/usr/include/libmstoolkit/mzParser.h is in libmstoolkit-dev 77.0.0-1.
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1422 1423 1424 1425 1426 1427 1428 1429 1430 1431 1432 1433 1434 1435 1436 1437 | /*
mzParser - This distribution contains novel code
and publicly available open source utilities. The novel code is
open source under the FreeBSD License, please see LICENSE file
for detailed information.
Copyright (C) 2011, Mike Hoopmann, Institute for Systems Biology
Version 1.0, January 4, 2011.
Version 1.1, March 14, 2012.
Additional code/libraries obtained from:
X!Tandem 2010.12.01: http://thegpm.org/
Copyright and license information for these free utilities are
provided in the LICENSE file. Note that many changes were made
to the code adapted from X!Tandem.
*/
#ifndef _MZPARSER_H
#define _MZPARSER_H
//------------------------------------------------
// Standard libraries
//------------------------------------------------
#include <vector>
#include <map>
#include <stdio.h>
#include <iostream>
#include <string>
#include <string.h>
#include "expat.h"
#include "zlib.h"
#include "MSNumpress.hpp"
#ifdef MZP_MZ5
#include "hdf5.h"
#include "H5Cpp.h"
#endif
using namespace std;
#ifdef MZP_MZ5
using namespace H5;
#endif
//------------------------------------------------
// MACROS
//------------------------------------------------
//#define OSX // to compile with cc on Macintosh OSX
//#define OSX_TIGER // use with OSX if OSX Tiger is being used
//#define OSX_INTEL // compile with cc on Macintosh OSX on Intel-style processors
//#define GCC // to compile with gcc (or g++) on LINUX
//#define __LINUX__ // to compile with gcc (or g++) on LINUX
//#define _MSC_VER // to compile with Microsoft Studio
#define XMLCLASS
#ifndef XML_STATIC
#define XML_STATIC // to statically link the expat libraries
#endif
//For Windows
#ifdef _MSC_VER
#define __inline__ _inline
typedef _int64 __int64_t;
typedef unsigned _int32 uint32_t;
typedef unsigned _int64 uint64_t;
typedef __int64 f_off;
#define mzpfseek(h,p,o) _fseeki64(h,p,o)
#define mzpftell(h) _ftelli64(h)
#define mzpatoi64(h) _atoi64(h)
#endif
//For Windows
#ifdef __MINGW__
#undef GCC
typedef __int64 f_off;
#define __int64_t int64_t
#define mzpfseek(h,p,o) fseeko64(h,p,o)
#define mzpftell(h) ftello64(h)
#define mzpatoi64(h) _atoi64(h)
#include <stdexcept>
#endif
#if defined(GCC) || defined(__LINUX__)
#include <stdint.h>
#include <stdexcept>
#ifndef _LARGEFILE_SOURCE
#error "need to define _LARGEFILE_SOURCE!!"
#endif /* end _LARGEFILE_SOURCE */
#if _FILE_OFFSET_BITS<64
#error "need to define _FILE_OFFSET_BITS=64"
#endif
typedef off_t f_off;
#define mzpfseek(h,p,o) fseeko(h,p,o)
#define mzpftell(h) ftello(h)
#define mzpatoi64(h) atoll(h)
#endif
#ifdef OSX
#define __inline__ inline
#ifndef OSX_TIGER
#define __int64_t int64_t
#endif
#endif
// this define for the INTEL-based OSX platform is untested and may not work
#ifdef OSX_INTEL
#define __inline__ inline
#endif
// this define should work for most LINUX and UNIX platforms
//------------------------------------------------
// mzMLParser structures, definitions, and enums
//------------------------------------------------
//specDP (Spectrum Data Point) is the basic content element of a mass spectrum.
typedef struct specDP{
double mz;
double intensity;
} specDP;
typedef struct TimeIntensityPair{
double time;
double intensity;
} TimeIntensityPair;
enum enumActivation {
none=0,
CID=1,
HCD=2,
ETD=3,
ETDSA=4,
ECD=5,
};
//------------------------------------------------
// mzMLParser classes
//------------------------------------------------
//For holding mzML and mzXML indexes
class cindex {
public:
static int compare (const void* a, const void* b) {
if( *(int*)a < *(int*)b ) return -1;
if( *(int*)a > *(int*)b ) return 1;
return 0;
}
int scanNum;
string idRef;
f_off offset;
};
//For instrument information
class instrumentInfo {
public:
string analyzer;
string detector;
string id;
string ionization;
string manufacturer;
string model;
instrumentInfo(){
analyzer="";
detector="";
id="";
ionization="";
manufacturer="";
model="";
}
void clear(){
analyzer="";
detector="";
id="";
ionization="";
manufacturer="";
model="";
}
};
class BasicSpectrum {
public:
//Constructors & Destructors
BasicSpectrum();
BasicSpectrum(const BasicSpectrum& s);
~BasicSpectrum();
//Operator overloads
BasicSpectrum& operator=(const BasicSpectrum& s);
specDP& operator[ ](const unsigned int index);
//Modifiers
void addDP(specDP dp);
void clear();
void setActivation(int a);
void setBasePeakIntensity(double d);
void setBasePeakMZ(double d);
void setCentroid(bool b);
void setCollisionEnergy(double d);
void setCompensationVoltage(double d);
void setFilterLine(char* str);
void setHighMZ(double d);
void setIDString(char* str);
void setLowMZ(double d);
void setMSLevel(int level);
void setPeaksCount(int i);
void setPositiveScan(bool b);
void setPrecursorCharge(int z);
void setPrecursorIntensity(double d);
void setPrecursorMonoMZ(double mz);
void setPrecursorMZ(double mz);
void setPrecursorScanNum(int i);
void setRTime(float t);
void setScanIndex(int num);
void setScanNum(int num);
void setTotalIonCurrent(double d);
//Accessors
int getActivation();
double getBasePeakIntensity();
double getBasePeakMZ();
bool getCentroid();
double getCollisionEnergy();
double getCompensationVoltage();
int getFilterLine(char* str);
double getHighMZ();
int getIDString(char* str);
double getLowMZ();
int getMSLevel();
int getPeaksCount();
bool getPositiveScan();
int getPrecursorCharge();
double getPrecursorIntensity();
double getPrecursorMonoMZ();
double getPrecursorMZ();
int getPrecursorScanNum();
float getRTime(bool min=true);
int getScanIndex();
int getScanNum();
double getTotalIonCurrent();
unsigned int size();
protected:
