libmstoolkit-77.0.0/0000755000175000017500000000000012455161123014247 5ustar rusconirusconilibmstoolkit-77.0.0/include/0000755000175000017500000000000012455161024015672 5ustar rusconirusconilibmstoolkit-77.0.0/include/mzParser.h0000644000175000017500000012014612455161024017652 0ustar rusconirusconi/* 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 #include #include #include #include #include #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 #endif #if defined(GCC) || defined(__LINUX__) #include #include #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 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& getData(); int getIDString(char* str); unsigned int size(); protected: //Data Members (protected) char idString[128]; vector 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* getChromatIndex(); f_off getIndexOffset(); vector* getInstrument(); int getPeaksCount(); vector* 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& d); //void decode32(vector& d); //void decode64(vector& d); //void decompress32(vector& d); //void decompress64(vector& 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 m_vIndex; cindex curIndex; int posIndex; f_off indexOffset; vector 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 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 m_vInstrument; BasicSpectrum* spec; vector vdI; vector 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* 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 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 m_vInstrument; BasicSpectrum* spec; vector vdI; vector 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&); 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&); 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 variableBufferSizes_; map variableChunkSizes_; map variableNames_; map variableTypes_; map 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* getChromatIndex(); void getData(vector& data, const MZ5DataSets v, const hsize_t start, const hsize_t end); const map& getFields(); vector* 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 m_vIndex; int posIndex; cMz5Index curChromatIndex; vector m_vChromatIndex; int posChromatIndex; map bufferMap_; BasicChromatogram* chromat; bool closed_; mzpMz5Config* config_; vector cvRef; vector cvParams_; map 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 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& 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* vChromatIndex; #ifdef MZP_MZ5 vector* 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 libmstoolkit-77.0.0/include/zconf.h0000644000175000017500000003207712455161024017173 0ustar rusconirusconi/* zconf.h -- configuration of the zlib compression library * Copyright (C) 1995-2010 Jean-loup Gailly. * For conditions of distribution and use, see copyright notice in zlib.h */ /* @(#) $Id$ */ #ifndef ZCONF_H #define ZCONF_H /* * If you *really* need a unique prefix for all types and library functions, * compile with -DZ_PREFIX. The "standard" zlib should be compiled without it. * Even better than compiling with -DZ_PREFIX would be to use configure to set * this permanently in zconf.h using "./configure --zprefix". */ #ifdef Z_PREFIX /* may be set to #if 1 by ./configure */ /* all linked symbols */ # define _dist_code z__dist_code # define _length_code z__length_code # define _tr_align z__tr_align # define _tr_flush_block z__tr_flush_block # define _tr_init z__tr_init # define _tr_stored_block z__tr_stored_block # define _tr_tally z__tr_tally # define adler32 z_adler32 # define adler32_combine z_adler32_combine # define adler32_combine64 z_adler32_combine64 # define compress z_compress # define compress2 z_compress2 # define compressBound z_compressBound # define crc32 z_crc32 # define crc32_combine z_crc32_combine # define crc32_combine64 z_crc32_combine64 # define deflate z_deflate # define deflateBound z_deflateBound # define deflateCopy z_deflateCopy # define deflateEnd z_deflateEnd # define deflateInit2_ z_deflateInit2_ # define deflateInit_ z_deflateInit_ # define deflateParams z_deflateParams # define deflatePrime z_deflatePrime # define deflateReset z_deflateReset # define deflateSetDictionary z_deflateSetDictionary # define deflateSetHeader z_deflateSetHeader # define deflateTune z_deflateTune # define deflate_copyright z_deflate_copyright # define get_crc_table z_get_crc_table # define gz_error z_gz_error # define gz_intmax z_gz_intmax # define gz_strwinerror z_gz_strwinerror # define gzbuffer z_gzbuffer # define gzclearerr z_gzclearerr # define gzclose z_gzclose # define gzclose_r z_gzclose_r # define gzclose_w z_gzclose_w # define gzdirect z_gzdirect # define gzdopen z_gzdopen # define gzeof z_gzeof # define gzerror z_gzerror # define gzflush z_gzflush # define gzgetc z_gzgetc # define gzgets z_gzgets # define gzoffset z_gzoffset # define gzoffset64 z_gzoffset64 # define gzopen z_gzopen # define gzopen64 z_gzopen64 # define gzprintf z_gzprintf # define gzputc z_gzputc # define gzputs z_gzputs # define gzread z_gzread # define gzrewind z_gzrewind # define gzseek z_gzseek # define gzseek64 z_gzseek64 # define gzsetparams z_gzsetparams # define gztell z_gztell # define gztell64 z_gztell64 # define gzungetc z_gzungetc # define gzwrite z_gzwrite # define inflate z_inflate # define inflateBack z_inflateBack # define inflateBackEnd z_inflateBackEnd # define inflateBackInit_ z_inflateBackInit_ # define inflateCopy z_inflateCopy # define inflateEnd z_inflateEnd # define inflateGetHeader z_inflateGetHeader # define inflateInit2_ z_inflateInit2_ # define inflateInit_ z_inflateInit_ # define inflateMark z_inflateMark # define inflatePrime z_inflatePrime # define inflateReset z_inflateReset # define inflateReset2 z_inflateReset2 # define inflateSetDictionary z_inflateSetDictionary # define inflateSync z_inflateSync # define inflateSyncPoint z_inflateSyncPoint # define inflateUndermine z_inflateUndermine # define inflate_copyright z_inflate_copyright # define inflate_fast z_inflate_fast # define inflate_table z_inflate_table # define uncompress z_uncompress # define zError z_zError # define zcalloc z_zcalloc # define zcfree z_zcfree # define zlibCompileFlags z_zlibCompileFlags # define zlibVersion z_zlibVersion /* all zlib typedefs in zlib.h and zconf.h */ # define Byte z_Byte # define Bytef z_Bytef # define alloc_func z_alloc_func # define charf z_charf # define free_func z_free_func # define gzFile z_gzFile # define gz_header z_gz_header # define gz_headerp z_gz_headerp # define in_func z_in_func # define intf z_intf # define out_func z_out_func # define uInt z_uInt # define uIntf z_uIntf # define uLong z_uLong # define uLongf z_uLongf # define voidp z_voidp # define voidpc z_voidpc # define voidpf z_voidpf /* all zlib structs in zlib.h and zconf.h */ # define gz_header_s z_gz_header_s # define internal_state z_internal_state #endif #if defined(__MSDOS__) && !defined(MSDOS) # define MSDOS #endif #if (defined(OS_2) || defined(__OS2__)) && !defined(OS2) # define OS2 #endif #if defined(_WINDOWS) && !defined(WINDOWS) # define WINDOWS #endif #if defined(_WIN32) || defined(_WIN32_WCE) || defined(__WIN32__) # ifndef WIN32 # define WIN32 # endif #endif #if (defined(MSDOS) || defined(OS2) || defined(WINDOWS)) && !defined(WIN32) # if !defined(__GNUC__) && !defined(__FLAT__) && !defined(__386__) # ifndef SYS16BIT # define SYS16BIT # endif # endif #endif /* * Compile with -DMAXSEG_64K if the alloc function cannot allocate more * than 64k bytes at a time (needed on systems with 16-bit int). */ #ifdef SYS16BIT # define MAXSEG_64K #endif #ifdef MSDOS # define UNALIGNED_OK #endif #ifdef __STDC_VERSION__ # ifndef STDC # define STDC # endif # if __STDC_VERSION__ >= 199901L # ifndef STDC99 # define STDC99 # endif # endif #endif #if !defined(STDC) && (defined(__STDC__) || defined(__cplusplus)) # define STDC #endif #if !defined(STDC) && (defined(__GNUC__) || defined(__BORLANDC__)) # define STDC #endif #if !defined(STDC) && (defined(MSDOS) || defined(WINDOWS) || defined(WIN32)) # define STDC #endif #if !defined(STDC) && (defined(OS2) || defined(__HOS_AIX__)) # define STDC #endif #if defined(__OS400__) && !defined(STDC) /* iSeries (formerly AS/400). */ # define STDC #endif #ifndef STDC # ifndef const /* cannot use !defined(STDC) && !defined(const) on Mac */ # define const /* note: need a more gentle solution here */ # endif #endif /* Some Mac compilers merge all .h files incorrectly: */ #if defined(__MWERKS__)||defined(applec)||defined(THINK_C)||defined(__SC__) # define NO_DUMMY_DECL #endif /* Maximum value for memLevel in deflateInit2 */ #ifndef MAX_MEM_LEVEL # ifdef MAXSEG_64K # define MAX_MEM_LEVEL 8 # else # define MAX_MEM_LEVEL 9 # endif #endif /* Maximum value for windowBits in deflateInit2 and inflateInit2. * WARNING: reducing MAX_WBITS makes minigzip unable to extract .gz files * created by gzip. (Files created by minigzip can still be extracted by * gzip.) */ #ifndef MAX_WBITS # define MAX_WBITS 15 /* 32K LZ77 window */ #endif /* The memory requirements for deflate are (in bytes): (1 << (windowBits+2)) + (1 << (memLevel+9)) that is: 128K for windowBits=15 + 128K for memLevel = 8 (default values) plus a few kilobytes for small objects. For example, if you want to reduce the default memory requirements from 256K to 128K, compile with make CFLAGS="-O -DMAX_WBITS=14 -DMAX_MEM_LEVEL=7" Of course this will generally degrade compression (there's no free lunch). The memory requirements for inflate are (in bytes) 1 << windowBits that is, 32K for windowBits=15 (default value) plus a few kilobytes for small objects. */ /* Type declarations */ #ifndef OF /* function prototypes */ # ifdef STDC # define OF(args) args # else # define OF(args) () # endif #endif /* The following definitions for FAR are needed only for MSDOS mixed * model programming (small or medium model with some far allocations). * This was tested only with MSC; for other MSDOS compilers you may have * to define NO_MEMCPY in zutil.h. If you don't need the mixed model, * just define FAR to be empty. */ #ifdef SYS16BIT # if defined(M_I86SM) || defined(M_I86MM) /* MSC small or medium model */ # define SMALL_MEDIUM # ifdef _MSC_VER # define FAR _far # else # define FAR far # endif # endif # if (defined(__SMALL__) || defined(__MEDIUM__)) /* Turbo C small or medium model */ # define SMALL_MEDIUM # ifdef __BORLANDC__ # define FAR _far # else # define FAR far # endif # endif #endif #if defined(WINDOWS) || defined(WIN32) /* If building or using zlib as a DLL, define ZLIB_DLL. * This is not mandatory, but it offers a little performance increase. */ # ifdef ZLIB_DLL # if defined(WIN32) && (!defined(__BORLANDC__) || (__BORLANDC__ >= 0x500)) # ifdef ZLIB_INTERNAL # define ZEXTERN extern __declspec(dllexport) # else # define ZEXTERN extern __declspec(dllimport) # endif # endif # endif /* ZLIB_DLL */ /* If building or using zlib with the WINAPI/WINAPIV calling convention, * define ZLIB_WINAPI. * Caution: the standard ZLIB1.DLL is NOT compiled using ZLIB_WINAPI. */ # ifdef ZLIB_WINAPI # ifdef FAR # undef FAR # endif # include /* No need for _export, use ZLIB.DEF instead. */ /* For complete Windows compatibility, use WINAPI, not __stdcall. */ # define ZEXPORT WINAPI # ifdef WIN32 # define ZEXPORTVA WINAPIV # else # define ZEXPORTVA FAR CDECL # endif # endif #endif #if defined (__BEOS__) # ifdef ZLIB_DLL # ifdef ZLIB_INTERNAL # define ZEXPORT __declspec(dllexport) # define ZEXPORTVA __declspec(dllexport) # else # define ZEXPORT __declspec(dllimport) # define ZEXPORTVA __declspec(dllimport) # endif # endif #endif #ifndef ZEXTERN # define ZEXTERN extern #endif #ifndef ZEXPORT # define ZEXPORT #endif #ifndef ZEXPORTVA # define ZEXPORTVA #endif #ifndef FAR # define FAR #endif #if !defined(__MACTYPES__) typedef unsigned char Byte; /* 8 bits */ #endif typedef unsigned int uInt; /* 16 bits or more */ typedef unsigned long uLong; /* 32 bits or more */ #ifdef SMALL_MEDIUM /* Borland C/C++ and some old MSC versions ignore FAR inside typedef */ # define Bytef Byte FAR #else typedef Byte FAR Bytef; #endif typedef char FAR charf; typedef int FAR intf; typedef uInt FAR uIntf; typedef uLong FAR uLongf; #ifdef STDC typedef void const *voidpc; typedef void FAR *voidpf; typedef void *voidp; #else typedef Byte const *voidpc; typedef Byte FAR *voidpf; typedef Byte *voidp; #endif #ifdef HAVE_UNISTD_H /* may be set to #if 1 by ./configure */ # define Z_HAVE_UNISTD_H #endif #ifdef STDC # include /* for off_t */ #endif /* a little trick to accommodate both "#define _LARGEFILE64_SOURCE" and * "#define _LARGEFILE64_SOURCE 1" as requesting 64-bit operations, (even * though the former does not conform to the LFS document), but considering * both "#undef _LARGEFILE64_SOURCE" and "#define _LARGEFILE64_SOURCE 0" as * equivalently requesting no 64-bit operations */ #if -_LARGEFILE64_SOURCE - -1 == 1 # undef _LARGEFILE64_SOURCE #endif #if defined(Z_HAVE_UNISTD_H) || defined(_LARGEFILE64_SOURCE) # include /* for SEEK_* and off_t */ # ifdef VMS # include /* for off_t */ # endif # ifndef z_off_t # define z_off_t off_t # endif #endif #ifndef SEEK_SET # define SEEK_SET 0 /* Seek from beginning of file. */ # define SEEK_CUR 1 /* Seek from current position. */ # define SEEK_END 2 /* Set file pointer to EOF plus "offset" */ #endif #ifndef z_off_t # define z_off_t long #endif #if defined(_LARGEFILE64_SOURCE) && _LFS64_LARGEFILE-0 # define z_off64_t off64_t #else # define z_off64_t z_off_t #endif #if defined(__OS400__) # define NO_vsnprintf #endif #if defined(__MVS__) # define NO_vsnprintf #endif /* MVS linker does not support external names larger than 8 bytes */ #if defined(__MVS__) #pragma map(deflateInit_,"DEIN") #pragma map(deflateInit2_,"DEIN2") #pragma map(deflateEnd,"DEEND") #pragma map(deflateBound,"DEBND") #pragma map(inflateInit_,"ININ") #pragma map(inflateInit2_,"ININ2") #pragma map(inflateEnd,"INEND") #pragma map(inflateSync,"INSY") #pragma map(inflateSetDictionary,"INSEDI") #pragma map(compressBound,"CMBND") #pragma map(inflate_table,"INTABL") #pragma map(inflate_fast,"INFA") #pragma map(inflate_copyright,"INCOPY") #endif #endif /* ZCONF_H */ libmstoolkit-77.0.0/include/inflate.h0000644000175000017500000001437712455161024017501 0ustar rusconirusconi/* inflate.h -- internal inflate state definition * Copyright (C) 1995-2009 Mark Adler * For conditions of distribution and use, see copyright notice in zlib.h */ /* WARNING: this file should *not* be used by applications. It is part of the implementation of the compression library and is subject to change. Applications should only use zlib.h. */ /* define NO_GZIP when compiling if you want to disable gzip header and trailer decoding by inflate(). NO_GZIP would be used to avoid linking in the crc code when it is not needed. For shared libraries, gzip decoding should be left enabled. */ #ifndef NO_GZIP # define GUNZIP #endif /* Possible inflate modes between inflate() calls */ typedef enum { HEAD, /* i: waiting for magic header */ FLAGS, /* i: waiting for method and flags (gzip) */ TIME, /* i: waiting for modification time (gzip) */ OS, /* i: waiting for extra flags and operating system (gzip) */ EXLEN, /* i: waiting for extra length (gzip) */ EXTRA, /* i: waiting for extra bytes (gzip) */ NAME, /* i: waiting for end of file name (gzip) */ COMMENT, /* i: waiting for end of comment (gzip) */ HCRC, /* i: waiting for header crc (gzip) */ DICTID, /* i: waiting for dictionary check value */ DICT, /* waiting for inflateSetDictionary() call */ TYPE, /* i: waiting for type bits, including last-flag bit */ TYPEDO, /* i: same, but skip check to exit inflate on new block */ STORED, /* i: waiting for stored size (length and complement) */ COPY_, /* i/o: same as COPY below, but only first time in */ COPY, /* i/o: waiting for input or output to copy stored block */ TABLE, /* i: waiting for dynamic block table lengths */ LENLENS, /* i: waiting for code length code lengths */ CODELENS, /* i: waiting for length/lit and distance code lengths */ LEN_, /* i: same as LEN below, but only first time in */ LEN, /* i: waiting for length/lit/eob code */ LENEXT, /* i: waiting for length extra bits */ DIST, /* i: waiting for distance code */ DISTEXT, /* i: waiting for distance extra bits */ MATCH, /* o: waiting for output space to copy string */ LIT, /* o: waiting for output space to write literal */ CHECK, /* i: waiting for 32-bit check value */ LENGTH, /* i: waiting for 32-bit length (gzip) */ DONE, /* finished check, done -- remain here until reset */ BAD, /* got a data error -- remain here until reset */ MEM, /* got an inflate() memory error -- remain here until reset */ SYNC /* looking for synchronization bytes to restart inflate() */ } inflate_mode; /* State transitions between above modes - (most modes can go to BAD or MEM on error -- not shown for clarity) Process header: HEAD -> (gzip) or (zlib) or (raw) (gzip) -> FLAGS -> TIME -> OS -> EXLEN -> EXTRA -> NAME -> COMMENT -> HCRC -> TYPE (zlib) -> DICTID or TYPE DICTID -> DICT -> TYPE (raw) -> TYPEDO Read deflate blocks: TYPE -> TYPEDO -> STORED or TABLE or LEN_ or CHECK STORED -> COPY_ -> COPY -> TYPE TABLE -> LENLENS -> CODELENS -> LEN_ LEN_ -> LEN Read deflate codes in fixed or dynamic block: LEN -> LENEXT or LIT or TYPE LENEXT -> DIST -> DISTEXT -> MATCH -> LEN LIT -> LEN Process trailer: CHECK -> LENGTH -> DONE */ /* state maintained between inflate() calls. Approximately 10K bytes. */ struct inflate_state { inflate_mode mode; /* current inflate mode */ int last; /* true if processing last block */ int wrap; /* bit 0 true for zlib, bit 1 true for gzip */ int havedict; /* true if dictionary provided */ int flags; /* gzip header method and flags (0 if zlib) */ unsigned dmax; /* zlib header max distance (INFLATE_STRICT) */ unsigned long check; /* protected copy of check value */ unsigned long total; /* protected copy of output count */ gz_headerp head; /* where to save gzip header information */ /* sliding window */ unsigned wbits; /* log base 2 of requested window size */ unsigned wsize; /* window size or zero if not using window */ unsigned whave; /* valid bytes in the window */ unsigned wnext; /* window write index */ unsigned char FAR *window; /* allocated sliding window, if needed */ /* bit accumulator */ unsigned long hold; /* input bit accumulator */ unsigned bits; /* number of bits in "in" */ /* for string and stored block copying */ unsigned length; /* literal or length of data to copy */ unsigned offset; /* distance back to copy string from */ /* for table and code decoding */ unsigned extra; /* extra bits needed */ /* fixed and dynamic code tables */ code const FAR *lencode; /* starting table for length/literal codes */ code const FAR *distcode; /* starting table for distance codes */ unsigned lenbits; /* index bits for lencode */ unsigned distbits; /* index bits for distcode */ /* dynamic table building */ unsigned ncode; /* number of code length code lengths */ unsigned nlen; /* number of length code lengths */ unsigned ndist; /* number of distance code lengths */ unsigned have; /* number of code lengths in lens[] */ code FAR *next; /* next available space in codes[] */ unsigned short lens[320]; /* temporary storage for code lengths */ unsigned short work[288]; /* work area for code table building */ code codes[ENOUGH]; /* space for code tables */ int sane; /* if false, allow invalid distance too far */ int back; /* bits back of last unprocessed length/lit */ unsigned was; /* initial length of match */ }; libmstoolkit-77.0.0/include/RAWReader.h0000644000175000017500000000362012455161024017620 0ustar rusconirusconi#ifndef _RAWREADER_H #define _RAWREADER_H #ifdef _MSC_VER #include "MSToolkitTypes.h" #include "Spectrum.h" #include #include #include //#include //#include //#include //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; using namespace std; namespace MSToolkit { class RAWReader { public: //Constructors & Destructors RAWReader(); ~RAWReader(); //Public Functions void getInstrument(char* str); long getLastScanNumber(); void getManufacturer(char* str); long getScanCount(); bool getStatus(); bool lookupRT(char* c, int scanNum, float& rt); bool readRawFile(const char* c, Spectrum& s, int scNum=0); 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 setMSLevelFilter(vector* v); void setRawFilter(char* c); void setRawFilterExact(bool b); private: //Data Members bool bRaw; bool rawAvg; bool rawFileOpen; bool rawLabel; bool rawUserFilterExact; char rawInstrument[256]; char rawManufacturer[256]; char rawUserFilter[256]; int rawAvgWidth; long rawAvgCutoff; long rawCurSpec; long rawTotSpec; IXRawfilePtr m_Raw; vector* msLevelFilter; //Private Functions int calcChargeState(double precursormz, double highmass, VARIANT* varMassList, long nArraySize); double calcPepMass(int chargestate, double precursormz); MSSpectrumType evaluateFilter(long scan, char* chFilter, vector& MZs, bool& bCentroid, double& cv, MSActivation& act); bool initRaw(); }; } #endif #endiflibmstoolkit-77.0.0/include/xmltok.h0000644000175000017500000002566012455161024017372 0ustar rusconirusconi/* Copyright (c) 1998, 1999 Thai Open Source Software Center Ltd See the file COPYING for copying permission. */ #ifndef XmlTok_INCLUDED #define XmlTok_INCLUDED 1 #ifdef __cplusplus extern "C" { #endif /* The following token may be returned by XmlContentTok */ #define XML_TOK_TRAILING_RSQB -5 /* ] or ]] at the end of the scan; might be start of illegal ]]> sequence */ /* The following tokens may be returned by both XmlPrologTok and XmlContentTok. */ #define XML_TOK_NONE -4 /* The string to be scanned is empty */ #define XML_TOK_TRAILING_CR -3 /* A CR at the end of the scan; might be part of CRLF sequence */ #define XML_TOK_PARTIAL_CHAR -2 /* only part of a multibyte sequence */ #define XML_TOK_PARTIAL -1 /* only part of a token */ #define XML_TOK_INVALID 0 /* The following tokens are returned by XmlContentTok; some are also returned by XmlAttributeValueTok, XmlEntityTok, XmlCdataSectionTok. */ #define XML_TOK_START_TAG_WITH_ATTS 1 #define XML_TOK_START_TAG_NO_ATTS 2 #define XML_TOK_EMPTY_ELEMENT_WITH_ATTS 3 /* empty element tag */ #define XML_TOK_EMPTY_ELEMENT_NO_ATTS 4 #define XML_TOK_END_TAG 5 #define XML_TOK_DATA_CHARS 6 #define XML_TOK_DATA_NEWLINE 7 #define XML_TOK_CDATA_SECT_OPEN 8 #define XML_TOK_ENTITY_REF 9 #define XML_TOK_CHAR_REF 10 /* numeric character reference */ /* The following tokens may be returned by both XmlPrologTok and XmlContentTok. */ #define XML_TOK_PI 11 /* processing instruction */ #define XML_TOK_XML_DECL 12 /* XML decl or text decl */ #define XML_TOK_COMMENT 13 #define XML_TOK_BOM 14 /* Byte order mark */ /* The following tokens are returned only by XmlPrologTok */ #define XML_TOK_PROLOG_S 15 #define XML_TOK_DECL_OPEN 16 /* */ #define XML_TOK_NAME 18 #define XML_TOK_NMTOKEN 19 #define XML_TOK_POUND_NAME 20 /* #name */ #define XML_TOK_OR 21 /* | */ #define XML_TOK_PERCENT 22 #define XML_TOK_OPEN_PAREN 23 #define XML_TOK_CLOSE_PAREN 24 #define XML_TOK_OPEN_BRACKET 25 #define XML_TOK_CLOSE_BRACKET 26 #define XML_TOK_LITERAL 27 #define XML_TOK_PARAM_ENTITY_REF 28 #define XML_TOK_INSTANCE_START 29 /* The following occur only in element type declarations */ #define XML_TOK_NAME_QUESTION 30 /* name? */ #define XML_TOK_NAME_ASTERISK 31 /* name* */ #define XML_TOK_NAME_PLUS 32 /* name+ */ #define XML_TOK_COND_SECT_OPEN 33 /* */ #define XML_TOK_CLOSE_PAREN_QUESTION 35 /* )? */ #define XML_TOK_CLOSE_PAREN_ASTERISK 36 /* )* */ #define XML_TOK_CLOSE_PAREN_PLUS 37 /* )+ */ #define XML_TOK_COMMA 38 /* The following token is returned only by XmlAttributeValueTok */ #define XML_TOK_ATTRIBUTE_VALUE_S 39 /* The following token is returned only by XmlCdataSectionTok */ #define XML_TOK_CDATA_SECT_CLOSE 40 /* With namespace processing this is returned by XmlPrologTok for a name with a colon. */ #define XML_TOK_PREFIXED_NAME 41 #ifdef XML_DTD #define XML_TOK_IGNORE_SECT 42 #endif /* XML_DTD */ #ifdef XML_DTD #define XML_N_STATES 4 #else /* not XML_DTD */ #define XML_N_STATES 3 #endif /* not XML_DTD */ #define XML_PROLOG_STATE 0 #define XML_CONTENT_STATE 1 #define XML_CDATA_SECTION_STATE 2 #ifdef XML_DTD #define XML_IGNORE_SECTION_STATE 3 #endif /* XML_DTD */ #define XML_N_LITERAL_TYPES 2 #define XML_ATTRIBUTE_VALUE_LITERAL 0 #define XML_ENTITY_VALUE_LITERAL 1 /* The size of the buffer passed to XmlUtf8Encode must be at least this. */ #define XML_UTF8_ENCODE_MAX 4 /* The size of the buffer passed to XmlUtf16Encode must be at least this. */ #define XML_UTF16_ENCODE_MAX 2 typedef struct position { /* first line and first column are 0 not 1 */ XML_Size lineNumber; XML_Size columnNumber; } POSITION; typedef struct { const char *name; const char *valuePtr; const char *valueEnd; char normalized; } ATTRIBUTE; struct encoding; typedef struct encoding ENCODING; typedef int (PTRCALL *SCANNER)(const ENCODING *, const char *, const char *, const char **); struct encoding { SCANNER scanners[XML_N_STATES]; SCANNER literalScanners[XML_N_LITERAL_TYPES]; int (PTRCALL *sameName)(const ENCODING *, const char *, const char *); int (PTRCALL *nameMatchesAscii)(const ENCODING *, const char *, const char *, const char *); int (PTRFASTCALL *nameLength)(const ENCODING *, const char *); const char *(PTRFASTCALL *skipS)(const ENCODING *, const char *); int (PTRCALL *getAtts)(const ENCODING *enc, const char *ptr, int attsMax, ATTRIBUTE *atts); int (PTRFASTCALL *charRefNumber)(const ENCODING *enc, const char *ptr); int (PTRCALL *predefinedEntityName)(const ENCODING *, const char *, const char *); void (PTRCALL *updatePosition)(const ENCODING *, const char *ptr, const char *end, POSITION *); int (PTRCALL *isPublicId)(const ENCODING *enc, const char *ptr, const char *end, const char **badPtr); void (PTRCALL *utf8Convert)(const ENCODING *enc, const char **fromP, const char *fromLim, char **toP, const char *toLim); void (PTRCALL *utf16Convert)(const ENCODING *enc, const char **fromP, const char *fromLim, unsigned short **toP, const unsigned short *toLim); int minBytesPerChar; char isUtf8; char isUtf16; }; /* Scan the string starting at ptr until the end of the next complete token, but do not scan past eptr. Return an integer giving the type of token. Return XML_TOK_NONE when ptr == eptr; nextTokPtr will not be set. Return XML_TOK_PARTIAL when the string does not contain a complete token; nextTokPtr will not be set. Return XML_TOK_INVALID when the string does not start a valid token; nextTokPtr will be set to point to the character which made the token invalid. Otherwise the string starts with a valid token; nextTokPtr will be set to point to the character following the end of that token. Each data character counts as a single token, but adjacent data characters may be returned together. Similarly for characters in the prolog outside literals, comments and processing instructions. */ #define XmlTok(enc, state, ptr, end, nextTokPtr) \ (((enc)->scanners[state])(enc, ptr, end, nextTokPtr)) #define XmlPrologTok(enc, ptr, end, nextTokPtr) \ XmlTok(enc, XML_PROLOG_STATE, ptr, end, nextTokPtr) #define XmlContentTok(enc, ptr, end, nextTokPtr) \ XmlTok(enc, XML_CONTENT_STATE, ptr, end, nextTokPtr) #define XmlCdataSectionTok(enc, ptr, end, nextTokPtr) \ XmlTok(enc, XML_CDATA_SECTION_STATE, ptr, end, nextTokPtr) #ifdef XML_DTD #define XmlIgnoreSectionTok(enc, ptr, end, nextTokPtr) \ XmlTok(enc, XML_IGNORE_SECTION_STATE, ptr, end, nextTokPtr) #endif /* XML_DTD */ /* This is used for performing a 2nd-level tokenization on the content of a literal that has already been returned by XmlTok. */ #define XmlLiteralTok(enc, literalType, ptr, end, nextTokPtr) \ (((enc)->literalScanners[literalType])(enc, ptr, end, nextTokPtr)) #define XmlAttributeValueTok(enc, ptr, end, nextTokPtr) \ XmlLiteralTok(enc, XML_ATTRIBUTE_VALUE_LITERAL, ptr, end, nextTokPtr) #define XmlEntityValueTok(enc, ptr, end, nextTokPtr) \ XmlLiteralTok(enc, XML_ENTITY_VALUE_LITERAL, ptr, end, nextTokPtr) #define XmlSameName(enc, ptr1, ptr2) (((enc)->sameName)(enc, ptr1, ptr2)) #define XmlNameMatchesAscii(enc, ptr1, end1, ptr2) \ (((enc)->nameMatchesAscii)(enc, ptr1, end1, ptr2)) #define XmlNameLength(enc, ptr) \ (((enc)->nameLength)(enc, ptr)) #define XmlSkipS(enc, ptr) \ (((enc)->skipS)(enc, ptr)) #define XmlGetAttributes(enc, ptr, attsMax, atts) \ (((enc)->getAtts)(enc, ptr, attsMax, atts)) #define XmlCharRefNumber(enc, ptr) \ (((enc)->charRefNumber)(enc, ptr)) #define XmlPredefinedEntityName(enc, ptr, end) \ (((enc)->predefinedEntityName)(enc, ptr, end)) #define XmlUpdatePosition(enc, ptr, end, pos) \ (((enc)->updatePosition)(enc, ptr, end, pos)) #define XmlIsPublicId(enc, ptr, end, badPtr) \ (((enc)->isPublicId)(enc, ptr, end, badPtr)) #define XmlUtf8Convert(enc, fromP, fromLim, toP, toLim) \ (((enc)->utf8Convert)(enc, fromP, fromLim, toP, toLim)) #define XmlUtf16Convert(enc, fromP, fromLim, toP, toLim) \ (((enc)->utf16Convert)(enc, fromP, fromLim, toP, toLim)) typedef struct { ENCODING initEnc; const ENCODING **encPtr; } INIT_ENCODING; int XmlParseXmlDecl(int isGeneralTextEntity, const ENCODING *enc, const char *ptr, const char *end, const char **badPtr, const char **versionPtr, const char **versionEndPtr, const char **encodingNamePtr, const ENCODING **namedEncodingPtr, int *standalonePtr); int XmlInitEncoding(INIT_ENCODING *, const ENCODING **, const char *name); const ENCODING *XmlGetUtf8InternalEncoding(void); const ENCODING *XmlGetUtf16InternalEncoding(void); int FASTCALL XmlUtf8Encode(int charNumber, char *buf); int FASTCALL XmlUtf16Encode(int charNumber, unsigned short *buf); int XmlSizeOfUnknownEncoding(void); typedef int (XMLCALL *CONVERTER) (void *userData, const char *p); ENCODING * XmlInitUnknownEncoding(void *mem, int *table, CONVERTER convert, void *userData); int XmlParseXmlDeclNS(int isGeneralTextEntity, const ENCODING *enc, const char *ptr, const char *end, const char **badPtr, const char **versionPtr, const char **versionEndPtr, const char **encodingNamePtr, const ENCODING **namedEncodingPtr, int *standalonePtr); int XmlInitEncodingNS(INIT_ENCODING *, const ENCODING **, const char *name); const ENCODING *XmlGetUtf8InternalEncodingNS(void); const ENCODING *XmlGetUtf16InternalEncodingNS(void); ENCODING * XmlInitUnknownEncodingNS(void *mem, int *table, CONVERTER convert, void *userData); #ifdef __cplusplus } #endif #endif /* not XmlTok_INCLUDED */ libmstoolkit-77.0.0/include/deflate.h0000644000175000017500000003060012455161024017446 0ustar rusconirusconi/* deflate.h -- internal compression state * Copyright (C) 1995-2010 Jean-loup Gailly * For conditions of distribution and use, see copyright notice in zlib.h */ /* WARNING: this file should *not* be used by applications. It is part of the implementation of the compression library and is subject to change. Applications should only use zlib.h. */ /* @(#) $Id$ */ #ifndef DEFLATE_H #define DEFLATE_H #include "zutil.h" /* define NO_GZIP when compiling if you want to disable gzip header and trailer creation by deflate(). NO_GZIP would be used to avoid linking in the crc code when it is not needed. For shared libraries, gzip encoding should be left enabled. */ #ifndef NO_GZIP # define GZIP #endif /* =========================================================================== * Internal compression state. */ #define LENGTH_CODES 29 /* number of length codes, not counting the special END_BLOCK code */ #define LITERALS 256 /* number of literal bytes 0..255 */ #define L_CODES (LITERALS+1+LENGTH_CODES) /* number of Literal or Length codes, including the END_BLOCK code */ #define D_CODES 30 /* number of distance codes */ #define BL_CODES 19 /* number of codes used to transfer the bit lengths */ #define HEAP_SIZE (2*L_CODES+1) /* maximum heap size */ #define MAX_BITS 15 /* All codes must not exceed MAX_BITS bits */ #define INIT_STATE 42 #define EXTRA_STATE 69 #define NAME_STATE 73 #define COMMENT_STATE 91 #define HCRC_STATE 103 #define BUSY_STATE 113 #define FINISH_STATE 666 /* Stream status */ /* Data structure describing a single value and its code string. */ typedef struct ct_data_s { union { ush freq; /* frequency count */ ush code; /* bit string */ } fc; union { ush dad; /* father node in Huffman tree */ ush len; /* length of bit string */ } dl; } FAR ct_data; #define Freq fc.freq #define Code fc.code #define Dad dl.dad #define Len dl.len typedef struct static_tree_desc_s static_tree_desc; typedef struct tree_desc_s { ct_data *dyn_tree; /* the dynamic tree */ int max_code; /* largest code with non zero frequency */ static_tree_desc *stat_desc; /* the corresponding static tree */ } FAR tree_desc; typedef ush Pos; typedef Pos FAR Posf; typedef unsigned IPos; /* A Pos is an index in the character window. We use short instead of int to * save space in the various tables. IPos is used only for parameter passing. */ typedef struct internal_state { z_streamp strm; /* pointer back to this zlib stream */ int status; /* as the name implies */ Bytef *pending_buf; /* output still pending */ ulg pending_buf_size; /* size of pending_buf */ Bytef *pending_out; /* next pending byte to output to the stream */ uInt pending; /* nb of bytes in the pending buffer */ int wrap; /* bit 0 true for zlib, bit 1 true for gzip */ gz_headerp gzhead; /* gzip header information to write */ uInt gzindex; /* where in extra, name, or comment */ Byte method; /* STORED (for zip only) or DEFLATED */ int last_flush; /* value of flush param for previous deflate call */ /* used by deflate.c: */ uInt w_size; /* LZ77 window size (32K by default) */ uInt w_bits; /* log2(w_size) (8..16) */ uInt w_mask; /* w_size - 1 */ Bytef *window; /* Sliding window. Input bytes are read into the second half of the window, * and move to the first half later to keep a dictionary of at least wSize * bytes. With this organization, matches are limited to a distance of * wSize-MAX_MATCH bytes, but this ensures that IO is always * performed with a length multiple of the block size. Also, it limits * the window size to 64K, which is quite useful on MSDOS. * To do: use the user input buffer as sliding window. */ ulg window_size; /* Actual size of window: 2*wSize, except when the user input buffer * is directly used as sliding window. */ Posf *prev; /* Link to older string with same hash index. To limit the size of this * array to 64K, this link is maintained only for the last 32K strings. * An index in this array is thus a window index modulo 32K. */ Posf *head; /* Heads of the hash chains or NIL. */ uInt ins_h; /* hash index of string to be inserted */ uInt hash_size; /* number of elements in hash table */ uInt hash_bits; /* log2(hash_size) */ uInt hash_mask; /* hash_size-1 */ uInt hash_shift; /* Number of bits by which ins_h must be shifted at each input * step. It must be such that after MIN_MATCH steps, the oldest * byte no longer takes part in the hash key, that is: * hash_shift * MIN_MATCH >= hash_bits */ long block_start; /* Window position at the beginning of the current output block. Gets * negative when the window is moved backwards. */ uInt match_length; /* length of best match */ IPos prev_match; /* previous match */ int match_available; /* set if previous match exists */ uInt strstart; /* start of string to insert */ uInt match_start; /* start of matching string */ uInt lookahead; /* number of valid bytes ahead in window */ uInt prev_length; /* Length of the best match at previous step. Matches not greater than this * are discarded. This is used in the lazy match evaluation. */ uInt max_chain_length; /* To speed up deflation, hash chains are never searched beyond this * length. A higher limit improves compression ratio but degrades the * speed. */ uInt max_lazy_match; /* Attempt to find a better match only when the current match is strictly * smaller than this value. This mechanism is used only for compression * levels >= 4. */ # define max_insert_length max_lazy_match /* Insert new strings in the hash table only if the match length is not * greater than this length. This saves time but degrades compression. * max_insert_length is used only for compression levels <= 3. */ int level; /* compression level (1..9) */ int strategy; /* favor or force Huffman coding*/ uInt good_match; /* Use a faster search when the previous match is longer than this */ int nice_match; /* Stop searching when current match exceeds this */ /* used by trees.c: */ /* Didn't use ct_data typedef below to supress compiler warning */ struct ct_data_s dyn_ltree[HEAP_SIZE]; /* literal and length tree */ struct ct_data_s dyn_dtree[2*D_CODES+1]; /* distance tree */ struct ct_data_s bl_tree[2*BL_CODES+1]; /* Huffman tree for bit lengths */ struct tree_desc_s l_desc; /* desc. for literal tree */ struct tree_desc_s d_desc; /* desc. for distance tree */ struct tree_desc_s bl_desc; /* desc. for bit length tree */ ush bl_count[MAX_BITS+1]; /* number of codes at each bit length for an optimal tree */ int heap[2*L_CODES+1]; /* heap used to build the Huffman trees */ int heap_len; /* number of elements in the heap */ int heap_max; /* element of largest frequency */ /* The sons of heap[n] are heap[2*n] and heap[2*n+1]. heap[0] is not used. * The same heap array is used to build all trees. */ uch depth[2*L_CODES+1]; /* Depth of each subtree used as tie breaker for trees of equal frequency */ uchf *l_buf; /* buffer for literals or lengths */ uInt lit_bufsize; /* Size of match buffer for literals/lengths. There are 4 reasons for * limiting lit_bufsize to 64K: * - frequencies can be kept in 16 bit counters * - if compression is not successful for the first block, all input * data is still in the window so we can still emit a stored block even * when input comes from standard input. (This can also be done for * all blocks if lit_bufsize is not greater than 32K.) * - if compression is not successful for a file smaller than 64K, we can * even emit a stored file instead of a stored block (saving 5 bytes). * This is applicable only for zip (not gzip or zlib). * - creating new Huffman trees less frequently may not provide fast * adaptation to changes in the input data statistics. (Take for * example a binary file with poorly compressible code followed by * a highly compressible string table.) Smaller buffer sizes give * fast adaptation but have of course the overhead of transmitting * trees more frequently. * - I can't count above 4 */ uInt last_lit; /* running index in l_buf */ ushf *d_buf; /* Buffer for distances. To simplify the code, d_buf and l_buf have * the same number of elements. To use different lengths, an extra flag * array would be necessary. */ ulg opt_len; /* bit length of current block with optimal trees */ ulg static_len; /* bit length of current block with static trees */ uInt matches; /* number of string matches in current block */ int last_eob_len; /* bit length of EOB code for last block */ #ifdef DEBUG ulg compressed_len; /* total bit length of compressed file mod 2^32 */ ulg bits_sent; /* bit length of compressed data sent mod 2^32 */ #endif ush bi_buf; /* Output buffer. bits are inserted starting at the bottom (least * significant bits). */ int bi_valid; /* Number of valid bits in bi_buf. All bits above the last valid bit * are always zero. */ ulg high_water; /* High water mark offset in window for initialized bytes -- bytes above * this are set to zero in order to avoid memory check warnings when * longest match routines access bytes past the input. This is then * updated to the new high water mark. */ } FAR deflate_state; /* Output a byte on the stream. * IN assertion: there is enough room in pending_buf. */ #define put_byte(s, c) {s->pending_buf[s->pending++] = (c);} #define MIN_LOOKAHEAD (MAX_MATCH+MIN_MATCH+1) /* Minimum amount of lookahead, except at the end of the input file. * See deflate.c for comments about the MIN_MATCH+1. */ #define MAX_DIST(s) ((s)->w_size-MIN_LOOKAHEAD) /* In order to simplify the code, particularly on 16 bit machines, match * distances are limited to MAX_DIST instead of WSIZE. */ #define WIN_INIT MAX_MATCH /* Number of bytes after end of data in window to initialize in order to avoid memory checker errors from longest match routines */ /* in trees.c */ void ZLIB_INTERNAL _tr_init OF((deflate_state *s)); int ZLIB_INTERNAL _tr_tally OF((deflate_state *s, unsigned dist, unsigned lc)); void ZLIB_INTERNAL _tr_flush_block OF((deflate_state *s, charf *buf, ulg stored_len, int last)); void ZLIB_INTERNAL _tr_align OF((deflate_state *s)); void ZLIB_INTERNAL _tr_stored_block OF((deflate_state *s, charf *buf, ulg stored_len, int last)); #define d_code(dist) \ ((dist) < 256 ? _dist_code[dist] : _dist_code[256+((dist)>>7)]) /* Mapping from a distance to a distance code. dist is the distance - 1 and * must not have side effects. _dist_code[256] and _dist_code[257] are never * used. */ #ifndef DEBUG /* Inline versions of _tr_tally for speed: */ #if defined(GEN_TREES_H) || !defined(STDC) extern uch ZLIB_INTERNAL _length_code[]; extern uch ZLIB_INTERNAL _dist_code[]; #else extern const uch ZLIB_INTERNAL _length_code[]; extern const uch ZLIB_INTERNAL _dist_code[]; #endif # define _tr_tally_lit(s, c, flush) \ { uch cc = (c); \ s->d_buf[s->last_lit] = 0; \ s->l_buf[s->last_lit++] = cc; \ s->dyn_ltree[cc].Freq++; \ flush = (s->last_lit == s->lit_bufsize-1); \ } # define _tr_tally_dist(s, distance, length, flush) \ { uch len = (length); \ ush dist = (distance); \ s->d_buf[s->last_lit] = dist; \ s->l_buf[s->last_lit++] = len; \ dist--; \ s->dyn_ltree[_length_code[len]+LITERALS+1].Freq++; \ s->dyn_dtree[d_code(dist)].Freq++; \ flush = (s->last_lit == s->lit_bufsize-1); \ } #else # define _tr_tally_lit(s, c, flush) flush = _tr_tally(s, 0, c) # define _tr_tally_dist(s, distance, length, flush) \ flush = _tr_tally(s, distance, length) #endif #endif /* DEFLATE_H */ libmstoolkit-77.0.0/include/iasciitab.h0000644000175000017500000000344612455161024020002 0ustar rusconirusconi/* Copyright (c) 1998, 1999 Thai Open Source Software Center Ltd See the file COPYING for copying permission. */ /* Like asciitab.h, except that 0xD has code BT_S rather than BT_CR */ /* 0x00 */ BT_NONXML, BT_NONXML, BT_NONXML, BT_NONXML, /* 0x04 */ BT_NONXML, BT_NONXML, BT_NONXML, BT_NONXML, /* 0x08 */ BT_NONXML, BT_S, BT_LF, BT_NONXML, /* 0x0C */ BT_NONXML, BT_S, BT_NONXML, BT_NONXML, /* 0x10 */ BT_NONXML, BT_NONXML, BT_NONXML, BT_NONXML, /* 0x14 */ BT_NONXML, BT_NONXML, BT_NONXML, BT_NONXML, /* 0x18 */ BT_NONXML, BT_NONXML, BT_NONXML, BT_NONXML, /* 0x1C */ BT_NONXML, BT_NONXML, BT_NONXML, BT_NONXML, /* 0x20 */ BT_S, BT_EXCL, BT_QUOT, BT_NUM, /* 0x24 */ BT_OTHER, BT_PERCNT, BT_AMP, BT_APOS, /* 0x28 */ BT_LPAR, BT_RPAR, BT_AST, BT_PLUS, /* 0x2C */ BT_COMMA, BT_MINUS, BT_NAME, BT_SOL, /* 0x30 */ BT_DIGIT, BT_DIGIT, BT_DIGIT, BT_DIGIT, /* 0x34 */ BT_DIGIT, BT_DIGIT, BT_DIGIT, BT_DIGIT, /* 0x38 */ BT_DIGIT, BT_DIGIT, BT_COLON, BT_SEMI, /* 0x3C */ BT_LT, BT_EQUALS, BT_GT, BT_QUEST, /* 0x40 */ BT_OTHER, BT_HEX, BT_HEX, BT_HEX, /* 0x44 */ BT_HEX, BT_HEX, BT_HEX, BT_NMSTRT, /* 0x48 */ BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, /* 0x4C */ BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, /* 0x50 */ BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, /* 0x54 */ BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, /* 0x58 */ BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, BT_LSQB, /* 0x5C */ BT_OTHER, BT_RSQB, BT_OTHER, BT_NMSTRT, /* 0x60 */ BT_OTHER, BT_HEX, BT_HEX, BT_HEX, /* 0x64 */ BT_HEX, BT_HEX, BT_HEX, BT_NMSTRT, /* 0x68 */ BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, /* 0x6C */ BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, /* 0x70 */ BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, /* 0x74 */ BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, /* 0x78 */ BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, BT_OTHER, /* 0x7C */ BT_VERBAR, BT_OTHER, BT_OTHER, BT_OTHER, libmstoolkit-77.0.0/include/zlib.h0000644000175000017500000023331412455161024017011 0ustar rusconirusconi/* zlib.h -- interface of the 'zlib' general purpose compression library version 1.2.5, April 19th, 2010 Copyright (C) 1995-2010 Jean-loup Gailly and Mark Adler This software is provided 'as-is', without any express or implied warranty. In no event will the authors be held liable for any damages arising from the use of this software. Permission is granted to anyone to use this software for any purpose, including commercial applications, and to alter it and redistribute it freely, subject to the following restrictions: 1. The origin of this software must not be misrepresented; you must not claim that you wrote the original software. If you use this software in a product, an acknowledgment in the product documentation would be appreciated but is not required. 2. Altered source versions must be plainly marked as such, and must not be misrepresented as being the original software. 3. This notice may not be removed or altered from any source distribution. Jean-loup Gailly Mark Adler jloup@gzip.org madler@alumni.caltech.edu The data format used by the zlib library is described by RFCs (Request for Comments) 1950 to 1952 in the files http://www.ietf.org/rfc/rfc1950.txt (zlib format), rfc1951.txt (deflate format) and rfc1952.txt (gzip format). */ #ifndef ZLIB_H #define ZLIB_H #include "zconf.h" #ifdef __cplusplus extern "C" { #endif #define ZLIB_VERSION "1.2.5" #define ZLIB_VERNUM 0x1250 #define ZLIB_VER_MAJOR 1 #define ZLIB_VER_MINOR 2 #define ZLIB_VER_REVISION 5 #define ZLIB_VER_SUBREVISION 0 /* The 'zlib' compression library provides in-memory compression and decompression functions, including integrity checks of the uncompressed data. This version of the library supports only one compression method (deflation) but other algorithms will be added later and will have the same stream interface. Compression can be done in a single step if the buffers are large enough, or can be done by repeated calls of the compression function. In the latter case, the application must provide more input and/or consume the output (providing more output space) before each call. The compressed data format used by default by the in-memory functions is the zlib format, which is a zlib wrapper documented in RFC 1950, wrapped around a deflate stream, which is itself documented in RFC 1951. The library also supports reading and writing files in gzip (.gz) format with an interface similar to that of stdio using the functions that start with "gz". The gzip format is different from the zlib format. gzip is a gzip wrapper, documented in RFC 1952, wrapped around a deflate stream. This library can optionally read and write gzip streams in memory as well. The zlib format was designed to be compact and fast for use in memory and on communications channels. The gzip format was designed for single- file compression on file systems, has a larger header than zlib to maintain directory information, and uses a different, slower check method than zlib. The library does not install any signal handler. The decoder checks the consistency of the compressed data, so the library should never crash even in case of corrupted input. */ typedef voidpf (*alloc_func) OF((voidpf opaque, uInt items, uInt size)); typedef void (*free_func) OF((voidpf opaque, voidpf address)); struct internal_state; typedef struct z_stream_s { Bytef *next_in; /* next input byte */ uInt avail_in; /* number of bytes available at next_in */ uLong total_in; /* total nb of input bytes read so far */ Bytef *next_out; /* next output byte should be put there */ uInt avail_out; /* remaining free space at next_out */ uLong total_out; /* total nb of bytes output so far */ char *msg; /* last error message, NULL if no error */ struct internal_state FAR *state; /* not visible by applications */ alloc_func zalloc; /* used to allocate the internal state */ free_func zfree; /* used to free the internal state */ voidpf opaque; /* private data object passed to zalloc and zfree */ int data_type; /* best guess about the data type: binary or text */ uLong adler; /* adler32 value of the uncompressed data */ uLong reserved; /* reserved for future use */ } z_stream; typedef z_stream FAR *z_streamp; /* gzip header information passed to and from zlib routines. See RFC 1952 for more details on the meanings of these fields. */ typedef struct gz_header_s { int text; /* true if compressed data believed to be text */ uLong time; /* modification time */ int xflags; /* extra flags (not used when writing a gzip file) */ int os; /* operating system */ Bytef *extra; /* pointer to extra field or Z_NULL if none */ uInt extra_len; /* extra field length (valid if extra != Z_NULL) */ uInt extra_max; /* space at extra (only when reading header) */ Bytef *name; /* pointer to zero-terminated file name or Z_NULL */ uInt name_max; /* space at name (only when reading header) */ Bytef *comment; /* pointer to zero-terminated comment or Z_NULL */ uInt comm_max; /* space at comment (only when reading header) */ int hcrc; /* true if there was or will be a header crc */ int done; /* true when done reading gzip header (not used when writing a gzip file) */ } gz_header; typedef gz_header FAR *gz_headerp; /* The application must update next_in and avail_in when avail_in has dropped to zero. It must update next_out and avail_out when avail_out has dropped to zero. The application must initialize zalloc, zfree and opaque before calling the init function. All other fields are set by the compression library and must not be updated by the application. The opaque value provided by the application will be passed as the first parameter for calls of zalloc and zfree. This can be useful for custom memory management. The compression library attaches no meaning to the opaque value. zalloc must return Z_NULL if there is not enough memory for the object. If zlib is used in a multi-threaded application, zalloc and zfree must be thread safe. On 16-bit systems, the functions zalloc and zfree must be able to allocate exactly 65536 bytes, but will not be required to allocate more than this if the symbol MAXSEG_64K is defined (see zconf.h). WARNING: On MSDOS, pointers returned by zalloc for objects of exactly 65536 bytes *must* have their offset normalized to zero. The default allocation function provided by this library ensures this (see zutil.c). To reduce memory requirements and avoid any allocation of 64K objects, at the expense of compression ratio, compile the library with -DMAX_WBITS=14 (see zconf.h). The fields total_in and total_out can be used for statistics or progress reports. After compression, total_in holds the total size of the uncompressed data and may be saved for use in the decompressor (particularly if the decompressor wants to decompress everything in a single step). */ /* constants */ #define Z_NO_FLUSH 0 #define Z_PARTIAL_FLUSH 1 #define Z_SYNC_FLUSH 2 #define Z_FULL_FLUSH 3 #define Z_FINISH 4 #define Z_BLOCK 5 #define Z_TREES 6 /* Allowed flush values; see deflate() and inflate() below for details */ #define Z_OK 0 #define Z_STREAM_END 1 #define Z_NEED_DICT 2 #define Z_ERRNO (-1) #define Z_STREAM_ERROR (-2) #define Z_DATA_ERROR (-3) #define Z_MEM_ERROR (-4) #define Z_BUF_ERROR (-5) #define Z_VERSION_ERROR (-6) /* Return codes for the compression/decompression functions. Negative values * are errors, positive values are used for special but normal events. */ #define Z_NO_COMPRESSION 0 #define Z_BEST_SPEED 1 #define Z_BEST_COMPRESSION 9 #define Z_DEFAULT_COMPRESSION (-1) /* compression levels */ #define Z_FILTERED 1 #define Z_HUFFMAN_ONLY 2 #define Z_RLE 3 #define Z_FIXED 4 #define Z_DEFAULT_STRATEGY 0 /* compression strategy; see deflateInit2() below for details */ #define Z_BINARY 0 #define Z_TEXT 1 #define Z_ASCII Z_TEXT /* for compatibility with 1.2.2 and earlier */ #define Z_UNKNOWN 2 /* Possible values of the data_type field (though see inflate()) */ #define Z_DEFLATED 8 /* The deflate compression method (the only one supported in this version) */ #define Z_NULL 0 /* for initializing zalloc, zfree, opaque */ #define zlib_version zlibVersion() /* for compatibility with versions < 1.0.2 */ /* basic functions */ ZEXTERN const char * ZEXPORT zlibVersion OF((void)); /* The application can compare zlibVersion and ZLIB_VERSION for consistency. If the first character differs, the library code actually used is not compatible with the zlib.h header file used by the application. This check is automatically made by deflateInit and inflateInit. */ /* ZEXTERN int ZEXPORT deflateInit OF((z_streamp strm, int level)); Initializes the internal stream state for compression. The fields zalloc, zfree and opaque must be initialized before by the caller. If zalloc and zfree are set to Z_NULL, deflateInit updates them to use default allocation functions. The compression level must be Z_DEFAULT_COMPRESSION, or between 0 and 9: 1 gives best speed, 9 gives best compression, 0 gives no compression at all (the input data is simply copied a block at a time). Z_DEFAULT_COMPRESSION requests a default compromise between speed and compression (currently equivalent to level 6). deflateInit returns Z_OK if success, Z_MEM_ERROR if there was not enough memory, Z_STREAM_ERROR if level is not a valid compression level, or Z_VERSION_ERROR if the zlib library version (zlib_version) is incompatible with the version assumed by the caller (ZLIB_VERSION). msg is set to null if there is no error message. deflateInit does not perform any compression: this will be done by deflate(). */ ZEXTERN int ZEXPORT deflate OF((z_streamp strm, int flush)); /* deflate compresses as much data as possible, and stops when the input buffer becomes empty or the output buffer becomes full. It may introduce some output latency (reading input without producing any output) except when forced to flush. The detailed semantics are as follows. deflate performs one or both of the following actions: - Compress more input starting at next_in and update next_in and avail_in accordingly. If not all input can be processed (because there is not enough room in the output buffer), next_in and avail_in are updated and processing will resume at this point for the next call of deflate(). - Provide more output starting at next_out and update next_out and avail_out accordingly. This action is forced if the parameter flush is non zero. Forcing flush frequently degrades the compression ratio, so this parameter should be set only when necessary (in interactive applications). Some output may be provided even if flush is not set. Before the call of deflate(), the application should ensure that at least one of the actions is possible, by providing more input and/or consuming more output, and updating avail_in or avail_out accordingly; avail_out should never be zero before the call. The application can consume the compressed output when it wants, for example when the output buffer is full (avail_out == 0), or after each call of deflate(). If deflate returns Z_OK and with zero avail_out, it must be called again after making room in the output buffer because there might be more output pending. Normally the parameter flush is set to Z_NO_FLUSH, which allows deflate to decide how much data to accumulate before producing output, in order to maximize compression. If the parameter flush is set to Z_SYNC_FLUSH, all pending output is flushed to the output buffer and the output is aligned on a byte boundary, so that the decompressor can get all input data available so far. (In particular avail_in is zero after the call if enough output space has been provided before the call.) Flushing may degrade compression for some compression algorithms and so it should be used only when necessary. This completes the current deflate block and follows it with an empty stored block that is three bits plus filler bits to the next byte, followed by four bytes (00 00 ff ff). If flush is set to Z_PARTIAL_FLUSH, all pending output is flushed to the output buffer, but the output is not aligned to a byte boundary. All of the input data so far will be available to the decompressor, as for Z_SYNC_FLUSH. This completes the current deflate block and follows it with an empty fixed codes block that is 10 bits long. This assures that enough bytes are output in order for the decompressor to finish the block before the empty fixed code block. If flush is set to Z_BLOCK, a deflate block is completed and emitted, as for Z_SYNC_FLUSH, but the output is not aligned on a byte boundary, and up to seven bits of the current block are held to be written as the next byte after the next deflate block is completed. In this case, the decompressor may not be provided enough bits at this point in order to complete decompression of the data provided so far to the compressor. It may need to wait for the next block to be emitted. This is for advanced applications that need to control the emission of deflate blocks. If flush is set to Z_FULL_FLUSH, all output is flushed as with Z_SYNC_FLUSH, and the compression state is reset so that decompression can restart from this point if previous compressed data has been damaged or if random access is desired. Using Z_FULL_FLUSH too often can seriously degrade compression. If deflate returns with avail_out == 0, this function must be called again with the same value of the flush parameter and more output space (updated avail_out), until the flush is complete (deflate returns with non-zero avail_out). In the case of a Z_FULL_FLUSH or Z_SYNC_FLUSH, make sure that avail_out is greater than six to avoid repeated flush markers due to avail_out == 0 on return. If the parameter flush is set to Z_FINISH, pending input is processed, pending output is flushed and deflate returns with Z_STREAM_END if there was enough output space; if deflate returns with Z_OK, this function must be called again with Z_FINISH and more output space (updated avail_out) but no more input data, until it returns with Z_STREAM_END or an error. After deflate has returned Z_STREAM_END, the only possible operations on the stream are deflateReset or deflateEnd. Z_FINISH can be used immediately after deflateInit if all the compression is to be done in a single step. In this case, avail_out must be at least the value returned by deflateBound (see below). If deflate does not return Z_STREAM_END, then it must be called again as described above. deflate() sets strm->adler to the adler32 checksum of all input read so far (that is, total_in bytes). deflate() may update strm->data_type if it can make a good guess about the input data type (Z_BINARY or Z_TEXT). In doubt, the data is considered binary. This field is only for information purposes and does not affect the compression algorithm in any manner. deflate() returns Z_OK if some progress has been made (more input processed or more output produced), Z_STREAM_END if all input has been consumed and all output has been produced (only when flush is set to Z_FINISH), Z_STREAM_ERROR if the stream state was inconsistent (for example if next_in or next_out was Z_NULL), Z_BUF_ERROR if no progress is possible (for example avail_in or avail_out was zero). Note that Z_BUF_ERROR is not fatal, and deflate() can be called again with more input and more output space to continue compressing. */ ZEXTERN int ZEXPORT deflateEnd OF((z_streamp strm)); /* All dynamically allocated data structures for this stream are freed. This function discards any unprocessed input and does not flush any pending output. deflateEnd returns Z_OK if success, Z_STREAM_ERROR if the stream state was inconsistent, Z_DATA_ERROR if the stream was freed prematurely (some input or output was discarded). In the error case, msg may be set but then points to a static string (which must not be deallocated). */ /* ZEXTERN int ZEXPORT inflateInit OF((z_streamp strm)); Initializes the internal stream state for decompression. The fields next_in, avail_in, zalloc, zfree and opaque must be initialized before by the caller. If next_in is not Z_NULL and avail_in is large enough (the exact value depends on the compression method), inflateInit determines the compression method from the zlib header and allocates all data structures accordingly; otherwise the allocation will be deferred to the first call of inflate. If zalloc and zfree are set to Z_NULL, inflateInit updates them to use default allocation functions. inflateInit returns Z_OK if success, Z_MEM_ERROR if there was not enough memory, Z_VERSION_ERROR if the zlib library version is incompatible with the version assumed by the caller, or Z_STREAM_ERROR if the parameters are invalid, such as a null pointer to the structure. msg is set to null if there is no error message. inflateInit does not perform any decompression apart from possibly reading the zlib header if present: actual decompression will be done by inflate(). (So next_in and avail_in may be modified, but next_out and avail_out are unused and unchanged.) The current implementation of inflateInit() does not process any header information -- that is deferred until inflate() is called. */ ZEXTERN int ZEXPORT inflate OF((z_streamp strm, int flush)); /* inflate decompresses as much data as possible, and stops when the input buffer becomes empty or the output buffer becomes full. It may introduce some output latency (reading input without producing any output) except when forced to flush. The detailed semantics are as follows. inflate performs one or both of the following actions: - Decompress more input starting at next_in and update next_in and avail_in accordingly. If not all input can be processed (because there is not enough room in the output buffer), next_in is updated and processing will resume at this point for the next call of inflate(). - Provide more output starting at next_out and update next_out and avail_out accordingly. inflate() provides as much output as possible, until there is no more input data or no more space in the output buffer (see below about the flush parameter). Before the call of inflate(), the application should ensure that at least one of the actions is possible, by providing more input and/or consuming more output, and updating the next_* and avail_* values accordingly. The application can consume the uncompressed output when it wants, for example when the output buffer is full (avail_out == 0), or after each call of inflate(). If inflate returns Z_OK and with zero avail_out, it must be called again after making room in the output buffer because there might be more output pending. The flush parameter of inflate() can be Z_NO_FLUSH, Z_SYNC_FLUSH, Z_FINISH, Z_BLOCK, or Z_TREES. Z_SYNC_FLUSH requests that inflate() flush as much output as possible to the output buffer. Z_BLOCK requests that inflate() stop if and when it gets to the next deflate block boundary. When decoding the zlib or gzip format, this will cause inflate() to return immediately after the header and before the first block. When doing a raw inflate, inflate() will go ahead and process the first block, and will return when it gets to the end of that block, or when it runs out of data. The Z_BLOCK option assists in appending to or combining deflate streams. Also to assist in this, on return inflate() will set strm->data_type to the number of unused bits in the last byte taken from strm->next_in, plus 64 if inflate() is currently decoding the last block in the deflate stream, plus 128 if inflate() returned immediately after decoding an end-of-block code or decoding the complete header up to just before the first byte of the deflate stream. The end-of-block will not be indicated until all of the uncompressed data from that block has been written to strm->next_out. The number of unused bits may in general be greater than seven, except when bit 7 of data_type is set, in which case the number of unused bits will be less than eight. data_type is set as noted here every time inflate() returns for all flush options, and so can be used to determine the amount of currently consumed input in bits. The Z_TREES option behaves as Z_BLOCK does, but it also returns when the end of each deflate block header is reached, before any actual data in that block is decoded. This allows the caller to determine the length of the deflate block header for later use in random access within a deflate block. 256 is added to the value of strm->data_type when inflate() returns immediately after reaching the end of the deflate block header. inflate() should normally be called until it returns Z_STREAM_END or an error. However if all decompression is to be performed in a single step (a single call of inflate), the parameter flush should be set to Z_FINISH. In this case all pending input is processed and all pending output is flushed; avail_out must be large enough to hold all the uncompressed data. (The size of the uncompressed data may have been saved by the compressor for this purpose.) The next operation on this stream must be inflateEnd to deallocate the decompression state. The use of Z_FINISH is never required, but can be used to inform inflate that a faster approach may be used for the single inflate() call. In this implementation, inflate() always flushes as much output as possible to the output buffer, and always uses the faster approach on the first call. So the only effect of the flush parameter in this implementation is on the return value of inflate(), as noted below, or when it returns early because Z_BLOCK or Z_TREES is used. If a preset dictionary is needed after this call (see inflateSetDictionary below), inflate sets strm->adler to the adler32 checksum of the dictionary chosen by the compressor and returns Z_NEED_DICT; otherwise it sets strm->adler to the adler32 checksum of all output produced so far (that is, total_out bytes) and returns Z_OK, Z_STREAM_END or an error code as described below. At the end of the stream, inflate() checks that its computed adler32 checksum is equal to that saved by the compressor and returns Z_STREAM_END only if the checksum is correct. inflate() can decompress and check either zlib-wrapped or gzip-wrapped deflate data. The header type is detected automatically, if requested when initializing with inflateInit2(). Any information contained in the gzip header is not retained, so applications that need that information should instead use raw inflate, see inflateInit2() below, or inflateBack() and perform their own processing of the gzip header and trailer. inflate() returns Z_OK if some progress has been made (more input processed or more output produced), Z_STREAM_END if the end of the compressed data has been reached and all uncompressed output has been produced, Z_NEED_DICT if a preset dictionary is needed at this point, Z_DATA_ERROR if the input data was corrupted (input stream not conforming to the zlib format or incorrect check value), Z_STREAM_ERROR if the stream structure was inconsistent (for example next_in or next_out was Z_NULL), Z_MEM_ERROR if there was not enough memory, Z_BUF_ERROR if no progress is possible or if there was not enough room in the output buffer when Z_FINISH is used. Note that Z_BUF_ERROR is not fatal, and inflate() can be called again with more input and more output space to continue decompressing. If Z_DATA_ERROR is returned, the application may then call inflateSync() to look for a good compression block if a partial recovery of the data is desired. */ ZEXTERN int ZEXPORT inflateEnd OF((z_streamp strm)); /* All dynamically allocated data structures for this stream are freed. This function discards any unprocessed input and does not flush any pending output. inflateEnd returns Z_OK if success, Z_STREAM_ERROR if the stream state was inconsistent. In the error case, msg may be set but then points to a static string (which must not be deallocated). */ /* Advanced functions */ /* The following functions are needed only in some special applications. */ /* ZEXTERN int ZEXPORT deflateInit2 OF((z_streamp strm, int level, int method, int windowBits, int memLevel, int strategy)); This is another version of deflateInit with more compression options. The fields next_in, zalloc, zfree and opaque must be initialized before by the caller. The method parameter is the compression method. It must be Z_DEFLATED in this version of the library. The windowBits parameter is the base two logarithm of the window size (the size of the history buffer). It should be in the range 8..15 for this version of the library. Larger values of this parameter result in better compression at the expense of memory usage. The default value is 15 if deflateInit is used instead. windowBits can also be -8..-15 for raw deflate. In this case, -windowBits determines the window size. deflate() will then generate raw deflate data with no zlib header or trailer, and will not compute an adler32 check value. windowBits can also be greater than 15 for optional gzip encoding. Add 16 to windowBits to write a simple gzip header and trailer around the compressed data instead of a zlib wrapper. The gzip header will have no file name, no extra data, no comment, no modification time (set to zero), no header crc, and the operating system will be set to 255 (unknown). If a gzip stream is being written, strm->adler is a crc32 instead of an adler32. The memLevel parameter specifies how much memory should be allocated for the internal compression state. memLevel=1 uses minimum memory but is slow and reduces compression ratio; memLevel=9 uses maximum memory for optimal speed. The default value is 8. See zconf.h for total memory usage as a function of windowBits and memLevel. The strategy parameter is used to tune the compression algorithm. Use the value Z_DEFAULT_STRATEGY for normal data, Z_FILTERED for data produced by a filter (or predictor), Z_HUFFMAN_ONLY to force Huffman encoding only (no string match), or Z_RLE to limit match distances to one (run-length encoding). Filtered data consists mostly of small values with a somewhat random distribution. In this case, the compression algorithm is tuned to compress them better. The effect of Z_FILTERED is to force more Huffman coding and less string matching; it is somewhat intermediate between Z_DEFAULT_STRATEGY and Z_HUFFMAN_ONLY. Z_RLE is designed to be almost as fast as Z_HUFFMAN_ONLY, but give better compression for PNG image data. The strategy parameter only affects the compression ratio but not the correctness of the compressed output even if it is not set appropriately. Z_FIXED prevents the use of dynamic Huffman codes, allowing for a simpler decoder for special applications. deflateInit2 returns Z_OK if success, Z_MEM_ERROR if there was not enough memory, Z_STREAM_ERROR if any parameter is invalid (such as an invalid method), or Z_VERSION_ERROR if the zlib library version (zlib_version) is incompatible with the version assumed by the caller (ZLIB_VERSION). msg is set to null if there is no error message. deflateInit2 does not perform any compression: this will be done by deflate(). */ ZEXTERN int ZEXPORT deflateSetDictionary OF((z_streamp strm, const Bytef *dictionary, uInt dictLength)); /* Initializes the compression dictionary from the given byte sequence without producing any compressed output. This function must be called immediately after deflateInit, deflateInit2 or deflateReset, before any call of deflate. The compressor and decompressor must use exactly the same dictionary (see inflateSetDictionary). The dictionary should consist of strings (byte sequences) that are likely to be encountered later in the data to be compressed, with the most commonly used strings preferably put towards the end of the dictionary. Using a dictionary is most useful when the data to be compressed is short and can be predicted with good accuracy; the data can then be compressed better than with the default empty dictionary. Depending on the size of the compression data structures selected by deflateInit or deflateInit2, a part of the dictionary may in effect be discarded, for example if the dictionary is larger than the window size provided in deflateInit or deflateInit2. Thus the strings most likely to be useful should be put at the end of the dictionary, not at the front. In addition, the current implementation of deflate will use at most the window size minus 262 bytes of the provided dictionary. Upon return of this function, strm->adler is set to the adler32 value of the dictionary; the decompressor may later use this value to determine which dictionary has been used by the compressor. (The adler32 value applies to the whole dictionary even if only a subset of the dictionary is actually used by the compressor.) If a raw deflate was requested, then the adler32 value is not computed and strm->adler is not set. deflateSetDictionary returns Z_OK if success, or Z_STREAM_ERROR if a parameter is invalid (e.g. dictionary being Z_NULL) or the stream state is inconsistent (for example if deflate has already been called for this stream or if the compression method is bsort). deflateSetDictionary does not perform any compression: this will be done by deflate(). */ ZEXTERN int ZEXPORT deflateCopy OF((z_streamp dest, z_streamp source)); /* Sets the destination stream as a complete copy of the source stream. This function can be useful when several compression strategies will be tried, for example when there are several ways of pre-processing the input data with a filter. The streams that will be discarded should then be freed by calling deflateEnd. Note that deflateCopy duplicates the internal compression state which can be quite large, so this strategy is slow and can consume lots of memory. deflateCopy returns Z_OK if success, Z_MEM_ERROR if there was not enough memory, Z_STREAM_ERROR if the source stream state was inconsistent (such as zalloc being Z_NULL). msg is left unchanged in both source and destination. */ ZEXTERN int ZEXPORT deflateReset OF((z_streamp strm)); /* This function is equivalent to deflateEnd followed by deflateInit, but does not free and reallocate all the internal compression state. The stream will keep the same compression level and any other attributes that may have been set by deflateInit2. deflateReset returns Z_OK if success, or Z_STREAM_ERROR if the source stream state was inconsistent (such as zalloc or state being Z_NULL). */ ZEXTERN int ZEXPORT deflateParams OF((z_streamp strm, int level, int strategy)); /* Dynamically update the compression level and compression strategy. The interpretation of level and strategy is as in deflateInit2. This can be used to switch between compression and straight copy of the input data, or to switch to a different kind of input data requiring a different strategy. If the compression level is changed, the input available so far is compressed with the old level (and may be flushed); the new level will take effect only at the next call of deflate(). Before the call of deflateParams, the stream state must be set as for a call of deflate(), since the currently available input may have to be compressed and flushed. In particular, strm->avail_out must be non-zero. deflateParams returns Z_OK if success, Z_STREAM_ERROR if the source stream state was inconsistent or if a parameter was invalid, Z_BUF_ERROR if strm->avail_out was zero. */ ZEXTERN int ZEXPORT deflateTune OF((z_streamp strm, int good_length, int max_lazy, int nice_length, int max_chain)); /* Fine tune deflate's internal compression parameters. This should only be used by someone who understands the algorithm used by zlib's deflate for searching for the best matching string, and even then only by the most fanatic optimizer trying to squeeze out the last compressed bit for their specific input data. Read the deflate.c source code for the meaning of the max_lazy, good_length, nice_length, and max_chain parameters. deflateTune() can be called after deflateInit() or deflateInit2(), and returns Z_OK on success, or Z_STREAM_ERROR for an invalid deflate stream. */ ZEXTERN uLong ZEXPORT deflateBound OF((z_streamp strm, uLong sourceLen)); /* deflateBound() returns an upper bound on the compressed size after deflation of sourceLen bytes. It must be called after deflateInit() or deflateInit2(), and after deflateSetHeader(), if used. This would be used to allocate an output buffer for deflation in a single pass, and so would be called before deflate(). */ ZEXTERN int ZEXPORT deflatePrime OF((z_streamp strm, int bits, int value)); /* deflatePrime() inserts bits in the deflate output stream. The intent is that this function is used to start off the deflate output with the bits leftover from a previous deflate stream when appending to it. As such, this function can only be used for raw deflate, and must be used before the first deflate() call after a deflateInit2() or deflateReset(). bits must be less than or equal to 16, and that many of the least significant bits of value will be inserted in the output. deflatePrime returns Z_OK if success, or Z_STREAM_ERROR if the source stream state was inconsistent. */ ZEXTERN int ZEXPORT deflateSetHeader OF((z_streamp strm, gz_headerp head)); /* deflateSetHeader() provides gzip header information for when a gzip stream is requested by deflateInit2(). deflateSetHeader() may be called after deflateInit2() or deflateReset() and before the first call of deflate(). The text, time, os, extra field, name, and comment information in the provided gz_header structure are written to the gzip header (xflag is ignored -- the extra flags are set according to the compression level). The caller must assure that, if not Z_NULL, name and comment are terminated with a zero byte, and that if extra is not Z_NULL, that extra_len bytes are available there. If hcrc is true, a gzip header crc is included. Note that the current versions of the command-line version of gzip (up through version 1.3.x) do not support header crc's, and will report that it is a "multi-part gzip file" and give up. If deflateSetHeader is not used, the default gzip header has text false, the time set to zero, and os set to 255, with no extra, name, or comment fields. The gzip header is returned to the default state by deflateReset(). deflateSetHeader returns Z_OK if success, or Z_STREAM_ERROR if the source stream state was inconsistent. */ /* ZEXTERN int ZEXPORT inflateInit2 OF((z_streamp strm, int windowBits)); This is another version of inflateInit with an extra parameter. The fields next_in, avail_in, zalloc, zfree and opaque must be initialized before by the caller. The windowBits parameter is the base two logarithm of the maximum window size (the size of the history buffer). It should be in the range 8..15 for this version of the library. The default value is 15 if inflateInit is used instead. windowBits must be greater than or equal to the windowBits value provided to deflateInit2() while compressing, or it must be equal to 15 if deflateInit2() was not used. If a compressed stream with a larger window size is given as input, inflate() will return with the error code Z_DATA_ERROR instead of trying to allocate a larger window. windowBits can also be zero to request that inflate use the window size in the zlib header of the compressed stream. windowBits can also be -8..-15 for raw inflate. In this case, -windowBits determines the window size. inflate() will then process raw deflate data, not looking for a zlib or gzip header, not generating a check value, and not looking for any check values for comparison at the end of the stream. This is for use with other formats that use the deflate compressed data format such as zip. Those formats provide their own check values. If a custom format is developed using the raw deflate format for compressed data, it is recommended that a check value such as an adler32 or a crc32 be applied to the uncompressed data as is done in the zlib, gzip, and zip formats. For most applications, the zlib format should be used as is. Note that comments above on the use in deflateInit2() applies to the magnitude of windowBits. windowBits can also be greater than 15 for optional gzip decoding. Add 32 to windowBits to enable zlib and gzip decoding with automatic header detection, or add 16 to decode only the gzip format (the zlib format will return a Z_DATA_ERROR). If a gzip stream is being decoded, strm->adler is a crc32 instead of an adler32. inflateInit2 returns Z_OK if success, Z_MEM_ERROR if there was not enough memory, Z_VERSION_ERROR if the zlib library version is incompatible with the version assumed by the caller, or Z_STREAM_ERROR if the parameters are invalid, such as a null pointer to the structure. msg is set to null if there is no error message. inflateInit2 does not perform any decompression apart from possibly reading the zlib header if present: actual decompression will be done by inflate(). (So next_in and avail_in may be modified, but next_out and avail_out are unused and unchanged.) The current implementation of inflateInit2() does not process any header information -- that is deferred until inflate() is called. */ ZEXTERN int ZEXPORT inflateSetDictionary OF((z_streamp strm, const Bytef *dictionary, uInt dictLength)); /* Initializes the decompression dictionary from the given uncompressed byte sequence. This function must be called immediately after a call of inflate, if that call returned Z_NEED_DICT. The dictionary chosen by the compressor can be determined from the adler32 value returned by that call of inflate. The compressor and decompressor must use exactly the same dictionary (see deflateSetDictionary). For raw inflate, this function can be called immediately after inflateInit2() or inflateReset() and before any call of inflate() to set the dictionary. The application must insure that the dictionary that was used for compression is provided. inflateSetDictionary returns Z_OK if success, Z_STREAM_ERROR if a parameter is invalid (e.g. dictionary being Z_NULL) or the stream state is inconsistent, Z_DATA_ERROR if the given dictionary doesn't match the expected one (incorrect adler32 value). inflateSetDictionary does not perform any decompression: this will be done by subsequent calls of inflate(). */ ZEXTERN int ZEXPORT inflateSync OF((z_streamp strm)); /* Skips invalid compressed data until a full flush point (see above the description of deflate with Z_FULL_FLUSH) can be found, or until all available input is skipped. No output is provided. inflateSync returns Z_OK if a full flush point has been found, Z_BUF_ERROR if no more input was provided, Z_DATA_ERROR if no flush point has been found, or Z_STREAM_ERROR if the stream structure was inconsistent. In the success case, the application may save the current current value of total_in which indicates where valid compressed data was found. In the error case, the application may repeatedly call inflateSync, providing more input each time, until success or end of the input data. */ ZEXTERN int ZEXPORT inflateCopy OF((z_streamp dest, z_streamp source)); /* Sets the destination stream as a complete copy of the source stream. This function can be useful when randomly accessing a large stream. The first pass through the stream can periodically record the inflate state, allowing restarting inflate at those points when randomly accessing the stream. inflateCopy returns Z_OK if success, Z_MEM_ERROR if there was not enough memory, Z_STREAM_ERROR if the source stream state was inconsistent (such as zalloc being Z_NULL). msg is left unchanged in both source and destination. */ ZEXTERN int ZEXPORT inflateReset OF((z_streamp strm)); /* This function is equivalent to inflateEnd followed by inflateInit, but does not free and reallocate all the internal decompression state. The stream will keep attributes that may have been set by inflateInit2. inflateReset returns Z_OK if success, or Z_STREAM_ERROR if the source stream state was inconsistent (such as zalloc or state being Z_NULL). */ ZEXTERN int ZEXPORT inflateReset2 OF((z_streamp strm, int windowBits)); /* This function is the same as inflateReset, but it also permits changing the wrap and window size requests. The windowBits parameter is interpreted the same as it is for inflateInit2. inflateReset2 returns Z_OK if success, or Z_STREAM_ERROR if the source stream state was inconsistent (such as zalloc or state being Z_NULL), or if the windowBits parameter is invalid. */ ZEXTERN int ZEXPORT inflatePrime OF((z_streamp strm, int bits, int value)); /* This function inserts bits in the inflate input stream. The intent is that this function is used to start inflating at a bit position in the middle of a byte. The provided bits will be used before any bytes are used from next_in. This function should only be used with raw inflate, and should be used before the first inflate() call after inflateInit2() or inflateReset(). bits must be less than or equal to 16, and that many of the least significant bits of value will be inserted in the input. If bits is negative, then the input stream bit buffer is emptied. Then inflatePrime() can be called again to put bits in the buffer. This is used to clear out bits leftover after feeding inflate a block description prior to feeding inflate codes. inflatePrime returns Z_OK if success, or Z_STREAM_ERROR if the source stream state was inconsistent. */ ZEXTERN long ZEXPORT inflateMark OF((z_streamp strm)); /* This function returns two values, one in the lower 16 bits of the return value, and the other in the remaining upper bits, obtained by shifting the return value down 16 bits. If the upper value is -1 and the lower value is zero, then inflate() is currently decoding information outside of a block. If the upper value is -1 and the lower value is non-zero, then inflate is in the middle of a stored block, with the lower value equaling the number of bytes from the input remaining to copy. If the upper value is not -1, then it is the number of bits back from the current bit position in the input of the code (literal or length/distance pair) currently being processed. In that case the lower value is the number of bytes already emitted for that code. A code is being processed if inflate is waiting for more input to complete decoding of the code, or if it has completed decoding but is waiting for more output space to write the literal or match data. inflateMark() is used to mark locations in the input data for random access, which may be at bit positions, and to note those cases where the output of a code may span boundaries of random access blocks. The current location in the input stream can be determined from avail_in and data_type as noted in the description for the Z_BLOCK flush parameter for inflate. inflateMark returns the value noted above or -1 << 16 if the provided source stream state was inconsistent. */ ZEXTERN int ZEXPORT inflateGetHeader OF((z_streamp strm, gz_headerp head)); /* inflateGetHeader() requests that gzip header information be stored in the provided gz_header structure. inflateGetHeader() may be called after inflateInit2() or inflateReset(), and before the first call of inflate(). As inflate() processes the gzip stream, head->done is zero until the header is completed, at which time head->done is set to one. If a zlib stream is being decoded, then head->done is set to -1 to indicate that there will be no gzip header information forthcoming. Note that Z_BLOCK or Z_TREES can be used to force inflate() to return immediately after header processing is complete and before any actual data is decompressed. The text, time, xflags, and os fields are filled in with the gzip header contents. hcrc is set to true if there is a header CRC. (The header CRC was valid if done is set to one.) If extra is not Z_NULL, then extra_max contains the maximum number of bytes to write to extra. Once done is true, extra_len contains the actual extra field length, and extra contains the extra field, or that field truncated if extra_max is less than extra_len. If name is not Z_NULL, then up to name_max characters are written there, terminated with a zero unless the length is greater than name_max. If comment is not Z_NULL, then up to comm_max characters are written there, terminated with a zero unless the length is greater than comm_max. When any of extra, name, or comment are not Z_NULL and the respective field is not present in the header, then that field is set to Z_NULL to signal its absence. This allows the use of deflateSetHeader() with the returned structure to duplicate the header. However if those fields are set to allocated memory, then the application will need to save those pointers elsewhere so that they can be eventually freed. If inflateGetHeader is not used, then the header information is simply discarded. The header is always checked for validity, including the header CRC if present. inflateReset() will reset the process to discard the header information. The application would need to call inflateGetHeader() again to retrieve the header from the next gzip stream. inflateGetHeader returns Z_OK if success, or Z_STREAM_ERROR if the source stream state was inconsistent. */ /* ZEXTERN int ZEXPORT inflateBackInit OF((z_streamp strm, int windowBits, unsigned char FAR *window)); Initialize the internal stream state for decompression using inflateBack() calls. The fields zalloc, zfree and opaque in strm must be initialized before the call. If zalloc and zfree are Z_NULL, then the default library- derived memory allocation routines are used. windowBits is the base two logarithm of the window size, in the range 8..15. window is a caller supplied buffer of that size. Except for special applications where it is assured that deflate was used with small window sizes, windowBits must be 15 and a 32K byte window must be supplied to be able to decompress general deflate streams. See inflateBack() for the usage of these routines. inflateBackInit will return Z_OK on success, Z_STREAM_ERROR if any of the paramaters are invalid, Z_MEM_ERROR if the internal state could not be allocated, or Z_VERSION_ERROR if the version of the library does not match the version of the header file. */ typedef unsigned (*in_func) OF((void FAR *, unsigned char FAR * FAR *)); typedef int (*out_func) OF((void FAR *, unsigned char FAR *, unsigned)); ZEXTERN int ZEXPORT inflateBack OF((z_streamp strm, in_func in, void FAR *in_desc, out_func out, void FAR *out_desc)); /* inflateBack() does a raw inflate with a single call using a call-back interface for input and output. This is more efficient than inflate() for file i/o applications in that it avoids copying between the output and the sliding window by simply making the window itself the output buffer. This function trusts the application to not change the output buffer passed by the output function, at least until inflateBack() returns. inflateBackInit() must be called first to allocate the internal state and to initialize the state with the user-provided window buffer. inflateBack() may then be used multiple times to inflate a complete, raw deflate stream with each call. inflateBackEnd() is then called to free the allocated state. A raw deflate stream is one with no zlib or gzip header or trailer. This routine would normally be used in a utility that reads zip or gzip files and writes out uncompressed files. The utility would decode the header and process the trailer on its own, hence this routine expects only the raw deflate stream to decompress. This is different from the normal behavior of inflate(), which expects either a zlib or gzip header and trailer around the deflate stream. inflateBack() uses two subroutines supplied by the caller that are then called by inflateBack() for input and output. inflateBack() calls those routines until it reads a complete deflate stream and writes out all of the uncompressed data, or until it encounters an error. The function's parameters and return types are defined above in the in_func and out_func typedefs. inflateBack() will call in(in_desc, &buf) which should return the number of bytes of provided input, and a pointer to that input in buf. If there is no input available, in() must return zero--buf is ignored in that case--and inflateBack() will return a buffer error. inflateBack() will call out(out_desc, buf, len) to write the uncompressed data buf[0..len-1]. out() should return zero on success, or non-zero on failure. If out() returns non-zero, inflateBack() will return with an error. Neither in() nor out() are permitted to change the contents of the window provided to inflateBackInit(), which is also the buffer that out() uses to write from. The length written by out() will be at most the window size. Any non-zero amount of input may be provided by in(). For convenience, inflateBack() can be provided input on the first call by setting strm->next_in and strm->avail_in. If that input is exhausted, then in() will be called. Therefore strm->next_in must be initialized before calling inflateBack(). If strm->next_in is Z_NULL, then in() will be called immediately for input. If strm->next_in is not Z_NULL, then strm->avail_in must also be initialized, and then if strm->avail_in is not zero, input will initially be taken from strm->next_in[0 .. strm->avail_in - 1]. The in_desc and out_desc parameters of inflateBack() is passed as the first parameter of in() and out() respectively when they are called. These descriptors can be optionally used to pass any information that the caller- supplied in() and out() functions need to do their job. On return, inflateBack() will set strm->next_in and strm->avail_in to pass back any unused input that was provided by the last in() call. The return values of inflateBack() can be Z_STREAM_END on success, Z_BUF_ERROR if in() or out() returned an error, Z_DATA_ERROR if there was a format error in the deflate stream (in which case strm->msg is set to indicate the nature of the error), or Z_STREAM_ERROR if the stream was not properly initialized. In the case of Z_BUF_ERROR, an input or output error can be distinguished using strm->next_in which will be Z_NULL only if in() returned an error. If strm->next_in is not Z_NULL, then the Z_BUF_ERROR was due to out() returning non-zero. (in() will always be called before out(), so strm->next_in is assured to be defined if out() returns non-zero.) Note that inflateBack() cannot return Z_OK. */ ZEXTERN int ZEXPORT inflateBackEnd OF((z_streamp strm)); /* All memory allocated by inflateBackInit() is freed. inflateBackEnd() returns Z_OK on success, or Z_STREAM_ERROR if the stream state was inconsistent. */ ZEXTERN uLong ZEXPORT zlibCompileFlags OF((void)); /* Return flags indicating compile-time options. Type sizes, two bits each, 00 = 16 bits, 01 = 32, 10 = 64, 11 = other: 1.0: size of uInt 3.2: size of uLong 5.4: size of voidpf (pointer) 7.6: size of z_off_t Compiler, assembler, and debug options: 8: DEBUG 9: ASMV or ASMINF -- use ASM code 10: ZLIB_WINAPI -- exported functions use the WINAPI calling convention 11: 0 (reserved) One-time table building (smaller code, but not thread-safe if true): 12: BUILDFIXED -- build static block decoding tables when needed 13: DYNAMIC_CRC_TABLE -- build CRC calculation tables when needed 14,15: 0 (reserved) Library content (indicates missing functionality): 16: NO_GZCOMPRESS -- gz* functions cannot compress (to avoid linking deflate code when not needed) 17: NO_GZIP -- deflate can't write gzip streams, and inflate can't detect and decode gzip streams (to avoid linking crc code) 18-19: 0 (reserved) Operation variations (changes in library functionality): 20: PKZIP_BUG_WORKAROUND -- slightly more permissive inflate 21: FASTEST -- deflate algorithm with only one, lowest compression level 22,23: 0 (reserved) The sprintf variant used by gzprintf (zero is best): 24: 0 = vs*, 1 = s* -- 1 means limited to 20 arguments after the format 25: 0 = *nprintf, 1 = *printf -- 1 means gzprintf() not secure! 