there refer to elements
in the same parent Model as the Port object. A Port object instance
therefore uses those attributes to define a port for a component in a
model. When other SBaseRef or SBaseRef-derived classes refer to a Port
object using a "portRef" attribute, the element being referenced is the
element the Port object itself points to.
In the present formulation of the Hierarchical Model Composition
package, the use of ports is not enforced, nor is there any
mechanism to restrict which ports may be used in what ways—they are
only an advisory construct. Future versions of this SBML package may
provide additional functionality to support explicit restrictions on
port use. For the present definition of Hierarchical Model Composition,
users of models containing ports are encouraged to respect the modeler's
intention in defining ports, and use the port definitions to interact
with components through their ports (when they have ports defined)
rather than interact directly with the components.
The required attribute "id" is used to give an identifier to a
Port object so that other objects can refer to it. The attribute has
type PortSId and is essentially identical to the SBML
primitive type SId, except that its namespace is limited to
the identifiers of Port objects defined within a Model object. In
parallel, the PortSId type has a companion type,
PortSIdRef, that corresponds to the SBML primitive type
SIdRef; the value space of PortSIdRef is limited
to PortSId values.
=over
=item Port::Port
Creates a new Port with the given level, version, and package version.
@param level the SBML Level
@param version the Version within the SBML Level
@param pkgVersion the version of the package
=item Port::Port
Creates a new Port with the given CompPkgNamespaces object.
@param compns the namespace to use
=item Port::Port
Copy constructor.
=item Port::clone
Creates and returns a deep copy of this Port object.
@return a (deep) copy of this Port object
=item Port::getId
Returns the value of the "id" attribute of this Port.
@return the value of the "id" attribute of this Port.
=item Port::isSetId
Predicate returning C<true> or C<false> depending on whether this
Port's "id" attribute has been set.
@return C<true> if this Port's "id" attribute has been set,
otherwise C<false> is returned.
=item Port::setId
Sets the value of the "id" attribute of this Port.
This method fails if the C<id> is not a valid syntax for an SId.
@param id the identifier for the port
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item Port::unsetId
Unsets the value of the "id" attribute of this Port.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item Port::getName
Returns the value of the "name" attribute of this Port.
@return the value of the "name" attribute of this Port.
=item Port::isSetName
Predicate returning C<true> or C<false> depending on whether this
Port's "name" attribute has been set.
@return C<true> if this Port's "name" attribute has been set,
otherwise C<false> is returned.
=item Port::setName
Sets the value of the "name" attribute of this Port.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item Port::unsetName
Unsets the value of the "name" attribute of this Port.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item Port::setPortRef
Overrides SBaseRef::setPortRef to always fail, because Port objects
themselves cannot refer to model elements by PortSId.
@param id the identifier to set for the port reference
@return integer value indicating failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif The possible value
returned by this function is:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item Port::hasRequiredAttributes
Returns true if the 'id' attribute is set, and if exactly one of
the optional attributes of SBaseRef (portRef, idRef, metaIdRef,
and unitRef)are set.
@return boolean: 'true' if the attributes are correctly set; 'false' if not.
=item Port::getElementName
Returns the XML element name of
this SBML object.
@return the string of the name of this element.
=item Port::getTypeCode
Returns the libSBML type code of this object instance.
C<opydetails> doc_what_are_typecodes
@return the SBML type code for this object:
@link SBMLCompTypeCode_t#SBML_COMP_PORT SBML_COMP_PORT@endlink
C<opydetails> doc_warning_typecodes_not_unique
@see getElementName()
@see getPackageName()
=item Port::saveReferencedElement
Finds and stores the referenced object by finding its Model parent,
calling 'getReferencedElementFrom()' on that model, and storing the
result.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item Port::renameSIdRefs
Renames the idRef attribute on this element if the oldid matches.
=item Port::renameUnitSIdRefs
Renames the unitRef attribute on this element if the oldid matches.
=item Port::renameMetaIdRefs
Renames the metaIdRef attribute on this element if the oldid matches.
=item Port::writeElements
@internal
Subclasses should override this method to write out their contained
SBML objects as XML elements. Be sure to call your parents
implementation of this method as well. For example:
SBase::writeElements(stream);
mReactants.write(stream);
mProducts.write(stream);
...
=item Port::accept
@internal
Accepts the given SBMLVisitor.
@return the result of calling C<v.visit()>, which indicates
whether or not the Visitor would like to visit the SBML object's next
sibling object (if available).
=item Port::addExpectedAttributes
@internal
Subclasses should override this method to get the list of
expected attributes.
This function is invoked from corresponding readAttributes()
function.
=item Port::readAttributes
@internal
Subclasses should override this method to read values from the given
XMLAttributes set into their specific fields. Be sure to call your
parents implementation of this method as well.
=item Port::writeAttributes
@internal
Subclasses should override this method to write their XML attributes
to the XMLOutputStream. Be sure to call your parents implementation
of this method as well. For example:
SBase::writeAttributes(stream);
stream.writeAttribute( "submodel", mSubmodel );
...
=back
=head2 ReplacedBy
@sbmlpackage{comp}
@htmlinclude pkg-marker-comp.html Implementation of the ReplacedBy construct from the
“comp” package.
The ReplacedBy class was introduced by the SBML Level 3 @ref comp
@if java "Hierarchical Model Composition"@endif@~
package (“comp”) to allow submodel elements to be 'canonical'
versions of the element while still allowing the parent model to reference
those elements. Whereas a ReplacedElement object indicates that the
containing object replaces another, a ReplacedBy object indicates the
converse: the parent object is to be replaced by another object.
As is the case with ReplacedElement, the ReplacedBy class inherits from SBaseRef.
It additionally defines one required attribute ("submodelRef"), defined in
libSBML in the Replacing class.
=over
=item ReplacedBy::ReplacedBy
Creates a new ReplacedBy with the given level, version, and package
version.
@param level the SBML Level
@param version the Version within the SBML Level
@param pkgVersion the version of the package
=item ReplacedBy::ReplacedBy
Creates a new ReplacedBy with the given CompPkgNamespaces object.
@param compns the namespace to use
=item ReplacedBy::ReplacedBy
Copy constructor.
=item ReplacedBy::clone
Creates and returns a deep copy of this ReplacedBy object.
@return a (deep) copy of this ReplacedBy object
=item ReplacedBy::getElementName
Returns the XML element name of
this SBML object.
@return the string of the name of this element.
=item ReplacedBy::getTypeCode
Returns the libSBML type code of this object instance.
C<opydetails> doc_what_are_typecodes
@return the SBML type code for this object:
@link SBMLCompTypeCode_t#SBML_COMP_REPLACEDBY SBML_COMP_REPLACEDBY@endlink
C<opydetails> doc_warning_typecodes_not_unique
@see getElementName()
@see getPackageName()
=item ReplacedBy::removeFromParentAndDelete
Finds this ReplacedBy's SBase parent, gets the “comp” plugin from it,
and tells that to remove this.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item ReplacedBy::updateIDs
@internal
Searches the model that C<oldnames> came from for references to any of its ids,
and replaces them with references to C<newnames>.
@param oldnames the object being replaced, and whose parent Model contains
the references that need to be updated.
@param newnames the object that should now be referenced instead, to which
any references to C<oldnames> should now point.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT @endlink
=item ReplacedBy::accept
@internal
Accepts the given SBMLVisitor.
@return the result of calling C<v.visit()>, which indicates
whether or not the Visitor would like to visit the SBML object's next
sibling object (if available).
=item ReplacedBy::performReplacementAndCollect
Updates all IDs and references to those IDs. Does not actually
remove the now-redundant element! The elements to be removed is instead
added to 'toremove', allowing one to remove the element carefully
to prevent double-deletion of elements, and to allow the correct
interpretation of 'nested' replacements and deletions.
The 'removed' argument is present to ensure that the replaced element was
not already removed, which would make it impossible to check it for its
old IDs. In normal comp flattening, 'removed' will only contain comp elements,
which should usually not be replaced, only deleted.
=back
=head2 ReplacedElement
@sbmlpackage{comp}
@htmlinclude pkg-marker-comp.html Implementation of the ReplacedElement construct from the
“comp” package.
The ReplacedElement class was introduced by the SBML Level 3
@ref comp @if java "Hierarchical Model Composition"@endif@~ package
(“comp”) to allow submodel elements to be replaced, but still
allow references to those elements to be valid. A ReplacedElement object
is essentially a pointer to a submodel object that should be considered
'replaced'. The object holding the ReplacedElement instance is the one
doing the replacing; the object pointed to by the ReplacedElement object
is the object being replaced.
A replacement implies that dependencies involving the replaced object
must be updated: all references to the replaced object elsewhere in the
model are taken to refer to the replacement object instead. For
example, if one species replaces another, then any reference to the
original species in mathematical formulas, or lists of reactants or
products or modifiers in reactions, or initial assignments, or any other
SBML construct, are taken to refer to the replacement species, with its
value possibly modified by either this object's "conversionFactor"
attribute or the relevant submodel's conversion factors. Moreover, any
annotations that refer to the
replaced species' "metaid" value must be made to refer to the
replacement species' "metaid" value instead; and anything else
that referred either to an object identifier (i.e., attributes such as
the "id" attribute whose types inherit from the SId
primitive data type) or the meta identifier (i.e., the "metaid"
attribute or any other attribute that inherits from the ID primitive
data type) must be made to refer to the replacement species object
instead.
It is worth noting that local parameters (inside Reaction objects) pose an
interesting edge case for these rules. In order to determine which element
is pointed to by a C<<cn>> element within the
C<<math>> element of a KineticLaw object, it is necessary
to examine the local parameters of that kinetic law's parent Reaction
object. Whether the C<<cn>> element is considered to
point to something new, then, depends on whether it pointed to the local
parameter and whether that local parameter was replaced, even if the text
of the element matched the SId value of another element in the model.
Note that local parameters may only effectively be replaced by global
parameters, since references to its SId are only valid from within the
Reaction element to which it belongs.
When referencing an element within the Submodel pointed to by the
"submodelRef" attribute (defined in libSBML in the Replacing class),
any of the four attributes inherited from
SBaseRef for the purpose may be used (portRef, idRef, unitRef, or
metaIdRef), or a new optional attribute "deletion" may be used. This
attribute must be the identifier of a Deletion
object in the parent Model of the ReplacedElement (i.e., the value of
some Deletion object's "id" attribute). When "deletion" is
set, it means the ReplacedElement object is actually an annotation to
indicate that the replacement object replaces something deleted
from a submodel. The use of the "deletion" attribute overrides
the use of the attributes inherited from SBaseRef: instead of using,
e.g., "portRef" or "idRef", the ReplacedElement instance
sets "deletion" to the identifier of the Deletion object. In
addition, the referenced Deletion must be a child of the Submodel
referenced by the "submodelRef" attribute.
The use of ReplacedElement objects to refer to deletions has no effect
on the composition of models or the mathematical properties of the
result. It serves instead to help record the decision-making process
that lead to a given model. It can be particularly useful for
visualization purposes, as well as to serve as scaffolding where other
types of annotations can be added using the normal Annotation
subcomponents available on all SBase objects in SBML.
As with the Submodel class, it may be that the units of the replaced
element may not match the units of the replacement element. In this case,
the optional "conversionFactor" attribute may be used. This attribute, if
present, defines how to transform or rescale the replaced object's value
so that it is appropriate for the new contexts in which the object
appears. This attribute takes a value of type SIdRef, and
the value must refer to a Parameter object instance defined in the
model. This parameter then acts as a conversion factor.
The value of the conversion factor should be defined such that a single
unit of the replaced element multiplied by the conversion factor should
equal a single unit of the replacement element, and the units of the
conversion factor should be commensurate with that transformation. The
referenced Parameter may be non-constant, particularly if a Species is
replaced by a Species with a different "hasOnlySubstanceUnits"
attribute value, thus changing amount to concentration, or visa versa.
=over
=item ReplacedElement::ReplacedElement
Creates a new ReplacedElement with the given level, version, and package
version.
@param level the SBML Level
@param version the Version within the SBML Level
@param pkgVersion the version of the package
=item ReplacedElement::ReplacedElement
Creates a new ReplacedElement with the given CompPkgNamespaces object.
@param compns the namespace to use
=item ReplacedElement::ReplacedElement
Copy constructor.
=item ReplacedElement::clone
Creates and returns a deep copy of this ReplacedElement object.
@return a (deep) copy of this ReplacedElement object
=item ReplacedElement::getConversionFactor
Returns the value of the "conversionFactor" attribute of this ReplacedElement.
@return the value of the "conversionFactor" attribute of this ReplacedElement.
=item ReplacedElement::isSetConversionFactor
Predicate returning C<true> or C<false> depending on whether this
ReplacedElement's "conversionFactor" attribute has been set.
@return C<true> if this ReplacedElement's "conversionFactor" attribute has been set,
otherwise C<false> is returned.
=item ReplacedElement::setConversionFactor
Sets the value of the "conversionFactor" attribute of this ReplacedElement.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item ReplacedElement::unsetConversionFactor
Unsets the value of the "conversionFactor" attribute of this ReplacedElement.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item ReplacedElement::getDeletion
Returns the value of the "deletion" attribute of this ReplacedElement.
@return the value of the "deletion" attribute of this ReplacedElement.
=item ReplacedElement::isSetDeletion
Predicate returning C<true> or C<false> depending on whether this
SBaseRef's "deletion" attribute has been set.
@return C<true> if this ReplacedElement's "deletion" attribute has been set,
otherwise C<false> is returned.
=item ReplacedElement::setDeletion
Sets the value of the "deletion" attribute of this ReplacedElement.
This method fails if the id is not a valid syntax for an SIdRef (@link
OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE
LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink), or if the SBaseRef already
points to an element of the submodel using a different interface (@link
OperationReturnValues_t#LIBSBML_OPERATION_FAILED
LIBSBML_OPERATION_FAILED @endlink). A ReplacedElement must use exactly
one method to point to a submodel element: deletion, port, idRef,
unitRef, or metaIdRef.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item ReplacedElement::unsetDeletion
Unsets the value of the "deletion" attribute of this ReplacedElement.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item ReplacedElement::getElementName
Returns the XML element name of
this SBML object.
@return the string of the name of this element.
=item ReplacedElement::getNumReferents
Returns how many elements are being referred to by this ReplacedElement. A
valid ReplacedElement will have exactly one. Possible referents are deletion,
port, idRef, unitRef, and metaIdRef.
@return integer value between 0 and 5: the number of different ways this
element points to its referent.
=item ReplacedElement::getTypeCode
Returns the libSBML type code of this object instance.
C<opydetails> doc_what_are_typecodes
@return the SBML type code for this object:
@link SBMLCompTypeCode_t#SBML_COMP_REPLACEDELEMENT SBML_COMP_REPLACEDELEMENT@endlink
C<opydetails> doc_warning_typecodes_not_unique
@see getElementName()
@see getPackageName()
=item ReplacedElement::renameSIdRefs
Renames all the SIdRef attributes on this element if they match
C<oldid>, but not any found in child or plugin elements.
=item ReplacedElement::getReferencedElementFrom
Finds the SBase object this ReplacedElement object points to, if any.
=item ReplacedElement::writeElements
@internal
Subclasses should override this method to write out their contained
SBML objects as XML elements. Be sure to call your parents
implementation of this method as well. For example:
SBase::writeElements(stream);
mReactants.write(stream);
mProducts.write(stream);
...
=item ReplacedElement::accept
@internal
Accepts the given SBMLVisitor.
@return the result of calling C<v.visit()>, which indicates
whether or not the Visitor would like to visit the SBML object's next
sibling object (if available).
=item ReplacedElement::addExpectedAttributes
@internal
Subclasses should override this method to get the list of
expected attributes.
This function is invoked from corresponding readAttributes()
function.
=item ReplacedElement::readAttributes
@internal
Subclasses should override this method to read values from the given
XMLAttributes set into their specific fields. Be sure to call your
parents implementation of this method as well.
=item ReplacedElement::writeAttributes
@internal
Subclasses should override this method to write their XML attributes
to the XMLOutputStream. Be sure to call your parents implementation
of this method as well. For example:
SBase::writeAttributes(stream);
stream.writeAttribute( "conversionFactor", mConversionFactor );
...
=item ReplacedElement::performReplacementAndCollect
Updates all IDs and references to those IDs, as well as performing all
necessary conversions based on the conversion factors. Does not actually
remove the now-redundant element! The elements to be removed is instead
added to 'toremove', allowing one to remove the element carefully
to prevent double-deletion of elements, and to allow the correct
interpretation of 'nested' replacements and deletions.
The 'removed' argument is present to ensure that the replaced element was
not already removed, which would make it impossible to check it for its
old IDs. In normal comp flattening, 'removed' will only contain comp elements,
which should usually not be replaced, only deleted.
=back
=head2 Submodel
@sbmlpackage{comp}
@htmlinclude pkg-marker-comp.html Implementation of the Submodel construct from the
“comp” package.
The Submodel class was introduced by the SBML Level 3 @ref comp
@if java "Hierarchical Model Composition"@endif@~ package
(“comp”) as the principle way by which models are structured
hierarchically. Submodels are instantiations of models contained within
other models. They reference another Model that is to be instantiated
within its parent Model, and additionally define how that Model is to be
modified before instantiation.
The Submodel object class has a required attribute "modelRef", which must
reference another Model or ExternalModelDefinition object present in the
SBML Document. This referenced Model is the model to be instantiated.
It also has a required attribute, "id", to give the submodel a unique
identifier by which other parts of an SBML model definition can refer to
it, and an optional "name" attribute of type C<string>. Identifiers and
names must be used according to the guidelines described in the SBML
specification.
The Submodel class also provides constructs that define how the referenced
Model object is to be modified before it is instantiated in the enclosing
model. If numerical values in the referenced model must be changed in order
to fit them into their new context as part of the submodel, the changes can
be handled through conversion factors. If one or more structural features
in the referenced model are undesirable and should be removed, the changes
can be handled through deletions. (For example, an initial assignment or
reaction may not be relevant in its new context and should be removed.)
In some cases, the referenced Model may have been written with different
units than the containing model. For most model elements, this is not a
problem: it is already possible to have Species and Parameter objects with
different units in a single model, for example, so in this case the
resulting hierarchical model would be treated in exactly the same way as
any other model with Species and Parameters with different units.
However, two units in SBML models are fixed and must not vary between SBML
elements: time and extent. The units of time are set once per model, and
affect the core elements of RateRule, KineticLaw, Delay, and the
csymbols 'time' and 'delay'. Even if the model does not explicitly state
what the units of time actually are, they are defined to be consistent
across the model, and therefore might differ from the units of time across
a parent model. To correct this imbalance, the optional attribute
"timeConversionFactor" may be used, which, if defined, must reference a
constant parameter in the parent model. The value of the time conversion
factor should be defined such that a single unit of time in the Submodel
multiplied by the time conversion factor should equal a single unit of
time in the parent model.
Extent is the unit in SBML that defines how the KineticLaw of a Reaction
affects species quantities: kinetic laws are defined to be in units of
extent/time. No other SBML core construct is defined in terms of extent.
If the effective units of extent in a submodel differ from the effective
units of extent in the parent model (regardless of whether either defined
what those units actually are), the optional attribute
"extentConversionFactor" may be used, which, if defined, must reference a
constant parameter in the parent model. The value of the extent conversion
factor should be defined such that a single unit of extent in the Submodel
multiplied by the extent conversion factor should equal a single unit of
extent in the parent model.
If features of the referenced model must be removed, a Deletion should be added
to the Submodel object. A Submodel may contain a child ListOfDeletions, which
in turn may contain one or more Deletion items. Each Deletion references a single
element of the referenced Model that must be removed before instantiating that
Model as a submodel of the parent Model.
=over
=item Submodel::Submodel
Creates a new Submodel with the given level, version, and package
version.
@param level the SBML Level
@param version the Version within the SBML Level
@param pkgVersion the version of the package
=item Submodel::Submodel
Creates a new Submodel with the given CompPkgNamespaces object.
@param compns the namespace to use
=item Submodel::Submodel
Copy constructor.
=item Submodel::clone
Creates and returns a deep copy of this Submodel object.
@return a (deep) copy of this Submodel object
=item Submodel::getElementBySId
Returns the first child element found that has the given C<id> in the
model-wide SId namespace, or C<NULL> if no such object is found.
@param id string representing the id of objects to find
@return a pointer to the SBase element with the given C<id>.
=item Submodel::getElementByMetaId
Returns the first child element it can find with the given C<metaid>, or
itself if it has the given C<metaid>, or C<NULL> if no such object is found.
@param metaid string representing the metaid of objects to find
@return a pointer to the SBase element with the given C<metaid>.
=item Submodel::getAllElements
Returns a List of all child SBase objects, including those nested to an
arbitrary depth.
@return a List of pointers to all children objects.
=item Submodel::getId
Returns the value of the "id" attribute of this Submodel.
@return the value of the "id" attribute of this Submodel.
=item Submodel::isSetId
Predicate returning C<true> or C<false> depending on whether this
Submodel's "id" attribute has been set.
@return C<true> if this Submodel's "id" attribute has been set,
otherwise C<false> is returned.