//Data Members (protected)
int activation;
double basePeakIntensity;
double basePeakMZ;
bool centroid;
double collisionEnergy;
double compensationVoltage; //FAIMS compensation voltage
char filterLine[128];
double highMZ;
char idString[128];
double lowMZ;
int msLevel;
int peaksCount;
bool positiveScan;
int precursorCharge; //Precursor ion charge; 0 if no precursor or unknown
double precursorIntensity; //Precursor ion intensity; 0 if no precursor or unknown
double precursorMonoMZ; //Might be reported in Thermo data
double precursorMZ; //Precursor ion m/z value; 0 if no precursor or unknown
int precursorScanNum; //Precursor scan number; 0 if no precursor or unknown
float rTime; //always stored in minutes
int scanIndex; //when scan numbers aren't enough, there are indexes (start at 1)
int scanNum; //identifying scan number
double totalIonCurrent;
vector<specDP> vData; //Spectrum data points
};
class BasicChromatogram {
public:
//Constructors & Destructors
BasicChromatogram();
BasicChromatogram(const BasicChromatogram& c);
~BasicChromatogram();
//Operator overloads
BasicChromatogram& operator=(const BasicChromatogram& c);
TimeIntensityPair& operator[ ](const unsigned int index);
//Modifiers
void addTIP(TimeIntensityPair tip);
void clear();
void setIDString(char* str);
//Accessors
vector<TimeIntensityPair>& getData();
int getIDString(char* str);
unsigned int size();
protected:
//Data Members (protected)
char idString[128];
vector<TimeIntensityPair> vData; //Chromatogram data points
};
//------------------------------------------------
// Random access gz (zran from zlib source code)
//------------------------------------------------
#define SPAN 1048576L // desired distance between access points
#define WINSIZE 32768U // sliding window size
#define CHUNK 32768 // file input buffer size
#define READCHUNK 16384
// access point entry
typedef struct point {
f_off out; // corresponding offset in uncompressed data
f_off in; // offset in input file of first full byte
int bits; // number of bits (1-7) from byte at in - 1, or 0
unsigned char window[WINSIZE]; // preceding 32K of uncompressed data
} point;
// access point list
typedef struct gz_access {
int have; // number of list entries filled in
int size; // number of list entries allocated
point *list; // allocated list
} gz_access;
class Czran{
public:
Czran();
~Czran();
void free_index();
gz_access *addpoint(int bits, f_off in, f_off out, unsigned left, unsigned char *window);
int build_index(FILE *in, f_off span);
int build_index(FILE *in, f_off span, gz_access **built);
int extract(FILE *in, f_off offset, unsigned char *buf, int len);
int extract(FILE *in, f_off offset);
f_off getfilesize();
protected:
private:
gz_access* index;
unsigned char* buffer;
f_off bufferOffset;
int bufferLen;
unsigned char* lastBuffer;
f_off lastBufferOffset;
int lastBufferLen;
f_off fileSize;
};
//------------------------------------------------
// X!Tandem borrowed headers
//------------------------------------------------
int b64_decode_mio (char *dest, char *src, size_t size);
class mzpSAXHandler{
public:
// SAXHandler constructors and destructors
mzpSAXHandler();
virtual ~mzpSAXHandler();
// SAXHandler eXpat event handlers
virtual void startElement(const XML_Char *el, const XML_Char **attr);
virtual void endElement(const XML_Char *el);
virtual void characters(const XML_Char *s, int len);
// SAXHandler Parsing functions.
bool open(const char* fileName);
bool parse();
bool parseOffset(f_off offset);
void setGZCompression(bool b);
inline void setFileName(const char* fileName) {
m_strFileName = fileName;
}
// SAXHandler helper functions
inline bool isElement(const char *n1, const XML_Char *n2)
{ return (strcmp(n1, n2) == 0); }
inline bool isAttr(const char *n1, const XML_Char *n2)
{ return (strcmp(n1, n2) == 0); }
inline const char* getAttrValue(const char* name, const XML_Char **attr) {
for (int i = 0; attr[i]; i += 2) {
if (isAttr(name, attr[i])) return attr[i + 1];
}
return "";
}
protected:
XML_Parser m_parser;
string m_strFileName;
bool m_bStopParse;
bool m_bGZCompression;
FILE* fptr;
Czran gzObj;
};
class mzpSAXMzmlHandler : public mzpSAXHandler {
public:
mzpSAXMzmlHandler(BasicSpectrum* bs);
mzpSAXMzmlHandler(BasicSpectrum* bs, BasicChromatogram* bc);
~mzpSAXMzmlHandler();
// Overrides of SAXHandler functions
void startElement(const XML_Char *el, const XML_Char **attr);
void endElement(const XML_Char *el);
void characters(const XML_Char *s, int len);
// SAXMzmlHandler public functions
vector<cindex>* getChromatIndex();
f_off getIndexOffset();
vector<instrumentInfo>* getInstrument();
int getPeaksCount();
vector<cindex>* getSpecIndex();
int highChromat();
int highScan();
bool load(const char* fileName);
int lowScan();
bool readChromatogram(int num=-1);
bool readHeader(int num=-1);
bool readSpectrum(int num=-1);
protected:
private:
// mzpSAXMzmlHandler subclasses
class cvParam {
public:
string refGroupName;
string name;
string accession;
string value;
string unitAccession;
string unitName;
};
// mzpSAXMzmlHandler private functions
void processData();
void processCVParam(const char* name, const char* accession, const char* value, const char* unitName="0", const char* unitAccession="0");
void pushChromatogram();
void pushSpectrum(); // Load current data into pvSpec, may have to guess charge
f_off readIndexOffset();
void stopParser();
// mzpSAXMzmlHandler Base64 conversion functions
void decode(vector<double>& d);
//void decode32(vector<double>& d);
//void decode64(vector<double>& d);
//void decompress32(vector<double>& d);
//void decompress64(vector<double>& d);
unsigned long dtohl(uint32_t l, bool bNet);
uint64_t dtohl(uint64_t l, bool bNet);
// mzpSAXMzmlHandler Flags indicating parser is inside a particular tag.