26: 0 = returns value, 1 = void -- 1 means inferred string length returned Remainder: 27-31: 0 (reserved) */ /* utility functions */ /* The following utility functions are implemented on top of the basic stream-oriented functions. To simplify the interface, some default options are assumed (compression level and memory usage, standard memory allocation functions). The source code of these utility functions can be modified if you need special options. */ ZEXTERN int ZEXPORT compress OF((Bytef *dest, uLongf *destLen, const Bytef *source, uLong sourceLen)); /* Compresses the source buffer into the destination buffer. sourceLen is the byte length of the source buffer. Upon entry, destLen is the total size of the destination buffer, which must be at least the value returned by compressBound(sourceLen). Upon exit, destLen is the actual size of the compressed buffer. compress returns Z_OK if success, Z_MEM_ERROR if there was not enough memory, Z_BUF_ERROR if there was not enough room in the output buffer. */ ZEXTERN int ZEXPORT compress2 OF((Bytef *dest, uLongf *destLen, const Bytef *source, uLong sourceLen, int level)); /* Compresses the source buffer into the destination buffer. The level parameter has the same meaning as in deflateInit. sourceLen is the byte length of the source buffer. Upon entry, destLen is the total size of the destination buffer, which must be at least the value returned by compressBound(sourceLen). Upon exit, destLen is the actual size of the compressed buffer. compress2 returns Z_OK if success, Z_MEM_ERROR if there was not enough memory, Z_BUF_ERROR if there was not enough room in the output buffer, Z_STREAM_ERROR if the level parameter is invalid. */ ZEXTERN uLong ZEXPORT compressBound OF((uLong sourceLen)); /* compressBound() returns an upper bound on the compressed size after compress() or compress2() on sourceLen bytes. It would be used before a compress() or compress2() call to allocate the destination buffer. */ ZEXTERN int ZEXPORT uncompress OF((Bytef *dest, uLongf *destLen, const Bytef *source, uLong sourceLen)); /* Decompresses the source buffer into the destination buffer. sourceLen is the byte length of the source buffer. Upon entry, destLen is the total size of the destination buffer, which must be large enough to hold the entire uncompressed data. (The size of the uncompressed data must have been saved previously by the compressor and transmitted to the decompressor by some mechanism outside the scope of this compression library.) Upon exit, destLen is the actual size of the uncompressed buffer. uncompress returns Z_OK if success, Z_MEM_ERROR if there was not enough memory, Z_BUF_ERROR if there was not enough room in the output buffer, or Z_DATA_ERROR if the input data was corrupted or incomplete. */ /* gzip file access functions */ /* This library supports reading and writing files in gzip (.gz) format with an interface similar to that of stdio, using the functions that start with "gz". The gzip format is different from the zlib format. gzip is a gzip wrapper, documented in RFC 1952, wrapped around a deflate stream. */ typedef voidp gzFile; /* opaque gzip file descriptor */ /* ZEXTERN gzFile ZEXPORT gzopen OF((const char *path, const char *mode)); Opens a gzip (.gz) file for reading or writing. The mode parameter is as in fopen ("rb" or "wb") but can also include a compression level ("wb9") or a strategy: 'f' for filtered data as in "wb6f", 'h' for Huffman-only compression as in "wb1h", 'R' for run-length encoding as in "wb1R", or 'F' for fixed code compression as in "wb9F". (See the description of deflateInit2 for more information about the strategy parameter.) Also "a" can be used instead of "w" to request that the gzip stream that will be written be appended to the file. "+" will result in an error, since reading and writing to the same gzip file is not supported. gzopen can be used to read a file which is not in gzip format; in this case gzread will directly read from the file without decompression. gzopen returns NULL if the file could not be opened, if there was insufficient memory to allocate the gzFile state, or if an invalid mode was specified (an 'r', 'w', or 'a' was not provided, or '+' was provided). errno can be checked to determine if the reason gzopen failed was that the file could not be opened. */ ZEXTERN gzFile ZEXPORT gzdopen OF((int fd, const char *mode)); /* gzdopen associates a gzFile with the file descriptor fd. File descriptors are obtained from calls like open, dup, creat, pipe or fileno (if the file has been previously opened with fopen). The mode parameter is as in gzopen. The next call of gzclose on the returned gzFile will also close the file descriptor fd, just like fclose(fdopen(fd, mode)) closes the file descriptor fd. If you want to keep fd open, use fd = dup(fd_keep); gz = gzdopen(fd, mode);. The duplicated descriptor should be saved to avoid a leak, since gzdopen does not close fd if it fails. gzdopen returns NULL if there was insufficient memory to allocate the gzFile state, if an invalid mode was specified (an 'r', 'w', or 'a' was not provided, or '+' was provided), or if fd is -1. The file descriptor is not used until the next gz* read, write, seek, or close operation, so gzdopen will not detect if fd is invalid (unless fd is -1). */ ZEXTERN int ZEXPORT gzbuffer OF((gzFile file, unsigned size)); /* Set the internal buffer size used by this library's functions. The default buffer size is 8192 bytes. This function must be called after gzopen() or gzdopen(), and before any other calls that read or write the file. The buffer memory allocation is always deferred to the first read or write. Two buffers are allocated, either both of the specified size when writing, or one of the specified size and the other twice that size when reading. A larger buffer size of, for example, 64K or 128K bytes will noticeably increase the speed of decompression (reading). The new buffer size also affects the maximum length for gzprintf(). gzbuffer() returns 0 on success, or -1 on failure, such as being called too late. */ ZEXTERN int ZEXPORT gzsetparams OF((gzFile file, int level, int strategy)); /* Dynamically update the compression level or strategy. See the description of deflateInit2 for the meaning of these parameters. gzsetparams returns Z_OK if success, or Z_STREAM_ERROR if the file was not opened for writing. */ ZEXTERN int ZEXPORT gzread OF((gzFile file, voidp buf, unsigned len)); /* Reads the given number of uncompressed bytes from the compressed file. If the input file was not in gzip format, gzread copies the given number of bytes into the buffer. After reaching the end of a gzip stream in the input, gzread will continue to read, looking for another gzip stream, or failing that, reading the rest of the input file directly without decompression. The entire input file will be read if gzread is called until it returns less than the requested len. gzread returns the number of uncompressed bytes actually read, less than len for end of file, or -1 for error. */ ZEXTERN int ZEXPORT gzwrite OF((gzFile file, voidpc buf, unsigned len)); /* Writes the given number of uncompressed bytes into the compressed file. gzwrite returns the number of uncompressed bytes written or 0 in case of error. */ ZEXTERN int ZEXPORTVA gzprintf OF((gzFile file, const char *format, ...)); /* Converts, formats, and writes the arguments to the compressed file under control of the format string, as in fprintf. gzprintf returns the number of uncompressed bytes actually written, or 0 in case of error. The number of uncompressed bytes written is limited to 8191, or one less than the buffer size given to gzbuffer(). The caller should assure that this limit is not exceeded. If it is exceeded, then gzprintf() will return an error (0) with nothing written. In this case, there may also be a buffer overflow with unpredictable consequences, which is possible only if zlib was compiled with the insecure functions sprintf() or vsprintf() because the secure snprintf() or vsnprintf() functions were not available. This can be determined using zlibCompileFlags(). */ ZEXTERN int ZEXPORT gzputs OF((gzFile file, const char *s)); /* Writes the given null-terminated string to the compressed file, excluding the terminating null character. gzputs returns the number of characters written, or -1 in case of error. */ ZEXTERN char * ZEXPORT gzgets OF((gzFile file, char *buf, int len)); /* Reads bytes from the compressed file until len-1 characters are read, or a newline character is read and transferred to buf, or an end-of-file condition is encountered. If any characters are read or if len == 1, the string is terminated with a null character. If no characters are read due to an end-of-file or len < 1, then the buffer is left untouched. gzgets returns buf which is a null-terminated string, or it returns NULL for end-of-file or in case of error. If there was an error, the contents at buf are indeterminate. */ ZEXTERN int ZEXPORT gzputc OF((gzFile file, int c)); /* Writes c, converted to an unsigned char, into the compressed file. gzputc returns the value that was written, or -1 in case of error. */ ZEXTERN int ZEXPORT gzgetc OF((gzFile file)); /* Reads one byte from the compressed file. gzgetc returns this byte or -1 in case of end of file or error. */ ZEXTERN int ZEXPORT gzungetc OF((int c, gzFile file)); /* Push one character back onto the stream to be read as the first character on the next read. At least one character of push-back is allowed. gzungetc() returns the character pushed, or -1 on failure. gzungetc() will fail if c is -1, and may fail if a character has been pushed but not read yet. If gzungetc is used immediately after gzopen or gzdopen, at least the output buffer size of pushed characters is allowed. (See gzbuffer above.) The pushed character will be discarded if the stream is repositioned with gzseek() or gzrewind(). */ ZEXTERN int ZEXPORT gzflush OF((gzFile file, int flush)); /* Flushes all pending output into the compressed file. The parameter flush is as in the deflate() function. The return value is the zlib error number (see function gzerror below). gzflush is only permitted when writing. If the flush parameter is Z_FINISH, the remaining data is written and the gzip stream is completed in the output. If gzwrite() is called again, a new gzip stream will be started in the output. gzread() is able to read such concatented gzip streams. gzflush should be called only when strictly necessary because it will degrade compression if called too often. */ /* ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile file, z_off_t offset, int whence)); Sets the starting position for the next gzread or gzwrite on the given compressed file. The offset represents a number of bytes in the uncompressed data stream. The whence parameter is defined as in lseek(2); the value SEEK_END is not supported. If the file is opened for reading, this function is emulated but can be extremely slow. If the file is opened for writing, only forward seeks are supported; gzseek then compresses a sequence of zeroes up to the new starting position. gzseek returns the resulting offset location as measured in bytes from the beginning of the uncompressed stream, or -1 in case of error, in particular if the file is opened for writing and the new starting position would be before the current position. */ ZEXTERN int ZEXPORT gzrewind OF((gzFile file)); /* Rewinds the given file. This function is supported only for reading. gzrewind(file) is equivalent to (int)gzseek(file, 0L, SEEK_SET) */ /* ZEXTERN z_off_t ZEXPORT gztell OF((gzFile file)); Returns the starting position for the next gzread or gzwrite on the given compressed file. This position represents a number of bytes in the uncompressed data stream, and is zero when starting, even if appending or reading a gzip stream from the middle of a file using gzdopen(). gztell(file) is equivalent to gzseek(file, 0L, SEEK_CUR) */ /* ZEXTERN z_off_t ZEXPORT gzoffset OF((gzFile file)); Returns the current offset in the file being read or written. This offset includes the count of bytes that precede the gzip stream, for example when appending or when using gzdopen() for reading. When reading, the offset does not include as yet unused buffered input. This information can be used for a progress indicator. On error, gzoffset() returns -1. */ ZEXTERN int ZEXPORT gzeof OF((gzFile file)); /* Returns true (1) if the end-of-file indicator has been set while reading, false (0) otherwise. Note that the end-of-file indicator is set only if the read tried to go past the end of the input, but came up short. Therefore, just like feof(), gzeof() may return false even if there is no more data to read, in the event that the last read request was for the exact number of bytes remaining in the input file. This will happen if the input file size is an exact multiple of the buffer size. If gzeof() returns true, then the read functions will return no more data, unless the end-of-file indicator is reset by gzclearerr() and the input file has grown since the previous end of file was detected. */ ZEXTERN int ZEXPORT gzdirect OF((gzFile file)); /* Returns true (1) if file is being copied directly while reading, or false (0) if file is a gzip stream being decompressed. This state can change from false to true while reading the input file if the end of a gzip stream is reached, but is followed by data that is not another gzip stream. If the input file is empty, gzdirect() will return true, since the input does not contain a gzip stream. If gzdirect() is used immediately after gzopen() or gzdopen() it will cause buffers to be allocated to allow reading the file to determine if it is a gzip file. Therefore if gzbuffer() is used, it should be called before gzdirect(). */ ZEXTERN int ZEXPORT gzclose OF((gzFile file)); /* Flushes all pending output if necessary, closes the compressed file and deallocates the (de)compression state. Note that once file is closed, you cannot call gzerror with file, since its structures have been deallocated. gzclose must not be called more than once on the same file, just as free must not be called more than once on the same allocation. gzclose will return Z_STREAM_ERROR if file is not valid, Z_ERRNO on a file operation error, or Z_OK on success. */ ZEXTERN int ZEXPORT gzclose_r OF((gzFile file)); ZEXTERN int ZEXPORT gzclose_w OF((gzFile file)); /* Same as gzclose(), but gzclose_r() is only for use when reading, and gzclose_w() is only for use when writing or appending. The advantage to using these instead of gzclose() is that they avoid linking in zlib compression or decompression code that is not used when only reading or only writing respectively. If gzclose() is used, then both compression and decompression code will be included the application when linking to a static zlib library. */ ZEXTERN const char * ZEXPORT gzerror OF((gzFile file, int *errnum)); /* Returns the error message for the last error which occurred on the given compressed file. errnum is set to zlib error number. If an error occurred in the file system and not in the compression library, errnum is set to Z_ERRNO and the application may consult errno to get the exact error code. The application must not modify the returned string. Future calls to this function may invalidate the previously returned string. If file is closed, then the string previously returned by gzerror will no longer be available. gzerror() should be used to distinguish errors from end-of-file for those functions above that do not distinguish those cases in their return values. */ ZEXTERN void ZEXPORT gzclearerr OF((gzFile file)); /* Clears the error and end-of-file flags for file. This is analogous to the clearerr() function in stdio. This is useful for continuing to read a gzip file that is being written concurrently. */ /* checksum functions */ /* These functions are not related to compression but are exported anyway because they might be useful in applications using the compression library. */ ZEXTERN uLong ZEXPORT adler32 OF((uLong adler, const Bytef *buf, uInt len)); /* Update a running Adler-32 checksum with the bytes buf[0..len-1] and return the updated checksum. If buf is Z_NULL, this function returns the required initial value for the checksum. An Adler-32 checksum is almost as reliable as a CRC32 but can be computed much faster. Usage example: uLong adler = adler32(0L, Z_NULL, 0); while (read_buffer(buffer, length) != EOF) { adler = adler32(adler, buffer, length); } if (adler != original_adler) error(); */ /* ZEXTERN uLong ZEXPORT adler32_combine OF((uLong adler1, uLong adler2, z_off_t len2)); Combine two Adler-32 checksums into one. For two sequences of bytes, seq1 and seq2 with lengths len1 and len2, Adler-32 checksums were calculated for each, adler1 and adler2. adler32_combine() returns the Adler-32 checksum of seq1 and seq2 concatenated, requiring only adler1, adler2, and len2. */ ZEXTERN uLong ZEXPORT crc32 OF((uLong crc, const Bytef *buf, uInt len)); /* Update a running CRC-32 with the bytes buf[0..len-1] and return the updated CRC-32. If buf is Z_NULL, this function returns the required initial value for the for the crc. Pre- and post-conditioning (one's complement) is performed within this function so it shouldn't be done by the application. Usage example: uLong crc = crc32(0L, Z_NULL, 0); while (read_buffer(buffer, length) != EOF) { crc = crc32(crc, buffer, length); } if (crc != original_crc) error(); */ /* ZEXTERN uLong ZEXPORT crc32_combine OF((uLong crc1, uLong crc2, z_off_t len2)); Combine two CRC-32 check values into one. For two sequences of bytes, seq1 and seq2 with lengths len1 and len2, CRC-32 check values were calculated for each, crc1 and crc2. crc32_combine() returns the CRC-32 check value of seq1 and seq2 concatenated, requiring only crc1, crc2, and len2. */ /* various hacks, don't look :) */ /* deflateInit and inflateInit are macros to allow checking the zlib version * and the compiler's view of z_stream: */ ZEXTERN int ZEXPORT deflateInit_ OF((z_streamp strm, int level, const char *version, int stream_size)); ZEXTERN int ZEXPORT inflateInit_ OF((z_streamp strm, const char *version, int stream_size)); ZEXTERN int ZEXPORT deflateInit2_ OF((z_streamp strm, int level, int method, int windowBits, int memLevel, int strategy, const char *version, int stream_size)); ZEXTERN int ZEXPORT inflateInit2_ OF((z_streamp strm, int windowBits, const char *version, int stream_size)); ZEXTERN int ZEXPORT inflateBackInit_ OF((z_streamp strm, int windowBits, unsigned char FAR *window, const char *version, int stream_size)); #define deflateInit(strm, level) \ deflateInit_((strm), (level), ZLIB_VERSION, sizeof(z_stream)) #define inflateInit(strm) \ inflateInit_((strm), ZLIB_VERSION, sizeof(z_stream)) #define deflateInit2(strm, level, method, windowBits, memLevel, strategy) \ deflateInit2_((strm),(level),(method),(windowBits),(memLevel),\ (strategy), ZLIB_VERSION, sizeof(z_stream)) #define inflateInit2(strm, windowBits) \ inflateInit2_((strm), (windowBits), ZLIB_VERSION, sizeof(z_stream)) #define inflateBackInit(strm, windowBits, window) \ inflateBackInit_((strm), (windowBits), (window), \ ZLIB_VERSION, sizeof(z_stream)) /* provide 64-bit offset functions if _LARGEFILE64_SOURCE defined, and/or * change the regular functions to 64 bits if _FILE_OFFSET_BITS is 64 (if * both are true, the application gets the *64 functions, and the regular * functions are changed to 64 bits) -- in case these are set on systems * without large file support, _LFS64_LARGEFILE must also be true */ #if defined(_LARGEFILE64_SOURCE) && _LFS64_LARGEFILE-0 ZEXTERN gzFile ZEXPORT gzopen64 OF((const char *, const char *)); ZEXTERN z_off64_t ZEXPORT gzseek64 OF((gzFile, z_off64_t, int)); ZEXTERN z_off64_t ZEXPORT gztell64 OF((gzFile)); ZEXTERN z_off64_t ZEXPORT gzoffset64 OF((gzFile)); ZEXTERN uLong ZEXPORT adler32_combine64 OF((uLong, uLong, z_off64_t)); ZEXTERN uLong ZEXPORT crc32_combine64 OF((uLong, uLong, z_off64_t)); #endif #if !defined(ZLIB_INTERNAL) && _FILE_OFFSET_BITS-0 == 64 && _LFS64_LARGEFILE-0 # define gzopen gzopen64 # define gzseek gzseek64 # define gztell gztell64 # define gzoffset gzoffset64 # define adler32_combine adler32_combine64 # define crc32_combine crc32_combine64 # ifdef _LARGEFILE64_SOURCE ZEXTERN gzFile ZEXPORT gzopen64 OF((const char *, const char *)); ZEXTERN z_off_t ZEXPORT gzseek64 OF((gzFile, z_off_t, int)); ZEXTERN z_off_t ZEXPORT gztell64 OF((gzFile)); ZEXTERN z_off_t ZEXPORT gzoffset64 OF((gzFile)); ZEXTERN uLong ZEXPORT adler32_combine64 OF((uLong, uLong, z_off_t)); ZEXTERN uLong ZEXPORT crc32_combine64 OF((uLong, uLong, z_off_t)); # endif #else ZEXTERN gzFile ZEXPORT gzopen OF((const char *, const char *)); ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int)); ZEXTERN z_off_t ZEXPORT gztell OF((gzFile)); ZEXTERN z_off_t ZEXPORT gzoffset OF((gzFile)); ZEXTERN uLong ZEXPORT adler32_combine OF((uLong, uLong, z_off_t)); ZEXTERN uLong ZEXPORT crc32_combine OF((uLong, uLong, z_off_t)); #endif /* hack for buggy compilers */ #if !defined(ZUTIL_H) && !defined(NO_DUMMY_DECL) struct internal_state {int dummy;}; #endif /* undocumented functions */ ZEXTERN const char * ZEXPORT zError OF((int)); ZEXTERN int ZEXPORT inflateSyncPoint OF((z_streamp)); ZEXTERN const uLongf * ZEXPORT get_crc_table OF((void)); ZEXTERN int ZEXPORT inflateUndermine OF((z_streamp, int)); #ifdef __cplusplus } #endif #endif /* ZLIB_H */ libmstoolkit-77.0.0/include/xmltok_impl.h0000644000175000017500000000122512455161024020402 0ustar rusconirusconi/* Copyright (c) 1998, 1999 Thai Open Source Software Center Ltd See the file COPYING for copying permission. */ enum { BT_NONXML, BT_MALFORM, BT_LT, BT_AMP, BT_RSQB, BT_LEAD2, BT_LEAD3, BT_LEAD4, BT_TRAIL, BT_CR, BT_LF, BT_GT, BT_QUOT, BT_APOS, BT_EQUALS, BT_QUEST, BT_EXCL, BT_SOL, BT_SEMI, BT_NUM, BT_LSQB, BT_S, BT_NMSTRT, BT_COLON, BT_HEX, BT_DIGIT, BT_NAME, BT_MINUS, BT_OTHER, /* known not to be a name or name start character */ BT_NONASCII, /* might be a name or name start character */ BT_PERCNT, BT_LPAR, BT_RPAR, BT_AST, BT_PLUS, BT_COMMA, BT_VERBAR }; #include libmstoolkit-77.0.0/include/MSObject.h0000644000175000017500000000151712455161024017515 0ustar rusconirusconi#ifndef _MSOBJECT_H #define _MSOBJECT_H #include "MSToolkitTypes.h" #include "Spectrum.h" #include using namespace std; namespace MSToolkit { class MSObject { public: //Constructors & Destructors MSObject(); MSObject(const MSObject&); ~MSObject(); //Operator Functions MSObject& operator=(const MSObject&); //Functions void add(Spectrum&); bool addToHeader(char*); bool addToHeader(string); Spectrum& at(unsigned int); Peak_T& at(unsigned int, unsigned int); void clear(); void erase(unsigned int); void erase(unsigned int, unsigned int); MSHeader& getHeader(); void setHeader(const MSHeader& h); int size(); protected: private: vector *vSpectrum; string fileName; MSHeader header; MSSpectrumType fileType; }; } #endif libmstoolkit-77.0.0/include/ascii.h0000644000175000017500000000370112455161024017134 0ustar rusconirusconi/* Copyright (c) 1998, 1999 Thai Open Source Software Center Ltd See the file COPYING for copying permission. */ #define ASCII_A 0x41 #define ASCII_B 0x42 #define ASCII_C 0x43 #define ASCII_D 0x44 #define ASCII_E 0x45 #define ASCII_F 0x46 #define ASCII_G 0x47 #define ASCII_H 0x48 #define ASCII_I 0x49 #define ASCII_J 0x4A #define ASCII_K 0x4B #define ASCII_L 0x4C #define ASCII_M 0x4D #define ASCII_N 0x4E #define ASCII_O 0x4F #define ASCII_P 0x50 #define ASCII_Q 0x51 #define ASCII_R 0x52 #define ASCII_S 0x53 #define ASCII_T 0x54 #define ASCII_U 0x55 #define ASCII_V 0x56 #define ASCII_W 0x57 #define ASCII_X 0x58 #define ASCII_Y 0x59 #define ASCII_Z 0x5A #define ASCII_a 0x61 #define ASCII_b 0x62 #define ASCII_c 0x63 #define ASCII_d 0x64 #define ASCII_e 0x65 #define ASCII_f 0x66 #define ASCII_g 0x67 #define ASCII_h 0x68 #define ASCII_i 0x69 #define ASCII_j 0x6A #define ASCII_k 0x6B #define ASCII_l 0x6C #define ASCII_m 0x6D #define ASCII_n 0x6E #define ASCII_o 0x6F #define ASCII_p 0x70 #define ASCII_q 0x71 #define ASCII_r 0x72 #define ASCII_s 0x73 #define ASCII_t 0x74 #define ASCII_u 0x75 #define ASCII_v 0x76 #define ASCII_w 0x77 #define ASCII_x 0x78 #define ASCII_y 0x79 #define ASCII_z 0x7A #define ASCII_0 0x30 #define ASCII_1 0x31 #define ASCII_2 0x32 #define ASCII_3 0x33 #define ASCII_4 0x34 #define ASCII_5 0x35 #define ASCII_6 0x36 #define ASCII_7 0x37 #define ASCII_8 0x38 #define ASCII_9 0x39 #define ASCII_TAB 0x09 #define ASCII_SPACE 0x20 #define ASCII_EXCL 0x21 #define ASCII_QUOT 0x22 #define ASCII_AMP 0x26 #define ASCII_APOS 0x27 #define ASCII_MINUS 0x2D #define ASCII_PERIOD 0x2E #define ASCII_COLON 0x3A #define ASCII_SEMI 0x3B #define ASCII_LT 0x3C #define ASCII_EQUALS 0x3D #define ASCII_GT 0x3E #define ASCII_LSQB 0x5B #define ASCII_RSQB 0x5D #define ASCII_UNDERSCORE 0x5F #define ASCII_LPAREN 0x28 #define ASCII_RPAREN 0x29 #define ASCII_FF 0x0C #define ASCII_SLASH 0x2F #define ASCII_HASH 0x23 #define ASCII_PIPE 0x7C #define ASCII_COMMA 0x2C libmstoolkit-77.0.0/include/Spectrum.h0000644000175000017500000001211612455161024017646 0ustar rusconirusconi#ifndef _SPECTRUM_H #define _SPECTRUM_H #include "MSToolkitTypes.h" #include #include #include #include using namespace std; namespace MSToolkit { class Spectrum { public: //Constructors & Destructors Spectrum(); Spectrum(char*); Spectrum(char, unsigned int); Spectrum(const Spectrum&); ~Spectrum(); //Operator Functions Spectrum& operator=(const Spectrum&); Peak_T& operator[](const int&); //Functions void add(Peak_T&); void add(double,float); void addEZState(int,double,float,float); void addEZState(EZState&); void addMZ(double, double mono=0); void addZState(int,double); void addZState(ZState&); Peak_T& at(const int&); Peak_T& at(const unsigned int&); EZState& atEZ(const int&); EZState& atEZ(const unsigned int&); ZState& atZ(const int&); ZState& atZ(const unsigned int&); void clear(); void clearMZ(); void clearPeaks(); void erase(unsigned int); void erase(unsigned int, unsigned int); void eraseEZ(unsigned int); void eraseEZ(unsigned int, unsigned int); void eraseZ(unsigned int); void eraseZ(unsigned int, unsigned int); MSActivation getActivationMethod(); float getArea(); float getBPI(); double getBPM(); int getCentroidStatus(); int getCharge(); double getCompensationVoltage(); double getConversionA(); double getConversionB(); double getConversionC(); double getConversionD(); double getConversionE(); double getConversionI(); MSSpectrumType getFileType(); float getIonInjectionTime(); double getMonoMZ(int index=0); double getMZ(int index=0); bool getNativeID(char*,int); bool getRawFilter(char*,int,bool bLock=false); float getRTime(); float getRTimeApex(); int getScanNumber(bool second=false); double getTIC(); int getMsLevel(); void setActivationMethod(MSActivation); void setArea(float); void setBPI(float); void setBPM(double); void setCentroidStatus(int); void setCharge(int); void setCompensationVoltage(double); void setConversionA(double); void setConversionB(double); void setConversionC(double); void setConversionD(double); void setConversionE(double); void setConversionI(double); void setFileType(MSSpectrumType); void setIonInjectionTime(float); void setMZ(double, double mono=0); void setNativeID(char*); void setRawFilter(char*); void setRTime(float); void setRTimeApex(float); void setScanNumber(int, bool second=false); void setTIC(double); void setMsLevel(int level); int size(); int sizeEZ(); int sizeMZ(); //also returns size of monoMZ int sizeZ(); void sortIntensity(); void sortIntensityRev(); void sortMZ(); void setPeaks( std::vector peaks); void sortMZRev(); //for sqlite format void setScanID(int scanID); int getScanID(); //const vector* getPeaks(); vector* getPeaks(); //void setPeaks(vector peaks); float getTotalIntensity(); //for debugging void printMe(); protected: //Data Members vector *vPeaks; vector *vEZ; vector *vZ; int charge; float rTime; int scanNumber; int scanNumber2; int msLevel; vector *monoMZ; vector *mz; MSSpectrumType fileType; MSActivation actMethod; int scanID; //index for sqlite float IIT; float BPI; //Base Peak Intensity double compensationVoltage; double convA; double convB; double convC; double convD; double convE; double convI; double TIC; double BPM; //Base Peak Mass float rTimeApex; //retention time of precursor apex (MS2) float area; //summed peak areas of precursor (MS2) char nativeID[256]; //spectrumNativeID in mzML files char rawFilter[256]; //RAW file header line int centroidStatus; //0=profile, 1=centroid, 2=unknown //private: //Functions static int compareIntensity(const void *p1,const void *p2); static int compareMZ(const void *p1,const void *p2); static int compareIntensityRev(const void *p1,const void *p2); static int compareMZRev(const void *p1,const void *p2); }; } #endif libmstoolkit-77.0.0/include/xmlrole.h0000644000175000017500000000571712455161024017537 0ustar rusconirusconi/* Copyright (c) 1998, 1999 Thai Open Source Software Center Ltd See the file COPYING for copying permission. */ #ifndef XmlRole_INCLUDED #define XmlRole_INCLUDED 1 #ifdef __VMS /* 0 1 2 3 0 1 2 3 1234567890123456789012345678901 1234567890123456789012345678901 */ #define XmlPrologStateInitExternalEntity XmlPrologStateInitExternalEnt #endif #include "xmltok.h" #ifdef __cplusplus extern "C" { #endif enum { XML_ROLE_ERROR = -1, XML_ROLE_NONE = 0, XML_ROLE_XML_DECL, XML_ROLE_INSTANCE_START, XML_ROLE_DOCTYPE_NONE, XML_ROLE_DOCTYPE_NAME, XML_ROLE_DOCTYPE_SYSTEM_ID, XML_ROLE_DOCTYPE_PUBLIC_ID, XML_ROLE_DOCTYPE_INTERNAL_SUBSET, XML_ROLE_DOCTYPE_CLOSE, XML_ROLE_GENERAL_ENTITY_NAME, XML_ROLE_PARAM_ENTITY_NAME, XML_ROLE_ENTITY_NONE, XML_ROLE_ENTITY_VALUE, XML_ROLE_ENTITY_SYSTEM_ID, XML_ROLE_ENTITY_PUBLIC_ID, XML_ROLE_ENTITY_COMPLETE, XML_ROLE_ENTITY_NOTATION_NAME, XML_ROLE_NOTATION_NONE, XML_ROLE_NOTATION_NAME, XML_ROLE_NOTATION_SYSTEM_ID, XML_ROLE_NOTATION_NO_SYSTEM_ID, XML_ROLE_NOTATION_PUBLIC_ID, XML_ROLE_ATTRIBUTE_NAME, XML_ROLE_ATTRIBUTE_TYPE_CDATA, XML_ROLE_ATTRIBUTE_TYPE_ID, XML_ROLE_ATTRIBUTE_TYPE_IDREF, XML_ROLE_ATTRIBUTE_TYPE_IDREFS, XML_ROLE_ATTRIBUTE_TYPE_ENTITY, XML_ROLE_ATTRIBUTE_TYPE_ENTITIES, XML_ROLE_ATTRIBUTE_TYPE_NMTOKEN, XML_ROLE_ATTRIBUTE_TYPE_NMTOKENS, XML_ROLE_ATTRIBUTE_ENUM_VALUE, XML_ROLE_ATTRIBUTE_NOTATION_VALUE, XML_ROLE_ATTLIST_NONE, XML_ROLE_ATTLIST_ELEMENT_NAME, XML_ROLE_IMPLIED_ATTRIBUTE_VALUE, XML_ROLE_REQUIRED_ATTRIBUTE_VALUE, XML_ROLE_DEFAULT_ATTRIBUTE_VALUE, XML_ROLE_FIXED_ATTRIBUTE_VALUE, XML_ROLE_ELEMENT_NONE, XML_ROLE_ELEMENT_NAME, XML_ROLE_CONTENT_ANY, XML_ROLE_CONTENT_EMPTY, XML_ROLE_CONTENT_PCDATA, XML_ROLE_GROUP_OPEN, XML_ROLE_GROUP_CLOSE, XML_ROLE_GROUP_CLOSE_REP, XML_ROLE_GROUP_CLOSE_OPT, XML_ROLE_GROUP_CLOSE_PLUS, XML_ROLE_GROUP_CHOICE, XML_ROLE_GROUP_SEQUENCE, XML_ROLE_CONTENT_ELEMENT, XML_ROLE_CONTENT_ELEMENT_REP, XML_ROLE_CONTENT_ELEMENT_OPT, XML_ROLE_CONTENT_ELEMENT_PLUS, XML_ROLE_PI, XML_ROLE_COMMENT, #ifdef XML_DTD XML_ROLE_TEXT_DECL, XML_ROLE_IGNORE_SECT, XML_ROLE_INNER_PARAM_ENTITY_REF, #endif /* XML_DTD */ XML_ROLE_PARAM_ENTITY_REF }; typedef struct prolog_state { int (PTRCALL *handler) (struct prolog_state *state, int tok, const char *ptr, const char *end, const ENCODING *enc); unsigned level; int role_none; #ifdef XML_DTD unsigned includeLevel; int documentEntity; int inEntityValue; #endif /* XML_DTD */ } PROLOG_STATE; void XmlPrologStateInit(PROLOG_STATE *); #ifdef XML_DTD void XmlPrologStateInitExternalEntity(PROLOG_STATE *); #endif /* XML_DTD */ #define XmlTokenRole(state, tok, ptr, end, enc) \ (((state)->handler)(state, tok, ptr, end, enc)) #ifdef __cplusplus } #endif #endif /* not XmlRole_INCLUDED */ libmstoolkit-77.0.0/include/zutil.h0000644000175000017500000001576112455161024017224 0ustar rusconirusconi/* zutil.h -- internal interface and configuration of the compression library * Copyright (C) 1995-2010 Jean-loup Gailly. * For conditions of distribution and use, see copyright notice in zlib.h */ /* WARNING: this file should *not* be used by applications. It is part of the implementation of the compression library and is subject to change. Applications should only use zlib.h. */ /* @(#) $Id$ */ #ifndef ZUTIL_H #define ZUTIL_H #if ((__GNUC__-0) * 10 + __GNUC_MINOR__-0 >= 33) && !defined(NO_VIZ) # define ZLIB_INTERNAL __attribute__((visibility ("hidden"))) #else # define ZLIB_INTERNAL #endif #include "zlib.h" #ifdef STDC # if !(defined(_WIN32_WCE) && defined(_MSC_VER)) # include # endif # include # include #endif #ifndef local # define local static #endif /* compile with -Dlocal if your debugger can't find static symbols */ typedef unsigned char uch; typedef uch FAR uchf; typedef unsigned short ush; typedef ush FAR ushf; typedef unsigned long ulg; extern const char * const z_errmsg[10]; /* indexed by 2-zlib_error */ /* (size given to avoid silly warnings with Visual C++) */ #define ERR_MSG(err) z_errmsg[Z_NEED_DICT-(err)] #define ERR_RETURN(strm,err) \ return (strm->msg = (char*)ERR_MSG(err), (err)) /* To be used only when the state is known to be valid */ /* common constants */ #ifndef DEF_WBITS # define DEF_WBITS MAX_WBITS #endif /* default windowBits for decompression. MAX_WBITS is for compression only */ #if MAX_MEM_LEVEL >= 8 # define DEF_MEM_LEVEL 8 #else # define DEF_MEM_LEVEL MAX_MEM_LEVEL #endif /* default memLevel */ #define STORED_BLOCK 0 #define STATIC_TREES 1 #define DYN_TREES 2 /* The three kinds of block type */ #define MIN_MATCH 3 #define MAX_MATCH 258 /* The minimum and maximum match lengths */ #define PRESET_DICT 0x20 /* preset dictionary flag in zlib header */ /* target dependencies */ #if defined(MSDOS) || (defined(WINDOWS) && !defined(WIN32)) # define OS_CODE 0x00 # if defined(__TURBOC__) || defined(__BORLANDC__) # if (__STDC__ == 1) && (defined(__LARGE__) || defined(__COMPACT__)) /* Allow compilation with ANSI keywords only enabled */ void _Cdecl farfree( void *block ); void *_Cdecl farmalloc( unsigned long nbytes ); # else # include # endif # else /* MSC or DJGPP */ # include # endif #endif #ifdef AMIGA # define OS_CODE 0x01 #endif #if defined(VAXC) || defined(VMS) # define OS_CODE 0x02 # define F_OPEN(name, mode) \ fopen((name), (mode), "mbc=60", "ctx=stm", "rfm=fix", "mrs=512") #endif #if defined(ATARI) || defined(atarist) # define OS_CODE 0x05 #endif #ifdef OS2 # define OS_CODE 0x06 # ifdef M_I86 # include # endif #endif #if defined(MACOS) || defined(TARGET_OS_MAC) # define OS_CODE 0x07 # if defined(__MWERKS__) && __dest_os != __be_os && __dest_os != __win32_os # include /* for fdopen */ # else # ifndef fdopen # define fdopen(fd,mode) NULL /* No fdopen() */ # endif # endif #endif #ifdef TOPS20 # define OS_CODE 0x0a #endif #ifdef WIN32 # ifndef __CYGWIN__ /* Cygwin is Unix, not Win32 */ # define OS_CODE 0x0b # endif #endif #ifdef __50SERIES /* Prime/PRIMOS */ # define OS_CODE 0x0f #endif #if defined(_BEOS_) || defined(RISCOS) # define fdopen(fd,mode) NULL /* No fdopen() */ #endif #if (defined(_MSC_VER) && (_MSC_VER > 600)) && !defined __INTERIX # if defined(_WIN32_WCE) # define fdopen(fd,mode) NULL /* No fdopen() */ # ifndef _PTRDIFF_T_DEFINED typedef int ptrdiff_t; # define _PTRDIFF_T_DEFINED # endif # else # define fdopen(fd,type) _fdopen(fd,type) # endif #endif #if defined(__BORLANDC__) #pragma warn -8004 #pragma warn -8008 #pragma warn -8066 #endif /* provide prototypes for these when building zlib without LFS */ #if !defined(_LARGEFILE64_SOURCE) || _LFS64_LARGEFILE-0 == 0 ZEXTERN uLong ZEXPORT adler32_combine64 OF((uLong, uLong, z_off_t)); ZEXTERN uLong ZEXPORT crc32_combine64 OF((uLong, uLong, z_off_t)); #endif /* common defaults */ #ifndef OS_CODE # define OS_CODE 0x03 /* assume Unix */ #endif #ifndef F_OPEN # define F_OPEN(name, mode) fopen((name), (mode)) #endif /* functions */ #if defined(STDC99) || (defined(__TURBOC__) && __TURBOC__ >= 0x550) # ifndef HAVE_VSNPRINTF # define HAVE_VSNPRINTF # endif #endif #if defined(__CYGWIN__) # ifndef HAVE_VSNPRINTF # define HAVE_VSNPRINTF # endif #endif #ifndef HAVE_VSNPRINTF # ifdef MSDOS /* vsnprintf may exist on some MS-DOS compilers (DJGPP?), but for now we just assume it doesn't. */ # define NO_vsnprintf # endif # ifdef __TURBOC__ # define NO_vsnprintf # endif # ifdef WIN32 /* In Win32, vsnprintf is available as the "non-ANSI" _vsnprintf. */ # if !defined(vsnprintf) && !defined(NO_vsnprintf) # if !defined(_MSC_VER) || ( defined(_MSC_VER) && _MSC_VER < 1500 ) # define vsnprintf _vsnprintf # endif # endif # endif # ifdef __SASC # define NO_vsnprintf # endif #endif #ifdef VMS # define NO_vsnprintf #endif #if defined(pyr) # define NO_MEMCPY #endif #if defined(SMALL_MEDIUM) && !defined(_MSC_VER) && !defined(__SC__) /* Use our own functions for small and medium model with MSC <= 5.0. * You may have to use the same strategy for Borland C (untested). * The __SC__ check is for Symantec. */ # define NO_MEMCPY #endif #if defined(STDC) && !defined(HAVE_MEMCPY) && !defined(NO_MEMCPY) # define HAVE_MEMCPY #endif #ifdef HAVE_MEMCPY # ifdef SMALL_MEDIUM /* MSDOS small or medium model */ # define zmemcpy _fmemcpy # define zmemcmp _fmemcmp # define zmemzero(dest, len) _fmemset(dest, 0, len) # else # define zmemcpy memcpy # define zmemcmp memcmp # define zmemzero(dest, len) memset(dest, 0, len) # endif #else void ZLIB_INTERNAL zmemcpy OF((Bytef* dest, const Bytef* source, uInt len)); int ZLIB_INTERNAL zmemcmp OF((const Bytef* s1, const Bytef* s2, uInt len)); void ZLIB_INTERNAL zmemzero OF((Bytef* dest, uInt len)); #endif /* Diagnostic functions */ #ifdef DEBUG # include extern int ZLIB_INTERNAL z_verbose; extern void ZLIB_INTERNAL z_error OF((char *m)); # define Assert(cond,msg) {if(!(cond)) z_error(msg);} # define Trace(x) {if (z_verbose>=0) fprintf x ;} # define Tracev(x) {if (z_verbose>0) fprintf x ;} # define Tracevv(x) {if (z_verbose>1) fprintf x ;} # define Tracec(c,x) {if (z_verbose>0 && (c)) fprintf x ;} # define Tracecv(c,x) {if (z_verbose>1 && (c)) fprintf x ;} #else # define Assert(cond,msg) # define Trace(x) # define Tracev(x) # define Tracevv(x) # define Tracec(c,x) # define Tracecv(c,x) #endif voidpf ZLIB_INTERNAL zcalloc OF((voidpf opaque, unsigned items, unsigned size)); void ZLIB_INTERNAL zcfree OF((voidpf opaque, voidpf ptr)); #define ZALLOC(strm, items, size) \ (*((strm)->zalloc))((strm)->opaque, (items), (size)) #define ZFREE(strm, addr) (*((strm)->zfree))((strm)->opaque, (voidpf)(addr)) #define TRY_FREE(s, p) {if (p) ZFREE(s, p);} #endif /* ZUTIL_H */ libmstoolkit-77.0.0/include/expat_external.h0000644000175000017500000000644412455161024021076 0ustar rusconirusconi/* Copyright (c) 1998, 1999, 2000 Thai Open Source Software Center Ltd See the file COPYING for copying permission. */ #ifndef Expat_External_INCLUDED #define Expat_External_INCLUDED 1 /* External API definitions */ #if defined(_MSC_EXTENSIONS) && !defined(__BEOS__) && !defined(__CYGWIN__) #define XML_USE_MSC_EXTENSIONS 1 #endif /* Expat tries very hard to make the API boundary very specifically defined. There are two macros defined to control this boundary; each of these can be defined before including this header to achieve some different behavior, but doing so it not recommended or tested frequently. XMLCALL - The calling convention to use for all calls across the "library boundary." This will default to cdecl, and try really hard to tell the compiler that's what we want. XMLIMPORT - Whatever magic is needed to note that a function is to be imported from a dynamically loaded library (.dll, .so, or .sl, depending on your platform). The XMLCALL macro was added in Expat 1.95.7. The only one which is expected to be directly useful in client code is XMLCALL. Note that on at least some Unix versions, the Expat library must be compiled with the cdecl calling convention as the default since system headers may assume the cdecl convention. */ #ifndef XMLCALL #if defined(_MSC_VER) #define XMLCALL __cdecl #elif defined(__GNUC__) && defined(__i386) && !defined(__INTEL_COMPILER) #define XMLCALL __attribute__((cdecl)) #else /* For any platform which uses this definition and supports more than one calling convention, we need to extend this definition to declare the convention used on that platform, if it's possible to do so. If this is the case for your platform, please file a bug report with information on how to identify your platform via the C pre-processor and how to specify the same calling convention as the platform's malloc() implementation. */ #define XMLCALL #endif #endif /* not defined XMLCALL */ #if !defined(XML_STATIC) && !defined(XMLIMPORT) #ifndef XML_BUILDING_EXPAT /* using Expat from an application */ #ifdef XML_USE_MSC_EXTENSIONS #define XMLIMPORT __declspec(dllimport) #endif #endif #endif /* not defined XML_STATIC */ /* If we didn't define it above, define it away: */ #ifndef XMLIMPORT #define XMLIMPORT #endif #define XMLPARSEAPI(type) XMLIMPORT type XMLCALL #ifdef __cplusplus extern "C" { #endif #ifdef XML_UNICODE_WCHAR_T #define XML_UNICODE #endif #ifdef XML_UNICODE /* Information is UTF-16 encoded. */ #ifdef XML_UNICODE_WCHAR_T typedef wchar_t XML_Char; typedef wchar_t XML_LChar; #else typedef unsigned short XML_Char; typedef char XML_LChar; #endif /* XML_UNICODE_WCHAR_T */ #else /* Information is UTF-8 encoded. */ typedef char XML_Char; typedef char XML_LChar; #endif /* XML_UNICODE */ #ifdef XML_LARGE_SIZE /* Use large integers for file/stream positions. */ #if defined(XML_USE_MSC_EXTENSIONS) && _MSC_VER < 1400 typedef __int64 XML_Index; typedef unsigned __int64 XML_Size; #else typedef long long XML_Index; typedef unsigned long long XML_Size; #endif #else typedef long XML_Index; typedef unsigned long XML_Size; #endif /* XML_LARGE_SIZE */ #ifdef __cplusplus } #endif #endif /* not Expat_External_INCLUDED */ libmstoolkit-77.0.0/include/inffixed.h0000644000175000017500000001430712455161024017644 0ustar rusconirusconi /* inffixed.h -- table for decoding fixed codes * Generated automatically by makefixed(). */ /* WARNING: this file should *not* be used by applications. It is part of the implementation of the compression library and is subject to change. Applications should only use zlib.h. */ static const code lenfix[512] = { {96,7,0},{0,8,80},{0,8,16},{20,8,115},{18,7,31},{0,8,112},{0,8,48}, {0,9,192},{16,7,10},{0,8,96},{0,8,32},{0,9,160},{0,8,0},{0,8,128}, {0,8,64},{0,9,224},{16,7,6},{0,8,88},{0,8,24},{0,9,144},{19,7,59}, {0,8,120},{0,8,56},{0,9,208},{17,7,17},{0,8,104},{0,8,40},{0,9,176}, {0,8,8},{0,8,136},{0,8,72},{0,9,240},{16,7,4},{0,8,84},{0,8,20}, {21,8,227},{19,7,43},{0,8,116},{0,8,52},{0,9,200},{17,7,13},{0,8,100}, {0,8,36},{0,9,168},{0,8,4},{0,8,132},{0,8,68},{0,9,232},{16,7,8}, {0,8,92},{0,8,28},{0,9,152},{20,7,83},{0,8,124},{0,8,60},{0,9,216}, {18,7,23},{0,8,108},{0,8,44},{0,9,184},{0,8,12},{0,8,140},{0,8,76}, {0,9,248},{16,7,3},{0,8,82},{0,8,18},{21,8,163},{19,7,35},{0,8,114}, {0,8,50},{0,9,196},{17,7,11},{0,8,98},{0,8,34},{0,9,164},{0,8,2}, {0,8,130},{0,8,66},{0,9,228},{16,7,7},{0,8,90},{0,8,26},{0,9,148}, {20,7,67},{0,8,122},{0,8,58},{0,9,212},{18,7,19},{0,8,106},{0,8,42}, {0,9,180},{0,8,10},{0,8,138},{0,8,74},{0,9,244},{16,7,5},{0,8,86}, {0,8,22},{64,8,0},{19,7,51},{0,8,118},{0,8,54},{0,9,204},{17,7,15}, {0,8,102},{0,8,38},{0,9,172},{0,8,6},{0,8,134},{0,8,70},{0,9,236}, {16,7,9},{0,8,94},{0,8,30},{0,9,156},{20,7,99},{0,8,126},{0,8,62}, {0,9,220},{18,7,27},{0,8,110},{0,8,46},{0,9,188},{0,8,14},{0,8,142}, {0,8,78},{0,9,252},{96,7,0},{0,8,81},{0,8,17},{21,8,131},{18,7,31}, {0,8,113},{0,8,49},{0,9,194},{16,7,10},{0,8,97},{0,8,33},{0,9,162}, {0,8,1},{0,8,129},{0,8,65},{0,9,226},{16,7,6},{0,8,89},{0,8,25}, {0,9,146},{19,7,59},{0,8,121},{0,8,57},{0,9,210},{17,7,17},{0,8,105}, {0,8,41},{0,9,178},{0,8,9},{0,8,137},{0,8,73},{0,9,242},{16,7,4}, {0,8,85},{0,8,21},{16,8,258},{19,7,43},{0,8,117},{0,8,53},{0,9,202}, {17,7,13},{0,8,101},{0,8,37},{0,9,170},{0,8,5},{0,8,133},{0,8,69}, {0,9,234},{16,7,8},{0,8,93},{0,8,29},{0,9,154},{20,7,83},{0,8,125}, {0,8,61},{0,9,218},{18,7,23},{0,8,109},{0,8,45},{0,9,186},{0,8,13}, {0,8,141},{0,8,77},{0,9,250},{16,7,3},{0,8,83},{0,8,19},{21,8,195}, {19,7,35},{0,8,115},{0,8,51},{0,9,198},{17,7,11},{0,8,99},{0,8,35}, {0,9,166},{0,8,3},{0,8,131},{0,8,67},{0,9,230},{16,7,7},{0,8,91}, {0,8,27},{0,9,150},{20,7,67},{0,8,123},{0,8,59},{0,9,214},{18,7,19}, {0,8,107},{0,8,43},{0,9,182},{0,8,11},{0,8,139},{0,8,75},{0,9,246}, {16,7,5},{0,8,87},{0,8,23},{64,8,0},{19,7,51},{0,8,119},{0,8,55}, {0,9,206},{17,7,15},{0,8,103},{0,8,39},{0,9,174},{0,8,7},{0,8,135}, {0,8,71},{0,9,238},{16,7,9},{0,8,95},{0,8,31},{0,9,158},{20,7,99}, {0,8,127},{0,8,63},{0,9,222},{18,7,27},{0,8,111},{0,8,47},{0,9,190}, {0,8,15},{0,8,143},{0,8,79},{0,9,254},{96,7,0},{0,8,80},{0,8,16}, {20,8,115},{18,7,31},{0,8,112},{0,8,48},{0,9,193},{16,7,10},{0,8,96}, {0,8,32},{0,9,161},{0,8,0},{0,8,128},{0,8,64},{0,9,225},{16,7,6}, {0,8,88},{0,8,24},{0,9,145},{19,7,59},{0,8,120},{0,8,56},{0,9,209}, {17,7,17},{0,8,104},{0,8,40},{0,9,177},{0,8,8},{0,8,136},{0,8,72}, {0,9,241},{16,7,4},{0,8,84},{0,8,20},{21,8,227},{19,7,43},{0,8,116}, {0,8,52},{0,9,201},{17,7,13},{0,8,100},{0,8,36},{0,9,169},{0,8,4}, {0,8,132},{0,8,68},{0,9,233},{16,7,8},{0,8,92},{0,8,28},{0,9,153}, {20,7,83},{0,8,124},{0,8,60},{0,9,217},{18,7,23},{0,8,108},{0,8,44}, {0,9,185},{0,8,12},{0,8,140},{0,8,76},{0,9,249},{16,7,3},{0,8,82}, {0,8,18},{21,8,163},{19,7,35},{0,8,114},{0,8,50},{0,9,197},{17,7,11}, {0,8,98},{0,8,34},{0,9,165},{0,8,2},{0,8,130},{0,8,66},{0,9,229}, {16,7,7},{0,8,90},{0,8,26},{0,9,149},{20,7,67},{0,8,122},{0,8,58}, {0,9,213},{18,7,19},{0,8,106},{0,8,42},{0,9,181},{0,8,10},{0,8,138}, {0,8,74},{0,9,245},{16,7,5},{0,8,86},{0,8,22},{64,8,0},{19,7,51}, {0,8,118},{0,8,54},{0,9,205},{17,7,15},{0,8,102},{0,8,38},{0,9,173}, {0,8,6},{0,8,134},{0,8,70},{0,9,237},{16,7,9},{0,8,94},{0,8,30}, {0,9,157},{20,7,99},{0,8,126},{0,8,62},{0,9,221},{18,7,27},{0,8,110}, {0,8,46},{0,9,189},{0,8,14},{0,8,142},{0,8,78},{0,9,253},{96,7,0}, {0,8,81},{0,8,17},{21,8,131},{18,7,31},{0,8,113},{0,8,49},{0,9,195}, {16,7,10},{0,8,97},{0,8,33},{0,9,163},{0,8,1},{0,8,129},{0,8,65}, {0,9,227},{16,7,6},{0,8,89},{0,8,25},{0,9,147},{19,7,59},{0,8,121}, {0,8,57},{0,9,211},{17,7,17},{0,8,105},{0,8,41},{0,9,179},{0,8,9}, {0,8,137},{0,8,73},{0,9,243},{16,7,4},{0,8,85},{0,8,21},{16,8,258}, {19,7,43},{0,8,117},{0,8,53},{0,9,203},{17,7,13},{0,8,101},{0,8,37}, {0,9,171},{0,8,5},{0,8,133},{0,8,69},{0,9,235},{16,7,8},{0,8,93}, {0,8,29},{0,9,155},{20,7,83},{0,8,125},{0,8,61},{0,9,219},{18,7,23}, {0,8,109},{0,8,45},{0,9,187},{0,8,13},{0,8,141},{0,8,77},{0,9,251}, {16,7,3},{0,8,83},{0,8,19},{21,8,195},{19,7,35},{0,8,115},{0,8,51}, {0,9,199},{17,7,11},{0,8,99},{0,8,35},{0,9,167},{0,8,3},{0,8,131}, {0,8,67},{0,9,231},{16,7,7},{0,8,91},{0,8,27},{0,9,151},{20,7,67}, {0,8,123},{0,8,59},{0,9,215},{18,7,19},{0,8,107},{0,8,43},{0,9,183}, {0,8,11},{0,8,139},{0,8,75},{0,9,247},{16,7,5},{0,8,87},{0,8,23}, {64,8,0},{19,7,51},{0,8,119},{0,8,55},{0,9,207},{17,7,15},{0,8,103}, {0,8,39},{0,9,175},{0,8,7},{0,8,135},{0,8,71},{0,9,239},{16,7,9}, {0,8,95},{0,8,31},{0,9,159},{20,7,99},{0,8,127},{0,8,63},{0,9,223}, {18,7,27},{0,8,111},{0,8,47},{0,9,191},{0,8,15},{0,8,143},{0,8,79}, {0,9,255} }; static const code distfix[32] = { {16,5,1},{23,5,257},{19,5,17},{27,5,4097},{17,5,5},{25,5,1025}, {21,5,65},{29,5,16385},{16,5,3},{24,5,513},{20,5,33},{28,5,8193}, {18,5,9},{26,5,2049},{22,5,129},{64,5,0},{16,5,2},{23,5,385}, {19,5,25},{27,5,6145},{17,5,7},{25,5,1537},{21,5,97},{29,5,24577}, {16,5,4},{24,5,769},{20,5,49},{28,5,12289},{18,5,13},{26,5,3073}, {22,5,193},{64,5,0} }; libmstoolkit-77.0.0/include/internal.h0000644000175000017500000000375412455161024017670 0ustar rusconirusconi/* internal.h Internal definitions used by Expat. This is not needed to compile client code. The following calling convention macros are defined for frequently called functions: FASTCALL - Used for those internal functions that have a simple body and a low number of arguments and local variables. PTRCALL - Used for functions called though function pointers. PTRFASTCALL - Like PTRCALL, but for low number of arguments. inline - Used for selected internal functions for which inlining may improve performance on some platforms. Note: Use of these macros is based on judgement, not hard rules, and therefore subject to change. */ #if defined(__GNUC__) && defined(__i386__) && !defined(__MINGW32__) /* We'll use this version by default only where we know it helps. regparm() generates warnings on Solaris boxes. See SF bug #692878. Instability reported with egcs on a RedHat Linux 7.3. Let's comment out: #define FASTCALL __attribute__((stdcall, regparm(3))) and let's try this: */ #define FASTCALL __attribute__((regparm(3))) #define PTRFASTCALL __attribute__((regparm(3))) #endif /* Using __fastcall seems to have an unexpected negative effect under MS VC++, especially for function pointers, so we won't use it for now on that platform. It may be reconsidered for a future release if it can be made more effective. Likely reason: __fastcall on Windows is like stdcall, therefore the compiler cannot perform stack optimizations for call clusters. */ /* Make sure all of these are defined if they aren't already. */ #ifndef FASTCALL #define FASTCALL #endif #ifndef PTRCALL #define PTRCALL #endif #ifndef PTRFASTCALL #define PTRFASTCALL #endif #ifndef XML_MIN_SIZE #if !defined(__cplusplus) && !defined(inline) #ifdef __GNUC__ #define inline __inline #endif /* __GNUC__ */ #endif #endif /* XML_MIN_SIZE */ #ifdef __cplusplus #define inline inline #else #ifndef inline #define inline #endif #endif libmstoolkit-77.0.0/include/MSNumpress.hpp0000644000175000017500000003075012455161024020464 0ustar rusconirusconi/* MSNumpress.hpp johan.teleman@immun.lth.se Copyright 2013 Johan Teleman 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. */ /* ==================== encodeInt ==================== Some of the encodings described below use a integer compression referred to simply as encodeInt() This encoding works on a 4 byte integer, by truncating initial zeros or ones. If the initial (most significant) half byte is 0x0 or 0xf, the number of such halfbytes starting from the most significant is stored in a halfbyte. This initial count is then followed by the rest of the ints halfbytes, in little-endian order. A count halfbyte c of 0 <= c <= 8 is interpreted as an initial c 0x0 halfbytes 9 <= c <= 15 is interpreted as an initial (c-8) 0xf halfbytes Ex: int c rest 0 => 0x8 -1 => 0xf 0xf 23 => 0x6 0x7 0x1 */ #ifndef _MSNUMPRESS_HPP_ #define _MSNUMPRESS_HPP_ #include #include namespace ms { namespace numpress { namespace MSNumpress { double optimalLinearFixedPoint( const double *data, size_t dataSize); /** * Encodes the doubles in data by first using a * - lossy conversion to a 4 byte 5 decimal fixed point representation * - storing the residuals from a linear prediction after first to values * - encoding by encodeInt (see above) * * The resulting binary is maximally dataSize * 5 bytes, but much less if the * data is reasonably smooth on the first order. * * This encoding is suitable for typical m/z or retention time binary arrays. * On a test set, the encoding was empirically show to be accurate to at least 0.002 ppm. * * @data pointer to array of double to be encoded (need memorycont. repr.) * @dataSize number of doubles from *data to encode * @result pointer to where resulting bytes should be stored * @fixedPoint the scaling factor used for getting the fixed point repr. * This is stored in the binary and automatically extracted * on decoding. * @return the number of encoded bytes */ size_t encodeLinear( const double *data, const size_t dataSize, unsigned char *result, double fixedPoint); /** * Calls lower level encodeLinear while handling vector sizes appropriately * * @data vector of doubles to be encoded * @result vector of resulting bytes (will be resized to the number of bytes) */ void encodeLinear( const std::vector &data, std::vector &result, double fixedPoint); /** * Decodes data encoded by encodeLinear. * * result vector guaranteed to be shorter than twice the data length (in nbr of values) * * Note that this method may throw a const char* if it deems the input data to be corrupt, ei. * that the last encoded int does not use the last byte in the data. In addition the last encoded * int need to use either the last halfbyte, or the second last followed by a 0x0 halfbyte. * * @data pointer to array of bytes to be decoded (need memorycont. repr.) * @dataSize number of bytes from *data to decode * @result pointer to were resulting doubles should be stored * @return the number of decoded doubles, or -1 if dataSize < 4 or 4 < dataSize < 8 */ size_t decodeLinear( const unsigned char *data, const size_t dataSize, double *result); /** * Calls lower level decodeLinear while handling vector sizes appropriately * * Note that this method may throw a const char* if it deems the input data to be corrupt, ei. * that the last encoded int does not use the last byte in the data. In addition the last encoded * int need to use either the last halfbyte, or the second last followed by a 0x0 halfbyte. * * @data vector of bytes to be decoded * @result vector of resulting double (will be resized to the number of doubles) */ void decodeLinear( const std::vector &data, std::vector &result); ///////////////////////////////////////////////////////////// /** * Encodes the doubles in data by storing the residuals from a linear prediction after first to values. * * The resulting binary is the same size as the input data. * * This encoding is suitable for typical m/z or retention time binary arrays, and is * intended to be used before zlib compression to improve compression. * * @data pointer to array of doubles to be encoded (need memorycont. repr.) * @dataSize number of doubles from *data to encode * @result pointer to were resulting bytes should be stored */ size_t encodeSafe( const double *data, const size_t dataSize, unsigned char *result); /** * Decodes data encoded by encodeSafe. * * result vector is the same size as the input data. * * @data pointer to array of bytes to be decoded (need memorycont. repr.) * @dataSize number of bytes from *data to decode * @result pointer to were resulting doubles should be stored * @return the number of decoded bytes or -1 if something went wrong. */ int decodeSafe( const unsigned char *data, const size_t dataSize, double *result); ///////////////////////////////////////////////////////////// /** * Encodes ion counts by simply rounding to the nearest 4 byte integer, * and compressing each integer with encodeInt. * * The handleable range is therefore 0 -> 4294967294. * The resulting binary is maximally dataSize * 5 bytes, but much less if the * data is close to 0 on average. * * @data pointer to array of double to be encoded (need memorycont. repr.) * @dataSize number of doubles from *data to encode * @result pointer to were resulting bytes should be stored * @return the number of encoded bytes */ size_t encodePic( const double *data, const size_t dataSize, unsigned char *result); /** * Calls lower level encodePic while handling vector sizes appropriately * * @data vector of doubles to be encoded * @result vector of resulting bytes (will be resized to the number of bytes) */ void encodePic( const std::vector &data, std::vector &result); /** * Decodes data encoded by encodePic * * result vector guaranteed to be shorter of equal to twice the data length (in nbr of values) * * Note that this method may throw a const char* if it deems the input data to be corrupt, ei. * that the last encoded int does not use the last byte in the data. In addition the last encoded * int need to use either the last halfbyte, or the second last followed by a 0x0 halfbyte. * * @data pointer to array of bytes to be decoded (need memorycont. repr.) * @dataSize number of bytes from *data to decode * @result pointer to were resulting doubles should be stored * @return the number of decoded doubles */ size_t decodePic( const unsigned char *data, const size_t dataSize, double *result); /** * Calls lower level decodePic while handling vector sizes appropriately * * Note that this method may throw a const char* if it deems the input data to be corrupt, ei. * that the last encoded int does not use the last byte in the data. In addition the last encoded * int need to use either the last halfbyte, or the second last followed by a 0x0 halfbyte. * * @data vector of bytes to be decoded * @result vector of resulting double (will be resized to the number of doubles) */ void decodePic( const std::vector &data, std::vector &result); ///////////////////////////////////////////////////////////// double optimalSlofFixedPoint( const double *data, size_t dataSize); /** * Encodes ion counts by taking the natural logarithm, and storing a * fixed point representation of this. This is calculated as * * unsigned short fp = log(d + 1) * fixedPoint + 0.5 * * result vector is exactly twice the data length (in nbr of values) * * @data pointer to array of double to be encoded (need memorycont. repr.) * @dataSize number of doubles from *data to encode * @result pointer to were resulting bytes should be stored * @return the number of encoded bytes */ size_t encodeSlof( const double *data, const size_t dataSize, unsigned char *result, double fixedPoint); /** * Calls lower level encodeSlof while handling vector sizes appropriately * * @data vector of doubles to be encoded * @result vector of resulting bytes (will be resized to the number of bytes) */ void encodeSlof( const std::vector &data, std::vector &result, double fixedPoint); /** * Decodes data encoded by encodeSlof * * Note that this method may throw a const char* if it deems the input data to be corrupt. * * @data pointer to array of bytes to be decoded (need memorycont. repr.) * @dataSize number of bytes from *data to decode * @result pointer to were resulting doubles should be stored * @return the number of decoded doubles */ size_t decodeSlof( const unsigned char *data, const size_t dataSize, double *result); /** * Calls lower level decodeSlof while handling vector sizes appropriately * * Note that this method may throw a const char* if it deems the input data to be corrupt. * * @data vector of bytes to be decoded * @result vector of resulting double (will be resized to the number of doubles) */ void decodeSlof( const std::vector &data, std::vector &result); } // namespace MSNumpress } // namespace msdata } // namespace pwiz #endif // _MSNUMPRESS_HPP_ libmstoolkit-77.0.0/include/utf8tab.h0000644000175000017500000000334312455161024017423 0ustar rusconirusconi/* Copyright (c) 1998, 1999 Thai Open Source Software Center Ltd See the file COPYING for copying permission. */ /* 0x80 */ BT_TRAIL, BT_TRAIL, BT_TRAIL, BT_TRAIL, /* 0x84 */ BT_TRAIL, BT_TRAIL, BT_TRAIL, BT_TRAIL, /* 0x88 */ BT_TRAIL, BT_TRAIL, BT_TRAIL, BT_TRAIL, /* 0x8C */ BT_TRAIL, BT_TRAIL, BT_TRAIL, BT_TRAIL, /* 0x90 */ BT_TRAIL, BT_TRAIL, BT_TRAIL, BT_TRAIL, /* 0x94 */ BT_TRAIL, BT_TRAIL, BT_TRAIL, BT_TRAIL, /* 0x98 */ BT_TRAIL, BT_TRAIL, BT_TRAIL, BT_TRAIL, /* 0x9C */ BT_TRAIL, BT_TRAIL, BT_TRAIL, BT_TRAIL, /* 0xA0 */ BT_TRAIL, BT_TRAIL, BT_TRAIL, BT_TRAIL, /* 0xA4 */ BT_TRAIL, BT_TRAIL, BT_TRAIL, BT_TRAIL, /* 0xA8 */ BT_TRAIL, BT_TRAIL, BT_TRAIL, BT_TRAIL, /* 0xAC */ BT_TRAIL, BT_TRAIL, BT_TRAIL, BT_TRAIL, /* 0xB0 */ BT_TRAIL, BT_TRAIL, BT_TRAIL, BT_TRAIL, /* 0xB4 */ BT_TRAIL, BT_TRAIL, BT_TRAIL, BT_TRAIL, /* 0xB8 */ BT_TRAIL, BT_TRAIL, BT_TRAIL, BT_TRAIL, /* 0xBC */ BT_TRAIL, BT_TRAIL, BT_TRAIL, BT_TRAIL, /* 0xC0 */ BT_LEAD2, BT_LEAD2, BT_LEAD2, BT_LEAD2, /* 0xC4 */ BT_LEAD2, BT_LEAD2, BT_LEAD2, BT_LEAD2, /* 0xC8 */ BT_LEAD2, BT_LEAD2, BT_LEAD2, BT_LEAD2, /* 0xCC */ BT_LEAD2, BT_LEAD2, BT_LEAD2, BT_LEAD2, /* 0xD0 */ BT_LEAD2, BT_LEAD2, BT_LEAD2, BT_LEAD2, /* 0xD4 */ BT_LEAD2, BT_LEAD2, BT_LEAD2, BT_LEAD2, /* 0xD8 */ BT_LEAD2, BT_LEAD2, BT_LEAD2, BT_LEAD2, /* 0xDC */ BT_LEAD2, BT_LEAD2, BT_LEAD2, BT_LEAD2, /* 0xE0 */ BT_LEAD3, BT_LEAD3, BT_LEAD3, BT_LEAD3, /* 0xE4 */ BT_LEAD3, BT_LEAD3, BT_LEAD3, BT_LEAD3, /* 0xE8 */ BT_LEAD3, BT_LEAD3, BT_LEAD3, BT_LEAD3, /* 0xEC */ BT_LEAD3, BT_LEAD3, BT_LEAD3, BT_LEAD3, /* 0xF0 */ BT_LEAD4, BT_LEAD4, BT_LEAD4, BT_LEAD4, /* 0xF4 */ BT_LEAD4, BT_NONXML, BT_NONXML, BT_NONXML, /* 0xF8 */ BT_NONXML, BT_NONXML, BT_NONXML, BT_NONXML, /* 0xFC */ BT_NONXML, BT_NONXML, BT_MALFORM, BT_MALFORM, libmstoolkit-77.0.0/include/MSToolkitTypes.h0000644000175000017500000000303012455161024020751 0ustar rusconirusconi#ifndef _MSTOOLKITTYPES_H #define _MSTOOLKITTYPES_H #include namespace MSToolkit { enum MSSpectrumType { MS1, MS2, MS3, ZS, UZS, IonSpec, SRM, REFERENCE, Unspecified, MSX }; enum MSFileFormat { bms1, bms2, cms1, cms2, mgf, ms1, ms2, msmat_ff, mzXML, mz5, mzML, raw, sqlite, psm, uzs, zs, mzXMLgz, mzMLgz, dunno }; enum MSTag { no, D, H, I, S, Z }; enum MSActivation { mstCID, mstECD, mstETD, mstPQD, mstHCD, mstIRMPD, mstNA }; struct MSHeader { char header[16][128]; }; struct MSScanInfo { int scanNumber[2]; int numDataPoints; int numEZStates; int numZStates; float rTime; float IIT; float BPI; double* mz; int mzCount; double convA; double convB; double convC; double convD; double convE; double convI; double TIC; double BPM; MSScanInfo(){ mz=NULL; scanNumber[0]=scanNumber[1]=0; numDataPoints=numEZStates=numZStates=0; rTime=IIT=BPI=0.0f; TIC=BPM=0.0; convA=convB=convC=convD=convE=convI=0.0; mzCount=0; } ~MSScanInfo(){ if(mz!=NULL) delete [] mz; } }; struct DataPeak { double dMass; double dIntensity; }; //For RAW files struct Peak_T { double mz; float intensity; }; struct ZState { int z; double mz; //M+H, not mz }; struct EZState { int z; double mh; //M+H float pRTime; //precursor area float pArea; //precursor retention time }; } #endif libmstoolkit-77.0.0/include/MSReader.h0000644000175000017500000001134012455161024017504 0ustar rusconirusconi#ifndef _MSREADER_H #define _MSREADER_H #include "Spectrum.h" #include "MSObject.h" #include "mzParser.h" #include #include #include #include //For mzXML Writing //#include "mzXMLWriter.h" //#include "MSToolkitInterface.h" #ifdef _MSC_VER //#include //#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 #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& 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 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 estimateCharge(Spectrum& s); #endif }; } #endif libmstoolkit-77.0.0/include/inftrees.h0000644000175000017500000000556012455161024017670 0ustar rusconirusconi/* inftrees.h -- header to use inftrees.c * Copyright (C) 1995-2005, 2010 Mark Adler * For conditions of distribution and use, see copyright notice in zlib.h */ /* WARNING: this file should *not* be used by applications. It is part of the implementation of the compression library and is subject to change. Applications should only use zlib.h. */ /* Structure for decoding tables. Each entry provides either the information needed to do the operation requested by the code that indexed that table entry, or it provides a pointer to another table that indexes more bits of the code. op indicates whether the entry is a pointer to another table, a literal, a length or distance, an end-of-block, or an invalid code. For a table pointer, the low four bits of op is the number of index bits of that table. For a length or distance, the low four bits of op is the number of extra bits to get after the code. bits is the number of bits in this code or part of the code to drop off of the bit buffer. val is the actual byte to output in the case of a literal, the base length or distance, or the offset from the current table to the next table. Each entry is four bytes. */ typedef struct { unsigned char op; /* operation, extra bits, table bits */ unsigned char bits; /* bits in this part of the code */ unsigned short val; /* offset in table or code value */ } code; /* op values as set by inflate_table(): 00000000 - literal 0000tttt - table link, tttt != 0 is the number of table index bits 0001eeee - length or distance, eeee is the number of extra bits 01100000 - end of block 01000000 - invalid code */ /* Maximum size of the dynamic table. The maximum number of code structures is 1444, which is the sum of 852 for literal/length codes and 592 for distance codes. These values were found by exhaustive searches using the program examples/enough.c found in the zlib distribtution. The arguments to that program are the number of symbols, the initial root table size, and the maximum bit length of a code. "enough 286 9 15" for literal/length codes returns returns 852, and "enough 30 6 15" for distance codes returns 592. The initial root table size (9 or 6) is found in the fifth argument of the inflate_table() calls in inflate.c and infback.c. If the root table size is changed, then these maximum sizes would be need to be recalculated and updated. */ #define ENOUGH_LENS 852 #define ENOUGH_DISTS 592 #define ENOUGH (ENOUGH_LENS+ENOUGH_DISTS) /* Type of code to build for inflate_table() */ typedef enum { CODES, LENS, DISTS } codetype; int ZLIB_INTERNAL inflate_table OF((codetype type, unsigned short FAR *lens, unsigned codes, code FAR * FAR *table, unsigned FAR *bits, unsigned short FAR *work)); libmstoolkit-77.0.0/include/sqlite3.h0000644000175000017500000116247612455161024017450 0ustar rusconirusconi/* ** 2001 September 15 ** ** The author disclaims copyright to this source code. In place of ** a legal notice, here is a blessing: ** ** May you do good and not evil. ** May you find forgiveness for yourself and forgive others. ** May you share freely, never taking more than you give. ** ************************************************************************* ** This header file defines the interface that the SQLite library ** presents to client programs. If a C-function, structure, datatype, ** or constant definition does not appear in this file, then it is ** not a published API of SQLite, is subject to change without ** notice, and should not be referenced by programs that use SQLite. ** ** Some of the definitions that are in this file are marked as ** "experimental". Experimental interfaces are normally new ** features recently added to SQLite. We do not anticipate changes ** to experimental interfaces but reserve the right to make minor changes ** if experience from use "in the wild" suggest such changes are prudent. ** ** The official C-language API documentation for SQLite is derived ** from comments in this file. This file is the authoritative source ** on how SQLite interfaces are suppose to operate. ** ** The name of this file under configuration management is "sqlite.h.in". ** The makefile makes some minor changes to this file (such as inserting ** the version number) and changes its name to "sqlite3.h" as ** part of the build process. */ #ifndef _SQLITE3_H_ #define _SQLITE3_H_ #include /* Needed for the definition of va_list */ /* ** Make sure we can call this stuff from C++. */ #ifdef __cplusplus extern "C" { #endif /* ** Add the ability to override 'extern' */ #ifndef SQLITE_EXTERN # define SQLITE_EXTERN extern #endif #ifndef SQLITE_API # define SQLITE_API #endif /* ** These no-op macros are used in front of interfaces to mark those ** interfaces as either deprecated or experimental. New applications ** should not use deprecated interfaces - they are support for backwards ** compatibility only. Application writers should be aware that ** experimental interfaces are subject to change in point releases. ** ** These macros used to resolve to various kinds of compiler magic that ** would generate warning messages when they were used. But that ** compiler magic ended up generating such a flurry of bug reports ** that we have taken it all out and gone back to using simple ** noop macros. */ #define SQLITE_DEPRECATED #define SQLITE_EXPERIMENTAL /* ** Ensure these symbols were not defined by some previous header file. */ #ifdef SQLITE_VERSION # undef SQLITE_VERSION #endif #ifdef SQLITE_VERSION_NUMBER # undef SQLITE_VERSION_NUMBER #endif /* ** CAPI3REF: Compile-Time Library Version Numbers ** ** ^(The [SQLITE_VERSION] C preprocessor macro in the sqlite3.h header ** evaluates to a string literal that is the SQLite version in the ** format "X.Y.Z" where X is the major version number (always 3 for ** SQLite3) and Y is the minor version number and Z is the release number.)^ ** ^(The [SQLITE_VERSION_NUMBER] C preprocessor macro resolves to an integer ** with the value (X*1000000 + Y*1000 + Z) where X, Y, and Z are the same ** numbers used in [SQLITE_VERSION].)^ ** The SQLITE_VERSION_NUMBER for any given release of SQLite will also ** be larger than the release from which it is derived. Either Y will ** be held constant and Z will be incremented or else Y will be incremented ** and Z will be reset to zero. ** ** Since version 3.6.18, SQLite source code has been stored in the ** Fossil configuration management ** system. ^The SQLITE_SOURCE_ID macro evaluates to ** a string which identifies a particular check-in of SQLite ** within its configuration management system. ^The SQLITE_SOURCE_ID ** string contains the date and time of the check-in (UTC) and an SHA1 ** hash of the entire source tree. ** ** See also: [sqlite3_libversion()], ** [sqlite3_libversion_number()], [sqlite3_sourceid()], ** [sqlite_version()] and [sqlite_source_id()]. */ #define SQLITE_VERSION "3.7.7.1" #define SQLITE_VERSION_NUMBER 3007007 #define SQLITE_SOURCE_ID "2011-06-28 17:39:05 af0d91adf497f5f36ec3813f04235a6e195a605f" /* ** CAPI3REF: Run-Time Library Version Numbers ** KEYWORDS: sqlite3_version, sqlite3_sourceid ** ** These interfaces provide the same information as the [SQLITE_VERSION], ** [SQLITE_VERSION_NUMBER], and [SQLITE_SOURCE_ID] C preprocessor macros ** but are associated with the library instead of the header file. ^(Cautious ** programmers might include assert() statements in their application to ** verify that values returned by these interfaces match the macros in ** the header, and thus insure that the application is ** compiled with matching library and header files. ** ** 
** assert( sqlite3_libversion_number()==SQLITE_VERSION_NUMBER );
** assert( strcmp(sqlite3_sourceid(),SQLITE_SOURCE_ID)==0 );
** assert( strcmp(sqlite3_libversion(),SQLITE_VERSION)==0 );
**
)^ ** ** ^The sqlite3_version[] string constant contains the text of [SQLITE_VERSION] ** macro. ^The sqlite3_libversion() function returns a pointer to the ** to the sqlite3_version[] string constant. The sqlite3_libversion() ** function is provided for use in DLLs since DLL users usually do not have ** direct access to string constants within the DLL. ^The ** sqlite3_libversion_number() function returns an integer equal to ** [SQLITE_VERSION_NUMBER]. ^The sqlite3_sourceid() function returns ** a pointer to a string constant whose value is the same as the ** [SQLITE_SOURCE_ID] C preprocessor macro. ** ** See also: [sqlite_version()] and [sqlite_source_id()]. */ SQLITE_API SQLITE_EXTERN const char sqlite3_version[]; SQLITE_API const char *sqlite3_libversion(void); SQLITE_API const char *sqlite3_sourceid(void); SQLITE_API int sqlite3_libversion_number(void); /* ** CAPI3REF: Run-Time Library Compilation Options Diagnostics ** ** ^The sqlite3_compileoption_used() function returns 0 or 1 ** indicating whether the specified option was defined at ** compile time. ^The SQLITE_ prefix may be omitted from the ** option name passed to sqlite3_compileoption_used(). ** ** ^The sqlite3_compileoption_get() function allows iterating ** over the list of options that were defined at compile time by ** returning the N-th compile time option string. ^If N is out of range, ** sqlite3_compileoption_get() returns a NULL pointer. ^The SQLITE_ ** prefix is omitted from any strings returned by ** sqlite3_compileoption_get(). ** ** ^Support for the diagnostic functions sqlite3_compileoption_used() ** and sqlite3_compileoption_get() may be omitted by specifying the ** [SQLITE_OMIT_COMPILEOPTION_DIAGS] option at compile time. ** ** See also: SQL functions [sqlite_compileoption_used()] and ** [sqlite_compileoption_get()] and the [compile_options pragma]. */ #ifndef SQLITE_OMIT_COMPILEOPTION_DIAGS SQLITE_API int sqlite3_compileoption_used(const char *zOptName); SQLITE_API const char *sqlite3_compileoption_get(int N); #endif /* ** CAPI3REF: Test To See If The Library Is Threadsafe ** ** ^The sqlite3_threadsafe() function returns zero if and only if ** SQLite was compiled mutexing code omitted due to the ** [SQLITE_THREADSAFE] compile-time option being set to 0. ** ** SQLite can be compiled with or without mutexes. When ** the [SQLITE_THREADSAFE] C preprocessor macro is 1 or 2, mutexes ** are enabled and SQLite is threadsafe. When the ** [SQLITE_THREADSAFE] macro is 0, ** the mutexes are omitted. Without the mutexes, it is not safe ** to use SQLite concurrently from more than one thread. ** ** Enabling mutexes incurs a measurable performance penalty. ** So if speed is of utmost importance, it makes sense to disable ** the mutexes. But for maximum safety, mutexes should be enabled. ** ^The default behavior is for mutexes to be enabled. ** ** This interface can be used by an application to make sure that the ** version of SQLite that it is linking against was compiled with ** the desired setting of the [SQLITE_THREADSAFE] macro. ** ** This interface only reports on the compile-time mutex setting ** of the [SQLITE_THREADSAFE] flag. If SQLite is compiled with ** SQLITE_THREADSAFE=1 or =2 then mutexes are enabled by default but ** can be fully or partially disabled using a call to [sqlite3_config()] ** with the verbs [SQLITE_CONFIG_SINGLETHREAD], [SQLITE_CONFIG_MULTITHREAD], ** or [SQLITE_CONFIG_MUTEX]. ^(The return value of the ** sqlite3_threadsafe() function shows only the compile-time setting of ** thread safety, not any run-time changes to that setting made by ** sqlite3_config(). In other words, the return value from sqlite3_threadsafe() ** is unchanged by calls to sqlite3_config().)^ ** ** See the [threading mode] documentation for additional information. */ SQLITE_API int sqlite3_threadsafe(void); /* ** CAPI3REF: Database Connection Handle ** KEYWORDS: {database connection} {database connections} ** ** Each open SQLite database is represented by a pointer to an instance of ** the opaque structure named "sqlite3". It is useful to think of an sqlite3 ** pointer as an object. The [sqlite3_open()], [sqlite3_open16()], and ** [sqlite3_open_v2()] interfaces are its constructors, and [sqlite3_close()] ** is its destructor. There are many other interfaces (such as ** [sqlite3_prepare_v2()], [sqlite3_create_function()], and ** [sqlite3_busy_timeout()] to name but three) that are methods on an ** sqlite3 object. */ typedef struct sqlite3 sqlite3; /* ** CAPI3REF: 64-Bit Integer Types ** KEYWORDS: sqlite_int64 sqlite_uint64 ** ** Because there is no cross-platform way to specify 64-bit integer types ** SQLite includes typedefs for 64-bit signed and unsigned integers. ** ** The sqlite3_int64 and sqlite3_uint64 are the preferred type definitions. ** The sqlite_int64 and sqlite_uint64 types are supported for backwards ** compatibility only. ** ** ^The sqlite3_int64 and sqlite_int64 types can store integer values ** between -9223372036854775808 and +9223372036854775807 inclusive. ^The ** sqlite3_uint64 and sqlite_uint64 types can store integer values ** between 0 and +18446744073709551615 inclusive. */ #ifdef SQLITE_INT64_TYPE typedef SQLITE_INT64_TYPE sqlite_int64; typedef unsigned SQLITE_INT64_TYPE sqlite_uint64; #elif defined(_MSC_VER) || defined(__BORLANDC__) typedef __int64 sqlite_int64; typedef unsigned __int64 sqlite_uint64; #else typedef long long int sqlite_int64; typedef unsigned long long int sqlite_uint64; #endif typedef sqlite_int64 sqlite3_int64; typedef sqlite_uint64 sqlite3_uint64; /* ** If compiling for a processor that lacks floating point support, ** substitute integer for floating-point. */ #ifdef SQLITE_OMIT_FLOATING_POINT # define double sqlite3_int64 #endif /* ** CAPI3REF: Closing A Database Connection ** ** ^The sqlite3_close() routine is the destructor for the [sqlite3] object. ** ^Calls to sqlite3_close() return SQLITE_OK if the [sqlite3] object is ** successfully destroyed and all associated resources are deallocated. ** ** Applications must [sqlite3_finalize | finalize] all [prepared statements] ** and [sqlite3_blob_close | close] all [BLOB handles] associated with ** the [sqlite3] object prior to attempting to close the object. ^If ** sqlite3_close() is called on a [database connection] that still has ** outstanding [prepared statements] or [BLOB handles], then it returns ** SQLITE_BUSY. ** ** ^If [sqlite3_close()] is invoked while a transaction is open, ** the transaction is automatically rolled back. ** ** The C parameter to [sqlite3_close(C)] must be either a NULL ** pointer or an [sqlite3] object pointer obtained ** from [sqlite3_open()], [sqlite3_open16()], or ** [sqlite3_open_v2()], and not previously closed. ** ^Calling sqlite3_close() with a NULL pointer argument is a ** harmless no-op. */ SQLITE_API int sqlite3_close(sqlite3 *); /* ** The type for a callback function. ** This is legacy and deprecated. It is included for historical ** compatibility and is not documented. */ typedef int (*sqlite3_callback)(void*,int,char**, char**); /* ** CAPI3REF: One-Step Query Execution Interface ** ** The sqlite3_exec() interface is a convenience wrapper around ** [sqlite3_prepare_v2()], [sqlite3_step()], and [sqlite3_finalize()], ** that allows an application to run multiple statements of SQL ** without having to use a lot of C code. ** ** ^The sqlite3_exec() interface runs zero or more UTF-8 encoded, ** semicolon-separate SQL statements passed into its 2nd argument, ** in the context of the [database connection] passed in as its 1st ** argument. ^If the callback function of the 3rd argument to ** sqlite3_exec() is not NULL, then it is invoked for each result row ** coming out of the evaluated SQL statements. ^The 4th argument to ** sqlite3_exec() is relayed through to the 1st argument of each ** callback invocation. ^If the callback pointer to sqlite3_exec() ** is NULL, then no callback is ever invoked and result rows are ** ignored. ** ** ^If an error occurs while evaluating the SQL statements passed into ** sqlite3_exec(), then execution of the current statement stops and ** subsequent statements are skipped. ^If the 5th parameter to sqlite3_exec() ** is not NULL then any error message is written into memory obtained ** from [sqlite3_malloc()] and passed back through the 5th parameter. ** To avoid memory leaks, the application should invoke [sqlite3_free()] ** on error message strings returned through the 5th parameter of ** of sqlite3_exec() after the error message string is no longer needed. ** ^If the 5th parameter to sqlite3_exec() is not NULL and no errors ** occur, then sqlite3_exec() sets the pointer in its 5th parameter to ** NULL before returning. ** ** ^If an sqlite3_exec() callback returns non-zero, the sqlite3_exec() ** routine returns SQLITE_ABORT without invoking the callback again and ** without running any subsequent SQL statements. ** ** ^The 2nd argument to the sqlite3_exec() callback function is the ** number of columns in the result. ^The 3rd argument to the sqlite3_exec() ** callback is an array of pointers to strings obtained as if from ** [sqlite3_column_text()], one for each column. ^If an element of a ** result row is NULL then the corresponding string pointer for the ** sqlite3_exec() callback is a NULL pointer. ^The 4th argument to the ** sqlite3_exec() callback is an array of pointers to strings where each ** entry represents the name of corresponding result column as obtained ** from [sqlite3_column_name()]. ** ** ^If the 2nd parameter to sqlite3_exec() is a NULL pointer, a pointer ** to an empty string, or a pointer that contains only whitespace and/or ** SQL comments, then no SQL statements are evaluated and the database ** is not changed. ** ** Restrictions: ** **
    **
  • The application must insure that the 1st parameter to sqlite3_exec() ** is a valid and open [database connection]. **
  • The application must not close [database connection] specified by ** the 1st parameter to sqlite3_exec() while sqlite3_exec() is running. **
  • The application must not modify the SQL statement text passed into ** the 2nd parameter of sqlite3_exec() while sqlite3_exec() is running. **
*/ SQLITE_API int sqlite3_exec( sqlite3*, /* An open database */ const char *sql, /* SQL to be evaluated */ int (*callback)(void*,int,char**,char**), /* Callback function */ void *, /* 1st argument to callback */ char **errmsg /* Error msg written here */ ); /* ** CAPI3REF: Result Codes ** KEYWORDS: SQLITE_OK {error code} {error codes} ** KEYWORDS: {result code} {result codes} ** ** Many SQLite functions return an integer result code from the set shown ** here in order to indicates success or failure. ** ** New error codes may be added in future versions of SQLite. ** ** See also: [SQLITE_IOERR_READ | extended result codes], ** [sqlite3_vtab_on_conflict()] [SQLITE_ROLLBACK | result codes]. */ #define SQLITE_OK 0 /* Successful result */ /* beginning-of-error-codes */ #define SQLITE_ERROR 1 /* SQL error or missing database */ #define SQLITE_INTERNAL 2 /* Internal logic error in SQLite */ #define SQLITE_PERM 3 /* Access permission denied */ #define SQLITE_ABORT 4 /* Callback routine requested an abort */ #define SQLITE_BUSY 5 /* The database file is locked */ #define SQLITE_LOCKED 6 /* A table in the database is locked */ #define SQLITE_NOMEM 7 /* A malloc() failed */ #define SQLITE_READONLY 8 /* Attempt to write a readonly database */ #define SQLITE_INTERRUPT 9 /* Operation terminated by sqlite3_interrupt()*/ #define SQLITE_IOERR 10 /* Some kind of disk I/O error occurred */ #define SQLITE_CORRUPT 11 /* The database disk image is malformed */ #define SQLITE_NOTFOUND 12 /* Unknown opcode in sqlite3_file_control() */ #define SQLITE_FULL 13 /* Insertion failed because database is full */ #define SQLITE_CANTOPEN 14 /* Unable to open the database file */ #define SQLITE_PROTOCOL 15 /* Database lock protocol error */ #define SQLITE_EMPTY 16 /* Database is empty */ #define SQLITE_SCHEMA 17 /* The database schema changed */ #define SQLITE_TOOBIG 18 /* String or BLOB exceeds size limit */ #define SQLITE_CONSTRAINT 19 /* Abort due to constraint violation */ #define SQLITE_MISMATCH 20 /* Data type mismatch */ #define SQLITE_MISUSE 21 /* Library used incorrectly */ #define SQLITE_NOLFS 22 /* Uses OS features not supported on host */ #define SQLITE_AUTH 23 /* Authorization denied */ #define SQLITE_FORMAT 24 /* Auxiliary database format error */ #define SQLITE_RANGE 25 /* 2nd parameter to sqlite3_bind out of range */ #define SQLITE_NOTADB 26 /* File opened that is not a database file */ #define SQLITE_ROW 100 /* sqlite3_step() has another row ready */ #define SQLITE_DONE 101 /* sqlite3_step() has finished executing */ /* end-of-error-codes */ /* ** CAPI3REF: Extended Result Codes ** KEYWORDS: {extended error code} {extended error codes} ** KEYWORDS: {extended result code} {extended result codes} ** ** In its default configuration, SQLite API routines return one of 26 integer ** [SQLITE_OK | result codes]. However, experience has shown that many of ** these result codes are too coarse-grained. They do not provide as ** much information about problems as programmers might like. In an effort to ** address this, newer versions of SQLite (version 3.3.8 and later) include ** support for additional result codes that provide more detailed information ** about errors. The extended result codes are enabled or disabled ** on a per database connection basis using the ** [sqlite3_extended_result_codes()] API. ** ** Some of the available extended result codes are listed here. ** One may expect the number of extended result codes will be expand ** over time. Software that uses extended result codes should expect ** to see new result codes in future releases of SQLite. ** ** The SQLITE_OK result code will never be extended. It will always ** be exactly zero. */ #define SQLITE_IOERR_READ (SQLITE_IOERR | (1<<8)) #define SQLITE_IOERR_SHORT_READ (SQLITE_IOERR | (2<<8)) #define SQLITE_IOERR_WRITE (SQLITE_IOERR | (3<<8)) #define SQLITE_IOERR_FSYNC (SQLITE_IOERR | (4<<8)) #define SQLITE_IOERR_DIR_FSYNC (SQLITE_IOERR | (5<<8)) #define SQLITE_IOERR_TRUNCATE (SQLITE_IOERR | (6<<8)) #define SQLITE_IOERR_FSTAT (SQLITE_IOERR | (7<<8)) #define SQLITE_IOERR_UNLOCK (SQLITE_IOERR | (8<<8)) #define SQLITE_IOERR_RDLOCK (SQLITE_IOERR | (9<<8)) #define SQLITE_IOERR_DELETE (SQLITE_IOERR | (10<<8)) #define SQLITE_IOERR_BLOCKED (SQLITE_IOERR | (11<<8)) #define SQLITE_IOERR_NOMEM (SQLITE_IOERR | (12<<8)) #define SQLITE_IOERR_ACCESS (SQLITE_IOERR | (13<<8)) #define SQLITE_IOERR_CHECKRESERVEDLOCK (SQLITE_IOERR | (14<<8)) #define SQLITE_IOERR_LOCK (SQLITE_IOERR | (15<<8)) #define SQLITE_IOERR_CLOSE (SQLITE_IOERR | (16<<8)) #define SQLITE_IOERR_DIR_CLOSE (SQLITE_IOERR | (17<<8)) #define SQLITE_IOERR_SHMOPEN (SQLITE_IOERR | (18<<8)) #define SQLITE_IOERR_SHMSIZE (SQLITE_IOERR | (19<<8)) #define SQLITE_IOERR_SHMLOCK (SQLITE_IOERR | (20<<8)) #define SQLITE_IOERR_SHMMAP (SQLITE_IOERR | (21<<8)) #define SQLITE_IOERR_SEEK (SQLITE_IOERR | (22<<8)) #define SQLITE_LOCKED_SHAREDCACHE (SQLITE_LOCKED | (1<<8)) #define SQLITE_BUSY_RECOVERY (SQLITE_BUSY | (1<<8)) #define SQLITE_CANTOPEN_NOTEMPDIR (SQLITE_CANTOPEN | (1<<8)) #define SQLITE_CORRUPT_VTAB (SQLITE_CORRUPT | (1<<8)) #define SQLITE_READONLY_RECOVERY (SQLITE_READONLY | (1<<8)) #define SQLITE_READONLY_CANTLOCK (SQLITE_READONLY | (2<<8)) /* ** CAPI3REF: Flags For File Open Operations ** ** These bit values are intended for use in the ** 3rd parameter to the [sqlite3_open_v2()] interface and ** in the 4th parameter to the [sqlite3_vfs.xOpen] method. */ #define SQLITE_OPEN_READONLY 0x00000001 /* Ok for sqlite3_open_v2() */ #define SQLITE_OPEN_READWRITE 0x00000002 /* Ok for sqlite3_open_v2() */ #define SQLITE_OPEN_CREATE 0x00000004 /* Ok for sqlite3_open_v2() */ #define SQLITE_OPEN_DELETEONCLOSE 0x00000008 /* VFS only */ #define SQLITE_OPEN_EXCLUSIVE 0x00000010 /* VFS only */ #define SQLITE_OPEN_AUTOPROXY 0x00000020 /* VFS only */ #define SQLITE_OPEN_URI 0x00000040 /* Ok for sqlite3_open_v2() */ #define SQLITE_OPEN_MAIN_DB 0x00000100 /* VFS only */ #define SQLITE_OPEN_TEMP_DB 0x00000200 /* VFS only */ #define SQLITE_OPEN_TRANSIENT_DB 0x00000400 /* VFS only */ #define SQLITE_OPEN_MAIN_JOURNAL 0x00000800 /* VFS only */ #define SQLITE_OPEN_TEMP_JOURNAL 0x00001000 /* VFS only */ #define SQLITE_OPEN_SUBJOURNAL 0x00002000 /* VFS only */ #define SQLITE_OPEN_MASTER_JOURNAL 0x00004000 /* VFS only */ #define SQLITE_OPEN_NOMUTEX 0x00008000 /* Ok for sqlite3_open_v2() */ #define SQLITE_OPEN_FULLMUTEX 0x00010000 /* Ok for sqlite3_open_v2() */ #define SQLITE_OPEN_SHAREDCACHE 0x00020000 /* Ok for sqlite3_open_v2() */ #define SQLITE_OPEN_PRIVATECACHE 0x00040000 /* Ok for sqlite3_open_v2() */ #define SQLITE_OPEN_WAL 0x00080000 /* VFS only */ /* Reserved: 0x00F00000 */ /* ** CAPI3REF: Device Characteristics ** ** The xDeviceCharacteristics method of the [sqlite3_io_methods] ** object returns an integer which is a vector of the these ** bit values expressing I/O characteristics of the mass storage ** device that holds the file that the [sqlite3_io_methods] ** refers to. ** ** The SQLITE_IOCAP_ATOMIC property means that all writes of ** any size are atomic. The SQLITE_IOCAP_ATOMICnnn values ** mean that writes of blocks that are nnn bytes in size and ** are aligned to an address which is an integer multiple of ** nnn are atomic. The SQLITE_IOCAP_SAFE_APPEND value means ** that when data is appended to a file, the data is appended ** first then the size of the file is extended, never the other ** way around. The SQLITE_IOCAP_SEQUENTIAL property means that ** information is written to disk in the same order as calls ** to xWrite(). */ #define SQLITE_IOCAP_ATOMIC 0x00000001 #define SQLITE_IOCAP_ATOMIC512 0x00000002 #define SQLITE_IOCAP_ATOMIC1K 0x00000004 #define SQLITE_IOCAP_ATOMIC2K 0x00000008 #define SQLITE_IOCAP_ATOMIC4K 0x00000010 #define SQLITE_IOCAP_ATOMIC8K 0x00000020 #define SQLITE_IOCAP_ATOMIC16K 0x00000040 #define SQLITE_IOCAP_ATOMIC32K 0x00000080 #define SQLITE_IOCAP_ATOMIC64K 0x00000100 #define SQLITE_IOCAP_SAFE_APPEND 0x00000200 #define SQLITE_IOCAP_SEQUENTIAL 0x00000400 #define SQLITE_IOCAP_UNDELETABLE_WHEN_OPEN 0x00000800 /* ** CAPI3REF: File Locking Levels ** ** SQLite uses one of these integer values as the second ** argument to calls it makes to the xLock() and xUnlock() methods ** of an [sqlite3_io_methods] object. */ #define SQLITE_LOCK_NONE 0 #define SQLITE_LOCK_SHARED 1 #define SQLITE_LOCK_RESERVED 2 #define SQLITE_LOCK_PENDING 3 #define SQLITE_LOCK_EXCLUSIVE 4 /* ** CAPI3REF: Synchronization Type Flags ** ** When SQLite invokes the xSync() method of an ** [sqlite3_io_methods] object it uses a combination of ** these integer values as the second argument. ** ** When the SQLITE_SYNC_DATAONLY flag is used, it means that the ** sync operation only needs to flush data to mass storage. Inode ** information need not be flushed. If the lower four bits of the flag ** equal SQLITE_SYNC_NORMAL, that means to use normal fsync() semantics. ** If the lower four bits equal SQLITE_SYNC_FULL, that means ** to use Mac OS X style fullsync instead of fsync(). ** ** Do not confuse the SQLITE_SYNC_NORMAL and SQLITE_SYNC_FULL flags ** with the [PRAGMA synchronous]=NORMAL and [PRAGMA synchronous]=FULL ** settings. The [synchronous pragma] determines when calls to the ** xSync VFS method occur and applies uniformly across all platforms. ** The SQLITE_SYNC_NORMAL and SQLITE_SYNC_FULL flags determine how ** energetic or rigorous or forceful the sync operations are and ** only make a difference on Mac OSX for the default SQLite code. ** (Third-party VFS implementations might also make the distinction ** between SQLITE_SYNC_NORMAL and SQLITE_SYNC_FULL, but among the ** operating systems natively supported by SQLite, only Mac OSX ** cares about the difference.) */ #define SQLITE_SYNC_NORMAL 0x00002 #define SQLITE_SYNC_FULL 0x00003 #define SQLITE_SYNC_DATAONLY 0x00010 /* ** CAPI3REF: OS Interface Open File Handle ** ** An [sqlite3_file] object represents an open file in the ** [sqlite3_vfs | OS interface layer]. Individual OS interface ** implementations will ** want to subclass this object by appending additional fields ** for their own use. The pMethods entry is a pointer to an ** [sqlite3_io_methods] object that defines methods for performing ** I/O operations on the open file. */ typedef struct sqlite3_file sqlite3_file; struct sqlite3_file { const struct sqlite3_io_methods *pMethods; /* Methods for an open file */ }; /* ** CAPI3REF: OS Interface File Virtual Methods Object ** ** Every file opened by the [sqlite3_vfs.xOpen] method populates an ** [sqlite3_file] object (or, more commonly, a subclass of the ** [sqlite3_file] object) with a pointer to an instance of this object. ** This object defines the methods used to perform various operations ** against the open file represented by the [sqlite3_file] object. ** ** If the [sqlite3_vfs.xOpen] method sets the sqlite3_file.pMethods element ** to a non-NULL pointer, then the sqlite3_io_methods.xClose method ** may be invoked even if the [sqlite3_vfs.xOpen] reported that it failed. The ** only way to prevent a call to xClose following a failed [sqlite3_vfs.xOpen] ** is for the [sqlite3_vfs.xOpen] to set the sqlite3_file.pMethods element ** to NULL. ** ** The flags argument to xSync may be one of [SQLITE_SYNC_NORMAL] or ** [SQLITE_SYNC_FULL]. The first choice is the normal fsync(). ** The second choice is a Mac OS X style fullsync. The [SQLITE_SYNC_DATAONLY] ** flag may be ORed in to indicate that only the data of the file ** and not its inode needs to be synced. ** ** The integer values to xLock() and xUnlock() are one of **