=item Submodel::setId
Sets the value of the "id" attribute of this Submodel. Fails if the id
is not a valid syntax for an SId.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item Submodel::unsetId
Unsets the value of the "id" attribute of this Submodel.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item Submodel::getName
Returns the value of the "name" attribute of this Submodel.
@return the value of the "name" attribute of this Submodel.
=item Submodel::isSetName
Predicate returning C<true> or C<false> depending on whether this
Submodel's "name" attribute has been set.
@return C<true> if this Submodel's "name" attribute has been set,
otherwise C<false> is returned.
=item Submodel::setName
Sets the value of the "name" attribute of this Submodel. Fails if the
name is empty.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item Submodel::unsetName
Unsets the value of the "name" attribute of this Submodel.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item Submodel::getModelRef
Returns the value of the "modelRef" attribute of this Submodel.
@return the value of the "modelRef" attribute of this Submodel.
=item Submodel::isSetModelRef
Predicate returning C<true> or C<false> depending on whether this
Submodel's "modelRef" attribute has been set.
@return C<true> if this Submodel's "modelRef" attribute has been set,
otherwise C<false> is returned.
=item Submodel::setModelRef
Sets the value of the "modelRef" attribute of this Submodel. Fails if
the modelRef is not a valid syntax for an SIdRef.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item Submodel::unsetModelRef
Unsets the value of the "modelRef" attribute of this Submodel.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item Submodel::getSubstanceConversionFactor
Returns an empty string, since "substanceConversionFactor" is not a part of the comp spec.
@return an empty string
=item Submodel::isSetSubstanceConversionFactor
Returns C<false>, since "substanceConversionFactor" is not a part of the comp spec.
@return C<false>.
=item Submodel::setSubstanceConversionFactor
Automatically fails, since "substanceConversionFactor" is not a part of the comp spec.
@return integer value indicating success/failure of the
operation. The possible return value is:
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item Submodel::unsetSubstanceConversionFactor
Automatically fails, since "substanceConversionFactor" is not a part of the comp spec.
@return integer value indicating success/failure of the
operation. The possible return value is:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item Submodel::getTimeConversionFactor
Returns the value of the "timeConversionFactor" attribute of this Submodel.
@return the value of the "timeConversionFactor" attribute of this Submodel.
=item Submodel::isSetTimeConversionFactor
Predicate returning C<true> or C<false> depending on whether this
Submodel's "timeConversionFactor" attribute has been set.
@return C<true> if this Submodel's "timeConversionFactor" attribute has been set,
otherwise C<false> is returned.
=item Submodel::setTimeConversionFactor
Sets the value of the "timeConversionFactor" attribute of this Submodel.
Fails if the id is not a valid syntax for an SIdRef.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item Submodel::unsetTimeConversionFactor
Unsets the value of the "timeConversionFactor" attribute of this Submodel.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item Submodel::getExtentConversionFactor
Returns the value of the "extentConversionFactor" attribute of this Submodel.
@return the value of the "extentConversionFactor" attribute of this Submodel.
=item Submodel::isSetExtentConversionFactor
Predicate returning C<true> or C<false> depending on whether this
Submodel's "extentConversionFactor" attribute has been set.
@return C<true> if this Submodel's "extentConversionFactor" attribute has been set,
otherwise C<false> is returned.
=item Submodel::setExtentConversionFactor
Sets the value of the "extentConversionFactor" attribute of this
Submodel. Fails if the id is not a valid syntax for an SIdRef.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item Submodel::unsetExtentConversionFactor
Unsets the value of the "extentConversionFactor" attribute of this
Submodel.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item Submodel::getListOfDeletions
Returns the ListOf object that holds all deletions.
@return the ListOf object that holds all deletions.
=item Submodel::getListOfDeletions
Returns the ListOf object that holds all deletions.
@return the ListOf object that holds all deletions.
=item Submodel::getDeletion
Returns the deletion with the given index.
If the index is invalid, C<NULL> is returned.
@param n the index number of the Deletion to get.
@return the nth Deletion in the ListOfDeletions.
=item Submodel::getDeletion
Returns the deletion with the given index.
If the index is invalid, C<NULL> is returned.
@param n the index number of the Deletion to get.
@return the nth Deletion in the ListOfDeletions.
=item Submodel::getDeletion
Returns the deletion with the given C<id>.
If the id is invalid, C<NULL> is returned.
@param id the id of the Deletion to get.
@return the Deletion in the ListOfDeletions with the given C<id>.
=item Submodel::getDeletion
Returns the deletion with the given C<id>.
If the id is invalid, C<NULL> is returned.
@param id the id of the Deletion to get.
@return the Deletion in the ListOfDeletions with the given C<id>.
=item Submodel::addDeletion
Adds a copy of the given Deletion object to the list of deletions.
@param deletion the Deletion object to be added to the list of
deletions. Fails if the added deletion is NULL, does not match the
level/version/package of the parent object, or cannot be added to the
list of deletions.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT @endlink
@li @link OperationReturnValues_t#LIBSBML_LEVEL_MISMATCH LIBSBML_LEVEL_MISMATCH @endlink
@li @link OperationReturnValues_t#LIBSBML_VERSION_MISMATCH LIBSBML_VERSION_MISMATCH @endlink
@li @link OperationReturnValues_t#LIBSBML_PKG_VERSION_MISMATCH LIBSBML_VERSION_MISMATCH @endlink
=item Submodel::getNumDeletions
Returns the number of deletions for this Submodel.
@return the number of deletions for this Submodel.
=item Submodel::createDeletion
Creates a Deletion object, adds it to the end of the
deletion objects list and returns a pointer to the newly
created object.
@return a newly created Deletion object
=item Submodel::removeDeletion
Removes the deletion with the given index from the Submodel.
A pointer to the deletion that was removed is returned.
If no deletion has been removed, C<NULL> is returned.
@param index the index of the Deletion object to remove
@return the Deletion object removed. As mentioned above,
the caller owns the returned object. C<NULL> is returned if
the given index is out of range.
=item Submodel::removeDeletion
Removes the deletion with the given identifier from the Submodel.
A pointer to the deletion that was removed is returned.
If no deletion has been removed, C<NULL> is returned.
@param sid string representing the identifier
of the Deletion object to remove
@return the Deletion object removed. As mentioned above,
the caller owns the returned object. C<NULL> is returned if
the given C<sid> is not found.
=item Submodel::hasRequiredAttributes
Returns true if the 'submodel' attribute is set, and if getNumReferents() is exactly 1.
@return boolean: 'true' if the attributes are correctly set; 'false' if not.
=item Submodel::getElementName
Returns the XML element name of
this SBML object.
@return the string of the name of this element.
=item Submodel::renameSIdRefs
Renames the conversion factor attributes on this element if C<oldid> matches.
=item Submodel::getTypeCode
Returns the libSBML type code of this object instance.
C<opydetails> doc_what_are_typecodes
@return the SBML type code for this object:
@link SBMLCompTypeCode_t#SBML_COMP_SUBMODEL SBML_COMP_SUBMODEL@endlink
C<opydetails> doc_warning_typecodes_not_unique
@see getElementName()
@see getPackageName()
=item Submodel::writeElements
@internal
Subclasses should override this method to write out their contained
SBML objects as XML elements. Be sure to call your parents
implementation of this method as well. For example:
SBase::writeElements(stream);
mReactants.write(stream);
mProducts.write(stream);
...
=item Submodel::accept
@internal
Accepts the given SBMLVisitor.
@return the result of calling C<v.visit()>, which indicates
whether or not the Visitor would like to visit the SBML object's next
sibling object (if available).
=item Submodel::setSBMLDocument
@internal
Sets the parent SBMLDocument of this SBML object.
@param d the SBMLDocument object to use
=item Submodel::connectToChild
@internal
Sets this SBML object to child SBML objects (if any).
(Creates a child-parent relationship by the parent)
Subclasses must override this function if they define
one ore more child elements.
Basically, this function needs to be called in
constructor, copy constructor, assignment operator.
@see setSBMLDocument
@see enablePackageInternal
=item Submodel::createObject
@internal
Create and return an SBML object of this class, if present.
@return the SBML object corresponding to next XMLToken in the
XMLInputStream or NULL if the token was not recognized.
=item Submodel::instantiate
Find and create a local copy of the Model object referenced by this
Submodel. Is recursive, in that if the instantiated Model contains any
Submodel objects, those Submodels will themselves be instantiated. If
an instantiated model previously existed, it is deleted and a new one is
created. For this reason, call this function only once, or
call Submodel::getInstantiation().
@return an integer value indicating success/failure of the operation.
Possible return values from this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
In this case, 'invalid object' means that this Submodel itself is invalid, and no Model can be instantiated from it.
=item Submodel::performDeletions
Delete elements in the instantiated submodel, based on any Deletions
from this Submodel's listOfDeletions.
@return an integer value indicating success/failure of the operation.
Possible return values from this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
In this case, 'invalid object' means that this Submodel itself is invalid, and no Model can be instantiated from it.
=item Submodel::replaceElement
Delete the element in question from the stored instantiated Model, and
replace all references to it with references to the replacement object.
@link OperationReturnValues_t#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT @endlink
means that this Submodel itself or one of the passed-in objects are invalid.
@link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
means that the routine failed for some othe reason.
@return an integer value indicating success/failure of the operation.
Possible return values from this function are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item Submodel::getInstantiation
Get the instantiated Model this Submodel contains rules to create.
Calls instantiate() automatically if this operation has not yet been
performed, and/or if the operation failed the last time it was called.
Any modifictions that have been performed with performDeletions(),
replaceElement(), or convertTimeAndExtent() function calls will be included.
@return the instantiated Model object: a clone of the original, modified
according to the performDeletions() and replaceElement() functions that
have been called. Returns NULL if any error is encountered.
=item Submodel::getInstantiation
Get the instantiated Model this Submodel contains rules to create.
Calls instantiate() automatically if this operation has not yet been
performed, and/or if the operation failed the last time it was called.
Any modifictions that have been performed with performDeletions(),
replaceElement(), or convertTimeAndExtent() function calls will be included.
@return the instantiated Model object: a clone of the original, modified
according to the performDeletions() and replaceElement() functions that
have been called. Returns NULL if any error is encountered.
=item Submodel::clearInstantiation
Delete the instantiated Model, if it exists.
=item Submodel::getAllInstantiatedElements
Get all instantiated sub-elements, including any elements from
instantiated submodels, etc.
=item Submodel::convertTimeAndExtent
Convert all references to time and extent in the instantiated
Model, according to the
timeConversionFactor and extentConversionFactor attributes.
=item Submodel::addExpectedAttributes
@internal
Subclasses should override this method to get the list of
expected attributes.
This function is invoked from corresponding readAttributes()
function.
=item Submodel::readAttributes
@internal
Subclasses should override this method to read values from the given
XMLAttributes set into their specific fields. Be sure to call your
parents implementation of this method as well.
=item Submodel::writeAttributes
@internal
Subclasses should override this method to write their XML attributes
to the XMLOutputStream. Be sure to call your parents implementation
of this method as well. For example:
SBase::writeAttributes(stream);
stream.writeAttribute( "submodel", mId );
...
=item Submodel::convertTimeAndExtentWith
Internal function to convert time and extent with the given ASTNodes.
=item Submodel::convertCSymbols
Internal function that changes 'math' according to the passed-in time conversion factors (pre-set-up for convenience)
=item Submodel::createNewConversionFactor
Internal function that creates a new conversion factor in the given Model based on newcf and oldcf, and sets 'cf' to be the name of that new conversion factor.
=back
=head2 FbcExtension
@sbmlpackage{fbc}
@htmlinclude pkg-marker-fbc.html The core module of the 'fbc' package extension.
=over
=back
=head2 FbcPkgNamespaces
@sbmlpackage{fbc}
@htmlinclude pkg-marker-fbc.html Extension of SBMLNamespaces for the SBML Level 3
'fbc' package.
=over
=item FbcExtension::getPackageName
Returns the package name of this extension.
=item FbcExtension::getDefaultLevel
Returns the default SBML Level this extension.
=item FbcExtension::getDefaultVersion
Returns the default SBML Version this extension.
=item FbcExtension::getDefaultPackageVersion
Returns the default SBML version this extension.
=item FbcExtension::getXmlnsL3V1V1
Returns URI of supported versions of this package.
=item FbcExtension::FbcExtension
Constructor
=item FbcExtension::FbcExtension
Copy constructor.
=item FbcExtension::clone
Creates and returns a deep copy of this FbcExtension object.
@return a (deep) copy of this FbcExtension object
=item FbcExtension::getName
Returns the name of this package ("fbc")
@return the name of this package ("fbc")
=item FbcExtension::getURI
Returns the namespace URI corresponding to the combination of the given
SBML Level, Version, and package version.
@param sbmlLevel the level of SBML
@param sbmlVersion the version of SBML
@param pkgVersion the version of package
@return a string of the package URI, or an empty string if no
corresponding URI exists.
=item FbcExtension::getLevel
Returns the SBML Level for the given URI of this package.
@param uri the string of URI that represents one of versions of the
“fbc” package
@return the SBML Level with the given URI of this package, or C<0> if
the given URI is invalid.
=item FbcExtension::getVersion
Returns the SBML Version for the given URI of this package.
@param uri the string of URI that represents one of versions of the
“fbc” package
@return the SBML version with the given URI of this package, or C<0> if
the given URI is invalid.
=item FbcExtension::getPackageVersion
Returns the package version for the given URI of this package.
@param uri the string of URI that represents one of versions of the
“fbc” package
@return the package version with the given URI of this package, or C<0
>
if the given URI is invalid.
=item FbcExtension::getSBMLExtensionNamespaces
Returns an FbcPkgNamespaces object.
@param uri the string of URI that represents one of versions of the
“fbc” package
@return an FbcPkgNamespace object corresponding to the given C<uri>, or
C<NULL> if the URI is not defined in the FBC package.
=item FbcExtension::getStringFromTypeCode
Takes a type code of the “fbc” package and returns a string
describing the code.
=item FbcExtension::init
@internal
Initializes fbc extension by creating an object of this class with
required SBasePlugin derived objects and registering the object
to the SBMLExtensionRegistry class.
(NOTE) This function is automatically invoked when creating the following
global object in FbcExtension.cpp
static SBMLExtensionRegister<FbcExtension> fbcExtensionRegister;
=item FbcExtension::getErrorTable
@internal
=item FbcExtension::getErrorTableIndex
@internal
=item FbcExtension::getErrorIdOffset
@internal
=back
=head2 FbcModelPlugin
@sbmlpackage{fbc}
@htmlinclude pkg-marker-fbc.html Implementation of the 'fbc' package extention to the
Model construct.
=over
=item FbcModelPlugin::FbcModelPlugin
Constructor
=item FbcModelPlugin::FbcModelPlugin
Copy constructor. Creates a copy of this FbcModelPlugin object.
=item FbcModelPlugin::clone
Creates and returns a deep copy of this FbcModelPlugin object.
@return a (deep) copy of this FbcModelPlugin object
=item FbcModelPlugin::createObject
@internal
Subclasses must override this method to create, store, and then
return an SBML object corresponding to the next XMLToken in the
XMLInputStream if they have their specific elements.
@return the SBML object corresponding to next XMLToken in the
XMLInputStream or NULL if the token was not recognized.
=item FbcModelPlugin::writeAttributes
@internal
This function is a bit tricky.
This function is used only for setting annotation element in case
gene associations are used.
Thus, no attribute is written by this function.
=item FbcModelPlugin::writeElements
@internal
Subclasses must override this method to write out their contained
SBML objects as XML elements if they have their specific elements.
=item FbcModelPlugin::hasRequiredElements
@internal
Checks if this plugin object has all the required elements.
Subclasses should override this function if they have their specific
elements.
@return true if this plugin object has all the required elements,
otherwise false will be returned.
=item FbcModelPlugin::readOtherXML
@internal
Parses Gene Annotation Extension
=item FbcModelPlugin::getElementBySId
Returns the first child element found that has the given C<id> in the model-wide SId namespace, or C<NULL> if no such object is found.
@param id string representing the id of objects to find
@return a pointer to the SBase element with the given C<id>.
=item FbcModelPlugin::getElementByMetaId
Returns the first child element it can find with the given C<metaid>, or itself if it has the given C<metaid>, or C<NULL> if no such object is found.
@param metaid string representing the metaid of objects to find
@return a pointer to the SBase element with the given C<metaid>.
=item FbcModelPlugin::getAllElements
Returns a List of all child SBase objects, including those nested to an arbitrary depth
@return a List of pointers to all children objects.
=item FbcModelPlugin::appendFrom
@internal
=item FbcModelPlugin::getListOfFluxBounds
Returns the ListOfFluxBounds in this plugin object.
@return ListOfFluxBounds object in this plugin object.
=item FbcModelPlugin::getListOfFluxBounds
Returns the ListOfFluxBounds in this plugin object.
@return ListOfFluxBounds object in this plugin object.
=item FbcModelPlugin::getFluxBound
Returns the FluxBound object that belongs to the given index. If the
index is invalid, C<NULL> is returned.
@param n the index number of the FluxBound to get.
@return the nth FluxBound in the ListOfFluxBounds.
=item FbcModelPlugin::getFluxBound
Returns the FluxBound object that belongs to the given index. If the
index is invalid, C<NULL> is returned.
@param n the index number of the FluxBound to get.
@return the nth FluxBound in the ListOfFluxBounds.
=item FbcModelPlugin::getFluxBound
Returns the FluxBound object based on its identifier.
@param sid a string representing the identifier
of the FluxBound to get.
@return FluxBound in the ListOfFluxBounds with the given C<sid
>
or NULL if no such FluxBound exists.
@see getFluxBound(unsigned int n)
@see getListOfFluxBounds()
=item FbcModelPlugin::getFluxBound
Returns the FluxBound object based on its identifier.
@param sid a string representing the identifier
of the FluxBound to get.
@return FluxBound in the ListOfFluxBounds with the given C<sid>
or NULL if no such FluxBound exists.
@see getFluxBound(unsigned int n)
@see getListOfFluxBounds()
=item FbcModelPlugin::addFluxBound
Adds a copy of the given FluxBound object to the list of FluxBounds.
@param bound the FluxBound object to be added to the list of FluxBounds.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
=item FbcModelPlugin::createFluxBound
Creates a new FluxBound object and adds it to the list of FluxBound objects
and returns it.
@return a newly created FluxBound object
=item FbcModelPlugin::removeFluxBound
Removes the nth FluxBound object from this plugin object and
returns a pointer to it.
The caller owns the returned object and is responsible for
deleting it.
@param n the index of the FluxBound object to remove
@return the FluxBound object removed. As mentioned above, the
caller owns the returned object. C<NULL> is returned if the
given index is out of range.
=item FbcModelPlugin::removeFluxBound
Removes the FluxBound object with the given C<sid> attribute from
this plugin object and returns a pointer to it.
The caller owns the returned object and is responsible for
deleting it.
@param sid the id attribute of the FluxBound object to remove
@return the FluxBound object removed. As mentioned above, the
caller owns the returned object. C<NULL> is returned if the
given index is out of range.
=item FbcModelPlugin::getNumFluxBounds
Returns the number of FluxBound object in this plugin object.
@return the number of FluxBound object in this plugin object.
=item FbcModelPlugin::getListOfObjectives
Returns the ListOfObjectives in this plugin object.
@return ListOfObjectives object in this plugin object.
=item FbcModelPlugin::getListOfObjectives
Returns the ListOfObjectives in this plugin object.
@return ListOfObjectives object in this plugin object.
=item FbcModelPlugin::getObjective
Returns the Objective object that belongs to the given index. If the
index is invalid, C<NULL> is returned.
@param n the index number of the Objective to get.
@return the nth Objective in the ListOfObjectives.
=item FbcModelPlugin::getObjective
Returns the Objective object that belongs to the given index. If the
index is invalid, C<NULL> is returned.
@param n the index number of the Objective to get.
@return the nth Objective in the ListOfObjectives.
=item FbcModelPlugin::getObjective
Returns the Objective object based on its identifier.
@param sid a string representing the identifier
of the Objective to get.
@return Objective in the ListOfObjectives with the given C<id
>
or NULL if no such Objective exists.
@see getObjective(unsigned int n)
@see getListOfObjectives()
=item FbcModelPlugin::getObjective
Returns the Objective object based on its identifier.
@param sid a string representing the identifier
of the Objective to get.
@return Objective in the ListOfObjectives with the given C<sid>
or NULL if no such Objective exists.
@see getObjective(unsigned int n)
@see getListOfObjectives()
=item FbcModelPlugin::addObjective
Adds a copy of the given Objective object to the list of Objectives.
@param bound the Objective object to be added to the list of Objectives.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
=item FbcModelPlugin::createObjective
Creates a new Objective object and adds it to the list of Objective objects
and returns it.
@return a newly created Objective object
=item FbcModelPlugin::removeObjective
Removes the nth Objective object from this plugin object and
returns a pointer to it.
The caller owns the returned object and is responsible for
deleting it.
@param n the index of the Objective object to remove
@return the Objective object removed. As mentioned above, the
caller owns the returned object. C<NULL> is returned if the
given index is out of range.
=item FbcModelPlugin::removeObjective
Removes the Objective object with the given C<sid> attribute from
this plugin object and returns a pointer to it.
The caller owns the returned object and is responsible for
deleting it.