bool m_bInIndexedMzML;
bool m_bInRefGroup;
bool m_bInmzArrayBinary;
bool m_bInintenArrayBinary;
bool m_bInSpectrumList;
bool m_bInChromatogramList;
bool m_bInIndexList;
// mzpSAXMzmlHandler procedural flags.
bool m_bChromatogramIndex;
bool m_bHeaderOnly;
bool m_bLowPrecision;
bool m_bNetworkData; // i.e. big endian
bool m_bNumpressLinear;
bool m_bNumpressPic;
bool m_bNumpressSlof;
bool m_bNoIndex;
bool m_bSpectrumIndex;
bool m_bZlib;
int m_iDataType; //0=unspecified, 1=32-bit float, 2=64-bit float
bool m_bIndexSorted;
// mzpSAXMzmlHandler index data members.
vector<cindex> m_vIndex;
cindex curIndex;
int posIndex;
f_off indexOffset;
vector<cindex> m_vChromatIndex;
cindex curChromatIndex;
int posChromatIndex;
// mzpSAXMzmlHandler data members.
BasicChromatogram* chromat;
string m_ccurrentRefGroupName;
long m_encodedLen; // For compressed data
instrumentInfo m_instrument;
int m_peaksCount; // Count of peaks in spectrum
vector<cvParam> m_refGroupCvParams;
int m_scanSPECCount;
int m_scanIDXCount;
int m_scanPRECCount;
double m_startTime; //in minutes
double m_stopTime; //in minutes
string m_strData; // For collecting character data.
vector<instrumentInfo> m_vInstrument;
BasicSpectrum* spec;
vector<double> vdI;
vector<double> vdM; // Peak list vectors (masses and charges)
};
class mzpSAXMzxmlHandler : public mzpSAXHandler {
public:
mzpSAXMzxmlHandler(BasicSpectrum* bs);
mzpSAXMzxmlHandler(BasicSpectrum* bs, BasicChromatogram* bc);
~mzpSAXMzxmlHandler();
// Overrides of SAXHandler functions
void startElement(const XML_Char *el, const XML_Char **attr);
void endElement(const XML_Char *el);
void characters(const XML_Char *s, int len);
// mzpSAXMzxmlHandler public functions
vector<cindex>* getIndex();
f_off getIndexOffset();
instrumentInfo getInstrument();
int getPeaksCount();
int highScan();
bool load(const char* fileName);
int lowScan();
bool readChromat(int num=-1);
bool readHeader(int num=-1);
bool readSpectrum(int num=-1);
protected:
private:
// mzpSAXMzxmlHandler private functions
void pushSpectrum(); // Load current data into pvSpec, may have to guess charge
f_off readIndexOffset();
void stopParser();
// mzpSAXMzxmlHandler Base64 conversion functions
void decode32();
void decode64();
void decompress32();
void decompress64();
unsigned long dtohl(uint32_t l, bool bNet);
uint64_t dtohl(uint64_t l, bool bNet);
// mzpSAXMzxmlHandler Flags indicating parser is inside a particular tag.
bool m_bInDataProcessing;
bool m_bInIndex;
bool m_bInMsInstrument;
bool m_bInMsRun;
bool m_bInPeaks;
bool m_bInPrecursorMz;
bool m_bInScan;
// mzpSAXMzxmlHandler procedural flags.
bool m_bCompressedData;
bool m_bHeaderOnly;
bool m_bLowPrecision;
bool m_bNetworkData; // i.e. big endian
bool m_bNoIndex;
bool m_bScanIndex;
bool m_bIndexSorted;
// mzpSAXMzxmlHandler index data members.
vector<cindex> m_vIndex;
cindex curIndex;
int posIndex;
f_off indexOffset;
// mzpSAXMzxmlHandler data members.
uLong m_compressLen; // For compressed data
instrumentInfo m_instrument;
int m_peaksCount; // Count of peaks in spectrum
string m_strData; // For collecting character data.