    **
  • [SQLITE_LOCK_NONE], **
  • [SQLITE_LOCK_SHARED], **
  • [SQLITE_LOCK_RESERVED], **
  • [SQLITE_LOCK_PENDING], or **
  • [SQLITE_LOCK_EXCLUSIVE]. **
** xLock() increases the lock. xUnlock() decreases the lock. ** The xCheckReservedLock() method checks whether any database connection, ** either in this process or in some other process, is holding a RESERVED, ** PENDING, or EXCLUSIVE lock on the file. It returns true ** if such a lock exists and false otherwise. ** ** The xFileControl() method is a generic interface that allows custom ** VFS implementations to directly control an open file using the ** [sqlite3_file_control()] interface. The second "op" argument is an ** integer opcode. The third argument is a generic pointer intended to ** point to a structure that may contain arguments or space in which to ** write return values. Potential uses for xFileControl() might be ** functions to enable blocking locks with timeouts, to change the ** locking strategy (for example to use dot-file locks), to inquire ** about the status of a lock, or to break stale locks. The SQLite ** core reserves all opcodes less than 100 for its own use. ** A [SQLITE_FCNTL_LOCKSTATE | list of opcodes] less than 100 is available. ** Applications that define a custom xFileControl method should use opcodes ** greater than 100 to avoid conflicts. VFS implementations should ** return [SQLITE_NOTFOUND] for file control opcodes that they do not ** recognize. ** ** The xSectorSize() method returns the sector size of the ** device that underlies the file. The sector size is the ** minimum write that can be performed without disturbing ** other bytes in the file. The xDeviceCharacteristics() ** method returns a bit vector describing behaviors of the ** underlying device: ** **
    **
  • [SQLITE_IOCAP_ATOMIC] **
  • [SQLITE_IOCAP_ATOMIC512] **
  • [SQLITE_IOCAP_ATOMIC1K] **
  • [SQLITE_IOCAP_ATOMIC2K] **
  • [SQLITE_IOCAP_ATOMIC4K] **
  • [SQLITE_IOCAP_ATOMIC8K] **
  • [SQLITE_IOCAP_ATOMIC16K] **
  • [SQLITE_IOCAP_ATOMIC32K] **
  • [SQLITE_IOCAP_ATOMIC64K] **
  • [SQLITE_IOCAP_SAFE_APPEND] **
  • [SQLITE_IOCAP_SEQUENTIAL] **
** ** The SQLITE_IOCAP_ATOMIC property means that all writes of ** any size are atomic. The SQLITE_IOCAP_ATOMICnnn values ** mean that writes of blocks that are nnn bytes in size and ** are aligned to an address which is an integer multiple of ** nnn are atomic. The SQLITE_IOCAP_SAFE_APPEND value means ** that when data is appended to a file, the data is appended ** first then the size of the file is extended, never the other ** way around. The SQLITE_IOCAP_SEQUENTIAL property means that ** information is written to disk in the same order as calls ** to xWrite(). ** ** If xRead() returns SQLITE_IOERR_SHORT_READ it must also fill ** in the unread portions of the buffer with zeros. A VFS that ** fails to zero-fill short reads might seem to work. However, ** failure to zero-fill short reads will eventually lead to ** database corruption. */ typedef struct sqlite3_io_methods sqlite3_io_methods; struct sqlite3_io_methods { int iVersion; int (*xClose)(sqlite3_file*); int (*xRead)(sqlite3_file*, void*, int iAmt, sqlite3_int64 iOfst); int (*xWrite)(sqlite3_file*, const void*, int iAmt, sqlite3_int64 iOfst); int (*xTruncate)(sqlite3_file*, sqlite3_int64 size); int (*xSync)(sqlite3_file*, int flags); int (*xFileSize)(sqlite3_file*, sqlite3_int64 *pSize); int (*xLock)(sqlite3_file*, int); int (*xUnlock)(sqlite3_file*, int); int (*xCheckReservedLock)(sqlite3_file*, int *pResOut); int (*xFileControl)(sqlite3_file*, int op, void *pArg); int (*xSectorSize)(sqlite3_file*); int (*xDeviceCharacteristics)(sqlite3_file*); /* Methods above are valid for version 1 */ int (*xShmMap)(sqlite3_file*, int iPg, int pgsz, int, void volatile**); int (*xShmLock)(sqlite3_file*, int offset, int n, int flags); void (*xShmBarrier)(sqlite3_file*); int (*xShmUnmap)(sqlite3_file*, int deleteFlag); /* Methods above are valid for version 2 */ /* Additional methods may be added in future releases */ }; /* ** CAPI3REF: Standard File Control Opcodes ** ** These integer constants are opcodes for the xFileControl method ** of the [sqlite3_io_methods] object and for the [sqlite3_file_control()] ** interface. ** ** The [SQLITE_FCNTL_LOCKSTATE] opcode is used for debugging. This ** opcode causes the xFileControl method to write the current state of ** the lock (one of [SQLITE_LOCK_NONE], [SQLITE_LOCK_SHARED], ** [SQLITE_LOCK_RESERVED], [SQLITE_LOCK_PENDING], or [SQLITE_LOCK_EXCLUSIVE]) ** into an integer that the pArg argument points to. This capability ** is used during testing and only needs to be supported when SQLITE_TEST ** is defined. ** ** The [SQLITE_FCNTL_SIZE_HINT] opcode is used by SQLite to give the VFS ** layer a hint of how large the database file will grow to be during the ** current transaction. This hint is not guaranteed to be accurate but it ** is often close. The underlying VFS might choose to preallocate database ** file space based on this hint in order to help writes to the database ** file run faster. ** ** The [SQLITE_FCNTL_CHUNK_SIZE] opcode is used to request that the VFS ** extends and truncates the database file in chunks of a size specified ** by the user. The fourth argument to [sqlite3_file_control()] should ** point to an integer (type int) containing the new chunk-size to use ** for the nominated database. Allocating database file space in large ** chunks (say 1MB at a time), may reduce file-system fragmentation and ** improve performance on some systems. ** ** The [SQLITE_FCNTL_FILE_POINTER] opcode is used to obtain a pointer ** to the [sqlite3_file] object associated with a particular database ** connection. See the [sqlite3_file_control()] documentation for ** additional information. ** ** ^(The [SQLITE_FCNTL_SYNC_OMITTED] opcode is generated internally by ** SQLite and sent to all VFSes in place of a call to the xSync method ** when the database connection has [PRAGMA synchronous] set to OFF.)^ ** Some specialized VFSes need this signal in order to operate correctly ** when [PRAGMA synchronous | PRAGMA synchronous=OFF] is set, but most ** VFSes do not need this signal and should silently ignore this opcode. ** Applications should not call [sqlite3_file_control()] with this ** opcode as doing so may disrupt the operation of the specialized VFSes ** that do require it. */ #define SQLITE_FCNTL_LOCKSTATE 1 #define SQLITE_GET_LOCKPROXYFILE 2 #define SQLITE_SET_LOCKPROXYFILE 3 #define SQLITE_LAST_ERRNO 4 #define SQLITE_FCNTL_SIZE_HINT 5 #define SQLITE_FCNTL_CHUNK_SIZE 6 #define SQLITE_FCNTL_FILE_POINTER 7 #define SQLITE_FCNTL_SYNC_OMITTED 8 /* ** CAPI3REF: Mutex Handle ** ** The mutex module within SQLite defines [sqlite3_mutex] to be an ** abstract type for a mutex object. The SQLite core never looks ** at the internal representation of an [sqlite3_mutex]. It only ** deals with pointers to the [sqlite3_mutex] object. ** ** Mutexes are created using [sqlite3_mutex_alloc()]. */ typedef struct sqlite3_mutex sqlite3_mutex; /* ** CAPI3REF: OS Interface Object ** ** An instance of the sqlite3_vfs object defines the interface between ** the SQLite core and the underlying operating system. The "vfs" ** in the name of the object stands for "virtual file system". See ** the [VFS | VFS documentation] for further information. ** ** The value of the iVersion field is initially 1 but may be larger in ** future versions of SQLite. Additional fields may be appended to this ** object when the iVersion value is increased. Note that the structure ** of the sqlite3_vfs object changes in the transaction between ** SQLite version 3.5.9 and 3.6.0 and yet the iVersion field was not ** modified. ** ** The szOsFile field is the size of the subclassed [sqlite3_file] ** structure used by this VFS. mxPathname is the maximum length of ** a pathname in this VFS. ** ** Registered sqlite3_vfs objects are kept on a linked list formed by ** the pNext pointer. The [sqlite3_vfs_register()] ** and [sqlite3_vfs_unregister()] interfaces manage this list ** in a thread-safe way. The [sqlite3_vfs_find()] interface ** searches the list. Neither the application code nor the VFS ** implementation should use the pNext pointer. ** ** The pNext field is the only field in the sqlite3_vfs ** structure that SQLite will ever modify. SQLite will only access ** or modify this field while holding a particular static mutex. ** The application should never modify anything within the sqlite3_vfs ** object once the object has been registered. ** ** The zName field holds the name of the VFS module. The name must ** be unique across all VFS modules. ** ** [[sqlite3_vfs.xOpen]] ** ^SQLite guarantees that the zFilename parameter to xOpen ** is either a NULL pointer or string obtained ** from xFullPathname() with an optional suffix added. ** ^If a suffix is added to the zFilename parameter, it will ** consist of a single "-" character followed by no more than ** 10 alphanumeric and/or "-" characters. ** ^SQLite further guarantees that ** the string will be valid and unchanged until xClose() is ** called. Because of the previous sentence, ** the [sqlite3_file] can safely store a pointer to the ** filename if it needs to remember the filename for some reason. ** If the zFilename parameter to xOpen is a NULL pointer then xOpen ** must invent its own temporary name for the file. ^Whenever the ** xFilename parameter is NULL it will also be the case that the ** flags parameter will include [SQLITE_OPEN_DELETEONCLOSE]. ** ** The flags argument to xOpen() includes all bits set in ** the flags argument to [sqlite3_open_v2()]. Or if [sqlite3_open()] ** or [sqlite3_open16()] is used, then flags includes at least ** [SQLITE_OPEN_READWRITE] | [SQLITE_OPEN_CREATE]. ** If xOpen() opens a file read-only then it sets *pOutFlags to ** include [SQLITE_OPEN_READONLY]. Other bits in *pOutFlags may be set. ** ** ^(SQLite will also add one of the following flags to the xOpen() ** call, depending on the object being opened: ** **
    **
  • [SQLITE_OPEN_MAIN_DB] **
  • [SQLITE_OPEN_MAIN_JOURNAL] **
  • [SQLITE_OPEN_TEMP_DB] **
  • [SQLITE_OPEN_TEMP_JOURNAL] **
  • [SQLITE_OPEN_TRANSIENT_DB] **
  • [SQLITE_OPEN_SUBJOURNAL] **
  • [SQLITE_OPEN_MASTER_JOURNAL] **
  • [SQLITE_OPEN_WAL] **
)^ ** ** The file I/O implementation can use the object type flags to ** change the way it deals with files. For example, an application ** that does not care about crash recovery or rollback might make ** the open of a journal file a no-op. Writes to this journal would ** also be no-ops, and any attempt to read the journal would return ** SQLITE_IOERR. Or the implementation might recognize that a database ** file will be doing page-aligned sector reads and writes in a random ** order and set up its I/O subsystem accordingly. ** ** SQLite might also add one of the following flags to the xOpen method: ** **
    **
  • [SQLITE_OPEN_DELETEONCLOSE] **
  • [SQLITE_OPEN_EXCLUSIVE] **
** ** The [SQLITE_OPEN_DELETEONCLOSE] flag means the file should be ** deleted when it is closed. ^The [SQLITE_OPEN_DELETEONCLOSE] ** will be set for TEMP databases and their journals, transient ** databases, and subjournals. ** ** ^The [SQLITE_OPEN_EXCLUSIVE] flag is always used in conjunction ** with the [SQLITE_OPEN_CREATE] flag, which are both directly ** analogous to the O_EXCL and O_CREAT flags of the POSIX open() ** API. The SQLITE_OPEN_EXCLUSIVE flag, when paired with the ** SQLITE_OPEN_CREATE, is used to indicate that file should always ** be created, and that it is an error if it already exists. ** It is not used to indicate the file should be opened ** for exclusive access. ** ** ^At least szOsFile bytes of memory are allocated by SQLite ** to hold the [sqlite3_file] structure passed as the third ** argument to xOpen. The xOpen method does not have to ** allocate the structure; it should just fill it in. Note that ** the xOpen method must set the sqlite3_file.pMethods to either ** a valid [sqlite3_io_methods] object or to NULL. xOpen must do ** this even if the open fails. SQLite expects that the sqlite3_file.pMethods ** element will be valid after xOpen returns regardless of the success ** or failure of the xOpen call. ** ** [[sqlite3_vfs.xAccess]] ** ^The flags argument to xAccess() may be [SQLITE_ACCESS_EXISTS] ** to test for the existence of a file, or [SQLITE_ACCESS_READWRITE] to ** test whether a file is readable and writable, or [SQLITE_ACCESS_READ] ** to test whether a file is at least readable. The file can be a ** directory. ** ** ^SQLite will always allocate at least mxPathname+1 bytes for the ** output buffer xFullPathname. The exact size of the output buffer ** is also passed as a parameter to both methods. If the output buffer ** is not large enough, [SQLITE_CANTOPEN] should be returned. Since this is ** handled as a fatal error by SQLite, vfs implementations should endeavor ** to prevent this by setting mxPathname to a sufficiently large value. ** ** The xRandomness(), xSleep(), xCurrentTime(), and xCurrentTimeInt64() ** interfaces are not strictly a part of the filesystem, but they are ** included in the VFS structure for completeness. ** The xRandomness() function attempts to return nBytes bytes ** of good-quality randomness into zOut. The return value is ** the actual number of bytes of randomness obtained. ** The xSleep() method causes the calling thread to sleep for at ** least the number of microseconds given. ^The xCurrentTime() ** method returns a Julian Day Number for the current date and time as ** a floating point value. ** ^The xCurrentTimeInt64() method returns, as an integer, the Julian ** Day Number multiplied by 86400000 (the number of milliseconds in ** a 24-hour day). ** ^SQLite will use the xCurrentTimeInt64() method to get the current ** date and time if that method is available (if iVersion is 2 or ** greater and the function pointer is not NULL) and will fall back ** to xCurrentTime() if xCurrentTimeInt64() is unavailable. ** ** ^The xSetSystemCall(), xGetSystemCall(), and xNestSystemCall() interfaces ** are not used by the SQLite core. These optional interfaces are provided ** by some VFSes to facilitate testing of the VFS code. By overriding ** system calls with functions under its control, a test program can ** simulate faults and error conditions that would otherwise be difficult ** or impossible to induce. The set of system calls that can be overridden ** varies from one VFS to another, and from one version of the same VFS to the ** next. Applications that use these interfaces must be prepared for any ** or all of these interfaces to be NULL or for their behavior to change ** from one release to the next. Applications must not attempt to access ** any of these methods if the iVersion of the VFS is less than 3. */ typedef struct sqlite3_vfs sqlite3_vfs; typedef void (*sqlite3_syscall_ptr)(void); struct sqlite3_vfs { int iVersion; /* Structure version number (currently 3) */ int szOsFile; /* Size of subclassed sqlite3_file */ int mxPathname; /* Maximum file pathname length */ sqlite3_vfs *pNext; /* Next registered VFS */ const char *zName; /* Name of this virtual file system */ void *pAppData; /* Pointer to application-specific data */ int (*xOpen)(sqlite3_vfs*, const char *zName, sqlite3_file*, int flags, int *pOutFlags); int (*xDelete)(sqlite3_vfs*, const char *zName, int syncDir); int (*xAccess)(sqlite3_vfs*, const char *zName, int flags, int *pResOut); int (*xFullPathname)(sqlite3_vfs*, const char *zName, int nOut, char *zOut); void *(*xDlOpen)(sqlite3_vfs*, const char *zFilename); void (*xDlError)(sqlite3_vfs*, int nByte, char *zErrMsg); void (*(*xDlSym)(sqlite3_vfs*,void*, const char *zSymbol))(void); void (*xDlClose)(sqlite3_vfs*, void*); int (*xRandomness)(sqlite3_vfs*, int nByte, char *zOut); int (*xSleep)(sqlite3_vfs*, int microseconds); int (*xCurrentTime)(sqlite3_vfs*, double*); int (*xGetLastError)(sqlite3_vfs*, int, char *); /* ** The methods above are in version 1 of the sqlite_vfs object ** definition. Those that follow are added in version 2 or later */ int (*xCurrentTimeInt64)(sqlite3_vfs*, sqlite3_int64*); /* ** The methods above are in versions 1 and 2 of the sqlite_vfs object. ** Those below are for version 3 and greater. */ int (*xSetSystemCall)(sqlite3_vfs*, const char *zName, sqlite3_syscall_ptr); sqlite3_syscall_ptr (*xGetSystemCall)(sqlite3_vfs*, const char *zName); const char *(*xNextSystemCall)(sqlite3_vfs*, const char *zName); /* ** The methods above are in versions 1 through 3 of the sqlite_vfs object. ** New fields may be appended in figure versions. The iVersion ** value will increment whenever this happens. */ }; /* ** CAPI3REF: Flags for the xAccess VFS method ** ** These integer constants can be used as the third parameter to ** the xAccess method of an [sqlite3_vfs] object. They determine ** what kind of permissions the xAccess method is looking for. ** With SQLITE_ACCESS_EXISTS, the xAccess method ** simply checks whether the file exists. ** With SQLITE_ACCESS_READWRITE, the xAccess method ** checks whether the named directory is both readable and writable ** (in other words, if files can be added, removed, and renamed within ** the directory). ** The SQLITE_ACCESS_READWRITE constant is currently used only by the ** [temp_store_directory pragma], though this could change in a future ** release of SQLite. ** With SQLITE_ACCESS_READ, the xAccess method ** checks whether the file is readable. The SQLITE_ACCESS_READ constant is ** currently unused, though it might be used in a future release of ** SQLite. */ #define SQLITE_ACCESS_EXISTS 0 #define SQLITE_ACCESS_READWRITE 1 /* Used by PRAGMA temp_store_directory */ #define SQLITE_ACCESS_READ 2 /* Unused */ /* ** CAPI3REF: Flags for the xShmLock VFS method ** ** These integer constants define the various locking operations ** allowed by the xShmLock method of [sqlite3_io_methods]. The ** following are the only legal combinations of flags to the ** xShmLock method: ** **
    **
  • SQLITE_SHM_LOCK | SQLITE_SHM_SHARED **
  • SQLITE_SHM_LOCK | SQLITE_SHM_EXCLUSIVE **
  • SQLITE_SHM_UNLOCK | SQLITE_SHM_SHARED **
  • SQLITE_SHM_UNLOCK | SQLITE_SHM_EXCLUSIVE **
** ** When unlocking, the same SHARED or EXCLUSIVE flag must be supplied as ** was given no the corresponding lock. ** ** The xShmLock method can transition between unlocked and SHARED or ** between unlocked and EXCLUSIVE. It cannot transition between SHARED ** and EXCLUSIVE. */ #define SQLITE_SHM_UNLOCK 1 #define SQLITE_SHM_LOCK 2 #define SQLITE_SHM_SHARED 4 #define SQLITE_SHM_EXCLUSIVE 8 /* ** CAPI3REF: Maximum xShmLock index ** ** The xShmLock method on [sqlite3_io_methods] may use values ** between 0 and this upper bound as its "offset" argument. ** The SQLite core will never attempt to acquire or release a ** lock outside of this range */ #define SQLITE_SHM_NLOCK 8 /* ** CAPI3REF: Initialize The SQLite Library ** ** ^The sqlite3_initialize() routine initializes the ** SQLite library. ^The sqlite3_shutdown() routine ** deallocates any resources that were allocated by sqlite3_initialize(). ** These routines are designed to aid in process initialization and ** shutdown on embedded systems. Workstation applications using ** SQLite normally do not need to invoke either of these routines. ** ** A call to sqlite3_initialize() is an "effective" call if it is ** the first time sqlite3_initialize() is invoked during the lifetime of ** the process, or if it is the first time sqlite3_initialize() is invoked ** following a call to sqlite3_shutdown(). ^(Only an effective call ** of sqlite3_initialize() does any initialization. All other calls ** are harmless no-ops.)^ ** ** A call to sqlite3_shutdown() is an "effective" call if it is the first ** call to sqlite3_shutdown() since the last sqlite3_initialize(). ^(Only ** an effective call to sqlite3_shutdown() does any deinitialization. ** All other valid calls to sqlite3_shutdown() are harmless no-ops.)^ ** ** The sqlite3_initialize() interface is threadsafe, but sqlite3_shutdown() ** is not. The sqlite3_shutdown() interface must only be called from a ** single thread. All open [database connections] must be closed and all ** other SQLite resources must be deallocated prior to invoking ** sqlite3_shutdown(). ** ** Among other things, ^sqlite3_initialize() will invoke ** sqlite3_os_init(). Similarly, ^sqlite3_shutdown() ** will invoke sqlite3_os_end(). ** ** ^The sqlite3_initialize() routine returns [SQLITE_OK] on success. ** ^If for some reason, sqlite3_initialize() is unable to initialize ** the library (perhaps it is unable to allocate a needed resource such ** as a mutex) it returns an [error code] other than [SQLITE_OK]. ** ** ^The sqlite3_initialize() routine is called internally by many other ** SQLite interfaces so that an application usually does not need to ** invoke sqlite3_initialize() directly. For example, [sqlite3_open()] ** calls sqlite3_initialize() so the SQLite library will be automatically ** initialized when [sqlite3_open()] is called if it has not be initialized ** already. ^However, if SQLite is compiled with the [SQLITE_OMIT_AUTOINIT] ** compile-time option, then the automatic calls to sqlite3_initialize() ** are omitted and the application must call sqlite3_initialize() directly ** prior to using any other SQLite interface. For maximum portability, ** it is recommended that applications always invoke sqlite3_initialize() ** directly prior to using any other SQLite interface. Future releases ** of SQLite may require this. In other words, the behavior exhibited ** when SQLite is compiled with [SQLITE_OMIT_AUTOINIT] might become the ** default behavior in some future release of SQLite. ** ** The sqlite3_os_init() routine does operating-system specific ** initialization of the SQLite library. The sqlite3_os_end() ** routine undoes the effect of sqlite3_os_init(). Typical tasks ** performed by these routines include allocation or deallocation ** of static resources, initialization of global variables, ** setting up a default [sqlite3_vfs] module, or setting up ** a default configuration using [sqlite3_config()]. ** ** The application should never invoke either sqlite3_os_init() ** or sqlite3_os_end() directly. The application should only invoke ** sqlite3_initialize() and sqlite3_shutdown(). The sqlite3_os_init() ** interface is called automatically by sqlite3_initialize() and ** sqlite3_os_end() is called by sqlite3_shutdown(). Appropriate ** implementations for sqlite3_os_init() and sqlite3_os_end() ** are built into SQLite when it is compiled for Unix, Windows, or OS/2. ** When [custom builds | built for other platforms] ** (using the [SQLITE_OS_OTHER=1] compile-time ** option) the application must supply a suitable implementation for ** sqlite3_os_init() and sqlite3_os_end(). An application-supplied ** implementation of sqlite3_os_init() or sqlite3_os_end() ** must return [SQLITE_OK] on success and some other [error code] upon ** failure. */ SQLITE_API int sqlite3_initialize(void); SQLITE_API int sqlite3_shutdown(void); SQLITE_API int sqlite3_os_init(void); SQLITE_API int sqlite3_os_end(void); /* ** CAPI3REF: Configuring The SQLite Library ** ** The sqlite3_config() interface is used to make global configuration ** changes to SQLite in order to tune SQLite to the specific needs of ** the application. The default configuration is recommended for most ** applications and so this routine is usually not necessary. It is ** provided to support rare applications with unusual needs. ** ** The sqlite3_config() interface is not threadsafe. The application ** must insure that no other SQLite interfaces are invoked by other ** threads while sqlite3_config() is running. Furthermore, sqlite3_config() ** may only be invoked prior to library initialization using ** [sqlite3_initialize()] or after shutdown by [sqlite3_shutdown()]. ** ^If sqlite3_config() is called after [sqlite3_initialize()] and before ** [sqlite3_shutdown()] then it will return SQLITE_MISUSE. ** Note, however, that ^sqlite3_config() can be called as part of the ** implementation of an application-defined [sqlite3_os_init()]. ** ** The first argument to sqlite3_config() is an integer ** [configuration option] that determines ** what property of SQLite is to be configured. Subsequent arguments ** vary depending on the [configuration option] ** in the first argument. ** ** ^When a configuration option is set, sqlite3_config() returns [SQLITE_OK]. ** ^If the option is unknown or SQLite is unable to set the option ** then this routine returns a non-zero [error code]. */ SQLITE_API int sqlite3_config(int, ...); /* ** CAPI3REF: Configure database connections ** ** The sqlite3_db_config() interface is used to make configuration ** changes to a [database connection]. The interface is similar to ** [sqlite3_config()] except that the changes apply to a single ** [database connection] (specified in the first argument). ** ** The second argument to sqlite3_db_config(D,V,...) is the ** [SQLITE_DBCONFIG_LOOKASIDE | configuration verb] - an integer code ** that indicates what aspect of the [database connection] is being configured. ** Subsequent arguments vary depending on the configuration verb. ** ** ^Calls to sqlite3_db_config() return SQLITE_OK if and only if ** the call is considered successful. */ SQLITE_API int sqlite3_db_config(sqlite3*, int op, ...); /* ** CAPI3REF: Memory Allocation Routines ** ** An instance of this object defines the interface between SQLite ** and low-level memory allocation routines. ** ** This object is used in only one place in the SQLite interface. ** A pointer to an instance of this object is the argument to ** [sqlite3_config()] when the configuration option is ** [SQLITE_CONFIG_MALLOC] or [SQLITE_CONFIG_GETMALLOC]. ** By creating an instance of this object ** and passing it to [sqlite3_config]([SQLITE_CONFIG_MALLOC]) ** during configuration, an application can specify an alternative ** memory allocation subsystem for SQLite to use for all of its ** dynamic memory needs. ** ** Note that SQLite comes with several [built-in memory allocators] ** that are perfectly adequate for the overwhelming majority of applications ** and that this object is only useful to a tiny minority of applications ** with specialized memory allocation requirements. This object is ** also used during testing of SQLite in order to specify an alternative ** memory allocator that simulates memory out-of-memory conditions in ** order to verify that SQLite recovers gracefully from such ** conditions. ** ** The xMalloc and xFree methods must work like the ** malloc() and free() functions from the standard C library. ** The xRealloc method must work like realloc() from the standard C library ** with the exception that if the second argument to xRealloc is zero, ** xRealloc must be a no-op - it must not perform any allocation or ** deallocation. ^SQLite guarantees that the second argument to ** xRealloc is always a value returned by a prior call to xRoundup. ** And so in cases where xRoundup always returns a positive number, ** xRealloc can perform exactly as the standard library realloc() and ** still be in compliance with this specification. ** ** xSize should return the allocated size of a memory allocation ** previously obtained from xMalloc or xRealloc. The allocated size ** is always at least as big as the requested size but may be larger. ** ** The xRoundup method returns what would be the allocated size of ** a memory allocation given a particular requested size. Most memory ** allocators round up memory allocations at least to the next multiple ** of 8. Some allocators round up to a larger multiple or to a power of 2. ** Every memory allocation request coming in through [sqlite3_malloc()] ** or [sqlite3_realloc()] first calls xRoundup. If xRoundup returns 0, ** that causes the corresponding memory allocation to fail. ** ** The xInit method initializes the memory allocator. (For example, ** it might allocate any require mutexes or initialize internal data ** structures. The xShutdown method is invoked (indirectly) by ** [sqlite3_shutdown()] and should deallocate any resources acquired ** by xInit. The pAppData pointer is used as the only parameter to ** xInit and xShutdown. ** ** SQLite holds the [SQLITE_MUTEX_STATIC_MASTER] mutex when it invokes ** the xInit method, so the xInit method need not be threadsafe. The ** xShutdown method is only called from [sqlite3_shutdown()] so it does ** not need to be threadsafe either. For all other methods, SQLite ** holds the [SQLITE_MUTEX_STATIC_MEM] mutex as long as the ** [SQLITE_CONFIG_MEMSTATUS] configuration option is turned on (which ** it is by default) and so the methods are automatically serialized. ** However, if [SQLITE_CONFIG_MEMSTATUS] is disabled, then the other ** methods must be threadsafe or else make their own arrangements for ** serialization. ** ** SQLite will never invoke xInit() more than once without an intervening ** call to xShutdown(). */ typedef struct sqlite3_mem_methods sqlite3_mem_methods; struct sqlite3_mem_methods { void *(*xMalloc)(int); /* Memory allocation function */ void (*xFree)(void*); /* Free a prior allocation */ void *(*xRealloc)(void*,int); /* Resize an allocation */ int (*xSize)(void*); /* Return the size of an allocation */ int (*xRoundup)(int); /* Round up request size to allocation size */ int (*xInit)(void*); /* Initialize the memory allocator */ void (*xShutdown)(void*); /* Deinitialize the memory allocator */ void *pAppData; /* Argument to xInit() and xShutdown() */ }; /* ** CAPI3REF: Configuration Options ** KEYWORDS: {configuration option} ** ** These constants are the available integer configuration options that ** can be passed as the first argument to the [sqlite3_config()] interface. ** ** New configuration options may be added in future releases of SQLite. ** Existing configuration options might be discontinued. Applications ** should check the return code from [sqlite3_config()] to make sure that ** the call worked. The [sqlite3_config()] interface will return a ** non-zero [error code] if a discontinued or unsupported configuration option ** is invoked. ** **
** [[SQLITE_CONFIG_SINGLETHREAD]]
SQLITE_CONFIG_SINGLETHREAD
**
There are no arguments to this option. ^This option sets the ** [threading mode] to Single-thread. In other words, it disables ** all mutexing and puts SQLite into a mode where it can only be used ** by a single thread. ^If SQLite is compiled with ** the [SQLITE_THREADSAFE | SQLITE_THREADSAFE=0] compile-time option then ** it is not possible to change the [threading mode] from its default ** value of Single-thread and so [sqlite3_config()] will return ** [SQLITE_ERROR] if called with the SQLITE_CONFIG_SINGLETHREAD ** configuration option.
** ** [[SQLITE_CONFIG_MULTITHREAD]]
SQLITE_CONFIG_MULTITHREAD
**
There are no arguments to this option. ^This option sets the ** [threading mode] to Multi-thread. In other words, it disables ** mutexing on [database connection] and [prepared statement] objects. ** The application is responsible for serializing access to ** [database connections] and [prepared statements]. But other mutexes ** are enabled so that SQLite will be safe to use in a multi-threaded ** environment as long as no two threads attempt to use the same ** [database connection] at the same time. ^If SQLite is compiled with ** the [SQLITE_THREADSAFE | SQLITE_THREADSAFE=0] compile-time option then ** it is not possible to set the Multi-thread [threading mode] and ** [sqlite3_config()] will return [SQLITE_ERROR] if called with the ** SQLITE_CONFIG_MULTITHREAD configuration option.
** ** [[SQLITE_CONFIG_SERIALIZED]]
SQLITE_CONFIG_SERIALIZED
**
There are no arguments to this option. ^This option sets the ** [threading mode] to Serialized. In other words, this option enables ** all mutexes including the recursive ** mutexes on [database connection] and [prepared statement] objects. ** In this mode (which is the default when SQLite is compiled with ** [SQLITE_THREADSAFE=1]) the SQLite library will itself serialize access ** to [database connections] and [prepared statements] so that the ** application is free to use the same [database connection] or the ** same [prepared statement] in different threads at the same time. ** ^If SQLite is compiled with ** the [SQLITE_THREADSAFE | SQLITE_THREADSAFE=0] compile-time option then ** it is not possible to set the Serialized [threading mode] and ** [sqlite3_config()] will return [SQLITE_ERROR] if called with the ** SQLITE_CONFIG_SERIALIZED configuration option.
** ** [[SQLITE_CONFIG_MALLOC]]
SQLITE_CONFIG_MALLOC
**
^(This option takes a single argument which is a pointer to an ** instance of the [sqlite3_mem_methods] structure. The argument specifies ** alternative low-level memory allocation routines to be used in place of ** the memory allocation routines built into SQLite.)^ ^SQLite makes ** its own private copy of the content of the [sqlite3_mem_methods] structure ** before the [sqlite3_config()] call returns.
** ** [[SQLITE_CONFIG_GETMALLOC]]
SQLITE_CONFIG_GETMALLOC
**
^(This option takes a single argument which is a pointer to an ** instance of the [sqlite3_mem_methods] structure. The [sqlite3_mem_methods] ** structure is filled with the currently defined memory allocation routines.)^ ** This option can be used to overload the default memory allocation ** routines with a wrapper that simulations memory allocation failure or ** tracks memory usage, for example.
** ** [[SQLITE_CONFIG_MEMSTATUS]]
SQLITE_CONFIG_MEMSTATUS
**
^This option takes single argument of type int, interpreted as a ** boolean, which enables or disables the collection of memory allocation ** statistics. ^(When memory allocation statistics are disabled, the ** following SQLite interfaces become non-operational: **
    **
  • [sqlite3_memory_used()] **
  • [sqlite3_memory_highwater()] **
  • [sqlite3_soft_heap_limit64()] **
  • [sqlite3_status()] **
)^ ** ^Memory allocation statistics are enabled by default unless SQLite is ** compiled with [SQLITE_DEFAULT_MEMSTATUS]=0 in which case memory ** allocation statistics are disabled by default. **
** ** [[SQLITE_CONFIG_SCRATCH]]
SQLITE_CONFIG_SCRATCH
**
^This option specifies a static memory buffer that SQLite can use for ** scratch memory. There are three arguments: A pointer an 8-byte ** aligned memory buffer from which the scratch allocations will be ** drawn, the size of each scratch allocation (sz), ** and the maximum number of scratch allocations (N). The sz ** argument must be a multiple of 16. ** The first argument must be a pointer to an 8-byte aligned buffer ** of at least sz*N bytes of memory. ** ^SQLite will use no more than two scratch buffers per thread. So ** N should be set to twice the expected maximum number of threads. ** ^SQLite will never require a scratch buffer that is more than 6 ** times the database page size. ^If SQLite needs needs additional ** scratch memory beyond what is provided by this configuration option, then ** [sqlite3_malloc()] will be used to obtain the memory needed.
** ** [[SQLITE_CONFIG_PAGECACHE]]
SQLITE_CONFIG_PAGECACHE
**
^This option specifies a static memory buffer that SQLite can use for ** the database page cache with the default page cache implementation. ** This configuration should not be used if an application-define page ** cache implementation is loaded using the SQLITE_CONFIG_PCACHE option. ** There are three arguments to this option: A pointer to 8-byte aligned ** memory, the size of each page buffer (sz), and the number of pages (N). ** The sz argument should be the size of the largest database page ** (a power of two between 512 and 32768) plus a little extra for each ** page header. ^The page header size is 20 to 40 bytes depending on ** the host architecture. ^It is harmless, apart from the wasted memory, ** to make sz a little too large. The first ** argument should point to an allocation of at least sz*N bytes of memory. ** ^SQLite will use the memory provided by the first argument to satisfy its ** memory needs for the first N pages that it adds to cache. ^If additional ** page cache memory is needed beyond what is provided by this option, then ** SQLite goes to [sqlite3_malloc()] for the additional storage space. ** The pointer in the first argument must ** be aligned to an 8-byte boundary or subsequent behavior of SQLite ** will be undefined.
** ** [[SQLITE_CONFIG_HEAP]]
SQLITE_CONFIG_HEAP
**
^This option specifies a static memory buffer that SQLite will use ** for all of its dynamic memory allocation needs beyond those provided ** for by [SQLITE_CONFIG_SCRATCH] and [SQLITE_CONFIG_PAGECACHE]. ** There are three arguments: An 8-byte aligned pointer to the memory, ** the number of bytes in the memory buffer, and the minimum allocation size. ** ^If the first pointer (the memory pointer) is NULL, then SQLite reverts ** to using its default memory allocator (the system malloc() implementation), ** undoing any prior invocation of [SQLITE_CONFIG_MALLOC]. ^If the ** memory pointer is not NULL and either [SQLITE_ENABLE_MEMSYS3] or ** [SQLITE_ENABLE_MEMSYS5] are defined, then the alternative memory ** allocator is engaged to handle all of SQLites memory allocation needs. ** The first pointer (the memory pointer) must be aligned to an 8-byte ** boundary or subsequent behavior of SQLite will be undefined. ** The minimum allocation size is capped at 2^12. Reasonable values ** for the minimum allocation size are 2^5 through 2^8.
** ** [[SQLITE_CONFIG_MUTEX]]
SQLITE_CONFIG_MUTEX
**
^(This option takes a single argument which is a pointer to an ** instance of the [sqlite3_mutex_methods] structure. The argument specifies ** alternative low-level mutex routines to be used in place ** the mutex routines built into SQLite.)^ ^SQLite makes a copy of the ** content of the [sqlite3_mutex_methods] structure before the call to ** [sqlite3_config()] returns. ^If SQLite is compiled with ** the [SQLITE_THREADSAFE | SQLITE_THREADSAFE=0] compile-time option then ** the entire mutexing subsystem is omitted from the build and hence calls to ** [sqlite3_config()] with the SQLITE_CONFIG_MUTEX configuration option will ** return [SQLITE_ERROR].
** ** [[SQLITE_CONFIG_GETMUTEX]]
SQLITE_CONFIG_GETMUTEX
**
^(This option takes a single argument which is a pointer to an ** instance of the [sqlite3_mutex_methods] structure. The ** [sqlite3_mutex_methods] ** structure is filled with the currently defined mutex routines.)^ ** This option can be used to overload the default mutex allocation ** routines with a wrapper used to track mutex usage for performance ** profiling or testing, for example. ^If SQLite is compiled with ** the [SQLITE_THREADSAFE | SQLITE_THREADSAFE=0] compile-time option then ** the entire mutexing subsystem is omitted from the build and hence calls to ** [sqlite3_config()] with the SQLITE_CONFIG_GETMUTEX configuration option will ** return [SQLITE_ERROR].
** ** [[SQLITE_CONFIG_LOOKASIDE]]
SQLITE_CONFIG_LOOKASIDE
**
^(This option takes two arguments that determine the default ** memory allocation for the lookaside memory allocator on each ** [database connection]. The first argument is the ** size of each lookaside buffer slot and the second is the number of ** slots allocated to each database connection.)^ ^(This option sets the ** default lookaside size. The [SQLITE_DBCONFIG_LOOKASIDE] ** verb to [sqlite3_db_config()] can be used to change the lookaside ** configuration on individual connections.)^
** ** [[SQLITE_CONFIG_PCACHE]]
SQLITE_CONFIG_PCACHE
**
^(This option takes a single argument which is a pointer to ** an [sqlite3_pcache_methods] object. This object specifies the interface ** to a custom page cache implementation.)^ ^SQLite makes a copy of the ** object and uses it for page cache memory allocations.
** ** [[SQLITE_CONFIG_GETPCACHE]]
SQLITE_CONFIG_GETPCACHE
**
^(This option takes a single argument which is a pointer to an ** [sqlite3_pcache_methods] object. SQLite copies of the current ** page cache implementation into that object.)^
** ** [[SQLITE_CONFIG_LOG]]
SQLITE_CONFIG_LOG
**
^The SQLITE_CONFIG_LOG option takes two arguments: a pointer to a ** function with a call signature of void(*)(void*,int,const char*), ** and a pointer to void. ^If the function pointer is not NULL, it is ** invoked by [sqlite3_log()] to process each logging event. ^If the ** function pointer is NULL, the [sqlite3_log()] interface becomes a no-op. ** ^The void pointer that is the second argument to SQLITE_CONFIG_LOG is ** passed through as the first parameter to the application-defined logger ** function whenever that function is invoked. ^The second parameter to ** the logger function is a copy of the first parameter to the corresponding ** [sqlite3_log()] call and is intended to be a [result code] or an ** [extended result code]. ^The third parameter passed to the logger is ** log message after formatting via [sqlite3_snprintf()]. ** The SQLite logging interface is not reentrant; the logger function ** supplied by the application must not invoke any SQLite interface. ** In a multi-threaded application, the application-defined logger ** function must be threadsafe.
** ** [[SQLITE_CONFIG_URI]]
SQLITE_CONFIG_URI **
This option takes a single argument of type int. If non-zero, then ** URI handling is globally enabled. If the parameter is zero, then URI handling ** is globally disabled. If URI handling is globally enabled, all filenames ** passed to [sqlite3_open()], [sqlite3_open_v2()], [sqlite3_open16()] or ** specified as part of [ATTACH] commands are interpreted as URIs, regardless ** of whether or not the [SQLITE_OPEN_URI] flag is set when the database ** connection is opened. If it is globally disabled, filenames are ** only interpreted as URIs if the SQLITE_OPEN_URI flag is set when the ** database connection is opened. By default, URI handling is globally ** disabled. The default value may be changed by compiling with the ** [SQLITE_USE_URI] symbol defined. **
*/ #define SQLITE_CONFIG_SINGLETHREAD 1 /* nil */ #define SQLITE_CONFIG_MULTITHREAD 2 /* nil */ #define SQLITE_CONFIG_SERIALIZED 3 /* nil */ #define SQLITE_CONFIG_MALLOC 4 /* sqlite3_mem_methods* */ #define SQLITE_CONFIG_GETMALLOC 5 /* sqlite3_mem_methods* */ #define SQLITE_CONFIG_SCRATCH 6 /* void*, int sz, int N */ #define SQLITE_CONFIG_PAGECACHE 7 /* void*, int sz, int N */ #define SQLITE_CONFIG_HEAP 8 /* void*, int nByte, int min */ #define SQLITE_CONFIG_MEMSTATUS 9 /* boolean */ #define SQLITE_CONFIG_MUTEX 10 /* sqlite3_mutex_methods* */ #define SQLITE_CONFIG_GETMUTEX 11 /* sqlite3_mutex_methods* */ /* previously SQLITE_CONFIG_CHUNKALLOC 12 which is now unused. */ #define SQLITE_CONFIG_LOOKASIDE 13 /* int int */ #define SQLITE_CONFIG_PCACHE 14 /* sqlite3_pcache_methods* */ #define SQLITE_CONFIG_GETPCACHE 15 /* sqlite3_pcache_methods* */ #define SQLITE_CONFIG_LOG 16 /* xFunc, void* */ #define SQLITE_CONFIG_URI 17 /* int */ /* ** CAPI3REF: Database Connection Configuration Options ** ** These constants are the available integer configuration options that ** can be passed as the second argument to the [sqlite3_db_config()] interface. ** ** New configuration options may be added in future releases of SQLite. ** Existing configuration options might be discontinued. Applications ** should check the return code from [sqlite3_db_config()] to make sure that ** the call worked. ^The [sqlite3_db_config()] interface will return a ** non-zero [error code] if a discontinued or unsupported configuration option ** is invoked. ** **
**
SQLITE_DBCONFIG_LOOKASIDE
**
^This option takes three additional arguments that determine the ** [lookaside memory allocator] configuration for the [database connection]. ** ^The first argument (the third parameter to [sqlite3_db_config()] is a ** pointer to a memory buffer to use for lookaside memory. ** ^The first argument after the SQLITE_DBCONFIG_LOOKASIDE verb ** may be NULL in which case SQLite will allocate the ** lookaside buffer itself using [sqlite3_malloc()]. ^The second argument is the ** size of each lookaside buffer slot. ^The third argument is the number of ** slots. The size of the buffer in the first argument must be greater than ** or equal to the product of the second and third arguments. The buffer ** must be aligned to an 8-byte boundary. ^If the second argument to ** SQLITE_DBCONFIG_LOOKASIDE is not a multiple of 8, it is internally ** rounded down to the next smaller multiple of 8. ^(The lookaside memory ** configuration for a database connection can only be changed when that ** connection is not currently using lookaside memory, or in other words ** when the "current value" returned by ** [sqlite3_db_status](D,[SQLITE_CONFIG_LOOKASIDE],...) is zero. ** Any attempt to change the lookaside memory configuration when lookaside ** memory is in use leaves the configuration unchanged and returns ** [SQLITE_BUSY].)^
** **
SQLITE_DBCONFIG_ENABLE_FKEY
**
^This option is used to enable or disable the enforcement of ** [foreign key constraints]. There should be two additional arguments. ** The first argument is an integer which is 0 to disable FK enforcement, ** positive to enable FK enforcement or negative to leave FK enforcement ** unchanged. The second parameter is a pointer to an integer into which ** is written 0 or 1 to indicate whether FK enforcement is off or on ** following this call. The second parameter may be a NULL pointer, in ** which case the FK enforcement setting is not reported back.
** **
SQLITE_DBCONFIG_ENABLE_TRIGGER
**
^This option is used to enable or disable [CREATE TRIGGER | triggers]. ** There should be two additional arguments. ** The first argument is an integer which is 0 to disable triggers, ** positive to enable triggers or negative to leave the setting unchanged. ** The second parameter is a pointer to an integer into which ** is written 0 or 1 to indicate whether triggers are disabled or enabled ** following this call. The second parameter may be a NULL pointer, in ** which case the trigger setting is not reported back.
** **
*/ #define SQLITE_DBCONFIG_LOOKASIDE 1001 /* void* int int */ #define SQLITE_DBCONFIG_ENABLE_FKEY 1002 /* int int* */ #define SQLITE_DBCONFIG_ENABLE_TRIGGER 1003 /* int int* */ /* ** CAPI3REF: Enable Or Disable Extended Result Codes ** ** ^The sqlite3_extended_result_codes() routine enables or disables the ** [extended result codes] feature of SQLite. ^The extended result ** codes are disabled by default for historical compatibility. */ SQLITE_API int sqlite3_extended_result_codes(sqlite3*, int onoff); /* ** CAPI3REF: Last Insert Rowid ** ** ^Each entry in an SQLite table has a unique 64-bit signed ** integer key called the [ROWID | "rowid"]. ^The rowid is always available ** as an undeclared column named ROWID, OID, or _ROWID_ as long as those ** names are not also used by explicitly declared columns. ^If ** the table has a column of type [INTEGER PRIMARY KEY] then that column ** is another alias for the rowid. ** ** ^This routine returns the [rowid] of the most recent ** successful [INSERT] into the database from the [database connection] ** in the first argument. ^As of SQLite version 3.7.7, this routines ** records the last insert rowid of both ordinary tables and [virtual tables]. ** ^If no successful [INSERT]s ** have ever occurred on that database connection, zero is returned. ** ** ^(If an [INSERT] occurs within a trigger or within a [virtual table] ** method, then this routine will return the [rowid] of the inserted ** row as long as the trigger or virtual table method is running. ** But once the trigger or virtual table method ends, the value returned ** by this routine reverts to what it was before the trigger or virtual ** table method began.)^ ** ** ^An [INSERT] that fails due to a constraint violation is not a ** successful [INSERT] and does not change the value returned by this ** routine. ^Thus INSERT OR FAIL, INSERT OR IGNORE, INSERT OR ROLLBACK, ** and INSERT OR ABORT make no changes to the return value of this ** routine when their insertion fails. ^(When INSERT OR REPLACE ** encounters a constraint violation, it does not fail. The ** INSERT continues to completion after deleting rows that caused ** the constraint problem so INSERT OR REPLACE will always change ** the return value of this interface.)^ ** ** ^For the purposes of this routine, an [INSERT] is considered to ** be successful even if it is subsequently rolled back. ** ** This function is accessible to SQL statements via the ** [last_insert_rowid() SQL function]. ** ** If a separate thread performs a new [INSERT] on the same ** database connection while the [sqlite3_last_insert_rowid()] ** function is running and thus changes the last insert [rowid], ** then the value returned by [sqlite3_last_insert_rowid()] is ** unpredictable and might not equal either the old or the new ** last insert [rowid]. */ SQLITE_API sqlite3_int64 sqlite3_last_insert_rowid(sqlite3*); /* ** CAPI3REF: Count The Number Of Rows Modified ** ** ^This function returns the number of database rows that were changed ** or inserted or deleted by the most recently completed SQL statement ** on the [database connection] specified by the first parameter. ** ^(Only changes that are directly specified by the [INSERT], [UPDATE], ** or [DELETE] statement are counted. Auxiliary changes caused by ** triggers or [foreign key actions] are not counted.)^ Use the ** [sqlite3_total_changes()] function to find the total number of changes ** including changes caused by triggers and foreign key actions. ** ** ^Changes to a view that are simulated by an [INSTEAD OF trigger] ** are not counted. Only real table changes are counted. ** ** ^(A "row change" is a change to a single row of a single table ** caused by an INSERT, DELETE, or UPDATE statement. Rows that ** are changed as side effects of [REPLACE] constraint resolution, ** rollback, ABORT processing, [DROP TABLE], or by any other ** mechanisms do not count as direct row changes.)^ ** ** A "trigger context" is a scope of execution that begins and ** ends with the script of a [CREATE TRIGGER | trigger]. ** Most SQL statements are ** evaluated outside of any trigger. This is the "top level" ** trigger context. If a trigger fires from the top level, a ** new trigger context is entered for the duration of that one ** trigger. Subtriggers create subcontexts for their duration. ** ** ^Calling [sqlite3_exec()] or [sqlite3_step()] recursively does ** not create a new trigger context. ** ** ^This function returns the number of direct row changes in the ** most recent INSERT, UPDATE, or DELETE statement within the same ** trigger context. ** ** ^Thus, when called from the top level, this function returns the ** number of changes in the most recent INSERT, UPDATE, or DELETE ** that also occurred at the top level. ^(Within the body of a trigger, ** the sqlite3_changes() interface can be called to find the number of ** changes in the most recently completed INSERT, UPDATE, or DELETE ** statement within the body of the same trigger. ** However, the number returned does not include changes ** caused by subtriggers since those have their own context.)^ ** ** See also the [sqlite3_total_changes()] interface, the ** [count_changes pragma], and the [changes() SQL function]. ** ** If a separate thread makes changes on the same database connection ** while [sqlite3_changes()] is running then the value returned ** is unpredictable and not meaningful. */ SQLITE_API int sqlite3_changes(sqlite3*); /* ** CAPI3REF: Total Number Of Rows Modified ** ** ^This function returns the number of row changes caused by [INSERT], ** [UPDATE] or [DELETE] statements since the [database connection] was opened. ** ^(The count returned by sqlite3_total_changes() includes all changes ** from all [CREATE TRIGGER | trigger] contexts and changes made by ** [foreign key actions]. However, ** the count does not include changes used to implement [REPLACE] constraints, ** do rollbacks or ABORT processing, or [DROP TABLE] processing. The ** count does not include rows of views that fire an [INSTEAD OF trigger], ** though if the INSTEAD OF trigger makes changes of its own, those changes ** are counted.)^ ** ^The sqlite3_total_changes() function counts the changes as soon as ** the statement that makes them is completed (when the statement handle ** is passed to [sqlite3_reset()] or [sqlite3_finalize()]). ** ** See also the [sqlite3_changes()] interface, the ** [count_changes pragma], and the [total_changes() SQL function]. ** ** If a separate thread makes changes on the same database connection ** while [sqlite3_total_changes()] is running then the value ** returned is unpredictable and not meaningful. */ SQLITE_API int sqlite3_total_changes(sqlite3*); /* ** CAPI3REF: Interrupt A Long-Running Query ** ** ^This function causes any pending database operation to abort and ** return at its earliest opportunity. This routine is typically ** called in response to a user action such as pressing "Cancel" ** or Ctrl-C where the user wants a long query operation to halt ** immediately. ** ** ^It is safe to call this routine from a thread different from the ** thread that is currently running the database operation. But it ** is not safe to call this routine with a [database connection] that ** is closed or might close before sqlite3_interrupt() returns. ** ** ^If an SQL operation is very nearly finished at the time when ** sqlite3_interrupt() is called, then it might not have an opportunity ** to be interrupted and might continue to completion. ** ** ^An SQL operation that is interrupted will return [SQLITE_INTERRUPT]. ** ^If the interrupted SQL operation is an INSERT, UPDATE, or DELETE ** that is inside an explicit transaction, then the entire transaction ** will be rolled back automatically. ** ** ^The sqlite3_interrupt(D) call is in effect until all currently running ** SQL statements on [database connection] D complete. ^Any new SQL statements ** that are started after the sqlite3_interrupt() call and before the ** running statements reaches zero are interrupted as if they had been ** running prior to the sqlite3_interrupt() call. ^New SQL statements ** that are started after the running statement count reaches zero are ** not effected by the sqlite3_interrupt(). ** ^A call to sqlite3_interrupt(D) that occurs when there are no running ** SQL statements is a no-op and has no effect on SQL statements ** that are started after the sqlite3_interrupt() call returns. ** ** If the database connection closes while [sqlite3_interrupt()] ** is running then bad things will likely happen. */ SQLITE_API void sqlite3_interrupt(sqlite3*); /* ** CAPI3REF: Determine If An SQL Statement Is Complete ** ** These routines are useful during command-line input to determine if the ** currently entered text seems to form a complete SQL statement or ** if additional input is needed before sending the text into ** SQLite for parsing. ^These routines return 1 if the input string ** appears to be a complete SQL statement. ^A statement is judged to be ** complete if it ends with a semicolon token and is not a prefix of a ** well-formed CREATE TRIGGER statement. ^Semicolons that are embedded within ** string literals or quoted identifier names or comments are not ** independent tokens (they are part of the token in which they are ** embedded) and thus do not count as a statement terminator. ^Whitespace ** and comments that follow the final semicolon are ignored. ** ** ^These routines return 0 if the statement is incomplete. ^If a ** memory allocation fails, then SQLITE_NOMEM is returned. ** ** ^These routines do not parse the SQL statements thus ** will not detect syntactically incorrect SQL. ** ** ^(If SQLite has not been initialized using [sqlite3_initialize()] prior ** to invoking sqlite3_complete16() then sqlite3_initialize() is invoked ** automatically by sqlite3_complete16(). If that initialization fails, ** then the return value from sqlite3_complete16() will be non-zero ** regardless of whether or not the input SQL is complete.)^ ** ** The input to [sqlite3_complete()] must be a zero-terminated ** UTF-8 string. ** ** The input to [sqlite3_complete16()] must be a zero-terminated ** UTF-16 string in native byte order. */ SQLITE_API int sqlite3_complete(const char *sql); SQLITE_API int sqlite3_complete16(const void *sql); /* ** CAPI3REF: Register A Callback To Handle SQLITE_BUSY Errors ** ** ^This routine sets a callback function that might be invoked whenever ** an attempt is made to open a database table that another thread ** or process has locked. ** ** ^If the busy callback is NULL, then [SQLITE_BUSY] or [SQLITE_IOERR_BLOCKED] ** is returned immediately upon encountering the lock. ^If the busy callback ** is not NULL, then the callback might be invoked with two arguments. ** ** ^The first argument to the busy handler is a copy of the void* pointer which ** is the third argument to sqlite3_busy_handler(). ^The second argument to ** the busy handler callback is the number of times that the busy handler has ** been invoked for this locking event. ^If the ** busy callback returns 0, then no additional attempts are made to ** access the database and [SQLITE_BUSY] or [SQLITE_IOERR_BLOCKED] is returned. ** ^If the callback returns non-zero, then another attempt ** is made to open the database for reading and the cycle repeats. ** ** The presence of a busy handler does not guarantee that it will be invoked ** when there is lock contention. ^If SQLite determines that invoking the busy ** handler could result in a deadlock, it will go ahead and return [SQLITE_BUSY] ** or [SQLITE_IOERR_BLOCKED] instead of invoking the busy handler. ** Consider a scenario where one process is holding a read lock that ** it is trying to promote to a reserved lock and ** a second process is holding a reserved lock that it is trying ** to promote to an exclusive lock. The first process cannot proceed ** because it is blocked by the second and the second process cannot ** proceed because it is blocked by the first. If both processes ** invoke the busy handlers, neither will make any progress. Therefore, ** SQLite returns [SQLITE_BUSY] for the first process, hoping that this ** will induce the first process to release its read lock and allow ** the second process to proceed. ** ** ^The default busy callback is NULL. ** ** ^The [SQLITE_BUSY] error is converted to [SQLITE_IOERR_BLOCKED] ** when SQLite is in the middle of a large transaction where all the ** changes will not fit into the in-memory cache. SQLite will ** already hold a RESERVED lock on the database file, but it needs ** to promote this lock to EXCLUSIVE so that it can spill cache ** pages into the database file without harm to concurrent ** readers. ^If it is unable to promote the lock, then the in-memory ** cache will be left in an inconsistent state and so the error ** code is promoted from the relatively benign [SQLITE_BUSY] to ** the more severe [SQLITE_IOERR_BLOCKED]. ^This error code promotion ** forces an automatic rollback of the changes. See the ** ** CorruptionFollowingBusyError wiki page for a discussion of why ** this is important. ** ** ^(There can only be a single busy handler defined for each ** [database connection]. Setting a new busy handler clears any ** previously set handler.)^ ^Note that calling [sqlite3_busy_timeout()] ** will also set or clear the busy handler. ** ** The busy callback should not take any actions which modify the ** database connection that invoked the busy handler. Any such actions ** result in undefined behavior. ** ** A busy handler must not close the database connection ** or [prepared statement] that invoked the busy handler. */ SQLITE_API int sqlite3_busy_handler(sqlite3*, int(*)(void*,int), void*); /* ** CAPI3REF: Set A Busy Timeout ** ** ^This routine sets a [sqlite3_busy_handler | busy handler] that sleeps ** for a specified amount of time when a table is locked. ^The handler ** will sleep multiple times until at least "ms" milliseconds of sleeping ** have accumulated. ^After at least "ms" milliseconds of sleeping, ** the handler returns 0 which causes [sqlite3_step()] to return ** [SQLITE_BUSY] or [SQLITE_IOERR_BLOCKED]. ** ** ^Calling this routine with an argument less than or equal to zero ** turns off all busy handlers. ** ** ^(There can only be a single busy handler for a particular ** [database connection] any any given moment. If another busy handler ** was defined (using [sqlite3_busy_handler()]) prior to calling ** this routine, that other busy handler is cleared.)^ */ SQLITE_API int sqlite3_busy_timeout(sqlite3*, int ms); /* ** CAPI3REF: Convenience Routines For Running Queries ** ** This is a legacy interface that is preserved for backwards compatibility. ** Use of this interface is not recommended. ** ** Definition: A result table is memory data structure created by the ** [sqlite3_get_table()] interface. A result table records the ** complete query results from one or more queries. ** ** The table conceptually has a number of rows and columns. But ** these numbers are not part of the result table itself. These ** numbers are obtained separately. Let N be the number of rows ** and M be the number of columns. ** ** A result table is an array of pointers to zero-terminated UTF-8 strings. ** There are (N+1)*M elements in the array. The first M pointers point ** to zero-terminated strings that contain the names of the columns. ** The remaining entries all point to query results. NULL values result ** in NULL pointers. All other values are in their UTF-8 zero-terminated ** string representation as returned by [sqlite3_column_text()]. ** ** A result table might consist of one or more memory allocations. ** It is not safe to pass a result table directly to [sqlite3_free()]. ** A result table should be deallocated using [sqlite3_free_table()]. ** ** ^(As an example of the result table format, suppose a query result ** is as follows: ** ** 
**        Name        | Age
**        -----------------------
**        Alice       | 43
**        Bob         | 28
**        Cindy       | 21
**
** ** There are two column (M==2) and three rows (N==3). Thus the ** result table has 8 entries. Suppose the result table is stored ** in an array names azResult. Then azResult holds this content: ** ** 
**        azResult[0] = "Name";
**        azResult[1] = "Age";
**        azResult[2] = "Alice";
**        azResult[3] = "43";
**        azResult[4] = "Bob";
**        azResult[5] = "28";
**        azResult[6] = "Cindy";
**        azResult[7] = "21";
**
)^ ** ** ^The sqlite3_get_table() function evaluates one or more ** semicolon-separated SQL statements in the zero-terminated UTF-8 ** string of its 2nd parameter and returns a result table to the ** pointer given in its 3rd parameter. ** ** After the application has finished with the result from sqlite3_get_table(), ** it must pass the result table pointer to sqlite3_free_table() in order to ** release the memory that was malloced. Because of the way the ** [sqlite3_malloc()] happens within sqlite3_get_table(), the calling ** function must not try to call [sqlite3_free()] directly. Only ** [sqlite3_free_table()] is able to release the memory properly and safely. ** ** The sqlite3_get_table() interface is implemented as a wrapper around ** [sqlite3_exec()]. The sqlite3_get_table() routine does not have access ** to any internal data structures of SQLite. It uses only the public ** interface defined here. As a consequence, errors that occur in the ** wrapper layer outside of the internal [sqlite3_exec()] call are not ** reflected in subsequent calls to [sqlite3_errcode()] or ** [sqlite3_errmsg()]. */ SQLITE_API int sqlite3_get_table( sqlite3 *db, /* An open database */ const char *zSql, /* SQL to be evaluated */ char ***pazResult, /* Results of the query */ int *pnRow, /* Number of result rows written here */ int *pnColumn, /* Number of result columns written here */ char **pzErrmsg /* Error msg written here */ ); SQLITE_API void sqlite3_free_table(char **result); /* ** CAPI3REF: Formatted String Printing Functions ** ** These routines are work-alikes of the "printf()" family of functions ** from the standard C library. ** ** ^The sqlite3_mprintf() and sqlite3_vmprintf() routines write their ** results into memory obtained from [sqlite3_malloc()]. ** The strings returned by these two routines should be ** released by [sqlite3_free()]. ^Both routines return a ** NULL pointer if [sqlite3_malloc()] is unable to allocate enough ** memory to hold the resulting string. ** ** ^(The sqlite3_snprintf() routine is similar to "snprintf()" from ** the standard C library. The result is written into the ** buffer supplied as the second parameter whose size is given by ** the first parameter. Note that the order of the ** first two parameters is reversed from snprintf().)^ This is an ** historical accident that cannot be fixed without breaking ** backwards compatibility. ^(Note also that sqlite3_snprintf() ** returns a pointer to its buffer instead of the number of ** characters actually written into the buffer.)^ We admit that ** the number of characters written would be a more useful return ** value but we cannot change the implementation of sqlite3_snprintf() ** now without breaking compatibility. ** ** ^As long as the buffer size is greater than zero, sqlite3_snprintf() ** guarantees that the buffer is always zero-terminated. ^The first ** parameter "n" is the total size of the buffer, including space for ** the zero terminator. So the longest string that can be completely ** written will be n-1 characters. ** ** ^The sqlite3_vsnprintf() routine is a varargs version of sqlite3_snprintf(). ** ** These routines all implement some additional formatting ** options that are useful for constructing SQL statements. ** All of the usual printf() formatting options apply. In addition, there ** is are "%q", "%Q", and "%z" options. ** ** ^(The %q option works like %s in that it substitutes a null-terminated ** string from the argument list. But %q also doubles every '\'' character. ** %q is designed for use inside a string literal.)^ By doubling each '\'' ** character it escapes that character and allows it to be inserted into ** the string. ** ** For example, assume the string variable zText contains text as follows: ** ** 
**  char *zText = "It's a happy day!";
**
** ** One can use this text in an SQL statement as follows: ** ** 
**  char *zSQL = sqlite3_mprintf("INSERT INTO table VALUES('%q')", zText);
**  sqlite3_exec(db, zSQL, 0, 0, 0);
**  sqlite3_free(zSQL);
**
** ** Because the %q format string is used, the '\'' character in zText ** is escaped and the SQL generated is as follows: ** ** 
**  INSERT INTO table1 VALUES('It''s a happy day!')
**
** ** This is correct. Had we used %s instead of %q, the generated SQL ** would have looked like this: ** ** 
**  INSERT INTO table1 VALUES('It's a happy day!');
**
** ** This second example is an SQL syntax error. As a general rule you should ** always use %q instead of %s when inserting text into a string literal. ** ** ^(The %Q option works like %q except it also adds single quotes around ** the outside of the total string. Additionally, if the parameter in the ** argument list is a NULL pointer, %Q substitutes the text "NULL" (without ** single quotes).)^ So, for example, one could say: ** ** 
**  char *zSQL = sqlite3_mprintf("INSERT INTO table VALUES(%Q)", zText);
**  sqlite3_exec(db, zSQL, 0, 0, 0);
**  sqlite3_free(zSQL);
**
** ** The code above will render a correct SQL statement in the zSQL ** variable even if the zText variable is a NULL pointer. ** ** ^(The "%z" formatting option works like "%s" but with the ** addition that after the string has been read and copied into ** the result, [sqlite3_free()] is called on the input string.)^ */ SQLITE_API char *sqlite3_mprintf(const char*,...); SQLITE_API char *sqlite3_vmprintf(const char*, va_list); SQLITE_API char *sqlite3_snprintf(int,char*,const char*, ...); SQLITE_API char *sqlite3_vsnprintf(int,char*,const char*, va_list); /* ** CAPI3REF: Memory Allocation Subsystem ** ** The SQLite core uses these three routines for all of its own ** internal memory allocation needs. "Core" in the previous sentence ** does not include operating-system specific VFS implementation. The ** Windows VFS uses native malloc() and free() for some operations. ** ** ^The sqlite3_malloc() routine returns a pointer to a block ** of memory at least N bytes in length, where N is the parameter. ** ^If sqlite3_malloc() is unable to obtain sufficient free ** memory, it returns a NULL pointer. ^If the parameter N to ** sqlite3_malloc() is zero or negative then sqlite3_malloc() returns ** a NULL pointer. ** ** ^Calling sqlite3_free() with a pointer previously returned ** by sqlite3_malloc() or sqlite3_realloc() releases that memory so ** that it might be reused. ^The sqlite3_free() routine is ** a no-op if is called with a NULL pointer. Passing a NULL pointer ** to sqlite3_free() is harmless. After being freed, memory ** should neither be read nor written. Even reading previously freed ** memory might result in a segmentation fault or other severe error. ** Memory corruption, a segmentation fault, or other severe error ** might result if sqlite3_free() is called with a non-NULL pointer that ** was not obtained from sqlite3_malloc() or sqlite3_realloc(). ** ** ^(The sqlite3_realloc() interface attempts to resize a ** prior memory allocation to be at least N bytes, where N is the ** second parameter. The memory allocation to be resized is the first ** parameter.)^ ^ If the first parameter to sqlite3_realloc() ** is a NULL pointer then its behavior is identical to calling ** sqlite3_malloc(N) where N is the second parameter to sqlite3_realloc(). ** ^If the second parameter to sqlite3_realloc() is zero or ** negative then the behavior is exactly the same as calling ** sqlite3_free(P) where P is the first parameter to sqlite3_realloc(). ** ^sqlite3_realloc() returns a pointer to a memory allocation ** of at least N bytes in size or NULL if sufficient memory is unavailable. ** ^If M is the size of the prior allocation, then min(N,M) bytes ** of the prior allocation are copied into the beginning of buffer returned ** by sqlite3_realloc() and the prior allocation is freed. ** ^If sqlite3_realloc() returns NULL, then the prior allocation ** is not freed. ** ** ^The memory returned by sqlite3_malloc() and sqlite3_realloc() ** is always aligned to at least an 8 byte boundary, or to a ** 4 byte boundary if the [SQLITE_4_BYTE_ALIGNED_MALLOC] compile-time ** option is used. ** ** In SQLite version 3.5.0 and 3.5.1, it was possible to define ** the SQLITE_OMIT_MEMORY_ALLOCATION which would cause the built-in ** implementation of these routines to be omitted. That capability ** is no longer provided. Only built-in memory allocators can be used. ** ** The Windows OS interface layer calls ** the system malloc() and free() directly when converting ** filenames between the UTF-8 encoding used by SQLite ** and whatever filename encoding is used by the particular Windows ** installation. Memory allocation errors are detected, but ** they are reported back as [SQLITE_CANTOPEN] or ** [SQLITE_IOERR] rather than [SQLITE_NOMEM]. ** ** The pointer arguments to [sqlite3_free()] and [sqlite3_realloc()] ** must be either NULL or else pointers obtained from a prior ** invocation of [sqlite3_malloc()] or [sqlite3_realloc()] that have ** not yet been released. ** ** The application must not read or write any part of ** a block of memory after it has been released using ** [sqlite3_free()] or [sqlite3_realloc()]. */ SQLITE_API void *sqlite3_malloc(int); SQLITE_API void *sqlite3_realloc(void*, int); SQLITE_API void sqlite3_free(void*); /* ** CAPI3REF: Memory Allocator Statistics ** ** SQLite provides these two interfaces for reporting on the status ** of the [sqlite3_malloc()], [sqlite3_free()], and [sqlite3_realloc()] ** routines, which form the built-in memory allocation subsystem. ** ** ^The [sqlite3_memory_used()] routine returns the number of bytes ** of memory currently outstanding (malloced but not freed). ** ^The [sqlite3_memory_highwater()] routine returns the maximum ** value of [sqlite3_memory_used()] since the high-water mark ** was last reset. ^The values returned by [sqlite3_memory_used()] and ** [sqlite3_memory_highwater()] include any overhead ** added by SQLite in its implementation of [sqlite3_malloc()], ** but not overhead added by the any underlying system library ** routines that [sqlite3_malloc()] may call. ** ** ^The memory high-water mark is reset to the current value of ** [sqlite3_memory_used()] if and only if the parameter to ** [sqlite3_memory_highwater()] is true. ^The value returned ** by [sqlite3_memory_highwater(1)] is the high-water mark ** prior to the reset. */ SQLITE_API sqlite3_int64 sqlite3_memory_used(void); SQLITE_API sqlite3_int64 sqlite3_memory_highwater(int resetFlag); /* ** CAPI3REF: Pseudo-Random Number Generator ** ** SQLite contains a high-quality pseudo-random number generator (PRNG) used to ** select random [ROWID | ROWIDs] when inserting new records into a table that ** already uses the largest possible [ROWID]. The PRNG is also used for ** the build-in random() and randomblob() SQL functions. This interface allows ** applications to access the same PRNG for other purposes. ** ** ^A call to this routine stores N bytes of randomness into buffer P. ** ** ^The first time this routine is invoked (either internally or by ** the application) the PRNG is seeded using randomness obtained ** from the xRandomness method of the default [sqlite3_vfs] object. ** ^On all subsequent invocations, the pseudo-randomness is generated ** internally and without recourse to the [sqlite3_vfs] xRandomness ** method. */ SQLITE_API void sqlite3_randomness(int N, void *P); /* ** CAPI3REF: Compile-Time Authorization Callbacks ** ** ^This routine registers an authorizer callback with a particular ** [database connection], supplied in the first argument. ** ^The authorizer callback is invoked as SQL statements are being compiled ** by [sqlite3_prepare()] or its variants [sqlite3_prepare_v2()], ** [sqlite3_prepare16()] and [sqlite3_prepare16_v2()]. ^At various ** points during the compilation process, as logic is being created ** to perform various actions, the authorizer callback is invoked to ** see if those actions are allowed. ^The authorizer callback should ** return [SQLITE_OK] to allow the action, [SQLITE_IGNORE] to disallow the ** specific action but allow the SQL statement to continue to be ** compiled, or [SQLITE_DENY] to cause the entire SQL statement to be ** rejected with an error. ^If the authorizer callback returns ** any value other than [SQLITE_IGNORE], [SQLITE_OK], or [SQLITE_DENY] ** then the [sqlite3_prepare_v2()] or equivalent call that triggered ** the authorizer will fail with an error message. ** ** When the callback returns [SQLITE_OK], that means the operation ** requested is ok. ^When the callback returns [SQLITE_DENY], the ** [sqlite3_prepare_v2()] or equivalent call that triggered the ** authorizer will fail with an error message explaining that ** access is denied. ** ** ^The first parameter to the authorizer callback is a copy of the third ** parameter to the sqlite3_set_authorizer() interface. ^The second parameter ** to the callback is an integer [SQLITE_COPY | action code] that specifies ** the particular action to be authorized. ^The third through sixth parameters ** to the callback are zero-terminated strings that contain additional ** details about the action to be authorized. ** ** ^If the action code is [SQLITE_READ] ** and the callback returns [SQLITE_IGNORE] then the ** [prepared statement] statement is constructed to substitute ** a NULL value in place of the table column that would have ** been read if [SQLITE_OK] had been returned. The [SQLITE_IGNORE] ** return can be used to deny an untrusted user access to individual ** columns of a table. ** ^If the action code is [SQLITE_DELETE] and the callback returns ** [SQLITE_IGNORE] then the [DELETE] operation proceeds but the ** [truncate optimization] is disabled and all rows are deleted individually. ** ** An authorizer is used when [sqlite3_prepare | preparing] ** SQL statements from an untrusted source, to ensure that the SQL statements ** do not try to access data they are not allowed to see, or that they do not ** try to execute malicious statements that damage the database. For ** example, an application may allow a user to enter arbitrary ** SQL queries for evaluation by a database. But the application does ** not want the user to be able to make arbitrary changes to the ** database. An authorizer could then be put in place while the ** user-entered SQL is being [sqlite3_prepare | prepared] that ** disallows everything except [SELECT] statements. ** ** Applications that need to process SQL from untrusted sources ** might also consider lowering resource limits using [sqlite3_limit()] ** and limiting database size using the [max_page_count] [PRAGMA] ** in addition to using an authorizer. ** ** ^(Only a single authorizer can be in place on a database connection ** at a time. Each call to sqlite3_set_authorizer overrides the ** previous call.)^ ^Disable the authorizer by installing a NULL callback. ** The authorizer is disabled by default. ** ** The authorizer callback must not do anything that will modify ** the database connection that invoked the authorizer callback. ** Note that [sqlite3_prepare_v2()] and [sqlite3_step()] both modify their ** database connections for the meaning of "modify" in this paragraph. ** ** ^When [sqlite3_prepare_v2()] is used to prepare a statement, the ** statement might be re-prepared during [sqlite3_step()] due to a ** schema change. Hence, the application should ensure that the ** correct authorizer callback remains in place during the [sqlite3_step()]. ** ** ^Note that the authorizer callback is invoked only during ** [sqlite3_prepare()] or its variants. Authorization is not ** performed during statement evaluation in [sqlite3_step()], unless ** as stated in the previous paragraph, sqlite3_step() invokes ** sqlite3_prepare_v2() to reprepare a statement after a schema change. */ SQLITE_API int sqlite3_set_authorizer( sqlite3*, int (*xAuth)(void*,int,const char*,const char*,const char*,const char*), void *pUserData ); /* ** CAPI3REF: Authorizer Return Codes ** ** The [sqlite3_set_authorizer | authorizer callback function] must ** return either [SQLITE_OK] or one of these two constants in order ** to signal SQLite whether or not the action is permitted. See the ** [sqlite3_set_authorizer | authorizer documentation] for additional ** information. ** ** Note that SQLITE_IGNORE is also used as a [SQLITE_ROLLBACK | return code] ** from the [sqlite3_vtab_on_conflict()] interface. */ #define SQLITE_DENY 1 /* Abort the SQL statement with an error */ #define SQLITE_IGNORE 2 /* Don't allow access, but don't generate an error */ /* ** CAPI3REF: Authorizer Action Codes ** ** The [sqlite3_set_authorizer()] interface registers a callback function ** that is invoked to authorize certain SQL statement actions. The ** second parameter to the callback is an integer code that specifies ** what action is being authorized. These are the integer action codes that ** the authorizer callback may be passed. ** ** These action code values signify what kind of operation is to be ** authorized. The 3rd and 4th parameters to the authorization ** callback function will be parameters or NULL depending on which of these ** codes is used as the second parameter. ^(The 5th parameter to the ** authorizer callback is the name of the database ("main", "temp", ** etc.) if applicable.)^ ^The 6th parameter to the authorizer callback ** is the name of the inner-most trigger or view that is responsible for ** the access attempt or NULL if this access attempt is directly from ** top-level SQL code. */ /******************************************* 3rd ************ 4th ***********/ #define SQLITE_CREATE_INDEX 1 /* Index Name Table Name */ #define SQLITE_CREATE_TABLE 2 /* Table Name NULL */ #define SQLITE_CREATE_TEMP_INDEX 3 /* Index Name Table Name */ #define SQLITE_CREATE_TEMP_TABLE 4 /* Table Name NULL */ #define SQLITE_CREATE_TEMP_TRIGGER 5 /* Trigger Name Table Name */ #define SQLITE_CREATE_TEMP_VIEW 6 /* View Name NULL */ #define SQLITE_CREATE_TRIGGER 7 /* Trigger Name Table Name */ #define SQLITE_CREATE_VIEW 8 /* View Name NULL */ #define SQLITE_DELETE 9 /* Table Name NULL */ #define SQLITE_DROP_INDEX 10 /* Index Name Table Name */ #define SQLITE_DROP_TABLE 11 /* Table Name NULL */ #define SQLITE_DROP_TEMP_INDEX 12 /* Index Name Table Name */ #define SQLITE_DROP_TEMP_TABLE 13 /* Table Name NULL */ #define SQLITE_DROP_TEMP_TRIGGER 14 /* Trigger Name Table Name */ #define SQLITE_DROP_TEMP_VIEW 15 /* View Name NULL */ #define SQLITE_DROP_TRIGGER 16 /* Trigger Name Table Name */ #define SQLITE_DROP_VIEW 17 /* View Name NULL */ #define SQLITE_INSERT 18 /* Table Name NULL */ #define SQLITE_PRAGMA 19 /* Pragma Name 1st arg or NULL */ #define SQLITE_READ 20 /* Table Name Column Name */ #define SQLITE_SELECT 21 /* NULL NULL */ #define SQLITE_TRANSACTION 22 /* Operation NULL */ #define SQLITE_UPDATE 23 /* Table Name Column Name */ #define SQLITE_ATTACH 24 /* Filename NULL */ #define SQLITE_DETACH 25 /* Database Name NULL */ #define SQLITE_ALTER_TABLE 26 /* Database Name Table Name */ #define SQLITE_REINDEX 27 /* Index Name NULL */ #define SQLITE_ANALYZE 28 /* Table Name NULL */ #define SQLITE_CREATE_VTABLE 29 /* Table Name Module Name */ #define SQLITE_DROP_VTABLE 30 /* Table Name Module Name */ #define SQLITE_FUNCTION 31 /* NULL Function Name */ #define SQLITE_SAVEPOINT 32 /* Operation Savepoint Name */ #define SQLITE_COPY 0 /* No longer used */ /* ** CAPI3REF: Tracing And Profiling Functions ** ** These routines register callback functions that can be used for ** tracing and profiling the execution of SQL statements. ** ** ^The callback function registered by sqlite3_trace() is invoked at ** various times when an SQL statement is being run by [sqlite3_step()]. ** ^The sqlite3_trace() callback is invoked with a UTF-8 rendering of the ** SQL statement text as the statement first begins executing. ** ^(Additional sqlite3_trace() callbacks might occur ** as each triggered subprogram is entered. The callbacks for triggers ** contain a UTF-8 SQL comment that identifies the trigger.)^ ** ** ^The callback function registered by sqlite3_profile() is invoked ** as each SQL statement finishes. ^The profile callback contains ** the original statement text and an estimate of wall-clock time ** of how long that statement took to run. ^The profile callback ** time is in units of nanoseconds, however the current implementation ** is only capable of millisecond resolution so the six least significant ** digits in the time are meaningless. Future versions of SQLite ** might provide greater resolution on the profiler callback. The ** sqlite3_profile() function is considered experimental and is ** subject to change in future versions of SQLite. */ SQLITE_API void *sqlite3_trace(sqlite3*, void(*xTrace)(void*,const char*), void*); SQLITE_API SQLITE_EXPERIMENTAL void *sqlite3_profile(sqlite3*, void(*xProfile)(void*,const char*,sqlite3_uint64), void*); /* ** CAPI3REF: Query Progress Callbacks ** ** ^The sqlite3_progress_handler(D,N,X,P) interface causes the callback ** function X to be invoked periodically during long running calls to ** [sqlite3_exec()], [sqlite3_step()] and [sqlite3_get_table()] for ** database connection D. An example use for this ** interface is to keep a GUI updated during a large query. ** ** ^The parameter P is passed through as the only parameter to the ** callback function X. ^The parameter N is the number of ** [virtual machine instructions] that are evaluated between successive ** invocations of the callback X. ** ** ^Only a single progress handler may be defined at one time per ** [database connection]; setting a new progress handler cancels the ** old one. ^Setting parameter X to NULL disables the progress handler. ** ^The progress handler is also disabled by setting N to a value less ** than 1. ** ** ^If the progress callback returns non-zero, the operation is ** interrupted. This feature can be used to implement a ** "Cancel" button on a GUI progress dialog box. ** ** The progress handler callback must not do anything that will modify ** the database connection that invoked the progress handler. ** Note that [sqlite3_prepare_v2()] and [sqlite3_step()] both modify their ** database connections for the meaning of "modify" in this paragraph. ** */ SQLITE_API void sqlite3_progress_handler(sqlite3*, int, int(*)(void*), void*); /* ** CAPI3REF: Opening A New Database Connection ** ** ^These routines open an SQLite database file as specified by the ** filename argument. ^The filename argument is interpreted as UTF-8 for ** sqlite3_open() and sqlite3_open_v2() and as UTF-16 in the native byte ** order for sqlite3_open16(). ^(A [database connection] handle is usually ** returned in *ppDb, even if an error occurs. The only exception is that ** if SQLite is unable to allocate memory to hold the [sqlite3] object, ** a NULL will be written into *ppDb instead of a pointer to the [sqlite3] ** object.)^ ^(If the database is opened (and/or created) successfully, then ** [SQLITE_OK] is returned. Otherwise an [error code] is returned.)^ ^The ** [sqlite3_errmsg()] or [sqlite3_errmsg16()] routines can be used to obtain ** an English language description of the error following a failure of any ** of the sqlite3_open() routines. ** ** ^The default encoding for the database will be UTF-8 if ** sqlite3_open() or sqlite3_open_v2() is called and ** UTF-16 in the native byte order if sqlite3_open16() is used. ** ** Whether or not an error occurs when it is opened, resources ** associated with the [database connection] handle should be released by ** passing it to [sqlite3_close()] when it is no longer required. ** ** The sqlite3_open_v2() interface works like sqlite3_open() ** except that it accepts two additional parameters for additional control ** over the new database connection. ^(The flags parameter to ** sqlite3_open_v2() can take one of ** the following three values, optionally combined with the ** [SQLITE_OPEN_NOMUTEX], [SQLITE_OPEN_FULLMUTEX], [SQLITE_OPEN_SHAREDCACHE], ** [SQLITE_OPEN_PRIVATECACHE], and/or [SQLITE_OPEN_URI] flags:)^ ** **
** ^(
[SQLITE_OPEN_READONLY]
**
The database is opened in read-only mode. If the database does not ** already exist, an error is returned.
)^ ** ** ^(
[SQLITE_OPEN_READWRITE]
**
The database is opened for reading and writing if possible, or reading ** only if the file is write protected by the operating system. In either ** case the database must already exist, otherwise an error is returned.
)^ ** ** ^(
[SQLITE_OPEN_READWRITE] | [SQLITE_OPEN_CREATE]
**
The database is opened for reading and writing, and is created if ** it does not already exist. This is the behavior that is always used for ** sqlite3_open() and sqlite3_open16().