@param sid the id attribute of the Objective object to remove
@return the Objective object removed. As mentioned above, the
caller owns the returned object. C<NULL> is returned if the
given index is out of range.
=item FbcModelPlugin::getNumObjectives
Returns the number of Objective object in this plugin object.
@return the number of Objective object in this plugin object.
=item FbcModelPlugin::getActiveObjective
Returns the current active objective.
=item FbcModelPlugin::*getActiveObjective
Returns the current active objective.
=item FbcModelPlugin::setActiveObjectiveId
Sets the id of the active objective.
=item FbcModelPlugin::getActiveObjectiveId
returns the id of the current active objective.
=item FbcModelPlugin::unsetActiveObjectiveId
Unsets the active objective.
=item FbcModelPlugin::getListOfGeneAssociations
Returns the ListOfObjectives in this plugin object.
@return ListOfObjectives object in this plugin object.
=item FbcModelPlugin::getListOfGeneAssociations
Returns the ListOfGeneAssociations in this plugin object.
@return ListOfGeneAssociations object in this plugin object.
=item FbcModelPlugin::getGeneAssociation
Returns the GeneAssociation object that belongs to the given index. If the
index is invalid, C<NULL> is returned.
@param n the index number of the GeneAssociation to get.
@return the nth GeneAssociation in the ListOfGeneAssociations.
=item FbcModelPlugin::getGeneAssociation
Returns the GeneAssociation object that belongs to the given index. If the
index is invalid, C<NULL> is returned.
@param n the index number of the GeneAssociation to get.
@return the nth GeneAssociation in the ListOfGeneAssociations.
=item FbcModelPlugin::getGeneAssociation
Returns the GeneAssociation object based on its identifier.
@param sid a string representing the identifier
of the GeneAssociation to get.
@return GeneAssociation in the ListOfGeneAssociations with the given C<sid
>
or NULL if no such GeneAssociation exists.
@see getGeneAssociation(unsigned int n)
@see getListOfGeneAssociations()
=item FbcModelPlugin::getGeneAssociation
Returns the GeneAssociation object based on its identifier.
@param sid a string representing the identifier
of the GeneAssociation to get.
@return GeneAssociation in the ListOfGeneAssociations with the given C<sid>
or NULL if no such GeneAssociation exists.
@see getGeneAssociation(unsigned int n)
@see getListOfGeneAssociations()
=item FbcModelPlugin::addGeneAssociation
Adds a copy of the given GeneAssociation object to the list of GeneAssociations.
@param association the GeneAssociation object to be added to the list of GeneAssociations.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
=item FbcModelPlugin::createGeneAssociation
Creates a new GeneAssociation object and adds it to the list of GeneAssociation objects
and returns it.
@return a newly created GeneAssociation object
=item FbcModelPlugin::removeGeneAssociation
Removes the nth GeneAssociation object from this plugin object and
returns a pointer to it.
The caller owns the returned object and is responsible for
deleting it.
@param n the index of the GeneAssociation object to remove
@return the GeneAssociation object removed. As mentioned above, the
caller owns the returned object. C<NULL> is returned if the
given index is out of range.
=item FbcModelPlugin::removeGeneAssociation
Removes the GeneAssociation object with the given C<sid> attribute from
this plugin object and returns a pointer to it.
The caller owns the returned object and is responsible for
deleting it.
@param sid the id attribute of the GeneAssociation object to remove
@return the GeneAssociation object removed. As mentioned above, the
caller owns the returned object. C<NULL> is returned if the
given index is out of range.
=item FbcModelPlugin::getNumGeneAssociations
Returns the number of GeneAssociation object in this plugin object.
@return the number of GeneAssociation object in this plugin object.
=item FbcModelPlugin::setSBMLDocument
@internal
Sets the parent SBMLDocument of this plugin object.
Subclasses which contain one or more SBase derived elements must
override this function.
@param d the SBMLDocument object to use
@see connectToParent
@see enablePackageInternal
=item FbcModelPlugin::connectToChild
@internal
Sets the parent of this SBML object to child SBML objects (if any).
(Creates a child-parent relationship by the parent)
@see setSBMLDocument
@see enablePackageInternal
=item FbcModelPlugin::connectToParent
@internal
Sets the parent SBML object of this plugin object to
this object and child elements (if any).
(Creates a child-parent relationship by this plugin object)
This function is called when this object is created by
the parent element.
Subclasses must override this this function if they have one
or more child elements.Also, SBasePlugin::connectToParent()
must be called in the overridden function.
@param sbase the SBase object to use
@see setSBMLDocument
@see enablePackageInternal
=item FbcModelPlugin::enablePackageInternal
@internal
Enables/Disables the given package with child elements in this plugin
object (if any).
(This is an internal implementation invoked from
SBase::enablePackageInternal() function)
@note Subclasses in which one or more SBase derived elements are
defined must override this function.
@see setSBMLDocument
@see connectToParent
=item FbcModelPlugin::accept
@internal
=item FbcModelPlugin::getFluxBoundsForReaction
=item FbcModelPlugin::parseAnnotation
@internal
Parse L2 annotation if supported
=back
=head2 FbcSpeciesPlugin
@sbmlpackage{fbc}
@htmlinclude pkg-marker-fbc.html Implementation of the 'fbc' package extention to the
Species construct.
The Flux Balance Constraints package extends the SBML Level 3 Version 1 Core Species class with the addition of two attributes: 'charge' and 'chemicalFormula'.
=over
=item FbcSpeciesPlugin::FbcSpeciesPlugin
Constructor
=item FbcSpeciesPlugin::FbcSpeciesPlugin
Copy constructor. Creates a copy of this FbcSpeciesPlugin object.
=item FbcSpeciesPlugin::clone
Creates and returns a deep copy of this FbcSpeciesPlugin object.
@return a (deep) copy of this FbcSpeciesPlugin object
=item FbcSpeciesPlugin::isSetCharge
Predicate returning C<true> or C<false> depending on whether this
FbcSpeciesPlugin "charge" attribute has been set.
@return C<true> if this FbcSpeciesPlugin "charge" attribute has been set,
otherwise C<false> is returned.
=item FbcSpeciesPlugin::setCharge
Sets the value of the "charge" attribute of this FbcSpeciesPlugin.
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif The only possible value
returned by this function is:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
=item FbcSpeciesPlugin::getCharge
Returns the value of the "charge" attribute of this FbcSpeciesPlugin.
@return the value of the "charge" attribute of this FbcSpeciesPlugin.
=item FbcSpeciesPlugin::unsetCharge
Unsets the value of the "charge" attribute of this FbcSpeciesPlugin.
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif The only possible value
returned by this function is:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
=item FbcSpeciesPlugin::isSetChemicalFormula
Predicate returning C<true> or C<false> depending on whether this
FbcSpeciesPlugin "chemicalFormula" attribute has been set.
@return C<true> if this FbcSpeciesPlugin "chemicalFormula" attribute has been set,
otherwise C<false> is returned.
=item FbcSpeciesPlugin::setChemicalFormula
Sets the value of the "chemicalFormula" attribute of this FbcSpeciesPlugin.
The format of chemicalFormula must consist only of atomic names (as in the Periodic Table) or user defined compounds either of which take the form of a single capital letter followed by zero or more lowercase letters. Where there is more than a single atom present, this is indicated with an integer. With regards to order (and enhance inter-operability) it is recommended to use the Hill system order. (However, no error-checking is performed by this routine.)
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif The only possible value
returned by this function is:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
=item FbcSpeciesPlugin::getChemicalFormula
Returns the value of the "chemicalFormula" attribute of this FbcSpeciesPlugin.
@return the value of the "chemicalFormula" attribute of this FbcSpeciesPlugin.
=item FbcSpeciesPlugin::unsetChemicalFormula
Unsets the value of the "chemicalFormula" attribute of this FbcSpeciesPlugin.
@return integer value indicating success/failure of the
function. @if clike The value is drawn from the
enumeration #OperationReturnValues_t. @endif The only possible value
returned by this function is:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
=item FbcSpeciesPlugin::setSBMLDocument
@internal
Sets the parent SBMLDocument of this plugin object.
Subclasses which contain one or more SBase derived elements must
override this function.
@param d the SBMLDocument object to use
@see connectToParent
@see enablePackageInternal
=item FbcSpeciesPlugin::connectToParent
@internal
Sets the parent SBML object of this plugin object to
this object and child elements (if any).
(Creates a child-parent relationship by this plugin object)
This function is called when this object is created by
the parent element.
Subclasses must override this this function if they have one
or more child elements.Also, SBasePlugin::connectToParent()
must be called in the overridden function.
@param sbase the SBase object to use
@see setSBMLDocument
@see enablePackageInternal
=item FbcSpeciesPlugin::enablePackageInternal
@internal
Enables/Disables the given package with child elements in this plugin
object (if any).
(This is an internal implementation invoked from
SBase::enablePakcageInternal() function)
@note Subclasses in which one or more SBase derived elements are
defined must override this function.
@see setSBMLDocument
@see connectToParent
=item FbcSpeciesPlugin::addExpectedAttributes
@internal
Subclasses should override this method to get the list of
expected attributes.
This function is invoked from corresponding readAttributes()
function.
=item FbcSpeciesPlugin::readAttributes
@internal
Reads the attributes of corresponding package in SBMLDocument element.
=item FbcSpeciesPlugin::writeAttributes
@internal
Writes the attributes of corresponding package in SBMLDocument element.
=back
=head2 Association
@sbmlpackage{fbc}
@htmlinclude pkg-marker-fbc.html Implementation of the 'fbc' proposed package Association
construct.
The Association class is not part of the official Flux Balance
specification, but is instead a proposed future development of the
package. If adopted, it would be a child of a GeneAssociation that would
describe a single 'and' or 'or' relationship between two or more genes or
other associations.
=over
=item Association::Association
Creates a new Association with the given level, version, and package version.
=item Association::Association
=item Association::Association
Creates a new Association with the given FbcPkgNamespaces object.
=item Association::Association
Copy constructor.
=item Association::getType
Returns the string of the "type" attribute of this Association.
@return the string of the "type" attribute of this Association.
=item Association::isSetType
Predicate returning C<true> or C<false> depending on whether this
Association's "type" attribute has been set.
@return C<true> if this Association's "type" attribute has been set,
otherwise C<false> is returned.
=item Association::setType
Sets the SIdRef string of the "type" attribute of this Association.
@param type a SIdRef string to be set.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item Association::unsetType
Unsets the value of the "id" attribute of this Association.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item Association::getReference
Returns the string of the "reference" attribute of this Association.
@return the string of the "reference" attribute of this Association.
=item Association::isSetReference
Predicate returning C<true> or C<false> depending on whether this
Association's "reference" attribute has been set.
@return C<true> if this Association's "reference" attribute has been set,
otherwise C<false> is returned.
=item Association::setReference
Sets the SIdRef string of the "reference" attribute of this Association.
@param reference a SIdRef string to be set.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item Association::unsetReference
Unsets the value of the "id" attribute of this Association.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item Association::addGene
Add a gene with the given C<id> to the association.
=item Association::getNumAssociations
Returns the number of child Associations of this Association.
=item Association::addAssociation
Adds a child Association to this Association.
=item Association::removeAssociation
Removes the child Associations with the given C<index> from this Association.
=item Association::clearAssociations
Returns the number of child Associations of this Association.
=item Association::createAnd
Creates and returns a new Association of type 'and'. Does not actually add the created Association as a child of this Association or do anything else with it--the returning pointer is now owned by the caller.
=item Association::createOr
Creates and returns a new Association of type 'or'. Does not actually add the created Association as a child of this Association or do anything else with it--the returning pointer is now owned by the caller.
=item Association::createGene
Creates and returns a new Association of type 'and', and with the gene reference C<reference>. Does not actually add the created Association as a child of this Association or do anything else with it--the returning pointer is now owned by the caller.
=item Association::toXML
Creates an XMLNode object from this.
=item Association::getElementName
Returns the XML element name of
this SBML object.
@return the string of the name of this element.
=item Association::clone
Creates and returns a deep copy of this Association.
@return a (deep) copy of this Association.
=item Association::getTypeCode
Returns the libSBML type code of this object instance.
C<opydetails> doc_what_are_typecodes
@return the SBML type code for this object:
@link SBMLFbcTypeCode_t#SBML_FBC_ASSOCIATION SBML_FBC_ASSOCIATION@endlink
C<opydetails> doc_warning_typecodes_not_unique
@see getElementName()
@see getPackageName()
=item Association::writeElements
@internal
Subclasses should override this method to write out their contained
SBML objects as XML elements. Be sure to call your parents
implementation of this method as well. For example:
SBase::writeElements(stream);
mReactants.write(stream);
mProducts.write(stream);
...
=item Association::accept
Accepts the given SBMLVisitor.
@return the result of calling C<v.visit()>, which indicates
whether or not the Visitor would like to visit the SBML object's next
sibling object (if available).
=item Association::parseInfixAssociation
Parses a gene association in infix format. These look like this:
(b2422) and (b2425) and (b2423) and (b2424) or (b2422) and (b2423) and (b2424) and (b2413) and (b3917)
@return the parsed association, or C<NULL> in case of an error.
=item Association::toInfix
Converts this association into an infix string.
@return the association as infix string.
=item Association::createObject
@internal
Create and return an SBML object of this class, if present.
@return the SBML object corresponding to next XMLToken in the
XMLInputStream or NULL if the token was not recognized.
=item Association::addExpectedAttributes
@internal
Subclasses should override this method to get the list of
expected attributes.
This function is invoked from corresponding readAttributes()
function.
=item Association::readAttributes
@internal
Subclasses should override this method to read values from the given
XMLAttributes set into their specific fields. Be sure to call your
parents implementation of this method as well.
=item Association::writeAttributes
@internal
Subclasses should override this method to write their XML attributes
to the XMLOutputStream. Be sure to call your parents implementation
of this method as well. For example:
SBase::writeAttributes(stream);
stream.writeAttribute( "id" , mId );
stream.writeAttribute( "name", mName );
...
=back
=head2 FluxBound
@sbmlpackage{fbc}
@htmlinclude pkg-marker-fbc.html Implementation of the 'fbc' package FluxBound construct.
The FluxBound object holds a single (in)equality that provides the maximum
or minimum value that a reaction flux can obtain at steady state.
=over
=back
=head2 ListOfFluxBounds
@sbmlpackage{fbc}
@htmlinclude pkg-marker-fbc.html Implementation of the ListOfFluxBounds construct from the
'fbc' package.
The ListOfFluxBounds is a container for the FluxBound elements of a Model.
C<opydetails> doc_what_is_listof
=over
=item FluxBound::FluxBound
Creates a new FluxBound with the given level, version, and package version.
=item FluxBound::FluxBound
Creates a new FluxBound with the given FbcPkgNamespaces object.
=item FluxBound::FluxBound
Copy constructor.
=item FluxBound::getId
Returns the value of the "id" attribute of this FluxBound.
@return the value of the "id" attribute of this FluxBound.
=item FluxBound::isSetId
Predicate returning C<true> or C<false> depending on whether this
FluxBound's "id" attribute has been set.
@return C<true> if this FluxBound's "id" attribute has been set,
otherwise C<false> is returned.
=item FluxBound::setId
Sets the value of the "id" attribute of this FluxBound.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item FluxBound::unsetId
Unsets the value of the "id" attribute of this FluxBound.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item FluxBound::getName
Returns the value of the "name" attribute of this FluxBound.
@return the value of the "name" attribute of this FluxBound.
=item FluxBound::isSetName
Predicate returning C<true> or C<false> depending on whether this
FluxBound's "name" attribute has been set.
@return C<true> if this FluxBound's "id" attribute has been set,
otherwise C<false> is returned.
=item FluxBound::setName
Sets the value of the "name" attribute of this FluxBound.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item FluxBound::unsetName
Unsets the value of the "name" attribute of this FluxBound.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item FluxBound::getReaction
Returns the value of the "reaction" attribute of this FluxBound.
@return the value of the "reaction" attribute of this FluxBound.
=item FluxBound::isSetReaction
Predicate returning C<true> or C<false> depending on whether this
FluxBound's "reaction" attribute has been set.
@return C<true> if this FluxBound's "reaction" attribute has been set,
otherwise C<false> is returned.
=item FluxBound::setReaction
Sets the value of the "reaction" attribute of this FluxBound.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item FluxBound::unsetReaction
Unsets the value of the "reaction" attribute of this FluxBound.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item FluxBound::getOperation
Returns the value of the "operation" attribute of this FluxBound.
@return the value of the "operation" attribute of this FluxBound.
=item FluxBound::getFluxBoundOperation
Returns the value of the "operation" attribute of this FluxBound.
@return the value of the "operation" attribute of this FluxBound.
=item FluxBound::isSetOperation
Predicate returning C<true> or C<false> depending on whether this
FluxBound's "operation" attribute has been set.
@return C<true> if this FluxBound's "operation" attribute has been set,
otherwise C<false> is returned.
=item FluxBound::setOperation
Sets the value of the "operation" attribute of this FluxBound.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item FluxBound::setOperation
Sets the value of the "operation" attribute of this FluxBound.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item FluxBound::unsetOperation
Unsets the value of the "operation" attribute of this FluxBound.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item FluxBound::getValue
Returns the value of the "value" attribute of this FluxBound.
@return the value of the "value" attribute of this FluxBound.
=item FluxBound::isSetValue
Predicate returning C<true> or C<false> depending on whether this
FluxBound's "value" attribute has been set.
@return C<true> if this FluxBound's "value" attribute has been set,
otherwise C<false> is returned.
=item FluxBound::setValue
Sets the value of the "value" attribute of this FluxBound.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item FluxBound::unsetValue
Unsets the value of the "value" attribute of this FluxBound.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item FluxBound::renameSIdRefs
Renames all the C<SIdRef> attributes on this element, including any
found in MathML content (if such exists).
This method works by looking at all attributes and (if appropriate)
mathematical formulas, comparing the identifiers to the value of @p
oldid. If any matches are found, the matching identifiers are replaced
with C<newid>. The method does I<not> descend into child elements.
@param oldid the old identifier
@param newid the new identifier
=item FluxBound::getElementName
Returns the XML element name of
this SBML object.
@return the string of the name of this element.
=item FluxBound::clone
Creates and returns a deep copy of this FluxBound.
@return a (deep) copy of this FluxBound.
=item FluxBound::getTypeCode
Returns the libSBML type code of this object instance.
C<opydetails> doc_what_are_typecodes
@return the SBML type code for this object:
@link SBMLFbcTypeCode_t#SBML_FBC_FLUXBOUND SBML_FBC_FLUXBOUND@endlink
C<opydetails> doc_warning_typecodes_not_unique
@see getElementName()
@see getPackageName()
=item FluxBound::writeElements
@internal
Subclasses should override this method to write out their contained
SBML objects as XML elements. Be sure to call your parents
implementation of this method as well. For example:
SBase::writeElements(stream);
mReactants.write(stream);
mProducts.write(stream);
...
=item FluxBound::accept
Accepts the given SBMLVisitor.
@return the result of calling C<v.visit()>, which indicates
whether or not the Visitor would like to visit the SBML object's next
sibling object (if available).
=item FluxBound::setSBMLDocument
@internal
Sets the parent SBMLDocument of this SBML object.
@param d the SBMLDocument object to use
=item FluxBound::enablePackageInternal
@internal
Enables/Disables the given package with this element and child
elements (if any).
(This is an internal implementation for enablePakcage function)
@note Subclasses in which one or more child elements are defined
must override this function.
=item FluxBound::hasRequiredElements
@internal
=item FluxBound::createObject
@internal
Create and return an SBML object of this class, if present.
@return the SBML object corresponding to next XMLToken in the
XMLInputStream or NULL if the token was not recognized.
=item FluxBound::addExpectedAttributes
@internal
Subclasses should override this method to get the list of
expected attributes.
This function is invoked from corresponding readAttributes()
function.
=item FluxBound::readAttributes
@internal
Subclasses should override this method to read values from the given
XMLAttributes set into their specific fields. Be sure to call your
parents implementation of this method as well.
=item FluxBound::writeAttributes
@internal
Subclasses should override this method to write their XML attributes
to the XMLOutputStream. Be sure to call your parents implementation
of this method as well. For example:
SBase::writeAttributes(stream);
stream.writeAttribute( "id" , mId );
stream.writeAttribute( "name", mName );
...
=item ListOfFluxBounds::clone
Creates and returns a deep copy of this ListOfFluxBounds.
@return a (deep) copy of this ListOfFluxBounds.
=item ListOfFluxBounds::ListOfFluxBounds
Creates a new ListOfFluxBounds with the given level, version, and package version.
=item ListOfFluxBounds::ListOfFluxBounds
Creates a new ListOfFluxBounds with the given FbcPkgNamespaces object.
=item ListOfFluxBounds::get
Get a FluxBound from the ListOfFluxBounds.
@param n the index number of the FluxBound to get.
@return the nth FluxBound in this ListOfFluxBounds.
@see size()
=item ListOfFluxBounds::get
Get a FluxBound from the ListOfFluxBounds.
@param n the index number of the FluxBound to get.
@return the nth FluxBound in this ListOfFluxBounds.
@see size()
=item ListOfFluxBounds::get
Get a FluxBound from the ListOfFluxBounds
based on its identifier.