vector<instrumentInfo> m_vInstrument;
BasicSpectrum* spec;
vector<double> vdI;
vector<double> vdM; // Peak list vectors (masses and charges)
};
//------------------------------------------------
// mz5 Support
//------------------------------------------------
#ifdef MZP_MZ5
//mz5 constants
#define CVL 128
#define USRVL 128
#define USRNL 256
#define USRTL 64
static unsigned short MZ5_FILE_MAJOR_VERSION = 0;
static unsigned short MZ5_FILE_MINOR_VERSION = 9;
//forward declarations
class mzpMz5Config;
enum MZ5DataSets {
ControlledVocabulary,
FileContent,
Contact,
CVReference,
CVParam,
UserParam,
RefParam,
ParamGroups,
SourceFiles,
Samples,
Software,
ScanSetting,
InstrumentConfiguration,
DataProcessing,
Run,
SpectrumMetaData,
SpectrumBinaryMetaData,
SpectrumIndex,
SpectrumMZ,
SpectrumIntensity,
ChromatogramMetaData,
ChromatogramBinaryMetaData,
ChromatogramIndex,
ChromatogramTime,
ChromatogramIntensity,
FileInformation
};
enum SpectrumLoadPolicy {
SLP_InitializeAllOnCreation,
SLP_InitializeAllOnFirstCall
};
enum ChromatogramLoadPolicy {
CLP_InitializeAllOnCreation,
CLP_InitializeAllOnFirstCall
};
struct FileInformationMZ5Data {
unsigned short majorVersion;
unsigned short minorVersion;
unsigned short didFiltering;
unsigned short deltaMZ;
unsigned short translateInten;
};
struct FileInformationMZ5: public FileInformationMZ5Data {
FileInformationMZ5();
FileInformationMZ5(const FileInformationMZ5&);
FileInformationMZ5(const mzpMz5Config&);
~FileInformationMZ5();
FileInformationMZ5& operator=(const FileInformationMZ5&);
void init(const unsigned short majorVersion, const unsigned short minorVersion, const unsigned didFiltering, const unsigned deltaMZ, const unsigned translateInten);
static CompType getType();
};
struct ContVocabMZ5Data {
char* uri;
char* fullname;
char* id;
char* version;
};
struct ContVocabMZ5: public ContVocabMZ5Data {
ContVocabMZ5();
ContVocabMZ5(const string& uri, const string& fullname, const string& id, const string& version);
ContVocabMZ5(const char* uri, const char* fullname, const char* id, const char* version);
ContVocabMZ5(const ContVocabMZ5&);
ContVocabMZ5& operator=(const ContVocabMZ5&);
~ContVocabMZ5();
void init(const string&, const string&, const string&, const string&);
static CompType getType();
};
struct CVRefMZ5Data {
char* name;
char* prefix;
unsigned long accession;
};
struct CVRefMZ5: public CVRefMZ5Data {
CVRefMZ5();
CVRefMZ5(const CVRefMZ5&);
CVRefMZ5& operator=(const CVRefMZ5&);
~CVRefMZ5();
void init(const char* name, const char* prefix, const unsigned long accession);
static CompType getType();
};
struct UserParamMZ5Data {
char name[USRNL];
char value[USRVL];
char type[USRTL];
unsigned long unitCVRefID;
};
struct UserParamMZ5: public UserParamMZ5Data {
UserParamMZ5();
UserParamMZ5(const UserParamMZ5&);
UserParamMZ5& operator=(const UserParamMZ5&);
~UserParamMZ5();
void init(const char* name, const char* value, const char* type, const unsigned long urefid);
static CompType getType();
};
struct CVParamMZ5Data {
char value[CVL];
unsigned long typeCVRefID;
unsigned long unitCVRefID;
};
struct CVParamMZ5: public CVParamMZ5Data {
CVParamMZ5();
CVParamMZ5(const CVParamMZ5&);
CVParamMZ5& operator=(const CVParamMZ5&);
~CVParamMZ5();
void init(const char* value, const unsigned long& cvrefid, const unsigned long& urefid);
static CompType getType();
};
struct RefMZ5Data {
unsigned long refID;
};
struct RefMZ5: public RefMZ5Data {
RefMZ5();
RefMZ5(const RefMZ5&);
RefMZ5& operator=(const RefMZ5&);
~RefMZ5();
static CompType getType();
};
struct RefListMZ5Data {
size_t len;
RefMZ5* list;
};
struct RefListMZ5: RefListMZ5Data {
RefListMZ5();
RefListMZ5(const RefListMZ5&);
RefListMZ5& operator=(const RefListMZ5&);
~RefListMZ5();
void init(const RefMZ5* list, const size_t len);
static VarLenType getType();
};
struct ParamListMZ5Data {
unsigned long cvParamStartID;
unsigned long cvParamEndID;
unsigned long userParamStartID;
unsigned long userParamEndID;
unsigned long refParamGroupStartID;
unsigned long refParamGroupEndID;
};
struct ParamListMZ5: ParamListMZ5Data {
ParamListMZ5();
ParamListMZ5(const ParamListMZ5&);
ParamListMZ5& operator=(const ParamListMZ5&);
~ParamListMZ5();
void init(const unsigned long cvstart, const unsigned long cvend, const unsigned long usrstart, const unsigned long usrend, const unsigned long refstart, const unsigned long refend);
static CompType getType();
};
struct ParamGroupMZ5 {
char* id;
ParamListMZ5 paramList;
ParamGroupMZ5();
ParamGroupMZ5(const ParamGroupMZ5&);
ParamGroupMZ5& operator=(const ParamGroupMZ5&);
~ParamGroupMZ5();
void init(const ParamListMZ5& params, const char* id);
