/usr/include/libmstoolkit/MSReader.h is in libmstoolkit-dev 77.0.0-1.
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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 | #ifndef _MSREADER_H
#define _MSREADER_H
#include "Spectrum.h"
#include "MSObject.h"
#include "mzParser.h"
#include <cstring>
#include <algorithm>
#include <cstdio>
#include <cstdlib>
//For mzXML Writing
//#include "mzXMLWriter.h"
//#include "MSToolkitInterface.h"
#ifdef _MSC_VER
//#include <atlstr.h>
//#import "XRawfile2.dll" rename_namespace("XRawfile")
//using namespace XRAWFILE2Lib;
//Explicit path is needed on systems where Xcalibur installs with errors
//For example, Vista-64bit
//#import "C:\Xcalibur\system\programs\XRawfile2.dll"
#import "MSFileReader.XRawfile2.dll" rename_namespace("XRawfile")
using namespace XRawfile;
#endif
#ifndef _NOSQLITE
#include <sqlite3.h>
#endif
//Macros for 64-bit file support
#ifdef _MSC_VER
#include "RAWReader.h"
//extern "C" int __cdecl _fseeki64(FILE *, __int64, int);
//extern "C" __int64 __cdecl _ftelli64(FILE *);
typedef __int64 f_off;
#define fseek(h,p,o) _fseeki64(h,p,o)
#define ftell(h) _ftelli64(h)
#else
#ifndef _LARGEFILE_SOURCE
#error "need to define _LARGEFILE_SOURCE!!"
#endif /* end _LARGEFILE_SOURCE */
typedef off_t f_off;
#define fseek(h,p,o) fseeko(h,p,o)
#define ftell(h) ftello(h)
#endif /* end _MSC_VER */
using namespace std;
namespace MSToolkit {
class MSReader {
public:
//Constructors & Destructors
MSReader();
~MSReader();
//Functions
void addFilter(MSSpectrumType m);
void appendFile(char* c, bool text, Spectrum& s);
void appendFile(char* c, bool text, MSObject& m);
void appendFile(char* c, Spectrum& s);
void appendFile(char* c, MSObject& m);
MSFileFormat checkFileFormat(const char *fn);
MSSpectrumType getFileType();
MSHeader& getHeader();
void getInstrument(char* str);
int getLastScan();
void getManufacturer(char* str);
int getPercent();
//get specific header informations
void setPrecision(int i, int j);
void setPrecisionInt(int i);
void setPrecisionMZ(int i);
void writeFile(const char* c, bool text, MSObject& m);
void writeFile(const char* c, MSFileFormat ff, MSObject& m, char* sha1Report='\0');
bool readMSTFile(const char* c, bool text, Spectrum& s, int scNum=0);
bool readMZPFile(const char* c, Spectrum& s, int scNum=0);
bool readFile(const char* c, Spectrum& s, int scNum=0);
void setFilter(vector<MSSpectrumType>& m);
void setFilter(MSSpectrumType m);
//For RAW files
bool lookupRT(char* c, int scanNum, float& rt);
void setAverageRaw(bool b, int width=1, long cutoff=1000);
void setLabel(bool b); //label data contains all centroids (including noise and excluded peaks)
void setRawFilter(char* c);
void setRawFilterExact(bool b);
//For MGF files
void setHighResMGF(bool b);
//File compression
void setCompression(bool b);
//for Sqlite
void createIndex();
protected:
private:
//Data Members
FILE *fileIn;
MSHeader header;
int headerIndex;
MSSpectrumType fileType;
f_off lEnd;
f_off lPivot;
f_off lFWidth;
int iIntensityPrecision;
int iMZPrecision;
int iVersion;
int iFType;
MSFileFormat lastFileFormat;
string sInstrument;
string sManufacturer;
//File compression
bool compressMe;
//mzXML support variables;
ramp_fileoffset_t *pScanIndex;
RAMPFILE *rampFileIn;
bool rampFileOpen;
int rampLastScan;
int rampIndex;
vector<MSSpectrumType> filter;
//for RAW file support (even if not on windows)
bool rawFileOpen;
//for mgf output
bool exportMGF;
bool highResMGF;
//Functions
void closeFile();
int openFile(const char* c, bool text=false);
bool findSpectrum(int i);
void readCompressSpec(FILE* fileIn, MSScanInfo& ms, Spectrum& s);
void readSpecHeader(FILE* fileIn, MSScanInfo& ms);
void writeBinarySpec(FILE* fileOut, Spectrum& s);
void writeCompressSpec(FILE* fileOut, Spectrum& s);
void writeTextSpec(FILE* fileOut, Spectrum& s);
void writeSpecHeader(FILE* fileOut, bool text, Spectrum& s);
//support for rawfiles
#ifdef _MSC_VER
RAWReader cRAW;
#endif
//support for sqlite
#ifndef _NOSQLITE
bool readSqlite(const char* c, Spectrum& s, int scNum);
void getUncompressedPeaks(Spectrum& s, int& numPeaks, int& mzLen, unsigned char* comprM, int& intensityLen, unsigned char* comprI);
int curIndex; //remember where we are
int lastScanNumber;
int lastIndex;
sqlite3* db;
void sql_stmt(const char* stmt);
bool executeSqlStmt(Spectrum& s, char* zSql);
void appendFile(Spectrum& s);
void writeSqlite(const char* c, MSObject& m, char* sha1Report);
void readChargeTable(int scanID, Spectrum& s);
vector<int> estimateCharge(Spectrum& s);
#endif
};
}
#endif
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