@param sid a string representing the identifier
of the FluxBound to get.
@return FluxBound in this ListOfFluxBounds
with the given C<sid> or C<NULL> if no such
FluxBound exists.
@see get(unsigned int n)
@see size()
=item ListOfFluxBounds::get
Get a FluxBound from the ListOfFluxBounds
based on its identifier.
@param sid a string representing the identifier
of the FluxBound to get.
@return FluxBound in this ListOfFluxBounds
with the given C<sid> or C<NULL> if no such
FluxBound exists.
@see get(unsigned int n)
@see size()
=item ListOfFluxBounds::remove
Removes the nth item from this ListOfFluxBounds items and returns a pointer to
it.
The caller owns the returned item and is responsible for deleting it.
@param n the index of the item to remove
@see size()
=item ListOfFluxBounds::remove
Removes item in this ListOfFluxBounds items with the given identifier.
The caller owns the returned item and is responsible for deleting it.
If none of the items in this list have the identifier C<sid>, then C<
>
NULL is returned.
@param sid the identifier of the item to remove
@return the item removed. As mentioned above, the caller owns the
returned item.
=item ListOfFluxBounds::getItemTypeCode
Returns the libSBML type code for the SBML objects
contained in this ListOf object.
C<opydetails> doc_what_are_typecodes
@return the SBML type code for objects contained in this list:
@link SBMLTypeCode_t#SBML_FBC_FLUXBOUND SBML_FBC_FLUXBOUND@endlink (default).
@see getElementName()
@see getPackageName()
=item ListOfFluxBounds::getElementName
Returns the XML element name of
this SBML object.
@return the string of the name of this element.
=item ListOfFluxBounds::createObject
@internal
Create and return an SBML object of this class, if present.
@return the SBML object corresponding to next XMLToken in the
XMLInputStream or NULL if the token was not recognized.
=item ListOfFluxBounds::writeXMLNS
@internal
=back
=head2 FluxObjective
@sbmlpackage{fbc}
@htmlinclude pkg-marker-fbc.html Implementation of the 'fbc' package FluxObjective
construct.
An integral component in a complete description of a steady-state model is the so-called 'objective function' which generally consists of a linear combination of model variables (fluxes) and a sense (direction). In the FBC package this concept is succinctly captured in the Objective class.
=over
=back
=head2 ListOfFluxObjectives
@sbmlpackage{fbc}
@htmlinclude pkg-marker-fbc.html Implementation of the 'fbc' package ListOfFluxObjectives
construct.
The ListOfFluxObjectives is a container for the FluxObjective elements of a Model annotation.
C<opydetails> doc_what_is_listof
@see FluxObjective
=over
=item FluxObjective::FluxObjective
Creates a new FluxObjective with the given level, version, and package version.
=item FluxObjective::FluxObjective
Creates a new FluxObjective with the given FbcPkgNamespaces object.
=item FluxObjective::FluxObjective
Copy constructor.
=item FluxObjective::getId
Returns the value of the "id" attribute of this FluxObjective.
@return the value of the "id" attribute of this FluxObjective.
=item FluxObjective::isSetId
Predicate returning C<true> or C<false> depending on whether this
FluxObjective "id" attribute has been set.
@return C<true> if this FluxObjective "id" attribute has been set,
otherwise C<false> is returned.
=item FluxObjective::setId
Sets the value of the "id" attribute of this FluxObjective.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item FluxObjective::unsetId
Unsets the value of the "id" attribute of this FluxObjective.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item FluxObjective::getName
Returns the value of the "name" attribute of this FluxObjective.
@return the value of the "name" attribute of this FluxObjective.
=item FluxObjective::isSetName
Predicate returning C<true> or C<false> depending on whether this
FluxObjective "name" attribute has been set.
@return C<true> if this FluxObjective "id" attribute has been set,
otherwise C<false> is returned.
=item FluxObjective::setName
Sets the value of the "name" attribute of this FluxObjective.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item FluxObjective::unsetName
Unsets the value of the "name" attribute of this FluxObjective.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item FluxObjective::getReaction
Returns the string of the "reaction" attribute of this FluxObjective.
@return the string of the "reaction" attribute of this FluxObjective.
=item FluxObjective::isSetReaction
Predicate returning C<true> or C<false> depending on whether this
FluxObjective's "reaction" attribute has been set.
@return C<true> if this FluxObjective's "reaction" attribute has been set,
otherwise C<false> is returned.
=item FluxObjective::setReaction
Sets the SIdRef string of the "reaction" attribute of this FluxObjective.
@param reaction a SIdRef string to be set.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item FluxObjective::unsetReaction
Unsets the value of the "id" attribute of this FluxObjective.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item FluxObjective::getCoefficient
Returns the value of the "coefficient" attribute of this FluxObjective.
@return the value of the "coefficient" attribute of this FluxObjective.
=item FluxObjective::isSetCoefficient
Predicate returning C<true> or C<false> depending on whether this
FluxObjective's "coefficient" attribute has been set.
@return C<true> if this FluxObjective's "coefficient" attribute has been set,
otherwise C<false> is returned.
=item FluxObjective::setCoefficient
Sets the value of the "coefficient" attribute of this FluxObjective.
@param coefficient a double coefficient to be set.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item FluxObjective::unsetCoefficient
Unsets the value of the "id" attribute of this FluxObjective.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item FluxObjective::renameSIdRefs
Renames all the C<SIdRef> attributes on this element, including any
found in MathML content (if such exists).
This method works by looking at all attributes and (if appropriate)
mathematical formulas, comparing the identifiers to the value of @p
oldid. If any matches are found, the matching identifiers are replaced
with C<newid>. The method does I<not> descend into child elements.
@param oldid the old identifier
@param newid the new identifier
=item FluxObjective::getElementName
Returns the XML element name of
this SBML object.
@return the string of the name of this element.
=item FluxObjective::clone
Creates and returns a deep copy of this FluxObjective.
@return a (deep) copy of this FluxObjective.
=item FluxObjective::getTypeCode
Returns the libSBML type code of this object instance.
C<opydetails> doc_what_are_typecodes
@return the SBML type code for this object:
@link SBMLFbcTypeCode_t#SBML_FBC_FLUXOBJECTIVE SBML_FBC_FLUXOBJECTIVE@endlink
C<opydetails> doc_warning_typecodes_not_unique
@see getElementName()
@see getPackageName()
=item FluxObjective::writeElements
@internal
Subclasses should override this method to write out their contained
SBML objects as XML elements. Be sure to call your parents
implementation of this method as well. For example:
SBase::writeElements(stream);
mReactants.write(stream);
mProducts.write(stream);
...
=item FluxObjective::accept
Accepts the given SBMLVisitor.
@return the result of calling C<v.visit()>, which indicates
whether or not the Visitor would like to visit the SBML object's next
sibling object (if available).
=item FluxObjective::createObject
@internal
Create and return an SBML object of this class, if present.
@return the SBML object corresponding to next XMLToken in the
XMLInputStream or NULL if the token was not recognized.
=item FluxObjective::addExpectedAttributes
@internal
Subclasses should override this method to get the list of
expected attributes.
This function is invoked from corresponding readAttributes()
function.
=item FluxObjective::readAttributes
@internal
Subclasses should override this method to read values from the given
XMLAttributes set into their specific fields. Be sure to call your
parents implementation of this method as well.
=item FluxObjective::writeAttributes
@internal
Subclasses should override this method to write their XML attributes
to the XMLOutputStream. Be sure to call your parents implementation
of this method as well. For example:
SBase::writeAttributes(stream);
stream.writeAttribute( "id" , mId );
stream.writeAttribute( "name", mName );
...
=item ListOfFluxObjectives::clone
Creates and returns a deep copy of this ListOfFluxObjectives.
@return a (deep) copy of this ListOfFluxObjectives.
=item ListOfFluxObjectives::ListOfFluxObjectives
Creates a new ListOfFluxObjectives with the given level, version, and package version.
=item ListOfFluxObjectives::ListOfFluxObjectives
Creates a new ListOfFluxObjectives with the given FbcPkgNamespaces object.
=item ListOfFluxObjectives::get
Get a FluxObjective from the ListOfFluxObjectives.
@param n the index number of the FluxObjective to get.
@return the nth FluxObjective in this ListOfFluxObjectives.
@see size()
=item ListOfFluxObjectives::get
Get a FluxObjective from the ListOfFluxObjectives.
@param n the index number of the FluxObjective to get.
@return the nth FluxObjective in this ListOfFluxObjectives.
@see size()
=item ListOfFluxObjectives::get
Get a FluxObjective from the ListOfFluxObjectives
based on its identifier.
@param sid a string representing the identifier
of the FluxObjective to get.
@return FluxObjective in this ListOfFluxObjectives
with the given C<sid> or C<NULL> if no such
FluxObjective exists.
@see get(unsigned int n)
@see size()
=item ListOfFluxObjectives::get
Get a FluxObjective from the ListOfFluxObjectives
based on its identifier.
@param sid a string representing the identifier
of the FluxObjective to get.
@return FluxObjective in this ListOfFluxObjectives
with the given C<sid> or C<NULL> if no such
FluxObjective exists.
@see get(unsigned int n)
@see size()
=item ListOfFluxObjectives::remove
Removes the nth item from this ListOfFluxObjectives items and returns a pointer to
it.
The caller owns the returned item and is responsible for deleting it.
@param n the index of the item to remove
@return the item removed. As mentioned above, the caller owns the
returned item.
@see size()
=item ListOfFluxObjectives::remove
Removes item in this ListOfFluxObjectives items with the given identifier.
The caller owns the returned item and is responsible for deleting it.
If none of the items in this list have the identifier C<sid>, then C<
>
NULL is returned.
@param sid the identifier of the item to remove
@return the item removed. As mentioned above, the caller owns the
returned item.
=item ListOfFluxObjectives::getItemTypeCode
Returns the libSBML type code for the SBML objects
contained in this ListOf object.
C<opydetails> doc_what_are_typecodes
@return the SBML type code for objects contained in this list:
@link SBMLTypeCode_t#SBML_FBC_FLUXOBJECTIVE SBML_FBC_FLUXOBJECTIVE@endlink (default).
@see getElementName()
@see getPackageName()
=item ListOfFluxObjectives::getElementName
Returns the XML element name of
this SBML object.
@return the string of the name of this element.
=item ListOfFluxObjectives::createObject
@internal
Create and return an SBML object of this class, if present.
@return the SBML object corresponding to next XMLToken in the
XMLInputStream or NULL if the token was not recognized.
=back
=head2 GeneAssociation
@sbmlpackage{fbc}
@htmlinclude pkg-marker-fbc.html Implementation of the 'fbc' package GeneAssociation
construct.
Gene associations are not part of the core FBC specification, but rather are a proposed annotation.
=over
=back
=head2 ListOfGeneAssociations
@sbmlpackage{fbc}
@htmlinclude pkg-marker-fbc.html Implementation of the 'fbc' package suggested
ListOfGeneAssociations annotation construct.
The ListOfGeneAssociations is a container for the GeneAssociation elements of the proposed Model annotation, and is not part of the official FBC specification.
C<opydetails> doc_what_is_listof
@see GeneAssociation
=over
=item GeneAssociation::GeneAssociation
Creates a new GeneAssociation with the given C<level>, C<version>, and C<pkgVersion>.
=item GeneAssociation::GeneAssociation
Creates a new GeneAssociation with the given C<node> and FbcPkgNamespaces C<fbcns>.
=item GeneAssociation::GeneAssociation
Creates a new GeneAssociation with the given FbcPkgNamespaces object.
=item GeneAssociation::GeneAssociation
Copy constructor.
=item GeneAssociation::getId
Returns the string of the "id" attribute of this GeneAssociation.
@return the string of the "id" attribute of this GeneAssociation.
=item GeneAssociation::isSetId
Predicate returning C<true> or C<false> depending on whether this
GeneAssociation's "id" attribute has been set.
@return C<true> if this GeneAssociation's "id" attribute has been set,
otherwise C<false> is returned.
=item GeneAssociation::setId
Sets the SIdRef string of the "id" attribute of this GeneAssociation.
@param id a SIdRef string to be set.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item GeneAssociation::unsetId
Unsets the value of the "id" attribute of this GeneAssociation.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item GeneAssociation::getReaction
Returns the string of the "reaction" attribute of this GeneAssociation.
@return the string of the "reaction" attribute of this GeneAssociation.
=item GeneAssociation::isSetReaction
Predicate returning C<true> or C<false> depending on whether this
GeneAssociation's "reaction" attribute has been set.
@return C<true> if this GeneAssociation's "reaction" attribute has been set,
otherwise C<false> is returned.
=item GeneAssociation::setReaction
Sets the SIdRef string of the "reaction" attribute of this GeneAssociation.
@param reaction a SIdRef string to be set.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item GeneAssociation::unsetReaction
Unsets the value of the "id" attribute of this GeneAssociation.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item GeneAssociation::createAssociation
Creates a new association, sets it to this element and returns it.
=item GeneAssociation::getAssociation
Returns Association object of this GeneAssociation.
@return Association object of this GeneAssociation.
=item GeneAssociation::getAssociation
Returns Association object of this GeneAssociation.
@return Association object of this GeneAssociation.
=item GeneAssociation::isSetAssociation
Predicate returning C<true> or C<false> depending on whether this
GeneAssociation's "association" element has been set.
@return C<true> if this GeneAssociation's "association" element has been set,
otherwise C<false> is returned.
=item GeneAssociation::setAssociation
Sets the Association object of this GeneAssociation.
@param association a Association object to be set.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item GeneAssociation::unsetAssociation
Unsets the Association object of this GeneAssociation.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item GeneAssociation::getElementName
Returns the XML element name of
this SBML object.
@return the string of the name of this element.
=item GeneAssociation::clone
Creates and returns a deep copy of this GeneAssociation.
@return a (deep) copy of this GeneAssociation.
=item GeneAssociation::getTypeCode
Returns the libSBML type code of this object instance.
C<opydetails> doc_what_are_typecodes
@return the SBML type code for this object:
@link SBMLFbcTypeCode_t#SBML_FBC_GENEASSOCIATION SBML_FBC_GENEASSOCIATION@endlink
C<opydetails> doc_warning_typecodes_not_unique
@see getElementName()
@see getPackageName()
=item GeneAssociation::writeElements
@internal
Subclasses should override this method to write out their contained
SBML objects as XML elements. Be sure to call your parents
implementation of this method as well. For example:
SBase::writeElements(stream);
mReactants.write(stream);
mProducts.write(stream);
...
=item GeneAssociation::accept
Accepts the given SBMLVisitor.
@return the result of calling C<v.visit()>, which indicates
whether or not the Visitor would like to visit the SBML object's next
sibling object (if available).
=item GeneAssociation::toXML
Creates an XMLNode object from this.
=item GeneAssociation::createObject
@internal
Creates and returns an SBML object corresponding to the next
XMLToken in the C<stream>, or NULL if the token was not recognized.
@return the SBML object corresponding to next XMLToken in the
XMLInputStream or NULL if the token was not recognized.
=item GeneAssociation::addExpectedAttributes
@internal
Subclasses should override this method to get the list of
expected attributes.
This function is invoked from corresponding readAttributes()
function.
=item GeneAssociation::readAttributes
@internal
Subclasses should override this method to read values from the given
XMLAttributes set into their specific fields. Be sure to call your
parents implementation of this method as well.
=item GeneAssociation::writeAttributes
@internal
Subclasses should override this method to write their XML attributes
to the XMLOutputStream. Be sure to call your parents implementation
of this method as well. For example:
SBase::writeAttributes(stream);
stream.writeAttribute( "id" , mId );
stream.writeAttribute( "name", mName );
...
=item ListOfGeneAssociations::clone
Creates and returns a deep copy of this ListOfGeneAssociations.
@return a (deep) copy of this ListOfGeneAssociations.
=item ListOfGeneAssociations::ListOfGeneAssociations
Creates a new ListOfGeneAssociations with the given level, version, and package version.
=item ListOfGeneAssociations::ListOfGeneAssociations
Creates a new ListOfGeneAssociations with the given FbcPkgNamespaces object.
=item ListOfGeneAssociations::get
Get a GeneAssociation from the ListOfGeneAssociations.
@param n the index number of the GeneAssociation to get.
@return the nth GeneAssociation in this ListOfGeneAssociations.
@see size()
=item ListOfGeneAssociations::get
Get a GeneAssociation from the ListOfGeneAssociations.
@param n the index number of the GeneAssociation to get.
@return the nth GeneAssociation in this ListOfGeneAssociations.
@see size()
=item ListOfGeneAssociations::get
Get a GeneAssociation from the ListOfGeneAssociations
based on its identifier.
@param sid a string representing the identifier
of the GeneAssociation to get.
@return GeneAssociation in this ListOfGeneAssociations
with the given C<sid> or C<NULL> if no such
GeneAssociation exists.
@see get(unsigned int n)
@see size()
=item ListOfGeneAssociations::get
Get a GeneAssociation from the ListOfGeneAssociations
based on its identifier.
@param sid a string representing the identifier
of the GeneAssociation to get.
@return GeneAssociation in this ListOfGeneAssociations
with the given C<sid> or C<NULL> if no such
GeneAssociation exists.
@see get(unsigned int n)
@see size()
=item ListOfGeneAssociations::remove
Removes the nth item from this ListOfGeneAssociations items and returns a pointer to
it.
The caller owns the returned item and is responsible for deleting it.
@param n the index of the item to remove
@return the item removed. As mentioned above, the caller owns the
returned item.
@see size()
=item ListOfGeneAssociations::remove
Removes item in this ListOfGeneAssociations items with the given identifier.
The caller owns the returned item and is responsible for deleting it.
If none of the items in this list have the identifier C<sid>, then C<
>
NULL is returned.
@param sid the identifier of the item to remove
@return the item removed. As mentioned above, the caller owns the
returned item.
=item ListOfGeneAssociations::getItemTypeCode
Returns the libSBML type code for the SBML objects
contained in this ListOf object.
C<opydetails> doc_what_are_typecodes
@return the SBML type code for objects contained in this list:
@link SBMLTypeCode_t#SBML_FBC_GENEASSOCIATION SBML_FBC_GENEASSOCIATION@endlink (default).
@see getElementName()
@see getPackageName()
=item ListOfGeneAssociations::getElementName
Returns the XML element name of
this SBML object.
@return the string of the name of this element.
=item ListOfGeneAssociations::createObject
@internal
Create and return a geneAssociation object, if present.
@return the SBML object corresponding to next XMLToken in the
XMLInputStream or NULL if the token was not recognized.
=back
=head2 Objective
@sbmlpackage{fbc}
@htmlinclude pkg-marker-fbc.html Implementation of the 'fbc' package Objective construct.
The FBC Objective class is derived from SBML SBase and inherits metaid and
sboTerm, as well as the subcomponents for Annotation and Notes. An
integral component in a complete description of a steady-state model is
the so-called 'objective function' which generally consists of a linear
combination of model variables (fluxes) and a sense (direction). In the
FBC package this concept is succinctly captured in the Objective class.
=over
=back
=head2 ListOfObjectives
@sbmlpackage{fbc}
@htmlinclude pkg-marker-fbc.html Implementation of the ListOfObjectives construct from the
'fbc' package.
The ListOfObjectives is a container for the Objective elements of Model.
C<opydetails> doc_what_is_listof
@see Objective
=over
=item Objective::Objective
Creates a new Objective with the given level, version, and package version.
=item Objective::Objective
Creates a new Objective with the given FbcPkgNamespaces object.
=item Objective::Objective
Copy constructor.
=item Objective::getElementBySId
Returns the first child element found that has the given C<id> in the model-wide SId namespace, or C<NULL> if no such object is found.
@param id string representing the id of objects to find
@return a pointer to the SBase element with the given C<id>.
=item Objective::getElementByMetaId
Returns the first child element it can find with the given C<metaid>, or itself if it has the given C<metaid>, or C<NULL> if no such object is found.
@param metaid string representing the metaid of objects to find
@return a pointer to the SBase element with the given C<metaid>.
=item Objective::getAllElements
Returns a List of all child SBase objects, including those nested to an arbitrary depth
@return a List of pointers to all children objects.
=item Objective::getName
Returns the value of the "name" attribute of this Objective.
@return the value of the "name" attribute of this Objective.
=item Objective::isSetName
Predicate returning C<true> or C<false> depending on whether this
Objective's "name" attribute has been set.
@return C<true> if this Objective's "id" attribute has been set,
otherwise C<false> is returned.
=item Objective::setName
Sets the value of the "name" attribute of this Objective.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item Objective::unsetName
Unsets the value of the "name" attribute of this Objective.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item Objective::getType
Returns the string of the "type" attribute of this Objective.
@return the string of the "type" attribute of this Objective.
=item Objective::getObjectiveType
Returns the ObjectiveType_t of the "type" attribute of this Objective.
@return the ObjectiveType_t of the "type" attribute of this Objective.
=item Objective::isSetType
Predicate returning C<true> or C<false> depending on whether this
Objective's "type" attribute has been set.
@return C<true> if this Objective's "type" attribute has been set,
otherwise C<false> is returned.
=item Objective::setType
Sets the SIdRef string of the "type" attribute of this Objective.