static CompType getType();
};
struct SourceFileMZ5 {
char* id;
char* location;
char* name;
ParamListMZ5 paramList;
SourceFileMZ5();
SourceFileMZ5(const SourceFileMZ5&);
SourceFileMZ5& operator=(const SourceFileMZ5&);
~SourceFileMZ5();
void init(const ParamListMZ5& params, const char* id, const char* location, const char* name);
static CompType getType();
};
struct SampleMZ5 {
char* id;
char* name;
ParamListMZ5 paramList;
SampleMZ5();
SampleMZ5(const SampleMZ5&);
SampleMZ5& operator=(const SampleMZ5&);
~SampleMZ5();
void init(const ParamListMZ5& params, const char* id, const char* name);
static CompType getType();
};
struct SoftwareMZ5 {
char* id;
char* version;
ParamListMZ5 paramList;
SoftwareMZ5();
SoftwareMZ5(const SoftwareMZ5&);
SoftwareMZ5& operator=(const SoftwareMZ5&);
~SoftwareMZ5();
void init(const ParamListMZ5& params, const char* id, const char* version);
static CompType getType();
};
struct ParamListsMZ5 {
size_t len;
ParamListMZ5* lists;
ParamListsMZ5();
ParamListsMZ5(const ParamListsMZ5&);
ParamListsMZ5& operator=(const ParamListsMZ5&);
~ParamListsMZ5();
void init(const ParamListMZ5* list, const size_t len);
static VarLenType getType();
};
struct ScanSettingMZ5 {
char* id;
ParamListMZ5 paramList;
RefListMZ5 sourceFileIDs;
ParamListsMZ5 targetList;
ScanSettingMZ5();
ScanSettingMZ5(const ScanSettingMZ5&);
ScanSettingMZ5& operator=(const ScanSettingMZ5&);
~ScanSettingMZ5();
void init(const ParamListMZ5& params, const RefListMZ5& refSourceFiles, const ParamListsMZ5 targets, const char* id);
static CompType getType();
};
struct ComponentMZ5 {
ParamListMZ5 paramList;
unsigned long order;
ComponentMZ5();
ComponentMZ5(const ComponentMZ5&);
ComponentMZ5& operator=(const ComponentMZ5&);
~ComponentMZ5();
void init(const ParamListMZ5&, const unsigned long order);
static CompType getType();
};
struct ComponentListMZ5 {
size_t len;
ComponentMZ5* list;
ComponentListMZ5();
ComponentListMZ5(const ComponentListMZ5&);
ComponentListMZ5(const vector<ComponentMZ5>&);
ComponentListMZ5& operator=(const ComponentListMZ5&);
~ComponentListMZ5();
void init(const ComponentMZ5*, const size_t&);
static VarLenType getType();
};
struct ComponentsMZ5 {
ComponentListMZ5 sources;
ComponentListMZ5 analyzers;
ComponentListMZ5 detectors;
ComponentsMZ5();
ComponentsMZ5(const ComponentsMZ5&);
ComponentsMZ5& operator=(const ComponentsMZ5&);
~ComponentsMZ5();
void init(const ComponentListMZ5& sources, const ComponentListMZ5& analyzers, const ComponentListMZ5& detectors);
static CompType getType();
};
struct InstrumentConfigurationMZ5 {
char* id;
ParamListMZ5 paramList;
ComponentsMZ5 components;
RefMZ5 scanSettingRefID;
RefMZ5 softwareRefID;
InstrumentConfigurationMZ5();
InstrumentConfigurationMZ5(const InstrumentConfigurationMZ5&);
InstrumentConfigurationMZ5& operator=(const InstrumentConfigurationMZ5&);
~InstrumentConfigurationMZ5();
void init(const ParamListMZ5& params, const ComponentsMZ5& components, const RefMZ5& refScanSetting, const RefMZ5& refSoftware, const char* id);
static CompType getType();
};
struct ProcessingMethodMZ5 {
ParamListMZ5 paramList;
RefMZ5 softwareRefID;
unsigned long order;
ProcessingMethodMZ5();
ProcessingMethodMZ5(const ProcessingMethodMZ5&);
ProcessingMethodMZ5& operator=(const ProcessingMethodMZ5&);
~ProcessingMethodMZ5();
void init(const ParamListMZ5& params, const RefMZ5& refSoftware, const unsigned long order);
static CompType getType();
};
struct ProcessingMethodListMZ5 {
size_t len;
ProcessingMethodMZ5* list;
ProcessingMethodListMZ5();
ProcessingMethodListMZ5(const ProcessingMethodListMZ5&);
ProcessingMethodListMZ5& operator=(const ProcessingMethodListMZ5&);
~ProcessingMethodListMZ5();
void init(const ProcessingMethodMZ5* list, const size_t len);
static VarLenType getType();
};
struct DataProcessingMZ5 {
char* id;
ProcessingMethodListMZ5 processingMethodList;
DataProcessingMZ5();
DataProcessingMZ5(const DataProcessingMZ5&);
DataProcessingMZ5& operator=(const DataProcessingMZ5&);
~DataProcessingMZ5();
void init(const ProcessingMethodListMZ5&, const char* id);
static CompType getType();
};
struct PrecursorMZ5 {
char* externalSpectrumId;
ParamListMZ5 activation;
ParamListMZ5 isolationWindow;
ParamListsMZ5 selectedIonList;
RefMZ5 spectrumRefID;
RefMZ5 sourceFileRefID;
PrecursorMZ5();
PrecursorMZ5(const PrecursorMZ5&);
PrecursorMZ5& operator=(const PrecursorMZ5&);
~PrecursorMZ5();
void init(const ParamListMZ5& activation, const ParamListMZ5& isolationWindow, const ParamListsMZ5 selectedIonList, const RefMZ5& refSpectrum, const RefMZ5& refSourceFile, const char* externalSpectrumId);
