/usr/include/libmstoolkit/mzMLWriter.h is in libmstoolkit-dev 82-6.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 | /*
Copyright 2005-2016, Michael R. Hoopmann
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
*/
#ifndef _MZMLWRITER_H
#define _MZMLWRITER_H
#include <string>
#include <iostream>
#include "MSObject.h"
#include "MSReader.h"
#include "Spectrum.h"
#include "mzParser.h"
using namespace std;
namespace MSToolkit {
typedef struct sMzMLIndex{
string id;
f_off offset;
} sMzMLIndex;
class MzMLWriter {
public:
MzMLWriter();
~MzMLWriter();
bool closeList(); //false is chromatogram list
bool closeMzML();
bool createList(bool specList=true); //false is chromatogram list
bool createMzML(char* fn);
int checkState();
void setNumpress(bool b);
void setTabs(bool b);
void setZlib(bool b);
bool writeRunInformation();
bool writeSpectra(MSObject& o);
bool writeSpectra(Spectrum& s);
bool writeChromatogram(BasicChromatogram& c);
bool writeIndex();
private:
bool exportActivation(Spectrum& s, int tabs=0);
bool exportAnalyzer();
bool exportBinary(char* str, int len, int tabs=0);
bool exportBinaryDataArray(BasicChromatogram& c, bool bRT, int tabs = 0);
bool exportBinaryDataArray(Spectrum& s, bool bMZ, int tabs=0);
bool exportBinaryDataArrayList(BasicChromatogram& c, int tabs = 0);
bool exportBinaryDataArrayList(Spectrum& s, int tabs=0);
bool exportChromatogram(BasicChromatogram& c, int tabs);
bool exportChromatogramList();
bool exportComponentList();
bool exportContact();
bool exportCv();
bool exportCvList();
bool exportCvParam(string ac, string ref, string name, string unitAc="", string unitRef="", string unitName="", string value="", int tabs=0);
bool exportDataProcessing();
bool exportDataProcessingList();
bool exportFileContent();
bool exportFileDescription();
bool exportInstrumentConfiguration();
bool exportInstrumentConfigurationList();
bool exportIsolationWindow(BasicChromatogram& c, bool bPre, int tabs = 0);
bool exportIsolationWindow(Spectrum& s, int tabs=0);
bool exportMzML();
bool exportOffset(string idRef, f_off offset, int tabs=0);
bool exportPrecursor(BasicChromatogram& c, int tabs = 0);
bool exportPrecursor(Spectrum& s, int tabs=0);
bool exportPrecursorList(Spectrum& s, int tabs=0);
bool exportProcessingMethod();
bool exportProduct(BasicChromatogram&c, int tabs = 0);
bool exportProductList();
bool exportReferencableParamGroup();
bool exportReferenceableParamGroupList();
bool exportReferenceableParamGroupRef();
bool exportRun();
bool exportSample();
bool exportSampleList();
bool exportScan(Spectrum& s, int tabs=0);
bool exportScanList(Spectrum& s, int tabs=0);
bool exportScanSettings();
bool exportScanSettingsList();
bool exportScanWindow(Spectrum& s, int tabs = 0);
bool exportScanWindowList(Spectrum& s, int tabs = 0);
bool exportSelectedIon(BasicChromatogram& c, int tabs = 0);
bool exportSelectedIon(Spectrum& s, int tabs=0);
bool exportSelectedIonList(BasicChromatogram& c, int tabs = 0);
bool exportSelectedIonList(Spectrum& s, int tabs=0);
bool exportSoftware();
bool exportSoftwareList();
bool exportSoftwareRef();
bool exportSource();
bool exportSouceFile();
bool exportSourceFileList();
bool exportSourceFileRef();
bool exportSourceFileRefList();
bool exportSpectrum(Spectrum& s, int tabs=0);
bool exportSpectrumList();
void exportTabs(int tabs);
bool exportTarget();
bool exportTargetList();
bool exportDetector();
bool exportUserParam();
int index;
int chromIndex;
FILE* fptr;
f_off fSpecList;
f_off fChromList;
int iSpecList;
int iChromList;
bool bTabs;
bool bFileOpen;
bool bZlib;
bool bNumpress;
vector<sMzMLIndex> vIndex;
vector<sMzMLIndex> vChromIndex;
};
}
#endif
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