@param type a SIdRef string to be set.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item Objective::setType
Sets the SIdRef string of the "type" attribute of this Objective.
@param type a SIdRef string to be set.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item Objective::unsetType
Unsets the value of the "id" attribute of this Objective.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item Objective::getId
Returns the string of the "id" attribute of this Objective.
@return the string of the "id" attribute of this Objective.
=item Objective::isSetId
Predicate returning C<true> or C<false> depending on whether this
Objective's "id" attribute has been set.
@return C<true> if this Objective's "id" attribute has been set,
otherwise C<false> is returned.
=item Objective::setId
Sets the SIdRef string of the "id" attribute of this Objective.
@param id a SIdRef string to be set.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item Objective::unsetId
Unsets the value of the "id" attribute of this Objective.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item Objective::getListOfFluxObjectives
Returns the ListOf object that holds all members.
@return the ListOf object that holds all members.
=item Objective::getFluxObjective
Returns the member with the given index.
If the index is invalid, C<NULL> is returned.
@param n the index number of the FluxObjective to get.
@return the nth FluxObjective in the ListOfFluxObjectives.
=item Objective::getFluxObjective
Returns the member with the given index.
If the index is invalid, C<NULL> is returned.
@param n the index number of the FluxObjective to get.
@return the nth FluxObjective in the ListOfFluxObjectives.
=item Objective::getFluxObjective
Returns the member with the given symbol.
If the index is invalid, C<NULL> is returned.
@param symbol a string representing the symbol attribute
of the FluxObjective to get.
@return FluxObjective in the ListOfFluxObjectives with the given symbol
or NULL if no such FluxObjective exists.
=item Objective::getFluxObjective
Returns the member with the given symbol.
If the index is invalid, C<NULL> is returned.
@param symbol a string representing the symbol attribute
of the FluxObjective to get.
@return FluxObjective in the ListOfFluxObjectives with the given symbol
or NULL if no such FluxObjective exists.
=item Objective::addFluxObjective
Adds a copy of the given FluxObjective object to the list of members.
@param member the FluxObjective object to be added to the list of
members.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_LEVEL_MISMATCH LIBSBML_LEVEL_MISMATCH @endlink
@li @link OperationReturnValues_t#LIBSBML_VERSION_MISMATCH LIBSBML_VERSION_MISMATCH @endlink
@li @link OperationReturnValues_t#LIBSBML_PKG_VERSION_MISMATCH LIBSBML_PKG_VERSION_MISMATCH @endlink
@li @link OperationReturnValues_t#LIBSBML_DUPLICATE_OBJECT_ID LIBSBML_DUPLICATE_OBJECT_ID @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item Objective::getNumFluxObjectives
Returns the number of members for this objective.
@return the number of members for this objective.
=item Objective::createFluxObjective
Creates a FluxObjective object, adds it to the end of the
member objects list and returns a pointer to the newly
created object.
@return a newly created FluxObjective object
=item Objective::removeFluxObjective
Removes the member with the given index from the objective.
A pointer to the member that was removed is returned.
If no member has been removed, C<NULL> is returned.
@param index the index of the FluxObjective object to remove
@return the FluxObjective object removed. As mentioned above,
the caller owns the returned object. C<NULL> is returned if
the given index is out of range.
=item Objective::removeFluxObjective
Removes the member with the given symbol from the objective.
A pointer to the member that was removed is returned.
If no member has been removed, C<NULL> is returned.
@param symbol the symbol attribute of the FluxObjective object to remove
@return the FluxObjective object removed. As mentioned above,
the caller owns the returned object. C<NULL> is returned if
the given index is out of range.
=item Objective::getElementName
Returns the XML element name of
this SBML object.
@return the string of the name of this element.
=item Objective::clone
Creates and returns a deep copy of this Objective object.
@return a (deep) copy of this Objective.
=item Objective::getTypeCode
Returns the libSBML type code of this object instance.
C<opydetails> doc_what_are_typecodes
@return the SBML type code for this object:
@link SBMLFbcTypeCode_t#SBML_FBC_OBJECTIVE SBML_FBC_OBJECTIVE@endlink
C<opydetails> doc_warning_typecodes_not_unique
@see getElementName()
@see getPackageName()
=item Objective::writeElements
@internal
Subclasses should override this method to write out their contained
SBML objects as XML elements. Be sure to call your parents
implementation of this method as well. For example:
SBase::writeElements(stream);
mReactants.write(stream);
mProducts.write(stream);
...
=item Objective::accept
Accepts the given SBMLVisitor.
@return the result of calling C<v.visit()>, which indicates
whether or not the Visitor would like to visit the SBML object's next
sibling object (if available).
=item Objective::setSBMLDocument
@internal
Sets the parent SBMLDocument of this SBML object.
@param d the SBMLDocument object to use
=item Objective::connectToChild
@internal
Sets this SBML object to child SBML objects (if any).
(Creates a child-parent relationship by the parent)
Subclasses must override this function if they define
one ore more child elements.
Basically, this function needs to be called in
constructor, copy constructor, assignment operator.
@see setSBMLDocument
@see enablePackageInternal
=item Objective::enablePackageInternal
@internal
Enables/Disables the given package with this element and child
elements (if any).
(This is an internal implementation for enablePakcage function)
@note Subclasses in which one or more child elements are defined
must override this function.
=item Objective::hasRequiredElements
@internal
=item Objective::getIsSetListOfFluxObjectives
@internal
=item Objective::createObject
@internal
Create and return an SBML object of this class, if present.
@return the SBML object corresponding to next XMLToken in the
XMLInputStream or NULL if the token was not recognized.
=item Objective::addExpectedAttributes
@internal
Subclasses should override this method to get the list of
expected attributes.
This function is invoked from corresponding readAttributes()
function.
=item Objective::readAttributes
@internal
Subclasses should override this method to read values from the given
XMLAttributes set into their specific fields. Be sure to call your
parents implementation of this method as well.
=item Objective::writeAttributes
@internal
Subclasses should override this method to write their XML attributes
to the XMLOutputStream. Be sure to call your parents implementation
of this method as well. For example:
SBase::writeAttributes(stream);
stream.writeAttribute( "id" , mId );
stream.writeAttribute( "name", mName );
...
=item ListOfObjectives::clone
Creates and returns a deep copy of this ListOfObjectives object.
@return a (deep) copy of this ListOfObjectives.
=item ListOfObjectives::ListOfObjectives
Creates a new ListOfObjectives with the given level, version, and package version.
=item ListOfObjectives::ListOfObjectives
Creates a new ListOfObjectives with the given FbcPkgNamespaces object.
=item ListOfObjectives::get
Get a Objective from the ListOfObjectives.
@param n the index number of the Objective to get.
@return the nth Objective in this ListOfObjectives.
@see size()
=item ListOfObjectives::get
Get a Objective from the ListOfObjectives.
@param n the index number of the Objective to get.
@return the nth Objective in this ListOfObjectives.
@see size()
=item ListOfObjectives::get
Get a Objective from the ListOfObjectives
based on its identifier.
@param sid a string representing the identifier
of the Objective to get.
@return Objective in this ListOfObjectives
with the given C<sid> or C<NULL> if no such
Objective exists.
@see get(unsigned int n)
@see size()
=item ListOfObjectives::get
Get a Objective from the ListOfObjectives
based on its identifier.
@param sid a string representing the identifier
of the Objective to get.
@return Objective in this ListOfObjectives
with the given C<sid> or C<NULL> if no such
Objective exists.
@see get(unsigned int n)
@see size()
=item ListOfObjectives::remove
Removes the nth item from this ListOfObjectives items and returns a pointer to
it.
The caller owns the returned item and is responsible for deleting it.
@param n the index of the item to remove
@return the item removed. As mentioned above, the caller owns the
returned item.
@see size()
=item ListOfObjectives::remove
Removes item in this ListOfObjectives items with the given identifier.
The caller owns the returned item and is responsible for deleting it.
If none of the items in this list have the identifier C<sid>, then C<
>
NULL is returned.
@param sid the identifier of the item to remove
@return the item removed. As mentioned above, the caller owns the
returned item.
=item ListOfObjectives::getItemTypeCode
Returns the libSBML type code for the objects contained in this ListOf
(i.e., @link SBMLFbcTypeCode_t#SBML_FBC_OBJECTIVE SBML_FBC_OBJECTIVE@endlink).
C<opydetails> doc_what_are_typecodes
@return the SBML type code for objects contained in this list:
@link SBMLFbcTypeCode_t#SBML_FBC_OBJECTIVE SBML_FBC_OBJECTIVE@endlink
@see getElementName()
@see getPackageName()
=item ListOfObjectives::getElementName
Returns the XML element name of
this SBML object.
@return the string of the name of this element.
=item ListOfObjectives::isSetActiveObjective
Predicate returning C<true> or C<false> depending on whether this
ListOfObjective's "activeObjective" attribute has been set.
@return C<true> if this ListOfObjective's "activeObjective" attribute has been set,
otherwise C<false> is returned.
=item ListOfObjectives::setActiveObjective
Sets the value of the "activeObjective" attribute of this ListOfObjectives.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item ListOfObjectives::getActiveObjective
Returns the value of the "activeObjective" attribute of this ListOfObjectives.
@return the value of the "activeObjective" attribute of this ListOfObjectives.
=item ListOfObjectives::unsetActiveObjective
Unsets the value of the "activeObjective" attribute of this ListOfObjectives.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item ListOfObjectives::accept
@internal
=item ListOfObjectives::appendFrom
Adds a clone of all items in the provided ListOf to this object. This means that when this ListOf is destroyed, the original items will not be destroyed. In addition, copy over the input ListOfObjectives' 'activeObjective' attribute, if none is set for this element.
@param list A list of items to be added.
@see append(const SBase item)
=item ListOfObjectives::renameSIdRefs
Renames all the SIdRef attributes on this element if they match
C<oldid>, but not any found in child or plugin elements.
=item ListOfObjectives::createObject
@internal
Create and return an SBML object of this class, if present.
@return the SBML object corresponding to next XMLToken in the
XMLInputStream or NULL if the token was not recognized.
=item ListOfObjectives::addExpectedAttributes
@internal
Subclasses should override this method to get the list of
expected attributes.
This function is invoked from corresponding readAttributes()
function.
=item ListOfObjectives::readAttributes
@internal
Reads the attributes of corresponding package in SBMLDocument element.
=item ListOfObjectives::writeAttributes
@internal
Writes the attributes of corresponding package in SBMLDocument element.
=back
=head2 QualExtension
@sbmlpackage{qual}
@htmlinclude pkg-marker-qual.html The core module of the 'qual' package extension.
=over
=back
=head2 QualPkgNamespaces
@sbmlpackage{qual}
@htmlinclude pkg-marker-qual.html Extension of SBMLNamespaces for the SBML Level 3
'qual' package.
=over
=item QualExtension::getPackageName
Returns the package name of this extension.
=item QualExtension::getDefaultLevel
Returns the default SBML Level this extension.
=item QualExtension::getDefaultVersion
Returns the default SBML Version this extension.
=item QualExtension::getDefaultPackageVersion
Returns the default SBML version this extension.
=item QualExtension::getXmlnsL3V1V1
Returns URI of supported versions of this package.
=item QualExtension::QualExtension
Constructor
=item QualExtension::QualExtension
Copy constructor.
=item QualExtension::clone
Creates and returns a deep copy of this QualExtension object.
@return a (deep) copy of this SBase object
=item QualExtension::getName
Returns the name of this package ("qual")
@return a string representing the name of this package ("qual")
=item QualExtension::getURI
Returns the namespace URI corresponding to the combination of the given
SBML Level, Version, and package version.
@param sbmlLevel the level of SBML
@param sbmlVersion the version of SBML
@param pkgVersion the version of package
@return a string of the package URI, or an empty string if no
corresponding URI exists.
=item QualExtension::getLevel
Returns the SBML Level for the given URI of this package.
@param uri the string of URI that represents one of versions of the
“qual” package
@return the SBML Level with the given URI of this package, or C<0> if
the given URI is invalid.
=item QualExtension::getVersion
Returns the SBML Version for the given URI of this package.
@param uri the string of URI that represents one of versions of the
“qual” package
@return the SBML version with the given URI of this package, or C<0> if
the given URI is invalid.
=item QualExtension::getPackageVersion
Returns the package version for the given URI of this package.
@param uri the string of URI that represents one of versions of the
“qual” package
@return the package version with the given URI of this package, or C<0
>
if the given URI is invalid.
=item QualExtension::getSBMLExtensionNamespaces
Returns an QualPkgNamespaces object.
@param uri the string of URI that represents one of versions of the
“qual” package
@return an QualPkgNamespace object corresponding to the given C<uri>, or
C<NULL> if the URI is not defined in the Hierarchical Model Qualosition
package.
=item QualExtension::getStringFromTypeCode
Takes a type code of the “qual” package and returns a string
describing the code.
=item QualExtension::init
@internal
Initializes qual extension by creating an object of this class with
required SBasePlugin derived objects and registering the object
to the SBMLExtensionRegistry class.
(NOTE) This function is automatically invoked when creating the following
global object in QualExtension.cpp
static SBMLExtensionRegister<QualExtension> qualExtensionRegistry;
=item QualExtension::getErrorTable
@internal
Return the entry in the error table at this index.
@param index an unsigned intgere representing the index of the error in the QualSBMLErrorTable
@return packageErrorTableEntry object in the QualSBMLErrorTable corresponding to the index given.
=item QualExtension::getErrorTableIndex
@internal
Return the index in the error table with the given errorId.
@param errorId an unsigned intgere representing the errorId of the error in the QualSBMLErrorTable
@return unsigned integer representing the index in the QualSBMLErrorTable corresponding to the errorId given.
=item QualExtension::getErrorIdOffset
@internal
Return the offset for the errorId range for the qual L3 package.
@return unsigned intege representing the offset for errors QualSBMLErrorTable.
=back
=head2 QualModelPlugin
@sbmlpackage{qual}
@htmlinclude pkg-marker-qual.html Implementation of the 'qual' package extention to the
Model construct. The extension of SBML Level 3 Core's Model class is
relatively straightforward: the Qualitative Models Package adds two lists,
one for holding qualitativeSpecies (ListOfQualitativeSpecies), and the
other for holding transitions (ListOfTransitions). The Model element may
contain at most one ListOfQualitativeSpecies, which must contain at least
one QualitativeSpecies. It may also contain at most one ListOfTransitions
which must contain at least one Transition.
=over
=item QualModelPlugin::QualModelPlugin
Constructor
=item QualModelPlugin::QualModelPlugin
Copy constructor. Creates a copy of this SBase object.
=item QualModelPlugin::clone
Creates and returns a deep copy of this QualModelPlugin object.
@return a (deep) copy of this SBase object
=item QualModelPlugin::createObject
@internal
Subclasses must override this method to create, store, and then
return an SBML object corresponding to the next XMLToken in the
XMLInputStream if they have their specific elements.
@return the SBML object corresponding to next XMLToken in the
XMLInputStream or NULL if the token was not recognized.
=item QualModelPlugin::writeElements
@internal
Subclasses must override this method to write out their contained
SBML objects as XML elements if they have their specific elements.
=item QualModelPlugin::hasRequiredElements
@internal
Checks if this plugin object has all the required elements.
Subclasses should override this function if they have their specific
elements.
@return true if this plugin object has all the required elements,
otherwise false will be returned.
=item QualModelPlugin::appendFrom
@internal
=item QualModelPlugin::getAllElements
Returns a List of all child SBase objects, including those nested to an
arbitary depth.
@return a List of pointers to all child objects.
=item QualModelPlugin::getListOfQualitativeSpecies
Returns the ListOfQualitativeSpecies in this plugin object.
@return ListOfQualitativeSpecies object in this plugin object.
=item QualModelPlugin::getListOfQualitativeSpecies
Returns the ListOfQualitativeSpecies in this plugin object.
@return ListOfQualitativeSpecies object in this plugin object.
=item QualModelPlugin::getQualitativeSpecies
Returns the QualitativeSpecies object that belongs to the given index. If the
index is invalid, NULL is returned.
@param n the index number of the QualitativeSpecies to get.
@return the nth QualitativeSpecies in the ListOfQualitativeSpecies.
=item QualModelPlugin::getQualitativeSpecies
Returns the QualitativeSpecies object that belongs to the given index. If the
index is invalid, NULL is returned.
@param n the index number of the QualitativeSpecies to get.
@return the nth QualitativeSpecies in the ListOfQualitativeSpecies.
=item QualModelPlugin::getQualitativeSpecies
Returns the qualitativeSpecies object based on its identifier.
@param sid a string representing the identifier
of the QualitativeSpecies to get.
@return QualitativeSpecies in the ListOfQualitativeSpecies with the given id
or NULL if no such QualitativeSpecies exists.
@see getQualitativeSpecies(unsigned int n)
@see getListOfQualitativeSpecies()
=item QualModelPlugin::getQualitativeSpecies
Returns the qualitativeSpecies object based on its identifier.
@param sid a string representing the identifier
of the QualitativeSpecies to get.
@return QualitativeSpecies in the ListOfQualitativeSpecies with the given id
or NULL if no such QualitativeSpecies exists.
@see getQualitativeSpecies(unsigned int n)
@see getListOfQualitativeSpecies()
=item QualModelPlugin::addQualitativeSpecies
Adds a copy of the given QualitativeSpecies object to the list of qual.
@param qualitativeSpecies the QualitativeSpecies object to be added to the list of qual.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
=item QualModelPlugin::createQualitativeSpecies
Creates a new qual object and adds it to the list of qual objects
and returns it.
@return a newly created QualitativeSpecies object
=item QualModelPlugin::removeQualitativeSpecies
Removes the nth QualitativeSpecies object from this plugin object and
returns a pointer to it.
The caller owns the returned object and is responsible for
deleting it.
@param n the index of the QualitativeSpecies object to remove
@return the QualitativeSpecies object removed. As mentioned above, the
caller owns the returned object. NULL is returned if the
given index is out of range.
=item QualModelPlugin::removeQualitativeSpecies
Removes the QualitativeSpecies object with the given id attribute from
this plugin object and returns a pointer to it.
The caller owns the returned object and is responsible for
deleting it.
@param sid the id attribute of the QualitativeSpecies object to remove
@return the QualitativeSpecies object removed. As mentioned above, the
caller owns the returned object. NULL is returned if the
given index is out of range.
=item QualModelPlugin::getNumQualitativeSpecies
Returns the number of QualitativeSpecies object in this plugin object.
@return the number of QualitativeSpecies object in this plugin object.
=item QualModelPlugin::getListOfTransitions
Returns the ListOfTransitions in this plugin object.
@return ListOfTransitions object in this plugin object.
=item QualModelPlugin::getListOfTransitions
Returns the ListOfTransitions in this plugin object.
@return ListOfTransitions object in this plugin object.
=item QualModelPlugin::getTransition
Returns the Transition object that belongs to the given index. If the
index is invalid, NULL is returned.
@param n the index number of the Transition to get.
@return the nth Transition in the ListOfTransitions.
=item QualModelPlugin::getTransition
Returns the Transition object that belongs to the given index. If the
index is invalid, NULL is returned.
@param n the index number of the Transition to get.
@return the nth Transition in the ListOfTransitions.
=item QualModelPlugin::getTransition
Returns the qualitativeSpecies object based on its identifier.
@param sid a string representing the identifier
of the Transition to get.
@return Transition in the ListOfTransitions with the given id
or NULL if no such Transition exists.
@see getTransition(unsigned int n)
@see getListOfTransitions()
=item QualModelPlugin::getTransition
Returns the qualitativeSpecies object based on its identifier.
@param sid a string representing the identifier
of the Transition to get.
@return Transition in the ListOfTransitions with the given id
or NULL if no such Transition exists.
@see getTransition(unsigned int n)
@see getListOfTransitions()
=item QualModelPlugin::addTransition
Adds a copy of the given Transition object to the list of qual.
@param transition the Transition object to be added to the list of qual.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
=item QualModelPlugin::createTransition
Creates a new qual object and adds it to the list of qual objects
and returns it.
@return a newly created Transition object
=item QualModelPlugin::removeTransition
Removes the nth Transition object from this plugin object and
returns a pointer to it.
The caller owns the returned object and is responsible for
deleting it.
@param n the index of the Transition object to remove
@return the Transition object removed. As mentioned above, the
caller owns the returned object. NULL is returned if the
given index is out of range.
=item QualModelPlugin::removeTransition
Removes the Transition object with the given id attribute from
this plugin object and returns a pointer to it.
The caller owns the returned object and is responsible for
deleting it.
@param sid the id attribute of the Transition object to remove
@return the Transition object removed. As mentioned above, the
caller owns the returned object. NULL is returned if the
given index is out of range.
=item QualModelPlugin::getNumTransitions
Returns the number of Transition object in this plugin object.
@return the number of Transition object in this plugin object.
=item QualModelPlugin::setSBMLDocument
@internal
Sets the parent SBMLDocument of this plugin object.
Subclasses which contain one or more SBase derived elements must
override this function.
@param d the SBMLDocument object to use
@see connectToParent
@see enablePackageInternal
=item QualModelPlugin::connectToChild
@internal
Sets the parent of this SBML object to child SBML objects (if any).