static CompType getType();
};
struct PrecursorListMZ5 {
size_t len;
PrecursorMZ5* list;
PrecursorListMZ5();
PrecursorListMZ5(const PrecursorListMZ5&);
PrecursorListMZ5& operator=(const PrecursorListMZ5&);
~PrecursorListMZ5();
void init(const PrecursorMZ5*, const size_t len);
static VarLenType getType();
};
struct ChromatogramMZ5 {
char* id;
ParamListMZ5 paramList;
PrecursorMZ5 precursor;
ParamListMZ5 productIsolationWindow;
RefMZ5 dataProcessingRefID;
unsigned long index;
ChromatogramMZ5();
ChromatogramMZ5(const ChromatogramMZ5&);
ChromatogramMZ5& operator=(const ChromatogramMZ5&);
~ChromatogramMZ5();
void init(const ParamListMZ5& params, const PrecursorMZ5& precursor, const ParamListMZ5& productIsolationWindow, const RefMZ5& refDataProcessing, const unsigned long index, const char* id);
static CompType getType();
};
struct ScanMZ5 {
char* externalSpectrumID;
ParamListMZ5 paramList;
ParamListsMZ5 scanWindowList;
RefMZ5 instrumentConfigurationRefID;
RefMZ5 sourceFileRefID;
RefMZ5 spectrumRefID;
ScanMZ5();
ScanMZ5(const ScanMZ5&);
ScanMZ5& operator=(const ScanMZ5&);
~ScanMZ5();
void init(const ParamListMZ5& params, const ParamListsMZ5& scanWindowList, const RefMZ5& refInstrument, const RefMZ5& refSourceFile, const RefMZ5& refSpectrum, const char* externalSpectrumID);
static CompType getType();
};
struct ScanListMZ5 {
size_t len;
ScanMZ5* list;
ScanListMZ5();
ScanListMZ5(const ScanListMZ5&);
ScanListMZ5(const vector<ScanMZ5>&);
ScanListMZ5& operator=(const ScanListMZ5&);
~ScanListMZ5();
void init(const ScanMZ5* list, const size_t len);
static VarLenType getType();
};
struct ScansMZ5 {
ParamListMZ5 paramList;
ScanListMZ5 scanList;
ScansMZ5();
ScansMZ5(const ScansMZ5&);
ScansMZ5& operator=(const ScansMZ5&);
~ScansMZ5();
void init(const ParamListMZ5& params, const ScanListMZ5& scanList);
static CompType getType();
};
struct SpectrumMZ5 {
char* id;
char* spotID;
ParamListMZ5 paramList;
ScansMZ5 scanList;
PrecursorListMZ5 precursorList;
ParamListsMZ5 productList;
RefMZ5 dataProcessingRefID;
RefMZ5 sourceFileRefID;
unsigned int index;
SpectrumMZ5();
SpectrumMZ5(const SpectrumMZ5&);
SpectrumMZ5& operator=(const SpectrumMZ5&);
~SpectrumMZ5();
void init(const ParamListMZ5& params, const ScansMZ5& scanList, const PrecursorListMZ5& precursors, const ParamListsMZ5& productIonIsolationWindows, const RefMZ5& refDataProcessing, const RefMZ5& refSourceFile, const unsigned long index, const char* id, const char* spotID);
static CompType getType();
};
struct RunMZ5 {
char* id;
char* startTimeStamp;
char* fid;
char* facc;
ParamListMZ5 paramList;
RefMZ5 defaultSpectrumDataProcessingRefID;
RefMZ5 defaultChromatogramDataProcessingRefID;
RefMZ5 defaultInstrumentConfigurationRefID;
RefMZ5 sourceFileRefID;
RefMZ5 sampleRefID;
RunMZ5();
RunMZ5(const RunMZ5&);
RunMZ5& operator=(const RunMZ5&);
~RunMZ5();
void init(const ParamListMZ5& params, const RefMZ5& refSpectrumDP, const RefMZ5& refChromatogramDP, const RefMZ5& refDefaultInstrument, const RefMZ5& refSourceFile, const RefMZ5& refSample, const char* id, const char* startTimeStamp, const char* fid, const char* facc);
static CompType getType();
};
struct BinaryDataMZ5 {
ParamListMZ5 xParamList;
ParamListMZ5 yParamList;
RefMZ5 xDataProcessingRefID;
RefMZ5 yDataProcessingRefID;
BinaryDataMZ5();
BinaryDataMZ5(const BinaryDataMZ5&);
BinaryDataMZ5& operator=(const BinaryDataMZ5&);
~BinaryDataMZ5();
void init(const ParamListMZ5& xParams, const ParamListMZ5& yParams, const RefMZ5& refDPx, const RefMZ5& refDPy);
static CompType getType();
};
struct CVRefItem {
int group; //0=MS, 1=UO, don't know what others there are.
int ref;
};
class mzpMz5Config{
public:
mzpMz5Config();
~mzpMz5Config();
static bool PRINT_HDF5_EXCEPTIONS;
const bool doFiltering() const;
const bool doTranslating() const;
const size_t getBufferInB();
const DataType& getDataTypeFor(const MZ5DataSets v);
const string& getNameFor(const MZ5DataSets v);
const size_t& getRdccSlots();
MZ5DataSets getVariableFor(const string& name);
void setFiltering(const bool flag) const;
void setTranslating(const bool flag) const;
protected:
private:
size_t bufferInMB_;
ChromatogramLoadPolicy chromatogramLoadPolicy_;
int deflateLvl_;
mutable bool doFiltering_;
mutable bool doTranslating_;
size_t rdccSolts_;
SpectrumLoadPolicy spectrumLoadPolicy_;
map<MZ5DataSets, size_t> variableBufferSizes_;
map<MZ5DataSets, hsize_t> variableChunkSizes_;
map<MZ5DataSets, string> variableNames_;
map<MZ5DataSets, DataType> variableTypes_;
map<string, MZ5DataSets> variableVariables_; //Really? variableVariables? Was this written by Donald Rumsfeld?