)^ **
** ** If the 3rd parameter to sqlite3_open_v2() is not one of the ** combinations shown above optionally combined with other ** [SQLITE_OPEN_READONLY | SQLITE_OPEN_* bits] ** then the behavior is undefined. ** ** ^If the [SQLITE_OPEN_NOMUTEX] flag is set, then the database connection ** opens in the multi-thread [threading mode] as long as the single-thread ** mode has not been set at compile-time or start-time. ^If the ** [SQLITE_OPEN_FULLMUTEX] flag is set then the database connection opens ** in the serialized [threading mode] unless single-thread was ** previously selected at compile-time or start-time. ** ^The [SQLITE_OPEN_SHAREDCACHE] flag causes the database connection to be ** eligible to use [shared cache mode], regardless of whether or not shared ** cache is enabled using [sqlite3_enable_shared_cache()]. ^The ** [SQLITE_OPEN_PRIVATECACHE] flag causes the database connection to not ** participate in [shared cache mode] even if it is enabled. ** ** ^The fourth parameter to sqlite3_open_v2() is the name of the ** [sqlite3_vfs] object that defines the operating system interface that ** the new database connection should use. ^If the fourth parameter is ** a NULL pointer then the default [sqlite3_vfs] object is used. ** ** ^If the filename is ":memory:", then a private, temporary in-memory database ** is created for the connection. ^This in-memory database will vanish when ** the database connection is closed. Future versions of SQLite might ** make use of additional special filenames that begin with the ":" character. ** It is recommended that when a database filename actually does begin with ** a ":" character you should prefix the filename with a pathname such as ** "./" to avoid ambiguity. ** ** ^If the filename is an empty string, then a private, temporary ** on-disk database will be created. ^This private database will be ** automatically deleted as soon as the database connection is closed. ** ** [[URI filenames in sqlite3_open()]]

URI Filenames

** ** ^If [URI filename] interpretation is enabled, and the filename argument ** begins with "file:", then the filename is interpreted as a URI. ^URI ** filename interpretation is enabled if the [SQLITE_OPEN_URI] flag is ** set in the fourth argument to sqlite3_open_v2(), or if it has ** been enabled globally using the [SQLITE_CONFIG_URI] option with the ** [sqlite3_config()] method or by the [SQLITE_USE_URI] compile-time option. ** As of SQLite version 3.7.7, URI filename interpretation is turned off ** by default, but future releases of SQLite might enable URI filename ** interpretation by default. See "[URI filenames]" for additional ** information. ** ** URI filenames are parsed according to RFC 3986. ^If the URI contains an ** authority, then it must be either an empty string or the string ** "localhost". ^If the authority is not an empty string or "localhost", an ** error is returned to the caller. ^The fragment component of a URI, if ** present, is ignored. ** ** ^SQLite uses the path component of the URI as the name of the disk file ** which contains the database. ^If the path begins with a '/' character, ** then it is interpreted as an absolute path. ^If the path does not begin ** with a '/' (meaning that the authority section is omitted from the URI) ** then the path is interpreted as a relative path. ** ^On windows, the first component of an absolute path ** is a drive specification (e.g. "C:"). ** ** [[core URI query parameters]] ** The query component of a URI may contain parameters that are interpreted ** either by SQLite itself, or by a [VFS | custom VFS implementation]. ** SQLite interprets the following three query parameters: ** **
    **
  • vfs: ^The "vfs" parameter may be used to specify the name of ** a VFS object that provides the operating system interface that should ** be used to access the database file on disk. ^If this option is set to ** an empty string the default VFS object is used. ^Specifying an unknown ** VFS is an error. ^If sqlite3_open_v2() is used and the vfs option is ** present, then the VFS specified by the option takes precedence over ** the value passed as the fourth parameter to sqlite3_open_v2(). ** **
  • mode: ^(The mode parameter may be set to either "ro", "rw" or ** "rwc". Attempting to set it to any other value is an error)^. ** ^If "ro" is specified, then the database is opened for read-only ** access, just as if the [SQLITE_OPEN_READONLY] flag had been set in the ** third argument to sqlite3_prepare_v2(). ^If the mode option is set to ** "rw", then the database is opened for read-write (but not create) ** access, as if SQLITE_OPEN_READWRITE (but not SQLITE_OPEN_CREATE) had ** been set. ^Value "rwc" is equivalent to setting both ** SQLITE_OPEN_READWRITE and SQLITE_OPEN_CREATE. ^If sqlite3_open_v2() is ** used, it is an error to specify a value for the mode parameter that is ** less restrictive than that specified by the flags passed as the third ** parameter. ** **
  • cache: ^The cache parameter may be set to either "shared" or ** "private". ^Setting it to "shared" is equivalent to setting the ** SQLITE_OPEN_SHAREDCACHE bit in the flags argument passed to ** sqlite3_open_v2(). ^Setting the cache parameter to "private" is ** equivalent to setting the SQLITE_OPEN_PRIVATECACHE bit. ** ^If sqlite3_open_v2() is used and the "cache" parameter is present in ** a URI filename, its value overrides any behaviour requested by setting ** SQLITE_OPEN_PRIVATECACHE or SQLITE_OPEN_SHAREDCACHE flag. **
** ** ^Specifying an unknown parameter in the query component of a URI is not an ** error. Future versions of SQLite might understand additional query ** parameters. See "[query parameters with special meaning to SQLite]" for ** additional information. ** ** [[URI filename examples]]

URI filename examples

** ** **
URI filenames Results **
file:data.db ** Open the file "data.db" in the current directory. **
file:/home/fred/data.db
** file:///home/fred/data.db
** file://localhost/home/fred/data.db
** Open the database file "/home/fred/data.db". **
file://darkstar/home/fred/data.db ** An error. "darkstar" is not a recognized authority. **
** file:///C:/Documents%20and%20Settings/fred/Desktop/data.db ** Windows only: Open the file "data.db" on fred's desktop on drive ** C:. Note that the %20 escaping in this example is not strictly ** necessary - space characters can be used literally ** in URI filenames. **
file:data.db?mode=ro&cache=private ** Open file "data.db" in the current directory for read-only access. ** Regardless of whether or not shared-cache mode is enabled by ** default, use a private cache. **
file:/home/fred/data.db?vfs=unix-nolock ** Open file "/home/fred/data.db". Use the special VFS "unix-nolock". **
file:data.db?mode=readonly ** An error. "readonly" is not a valid option for the "mode" parameter. **
** ** ^URI hexadecimal escape sequences (%HH) are supported within the path and ** query components of a URI. A hexadecimal escape sequence consists of a ** percent sign - "%" - followed by exactly two hexadecimal digits ** specifying an octet value. ^Before the path or query components of a ** URI filename are interpreted, they are encoded using UTF-8 and all ** hexadecimal escape sequences replaced by a single byte containing the ** corresponding octet. If this process generates an invalid UTF-8 encoding, ** the results are undefined. ** ** Note to Windows users: The encoding used for the filename argument ** of sqlite3_open() and sqlite3_open_v2() must be UTF-8, not whatever ** codepage is currently defined. Filenames containing international ** characters must be converted to UTF-8 prior to passing them into ** sqlite3_open() or sqlite3_open_v2(). */ SQLITE_API int sqlite3_open( const char *filename, /* Database filename (UTF-8) */ sqlite3 **ppDb /* OUT: SQLite db handle */ ); SQLITE_API int sqlite3_open16( const void *filename, /* Database filename (UTF-16) */ sqlite3 **ppDb /* OUT: SQLite db handle */ ); SQLITE_API int sqlite3_open_v2( const char *filename, /* Database filename (UTF-8) */ sqlite3 **ppDb, /* OUT: SQLite db handle */ int flags, /* Flags */ const char *zVfs /* Name of VFS module to use */ ); /* ** CAPI3REF: Obtain Values For URI Parameters ** ** This is a utility routine, useful to VFS implementations, that checks ** to see if a database file was a URI that contained a specific query ** parameter, and if so obtains the value of the query parameter. ** ** The zFilename argument is the filename pointer passed into the xOpen() ** method of a VFS implementation. The zParam argument is the name of the ** query parameter we seek. This routine returns the value of the zParam ** parameter if it exists. If the parameter does not exist, this routine ** returns a NULL pointer. ** ** If the zFilename argument to this function is not a pointer that SQLite ** passed into the xOpen VFS method, then the behavior of this routine ** is undefined and probably undesirable. */ SQLITE_API const char *sqlite3_uri_parameter(const char *zFilename, const char *zParam); /* ** CAPI3REF: Error Codes And Messages ** ** ^The sqlite3_errcode() interface returns the numeric [result code] or ** [extended result code] for the most recent failed sqlite3_* API call ** associated with a [database connection]. If a prior API call failed ** but the most recent API call succeeded, the return value from ** sqlite3_errcode() is undefined. ^The sqlite3_extended_errcode() ** interface is the same except that it always returns the ** [extended result code] even when extended result codes are ** disabled. ** ** ^The sqlite3_errmsg() and sqlite3_errmsg16() return English-language ** text that describes the error, as either UTF-8 or UTF-16 respectively. ** ^(Memory to hold the error message string is managed internally. ** The application does not need to worry about freeing the result. ** However, the error string might be overwritten or deallocated by ** subsequent calls to other SQLite interface functions.)^ ** ** When the serialized [threading mode] is in use, it might be the ** case that a second error occurs on a separate thread in between ** the time of the first error and the call to these interfaces. ** When that happens, the second error will be reported since these ** interfaces always report the most recent result. To avoid ** this, each thread can obtain exclusive use of the [database connection] D ** by invoking [sqlite3_mutex_enter]([sqlite3_db_mutex](D)) before beginning ** to use D and invoking [sqlite3_mutex_leave]([sqlite3_db_mutex](D)) after ** all calls to the interfaces listed here are completed. ** ** If an interface fails with SQLITE_MISUSE, that means the interface ** was invoked incorrectly by the application. In that case, the ** error code and message may or may not be set. */ SQLITE_API int sqlite3_errcode(sqlite3 *db); SQLITE_API int sqlite3_extended_errcode(sqlite3 *db); SQLITE_API const char *sqlite3_errmsg(sqlite3*); SQLITE_API const void *sqlite3_errmsg16(sqlite3*); /* ** CAPI3REF: SQL Statement Object ** KEYWORDS: {prepared statement} {prepared statements} ** ** An instance of this object represents a single SQL statement. ** This object is variously known as a "prepared statement" or a ** "compiled SQL statement" or simply as a "statement". ** ** The life of a statement object goes something like this: ** **
    **
  1. Create the object using [sqlite3_prepare_v2()] or a related ** function. **
  2. Bind values to [host parameters] using the sqlite3_bind_*() ** interfaces. **
  3. Run the SQL by calling [sqlite3_step()] one or more times. **
  4. Reset the statement using [sqlite3_reset()] then go back ** to step 2. Do this zero or more times. **
  5. Destroy the object using [sqlite3_finalize()]. **
** ** Refer to documentation on individual methods above for additional ** information. */ typedef struct sqlite3_stmt sqlite3_stmt; /* ** CAPI3REF: Run-time Limits ** ** ^(This interface allows the size of various constructs to be limited ** on a connection by connection basis. The first parameter is the ** [database connection] whose limit is to be set or queried. The ** second parameter is one of the [limit categories] that define a ** class of constructs to be size limited. The third parameter is the ** new limit for that construct.)^ ** ** ^If the new limit is a negative number, the limit is unchanged. ** ^(For each limit category SQLITE_LIMIT_NAME there is a ** [limits | hard upper bound] ** set at compile-time by a C preprocessor macro called ** [limits | SQLITE_MAX_NAME]. ** (The "_LIMIT_" in the name is changed to "_MAX_".))^ ** ^Attempts to increase a limit above its hard upper bound are ** silently truncated to the hard upper bound. ** ** ^Regardless of whether or not the limit was changed, the ** [sqlite3_limit()] interface returns the prior value of the limit. ** ^Hence, to find the current value of a limit without changing it, ** simply invoke this interface with the third parameter set to -1. ** ** Run-time limits are intended for use in applications that manage ** both their own internal database and also databases that are controlled ** by untrusted external sources. An example application might be a ** web browser that has its own databases for storing history and ** separate databases controlled by JavaScript applications downloaded ** off the Internet. The internal databases can be given the ** large, default limits. Databases managed by external sources can ** be given much smaller limits designed to prevent a denial of service ** attack. Developers might also want to use the [sqlite3_set_authorizer()] ** interface to further control untrusted SQL. The size of the database ** created by an untrusted script can be contained using the ** [max_page_count] [PRAGMA]. ** ** New run-time limit categories may be added in future releases. */ SQLITE_API int sqlite3_limit(sqlite3*, int id, int newVal); /* ** CAPI3REF: Run-Time Limit Categories ** KEYWORDS: {limit category} {*limit categories} ** ** These constants define various performance limits ** that can be lowered at run-time using [sqlite3_limit()]. ** The synopsis of the meanings of the various limits is shown below. ** Additional information is available at [limits | Limits in SQLite]. ** **
** [[SQLITE_LIMIT_LENGTH]] ^(
SQLITE_LIMIT_LENGTH
**
The maximum size of any string or BLOB or table row, in bytes.
)^ ** ** [[SQLITE_LIMIT_SQL_LENGTH]] ^(
SQLITE_LIMIT_SQL_LENGTH
**
The maximum length of an SQL statement, in bytes.
)^ ** ** [[SQLITE_LIMIT_COLUMN]] ^(
SQLITE_LIMIT_COLUMN
**
The maximum number of columns in a table definition or in the ** result set of a [SELECT] or the maximum number of columns in an index ** or in an ORDER BY or GROUP BY clause.
)^ ** ** [[SQLITE_LIMIT_EXPR_DEPTH]] ^(
SQLITE_LIMIT_EXPR_DEPTH
**
The maximum depth of the parse tree on any expression.
)^ ** ** [[SQLITE_LIMIT_COMPOUND_SELECT]] ^(
SQLITE_LIMIT_COMPOUND_SELECT
**
The maximum number of terms in a compound SELECT statement.
)^ ** ** [[SQLITE_LIMIT_VDBE_OP]] ^(
SQLITE_LIMIT_VDBE_OP
**
The maximum number of instructions in a virtual machine program ** used to implement an SQL statement. This limit is not currently ** enforced, though that might be added in some future release of ** SQLite.
)^ ** ** [[SQLITE_LIMIT_FUNCTION_ARG]] ^(
SQLITE_LIMIT_FUNCTION_ARG
**
The maximum number of arguments on a function.
)^ ** ** [[SQLITE_LIMIT_ATTACHED]] ^(
SQLITE_LIMIT_ATTACHED
**
The maximum number of [ATTACH | attached databases].)^
** ** [[SQLITE_LIMIT_LIKE_PATTERN_LENGTH]] ** ^(
SQLITE_LIMIT_LIKE_PATTERN_LENGTH
**
The maximum length of the pattern argument to the [LIKE] or ** [GLOB] operators.
)^ ** ** [[SQLITE_LIMIT_VARIABLE_NUMBER]] ** ^(
SQLITE_LIMIT_VARIABLE_NUMBER
**
The maximum index number of any [parameter] in an SQL statement.)^ ** ** [[SQLITE_LIMIT_TRIGGER_DEPTH]] ^(
SQLITE_LIMIT_TRIGGER_DEPTH
**
The maximum depth of recursion for triggers.
)^ **
*/ #define SQLITE_LIMIT_LENGTH 0 #define SQLITE_LIMIT_SQL_LENGTH 1 #define SQLITE_LIMIT_COLUMN 2 #define SQLITE_LIMIT_EXPR_DEPTH 3 #define SQLITE_LIMIT_COMPOUND_SELECT 4 #define SQLITE_LIMIT_VDBE_OP 5 #define SQLITE_LIMIT_FUNCTION_ARG 6 #define SQLITE_LIMIT_ATTACHED 7 #define SQLITE_LIMIT_LIKE_PATTERN_LENGTH 8 #define SQLITE_LIMIT_VARIABLE_NUMBER 9 #define SQLITE_LIMIT_TRIGGER_DEPTH 10 /* ** CAPI3REF: Compiling An SQL Statement ** KEYWORDS: {SQL statement compiler} ** ** To execute an SQL query, it must first be compiled into a byte-code ** program using one of these routines. ** ** The first argument, "db", is a [database connection] obtained from a ** prior successful call to [sqlite3_open()], [sqlite3_open_v2()] or ** [sqlite3_open16()]. The database connection must not have been closed. ** ** The second argument, "zSql", is the statement to be compiled, encoded ** as either UTF-8 or UTF-16. The sqlite3_prepare() and sqlite3_prepare_v2() ** interfaces use UTF-8, and sqlite3_prepare16() and sqlite3_prepare16_v2() ** use UTF-16. ** ** ^If the nByte argument is less than zero, then zSql is read up to the ** first zero terminator. ^If nByte is non-negative, then it is the maximum ** number of bytes read from zSql. ^When nByte is non-negative, the ** zSql string ends at either the first '\000' or '\u0000' character or ** the nByte-th byte, whichever comes first. If the caller knows ** that the supplied string is nul-terminated, then there is a small ** performance advantage to be gained by passing an nByte parameter that ** is equal to the number of bytes in the input string including ** the nul-terminator bytes. ** ** ^If pzTail is not NULL then *pzTail is made to point to the first byte ** past the end of the first SQL statement in zSql. These routines only ** compile the first statement in zSql, so *pzTail is left pointing to ** what remains uncompiled. ** ** ^*ppStmt is left pointing to a compiled [prepared statement] that can be ** executed using [sqlite3_step()]. ^If there is an error, *ppStmt is set ** to NULL. ^If the input text contains no SQL (if the input is an empty ** string or a comment) then *ppStmt is set to NULL. ** The calling procedure is responsible for deleting the compiled ** SQL statement using [sqlite3_finalize()] after it has finished with it. ** ppStmt may not be NULL. ** ** ^On success, the sqlite3_prepare() family of routines return [SQLITE_OK]; ** otherwise an [error code] is returned. ** ** The sqlite3_prepare_v2() and sqlite3_prepare16_v2() interfaces are ** recommended for all new programs. The two older interfaces are retained ** for backwards compatibility, but their use is discouraged. ** ^In the "v2" interfaces, the prepared statement ** that is returned (the [sqlite3_stmt] object) contains a copy of the ** original SQL text. This causes the [sqlite3_step()] interface to ** behave differently in three ways: ** **
    **
  1. ** ^If the database schema changes, instead of returning [SQLITE_SCHEMA] as it ** always used to do, [sqlite3_step()] will automatically recompile the SQL ** statement and try to run it again. **
    2. ** **
  2. ** ^When an error occurs, [sqlite3_step()] will return one of the detailed ** [error codes] or [extended error codes]. ^The legacy behavior was that ** [sqlite3_step()] would only return a generic [SQLITE_ERROR] result code ** and the application would have to make a second call to [sqlite3_reset()] ** in order to find the underlying cause of the problem. With the "v2" prepare ** interfaces, the underlying reason for the error is returned immediately. **
    3. ** **
  3. ** ^If the specific value bound to [parameter | host parameter] in the ** WHERE clause might influence the choice of query plan for a statement, ** then the statement will be automatically recompiled, as if there had been ** a schema change, on the first [sqlite3_step()] call following any change ** to the [sqlite3_bind_text | bindings] of that [parameter]. ** ^The specific value of WHERE-clause [parameter] might influence the ** choice of query plan if the parameter is the left-hand side of a [LIKE] ** or [GLOB] operator or if the parameter is compared to an indexed column ** and the [SQLITE_ENABLE_STAT2] compile-time option is enabled. ** the **
    4. **
*/ SQLITE_API int sqlite3_prepare( sqlite3 *db, /* Database handle */ const char *zSql, /* SQL statement, UTF-8 encoded */ int nByte, /* Maximum length of zSql in bytes. */ sqlite3_stmt **ppStmt, /* OUT: Statement handle */ const char **pzTail /* OUT: Pointer to unused portion of zSql */ ); SQLITE_API int sqlite3_prepare_v2( sqlite3 *db, /* Database handle */ const char *zSql, /* SQL statement, UTF-8 encoded */ int nByte, /* Maximum length of zSql in bytes. */ sqlite3_stmt **ppStmt, /* OUT: Statement handle */ const char **pzTail /* OUT: Pointer to unused portion of zSql */ ); SQLITE_API int sqlite3_prepare16( sqlite3 *db, /* Database handle */ const void *zSql, /* SQL statement, UTF-16 encoded */ int nByte, /* Maximum length of zSql in bytes. */ sqlite3_stmt **ppStmt, /* OUT: Statement handle */ const void **pzTail /* OUT: Pointer to unused portion of zSql */ ); SQLITE_API int sqlite3_prepare16_v2( sqlite3 *db, /* Database handle */ const void *zSql, /* SQL statement, UTF-16 encoded */ int nByte, /* Maximum length of zSql in bytes. */ sqlite3_stmt **ppStmt, /* OUT: Statement handle */ const void **pzTail /* OUT: Pointer to unused portion of zSql */ ); /* ** CAPI3REF: Retrieving Statement SQL ** ** ^This interface can be used to retrieve a saved copy of the original ** SQL text used to create a [prepared statement] if that statement was ** compiled using either [sqlite3_prepare_v2()] or [sqlite3_prepare16_v2()]. */ SQLITE_API const char *sqlite3_sql(sqlite3_stmt *pStmt); /* ** CAPI3REF: Determine If An SQL Statement Writes The Database ** ** ^The sqlite3_stmt_readonly(X) interface returns true (non-zero) if ** and only if the [prepared statement] X makes no direct changes to ** the content of the database file. ** ** Note that [application-defined SQL functions] or ** [virtual tables] might change the database indirectly as a side effect. ** ^(For example, if an application defines a function "eval()" that ** calls [sqlite3_exec()], then the following SQL statement would ** change the database file through side-effects: ** ** 
**    SELECT eval('DELETE FROM t1') FROM t2;
**
** ** But because the [SELECT] statement does not change the database file ** directly, sqlite3_stmt_readonly() would still return true.)^ ** ** ^Transaction control statements such as [BEGIN], [COMMIT], [ROLLBACK], ** [SAVEPOINT], and [RELEASE] cause sqlite3_stmt_readonly() to return true, ** since the statements themselves do not actually modify the database but ** rather they control the timing of when other statements modify the ** database. ^The [ATTACH] and [DETACH] statements also cause ** sqlite3_stmt_readonly() to return true since, while those statements ** change the configuration of a database connection, they do not make ** changes to the content of the database files on disk. */ SQLITE_API int sqlite3_stmt_readonly(sqlite3_stmt *pStmt); /* ** CAPI3REF: Dynamically Typed Value Object ** KEYWORDS: {protected sqlite3_value} {unprotected sqlite3_value} ** ** SQLite uses the sqlite3_value object to represent all values ** that can be stored in a database table. SQLite uses dynamic typing ** for the values it stores. ^Values stored in sqlite3_value objects ** can be integers, floating point values, strings, BLOBs, or NULL. ** ** An sqlite3_value object may be either "protected" or "unprotected". ** Some interfaces require a protected sqlite3_value. Other interfaces ** will accept either a protected or an unprotected sqlite3_value. ** Every interface that accepts sqlite3_value arguments specifies ** whether or not it requires a protected sqlite3_value. ** ** The terms "protected" and "unprotected" refer to whether or not ** a mutex is held. An internal mutex is held for a protected ** sqlite3_value object but no mutex is held for an unprotected ** sqlite3_value object. If SQLite is compiled to be single-threaded ** (with [SQLITE_THREADSAFE=0] and with [sqlite3_threadsafe()] returning 0) ** or if SQLite is run in one of reduced mutex modes ** [SQLITE_CONFIG_SINGLETHREAD] or [SQLITE_CONFIG_MULTITHREAD] ** then there is no distinction between protected and unprotected ** sqlite3_value objects and they can be used interchangeably. However, ** for maximum code portability it is recommended that applications ** still make the distinction between protected and unprotected ** sqlite3_value objects even when not strictly required. ** ** ^The sqlite3_value objects that are passed as parameters into the ** implementation of [application-defined SQL functions] are protected. ** ^The sqlite3_value object returned by ** [sqlite3_column_value()] is unprotected. ** Unprotected sqlite3_value objects may only be used with ** [sqlite3_result_value()] and [sqlite3_bind_value()]. ** The [sqlite3_value_blob | sqlite3_value_type()] family of ** interfaces require protected sqlite3_value objects. */ typedef struct Mem sqlite3_value; /* ** CAPI3REF: SQL Function Context Object ** ** The context in which an SQL function executes is stored in an ** sqlite3_context object. ^A pointer to an sqlite3_context object ** is always first parameter to [application-defined SQL functions]. ** The application-defined SQL function implementation will pass this ** pointer through into calls to [sqlite3_result_int | sqlite3_result()], ** [sqlite3_aggregate_context()], [sqlite3_user_data()], ** [sqlite3_context_db_handle()], [sqlite3_get_auxdata()], ** and/or [sqlite3_set_auxdata()]. */ typedef struct sqlite3_context sqlite3_context; /* ** CAPI3REF: Binding Values To Prepared Statements ** KEYWORDS: {host parameter} {host parameters} {host parameter name} ** KEYWORDS: {SQL parameter} {SQL parameters} {parameter binding} ** ** ^(In the SQL statement text input to [sqlite3_prepare_v2()] and its variants, ** literals may be replaced by a [parameter] that matches one of following ** templates: ** **
    **
  • ? **
  • ?NNN **
  • :VVV **
  • @VVV **
  • $VVV **
** ** In the templates above, NNN represents an integer literal, ** and VVV represents an alphanumeric identifier.)^ ^The values of these ** parameters (also called "host parameter names" or "SQL parameters") ** can be set using the sqlite3_bind_*() routines defined here. ** ** ^The first argument to the sqlite3_bind_*() routines is always ** a pointer to the [sqlite3_stmt] object returned from ** [sqlite3_prepare_v2()] or its variants. ** ** ^The second argument is the index of the SQL parameter to be set. ** ^The leftmost SQL parameter has an index of 1. ^When the same named ** SQL parameter is used more than once, second and subsequent ** occurrences have the same index as the first occurrence. ** ^The index for named parameters can be looked up using the ** [sqlite3_bind_parameter_index()] API if desired. ^The index ** for "?NNN" parameters is the value of NNN. ** ^The NNN value must be between 1 and the [sqlite3_limit()] ** parameter [SQLITE_LIMIT_VARIABLE_NUMBER] (default value: 999). ** ** ^The third argument is the value to bind to the parameter. ** ** ^(In those routines that have a fourth argument, its value is the ** number of bytes in the parameter. To be clear: the value is the ** number of bytes in the value, not the number of characters.)^ ** ^If the fourth parameter is negative, the length of the string is ** the number of bytes up to the first zero terminator. ** ** ^The fifth argument to sqlite3_bind_blob(), sqlite3_bind_text(), and ** sqlite3_bind_text16() is a destructor used to dispose of the BLOB or ** string after SQLite has finished with it. ^The destructor is called ** to dispose of the BLOB or string even if the call to sqlite3_bind_blob(), ** sqlite3_bind_text(), or sqlite3_bind_text16() fails. ** ^If the fifth argument is ** the special value [SQLITE_STATIC], then SQLite assumes that the ** information is in static, unmanaged space and does not need to be freed. ** ^If the fifth argument has the value [SQLITE_TRANSIENT], then ** SQLite makes its own private copy of the data immediately, before ** the sqlite3_bind_*() routine returns. ** ** ^The sqlite3_bind_zeroblob() routine binds a BLOB of length N that ** is filled with zeroes. ^A zeroblob uses a fixed amount of memory ** (just an integer to hold its size) while it is being processed. ** Zeroblobs are intended to serve as placeholders for BLOBs whose ** content is later written using ** [sqlite3_blob_open | incremental BLOB I/O] routines. ** ^A negative value for the zeroblob results in a zero-length BLOB. ** ** ^If any of the sqlite3_bind_*() routines are called with a NULL pointer ** for the [prepared statement] or with a prepared statement for which ** [sqlite3_step()] has been called more recently than [sqlite3_reset()], ** then the call will return [SQLITE_MISUSE]. If any sqlite3_bind_() ** routine is passed a [prepared statement] that has been finalized, the ** result is undefined and probably harmful. ** ** ^Bindings are not cleared by the [sqlite3_reset()] routine. ** ^Unbound parameters are interpreted as NULL. ** ** ^The sqlite3_bind_* routines return [SQLITE_OK] on success or an ** [error code] if anything goes wrong. ** ^[SQLITE_RANGE] is returned if the parameter ** index is out of range. ^[SQLITE_NOMEM] is returned if malloc() fails. ** ** See also: [sqlite3_bind_parameter_count()], ** [sqlite3_bind_parameter_name()], and [sqlite3_bind_parameter_index()]. */ SQLITE_API int sqlite3_bind_blob(sqlite3_stmt*, int, const void*, int n, void(*)(void*)); SQLITE_API int sqlite3_bind_double(sqlite3_stmt*, int, double); SQLITE_API int sqlite3_bind_int(sqlite3_stmt*, int, int); SQLITE_API int sqlite3_bind_int64(sqlite3_stmt*, int, sqlite3_int64); SQLITE_API int sqlite3_bind_null(sqlite3_stmt*, int); SQLITE_API int sqlite3_bind_text(sqlite3_stmt*, int, const char*, int n, void(*)(void*)); SQLITE_API int sqlite3_bind_text16(sqlite3_stmt*, int, const void*, int, void(*)(void*)); SQLITE_API int sqlite3_bind_value(sqlite3_stmt*, int, const sqlite3_value*); SQLITE_API int sqlite3_bind_zeroblob(sqlite3_stmt*, int, int n); /* ** CAPI3REF: Number Of SQL Parameters ** ** ^This routine can be used to find the number of [SQL parameters] ** in a [prepared statement]. SQL parameters are tokens of the ** form "?", "?NNN", ":AAA", "$AAA", or "@AAA" that serve as ** placeholders for values that are [sqlite3_bind_blob | bound] ** to the parameters at a later time. ** ** ^(This routine actually returns the index of the largest (rightmost) ** parameter. For all forms except ?NNN, this will correspond to the ** number of unique parameters. If parameters of the ?NNN form are used, ** there may be gaps in the list.)^ ** ** See also: [sqlite3_bind_blob|sqlite3_bind()], ** [sqlite3_bind_parameter_name()], and ** [sqlite3_bind_parameter_index()]. */ SQLITE_API int sqlite3_bind_parameter_count(sqlite3_stmt*); /* ** CAPI3REF: Name Of A Host Parameter ** ** ^The sqlite3_bind_parameter_name(P,N) interface returns ** the name of the N-th [SQL parameter] in the [prepared statement] P. ** ^(SQL parameters of the form "?NNN" or ":AAA" or "@AAA" or "$AAA" ** have a name which is the string "?NNN" or ":AAA" or "@AAA" or "$AAA" ** respectively. ** In other words, the initial ":" or "$" or "@" or "?" ** is included as part of the name.)^ ** ^Parameters of the form "?" without a following integer have no name ** and are referred to as "nameless" or "anonymous parameters". ** ** ^The first host parameter has an index of 1, not 0. ** ** ^If the value N is out of range or if the N-th parameter is ** nameless, then NULL is returned. ^The returned string is ** always in UTF-8 encoding even if the named parameter was ** originally specified as UTF-16 in [sqlite3_prepare16()] or ** [sqlite3_prepare16_v2()]. ** ** See also: [sqlite3_bind_blob|sqlite3_bind()], ** [sqlite3_bind_parameter_count()], and ** [sqlite3_bind_parameter_index()]. */ SQLITE_API const char *sqlite3_bind_parameter_name(sqlite3_stmt*, int); /* ** CAPI3REF: Index Of A Parameter With A Given Name ** ** ^Return the index of an SQL parameter given its name. ^The ** index value returned is suitable for use as the second ** parameter to [sqlite3_bind_blob|sqlite3_bind()]. ^A zero ** is returned if no matching parameter is found. ^The parameter ** name must be given in UTF-8 even if the original statement ** was prepared from UTF-16 text using [sqlite3_prepare16_v2()]. ** ** See also: [sqlite3_bind_blob|sqlite3_bind()], ** [sqlite3_bind_parameter_count()], and ** [sqlite3_bind_parameter_index()]. */ SQLITE_API int sqlite3_bind_parameter_index(sqlite3_stmt*, const char *zName); /* ** CAPI3REF: Reset All Bindings On A Prepared Statement ** ** ^Contrary to the intuition of many, [sqlite3_reset()] does not reset ** the [sqlite3_bind_blob | bindings] on a [prepared statement]. ** ^Use this routine to reset all host parameters to NULL. */ SQLITE_API int sqlite3_clear_bindings(sqlite3_stmt*); /* ** CAPI3REF: Number Of Columns In A Result Set ** ** ^Return the number of columns in the result set returned by the ** [prepared statement]. ^This routine returns 0 if pStmt is an SQL ** statement that does not return data (for example an [UPDATE]). ** ** See also: [sqlite3_data_count()] */ SQLITE_API int sqlite3_column_count(sqlite3_stmt *pStmt); /* ** CAPI3REF: Column Names In A Result Set ** ** ^These routines return the name assigned to a particular column ** in the result set of a [SELECT] statement. ^The sqlite3_column_name() ** interface returns a pointer to a zero-terminated UTF-8 string ** and sqlite3_column_name16() returns a pointer to a zero-terminated ** UTF-16 string. ^The first parameter is the [prepared statement] ** that implements the [SELECT] statement. ^The second parameter is the ** column number. ^The leftmost column is number 0. ** ** ^The returned string pointer is valid until either the [prepared statement] ** is destroyed by [sqlite3_finalize()] or until the statement is automatically ** reprepared by the first call to [sqlite3_step()] for a particular run ** or until the next call to ** sqlite3_column_name() or sqlite3_column_name16() on the same column. ** ** ^If sqlite3_malloc() fails during the processing of either routine ** (for example during a conversion from UTF-8 to UTF-16) then a ** NULL pointer is returned. ** ** ^The name of a result column is the value of the "AS" clause for ** that column, if there is an AS clause. If there is no AS clause ** then the name of the column is unspecified and may change from ** one release of SQLite to the next. */ SQLITE_API const char *sqlite3_column_name(sqlite3_stmt*, int N); SQLITE_API const void *sqlite3_column_name16(sqlite3_stmt*, int N); /* ** CAPI3REF: Source Of Data In A Query Result ** ** ^These routines provide a means to determine the database, table, and ** table column that is the origin of a particular result column in ** [SELECT] statement. ** ^The name of the database or table or column can be returned as ** either a UTF-8 or UTF-16 string. ^The _database_ routines return ** the database name, the _table_ routines return the table name, and ** the origin_ routines return the column name. ** ^The returned string is valid until the [prepared statement] is destroyed ** using [sqlite3_finalize()] or until the statement is automatically ** reprepared by the first call to [sqlite3_step()] for a particular run ** or until the same information is requested ** again in a different encoding. ** ** ^The names returned are the original un-aliased names of the ** database, table, and column. ** ** ^The first argument to these interfaces is a [prepared statement]. ** ^These functions return information about the Nth result column returned by ** the statement, where N is the second function argument. ** ^The left-most column is column 0 for these routines. ** ** ^If the Nth column returned by the statement is an expression or ** subquery and is not a column value, then all of these functions return ** NULL. ^These routine might also return NULL if a memory allocation error ** occurs. ^Otherwise, they return the name of the attached database, table, ** or column that query result column was extracted from. ** ** ^As with all other SQLite APIs, those whose names end with "16" return ** UTF-16 encoded strings and the other functions return UTF-8. ** ** ^These APIs are only available if the library was compiled with the ** [SQLITE_ENABLE_COLUMN_METADATA] C-preprocessor symbol. ** ** If two or more threads call one or more of these routines against the same ** prepared statement and column at the same time then the results are ** undefined. ** ** If two or more threads call one or more ** [sqlite3_column_database_name | column metadata interfaces] ** for the same [prepared statement] and result column ** at the same time then the results are undefined. */ SQLITE_API const char *sqlite3_column_database_name(sqlite3_stmt*,int); SQLITE_API const void *sqlite3_column_database_name16(sqlite3_stmt*,int); SQLITE_API const char *sqlite3_column_table_name(sqlite3_stmt*,int); SQLITE_API const void *sqlite3_column_table_name16(sqlite3_stmt*,int); SQLITE_API const char *sqlite3_column_origin_name(sqlite3_stmt*,int); SQLITE_API const void *sqlite3_column_origin_name16(sqlite3_stmt*,int); /* ** CAPI3REF: Declared Datatype Of A Query Result ** ** ^(The first parameter is a [prepared statement]. ** If this statement is a [SELECT] statement and the Nth column of the ** returned result set of that [SELECT] is a table column (not an ** expression or subquery) then the declared type of the table ** column is returned.)^ ^If the Nth column of the result set is an ** expression or subquery, then a NULL pointer is returned. ** ^The returned string is always UTF-8 encoded. ** ** ^(For example, given the database schema: ** ** CREATE TABLE t1(c1 VARIANT); ** ** and the following statement to be compiled: ** ** SELECT c1 + 1, c1 FROM t1; ** ** this routine would return the string "VARIANT" for the second result ** column (i==1), and a NULL pointer for the first result column (i==0).)^ ** ** ^SQLite uses dynamic run-time typing. ^So just because a column ** is declared to contain a particular type does not mean that the ** data stored in that column is of the declared type. SQLite is ** strongly typed, but the typing is dynamic not static. ^Type ** is associated with individual values, not with the containers ** used to hold those values. */ SQLITE_API const char *sqlite3_column_decltype(sqlite3_stmt*,int); SQLITE_API const void *sqlite3_column_decltype16(sqlite3_stmt*,int); /* ** CAPI3REF: Evaluate An SQL Statement ** ** After a [prepared statement] has been prepared using either ** [sqlite3_prepare_v2()] or [sqlite3_prepare16_v2()] or one of the legacy ** interfaces [sqlite3_prepare()] or [sqlite3_prepare16()], this function ** must be called one or more times to evaluate the statement. ** ** The details of the behavior of the sqlite3_step() interface depend ** on whether the statement was prepared using the newer "v2" interface ** [sqlite3_prepare_v2()] and [sqlite3_prepare16_v2()] or the older legacy ** interface [sqlite3_prepare()] and [sqlite3_prepare16()]. The use of the ** new "v2" interface is recommended for new applications but the legacy ** interface will continue to be supported. ** ** ^In the legacy interface, the return value will be either [SQLITE_BUSY], ** [SQLITE_DONE], [SQLITE_ROW], [SQLITE_ERROR], or [SQLITE_MISUSE]. ** ^With the "v2" interface, any of the other [result codes] or ** [extended result codes] might be returned as well. ** ** ^[SQLITE_BUSY] means that the database engine was unable to acquire the ** database locks it needs to do its job. ^If the statement is a [COMMIT] ** or occurs outside of an explicit transaction, then you can retry the ** statement. If the statement is not a [COMMIT] and occurs within an ** explicit transaction then you should rollback the transaction before ** continuing. ** ** ^[SQLITE_DONE] means that the statement has finished executing ** successfully. sqlite3_step() should not be called again on this virtual ** machine without first calling [sqlite3_reset()] to reset the virtual ** machine back to its initial state. ** ** ^If the SQL statement being executed returns any data, then [SQLITE_ROW] ** is returned each time a new row of data is ready for processing by the ** caller. The values may be accessed using the [column access functions]. ** sqlite3_step() is called again to retrieve the next row of data. ** ** ^[SQLITE_ERROR] means that a run-time error (such as a constraint ** violation) has occurred. sqlite3_step() should not be called again on ** the VM. More information may be found by calling [sqlite3_errmsg()]. ** ^With the legacy interface, a more specific error code (for example, ** [SQLITE_INTERRUPT], [SQLITE_SCHEMA], [SQLITE_CORRUPT], and so forth) ** can be obtained by calling [sqlite3_reset()] on the ** [prepared statement]. ^In the "v2" interface, ** the more specific error code is returned directly by sqlite3_step(). ** ** [SQLITE_MISUSE] means that the this routine was called inappropriately. ** Perhaps it was called on a [prepared statement] that has ** already been [sqlite3_finalize | finalized] or on one that had ** previously returned [SQLITE_ERROR] or [SQLITE_DONE]. Or it could ** be the case that the same database connection is being used by two or ** more threads at the same moment in time. ** ** For all versions of SQLite up to and including 3.6.23.1, a call to ** [sqlite3_reset()] was required after sqlite3_step() returned anything ** other than [SQLITE_ROW] before any subsequent invocation of ** sqlite3_step(). Failure to reset the prepared statement using ** [sqlite3_reset()] would result in an [SQLITE_MISUSE] return from ** sqlite3_step(). But after version 3.6.23.1, sqlite3_step() began ** calling [sqlite3_reset()] automatically in this circumstance rather ** than returning [SQLITE_MISUSE]. This is not considered a compatibility ** break because any application that ever receives an SQLITE_MISUSE error ** is broken by definition. The [SQLITE_OMIT_AUTORESET] compile-time option ** can be used to restore the legacy behavior. ** ** Goofy Interface Alert: In the legacy interface, the sqlite3_step() ** API always returns a generic error code, [SQLITE_ERROR], following any ** error other than [SQLITE_BUSY] and [SQLITE_MISUSE]. You must call ** [sqlite3_reset()] or [sqlite3_finalize()] in order to find one of the ** specific [error codes] that better describes the error. ** We admit that this is a goofy design. The problem has been fixed ** with the "v2" interface. If you prepare all of your SQL statements ** using either [sqlite3_prepare_v2()] or [sqlite3_prepare16_v2()] instead ** of the legacy [sqlite3_prepare()] and [sqlite3_prepare16()] interfaces, ** then the more specific [error codes] are returned directly ** by sqlite3_step(). The use of the "v2" interface is recommended. */ SQLITE_API int sqlite3_step(sqlite3_stmt*); /* ** CAPI3REF: Number of columns in a result set ** ** ^The sqlite3_data_count(P) interface returns the number of columns in the ** current row of the result set of [prepared statement] P. ** ^If prepared statement P does not have results ready to return ** (via calls to the [sqlite3_column_int | sqlite3_column_*()] of ** interfaces) then sqlite3_data_count(P) returns 0. ** ^The sqlite3_data_count(P) routine also returns 0 if P is a NULL pointer. ** ** See also: [sqlite3_column_count()] */ SQLITE_API int sqlite3_data_count(sqlite3_stmt *pStmt); /* ** CAPI3REF: Fundamental Datatypes ** KEYWORDS: SQLITE_TEXT ** ** ^(Every value in SQLite has one of five fundamental datatypes: ** **
    **
  • 64-bit signed integer **
  • 64-bit IEEE floating point number **
  • string **
  • BLOB **
  • NULL **
)^ ** ** These constants are codes for each of those types. ** ** Note that the SQLITE_TEXT constant was also used in SQLite version 2 ** for a completely different meaning. Software that links against both ** SQLite version 2 and SQLite version 3 should use SQLITE3_TEXT, not ** SQLITE_TEXT. */ #define SQLITE_INTEGER 1 #define SQLITE_FLOAT 2 #define SQLITE_BLOB 4 #define SQLITE_NULL 5 #ifdef SQLITE_TEXT # undef SQLITE_TEXT #else # define SQLITE_TEXT 3 #endif #define SQLITE3_TEXT 3 /* ** CAPI3REF: Result Values From A Query ** KEYWORDS: {column access functions} ** ** These routines form the "result set" interface. ** ** ^These routines return information about a single column of the current ** result row of a query. ^In every case the first argument is a pointer ** to the [prepared statement] that is being evaluated (the [sqlite3_stmt*] ** that was returned from [sqlite3_prepare_v2()] or one of its variants) ** and the second argument is the index of the column for which information ** should be returned. ^The leftmost column of the result set has the index 0. ** ^The number of columns in the result can be determined using ** [sqlite3_column_count()]. ** ** If the SQL statement does not currently point to a valid row, or if the ** column index is out of range, the result is undefined. ** These routines may only be called when the most recent call to ** [sqlite3_step()] has returned [SQLITE_ROW] and neither ** [sqlite3_reset()] nor [sqlite3_finalize()] have been called subsequently. ** If any of these routines are called after [sqlite3_reset()] or ** [sqlite3_finalize()] or after [sqlite3_step()] has returned ** something other than [SQLITE_ROW], the results are undefined. ** If [sqlite3_step()] or [sqlite3_reset()] or [sqlite3_finalize()] ** are called from a different thread while any of these routines ** are pending, then the results are undefined. ** ** ^The sqlite3_column_type() routine returns the ** [SQLITE_INTEGER | datatype code] for the initial data type ** of the result column. ^The returned value is one of [SQLITE_INTEGER], ** [SQLITE_FLOAT], [SQLITE_TEXT], [SQLITE_BLOB], or [SQLITE_NULL]. The value ** returned by sqlite3_column_type() is only meaningful if no type ** conversions have occurred as described below. After a type conversion, ** the value returned by sqlite3_column_type() is undefined. Future ** versions of SQLite may change the behavior of sqlite3_column_type() ** following a type conversion. ** ** ^If the result is a BLOB or UTF-8 string then the sqlite3_column_bytes() ** routine returns the number of bytes in that BLOB or string. ** ^If the result is a UTF-16 string, then sqlite3_column_bytes() converts ** the string to UTF-8 and then returns the number of bytes. ** ^If the result is a numeric value then sqlite3_column_bytes() uses ** [sqlite3_snprintf()] to convert that value to a UTF-8 string and returns ** the number of bytes in that string. ** ^If the result is NULL, then sqlite3_column_bytes() returns zero. ** ** ^If the result is a BLOB or UTF-16 string then the sqlite3_column_bytes16() ** routine returns the number of bytes in that BLOB or string. ** ^If the result is a UTF-8 string, then sqlite3_column_bytes16() converts ** the string to UTF-16 and then returns the number of bytes. ** ^If the result is a numeric value then sqlite3_column_bytes16() uses ** [sqlite3_snprintf()] to convert that value to a UTF-16 string and returns ** the number of bytes in that string. ** ^If the result is NULL, then sqlite3_column_bytes16() returns zero. ** ** ^The values returned by [sqlite3_column_bytes()] and ** [sqlite3_column_bytes16()] do not include the zero terminators at the end ** of the string. ^For clarity: the values returned by ** [sqlite3_column_bytes()] and [sqlite3_column_bytes16()] are the number of ** bytes in the string, not the number of characters. ** ** ^Strings returned by sqlite3_column_text() and sqlite3_column_text16(), ** even empty strings, are always zero terminated. ^The return ** value from sqlite3_column_blob() for a zero-length BLOB is a NULL pointer. ** ** ^The object returned by [sqlite3_column_value()] is an ** [unprotected sqlite3_value] object. An unprotected sqlite3_value object ** may only be used with [sqlite3_bind_value()] and [sqlite3_result_value()]. ** If the [unprotected sqlite3_value] object returned by ** [sqlite3_column_value()] is used in any other way, including calls ** to routines like [sqlite3_value_int()], [sqlite3_value_text()], ** or [sqlite3_value_bytes()], then the behavior is undefined. ** ** These routines attempt to convert the value where appropriate. ^For ** example, if the internal representation is FLOAT and a text result ** is requested, [sqlite3_snprintf()] is used internally to perform the ** conversion automatically. ^(The following table details the conversions ** that are applied: ** **
** **
Internal
Type 		Requested
Type 		Conversion ** **
NULL INTEGER Result is 0 **
NULL FLOAT Result is 0.0 **
NULL TEXT Result is NULL pointer **
NULL BLOB Result is NULL pointer **
INTEGER FLOAT Convert from integer to float **
INTEGER TEXT ASCII rendering of the integer **
INTEGER BLOB Same as INTEGER->TEXT **
FLOAT INTEGER Convert from float to integer **
FLOAT TEXT ASCII rendering of the float **
FLOAT BLOB Same as FLOAT->TEXT **
TEXT INTEGER Use atoi() **
TEXT FLOAT Use atof() **
TEXT BLOB No change **
BLOB INTEGER Convert to TEXT then use atoi() **
BLOB FLOAT Convert to TEXT then use atof() **
BLOB TEXT Add a zero terminator if needed **
**
)^ ** ** The table above makes reference to standard C library functions atoi() ** and atof(). SQLite does not really use these functions. It has its ** own equivalent internal routines. The atoi() and atof() names are ** used in the table for brevity and because they are familiar to most ** C programmers. ** ** Note that when type conversions occur, pointers returned by prior ** calls to sqlite3_column_blob(), sqlite3_column_text(), and/or ** sqlite3_column_text16() may be invalidated. ** Type conversions and pointer invalidations might occur ** in the following cases: ** **
    **
  • The initial content is a BLOB and sqlite3_column_text() or ** sqlite3_column_text16() is called. A zero-terminator might ** need to be added to the string.
    • **
  • The initial content is UTF-8 text and sqlite3_column_bytes16() or ** sqlite3_column_text16() is called. The content must be converted ** to UTF-16.
    • **
  • The initial content is UTF-16 text and sqlite3_column_bytes() or ** sqlite3_column_text() is called. The content must be converted ** to UTF-8.
    • **
** ** ^Conversions between UTF-16be and UTF-16le are always done in place and do ** not invalidate a prior pointer, though of course the content of the buffer ** that the prior pointer references will have been modified. Other kinds ** of conversion are done in place when it is possible, but sometimes they ** are not possible and in those cases prior pointers are invalidated. ** ** The safest and easiest to remember policy is to invoke these routines ** in one of the following ways: ** **
    **
  • sqlite3_column_text() followed by sqlite3_column_bytes()
    • **
  • sqlite3_column_blob() followed by sqlite3_column_bytes()
    • **
  • sqlite3_column_text16() followed by sqlite3_column_bytes16()
    • **
** ** In other words, you should call sqlite3_column_text(), ** sqlite3_column_blob(), or sqlite3_column_text16() first to force the result ** into the desired format, then invoke sqlite3_column_bytes() or ** sqlite3_column_bytes16() to find the size of the result. Do not mix calls ** to sqlite3_column_text() or sqlite3_column_blob() with calls to ** sqlite3_column_bytes16(), and do not mix calls to sqlite3_column_text16() ** with calls to sqlite3_column_bytes(). ** ** ^The pointers returned are valid until a type conversion occurs as ** described above, or until [sqlite3_step()] or [sqlite3_reset()] or ** [sqlite3_finalize()] is called. ^The memory space used to hold strings ** and BLOBs is freed automatically. Do not pass the pointers returned ** [sqlite3_column_blob()], [sqlite3_column_text()], etc. into ** [sqlite3_free()]. ** ** ^(If a memory allocation error occurs during the evaluation of any ** of these routines, a default value is returned. The default value ** is either the integer 0, the floating point number 0.0, or a NULL ** pointer. Subsequent calls to [sqlite3_errcode()] will return ** [SQLITE_NOMEM].)^ */ SQLITE_API const void *sqlite3_column_blob(sqlite3_stmt*, int iCol); SQLITE_API int sqlite3_column_bytes(sqlite3_stmt*, int iCol); SQLITE_API int sqlite3_column_bytes16(sqlite3_stmt*, int iCol); SQLITE_API double sqlite3_column_double(sqlite3_stmt*, int iCol); SQLITE_API int sqlite3_column_int(sqlite3_stmt*, int iCol); SQLITE_API sqlite3_int64 sqlite3_column_int64(sqlite3_stmt*, int iCol); SQLITE_API const unsigned char *sqlite3_column_text(sqlite3_stmt*, int iCol); SQLITE_API const void *sqlite3_column_text16(sqlite3_stmt*, int iCol); SQLITE_API int sqlite3_column_type(sqlite3_stmt*, int iCol); SQLITE_API sqlite3_value *sqlite3_column_value(sqlite3_stmt*, int iCol); /* ** CAPI3REF: Destroy A Prepared Statement Object ** ** ^The sqlite3_finalize() function is called to delete a [prepared statement]. ** ^If the most recent evaluation of the statement encountered no errors ** or if the statement is never been evaluated, then sqlite3_finalize() returns ** SQLITE_OK. ^If the most recent evaluation of statement S failed, then ** sqlite3_finalize(S) returns the appropriate [error code] or ** [extended error code]. ** ** ^The sqlite3_finalize(S) routine can be called at any point during ** the life cycle of [prepared statement] S: ** before statement S is ever evaluated, after ** one or more calls to [sqlite3_reset()], or after any call ** to [sqlite3_step()] regardless of whether or not the statement has ** completed execution. ** ** ^Invoking sqlite3_finalize() on a NULL pointer is a harmless no-op. ** ** The application must finalize every [prepared statement] in order to avoid ** resource leaks. It is a grievous error for the application to try to use ** a prepared statement after it has been finalized. Any use of a prepared ** statement after it has been finalized can result in undefined and ** undesirable behavior such as segfaults and heap corruption. */ SQLITE_API int sqlite3_finalize(sqlite3_stmt *pStmt); /* ** CAPI3REF: Reset A Prepared Statement Object ** ** The sqlite3_reset() function is called to reset a [prepared statement] ** object back to its initial state, ready to be re-executed. ** ^Any SQL statement variables that had values bound to them using ** the [sqlite3_bind_blob | sqlite3_bind_*() API] retain their values. ** Use [sqlite3_clear_bindings()] to reset the bindings. ** ** ^The [sqlite3_reset(S)] interface resets the [prepared statement] S ** back to the beginning of its program. ** ** ^If the most recent call to [sqlite3_step(S)] for the ** [prepared statement] S returned [SQLITE_ROW] or [SQLITE_DONE], ** or if [sqlite3_step(S)] has never before been called on S, ** then [sqlite3_reset(S)] returns [SQLITE_OK]. ** ** ^If the most recent call to [sqlite3_step(S)] for the ** [prepared statement] S indicated an error, then ** [sqlite3_reset(S)] returns an appropriate [error code]. ** ** ^The [sqlite3_reset(S)] interface does not change the values ** of any [sqlite3_bind_blob|bindings] on the [prepared statement] S. */ SQLITE_API int sqlite3_reset(sqlite3_stmt *pStmt); /* ** CAPI3REF: Create Or Redefine SQL Functions ** KEYWORDS: {function creation routines} ** KEYWORDS: {application-defined SQL function} ** KEYWORDS: {application-defined SQL functions} ** ** ^These functions (collectively known as "function creation routines") ** are used to add SQL functions or aggregates or to redefine the behavior ** of existing SQL functions or aggregates. The only differences between ** these routines are the text encoding expected for ** the second parameter (the name of the function being created) ** and the presence or absence of a destructor callback for ** the application data pointer. ** ** ^The first parameter is the [database connection] to which the SQL ** function is to be added. ^If an application uses more than one database ** connection then application-defined SQL functions must be added ** to each database connection separately. ** ** ^The second parameter is the name of the SQL function to be created or ** redefined. ^The length of the name is limited to 255 bytes in a UTF-8 ** representation, exclusive of the zero-terminator. ^Note that the name ** length limit is in UTF-8 bytes, not characters nor UTF-16 bytes. ** ^Any attempt to create a function with a longer name ** will result in [SQLITE_MISUSE] being returned. ** ** ^The third parameter (nArg) ** is the number of arguments that the SQL function or ** aggregate takes. ^If this parameter is -1, then the SQL function or ** aggregate may take any number of arguments between 0 and the limit ** set by [sqlite3_limit]([SQLITE_LIMIT_FUNCTION_ARG]). If the third ** parameter is less than -1 or greater than 127 then the behavior is ** undefined. ** ** ^The fourth parameter, eTextRep, specifies what ** [SQLITE_UTF8 | text encoding] this SQL function prefers for ** its parameters. Every SQL function implementation must be able to work ** with UTF-8, UTF-16le, or UTF-16be. But some implementations may be ** more efficient with one encoding than another. ^An application may ** invoke sqlite3_create_function() or sqlite3_create_function16() multiple ** times with the same function but with different values of eTextRep. ** ^When multiple implementations of the same function are available, SQLite ** will pick the one that involves the least amount of data conversion. ** If there is only a single implementation which does not care what text ** encoding is used, then the fourth argument should be [SQLITE_ANY]. ** ** ^(The fifth parameter is an arbitrary pointer. The implementation of the ** function can gain access to this pointer using [sqlite3_user_data()].)^ ** ** ^The sixth, seventh and eighth parameters, xFunc, xStep and xFinal, are ** pointers to C-language functions that implement the SQL function or ** aggregate. ^A scalar SQL function requires an implementation of the xFunc ** callback only; NULL pointers must be passed as the xStep and xFinal ** parameters. ^An aggregate SQL function requires an implementation of xStep ** and xFinal and NULL pointer must be passed for xFunc. ^To delete an existing ** SQL function or aggregate, pass NULL pointers for all three function ** callbacks. ** ** ^(If the ninth parameter to sqlite3_create_function_v2() is not NULL, ** then it is destructor for the application data pointer. ** The destructor is invoked when the function is deleted, either by being ** overloaded or when the database connection closes.)^ ** ^The destructor is also invoked if the call to ** sqlite3_create_function_v2() fails. ** ^When the destructor callback of the tenth parameter is invoked, it ** is passed a single argument which is a copy of the application data ** pointer which was the fifth parameter to sqlite3_create_function_v2(). ** ** ^It is permitted to register multiple implementations of the same ** functions with the same name but with either differing numbers of ** arguments or differing preferred text encodings. ^SQLite will use ** the implementation that most closely matches the way in which the ** SQL function is used. ^A function implementation with a non-negative ** nArg parameter is a better match than a function implementation with ** a negative nArg. ^A function where the preferred text encoding ** matches the database encoding is a better ** match than a function where the encoding is different. ** ^A function where the encoding difference is between UTF16le and UTF16be ** is a closer match than a function where the encoding difference is ** between UTF8 and UTF16. ** ** ^Built-in functions may be overloaded by new application-defined functions. ** ** ^An application-defined function is permitted to call other ** SQLite interfaces. However, such calls must not ** close the database connection nor finalize or reset the prepared ** statement in which the function is running. */ SQLITE_API int sqlite3_create_function( sqlite3 *db, const char *zFunctionName, int nArg, int eTextRep, void *pApp, void (*xFunc)(sqlite3_context*,int,sqlite3_value**), void (*xStep)(sqlite3_context*,int,sqlite3_value**), void (*xFinal)(sqlite3_context*) ); SQLITE_API int sqlite3_create_function16( sqlite3 *db, const void *zFunctionName, int nArg, int eTextRep, void *pApp, void (*xFunc)(sqlite3_context*,int,sqlite3_value**), void (*xStep)(sqlite3_context*,int,sqlite3_value**), void (*xFinal)(sqlite3_context*) ); SQLITE_API int sqlite3_create_function_v2( sqlite3 *db, const char *zFunctionName, int nArg, int eTextRep, void *pApp, void (*xFunc)(sqlite3_context*,int,sqlite3_value**), void (*xStep)(sqlite3_context*,int,sqlite3_value**), void (*xFinal)(sqlite3_context*), void(*xDestroy)(void*) ); /* ** CAPI3REF: Text Encodings ** ** These constant define integer codes that represent the various ** text encodings supported by SQLite. */ #define SQLITE_UTF8 1 #define SQLITE_UTF16LE 2 #define SQLITE_UTF16BE 3 #define SQLITE_UTF16 4 /* Use native byte order */ #define SQLITE_ANY 5 /* sqlite3_create_function only */ #define SQLITE_UTF16_ALIGNED 8 /* sqlite3_create_collation only */ /* ** CAPI3REF: Deprecated Functions ** DEPRECATED ** ** These functions are [deprecated]. In order to maintain ** backwards compatibility with older code, these functions continue ** to be supported. However, new applications should avoid ** the use of these functions. To help encourage people to avoid ** using these functions, we are not going to tell you what they do. */ #ifndef SQLITE_OMIT_DEPRECATED SQLITE_API SQLITE_DEPRECATED int sqlite3_aggregate_count(sqlite3_context*); SQLITE_API SQLITE_DEPRECATED int sqlite3_expired(sqlite3_stmt*); SQLITE_API SQLITE_DEPRECATED int sqlite3_transfer_bindings(sqlite3_stmt*, sqlite3_stmt*); SQLITE_API SQLITE_DEPRECATED int sqlite3_global_recover(void); SQLITE_API SQLITE_DEPRECATED void sqlite3_thread_cleanup(void); SQLITE_API SQLITE_DEPRECATED int sqlite3_memory_alarm(void(*)(void*,sqlite3_int64,int),void*,sqlite3_int64); #endif /* ** CAPI3REF: Obtaining SQL Function Parameter Values ** ** The C-language implementation of SQL functions and aggregates uses ** this set of interface routines to access the parameter values on ** the function or aggregate. ** ** The xFunc (for scalar functions) or xStep (for aggregates) parameters ** to [sqlite3_create_function()] and [sqlite3_create_function16()] ** define callbacks that implement the SQL functions and aggregates. ** The 3rd parameter to these callbacks is an array of pointers to ** [protected sqlite3_value] objects. There is one [sqlite3_value] object for ** each parameter to the SQL function. These routines are used to ** extract values from the [sqlite3_value] objects. ** ** These routines work only with [protected sqlite3_value] objects. ** Any attempt to use these routines on an [unprotected sqlite3_value] ** object results in undefined behavior. ** ** ^These routines work just like the corresponding [column access functions] ** except that these routines take a single [protected sqlite3_value] object ** pointer instead of a [sqlite3_stmt*] pointer and an integer column number. ** ** ^The sqlite3_value_text16() interface extracts a UTF-16 string ** in the native byte-order of the host machine. ^The ** sqlite3_value_text16be() and sqlite3_value_text16le() interfaces ** extract UTF-16 strings as big-endian and little-endian respectively. ** ** ^(The sqlite3_value_numeric_type() interface attempts to apply ** numeric affinity to the value. This means that an attempt is ** made to convert the value to an integer or floating point. If ** such a conversion is possible without loss of information (in other ** words, if the value is a string that looks like a number) ** then the conversion is performed. Otherwise no conversion occurs. ** The [SQLITE_INTEGER | datatype] after conversion is returned.)^ ** ** Please pay particular attention to the fact that the pointer returned ** from [sqlite3_value_blob()], [sqlite3_value_text()], or ** [sqlite3_value_text16()] can be invalidated by a subsequent call to ** [sqlite3_value_bytes()], [sqlite3_value_bytes16()], [sqlite3_value_text()], ** or [sqlite3_value_text16()]. ** ** These routines must be called from the same thread as ** the SQL function that supplied the [sqlite3_value*] parameters. */ SQLITE_API const void *sqlite3_value_blob(sqlite3_value*); SQLITE_API int sqlite3_value_bytes(sqlite3_value*); SQLITE_API int sqlite3_value_bytes16(sqlite3_value*); SQLITE_API double sqlite3_value_double(sqlite3_value*); SQLITE_API int sqlite3_value_int(sqlite3_value*); SQLITE_API sqlite3_int64 sqlite3_value_int64(sqlite3_value*); SQLITE_API const unsigned char *sqlite3_value_text(sqlite3_value*); SQLITE_API const void *sqlite3_value_text16(sqlite3_value*); SQLITE_API const void *sqlite3_value_text16le(sqlite3_value*); SQLITE_API const void *sqlite3_value_text16be(sqlite3_value*); SQLITE_API int sqlite3_value_type(sqlite3_value*); SQLITE_API int sqlite3_value_numeric_type(sqlite3_value*); /* ** CAPI3REF: Obtain Aggregate Function Context ** ** Implementations of aggregate SQL functions use this ** routine to allocate memory for storing their state. ** ** ^The first time the sqlite3_aggregate_context(C,N) routine is called ** for a particular aggregate function, SQLite ** allocates N of memory, zeroes out that memory, and returns a pointer ** to the new memory. ^On second and subsequent calls to ** sqlite3_aggregate_context() for the same aggregate function instance, ** the same buffer is returned. Sqlite3_aggregate_context() is normally ** called once for each invocation of the xStep callback and then one ** last time when the xFinal callback is invoked. ^(When no rows match ** an aggregate query, the xStep() callback of the aggregate function ** implementation is never called and xFinal() is called exactly once. ** In those cases, sqlite3_aggregate_context() might be called for the ** first time from within xFinal().)^ ** ** ^The sqlite3_aggregate_context(C,N) routine returns a NULL pointer if N is ** less than or equal to zero or if a memory allocate error occurs. ** ** ^(The amount of space allocated by sqlite3_aggregate_context(C,N) is ** determined by the N parameter on first successful call. Changing the ** value of N in subsequent call to sqlite3_aggregate_context() within ** the same aggregate function instance will not resize the memory ** allocation.)^ ** ** ^SQLite automatically frees the memory allocated by ** sqlite3_aggregate_context() when the aggregate query concludes. ** ** The first parameter must be a copy of the ** [sqlite3_context | SQL function context] that is the first parameter ** to the xStep or xFinal callback routine that implements the aggregate ** function. ** ** This routine must be called from the same thread in which ** the aggregate SQL function is running. */ SQLITE_API void *sqlite3_aggregate_context(sqlite3_context*, int nBytes); /* ** CAPI3REF: User Data For Functions ** ** ^The sqlite3_user_data() interface returns a copy of ** the pointer that was the pUserData parameter (the 5th parameter) ** of the [sqlite3_create_function()] ** and [sqlite3_create_function16()] routines that originally ** registered the application defined function. ** ** This routine must be called from the same thread in which ** the application-defined function is running. */ SQLITE_API void *sqlite3_user_data(sqlite3_context*); /* ** CAPI3REF: Database Connection For Functions ** ** ^The sqlite3_context_db_handle() interface returns a copy of ** the pointer to the [database connection] (the 1st parameter) ** of the [sqlite3_create_function()] ** and [sqlite3_create_function16()] routines that originally ** registered the application defined function. */ SQLITE_API sqlite3 *sqlite3_context_db_handle(sqlite3_context*); /* ** CAPI3REF: Function Auxiliary Data ** ** The following two functions may be used by scalar SQL functions to ** associate metadata with argument values. If the same value is passed to ** multiple invocations of the same SQL function during query execution, under ** some circumstances the associated metadata may be preserved. This may ** be used, for example, to add a regular-expression matching scalar ** function. The compiled version of the regular expression is stored as ** metadata associated with the SQL value passed as the regular expression ** pattern. The compiled regular expression can be reused on multiple ** invocations of the same function so that the original pattern string ** does not need to be recompiled on each invocation. ** ** ^The sqlite3_get_auxdata() interface returns a pointer to the metadata ** associated by the sqlite3_set_auxdata() function with the Nth argument ** value to the application-defined function. ^If no metadata has been ever ** been set for the Nth argument of the function, or if the corresponding ** function parameter has changed since the meta-data was set, ** then sqlite3_get_auxdata() returns a NULL pointer. ** ** ^The sqlite3_set_auxdata() interface saves the metadata ** pointed to by its 3rd parameter as the metadata for the N-th ** argument of the application-defined function. Subsequent ** calls to sqlite3_get_auxdata() might return this data, if it has ** not been destroyed. ** ^If it is not NULL, SQLite will invoke the destructor ** function given by the 4th parameter to sqlite3_set_auxdata() on ** the metadata when the corresponding function parameter changes ** or when the SQL statement completes, whichever comes first. ** ** SQLite is free to call the destructor and drop metadata on any ** parameter of any function at any time. ^The only guarantee is that ** the destructor will be called before the metadata is dropped. ** ** ^(In practice, metadata is preserved between function calls for ** expressions that are constant at compile time. This includes literal ** values and [parameters].)^ ** ** These routines must be called from the same thread in which ** the SQL function is running. */ SQLITE_API void *sqlite3_get_auxdata(sqlite3_context*, int N); SQLITE_API void sqlite3_set_auxdata(sqlite3_context*, int N, void*, void (*)(void*)); /* ** CAPI3REF: Constants Defining Special Destructor Behavior ** ** These are special values for the destructor that is passed in as the ** final argument to routines like [sqlite3_result_blob()]. ^If the destructor ** argument is SQLITE_STATIC, it means that the content pointer is constant ** and will never change. It does not need to be destroyed. ^The ** SQLITE_TRANSIENT value means that the content will likely change in ** the near future and that SQLite should make its own private copy of ** the content before returning. ** ** The typedef is necessary to work around problems in certain ** C++ compilers. See ticket #2191. */ typedef void (*sqlite3_destructor_type)(void*); #define SQLITE_STATIC ((sqlite3_destructor_type)0) #define SQLITE_TRANSIENT ((sqlite3_destructor_type)-1) /* ** CAPI3REF: Setting The Result Of An SQL Function ** ** These routines are used by the xFunc or xFinal callbacks that ** implement SQL functions and aggregates. See ** [sqlite3_create_function()] and [sqlite3_create_function16()] ** for additional information. ** ** These functions work very much like the [parameter binding] family of ** functions used to bind values to host parameters in prepared statements. ** Refer to the [SQL parameter] documentation for additional information. ** ** ^The sqlite3_result_blob() interface sets the result from ** an application-defined function to be the BLOB whose content is pointed ** to by the second parameter and which is N bytes long where N is the ** third parameter. ** ** ^The sqlite3_result_zeroblob() interfaces set the result of ** the application-defined function to be a BLOB containing all zero ** bytes and N bytes in size, where N is the value of the 2nd parameter. ** ** ^The sqlite3_result_double() interface sets the result from ** an application-defined function to be a floating point value specified ** by its 2nd argument. ** ** ^The sqlite3_result_error() and sqlite3_result_error16() functions ** cause the implemented SQL function to throw an exception. ** ^SQLite uses the string pointed to by the ** 2nd parameter of sqlite3_result_error() or sqlite3_result_error16() ** as the text of an error message. ^SQLite interprets the error ** message string from sqlite3_result_error() as UTF-8. ^SQLite ** interprets the string from sqlite3_result_error16() as UTF-16 in native ** byte order. ^If the third parameter to sqlite3_result_error() ** or sqlite3_result_error16() is negative then SQLite takes as the error ** message all text up through the first zero character. ** ^If the third parameter to sqlite3_result_error() or ** sqlite3_result_error16() is non-negative then SQLite takes that many ** bytes (not characters) from the 2nd parameter as the error message. ** ^The sqlite3_result_error() and sqlite3_result_error16() ** routines make a private copy of the error message text before ** they return. Hence, the calling function can deallocate or ** modify the text after they return without harm. ** ^The sqlite3_result_error_code() function changes the error code ** returned by SQLite as a result of an error in a function. ^By default, ** the error code is SQLITE_ERROR. ^A subsequent call to sqlite3_result_error() ** or sqlite3_result_error16() resets the error code to SQLITE_ERROR. ** ** ^The sqlite3_result_toobig() interface causes SQLite to throw an error ** indicating that a string or BLOB is too long to represent. ** ** ^The sqlite3_result_nomem() interface causes SQLite to throw an error ** indicating that a memory allocation failed. ** ** ^The sqlite3_result_int() interface sets the return value ** of the application-defined function to be the 32-bit signed integer ** value given in the 2nd argument. ** ^The sqlite3_result_int64() interface sets the return value ** of the application-defined function to be the 64-bit signed integer ** value given in the 2nd argument. ** ** ^The sqlite3_result_null() interface sets the return value ** of the application-defined function to be NULL. ** ** ^The sqlite3_result_text(), sqlite3_result_text16(), ** sqlite3_result_text16le(), and sqlite3_result_text16be() interfaces ** set the return value of the application-defined function to be ** a text string which is represented as UTF-8, UTF-16 native byte order, ** UTF-16 little endian, or UTF-16 big endian, respectively. ** ^SQLite takes the text result from the application from ** the 2nd parameter of the sqlite3_result_text* interfaces. ** ^If the 3rd parameter to the sqlite3_result_text* interfaces ** is negative, then SQLite takes result text from the 2nd parameter ** through the first zero character. ** ^If the 3rd parameter to the sqlite3_result_text* interfaces ** is non-negative, then as many bytes (not characters) of the text ** pointed to by the 2nd parameter are taken as the application-defined ** function result. ** ^If the 4th parameter to the sqlite3_result_text* interfaces ** or sqlite3_result_blob is a non-NULL pointer, then SQLite calls that ** function as the destructor on the text or BLOB result when it has ** finished using that result. ** ^If the 4th parameter to the sqlite3_result_text* interfaces or to ** sqlite3_result_blob is the special constant SQLITE_STATIC, then SQLite ** assumes that the text or BLOB result is in constant space and does not ** copy the content of the parameter nor call a destructor on the content ** when it has finished using that result. ** ^If the 4th parameter to the sqlite3_result_text* interfaces ** or sqlite3_result_blob is the special constant SQLITE_TRANSIENT ** then SQLite makes a copy of the result into space obtained from ** from [sqlite3_malloc()] before it returns. ** ** ^The sqlite3_result_value() interface sets the result of ** the application-defined function to be a copy the ** [unprotected sqlite3_value] object specified by the 2nd parameter. ^The ** sqlite3_result_value() interface makes a copy of the [sqlite3_value] ** so that the [sqlite3_value] specified in the parameter may change or ** be deallocated after sqlite3_result_value() returns without harm. ** ^A [protected sqlite3_value] object may always be used where an ** [unprotected sqlite3_value] object is required, so either ** kind of [sqlite3_value] object can be used with this interface. ** ** If these routines are called from within the different thread ** than the one containing the application-defined function that received ** the [sqlite3_context] pointer, the results are undefined. */ SQLITE_API void sqlite3_result_blob(sqlite3_context*, const void*, int, void(*)(void*)); SQLITE_API void sqlite3_result_double(sqlite3_context*, double); SQLITE_API void sqlite3_result_error(sqlite3_context*, const char*, int); SQLITE_API void sqlite3_result_error16(sqlite3_context*, const void*, int); SQLITE_API void sqlite3_result_error_toobig(sqlite3_context*); SQLITE_API void sqlite3_result_error_nomem(sqlite3_context*); SQLITE_API void sqlite3_result_error_code(sqlite3_context*, int); SQLITE_API void sqlite3_result_int(sqlite3_context*, int); SQLITE_API void sqlite3_result_int64(sqlite3_context*, sqlite3_int64); SQLITE_API void sqlite3_result_null(sqlite3_context*); SQLITE_API void sqlite3_result_text(sqlite3_context*, const char*, int, void(*)(void*)); SQLITE_API void sqlite3_result_text16(sqlite3_context*, const void*, int, void(*)(void*)); SQLITE_API void sqlite3_result_text16le(sqlite3_context*, const void*, int,void(*)(void*)); SQLITE_API void sqlite3_result_text16be(sqlite3_context*, const void*, int,void(*)(void*)); SQLITE_API void sqlite3_result_value(sqlite3_context*, sqlite3_value*); SQLITE_API void sqlite3_result_zeroblob(sqlite3_context*, int n); /* ** CAPI3REF: Define New Collating Sequences ** ** ^These functions add, remove, or modify a [collation] associated ** with the [database connection] specified as the first argument. ** ** ^The name of the collation is a UTF-8 string ** for sqlite3_create_collation() and sqlite3_create_collation_v2() ** and a UTF-16 string in native byte order for sqlite3_create_collation16(). ** ^Collation names that compare equal according to [sqlite3_strnicmp()] are ** considered to be the same name. ** ** ^(The third argument (eTextRep) must be one of the constants: **
    **
  • [SQLITE_UTF8], **
  • [SQLITE_UTF16LE], **
  • [SQLITE_UTF16BE], **
  • [SQLITE_UTF16], or **
  • [SQLITE_UTF16_ALIGNED]. **
)^ ** ^The eTextRep argument determines the encoding of strings passed ** to the collating function callback, xCallback. ** ^The [SQLITE_UTF16] and [SQLITE_UTF16_ALIGNED] values for eTextRep ** force strings to be UTF16 with native byte order. ** ^The [SQLITE_UTF16_ALIGNED] value for eTextRep forces strings to begin ** on an even byte address. ** ** ^The fourth argument, pArg, is an application data pointer that is passed ** through as the first argument to the collating function callback. ** ** ^The fifth argument, xCallback, is a pointer to the collating function. ** ^Multiple collating functions can be registered using the same name but ** with different eTextRep parameters and SQLite will use whichever ** function requires the least amount of data transformation. ** ^If the xCallback argument is NULL then the collating function is ** deleted. ^When all collating functions having the same name are deleted, ** that collation is no longer usable. ** ** ^The collating function callback is invoked with a copy of the pArg ** application data pointer and with two strings in the encoding specified ** by the eTextRep argument. The collating function must return an ** integer that is negative, zero, or positive ** if the first string is less than, equal to, or greater than the second, ** respectively. A collating function must always return the same answer ** given the same inputs. If two or more collating functions are registered ** to the same collation name (using different eTextRep values) then all ** must give an equivalent answer when invoked with equivalent strings. ** The collating function must obey the following properties for all ** strings A, B, and C: ** **
    **
  1. If A==B then B==A. **
  2. If A==B and B==C then A==C. **
  3. If A<B THEN B>A. **
  4. If A<B and B<C then A<C. **