(Creates a child-parent relationship by the parent)
@see setSBMLDocument
@see enablePackageInternal
=item QualModelPlugin::connectToParent
@internal
Sets the parent SBML object of this plugin object to
this object and child elements (if any).
(Creates a child-parent relationship by this plugin object)
This function is called when this object is created by
the parent element.
Subclasses must override this this function if they have one
or more child elements.Also, SBasePlugin::connectToParent()
must be called in the overridden function.
@param sbase the SBase object to use
@see setSBMLDocument
@see enablePackageInternal
=item QualModelPlugin::enablePackageInternal
@internal
Enables/Disables the given package with child elements in this plugin
object (if any).
(This is an internal implementation invoked from
SBase::enablePackageInternal() function)
@note Subclasses in which one or more SBase derived elements are
defined must override this function.
@see setSBMLDocument
@see connectToParent
=item QualModelPlugin::accept
@internal
Accepts the given SBMLVisitor.
=back
=head2 FunctionTerm
@sbmlpackage{qual}
@htmlinclude pkg-marker-qual.html The FunctionTerm class for the Qualitative Models
package.
Each FunctionTerm is associated with a result and with a Boolean function
inside a Math element that can be used to set the conditions under which
this term is selected.
=over
=back
=head2 ListOfFunctionTerms
@sbmlpackage{qual}
@htmlinclude pkg-marker-qual.html Implementation of the ListOfFunctionTerms construct from
the 'qual' package.
The ListOfFunctionTerms is a container for the FunctionTerms of a Transition.
C<opydetails> doc_what_is_listof
@see Input
=over
=item FunctionTerm::FunctionTerm
Creates a new FunctionTerm with the given level, version, and package version.
@param level an unsigned int, the SBML Level to assign to this FunctionTerm
@param version an unsigned int, the SBML Version to assign to this FunctionTerm
@param pkgVersion an unsigned int, the SBML Qual Version to assign to this FunctionTerm
=item FunctionTerm::FunctionTerm
Creates a new FunctionTerm with the given QualPkgNamespaces object.
@param qualns the QualPkgNamespaces object
=item FunctionTerm::FunctionTerm
Copy constructor for FunctionTerm.
@param orig the FunctionTerm instance to copy.
=item FunctionTerm::clone
Creates and returns a deep copy of this FunctionTerm object.
@return a (deep) copy of this FunctionTerm object.
=item FunctionTerm::getResultLevel
Returns the value of the "resultLevel" attribute of this FunctionTerm.
@return the value of the "resultLevel" attribute of this FunctionTerm as a integer.
=item FunctionTerm::isSetResultLevel
Predicate returning C<true> or C<false> depending on whether this
FunctionTerm's "resultLevel" attribute has been set.
@return C<true> if this FunctionTerm's "resultLevel" attribute has been set,
otherwise C<false> is returned.
=item FunctionTerm::setResultLevel
Sets the value of the "resultLevel" attribute of this FunctionTerm.
@param resultLevel int value of the "resultLevel" attribute to be set
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item FunctionTerm::unsetResultLevel
Unsets the value of the "resultLevel" attribute of this FunctionTerm.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item FunctionTerm::getMath
Returns the "math" element of this FunctionTerm.
@return the "math" element of this FunctionTerm.
=item FunctionTerm::isSetMath
Predicate returning C<true> or C<false> depending on whether this
FunctionTerm's "math" element has been set.
@return C<true> if this FunctionTerm's "math" element has been set,
otherwise C<false> is returned.
=item FunctionTerm::setMath
Sets the "math" element of this FunctionTerm.
@param math ASTNode math of the "resultLevel" attribute to be set
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item FunctionTerm::unsetMath
Unsets the "math" element of this FunctionTerm.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item FunctionTerm::renameSIdRefs
Renames all the C<SIdRef> attributes on this element, including any
found in MathML content (if such exists).
This method works by looking at all attributes and (if appropriate)
mathematical formulas, comparing the identifiers to the value of @p
oldid. If any matches are found, the matching identifiers are replaced
with C<newid>. The method does I<not> descend into child elements.
@param oldid the old identifier
@param newid the new identifier
=item FunctionTerm::getElementName
Returns the XML element name of this object, which for FunctionTerm, is
always C<"functionTerm">.
@return the name of this element, i.e. C<"functionTerm">.
=item FunctionTerm::getTypeCode
Returns the libSBML type code of this object instance.
C<opydetails> doc_what_are_typecodes
@return the SBML type code for this object:
@link SBMLQualTypeCode_t#SBML_QUAL_FUNCTION_TERM SBML_QUAL_FUNCTION_TERM@endlink
C<opydetails> doc_warning_typecodes_not_unique
@see getElementName()
@see getPackageName()
=item FunctionTerm::hasRequiredAttributes
Predicate returning C<true> if all the required attributes
for this FunctionTerm object have been set.
@note The required attributes for a FunctionTerm object are:
@return a boolean value indicating whether all the required
attributes for this object have been defined.
=item FunctionTerm::hasRequiredElements
Predicate returning C<true> if all the required elements
for this FunctionTerm object have been set.
@note The required elements for a FunctionTerm object are:
@li "math"
@return a boolean value indicating whether all the required
elements for this object have been defined.
=item FunctionTerm::writeElements
@internal
Subclasses should override this method to write out their contained
SBML objects as XML elements. Be sure to call your parents
implementation of this method as well.
=item FunctionTerm::accept
@internal
Accepts the given SBMLVisitor.
=item FunctionTerm::setSBMLDocument
@internal
Sets the parent SBMLDocument.
=item FunctionTerm::enablePackageInternal
@internal
Enables/Disables the given package with this element.
=item FunctionTerm::addExpectedAttributes
@internal
Get the list of expected attributes for this element.
=item FunctionTerm::readAttributes
@internal
Read values from the given XMLAttributes set into their specific fields.
=item FunctionTerm::readOtherXML
@internal
Subclasses should override this method to read (and store) XHTML,
MathML, etc. directly from the XMLInputStream.
@return true if the subclass read from the stream, false otherwise.
=item FunctionTerm::writeAttributes
@internal
Write values of XMLAttributes to the output stream.
=item ListOfFunctionTerms::ListOfFunctionTerms
Creates a new ListOfFunctionTerms with the given level, version, and package version.
@param level an unsigned int, the SBML Level to assign to this ListOfFunctionTerms
@param version an unsigned int, the SBML Version to assign to this ListOfFunctionTerms
@param pkgVersion an unsigned int, the SBML Qual Version to assign to this ListOfFunctionTerms
=item ListOfFunctionTerms::ListOfFunctionTerms
Creates a new ListOfFunctionTerms with the given QualPkgNamespaces object.
@param qualns the QualPkgNamespaces object
=item ListOfFunctionTerms::ListOfFunctionTerms
=item ListOfFunctionTerms::clone
Creates and returns a deep copy of this ListOfFunctionTerms object.
@return a (deep) copy of this ListOfFunctionTerms object.
=item ListOfFunctionTerms::get
Get a FunctionTerm from the ListOfFunctionTerms.
@param n the index number of the FunctionTerm to get.
@return the nth FunctionTerm in this ListOfFunctionTerms.
@see size()
=item ListOfFunctionTerms::get
Get a FunctionTerm from the ListOfFunctionTerms.
@param n the index number of the FunctionTerm to get.
@return the nth FunctionTerm in this ListOfFunctionTerms.
@see size()
=item ListOfFunctionTerms::get
Get a FunctionTerm from the ListOfFunctionTerms
based on its identifier.
@param sid a string representing the identifier
of the FunctionTerm to get.
@return FunctionTerm in this ListOfFunctionTerms
with the given id or NULL if no such
FunctionTerm exists.
@see get(unsigned int n)
@see size()
=item ListOfFunctionTerms::get
Get a FunctionTerm from the ListOfFunctionTerms
based on its identifier.
@param sid a string representing the identifier
of the FunctionTerm to get.
@return FunctionTerm in this ListOfFunctionTerms
with the given id or NULL if no such
FunctionTerm exists.
@see get(unsigned int n)
@see size()
=item ListOfFunctionTerms::remove
Removes the nth FunctionTerm from this ListOfFunctionTerms
and returns a pointer to it.
The caller owns the returned item and is responsible for deleting it.
@param n the index of the FunctionTerm to remove.
@see size()
=item ListOfFunctionTerms::remove
Removes the FunctionTerm from this ListOfFunctionTerms with the given identifier
and returns a pointer to it.
The caller owns the returned item and is responsible for deleting it.
If none of the items in this list have the identifier C<sid>, then
C<NULL> is returned.
@param sid the identifier of the FunctionTerm to remove.
@return the FunctionTerm removed. As mentioned above, the caller owns the
returned item.
=item ListOfFunctionTerms::getAllElements
Returns a List of all child SBase objects, including those nested to an
arbitary depth.
@return a List of pointers to all child objects.
=item ListOfFunctionTerms::getElementName
Returns the XML element name of this object, which for ListOfFunctionTerms, is
always C<"listOfFunctionTerms">.
@return the name of this element, i.e. C<"listOfFunctionTerms">.
=item ListOfFunctionTerms::getItemTypeCode
Returns the libSBML type code for the SBML objects
contained in this ListOf object.
C<opydetails> doc_what_are_typecodes
@return the SBML type code for objects contained in this list:
@link SBMLTypeCode_t#SBML_QUAL_FUNCTION_TERM SBML_QUAL_FUNCTION_TERM@endlink (default).
@see getElementName()
@see getPackageName()
=item ListOfFunctionTerms::getDefaultTerm
Get the DefaultTerm from this ListOfFunctionTerms.
@return the DefaultTerm in this ListOfFunctionTerms, or NULL if no such value is set.
@see Transition::getDefaultTerm
=item ListOfFunctionTerms::getDefaultTerm
Get the DefaultTerm from this ListOfFunctionTerms.
@return the DefaultTerm in this ListOfFunctionTerms, or NULL if no such value is set.
@see Transition::getDefaultTerm
=item ListOfFunctionTerms::setDefaultTerm
Sets the given DefaultTerm to this Transition.
@param dt the DefaultTerm object to add
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item ListOfFunctionTerms::isSetDefaultTerm
Predicate returning C<true> if the defaultTerm
for this ListOfFunctionTerms object has been set.
@return a boolean value indicating whether the defaultTerm
child for this object has been defined.
=item ListOfFunctionTerms::setSBMLDocument
@internal
Connects to child elements.
=item ListOfFunctionTerms::accept
@internal
Connects to child elements.
=item ListOfFunctionTerms::createObject
@internal
Creates a new FunctionTerm in this ListOfFunctionTerms
=item ListOfFunctionTerms::writeXMLNS
@internal
Write the namespace for the Qual package.
=item ListOfFunctionTerms::writeElements
@internal
Write the namespace for the Qual package.
=item ListOfFunctionTerms::connectToChild
@internal
Connects to child elements.
=back
=head2 DefaultTerm
@sbmlpackage{qual}
@htmlinclude pkg-marker-qual.html The DefaultTerm class for the Qualitative Models package.
The DefaultTerm defines the default result of a Transition. This term is
used if there are no other FunctionTerm elements or if none of the Math
elements of the FunctionTerm elements evaluates to C<true>.
=over
=item DefaultTerm::DefaultTerm
Creates a new DefaultTerm with the given level, version, and package version.
@param level an unsigned int, the SBML Level to assign to this DefaultTerm
@param version an unsigned int, the SBML Version to assign to this DefaultTerm
@param pkgVersion an unsigned int, the SBML Qual Version to assign to this DefaultTerm
=item DefaultTerm::DefaultTerm
Creates a new DefaultTerm with the given QualPkgNamespaces object.
@param qualns the QualPkgNamespaces object
=item DefaultTerm::DefaultTerm
Copy constructor for DefaultTerm.
@param orig the DefaultTerm instance to copy.
=item DefaultTerm::clone
Creates and returns a deep copy of this DefaultTerm object.
@return a (deep) copy of this DefaultTerm object.
=item DefaultTerm::getResultLevel
Returns the value of the "resultLevel" attribute of this DefaultTerm.
@return the value of the "resultLevel" attribute of this DefaultTerm as a integer.
=item DefaultTerm::isSetResultLevel
Predicate returning C<true> or C<false> depending on whether this
DefaultTerm's "resultLevel" attribute has been set.
@return C<true> if this DefaultTerm's "resultLevel" attribute has been set,
otherwise C<false> is returned.
=item DefaultTerm::setResultLevel
Sets the value of the "resultLevel" attribute of this DefaultTerm.
@param resultLevel int value of the "resultLevel" attribute to be set
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item DefaultTerm::unsetResultLevel
Unsets the value of the "resultLevel" attribute of this DefaultTerm.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item DefaultTerm::getElementName
Returns the XML element name of this object, which for DefaultTerm, is
always C<"defaultTerm">.
@return the name of this element, i.e. C<"defaultTerm">.
=item DefaultTerm::getTypeCode
Returns the libSBML type code of this object instance.
C<opydetails> doc_what_are_typecodes
@return the SBML type code for this object:
@link SBMLQualTypeCode_t#SBML_QUAL_DEFAULT_TERM SBML_QUAL_DEFAULT_TERM@endlink
C<opydetails> doc_warning_typecodes_not_unique
@see getElementName()
@see getPackageName()
=item DefaultTerm::hasRequiredAttributes
Predicate returning C<true> if all the required attributes
for this DefaultTerm object have been set.
@note The required attributes for a DefaultTerm object are:
@return a boolean value indicating whether all the required
attributes for this object have been defined.
=item DefaultTerm::writeElements
@internal
Subclasses should override this method to write out their contained
SBML objects as XML elements. Be sure to call your parents
implementation of this method as well.
=item DefaultTerm::accept
@internal
Accepts the given SBMLVisitor.
=item DefaultTerm::setSBMLDocument
@internal
Sets the parent SBMLDocument.
=item DefaultTerm::enablePackageInternal
@internal
Enables/Disables the given package with this element.
=item DefaultTerm::addExpectedAttributes
@internal
Get the list of expected attributes for this element.
=item DefaultTerm::readAttributes
@internal
Read values from the given XMLAttributes set into their specific fields.
=item DefaultTerm::writeAttributes
@internal
Write values of XMLAttributes to the output stream.
=back
=head2 Input
@sbmlpackage{qual}
@htmlinclude pkg-marker-qual.html The Input class for the Qualitative Models package.
Each Input refers to a QualitativeSpecies that participates in the
corresponding Transition. In Petri nets, these are the input places of the
transition. In logical models, they are the regulators of the species
whose behaviour is defined by the transition.
=over
=back
=head2 ListOfInputs
@sbmlpackage{qual}
@htmlinclude pkg-marker-qual.html Implementation of the ListOfInputs construct from the
'qual' package.
The ListOfInputs is a container for the Inputs of a Transition.
C<opydetails> doc_what_is_listof
@see Input
=over
=item Input::Input
Creates a new Input with the given level, version, and package version.
@param level an unsigned int, the SBML Level to assign to this Input
@param version an unsigned int, the SBML Version to assign to this Input
@param pkgVersion an unsigned int, the SBML Qual Version to assign to this Input
=item Input::Input
Creates a new Input with the given QualPkgNamespaces object.
@param qualns the QualPkgNamespaces object
=item Input::Input
Copy constructor for Input.
@param orig the Input instance to copy.
=item Input::clone
Creates and returns a deep copy of this Input object.
@return a (deep) copy of this Input object.
=item Input::getId
Returns the value of the "id" attribute of this Input.
@return the value of the "id" attribute of this Input as a string.
=item Input::getQualitativeSpecies
Returns the value of the "qualitativeSpecies" attribute of this Input.
@return the value of the "qualitativeSpecies" attribute of this Input as a string.
=item Input::getTransitionEffect
Returns the value of the "transitionEffect" attribute of this Input.
@return the value of the "transitionEffect" attribute of this Input as a string.
=item Input::getName
Returns the value of the "name" attribute of this Input.
@return the value of the "name" attribute of this Input as a string.
=item Input::getSign
Returns the value of the "sign" attribute of this Input.
@return the value of the "sign" attribute of this Input as a string.
=item Input::getThresholdLevel
Returns the value of the "thresholdLevel" attribute of this Input.
@return the value of the "thresholdLevel" attribute of this Input as a integer.
=item Input::isSetId
Predicate returning C<true> or C<false> depending on whether this
Input's "id" attribute has been set.
@return C<true> if this Input's "id" attribute has been set,
otherwise C<false> is returned.
=item Input::isSetQualitativeSpecies
Predicate returning C<true> or C<false> depending on whether this
Input's "qualitativeSpecies" attribute has been set.
@return C<true> if this Input's "qualitativeSpecies" attribute has been set,
otherwise C<false> is returned.
=item Input::isSetTransitionEffect
Predicate returning C<true> or C<false> depending on whether this
Input's "transitionEffect" attribute has been set.
@return C<true> if this Input's "transitionEffect" attribute has been set,
otherwise C<false> is returned.
=item Input::isSetName
Predicate returning C<true> or C<false> depending on whether this
Input's "name" attribute has been set.
@return C<true> if this Input's "name" attribute has been set,
otherwise C<false> is returned.
=item Input::isSetSign
Predicate returning C<true> or C<false> depending on whether this
Input's "sign" attribute has been set.
@return C<true> if this Input's "sign" attribute has been set,
otherwise C<false> is returned.
=item Input::isSetThresholdLevel
Predicate returning C<true> or C<false> depending on whether this
Input's "thresholdLevel" attribute has been set.
@return C<true> if this Input's "thresholdLevel" attribute has been set,
otherwise C<false> is returned.
=item Input::setId
Sets the value of the "id" attribute of this Input.
@param id const std::string& value of the "id" attribute to be set
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item Input::setQualitativeSpecies
Sets the value of the "qualitativeSpecies" attribute of this Input.
@param qualitativeSpecies const std::string& value of the "qualitativeSpecies" attribute to be set
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item Input::setTransitionEffect
Sets the value of the "transitionEffect" attribute of this Input.
@param transitionEffect const std::string& value of the "transitionEffect" attribute to be set
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item Input::setName
Sets the value of the "name" attribute of this Input.
@param name const std::string& value of the "name" attribute to be set
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item Input::setSign
Sets the value of the "sign" attribute of this Input.
@param sign const std::string& value of the "sign" attribute to be set
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item Input::setThresholdLevel
Sets the value of the "thresholdLevel" attribute of this Input.
@param thresholdLevel int value of the "thresholdLevel" attribute to be set
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item Input::unsetId
Unsets the value of the "id" attribute of this Input.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item Input::unsetQualitativeSpecies
Unsets the value of the "qualitativeSpecies" attribute of this Input.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item Input::unsetTransitionEffect
Unsets the value of the "transitionEffect" attribute of this Input.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item Input::unsetName
Unsets the value of the "name" attribute of this Input.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item Input::unsetSign
Unsets the value of the "sign" attribute of this Input.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item Input::unsetThresholdLevel
Unsets the value of the "thresholdLevel" attribute of this Input.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item Input::renameSIdRefs
Renames all the C<SIdRef> attributes on this element, including any
found in MathML content (if such exists).
This method works by looking at all attributes and (if appropriate)
mathematical formulas, comparing the identifiers to the value of @p
oldid. If any matches are found, the matching identifiers are replaced
with C<newid>. The method does I<not> descend into child elements.
@param oldid the old identifier
@param newid the new identifier
=item Input::getElementName
Returns the XML element name of this object, which for Input, is
always C<"input">.
@return the name of this element, i.e. C<"input">.
=item Input::getTypeCode
Returns the libSBML type code of this object instance.
C<opydetails> doc_what_are_typecodes
@return the SBML type code for this object:
@link SBMLQualTypeCode_t#SBML_QUAL_INPUT SBML_QUAL_INPUT@endlink
C<opydetails> doc_warning_typecodes_not_unique
@see getElementName()
@see getPackageName()
=item Input::hasRequiredAttributes
Predicate returning C<true> if all the required attributes
for this Input object have been set.
@note The required attributes for a Input object are:
@li "qualitativeSpecies"
@li "transitionEffect"
@return a boolean value indicating whether all the required
attributes for this object have been defined.
=item Input::writeElements
@internal
Subclasses should override this method to write out their contained
SBML objects as XML elements. Be sure to call your parents
implementation of this method as well.
=item Input::accept
@internal
Accepts the given SBMLVisitor.
=item Input::setSBMLDocument
@internal
Sets the parent SBMLDocument.
=item Input::enablePackageInternal
@internal
Enables/Disables the given package with this element.
=item Input::addExpectedAttributes
@internal
Get the list of expected attributes for this element.
=item Input::readAttributes
@internal
Read values from the given XMLAttributes set into their specific fields.
=item Input::writeAttributes
@internal
Write values of XMLAttributes to the output stream.
=item ListOfInputs::ListOfInputs
Creates a new ListOfInputs with the given level, version, and package version.
@param level an unsigned int, the SBML Level to assign to this ListOfInputs
@param version an unsigned int, the SBML Version to assign to this ListOfInputs
@param pkgVersion an unsigned int, the SBML Qual Version to assign to this ListOfInputs
=item ListOfInputs::ListOfInputs
Creates a new ListOfInputs with the given QualPkgNamespaces object.
@param qualns the QualPkgNamespaces object
=item ListOfInputs::clone
Creates and returns a deep copy of this ListOfInputs object.