void init(const bool filter, const bool deltamz, const bool translateinten);
};
class cMz5Index : public cindex {
public:
unsigned long cvStart;
unsigned long cvLen;
};
class mzpMz5Handler{
public:
mzpMz5Handler(mzpMz5Config* c, BasicSpectrum* s);
mzpMz5Handler(mzpMz5Config* c, BasicSpectrum* s, BasicChromatogram* bc);
~mzpMz5Handler();
void clean(const MZ5DataSets v, void* data, const size_t dsend);
vector<cMz5Index>* getChromatIndex();
void getData(vector<double>& data, const MZ5DataSets v, const hsize_t start, const hsize_t end);
const map<MZ5DataSets, size_t>& getFields();
vector<cMz5Index>* getSpecIndex();
int highChromat();
int highScan();
int lowScan();
void processCVParams(unsigned long index);
bool readChromatogram(int num=-1);
void* readDataSet(const MZ5DataSets v, size_t& dsend, void* ptr=0);
bool readFile(const string filename);
bool readHeader(int num=-1);
bool readSpectrum(int num=-1);
protected:
private:
// mzpMz5Handler index data members.
cMz5Index curIndex;
f_off indexOffset;
int m_scanIDXCount;
vector<cMz5Index> m_vIndex;
int posIndex;
cMz5Index curChromatIndex;
vector<cMz5Index> m_vChromatIndex;
int posChromatIndex;
map<MZ5DataSets, DataSet> bufferMap_;
BasicChromatogram* chromat;
bool closed_;
mzpMz5Config* config_;
vector<CVRefItem> cvRef;
vector<CVParamMZ5> cvParams_;
map<MZ5DataSets, size_t> fields_;
H5File* file_;
BasicSpectrum* spec;
};
#endif
//------------------------------------------------
// RAMP API
//------------------------------------------------
#define INSTRUMENT_LENGTH 2000
#define SCANTYPE_LENGTH 32
#define CHARGEARRAY_LENGTH 128
typedef double RAMPREAL;
typedef f_off ramp_fileoffset_t;
typedef struct RAMPFILE{
BasicSpectrum* bs;
mzpSAXMzmlHandler* mzML;
mzpSAXMzxmlHandler* mzXML;
#ifdef MZP_MZ5
mzpMz5Config* mz5Config;
mzpMz5Handler* mz5;
#endif
int fileType;
int bIsMzData;
RAMPFILE(){
bs=NULL;
mzML=NULL;
mzXML=NULL;
#ifdef MZP_MZ5
mz5=NULL;
mz5Config=NULL;
#endif
fileType=0;
bIsMzData=0;
}
~RAMPFILE(){
if(bs!=NULL) delete bs;
if(mzML!=NULL) delete mzML;
if(mzXML!=NULL) delete mzXML;
bs=NULL;
mzML=NULL;
mzXML=NULL;
#ifdef MZP_MZ5
if(mz5!=NULL) delete mz5;
if(mz5Config!=NULL) delete mz5Config;
mz5=NULL;
mz5Config=NULL;
#endif
}
} RAMPFILE;
static vector<const char *> data_Ext;
struct ScanHeaderStruct {
int acquisitionNum; // scan number as declared in File (may be gaps)
int mergedScan; /* only if MS level > 1 */
int mergedResultScanNum; /* scan number of the resultant merged scan */
int mergedResultStartScanNum; /* smallest scan number of the scanOrigin for merged scan */
int mergedResultEndScanNum; /* largest scan number of the scanOrigin for merged scan */
int msLevel;
int numPossibleCharges;
int peaksCount;
int precursorCharge; /* only if MS level > 1 */
int precursorScanNum; /* only if MS level > 1 */
int scanIndex; //a sequential index for non-sequential scan numbers (1-based)
int seqNum; // number in sequence observed file (1-based)
double basePeakIntensity;
double basePeakMZ;
double collisionEnergy;
double compensationVoltage; /* only if MS level > 1 */
double highMZ;
double ionisationEnergy;
double lowMZ;
double precursorIntensity; /* only if MS level > 1 */
double precursorMonoMZ;
double precursorMZ; /* only if MS level > 1 */
double retentionTime; /* in seconds */
double totIonCurrent;
char activationMethod[SCANTYPE_LENGTH];
char filterLine[CHARGEARRAY_LENGTH];
char possibleCharges[SCANTYPE_LENGTH];
char scanType[SCANTYPE_LENGTH];
char idString[CHARGEARRAY_LENGTH];
bool centroid; //true if spectrum is centroided
bool possibleChargesArray[CHARGEARRAY_LENGTH]; /* NOTE: does NOT include "precursorCharge" information; only from "possibleCharges" */
ramp_fileoffset_t filePosition; /* where in the file is this header? */
};
struct RunHeaderStruct {
int scanCount;
double dEndTime;
double dStartTime;
double endMZ;
double highMZ;
double lowMZ;
double startMZ;
};
typedef struct InstrumentStruct {
char manufacturer[INSTRUMENT_LENGTH];
char model[INSTRUMENT_LENGTH];
char ionisation[INSTRUMENT_LENGTH];
char analyzer[INSTRUMENT_LENGTH];
char detector[INSTRUMENT_LENGTH];
} InstrumentStruct;
struct ScanCacheStruct {
int seqNumStart; // scan at which the cache starts
int size; // number of scans in the cache
struct ScanHeaderStruct *headers;
RAMPREAL **peaks;
};
int checkFileType(const char* fname);
ramp_fileoffset_t getIndexOffset(RAMPFILE *pFI);
InstrumentStruct* getInstrumentStruct(RAMPFILE *pFI);