** ** If a collating function fails any of the above constraints and that ** collating function is registered and used, then the behavior of SQLite ** is undefined. ** ** ^The sqlite3_create_collation_v2() works like sqlite3_create_collation() ** with the addition that the xDestroy callback is invoked on pArg when ** the collating function is deleted. ** ^Collating functions are deleted when they are overridden by later ** calls to the collation creation functions or when the ** [database connection] is closed using [sqlite3_close()]. ** ** ^The xDestroy callback is not called if the ** sqlite3_create_collation_v2() function fails. Applications that invoke ** sqlite3_create_collation_v2() with a non-NULL xDestroy argument should ** check the return code and dispose of the application data pointer ** themselves rather than expecting SQLite to deal with it for them. ** This is different from every other SQLite interface. The inconsistency ** is unfortunate but cannot be changed without breaking backwards ** compatibility. ** ** See also: [sqlite3_collation_needed()] and [sqlite3_collation_needed16()]. */ SQLITE_API int sqlite3_create_collation( sqlite3*, const char *zName, int eTextRep, void *pArg, int(*xCompare)(void*,int,const void*,int,const void*) ); SQLITE_API int sqlite3_create_collation_v2( sqlite3*, const char *zName, int eTextRep, void *pArg, int(*xCompare)(void*,int,const void*,int,const void*), void(*xDestroy)(void*) ); SQLITE_API int sqlite3_create_collation16( sqlite3*, const void *zName, int eTextRep, void *pArg, int(*xCompare)(void*,int,const void*,int,const void*) ); /* ** CAPI3REF: Collation Needed Callbacks ** ** ^To avoid having to register all collation sequences before a database ** can be used, a single callback function may be registered with the ** [database connection] to be invoked whenever an undefined collation ** sequence is required. ** ** ^If the function is registered using the sqlite3_collation_needed() API, ** then it is passed the names of undefined collation sequences as strings ** encoded in UTF-8. ^If sqlite3_collation_needed16() is used, ** the names are passed as UTF-16 in machine native byte order. ** ^A call to either function replaces the existing collation-needed callback. ** ** ^(When the callback is invoked, the first argument passed is a copy ** of the second argument to sqlite3_collation_needed() or ** sqlite3_collation_needed16(). The second argument is the database ** connection. The third argument is one of [SQLITE_UTF8], [SQLITE_UTF16BE], ** or [SQLITE_UTF16LE], indicating the most desirable form of the collation ** sequence function required. The fourth parameter is the name of the ** required collation sequence.)^ ** ** The callback function should register the desired collation using ** [sqlite3_create_collation()], [sqlite3_create_collation16()], or ** [sqlite3_create_collation_v2()]. */ SQLITE_API int sqlite3_collation_needed( sqlite3*, void*, void(*)(void*,sqlite3*,int eTextRep,const char*) ); SQLITE_API int sqlite3_collation_needed16( sqlite3*, void*, void(*)(void*,sqlite3*,int eTextRep,const void*) ); #ifdef SQLITE_HAS_CODEC /* ** Specify the key for an encrypted database. This routine should be ** called right after sqlite3_open(). ** ** The code to implement this API is not available in the public release ** of SQLite. */ SQLITE_API int sqlite3_key( sqlite3 *db, /* Database to be rekeyed */ const void *pKey, int nKey /* The key */ ); /* ** Change the key on an open database. If the current database is not ** encrypted, this routine will encrypt it. If pNew==0 or nNew==0, the ** database is decrypted. ** ** The code to implement this API is not available in the public release ** of SQLite. */ SQLITE_API int sqlite3_rekey( sqlite3 *db, /* Database to be rekeyed */ const void *pKey, int nKey /* The new key */ ); /* ** Specify the activation key for a SEE database. Unless ** activated, none of the SEE routines will work. */ SQLITE_API void sqlite3_activate_see( const char *zPassPhrase /* Activation phrase */ ); #endif #ifdef SQLITE_ENABLE_CEROD /* ** Specify the activation key for a CEROD database. Unless ** activated, none of the CEROD routines will work. */ SQLITE_API void sqlite3_activate_cerod( const char *zPassPhrase /* Activation phrase */ ); #endif /* ** CAPI3REF: Suspend Execution For A Short Time ** ** The sqlite3_sleep() function causes the current thread to suspend execution ** for at least a number of milliseconds specified in its parameter. ** ** If the operating system does not support sleep requests with ** millisecond time resolution, then the time will be rounded up to ** the nearest second. The number of milliseconds of sleep actually ** requested from the operating system is returned. ** ** ^SQLite implements this interface by calling the xSleep() ** method of the default [sqlite3_vfs] object. If the xSleep() method ** of the default VFS is not implemented correctly, or not implemented at ** all, then the behavior of sqlite3_sleep() may deviate from the description ** in the previous paragraphs. */ SQLITE_API int sqlite3_sleep(int); /* ** CAPI3REF: Name Of The Folder Holding Temporary Files ** ** ^(If this global variable is made to point to a string which is ** the name of a folder (a.k.a. directory), then all temporary files ** created by SQLite when using a built-in [sqlite3_vfs | VFS] ** will be placed in that directory.)^ ^If this variable ** is a NULL pointer, then SQLite performs a search for an appropriate ** temporary file directory. ** ** It is not safe to read or modify this variable in more than one ** thread at a time. It is not safe to read or modify this variable ** if a [database connection] is being used at the same time in a separate ** thread. ** It is intended that this variable be set once ** as part of process initialization and before any SQLite interface ** routines have been called and that this variable remain unchanged ** thereafter. ** ** ^The [temp_store_directory pragma] may modify this variable and cause ** it to point to memory obtained from [sqlite3_malloc]. ^Furthermore, ** the [temp_store_directory pragma] always assumes that any string ** that this variable points to is held in memory obtained from ** [sqlite3_malloc] and the pragma may attempt to free that memory ** using [sqlite3_free]. ** Hence, if this variable is modified directly, either it should be ** made NULL or made to point to memory obtained from [sqlite3_malloc] ** or else the use of the [temp_store_directory pragma] should be avoided. */ SQLITE_API SQLITE_EXTERN char *sqlite3_temp_directory; /* ** CAPI3REF: Test For Auto-Commit Mode ** KEYWORDS: {autocommit mode} ** ** ^The sqlite3_get_autocommit() interface returns non-zero or ** zero if the given database connection is or is not in autocommit mode, ** respectively. ^Autocommit mode is on by default. ** ^Autocommit mode is disabled by a [BEGIN] statement. ** ^Autocommit mode is re-enabled by a [COMMIT] or [ROLLBACK]. ** ** If certain kinds of errors occur on a statement within a multi-statement ** transaction (errors including [SQLITE_FULL], [SQLITE_IOERR], ** [SQLITE_NOMEM], [SQLITE_BUSY], and [SQLITE_INTERRUPT]) then the ** transaction might be rolled back automatically. The only way to ** find out whether SQLite automatically rolled back the transaction after ** an error is to use this function. ** ** If another thread changes the autocommit status of the database ** connection while this routine is running, then the return value ** is undefined. */ SQLITE_API int sqlite3_get_autocommit(sqlite3*); /* ** CAPI3REF: Find The Database Handle Of A Prepared Statement ** ** ^The sqlite3_db_handle interface returns the [database connection] handle ** to which a [prepared statement] belongs. ^The [database connection] ** returned by sqlite3_db_handle is the same [database connection] ** that was the first argument ** to the [sqlite3_prepare_v2()] call (or its variants) that was used to ** create the statement in the first place. */ SQLITE_API sqlite3 *sqlite3_db_handle(sqlite3_stmt*); /* ** CAPI3REF: Find the next prepared statement ** ** ^This interface returns a pointer to the next [prepared statement] after ** pStmt associated with the [database connection] pDb. ^If pStmt is NULL ** then this interface returns a pointer to the first prepared statement ** associated with the database connection pDb. ^If no prepared statement ** satisfies the conditions of this routine, it returns NULL. ** ** The [database connection] pointer D in a call to ** [sqlite3_next_stmt(D,S)] must refer to an open database ** connection and in particular must not be a NULL pointer. */ SQLITE_API sqlite3_stmt *sqlite3_next_stmt(sqlite3 *pDb, sqlite3_stmt *pStmt); /* ** CAPI3REF: Commit And Rollback Notification Callbacks ** ** ^The sqlite3_commit_hook() interface registers a callback ** function to be invoked whenever a transaction is [COMMIT | committed]. ** ^Any callback set by a previous call to sqlite3_commit_hook() ** for the same database connection is overridden. ** ^The sqlite3_rollback_hook() interface registers a callback ** function to be invoked whenever a transaction is [ROLLBACK | rolled back]. ** ^Any callback set by a previous call to sqlite3_rollback_hook() ** for the same database connection is overridden. ** ^The pArg argument is passed through to the callback. ** ^If the callback on a commit hook function returns non-zero, ** then the commit is converted into a rollback. ** ** ^The sqlite3_commit_hook(D,C,P) and sqlite3_rollback_hook(D,C,P) functions ** return the P argument from the previous call of the same function ** on the same [database connection] D, or NULL for ** the first call for each function on D. ** ** The callback implementation must not do anything that will modify ** the database connection that invoked the callback. Any actions ** to modify the database connection must be deferred until after the ** completion of the [sqlite3_step()] call that triggered the commit ** or rollback hook in the first place. ** Note that [sqlite3_prepare_v2()] and [sqlite3_step()] both modify their ** database connections for the meaning of "modify" in this paragraph. ** ** ^Registering a NULL function disables the callback. ** ** ^When the commit hook callback routine returns zero, the [COMMIT] ** operation is allowed to continue normally. ^If the commit hook ** returns non-zero, then the [COMMIT] is converted into a [ROLLBACK]. ** ^The rollback hook is invoked on a rollback that results from a commit ** hook returning non-zero, just as it would be with any other rollback. ** ** ^For the purposes of this API, a transaction is said to have been ** rolled back if an explicit "ROLLBACK" statement is executed, or ** an error or constraint causes an implicit rollback to occur. ** ^The rollback callback is not invoked if a transaction is ** automatically rolled back because the database connection is closed. ** ** See also the [sqlite3_update_hook()] interface. */ SQLITE_API void *sqlite3_commit_hook(sqlite3*, int(*)(void*), void*); SQLITE_API void *sqlite3_rollback_hook(sqlite3*, void(*)(void *), void*); /* ** CAPI3REF: Data Change Notification Callbacks ** ** ^The sqlite3_update_hook() interface registers a callback function ** with the [database connection] identified by the first argument ** to be invoked whenever a row is updated, inserted or deleted. ** ^Any callback set by a previous call to this function ** for the same database connection is overridden. ** ** ^The second argument is a pointer to the function to invoke when a ** row is updated, inserted or deleted. ** ^The first argument to the callback is a copy of the third argument ** to sqlite3_update_hook(). ** ^The second callback argument is one of [SQLITE_INSERT], [SQLITE_DELETE], ** or [SQLITE_UPDATE], depending on the operation that caused the callback ** to be invoked. ** ^The third and fourth arguments to the callback contain pointers to the ** database and table name containing the affected row. ** ^The final callback parameter is the [rowid] of the row. ** ^In the case of an update, this is the [rowid] after the update takes place. ** ** ^(The update hook is not invoked when internal system tables are ** modified (i.e. sqlite_master and sqlite_sequence).)^ ** ** ^In the current implementation, the update hook ** is not invoked when duplication rows are deleted because of an ** [ON CONFLICT | ON CONFLICT REPLACE] clause. ^Nor is the update hook ** invoked when rows are deleted using the [truncate optimization]. ** The exceptions defined in this paragraph might change in a future ** release of SQLite. ** ** The update hook implementation must not do anything that will modify ** the database connection that invoked the update hook. Any actions ** to modify the database connection must be deferred until after the ** completion of the [sqlite3_step()] call that triggered the update hook. ** Note that [sqlite3_prepare_v2()] and [sqlite3_step()] both modify their ** database connections for the meaning of "modify" in this paragraph. ** ** ^The sqlite3_update_hook(D,C,P) function ** returns the P argument from the previous call ** on the same [database connection] D, or NULL for ** the first call on D. ** ** See also the [sqlite3_commit_hook()] and [sqlite3_rollback_hook()] ** interfaces. */ SQLITE_API void *sqlite3_update_hook( sqlite3*, void(*)(void *,int ,char const *,char const *,sqlite3_int64), void* ); /* ** CAPI3REF: Enable Or Disable Shared Pager Cache ** KEYWORDS: {shared cache} ** ** ^(This routine enables or disables the sharing of the database cache ** and schema data structures between [database connection | connections] ** to the same database. Sharing is enabled if the argument is true ** and disabled if the argument is false.)^ ** ** ^Cache sharing is enabled and disabled for an entire process. ** This is a change as of SQLite version 3.5.0. In prior versions of SQLite, ** sharing was enabled or disabled for each thread separately. ** ** ^(The cache sharing mode set by this interface effects all subsequent ** calls to [sqlite3_open()], [sqlite3_open_v2()], and [sqlite3_open16()]. ** Existing database connections continue use the sharing mode ** that was in effect at the time they were opened.)^ ** ** ^(This routine returns [SQLITE_OK] if shared cache was enabled or disabled ** successfully. An [error code] is returned otherwise.)^ ** ** ^Shared cache is disabled by default. But this might change in ** future releases of SQLite. Applications that care about shared ** cache setting should set it explicitly. ** ** See Also: [SQLite Shared-Cache Mode] */ SQLITE_API int sqlite3_enable_shared_cache(int); /* ** CAPI3REF: Attempt To Free Heap Memory ** ** ^The sqlite3_release_memory() interface attempts to free N bytes ** of heap memory by deallocating non-essential memory allocations ** held by the database library. Memory used to cache database ** pages to improve performance is an example of non-essential memory. ** ^sqlite3_release_memory() returns the number of bytes actually freed, ** which might be more or less than the amount requested. ** ^The sqlite3_release_memory() routine is a no-op returning zero ** if SQLite is not compiled with [SQLITE_ENABLE_MEMORY_MANAGEMENT]. */ SQLITE_API int sqlite3_release_memory(int); /* ** CAPI3REF: Impose A Limit On Heap Size ** ** ^The sqlite3_soft_heap_limit64() interface sets and/or queries the ** soft limit on the amount of heap memory that may be allocated by SQLite. ** ^SQLite strives to keep heap memory utilization below the soft heap ** limit by reducing the number of pages held in the page cache ** as heap memory usages approaches the limit. ** ^The soft heap limit is "soft" because even though SQLite strives to stay ** below the limit, it will exceed the limit rather than generate ** an [SQLITE_NOMEM] error. In other words, the soft heap limit ** is advisory only. ** ** ^The return value from sqlite3_soft_heap_limit64() is the size of ** the soft heap limit prior to the call. ^If the argument N is negative ** then no change is made to the soft heap limit. Hence, the current ** size of the soft heap limit can be determined by invoking ** sqlite3_soft_heap_limit64() with a negative argument. ** ** ^If the argument N is zero then the soft heap limit is disabled. ** ** ^(The soft heap limit is not enforced in the current implementation ** if one or more of following conditions are true: ** **
    **
  • The soft heap limit is set to zero. **
  • Memory accounting is disabled using a combination of the ** [sqlite3_config]([SQLITE_CONFIG_MEMSTATUS],...) start-time option and ** the [SQLITE_DEFAULT_MEMSTATUS] compile-time option. **
  • An alternative page cache implementation is specified using ** [sqlite3_config]([SQLITE_CONFIG_PCACHE],...). **
  • The page cache allocates from its own memory pool supplied ** by [sqlite3_config]([SQLITE_CONFIG_PAGECACHE],...) rather than ** from the heap. **
)^ ** ** Beginning with SQLite version 3.7.3, the soft heap limit is enforced ** regardless of whether or not the [SQLITE_ENABLE_MEMORY_MANAGEMENT] ** compile-time option is invoked. With [SQLITE_ENABLE_MEMORY_MANAGEMENT], ** the soft heap limit is enforced on every memory allocation. Without ** [SQLITE_ENABLE_MEMORY_MANAGEMENT], the soft heap limit is only enforced ** when memory is allocated by the page cache. Testing suggests that because ** the page cache is the predominate memory user in SQLite, most ** applications will achieve adequate soft heap limit enforcement without ** the use of [SQLITE_ENABLE_MEMORY_MANAGEMENT]. ** ** The circumstances under which SQLite will enforce the soft heap limit may ** changes in future releases of SQLite. */ SQLITE_API sqlite3_int64 sqlite3_soft_heap_limit64(sqlite3_int64 N); /* ** CAPI3REF: Deprecated Soft Heap Limit Interface ** DEPRECATED ** ** This is a deprecated version of the [sqlite3_soft_heap_limit64()] ** interface. This routine is provided for historical compatibility ** only. All new applications should use the ** [sqlite3_soft_heap_limit64()] interface rather than this one. */ SQLITE_API SQLITE_DEPRECATED void sqlite3_soft_heap_limit(int N); /* ** CAPI3REF: Extract Metadata About A Column Of A Table ** ** ^This routine returns metadata about a specific column of a specific ** database table accessible using the [database connection] handle ** passed as the first function argument. ** ** ^The column is identified by the second, third and fourth parameters to ** this function. ^The second parameter is either the name of the database ** (i.e. "main", "temp", or an attached database) containing the specified ** table or NULL. ^If it is NULL, then all attached databases are searched ** for the table using the same algorithm used by the database engine to ** resolve unqualified table references. ** ** ^The third and fourth parameters to this function are the table and column ** name of the desired column, respectively. Neither of these parameters ** may be NULL. ** ** ^Metadata is returned by writing to the memory locations passed as the 5th ** and subsequent parameters to this function. ^Any of these arguments may be ** NULL, in which case the corresponding element of metadata is omitted. ** ** ^(
** **
Parameter Output
Type 		Description ** **
5th const char* Data type **
6th const char* Name of default collation sequence **
7th int True if column has a NOT NULL constraint **
8th int True if column is part of the PRIMARY KEY **
9th int True if column is [AUTOINCREMENT] **
**
)^ ** ** ^The memory pointed to by the character pointers returned for the ** declaration type and collation sequence is valid only until the next ** call to any SQLite API function. ** ** ^If the specified table is actually a view, an [error code] is returned. ** ** ^If the specified column is "rowid", "oid" or "_rowid_" and an ** [INTEGER PRIMARY KEY] column has been explicitly declared, then the output ** parameters are set for the explicitly declared column. ^(If there is no ** explicitly declared [INTEGER PRIMARY KEY] column, then the output ** parameters are set as follows: ** ** 
**     data type: "INTEGER"
**     collation sequence: "BINARY"
**     not null: 0
**     primary key: 1
**     auto increment: 0
**
)^ ** ** ^(This function may load one or more schemas from database files. If an ** error occurs during this process, or if the requested table or column ** cannot be found, an [error code] is returned and an error message left ** in the [database connection] (to be retrieved using sqlite3_errmsg()).)^ ** ** ^This API is only available if the library was compiled with the ** [SQLITE_ENABLE_COLUMN_METADATA] C-preprocessor symbol defined. */ SQLITE_API int sqlite3_table_column_metadata( sqlite3 *db, /* Connection handle */ const char *zDbName, /* Database name or NULL */ const char *zTableName, /* Table name */ const char *zColumnName, /* Column name */ char const **pzDataType, /* OUTPUT: Declared data type */ char const **pzCollSeq, /* OUTPUT: Collation sequence name */ int *pNotNull, /* OUTPUT: True if NOT NULL constraint exists */ int *pPrimaryKey, /* OUTPUT: True if column part of PK */ int *pAutoinc /* OUTPUT: True if column is auto-increment */ ); /* ** CAPI3REF: Load An Extension ** ** ^This interface loads an SQLite extension library from the named file. ** ** ^The sqlite3_load_extension() interface attempts to load an ** SQLite extension library contained in the file zFile. ** ** ^The entry point is zProc. ** ^zProc may be 0, in which case the name of the entry point ** defaults to "sqlite3_extension_init". ** ^The sqlite3_load_extension() interface returns ** [SQLITE_OK] on success and [SQLITE_ERROR] if something goes wrong. ** ^If an error occurs and pzErrMsg is not 0, then the ** [sqlite3_load_extension()] interface shall attempt to ** fill *pzErrMsg with error message text stored in memory ** obtained from [sqlite3_malloc()]. The calling function ** should free this memory by calling [sqlite3_free()]. ** ** ^Extension loading must be enabled using ** [sqlite3_enable_load_extension()] prior to calling this API, ** otherwise an error will be returned. ** ** See also the [load_extension() SQL function]. */ SQLITE_API int sqlite3_load_extension( sqlite3 *db, /* Load the extension into this database connection */ const char *zFile, /* Name of the shared library containing extension */ const char *zProc, /* Entry point. Derived from zFile if 0 */ char **pzErrMsg /* Put error message here if not 0 */ ); /* ** CAPI3REF: Enable Or Disable Extension Loading ** ** ^So as not to open security holes in older applications that are ** unprepared to deal with extension loading, and as a means of disabling ** extension loading while evaluating user-entered SQL, the following API ** is provided to turn the [sqlite3_load_extension()] mechanism on and off. ** ** ^Extension loading is off by default. See ticket #1863. ** ^Call the sqlite3_enable_load_extension() routine with onoff==1 ** to turn extension loading on and call it with onoff==0 to turn ** it back off again. */ SQLITE_API int sqlite3_enable_load_extension(sqlite3 *db, int onoff); /* ** CAPI3REF: Automatically Load Statically Linked Extensions ** ** ^This interface causes the xEntryPoint() function to be invoked for ** each new [database connection] that is created. The idea here is that ** xEntryPoint() is the entry point for a statically linked SQLite extension ** that is to be automatically loaded into all new database connections. ** ** ^(Even though the function prototype shows that xEntryPoint() takes ** no arguments and returns void, SQLite invokes xEntryPoint() with three ** arguments and expects and integer result as if the signature of the ** entry point where as follows: ** ** 
**    int xEntryPoint(
**      sqlite3 *db,
**      const char **pzErrMsg,
**      const struct sqlite3_api_routines *pThunk
**    );
**
)^ ** ** If the xEntryPoint routine encounters an error, it should make *pzErrMsg ** point to an appropriate error message (obtained from [sqlite3_mprintf()]) ** and return an appropriate [error code]. ^SQLite ensures that *pzErrMsg ** is NULL before calling the xEntryPoint(). ^SQLite will invoke ** [sqlite3_free()] on *pzErrMsg after xEntryPoint() returns. ^If any ** xEntryPoint() returns an error, the [sqlite3_open()], [sqlite3_open16()], ** or [sqlite3_open_v2()] call that provoked the xEntryPoint() will fail. ** ** ^Calling sqlite3_auto_extension(X) with an entry point X that is already ** on the list of automatic extensions is a harmless no-op. ^No entry point ** will be called more than once for each database connection that is opened. ** ** See also: [sqlite3_reset_auto_extension()]. */ SQLITE_API int sqlite3_auto_extension(void (*xEntryPoint)(void)); /* ** CAPI3REF: Reset Automatic Extension Loading ** ** ^This interface disables all automatic extensions previously ** registered using [sqlite3_auto_extension()]. */ SQLITE_API void sqlite3_reset_auto_extension(void); /* ** The interface to the virtual-table mechanism is currently considered ** to be experimental. The interface might change in incompatible ways. ** If this is a problem for you, do not use the interface at this time. ** ** When the virtual-table mechanism stabilizes, we will declare the ** interface fixed, support it indefinitely, and remove this comment. */ /* ** Structures used by the virtual table interface */ typedef struct sqlite3_vtab sqlite3_vtab; typedef struct sqlite3_index_info sqlite3_index_info; typedef struct sqlite3_vtab_cursor sqlite3_vtab_cursor; typedef struct sqlite3_module sqlite3_module; /* ** CAPI3REF: Virtual Table Object ** KEYWORDS: sqlite3_module {virtual table module} ** ** This structure, sometimes called a "virtual table module", ** defines the implementation of a [virtual tables]. ** This structure consists mostly of methods for the module. ** ** ^A virtual table module is created by filling in a persistent ** instance of this structure and passing a pointer to that instance ** to [sqlite3_create_module()] or [sqlite3_create_module_v2()]. ** ^The registration remains valid until it is replaced by a different ** module or until the [database connection] closes. The content ** of this structure must not change while it is registered with ** any database connection. */ struct sqlite3_module { int iVersion; int (*xCreate)(sqlite3*, void *pAux, int argc, const char *const*argv, sqlite3_vtab **ppVTab, char**); int (*xConnect)(sqlite3*, void *pAux, int argc, const char *const*argv, sqlite3_vtab **ppVTab, char**); int (*xBestIndex)(sqlite3_vtab *pVTab, sqlite3_index_info*); int (*xDisconnect)(sqlite3_vtab *pVTab); int (*xDestroy)(sqlite3_vtab *pVTab); int (*xOpen)(sqlite3_vtab *pVTab, sqlite3_vtab_cursor **ppCursor); int (*xClose)(sqlite3_vtab_cursor*); int (*xFilter)(sqlite3_vtab_cursor*, int idxNum, const char *idxStr, int argc, sqlite3_value **argv); int (*xNext)(sqlite3_vtab_cursor*); int (*xEof)(sqlite3_vtab_cursor*); int (*xColumn)(sqlite3_vtab_cursor*, sqlite3_context*, int); int (*xRowid)(sqlite3_vtab_cursor*, sqlite3_int64 *pRowid); int (*xUpdate)(sqlite3_vtab *, int, sqlite3_value **, sqlite3_int64 *); int (*xBegin)(sqlite3_vtab *pVTab); int (*xSync)(sqlite3_vtab *pVTab); int (*xCommit)(sqlite3_vtab *pVTab); int (*xRollback)(sqlite3_vtab *pVTab); int (*xFindFunction)(sqlite3_vtab *pVtab, int nArg, const char *zName, void (**pxFunc)(sqlite3_context*,int,sqlite3_value**), void **ppArg); int (*xRename)(sqlite3_vtab *pVtab, const char *zNew); /* The methods above are in version 1 of the sqlite_module object. Those ** below are for version 2 and greater. */ int (*xSavepoint)(sqlite3_vtab *pVTab, int); int (*xRelease)(sqlite3_vtab *pVTab, int); int (*xRollbackTo)(sqlite3_vtab *pVTab, int); }; /* ** CAPI3REF: Virtual Table Indexing Information ** KEYWORDS: sqlite3_index_info ** ** The sqlite3_index_info structure and its substructures is used as part ** of the [virtual table] interface to ** pass information into and receive the reply from the [xBestIndex] ** method of a [virtual table module]. The fields under **Inputs** are the ** inputs to xBestIndex and are read-only. xBestIndex inserts its ** results into the **Outputs** fields. ** ** ^(The aConstraint[] array records WHERE clause constraints of the form: ** **
column OP expr
** ** where OP is =, <, <=, >, or >=.)^ ^(The particular operator is ** stored in aConstraint[].op using one of the ** [SQLITE_INDEX_CONSTRAINT_EQ | SQLITE_INDEX_CONSTRAINT_ values].)^ ** ^(The index of the column is stored in ** aConstraint[].iColumn.)^ ^(aConstraint[].usable is TRUE if the ** expr on the right-hand side can be evaluated (and thus the constraint ** is usable) and false if it cannot.)^ ** ** ^The optimizer automatically inverts terms of the form "expr OP column" ** and makes other simplifications to the WHERE clause in an attempt to ** get as many WHERE clause terms into the form shown above as possible. ** ^The aConstraint[] array only reports WHERE clause terms that are ** relevant to the particular virtual table being queried. ** ** ^Information about the ORDER BY clause is stored in aOrderBy[]. ** ^Each term of aOrderBy records a column of the ORDER BY clause. ** ** The [xBestIndex] method must fill aConstraintUsage[] with information ** about what parameters to pass to xFilter. ^If argvIndex>0 then ** the right-hand side of the corresponding aConstraint[] is evaluated ** and becomes the argvIndex-th entry in argv. ^(If aConstraintUsage[].omit ** is true, then the constraint is assumed to be fully handled by the ** virtual table and is not checked again by SQLite.)^ ** ** ^The idxNum and idxPtr values are recorded and passed into the ** [xFilter] method. ** ^[sqlite3_free()] is used to free idxPtr if and only if ** needToFreeIdxPtr is true. ** ** ^The orderByConsumed means that output from [xFilter]/[xNext] will occur in ** the correct order to satisfy the ORDER BY clause so that no separate ** sorting step is required. ** ** ^The estimatedCost value is an estimate of the cost of doing the ** particular lookup. A full scan of a table with N entries should have ** a cost of N. A binary search of a table of N entries should have a ** cost of approximately log(N). */ struct sqlite3_index_info { /* Inputs */ int nConstraint; /* Number of entries in aConstraint */ struct sqlite3_index_constraint { int iColumn; /* Column on left-hand side of constraint */ unsigned char op; /* Constraint operator */ unsigned char usable; /* True if this constraint is usable */ int iTermOffset; /* Used internally - xBestIndex should ignore */ } *aConstraint; /* Table of WHERE clause constraints */ int nOrderBy; /* Number of terms in the ORDER BY clause */ struct sqlite3_index_orderby { int iColumn; /* Column number */ unsigned char desc; /* True for DESC. False for ASC. */ } *aOrderBy; /* The ORDER BY clause */ /* Outputs */ struct sqlite3_index_constraint_usage { int argvIndex; /* if >0, constraint is part of argv to xFilter */ unsigned char omit; /* Do not code a test for this constraint */ } *aConstraintUsage; int idxNum; /* Number used to identify the index */ char *idxStr; /* String, possibly obtained from sqlite3_malloc */ int needToFreeIdxStr; /* Free idxStr using sqlite3_free() if true */ int orderByConsumed; /* True if output is already ordered */ double estimatedCost; /* Estimated cost of using this index */ }; /* ** CAPI3REF: Virtual Table Constraint Operator Codes ** ** These macros defined the allowed values for the ** [sqlite3_index_info].aConstraint[].op field. Each value represents ** an operator that is part of a constraint term in the wHERE clause of ** a query that uses a [virtual table]. */ #define SQLITE_INDEX_CONSTRAINT_EQ 2 #define SQLITE_INDEX_CONSTRAINT_GT 4 #define SQLITE_INDEX_CONSTRAINT_LE 8 #define SQLITE_INDEX_CONSTRAINT_LT 16 #define SQLITE_INDEX_CONSTRAINT_GE 32 #define SQLITE_INDEX_CONSTRAINT_MATCH 64 /* ** CAPI3REF: Register A Virtual Table Implementation ** ** ^These routines are used to register a new [virtual table module] name. ** ^Module names must be registered before ** creating a new [virtual table] using the module and before using a ** preexisting [virtual table] for the module. ** ** ^The module name is registered on the [database connection] specified ** by the first parameter. ^The name of the module is given by the ** second parameter. ^The third parameter is a pointer to ** the implementation of the [virtual table module]. ^The fourth ** parameter is an arbitrary client data pointer that is passed through ** into the [xCreate] and [xConnect] methods of the virtual table module ** when a new virtual table is be being created or reinitialized. ** ** ^The sqlite3_create_module_v2() interface has a fifth parameter which ** is a pointer to a destructor for the pClientData. ^SQLite will ** invoke the destructor function (if it is not NULL) when SQLite ** no longer needs the pClientData pointer. ^The destructor will also ** be invoked if the call to sqlite3_create_module_v2() fails. ** ^The sqlite3_create_module() ** interface is equivalent to sqlite3_create_module_v2() with a NULL ** destructor. */ SQLITE_API int sqlite3_create_module( sqlite3 *db, /* SQLite connection to register module with */ const char *zName, /* Name of the module */ const sqlite3_module *p, /* Methods for the module */ void *pClientData /* Client data for xCreate/xConnect */ ); SQLITE_API int sqlite3_create_module_v2( sqlite3 *db, /* SQLite connection to register module with */ const char *zName, /* Name of the module */ const sqlite3_module *p, /* Methods for the module */ void *pClientData, /* Client data for xCreate/xConnect */ void(*xDestroy)(void*) /* Module destructor function */ ); /* ** CAPI3REF: Virtual Table Instance Object ** KEYWORDS: sqlite3_vtab ** ** Every [virtual table module] implementation uses a subclass ** of this object to describe a particular instance ** of the [virtual table]. Each subclass will ** be tailored to the specific needs of the module implementation. ** The purpose of this superclass is to define certain fields that are ** common to all module implementations. ** ** ^Virtual tables methods can set an error message by assigning a ** string obtained from [sqlite3_mprintf()] to zErrMsg. The method should ** take care that any prior string is freed by a call to [sqlite3_free()] ** prior to assigning a new string to zErrMsg. ^After the error message ** is delivered up to the client application, the string will be automatically ** freed by sqlite3_free() and the zErrMsg field will be zeroed. */ struct sqlite3_vtab { const sqlite3_module *pModule; /* The module for this virtual table */ int nRef; /* NO LONGER USED */ char *zErrMsg; /* Error message from sqlite3_mprintf() */ /* Virtual table implementations will typically add additional fields */ }; /* ** CAPI3REF: Virtual Table Cursor Object ** KEYWORDS: sqlite3_vtab_cursor {virtual table cursor} ** ** Every [virtual table module] implementation uses a subclass of the ** following structure to describe cursors that point into the ** [virtual table] and are used ** to loop through the virtual table. Cursors are created using the ** [sqlite3_module.xOpen | xOpen] method of the module and are destroyed ** by the [sqlite3_module.xClose | xClose] method. Cursors are used ** by the [xFilter], [xNext], [xEof], [xColumn], and [xRowid] methods ** of the module. Each module implementation will define ** the content of a cursor structure to suit its own needs. ** ** This superclass exists in order to define fields of the cursor that ** are common to all implementations. */ struct sqlite3_vtab_cursor { sqlite3_vtab *pVtab; /* Virtual table of this cursor */ /* Virtual table implementations will typically add additional fields */ }; /* ** CAPI3REF: Declare The Schema Of A Virtual Table ** ** ^The [xCreate] and [xConnect] methods of a ** [virtual table module] call this interface ** to declare the format (the names and datatypes of the columns) of ** the virtual tables they implement. */ SQLITE_API int sqlite3_declare_vtab(sqlite3*, const char *zSQL); /* ** CAPI3REF: Overload A Function For A Virtual Table ** ** ^(Virtual tables can provide alternative implementations of functions ** using the [xFindFunction] method of the [virtual table module]. ** But global versions of those functions ** must exist in order to be overloaded.)^ ** ** ^(This API makes sure a global version of a function with a particular ** name and number of parameters exists. If no such function exists ** before this API is called, a new function is created.)^ ^The implementation ** of the new function always causes an exception to be thrown. So ** the new function is not good for anything by itself. Its only ** purpose is to be a placeholder function that can be overloaded ** by a [virtual table]. */ SQLITE_API int sqlite3_overload_function(sqlite3*, const char *zFuncName, int nArg); /* ** The interface to the virtual-table mechanism defined above (back up ** to a comment remarkably similar to this one) is currently considered ** to be experimental. The interface might change in incompatible ways. ** If this is a problem for you, do not use the interface at this time. ** ** When the virtual-table mechanism stabilizes, we will declare the ** interface fixed, support it indefinitely, and remove this comment. */ /* ** CAPI3REF: A Handle To An Open BLOB ** KEYWORDS: {BLOB handle} {BLOB handles} ** ** An instance of this object represents an open BLOB on which ** [sqlite3_blob_open | incremental BLOB I/O] can be performed. ** ^Objects of this type are created by [sqlite3_blob_open()] ** and destroyed by [sqlite3_blob_close()]. ** ^The [sqlite3_blob_read()] and [sqlite3_blob_write()] interfaces ** can be used to read or write small subsections of the BLOB. ** ^The [sqlite3_blob_bytes()] interface returns the size of the BLOB in bytes. */ typedef struct sqlite3_blob sqlite3_blob; /* ** CAPI3REF: Open A BLOB For Incremental I/O ** ** ^(This interfaces opens a [BLOB handle | handle] to the BLOB located ** in row iRow, column zColumn, table zTable in database zDb; ** in other words, the same BLOB that would be selected by: ** ** 
**     SELECT zColumn FROM zDb.zTable WHERE [rowid] = iRow;
**
)^ ** ** ^If the flags parameter is non-zero, then the BLOB is opened for read ** and write access. ^If it is zero, the BLOB is opened for read access. ** ^It is not possible to open a column that is part of an index or primary ** key for writing. ^If [foreign key constraints] are enabled, it is ** not possible to open a column that is part of a [child key] for writing. ** ** ^Note that the database name is not the filename that contains ** the database but rather the symbolic name of the database that ** appears after the AS keyword when the database is connected using [ATTACH]. ** ^For the main database file, the database name is "main". ** ^For TEMP tables, the database name is "temp". ** ** ^(On success, [SQLITE_OK] is returned and the new [BLOB handle] is written ** to *ppBlob. Otherwise an [error code] is returned and *ppBlob is set ** to be a null pointer.)^ ** ^This function sets the [database connection] error code and message ** accessible via [sqlite3_errcode()] and [sqlite3_errmsg()] and related ** functions. ^Note that the *ppBlob variable is always initialized in a ** way that makes it safe to invoke [sqlite3_blob_close()] on *ppBlob ** regardless of the success or failure of this routine. ** ** ^(If the row that a BLOB handle points to is modified by an ** [UPDATE], [DELETE], or by [ON CONFLICT] side-effects ** then the BLOB handle is marked as "expired". ** This is true if any column of the row is changed, even a column ** other than the one the BLOB handle is open on.)^ ** ^Calls to [sqlite3_blob_read()] and [sqlite3_blob_write()] for ** an expired BLOB handle fail with a return code of [SQLITE_ABORT]. ** ^(Changes written into a BLOB prior to the BLOB expiring are not ** rolled back by the expiration of the BLOB. Such changes will eventually ** commit if the transaction continues to completion.)^ ** ** ^Use the [sqlite3_blob_bytes()] interface to determine the size of ** the opened blob. ^The size of a blob may not be changed by this ** interface. Use the [UPDATE] SQL command to change the size of a ** blob. ** ** ^The [sqlite3_bind_zeroblob()] and [sqlite3_result_zeroblob()] interfaces ** and the built-in [zeroblob] SQL function can be used, if desired, ** to create an empty, zero-filled blob in which to read or write using ** this interface. ** ** To avoid a resource leak, every open [BLOB handle] should eventually ** be released by a call to [sqlite3_blob_close()]. */ SQLITE_API int sqlite3_blob_open( sqlite3*, const char *zDb, const char *zTable, const char *zColumn, sqlite3_int64 iRow, int flags, sqlite3_blob **ppBlob ); /* ** CAPI3REF: Move a BLOB Handle to a New Row ** ** ^This function is used to move an existing blob handle so that it points ** to a different row of the same database table. ^The new row is identified ** by the rowid value passed as the second argument. Only the row can be ** changed. ^The database, table and column on which the blob handle is open ** remain the same. Moving an existing blob handle to a new row can be ** faster than closing the existing handle and opening a new one. ** ** ^(The new row must meet the same criteria as for [sqlite3_blob_open()] - ** it must exist and there must be either a blob or text value stored in ** the nominated column.)^ ^If the new row is not present in the table, or if ** it does not contain a blob or text value, or if another error occurs, an ** SQLite error code is returned and the blob handle is considered aborted. ** ^All subsequent calls to [sqlite3_blob_read()], [sqlite3_blob_write()] or ** [sqlite3_blob_reopen()] on an aborted blob handle immediately return ** SQLITE_ABORT. ^Calling [sqlite3_blob_bytes()] on an aborted blob handle ** always returns zero. ** ** ^This function sets the database handle error code and message. */ SQLITE_API SQLITE_EXPERIMENTAL int sqlite3_blob_reopen(sqlite3_blob *, sqlite3_int64); /* ** CAPI3REF: Close A BLOB Handle ** ** ^Closes an open [BLOB handle]. ** ** ^Closing a BLOB shall cause the current transaction to commit ** if there are no other BLOBs, no pending prepared statements, and the ** database connection is in [autocommit mode]. ** ^If any writes were made to the BLOB, they might be held in cache ** until the close operation if they will fit. ** ** ^(Closing the BLOB often forces the changes ** out to disk and so if any I/O errors occur, they will likely occur ** at the time when the BLOB is closed. Any errors that occur during ** closing are reported as a non-zero return value.)^ ** ** ^(The BLOB is closed unconditionally. Even if this routine returns ** an error code, the BLOB is still closed.)^ ** ** ^Calling this routine with a null pointer (such as would be returned ** by a failed call to [sqlite3_blob_open()]) is a harmless no-op. */ SQLITE_API int sqlite3_blob_close(sqlite3_blob *); /* ** CAPI3REF: Return The Size Of An Open BLOB ** ** ^Returns the size in bytes of the BLOB accessible via the ** successfully opened [BLOB handle] in its only argument. ^The ** incremental blob I/O routines can only read or overwriting existing ** blob content; they cannot change the size of a blob. ** ** This routine only works on a [BLOB handle] which has been created ** by a prior successful call to [sqlite3_blob_open()] and which has not ** been closed by [sqlite3_blob_close()]. Passing any other pointer in ** to this routine results in undefined and probably undesirable behavior. */ SQLITE_API int sqlite3_blob_bytes(sqlite3_blob *); /* ** CAPI3REF: Read Data From A BLOB Incrementally ** ** ^(This function is used to read data from an open [BLOB handle] into a ** caller-supplied buffer. N bytes of data are copied into buffer Z ** from the open BLOB, starting at offset iOffset.)^ ** ** ^If offset iOffset is less than N bytes from the end of the BLOB, ** [SQLITE_ERROR] is returned and no data is read. ^If N or iOffset is ** less than zero, [SQLITE_ERROR] is returned and no data is read. ** ^The size of the blob (and hence the maximum value of N+iOffset) ** can be determined using the [sqlite3_blob_bytes()] interface. ** ** ^An attempt to read from an expired [BLOB handle] fails with an ** error code of [SQLITE_ABORT]. ** ** ^(On success, sqlite3_blob_read() returns SQLITE_OK. ** Otherwise, an [error code] or an [extended error code] is returned.)^ ** ** This routine only works on a [BLOB handle] which has been created ** by a prior successful call to [sqlite3_blob_open()] and which has not ** been closed by [sqlite3_blob_close()]. Passing any other pointer in ** to this routine results in undefined and probably undesirable behavior. ** ** See also: [sqlite3_blob_write()]. */ SQLITE_API int sqlite3_blob_read(sqlite3_blob *, void *Z, int N, int iOffset); /* ** CAPI3REF: Write Data Into A BLOB Incrementally ** ** ^This function is used to write data into an open [BLOB handle] from a ** caller-supplied buffer. ^N bytes of data are copied from the buffer Z ** into the open BLOB, starting at offset iOffset. ** ** ^If the [BLOB handle] passed as the first argument was not opened for ** writing (the flags parameter to [sqlite3_blob_open()] was zero), ** this function returns [SQLITE_READONLY]. ** ** ^This function may only modify the contents of the BLOB; it is ** not possible to increase the size of a BLOB using this API. ** ^If offset iOffset is less than N bytes from the end of the BLOB, ** [SQLITE_ERROR] is returned and no data is written. ^If N is ** less than zero [SQLITE_ERROR] is returned and no data is written. ** The size of the BLOB (and hence the maximum value of N+iOffset) ** can be determined using the [sqlite3_blob_bytes()] interface. ** ** ^An attempt to write to an expired [BLOB handle] fails with an ** error code of [SQLITE_ABORT]. ^Writes to the BLOB that occurred ** before the [BLOB handle] expired are not rolled back by the ** expiration of the handle, though of course those changes might ** have been overwritten by the statement that expired the BLOB handle ** or by other independent statements. ** ** ^(On success, sqlite3_blob_write() returns SQLITE_OK. ** Otherwise, an [error code] or an [extended error code] is returned.)^ ** ** This routine only works on a [BLOB handle] which has been created ** by a prior successful call to [sqlite3_blob_open()] and which has not ** been closed by [sqlite3_blob_close()]. Passing any other pointer in ** to this routine results in undefined and probably undesirable behavior. ** ** See also: [sqlite3_blob_read()]. */ SQLITE_API int sqlite3_blob_write(sqlite3_blob *, const void *z, int n, int iOffset); /* ** CAPI3REF: Virtual File System Objects ** ** A virtual filesystem (VFS) is an [sqlite3_vfs] object ** that SQLite uses to interact ** with the underlying operating system. Most SQLite builds come with a ** single default VFS that is appropriate for the host computer. ** New VFSes can be registered and existing VFSes can be unregistered. ** The following interfaces are provided. ** ** ^The sqlite3_vfs_find() interface returns a pointer to a VFS given its name. ** ^Names are case sensitive. ** ^Names are zero-terminated UTF-8 strings. ** ^If there is no match, a NULL pointer is returned. ** ^If zVfsName is NULL then the default VFS is returned. ** ** ^New VFSes are registered with sqlite3_vfs_register(). ** ^Each new VFS becomes the default VFS if the makeDflt flag is set. ** ^The same VFS can be registered multiple times without injury. ** ^To make an existing VFS into the default VFS, register it again ** with the makeDflt flag set. If two different VFSes with the ** same name are registered, the behavior is undefined. If a ** VFS is registered with a name that is NULL or an empty string, ** then the behavior is undefined. ** ** ^Unregister a VFS with the sqlite3_vfs_unregister() interface. ** ^(If the default VFS is unregistered, another VFS is chosen as ** the default. The choice for the new VFS is arbitrary.)^ */ SQLITE_API sqlite3_vfs *sqlite3_vfs_find(const char *zVfsName); SQLITE_API int sqlite3_vfs_register(sqlite3_vfs*, int makeDflt); SQLITE_API int sqlite3_vfs_unregister(sqlite3_vfs*); /* ** CAPI3REF: Mutexes ** ** The SQLite core uses these routines for thread ** synchronization. Though they are intended for internal ** use by SQLite, code that links against SQLite is ** permitted to use any of these routines. ** ** The SQLite source code contains multiple implementations ** of these mutex routines. An appropriate implementation ** is selected automatically at compile-time. ^(The following ** implementations are available in the SQLite core: ** **
    **
  • SQLITE_MUTEX_OS2 **
  • SQLITE_MUTEX_PTHREAD **
  • SQLITE_MUTEX_W32 **
  • SQLITE_MUTEX_NOOP **
)^ ** ** ^The SQLITE_MUTEX_NOOP implementation is a set of routines ** that does no real locking and is appropriate for use in ** a single-threaded application. ^The SQLITE_MUTEX_OS2, ** SQLITE_MUTEX_PTHREAD, and SQLITE_MUTEX_W32 implementations ** are appropriate for use on OS/2, Unix, and Windows. ** ** ^(If SQLite is compiled with the SQLITE_MUTEX_APPDEF preprocessor ** macro defined (with "-DSQLITE_MUTEX_APPDEF=1"), then no mutex ** implementation is included with the library. In this case the ** application must supply a custom mutex implementation using the ** [SQLITE_CONFIG_MUTEX] option of the sqlite3_config() function ** before calling sqlite3_initialize() or any other public sqlite3_ ** function that calls sqlite3_initialize().)^ ** ** ^The sqlite3_mutex_alloc() routine allocates a new ** mutex and returns a pointer to it. ^If it returns NULL ** that means that a mutex could not be allocated. ^SQLite ** will unwind its stack and return an error. ^(The argument ** to sqlite3_mutex_alloc() is one of these integer constants: ** **
    **
  • SQLITE_MUTEX_FAST **
  • SQLITE_MUTEX_RECURSIVE **
  • SQLITE_MUTEX_STATIC_MASTER **
  • SQLITE_MUTEX_STATIC_MEM **
  • SQLITE_MUTEX_STATIC_MEM2 **
  • SQLITE_MUTEX_STATIC_PRNG **
  • SQLITE_MUTEX_STATIC_LRU **
  • SQLITE_MUTEX_STATIC_LRU2 **
)^ ** ** ^The first two constants (SQLITE_MUTEX_FAST and SQLITE_MUTEX_RECURSIVE) ** cause sqlite3_mutex_alloc() to create ** a new mutex. ^The new mutex is recursive when SQLITE_MUTEX_RECURSIVE ** is used but not necessarily so when SQLITE_MUTEX_FAST is used. ** The mutex implementation does not need to make a distinction ** between SQLITE_MUTEX_RECURSIVE and SQLITE_MUTEX_FAST if it does ** not want to. ^SQLite will only request a recursive mutex in ** cases where it really needs one. ^If a faster non-recursive mutex ** implementation is available on the host platform, the mutex subsystem ** might return such a mutex in response to SQLITE_MUTEX_FAST. ** ** ^The other allowed parameters to sqlite3_mutex_alloc() (anything other ** than SQLITE_MUTEX_FAST and SQLITE_MUTEX_RECURSIVE) each return ** a pointer to a static preexisting mutex. ^Six static mutexes are ** used by the current version of SQLite. Future versions of SQLite ** may add additional static mutexes. Static mutexes are for internal ** use by SQLite only. Applications that use SQLite mutexes should ** use only the dynamic mutexes returned by SQLITE_MUTEX_FAST or ** SQLITE_MUTEX_RECURSIVE. ** ** ^Note that if one of the dynamic mutex parameters (SQLITE_MUTEX_FAST ** or SQLITE_MUTEX_RECURSIVE) is used then sqlite3_mutex_alloc() ** returns a different mutex on every call. ^But for the static ** mutex types, the same mutex is returned on every call that has ** the same type number. ** ** ^The sqlite3_mutex_free() routine deallocates a previously ** allocated dynamic mutex. ^SQLite is careful to deallocate every ** dynamic mutex that it allocates. The dynamic mutexes must not be in ** use when they are deallocated. Attempting to deallocate a static ** mutex results in undefined behavior. ^SQLite never deallocates ** a static mutex. ** ** ^The sqlite3_mutex_enter() and sqlite3_mutex_try() routines attempt ** to enter a mutex. ^If another thread is already within the mutex, ** sqlite3_mutex_enter() will block and sqlite3_mutex_try() will return ** SQLITE_BUSY. ^The sqlite3_mutex_try() interface returns [SQLITE_OK] ** upon successful entry. ^(Mutexes created using ** SQLITE_MUTEX_RECURSIVE can be entered multiple times by the same thread. ** In such cases the, ** mutex must be exited an equal number of times before another thread ** can enter.)^ ^(If the same thread tries to enter any other ** kind of mutex more than once, the behavior is undefined. ** SQLite will never exhibit ** such behavior in its own use of mutexes.)^ ** ** ^(Some systems (for example, Windows 95) do not support the operation ** implemented by sqlite3_mutex_try(). On those systems, sqlite3_mutex_try() ** will always return SQLITE_BUSY. The SQLite core only ever uses ** sqlite3_mutex_try() as an optimization so this is acceptable behavior.)^ ** ** ^The sqlite3_mutex_leave() routine exits a mutex that was ** previously entered by the same thread. ^(The behavior ** is undefined if the mutex is not currently entered by the ** calling thread or is not currently allocated. SQLite will ** never do either.)^ ** ** ^If the argument to sqlite3_mutex_enter(), sqlite3_mutex_try(), or ** sqlite3_mutex_leave() is a NULL pointer, then all three routines ** behave as no-ops. ** ** See also: [sqlite3_mutex_held()] and [sqlite3_mutex_notheld()]. */ SQLITE_API sqlite3_mutex *sqlite3_mutex_alloc(int); SQLITE_API void sqlite3_mutex_free(sqlite3_mutex*); SQLITE_API void sqlite3_mutex_enter(sqlite3_mutex*); SQLITE_API int sqlite3_mutex_try(sqlite3_mutex*); SQLITE_API void sqlite3_mutex_leave(sqlite3_mutex*); /* ** CAPI3REF: Mutex Methods Object ** ** An instance of this structure defines the low-level routines ** used to allocate and use mutexes. ** ** Usually, the default mutex implementations provided by SQLite are ** sufficient, however the user has the option of substituting a custom ** implementation for specialized deployments or systems for which SQLite ** does not provide a suitable implementation. In this case, the user ** creates and populates an instance of this structure to pass ** to sqlite3_config() along with the [SQLITE_CONFIG_MUTEX] option. ** Additionally, an instance of this structure can be used as an ** output variable when querying the system for the current mutex ** implementation, using the [SQLITE_CONFIG_GETMUTEX] option. ** ** ^The xMutexInit method defined by this structure is invoked as ** part of system initialization by the sqlite3_initialize() function. ** ^The xMutexInit routine is called by SQLite exactly once for each ** effective call to [sqlite3_initialize()]. ** ** ^The xMutexEnd method defined by this structure is invoked as ** part of system shutdown by the sqlite3_shutdown() function. The ** implementation of this method is expected to release all outstanding ** resources obtained by the mutex methods implementation, especially ** those obtained by the xMutexInit method. ^The xMutexEnd() ** interface is invoked exactly once for each call to [sqlite3_shutdown()]. ** ** ^(The remaining seven methods defined by this structure (xMutexAlloc, ** xMutexFree, xMutexEnter, xMutexTry, xMutexLeave, xMutexHeld and ** xMutexNotheld) implement the following interfaces (respectively): ** **
    **
  • [sqlite3_mutex_alloc()]
    • **
  • [sqlite3_mutex_free()]
    • **
  • [sqlite3_mutex_enter()]
    • **
  • [sqlite3_mutex_try()]
    • **
  • [sqlite3_mutex_leave()]
    • **
  • [sqlite3_mutex_held()]
    • **
  • [sqlite3_mutex_notheld()]
    • **
)^ ** ** The only difference is that the public sqlite3_XXX functions enumerated ** above silently ignore any invocations that pass a NULL pointer instead ** of a valid mutex handle. The implementations of the methods defined ** by this structure are not required to handle this case, the results ** of passing a NULL pointer instead of a valid mutex handle are undefined ** (i.e. it is acceptable to provide an implementation that segfaults if ** it is passed a NULL pointer). ** ** The xMutexInit() method must be threadsafe. ^It must be harmless to ** invoke xMutexInit() multiple times within the same process and without ** intervening calls to xMutexEnd(). Second and subsequent calls to ** xMutexInit() must be no-ops. ** ** ^xMutexInit() must not use SQLite memory allocation ([sqlite3_malloc()] ** and its associates). ^Similarly, xMutexAlloc() must not use SQLite memory ** allocation for a static mutex. ^However xMutexAlloc() may use SQLite ** memory allocation for a fast or recursive mutex. ** ** ^SQLite will invoke the xMutexEnd() method when [sqlite3_shutdown()] is ** called, but only if the prior call to xMutexInit returned SQLITE_OK. ** If xMutexInit fails in any way, it is expected to clean up after itself ** prior to returning. */ typedef struct sqlite3_mutex_methods sqlite3_mutex_methods; struct sqlite3_mutex_methods { int (*xMutexInit)(void); int (*xMutexEnd)(void); sqlite3_mutex *(*xMutexAlloc)(int); void (*xMutexFree)(sqlite3_mutex *); void (*xMutexEnter)(sqlite3_mutex *); int (*xMutexTry)(sqlite3_mutex *); void (*xMutexLeave)(sqlite3_mutex *); int (*xMutexHeld)(sqlite3_mutex *); int (*xMutexNotheld)(sqlite3_mutex *); }; /* ** CAPI3REF: Mutex Verification Routines ** ** The sqlite3_mutex_held() and sqlite3_mutex_notheld() routines ** are intended for use inside assert() statements. ^The SQLite core ** never uses these routines except inside an assert() and applications ** are advised to follow the lead of the core. ^The SQLite core only ** provides implementations for these routines when it is compiled ** with the SQLITE_DEBUG flag. ^External mutex implementations ** are only required to provide these routines if SQLITE_DEBUG is ** defined and if NDEBUG is not defined. ** ** ^These routines should return true if the mutex in their argument ** is held or not held, respectively, by the calling thread. ** ** ^The implementation is not required to provided versions of these ** routines that actually work. If the implementation does not provide working ** versions of these routines, it should at least provide stubs that always ** return true so that one does not get spurious assertion failures. ** ** ^If the argument to sqlite3_mutex_held() is a NULL pointer then ** the routine should return 1. This seems counter-intuitive since ** clearly the mutex cannot be held if it does not exist. But ** the reason the mutex does not exist is because the build is not ** using mutexes. And we do not want the assert() containing the ** call to sqlite3_mutex_held() to fail, so a non-zero return is ** the appropriate thing to do. ^The sqlite3_mutex_notheld() ** interface should also return 1 when given a NULL pointer. */ #ifndef NDEBUG SQLITE_API int sqlite3_mutex_held(sqlite3_mutex*); SQLITE_API int sqlite3_mutex_notheld(sqlite3_mutex*); #endif /* ** CAPI3REF: Mutex Types ** ** The [sqlite3_mutex_alloc()] interface takes a single argument ** which is one of these integer constants. ** ** The set of static mutexes may change from one SQLite release to the ** next. Applications that override the built-in mutex logic must be ** prepared to accommodate additional static mutexes. */ #define SQLITE_MUTEX_FAST 0 #define SQLITE_MUTEX_RECURSIVE 1 #define SQLITE_MUTEX_STATIC_MASTER 2 #define SQLITE_MUTEX_STATIC_MEM 3 /* sqlite3_malloc() */ #define SQLITE_MUTEX_STATIC_MEM2 4 /* NOT USED */ #define SQLITE_MUTEX_STATIC_OPEN 4 /* sqlite3BtreeOpen() */ #define SQLITE_MUTEX_STATIC_PRNG 5 /* sqlite3_random() */ #define SQLITE_MUTEX_STATIC_LRU 6 /* lru page list */ #define SQLITE_MUTEX_STATIC_LRU2 7 /* NOT USED */ #define SQLITE_MUTEX_STATIC_PMEM 7 /* sqlite3PageMalloc() */ /* ** CAPI3REF: Retrieve the mutex for a database connection ** ** ^This interface returns a pointer the [sqlite3_mutex] object that ** serializes access to the [database connection] given in the argument ** when the [threading mode] is Serialized. ** ^If the [threading mode] is Single-thread or Multi-thread then this ** routine returns a NULL pointer. */ SQLITE_API sqlite3_mutex *sqlite3_db_mutex(sqlite3*); /* ** CAPI3REF: Low-Level Control Of Database Files ** ** ^The [sqlite3_file_control()] interface makes a direct call to the ** xFileControl method for the [sqlite3_io_methods] object associated ** with a particular database identified by the second argument. ^The ** name of the database is "main" for the main database or "temp" for the ** TEMP database, or the name that appears after the AS keyword for ** databases that are added using the [ATTACH] SQL command. ** ^A NULL pointer can be used in place of "main" to refer to the ** main database file. ** ^The third and fourth parameters to this routine ** are passed directly through to the second and third parameters of ** the xFileControl method. ^The return value of the xFileControl ** method becomes the return value of this routine. ** ** ^The SQLITE_FCNTL_FILE_POINTER value for the op parameter causes ** a pointer to the underlying [sqlite3_file] object to be written into ** the space pointed to by the 4th parameter. ^The SQLITE_FCNTL_FILE_POINTER ** case is a short-circuit path which does not actually invoke the ** underlying sqlite3_io_methods.xFileControl method. ** ** ^If the second parameter (zDbName) does not match the name of any ** open database file, then SQLITE_ERROR is returned. ^This error ** code is not remembered and will not be recalled by [sqlite3_errcode()] ** or [sqlite3_errmsg()]. The underlying xFileControl method might ** also return SQLITE_ERROR. There is no way to distinguish between ** an incorrect zDbName and an SQLITE_ERROR return from the underlying ** xFileControl method. ** ** See also: [SQLITE_FCNTL_LOCKSTATE] */ SQLITE_API int sqlite3_file_control(sqlite3*, const char *zDbName, int op, void*); /* ** CAPI3REF: Testing Interface ** ** ^The sqlite3_test_control() interface is used to read out internal ** state of SQLite and to inject faults into SQLite for testing ** purposes. ^The first parameter is an operation code that determines ** the number, meaning, and operation of all subsequent parameters. ** ** This interface is not for use by applications. It exists solely ** for verifying the correct operation of the SQLite library. Depending ** on how the SQLite library is compiled, this interface might not exist. ** ** The details of the operation codes, their meanings, the parameters ** they take, and what they do are all subject to change without notice. ** Unlike most of the SQLite API, this function is not guaranteed to ** operate consistently from one release to the next. */ SQLITE_API int sqlite3_test_control(int op, ...); /* ** CAPI3REF: Testing Interface Operation Codes ** ** These constants are the valid operation code parameters used ** as the first argument to [sqlite3_test_control()]. ** ** These parameters and their meanings are subject to change ** without notice. These values are for testing purposes only. ** Applications should not use any of these parameters or the ** [sqlite3_test_control()] interface. */ #define SQLITE_TESTCTRL_FIRST 5 #define SQLITE_TESTCTRL_PRNG_SAVE 5 #define SQLITE_TESTCTRL_PRNG_RESTORE 6 #define SQLITE_TESTCTRL_PRNG_RESET 7 #define SQLITE_TESTCTRL_BITVEC_TEST 8 #define SQLITE_TESTCTRL_FAULT_INSTALL 9 #define SQLITE_TESTCTRL_BENIGN_MALLOC_HOOKS 10 #define SQLITE_TESTCTRL_PENDING_BYTE 11 #define SQLITE_TESTCTRL_ASSERT 12 #define SQLITE_TESTCTRL_ALWAYS 13 #define SQLITE_TESTCTRL_RESERVE 14 #define SQLITE_TESTCTRL_OPTIMIZATIONS 15 #define SQLITE_TESTCTRL_ISKEYWORD 16 #define SQLITE_TESTCTRL_PGHDRSZ 17 #define SQLITE_TESTCTRL_SCRATCHMALLOC 18 #define SQLITE_TESTCTRL_LOCALTIME_FAULT 19 #define SQLITE_TESTCTRL_LAST 19 /* ** CAPI3REF: SQLite Runtime Status ** ** ^This interface is used to retrieve runtime status information ** about the performance of SQLite, and optionally to reset various ** highwater marks. ^The first argument is an integer code for ** the specific parameter to measure. ^(Recognized integer codes ** are of the form [status parameters | SQLITE_STATUS_...].)^ ** ^The current value of the parameter is returned into *pCurrent. ** ^The highest recorded value is returned in *pHighwater. ^If the ** resetFlag is true, then the highest record value is reset after ** *pHighwater is written. ^(Some parameters do not record the highest ** value. For those parameters ** nothing is written into *pHighwater and the resetFlag is ignored.)^ ** ^(Other parameters record only the highwater mark and not the current ** value. For these latter parameters nothing is written into *pCurrent.)^ ** ** ^The sqlite3_status() routine returns SQLITE_OK on success and a ** non-zero [error code] on failure. ** ** This routine is threadsafe but is not atomic. This routine can be ** called while other threads are running the same or different SQLite ** interfaces. However the values returned in *pCurrent and ** *pHighwater reflect the status of SQLite at different points in time ** and it is possible that another thread might change the parameter ** in between the times when *pCurrent and *pHighwater are written. ** ** See also: [sqlite3_db_status()] */ SQLITE_API int sqlite3_status(int op, int *pCurrent, int *pHighwater, int resetFlag); /* ** CAPI3REF: Status Parameters ** KEYWORDS: {status parameters} ** ** These integer constants designate various run-time status parameters ** that can be returned by [sqlite3_status()]. ** **
** [[SQLITE_STATUS_MEMORY_USED]] ^(
SQLITE_STATUS_MEMORY_USED
**
This parameter is the current amount of memory checked out ** using [sqlite3_malloc()], either directly or indirectly. The ** figure includes calls made to [sqlite3_malloc()] by the application ** and internal memory usage by the SQLite library. Scratch memory ** controlled by [SQLITE_CONFIG_SCRATCH] and auxiliary page-cache ** memory controlled by [SQLITE_CONFIG_PAGECACHE] is not included in ** this parameter. The amount returned is the sum of the allocation ** sizes as reported by the xSize method in [sqlite3_mem_methods].
)^ ** ** [[SQLITE_STATUS_MALLOC_SIZE]] ^(
SQLITE_STATUS_MALLOC_SIZE
**
This parameter records the largest memory allocation request ** handed to [sqlite3_malloc()] or [sqlite3_realloc()] (or their ** internal equivalents). Only the value returned in the ** *pHighwater parameter to [sqlite3_status()] is of interest. ** The value written into the *pCurrent parameter is undefined.
)^ ** ** [[SQLITE_STATUS_MALLOC_COUNT]] ^(
SQLITE_STATUS_MALLOC_COUNT
**
This parameter records the number of separate memory allocations ** currently checked out.
)^ ** ** [[SQLITE_STATUS_PAGECACHE_USED]] ^(
SQLITE_STATUS_PAGECACHE_USED
**
This parameter returns the number of pages used out of the ** [pagecache memory allocator] that was configured using ** [SQLITE_CONFIG_PAGECACHE]. The ** value returned is in pages, not in bytes.
)^ ** ** [[SQLITE_STATUS_PAGECACHE_OVERFLOW]] ** ^(
SQLITE_STATUS_PAGECACHE_OVERFLOW
**
This parameter returns the number of bytes of page cache ** allocation which could not be satisfied by the [SQLITE_CONFIG_PAGECACHE] ** buffer and where forced to overflow to [sqlite3_malloc()]. The ** returned value includes allocations that overflowed because they ** where too large (they were larger than the "sz" parameter to ** [SQLITE_CONFIG_PAGECACHE]) and allocations that overflowed because ** no space was left in the page cache.
)^ ** ** [[SQLITE_STATUS_PAGECACHE_SIZE]] ^(
SQLITE_STATUS_PAGECACHE_SIZE
**
This parameter records the largest memory allocation request ** handed to [pagecache memory allocator]. Only the value returned in the ** *pHighwater parameter to [sqlite3_status()] is of interest. ** The value written into the *pCurrent parameter is undefined.
)^ ** ** [[SQLITE_STATUS_SCRATCH_USED]] ^(
SQLITE_STATUS_SCRATCH_USED
**
This parameter returns the number of allocations used out of the ** [scratch memory allocator] configured using ** [SQLITE_CONFIG_SCRATCH]. The value returned is in allocations, not ** in bytes. Since a single thread may only have one scratch allocation ** outstanding at time, this parameter also reports the number of threads ** using scratch memory at the same time.
)^ ** ** [[SQLITE_STATUS_SCRATCH_OVERFLOW]] ^(
SQLITE_STATUS_SCRATCH_OVERFLOW
**
This parameter returns the number of bytes of scratch memory ** allocation which could not be satisfied by the [SQLITE_CONFIG_SCRATCH] ** buffer and where forced to overflow to [sqlite3_malloc()]. The values ** returned include overflows because the requested allocation was too ** larger (that is, because the requested allocation was larger than the ** "sz" parameter to [SQLITE_CONFIG_SCRATCH]) and because no scratch buffer ** slots were available. **
)^ ** ** [[SQLITE_STATUS_SCRATCH_SIZE]] ^(
SQLITE_STATUS_SCRATCH_SIZE
**
This parameter records the largest memory allocation request ** handed to [scratch memory allocator]. Only the value returned in the ** *pHighwater parameter to [sqlite3_status()] is of interest. ** The value written into the *pCurrent parameter is undefined.
)^ ** ** [[SQLITE_STATUS_PARSER_STACK]] ^(
SQLITE_STATUS_PARSER_STACK
**
This parameter records the deepest parser stack. It is only ** meaningful if SQLite is compiled with [YYTRACKMAXSTACKDEPTH].
)^ **
** ** New status parameters may be added from time to time. */ #define SQLITE_STATUS_MEMORY_USED 0 #define SQLITE_STATUS_PAGECACHE_USED 1 #define SQLITE_STATUS_PAGECACHE_OVERFLOW 2 #define SQLITE_STATUS_SCRATCH_USED 3 #define SQLITE_STATUS_SCRATCH_OVERFLOW 4 #define SQLITE_STATUS_MALLOC_SIZE 5 #define SQLITE_STATUS_PARSER_STACK 6 #define SQLITE_STATUS_PAGECACHE_SIZE 7 #define SQLITE_STATUS_SCRATCH_SIZE 8 #define SQLITE_STATUS_MALLOC_COUNT 9 /* ** CAPI3REF: Database Connection Status ** ** ^This interface is used to retrieve runtime status information ** about a single [database connection]. ^The first argument is the ** database connection object to be interrogated. ^The second argument ** is an integer constant, taken from the set of ** [SQLITE_DBSTATUS options], that ** determines the parameter to interrogate. The set of ** [SQLITE_DBSTATUS options] is likely ** to grow in future releases of SQLite. ** ** ^The current value of the requested parameter is written into *pCur ** and the highest instantaneous value is written into *pHiwtr. ^If ** the resetFlg is true, then the highest instantaneous value is ** reset back down to the current value. ** ** ^The sqlite3_db_status() routine returns SQLITE_OK on success and a ** non-zero [error code] on failure. ** ** See also: [sqlite3_status()] and [sqlite3_stmt_status()]. */ SQLITE_API int sqlite3_db_status(sqlite3*, int op, int *pCur, int *pHiwtr, int resetFlg); /* ** CAPI3REF: Status Parameters for database connections ** KEYWORDS: {SQLITE_DBSTATUS options} ** ** These constants are the available integer "verbs" that can be passed as ** the second argument to the [sqlite3_db_status()] interface. ** ** New verbs may be added in future releases of SQLite. Existing verbs ** might be discontinued. Applications should check the return code from ** [sqlite3_db_status()] to make sure that the call worked. ** The [sqlite3_db_status()] interface will return a non-zero error code ** if a discontinued or unsupported verb is invoked. ** **
** [[SQLITE_DBSTATUS_LOOKASIDE_USED]] ^(
SQLITE_DBSTATUS_LOOKASIDE_USED
**
This parameter returns the number of lookaside memory slots currently ** checked out.
)^ ** ** [[SQLITE_DBSTATUS_LOOKASIDE_HIT]] ^(
SQLITE_DBSTATUS_LOOKASIDE_HIT
**
This parameter returns the number malloc attempts that were ** satisfied using lookaside memory. Only the high-water value is meaningful; ** the current value is always zero.)^ ** ** [[SQLITE_DBSTATUS_LOOKASIDE_MISS_SIZE]] ** ^(
SQLITE_DBSTATUS_LOOKASIDE_MISS_SIZE
**
This parameter returns the number malloc attempts that might have ** been satisfied using lookaside memory but failed due to the amount of ** memory requested being larger than the lookaside slot size. ** Only the high-water value is meaningful; ** the current value is always zero.)^ ** ** [[SQLITE_DBSTATUS_LOOKASIDE_MISS_FULL]] ** ^(
SQLITE_DBSTATUS_LOOKASIDE_MISS_FULL
**
This parameter returns the number malloc attempts that might have ** been satisfied using lookaside memory but failed due to all lookaside ** memory already being in use. ** Only the high-water value is meaningful; ** the current value is always zero.)^ ** ** [[SQLITE_DBSTATUS_CACHE_USED]] ^(
SQLITE_DBSTATUS_CACHE_USED
**
This parameter returns the approximate number of of bytes of heap ** memory used by all pager caches associated with the database connection.)^ ** ^The highwater mark associated with SQLITE_DBSTATUS_CACHE_USED is always 0. ** ** [[SQLITE_DBSTATUS_SCHEMA_USED]] ^(
SQLITE_DBSTATUS_SCHEMA_USED
**
This parameter returns the approximate number of of bytes of heap ** memory used to store the schema for all databases associated ** with the connection - main, temp, and any [ATTACH]-ed databases.)^ ** ^The full amount of memory used by the schemas is reported, even if the ** schema memory is shared with other database connections due to ** [shared cache mode] being enabled. ** ^The highwater mark associated with SQLITE_DBSTATUS_SCHEMA_USED is always 0. ** ** [[SQLITE_DBSTATUS_STMT_USED]] ^(
SQLITE_DBSTATUS_STMT_USED
**
This parameter returns the approximate number of of bytes of heap ** and lookaside memory used by all prepared statements associated with ** the database connection.)^ ** ^The highwater mark associated with SQLITE_DBSTATUS_STMT_USED is always 0. **
**
*/ #define SQLITE_DBSTATUS_LOOKASIDE_USED 0 #define SQLITE_DBSTATUS_CACHE_USED 1 #define SQLITE_DBSTATUS_SCHEMA_USED 2 #define SQLITE_DBSTATUS_STMT_USED 3 #define SQLITE_DBSTATUS_LOOKASIDE_HIT 4 #define SQLITE_DBSTATUS_LOOKASIDE_MISS_SIZE 5 #define SQLITE_DBSTATUS_LOOKASIDE_MISS_FULL 6 #define SQLITE_DBSTATUS_MAX 6 /* Largest defined DBSTATUS */ /* ** CAPI3REF: Prepared Statement Status ** ** ^(Each prepared statement maintains various ** [SQLITE_STMTSTATUS counters] that measure the number ** of times it has performed specific operations.)^ These counters can ** be used to monitor the performance characteristics of the prepared ** statements. For example, if the number of table steps greatly exceeds ** the number of table searches or result rows, that would tend to indicate ** that the prepared statement is using a full table scan rather than ** an index. ** ** ^(This interface is used to retrieve and reset counter values from ** a [prepared statement]. The first argument is the prepared statement ** object to be interrogated. The second argument ** is an integer code for a specific [SQLITE_STMTSTATUS counter] ** to be interrogated.)^ ** ^The current value of the requested counter is returned. ** ^If the resetFlg is true, then the counter is reset to zero after this ** interface call returns. ** ** See also: [sqlite3_status()] and [sqlite3_db_status()]. */ SQLITE_API int sqlite3_stmt_status(sqlite3_stmt*, int op,int resetFlg); /* ** CAPI3REF: Status Parameters for prepared statements ** KEYWORDS: {SQLITE_STMTSTATUS counter} {SQLITE_STMTSTATUS counters} ** ** These preprocessor macros define integer codes that name counter ** values associated with the [sqlite3_stmt_status()] interface. ** The meanings of the various counters are as follows: ** **
** [[SQLITE_STMTSTATUS_FULLSCAN_STEP]]
SQLITE_STMTSTATUS_FULLSCAN_STEP
**
^This is the number of times that SQLite has stepped forward in ** a table as part of a full table scan. Large numbers for this counter ** may indicate opportunities for performance improvement through ** careful use of indices.
** ** [[SQLITE_STMTSTATUS_SORT]]
SQLITE_STMTSTATUS_SORT
**
^This is the number of sort operations that have occurred. ** A non-zero value in this counter may indicate an opportunity to ** improvement performance through careful use of indices.
** ** [[SQLITE_STMTSTATUS_AUTOINDEX]]
SQLITE_STMTSTATUS_AUTOINDEX
**
^This is the number of rows inserted into transient indices that ** were created automatically in order to help joins run faster. ** A non-zero value in this counter may indicate an opportunity to ** improvement performance by adding permanent indices that do not ** need to be reinitialized each time the statement is run.
** **
*/ #define SQLITE_STMTSTATUS_FULLSCAN_STEP 1 #define SQLITE_STMTSTATUS_SORT 2 #define SQLITE_STMTSTATUS_AUTOINDEX 3 /* ** CAPI3REF: Custom Page Cache Object ** ** The sqlite3_pcache type is opaque. It is implemented by ** the pluggable module. The SQLite core has no knowledge of ** its size or internal structure and never deals with the ** sqlite3_pcache object except by holding and passing pointers ** to the object. ** ** See [sqlite3_pcache_methods] for additional information. */ typedef struct sqlite3_pcache sqlite3_pcache; /* ** CAPI3REF: Application Defined Page Cache. ** KEYWORDS: {page cache} ** ** ^(The [sqlite3_config]([SQLITE_CONFIG_PCACHE], ...) interface can ** register an alternative page cache implementation by passing in an ** instance of the sqlite3_pcache_methods structure.)^ ** In many applications, most of the heap memory allocated by ** SQLite is used for the page cache. ** By implementing a ** custom page cache using this API, an application can better control ** the amount of memory consumed by SQLite, the way in which ** that memory is allocated and released, and the policies used to ** determine exactly which parts of a database file are cached and for ** how long. ** ** The alternative page cache mechanism is an ** extreme measure that is only needed by the most demanding applications. ** The built-in page cache is recommended for most uses. ** ** ^(The contents of the sqlite3_pcache_methods structure are copied to an ** internal buffer by SQLite within the call to [sqlite3_config]. Hence ** the application may discard the parameter after the call to ** [sqlite3_config()] returns.)^ ** ** [[the xInit() page cache method]] ** ^(The xInit() method is called once for each effective ** call to [sqlite3_initialize()])^ ** (usually only once during the lifetime of the process). ^(The xInit() ** method is passed a copy of the sqlite3_pcache_methods.pArg value.)^ ** The intent of the xInit() method is to set up global data structures ** required by the custom page cache implementation. ** ^(If the xInit() method is NULL, then the ** built-in default page cache is used instead of the application defined ** page cache.)^ ** ** [[the xShutdown() page cache method]] ** ^The xShutdown() method is called by [sqlite3_shutdown()]. ** It can be used to clean up ** any outstanding resources before process shutdown, if required. ** ^The xShutdown() method may be NULL. ** ** ^SQLite automatically serializes calls to the xInit method, ** so the xInit method need not be threadsafe. ^The ** xShutdown method is only called from [sqlite3_shutdown()] so it does ** not need to be threadsafe either. All other methods must be threadsafe ** in multithreaded applications. ** ** ^SQLite will never invoke xInit() more than once without an intervening ** call to xShutdown(). ** ** [[the xCreate() page cache methods]] ** ^SQLite invokes the xCreate() method to construct a new cache instance. ** SQLite will typically create one cache instance for each open database file, ** though this is not guaranteed. ^The ** first parameter, szPage, is the size in bytes of the pages that must ** be allocated by the cache. ^szPage will not be a power of two. ^szPage ** will the page size of the database file that is to be cached plus an ** increment (here called "R") of less than 250. SQLite will use the ** extra R bytes on each page to store metadata about the underlying ** database page on disk. The value of R depends ** on the SQLite version, the target platform, and how SQLite was compiled. ** ^(R is constant for a particular build of SQLite. Except, there are two ** distinct values of R when SQLite is compiled with the proprietary ** ZIPVFS extension.)^ ^The second argument to ** xCreate(), bPurgeable, is true if the cache being created will ** be used to cache database pages of a file stored on disk, or ** false if it is used for an in-memory database. The cache implementation ** does not have to do anything special based with the value of bPurgeable; ** it is purely advisory. ^On a cache where bPurgeable is false, SQLite will ** never invoke xUnpin() except to deliberately delete a page. ** ^In other words, calls to xUnpin() on a cache with bPurgeable set to ** false will always have the "discard" flag set to true. ** ^Hence, a cache created with bPurgeable false will ** never contain any unpinned pages. ** ** [[the xCachesize() page cache method]] ** ^(The xCachesize() method may be called at any time by SQLite to set the ** suggested maximum cache-size (number of pages stored by) the cache ** instance passed as the first argument. This is the value configured using ** the SQLite "[PRAGMA cache_size]" command.)^ As with the bPurgeable ** parameter, the implementation is not required to do anything with this ** value; it is advisory only. ** ** [[the xPagecount() page cache methods]] ** The xPagecount() method must return the number of pages currently ** stored in the cache, both pinned and unpinned. ** ** [[the xFetch() page cache methods]] ** The xFetch() method locates a page in the cache and returns a pointer to ** the page, or a NULL pointer. ** A "page", in this context, means a buffer of szPage bytes aligned at an ** 8-byte boundary. The page to be fetched is determined by the key. ^The ** minimum key value is 1. After it has been retrieved using xFetch, the page ** is considered to be "pinned". ** ** If the requested page is already in the page cache, then the page cache ** implementation must return a pointer to the page buffer with its content ** intact. If the requested page is not already in the cache, then the ** cache implementation should use the value of the createFlag ** parameter to help it determined what action to take: ** ** **
createFlag Behaviour when page is not already in cache **
0 Do not allocate a new page. Return NULL. **
1 Allocate a new page if it easy and convenient to do so. ** Otherwise return NULL. **
2 Make every effort to allocate a new page. Only return ** NULL if allocating a new page is effectively impossible. **
** ** ^(SQLite will normally invoke xFetch() with a createFlag of 0 or 1. SQLite ** will only use a createFlag of 2 after a prior call with a createFlag of 1 ** failed.)^ In between the to xFetch() calls, SQLite may ** attempt to unpin one or more cache pages by spilling the content of ** pinned pages to disk and synching the operating system disk cache. ** ** [[the xUnpin() page cache method]] ** ^xUnpin() is called by SQLite with a pointer to a currently pinned page ** as its second argument. If the third parameter, discard, is non-zero, ** then the page must be evicted from the cache. ** ^If the discard parameter is ** zero, then the page may be discarded or retained at the discretion of ** page cache implementation. ^The page cache implementation ** may choose to evict unpinned pages at any time. ** ** The cache must not perform any reference counting. A single ** call to xUnpin() unpins the page regardless of the number of prior calls ** to xFetch(). ** ** [[the xRekey() page cache methods]] ** The xRekey() method is used to change the key value associated with the ** page passed as the second argument. If the cache ** previously contains an entry associated with newKey, it must be ** discarded. ^Any prior cache entry associated with newKey is guaranteed not ** to be pinned. ** ** When SQLite calls the xTruncate() method, the cache must discard all ** existing cache entries with page numbers (keys) greater than or equal ** to the value of the iLimit parameter passed to xTruncate(). If any ** of these pages are pinned, they are implicitly unpinned, meaning that ** they can be safely discarded. ** ** [[the xDestroy() page cache method]] ** ^The xDestroy() method is used to delete a cache allocated by xCreate(). ** All resources associated with the specified cache should be freed. ^After ** calling the xDestroy() method, SQLite considers the [sqlite3_pcache*] ** handle invalid, and will not use it with any other sqlite3_pcache_methods ** functions. */ typedef struct sqlite3_pcache_methods sqlite3_pcache_methods; struct sqlite3_pcache_methods { void *pArg; int (*xInit)(void*); void (*xShutdown)(void*); sqlite3_pcache *(*xCreate)(int szPage, int bPurgeable); void (*xCachesize)(sqlite3_pcache*, int nCachesize); int (*xPagecount)(sqlite3_pcache*); void *(*xFetch)(sqlite3_pcache*, unsigned key, int createFlag); void (*xUnpin)(sqlite3_pcache*, void*, int discard); void (*xRekey)(sqlite3_pcache*, void*, unsigned oldKey, unsigned newKey); void (*xTruncate)(sqlite3_pcache*, unsigned iLimit); void (*xDestroy)(sqlite3_pcache*); }; /* ** CAPI3REF: Online Backup Object ** ** The sqlite3_backup object records state information about an ongoing ** online backup operation. ^The sqlite3_backup object is created by ** a call to [sqlite3_backup_init()] and is destroyed by a call to ** [sqlite3_backup_finish()]. ** ** See Also: [Using the SQLite Online Backup API] */ typedef struct sqlite3_backup sqlite3_backup; /* ** CAPI3REF: Online Backup API. ** ** The backup API copies the content of one database into another. ** It is useful either for creating backups of databases or ** for copying in-memory databases to or from persistent files. ** ** See Also: [Using the SQLite Online Backup API] ** ** ^SQLite holds a write transaction open on the destination database file ** for the duration of the backup operation. ** ^The source database is read-locked only while it is being read; ** it is not locked continuously for the entire backup operation. ** ^Thus, the backup may be performed on a live source database without ** preventing other database connections from ** reading or writing to the source database while the backup is underway. ** ** ^(To perform a backup operation: **
    **
  1. sqlite3_backup_init() is called once to initialize the ** backup, **
  2. sqlite3_backup_step() is called one or more times to transfer ** the data between the two databases, and finally **
  3. sqlite3_backup_finish() is called to release all resources ** associated with the backup operation. **