@return a (deep) copy of this ListOfInputs object.
=item ListOfInputs::get
Get a Input from the ListOfInputs.
@param n the index number of the Input to get.
@return the nth Input in this ListOfInputs.
@see size()
=item ListOfInputs::get
Get a Input from the ListOfInputs.
@param n the index number of the Input to get.
@return the nth Input in this ListOfInputs.
@see size()
=item ListOfInputs::get
Get a Input from the ListOfInputs
based on its identifier.
@param sid a string representing the identifier
of the Input to get.
@return Input in this ListOfInputs
with the given id or NULL if no such
Input exists.
@see get(unsigned int n)
@see size()
=item ListOfInputs::get
Get a Input from the ListOfInputs
based on its identifier.
@param sid a string representing the identifier
of the Input to get.
@return Input in this ListOfInputs
with the given id or NULL if no such
Input exists.
@see get(unsigned int n)
@see size()
=item ListOfInputs::getBySpecies
Get a Input from the ListOfInputs
based on the qualitativeSpecies to which it refers.
@param sid a string representing the qualitativeSpecies attribute
of the Input to get.
@return the first Input in this ListOfInputs
with the given qualitativeSpecies or NULL if no such
Input exists.
@see get(unsigned int n)
@see size()
=item ListOfInputs::getBySpecies
Get a Input from the ListOfInputs
based on the qualitativeSpecies to which it refers.
@param sid a string representing the qualitativeSpecies attribute
of the Input to get.
@return the first Input in this ListOfInputs
with the given qualitativeSpecies or NULL if no such
Input exists.
@see get(unsigned int n)
@see size()
=item ListOfInputs::remove
Removes the nth Input from this ListOfInputs
and returns a pointer to it.
The caller owns the returned item and is responsible for deleting it.
@param n the index of the Input to remove.
@see size()
=item ListOfInputs::remove
Removes the Input from this ListOfInputs with the given identifier
and returns a pointer to it.
The caller owns the returned item and is responsible for deleting it.
If none of the items in this list have the identifier C<sid>, then
C<NULL> is returned.
@param sid the identifier of the Input to remove.
@return the Input removed. As mentioned above, the caller owns the
returned item.
=item ListOfInputs::getElementName
Returns the XML element name of this object, which for ListOfInputs, is
always C<"listOfInputs">.
@return the name of this element, i.e. C<"listOfInputs">.
=item ListOfInputs::getItemTypeCode
Returns the libSBML type code for the SBML objects
contained in this ListOf object.
C<opydetails> doc_what_are_typecodes
@return the SBML type code for objects contained in this list:
@link SBMLTypeCode_t#SBML_QUAL_INPUT SBML_QUAL_INPUT@endlink (default).
@see getElementName()
@see getPackageName()
=item ListOfInputs::createObject
@internal
Creates a new Input in this ListOfInputs
=item ListOfInputs::writeXMLNS
@internal
Write the namespace for the Qual package.
=back
=head2 Output
@sbmlpackage{qual}
@htmlinclude pkg-marker-qual.html The Output class for the Qualitative Models package.
Each Output refers to a QualitativeSpecies that participates in (is
affected by) the corresponding Transition. In Petri net models these are
the output places of the transition.
In a logical model, a QualitativeSpecies should be referenced in at most
one ListOfOutputs, (that of the Transition defining the evolution of this
species). When a Transition has several outputs, it is because the
referenced species share the same regulators and the same logical rules.
=over
=back
=head2 ListOfOutputs
@sbmlpackage{qual}
@htmlinclude pkg-marker-qual.html Implementation of the ListOfOutputs construct from the
'qual' package.
The ListOfOutputs is a container for the Output elements of a Transition.
C<opydetails> doc_what_is_listof
@see Output
=over
=item Output::Output
Creates a new Output with the given level, version, and package version.
@param level an unsigned int, the SBML Level to assign to this Output
@param version an unsigned int, the SBML Version to assign to this Output
@param pkgVersion an unsigned int, the SBML Qual Version to assign to this Output
=item Output::Output
Creates a new Output with the given QualPkgNamespaces object.
@param qualns the QualPkgNamespaces object
=item Output::Output
Copy constructor for Output.
@param orig the Output instance to copy.
=item Output::clone
Creates and returns a deep copy of this Output object.
@return a (deep) copy of this Output object.
=item Output::getId
Returns the value of the "id" attribute of this Output.
@return the value of the "id" attribute of this Output as a string.
=item Output::getQualitativeSpecies
Returns the value of the "qualitativeSpecies" attribute of this Output.
@return the value of the "qualitativeSpecies" attribute of this Output as a string.
=item Output::getTransitionEffect
Returns the value of the "transitionEffect" attribute of this Output.
@return the value of the "transitionEffect" attribute of this Output as a string.
=item Output::getName
Returns the value of the "name" attribute of this Output.
@return the value of the "name" attribute of this Output as a string.
=item Output::getOutputLevel
Returns the value of the "outputLevel" attribute of this Output.
@return the value of the "outputLevel" attribute of this Output as a integer.
=item Output::isSetId
Predicate returning C<true> or C<false> depending on whether this
Output's "id" attribute has been set.
@return C<true> if this Output's "id" attribute has been set,
otherwise C<false> is returned.
=item Output::isSetQualitativeSpecies
Predicate returning C<true> or C<false> depending on whether this
Output's "qualitativeSpecies" attribute has been set.
@return C<true> if this Output's "qualitativeSpecies" attribute has been set,
otherwise C<false> is returned.
=item Output::isSetTransitionEffect
Predicate returning C<true> or C<false> depending on whether this
Output's "transitionEffect" attribute has been set.
@return C<true> if this Output's "transitionEffect" attribute has been set,
otherwise C<false> is returned.
=item Output::isSetName
Predicate returning C<true> or C<false> depending on whether this
Output's "name" attribute has been set.
@return C<true> if this Output's "name" attribute has been set,
otherwise C<false> is returned.
=item Output::isSetOutputLevel
Predicate returning C<true> or C<false> depending on whether this
Output's "outputLevel" attribute has been set.
@return C<true> if this Output's "outputLevel" attribute has been set,
otherwise C<false> is returned.
=item Output::setId
Sets the value of the "id" attribute of this Output.
@param id const std::string& value of the "id" attribute to be set
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item Output::setQualitativeSpecies
Sets the value of the "qualitativeSpecies" attribute of this Output.
@param qualitativeSpecies const std::string& value of the "qualitativeSpecies" attribute to be set
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item Output::setTransitionEffect
Sets the value of the "transitionEffect" attribute of this Output.
@param transitionEffect const std::string& value of the "transitionEffect" attribute to be set
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item Output::setName
Sets the value of the "name" attribute of this Output.
@param name const std::string& value of the "name" attribute to be set
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item Output::setOutputLevel
Sets the value of the "outputLevel" attribute of this Output.
@param outputLevel int value of the "outputLevel" attribute to be set
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item Output::unsetId
Unsets the value of the "id" attribute of this Output.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item Output::unsetQualitativeSpecies
Unsets the value of the "qualitativeSpecies" attribute of this Output.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item Output::unsetTransitionEffect
Unsets the value of the "transitionEffect" attribute of this Output.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item Output::unsetName
Unsets the value of the "name" attribute of this Output.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item Output::unsetOutputLevel
Unsets the value of the "outputLevel" attribute of this Output.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item Output::renameSIdRefs
Renames all the C<SIdRef> attributes on this element, including any
found in MathML content (if such exists).
This method works by looking at all attributes and (if appropriate)
mathematical formulas, comparing the identifiers to the value of @p
oldid. If any matches are found, the matching identifiers are replaced
with C<newid>. The method does I<not> descend into child elements.
@param oldid the old identifier
@param newid the new identifier
=item Output::getElementName
Returns the XML element name of this object, which for Output, is
always C<"output">.
@return the name of this element, i.e. C<"output">.
=item Output::getTypeCode
Returns the libSBML type code of this object instance.
C<opydetails> doc_what_are_typecodes
@return the SBML type code for this object:
@link SBMLQualTypeCode_t#SBML_QUAL_OUTPUT SBML_QUAL_OUTPUT@endlink
C<opydetails> doc_warning_typecodes_not_unique
@see getElementName()
@see getPackageName()
=item Output::hasRequiredAttributes
Predicate returning C<true> if all the required attributes
for this Output object have been set.
@note The required attributes for a Output object are:
@li "qualitativeSpecies"
@li "transitionEffect"
@return a boolean value indicating whether all the required
attributes for this object have been defined.
=item Output::writeElements
@internal
Subclasses should override this method to write out their contained
SBML objects as XML elements. Be sure to call your parents
implementation of this method as well.
=item Output::accept
@internal
Accepts the given SBMLVisitor.
=item Output::setSBMLDocument
@internal
Sets the parent SBMLDocument.
=item Output::enablePackageInternal
@internal
Enables/Disables the given package with this element.
=item Output::addExpectedAttributes
@internal
Get the list of expected attributes for this element.
=item Output::readAttributes
@internal
Read values from the given XMLAttributes set into their specific fields.
=item Output::writeAttributes
@internal
Write values of XMLAttributes to the output stream.
=item ListOfOutputs::ListOfOutputs
Creates a new ListOfOutputs with the given level, version, and package version.
@param level an unsigned int, the SBML Level to assign to this ListOfOutputs
@param version an unsigned int, the SBML Version to assign to this ListOfOutputs
@param pkgVersion an unsigned int, the SBML Qual Version to assign to this ListOfOutputs
=item ListOfOutputs::ListOfOutputs
Creates a new ListOfOutputs with the given QualPkgNamespaces object.
@param qualns the QualPkgNamespaces object
=item ListOfOutputs::clone
Creates and returns a deep copy of this ListOfOutputs object.
@return a (deep) copy of this ListOfOutputs object.
=item ListOfOutputs::get
Get a Output from the ListOfOutputs.
@param n the index number of the Output to get.
@return the nth Output in this ListOfOutputs.
@see size()
=item ListOfOutputs::get
Get a Output from the ListOfOutputs.
@param n the index number of the Output to get.
@return the nth Output in this ListOfOutputs.
@see size()
=item ListOfOutputs::get
Get a Output from the ListOfOutputs
based on its identifier.
@param sid a string representing the identifier
of the Output to get.
@return Output in this ListOfOutputs
with the given id or NULL if no such
Output exists.
@see get(unsigned int n)
@see size()
=item ListOfOutputs::get
Get a Output from the ListOfOutputs
based on its identifier.
@param sid a string representing the identifier
of the Output to get.
@return Output in this ListOfOutputs
with the given id or NULL if no such
Output exists.
@see get(unsigned int n)
@see size()
=item ListOfOutputs::getBySpecies
Get a Output from the ListOfOutputs
based on the qualitativeSpecies to which it refers.
@param sid a string representing the qualitativeSpecies attribute
of the Output to get.
@return the first Output in this ListOfOutputs
with the given qualitativeSpecies or NULL if no such
Output exists.
@see get(unsigned int n)
@see size()
=item ListOfOutputs::getBySpecies
Get a Output from the ListOfOutputs
based on the qualitativeSpecies to which it refers.
@param sid a string representing the qualitativeSpecies attribute
of the Output to get.
@return the first Output in this ListOfOutputs
with the given qualitativeSpecies or NULL if no such
Output exists.
@see get(unsigned int n)
@see size()
=item ListOfOutputs::remove
Removes the nth Output from this ListOfOutputs
and returns a pointer to it.
The caller owns the returned item and is responsible for deleting it.
@param n the index of the Output to remove.
@see size()
=item ListOfOutputs::remove
Removes the Output from this ListOfOutputs with the given identifier
and returns a pointer to it.
The caller owns the returned item and is responsible for deleting it.
If none of the items in this list have the identifier C<sid>, then
C<NULL> is returned.
@param sid the identifier of the Output to remove.
@return the Output removed. As mentioned above, the caller owns the
returned item.
=item ListOfOutputs::getElementName
Returns the XML element name of this object, which for ListOfOutputs, is
always C<"listOfOutputs">.
@return the name of this element, i.e. C<"listOfOutputs">.
=item ListOfOutputs::getItemTypeCode
Returns the libSBML type code for the SBML objects
contained in this ListOf object.
C<opydetails> doc_what_are_typecodes
@return the SBML type code for objects contained in this list:
@link SBMLTypeCode_t#SBML_QUAL_OUTPUT SBML_QUAL_OUTPUT@endlink (default).
@see getElementName()
@see getPackageName()
=item ListOfOutputs::createObject
@internal
Creates a new Output in this ListOfOutputs
=item ListOfOutputs::writeXMLNS
@internal
Write the namespace for the Qual package.
=back
=head2 QualitativeSpecies
@sbmlpackage{qual}
@htmlinclude pkg-marker-qual.html The QualitativeSpecies class for the Qualitative Models
package.
Similarly to the Species in SBML, the components of qualitative models
refer to pools of entities that are considered indistinguishable and are
each located in a specific Compartment. However, here components are
characterised by their qualitative influences rather than by taking part
in reactions. Therefore, we define the QualitativeSpecies element to
represent such pools of entities.
In a Petri net, qualitative species refer to the places of the model,
while in a logical model, they refer to the variables of this model
(i.e. nodes of the influence graph).
A QualitativeSpecies describes a pool of indistinguishable entities in a
Compartment. It is associated with a level (an integer representing
e.g. an activity state, or a functional level of concentration, etc.)
=over
=back
=head2 ListOfQualitativeSpecies
@sbmlpackage{qual}
@htmlinclude pkg-marker-qual.html Implementation of the ListOfQualitativeSpecies construct
from the 'qual' package.
The ListOfQualitativeSpecies is a container for the QualitativeSpecies elements of a Model.
C<opydetails> doc_what_is_listof
@see QualitativeSpecies
=over
=item QualitativeSpecies::QualitativeSpecies
Creates a new QualitativeSpecies with the given level, version, and package version.
@param level an unsigned int, the SBML Level to assign to this QualitativeSpecies
@param version an unsigned int, the SBML Version to assign to this QualitativeSpecies
@param pkgVersion an unsigned int, the SBML Qual Version to assign to this QualitativeSpecies
=item QualitativeSpecies::QualitativeSpecies
Creates a new QualitativeSpecies with the given QualPkgNamespaces object.
@param qualns the QualPkgNamespaces object
=item QualitativeSpecies::QualitativeSpecies
Copy constructor for QualitativeSpecies.
@param orig the QualitativeSpecies instance to copy.
=item QualitativeSpecies::clone
Creates and returns a deep copy of this QualitativeSpecies object.
@return a (deep) copy of this QualitativeSpecies object.
=item QualitativeSpecies::getId
Returns the value of the "id" attribute of this QualitativeSpecies.
@return the value of the "id" attribute of this QualitativeSpecies as a string.
=item QualitativeSpecies::getCompartment
Returns the value of the "compartment" attribute of this QualitativeSpecies.
@return the value of the "compartment" attribute of this QualitativeSpecies as a string.
=item QualitativeSpecies::getConstant
Returns the value of the "constant" attribute of this QualitativeSpecies.
@return the value of the "constant" attribute of this QualitativeSpecies as a boolean.
=item QualitativeSpecies::getName
Returns the value of the "name" attribute of this QualitativeSpecies.
@return the value of the "name" attribute of this QualitativeSpecies as a string.
=item QualitativeSpecies::getInitialLevel
Returns the value of the "initialLevel" attribute of this QualitativeSpecies.
@return the value of the "initialLevel" attribute of this QualitativeSpecies as a integer.
=item QualitativeSpecies::getMaxLevel
Returns the value of the "maxLevel" attribute of this QualitativeSpecies.
@return the value of the "maxLevel" attribute of this QualitativeSpecies as a integer.
=item QualitativeSpecies::isSetId
Predicate returning C<true> or C<false> depending on whether this
QualitativeSpecies's "id" attribute has been set.
@return C<true> if this QualitativeSpecies's "id" attribute has been set,
otherwise C<false> is returned.
=item QualitativeSpecies::isSetCompartment
Predicate returning C<true> or C<false> depending on whether this
QualitativeSpecies's "compartment" attribute has been set.
@return C<true> if this QualitativeSpecies's "compartment" attribute has been set,
otherwise C<false> is returned.
=item QualitativeSpecies::isSetConstant
Predicate returning C<true> or C<false> depending on whether this
QualitativeSpecies's "constant" attribute has been set.
@return C<true> if this QualitativeSpecies's "constant" attribute has been set,
otherwise C<false> is returned.
=item QualitativeSpecies::isSetName
Predicate returning C<true> or C<false> depending on whether this
QualitativeSpecies's "name" attribute has been set.
@return C<true> if this QualitativeSpecies's "name" attribute has been set,
otherwise C<false> is returned.
=item QualitativeSpecies::isSetInitialLevel
Predicate returning C<true> or C<false> depending on whether this
QualitativeSpecies's "initialLevel" attribute has been set.
@return C<true> if this QualitativeSpecies's "initialLevel" attribute has been set,
otherwise C<false> is returned.
=item QualitativeSpecies::isSetMaxLevel
Predicate returning C<true> or C<false> depending on whether this
QualitativeSpecies's "maxLevel" attribute has been set.
@return C<true> if this QualitativeSpecies's "maxLevel" attribute has been set,
otherwise C<false> is returned.
=item QualitativeSpecies::setId
Sets the value of the "id" attribute of this QualitativeSpecies.
@param id const std::string& value of the "id" attribute to be set
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item QualitativeSpecies::setCompartment
Sets the value of the "compartment" attribute of this QualitativeSpecies.
@param compartment const std::string& value of the "compartment" attribute to be set
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item QualitativeSpecies::setConstant
Sets the value of the "constant" attribute of this QualitativeSpecies.
@param constant bool value of the "constant" attribute to be set
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item QualitativeSpecies::setName
Sets the value of the "name" attribute of this QualitativeSpecies.
@param name const std::string& value of the "name" attribute to be set
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item QualitativeSpecies::setInitialLevel
Sets the value of the "initialLevel" attribute of this QualitativeSpecies.
@param initialLevel int value of the "initialLevel" attribute to be set
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item QualitativeSpecies::setMaxLevel
Sets the value of the "maxLevel" attribute of this QualitativeSpecies.
@param maxLevel int value of the "maxLevel" attribute to be set
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item QualitativeSpecies::unsetId
Unsets the value of the "id" attribute of this QualitativeSpecies.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item QualitativeSpecies::unsetCompartment
Unsets the value of the "compartment" attribute of this QualitativeSpecies.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item QualitativeSpecies::unsetConstant
Unsets the value of the "constant" attribute of this QualitativeSpecies.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item QualitativeSpecies::unsetName
Unsets the value of the "name" attribute of this QualitativeSpecies.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item QualitativeSpecies::unsetInitialLevel
Unsets the value of the "initialLevel" attribute of this QualitativeSpecies.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item QualitativeSpecies::unsetMaxLevel
Unsets the value of the "maxLevel" attribute of this QualitativeSpecies.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item QualitativeSpecies::renameSIdRefs
Renames all the C<SIdRef> attributes on this element, including any
found in MathML content (if such exists).
This method works by looking at all attributes and (if appropriate)
mathematical formulas, comparing the identifiers to the value of @p
oldid. If any matches are found, the matching identifiers are replaced
with C<newid>. The method does I<not> descend into child elements.
@param oldid the old identifier
@param newid the new identifier
=item QualitativeSpecies::getElementName
Returns the XML element name of this object, which for QualitativeSpecies, is
always C<"qualitativeSpecies">.
@return the name of this element, i.e. C<"qualitativeSpecies">.
=item QualitativeSpecies::getTypeCode
Returns the libSBML type code of this object instance.
C<opydetails> doc_what_are_typecodes
@return the SBML type code for this object:
@link SBMLQualTypeCode_t#SBML_QUAL_QUALITATIVE_SPECIES SBML_QUAL_QUALITATIVE_SPECIES@endlink
C<opydetails> doc_warning_typecodes_not_unique
@see getElementName()
@see getPackageName()
=item QualitativeSpecies::hasRequiredAttributes
Predicate returning C<true> if all the required attributes
for this QualitativeSpecies object have been set.
@note The required attributes for a QualitativeSpecies object are:
@li "id"
@li "compartment"
@li "constant"
@return a boolean value indicating whether all the required
attributes for this object have been defined.
=item QualitativeSpecies::writeElements
@internal
Subclasses should override this method to write out their contained
SBML objects as XML elements. Be sure to call your parents
implementation of this method as well.
=item QualitativeSpecies::accept
@internal
Accepts the given SBMLVisitor.
=item QualitativeSpecies::setSBMLDocument
@internal
Sets the parent SBMLDocument.
=item QualitativeSpecies::enablePackageInternal
@internal
Enables/Disables the given package with this element.
=item QualitativeSpecies::addExpectedAttributes
@internal
Get the list of expected attributes for this element.
=item QualitativeSpecies::readAttributes
@internal
Read values from the given XMLAttributes set into their specific fields.
=item QualitativeSpecies::writeAttributes
@internal
Write values of XMLAttributes to the output stream.
=item ListOfQualitativeSpecies::ListOfQualitativeSpecies
Creates a new ListOfQualitativeSpecies with the given level, version, and package version.