void getScanSpanRange(const struct ScanHeaderStruct *scanHeader, int *startScanNum, int *endScanNum);
void rampCloseFile(RAMPFILE *pFI);
string rampConstructInputFileName(const string &basename);
char* rampConstructInputFileName(char *buf,int buflen,const char *basename);
char* rampConstructInputPath(char *buf, int inbuflen, const char *dir_in, const char *basename);
const char** rampListSupportedFileTypes();
RAMPFILE* rampOpenFile(const char *filename);
char* rampValidFileType(const char *buf);
void readHeader(RAMPFILE *pFI, ramp_fileoffset_t lScanIndex, struct ScanHeaderStruct *scanHeader);
ramp_fileoffset_t* readIndex(RAMPFILE *pFI, ramp_fileoffset_t indexOffset, int *iLastScan);
int readMsLevel(RAMPFILE *pFI, ramp_fileoffset_t lScanIndex);
void readMSRun(RAMPFILE *pFI, struct RunHeaderStruct *runHeader);
RAMPREAL* readPeaks(RAMPFILE *pFI, ramp_fileoffset_t lScanIndex);
int readPeaksCount(RAMPFILE *pFI, ramp_fileoffset_t lScanIndex);
void readRunHeader(RAMPFILE *pFI, ramp_fileoffset_t *pScanIndex, struct RunHeaderStruct *runHeader, int iLastScan);
//MH:Cached RAMP functions
void clearScanCache(struct ScanCacheStruct* cache);
void freeScanCache(struct ScanCacheStruct* cache);
int getCacheIndex(struct ScanCacheStruct* cache, int seqNum);
struct ScanCacheStruct* getScanCache(int size);
const struct ScanHeaderStruct* readHeaderCached(struct ScanCacheStruct* cache, int seqNum, RAMPFILE* pFI, ramp_fileoffset_t lScanIndex);
int readMsLevelCached(struct ScanCacheStruct* cache, int seqNum, RAMPFILE* pFI, ramp_fileoffset_t lScanIndex);
const RAMPREAL* readPeaksCached(struct ScanCacheStruct* cache, int seqNum, RAMPFILE* pFI, ramp_fileoffset_t lScanIndex);
void shiftScanCache(struct ScanCacheStruct* cache, int nScans);
//MH:Unimplimented functions. These just bark cerr when used.
int isScanAveraged(struct ScanHeaderStruct *scanHeader);
int isScanMergedResult(struct ScanHeaderStruct *scanHeader);
int rampSelfTest(char *filename);
char* rampTrimBaseName(char *buf);
int rampValidateOrDeriveInputFilename(char *inbuf, int inbuflen, char *spectrumName);
double readStartMz(RAMPFILE *pFI, ramp_fileoffset_t lScanIndex);
double readEndMz(RAMPFILE *pFI, ramp_fileoffset_t lScanIndex);
void setRampOption(long option);
//------------------------------------------------
// PWiz API
//------------------------------------------------
class Chromatogram{
public:
Chromatogram();
~Chromatogram();
BasicChromatogram* bc;
string id;
void getTimeIntensityPairs(vector<TimeIntensityPair>& v);
};
typedef class Chromatogram* ChromatogramPtr;
class ChromatogramList{
public:
ChromatogramList();
ChromatogramList(mzpSAXMzmlHandler* ml, void* m5, BasicChromatogram* bc);
~ChromatogramList();
ChromatogramPtr chromatogram(int index, bool binaryData = false);
bool get();
unsigned int size();
vector<cindex>* vChromatIndex;
#ifdef MZP_MZ5
vector<cMz5Index>* vMz5Index;
#endif
private:
mzpSAXMzmlHandler* mzML;
#ifdef MZP_MZ5
mzpMz5Handler* mz5;
#endif
ChromatogramPtr chromat;
};
typedef class ChromatogramList* ChromatogramListPtr;
class PwizRun{
public:
PwizRun();
PwizRun(mzpSAXMzmlHandler* ml, void* m5, BasicChromatogram* b);
~PwizRun();
ChromatogramListPtr chromatogramListPtr;
void set(mzpSAXMzmlHandler* ml, void* m5, BasicChromatogram* b);
private:
mzpSAXMzmlHandler* mzML;
#ifdef MZP_MZ5
mzpMz5Handler* mz5;
#endif
BasicChromatogram* bc;
};
class MSDataFile{
public:
MSDataFile(string s);
~MSDataFile();
PwizRun run;
private:
BasicSpectrum* bs;
BasicChromatogram* bc;
mzpSAXMzmlHandler* mzML;
#ifdef MZP_MZ5
mzpMz5Config* mz5Config;
mzpMz5Handler* mz5;
#endif
};
//------------------------------------------------
// MzParser Interface
//------------------------------------------------
class MzParser {
public:
//Constructors and Destructors
MzParser(BasicSpectrum* s);
MzParser(BasicSpectrum* s, BasicChromatogram* c);
~MzParser();
//User functions
int highChromat();
int highScan();
bool load(char* fname);
int lowScan();
bool readChromatogram(int num=-1);
bool readSpectrum(int num=-1);
bool readSpectrumHeader(int num=-1);
protected:
mzpSAXMzmlHandler* mzML;
mzpSAXMzxmlHandler* mzXML;
#ifdef MZP_MZ5
mzpMz5Handler* mz5;
mzpMz5Config* mz5Config;
#endif
private:
//private functions
int checkFileType(char* fname);
//private data members
BasicChromatogram* chromat;
int fileType;
BasicSpectrum* spec;
};
#endif
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