)^ ** There should be exactly one call to sqlite3_backup_finish() for each ** successful call to sqlite3_backup_init(). ** ** [[sqlite3_backup_init()]] sqlite3_backup_init() ** ** ^The D and N arguments to sqlite3_backup_init(D,N,S,M) are the ** [database connection] associated with the destination database ** and the database name, respectively. ** ^The database name is "main" for the main database, "temp" for the ** temporary database, or the name specified after the AS keyword in ** an [ATTACH] statement for an attached database. ** ^The S and M arguments passed to ** sqlite3_backup_init(D,N,S,M) identify the [database connection] ** and database name of the source database, respectively. ** ^The source and destination [database connections] (parameters S and D) ** must be different or else sqlite3_backup_init(D,N,S,M) will fail with ** an error. ** ** ^If an error occurs within sqlite3_backup_init(D,N,S,M), then NULL is ** returned and an error code and error message are stored in the ** destination [database connection] D. ** ^The error code and message for the failed call to sqlite3_backup_init() ** can be retrieved using the [sqlite3_errcode()], [sqlite3_errmsg()], and/or ** [sqlite3_errmsg16()] functions. ** ^A successful call to sqlite3_backup_init() returns a pointer to an ** [sqlite3_backup] object. ** ^The [sqlite3_backup] object may be used with the sqlite3_backup_step() and ** sqlite3_backup_finish() functions to perform the specified backup ** operation. ** ** [[sqlite3_backup_step()]] sqlite3_backup_step() ** ** ^Function sqlite3_backup_step(B,N) will copy up to N pages between ** the source and destination databases specified by [sqlite3_backup] object B. ** ^If N is negative, all remaining source pages are copied. ** ^If sqlite3_backup_step(B,N) successfully copies N pages and there ** are still more pages to be copied, then the function returns [SQLITE_OK]. ** ^If sqlite3_backup_step(B,N) successfully finishes copying all pages ** from source to destination, then it returns [SQLITE_DONE]. ** ^If an error occurs while running sqlite3_backup_step(B,N), ** then an [error code] is returned. ^As well as [SQLITE_OK] and ** [SQLITE_DONE], a call to sqlite3_backup_step() may return [SQLITE_READONLY], ** [SQLITE_NOMEM], [SQLITE_BUSY], [SQLITE_LOCKED], or an ** [SQLITE_IOERR_ACCESS | SQLITE_IOERR_XXX] extended error code. ** ** ^(The sqlite3_backup_step() might return [SQLITE_READONLY] if **
    **
  1. the destination database was opened read-only, or **
  2. the destination database is using write-ahead-log journaling ** and the destination and source page sizes differ, or **
  3. the destination database is an in-memory database and the ** destination and source page sizes differ. **
)^ ** ** ^If sqlite3_backup_step() cannot obtain a required file-system lock, then ** the [sqlite3_busy_handler | busy-handler function] ** is invoked (if one is specified). ^If the ** busy-handler returns non-zero before the lock is available, then ** [SQLITE_BUSY] is returned to the caller. ^In this case the call to ** sqlite3_backup_step() can be retried later. ^If the source ** [database connection] ** is being used to write to the source database when sqlite3_backup_step() ** is called, then [SQLITE_LOCKED] is returned immediately. ^Again, in this ** case the call to sqlite3_backup_step() can be retried later on. ^(If ** [SQLITE_IOERR_ACCESS | SQLITE_IOERR_XXX], [SQLITE_NOMEM], or ** [SQLITE_READONLY] is returned, then ** there is no point in retrying the call to sqlite3_backup_step(). These ** errors are considered fatal.)^ The application must accept ** that the backup operation has failed and pass the backup operation handle ** to the sqlite3_backup_finish() to release associated resources. ** ** ^The first call to sqlite3_backup_step() obtains an exclusive lock ** on the destination file. ^The exclusive lock is not released until either ** sqlite3_backup_finish() is called or the backup operation is complete ** and sqlite3_backup_step() returns [SQLITE_DONE]. ^Every call to ** sqlite3_backup_step() obtains a [shared lock] on the source database that ** lasts for the duration of the sqlite3_backup_step() call. ** ^Because the source database is not locked between calls to ** sqlite3_backup_step(), the source database may be modified mid-way ** through the backup process. ^If the source database is modified by an ** external process or via a database connection other than the one being ** used by the backup operation, then the backup will be automatically ** restarted by the next call to sqlite3_backup_step(). ^If the source ** database is modified by the using the same database connection as is used ** by the backup operation, then the backup database is automatically ** updated at the same time. ** ** [[sqlite3_backup_finish()]] sqlite3_backup_finish() ** ** When sqlite3_backup_step() has returned [SQLITE_DONE], or when the ** application wishes to abandon the backup operation, the application ** should destroy the [sqlite3_backup] by passing it to sqlite3_backup_finish(). ** ^The sqlite3_backup_finish() interfaces releases all ** resources associated with the [sqlite3_backup] object. ** ^If sqlite3_backup_step() has not yet returned [SQLITE_DONE], then any ** active write-transaction on the destination database is rolled back. ** The [sqlite3_backup] object is invalid ** and may not be used following a call to sqlite3_backup_finish(). ** ** ^The value returned by sqlite3_backup_finish is [SQLITE_OK] if no ** sqlite3_backup_step() errors occurred, regardless or whether or not ** sqlite3_backup_step() completed. ** ^If an out-of-memory condition or IO error occurred during any prior ** sqlite3_backup_step() call on the same [sqlite3_backup] object, then ** sqlite3_backup_finish() returns the corresponding [error code]. ** ** ^A return of [SQLITE_BUSY] or [SQLITE_LOCKED] from sqlite3_backup_step() ** is not a permanent error and does not affect the return value of ** sqlite3_backup_finish(). ** ** [[sqlite3_backup__remaining()]] [[sqlite3_backup_pagecount()]] ** sqlite3_backup_remaining() and sqlite3_backup_pagecount() ** ** ^Each call to sqlite3_backup_step() sets two values inside ** the [sqlite3_backup] object: the number of pages still to be backed ** up and the total number of pages in the source database file. ** The sqlite3_backup_remaining() and sqlite3_backup_pagecount() interfaces ** retrieve these two values, respectively. ** ** ^The values returned by these functions are only updated by ** sqlite3_backup_step(). ^If the source database is modified during a backup ** operation, then the values are not updated to account for any extra ** pages that need to be updated or the size of the source database file ** changing. ** ** Concurrent Usage of Database Handles ** ** ^The source [database connection] may be used by the application for other ** purposes while a backup operation is underway or being initialized. ** ^If SQLite is compiled and configured to support threadsafe database ** connections, then the source database connection may be used concurrently ** from within other threads. ** ** However, the application must guarantee that the destination ** [database connection] is not passed to any other API (by any thread) after ** sqlite3_backup_init() is called and before the corresponding call to ** sqlite3_backup_finish(). SQLite does not currently check to see ** if the application incorrectly accesses the destination [database connection] ** and so no error code is reported, but the operations may malfunction ** nevertheless. Use of the destination database connection while a ** backup is in progress might also also cause a mutex deadlock. ** ** If running in [shared cache mode], the application must ** guarantee that the shared cache used by the destination database ** is not accessed while the backup is running. In practice this means ** that the application must guarantee that the disk file being ** backed up to is not accessed by any connection within the process, ** not just the specific connection that was passed to sqlite3_backup_init(). ** ** The [sqlite3_backup] object itself is partially threadsafe. Multiple ** threads may safely make multiple concurrent calls to sqlite3_backup_step(). ** However, the sqlite3_backup_remaining() and sqlite3_backup_pagecount() ** APIs are not strictly speaking threadsafe. If they are invoked at the ** same time as another thread is invoking sqlite3_backup_step() it is ** possible that they return invalid values. */ SQLITE_API sqlite3_backup *sqlite3_backup_init( sqlite3 *pDest, /* Destination database handle */ const char *zDestName, /* Destination database name */ sqlite3 *pSource, /* Source database handle */ const char *zSourceName /* Source database name */ ); SQLITE_API int sqlite3_backup_step(sqlite3_backup *p, int nPage); SQLITE_API int sqlite3_backup_finish(sqlite3_backup *p); SQLITE_API int sqlite3_backup_remaining(sqlite3_backup *p); SQLITE_API int sqlite3_backup_pagecount(sqlite3_backup *p); /* ** CAPI3REF: Unlock Notification ** ** ^When running in shared-cache mode, a database operation may fail with ** an [SQLITE_LOCKED] error if the required locks on the shared-cache or ** individual tables within the shared-cache cannot be obtained. See ** [SQLite Shared-Cache Mode] for a description of shared-cache locking. ** ^This API may be used to register a callback that SQLite will invoke ** when the connection currently holding the required lock relinquishes it. ** ^This API is only available if the library was compiled with the ** [SQLITE_ENABLE_UNLOCK_NOTIFY] C-preprocessor symbol defined. ** ** See Also: [Using the SQLite Unlock Notification Feature]. ** ** ^Shared-cache locks are released when a database connection concludes ** its current transaction, either by committing it or rolling it back. ** ** ^When a connection (known as the blocked connection) fails to obtain a ** shared-cache lock and SQLITE_LOCKED is returned to the caller, the ** identity of the database connection (the blocking connection) that ** has locked the required resource is stored internally. ^After an ** application receives an SQLITE_LOCKED error, it may call the ** sqlite3_unlock_notify() method with the blocked connection handle as ** the first argument to register for a callback that will be invoked ** when the blocking connections current transaction is concluded. ^The ** callback is invoked from within the [sqlite3_step] or [sqlite3_close] ** call that concludes the blocking connections transaction. ** ** ^(If sqlite3_unlock_notify() is called in a multi-threaded application, ** there is a chance that the blocking connection will have already ** concluded its transaction by the time sqlite3_unlock_notify() is invoked. ** If this happens, then the specified callback is invoked immediately, ** from within the call to sqlite3_unlock_notify().)^ ** ** ^If the blocked connection is attempting to obtain a write-lock on a ** shared-cache table, and more than one other connection currently holds ** a read-lock on the same table, then SQLite arbitrarily selects one of ** the other connections to use as the blocking connection. ** ** ^(There may be at most one unlock-notify callback registered by a ** blocked connection. If sqlite3_unlock_notify() is called when the ** blocked connection already has a registered unlock-notify callback, ** then the new callback replaces the old.)^ ^If sqlite3_unlock_notify() is ** called with a NULL pointer as its second argument, then any existing ** unlock-notify callback is canceled. ^The blocked connections ** unlock-notify callback may also be canceled by closing the blocked ** connection using [sqlite3_close()]. ** ** The unlock-notify callback is not reentrant. If an application invokes ** any sqlite3_xxx API functions from within an unlock-notify callback, a ** crash or deadlock may be the result. ** ** ^Unless deadlock is detected (see below), sqlite3_unlock_notify() always ** returns SQLITE_OK. ** ** Callback Invocation Details ** ** When an unlock-notify callback is registered, the application provides a ** single void* pointer that is passed to the callback when it is invoked. ** However, the signature of the callback function allows SQLite to pass ** it an array of void* context pointers. The first argument passed to ** an unlock-notify callback is a pointer to an array of void* pointers, ** and the second is the number of entries in the array. ** ** When a blocking connections transaction is concluded, there may be ** more than one blocked connection that has registered for an unlock-notify ** callback. ^If two or more such blocked connections have specified the ** same callback function, then instead of invoking the callback function ** multiple times, it is invoked once with the set of void* context pointers ** specified by the blocked connections bundled together into an array. ** This gives the application an opportunity to prioritize any actions ** related to the set of unblocked database connections. ** ** Deadlock Detection ** ** Assuming that after registering for an unlock-notify callback a ** database waits for the callback to be issued before taking any further ** action (a reasonable assumption), then using this API may cause the ** application to deadlock. For example, if connection X is waiting for ** connection Y's transaction to be concluded, and similarly connection ** Y is waiting on connection X's transaction, then neither connection ** will proceed and the system may remain deadlocked indefinitely. ** ** To avoid this scenario, the sqlite3_unlock_notify() performs deadlock ** detection. ^If a given call to sqlite3_unlock_notify() would put the ** system in a deadlocked state, then SQLITE_LOCKED is returned and no ** unlock-notify callback is registered. The system is said to be in ** a deadlocked state if connection A has registered for an unlock-notify ** callback on the conclusion of connection B's transaction, and connection ** B has itself registered for an unlock-notify callback when connection ** A's transaction is concluded. ^Indirect deadlock is also detected, so ** the system is also considered to be deadlocked if connection B has ** registered for an unlock-notify callback on the conclusion of connection ** C's transaction, where connection C is waiting on connection A. ^Any ** number of levels of indirection are allowed. ** ** The "DROP TABLE" Exception ** ** When a call to [sqlite3_step()] returns SQLITE_LOCKED, it is almost ** always appropriate to call sqlite3_unlock_notify(). There is however, ** one exception. When executing a "DROP TABLE" or "DROP INDEX" statement, ** SQLite checks if there are any currently executing SELECT statements ** that belong to the same connection. If there are, SQLITE_LOCKED is ** returned. In this case there is no "blocking connection", so invoking ** sqlite3_unlock_notify() results in the unlock-notify callback being ** invoked immediately. If the application then re-attempts the "DROP TABLE" ** or "DROP INDEX" query, an infinite loop might be the result. ** ** One way around this problem is to check the extended error code returned ** by an sqlite3_step() call. ^(If there is a blocking connection, then the ** extended error code is set to SQLITE_LOCKED_SHAREDCACHE. Otherwise, in ** the special "DROP TABLE/INDEX" case, the extended error code is just ** SQLITE_LOCKED.)^ */ SQLITE_API int sqlite3_unlock_notify( sqlite3 *pBlocked, /* Waiting connection */ void (*xNotify)(void **apArg, int nArg), /* Callback function to invoke */ void *pNotifyArg /* Argument to pass to xNotify */ ); /* ** CAPI3REF: String Comparison ** ** ^The [sqlite3_strnicmp()] API allows applications and extensions to ** compare the contents of two buffers containing UTF-8 strings in a ** case-independent fashion, using the same definition of case independence ** that SQLite uses internally when comparing identifiers. */ SQLITE_API int sqlite3_strnicmp(const char *, const char *, int); /* ** CAPI3REF: Error Logging Interface ** ** ^The [sqlite3_log()] interface writes a message into the error log ** established by the [SQLITE_CONFIG_LOG] option to [sqlite3_config()]. ** ^If logging is enabled, the zFormat string and subsequent arguments are ** used with [sqlite3_snprintf()] to generate the final output string. ** ** The sqlite3_log() interface is intended for use by extensions such as ** virtual tables, collating functions, and SQL functions. While there is ** nothing to prevent an application from calling sqlite3_log(), doing so ** is considered bad form. ** ** The zFormat string must not be NULL. ** ** To avoid deadlocks and other threading problems, the sqlite3_log() routine ** will not use dynamically allocated memory. The log message is stored in ** a fixed-length buffer on the stack. If the log message is longer than ** a few hundred characters, it will be truncated to the length of the ** buffer. */ SQLITE_API void sqlite3_log(int iErrCode, const char *zFormat, ...); /* ** CAPI3REF: Write-Ahead Log Commit Hook ** ** ^The [sqlite3_wal_hook()] function is used to register a callback that ** will be invoked each time a database connection commits data to a ** [write-ahead log] (i.e. whenever a transaction is committed in ** [journal_mode | journal_mode=WAL mode]). ** ** ^The callback is invoked by SQLite after the commit has taken place and ** the associated write-lock on the database released, so the implementation ** may read, write or [checkpoint] the database as required. ** ** ^The first parameter passed to the callback function when it is invoked ** is a copy of the third parameter passed to sqlite3_wal_hook() when ** registering the callback. ^The second is a copy of the database handle. ** ^The third parameter is the name of the database that was written to - ** either "main" or the name of an [ATTACH]-ed database. ^The fourth parameter ** is the number of pages currently in the write-ahead log file, ** including those that were just committed. ** ** The callback function should normally return [SQLITE_OK]. ^If an error ** code is returned, that error will propagate back up through the ** SQLite code base to cause the statement that provoked the callback ** to report an error, though the commit will have still occurred. If the ** callback returns [SQLITE_ROW] or [SQLITE_DONE], or if it returns a value ** that does not correspond to any valid SQLite error code, the results ** are undefined. ** ** A single database handle may have at most a single write-ahead log callback ** registered at one time. ^Calling [sqlite3_wal_hook()] replaces any ** previously registered write-ahead log callback. ^Note that the ** [sqlite3_wal_autocheckpoint()] interface and the ** [wal_autocheckpoint pragma] both invoke [sqlite3_wal_hook()] and will ** those overwrite any prior [sqlite3_wal_hook()] settings. */ SQLITE_API void *sqlite3_wal_hook( sqlite3*, int(*)(void *,sqlite3*,const char*,int), void* ); /* ** CAPI3REF: Configure an auto-checkpoint ** ** ^The [sqlite3_wal_autocheckpoint(D,N)] is a wrapper around ** [sqlite3_wal_hook()] that causes any database on [database connection] D ** to automatically [checkpoint] ** after committing a transaction if there are N or ** more frames in the [write-ahead log] file. ^Passing zero or ** a negative value as the nFrame parameter disables automatic ** checkpoints entirely. ** ** ^The callback registered by this function replaces any existing callback ** registered using [sqlite3_wal_hook()]. ^Likewise, registering a callback ** using [sqlite3_wal_hook()] disables the automatic checkpoint mechanism ** configured by this function. ** ** ^The [wal_autocheckpoint pragma] can be used to invoke this interface ** from SQL. ** ** ^Every new [database connection] defaults to having the auto-checkpoint ** enabled with a threshold of 1000 or [SQLITE_DEFAULT_WAL_AUTOCHECKPOINT] ** pages. The use of this interface ** is only necessary if the default setting is found to be suboptimal ** for a particular application. */ SQLITE_API int sqlite3_wal_autocheckpoint(sqlite3 *db, int N); /* ** CAPI3REF: Checkpoint a database ** ** ^The [sqlite3_wal_checkpoint(D,X)] interface causes database named X ** on [database connection] D to be [checkpointed]. ^If X is NULL or an ** empty string, then a checkpoint is run on all databases of ** connection D. ^If the database connection D is not in ** [WAL | write-ahead log mode] then this interface is a harmless no-op. ** ** ^The [wal_checkpoint pragma] can be used to invoke this interface ** from SQL. ^The [sqlite3_wal_autocheckpoint()] interface and the ** [wal_autocheckpoint pragma] can be used to cause this interface to be ** run whenever the WAL reaches a certain size threshold. ** ** See also: [sqlite3_wal_checkpoint_v2()] */ SQLITE_API int sqlite3_wal_checkpoint(sqlite3 *db, const char *zDb); /* ** CAPI3REF: Checkpoint a database ** ** Run a checkpoint operation on WAL database zDb attached to database ** handle db. The specific operation is determined by the value of the ** eMode parameter: ** **
**
SQLITE_CHECKPOINT_PASSIVE
** Checkpoint as many frames as possible without waiting for any database ** readers or writers to finish. Sync the db file if all frames in the log ** are checkpointed. This mode is the same as calling ** sqlite3_wal_checkpoint(). The busy-handler callback is never invoked. ** **
SQLITE_CHECKPOINT_FULL
** This mode blocks (calls the busy-handler callback) until there is no ** database writer and all readers are reading from the most recent database ** snapshot. It then checkpoints all frames in the log file and syncs the ** database file. This call blocks database writers while it is running, ** but not database readers. ** **
SQLITE_CHECKPOINT_RESTART
** This mode works the same way as SQLITE_CHECKPOINT_FULL, except after ** checkpointing the log file it blocks (calls the busy-handler callback) ** until all readers are reading from the database file only. This ensures ** that the next client to write to the database file restarts the log file ** from the beginning. This call blocks database writers while it is running, ** but not database readers. **
** ** If pnLog is not NULL, then *pnLog is set to the total number of frames in ** the log file before returning. If pnCkpt is not NULL, then *pnCkpt is set to ** the total number of checkpointed frames (including any that were already ** checkpointed when this function is called). *pnLog and *pnCkpt may be ** populated even if sqlite3_wal_checkpoint_v2() returns other than SQLITE_OK. ** If no values are available because of an error, they are both set to -1 ** before returning to communicate this to the caller. ** ** All calls obtain an exclusive "checkpoint" lock on the database file. If ** any other process is running a checkpoint operation at the same time, the ** lock cannot be obtained and SQLITE_BUSY is returned. Even if there is a ** busy-handler configured, it will not be invoked in this case. ** ** The SQLITE_CHECKPOINT_FULL and RESTART modes also obtain the exclusive ** "writer" lock on the database file. If the writer lock cannot be obtained ** immediately, and a busy-handler is configured, it is invoked and the writer ** lock retried until either the busy-handler returns 0 or the lock is ** successfully obtained. The busy-handler is also invoked while waiting for ** database readers as described above. If the busy-handler returns 0 before ** the writer lock is obtained or while waiting for database readers, the ** checkpoint operation proceeds from that point in the same way as ** SQLITE_CHECKPOINT_PASSIVE - checkpointing as many frames as possible ** without blocking any further. SQLITE_BUSY is returned in this case. ** ** If parameter zDb is NULL or points to a zero length string, then the ** specified operation is attempted on all WAL databases. In this case the ** values written to output parameters *pnLog and *pnCkpt are undefined. If ** an SQLITE_BUSY error is encountered when processing one or more of the ** attached WAL databases, the operation is still attempted on any remaining ** attached databases and SQLITE_BUSY is returned to the caller. If any other ** error occurs while processing an attached database, processing is abandoned ** and the error code returned to the caller immediately. If no error ** (SQLITE_BUSY or otherwise) is encountered while processing the attached ** databases, SQLITE_OK is returned. ** ** If database zDb is the name of an attached database that is not in WAL ** mode, SQLITE_OK is returned and both *pnLog and *pnCkpt set to -1. If ** zDb is not NULL (or a zero length string) and is not the name of any ** attached database, SQLITE_ERROR is returned to the caller. */ SQLITE_API int sqlite3_wal_checkpoint_v2( sqlite3 *db, /* Database handle */ const char *zDb, /* Name of attached database (or NULL) */ int eMode, /* SQLITE_CHECKPOINT_* value */ int *pnLog, /* OUT: Size of WAL log in frames */ int *pnCkpt /* OUT: Total number of frames checkpointed */ ); /* ** CAPI3REF: Checkpoint operation parameters ** ** These constants can be used as the 3rd parameter to ** [sqlite3_wal_checkpoint_v2()]. See the [sqlite3_wal_checkpoint_v2()] ** documentation for additional information about the meaning and use of ** each of these values. */ #define SQLITE_CHECKPOINT_PASSIVE 0 #define SQLITE_CHECKPOINT_FULL 1 #define SQLITE_CHECKPOINT_RESTART 2 /* ** CAPI3REF: Virtual Table Interface Configuration ** ** This function may be called by either the [xConnect] or [xCreate] method ** of a [virtual table] implementation to configure ** various facets of the virtual table interface. ** ** If this interface is invoked outside the context of an xConnect or ** xCreate virtual table method then the behavior is undefined. ** ** At present, there is only one option that may be configured using ** this function. (See [SQLITE_VTAB_CONSTRAINT_SUPPORT].) Further options ** may be added in the future. */ SQLITE_API int sqlite3_vtab_config(sqlite3*, int op, ...); /* ** CAPI3REF: Virtual Table Configuration Options ** ** These macros define the various options to the ** [sqlite3_vtab_config()] interface that [virtual table] implementations ** can use to customize and optimize their behavior. ** **
**
SQLITE_VTAB_CONSTRAINT_SUPPORT **
Calls of the form ** [sqlite3_vtab_config](db,SQLITE_VTAB_CONSTRAINT_SUPPORT,X) are supported, ** where X is an integer. If X is zero, then the [virtual table] whose ** [xCreate] or [xConnect] method invoked [sqlite3_vtab_config()] does not ** support constraints. In this configuration (which is the default) if ** a call to the [xUpdate] method returns [SQLITE_CONSTRAINT], then the entire ** statement is rolled back as if [ON CONFLICT | OR ABORT] had been ** specified as part of the users SQL statement, regardless of the actual ** ON CONFLICT mode specified. ** ** If X is non-zero, then the virtual table implementation guarantees ** that if [xUpdate] returns [SQLITE_CONSTRAINT], it will do so before ** any modifications to internal or persistent data structures have been made. ** If the [ON CONFLICT] mode is ABORT, FAIL, IGNORE or ROLLBACK, SQLite ** is able to roll back a statement or database transaction, and abandon ** or continue processing the current SQL statement as appropriate. ** If the ON CONFLICT mode is REPLACE and the [xUpdate] method returns ** [SQLITE_CONSTRAINT], SQLite handles this as if the ON CONFLICT mode ** had been ABORT. ** ** Virtual table implementations that are required to handle OR REPLACE ** must do so within the [xUpdate] method. If a call to the ** [sqlite3_vtab_on_conflict()] function indicates that the current ON ** CONFLICT policy is REPLACE, the virtual table implementation should ** silently replace the appropriate rows within the xUpdate callback and ** return SQLITE_OK. Or, if this is not possible, it may return ** SQLITE_CONSTRAINT, in which case SQLite falls back to OR ABORT ** constraint handling. **
*/ #define SQLITE_VTAB_CONSTRAINT_SUPPORT 1 /* ** CAPI3REF: Determine The Virtual Table Conflict Policy ** ** This function may only be called from within a call to the [xUpdate] method ** of a [virtual table] implementation for an INSERT or UPDATE operation. ^The ** value returned is one of [SQLITE_ROLLBACK], [SQLITE_IGNORE], [SQLITE_FAIL], ** [SQLITE_ABORT], or [SQLITE_REPLACE], according to the [ON CONFLICT] mode ** of the SQL statement that triggered the call to the [xUpdate] method of the ** [virtual table]. */ SQLITE_API int sqlite3_vtab_on_conflict(sqlite3 *); /* ** CAPI3REF: Conflict resolution modes ** ** These constants are returned by [sqlite3_vtab_on_conflict()] to ** inform a [virtual table] implementation what the [ON CONFLICT] mode ** is for the SQL statement being evaluated. ** ** Note that the [SQLITE_IGNORE] constant is also used as a potential ** return value from the [sqlite3_set_authorizer()] callback and that ** [SQLITE_ABORT] is also a [result code]. */ #define SQLITE_ROLLBACK 1 /* #define SQLITE_IGNORE 2 // Also used by sqlite3_authorizer() callback */ #define SQLITE_FAIL 3 /* #define SQLITE_ABORT 4 // Also an error code */ #define SQLITE_REPLACE 5 /* ** Undo the hack that converts floating point types to integer for ** builds on processors without floating point support. */ #ifdef SQLITE_OMIT_FLOATING_POINT # undef double #endif #ifdef __cplusplus } /* End of the 'extern "C"' block */ #endif #endif /* ** 2010 August 30 ** ** The author disclaims copyright to this source code. In place of ** a legal notice, here is a blessing: ** ** May you do good and not evil. ** May you find forgiveness for yourself and forgive others. ** May you share freely, never taking more than you give. ** ************************************************************************* */ #ifndef _SQLITE3RTREE_H_ #define _SQLITE3RTREE_H_ #ifdef __cplusplus extern "C" { #endif typedef struct sqlite3_rtree_geometry sqlite3_rtree_geometry; /* ** Register a geometry callback named zGeom that can be used as part of an ** R-Tree geometry query as follows: ** ** SELECT ... FROM WHERE MATCH $zGeom(... params ...) */ SQLITE_API int sqlite3_rtree_geometry_callback( sqlite3 *db, const char *zGeom, int (*xGeom)(sqlite3_rtree_geometry *, int nCoord, double *aCoord, int *pRes), void *pContext ); /* ** A pointer to a structure of the following type is passed as the first ** argument to callbacks registered using rtree_geometry_callback(). */ struct sqlite3_rtree_geometry { void *pContext; /* Copy of pContext passed to s_r_g_c() */ int nParam; /* Size of array aParam[] */ double *aParam; /* Parameters passed to SQL geom function */ void *pUser; /* Callback implementation user data */ void (*xDelUser)(void *); /* Called by SQLite to clean up pUser */ }; #ifdef __cplusplus } /* end of the 'extern "C"' block */ #endif #endif /* ifndef _SQLITE3RTREE_H_ */ libmstoolkit-77.0.0/include/inffast.h0000644000175000017500000000065312455161024017501 0ustar rusconirusconi/* inffast.h -- header to use inffast.c * Copyright (C) 1995-2003, 2010 Mark Adler * For conditions of distribution and use, see copyright notice in zlib.h */ /* WARNING: this file should *not* be used by applications. It is part of the implementation of the compression library and is subject to change. Applications should only use zlib.h. */ void ZLIB_INTERNAL inflate_fast OF((z_streamp strm, unsigned start)); libmstoolkit-77.0.0/include/gzguts.h0000644000175000017500000001110512455161024017364 0ustar rusconirusconi/* gzguts.h -- zlib internal header definitions for gz* operations * Copyright (C) 2004, 2005, 2010 Mark Adler * For conditions of distribution and use, see copyright notice in zlib.h */ #ifdef _LARGEFILE64_SOURCE # ifndef _LARGEFILE_SOURCE # define _LARGEFILE_SOURCE 1 # endif # ifdef _FILE_OFFSET_BITS # undef _FILE_OFFSET_BITS # endif #endif #if ((__GNUC__-0) * 10 + __GNUC_MINOR__-0 >= 33) && !defined(NO_VIZ) # define ZLIB_INTERNAL __attribute__((visibility ("hidden"))) #else # define ZLIB_INTERNAL #endif #include #include "zlib.h" #ifdef STDC # include # include # include #endif #include #ifdef NO_DEFLATE /* for compatibility with old definition */ # define NO_GZCOMPRESS #endif #ifdef _MSC_VER # include # define vsnprintf _vsnprintf #endif #ifndef local # define local static #endif /* compile with -Dlocal if your debugger can't find static symbols */ /* gz* functions always use library allocation functions */ #ifndef STDC extern voidp malloc OF((uInt size)); extern void free OF((voidpf ptr)); #endif /* get errno and strerror definition */ #if defined UNDER_CE # include # define zstrerror() gz_strwinerror((DWORD)GetLastError()) #else # ifdef STDC # include # define zstrerror() strerror(errno) # else # define zstrerror() "stdio error (consult errno)" # endif #endif /* provide prototypes for these when building zlib without LFS */ #if !defined(_LARGEFILE64_SOURCE) || _LFS64_LARGEFILE-0 == 0 ZEXTERN gzFile ZEXPORT gzopen64 OF((const char *, const char *)); ZEXTERN z_off64_t ZEXPORT gzseek64 OF((gzFile, z_off64_t, int)); ZEXTERN z_off64_t ZEXPORT gztell64 OF((gzFile)); ZEXTERN z_off64_t ZEXPORT gzoffset64 OF((gzFile)); #endif /* default i/o buffer size -- double this for output when reading */ #define GZBUFSIZE 8192 /* gzip modes, also provide a little integrity check on the passed structure */ #define GZ_NONE 0 #define GZ_READ 7247 #define GZ_WRITE 31153 #define GZ_APPEND 1 /* mode set to GZ_WRITE after the file is opened */ /* values for gz_state how */ #define LOOK 0 /* look for a gzip header */ #define COPY 1 /* copy input directly */ #define GZIP 2 /* decompress a gzip stream */ /* internal gzip file state data structure */ typedef struct { /* used for both reading and writing */ int mode; /* see gzip modes above */ int fd; /* file descriptor */ char *path; /* path or fd for error messages */ z_off64_t pos; /* current position in uncompressed data */ unsigned size; /* buffer size, zero if not allocated yet */ unsigned want; /* requested buffer size, default is GZBUFSIZE */ unsigned char *in; /* input buffer */ unsigned char *out; /* output buffer (double-sized when reading) */ unsigned char *next; /* next output data to deliver or write */ /* just for reading */ unsigned have; /* amount of output data unused at next */ int eof; /* true if end of input file reached */ z_off64_t start; /* where the gzip data started, for rewinding */ z_off64_t raw; /* where the raw data started, for seeking */ int how; /* 0: get header, 1: copy, 2: decompress */ int direct; /* true if last read direct, false if gzip */ /* just for writing */ int level; /* compression level */ int strategy; /* compression strategy */ /* seek request */ z_off64_t skip; /* amount to skip (already rewound if backwards) */ int seek; /* true if seek request pending */ /* error information */ int err; /* error code */ char *msg; /* error message */ /* zlib inflate or deflate stream */ z_stream strm; /* stream structure in-place (not a pointer) */ } gz_state; typedef gz_state FAR *gz_statep; /* shared functions */ void ZLIB_INTERNAL gz_error OF((gz_statep, int, const char *)); #if defined UNDER_CE char ZLIB_INTERNAL *gz_strwinerror OF((DWORD error)); #endif /* GT_OFF(x), where x is an unsigned value, is true if x > maximum z_off64_t value -- needed when comparing unsigned to z_off64_t, which is signed (possible z_off64_t types off_t, off64_t, and long are all signed) */ #ifdef INT_MAX # define GT_OFF(x) (sizeof(int) == sizeof(z_off64_t) && (x) > INT_MAX) #else unsigned ZLIB_INTERNAL gz_intmax OF((void)); # define GT_OFF(x) (sizeof(int) == sizeof(z_off64_t) && (x) > gz_intmax()) #endif libmstoolkit-77.0.0/include/latin1tab.h0000644000175000017500000000342512455161024017726 0ustar rusconirusconi/* Copyright (c) 1998, 1999 Thai Open Source Software Center Ltd See the file COPYING for copying permission. */ /* 0x80 */ BT_OTHER, BT_OTHER, BT_OTHER, BT_OTHER, /* 0x84 */ BT_OTHER, BT_OTHER, BT_OTHER, BT_OTHER, /* 0x88 */ BT_OTHER, BT_OTHER, BT_OTHER, BT_OTHER, /* 0x8C */ BT_OTHER, BT_OTHER, BT_OTHER, BT_OTHER, /* 0x90 */ BT_OTHER, BT_OTHER, BT_OTHER, BT_OTHER, /* 0x94 */ BT_OTHER, BT_OTHER, BT_OTHER, BT_OTHER, /* 0x98 */ BT_OTHER, BT_OTHER, BT_OTHER, BT_OTHER, /* 0x9C */ BT_OTHER, BT_OTHER, BT_OTHER, BT_OTHER, /* 0xA0 */ BT_OTHER, BT_OTHER, BT_OTHER, BT_OTHER, /* 0xA4 */ BT_OTHER, BT_OTHER, BT_OTHER, BT_OTHER, /* 0xA8 */ BT_OTHER, BT_OTHER, BT_NMSTRT, BT_OTHER, /* 0xAC */ BT_OTHER, BT_OTHER, BT_OTHER, BT_OTHER, /* 0xB0 */ BT_OTHER, BT_OTHER, BT_OTHER, BT_OTHER, /* 0xB4 */ BT_OTHER, BT_NMSTRT, BT_OTHER, BT_NAME, /* 0xB8 */ BT_OTHER, BT_OTHER, BT_NMSTRT, BT_OTHER, /* 0xBC */ BT_OTHER, BT_OTHER, BT_OTHER, BT_OTHER, /* 0xC0 */ BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, /* 0xC4 */ BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, /* 0xC8 */ BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, /* 0xCC */ BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, /* 0xD0 */ BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, /* 0xD4 */ BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, BT_OTHER, /* 0xD8 */ BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, /* 0xDC */ BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, /* 0xE0 */ BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, /* 0xE4 */ BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, /* 0xE8 */ BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, /* 0xEC */ BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, /* 0xF0 */ BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, /* 0xF4 */ BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, BT_OTHER, /* 0xF8 */ BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, /* 0xFC */ BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, libmstoolkit-77.0.0/include/expat_config.h0000644000175000017500000000516512455161024020520 0ustar rusconirusconi/* expat_config.h. Generated by configure. */ /* expat_config.h.in. Generated from configure.in by autoheader. */ /* 1234 = LIL_ENDIAN, 4321 = BIGENDIAN */ #define BYTEORDER 1234 /* Define to 1 if you have the `bcopy' function. */ #define HAVE_BCOPY 1 /* Define to 1 if you have the header file. */ #define HAVE_DLFCN_H 1 /* Define to 1 if you have the header file. */ #define HAVE_FCNTL_H 1 /* Define to 1 if you have the `getpagesize' function. */ #define HAVE_GETPAGESIZE 1 /* Define to 1 if you have the header file. */ #define HAVE_INTTYPES_H 1 /* Define to 1 if you have the `memmove' function. */ #define HAVE_MEMMOVE 1 /* Define to 1 if you have the header file. */ #define HAVE_MEMORY_H 1 /* Define to 1 if you have a working `mmap' system call. */ #define HAVE_MMAP 1 /* Define to 1 if you have the header file. */ #define HAVE_STDINT_H 1 /* Define to 1 if you have the header file. */ #define HAVE_STDLIB_H 1 /* Define to 1 if you have the header file. */ #define HAVE_STRINGS_H 1 /* Define to 1 if you have the header file. */ #define HAVE_STRING_H 1 /* Define to 1 if you have the header file. */ #define HAVE_SYS_STAT_H 1 /* Define to 1 if you have the header file. */ #define HAVE_SYS_TYPES_H 1 /* Define to 1 if you have the header file. */ #define HAVE_UNISTD_H 1 /* Define to the address where bug reports for this package should be sent. */ #define PACKAGE_BUGREPORT "expat-bugs@libexpat.org" /* Define to the full name of this package. */ #define PACKAGE_NAME "expat" /* Define to the full name and version of this package. */ #define PACKAGE_STRING "expat 2.0.1" /* Define to the one symbol short name of this package. */ #define PACKAGE_TARNAME "expat" /* Define to the version of this package. */ #define PACKAGE_VERSION "2.0.1" /* Define to 1 if you have the ANSI C header files. */ #define STDC_HEADERS 1 /* whether byteorder is bigendian */ /* #undef WORDS_BIGENDIAN */ /* Define to specify how much context to retain around the current parse point. */ #define XML_CONTEXT_BYTES 1024 /* Define to make parameter entity parsing functionality available. */ #define XML_DTD 1 /* Define to make XML Namespaces functionality available. */ #define XML_NS 1 /* Define to __FUNCTION__ or "" if `__func__' does not conform to ANSI C. */ /* #undef __func__ */ /* Define to empty if `const' does not conform to ANSI C. */ /* #undef const */ /* Define to `long' if does not define. */ /* #undef off_t */ /* Define to `unsigned' if does not define. */ /* #undef size_t */ libmstoolkit-77.0.0/include/nametab.h0000644000175000017500000001561212455161024017457 0ustar rusconirusconistatic const unsigned namingBitmap[] = { 0x00000000, 0x00000000, 0x00000000, 0x00000000, 0x00000000, 0x00000000, 0x00000000, 0x00000000, 0xFFFFFFFF, 0xFFFFFFFF, 0xFFFFFFFF, 0xFFFFFFFF, 0xFFFFFFFF, 0xFFFFFFFF, 0xFFFFFFFF, 0xFFFFFFFF, 0x00000000, 0x04000000, 0x87FFFFFE, 0x07FFFFFE, 0x00000000, 0x00000000, 0xFF7FFFFF, 0xFF7FFFFF, 0xFFFFFFFF, 0x7FF3FFFF, 0xFFFFFDFE, 0x7FFFFFFF, 0xFFFFFFFF, 0xFFFFFFFF, 0xFFFFE00F, 0xFC31FFFF, 0x00FFFFFF, 0x00000000, 0xFFFF0000, 0xFFFFFFFF, 0xFFFFFFFF, 0xF80001FF, 0x00000003, 0x00000000, 0x00000000, 0x00000000, 0x00000000, 0x00000000, 0xFFFFD740, 0xFFFFFFFB, 0x547F7FFF, 0x000FFFFD, 0xFFFFDFFE, 0xFFFFFFFF, 0xDFFEFFFF, 0xFFFFFFFF, 0xFFFF0003, 0xFFFFFFFF, 0xFFFF199F, 0x033FCFFF, 0x00000000, 0xFFFE0000, 0x027FFFFF, 0xFFFFFFFE, 0x0000007F, 0x00000000, 0xFFFF0000, 0x000707FF, 0x00000000, 0x07FFFFFE, 0x000007FE, 0xFFFE0000, 0xFFFFFFFF, 0x7CFFFFFF, 0x002F7FFF, 0x00000060, 0xFFFFFFE0, 0x23FFFFFF, 0xFF000000, 0x00000003, 0xFFF99FE0, 0x03C5FDFF, 0xB0000000, 0x00030003, 0xFFF987E0, 0x036DFDFF, 0x5E000000, 0x001C0000, 0xFFFBAFE0, 0x23EDFDFF, 0x00000000, 0x00000001, 0xFFF99FE0, 0x23CDFDFF, 0xB0000000, 0x00000003, 0xD63DC7E0, 0x03BFC718, 0x00000000, 0x00000000, 0xFFFDDFE0, 0x03EFFDFF, 0x00000000, 0x00000003, 0xFFFDDFE0, 0x03EFFDFF, 0x40000000, 0x00000003, 0xFFFDDFE0, 0x03FFFDFF, 0x00000000, 0x00000003, 0x00000000, 0x00000000, 0x00000000, 0x00000000, 0xFFFFFFFE, 0x000D7FFF, 0x0000003F, 0x00000000, 0xFEF02596, 0x200D6CAE, 0x0000001F, 0x00000000, 0x00000000, 0x00000000, 0xFFFFFEFF, 0x000003FF, 0x00000000, 0x00000000, 0x00000000, 0x00000000, 0x00000000, 0x00000000, 0x00000000, 0x00000000, 0x00000000, 0xFFFFFFFF, 0xFFFF003F, 0x007FFFFF, 0x0007DAED, 0x50000000, 0x82315001, 0x002C62AB, 0x40000000, 0xF580C900, 0x00000007, 0x02010800, 0xFFFFFFFF, 0xFFFFFFFF, 0xFFFFFFFF, 0xFFFFFFFF, 0x0FFFFFFF, 0xFFFFFFFF, 0xFFFFFFFF, 0x03FFFFFF, 0x3F3FFFFF, 0xFFFFFFFF, 0xAAFF3F3F, 0x3FFFFFFF, 0xFFFFFFFF, 0x5FDFFFFF, 0x0FCF1FDC, 0x1FDC1FFF, 0x00000000, 0x00004C40, 0x00000000, 0x00000000, 0x00000007, 0x00000000, 0x00000000, 0x00000000, 0x00000080, 0x000003FE, 0xFFFFFFFE, 0xFFFFFFFF, 0x001FFFFF, 0xFFFFFFFE, 0xFFFFFFFF, 0x07FFFFFF, 0xFFFFFFE0, 0x00001FFF, 0x00000000, 0x00000000, 0x00000000, 0x00000000, 0x00000000, 0x00000000, 0xFFFFFFFF, 0xFFFFFFFF, 0xFFFFFFFF, 0xFFFFFFFF, 0xFFFFFFFF, 0x0000003F, 0x00000000, 0x00000000, 0xFFFFFFFF, 0xFFFFFFFF, 0xFFFFFFFF, 0xFFFFFFFF, 0xFFFFFFFF, 0x0000000F, 0x00000000, 0x00000000, 0x00000000, 0x07FF6000, 0x87FFFFFE, 0x07FFFFFE, 0x00000000, 0x00800000, 0xFF7FFFFF, 0xFF7FFFFF, 0x00FFFFFF, 0x00000000, 0xFFFF0000, 0xFFFFFFFF, 0xFFFFFFFF, 0xF80001FF, 0x00030003, 0x00000000, 0xFFFFFFFF, 0xFFFFFFFF, 0x0000003F, 0x00000003, 0xFFFFD7C0, 0xFFFFFFFB, 0x547F7FFF, 0x000FFFFD, 0xFFFFDFFE, 0xFFFFFFFF, 0xDFFEFFFF, 0xFFFFFFFF, 0xFFFF007B, 0xFFFFFFFF, 0xFFFF199F, 0x033FCFFF, 0x00000000, 0xFFFE0000, 0x027FFFFF, 0xFFFFFFFE, 0xFFFE007F, 0xBBFFFFFB, 0xFFFF0016, 0x000707FF, 0x00000000, 0x07FFFFFE, 0x0007FFFF, 0xFFFF03FF, 0xFFFFFFFF, 0x7CFFFFFF, 0xFFEF7FFF, 0x03FF3DFF, 0xFFFFFFEE, 0xF3FFFFFF, 0xFF1E3FFF, 0x0000FFCF, 0xFFF99FEE, 0xD3C5FDFF, 0xB080399F, 0x0003FFCF, 0xFFF987E4, 0xD36DFDFF, 0x5E003987, 0x001FFFC0, 0xFFFBAFEE, 0xF3EDFDFF, 0x00003BBF, 0x0000FFC1, 0xFFF99FEE, 0xF3CDFDFF, 0xB0C0398F, 0x0000FFC3, 0xD63DC7EC, 0xC3BFC718, 0x00803DC7, 0x0000FF80, 0xFFFDDFEE, 0xC3EFFDFF, 0x00603DDF, 0x0000FFC3, 0xFFFDDFEC, 0xC3EFFDFF, 0x40603DDF, 0x0000FFC3, 0xFFFDDFEC, 0xC3FFFDFF, 0x00803DCF, 0x0000FFC3, 0x00000000, 0x00000000, 0x00000000, 0x00000000, 0xFFFFFFFE, 0x07FF7FFF, 0x03FF7FFF, 0x00000000, 0xFEF02596, 0x3BFF6CAE, 0x03FF3F5F, 0x00000000, 0x03000000, 0xC2A003FF, 0xFFFFFEFF, 0xFFFE03FF, 0xFEBF0FDF, 0x02FE3FFF, 0x00000000, 0x00000000, 0x00000000, 0x00000000, 0x00000000, 0x00000000, 0x00000000, 0x00000000, 0x1FFF0000, 0x00000002, 0x000000A0, 0x003EFFFE, 0xFFFFFFFE, 0xFFFFFFFF, 0x661FFFFF, 0xFFFFFFFE, 0xFFFFFFFF, 0x77FFFFFF, }; static const unsigned char nmstrtPages[] = { 0x02, 0x03, 0x04, 0x05, 0x06, 0x07, 0x08, 0x00, 0x00, 0x09, 0x0A, 0x0B, 0x0C, 0x0D, 0x0E, 0x0F, 0x10, 0x11, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x12, 0x13, 0x00, 0x14, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x15, 0x16, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x17, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x18, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, }; static const unsigned char namePages[] = { 0x19, 0x03, 0x1A, 0x1B, 0x1C, 0x1D, 0x1E, 0x00, 0x00, 0x1F, 0x20, 0x21, 0x22, 0x23, 0x24, 0x25, 0x10, 0x11, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x12, 0x13, 0x26, 0x14, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x27, 0x16, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x17, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x18, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, }; libmstoolkit-77.0.0/include/trees.h0000644000175000017500000002043012455161024017164 0ustar rusconirusconi/* header created automatically with -DGEN_TREES_H */ local const ct_data static_ltree[L_CODES+2] = { {{ 12},{ 8}}, {{140},{ 8}}, {{ 76},{ 8}}, {{204},{ 8}}, {{ 44},{ 8}}, {{172},{ 8}}, {{108},{ 8}}, {{236},{ 8}}, {{ 28},{ 8}}, {{156},{ 8}}, {{ 92},{ 8}}, {{220},{ 8}}, {{ 60},{ 8}}, {{188},{ 8}}, {{124},{ 8}}, {{252},{ 8}}, {{ 2},{ 8}}, {{130},{ 8}}, {{ 66},{ 8}}, {{194},{ 8}}, {{ 34},{ 8}}, {{162},{ 8}}, {{ 98},{ 8}}, {{226},{ 8}}, {{ 18},{ 8}}, {{146},{ 8}}, {{ 82},{ 8}}, {{210},{ 8}}, {{ 50},{ 8}}, {{178},{ 8}}, {{114},{ 8}}, {{242},{ 8}}, {{ 10},{ 8}}, {{138},{ 8}}, {{ 74},{ 8}}, {{202},{ 8}}, {{ 42},{ 8}}, {{170},{ 8}}, {{106},{ 8}}, {{234},{ 8}}, {{ 26},{ 8}}, {{154},{ 8}}, {{ 90},{ 8}}, {{218},{ 8}}, {{ 58},{ 8}}, {{186},{ 8}}, {{122},{ 8}}, {{250},{ 8}}, {{ 6},{ 8}}, {{134},{ 8}}, {{ 70},{ 8}}, {{198},{ 8}}, {{ 38},{ 8}}, {{166},{ 8}}, {{102},{ 8}}, {{230},{ 8}}, {{ 22},{ 8}}, {{150},{ 8}}, {{ 86},{ 8}}, {{214},{ 8}}, {{ 54},{ 8}}, {{182},{ 8}}, {{118},{ 8}}, {{246},{ 8}}, {{ 14},{ 8}}, {{142},{ 8}}, {{ 78},{ 8}}, {{206},{ 8}}, {{ 46},{ 8}}, {{174},{ 8}}, {{110},{ 8}}, {{238},{ 8}}, {{ 30},{ 8}}, {{158},{ 8}}, {{ 94},{ 8}}, {{222},{ 8}}, {{ 62},{ 8}}, {{190},{ 8}}, {{126},{ 8}}, {{254},{ 8}}, {{ 1},{ 8}}, {{129},{ 8}}, {{ 65},{ 8}}, {{193},{ 8}}, {{ 33},{ 8}}, {{161},{ 8}}, {{ 97},{ 8}}, {{225},{ 8}}, {{ 17},{ 8}}, {{145},{ 8}}, {{ 81},{ 8}}, {{209},{ 8}}, {{ 49},{ 8}}, {{177},{ 8}}, {{113},{ 8}}, {{241},{ 8}}, {{ 9},{ 8}}, {{137},{ 8}}, {{ 73},{ 8}}, {{201},{ 8}}, {{ 41},{ 8}}, {{169},{ 8}}, {{105},{ 8}}, {{233},{ 8}}, {{ 25},{ 8}}, {{153},{ 8}}, {{ 89},{ 8}}, {{217},{ 8}}, {{ 57},{ 8}}, {{185},{ 8}}, {{121},{ 8}}, {{249},{ 8}}, {{ 5},{ 8}}, {{133},{ 8}}, {{ 69},{ 8}}, {{197},{ 8}}, {{ 37},{ 8}}, {{165},{ 8}}, {{101},{ 8}}, {{229},{ 8}}, {{ 21},{ 8}}, {{149},{ 8}}, {{ 85},{ 8}}, {{213},{ 8}}, {{ 53},{ 8}}, {{181},{ 8}}, {{117},{ 8}}, {{245},{ 8}}, {{ 13},{ 8}}, {{141},{ 8}}, {{ 77},{ 8}}, {{205},{ 8}}, {{ 45},{ 8}}, {{173},{ 8}}, {{109},{ 8}}, {{237},{ 8}}, {{ 29},{ 8}}, {{157},{ 8}}, {{ 93},{ 8}}, {{221},{ 8}}, {{ 61},{ 8}}, {{189},{ 8}}, {{125},{ 8}}, {{253},{ 8}}, {{ 19},{ 9}}, {{275},{ 9}}, {{147},{ 9}}, {{403},{ 9}}, {{ 83},{ 9}}, {{339},{ 9}}, {{211},{ 9}}, {{467},{ 9}}, {{ 51},{ 9}}, {{307},{ 9}}, {{179},{ 9}}, {{435},{ 9}}, {{115},{ 9}}, {{371},{ 9}}, {{243},{ 9}}, {{499},{ 9}}, {{ 11},{ 9}}, {{267},{ 9}}, {{139},{ 9}}, {{395},{ 9}}, {{ 75},{ 9}}, {{331},{ 9}}, {{203},{ 9}}, {{459},{ 9}}, {{ 43},{ 9}}, {{299},{ 9}}, {{171},{ 9}}, {{427},{ 9}}, {{107},{ 9}}, {{363},{ 9}}, {{235},{ 9}}, {{491},{ 9}}, {{ 27},{ 9}}, {{283},{ 9}}, {{155},{ 9}}, {{411},{ 9}}, {{ 91},{ 9}}, {{347},{ 9}}, {{219},{ 9}}, {{475},{ 9}}, {{ 59},{ 9}}, {{315},{ 9}}, {{187},{ 9}}, {{443},{ 9}}, {{123},{ 9}}, {{379},{ 9}}, {{251},{ 9}}, {{507},{ 9}}, {{ 7},{ 9}}, {{263},{ 9}}, {{135},{ 9}}, {{391},{ 9}}, {{ 71},{ 9}}, {{327},{ 9}}, {{199},{ 9}}, {{455},{ 9}}, {{ 39},{ 9}}, {{295},{ 9}}, {{167},{ 9}}, {{423},{ 9}}, {{103},{ 9}}, {{359},{ 9}}, {{231},{ 9}}, {{487},{ 9}}, {{ 23},{ 9}}, {{279},{ 9}}, {{151},{ 9}}, {{407},{ 9}}, {{ 87},{ 9}}, {{343},{ 9}}, {{215},{ 9}}, {{471},{ 9}}, {{ 55},{ 9}}, {{311},{ 9}}, {{183},{ 9}}, {{439},{ 9}}, {{119},{ 9}}, {{375},{ 9}}, {{247},{ 9}}, {{503},{ 9}}, {{ 15},{ 9}}, {{271},{ 9}}, {{143},{ 9}}, {{399},{ 9}}, {{ 79},{ 9}}, {{335},{ 9}}, {{207},{ 9}}, {{463},{ 9}}, {{ 47},{ 9}}, {{303},{ 9}}, {{175},{ 9}}, {{431},{ 9}}, {{111},{ 9}}, {{367},{ 9}}, {{239},{ 9}}, {{495},{ 9}}, {{ 31},{ 9}}, {{287},{ 9}}, {{159},{ 9}}, {{415},{ 9}}, {{ 95},{ 9}}, {{351},{ 9}}, {{223},{ 9}}, {{479},{ 9}}, {{ 63},{ 9}}, {{319},{ 9}}, {{191},{ 9}}, {{447},{ 9}}, {{127},{ 9}}, {{383},{ 9}}, {{255},{ 9}}, {{511},{ 9}}, {{ 0},{ 7}}, {{ 64},{ 7}}, {{ 32},{ 7}}, {{ 96},{ 7}}, {{ 16},{ 7}}, {{ 80},{ 7}}, {{ 48},{ 7}}, {{112},{ 7}}, {{ 8},{ 7}}, {{ 72},{ 7}}, {{ 40},{ 7}}, {{104},{ 7}}, {{ 24},{ 7}}, {{ 88},{ 7}}, {{ 56},{ 7}}, {{120},{ 7}}, {{ 4},{ 7}}, {{ 68},{ 7}}, {{ 36},{ 7}}, {{100},{ 7}}, {{ 20},{ 7}}, {{ 84},{ 7}}, {{ 52},{ 7}}, {{116},{ 7}}, {{ 3},{ 8}}, {{131},{ 8}}, {{ 67},{ 8}}, {{195},{ 8}}, {{ 35},{ 8}}, {{163},{ 8}}, {{ 99},{ 8}}, {{227},{ 8}} }; local const ct_data static_dtree[D_CODES] = { {{ 0},{ 5}}, {{16},{ 5}}, {{ 8},{ 5}}, {{24},{ 5}}, {{ 4},{ 5}}, {{20},{ 5}}, {{12},{ 5}}, {{28},{ 5}}, {{ 2},{ 5}}, {{18},{ 5}}, {{10},{ 5}}, {{26},{ 5}}, {{ 6},{ 5}}, {{22},{ 5}}, {{14},{ 5}}, {{30},{ 5}}, {{ 1},{ 5}}, {{17},{ 5}}, {{ 9},{ 5}}, {{25},{ 5}}, {{ 5},{ 5}}, {{21},{ 5}}, {{13},{ 5}}, {{29},{ 5}}, {{ 3},{ 5}}, {{19},{ 5}}, {{11},{ 5}}, {{27},{ 5}}, {{ 7},{ 5}}, {{23},{ 5}} }; const uch ZLIB_INTERNAL _dist_code[DIST_CODE_LEN] = { 0, 1, 2, 3, 4, 4, 5, 5, 6, 6, 6, 6, 7, 7, 7, 7, 8, 8, 8, 8, 8, 8, 8, 8, 9, 9, 9, 9, 9, 9, 9, 9, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 0, 0, 16, 17, 18, 18, 19, 19, 20, 20, 20, 20, 21, 21, 21, 21, 22, 22, 22, 22, 22, 22, 22, 22, 23, 23, 23, 23, 23, 23, 23, 23, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29 }; const uch ZLIB_INTERNAL _length_code[MAX_MATCH-MIN_MATCH+1]= { 0, 1, 2, 3, 4, 5, 6, 7, 8, 8, 9, 9, 10, 10, 11, 11, 12, 12, 12, 12, 13, 13, 13, 13, 14, 14, 14, 14, 15, 15, 15, 15, 16, 16, 16, 16, 16, 16, 16, 16, 17, 17, 17, 17, 17, 17, 17, 17, 18, 18, 18, 18, 18, 18, 18, 18, 19, 19, 19, 19, 19, 19, 19, 19, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 28 }; local const int base_length[LENGTH_CODES] = { 0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 12, 14, 16, 20, 24, 28, 32, 40, 48, 56, 64, 80, 96, 112, 128, 160, 192, 224, 0 }; local const int base_dist[D_CODES] = { 0, 1, 2, 3, 4, 6, 8, 12, 16, 24, 32, 48, 64, 96, 128, 192, 256, 384, 512, 768, 1024, 1536, 2048, 3072, 4096, 6144, 8192, 12288, 16384, 24576 }; libmstoolkit-77.0.0/include/asciitab.h0000644000175000017500000000334012455161024017622 0ustar rusconirusconi/* Copyright (c) 1998, 1999 Thai Open Source Software Center Ltd See the file COPYING for copying permission. */ /* 0x00 */ BT_NONXML, BT_NONXML, BT_NONXML, BT_NONXML, /* 0x04 */ BT_NONXML, BT_NONXML, BT_NONXML, BT_NONXML, /* 0x08 */ BT_NONXML, BT_S, BT_LF, BT_NONXML, /* 0x0C */ BT_NONXML, BT_CR, BT_NONXML, BT_NONXML, /* 0x10 */ BT_NONXML, BT_NONXML, BT_NONXML, BT_NONXML, /* 0x14 */ BT_NONXML, BT_NONXML, BT_NONXML, BT_NONXML, /* 0x18 */ BT_NONXML, BT_NONXML, BT_NONXML, BT_NONXML, /* 0x1C */ BT_NONXML, BT_NONXML, BT_NONXML, BT_NONXML, /* 0x20 */ BT_S, BT_EXCL, BT_QUOT, BT_NUM, /* 0x24 */ BT_OTHER, BT_PERCNT, BT_AMP, BT_APOS, /* 0x28 */ BT_LPAR, BT_RPAR, BT_AST, BT_PLUS, /* 0x2C */ BT_COMMA, BT_MINUS, BT_NAME, BT_SOL, /* 0x30 */ BT_DIGIT, BT_DIGIT, BT_DIGIT, BT_DIGIT, /* 0x34 */ BT_DIGIT, BT_DIGIT, BT_DIGIT, BT_DIGIT, /* 0x38 */ BT_DIGIT, BT_DIGIT, BT_COLON, BT_SEMI, /* 0x3C */ BT_LT, BT_EQUALS, BT_GT, BT_QUEST, /* 0x40 */ BT_OTHER, BT_HEX, BT_HEX, BT_HEX, /* 0x44 */ BT_HEX, BT_HEX, BT_HEX, BT_NMSTRT, /* 0x48 */ BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, /* 0x4C */ BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, /* 0x50 */ BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, /* 0x54 */ BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, /* 0x58 */ BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, BT_LSQB, /* 0x5C */ BT_OTHER, BT_RSQB, BT_OTHER, BT_NMSTRT, /* 0x60 */ BT_OTHER, BT_HEX, BT_HEX, BT_HEX, /* 0x64 */ BT_HEX, BT_HEX, BT_HEX, BT_NMSTRT, /* 0x68 */ BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, /* 0x6C */ BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, /* 0x70 */ BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, /* 0x74 */ BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, /* 0x78 */ BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, BT_OTHER, /* 0x7C */ BT_VERBAR, BT_OTHER, BT_OTHER, BT_OTHER, libmstoolkit-77.0.0/include/crc32.h0000644000175000017500000007355012455161024016771 0ustar rusconirusconi/* crc32.h -- tables for rapid CRC calculation * Generated automatically by crc32.c */ local const unsigned long FAR crc_table[TBLS][256] = { { 0x00000000UL, 0x77073096UL, 0xee0e612cUL, 0x990951baUL, 0x076dc419UL, 0x706af48fUL, 0xe963a535UL, 0x9e6495a3UL, 0x0edb8832UL, 0x79dcb8a4UL, 0xe0d5e91eUL, 0x97d2d988UL, 0x09b64c2bUL, 0x7eb17cbdUL, 0xe7b82d07UL, 0x90bf1d91UL, 0x1db71064UL, 0x6ab020f2UL, 0xf3b97148UL, 0x84be41deUL, 0x1adad47dUL, 0x6ddde4ebUL, 0xf4d4b551UL, 0x83d385c7UL, 0x136c9856UL, 0x646ba8c0UL, 0xfd62f97aUL, 0x8a65c9ecUL, 0x14015c4fUL, 0x63066cd9UL, 0xfa0f3d63UL, 0x8d080df5UL, 0x3b6e20c8UL, 0x4c69105eUL, 0xd56041e4UL, 0xa2677172UL, 0x3c03e4d1UL, 0x4b04d447UL, 0xd20d85fdUL, 0xa50ab56bUL, 0x35b5a8faUL, 0x42b2986cUL, 0xdbbbc9d6UL, 0xacbcf940UL, 0x32d86ce3UL, 0x45df5c75UL, 0xdcd60dcfUL, 0xabd13d59UL, 0x26d930acUL, 0x51de003aUL, 0xc8d75180UL, 0xbfd06116UL, 0x21b4f4b5UL, 0x56b3c423UL, 0xcfba9599UL, 0xb8bda50fUL, 0x2802b89eUL, 0x5f058808UL, 0xc60cd9b2UL, 0xb10be924UL, 0x2f6f7c87UL, 0x58684c11UL, 0xc1611dabUL, 0xb6662d3dUL, 0x76dc4190UL, 0x01db7106UL, 0x98d220bcUL, 0xefd5102aUL, 0x71b18589UL, 0x06b6b51fUL, 0x9fbfe4a5UL, 0xe8b8d433UL, 0x7807c9a2UL, 0x0f00f934UL, 0x9609a88eUL, 0xe10e9818UL, 0x7f6a0dbbUL, 0x086d3d2dUL, 0x91646c97UL, 0xe6635c01UL, 0x6b6b51f4UL, 0x1c6c6162UL, 0x856530d8UL, 0xf262004eUL, 0x6c0695edUL, 0x1b01a57bUL, 0x8208f4c1UL, 0xf50fc457UL, 0x65b0d9c6UL, 0x12b7e950UL, 0x8bbeb8eaUL, 0xfcb9887cUL, 0x62dd1ddfUL, 0x15da2d49UL, 0x8cd37cf3UL, 0xfbd44c65UL, 0x4db26158UL, 0x3ab551ceUL, 0xa3bc0074UL, 0xd4bb30e2UL, 0x4adfa541UL, 0x3dd895d7UL, 0xa4d1c46dUL, 0xd3d6f4fbUL, 0x4369e96aUL, 0x346ed9fcUL, 0xad678846UL, 0xda60b8d0UL, 0x44042d73UL, 0x33031de5UL, 0xaa0a4c5fUL, 0xdd0d7cc9UL, 0x5005713cUL, 0x270241aaUL, 0xbe0b1010UL, 0xc90c2086UL, 0x5768b525UL, 0x206f85b3UL, 0xb966d409UL, 0xce61e49fUL, 0x5edef90eUL, 0x29d9c998UL, 0xb0d09822UL, 0xc7d7a8b4UL, 0x59b33d17UL, 0x2eb40d81UL, 0xb7bd5c3bUL, 0xc0ba6cadUL, 0xedb88320UL, 0x9abfb3b6UL, 0x03b6e20cUL, 0x74b1d29aUL, 0xead54739UL, 0x9dd277afUL, 0x04db2615UL, 0x73dc1683UL, 0xe3630b12UL, 0x94643b84UL, 0x0d6d6a3eUL, 0x7a6a5aa8UL, 0xe40ecf0bUL, 0x9309ff9dUL, 0x0a00ae27UL, 0x7d079eb1UL, 0xf00f9344UL, 0x8708a3d2UL, 0x1e01f268UL, 0x6906c2feUL, 0xf762575dUL, 0x806567cbUL, 0x196c3671UL, 0x6e6b06e7UL, 0xfed41b76UL, 0x89d32be0UL, 0x10da7a5aUL, 0x67dd4accUL, 0xf9b9df6fUL, 0x8ebeeff9UL, 0x17b7be43UL, 0x60b08ed5UL, 0xd6d6a3e8UL, 0xa1d1937eUL, 0x38d8c2c4UL, 0x4fdff252UL, 0xd1bb67f1UL, 0xa6bc5767UL, 0x3fb506ddUL, 0x48b2364bUL, 0xd80d2bdaUL, 0xaf0a1b4cUL, 0x36034af6UL, 0x41047a60UL, 0xdf60efc3UL, 0xa867df55UL, 0x316e8eefUL, 0x4669be79UL, 0xcb61b38cUL, 0xbc66831aUL, 0x256fd2a0UL, 0x5268e236UL, 0xcc0c7795UL, 0xbb0b4703UL, 0x220216b9UL, 0x5505262fUL, 0xc5ba3bbeUL, 0xb2bd0b28UL, 0x2bb45a92UL, 0x5cb36a04UL, 0xc2d7ffa7UL, 0xb5d0cf31UL, 0x2cd99e8bUL, 0x5bdeae1dUL, 0x9b64c2b0UL, 0xec63f226UL, 0x756aa39cUL, 0x026d930aUL, 0x9c0906a9UL, 0xeb0e363fUL, 0x72076785UL, 0x05005713UL, 0x95bf4a82UL, 0xe2b87a14UL, 0x7bb12baeUL, 0x0cb61b38UL, 0x92d28e9bUL, 0xe5d5be0dUL, 0x7cdcefb7UL, 0x0bdbdf21UL, 0x86d3d2d4UL, 0xf1d4e242UL, 0x68ddb3f8UL, 0x1fda836eUL, 0x81be16cdUL, 0xf6b9265bUL, 0x6fb077e1UL, 0x18b74777UL, 0x88085ae6UL, 0xff0f6a70UL, 0x66063bcaUL, 0x11010b5cUL, 0x8f659effUL, 0xf862ae69UL, 0x616bffd3UL, 0x166ccf45UL, 0xa00ae278UL, 0xd70dd2eeUL, 0x4e048354UL, 0x3903b3c2UL, 0xa7672661UL, 0xd06016f7UL, 0x4969474dUL, 0x3e6e77dbUL, 0xaed16a4aUL, 0xd9d65adcUL, 0x40df0b66UL, 0x37d83bf0UL, 0xa9bcae53UL, 0xdebb9ec5UL, 0x47b2cf7fUL, 0x30b5ffe9UL, 0xbdbdf21cUL, 0xcabac28aUL, 0x53b39330UL, 0x24b4a3a6UL, 0xbad03605UL, 0xcdd70693UL, 0x54de5729UL, 0x23d967bfUL, 0xb3667a2eUL, 0xc4614ab8UL, 0x5d681b02UL, 0x2a6f2b94UL, 0xb40bbe37UL, 0xc30c8ea1UL, 0x5a05df1bUL, 0x2d02ef8dUL #ifdef BYFOUR }, { 0x00000000UL, 0x191b3141UL, 0x32366282UL, 0x2b2d53c3UL, 0x646cc504UL, 0x7d77f445UL, 0x565aa786UL, 0x4f4196c7UL, 0xc8d98a08UL, 0xd1c2bb49UL, 0xfaefe88aUL, 0xe3f4d9cbUL, 0xacb54f0cUL, 0xb5ae7e4dUL, 0x9e832d8eUL, 0x87981ccfUL, 0x4ac21251UL, 0x53d92310UL, 0x78f470d3UL, 0x61ef4192UL, 0x2eaed755UL, 0x37b5e614UL, 0x1c98b5d7UL, 0x05838496UL, 0x821b9859UL, 0x9b00a918UL, 0xb02dfadbUL, 0xa936cb9aUL, 0xe6775d5dUL, 0xff6c6c1cUL, 0xd4413fdfUL, 0xcd5a0e9eUL, 0x958424a2UL, 0x8c9f15e3UL, 0xa7b24620UL, 0xbea97761UL, 0xf1e8e1a6UL, 0xe8f3d0e7UL, 0xc3de8324UL, 0xdac5b265UL, 0x5d5daeaaUL, 0x44469febUL, 0x6f6bcc28UL, 0x7670fd69UL, 0x39316baeUL, 0x202a5aefUL, 0x0b07092cUL, 0x121c386dUL, 0xdf4636f3UL, 0xc65d07b2UL, 0xed705471UL, 0xf46b6530UL, 0xbb2af3f7UL, 0xa231c2b6UL, 0x891c9175UL, 0x9007a034UL, 0x179fbcfbUL, 0x0e848dbaUL, 0x25a9de79UL, 0x3cb2ef38UL, 0x73f379ffUL, 0x6ae848beUL, 0x41c51b7dUL, 0x58de2a3cUL, 0xf0794f05UL, 0xe9627e44UL, 0xc24f2d87UL, 0xdb541cc6UL, 0x94158a01UL, 0x8d0ebb40UL, 0xa623e883UL, 0xbf38d9c2UL, 0x38a0c50dUL, 0x21bbf44cUL, 0x0a96a78fUL, 0x138d96ceUL, 0x5ccc0009UL, 0x45d73148UL, 0x6efa628bUL, 0x77e153caUL, 0xbabb5d54UL, 0xa3a06c15UL, 0x888d3fd6UL, 0x91960e97UL, 0xded79850UL, 0xc7cca911UL, 0xece1fad2UL, 0xf5facb93UL, 0x7262d75cUL, 0x6b79e61dUL, 0x4054b5deUL, 0x594f849fUL, 0x160e1258UL, 0x0f152319UL, 0x243870daUL, 0x3d23419bUL, 0x65fd6ba7UL, 0x7ce65ae6UL, 0x57cb0925UL, 0x4ed03864UL, 0x0191aea3UL, 0x188a9fe2UL, 0x33a7cc21UL, 0x2abcfd60UL, 0xad24e1afUL, 0xb43fd0eeUL, 0x9f12832dUL, 0x8609b26cUL, 0xc94824abUL, 0xd05315eaUL, 0xfb7e4629UL, 0xe2657768UL, 0x2f3f79f6UL, 0x362448b7UL, 0x1d091b74UL, 0x04122a35UL, 0x4b53bcf2UL, 0x52488db3UL, 0x7965de70UL, 0x607eef31UL, 0xe7e6f3feUL, 0xfefdc2bfUL, 0xd5d0917cUL, 0xcccba03dUL, 0x838a36faUL, 0x9a9107bbUL, 0xb1bc5478UL, 0xa8a76539UL, 0x3b83984bUL, 0x2298a90aUL, 0x09b5fac9UL, 0x10aecb88UL, 0x5fef5d4fUL, 0x46f46c0eUL, 0x6dd93fcdUL, 0x74c20e8cUL, 0xf35a1243UL, 0xea412302UL, 0xc16c70c1UL, 0xd8774180UL, 0x9736d747UL, 0x8e2de606UL, 0xa500b5c5UL, 0xbc1b8484UL, 0x71418a1aUL, 0x685abb5bUL, 0x4377e898UL, 0x5a6cd9d9UL, 0x152d4f1eUL, 0x0c367e5fUL, 0x271b2d9cUL, 0x3e001cddUL, 0xb9980012UL, 0xa0833153UL, 0x8bae6290UL, 0x92b553d1UL, 0xddf4c516UL, 0xc4eff457UL, 0xefc2a794UL, 0xf6d996d5UL, 0xae07bce9UL, 0xb71c8da8UL, 0x9c31de6bUL, 0x852aef2aUL, 0xca6b79edUL, 0xd37048acUL, 0xf85d1b6fUL, 0xe1462a2eUL, 0x66de36e1UL, 0x7fc507a0UL, 0x54e85463UL, 0x4df36522UL, 0x02b2f3e5UL, 0x1ba9c2a4UL, 0x30849167UL, 0x299fa026UL, 0xe4c5aeb8UL, 0xfdde9ff9UL, 0xd6f3cc3aUL, 0xcfe8fd7bUL, 0x80a96bbcUL, 0x99b25afdUL, 0xb29f093eUL, 0xab84387fUL, 0x2c1c24b0UL, 0x350715f1UL, 0x1e2a4632UL, 0x07317773UL, 0x4870e1b4UL, 0x516bd0f5UL, 0x7a468336UL, 0x635db277UL, 0xcbfad74eUL, 0xd2e1e60fUL, 0xf9ccb5ccUL, 0xe0d7848dUL, 0xaf96124aUL, 0xb68d230bUL, 0x9da070c8UL, 0x84bb4189UL, 0x03235d46UL, 0x1a386c07UL, 0x31153fc4UL, 0x280e0e85UL, 0x674f9842UL, 0x7e54a903UL, 0x5579fac0UL, 0x4c62cb81UL, 0x8138c51fUL, 0x9823f45eUL, 0xb30ea79dUL, 0xaa1596dcUL, 0xe554001bUL, 0xfc4f315aUL, 0xd7626299UL, 0xce7953d8UL, 0x49e14f17UL, 0x50fa7e56UL, 0x7bd72d95UL, 0x62cc1cd4UL, 0x2d8d8a13UL, 0x3496bb52UL, 0x1fbbe891UL, 0x06a0d9d0UL, 0x5e7ef3ecUL, 0x4765c2adUL, 0x6c48916eUL, 0x7553a02fUL, 0x3a1236e8UL, 0x230907a9UL, 0x0824546aUL, 0x113f652bUL, 0x96a779e4UL, 0x8fbc48a5UL, 0xa4911b66UL, 0xbd8a2a27UL, 0xf2cbbce0UL, 0xebd08da1UL, 0xc0fdde62UL, 0xd9e6ef23UL, 0x14bce1bdUL, 0x0da7d0fcUL, 0x268a833fUL, 0x3f91b27eUL, 0x70d024b9UL, 0x69cb15f8UL, 0x42e6463bUL, 0x5bfd777aUL, 0xdc656bb5UL, 0xc57e5af4UL, 0xee530937UL, 0xf7483876UL, 0xb809aeb1UL, 0xa1129ff0UL, 0x8a3fcc33UL, 0x9324fd72UL }, { 0x00000000UL, 0x01c26a37UL, 0x0384d46eUL, 0x0246be59UL, 0x0709a8dcUL, 0x06cbc2ebUL, 0x048d7cb2UL, 0x054f1685UL, 0x0e1351b8UL, 0x0fd13b8fUL, 0x0d9785d6UL, 0x0c55efe1UL, 0x091af964UL, 0x08d89353UL, 0x0a9e2d0aUL, 0x0b5c473dUL, 0x1c26a370UL, 0x1de4c947UL, 0x1fa2771eUL, 0x1e601d29UL, 0x1b2f0bacUL, 0x1aed619bUL, 0x18abdfc2UL, 0x1969b5f5UL, 0x1235f2c8UL, 0x13f798ffUL, 0x11b126a6UL, 0x10734c91UL, 0x153c5a14UL, 0x14fe3023UL, 0x16b88e7aUL, 0x177ae44dUL, 0x384d46e0UL, 0x398f2cd7UL, 0x3bc9928eUL, 0x3a0bf8b9UL, 0x3f44ee3cUL, 0x3e86840bUL, 0x3cc03a52UL, 0x3d025065UL, 0x365e1758UL, 0x379c7d6fUL, 0x35dac336UL, 0x3418a901UL, 0x3157bf84UL, 0x3095d5b3UL, 0x32d36beaUL, 0x331101ddUL, 0x246be590UL, 0x25a98fa7UL, 0x27ef31feUL, 0x262d5bc9UL, 0x23624d4cUL, 0x22a0277bUL, 0x20e69922UL, 0x2124f315UL, 0x2a78b428UL, 0x2bbade1fUL, 0x29fc6046UL, 0x283e0a71UL, 0x2d711cf4UL, 0x2cb376c3UL, 0x2ef5c89aUL, 0x2f37a2adUL, 0x709a8dc0UL, 0x7158e7f7UL, 0x731e59aeUL, 0x72dc3399UL, 0x7793251cUL, 0x76514f2bUL, 0x7417f172UL, 0x75d59b45UL, 0x7e89dc78UL, 0x7f4bb64fUL, 0x7d0d0816UL, 0x7ccf6221UL, 0x798074a4UL, 0x78421e93UL, 0x7a04a0caUL, 0x7bc6cafdUL, 0x6cbc2eb0UL, 0x6d7e4487UL, 0x6f38fadeUL, 0x6efa90e9UL, 0x6bb5866cUL, 0x6a77ec5bUL, 0x68315202UL, 0x69f33835UL, 0x62af7f08UL, 0x636d153fUL, 0x612bab66UL, 0x60e9c151UL, 0x65a6d7d4UL, 0x6464bde3UL, 0x662203baUL, 0x67e0698dUL, 0x48d7cb20UL, 0x4915a117UL, 0x4b531f4eUL, 0x4a917579UL, 0x4fde63fcUL, 0x4e1c09cbUL, 0x4c5ab792UL, 0x4d98dda5UL, 0x46c49a98UL, 0x4706f0afUL, 0x45404ef6UL, 0x448224c1UL, 0x41cd3244UL, 0x400f5873UL, 0x4249e62aUL, 0x438b8c1dUL, 0x54f16850UL, 0x55330267UL, 0x5775bc3eUL, 0x56b7d609UL, 0x53f8c08cUL, 0x523aaabbUL, 0x507c14e2UL, 0x51be7ed5UL, 0x5ae239e8UL, 0x5b2053dfUL, 0x5966ed86UL, 0x58a487b1UL, 0x5deb9134UL, 0x5c29fb03UL, 0x5e6f455aUL, 0x5fad2f6dUL, 0xe1351b80UL, 0xe0f771b7UL, 0xe2b1cfeeUL, 0xe373a5d9UL, 0xe63cb35cUL, 0xe7fed96bUL, 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#define Expat_INCLUDED 1 #ifdef __VMS /* 0 1 2 3 0 1 2 3 1234567890123456789012345678901 1234567890123456789012345678901 */ #define XML_SetProcessingInstructionHandler XML_SetProcessingInstrHandler #define XML_SetUnparsedEntityDeclHandler XML_SetUnparsedEntDeclHandler #define XML_SetStartNamespaceDeclHandler XML_SetStartNamespcDeclHandler #define XML_SetExternalEntityRefHandlerArg XML_SetExternalEntRefHandlerArg #endif #include #include "expat_external.h" #ifdef __cplusplus extern "C" { #endif struct XML_ParserStruct; typedef struct XML_ParserStruct *XML_Parser; /* Should this be defined using stdbool.h when C99 is available? */ typedef unsigned char XML_Bool; #define XML_TRUE ((XML_Bool) 1) #define XML_FALSE ((XML_Bool) 0) /* The XML_Status enum gives the possible return values for several API functions. The preprocessor #defines are included so this stanza can be added to code that still needs to support older versions of Expat 1.95.x: #ifndef XML_STATUS_OK #define XML_STATUS_OK 1 #define XML_STATUS_ERROR 0 #endif Otherwise, the #define hackery is quite ugly and would have been dropped. */ enum XML_Status { XML_STATUS_ERROR = 0, #define XML_STATUS_ERROR XML_STATUS_ERROR XML_STATUS_OK = 1, #define XML_STATUS_OK XML_STATUS_OK XML_STATUS_SUSPENDED = 2 #define XML_STATUS_SUSPENDED XML_STATUS_SUSPENDED }; enum XML_Error { XML_ERROR_NONE, XML_ERROR_NO_MEMORY, XML_ERROR_SYNTAX, XML_ERROR_NO_ELEMENTS, XML_ERROR_INVALID_TOKEN, XML_ERROR_UNCLOSED_TOKEN, XML_ERROR_PARTIAL_CHAR, XML_ERROR_TAG_MISMATCH, XML_ERROR_DUPLICATE_ATTRIBUTE, XML_ERROR_JUNK_AFTER_DOC_ELEMENT, XML_ERROR_PARAM_ENTITY_REF, XML_ERROR_UNDEFINED_ENTITY, XML_ERROR_RECURSIVE_ENTITY_REF, XML_ERROR_ASYNC_ENTITY, XML_ERROR_BAD_CHAR_REF, XML_ERROR_BINARY_ENTITY_REF, XML_ERROR_ATTRIBUTE_EXTERNAL_ENTITY_REF, XML_ERROR_MISPLACED_XML_PI, XML_ERROR_UNKNOWN_ENCODING, XML_ERROR_INCORRECT_ENCODING, XML_ERROR_UNCLOSED_CDATA_SECTION, XML_ERROR_EXTERNAL_ENTITY_HANDLING, XML_ERROR_NOT_STANDALONE, XML_ERROR_UNEXPECTED_STATE, XML_ERROR_ENTITY_DECLARED_IN_PE, XML_ERROR_FEATURE_REQUIRES_XML_DTD, XML_ERROR_CANT_CHANGE_FEATURE_ONCE_PARSING, /* Added in 1.95.7. */ XML_ERROR_UNBOUND_PREFIX, /* Added in 1.95.8. */ XML_ERROR_UNDECLARING_PREFIX, XML_ERROR_INCOMPLETE_PE, XML_ERROR_XML_DECL, XML_ERROR_TEXT_DECL, XML_ERROR_PUBLICID, XML_ERROR_SUSPENDED, XML_ERROR_NOT_SUSPENDED, XML_ERROR_ABORTED, XML_ERROR_FINISHED, XML_ERROR_SUSPEND_PE, /* Added in 2.0. */ XML_ERROR_RESERVED_PREFIX_XML, XML_ERROR_RESERVED_PREFIX_XMLNS, XML_ERROR_RESERVED_NAMESPACE_URI }; enum XML_Content_Type { XML_CTYPE_EMPTY = 1, XML_CTYPE_ANY, XML_CTYPE_MIXED, XML_CTYPE_NAME, XML_CTYPE_CHOICE, XML_CTYPE_SEQ }; enum XML_Content_Quant { XML_CQUANT_NONE, XML_CQUANT_OPT, XML_CQUANT_REP, XML_CQUANT_PLUS }; /* If type == XML_CTYPE_EMPTY or XML_CTYPE_ANY, then quant will be XML_CQUANT_NONE, and the other fields will be zero or NULL. If type == XML_CTYPE_MIXED, then quant will be NONE or REP and numchildren will contain number of elements that may be mixed in and children point to an array of XML_Content cells that will be all of XML_CTYPE_NAME type with no quantification. If type == XML_CTYPE_NAME, then the name points to the name, and the numchildren field will be zero and children will be NULL. The quant fields indicates any quantifiers placed on the name. CHOICE and SEQ will have name NULL, the number of children in numchildren and children will point, recursively, to an array of XML_Content cells. The EMPTY, ANY, and MIXED types will only occur at top level. */ typedef struct XML_cp XML_Content; struct XML_cp { enum XML_Content_Type type; enum XML_Content_Quant quant; XML_Char * name; unsigned int numchildren; XML_Content * children; }; /* This is called for an element declaration. See above for description of the model argument. It's the caller's responsibility to free model when finished with it. */ typedef void (XMLCALL *XML_ElementDeclHandler) (void *userData, const XML_Char *name, XML_Content *model); XMLPARSEAPI(void) XML_SetElementDeclHandler(XML_Parser parser, XML_ElementDeclHandler eldecl); /* The Attlist declaration handler is called for *each* attribute. So a single Attlist declaration with multiple attributes declared will generate multiple calls to this handler. The "default" parameter may be NULL in the case of the "#IMPLIED" or "#REQUIRED" keyword. The "isrequired" parameter will be true and the default value will be NULL in the case of "#REQUIRED". If "isrequired" is true and default is non-NULL, then this is a "#FIXED" default. */ typedef void (XMLCALL *XML_AttlistDeclHandler) ( void *userData, const XML_Char *elname, const XML_Char *attname, const XML_Char *att_type, const XML_Char *dflt, int isrequired); XMLPARSEAPI(void) XML_SetAttlistDeclHandler(XML_Parser parser, XML_AttlistDeclHandler attdecl); /* The XML declaration handler is called for *both* XML declarations and text declarations. The way to distinguish is that the version parameter will be NULL for text declarations. The encoding parameter may be NULL for XML declarations. The standalone parameter will be -1, 0, or 1 indicating respectively that there was no standalone parameter in the declaration, that it was given as no, or that it was given as yes. */ typedef void (XMLCALL *XML_XmlDeclHandler) (void *userData, const XML_Char *version, const XML_Char *encoding, int standalone); XMLPARSEAPI(void) XML_SetXmlDeclHandler(XML_Parser parser, XML_XmlDeclHandler xmldecl); typedef struct { void *(*malloc_fcn)(size_t size); void *(*realloc_fcn)(void *ptr, size_t size); void (*free_fcn)(void *ptr); } XML_Memory_Handling_Suite; /* Constructs a new parser; encoding is the encoding specified by the external protocol or NULL if there is none specified. */ XMLPARSEAPI(XML_Parser) XML_ParserCreate(const XML_Char *encoding); /* Constructs a new parser and namespace processor. Element type names and attribute names that belong to a namespace will be expanded; unprefixed attribute names are never expanded; unprefixed element type names are expanded only if there is a default namespace. The expanded name is the concatenation of the namespace URI, the namespace separator character, and the local part of the name. If the namespace separator is '\0' then the namespace URI and the local part will be concatenated without any separator. It is a programming error to use the separator '\0' with namespace triplets (see XML_SetReturnNSTriplet). */ XMLPARSEAPI(XML_Parser) XML_ParserCreateNS(const XML_Char *encoding, XML_Char namespaceSeparator); /* Constructs a new parser using the memory management suite referred to by memsuite. If memsuite is NULL, then use the standard library memory suite. If namespaceSeparator is non-NULL it creates a parser with namespace processing as described above. The character pointed at will serve as the namespace separator. All further memory operations used for the created parser will come from the given suite. */ XMLPARSEAPI(XML_Parser) XML_ParserCreate_MM(const XML_Char *encoding, const XML_Memory_Handling_Suite *memsuite, const XML_Char *namespaceSeparator); /* Prepare a parser object to be re-used. This is particularly valuable when memory allocation overhead is disproportionatly high, such as when a large number of small documnents need to be parsed. All handlers are cleared from the parser, except for the unknownEncodingHandler. The parser's external state is re-initialized except for the values of ns and ns_triplets. Added in Expat 1.95.3. */ XMLPARSEAPI(XML_Bool) XML_ParserReset(XML_Parser parser, const XML_Char *encoding); /* atts is array of name/value pairs, terminated by 0; names and values are 0 terminated. */ typedef void (XMLCALL *XML_StartElementHandler) (void *userData, const XML_Char *name, const XML_Char **atts); typedef void (XMLCALL *XML_EndElementHandler) (void *userData, const XML_Char *name); /* s is not 0 terminated. */ typedef void (XMLCALL *XML_CharacterDataHandler) (void *userData, const XML_Char *s, int len); /* target and data are 0 terminated */ typedef void (XMLCALL *XML_ProcessingInstructionHandler) ( void *userData, const XML_Char *target, const XML_Char *data); /* data is 0 terminated */ typedef void (XMLCALL *XML_CommentHandler) (void *userData, const XML_Char *data); typedef void (XMLCALL *XML_StartCdataSectionHandler) (void *userData); typedef void (XMLCALL *XML_EndCdataSectionHandler) (void *userData); /* This is called for any characters in the XML document for which there is no applicable handler. This includes both characters that are part of markup which is of a kind that is not reported (comments, markup declarations), or characters that are part of a construct which could be reported but for which no handler has been supplied. The characters are passed exactly as they were in the XML document except that they will be encoded in UTF-8 or UTF-16. Line boundaries are not normalized. Note that a byte order mark character is not passed to the default handler. There are no guarantees about how characters are divided between calls to the default handler: for example, a comment might be split between multiple calls. */ typedef void (XMLCALL *XML_DefaultHandler) (void *userData, const XML_Char *s, int len); /* This is called for the start of the DOCTYPE declaration, before any DTD or internal subset is parsed. */ typedef void (XMLCALL *XML_StartDoctypeDeclHandler) ( void *userData, const XML_Char *doctypeName, const XML_Char *sysid, const XML_Char *pubid, int has_internal_subset); /* This is called for the start of the DOCTYPE declaration when the closing > is encountered, but after processing any external subset. */ typedef void (XMLCALL *XML_EndDoctypeDeclHandler)(void *userData); /* This is called for entity declarations. The is_parameter_entity argument will be non-zero if the entity is a parameter entity, zero otherwise. For internal entities (), value will be non-NULL and systemId, publicID, and notationName will be NULL. The value string is NOT nul-terminated; the length is provided in the value_length argument. Since it is legal to have zero-length values, do not use this argument to test for internal entities. For external entities, value will be NULL and systemId will be non-NULL. The publicId argument will be NULL unless a public identifier was provided. The notationName argument will have a non-NULL value only for unparsed entity declarations. Note that is_parameter_entity can't be changed to XML_Bool, since that would break binary compatibility. */ typedef void (XMLCALL *XML_EntityDeclHandler) ( void *userData, const XML_Char *entityName, int is_parameter_entity, const XML_Char *value, int value_length, const XML_Char *base, const XML_Char *systemId, const XML_Char *publicId, const XML_Char *notationName); XMLPARSEAPI(void) XML_SetEntityDeclHandler(XML_Parser parser, XML_EntityDeclHandler handler); /* OBSOLETE -- OBSOLETE -- OBSOLETE This handler has been superceded by the EntityDeclHandler above. It is provided here for backward compatibility. This is called for a declaration of an unparsed (NDATA) entity. The base argument is whatever was set by XML_SetBase. The entityName, systemId and notationName arguments will never be NULL. The other arguments may be. */ typedef void (XMLCALL *XML_UnparsedEntityDeclHandler) ( void *userData, const XML_Char *entityName, const XML_Char *base, const XML_Char *systemId, const XML_Char *publicId, const XML_Char *notationName); /* This is called for a declaration of notation. The base argument is whatever was set by XML_SetBase. The notationName will never be NULL. The other arguments can be. */ typedef void (XMLCALL *XML_NotationDeclHandler) ( void *userData, const XML_Char *notationName, const XML_Char *base, const XML_Char *systemId, const XML_Char *publicId); /* When namespace processing is enabled, these are called once for each namespace declaration. The call to the start and end element handlers occur between the calls to the start and end namespace declaration handlers. For an xmlns attribute, prefix will be NULL. For an xmlns="" attribute, uri will be NULL. */ typedef void (XMLCALL *XML_StartNamespaceDeclHandler) ( void *userData, const XML_Char *prefix, const XML_Char *uri); typedef void (XMLCALL *XML_EndNamespaceDeclHandler) ( void *userData, const XML_Char *prefix); /* This is called if the document is not standalone, that is, it has an external subset or a reference to a parameter entity, but does not have standalone="yes". If this handler returns XML_STATUS_ERROR, then processing will not continue, and the parser will return a XML_ERROR_NOT_STANDALONE error. If parameter entity parsing is enabled, then in addition to the conditions above this handler will only be called if the referenced entity was actually read. */ typedef int (XMLCALL *XML_NotStandaloneHandler) (void *userData); /* This is called for a reference to an external parsed general entity. The referenced entity is not automatically parsed. The application can parse it immediately or later using XML_ExternalEntityParserCreate. The parser argument is the parser parsing the entity containing the reference; it can be passed as the parser argument to XML_ExternalEntityParserCreate. The systemId argument is the system identifier as specified in the entity declaration; it will not be NULL. The base argument is the system identifier that should be used as the base for resolving systemId if systemId was relative; this is set by XML_SetBase; it may be NULL. The publicId argument is the public identifier as specified in the entity declaration, or NULL if none was specified; the whitespace in the public identifier will have been normalized as required by the XML spec. The context argument specifies the parsing context in the format expected by the context argument to XML_ExternalEntityParserCreate; context is valid only until the handler returns, so if the referenced entity is to be parsed later, it must be copied. context is NULL only when the entity is a parameter entity. The handler should return XML_STATUS_ERROR if processing should not continue because of a fatal error in the handling of the external entity. In this case the calling parser will return an XML_ERROR_EXTERNAL_ENTITY_HANDLING error. Note that unlike other handlers the first argument is the parser, not userData. */ typedef int (XMLCALL *XML_ExternalEntityRefHandler) ( XML_Parser parser, const XML_Char *context, const XML_Char *base, const XML_Char *systemId, const XML_Char *publicId); /* This is called in two situations: 1) An entity reference is encountered for which no declaration has been read *and* this is not an error. 2) An internal entity reference is read, but not expanded, because XML_SetDefaultHandler has been called. Note: skipped parameter entities in declarations and skipped general entities in attribute values cannot be reported, because the event would be out of sync with the reporting of the declarations or attribute values */ typedef void (XMLCALL *XML_SkippedEntityHandler) ( void *userData, const XML_Char *entityName, int is_parameter_entity); /* This structure is filled in by the XML_UnknownEncodingHandler to provide information to the parser about encodings that are unknown to the parser. The map[b] member gives information about byte sequences whose first byte is b. If map[b] is c where c is >= 0, then b by itself encodes the Unicode scalar value c. If map[b] is -1, then the byte sequence is malformed. If map[b] is -n, where n >= 2, then b is the first byte of an n-byte sequence that encodes a single Unicode scalar value. The data member will be passed as the first argument to the convert function. The convert function is used to convert multibyte sequences; s will point to a n-byte sequence where map[(unsigned char)*s] == -n. The convert function must return the Unicode scalar value represented by this byte sequence or -1 if the byte sequence is malformed. The convert function may be NULL if the encoding is a single-byte encoding, that is if map[b] >= -1 for all bytes b. When the parser is finished with the encoding, then if release is not NULL, it will call release passing it the data member; once release has been called, the convert function will not be called again. Expat places certain restrictions on the encodings that are supported using this mechanism. 1. Every ASCII character that can appear in a well-formed XML document, other than the characters $@\^`{}~ must be represented by a single byte, and that byte must be the same byte that represents that character in ASCII. 2. No character may require more than 4 bytes to encode. 3. All characters encoded must have Unicode scalar values <= 0xFFFF, (i.e., characters that would be encoded by surrogates in UTF-16 are not allowed). Note that this restriction doesn't apply to the built-in support for UTF-8 and UTF-16. 