@param level an unsigned int, the SBML Level to assign to this ListOfQualitativeSpecies
@param version an unsigned int, the SBML Version to assign to this ListOfQualitativeSpecies
@param pkgVersion an unsigned int, the SBML Qual Version to assign to this ListOfQualitativeSpecies
=item ListOfQualitativeSpecies::ListOfQualitativeSpecies
Creates a new ListOfQualitativeSpecies with the given QualPkgNamespaces object.
@param qualns the QualPkgNamespaces object
=item ListOfQualitativeSpecies::clone
Creates and returns a deep copy of this ListOfQualitativeSpecies object.
@return a (deep) copy of this ListOfQualitativeSpecies object.
=item ListOfQualitativeSpecies::get
Get a QualitativeSpecies from the ListOfQualitativeSpecies.
@param n the index number of the QualitativeSpecies to get.
@return the nth QualitativeSpecies in this ListOfQualitativeSpecies.
@see size()
=item ListOfQualitativeSpecies::get
Get a QualitativeSpecies from the ListOfQualitativeSpecies.
@param n the index number of the QualitativeSpecies to get.
@return the nth QualitativeSpecies in this ListOfQualitativeSpecies.
@see size()
=item ListOfQualitativeSpecies::get
Get a QualitativeSpecies from the ListOfQualitativeSpecies
based on its identifier.
@param sid a string representing the identifier
of the QualitativeSpecies to get.
@return QualitativeSpecies in this ListOfQualitativeSpecies
with the given id or NULL if no such
QualitativeSpecies exists.
@see get(unsigned int n)
@see size()
=item ListOfQualitativeSpecies::get
Get a QualitativeSpecies from the ListOfQualitativeSpecies
based on its identifier.
@param sid a string representing the identifier
of the QualitativeSpecies to get.
@return QualitativeSpecies in this ListOfQualitativeSpecies
with the given id or NULL if no such
QualitativeSpecies exists.
@see get(unsigned int n)
@see size()
=item ListOfQualitativeSpecies::remove
Removes the nth QualitativeSpecies from this ListOfQualitativeSpecies
and returns a pointer to it.
The caller owns the returned item and is responsible for deleting it.
@param n the index of the QualitativeSpecies to remove.
@see size()
=item ListOfQualitativeSpecies::remove
Removes the QualitativeSpecies from this ListOfQualitativeSpecies with the given identifier
and returns a pointer to it.
The caller owns the returned item and is responsible for deleting it.
If none of the items in this list have the identifier C<sid>, then
C<NULL> is returned.
@param sid the identifier of the QualitativeSpecies to remove.
@return the QualitativeSpecies removed. As mentioned above, the caller owns the
returned item.
=item ListOfQualitativeSpecies::getElementName
Returns the XML element name of this object, which for ListOfQualitativeSpecies, is
always C<"listOfQualitativeSpecies">.
@return the name of this element, i.e. C<"listOfQualitativeSpecies">.
=item ListOfQualitativeSpecies::getItemTypeCode
Returns the libSBML type code for the SBML objects
contained in this ListOf object.
C<opydetails> doc_what_are_typecodes
@return the SBML type code for objects contained in this list:
@link SBMLTypeCode_t#SBML_QUAL_QUALITATIVE_SPECIES SBML_QUAL_QUALITATIVE_SPECIES@endlink (default).
@see getElementName()
@see getPackageName()
=item ListOfQualitativeSpecies::createObject
@internal
Creates a new QualitativeSpecies in this ListOfQualitativeSpecies
=item ListOfQualitativeSpecies::writeXMLNS
@internal
Write the namespace for the Qual package.
=back
=head2 Transition
@sbmlpackage{qual}
@htmlinclude pkg-marker-qual.html The Transition class for the Qualitative Models package.
A Transition element contains at most one ListOfInputs and one
ListOfOutputs and exactly one ListOfFunctionTerms.
A Transition defines the changes in level associated with the
QualitativeSpecies that occur when a Transition is enabled.
In logical models, a Transition is used to specify the logical rule
associated with a QualitativeSpecies (that appears as an Output of this
Transition). For example, the rule "if A E<gt> 1 : B = 2" would be
encapsulated as a Transition with QualitativeSpecies "A" as an Input and
"B" as an Output; the "if A E<gt> 1" rule being encode by the math element of
a FunctionTerm with the resultLevel attribute having a value "2".
In Petri net models, a Transition is interpreted, using the common Petri
net semantics, as events that might occur within the system causing tokens
to be moved.
=over
=back
=head2 ListOfTransitions
@sbmlpackage{qual}
@htmlinclude pkg-marker-qual.html Implementation of the ListOfTransitions construct from
the 'qual' package.
The ListOfTransitions is a container for the Transition elements of a Model.
C<opydetails> doc_what_is_listof
@see Transition
=over
=item Transition::Transition
Creates a new Transition with the given level, version, and package version.
@param level an unsigned int, the SBML Level to assign to this Transition
@param version an unsigned int, the SBML Version to assign to this Transition
@param pkgVersion an unsigned int, the SBML Qual Version to assign to this Transition
=item Transition::Transition
Creates a new Transition with the given QualPkgNamespaces object.
@param qualns the QualPkgNamespaces object
=item Transition::Transition
Copy constructor for Transition.
@param orig the Transition instance to copy.
=item Transition::clone
Creates and returns a deep copy of this Transition object.
@return a (deep) copy of this Transition object.
=item Transition::getElementBySId
Returns the first child element found that has the given C<id>
in the model-wide SId namespace, or C<NULL> if no such object is found.
@param id string representing the id of objects to find
@return a pointer to the SBase element with the given C<id>.
=item Transition::getElementByMetaId
Returns the first child element it can find with the given C<metaid>,
or itself if it has the given C<metaid>, or C<NULL> if no such object
is found.
@param metaid string representing the metaid of objects to find
@return a pointer to the SBase element with the given C<metaid>.
=item Transition::getId
Returns the value of the "id" attribute of this Transition.
@return the value of the "id" attribute of this Transition as a string.
=item Transition::getName
Returns the value of the "name" attribute of this Transition.
@return the value of the "name" attribute of this Transition as a string.
=item Transition::isSetId
Predicate returning C<true> or C<false> depending on whether this
Transition's "id" attribute has been set.
@return C<true> if this Transition's "id" attribute has been set,
otherwise C<false> is returned.
=item Transition::isSetName
Predicate returning C<true> or C<false> depending on whether this
Transition's "name" attribute has been set.
@return C<true> if this Transition's "name" attribute has been set,
otherwise C<false> is returned.
=item Transition::setId
Sets the value of the "id" attribute of this Transition.
@param id const std::string& value of the "id" attribute to be set
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item Transition::setName
Sets the value of the "name" attribute of this Transition.
@param name const std::string& value of the "name" attribute to be set
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item Transition::unsetId
Unsets the value of the "id" attribute of this Transition.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item Transition::unsetName
Unsets the value of the "name" attribute of this Transition.
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
=item Transition::getListOfInputs
Returns the "ListOfInputs" in this Transition object.
@return the "ListOfInputs" attribute of this Transition.
=item Transition::getListOfInputs
Returns the "ListOfInputs" in this Transition object.
@return the "ListOfInputs" attribute of this Transition.
=item Transition::getInput
Get a Input from the ListOfInputs.
@param n the index number of the Input to get.
@return the nth Input in the ListOfInputs within this Transition.
@see getNumInputs()
=item Transition::getInput
Get a Input from the ListOfInputs.
@param n the index number of the Input to get.
@return the nth Input in the ListOfInputs within this Transition.
@see getNumInputs()
=item Transition::getInput
Get a Input from the ListOfInputs
based on its identifier.
@param sid a string representing the identifier
of the Input to get.
@return the Input in the ListOfInputs
with the given id or NULL if no such
Input exists.
@see getInput(unsigned int n)
@see getNumInputs()
=item Transition::getInput
Get a Input from the ListOfInputs
based on its identifier.
@param sid a string representing the identifier
of the Input to get.
@return the Input in the ListOfInputs
with the given id or NULL if no such
Input exists.
@see getInput(unsigned int n)
@see getNumInputs()
=item Transition::getInputBySpecies
Get a Input from the ListOfInputs
based on its qualitativeSpecies attribute.
@param sid a string representing the qualitativeSpecies
of the Input to get.
@return the first Input in the ListOfInputs
with the given qualitativeSpecies or NULL if no such
Input exists.
@see getInput(unsigned int n)
@see getNumInputs()
=item Transition::getInputBySpecies
Get a Input from the ListOfInputs
based on its qualitativeSpecies attribute.
@param sid a string representing the qualitativeSpecies
of the Input to get.
@return the first Input in the ListOfInputs
with the given qualitativeSpecies or NULL if no such
Input exists.
@see getInput(unsigned int n)
@see getNumInputs()
=item Transition::addInput
Adds a copy the given "Input" to this Transition.
@param i the Input object to add
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item Transition::getNumInputs
Get the number of Input objects in this Transition.
@return the number of Input objects in this Transition
=item Transition::createInput
Creates a new Input object, adds it to this Transitions
ListOfInputs and returns the Input object created.
@return a new Input object instance
@see addInput(const Input i)
=item Transition::removeInput
Removes the nth Input from the ListOfInputs within this Transition.
and returns a pointer to it.
The caller owns the returned item and is responsible for deleting it.
@param n the index of the Input to remove.
@see getNumInputs()
=item Transition::removeInput
Removes the Input with the given identifier from the ListOfInputs within this Transition
and returns a pointer to it.
The caller owns the returned item and is responsible for deleting it.
If none of the items in this list have the identifier C<sid>, then
C<NULL> is returned.
@param sid the identifier of the Input to remove.
@return the Input removed. As mentioned above, the caller owns the
returned item.
=item Transition::getListOfOutputs
Returns the "ListOfOutputs" in this Transition object.
@return the "ListOfOutputs" attribute of this Transition.
=item Transition::getListOfOutputs
Returns the "ListOfOutputs" in this Transition object.
@return the "ListOfOutputs" attribute of this Transition.
=item Transition::getOutput
Get a Output from the ListOfOutputs.
@param n the index number of the Output to get.
@return the nth Output in the ListOfOutputs within this Transition.
@see getNumOutputs()
=item Transition::getOutput
Get a Output from the ListOfOutputs.
@param n the index number of the Output to get.
@return the nth Output in the ListOfOutputs within this Transition.
@see getNumOutputs()
=item Transition::getOutput
Get a Output from the ListOfOutputs
based on its identifier.
@param sid a string representing the identifier
of the Output to get.
@return the Output in the ListOfOutputs
with the given id or NULL if no such
Output exists.
@see getOutput(unsigned int n)
@see getNumOutputs()
=item Transition::getOutput
Get a Output from the ListOfOutputs
based on its identifier.
@param sid a string representing the identifier
of the Output to get.
@return the Output in the ListOfOutputs
with the given id or NULL if no such
Output exists.
@see getOutput(unsigned int n)
@see getNumOutputs()
=item Transition::getOutputBySpecies
Get a Output from the ListOfOutputs
based on its qualitativeSpecies attribute.
@param sid a string representing the qualitativeSpecies
of the Output to get.
@return the first Output in the ListOfOutputs
with the given qualitativeSpecies or NULL if no such
Output exists.
@see getOutput(unsigned int n)
@see getNumOutputs()
=item Transition::getOutputBySpecies
Get a Output from the ListOfOutputs
based on its qualitativeSpecies attribute.
@param sid a string representing the qualitativeSpecies
of the Output to get.
@return the first Output in the ListOfOutputs
with the given qualitativeSpecies or NULL if no such
Output exists.
@see getOutput(unsigned int n)
@see getNumOutputs()
=item Transition::addOutput
Adds a copy the given "Output" to this Transition.
@param o the Output object to add
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item Transition::getNumOutputs
Get the number of Output objects in this Transition.
@return the number of Output objects in this Transition
=item Transition::createOutput
Creates a new Output object, adds it to this Transitions
ListOfOutputs and returns the Output object created.
@return a new Output object instance
@see addOutput(const Output o)
=item Transition::removeOutput
Removes the nth Output from the ListOfOutputs within this Transition.
and returns a pointer to it.
The caller owns the returned item and is responsible for deleting it.
@param n the index of the Output to remove.
@see getNumOutputs()
=item Transition::removeOutput
Removes the Output with the given identifier from the ListOfOutputs within this Transition
and returns a pointer to it.
The caller owns the returned item and is responsible for deleting it.
If none of the items in this list have the identifier C<sid>, then
C<NULL> is returned.
@param sid the identifier of the Output to remove.
@return the Output removed. As mentioned above, the caller owns the
returned item.
=item Transition::getListOfFunctionTerms
Returns the "ListOfFunctionTerms" in this Transition object.
@return the "ListOfFunctionTerms" attribute of this Transition.
=item Transition::getListOfFunctionTerms
Returns the "ListOfFunctionTerms" in this Transition object.
@return the "ListOfFunctionTerms" attribute of this Transition.
=item Transition::getFunctionTerm
Get a FunctionTerm from the ListOfFunctionTerms.
@param n the index number of the FunctionTerm to get.
@return the nth FunctionTerm in the ListOfFunctionTerms within this Transition.
@see getNumFunctionTerms()
=item Transition::getFunctionTerm
Get a FunctionTerm from the ListOfFunctionTerms.
@param n the index number of the FunctionTerm to get.
@return the nth FunctionTerm in the ListOfFunctionTerms within this Transition.
@see getNumFunctionTerms()
=item Transition::getFunctionTerm
Get a FunctionTerm from the ListOfFunctionTerms
based on its identifier.
@param sid a string representing the identifier
of the FunctionTerm to get.
@return the FunctionTerm in the ListOfFunctionTerms
with the given id or NULL if no such
FunctionTerm exists.
@see getFunctionTerm(unsigned int n)
@see getNumFunctionTerms()
=item Transition::getFunctionTerm
Get a FunctionTerm from the ListOfFunctionTerms
based on its identifier.
@param sid a string representing the identifier
of the FunctionTerm to get.
@return the FunctionTerm in the ListOfFunctionTerms
with the given id or NULL if no such
FunctionTerm exists.
@see getFunctionTerm(unsigned int n)
@see getNumFunctionTerms()
=item Transition::addFunctionTerm
Adds a copy the given "FunctionTerm" to this Transition.
@param ft the FunctionTerm object to add
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item Transition::getNumFunctionTerms
Get the number of FunctionTerm objects in this Transition.
@return the number of FunctionTerm objects in this Transition
=item Transition::createFunctionTerm
Creates a new FunctionTerm object, adds it to this Transitions
ListOfFunctionTerms and returns the FunctionTerm object created.
@return a new FunctionTerm object instance
@see addFunctionTerm(const FunctionTerm ft)
=item Transition::removeFunctionTerm
Removes the nth FunctionTerm from the ListOfFunctionTerms within this Transition.
and returns a pointer to it.
The caller owns the returned item and is responsible for deleting it.
@param n the index of the FunctionTerm to remove.
@see getNumFunctionTerms()
=item Transition::removeFunctionTerm
Removes the FunctionTerm with the given identifier from the ListOfFunctionTerms within this Transition
and returns a pointer to it.
The caller owns the returned item and is responsible for deleting it.
If none of the items in this list have the identifier C<sid>, then
C<NULL> is returned.
@param sid the identifier of the FunctionTerm to remove.
@return the FunctionTerm removed. As mentioned above, the caller owns the
returned item.
=item Transition::createDefaultTerm
Creates a new DefaultTerm object, adds it to this Transitions
ListOfFunctionTerms and returns the DefaultTerm object created.
@return a new DefaultTerm object instance
@see setDefaultTerm(const DefaultTerm ft)
=item Transition::setDefaultTerm
Sets the given "DefaultTerm" to this Transition.
@param dt the DefaultTerm object to add
@return integer value indicating success/failure of the
operation. The possible return values are:
@li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
=item Transition::isSetDefaultTerm
Predicate returning C<true> if the defaultTerm
for this Transition object has been set.
@return a boolean value indicating whether the defaultTerm
child for this object has been defined.
=item Transition::getDefaultTerm
Get the DefaultTerm from the ListOfFunctionTerms.
@return the DefaultTerm in the ListOfFunctionTerms within this Transition, or NULL if no such value is set.
=item Transition::getDefaultTerm
Get the DefaultTerm from the ListOfFunctionTerms.
@return the DefaultTerm in the ListOfFunctionTerms within this Transition, or NULL if no such value is set.
=item Transition::getAllElements
Returns a List of all child SBase objects, including those nested to an
arbitary depth.
@return a List of pointers to all child objects.
=item Transition::getElementName
Returns the XML element name of this object, which for Transition, is
always C<"transition">.
@return the name of this element, i.e. C<"transition">.
=item Transition::getTypeCode
Returns the libSBML type code of this object instance.
C<opydetails> doc_what_are_typecodes
@return the SBML type code for this object:
@link SBMLQualTypeCode_t#SBML_QUAL_TRANSITION SBML_QUAL_TRANSITION@endlink
C<opydetails> doc_warning_typecodes_not_unique
@see getElementName()
@see getPackageName()
=item Transition::hasRequiredAttributes
Predicate returning C<true> if all the required attributes
for this Transition object have been set.
@note The required attributes for a Transition object are:
@li "output"
@return a boolean value indicating whether all the required
attributes for this object have been defined.
=item Transition::hasRequiredElements
Predicate returning C<true> if all the required attributes
for this Transition object have been set.
@note The required elements for a Transition object are:
@li "output"
@return a boolean value indicating whether all the required
elements for this object have been defined.
=item Transition::writeElements
@internal
Subclasses should override this method to write out their contained
SBML objects as XML elements. Be sure to call your parents
implementation of this method as well.
=item Transition::accept
@internal
Accepts the given SBMLVisitor.
=item Transition::setSBMLDocument
@internal
Sets the parent SBMLDocument.
=item Transition::connectToChild
@internal
Connects to child elements.
=item Transition::enablePackageInternal
@internal
Enables/Disables the given package with this element.
=item Transition::createObject
@internal
Create and return an SBML object of this class, if present.
@return the SBML object corresponding to next XMLToken in the
XMLInputStream or C<NULL> if the token was not recognized.
=item Transition::addExpectedAttributes
@internal
Get the list of expected attributes for this element.
=item Transition::readAttributes
@internal
Read values from the given XMLAttributes set into their specific fields.
=item Transition::writeAttributes
@internal
Write values of XMLAttributes to the output stream.
=item ListOfTransitions::ListOfTransitions
Creates a new ListOfTransitions with the given level, version, and package version.
@param level an unsigned int, the SBML Level to assign to this ListOfTransitions
@param version an unsigned int, the SBML Version to assign to this ListOfTransitions
@param pkgVersion an unsigned int, the SBML Qual Version to assign to this ListOfTransitions
=item ListOfTransitions::ListOfTransitions
Creates a new ListOfTransitions with the given QualPkgNamespaces object.
@param qualns the QualPkgNamespaces object
=item ListOfTransitions::clone
Creates and returns a deep copy of this ListOfTransitions object.
@return a (deep) copy of this ListOfTransitions object.
=item ListOfTransitions::get
Get a Transition from the ListOfTransitions.
@param n the index number of the Transition to get.
@return the nth Transition in this ListOfTransitions.
@see size()
=item ListOfTransitions::get
Get a Transition from the ListOfTransitions.
@param n the index number of the Transition to get.
@return the nth Transition in this ListOfTransitions.
@see size()
=item ListOfTransitions::get
Get a Transition from the ListOfTransitions
based on its identifier.
@param sid a string representing the identifier
of the Transition to get.
@return Transition in this ListOfTransitions
with the given id or NULL if no such
Transition exists.
@see get(unsigned int n)
@see size()
=item ListOfTransitions::get
Get a Transition from the ListOfTransitions
based on its identifier.
@param sid a string representing the identifier
of the Transition to get.
@return Transition in this ListOfTransitions
with the given id or NULL if no such
Transition exists.
@see get(unsigned int n)
@see size()
=item ListOfTransitions::remove
Removes the nth Transition from this ListOfTransitions
and returns a pointer to it.
The caller owns the returned item and is responsible for deleting it.
@param n the index of the Transition to remove.
@see size()
=item ListOfTransitions::remove
Removes the Transition from this ListOfTransitions with the given identifier
and returns a pointer to it.
The caller owns the returned item and is responsible for deleting it.
If none of the items in this list have the identifier C<sid>, then
C<NULL> is returned.
@param sid the identifier of the Transition to remove.
@return the Transition removed. As mentioned above, the caller owns the
returned item.
=item ListOfTransitions::getElementName
Returns the XML element name of this object, which for ListOfTransitions, is
always C<"listOfTransitions">.
@return the name of this element, i.e. C<"listOfTransitions">.
=item ListOfTransitions::getItemTypeCode
Returns the libSBML type code for the SBML objects
contained in this ListOf object.
C<opydetails> doc_what_are_typecodes
@return the SBML type code for objects contained in this list:
@link SBMLTypeCode_t#SBML_QUAL_TRANSITION SBML_QUAL_TRANSITION@endlink (default).
@see getElementName()
@see getPackageName()
=item ListOfTransitions::createObject
@internal
Creates a new Transition in this ListOfTransitions
=item ListOfTransitions::writeXMLNS
@internal
Write the namespace for the Qual package.
=cut
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