4. No Unicode character may be encoded by more than one distinct sequence of bytes. */ typedef struct { int map[256]; void *data; int (XMLCALL *convert)(void *data, const char *s); void (XMLCALL *release)(void *data); } XML_Encoding; /* This is called for an encoding that is unknown to the parser. The encodingHandlerData argument is that which was passed as the second argument to XML_SetUnknownEncodingHandler. The name argument gives the name of the encoding as specified in the encoding declaration. If the callback can provide information about the encoding, it must fill in the XML_Encoding structure, and return XML_STATUS_OK. Otherwise it must return XML_STATUS_ERROR. If info does not describe a suitable encoding, then the parser will return an XML_UNKNOWN_ENCODING error. */ typedef int (XMLCALL *XML_UnknownEncodingHandler) ( void *encodingHandlerData, const XML_Char *name, XML_Encoding *info); XMLPARSEAPI(void) XML_SetElementHandler(XML_Parser parser, XML_StartElementHandler start, XML_EndElementHandler end); XMLPARSEAPI(void) XML_SetStartElementHandler(XML_Parser parser, XML_StartElementHandler handler); XMLPARSEAPI(void) XML_SetEndElementHandler(XML_Parser parser, XML_EndElementHandler handler); XMLPARSEAPI(void) XML_SetCharacterDataHandler(XML_Parser parser, XML_CharacterDataHandler handler); XMLPARSEAPI(void) XML_SetProcessingInstructionHandler(XML_Parser parser, XML_ProcessingInstructionHandler handler); XMLPARSEAPI(void) XML_SetCommentHandler(XML_Parser parser, XML_CommentHandler handler); XMLPARSEAPI(void) XML_SetCdataSectionHandler(XML_Parser parser, XML_StartCdataSectionHandler start, XML_EndCdataSectionHandler end); XMLPARSEAPI(void) XML_SetStartCdataSectionHandler(XML_Parser parser, XML_StartCdataSectionHandler start); XMLPARSEAPI(void) XML_SetEndCdataSectionHandler(XML_Parser parser, XML_EndCdataSectionHandler end); /* This sets the default handler and also inhibits expansion of internal entities. These entity references will be passed to the default handler, or to the skipped entity handler, if one is set. */ XMLPARSEAPI(void) XML_SetDefaultHandler(XML_Parser parser, XML_DefaultHandler handler); /* This sets the default handler but does not inhibit expansion of internal entities. The entity reference will not be passed to the default handler. */ XMLPARSEAPI(void) XML_SetDefaultHandlerExpand(XML_Parser parser, XML_DefaultHandler handler); XMLPARSEAPI(void) XML_SetDoctypeDeclHandler(XML_Parser parser, XML_StartDoctypeDeclHandler start, XML_EndDoctypeDeclHandler end); XMLPARSEAPI(void) XML_SetStartDoctypeDeclHandler(XML_Parser parser, XML_StartDoctypeDeclHandler start); XMLPARSEAPI(void) XML_SetEndDoctypeDeclHandler(XML_Parser parser, XML_EndDoctypeDeclHandler end); XMLPARSEAPI(void) XML_SetUnparsedEntityDeclHandler(XML_Parser parser, XML_UnparsedEntityDeclHandler handler); XMLPARSEAPI(void) XML_SetNotationDeclHandler(XML_Parser parser, XML_NotationDeclHandler handler); XMLPARSEAPI(void) XML_SetNamespaceDeclHandler(XML_Parser parser, XML_StartNamespaceDeclHandler start, XML_EndNamespaceDeclHandler end); XMLPARSEAPI(void) XML_SetStartNamespaceDeclHandler(XML_Parser parser, XML_StartNamespaceDeclHandler start); XMLPARSEAPI(void) XML_SetEndNamespaceDeclHandler(XML_Parser parser, XML_EndNamespaceDeclHandler end); XMLPARSEAPI(void) XML_SetNotStandaloneHandler(XML_Parser parser, XML_NotStandaloneHandler handler); XMLPARSEAPI(void) XML_SetExternalEntityRefHandler(XML_Parser parser, XML_ExternalEntityRefHandler handler); /* If a non-NULL value for arg is specified here, then it will be passed as the first argument to the external entity ref handler instead of the parser object. */ XMLPARSEAPI(void) XML_SetExternalEntityRefHandlerArg(XML_Parser parser, void *arg); XMLPARSEAPI(void) XML_SetSkippedEntityHandler(XML_Parser parser, XML_SkippedEntityHandler handler); XMLPARSEAPI(void) XML_SetUnknownEncodingHandler(XML_Parser parser, XML_UnknownEncodingHandler handler, void *encodingHandlerData); /* This can be called within a handler for a start element, end element, processing instruction or character data. It causes the corresponding markup to be passed to the default handler. */ XMLPARSEAPI(void) XML_DefaultCurrent(XML_Parser parser); /* If do_nst is non-zero, and namespace processing is in effect, and a name has a prefix (i.e. an explicit namespace qualifier) then that name is returned as a triplet in a single string separated by the separator character specified when the parser was created: URI + sep + local_name + sep + prefix. If do_nst is zero, then namespace information is returned in the default manner (URI + sep + local_name) whether or not the name has a prefix. Note: Calling XML_SetReturnNSTriplet after XML_Parse or XML_ParseBuffer has no effect. */ XMLPARSEAPI(void) XML_SetReturnNSTriplet(XML_Parser parser, int do_nst); /* This value is passed as the userData argument to callbacks. */ XMLPARSEAPI(void) XML_SetUserData(XML_Parser parser, void *userData); /* Returns the last value set by XML_SetUserData or NULL. */ #define XML_GetUserData(parser) (*(void **)(parser)) /* This is equivalent to supplying an encoding argument to XML_ParserCreate. On success XML_SetEncoding returns non-zero, zero otherwise. Note: Calling XML_SetEncoding after XML_Parse or XML_ParseBuffer has no effect and returns XML_STATUS_ERROR. */ XMLPARSEAPI(enum XML_Status) XML_SetEncoding(XML_Parser parser, const XML_Char *encoding); /* If this function is called, then the parser will be passed as the first argument to callbacks instead of userData. The userData will still be accessible using XML_GetUserData. */ XMLPARSEAPI(void) XML_UseParserAsHandlerArg(XML_Parser parser); /* If useDTD == XML_TRUE is passed to this function, then the parser will assume that there is an external subset, even if none is specified in the document. In such a case the parser will call the externalEntityRefHandler with a value of NULL for the systemId argument (the publicId and context arguments will be NULL as well). Note: For the purpose of checking WFC: Entity Declared, passing useDTD == XML_TRUE will make the parser behave as if the document had a DTD with an external subset. Note: If this function is called, then this must be done before the first call to XML_Parse or XML_ParseBuffer, since it will have no effect after that. Returns XML_ERROR_CANT_CHANGE_FEATURE_ONCE_PARSING. Note: If the document does not have a DOCTYPE declaration at all, then startDoctypeDeclHandler and endDoctypeDeclHandler will not be called, despite an external subset being parsed. Note: If XML_DTD is not defined when Expat is compiled, returns XML_ERROR_FEATURE_REQUIRES_XML_DTD. */ XMLPARSEAPI(enum XML_Error) XML_UseForeignDTD(XML_Parser parser, XML_Bool useDTD); /* Sets the base to be used for resolving relative URIs in system identifiers in declarations. Resolving relative identifiers is left to the application: this value will be passed through as the base argument to the XML_ExternalEntityRefHandler, XML_NotationDeclHandler and XML_UnparsedEntityDeclHandler. The base argument will be copied. Returns XML_STATUS_ERROR if out of memory, XML_STATUS_OK otherwise. */ XMLPARSEAPI(enum XML_Status) XML_SetBase(XML_Parser parser, const XML_Char *base); XMLPARSEAPI(const XML_Char *) XML_GetBase(XML_Parser parser); /* Returns the number of the attribute/value pairs passed in last call to the XML_StartElementHandler that were specified in the start-tag rather than defaulted. Each attribute/value pair counts as 2; thus this correspondds to an index into the atts array passed to the XML_StartElementHandler. */ XMLPARSEAPI(int) XML_GetSpecifiedAttributeCount(XML_Parser parser); /* Returns the index of the ID attribute passed in the last call to XML_StartElementHandler, or -1 if there is no ID attribute. Each attribute/value pair counts as 2; thus this correspondds to an index into the atts array passed to the XML_StartElementHandler. */ XMLPARSEAPI(int) XML_GetIdAttributeIndex(XML_Parser parser); /* Parses some input. Returns XML_STATUS_ERROR if a fatal error is detected. The last call to XML_Parse must have isFinal true; len may be zero for this call (or any other). Though the return values for these functions has always been described as a Boolean value, the implementation, at least for the 1.95.x series, has always returned exactly one of the XML_Status values. */ XMLPARSEAPI(enum XML_Status) XML_Parse(XML_Parser parser, const char *s, int len, int isFinal); XMLPARSEAPI(void *) XML_GetBuffer(XML_Parser parser, int len); XMLPARSEAPI(enum XML_Status) XML_ParseBuffer(XML_Parser parser, int len, int isFinal); /* Stops parsing, causing XML_Parse() or XML_ParseBuffer() to return. Must be called from within a call-back handler, except when aborting (resumable = 0) an already suspended parser. Some call-backs may still follow because they would otherwise get lost. Examples: - endElementHandler() for empty elements when stopped in startElementHandler(), - endNameSpaceDeclHandler() when stopped in endElementHandler(), and possibly others. Can be called from most handlers, including DTD related call-backs, except when parsing an external parameter entity and resumable != 0. Returns XML_STATUS_OK when successful, XML_STATUS_ERROR otherwise. Possible error codes: - XML_ERROR_SUSPENDED: when suspending an already suspended parser. - XML_ERROR_FINISHED: when the parser has already finished. - XML_ERROR_SUSPEND_PE: when suspending while parsing an external PE. When resumable != 0 (true) then parsing is suspended, that is, XML_Parse() and XML_ParseBuffer() return XML_STATUS_SUSPENDED. Otherwise, parsing is aborted, that is, XML_Parse() and XML_ParseBuffer() return XML_STATUS_ERROR with error code XML_ERROR_ABORTED. *Note*: This will be applied to the current parser instance only, that is, if there is a parent parser then it will continue parsing when the externalEntityRefHandler() returns. It is up to the implementation of the externalEntityRefHandler() to call XML_StopParser() on the parent parser (recursively), if one wants to stop parsing altogether. When suspended, parsing can be resumed by calling XML_ResumeParser(). */ XMLPARSEAPI(enum XML_Status) XML_StopParser(XML_Parser parser, XML_Bool resumable); /* Resumes parsing after it has been suspended with XML_StopParser(). Must not be called from within a handler call-back. Returns same status codes as XML_Parse() or XML_ParseBuffer(). Additional error code XML_ERROR_NOT_SUSPENDED possible. *Note*: This must be called on the most deeply nested child parser instance first, and on its parent parser only after the child parser has finished, to be applied recursively until the document entity's parser is restarted. That is, the parent parser will not resume by itself and it is up to the application to call XML_ResumeParser() on it at the appropriate moment. */ XMLPARSEAPI(enum XML_Status) XML_ResumeParser(XML_Parser parser); enum XML_Parsing { XML_INITIALIZED, XML_PARSING, XML_FINISHED, XML_SUSPENDED }; typedef struct { enum XML_Parsing parsing; XML_Bool finalBuffer; } XML_ParsingStatus; /* Returns status of parser with respect to being initialized, parsing, finished, or suspended and processing the final buffer. XXX XML_Parse() and XML_ParseBuffer() should return XML_ParsingStatus, XXX with XML_FINISHED_OK or XML_FINISHED_ERROR replacing XML_FINISHED */ XMLPARSEAPI(void) XML_GetParsingStatus(XML_Parser parser, XML_ParsingStatus *status); /* Creates an XML_Parser object that can parse an external general entity; context is a '\0'-terminated string specifying the parse context; encoding is a '\0'-terminated string giving the name of the externally specified encoding, or NULL if there is no externally specified encoding. The context string consists of a sequence of tokens separated by formfeeds (\f); a token consisting of a name specifies that the general entity of the name is open; a token of the form prefix=uri specifies the namespace for a particular prefix; a token of the form =uri specifies the default namespace. This can be called at any point after the first call to an ExternalEntityRefHandler so longer as the parser has not yet been freed. The new parser is completely independent and may safely be used in a separate thread. The handlers and userData are initialized from the parser argument. Returns NULL if out of memory. Otherwise returns a new XML_Parser object. */ XMLPARSEAPI(XML_Parser) XML_ExternalEntityParserCreate(XML_Parser parser, const XML_Char *context, const XML_Char *encoding); enum XML_ParamEntityParsing { XML_PARAM_ENTITY_PARSING_NEVER, XML_PARAM_ENTITY_PARSING_UNLESS_STANDALONE, XML_PARAM_ENTITY_PARSING_ALWAYS }; /* Controls parsing of parameter entities (including the external DTD subset). If parsing of parameter entities is enabled, then references to external parameter entities (including the external DTD subset) will be passed to the handler set with XML_SetExternalEntityRefHandler. The context passed will be 0. Unlike external general entities, external parameter entities can only be parsed synchronously. If the external parameter entity is to be parsed, it must be parsed during the call to the external entity ref handler: the complete sequence of XML_ExternalEntityParserCreate, XML_Parse/XML_ParseBuffer and XML_ParserFree calls must be made during this call. After XML_ExternalEntityParserCreate has been called to create the parser for the external parameter entity (context must be 0 for this call), it is illegal to make any calls on the old parser until XML_ParserFree has been called on the newly created parser. If the library has been compiled without support for parameter entity parsing (ie without XML_DTD being defined), then XML_SetParamEntityParsing will return 0 if parsing of parameter entities is requested; otherwise it will return non-zero. Note: If XML_SetParamEntityParsing is called after XML_Parse or XML_ParseBuffer, then it has no effect and will always return 0. */ XMLPARSEAPI(int) XML_SetParamEntityParsing(XML_Parser parser, enum XML_ParamEntityParsing parsing); /* If XML_Parse or XML_ParseBuffer have returned XML_STATUS_ERROR, then XML_GetErrorCode returns information about the error. */ XMLPARSEAPI(enum XML_Error) XML_GetErrorCode(XML_Parser parser); /* These functions return information about the current parse location. They may be called from any callback called to report some parse event; in this case the location is the location of the first of the sequence of characters that generated the event. When called from callbacks generated by declarations in the document prologue, the location identified isn't as neatly defined, but will be within the relevant markup. When called outside of the callback functions, the position indicated will be just past the last parse event (regardless of whether there was an associated callback). They may also be called after returning from a call to XML_Parse or XML_ParseBuffer. If the return value is XML_STATUS_ERROR then the location is the location of the character at which the error was detected; otherwise the location is the location of the last parse event, as described above. */ XMLPARSEAPI(XML_Size) XML_GetCurrentLineNumber(XML_Parser parser); XMLPARSEAPI(XML_Size) XML_GetCurrentColumnNumber(XML_Parser parser); XMLPARSEAPI(XML_Index) XML_GetCurrentByteIndex(XML_Parser parser); /* Return the number of bytes in the current event. Returns 0 if the event is in an internal entity. */ XMLPARSEAPI(int) XML_GetCurrentByteCount(XML_Parser parser); /* If XML_CONTEXT_BYTES is defined, returns the input buffer, sets the integer pointed to by offset to the offset within this buffer of the current parse position, and sets the integer pointed to by size to the size of this buffer (the number of input bytes). Otherwise returns a NULL pointer. Also returns a NULL pointer if a parse isn't active. NOTE: The character pointer returned should not be used outside the handler that makes the call. */ XMLPARSEAPI(const char *) XML_GetInputContext(XML_Parser parser, int *offset, int *size); /* For backwards compatibility with previous versions. */ #define XML_GetErrorLineNumber XML_GetCurrentLineNumber #define XML_GetErrorColumnNumber XML_GetCurrentColumnNumber #define XML_GetErrorByteIndex XML_GetCurrentByteIndex /* Frees the content model passed to the element declaration handler */ XMLPARSEAPI(void) XML_FreeContentModel(XML_Parser parser, XML_Content *model); /* Exposing the memory handling functions used in Expat */ XMLPARSEAPI(void *) XML_MemMalloc(XML_Parser parser, size_t size); XMLPARSEAPI(void *) XML_MemRealloc(XML_Parser parser, void *ptr, size_t size); XMLPARSEAPI(void) XML_MemFree(XML_Parser parser, void *ptr); /* Frees memory used by the parser. */ XMLPARSEAPI(void) XML_ParserFree(XML_Parser parser); /* Returns a string describing the error. */ XMLPARSEAPI(const XML_LChar *) XML_ErrorString(enum XML_Error code); /* Return a string containing the version number of this expat */ XMLPARSEAPI(const XML_LChar *) XML_ExpatVersion(void); typedef struct { int major; int minor; int micro; } XML_Expat_Version; /* Return an XML_Expat_Version structure containing numeric version number information for this version of expat. */ XMLPARSEAPI(XML_Expat_Version) XML_ExpatVersionInfo(void); /* Added in Expat 1.95.5. */ enum XML_FeatureEnum { XML_FEATURE_END = 0, XML_FEATURE_UNICODE, XML_FEATURE_UNICODE_WCHAR_T, XML_FEATURE_DTD, XML_FEATURE_CONTEXT_BYTES, XML_FEATURE_MIN_SIZE, XML_FEATURE_SIZEOF_XML_CHAR, XML_FEATURE_SIZEOF_XML_LCHAR, XML_FEATURE_NS, XML_FEATURE_LARGE_SIZE /* Additional features must be added to the end of this enum. */ }; typedef struct { enum XML_FeatureEnum feature; const XML_LChar *name; long int value; } XML_Feature; XMLPARSEAPI(const XML_Feature *) XML_GetFeatureList(void); /* Expat follows the GNU/Linux convention of odd number minor version for beta/development releases and even number minor version for stable releases. Micro is bumped with each release, and set to 0 with each change to major or minor version. */ #define XML_MAJOR_VERSION 2 #define XML_MINOR_VERSION 0 #define XML_MICRO_VERSION 1 #ifdef __cplusplus } #endif #endif /* not Expat_INCLUDED */ libmstoolkit-77.0.0/include/winconfig.h0000644000175000017500000000130512455161024020025 0ustar rusconirusconi/*================================================================ ** Copyright 2000, Clark Cooper ** All rights reserved. ** ** This is free software. You are permitted to copy, distribute, or modify ** it under the terms of the MIT/X license (contained in the COPYING file ** with this distribution.) */ #ifndef WINCONFIG_H #define WINCONFIG_H #define WIN32_LEAN_AND_MEAN #include #undef WIN32_LEAN_AND_MEAN #include #include #define XML_NS 1 #define XML_DTD 1 #define XML_CONTEXT_BYTES 1024 /* we will assume all Windows platforms are little endian */ #define BYTEORDER 1234 /* Windows has memmove() available. */ #define HAVE_MEMMOVE #endif /* ndef WINCONFIG_H */ libmstoolkit-77.0.0/src/0000755000175000017500000000000012455161123015036 5ustar rusconirusconilibmstoolkit-77.0.0/src/MSToolkit/0000755000175000017500000000000012455161024016723 5ustar rusconirusconilibmstoolkit-77.0.0/src/MSToolkit/RAWReader.cpp0000644000175000017500000004032112455161024021203 0ustar rusconirusconi#include "RAWReader.h" using namespace MSToolkit; // ========================== // Constructors & Destructors // ========================== RAWReader::RAWReader(){ CoInitialize( NULL ); bRaw = initRaw(); rawCurSpec=0; rawTotSpec=0; rawAvg=false; rawAvgWidth=1; rawAvgCutoff=1000; rawFileOpen=false; rawLabel=false; rawUserFilterExact=true; strcpy(rawInstrument,"unknown"); strcpy(rawManufacturer,"Thermo Scientific"); strcpy(rawUserFilter,""); msLevelFilter=NULL; } RAWReader::~RAWReader(){ if(bRaw){ if(rawFileOpen) m_Raw->Close(); m_Raw.Release(); m_Raw=NULL; } msLevelFilter=NULL; } int RAWReader::calcChargeState(double precursormz, double highmass, VARIANT* varMassList, long nArraySize) { // Assumes spectrum is +1 or +2. Figures out charge by // seeing if signal is present above the parent mass // indicating +2 (by taking ratio above/below precursor) bool bFound; long i, iStart; double dLeftSum,dRightSum; double FractionWindow; double CorrectionFactor; dLeftSum = 0.00001; dRightSum = 0.00001; DataPeak* pDataPeaks = NULL; SAFEARRAY FAR* psa = varMassList->parray; SafeArrayAccessData( psa, (void**)(&pDataPeaks) ); //------------- // calc charge //------------- bFound=false; i=0; while(i 0 && (dRightSum / dLeftSum) < (0.2 * CorrectionFactor)){ SafeArrayUnaccessData( psa ); psa=NULL; pDataPeaks=NULL; return 1; } else { SafeArrayUnaccessData( psa ); psa=NULL; pDataPeaks=NULL; return 0; //Set charge to 0 to indicate that both +2 and +3 spectra should be created } //When all else fails, return 0 return 0; } MSSpectrumType RAWReader::evaluateFilter(long scan, char* chFilter, vector& MZs, bool& bCentroid, double& cv, MSActivation& act) { BSTR Filter = NULL; char cStr[256]; string tStr; string mzVal; int stop; //For non-ATL and non-MFC conversions int sl; //Initialize raw values to default MZs.clear(); cv=0; m_Raw->GetFilterForScanNum(scan, &Filter); sl = SysStringLen(Filter)+1; WideCharToMultiByte(CP_ACP,0,Filter,-1,chFilter,sl,NULL,NULL); SysFreeString(Filter); strcpy(cStr,chFilter); MSSpectrumType mst=Unspecified; char* tok; tok=strtok(cStr," \n"); while(tok!=NULL){ if(strcmp(tok,"c")==0){ bCentroid=true; } else if(strlen(tok)>2 && tok[0]=='c' && tok[1]=='v'){ cv=atof(tok+3); } else if(strcmp(tok,"d")==0){ } else if(strcmp(tok,"ESI")==0){ } else if(strcmp(tok,"FTMS")==0){ } else if(strcmp(tok,"Full")==0){ } else if(strcmp(tok,"ITMS")==0){ } else if(strcmp(tok,"lock")==0){ } else if(strcmp(tok,"ms")==0){ mst=MS1; } else if(strcmp(tok,"msx")==0){ mst=MSX; } else if(strcmp(tok,"ms2")==0){ if(mst!=MSX) mst=MS2; } else if(strcmp(tok,"ms3")==0){ if(mst!=MSX) mst=MS3; } else if(strcmp(tok,"NSI")==0){ } else if(strcmp(tok,"p")==0){ bCentroid=false; } else if(strcmp(tok,"r")==0){ //appears in fusion data, no documentation } else if(strncmp(tok,"sid",3)==0){ } else if(strcmp(tok,"SRM")==0){ mst=SRM; } else if(strcmp(tok,"u")==0){ mst=UZS; } else if(strcmp(tok,"w")==0){ //wideband activation? } else if(strcmp(tok,"Z")==0){ if(mst!=UZS) mst=ZS; } else if(strcmp(tok,"+")==0){ } else if(strcmp(tok,"-")==0){ } else if(strchr(tok,'@')!=NULL){ tStr=tok; stop=tStr.find("@"); mzVal=tStr.substr(0,stop); MZs.push_back(atof(&mzVal[0])); mzVal=tStr.substr(stop+1,3); if(mzVal.compare("cid")==0){ act=mstCID; } else if(mzVal.compare("hcd")==0){ act=mstHCD; } else if(mzVal.compare("etd")==0){ act=mstETD; } else { cout << "Unknown activation method: " << &mzVal[0] << endl; act=mstNA; } } else if(strchr(tok,'[')!=NULL){ } else { cout << "Unknown token: " << tok << endl; } tok=strtok(NULL," \n"); } return mst; } void RAWReader::getInstrument(char* str){ strcpy(str,rawInstrument); } long RAWReader::getLastScanNumber(){ return rawCurSpec; } void RAWReader::getManufacturer(char* str){ strcpy(str,rawManufacturer); } long RAWReader::getScanCount(){ return rawTotSpec; } bool RAWReader::getStatus(){ return bRaw; } bool RAWReader::initRaw(){ int raw=0; IXRawfile2Ptr m_Raw2; IXRawfile3Ptr m_Raw3; IXRawfile4Ptr m_Raw4; IXRawfile5Ptr m_Raw5; //Example of Xcalibur/Foundation first //if(FAILED(m_Raw5.CreateInstance("XRawfile.XRawfile.1"))){ //Try MSFileReader - using ProteoWizard strategy if(FAILED(m_Raw5.CreateInstance("MSFileReader.XRawfile.1"))){ if(FAILED(m_Raw4.CreateInstance("MSFileReader.XRawfile.1"))){ if(FAILED(m_Raw3.CreateInstance("MSFileReader.XRawfile.1"))){ if(FAILED(m_Raw2.CreateInstance("MSFileReader.XRawfile.1"))){ if(FAILED(m_Raw.CreateInstance("MSFileReader.XRawfile.1"))){ raw=0; //cout << "Cannot load Thermo MSFileReader. Cannot read .RAW files." << endl; } else { raw=1; } } else { m_Raw=m_Raw2; raw=2; } } else { m_Raw=m_Raw3; raw=3; } } else { m_Raw=m_Raw4; raw=4; } } else { m_Raw=m_Raw5; raw=5; } if(raw>0) return true; return false; } bool RAWReader::readRawFile(const char *c, Spectrum &s, int scNum){ //General purpose function members bool bCheckNext; char chFilter[256]; char curFilter[256]; double dRTime; double highmass=0.0; double pm1; double pw; long i; long j; long lArraySize=0; vector MZs; DataPeak* pDataPeaks = NULL; HRESULT lRet; MSSpectrumType MSn; SAFEARRAY FAR* psa; TCHAR pth[MAX_PATH]; VARIANT varMassList; VARIANT varPeakFlags; //Members for gathering averaged scans int charge; int sl; int widthCount; long FirstBkg1=0; long FirstBkg2=0; long LastBkg1=0; long LastBkg2=0; long lowerBound; long upperBound; BSTR rawFilter=NULL; BSTR testStr; //Additional members for Scan Information bool bCentroid; double cv; //Compensation Voltage double BPI; //Base peak intensity double BPM; //Base peak mass double td; //temp double value double TIC; long tl; //temp long value MSActivation act; VARIANT Charge; VARIANT ConversionA; VARIANT ConversionB; VARIANT ConversionC; VARIANT ConversionD; VARIANT ConversionE; VARIANT ConversionI; VARIANT IIT; //ion injection time VARIANT MonoMZ; if(!bRaw) return false; //Clear spectrum object s.clear(); if(c==NULL){ //if file is closed and scan number requested, open file and grab scan number if(scNum>0) rawCurSpec=scNum; else rawCurSpec++; if(rawCurSpec>rawTotSpec) return false; } else { //close an open file, open the requested file. if(rawFileOpen) { lRet = m_Raw->Close(); rawFileOpen=false; } MultiByteToWideChar(CP_ACP,0,c,-1,(LPWSTR)pth,MAX_PATH); lRet = m_Raw->Open((LPWSTR)pth); if(lRet != ERROR_SUCCESS) { cerr << "Cannot open " << c << endl; return false; } else lRet = m_Raw->SetCurrentController(0,1); rawFileOpen=true; m_Raw->GetNumSpectra(&rawTotSpec); testStr=NULL; m_Raw->GetInstModel(&testStr); sl = SysStringLen(testStr)+1; WideCharToMultiByte(CP_ACP,0,testStr,-1,rawInstrument,sl,NULL,NULL); SysFreeString(testStr); //if scan number is requested, grab it if(scNum>0) rawCurSpec=scNum; else rawCurSpec=1; if(rawCurSpec>rawTotSpec) return false; } //Initialize members strcpy(chFilter,""); strcpy(curFilter,""); VariantInit(&varMassList); VariantInit(&varPeakFlags); VariantInit(&IIT); VariantInit(&ConversionA); VariantInit(&ConversionB); VariantInit(&ConversionC); VariantInit(&ConversionD); VariantInit(&ConversionE); VariantInit(&ConversionI); VariantInit(&Charge); VariantInit(&MonoMZ); //Rather than grab the next scan number, get the next scan based on a user-filter (if supplied). //if the filter was set, make sure we pass the filter while(true){ MSn = evaluateFilter(rawCurSpec, curFilter, MZs, bCentroid,cv,act); //check for spectrum filter (string) if(strlen(rawUserFilter)>0){ bCheckNext=false; if(rawUserFilterExact) { if(strcmp(curFilter,rawUserFilter)!=0) bCheckNext=true; } else { if(strstr(curFilter,rawUserFilter)==NULL) bCheckNext=true; } //if string doesn't match, get next scan until it does match or EOF if(bCheckNext){ if(scNum>0) return false; rawCurSpec++; if(rawCurSpec>rawTotSpec) return false; continue; } } //check for msLevel filter if(msLevelFilter->size()>0 && find(msLevelFilter->begin(), msLevelFilter->end(), MSn) == msLevelFilter->end()) { if(scNum>0) return false; rawCurSpec++; if(rawCurSpec>rawTotSpec) return false; } else { break; } } //Get spectrum meta data sl=lstrlenA("Monoisotopic M/Z:"); testStr = SysAllocStringLen(NULL,sl); MultiByteToWideChar(CP_ACP,0,"Monoisotopic M/Z:",sl,testStr,sl); m_Raw->GetTrailerExtraValueForScanNum(rawCurSpec, testStr, &MonoMZ); SysFreeString(testStr); sl=lstrlenA("Charge State:"); testStr = SysAllocStringLen(NULL,sl); MultiByteToWideChar(CP_ACP,0,"Charge State:",sl,testStr,sl); m_Raw->GetTrailerExtraValueForScanNum(rawCurSpec, testStr, &Charge); SysFreeString(testStr); sl=lstrlenA("Ion Injection Time (ms):"); testStr = SysAllocStringLen(NULL,sl); MultiByteToWideChar(CP_ACP,0,"Ion Injection Time (ms):",sl,testStr,sl); m_Raw->GetTrailerExtraValueForScanNum(rawCurSpec, testStr, &IIT); SysFreeString(testStr); sl=lstrlenA("Conversion Parameter A:"); testStr = SysAllocStringLen(NULL,sl); MultiByteToWideChar(CP_ACP,0,"Conversion Parameter A:",sl,testStr,sl); m_Raw->GetTrailerExtraValueForScanNum(rawCurSpec, testStr, &ConversionA); SysFreeString(testStr); testStr = SysAllocStringLen(NULL,sl); MultiByteToWideChar(CP_ACP,0,"Conversion Parameter B:",sl,testStr,sl); m_Raw->GetTrailerExtraValueForScanNum(rawCurSpec, testStr, &ConversionB); SysFreeString(testStr); testStr = SysAllocStringLen(NULL,sl); MultiByteToWideChar(CP_ACP,0,"Conversion Parameter C:",sl,testStr,sl); m_Raw->GetTrailerExtraValueForScanNum(rawCurSpec, testStr, &ConversionC); SysFreeString(testStr); testStr = SysAllocStringLen(NULL,sl); MultiByteToWideChar(CP_ACP,0,"Conversion Parameter D:",sl,testStr,sl); m_Raw->GetTrailerExtraValueForScanNum(rawCurSpec, testStr, &ConversionD); SysFreeString(testStr); testStr = SysAllocStringLen(NULL,sl); MultiByteToWideChar(CP_ACP,0,"Conversion Parameter E:",sl,testStr,sl); m_Raw->GetTrailerExtraValueForScanNum(rawCurSpec, testStr, &ConversionE); SysFreeString(testStr); testStr = SysAllocStringLen(NULL,sl); MultiByteToWideChar(CP_ACP,0,"Conversion Parameter I:",sl,testStr,sl); m_Raw->GetTrailerExtraValueForScanNum(rawCurSpec, testStr, &ConversionI); SysFreeString(testStr); m_Raw->GetScanHeaderInfoForScanNum(rawCurSpec, &tl, &td, &td, &td, &TIC, &BPM, &BPI, &tl, &tl, &td); m_Raw->RTFromScanNum(rawCurSpec,&dRTime); //Get the peaks //Average raw files if requested by user if(rawAvg){ widthCount=0; lowerBound=0; upperBound=0; for(i=rawCurSpec-1;i>0;i--){ evaluateFilter(i, chFilter, MZs, bCentroid,cv,act); if(strcmp(curFilter,chFilter)==0){ widthCount++; if(widthCount==rawAvgWidth) { lowerBound=i; break; } } } if(lowerBound==0) lowerBound=rawCurSpec; //this will have "edge" effects widthCount=0; for(i=rawCurSpec+1;iGetFilterForScanNum(i, &rawFilter); j=m_Raw->GetAverageMassList(&lowerBound, &upperBound, &FirstBkg1, &LastBkg1, &FirstBkg2, &LastBkg2, rawFilter, 1, rawAvgCutoff, 0, FALSE, &pw, &varMassList, &varPeakFlags, &lArraySize ); SysFreeString(rawFilter); rawFilter=NULL; } else { //Get regular spectrum data sl=lstrlenA(""); testStr = SysAllocStringLen(NULL,sl); MultiByteToWideChar(CP_ACP,0,"",sl,testStr,sl); j=m_Raw->GetMassListFromScanNum(&rawCurSpec,testStr,0,0,0,FALSE,&pw,&varMassList,&varPeakFlags,&lArraySize); SysFreeString(testStr); } //Handle MS2 and MS3 files differently to create Z-lines if(MSn==MS2 || MSn==MS3){ //if charge state is assigned to spectrum, add Z-lines. if(Charge.iVal>0){ if(MonoMZ.dblVal>0.01) { pm1 = MonoMZ.dblVal * Charge.iVal - ((Charge.iVal-1)*1.007276466); s.setMZ(MZs[0],MonoMZ.dblVal); } else { pm1 = MZs[0] * Charge.iVal - ((Charge.iVal-1)*1.007276466); s.setMZ(MZs[0]); } s.addZState(Charge.iVal,pm1); s.setCharge(Charge.iVal); } else { s.setMZ(MZs[0]); charge = calcChargeState(MZs[0], highmass, &varMassList, lArraySize); //Charge greater than 0 means the charge state is known if(charge>0){ pm1 = MZs[0]*charge - ((charge-1)*1.007276466); s.addZState(charge,pm1); //Charge of 0 means unknown charge state, therefore, compute +2 and +3 states. } else { pm1 = MZs[0]*2 - 1.007276466; s.addZState(2,pm1); pm1 = MZs[0]*3 - 2*1.007276466; s.addZState(3,pm1); } } } //endif MS2 and MS3 if(MSn==MSX){ for(i=0;i<(int)MZs.size();i++){ if(i==0) s.setMZ(MZs[i],0); else s.addMZ(MZs[i],0); } s.setCharge(0); } //Set basic scan info if(bCentroid) s.setCentroidStatus(1); else s.setCentroidStatus(0); s.setRawFilter(curFilter); s.setActivationMethod(act); s.setScanNumber((int)rawCurSpec); s.setScanNumber((int)rawCurSpec,true); s.setRTime((float)dRTime); s.setFileType(MSn); s.setBPI((float)BPI); s.setBPM(BPM); s.setCompensationVoltage(cv); s.setConversionA(ConversionA.dblVal); s.setConversionB(ConversionB.dblVal); s.setConversionC(ConversionC.dblVal); s.setConversionD(ConversionD.dblVal); s.setConversionE(ConversionE.dblVal); s.setConversionI(ConversionI.dblVal); s.setTIC(TIC); s.setIonInjectionTime(IIT.fltVal); if(MSn==SRM) s.setMZ(MZs[0]); switch(MSn){ case MS1: s.setMsLevel(1); break; case MS2: s.setMsLevel(2); break; case MS3: s.setMsLevel(3); break; case MSX: s.setMsLevel(2); break; default: s.setMsLevel(0); break; } psa = varMassList.parray; SafeArrayAccessData( psa, (void**)(&pDataPeaks) ); for(j=0;j* v){ msLevelFilter=v; } void RAWReader::setRawFilter(char *c){ strcpy(rawUserFilter,c); } libmstoolkit-77.0.0/src/MSToolkit/MSReader.cpp0000644000175000017500000014152712455161024021103 0ustar rusconirusconi#include "MSReader.h" #include using namespace std; using namespace MSToolkit; MSReader::MSReader(){ fileIn=NULL; rampFileIn=NULL; iIntensityPrecision=1; iMZPrecision=4; rampFileOpen=false; compressMe=false; rawFileOpen=false; exportMGF=false; highResMGF=false; iFType=0; iVersion=0; for(int i=0;i<16;i++) strcpy(header.header[i],"\0"); headerIndex=0; sInstrument="unknown"; sManufacturer="unknown"; #ifndef _NOSQLITE db = NULL; lastIndex=-1; lastScanNumber=-1; #endif } MSReader::~MSReader(){ closeFile(); if(rampFileOpen) { rampCloseFile(rampFileIn); free(pScanIndex); } #ifndef _NOSQLITE if(db != NULL) sqlite3_close(db); #endif } void MSReader::addFilter(MSSpectrumType m){ filter.push_back(m); } void MSReader::closeFile(){ if(fileIn!=NULL) fclose(fileIn); if(rampFileOpen) { rampCloseFile(rampFileIn); rampFileIn=NULL; rampFileOpen=false; free(pScanIndex); } } MSHeader& MSReader::getHeader(){ return header; } void MSReader::getInstrument(char* str){ strcpy(str,&sInstrument[0]); } void MSReader::getManufacturer(char* str){ strcpy(str,&sManufacturer[0]); } /* 0 = File opened correctly 1 = Could not open file */ int MSReader::openFile(const char *c,bool text){ int i; if(text) fileIn=fopen(c,"rt"); else fileIn=fopen(c,"rb"); if(fileIn==NULL) { for(i=0;i<16;i++) strcpy(header.header[i],"\0"); headerIndex=0; fileType=Unspecified; return 1; } else { fileType=Unspecified; //if we don't have the eof position, get it here. fseek(fileIn,0,2); lEnd=ftell(fileIn); lPivot = 0; lFWidth = lEnd/2; fseek(fileIn,0,0); if(text){ for(i=0;i<16;i++) strcpy(header.header[i],"\0"); headerIndex=0; } else { fread(&iFType,4,1,fileIn); fread(&iVersion,4,1,fileIn); fread(&header,sizeof(MSHeader),1,fileIn); } return 0; } } MSSpectrumType MSReader::getFileType(){ return fileType; } bool MSReader::readMSTFile(const char *c, bool text, Spectrum& s, int scNum){ MSScanInfo ms; Peak_T p; ZState z; EZState ez; int i; //variables for text reading only bool firstScan = false; bool bScan = true; bool bDoneHeader = false; char tstr[256]; char ch; char *tok; //variables for compressed files uLong mzLen, intensityLen; //clear any spectrum data s.clear(); s.setCentroidStatus(2); //unknown if centroided with these formats. //check for valid file and if we can access it if(c!=NULL){ closeFile(); if(openFile(c,text)==1) return false; lastFileFormat = checkFileFormat(c); } else if(fileIn==NULL) { return false; } //set the filetype switch(lastFileFormat){ case ms2: case cms2: case bms2: s.setFileType(MS2); break; case zs: s.setFileType(ZS); break; case uzs: s.setFileType(UZS); break; case ms1: case cms1: case bms1: s.setFileType(MS1); break; default: s.setFileType(Unspecified); break; } //Handle binary and text files differently if(!text){ //if binary file, read scan info sequentially, skipping to next scan if requested //fread(&ms,sizeof(MSScanInfo),1,fileIn); readSpecHeader(fileIn,ms); if(scNum!=0){ fseek(fileIn,sizeof(MSHeader)+8,0); //fread(&ms,sizeof(MSScanInfo),1,fileIn); readSpecHeader(fileIn,ms); while(ms.scanNumber[0]!=scNum){ fseek(fileIn,ms.numZStates*12,1); fseek(fileIn,ms.numEZStates*20,1); if(compressMe){ fread(&i,4,1,fileIn); mzLen = (uLong)i; fread(&i,4,1,fileIn); intensityLen = (uLong)i; fseek(fileIn,mzLen+intensityLen,1); } else { fseek(fileIn,ms.numDataPoints*12,1); } //fread(&ms,sizeof(MSScanInfo),1,fileIn); readSpecHeader(fileIn,ms); if(feof(fileIn)) return false; } } if(feof(fileIn)) return false; //read any charge states (for MS2 files) for(i=0;i0 && lPivot>0 && lPivot chgs; if(s.getMsLevel() >1) { chgs = estimateCharge(s); } if(s.sizeZ() == 1) charge = s.atZ(0).z; else if(s.sizeZ() > 1) charge = 0; else { if(chgs.size() == 1) charge = chgs.at(0); else charge = 0; } MSActivation act = s.getActivationMethod(); string actMethod; switch(act){ case mstETD: actMethod="ETD"; break; case mstCID: actMethod="CID"; break; case mstECD: actMethod="ECD"; break; case mstPQD: actMethod = "PQD"; break; case mstHCD: actMethod = "HCD"; break; case mstNA: default: actMethod="UNKNOWN"; break; } sprintf(zSql, "insert into msScan(runID,startScanNumber,endScanNumber,level,precursorMZ, precursorCharge,retentionTime,fragmentationType,peakCount) " "values (1,%d, %d,%d, %f, %d, %f,'%s', %d)", s.getScanNumber(), s.getScanNumber(true), s.getMsLevel(), s.getMZ(), charge, s.getRTime(), actMethod.c_str(), s.size()); sql_stmt(zSql); zSql[0]='\0'; //get scanID strcpy(zSql, "select MAX(id) from msScan"); int rc,iRow, iCol; char** result; int lastScanID; rc = sqlite3_get_table(db, zSql, &result, &iRow, &iCol, 0); if(rc == SQLITE_OK) { lastScanID=atoi(result[1]); } else { cout<<"Can't execute the SQL statement"< 1) { if(s.sizeZ() > 0) { for(int i=0; i MSReader::estimateCharge(Spectrum& s) { vector chgs; float totalIntensity = s.getTotalIntensity(); float beforeMZIntensity=0; double preMZ = s.getMZ(); for(int i=0; i= 0.95) { chgs.push_back(1); } else { chgs.push_back(2); chgs.push_back(3); } return chgs; } void MSReader::createIndex() { //create index for msScan table char* stmt1 = "create index idxScanNumber on msScan(startScanNumber)"; sql_stmt(stmt1); } #endif void MSReader::appendFile(char* c, bool text, MSObject& m){ FILE* fileOut; int i; //if a filename isn't specified, check to see if the //MSObject has a filename. if(c == NULL) { return; } else { if(text) fileOut=fopen(c,"at"); else fileOut=fopen(c,"ab"); } //output spectra; for(i=0;i lastScanNumber) { cout<<"Specified scan number doesn't exist!"< lastIndex) return false; sprintf(zSql, "select * from msScan, msScanData where id=%d " "AND id=scanID",curIndex); if(executeSqlStmt(s,zSql)) break; } } return true; } bool MSReader::executeSqlStmt(Spectrum& s, char* zSql) { bool isSameLevel=false; sqlite3_stmt *pStmt; int rc; rc = sqlite3_prepare(db, zSql, -1, &pStmt, 0); if( rc!=SQLITE_OK ){ cout<<"can't prepare SQL statement!"<(sqlite3_column_text(pStmt,10))); if(strcmp(actMethod,"CID") == 0) s.setActivationMethod(mstCID); if(strcmp(actMethod, "ETD") == 0) s.setActivationMethod(mstETD); if(strcmp(actMethod, "ECD") == 0) s.setActivationMethod(mstECD); if(strcmp(actMethod, "PQD") == 0) s.setActivationMethod(mstPQD); if(strcmp(actMethod, "HCD") == 0) s.setActivationMethod(mstHCD); if(strcmp(actMethod, "UNKNOWN") == 0) s.setActivationMethod(mstNA); int numPeaks = sqlite3_column_int(pStmt,12); int numBytes1=sqlite3_column_bytes(pStmt,14); unsigned char* comprM = (unsigned char*)sqlite3_column_blob(pStmt,14); int numBytes2=sqlite3_column_bytes(pStmt,15); unsigned char* comprI = (unsigned char*)sqlite3_column_blob(pStmt,15); getUncompressedPeaks(s,numPeaks, numBytes1,comprM, numBytes2,comprI); isSameLevel = true; } } rc = sqlite3_finalize(pStmt); return isSameLevel; } void MSReader::readChargeTable(int scanID, Spectrum& s) { char zSql[8192]; sprintf(zSql, "select charge, mass from MS2FileScanCharge where scanID=%d", scanID); sqlite3_stmt *pStmt; int rc; rc = sqlite3_prepare(db, zSql, -1, &pStmt, 0); if( rc!=SQLITE_OK ){ cout<<"can't prepare SQL statement!"< rampLastScan) return false; //clear any spectrum data s.clear(); MSSpectrumType mslevel; //read scan header if(scNum!=0) { rampIndex=scNum; readHeader(rampFileIn, pScanIndex[rampIndex], &scanHeader); if (scanHeader.acquisitionNum != scNum && scanHeader.acquisitionNum != -1) { cerr << "ERROR: Failure reading scan, index corrupted. Line endings may have changed during transfer." << flush; exit(1); } switch(scanHeader.msLevel){ case 1: mslevel = MS1; break; case 2: mslevel = MS2; break; case 3: mslevel = MS3; break; default: break; } if(find(filter.begin(), filter.end(), mslevel) != filter.end()) { if(scanHeader.centroid) s.setCentroidStatus(1); else s.setCentroidStatus(0); s.setNativeID(scanHeader.idString); s.setMsLevel(scanHeader.msLevel); s.setScanNumber(scanHeader.acquisitionNum); s.setScanNumber(scanHeader.acquisitionNum,true); s.setRTime((float)scanHeader.retentionTime/60.0f); s.setCompensationVoltage(scanHeader.compensationVoltage); if(strlen(scanHeader.activationMethod)>1){ if(strcmp(scanHeader.activationMethod,"CID")==0) s.setActivationMethod(mstCID); else if(strcmp(scanHeader.activationMethod,"ECD")==0) s.setActivationMethod(mstECD); else if(strcmp(scanHeader.activationMethod,"ETD")==0) s.setActivationMethod(mstETD); else if(strcmp(scanHeader.activationMethod,"PQD")==0) s.setActivationMethod(mstPQD); else if(strcmp(scanHeader.activationMethod,"HCD")==0) s.setActivationMethod(mstHCD); else s.setActivationMethod(mstNA); } if(scanHeader.msLevel>1) { s.setMZ(scanHeader.precursorMZ,scanHeader.precursorMonoMZ); s.setCharge(scanHeader.precursorCharge); } else { s.setMZ(0); } if(scanHeader.precursorCharge>0) s.addZState(scanHeader.precursorCharge,scanHeader.precursorMZ*scanHeader.precursorCharge-(scanHeader.precursorCharge-1)*1.007276466); pPeaks = readPeaks(rampFileIn, pScanIndex[rampIndex]); j=0; for(i=0;irampLastScan) return false; //read next index while(true){ rampIndex++; if(pScanIndex[rampIndex]<0) continue; //reached end of file if(rampIndex>rampLastScan) return false; readHeader(rampFileIn, pScanIndex[rampIndex], &scanHeader); switch(scanHeader.msLevel){ case 1: mslevel = MS1; break; case 2: mslevel = MS2; break; case 3: mslevel = MS3; break; default: break; } if(find(filter.begin(), filter.end(), mslevel) != filter.end()) break; } if(scanHeader.centroid) s.setCentroidStatus(1); else s.setCentroidStatus(0); s.setNativeID(scanHeader.idString); s.setMsLevel(scanHeader.msLevel); s.setScanNumber(scanHeader.acquisitionNum); s.setScanNumber(scanHeader.acquisitionNum,true); s.setRTime((float)scanHeader.retentionTime/60.0f); s.setCompensationVoltage(scanHeader.compensationVoltage); if(strlen(scanHeader.activationMethod)>1){ if(strcmp(scanHeader.activationMethod,"CID")==0) s.setActivationMethod(mstCID); else if(strcmp(scanHeader.activationMethod,"ECD")==0) s.setActivationMethod(mstECD); else if(strcmp(scanHeader.activationMethod,"ETD")==0) s.setActivationMethod(mstETD); else if(strcmp(scanHeader.activationMethod,"PQD")==0) s.setActivationMethod(mstPQD); else if(strcmp(scanHeader.activationMethod,"HCD")==0) s.setActivationMethod(mstHCD); else s.setActivationMethod(mstNA); } if(scanHeader.msLevel>1) { s.setMZ(scanHeader.precursorMZ,scanHeader.precursorMonoMZ); s.setCharge(scanHeader.precursorCharge); } else { s.setMZ(0); } if(scanHeader.precursorCharge>0) s.addZState(scanHeader.precursorCharge,scanHeader.precursorMZ*scanHeader.precursorCharge-(scanHeader.precursorCharge-1)*1.007276466); pPeaks = readPeaks(rampFileIn, pScanIndex[rampIndex]); j=0; for(i=0;i& m){ for(unsigned int i=0; i2 && iIntensityPrecision>0){ if(t[0]=='0'){ fprintf(fileOut,"%.*f 0\n",iMZPrecision,s.at(j).mz); } else if(t[k-1]=='0'){ fprintf(fileOut,"%.*f %.*f\n",iMZPrecision,s.at(j).mz,iIntensityPrecision-1,s.at(j).intensity); } else { fprintf(fileOut,"%.*f %.*f\n",iMZPrecision,s.at(j).mz,iIntensityPrecision,s.at(j).intensity); } } else { fprintf(fileOut,"%.*f %.*f\n",iMZPrecision,s.at(j).mz,iIntensityPrecision,s.at(j).intensity); } } fprintf(fileOut,"END IONS\n"); } } else { fprintf(fileOut,"BEGIN IONS\n"); fprintf(fileOut,"PEPMASS=%.*f\n",6,s.getMZ()); fprintf(fileOut,"RTINSECONDS=%d\n",(int)(s.getRTime()*60)); if(s.sizeZ()==1){ if(s.atZ(0).z==1) fprintf(fileOut,"CHARGE=1+\n"); fprintf(fileOut,"TITLE=%s.%d.%d.%d %d %.4f\n","test",s.getScanNumber(),s.getScanNumber(true),s.atZ(0).z,0,s.getRTime()); } else { fprintf(fileOut,"TITLE=%s.%d.%d.%d %d %.4f\n","test",s.getScanNumber(),s.getScanNumber(true),0,0,s.getRTime()); } for(j=0;j2 && iIntensityPrecision>0){ if(t[0]=='0'){ fprintf(fileOut,"%.*f 0\n",iMZPrecision,s.at(j).mz); } else if(t[k-1]=='0'){ fprintf(fileOut,"%.*f %.*f\n",iMZPrecision,s.at(j).mz,iIntensityPrecision-1,s.at(j).intensity); } else { fprintf(fileOut,"%.*f %.*f\n",iMZPrecision,s.at(j).mz,iIntensityPrecision,s.at(j).intensity); } } else { fprintf(fileOut,"%.*f %.*f\n",iMZPrecision,s.at(j).mz,iIntensityPrecision,s.at(j).intensity); } } fprintf(fileOut,"END IONS\n"); } return; } //Only use this code if not writing MGF file for(j=0;j2 && iIntensityPrecision>0){ if(t[0]=='0'){ fprintf(fileOut,"%.*f 0\n",iMZPrecision,s.at(j).mz); } else if(t[k-1]=='0'){ fprintf(fileOut,"%.*f %.*f\n",iMZPrecision,s.at(j).mz,iIntensityPrecision-1,s.at(j).intensity); } else { fprintf(fileOut,"%.*f %.*f\n",iMZPrecision,s.at(j).mz,iIntensityPrecision,s.at(j).intensity); } } else { fprintf(fileOut,"%.*f %.*f\n",iMZPrecision,s.at(j).mz,iIntensityPrecision,s.at(j).intensity); } } } void MSReader::writeBinarySpec(FILE* fileOut, Spectrum& s) { int j; for(j=0;j0) fprintf(fileOut,"I\tRTime\t%.*f\n",4,s.getRTime()); if(s.getBPI()>0) fprintf(fileOut,"I\tBPI\t%.*f\n",2,s.getBPI()); if(s.getBPM()>0) fprintf(fileOut,"I\tBPM\t%.*f\n",4,s.getBPM()); if(s.getConversionA()!=0) fprintf(fileOut,"I\tConvA\t%.*f\n",6,s.getConversionA()); if(s.getConversionB()!=0) fprintf(fileOut,"I\tConvB\t%.*f\n",6,s.getConversionB()); if(s.getConversionC()!=0) fprintf(fileOut,"I\tConvC\t%.*f\n",6,s.getConversionC()); if(s.getConversionD()!=0) fprintf(fileOut,"I\tConvD\t%.*f\n",6,s.getConversionD()); if(s.getConversionE()!=0) fprintf(fileOut,"I\tConvE\t%.*f\n",6,s.getConversionE()); if(s.getConversionI()!=0) fprintf(fileOut,"I\tConvI\t%.*f\n",6,s.getConversionI()); if(s.getTIC()>0) fprintf(fileOut,"I\tTIC\t%.*f\n",2,s.getTIC()); if(s.getIonInjectionTime()>0) fprintf(fileOut,"I\tIIT\t%.*f\n",4,s.getIonInjectionTime()); for(j=0;j=5){ fread(&ms.mzCount,4,1,fileIn); if(ms.mz!=NULL) delete [] ms.mz; ms.mz = new double[ms.mzCount]; for(int i=0;i=2){ fread(&ms.BPI,4,1,fileIn); fread(&ms.BPM,8,1,fileIn); fread(&ms.convA,8,1,fileIn); fread(&ms.convB,8,1,fileIn); if(iVersion>=4){ fread(&ms.convC,8,1,fileIn); fread(&ms.convD,8,1,fileIn); fread(&ms.convE,8,1,fileIn); fread(&ms.convI,8,1,fileIn); } fread(&ms.TIC,8,1,fileIn); fread(&ms.IIT,4,1,fileIn); } fread(&ms.numZStates,4,1,fileIn); if(iVersion>=3) fread(&ms.numEZStates,4,1,fileIn); else ms.numEZStates=0; fread(&ms.numDataPoints,4,1,fileIn); } MSFileFormat MSReader::checkFileFormat(const char *fn){ unsigned int i; char ext[32]; char tmp[1024]; char* c; //extract extension & capitalize c=(char*)strrchr(fn,'.'); if(c==NULL) return dunno; strcpy(ext,c); for(i=0;i #include using namespace std; using namespace MSToolkit; Spectrum::Spectrum(){ //cout<<"in Spectrum constructor!"<; mz=new vector; TIC=0; IIT=0; compensationVoltage=0; convA=0; convB=0; convC=0; convD=0; convE=0; convI=0; BPI=0; BPM=0; centroidStatus=2; fileType=Unspecified; vPeaks = new vector; vEZ = new vector; vZ = new vector; actMethod=mstNA; strcpy(rawFilter,""); strcpy(nativeID,""); } Spectrum::~Spectrum(){ if(vPeaks) delete vPeaks; if(vEZ) delete vEZ; if(vZ) delete vZ; if(mz) delete mz; if(monoMZ) delete monoMZ; } Spectrum::Spectrum(const Spectrum& s){ unsigned int i; rTime = s.rTime; charge = s.charge; scanNumber = s.scanNumber; scanNumber2 = s.scanNumber2; msLevel = s.msLevel; monoMZ = new vector; for(i=0;isize();i++){ monoMZ->push_back(s.monoMZ->at(i)); } mz = new vector; for(i=0;isize();i++){ mz->push_back(s.mz->at(i)); } fileType = s.fileType; IIT = s.IIT; TIC = s.TIC; compensationVoltage = s.compensationVoltage; convA = s.convA; convB = s.convB; convC = s.convC; convD = s.convD; convE = s.convE; convI = s.convI; BPI = s.BPI; BPM = s.BPM; centroidStatus = s.centroidStatus; vPeaks = new vector; for(i=0;isize();i++){ vPeaks->push_back(s.vPeaks->at(i)); } vEZ = new vector; for(i=0;isize();i++){ vEZ->push_back(s.vEZ->at(i)); } vZ = new vector; for(i=0;isize();i++){ vZ->push_back(s.vZ->at(i)); } strcpy(rawFilter,s.rawFilter); strcpy(nativeID,s.nativeID); } Spectrum& Spectrum::operator=(const Spectrum& s){ //cout<<"in Spectrum ="<; for(i=0;isize();i++){ monoMZ->push_back(s.monoMZ->at(i)); } mz = new vector; for(i=0;isize();i++){ mz->push_back(s.mz->at(i)); } vPeaks = new vector; for(i=0;isize();i++){ vPeaks->push_back(s.vPeaks->at(i)); } vEZ = new vector; for(i=0;isize();i++){ vEZ->push_back(s.vEZ->at(i)); } vZ = new vector; for(i=0;isize();i++){ vZ->push_back(s.vZ->at(i)); } rTime = s.rTime; charge = s.charge; scanNumber = s.scanNumber; scanNumber2 = s.scanNumber2; msLevel = s.msLevel; BPI = s.BPI; BPM = s.BPM; compensationVoltage = s.compensationVoltage; convA = s.convA; convB = s.convB; convC = s.convC; convD = s.convD; convE = s.convE; convI = s.convI; TIC = s.TIC; IIT = s.IIT; fileType = s.fileType; centroidStatus = s.centroidStatus; strcpy(rawFilter,s.rawFilter); strcpy(nativeID,s.nativeID); } return *this; } Peak_T& Spectrum::operator[](const int& i) { return vPeaks->operator[](i); } /* ----- Begin Functions ----- */ /* Adds Result struct to end of spectrum. */ void Spectrum::add(Peak_T& p){ vPeaks->push_back(p); } void Spectrum::add(double d1, float d2){ Peak_T p; p.mz=d1; p.intensity=d2; vPeaks->push_back(p); } void Spectrum::addEZState(EZState& z){ vEZ->push_back(z); } void Spectrum::addEZState(int i, double d, float f1, float f2){ EZState z; z.z=i; z.mh=d; z.pRTime=f1; z.pArea=f2; vEZ->push_back(z); } void Spectrum::addMZ(double d, double mono){ mz->push_back(d); monoMZ->push_back(mono); } void Spectrum::addZState(ZState& z){ vZ->push_back(z); } void Spectrum::addZState(int i, double d){ ZState z; z.z=i; z.mz=d; vZ->push_back(z); } /* Returns Result struct of single element in the spectrum. */ Peak_T& Spectrum::at(const int& i){ return vPeaks->operator [](i); } Peak_T& Spectrum::at(const unsigned int& i){ return vPeaks->operator [](i); } EZState& Spectrum::atEZ(const int& i){ return vEZ->operator [](i); } EZState& Spectrum::atEZ(const unsigned int& i){ return vEZ->operator [](i); } ZState& Spectrum::atZ(const int& i){ return vZ->operator [](i); } ZState& Spectrum::atZ(const unsigned int& i){ return vZ->operator [](i); } /* Clears the spectrum */ void Spectrum::clear(){ delete vPeaks; vPeaks = new vector; delete vEZ; vEZ = new vector; delete vZ; vZ = new vector; delete mz; mz = new vector; scanNumber = 0; scanNumber2 = 0; rTime = 0; charge = 0; msLevel = 2; convA = 0; convB = 0; TIC = 0; IIT = 0; BPI = 0; BPM = 0; fileType = Unspecified; actMethod=mstNA; } void Spectrum::clearMZ(){ delete mz; mz = new vector; delete monoMZ; monoMZ = new vector; } void Spectrum::clearPeaks(){ delete vPeaks; vPeaks = new vector; } /* Erases element i in the spectrum. */ void Spectrum::erase(unsigned int i){ vector::iterator vi; vi=vPeaks->begin()+i; vPeaks->erase(vi); } /* Erases element i to element j, inclusive, in the spectrum. */ void Spectrum::erase(unsigned int i, unsigned int j){ vector::iterator vi1; vector::iterator vi2; vi1=vPeaks->begin()+i; vi2=vPeaks->begin()+j+1; vPeaks->erase(vi1,vi2); } void Spectrum::eraseEZ(unsigned int i){ vector::iterator vi; vi=vEZ->begin()+i; vEZ->erase(vi); } /* Erases element i to element j, inclusive, in the spectrum. */ void Spectrum::eraseEZ(unsigned int i, unsigned int j){ vector::iterator vi1; vector::iterator vi2; vi1=vEZ->begin()+i; vi2=vEZ->begin()+j+1; vEZ->erase(vi1,vi2); } void Spectrum::eraseZ(unsigned int i){ vector::iterator vi; vi=vZ->begin()+i; vZ->erase(vi); } /* Erases element i to element j, inclusive, in the spectrum. */ void Spectrum::eraseZ(unsigned int i, unsigned int j){ vector::iterator vi1; vector::iterator vi2; vi1=vZ->begin()+i; vi2=vZ->begin()+j+1; vZ->erase(vi1,vi2); } MSActivation Spectrum::getActivationMethod(){ return actMethod; } float Spectrum::getBPI(){ return BPI; } double Spectrum::getBPM(){ return BPM; } int Spectrum::getCentroidStatus(){ return centroidStatus; } int Spectrum::getCharge(){ return charge; } double Spectrum::getCompensationVoltage(){ return compensationVoltage; } double Spectrum::getConversionA(){ return convA; } double Spectrum::getConversionB(){ return convB; } double Spectrum::getConversionC(){ return convC; } double Spectrum::getConversionD(){ return convD; } double Spectrum::getConversionE(){ return convE; } double Spectrum::getConversionI(){ return convI; } MSSpectrumType Spectrum::getFileType(){ return fileType; } float Spectrum::getIonInjectionTime(){ return IIT; } double Spectrum::getMonoMZ(int index){ if(index>(int)monoMZ->size()) return -1.0; return monoMZ->at(index); } double Spectrum::getMZ(int index){ if(index>(int)mz->size()) return -1.0; return mz->at(index); } bool Spectrum::getNativeID(char* c, int sz){ if(sz<(int)strlen(nativeID)) { cout << "Buffer too small to retrieve spectrumNativeID. " << sizeof(c) << " " << strlen(nativeID) << endl; return false; } else { strcpy(c,nativeID); return true; } } bool Spectrum::getRawFilter(char* c, int sz, bool bLock){ if(sz<(int)strlen(rawFilter)) { cout << "Buffer too small to retrieve RAW filter. " << sizeof(c) << " " << strlen(rawFilter) << endl; return false; } else { strcpy(c,rawFilter); char* chp=strstr(c,"lock"); if(!bLock && chp!=NULL) strcpy(chp,chp+5); return true; } } float Spectrum::getRTime(){ return rTime; } int Spectrum::getScanNumber(bool second){ if(second) return scanNumber2; else return scanNumber; } double Spectrum::getTIC(){ return TIC; } void Spectrum::setBPI(float f){ BPI=f; } void Spectrum::setBPM(double d){ BPM=d; } void Spectrum::setCentroidStatus(int i){ if(i>2) centroidStatus=2; else centroidStatus=i; } void Spectrum::setCharge(int i){ charge=i; } void Spectrum::setCompensationVoltage(double d){ compensationVoltage=d; } void Spectrum::setConversionA(double d){ convA=d; } void Spectrum::setConversionB(double d){ convB=d; } void Spectrum::setConversionC(double d){ convC=d; } void Spectrum::setConversionD(double d){ convD=d; } void Spectrum::setConversionE(double d){ convE=d; } void Spectrum::setConversionI(double d){ convI=d; } void Spectrum::setFileType(MSSpectrumType f){ fileType=f; } void Spectrum::setIonInjectionTime(float f){ IIT=f; } void Spectrum::setMZ(double d, double mono){ clearMZ(); mz->push_back(d); monoMZ->push_back(mono); } void Spectrum::setNativeID(char* c){ if(strlen(c)>256) cout << "Error - spectrumNativeID filter larger than 256 characters." << endl; else strcpy(nativeID,c); } void Spectrum::setRawFilter(char* c){ if(strlen(c)>256) cout << "Error - RAW filter larger than 256 characters." << endl; else strcpy(rawFilter,c); } void Spectrum::setRTime(float d){ rTime=d; } void Spectrum::setScanNumber(int i, bool second){ if(second)scanNumber2=i; else scanNumber=i; } void Spectrum::setTIC(double d){ TIC=d; } void Spectrum::setMsLevel(int level) { msLevel = level; } int Spectrum::getMsLevel() { return msLevel; } int Spectrum::getScanID(){ return scanID; } void Spectrum::setScanID(int scanid){ scanID = scanid; } /* Returns the number of elements in the spectrum. */ int Spectrum::size(){ return vPeaks->size(); } int Spectrum::sizeEZ(){ return vEZ->size(); } int Spectrum::sizeMZ(){ return mz->size(); } int Spectrum::sizeZ(){ return vZ->size(); } float Spectrum::getTotalIntensity(){ float totalIntensity = 0; for(unsigned int i=0; isize(); i++) totalIntensity += (vPeaks->at(i)).intensity; return totalIntensity; } /* Sorts the spectrum by Data. */ void Spectrum::sortIntensity(){ qsort(&vPeaks->at(0),vPeaks->size(),sizeof(Peak_T),compareIntensity); } /* Sorts the spectrum by Mass. */ void Spectrum::sortMZ(){ qsort(&vPeaks->at(0),vPeaks->size(),sizeof(Peak_T),compareMZ); } /* Sorts the spectrum by Data. */ void Spectrum::sortIntensityRev(){ qsort(&vPeaks->at(0),vPeaks->size(),sizeof(Peak_T),compareIntensityRev); } /* Sorts the spectrum by Mass. */ void Spectrum::sortMZRev(){ qsort(&vPeaks->at(0),vPeaks->size(),sizeof(Peak_T),compareMZRev); } //const vector* Spectrum::getPeaks(){ // return vPeaks; //}; vector* Spectrum::getPeaks(){ return vPeaks; } void Spectrum::setPeaks(vector peaks) { if(!vPeaks->empty()) vPeaks->clear(); for(unsigned int i=0; ipush_back(peaks.at(i)); } } void Spectrum::setActivationMethod(MSActivation m){ actMethod=m; } void Spectrum::printMe() { cout << "Scan Number: " << getScanNumber() << endl << "Mass to charge: " << getMZ() << endl << "S Charge: " << getCharge() << endl << "RT: " << getRTime() << endl; cout << fixed; for(unsigned int i=0; isize(); i++) { cout << setprecision(10) << vPeaks->at(i).mz << " " << vPeaks->at(i).intensity << endl; } } //Private Functions /* For the qsort */ int Spectrum::compareIntensity(const void *p1, const void *p2){ const Peak_T d1 = *(Peak_T *)p1; const Peak_T d2 = *(Peak_T *)p2; if(d1.intensityd2.intensity) return 1; else return 0; } /* For the qsort */ int Spectrum::compareMZ(const void *p1, const void *p2){ const Peak_T d1 = *(Peak_T *)p1; const Peak_T d2 = *(Peak_T *)p2; if(d1.mzd2.mz) return 1; else return 0; } /* For the qsort */ int Spectrum::compareIntensityRev(const void *p1, const void *p2){ const Peak_T d1 = *(Peak_T *)p1; const Peak_T d2 = *(Peak_T *)p2; if(d1.intensity>d2.intensity) return -1; else if(d1.intensityd2.mz) return -1; else if(d1.mz using namespace std; using namespace MSToolkit; MSObject::MSObject(){ vSpectrum = new vector; fileName=""; fileType=Unspecified; for(int i=0;i<16;i++) strcpy(header.header[i],"\0"); } MSObject::~MSObject(){ delete vSpectrum; } MSObject::MSObject(const MSObject& m){ unsigned int i; vSpectrum = new vector; for(i=0;isize();i++){ vSpectrum->push_back(m.vSpectrum->at(i)); } fileType = m.fileType; fileName = m.fileName; for(i=0;i<16;i++) strcpy(header.header[i],m.header.header[i]); } MSObject& MSObject::operator=(const MSObject& m){ unsigned int i; if (this!=&m){ delete vSpectrum; vSpectrum = new vector; for(i=0;isize();i++){ vSpectrum->push_back(m.vSpectrum->at(i)); } fileType = m.fileType; fileName = m.fileName; for(i=0;i<16;i++) strcpy(header.header[i],m.header.header[i]); } return *this; } void MSObject::add(Spectrum& s){ vSpectrum->push_back(s); }; bool MSObject::addToHeader(char* c){ if(strlen(c)>127) return false; for(int i=0;i<16;i++){ if(header.header[i][0]=='\0'){ strcpy(header.header[i],c); return true; }; }; return false; }; bool MSObject::addToHeader(string s){ if(s.size()>127) return false; for(int i=0;i<16;i++){ if(header.header[i][0]=='\0'){ strcpy(header.header[i],&s[0]); return true; }; }; return false; }; Spectrum& MSObject::at(unsigned int i){ return vSpectrum->at(i); }; Peak_T& MSObject::at(unsigned int i, unsigned int j){ return vSpectrum->at(i).at(j); }; void MSObject::clear(){ delete vSpectrum; vSpectrum = new vector; for(int i=0;i<16;i++) strcpy(header.header[i],"\0"); }; MSHeader& MSObject::getHeader(){ return header; }; void MSObject::setHeader(const MSHeader& h){ for(int i=0;i<16;i++) strcpy(header.header[i],h.header[i]); }; int MSObject::size(){ return vSpectrum->size(); }; libmstoolkit-77.0.0/src/mzParser/0000755000175000017500000000000012455161024016641 5ustar rusconirusconilibmstoolkit-77.0.0/src/mzParser/mzMLReader.cpp0000644000175000017500000000545612455161024021361 0ustar rusconirusconi#include "mzParser.h" using namespace std; int main(int argc, char* argv[]){ if(argc!=2) { cout << "USAGE: mzMLReader " << endl; exit(0); } MSDataFile* msd; ChromatogramListPtr sl; ChromatogramPtr s2; string st=argv[1]; vector pairs; msd = new MSDataFile(argv[1]); if(!msd->run.chromatogramListPtr->get()) cout << "WTF" << endl; sl = msd->run.chromatogramListPtr; for (int j=1; j<(int)sl->size(); j++) { s2 = sl->chromatogram(j, true); cout << j << "\t" << s2->id << endl; s2->getTimeIntensityPairs(pairs); for(int k=0;k<(int)pairs.size();k++) cout << pairs[k].time << " " << pairs[k].intensity << endl; } exit(1); BasicSpectrum s; BasicChromatogram chromat; MzParser sax(&s,&chromat); sax.load(argv[1]); bool bLastWasSpectrum=true; char c='a'; char str[256]; int num; while(c!='x'){ if(bLastWasSpectrum){ cout << "\nCurrent spectrum:" << endl; cout << "\tScan number: " << s.getScanNum() << endl; cout << "\tRetention Time: " << s.getRTime() << endl; cout << "\tMS Level: " << s.getMSLevel() << endl; cout << "\tNumber of Peaks: " << s.size() << endl; } else { chromat.getIDString(str); cout << "\nCurrent chromatogram:" << endl; cout << "\tID: " << str << endl; cout << "\tNumber of Peaks: " << chromat.size() << endl; } cout << "\nMenu:\n\t'c' to grab a new chromatogram\n\t's' to grab a new spectrum\n\t'p' to show peaks\n\t'x' to exit" << endl; cout << "Please enter your choice: "; cin >> c; switch(c){ case 'c': if(sax.highChromat()==0){ cout << "No chromatograms in the file." << endl; } else { cout << "Enter a number from 0 to " << sax.highChromat()-1 << ": "; cin >> str; num=(int)atoi(str); if(num<0 || num>sax.highChromat()-1) { cout << "Bad number! BOOOOO!" << endl; } else { if(!sax.readChromatogram(num)) cout << "Chromatogram number not in file." << endl; else bLastWasSpectrum=false; } } break; case 'p': if(bLastWasSpectrum){ for(unsigned int i=0;i> str; num=(int)atoi(str); if(numsax.highScan()) { cout << "Bad number! BOOOOO!" << endl; } else { if(!sax.readSpectrum(num)) cout << "Spectrum number not in file." << endl; else bLastWasSpectrum=true; } break; case 'x': break; default: cout << "\nInvalid command!" << endl; break; } } return 0; }libmstoolkit-77.0.0/src/mzParser/mzpMz5Structs.cpp0000644000175000017500000003744412455161024022153 0ustar rusconirusconi#include "mzParser.h" #ifdef MZP_MZ5 StrType getStringType() { StrType stringtype(PredType::C_S1, H5T_VARIABLE); return stringtype; } StrType getFStringType(const size_t len) { StrType stringtype(PredType::C_S1, len); return stringtype; } CompType BinaryDataMZ5::getType() { CompType ret(sizeof(BinaryDataMZ5)); size_t offset = 0; ret.insertMember("xParams", offset, ParamListMZ5::getType()); offset += ParamListMZ5::getType().getSize(); ret.insertMember("yParams", offset, ParamListMZ5::getType()); offset += ParamListMZ5::getType().getSize(); ret.insertMember("xrefDataProcessing", offset, RefMZ5::getType()); offset += RefMZ5::getType().getSize(); ret.insertMember("yrefDataProcessing", offset, RefMZ5::getType()); return ret; } CompType ChromatogramMZ5::getType() { CompType ret(sizeof(ChromatogramMZ5)); StrType stringtype = getStringType(); size_t offset = 0; ret.insertMember("id", offset, stringtype); offset += stringtype.getSize(); ret.insertMember("params", offset, ParamListMZ5::getType()); offset += sizeof(ParamListMZ5Data); ret.insertMember("precursor", offset, PrecursorMZ5::getType()); offset += sizeof(PrecursorMZ5); ret.insertMember("productIsolationWindow", offset, ParamListMZ5::getType()); offset += sizeof(ParamListMZ5Data); ret.insertMember("refDataProcessing", offset, RefMZ5::getType()); offset += sizeof(RefMZ5Data); ret.insertMember("index", offset, PredType::NATIVE_ULONG); offset += sizeof(unsigned long); return ret; } VarLenType ComponentListMZ5::getType() { CompType c = ComponentMZ5::getType(); VarLenType ret(&c); return ret; } CompType ComponentMZ5::getType() { CompType ret(sizeof(ComponentMZ5)); size_t offset = 0; ret.insertMember("paramList", offset, ParamListMZ5::getType()); offset += sizeof(ParamListMZ5Data); ret.insertMember("order", offset, PredType::NATIVE_ULONG); return ret; } CompType ComponentsMZ5::getType() { CompType ret(sizeof(ComponentsMZ5)); size_t offset = 0; ret.insertMember("sources", offset, ComponentListMZ5::getType()); offset += sizeof(ComponentListMZ5); ret.insertMember("analyzers", offset, ComponentListMZ5::getType()); offset += sizeof(ComponentListMZ5); ret.insertMember("detectors", offset, ComponentListMZ5::getType()); return ret; } CompType ContVocabMZ5::getType() { CompType cvtype(sizeof(ContVocabMZ5Data)); StrType stringtype = getStringType(); cvtype.insertMember("uri", HOFFSET(ContVocabMZ5Data, uri), stringtype); cvtype.insertMember("fullname", HOFFSET(ContVocabMZ5Data, fullname), stringtype); cvtype.insertMember("id", HOFFSET(ContVocabMZ5Data, id), stringtype); cvtype.insertMember("version", HOFFSET(ContVocabMZ5Data, version), stringtype); return cvtype; } CVParamMZ5::CVParamMZ5() { init(0, ULONG_MAX, ULONG_MAX); } CVParamMZ5::CVParamMZ5(const CVParamMZ5& cvparam) { init(cvparam.value, cvparam.typeCVRefID, cvparam.unitCVRefID); } CVParamMZ5& CVParamMZ5::operator=(const CVParamMZ5& rhs) { if (this != &rhs) init(rhs.value, rhs.typeCVRefID, rhs.unitCVRefID); return *this; } CVParamMZ5::~CVParamMZ5(){} CompType CVParamMZ5::getType() { CompType ret(sizeof(CVParamMZ5Data)); StrType stringtype = getFStringType(CVL); ret.insertMember("value", HOFFSET(CVParamMZ5Data, value), stringtype); ret.insertMember("cvRefID", HOFFSET(CVParamMZ5Data, typeCVRefID), PredType::NATIVE_ULONG); ret.insertMember("uRefID", HOFFSET(CVParamMZ5Data, unitCVRefID), PredType::NATIVE_ULONG); return ret; } void CVParamMZ5::init(const char* value, const unsigned long& cvrefid, const unsigned long& urefid) { if (value) strcpy(this->value, value); else this->value[0] = '\0'; this->value[CVL - 1] = '\0'; this->typeCVRefID = cvrefid; this->unitCVRefID = urefid; } CVRefMZ5::CVRefMZ5() { init("","",ULONG_MAX); } CVRefMZ5::CVRefMZ5(const CVRefMZ5& cvref) { init(cvref.name, cvref.prefix, cvref.accession); } CVRefMZ5::~CVRefMZ5() { delete [] name; delete [] prefix; } CVRefMZ5& CVRefMZ5::operator=(const CVRefMZ5& cvp) { if (this != &cvp){ delete [] name; delete [] prefix; init(cvp.name, cvp.prefix, cvp.accession); } return *this; } void CVRefMZ5::init(const char* name, const char* prefix, const unsigned long accession){ if(name) strcpy(this->name,name); strcpy(this->prefix,prefix); this->accession=accession; } CompType CVRefMZ5::getType() { CompType ret(sizeof(CVRefMZ5Data)); StrType stringtype = getStringType(); ret.insertMember("name", HOFFSET(CVRefMZ5Data, name), stringtype); ret.insertMember("prefix", HOFFSET(CVRefMZ5Data, prefix), stringtype); ret.insertMember("accession", HOFFSET(CVRefMZ5Data, accession), PredType::NATIVE_ULONG); return ret; } CompType DataProcessingMZ5::getType() { CompType ret(sizeof(DataProcessingMZ5)); StrType stringtype = getStringType(); size_t offset = 0; ret.insertMember("id", offset, stringtype); offset += stringtype.getSize(); ret.insertMember("method", offset, ProcessingMethodListMZ5::getType()); offset += sizeof(ProcessingMethodListMZ5); return ret; } FileInformationMZ5::FileInformationMZ5() { this->majorVersion = MZ5_FILE_MAJOR_VERSION; this->minorVersion = MZ5_FILE_MINOR_VERSION; this->didFiltering = 1; this->deltaMZ = 1; this->translateInten = 1; } FileInformationMZ5::FileInformationMZ5(const FileInformationMZ5& rhs) { init(rhs.majorVersion, rhs.minorVersion, rhs.didFiltering, rhs.deltaMZ, rhs.translateInten); } FileInformationMZ5::FileInformationMZ5(const mzpMz5Config& c) { unsigned short didfiltering = c.doFiltering() ? 1 : 0; unsigned short deltamz = c.doTranslating() ? 1 : 0; unsigned short translateinten = c.doTranslating() ? 1 : 0; init(MZ5_FILE_MAJOR_VERSION, MZ5_FILE_MINOR_VERSION, didfiltering, deltamz, translateinten); } FileInformationMZ5::~FileInformationMZ5(){} FileInformationMZ5& FileInformationMZ5::operator=(const FileInformationMZ5& rhs) { if (this != &rhs){ init(rhs.majorVersion, rhs.minorVersion, rhs.didFiltering, rhs.deltaMZ, rhs.translateInten); } return *this; } void FileInformationMZ5::init(const unsigned short majorVersion, const unsigned short minorVersion, const unsigned didFiltering, const unsigned deltaMZ, const unsigned translateInten) { this->majorVersion = majorVersion; this->minorVersion = minorVersion; this->didFiltering = didFiltering; this->deltaMZ = deltaMZ; this->translateInten = translateInten; } CompType FileInformationMZ5::getType() { CompType ret(sizeof(FileInformationMZ5Data)); ret.insertMember("majorVersion", HOFFSET(FileInformationMZ5Data, majorVersion), PredType::NATIVE_USHORT); ret.insertMember("minorVersion", HOFFSET(FileInformationMZ5Data, minorVersion), PredType::NATIVE_USHORT); ret.insertMember("didFiltering", HOFFSET(FileInformationMZ5Data, didFiltering), PredType::NATIVE_USHORT); ret.insertMember("deltaMZ", HOFFSET(FileInformationMZ5Data, deltaMZ), PredType::NATIVE_USHORT); ret.insertMember("translateInten", HOFFSET(FileInformationMZ5Data, translateInten), PredType::NATIVE_USHORT); return ret; } CompType InstrumentConfigurationMZ5::getType() { CompType ret(sizeof(InstrumentConfigurationMZ5)); StrType stringtype = getStringType(); size_t offset = 0; ret.insertMember("id", offset, stringtype); offset += stringtype.getSize(); ret.insertMember("params", offset, ParamListMZ5::getType()); offset += sizeof(ParamListMZ5Data); ret.insertMember("components", offset, ComponentsMZ5::getType()); offset += sizeof(ComponentsMZ5); ret.insertMember("refScanSetting", offset, RefMZ5::getType()); offset += sizeof(RefMZ5Data); ret.insertMember("refSoftware", offset, RefMZ5::getType()); offset += sizeof(RefMZ5Data); return ret; } CompType ParamGroupMZ5::getType() { CompType ret(sizeof(ParamGroupMZ5)); StrType stringtype = getStringType(); size_t offset = 0; ret.insertMember("id", offset, stringtype); offset += stringtype.getSize(); ret.insertMember("params", offset, ParamListMZ5::getType()); return ret; } CompType ParamListMZ5::getType() { CompType ret(sizeof(ParamListMZ5Data)); ret.insertMember("cvstart", HOFFSET(ParamListMZ5Data, cvParamStartID), PredType::NATIVE_ULONG); ret.insertMember("cvend", HOFFSET(ParamListMZ5Data, cvParamEndID), PredType::NATIVE_ULONG); ret.insertMember("usrstart", HOFFSET(ParamListMZ5Data, userParamStartID), PredType::NATIVE_ULONG); ret.insertMember("usrend", HOFFSET(ParamListMZ5Data, userParamEndID), PredType::NATIVE_ULONG); ret.insertMember("refstart", HOFFSET(ParamListMZ5Data, refParamGroupStartID), PredType::NATIVE_ULONG); ret.insertMember("refend", HOFFSET(ParamListMZ5Data, refParamGroupEndID), PredType::NATIVE_ULONG); return ret; } VarLenType ParamListsMZ5::getType() { CompType c(ParamListMZ5::getType()); VarLenType ret(&c); return ret; } VarLenType PrecursorListMZ5::getType() { CompType c(PrecursorMZ5::getType()); VarLenType ret(&c); return ret; } CompType PrecursorMZ5::getType() { CompType ret(sizeof(PrecursorMZ5)); StrType stringtype = getStringType(); size_t offset = 0; ret.insertMember("externalSpectrumId", offset, stringtype); offset += stringtype.getSize(); ret.insertMember("activation", offset, ParamListMZ5::getType()); offset += ParamListMZ5::getType().getSize(); ret.insertMember("isolationWindow", offset, ParamListMZ5::getType()); offset += ParamListMZ5::getType().getSize(); ret.insertMember("selectedIonList", offset, ParamListsMZ5::getType()); offset += ParamListsMZ5::getType().getSize(); ret.insertMember("refSpectrum", offset, RefMZ5::getType()); offset += RefMZ5::getType().getSize(); ret.insertMember("refSourceFile", offset, RefMZ5::getType()); offset += RefMZ5::getType().getSize(); return ret; } VarLenType ProcessingMethodListMZ5::getType() { CompType c = ProcessingMethodMZ5::getType(); VarLenType ret(&c); return ret; } CompType ProcessingMethodMZ5::getType() { CompType ret(sizeof(ProcessingMethodMZ5)); size_t offset = 0; ret.insertMember("params", offset, ParamListMZ5::getType()); offset += sizeof(ParamListMZ5Data); ret.insertMember("refSoftware", offset, RefMZ5::getType()); offset += sizeof(RefMZ5Data); ret.insertMember("order", offset, PredType::NATIVE_ULONG); return ret; } VarLenType RefListMZ5::getType() { CompType c = RefMZ5::getType(); VarLenType ret(&c); return ret; } CompType RefMZ5::getType() { CompType ret(sizeof(RefMZ5Data)); ret.insertMember("refID", HOFFSET(RefMZ5Data, refID), PredType::NATIVE_ULONG); return ret; } CompType RunMZ5::getType() { CompType ret(sizeof(RunMZ5)); StrType stringtype = getStringType(); size_t offset = 0; ret.insertMember("id", offset, stringtype); offset += stringtype.getSize(); ret.insertMember("startTimeStamp", offset, stringtype); offset += stringtype.getSize(); ret.insertMember("fid", offset, stringtype); offset += stringtype.getSize(); ret.insertMember("facc", offset, stringtype); offset += stringtype.getSize(); ret.insertMember("params", offset, ParamListMZ5::getType()); offset += sizeof(ParamListMZ5); ret.insertMember("refSpectrumDP", offset, RefMZ5::getType()); offset += sizeof(RefMZ5); ret.insertMember("refChromatogramDP", offset, RefMZ5::getType()); offset += sizeof(RefMZ5); ret.insertMember("refDefaultInstrument", offset, RefMZ5::getType()); offset += sizeof(RefMZ5); ret.insertMember("refSourceFile", offset, RefMZ5::getType()); offset += sizeof(RefMZ5); ret.insertMember("refSample", offset, RefMZ5::getType()); offset += sizeof(RefMZ5); return ret; } CompType SampleMZ5::getType() { CompType ret(sizeof(SampleMZ5)); StrType stringtype = getStringType(); size_t offset = 0; ret.insertMember("id", offset, stringtype); offset += stringtype.getSize(); ret.insertMember("name", offset, stringtype); offset += stringtype.getSize(); ret.insertMember("params", offset, ParamListMZ5::getType()); return ret; } VarLenType ScanListMZ5::getType() { CompType c = ScanMZ5::getType(); VarLenType ret(&c); return ret; } CompType ScanMZ5::getType() { CompType ret(sizeof(ScanMZ5)); StrType stringtype = getStringType(); size_t offset = 0; ret.insertMember("externalSpectrumID", offset, stringtype); offset += stringtype.getSize(); ret.insertMember("params", offset, ParamListMZ5::getType()); offset += sizeof(ParamListMZ5Data); ret.insertMember("scanWindowList", offset, ParamListsMZ5::getType()); offset += sizeof(ParamListsMZ5); ret.insertMember("refInstrumentConfiguration", offset, RefMZ5::getType()); offset += sizeof(RefMZ5Data); ret.insertMember("refSourceFile", offset, RefMZ5::getType()); offset += sizeof(RefMZ5Data); ret.insertMember("refSpectrum", offset, RefMZ5::getType()); offset += sizeof(RefMZ5Data); return ret; } CompType ScansMZ5::getType() { CompType ret(sizeof(ScansMZ5)); size_t offset = 0; ret.insertMember("params", offset, ParamListMZ5::getType()); offset += sizeof(ParamListMZ5); ret.insertMember("scanList", offset, ScanListMZ5::getType()); return ret; } CompType ScanSettingMZ5::getType() { CompType ret(sizeof(ScanSettingMZ5)); StrType stringtype = getStringType(); size_t offset = 0; ret.insertMember("id", offset, stringtype); offset += stringtype.getSize(); ret.insertMember("params", offset, ParamListMZ5::getType()); offset += sizeof(ParamListMZ5Data); ret.insertMember("refSourceFiles", offset, RefListMZ5::getType()); offset += sizeof(RefListMZ5Data); ret.insertMember("targets", offset, ParamListsMZ5::getType()); return ret; } CompType SoftwareMZ5::getType() { CompType ret(sizeof(SoftwareMZ5)); StrType stringtype = getStringType(); size_t offset = 0; ret.insertMember("id", offset, stringtype); offset += stringtype.getSize(); ret.insertMember("version", offset, stringtype); offset += stringtype.getSize(); ret.insertMember("params", offset, ParamListMZ5::getType()); return ret; } CompType SourceFileMZ5::getType() { CompType ret(sizeof(SourceFileMZ5)); StrType stringtype = getStringType(); size_t offset = 0; ret.insertMember("id", offset, stringtype); offset += stringtype.getSize(); ret.insertMember("location", offset, stringtype); offset += stringtype.getSize(); ret.insertMember("name", offset, stringtype); offset += stringtype.getSize(); ret.insertMember("params", offset, ParamListMZ5::getType()); return ret; } CompType SpectrumMZ5::getType() { CompType ret(sizeof(SpectrumMZ5)); StrType stringtype = getStringType(); size_t offset = 0; ret.insertMember("id", offset, stringtype); offset += stringtype.getSize(); ret.insertMember("spotID", offset, stringtype); offset += stringtype.getSize(); ret.insertMember("params", offset, ParamListMZ5::getType()); offset += sizeof(ParamListMZ5Data); ret.insertMember("scanList", offset, ScansMZ5::getType()); offset += sizeof(ScansMZ5); ret.insertMember("precursors", offset, PrecursorListMZ5::getType()); offset += sizeof(PrecursorListMZ5); ret.insertMember("products", offset, ParamListsMZ5::getType()); offset += sizeof(ParamListsMZ5); ret.insertMember("refDataProcessing", offset, RefMZ5::getType()); offset += sizeof(RefMZ5Data); ret.insertMember("refSourceFile", offset, RefMZ5::getType()); offset += sizeof(RefMZ5Data); ret.insertMember("index", offset, PredType::NATIVE_ULONG); offset += PredType::NATIVE_ULONG.getSize(); return ret; } CompType UserParamMZ5::getType() { CompType ret(sizeof(UserParamMZ5Data)); StrType namestringtype = getFStringType(USRNL); StrType valuestringtype = getFStringType(USRVL); StrType typestringtype = getFStringType(USRTL); ret.insertMember("name", HOFFSET(UserParamMZ5Data, name), namestringtype); ret.insertMember("value", HOFFSET(UserParamMZ5Data, value), valuestringtype); ret.insertMember("type", HOFFSET(UserParamMZ5Data, type), typestringtype); ret.insertMember("uRefID", HOFFSET(UserParamMZ5Data, unitCVRefID), PredType::NATIVE_ULONG); return ret; } #endif libmstoolkit-77.0.0/src/mzParser/RAMPface.cpp0000644000175000017500000006246012455161024020733 0ustar rusconirusconi#include "mzParser.h" int checkFileType(const char* fname){ char file[256]; char ext[256]; char *tok; char preExt[256]; unsigned int i; strcpy(ext,""); strcpy(file,fname); tok=strtok(file,".\n"); while(tok!=NULL){ strcpy(preExt,ext); strcpy(ext,tok); tok=strtok(NULL,".\n"); } for(i=0;ifileType){ case 1: case 3: return (ramp_fileoffset_t)pFI->mzML->getIndexOffset(); break; case 2: case 4: return (ramp_fileoffset_t)pFI->mzXML->getIndexOffset(); break; default: return -1; } } InstrumentStruct* getInstrumentStruct(RAMPFILE *pFI){ InstrumentStruct* r=(InstrumentStruct *) calloc(1,sizeof(InstrumentStruct)); if(r==NULL) { printf("Cannot allocate memory\n"); return NULL; } else { strcpy(r->analyzer,"UNKNOWN"); strcpy(r->detector,"UNKNOWN"); strcpy(r->ionisation,"UNKNOWN"); strcpy(r->manufacturer,"UNKNOWN"); strcpy(r->model,"UNKNOWN"); } switch(pFI->fileType){ case 1: case 3: if(pFI->mzML->getInstrument()->size()>0){ if(pFI->mzML->getInstrument()->at(0).analyzer.size()>1) strcpy(r->analyzer,&pFI->mzML->getInstrument()->at(0).analyzer[0]); if(pFI->mzML->getInstrument()->at(0).detector.size()>1) strcpy(r->detector,&pFI->mzML->getInstrument()->at(0).detector[0]); if(pFI->mzML->getInstrument()->at(0).ionization.size()>1) strcpy(r->ionisation,&pFI->mzML->getInstrument()->at(0).ionization[0]); if(pFI->mzML->getInstrument()->at(0).manufacturer.size()>1) strcpy(r->manufacturer,&pFI->mzML->getInstrument()->at(0).manufacturer[0]); if(pFI->mzML->getInstrument()->at(0).model.size()>1) strcpy(r->model,&pFI->mzML->getInstrument()->at(0).model[0]); } break; case 2: case 4: if(pFI->mzXML->getInstrument().analyzer.size()>1) strcpy(r->analyzer,&pFI->mzXML->getInstrument().analyzer[0]); if(pFI->mzXML->getInstrument().detector.size()>1) strcpy(r->detector,&pFI->mzXML->getInstrument().detector[0]); if(pFI->mzXML->getInstrument().ionization.size()>1) strcpy(r->ionisation,&pFI->mzXML->getInstrument().ionization[0]); if(pFI->mzXML->getInstrument().manufacturer.size()>1) strcpy(r->manufacturer,&pFI->mzXML->getInstrument().manufacturer[0]); if(pFI->mzXML->getInstrument().model.size()>1) strcpy(r->model,&pFI->mzXML->getInstrument().model[0]); break; case 5: default: break; } return r; } void getScanSpanRange(const struct ScanHeaderStruct *scanHeader, int *startScanNum, int *endScanNum) { if (0 == scanHeader->mergedResultStartScanNum || 0 == scanHeader->mergedResultEndScanNum) { *startScanNum = scanHeader->acquisitionNum; *endScanNum = scanHeader->acquisitionNum; } else { *startScanNum = scanHeader->mergedResultStartScanNum; *endScanNum = scanHeader->mergedResultEndScanNum; } } void rampCloseFile(RAMPFILE *pFI){ if(pFI!=NULL) { delete pFI; pFI=NULL; } } string rampConstructInputFileName(const string &basename){ int len; char *buf = new char[len = (int)(basename.length()+100)]; rampConstructInputPath(buf, len, "", basename.c_str()); string result(buf); delete[] buf; return result; } char* rampConstructInputFileName(char *buf,int buflen,const char *basename){ return rampConstructInputPath(buf, buflen, "", basename); } char* rampConstructInputPath(char *buf, int inbuflen, const char *dir_in, const char *basename){ if( (int)(strlen(dir_in)+strlen(basename)+1) > inbuflen ){ //Can't output error messages in TPP software that use this function //printf("rampConstructInputPath error: buffer too small for file\n"); return NULL; } FILE* f; char* result = NULL; char base[512]; strcpy(base,basename); //Try opening the base name first, then with directory: for(int j=0;j<2;j++){ for(int i=0;i<5;i++){ if(j==1){ strcpy(buf,dir_in); strcat(buf,"/"); strcat(buf,base); } else { strcpy(buf,base); } switch(i){ case 0: strcat(buf,".mzML"); break; case 1: strcat(buf,".mzXML"); break; case 2: strcat(buf,".mzML.gz"); break; case 3: strcat(buf,".mzXML.gz"); break; case 4: strcat(buf,".mz5"); break; default: break; } f=fopen(buf,"r"); if(f==NULL) continue; fclose(f); result=buf; return result; } } //Can't output error messages in TPP software that use this function //printf("rampConstructInputPath: file not found\n"); strcpy(buf,""); result=NULL; return result; } const char** rampListSupportedFileTypes(){ if (!data_Ext.size()) { // needs init data_Ext.push_back(".mzXML"); data_Ext.push_back(".mzML"); data_Ext.push_back(".mzXML.gz"); data_Ext.push_back(".mzML.gz"); data_Ext.push_back(".mz5"); data_Ext.push_back(NULL); // end of list } return &(data_Ext[0]); } RAMPFILE* rampOpenFile(const char* filename){ int i=checkFileType(filename); if(i==0){ return NULL; } else { RAMPFILE* r=new RAMPFILE(); r->bs = new BasicSpectrum(); r->fileType=i; switch(i){ case 1: //mzML case 3: r->mzML=new mzpSAXMzmlHandler(r->bs); if(i==3)r->mzML->setGZCompression(true); else r->mzML->setGZCompression(false); if(!r->mzML->load(filename)){ delete r; return NULL; } else { return r; } case 2: //mzXML case 4: r->mzXML=new mzpSAXMzxmlHandler(r->bs); if(i==4) r->mzXML->setGZCompression(true); else r->mzXML->setGZCompression(false); if(!r->mzXML->load(filename)){ delete r; return NULL; } else { return r; } #ifdef MZP_MZ5 case 5: //mz5 r->mz5Config = new mzpMz5Config(); r->mz5=new mzpMz5Handler(r->mz5Config, r->bs); if(!r->mz5->readFile(filename)){ delete r; return NULL; } else { return r; } #endif default: delete r; return NULL; } } } char* rampValidFileType(const char *buf){ char ext[256]; char preExt[256]; const char* result=NULL; const char* result2=NULL; const char* p; unsigned int i; p=strchr(buf,'.'); while(p!=NULL){ result2=result; result=p; p=strchr(p+1,'.'); } if(result==NULL) return (char*) result; strcpy(ext,result); for(i=0;i* v; #ifdef MZP_MZ5 vector* v2; #endif unsigned int i; //memset(scanHeader,0,sizeof(struct ScanHeaderStruct)); scanHeader->acquisitionNum=-1; scanHeader->activationMethod[0]='\0'; scanHeader->basePeakIntensity=0.0; scanHeader->basePeakMZ=0.0; scanHeader->centroid=false; scanHeader->collisionEnergy=0.0; scanHeader->compensationVoltage=0.0; scanHeader->filePosition=0; scanHeader->filterLine[0]='\0'; scanHeader->highMZ=0.0; scanHeader->idString[0]='\0'; scanHeader->ionisationEnergy=0.0; scanHeader->lowMZ=0.0; scanHeader->mergedScan=0; scanHeader->mergedResultScanNum=0; scanHeader->mergedResultStartScanNum=0; scanHeader->mergedResultEndScanNum=0; scanHeader->msLevel=0; scanHeader->numPossibleCharges=0; scanHeader->precursorCharge=0; scanHeader->precursorIntensity=0.0; scanHeader->precursorMonoMZ=0.0; scanHeader->precursorMZ=0.0; scanHeader->precursorScanNum=-1; scanHeader->retentionTime=0.0; scanHeader->totIonCurrent=0.0; scanHeader->scanIndex=0; scanHeader->seqNum=-1; if(lScanIndex<0) return; switch(pFI->fileType){ case 1: case 3: v=pFI->mzML->getSpecIndex(); for(i=0;isize();i++) { if(v->at(i).offset==(f_off)lScanIndex) { if(!pFI->mzML->readHeader(v->at(i).scanNum)){ v=NULL; return; } break; } } break; case 2: case 4: v=pFI->mzXML->getIndex(); for(i=0;isize();i++) { if(v->at(i).offset==(f_off)lScanIndex) { if(!pFI->mzXML->readHeader(v->at(i).scanNum)){ v=NULL; return; } break; } } break; #ifdef MZP_MZ5 case 5: v2=pFI->mz5->getSpecIndex(); for(i=0;isize();i++) { if(v2->at(i).offset==(f_off)lScanIndex) { if(!pFI->mz5->readHeader(v2->at(i).scanNum)){ v2=NULL; return; } break; } } break; #endif default: pFI->bs->clear(); v=NULL; #ifdef MZP_MZ5 v2=NULL; #endif return; } v=NULL; #ifdef MZP_MZ5 v2=NULL; #endif scanHeader->acquisitionNum=pFI->bs->getScanNum(); scanHeader->basePeakIntensity=pFI->bs->getBasePeakIntensity(); scanHeader->basePeakMZ=pFI->bs->getBasePeakMZ(); scanHeader->centroid=pFI->bs->getCentroid(); scanHeader->collisionEnergy=pFI->bs->getCollisionEnergy(); scanHeader->highMZ=pFI->bs->getHighMZ(); scanHeader->lowMZ=pFI->bs->getLowMZ(); scanHeader->msLevel=pFI->bs->getMSLevel(); scanHeader->peaksCount=pFI->bs->getPeaksCount(); scanHeader->precursorCharge=pFI->bs->getPrecursorCharge(); scanHeader->precursorIntensity=pFI->bs->getPrecursorIntensity(); scanHeader->compensationVoltage=pFI->bs->getCompensationVoltage(); scanHeader->precursorMonoMZ=pFI->bs->getPrecursorMonoMZ(); scanHeader->precursorMZ=pFI->bs->getPrecursorMZ(); scanHeader->precursorScanNum=pFI->bs->getPrecursorScanNum(); scanHeader->retentionTime=(double)pFI->bs->getRTime(false); scanHeader->totIonCurrent=pFI->bs->getTotalIonCurrent(); scanHeader->scanIndex=pFI->bs->getScanIndex(); scanHeader->seqNum=pFI->bs->getScanIndex(); pFI->bs->getFilterLine(scanHeader->filterLine); pFI->bs->getIDString(scanHeader->idString); switch(pFI->bs->getActivation()){ case 1: strcpy(scanHeader->activationMethod,"CID"); break; case 2: strcpy(scanHeader->activationMethod,"HCD"); break; case 3: strcpy(scanHeader->activationMethod,"ETD"); break; case 4: strcpy(scanHeader->activationMethod,"ETD+SA"); break; case 5: strcpy(scanHeader->activationMethod,"ECD"); break; default: strcpy(scanHeader->activationMethod,""); break; } } //MH: Indexes in RAMP are stored in an array indexed by scan number, with -1 for the offset //if the scan number does not exist. ramp_fileoffset_t* readIndex(RAMPFILE *pFI, ramp_fileoffset_t indexOffset, int *iLastScan){ vector* v; #ifdef MZP_MZ5 vector* v2; #endif ramp_fileoffset_t* rIndex; unsigned int i; switch(pFI->fileType){ case 1: case 3: v=pFI->mzML->getSpecIndex(); rIndex = (ramp_fileoffset_t *) malloc((pFI->mzML->highScan()+2)*sizeof(ramp_fileoffset_t)); memset(rIndex,-1,(pFI->mzML->highScan()+2)*sizeof(ramp_fileoffset_t)); for(i=0;isize();i++) rIndex[v->at(i).scanNum]=(ramp_fileoffset_t)v->at(i).offset; rIndex[v->at(i-1).scanNum+1]=-1; *iLastScan=v->at(i-1).scanNum; break; case 2: case 4: v=pFI->mzXML->getIndex(); rIndex = (ramp_fileoffset_t *) malloc((pFI->mzXML->highScan()+2)*sizeof(ramp_fileoffset_t)); memset(rIndex,-1,(pFI->mzXML->highScan()+2)*sizeof(ramp_fileoffset_t)); for(i=0;isize();i++) rIndex[v->at(i).scanNum]=(ramp_fileoffset_t)v->at(i).offset; rIndex[v->at(i-1).scanNum+1]=-1; *iLastScan=v->at(i-1).scanNum; break; #ifdef MZP_MZ5 case 5: v2=pFI->mz5->getSpecIndex(); rIndex = (ramp_fileoffset_t *) malloc((pFI->mz5->highScan()+2)*sizeof(ramp_fileoffset_t)); memset(rIndex,-1,(pFI->mz5->highScan()+2)*sizeof(ramp_fileoffset_t)); for(i=0;isize();i++) rIndex[v2->at(i).scanNum]=(ramp_fileoffset_t)v2->at(i).offset; rIndex[v2->at(i-1).scanNum+1]=-1; *iLastScan=v2->at(i-1).scanNum; break; #endif default: rIndex=NULL; *iLastScan=0; break; } v=NULL; #ifdef MZP_MZ5 v2=NULL; #endif return rIndex; } int readMsLevel(RAMPFILE *pFI, ramp_fileoffset_t lScanIndex){ vector* v; #ifdef MZP_MZ5 vector* v2; #endif unsigned int i; if(lScanIndex<0) return 0; switch(pFI->fileType){ case 1: case 3: v=pFI->mzML->getSpecIndex(); for(i=0;isize();i++) { if(v->at(i).offset==(f_off)lScanIndex) { pFI->mzML->readSpectrum(v->at(i).scanNum); break; } } break; case 2: case 4: v=pFI->mzXML->getIndex(); for(i=0;isize();i++) { if(v->at(i).offset==(f_off)lScanIndex) { pFI->mzXML->readSpectrum(v->at(i).scanNum); break; } } break; #ifdef MZP_MZ5 case 5: v2=pFI->mz5->getSpecIndex(); for(i=0;isize();i++) { if(v2->at(i).offset==(f_off)lScanIndex) { pFI->mz5->readSpectrum(v2->at(i).scanNum); break; } } break; #endif default: pFI->bs->clear(); break; } v=NULL; #ifdef MZP_MZ5 v2=NULL; #endif return pFI->bs->getMSLevel(); } void readMSRun(RAMPFILE *pFI, struct RunHeaderStruct *runHeader){ vector* v; #ifdef MZP_MZ5 vector* v2; #endif //memset(scanHeader,0,sizeof(struct ScanHeaderStruct)); runHeader->dEndTime=0.0; runHeader->dStartTime=0.0; runHeader->endMZ=0.0; runHeader->highMZ=0.0; runHeader->lowMZ=0.0; runHeader->scanCount=0; runHeader->startMZ=0.0; switch(pFI->fileType){ case 1: case 3: v=pFI->mzML->getSpecIndex(); runHeader->scanCount=v->size(); pFI->mzML->readHeader(v->at(0).scanNum); runHeader->dStartTime=pFI->bs->getRTime(false); pFI->mzML->readHeader(v->at(v->size()-1).scanNum); runHeader->dEndTime=pFI->bs->getRTime(false); pFI->bs->clear(); v=NULL; break; case 2: case 4: v=pFI->mzXML->getIndex(); runHeader->scanCount=v->size(); pFI->mzXML->readHeader(v->at(0).scanNum); runHeader->dStartTime=pFI->bs->getRTime(false); pFI->mzXML->readHeader(v->at(v->size()-1).scanNum); runHeader->dEndTime=pFI->bs->getRTime(false); pFI->bs->clear(); v=NULL; break; #ifdef MZP_MZ5 case 5: v2=pFI->mz5->getSpecIndex(); runHeader->scanCount=v2->size(); pFI->mz5->readHeader(v2->at(0).scanNum); runHeader->dStartTime=pFI->bs->getRTime(false); pFI->mz5->readHeader(v2->at(v2->size()-1).scanNum); runHeader->dEndTime=pFI->bs->getRTime(false); pFI->bs->clear(); v2=NULL; break; #endif default: break; } } //MH: Matching the index is very indirect, but requires less code, //making this wrapper much easier to read RAMPREAL* readPeaks(RAMPFILE* pFI, ramp_fileoffset_t lScanIndex){ vector* v; #ifdef MZP_MZ5 vector* v2; #endif unsigned int i; RAMPREAL* pPeaks=NULL; if(lScanIndex<0) return pPeaks; switch(pFI->fileType){ case 1: case 3: v=pFI->mzML->getSpecIndex(); for(i=0;isize();i++) { if(v->at(i).offset==(f_off)lScanIndex) { pFI->mzML->readSpectrum(v->at(i).scanNum); break; } } break; case 2: case 4: v=pFI->mzXML->getIndex(); for(i=0;isize();i++) { if(v->at(i).offset==(f_off)lScanIndex) { pFI->mzXML->readSpectrum(v->at(i).scanNum); break; } } break; #ifdef MZP_MZ5 case 5: v2=pFI->mz5->getSpecIndex(); for(i=0;isize();i++) { if(v2->at(i).offset==(f_off)lScanIndex) { pFI->mz5->readSpectrum(v2->at(i).scanNum); break; } } break; #endif default: pFI->bs->clear(); break; } v=NULL; #ifdef MZP_MZ5 v2=NULL; #endif unsigned int j=0; if(pFI->bs->size()>0){ pPeaks = (RAMPREAL *) malloc((pFI->bs->size()+1) * 2 * sizeof(RAMPREAL) + 1); for(i=0;ibs->size();i++){ pPeaks[j++]=pFI->bs->operator [](i).mz; pPeaks[j++]=pFI->bs->operator [](i).intensity; } } else { pPeaks = (RAMPREAL *) malloc(2 * sizeof(RAMPREAL)); } pPeaks[j]=-1; return pPeaks; } int readPeaksCount(RAMPFILE *pFI, ramp_fileoffset_t lScanIndex){ ScanHeaderStruct s; readHeader(pFI, lScanIndex, &s); return s.peaksCount; } void readRunHeader(RAMPFILE *pFI, ramp_fileoffset_t *pScanIndex, struct RunHeaderStruct *runHeader, int iLastScan){ vector* v; #ifdef MZP_MZ5 vector* v2; #endif unsigned int i; runHeader->scanCount=0; runHeader->dEndTime=0.0; runHeader->dStartTime=0.0; runHeader->endMZ=0.0; runHeader->highMZ=0.0; runHeader->lowMZ=0.0; runHeader->startMZ=0.0; switch(pFI->fileType){ case 1: case 3: v=pFI->mzML->getSpecIndex(); runHeader->scanCount=v->size(); pFI->mzML->readHeader(v->at(0).scanNum); runHeader->dStartTime=(double)pFI->bs->getRTime(false); runHeader->lowMZ=pFI->bs->getLowMZ(); runHeader->highMZ=pFI->bs->getHighMZ(); runHeader->startMZ=runHeader->lowMZ; runHeader->endMZ=runHeader->highMZ; for(i=1;isize();i++) { pFI->mzML->readHeader(v->at(i).scanNum); if(pFI->bs->getLowMZ()lowMZ) { runHeader->lowMZ=pFI->bs->getLowMZ(); runHeader->startMZ=runHeader->lowMZ; } if(pFI->bs->getHighMZ()>runHeader->highMZ){ runHeader->highMZ=pFI->bs->getHighMZ(); runHeader->endMZ=runHeader->highMZ; } } pFI->mzML->readHeader(v->at(v->size()-1).scanNum); break; case 2: case 4: v=pFI->mzXML->getIndex(); runHeader->scanCount=v->size(); pFI->mzXML->readHeader(v->at(0).scanNum); runHeader->dStartTime=(double)pFI->bs->getRTime(false); runHeader->lowMZ=pFI->bs->getLowMZ(); runHeader->highMZ=pFI->bs->getHighMZ(); runHeader->startMZ=runHeader->lowMZ; runHeader->endMZ=runHeader->highMZ; for(i=1;isize();i++) { pFI->mzXML->readHeader(v->at(i).scanNum); if(pFI->bs->getLowMZ()lowMZ) { runHeader->lowMZ=pFI->bs->getLowMZ(); runHeader->startMZ=runHeader->lowMZ; } if(pFI->bs->getHighMZ()>runHeader->highMZ){ runHeader->highMZ=pFI->bs->getHighMZ(); runHeader->endMZ=runHeader->highMZ; } } pFI->mzXML->readHeader(v->at(v->size()-1).scanNum); break; #ifdef MZP_MZ5 case 5: v2=pFI->mz5->getSpecIndex(); runHeader->scanCount=v2->size(); pFI->mz5->readHeader(v2->at(0).scanNum); runHeader->dStartTime=(double)pFI->bs->getRTime(false); runHeader->lowMZ=pFI->bs->getLowMZ(); runHeader->highMZ=pFI->bs->getHighMZ(); runHeader->startMZ=runHeader->lowMZ; runHeader->endMZ=runHeader->highMZ; for(i=1;isize();i++) { pFI->mz5->readHeader(v2->at(i).scanNum); if(pFI->bs->getLowMZ()lowMZ) { runHeader->lowMZ=pFI->bs->getLowMZ(); runHeader->startMZ=runHeader->lowMZ; } if(pFI->bs->getHighMZ()>runHeader->highMZ){ runHeader->highMZ=pFI->bs->getHighMZ(); runHeader->endMZ=runHeader->highMZ; } } pFI->mz5->readHeader(v2->at(v2->size()-1).scanNum); break; #endif default: pFI->bs->clear(); v=NULL; #ifdef MZP_MZ5 v2=NULL; #endif return; } v=NULL; #ifdef MZP_MZ5 v2=NULL; #endif } //-------------------------------------------------- // CACHED RAMP FUNCTIONS //-------------------------------------------------- void clearScanCache(struct ScanCacheStruct* cache){ for (int i=0; isize; i++) { if (cache->peaks[i] == NULL) continue; free(cache->peaks[i]); cache->peaks[i] = NULL; } memset(cache->headers, 0, cache->size * sizeof(struct ScanHeaderStruct)); } void freeScanCache(struct ScanCacheStruct* cache){ if (cache) { for (int i=0; isize; i++){ if (cache->peaks[i] != NULL) free(cache->peaks[i]); } free(cache->peaks); free(cache->headers); free(cache); } } int getCacheIndex(struct ScanCacheStruct* cache, int seqNum) { int seqNumStart = cache->seqNumStart; int size = cache->size; // First access, just set the start to seqNum. if (seqNumStart == 0) cache->seqNumStart = seqNum; // If requested scan is less than cache start, shift cache window // left to start at requested scan. else if (seqNum < seqNumStart) shiftScanCache(cache, (int) (seqNum - seqNumStart)); // If requested scan is greater than cache end, shift cache window // right so last entry is requested scan. else if (seqNum >= seqNumStart + size) shiftScanCache(cache, (int) (seqNum - (seqNumStart + size - 1))); return (int) (seqNum - cache->seqNumStart); } struct ScanCacheStruct* getScanCache(int size){ struct ScanCacheStruct* cache = (struct ScanCacheStruct*) malloc(sizeof(struct ScanCacheStruct)); cache->seqNumStart = 0; cache->size = size; cache->headers = (struct ScanHeaderStruct*) calloc(size, sizeof(struct ScanHeaderStruct)); cache->peaks = (RAMPREAL**) calloc(size, sizeof(RAMPREAL*)); return cache; } const struct ScanHeaderStruct* readHeaderCached(struct ScanCacheStruct* cache, int seqNum, RAMPFILE* pFI, ramp_fileoffset_t lScanIndex){ int i = getCacheIndex(cache, seqNum); if (cache->headers[i].msLevel == 0) readHeader(pFI, lScanIndex, cache->headers + i); return cache->headers + i; } int readMsLevelCached(struct ScanCacheStruct* cache, int seqNum, RAMPFILE* pFI, ramp_fileoffset_t lScanIndex){ const struct ScanHeaderStruct* header = readHeaderCached(cache, seqNum, pFI, lScanIndex); return header->msLevel; } const RAMPREAL* readPeaksCached(struct ScanCacheStruct* cache, int seqNum, RAMPFILE* pFI, ramp_fileoffset_t lScanIndex){ int i = getCacheIndex(cache, seqNum); if (cache->peaks[i] == NULL) cache->peaks[i] = readPeaks(pFI, lScanIndex); return cache->peaks[i]; } void shiftScanCache(struct ScanCacheStruct* cache, int nScans) { int i; cache->seqNumStart += nScans; if (abs(nScans) > cache->size) { // If the shift is larger than the size of the cache window, // just clear the whole cache. clearScanCache(cache); } else if (nScans > 0) { // Shifting window to the right. Memory moves right, with new // empty scans on the end. // Free the peaks that memmove will overwrite. for (i = 0; i < nScans; i++) { if (cache->peaks[i] != NULL) free(cache->peaks[i]); } memmove(cache->peaks, cache->peaks + nScans, (cache->size - nScans) * sizeof(RAMPREAL*)); memset(cache->peaks + cache->size - nScans, 0, nScans * sizeof(RAMPREAL*)); memmove(cache->headers, cache->headers + nScans,(cache->size - nScans) * sizeof(struct ScanHeaderStruct)); memset(cache->headers + cache->size - nScans, 0, nScans * sizeof(struct ScanHeaderStruct)); } else if (nScans < 0) { // Shifting window to the left. Memory moves right, with new // empty scans at the beginning. nScans = -nScans; // Free the peaks that memmove will overwrite. for (i = 0; i < nScans; i++) { if (cache->peaks[cache->size - 1 - i] != NULL) free(cache->peaks[cache->size - 1 - i]); } memmove(cache->peaks + nScans, cache->peaks, (cache->size - nScans) * sizeof(RAMPREAL*)); memset(cache->peaks, 0, nScans * sizeof(RAMPREAL*)); memmove(cache->headers + nScans, cache->headers, (cache->size - nScans) * sizeof(struct ScanHeaderStruct)); memset(cache->headers, 0, nScans * sizeof(struct ScanHeaderStruct)); } } //-------------------------------------------------- // DEAD FUNCTIONS //-------------------------------------------------- int isScanAveraged(struct ScanHeaderStruct *scanHeader){ cerr << "call to unsupported function: isScanAveraged(struct ScanHeaderStruct *scanHeader)" << endl; return 0; } int isScanMergedResult(struct ScanHeaderStruct *scanHeader){ cerr << "call to unsupported function: isScanMergedResult(struct ScanHeaderStruct *scanHeader)" << endl; return 0; } int rampSelfTest(char *filename){ cerr << "call to unsupported function: rampSelfTest(char *filename)" << endl; return 0; } char* rampTrimBaseName(char *buf){ cerr << "call to unsupported function: rampTrimBaseName(char *buf)" << endl; return buf; } int rampValidateOrDeriveInputFilename(char *inbuf, int inbuflen, char *spectrumName){ cerr << "call to unsupported function: rampValidateOrDeriveInputFilename(char *inbuf, int inbuflen, char *spectrumName)" << endl; return 0; } double readStartMz(RAMPFILE *pFI, ramp_fileoffset_t lScanIndex){ cerr << "call to unsupported function: readStartMz(RAMPFILE *pFI, ramp_fileoffset_t lScanIndex)" << endl; return 0.0; } double readEndMz(RAMPFILE *pFI, ramp_fileoffset_t lScanIndex){ cerr << "call to unsupported function: readEndMz(RAMPFILE *pFI, ramp_fileoffset_t lScanIndex)" << endl; return 0.0; } void setRampOption(long option){ cerr << "call to unsupported function: setRampOption(long option)" << endl; } libmstoolkit-77.0.0/src/mzParser/Czran.cpp0000644000175000017500000003207412455161024020430 0ustar rusconirusconi/* zran.c -- example of zlib/gzip stream indexing and random access * Copyright (C) 2005 Mark Adler * For conditions of distribution and use, see copyright notice in zlib.h Version 1.0 29 May 2005 Mark Adler */ /* Illustrate the use of Z_BLOCK, inflatePrime(), and inflateSetDictionary() for random access of a compressed file. A file containing a zlib or gzip stream is provided on the command line. The compressed stream is decoded in its entirety, and an index built with access points about every SPAN bytes in the uncompressed output. The compressed file is left open, and can then be read randomly, having to decompress on the average SPAN/2 uncompressed bytes before getting to the desired block of data. An access point can be created at the start of any deflate block, by saving the starting file offset and bit of that block, and the 32K bytes of uncompressed data that precede that block. Also the uncompressed offset of that block is saved to provide a referece for locating a desired starting point in the uncompressed stream. build_index() works by decompressing the input zlib or gzip stream a block at a time, and at the end of each block deciding if enough uncompressed data has gone by to justify the creation of a new access point. If so, that point is saved in a data structure that grows as needed to accommodate the points. To use the index, an offset in the uncompressed data is provided, for which the latest accees point at or preceding that offset is located in the index. The input file is positioned to the specified location in the index, and if necessary the first few bits of the compressed data is read from the file. inflate is initialized with those bits and the 32K of uncompressed data, and the decompression then proceeds until the desired offset in the file is reached. Then the decompression continues to read the desired uncompressed data from the file. Another approach would be to generate the index on demand. In that case, requests for random access reads from the compressed data would try to use the index, but if a read far enough past the end of the index is required, then further index entries would be generated and added. There is some fair bit of overhead to starting inflation for the random access, mainly copying the 32K byte dictionary. So if small pieces of the file are being accessed, it would make sense to implement a cache to hold some lookahead and avoid many calls to extract() for small lengths. Another way to build an index would be to use inflateCopy(). That would not be constrained to have access points at block boundaries, but requires more memory per access point, and also cannot be saved to file due to the use of pointers in the state. The approach here allows for storage of the index in a file. */ #include "mzParser.h" Czran::Czran(){ index=NULL; buffer=NULL; lastBuffer=NULL; bufferOffset=0; bufferLen=0; fileSize=0; lastBufferOffset=0; } Czran::~Czran(){ if(index!=NULL) free_index(); if(buffer!=NULL) free(buffer); if(lastBuffer!=NULL) free(lastBuffer); buffer=NULL; lastBuffer=NULL; } /* Deallocate an index built by build_index() */ void Czran::free_index(){ if (index != NULL) { free(index->list); free(index); index=NULL; } } /* Add an entry to the access point list. If out of memory, deallocate the existing list and return NULL. */ gz_access * Czran::addpoint(int bits,f_off in, f_off out, unsigned left, unsigned char *window) { point *next; /* if list is empty, create it (start with eight points) */ if (index == NULL) { index = (gz_access*)malloc(sizeof(gz_access)); if (index == NULL) return NULL; index->list = (point*)malloc(sizeof(point) << 3); if (index->list == NULL) { free(index); return NULL; } index->size = 8; index->have = 0; } /* if list is full, make it bigger */ else if (index->have == index->size) { index->size <<= 1; next = (point*)realloc(index->list, sizeof(point) * index->size); if (next == NULL) { free_index(); return NULL; } index->list = next; } /* fill in entry and increment how many we have */ next = index->list + index->have; next->bits = bits; next->in = in; next->out = out; if (left) memcpy(next->window, window + WINSIZE - left, left); if (left < WINSIZE) memcpy(next->window + left, window, WINSIZE - left); index->have++; /* return list, possibly reallocated */ return index; } /* Make one entire pass through the compressed stream and build an index, with access points about every span bytes of uncompressed output -- span is chosen to balance the speed of random access against the memory requirements of the list, about 32K bytes per access point. Note that data after the end of the first zlib or gzip stream in the file is ignored. build_index() returns the number of access points on success (>= 1), Z_MEM_ERROR for out of memory, Z_DATA_ERROR for an error in the input file, or Z_ERRNO for a file read error. On success, *built points to the resulting index. */ int Czran::build_index(FILE *in, f_off span){ return build_index(in,span,&index); } int Czran::build_index(FILE *in, f_off span, gz_access **built){ int ret; f_off totin, totout; /* our own total counters to avoid 4GB limit */ f_off last; /* totout value of last access point */ gz_access *index; /* access points being generated */ z_stream strm; unsigned char input[READCHUNK]; unsigned char window[WINSIZE]; /* initialize inflate */ strm.zalloc = Z_NULL; strm.zfree = Z_NULL; strm.opaque = Z_NULL; strm.avail_in = 0; strm.next_in = Z_NULL; ret = inflateInit2(&strm, 47); /* automatic zlib or gzip decoding */ if (ret != Z_OK) return ret; /* inflate the input, maintain a sliding window, and build an index -- this also validates the integrity of the compressed data using the check information at the end of the gzip or zlib stream */ totin = totout = last = 0; index = NULL; /* will be allocated by first addpoint() */ strm.avail_out = 0; do { /* get some compressed data from input file */ strm.avail_in = fread(input, 1, READCHUNK, in); if (ferror(in)) { ret = Z_ERRNO; goto build_index_error; } if (strm.avail_in == 0) { ret = Z_DATA_ERROR; goto build_index_error; } strm.next_in = input; /* process all of that, or until end of stream */ do { /* reset sliding window if necessary */ if (strm.avail_out == 0) { strm.avail_out = WINSIZE; strm.next_out = window; } /* inflate until out of input, output, or at end of block -- update the total input and output counters */ totin += strm.avail_in; totout += strm.avail_out; ret = inflate(&strm, Z_BLOCK); /* return at end of block */ totin -= strm.avail_in; totout -= strm.avail_out; if (ret == Z_NEED_DICT) ret = Z_DATA_ERROR; if (ret == Z_MEM_ERROR || ret == Z_DATA_ERROR) goto build_index_error; if (ret == Z_STREAM_END) break; /* if at end of block, consider adding an index entry (note that if data_type indicates an end-of-block, then all of the uncompressed data from that block has been delivered, and none of the compressed data after that block has been consumed, except for up to seven bits) -- the totout == 0 provides an entry point after the zlib or gzip header, and assures that the index always has at least one access point; we avoid creating an access point after the last block by checking bit 6 of data_type */ if ((strm.data_type & 128) && !(strm.data_type & 64) && (totout == 0 || totout - last > span)) { index = addpoint(strm.data_type & 7, totin, totout, strm.avail_out, window); if (index == NULL) { ret = Z_MEM_ERROR; goto build_index_error; } last = totout; } } while (strm.avail_in != 0); } while (ret != Z_STREAM_END); /* clean up and return index (release unused entries in list) */ fileSize=strm.total_out; (void)inflateEnd(&strm); index = (gz_access*)realloc(index, sizeof(point) * index->have); index->size = index->have; *built = index; return index->size; /* return error */ build_index_error: (void)inflateEnd(&strm); fileSize=0; if (index != NULL) free_index(); return ret; } /* Use the index to read len bytes from offset into buf, return bytes read or negative for error (Z_DATA_ERROR or Z_MEM_ERROR). If data is requested past the end of the uncompressed data, then extract() will return a value less than len, indicating how much as actually read into buf. This function should not return a data error unless the file was modified since the index was generated. extract() may also return Z_ERRNO if there is an error on reading or seeking the input file. */ int Czran::extract(FILE *in, f_off offset) { int ret, len; point *here; z_stream strm; unsigned char input[READCHUNK]; /* find where in stream to start */ here = index->list; ret = index->have; while (--ret && here[1].out <= offset) here++; /* initialize file and inflate state to start there */ strm.zalloc = Z_NULL; strm.zfree = Z_NULL; strm.opaque = Z_NULL; strm.avail_in = 0; strm.next_in = Z_NULL; ret = inflateInit2(&strm, -15); /* raw inflate */ if (ret != Z_OK) return ret; ret = mzpfseek(in, here->in - (here->bits ? 1 : 0), SEEK_SET); if (ret == -1) goto extract_ret; if (here->bits) { ret = getc(in); if (ret == -1) { ret = ferror(in) ? Z_ERRNO : Z_DATA_ERROR; goto extract_ret; } (void)inflatePrime(&strm, here->bits, ret >> (8 - here->bits)); } (void)inflateSetDictionary(&strm, here->window, WINSIZE); if(here[1].out>0) len = (int)(here[1].out-here->out); else len = (int)(fileSize-here->out); if(buffer!=NULL) free(buffer); buffer = (unsigned char*)malloc(len); if(buffer==NULL){ ret = Z_MEM_ERROR; goto extract_ret; } bufferOffset=here->out; strm.avail_in = 0; strm.avail_out = len; strm.next_out = buffer; /* uncompress until avail_out filled, or end of stream */ do { if (strm.avail_in == 0) { strm.avail_in = fread(input, 1, READCHUNK, in); if (ferror(in)) { ret = Z_ERRNO; goto extract_ret; } if (strm.avail_in == 0) { ret = Z_DATA_ERROR; goto extract_ret; } strm.next_in = input; } ret = inflate(&strm, Z_NO_FLUSH); /* normal inflate */ if (ret == Z_NEED_DICT) ret = Z_DATA_ERROR; if (ret == Z_MEM_ERROR || ret == Z_DATA_ERROR) goto extract_ret; if (ret == Z_STREAM_END) break; } while (strm.avail_out != 0); /* compute number of uncompressed bytes read after offset */ ret = len - strm.avail_out; /* clean up and return bytes read or error */ extract_ret: if(ret<0) bufferLen=0; else bufferLen=ret; (void)inflateEnd(&strm); return ret; } int Czran::extract(FILE *in, f_off offset, unsigned char *buf, int len){ int ret, seg; //see if request was to the last buffer //last buffer is only stored when it doesn't reside in large buffer if(lastBuffer!=NULL && offset==lastBufferOffset){ memcpy(buf,lastBuffer,lastBufferLen); return lastBufferLen; } //if we don't have the offset, grab it. if(buffer==NULL || offset=(bufferOffset+bufferLen)){ ret=extract(in,offset); } lastBufferOffset=offset; //check if we have all the requested bytes if( (offset+len) <= (bufferOffset+bufferLen) ){ memcpy(buf,buffer+(offset-bufferOffset),len); if(lastBuffer!=NULL){ free(lastBuffer); lastBuffer=NULL; } return len; } else { if(lastBuffer!=NULL) free(lastBuffer); lastBuffer=(unsigned char*)malloc(len); //otherwise grab what we can and try extending buffer seg=(int)(bufferLen-(offset-bufferOffset)); memcpy(buf,buffer+(offset-bufferOffset),seg); len-=seg; //get next block ret=extract(in,offset+seg); //add remaining bytes if(ret0) { cout << "Halting! Unknown compression type: " << &s[0] << endl; exit(-5); } s=getAttrValue("compressedLen", attr); if(s.length()>0) m_compressLen = (uLong)atoi(&s[0]); else m_compressLen=0; if(m_bHeaderOnly) stopParser(); } else if (isElement("precursorMz", el)) { m_strData.clear(); s=getAttrValue("precursorCharge", attr); if(s.length()>0) spec->setPrecursorCharge(atoi(&s[0])); else spec->setPrecursorCharge(0); s=getAttrValue("precursorIntensity", attr); if(s.length()>0) spec->setPrecursorIntensity(atof(&s[0])); else spec->setPrecursorIntensity(0.0); s=getAttrValue("precursorScanNum", attr); if(s.length()>0) spec->setPrecursorScanNum(atoi(&s[0])); else spec->setPrecursorScanNum(0); m_bInPrecursorMz = true; s=getAttrValue("activationMethod", attr); if(s.length()>0){ if(!strcmp("CID",&s[0])) spec->setActivation(CID); else if(!strcmp("ETD",&s[0])) spec->setActivation(ETD); else if(!strcmp("HCD",&s[0])) spec->setActivation(HCD); else if(!strcmp("ECD",&s[0])) spec->setActivation(ECD); else if(!strcmp("ETD+SA",&s[0])) spec->setActivation(ETDSA); } else { spec->setActivation(none); } s=getAttrValue("activationMethod", attr); if(s.length()>0){ if(!strcmp("CID",&s[0])) spec->setActivation(CID); else if(!strcmp("ETD",&s[0])) spec->setActivation(ETD); else if(!strcmp("HCD",&s[0])) spec->setActivation(HCD); else if(!strcmp("ECD",&s[0])) spec->setActivation(ECD); else if(!strcmp("ETD+SA",&s[0])) spec->setActivation(ETDSA); } } else if (isElement("scan", el)) { if(m_bInScan){ pushSpectrum(); stopParser(); } else { m_bInScan=true; spec->setScanNum(atoi(getAttrValue("num", attr))); spec->setMSLevel(atoi(getAttrValue("msLevel", attr))); spec->setBasePeakIntensity(atof(getAttrValue("basePeakIntensity", attr))); spec->setBasePeakMZ(atof(getAttrValue("basePeakMz", attr))); spec->setCentroid((bool)getAttrValue("centroided",attr)); spec->setCollisionEnergy(atof(getAttrValue("collisionEnergy", attr))); spec->setCompensationVoltage(atof(getAttrValue("CompensationVoltage", attr))); s=getAttrValue("filterLine", attr); spec->setFilterLine(&s[0]); spec->setHighMZ(atof(getAttrValue("highMz", attr))); spec->setLowMZ(atof(getAttrValue("lowMz", attr))); if(spec->getHighMZ()==0) spec->setHighMZ(atof(getAttrValue("endMz", attr))); if(spec->getLowMZ()==0) spec->setLowMZ(atof(getAttrValue("startMz", attr))); spec->setTotalIonCurrent(atof(getAttrValue("totIonCurrent",attr))); m_peaksCount = atoi(getAttrValue("peaksCount", attr)); spec->setPeaksCount(m_peaksCount); s=getAttrValue("retentionTime", attr); if(s.length()>0){ float f=(float)atof(&s[2]); if(s[s.length()-1]=='S') spec->setRTime(f/60.0f); else spec->setRTime(f); } else { spec->setRTime(0.0f); } } } } void mzpSAXMzxmlHandler::endElement(const XML_Char *el) { if(isElement("dataProcessing", el)) { m_bInDataProcessing=false; } else if(isElement("index",el)){ m_bInIndex=false; posIndex=-1; stopParser(); if (!m_bIndexSorted) { qsort(&m_vIndex[0],m_vIndex.size(),sizeof(cindex),cindex::compare); m_bIndexSorted=true; } } else if(isElement("msInstrument",el)){ m_vInstrument.push_back(m_instrument); m_bInMsInstrument=false; } else if(isElement("msRun",el)){ m_bInMsRun=false; } else if(isElement("offset",el) && m_bScanIndex){ if(!m_bInIndex){ //bad index reference cout << "Index offset points to wrong location. Please rebuild index." << endl; m_bNoIndex=true; stopParser(); } curIndex.offset=mzpatoi64(&m_strData[0]); m_vIndex.push_back(curIndex); if (m_bIndexSorted && m_vIndex.size() > 1) { if (m_vIndex[m_vIndex.size()-1].scanNumsetPrecursorMZ(atof(&m_strData[0])); m_bInPrecursorMz=false; } else if(isElement("scan",el)) { m_bInScan = false; pushSpectrum(); stopParser(); } } void mzpSAXMzxmlHandler::characters(const XML_Char *s, int len) { m_strData.append(s, len); } bool mzpSAXMzxmlHandler::readHeader(int num){ spec->clear(); if(m_bNoIndex){ cout << "Currently only supporting indexed mzXML" << endl; return false; } //if no scan was requested, grab the next one if(num<0){ posIndex++; if(posIndex>=(int)m_vIndex.size()) return false; m_bHeaderOnly=true; parseOffset(m_vIndex[posIndex].offset); m_bHeaderOnly=false; return true; } //Assumes scan numbers are in order int mid=m_vIndex.size()/2; int upper=m_vIndex.size(); int lower=0; while(m_vIndex[mid].scanNum!=num){ if(lower==upper) break; if(m_vIndex[mid].scanNum>num){ upper=mid-1; mid=(lower+upper)/2; } else { lower=mid+1; mid=(lower+upper)/2; } } //need something faster than this, perhaps binary search if(m_vIndex[mid].scanNum==num) { m_bHeaderOnly=true; parseOffset(m_vIndex[mid].offset); //force scan number; this was done for files where scan events are not numbered if(spec->getScanNum()!=m_vIndex[mid].scanNum) spec->setScanNum(m_vIndex[mid].scanNum); spec->setScanIndex(mid+1); //set the index, which starts from 1, so offset by 1 m_bHeaderOnly=false; posIndex=mid; return true; } return false; } bool mzpSAXMzxmlHandler::readSpectrum(int num){ spec->clear(); if(m_bNoIndex){ cout << "Currently only supporting indexed mzXML" << endl; return false; } //if no scan was requested, grab the next one if(num<0){ posIndex++; if(posIndex>=(int)m_vIndex.size()) return false; parseOffset(m_vIndex[posIndex].offset); return true; } //Assumes scan numbers are in order int mid=m_vIndex.size()/2; int upper=m_vIndex.size(); int lower=0; while(m_vIndex[mid].scanNum!=num){ if(lower==upper) break; if(m_vIndex[mid].scanNum>num){ upper=mid-1; mid=(lower+upper)/2; } else { lower=mid+1; mid=(lower+upper)/2; } } //need something faster than this perhaps if(m_vIndex[mid].scanNum==num) { parseOffset(m_vIndex[mid].offset); //force scan number; this was done for files where scan events are not numbered if(spec->getScanNum()!=m_vIndex[mid].scanNum) spec->setScanNum(m_vIndex[mid].scanNum); spec->setScanIndex(mid+1); //set the index, which starts from 1, so offset by 1 posIndex=mid; return true; } return false; } void mzpSAXMzxmlHandler::pushSpectrum(){ specDP dp; for(unsigned int i=0;iaddDP(dp); } } void mzpSAXMzxmlHandler::decompress32(){ vdM.clear(); vdI.clear(); if(m_peaksCount < 1) return; union udata { float f; uint32_t i; } uData; uLong uncomprLen; uint32_t* data; int length; const char* pData = m_strData.data(); size_t stringSize = m_strData.size(); //Decode base64 char* pDecoded = (char*) new char[m_compressLen]; memset(pDecoded, 0, m_compressLen); length = b64_decode_mio( (char*) pDecoded , (char*) pData, stringSize ); pData=NULL; //zLib decompression data = new uint32_t[m_peaksCount*2]; uncomprLen = m_peaksCount * 2 * sizeof(uint32_t); uncompress((Bytef*)data, &uncomprLen, (const Bytef*)pDecoded, length); delete [] pDecoded; //write data to arrays int n = 0; for(int i=0;i 0) { // Base64 decoding // By comparing the size of the unpacked data and the expected size // an additional check of the data file integrity can be performed int length = b64_decode_mio( (char*) pDecoded , (char*) pData, stringSize ); if(length != size) { cout << " decoded size " << length << " and required size " << (unsigned long)size << " dont match:\n"; cout << " Cause: possible corrupted file.\n"; exit(EXIT_FAILURE); } } // And byte order correction union udata { float fData; uint32_t iData; } uData; vdM.clear(); vdI.clear(); int n = 0; uint32_t* pDecodedInts = (uint32_t*)pDecoded; // cast to uint_32 for reading int sized chunks for(int i = 0; i < m_peaksCount; i++) { uData.iData = dtohl(pDecodedInts[n++], m_bNetworkData); vdM.push_back((double)uData.fData); uData.iData = dtohl(pDecodedInts[n++], m_bNetworkData); vdI.push_back((double)uData.fData); } // Free allocated memory delete[] pDecoded; } void mzpSAXMzxmlHandler::decode64(){ // This code block was revised so that it packs floats correctly // on both 64 and 32 bit machines, by making use of the uint32_t // data type. -S. Wiley const char* pData = m_strData.data(); size_t stringSize = m_strData.size(); size_t size = m_peaksCount * 2 * sizeof(uint64_t); char* pDecoded = (char *) new char[size]; memset(pDecoded, 0, size); if(m_peaksCount > 0) { // Base64 decoding // By comparing the size of the unpacked data and the expected size // an additional check of the data file integrity can be performed int length = b64_decode_mio( (char*) pDecoded , (char*) pData, stringSize ); if(length != size) { cout << " decoded size " << length << " and required size " << (unsigned long)size << " dont match:\n"; cout << " Cause: possible corrupted file.\n"; exit(EXIT_FAILURE); } } // And byte order correction union udata { double fData; uint64_t iData; } uData; vdM.clear(); vdI.clear(); int n = 0; uint64_t* pDecodedInts = (uint64_t*)pDecoded; // cast to uint_64 for reading int sized chunks for(int i = 0; i < m_peaksCount; i++) { uData.iData = dtohl(pDecodedInts[n++], m_bNetworkData); vdM.push_back(uData.fData); uData.iData = dtohl(pDecodedInts[n++], m_bNetworkData); vdI.push_back(uData.fData); } // Free allocated memory delete[] pDecoded; } unsigned long mzpSAXMzxmlHandler::dtohl(uint32_t l, bool bNet) { #ifdef OSX if (!bNet) { l = (l << 24) | ((l << 8) & 0xFF0000) | (l >> 24) | ((l >> 8) & 0x00FF00); } #else if (bNet) { l = (l << 24) | ((l << 8) & 0xFF0000) | (l >> 24) | ((l >> 8) & 0x00FF00); } #endif return l; } uint64_t mzpSAXMzxmlHandler::dtohl(uint64_t l, bool bNet) { #ifdef OSX if (!bNet) { l = (l << 56) | ((l << 40) & 0xFF000000000000LL) | ((l << 24) & 0x0000FF0000000000LL) | ((l << 8) & 0x000000FF00000000LL) | (l >> 56) | ((l >> 40) & 0x0000000000FF00LL) | ((l >> 24) & 0x0000000000FF0000LL) | ((l >> 8) & 0x00000000FF000000LL) ; } #else if (bNet) { l = (l << 56) | ((l << 40) & 0x00FF000000000000LL) | ((l << 24) & 0x0000FF0000000000LL) | ((l << 8) & 0x000000FF00000000LL) | (l >> 56) | ((l >> 40) & 0x000000000000FF00LL) | ((l >> 24) & 0x0000000000FF0000LL) | ((l >> 8) & 0x00000000FF000000LL) ; } #endif return l; } //Finding the index list offset is done without the xml parser //to speed things along. This can be problematic if the //tag is placed anywhere other than the end of the mzML file. f_off mzpSAXMzxmlHandler::readIndexOffset() { char buffer[200]; char chunk[CHUNK]; char* start; char* stop; int readBytes; size_t sz; if(!m_bGZCompression){ FILE* f=fopen(&m_strFileName[0],"r"); mzpfseek(f,-200,SEEK_END); sz = fread(buffer,1,200,f); fclose(f); start=strstr(buffer,""); stop=strstr(buffer,""); } else { readBytes = gzObj.extract(fptr, gzObj.getfilesize()-200, (unsigned char*)chunk, CHUNK); start=strstr(chunk,""); stop=strstr(chunk,""); } if(start==NULL || stop==NULL) { cerr << "No index list offset found. File will not be read." << endl; return 0; } char offset[64]; int len=(int)(stop-start-13); strncpy(offset,start+13,len); offset[len]='\0'; return mzpatoi64(offset); } bool mzpSAXMzxmlHandler::load(const char* fileName){ if(!open(fileName)) return false; indexOffset = readIndexOffset(); if(indexOffset==0){ m_bNoIndex=true; return false; } else { m_bNoIndex=false; if(!parseOffset(indexOffset)){ cerr << "Cannot parse index. Make sure index offset is correct or rebuild index." << endl; return false; } posIndex=-1; } m_vInstrument.clear(); parseOffset(0); return true; } void mzpSAXMzxmlHandler::stopParser(){ m_bStopParse=true; XML_StopParser(m_parser,false); //reset mzML flags m_bInMsInstrument=false; m_bInDataProcessing=false; m_bInScan=false; m_bInPrecursorMz=false; m_bInMsRun=false; m_bInIndex=false; m_bInPeaks=false; m_bLowPrecision=false; //reset other flags m_bScanIndex=false; } int mzpSAXMzxmlHandler::highScan() { if(m_vIndex.size()==0) return 0; return m_vIndex[m_vIndex.size()-1].scanNum; } int mzpSAXMzxmlHandler::lowScan() { if(m_vIndex.size()==0) return 0; return m_vIndex[0].scanNum; } vector* mzpSAXMzxmlHandler::getIndex(){ return &m_vIndex; } f_off mzpSAXMzxmlHandler::getIndexOffset(){ return indexOffset; } instrumentInfo mzpSAXMzxmlHandler::getInstrument(){ return m_instrument; } int mzpSAXMzxmlHandler::getPeaksCount(){ return m_peaksCount; } libmstoolkit-77.0.0/src/mzParser/mzParser.cpp0000644000175000017500000001025612455161024021154 0ustar rusconirusconi#include "mzParser.h" MzParser::MzParser(BasicSpectrum* s){ spec=s; fileType=0; mzML=NULL; mzXML=NULL; #ifdef MZP_MZ5 mz5=NULL; mz5Config=NULL; #endif } MzParser::MzParser(BasicSpectrum* s, BasicChromatogram* c){ spec=s; chromat=c; fileType=0; mzML=NULL; mzXML=NULL; #ifdef MZP_MZ5 mz5=NULL; mz5Config=NULL; #endif } MzParser::~MzParser(){ spec=NULL; chromat=NULL; if(mzML!=NULL) delete mzML; if(mzXML!=NULL) delete mzXML; #ifdef MZP_MZ5 if(mz5!=NULL) delete mz5; if(mz5Config!=NULL) delete mz5Config; #endif } int MzParser::highChromat(){ switch(fileType){ case 1: case 3: return mzML->highChromat(); break; case 2: case 4: return 0; break; #ifdef MZP_MZ5 case 5: return mz5->highChromat(); break; #endif default: break; } return 0; } int MzParser::highScan(){ switch(fileType){ case 1: case 3: return mzML->highScan(); break; case 2: case 4: return mzXML->highScan(); break; #ifdef MZP_MZ5 case 5: return mz5->highScan(); break; #endif default: break; } return 0; } bool MzParser::load(char* fname){ if(mzML!=NULL) { delete mzML; mzML=NULL; } if(mzXML!=NULL) { delete mzXML; mzXML=NULL; } #ifdef MZP_MZ5 if(mz5!=NULL) { delete mz5; delete mz5Config; mz5=NULL; mz5Config=NULL; } #endif fileType=checkFileType(fname); switch(fileType){ case 1: case 3: mzML = new mzpSAXMzmlHandler(spec,chromat); if(fileType==3) mzML->setGZCompression(true); else mzML->setGZCompression(false); return mzML->load(fname); break; case 2: case 4: mzXML = new mzpSAXMzxmlHandler(spec); if(fileType==4) mzXML->setGZCompression(true); else mzXML->setGZCompression(false); return mzXML->load(fname); break; #ifdef MZP_MZ5 case 5: mz5Config = new mzpMz5Config(); mz5 = new mzpMz5Handler(mz5Config,spec,chromat); return mz5->readFile(fname); break; #endif default: break; } return false; } int MzParser::lowScan(){ switch(fileType){ case 1: case 3: return mzML->lowScan(); break; case 2: case 4: return mzXML->lowScan(); break; #ifdef MZP_MZ5 case 5: return mz5->lowScan(); break; #endif default: break; } return 0; } bool MzParser::readChromatogram(int num){ switch(fileType){ case 1: case 3: return mzML->readChromatogram(num); break; #ifdef MZP_MZ5 case 5: return mz5->readChromatogram(num); break; #endif default: break; } return false; } bool MzParser::readSpectrum(int num){ switch(fileType){ case 1: case 3: return mzML->readSpectrum(num); break; case 2: case 4: return mzXML->readSpectrum(num); break; #ifdef MZP_MZ5 case 5: return mz5->readSpectrum(num); break; #endif default: break; } return false; } bool MzParser::readSpectrumHeader(int num){ switch(fileType){ case 1: case 3: return mzML->readHeader(num); break; case 2: case 4: return mzXML->readHeader(num); break; #ifdef MZP_MZ5 case 5: return mz5->readHeader(num); break; #endif default: break; } return false; } int MzParser::checkFileType(char* fname){ char file[256]; char ext[256]; char *tok; char preExt[256]; unsigned int i; strcpy(ext,""); strcpy(file,fname); tok=strtok(file,".\n"); while(tok!=NULL){ strcpy(preExt,ext); strcpy(ext,tok); tok=strtok(NULL,".\n"); } for(i=0;isecond; } throw out_of_range("[mzpMz5Config::getDataTypeFor]: out of range"); } const string& mzpMz5Config::getNameFor(const MZ5DataSets v) { if (variableNames_.find(v) != variableNames_.end()) { return variableNames_.find(v)->second; } throw out_of_range("[mzpMz5Config::getNameFor]: out of range"); } const size_t& mzpMz5Config::getRdccSlots() { return rdccSolts_; } MZ5DataSets mzpMz5Config::getVariableFor(const std::string& name) { if (variableVariables_.find(name) != variableVariables_.end()) { return variableVariables_.find(name)->second; } throw out_of_range("[mzpMz5Config::getVariableFor]: out of range"); } void mzpMz5Config::init(const bool filter, const bool deltamz, const bool translateinten) { variableNames_.insert(pair(ControlledVocabulary, "ControlledVocabulary")); variableNames_.insert(pair(CVReference, "CVReference")); variableNames_.insert(pair(CVParam, "CVParam")); variableNames_.insert(pair(UserParam, "UserParam")); variableNames_.insert(pair(RefParam, "RefParam")); variableNames_.insert(pair(FileContent, "FileContent")); variableNames_.insert(pair(Contact, "Contact")); variableNames_.insert(pair(ParamGroups, "ParamGroups")); variableNames_.insert(pair(SourceFiles, "SourceFiles")); variableNames_.insert(pair(Samples, "Samples")); variableNames_.insert(pair(Software, "Software")); variableNames_.insert(pair(ScanSetting, "ScanSetting")); variableNames_.insert(pair(InstrumentConfiguration, "InstrumentConfiguration")); variableNames_.insert(pair(DataProcessing, "DataProcessing")); variableNames_.insert(pair(Run, "Run")); variableNames_.insert(pair(SpectrumMetaData, "SpectrumMetaData")); variableNames_.insert(pair(SpectrumBinaryMetaData, "SpectrumListBinaryData")); variableNames_.insert(pair(ChromatogramMetaData, "ChromatogramList")); variableNames_.insert(pair(ChromatogramBinaryMetaData, "ChromatogramListBinaryData")); variableNames_.insert(pair(ChromatogramIndex, "ChromatogramIndex")); variableNames_.insert(pair(SpectrumIndex, "SpectrumIndex")); variableNames_.insert(pair(SpectrumMZ, "SpectrumMZ")); variableNames_.insert(pair(SpectrumIntensity, "SpectrumIntensity")); variableNames_.insert(pair(ChromatogramTime, "ChomatogramTime")); variableNames_.insert(pair(ChromatogramIntensity, "ChromatogramIntensity")); variableNames_.insert(pair(FileInformation, "FileInformation")); for (map::iterator it = variableNames_.begin(); it != variableNames_.end(); ++it) { variableVariables_.insert(pair(it->second, it->first)); } variableTypes_.insert(pair(ControlledVocabulary, ContVocabMZ5::getType())); variableTypes_.insert(pair(FileContent, ParamListMZ5::getType())); variableTypes_.insert(pair(Contact, ParamListMZ5::getType())); variableTypes_.insert(pair(CVReference, CVRefMZ5::getType())); variableTypes_.insert(pair(ParamGroups, ParamGroupMZ5::getType())); variableTypes_.insert(pair(SourceFiles, SourceFileMZ5::getType())); variableTypes_.insert(pair(Samples, SampleMZ5::getType())); variableTypes_.insert(pair(Software, SoftwareMZ5::getType())); variableTypes_.insert(pair(ScanSetting, ScanSettingMZ5::getType())); variableTypes_.insert(pair(InstrumentConfiguration, InstrumentConfigurationMZ5::getType())); variableTypes_.insert(pair(DataProcessing, DataProcessingMZ5::getType())); variableTypes_.insert(pair(Run, RunMZ5::getType())); variableTypes_.insert(pair(SpectrumMetaData, SpectrumMZ5::getType())); variableTypes_.insert(pair(SpectrumBinaryMetaData, BinaryDataMZ5::getType())); variableTypes_.insert(pair(ChromatogramMetaData, ChromatogramMZ5::getType())); variableTypes_.insert(pair(ChromatogramBinaryMetaData, BinaryDataMZ5::getType())); variableTypes_.insert(pair(ChromatogramIndex, PredType::NATIVE_ULONG)); variableTypes_.insert(pair(SpectrumIndex, PredType::NATIVE_ULONG)); variableTypes_.insert(pair(FileInformation, FileInformationMZ5::getType())); variableTypes_.insert(pair(SpectrumMZ, PredType::NATIVE_DOUBLE)); variableTypes_.insert(pair(SpectrumIntensity, PredType::NATIVE_DOUBLE)); variableTypes_.insert(pair(ChromatogramIntensity, PredType::NATIVE_DOUBLE)); variableTypes_.insert(pair(ChromatogramTime, PredType::NATIVE_DOUBLE)); variableTypes_.insert(pair(CVParam, CVParamMZ5::getType())); variableTypes_.insert(pair(UserParam, UserParamMZ5::getType())); variableTypes_.insert(pair(RefParam, RefMZ5::getType())); hsize_t spectrumChunkSize = 5000L; // 1000=faster random read, 10000=better compression hsize_t chromatogramChunkSize = 1000L; hsize_t spectrumMetaChunkSize = 2000L; // should be modified in case of on demand access // hsize_t chromatogramMetaChunkSize = 10L; // usually one experiment does not contain a lot of chromatograms, so this chunk size is small in order to save storage space hsize_t cvparamChunkSize = 5000L; hsize_t userparamChunkSize = 100L; variableChunkSizes_.insert(pair(SpectrumMZ, spectrumChunkSize)); variableChunkSizes_.insert(pair(SpectrumIntensity, spectrumChunkSize)); variableChunkSizes_.insert(pair(ChromatogramTime, chromatogramChunkSize)); variableChunkSizes_.insert(pair(ChromatogramIntensity, chromatogramChunkSize)); bufferInMB_ = 8L; // this affects all datasets. size_t sizeOfDouble = static_cast (sizeof(double)); size_t bufferInByte = bufferInMB_ * 1024L * 1024L; size_t numberOfChunksInBuffer = (bufferInByte / sizeOfDouble) / spectrumChunkSize; rdccSolts_ = 41957L; // for 32 mb, 10000 chunk size hsize_t spectrumBufferSize = spectrumChunkSize * (numberOfChunksInBuffer / 4L); hsize_t chromatogramBufferSize = chromatogramChunkSize * 10L; variableBufferSizes_.insert(pair(SpectrumMZ, spectrumBufferSize)); variableBufferSizes_.insert(pair(SpectrumIntensity, spectrumBufferSize)); variableBufferSizes_.insert(pair(ChromatogramTime, chromatogramBufferSize)); variableBufferSizes_.insert(pair(ChromatogramIntensity, chromatogramBufferSize)); //if (config_.binaryDataEncoderConfig.compression == pwiz::msdata::BinaryDataEncoder::Compression_Zlib) { doTranslating_ = deltamz && translateinten; deflateLvl_ = 1; variableChunkSizes_.insert(pair(SpectrumMetaData, spectrumMetaChunkSize)); variableChunkSizes_.insert(pair(SpectrumBinaryMetaData, spectrumMetaChunkSize)); variableChunkSizes_.insert(pair(SpectrumIndex, spectrumMetaChunkSize)); // should not affect file size to much, if chromatogram information are not compressed // variableChunkSizes_.insert(pair(ChromatogramMetaData, chromatogramMetaChunkSize)); // variableChunkSizes_.insert(pair(ChromatogramBinaryMetaData, chromatogramMetaChunkSize)); // variableChunkSizes_.insert(pair(ChromatogramIndex, chromatogramMetaChunkSize)); variableChunkSizes_.insert(pair(CVParam, cvparamChunkSize)); variableChunkSizes_.insert(pair(UserParam, userparamChunkSize)); //} else { // deflateLvl_ = 0; //} spectrumLoadPolicy_ = SLP_InitializeAllOnFirstCall; chromatogramLoadPolicy_ = CLP_InitializeAllOnFirstCall; doFiltering_ = filter; } void mzpMz5Config::setFiltering(const bool flag) const { doFiltering_ = flag; } void mzpMz5Config::setTranslating(const bool flag) const { doTranslating_ = flag; } #endif libmstoolkit-77.0.0/src/mzParser/saxmzmlhandler.cpp0000644000175000017500000006306412455161024022407 0ustar rusconirusconi/************************************************************ * SAXMzmlHandler.cpp * Adapted from SAXMzdataHandler.cpp * August 2008 * Ronald Beavis * * April 2009 - Support for referenceable param groups and mzML 1.1.0 * Fredrik Levander * * December 2010 - Drastically modified and cannibalized to create * robust, yet generic, mzML pareser * Mike Hoopmann, Institute for Systems Biology * * Premiere version janvier 2005 * Patrick Lacasse * placasse@mat.ulaval.ca * * 3/11/2005 (Brendan MacLean): Use eXpat SAX parser, and create SAXSpectraHandler * * November 2005 * Fredrik Levander * A few changes to handle MzData 1.05. * * Updated to handle version 1.04 and 1.05. (Rob Craig) * * * See http://psidev.sourceforge.net/ms/#mzdata for * mzData schema information. * * Inspired by DtaSAX2Handler.cpp * copyright : (C) 2002 by Pedrioli Patrick, ISB, Proteomics * email : ppatrick@systemsbiology.org * Artistic License granted 3/11/2005 *******************************************************/ #include "mzParser.h" mzpSAXMzmlHandler::mzpSAXMzmlHandler(BasicSpectrum* bs){ m_bChromatogramIndex = false; m_bInmzArrayBinary = false; m_bInintenArrayBinary = false; m_bInRefGroup = false; m_bNetworkData = false; //always little-endian for mzML m_bNumpressLinear = false; m_bNumpressPic = false; m_bNumpressSlof = false; m_bLowPrecision = false; m_bInSpectrumList=false; m_bInChromatogramList=false; m_bInIndexedMzML=false; m_bInIndexList=false; m_bHeaderOnly=false; m_bSpectrumIndex=false; m_bNoIndex=true; m_bIndexSorted = true; m_bZlib=false; m_iDataType=0; spec=bs; indexOffset=-1; m_scanPRECCount = 0; m_scanSPECCount = 0; m_scanIDXCount = 0; chromat=NULL; } mzpSAXMzmlHandler::mzpSAXMzmlHandler(BasicSpectrum* bs, BasicChromatogram* cs){ m_bChromatogramIndex = false; m_bInmzArrayBinary = false; m_bInintenArrayBinary = false; m_bInRefGroup = false; m_bNetworkData = false; //always little-endian for mzML m_bNumpressLinear = false; m_bNumpressPic = false; m_bNumpressSlof = false; m_bLowPrecision = false; m_bInSpectrumList=false; m_bInChromatogramList=false; m_bInIndexedMzML=false; m_bInIndexList=false; m_bHeaderOnly=false; m_bSpectrumIndex=false; m_bNoIndex=true; m_bIndexSorted = true; m_bZlib=false; m_iDataType=0; spec=bs; chromat=cs; indexOffset=-1; m_scanPRECCount = 0; m_scanSPECCount = 0; m_scanIDXCount = 0; } mzpSAXMzmlHandler::~mzpSAXMzmlHandler(){ chromat=NULL; spec=NULL; } void mzpSAXMzmlHandler::startElement(const XML_Char *el, const XML_Char **attr){ if (isElement("binaryDataArray",el)){ m_bNumpressLinear=false; string s=getAttrValue("encodedLength", attr); m_encodedLen=atoi(&s[0]); } else if (isElement("binaryDataArrayList",el)) { if(m_bHeaderOnly) stopParser(); } else if (isElement("chromatogram",el)) { string s=getAttrValue("id", attr); chromat->setIDString(&s[0]); m_peaksCount = atoi(getAttrValue("defaultArrayLength", attr)); } else if (isElement("chromatogramList",el)) { m_bInChromatogramList=true; } else if(isElement("index",el) && m_bInIndexList){ if(!strcmp(getAttrValue("name", attr),"spectrum")) m_bSpectrumIndex=true; if(!strcmp(getAttrValue("name", attr),"chromatogram")) m_bChromatogramIndex=true; } else if (isElement("indexedmzML",el)) { m_vIndex.clear(); m_bInIndexedMzML=true; } else if(isElement("indexList",el)) { m_bInIndexList=true; } else if(isElement("offset",el) && m_bChromatogramIndex){ m_strData.clear(); curIndex.idRef=string(getAttrValue("idRef", attr)); } else if(isElement("offset",el) && m_bSpectrumIndex){ m_strData.clear(); curIndex.idRef=string(getAttrValue("idRef", attr)); if(strstr(&curIndex.idRef[0],"scan=")!=NULL) { curIndex.scanNum=atoi(strstr(&curIndex.idRef[0],"scan=")+5); } else if(strstr(&curIndex.idRef[0],"scanId=")!=NULL) { curIndex.scanNum=atoi(strstr(&curIndex.idRef[0],"scanId=")+7); } else if(strstr(&curIndex.idRef[0],"S")!=NULL) { curIndex.scanNum=atoi(strstr(&curIndex.idRef[0],"S")+1); } else { curIndex.scanNum=++m_scanIDXCount; //Suppressing warning. //cout << "WARNING: Cannot extract scan number in index offset line: " << &curIndex.idRef[0] << "\tDefaulting to " << m_scanIDXCount << endl; } } else if(isElement("precursor",el)) { string s=getAttrValue("spectrumRef", attr); //if spectrumRef is not provided if(s.length()<1){ spec->setPrecursorScanNum(0); } else { if(strstr(&s[0],"scan=")!=NULL) { spec->setPrecursorScanNum(atoi(strstr(&s[0],"scan=")+5)); } else if(strstr(&s[0],"scanId=")!=NULL) { spec->setPrecursorScanNum(atoi(strstr(&s[0],"scanId=")+7)); } else if(strstr(&s[0],"S")!=NULL) { spec->setPrecursorScanNum(atoi(strstr(&s[0],"S")+1)); } else { spec->setPrecursorScanNum(++m_scanPRECCount); //Suppressing warning. //cout << "WARNING: Cannot extract precursor scan number spectrum line: " << &s[0] << "\tDefaulting to " << m_scanPRECCount << endl; } } } else if (isElement("referenceableParamGroup", el)) { const char* groupName = getAttrValue("id", attr); m_ccurrentRefGroupName = string(groupName); m_bInRefGroup = true; } else if (isElement("run", el)){ stopParser(); } else if (isElement("softwareParam", el)) { const char* name = getAttrValue("name", attr); const char* accession = getAttrValue("accession", attr); const char* version = getAttrValue("version", attr); } else if (isElement("spectrum", el)) { string s=getAttrValue("id", attr); spec->setIDString(&s[0]); if(strstr(&s[0],"scan=")!=NULL) { spec->setScanNum(atoi(strstr(&s[0],"scan=")+5)); } else if(strstr(&s[0],"scanId=")!=NULL) { spec->setScanNum(atoi(strstr(&s[0],"scanId=")+7)); } else if(strstr(&s[0],"S")!=NULL) { spec->setScanNum(atoi(strstr(&s[0],"S")+1)); } else { spec->setScanNum(++m_scanSPECCount); //Suppressing warning. //cout << "WARNING: Cannot extract scan number spectrum line: " << &s[0] << "\tDefaulting to " << m_scanSPECCount << endl; } m_peaksCount = atoi(getAttrValue("defaultArrayLength", attr)); spec->setPeaksCount(m_peaksCount); } else if (isElement("spectrumList",el)) { m_bInSpectrumList=true; } else if (isElement("cvParam", el)) { const char* name = getAttrValue("name", attr); const char* accession = getAttrValue("accession", attr); const char* value = getAttrValue("value", attr); const char* unitName = getAttrValue("unitName", attr); const char* unitAccession = getAttrValue("unitAccession", attr); if (m_bInRefGroup) { cvParam m_cvParam; m_cvParam.refGroupName = string(m_ccurrentRefGroupName); m_cvParam.name = string(name); m_cvParam.accession = string(accession); m_cvParam.value = string(value); m_cvParam.unitName = string(unitName); m_cvParam.unitAccession = string(unitAccession); m_refGroupCvParams.push_back(m_cvParam); } else { processCVParam(name,accession,value,unitName,unitAccession); } } else if (isElement("referenceableParamGroupRef", el)) { const char* groupName = getAttrValue("ref", attr); for (unsigned int i=0;isetPrecursorMonoMZ(atof(value)); } } if(isElement("binary", el)) { m_strData.clear(); } } void mzpSAXMzmlHandler::endElement(const XML_Char *el) { if(isElement("binary", el)) { processData(); m_strData.clear(); } else if(isElement("binaryDataArray", el)) { m_bZlib=false; m_bInintenArrayBinary = false; m_bInmzArrayBinary = false; m_bNumpressLinear=false; m_bNumpressSlof=false; m_bNumpressPic=false; m_iDataType=0; } else if(isElement("chromatogram",el)) { pushChromatogram(); stopParser(); } else if(isElement("chromatogramList",el)) { m_bInChromatogramList=false; } else if(isElement("componentList",el)) { m_vInstrument.push_back(m_instrument); } else if(isElement("index",el)){ m_bSpectrumIndex=false; m_bChromatogramIndex=false; } else if(isElement("indexList",el)){ m_bInIndexList=false; stopParser(); if (!m_bIndexSorted) { qsort(&m_vIndex[0],m_vIndex.size(),sizeof(cindex),cindex::compare); m_bIndexSorted=true; } } else if(isElement("offset",el) && m_bChromatogramIndex){ curChromatIndex.offset=mzpatoi64(&m_strData[0]); m_vChromatIndex.push_back(curChromatIndex); } else if(isElement("offset",el) && m_bSpectrumIndex){ curIndex.offset=mzpatoi64(&m_strData[0]); m_vIndex.push_back(curIndex); if (m_bIndexSorted && m_vIndex.size() > 1) { if (m_vIndex[m_vIndex.size()-1].scanNum < m_vIndex[m_vIndex.size()-2].scanNum) { m_bIndexSorted = false; } } } else if(isElement("precursorList",el)){ } else if (isElement("referenceableParamGroup", el)) { m_bInRefGroup = false; } else if(isElement("spectrum", el)) { pushSpectrum(); stopParser(); } else if(isElement("spectrumList",el)) { m_bInSpectrumList = false; } } void mzpSAXMzmlHandler::characters(const XML_Char *s, int len) { m_strData.append(s, len); } void mzpSAXMzmlHandler::processCVParam(const char* name, const char* accession, const char* value, const char* unitName, const char* unitAccession) { if(!strcmp(name, "32-bit float") || !strcmp(accession,"MS:1000521")) { m_bLowPrecision = true; m_iDataType=1; } else if(!strcmp(name, "64-bit float") || !strcmp(accession,"MS:1000523")) { m_bLowPrecision = false; m_iDataType=2; } else if(!strcmp(name, "base peak intensity") || !strcmp(accession,"MS:1000505")) { spec->setBasePeakIntensity(atof(value)); } else if(!strcmp(name, "base peak m/z") || !strcmp(accession,"MS:1000504")) { spec->setBasePeakMZ(atof(value)); } else if(!strcmp(name, "centroid spectrum") || !strcmp(accession,"MS:1000127")) { spec->setCentroid(true); } else if(!strcmp(name, "charge state") || !strcmp(accession,"MS:1000041")) { spec->setPrecursorCharge(atoi(value)); } else if(!strcmp(name, "collision-induced dissociation") || !strcmp(accession,"MS:1000133")) { if(spec->getActivation()==ETD) spec->setActivation(ETDSA); else spec->setActivation(CID); } else if(!strcmp(name, "collision energy") || !strcmp(accession,"MS:1000045")) { spec->setCollisionEnergy(atof(value)); } else if(!strcmp(name,"electron multiplier") || !strcmp(accession,"MS:1000253")) { m_instrument.detector=name; } else if(!strcmp(name, "electron transfer dissociation") || !strcmp(accession,"MS:1000598")) { if(spec->getActivation()==CID) spec->setActivation(ETDSA); else spec->setActivation(ETD); } else if(!strcmp(name, "FAIMS compensation voltage") || !strcmp(accession,"MS:1001581")) { spec->setCompensationVoltage(atof(value)); } else if(!strcmp(name, "filter string") || !strcmp(accession,"MS:1000512")) { char str[128]; strncpy(str,value,127); str[127]='\0'; spec->setFilterLine(str); } else if(!strcmp(name, "highest observed m/z") || !strcmp(accession,"MS:1000527")) { spec->setHighMZ(atof(value)); } else if(!strcmp(name,"inductive detector") || !strcmp(accession,"MS:1000624")) { m_instrument.detector=name; } else if(!strcmp(name, "intensity array") || !strcmp(accession,"MS:1000515")) { m_bInintenArrayBinary = true; m_bInmzArrayBinary = false; } else if(!strcmp(name,"LTQ Velos") || !strcmp(accession,"MS:1000855")) { m_instrument.model=name; } else if(!strcmp(name, "lowest observed m/z") || !strcmp(accession,"MS:1000528")) { spec->setLowMZ(atof(value)); } else if( !strcmp(name, "MS1 spectrum") || !strcmp(accession,"MS:1000579") ){ spec->setMSLevel(1); } else if( !strcmp(name, "ms level") || !strcmp(accession,"MS:1000511") ){ spec->setMSLevel(atoi(value)); } else if( !strcmp(name, "MS-Numpress linear prediction compression") || !strcmp(accession,"MS:1002312") ){ m_bNumpressLinear = true; } else if( !strcmp(name, "MS-Numpress positive integer compression") || !strcmp(accession,"MS:1002313") ){ m_bNumpressPic = true; } else if( !strcmp(name, "MS-Numpress short logged float compression") || !strcmp(accession,"MS:1002314") ){ m_bNumpressSlof = true; } else if(!strcmp(name, "m/z array") || !strcmp(accession,"MS:1000514")) { m_bInmzArrayBinary = true; m_bInintenArrayBinary = false; } else if(!strcmp(name,"nanoelectrospray") || !strcmp(accession,"MS:1000398")) { m_instrument.ionization=name; } else if(!strcmp(name,"orbitrap") || !strcmp(accession,"MS:1000484")) { m_instrument.analyzer=name; } else if(!strcmp(name,"peak intensity") || !strcmp(accession,"MS:1000042")) { spec->setPrecursorIntensity(atof(value)); } else if(!strcmp(name,"positive scan") || !strcmp(accession,"MS:1000130")) { spec->setPositiveScan(true); } else if(!strcmp(name,"profile spectrum") || !strcmp(accession,"MS:1000128")) { spec->setCentroid(false); } else if(!strcmp(name,"radial ejection linear ion trap") || !strcmp(accession,"MS:1000083")) { m_instrument.analyzer=name; } else if(!strcmp(name, "scan start time") || !strcmp(accession,"MS:1000016")) { if(!strcmp(unitName, "minute") || !strcmp(unitAccession,"UO:0000031")) { spec->setRTime((float)atof(value)); } else { spec->setRTime((float)atof(value)/60.0f); //assume if not minutes, then seconds } } else if(!strcmp(name, "scan window lower limit") || !strcmp(accession,"MS:1000501")) { //TODO: should we also check the units??? spec->setLowMZ(atof(value)); } else if(!strcmp(name, "scan window upper limit") || !strcmp(accession,"MS:1000500")) { //TODO: should we also check the units??? spec->setHighMZ(atof(value)); } else if(!strcmp(name, "selected ion m/z") || !strcmp(accession,"MS:1000744")) { spec->setPrecursorMZ(atof(value)); } else if(!strcmp(name, "time array") || !strcmp(accession,"MS:1000595")) { m_bInmzArrayBinary = true; //note that this uses the m/z designation, although it is a time series m_bInintenArrayBinary = false; } else if(!strcmp(name, "total ion current") || !strcmp(accession,"MS:1000285")) { spec->setTotalIonCurrent(atof(value)); } else if(!strcmp(name,"Thermo RAW file") || !strcmp(accession,"MS:1000563")) { m_instrument.manufacturer="Thermo Scientific"; } else if(!strcmp(name, "zlib compression") || !strcmp(accession,"MS:1000574")) { m_bZlib=true; } } void mzpSAXMzmlHandler::processData() { if(m_bInmzArrayBinary) { decode(vdM); //if(m_bLowPrecision && !m_bCompressedData) decode32(vdM); //else if(m_bLowPrecision && m_bCompressedData) decompress32(vdM); //else if(!m_bLowPrecision && !m_bCompressedData) decode64(vdM); //else decompress64(vdM); } else if(m_bInintenArrayBinary) { decode(vdI); //if(m_bLowPrecision && !m_bCompressedData) decode32(vdI); //else if(m_bLowPrecision && m_bCompressedData) decompress32(vdI); //else if(!m_bLowPrecision && !m_bCompressedData) decode64(vdI); //else decompress64(vdI); } //m_bCompressedData=false; } bool mzpSAXMzmlHandler::readChromatogram(int num){ if(chromat==NULL) return false; chromat->clear(); if(m_bNoIndex){ cout << "Currently only supporting indexed mzML" << endl; return false; } //if no scan was requested, grab the next one if(num<0) posChromatIndex++; else posChromatIndex=num; if(posChromatIndex>=(int)m_vChromatIndex.size()) return false; parseOffset(m_vChromatIndex[posChromatIndex].offset); return true; } bool mzpSAXMzmlHandler::readHeader(int num){ spec->clear(); if(m_bNoIndex){ cout << "Currently only supporting indexed mzML" << endl; return false; } //if no scan was requested, grab the next one if(num<0){ posIndex++; if(posIndex>=(int)m_vIndex.size()) return false; m_bHeaderOnly=true; parseOffset(m_vIndex[posIndex].offset); m_bHeaderOnly=false; return true; } //Assumes scan numbers are in order int mid=m_vIndex.size()/2; int upper=m_vIndex.size(); int lower=0; while(m_vIndex[mid].scanNum!=num){ if(lower==upper) break; if(m_vIndex[mid].scanNum>num){ upper=mid-1; mid=(lower+upper)/2; } else { lower=mid+1; mid=(lower+upper)/2; } } if(m_vIndex[mid].scanNum==num) { m_bHeaderOnly=true; parseOffset(m_vIndex[mid].offset); //force scan number; this was done for files where scan events are not numbered if(spec->getScanNum()!=m_vIndex[mid].scanNum) spec->setScanNum(m_vIndex[mid].scanNum); spec->setScanIndex(mid+1); //set the index, which starts from 1, so offset by 1 m_bHeaderOnly=false; posIndex=mid; return true; } return false; } bool mzpSAXMzmlHandler::readSpectrum(int num){ spec->clear(); if(m_bNoIndex){ cout << "Currently only supporting indexed mzML" << endl; return false; } //if no scan was requested, grab the next one if(num<0){ posIndex++; if(posIndex>=(int)m_vIndex.size()) return false; parseOffset(m_vIndex[posIndex].offset); return true; } //Assumes scan numbers are in order int mid=m_vIndex.size()/2; int upper=m_vIndex.size(); int lower=0; while(m_vIndex[mid].scanNum!=num){ if(lower==upper) break; if(m_vIndex[mid].scanNum>num){ upper=mid-1; mid=(lower+upper)/2; } else { lower=mid+1; mid=(lower+upper)/2; } } //need something faster than this perhaps //for(unsigned int i=0;igetScanNum()!=m_vIndex[mid].scanNum) spec->setScanNum(m_vIndex[mid].scanNum); spec->setScanIndex(mid+1); //set the index, which starts from 1, so offset by 1 posIndex=mid; return true; } //} return false; } void mzpSAXMzmlHandler::pushChromatogram(){ TimeIntensityPair tip; for(unsigned int i=0;iaddTIP(tip); } } void mzpSAXMzmlHandler::pushSpectrum(){ specDP dp; for(unsigned int i=0;iaddDP(dp); } } void mzpSAXMzmlHandler::decode(vector& d){ //If there is no data, back out now d.clear(); if(m_peaksCount < 1) return; //For byte order correction union udata32 { float d; uint32_t i; } uData32; union udata64 { double d; uint64_t i; } uData64; const char* pData = m_strData.data(); size_t stringSize = m_strData.size(); char* decoded = new char[m_encodedLen]; //array for decoded base64 string int decodeLen; Bytef* unzipped; uLong unzippedLen; int i; //Base64 decoding decodeLen = b64_decode_mio(decoded,(char*)pData,stringSize); //zlib decompression if(m_bZlib) { if(m_iDataType==1) { unzippedLen = m_peaksCount*sizeof(uint32_t); } else if(m_iDataType==2) { unzippedLen = m_peaksCount*sizeof(uint64_t); } else { if(!m_bNumpressLinear && !m_bNumpressSlof && !m_bNumpressPic){ cout << "Unknown data format to unzip. Stopping file read." << endl; exit(EXIT_FAILURE); } //don't know the unzipped size of numpressed data, so assume it to be no larger than unpressed 64-bit data unzippedLen = m_peaksCount*sizeof(uint64_t); } unzipped = new Bytef[unzippedLen]; uncompress((Bytef*)unzipped, &unzippedLen, (const Bytef*)decoded, (uLong)decodeLen); delete [] decoded; } //Numpress decompression if(m_bNumpressLinear || m_bNumpressSlof || m_bNumpressPic){ double* unpressed=new double[m_peaksCount]; try{ if(m_bNumpressLinear){ if(m_bZlib) ms::numpress::MSNumpress::decodeLinear((unsigned char*)unzipped,(const size_t)unzippedLen,unpressed); else ms::numpress::MSNumpress::decodeLinear((unsigned char*)decoded,decodeLen,unpressed); } else if(m_bNumpressSlof){ if(m_bZlib) ms::numpress::MSNumpress::decodeSlof((unsigned char*)unzipped,(const size_t)unzippedLen,unpressed); else ms::numpress::MSNumpress::decodeSlof((unsigned char*)decoded,decodeLen,unpressed); } else if(m_bNumpressPic){ if(m_bZlib) ms::numpress::MSNumpress::decodePic((unsigned char*)unzipped,(const size_t)unzippedLen,unpressed); else ms::numpress::MSNumpress::decodePic((unsigned char*)decoded,decodeLen,unpressed); } } catch (const char* ch){ cout << "Exception: " << ch << endl; exit(EXIT_FAILURE); } if(m_bZlib) delete [] unzipped; else delete [] decoded; for(i=0;i> 24) | ((l >> 8) & 0x00FF00); } #else if (bNet) { l = (l << 24) | ((l << 8) & 0xFF0000) | (l >> 24) | ((l >> 8) & 0x00FF00); } #endif return l; } uint64_t mzpSAXMzmlHandler::dtohl(uint64_t l, bool bNet) { #ifdef OSX if (!bNet) { l = (l << 56) | ((l << 40) & 0xFF000000000000LL) | ((l << 24) & 0x0000FF0000000000LL) | ((l << 8) & 0x000000FF00000000LL) | (l >> 56) | ((l >> 40) & 0x0000000000FF00LL) | ((l >> 24) & 0x0000000000FF0000LL) | ((l >> 8) & 0x00000000FF000000LL) ; } #else if (bNet) { l = (l << 56) | ((l << 40) & 0x00FF000000000000LL) | ((l << 24) & 0x0000FF0000000000LL) | ((l << 8) & 0x000000FF00000000LL) | (l >> 56) | ((l >> 40) & 0x000000000000FF00LL) | ((l >> 24) & 0x0000000000FF0000LL) | ((l >> 8) & 0x00000000FF000000LL) ; } #endif return l; } //Finding the index list offset is done without the xml parser //to speed things along. This can be problematic if the //tag is placed anywhere other than the end of the mzML file. f_off mzpSAXMzmlHandler::readIndexOffset() { char buffer[200]; char chunk[CHUNK]; char* start; char* stop; int readBytes; size_t sz; if(!m_bGZCompression){ FILE* f=fopen(&m_strFileName[0],"r"); mzpfseek(f,-200,SEEK_END); sz = fread(buffer,1,200,f); fclose(f); start=strstr(buffer,""); stop=strstr(buffer,""); } else { readBytes = gzObj.extract(fptr, gzObj.getfilesize()-200, (unsigned char*)chunk, CHUNK); start=strstr(chunk,""); stop=strstr(chunk,""); } if(start==NULL || stop==NULL) { cerr << "No index list offset found. File will not be read." << endl; return 0; } char offset[64]; int len=(int)(stop-start-17); strncpy(offset,start+17,len); offset[len]='\0'; return mzpatoi64(offset); } bool mzpSAXMzmlHandler::load(const char* fileName){ if(!open(fileName)) return false; m_vInstrument.clear(); m_vIndex.clear(); m_vChromatIndex.clear(); parseOffset(0); indexOffset = readIndexOffset(); if(indexOffset==0){ m_bNoIndex=true; return false; } else { m_bNoIndex=false; if(!parseOffset(indexOffset)){ cerr << "Cannot parse index. Make sure index offset is correct or rebuild index." << endl; return false; } posIndex=-1; posChromatIndex=-1; } return true; } void mzpSAXMzmlHandler::stopParser(){ m_bStopParse=true; XML_StopParser(m_parser,false); //reset mzML flags m_bInmzArrayBinary = false; m_bInintenArrayBinary = false; m_bInRefGroup = false; m_bInSpectrumList=false; m_bInChromatogramList=false; m_bInIndexedMzML=false; m_bInIndexList=false; //reset other flags m_bSpectrumIndex=false; } int mzpSAXMzmlHandler::highChromat() { return m_vChromatIndex.size(); } int mzpSAXMzmlHandler::highScan() { if(m_vIndex.size()==0) return 0; return m_vIndex[m_vIndex.size()-1].scanNum; } int mzpSAXMzmlHandler::lowScan() { if(m_vIndex.size()==0) return 0; return m_vIndex[0].scanNum; } vector* mzpSAXMzmlHandler::getChromatIndex(){ return &m_vChromatIndex; } f_off mzpSAXMzmlHandler::getIndexOffset(){ return indexOffset; } vector* mzpSAXMzmlHandler::getInstrument(){ return &m_vInstrument; } int mzpSAXMzmlHandler::getPeaksCount(){ return m_peaksCount; } vector* mzpSAXMzmlHandler::getSpecIndex(){ return &m_vIndex; } libmstoolkit-77.0.0/src/mzParser/MSNumpress.cpp0000644000175000017500000005341112455161024021425 0ustar rusconirusconi/* MSNumpress.cpp johan.teleman@immun.lth.se Copyright 2013 Johan Teleman 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. */ #include //#include #include #include #include #include #include "MSNumpress.hpp" namespace ms { namespace numpress { namespace MSNumpress { using std::cout; using std::cerr; using std::endl; using std::min; using std::max; using std::abs; const int ONE = 1; bool is_big_endian() { return *((char*)&(ONE)) == 1; } bool IS_BIG_ENDIAN = is_big_endian(); ///////////////////////////////////////////////////////////// void encodeFixedPoint( double fixedPoint, unsigned char *result ) { int i; unsigned char *fp = (unsigned char*)&fixedPoint; for (i=0; i<8; i++) { result[i] = fp[IS_BIG_ENDIAN ? (7-i) : i]; } } double decodeFixedPoint( const unsigned char *data ) { int i; double fixedPoint; unsigned char *fp = (unsigned char*)&fixedPoint; for (i=0; i<8; i++) { fp[i] = data[IS_BIG_ENDIAN ? (7-i) : i]; } return fixedPoint; } ///////////////////////////////////////////////////////////// /** * Encodes the int x as a number of halfbytes in res. * res_length is incremented by the number of halfbytes, * which will be 1 <= n <= 9 */ void encodeInt( const int x, unsigned char* res, size_t *res_length ) { int i, l, m; unsigned int mask = 0xf0000000; int init = x & mask; if (init == 0) { l = 8; for (i=0; i<8; i++) { m = mask >> (4*i); if ((x & m) != 0) { l = i; break; } } res[0] = l; for (i=l; i<8; i++) { res[1+i-l] = x >> (4*(i-l)); } *res_length += 1+8-l; } else if (init == mask) { l = 7; for (i=0; i<8; i++) { m = mask >> (4*i); if ((x & m) != m) { l = i; break; } } res[0] = l + 8; for (i=l; i<8; i++) { res[1+i-l] = x >> (4*(i-l)); } *res_length += 1+8-l; } else { res[0] = 0; for (i=0; i<8; i++) { res[1+i] = x >> (4*i); } *res_length += 9; } } /** * Decodes an int from the half bytes in bp. Lossless reverse of encodeInt */ void decodeInt( const unsigned char *data, size_t *di, size_t max_di, size_t *half, int *res ) { size_t n; size_t i; unsigned int mask, m; unsigned char head; unsigned char hb; if (*half == 0) { head = data[*di] >> 4; } else { head = data[*di] & 0xf; (*di)++; } *half = 1-(*half); *res = 0; if (head <= 8) { n = head; } else { // leading ones, fill n half bytes in res n = head - 8; mask = 0xf0000000; for (i=0; i> (4*i); *res = *res | m; } } if (n == 8) { return; } if (*di + ((8 - n) - (1 - *half)) / 2 >= max_di) { throw "[MSNumpress::decodeInt] Corrupt input data! "; } for (i=n; i<8; i++) { if (*half == 0) { hb = data[*di] >> 4; } else { hb = data[*di] & 0xf; (*di)++; } *res = *res | (hb << ((i-n)*4)); *half = 1 - (*half); } } ///////////////////////////////////////////////////////////// double optimalLinearFixedPoint( const double *data, size_t dataSize ) { /* * safer impl - apparently not needed though * if (dataSize == 0) return 0; double maxDouble = 0; double x; for (size_t i=0; i> (i*8)) & 0xff; } if (dataSize == 1) return 12; ints[2] = (unsigned long long)(data[1] * fixedPoint + 0.5); for (i=0; i<4; i++) { result[12+i] = (ints[2] >> (i*8)) & 0xff; } halfByteCount = 0; ri = 16; for (i=2; i> 8; } return ri; } size_t decodeSlof( const unsigned char *data, const size_t dataSize, double *result ) { size_t i, ri; unsigned short x; ri = 0; double fixedPoint; if (dataSize < 8) throw "[MSNumpress::decodeSlof] Corrupt input data: not enough bytes to read fixed point! "; fixedPoint = decodeFixedPoint(data); for (i=8; i &data, std::vector &result, double fixedPoint ) { size_t dataSize = data.size(); result.resize(dataSize * 2); size_t encodedLength = encodeSlof(&data[0], dataSize, &result[0], fixedPoint); result.resize(encodedLength); } void decodeSlof( const std::vector &data, std::vector &result ) { size_t dataSize = data.size(); result.resize(dataSize / 2); size_t decodedLength = decodeSlof(&data[0], dataSize, &result[0]); result.resize(decodedLength); } } } // namespace numpress } // namespace ms libmstoolkit-77.0.0/src/mzParser/mzp_base64.cpp0000644000175000017500000000754112455161024021326 0ustar rusconirusconi/* downloaded from web */ //#include //#include //#include "stdafx.h" //#include //#include "base64.h" #include "mzParser.h" inline int getPosition( char buf ); static const unsigned char *b64_tbl = (const unsigned char*) "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789+/"; static const unsigned char b64_pad = '='; /* base64 encode a group of between 1 and 3 input chars into a group of 4 output chars */ static void encode_group (unsigned char output[], const unsigned char input[], int n) { unsigned char ingrp[3]; ingrp[0] = n > 0 ? input[0] : 0; ingrp[1] = n > 1 ? input[1] : 0; ingrp[2] = n > 2 ? input[2] : 0; /* upper 6 bits of ingrp[0] */ output[0] = n > 0 ? b64_tbl[ingrp[0] >> 2] : b64_pad; /* lower 2 bits of ingrp[0] | upper 4 bits of ingrp[1] */ output[1] = n > 0 ? b64_tbl[((ingrp[0] & 0x3) << 4) | (ingrp[1] >> 4)] : b64_pad; /* lower 4 bits of ingrp[1] | upper 2 bits of ingrp[2] */ output[2] = n > 1 ? b64_tbl[((ingrp[1] & 0xf) << 2) | (ingrp[2] >> 6)] : b64_pad; /* lower 6 bits of ingrp[2] */ output[3] = n > 2 ? b64_tbl[ingrp[2] & 0x3f] : b64_pad; } /* base64 decode a group of 4 input chars into a group of between 0 and * 3 output chars */ static void decode_group (unsigned char output[], const unsigned char input[], int *n) { unsigned char *t1, *t2; *n = 0; if (input[0] == '=') return; t1 = (unsigned char*) strchr ((const char*)b64_tbl, input[0]); t2 = (unsigned char*) strchr ((const char*)b64_tbl, input[1]); output[(*n)++] = (unsigned char)(((t1 - b64_tbl) << 2) | ((t2 - b64_tbl) >> 4)); if (input[2] == '=') return; t1 = (unsigned char*) strchr ((const char*)b64_tbl, input[2]); output[(*n)++] = (unsigned char)(((t2 - b64_tbl) << 4) | ((t1 - b64_tbl) >> 2)); if (input[3] == '=') return; t2 = (unsigned char*) strchr ((const char*)b64_tbl, input[3]); output[(*n)++] = (unsigned char)(((t1 - b64_tbl) << 6) | (t2 - b64_tbl)); return; } inline int getPosition( char buf ) { if( buf > 96 ) // [a-z] return (buf - 71); else if( buf > 64 ) // [A-Z] return (buf - 65); else if( buf > 47 ) // [0-9] return (buf + 4); else if( buf == 43 ) return 63; else // buf == '/' return 64; } // Returns the total number of bytes decoded int b64_decode_mio ( char *dest, char *src, size_t size ) { char *temp = dest; char *end = dest + size; for (;;) { int register a; int register b; int t1,t2,t3,t4; if (!(t1 = *src++) || !(t2 = *src++) || !(t3 = *src++) || !(t4 = *src++)) return (int)(temp-dest); if (t1 == 61 || temp >= end) // if == '=' return(int)(temp-dest); if( t1 > 96 ) // [a-z] a = (t1 - 71); else if( t1 > 64 ) // [A-Z] a = (t1 - 65); else if( t1 > 47 ) // [0-9] a = (t1 + 4); else if( t1 == 43 ) a = 62; else // src[0] == '/' a = 63; if( t2 > 96 ) // [a-z] b = (t2 - 71); else if( t2 > 64 ) // [A-Z] b = (t2 - 65); else if( t2 > 47 ) // [0-9] b = (t2 + 4); else if( t2 == 43 ) b = 62; else // src[0] == '/' b = 63; *temp++ = ( a << 2) | ( b >> 4); if (t3 == 61 || temp >= end) return (int)(temp-dest);; if( t3 > 96 ) // [a-z] a = (t3 - 71); else if( t3 > 64 ) // [A-Z] a = (t3 - 65); else if( t3 > 47 ) // [0-9] a = (t3 + 4); else if( t3 == 43 ) a = 62; else // src[0] == '/' a = 63; *temp++ = ( b << 4) | ( a >> 2); if (t4 == 61 || temp >= end) return (int)(temp-dest);; if( t4 > 96 ) // [a-z] b = (t4 - 71); else if( t4 > 64 ) // [A-Z] b = (t4 - 65); else if( t4 > 47 ) // [0-9] b = (t4 + 4); else if( t4 == 43 ) b = 62; else // src[0] == '/' b = 63; *temp++ = ( a << 6) | ( b ); } } libmstoolkit-77.0.0/src/mzParser/mz5handler.cpp0000644000175000017500000003722012455161024021422 0ustar rusconirusconi#include "mzParser.h" #ifdef MZP_MZ5 mzpMz5Handler::mzpMz5Handler(mzpMz5Config* c, BasicSpectrum* s){ config_=c; spec=s; } mzpMz5Handler::mzpMz5Handler(mzpMz5Config* c, BasicSpectrum* s, BasicChromatogram* bc){ config_=c; spec=s; chromat=bc; } mzpMz5Handler::~mzpMz5Handler(){ config_=NULL; spec=NULL; chromat=NULL; } void mzpMz5Handler::clean(const MZ5DataSets v, void* data, const size_t dsend) { hsize_t dim[1] = { static_cast (dsend) }; DataSpace dsp(1, dim); DataSet::vlenReclaim(data, config_->getDataTypeFor(v), dsp); free(data); data = 0; dsp.close(); } vector* mzpMz5Handler::getChromatIndex(){ return &m_vChromatIndex; } void mzpMz5Handler::getData(vector& data, const MZ5DataSets v, const hsize_t start, const hsize_t end) { hsize_t scount = end - start; data.resize(scount); if (scount > 0) { map::iterator it = bufferMap_.find(v); if (it == bufferMap_.end()) { DataSet ds = file_->openDataSet(config_->getNameFor(v)); bufferMap_.insert(pair(v, ds)); it = bufferMap_.find(v); } DataSet dataset = it->second; DataSpace dataspace = dataset.getSpace(); hsize_t offset[1]; offset[0] = start; hsize_t count[1]; count[0] = scount; dataspace.selectHyperslab(H5S_SELECT_SET, count, offset); hsize_t dimsm[1]; dimsm[0] = scount; DataSpace memspace(1, dimsm); dataset.read(&data[0], PredType::NATIVE_DOUBLE, memspace, dataspace); if (v == SpectrumMZ && config_->doTranslating()) { size_t ms = data.size(); double s = 0; for (size_t i = 0; i < ms; ++i) { data[i] = data[i] + s; s = data[i]; } } if (v == SpectrumIntensity && config_->doTranslating()) { //there is no translating to do... //Translator_mz5::reverseTranslateIntensity(data); } memspace.close(); dataspace.close(); } } const map& mzpMz5Handler::getFields() { return fields_; } vector* mzpMz5Handler::getSpecIndex(){ return &m_vIndex; } int mzpMz5Handler::highChromat() { return m_vChromatIndex.size(); } int mzpMz5Handler::highScan() { if(m_vIndex.size()==0) return 0; return m_vIndex[m_vIndex.size()-1].scanNum; } int mzpMz5Handler::lowScan() { if(m_vIndex.size()==0) return 0; return m_vIndex[0].scanNum; } void mzpMz5Handler::processCVParams(unsigned long index){ if(cvRef[cvParams_[index].typeCVRefID].group==0){ //MS: switch(cvRef[cvParams_[index].typeCVRefID].ref) { case 1000016: if(cvRef[cvParams_[index].unitCVRefID].ref==31) spec->setRTime((float)atof(cvParams_[index].value)); else spec->setRTime((float)atof(cvParams_[index].value)/60.0f); //assume seconds if not minutes break; case 1000041: spec->setPrecursorCharge(atoi(cvParams_[index].value)); break; case 1000042: spec->setPrecursorIntensity(atof(cvParams_[index].value)); break; case 1000045: spec->setCollisionEnergy(atof(cvParams_[index].value)); break; case 1000127: spec->setCentroid(true); break; case 1000285: spec->setTotalIonCurrent(atof(cvParams_[index].value)); break; case 1000504: spec->setBasePeakMZ(atof(cvParams_[index].value)); break; case 1000505: spec->setBasePeakIntensity(atof(cvParams_[index].value)); break; case 1000511: spec->setMSLevel(atoi(cvParams_[index].value)); break; case 1000512: spec->setFilterLine(cvParams_[index].value); break; case 1000527: spec->setHighMZ(atof(cvParams_[index].value)); break; case 1000528: spec->setLowMZ(atof(cvParams_[index].value)); break; case 1000744: spec->setPrecursorMZ(atof(cvParams_[index].value)); break; default: //cout << "Unknown/Unparsed CV: " << cvRef[cvParams_[index].typeCVRefID].group << ":" << cvRef[cvParams_[index].typeCVRefID].ref << endl; break; } } else { //unknown: //cout << "Unknown/Unparsed CV: " << cvRef[cvParams_[index].typeCVRefID].group << ":" << cvRef[cvParams_[index].typeCVRefID].ref << endl; } } bool mzpMz5Handler::readChromatogram(int num){ if(chromat==NULL) return false; chromat->clear(); //if no chromatogram was requested, grab the next one if(num<0) posChromatIndex++; else posChromatIndex=num; if(posChromatIndex>=(int)m_vChromatIndex.size()) return false; //Read the chromatogram vector time, inten; TimeIntensityPair tip; if(posChromatIndex==0){ getData(time, ChromatogramTime, 0, (hsize_t)m_vChromatIndex[posChromatIndex].offset); getData(inten, ChromatogramIntensity, 0, (hsize_t)m_vChromatIndex[posChromatIndex].offset); } else { getData(time, ChromatogramTime, (hsize_t)m_vChromatIndex[posChromatIndex-1].offset, (hsize_t)m_vChromatIndex[posChromatIndex].offset); getData(inten, ChromatogramIntensity, (hsize_t)m_vChromatIndex[posChromatIndex-1].offset, (hsize_t)m_vChromatIndex[posChromatIndex].offset); } for(unsigned int i=0;iaddTIP(tip); } //Read the metadata unsigned long start=m_vChromatIndex[posChromatIndex].cvStart; unsigned long stop=start+m_vChromatIndex[posChromatIndex].cvLen; for(size_t i=start;isetIDString(&m_vChromatIndex[posChromatIndex].idRef[0]); return true; } void* mzpMz5Handler::readDataSet(const MZ5DataSets v, size_t& dsend, void* ptr) { DataSet ds = file_->openDataSet(config_->getNameFor(v)); DataSpace dsp = ds.getSpace(); hsize_t start[1], end[1]; dsp.getSelectBounds(start, end); dsend = (static_cast (end[0])) + 1; DataType dt = config_->getDataTypeFor(v); if (ptr == 0) ptr = calloc(dsend, dt.getSize()); ds.read(ptr, dt); dsp.close(); ds.close(); return ptr; } bool mzpMz5Handler::readFile(const string filename){ FileCreatPropList fcparm = FileCreatPropList::DEFAULT; FileAccPropList faparm = FileAccPropList::DEFAULT; int mds_nelemts; size_t rdcc_nelmts, rdcc_nbytes; double rdcc_w0; faparm.getCache(mds_nelemts, rdcc_nelmts, rdcc_nbytes, rdcc_w0); //TODO do not set global buffer size, instead set dataset specific buffer size rdcc_nbytes = config_->getBufferInB(); //TODO can be set to 1 if chunks that have been fully read/written will never be read/written again //rdcc_w0 = 1.0; rdcc_nelmts = config_->getRdccSlots(); faparm.setCache(mds_nelemts, rdcc_nelmts, rdcc_nbytes, rdcc_w0); try { file_ = new H5File(filename, H5F_ACC_RDONLY, fcparm, faparm); } catch (FileIException&){ return false; } closed_ = false; hsize_t start[1], end[1]; size_t dsend = 0; DataSet dataset; DataSpace dataspace; string oname; MZ5DataSets v; for (hsize_t i = 0; i < file_->getNumObjs(); ++i) { oname = file_->getObjnameByIdx(i); dataset = file_->openDataSet(oname); dataspace = dataset.getSpace(); dataspace.getSelectBounds(start, end); dsend = (static_cast (end[0])) + 1; try { v = config_->getVariableFor(oname); fields_.insert(pair(v, dsend)); } catch (out_of_range&) { } dataspace.close(); dataset.close(); } map::const_iterator it; it = fields_.find(FileInformation); if (it != fields_.end()) { DataSet ds = file_->openDataSet(config_->getNameFor(FileInformation)); DataSpace dsp = ds.getSpace(); hsize_t start[1], end[1]; dsp.getSelectBounds(start, end); dsend = (static_cast (end[0])) + 1; DataType dt = config_->getDataTypeFor(FileInformation); FileInformationMZ5* fi = (FileInformationMZ5*) (calloc(dsend, dt.getSize())); ds.read(fi, dt); dsp.close(); ds.close(); if (dsend == 1) { if (fi[0].majorVersion == MZ5_FILE_MAJOR_VERSION && fi[0].minorVersion == MZ5_FILE_MINOR_VERSION) { config_->setFiltering(fi[0].didFiltering > 0 ? true : false); config_->setTranslating(fi[0].deltaMZ && fi[0].translateInten); } } hsize_t dim[1] = { static_cast (dsend) }; DataSpace dspr(1, dim); DataSet::vlenReclaim(fi, config_->getDataTypeFor(FileInformation), dspr); free(fi); fi = 0; dspr.close(); } else { it = fields_.find(Run); if (it == fields_.end()) { throw runtime_error("mzpMz5Handler::readFile(): given file is not mz5."); return false; } } //Read the CV Reference List size_t numberOfRef = fields_.find(CVReference)->second; CVRefMZ5* cvrl = (CVRefMZ5*) readDataSet(CVReference, dsend); cvRef.clear(); CVRefItem cvr; for(int xx=0;xxsecond; cvParams_.resize(numberOfCV); readDataSet(CVParam, dsend, &cvParams_[0]); //Build the index m_vIndex.clear(); m_scanIDXCount=0; size_t numberOfSpectra_ = fields_.find(SpectrumMetaData)->second; vector index; index.resize(numberOfSpectra_); readDataSet(SpectrumIndex,dsend,&index[0]); BinaryDataMZ5* binaryParamsData_ = (BinaryDataMZ5*) calloc(numberOfSpectra_, sizeof(BinaryDataMZ5)); readDataSet(SpectrumBinaryMetaData, dsend, binaryParamsData_); SpectrumMZ5* spectrumData_ = (SpectrumMZ5*) calloc(numberOfSpectra_, sizeof(SpectrumMZ5)); readDataSet(SpectrumMetaData, dsend, spectrumData_); for(size_t i=0;isecond; index.clear(); index.resize(numberOfChromats_); readDataSet(ChromatogramIndex,dsend,&index[0]); free(binaryParamsData_); binaryParamsData_ = (BinaryDataMZ5*) calloc(numberOfChromats_, sizeof(BinaryDataMZ5)); readDataSet(ChromatogramBinaryMetaData, dsend, binaryParamsData_); ChromatogramMZ5* chromatogramData_ = (ChromatogramMZ5*) calloc(numberOfSpectra_, sizeof(ChromatogramMZ5)); readDataSet(ChromatogramMetaData, dsend, chromatogramData_); for(size_t i=0;iclear(); //if no scan was requested, grab the next one if(num<0){ posIndex++; if(posIndex>=(int)m_vIndex.size()) return false; } else { //otherwise do binary search for scan number //Assumes scan numbers are in order int mid=m_vIndex.size()/2; int upper=m_vIndex.size(); int lower=0; while(m_vIndex[mid].scanNum!=num){ if(lower==upper) break; if(m_vIndex[mid].scanNum>num){ upper=mid-1; mid=(lower+upper)/2; } else { lower=mid+1; mid=(lower+upper)/2; } } if(m_vIndex[mid].scanNum==num) posIndex=mid; } //Read the metadata unsigned long start=m_vIndex[posIndex].cvStart; unsigned long stop=start+m_vIndex[posIndex].cvLen; for(size_t i=start;i mz; if(posIndex==0) getData(mz, SpectrumMZ, 0, (hsize_t)m_vIndex[posIndex].offset); else getData(mz, SpectrumMZ, (hsize_t)m_vIndex[posIndex-1].offset, (hsize_t)m_vIndex[posIndex].offset); spec->setPeaksCount((int)mz.size()); if(spec->getScanNum()!=m_vIndex[posIndex].scanNum) spec->setScanNum(m_vIndex[posIndex].scanNum); spec->setScanIndex(posIndex+1); //set the index, which starts from 1, so offset by 1 return true; } bool mzpMz5Handler::readSpectrum(int num){ spec->clear(); //if no scan was requested, grab the next one if(num<0){ posIndex++; if(posIndex>=(int)m_vIndex.size()) return false; } else { //otherwise do binary search for scan number //Assumes scan numbers are in order int mid=m_vIndex.size()/2; int upper=m_vIndex.size(); int lower=0; while(m_vIndex[mid].scanNum!=num){ if(lower==upper) break; if(m_vIndex[mid].scanNum>num){ upper=mid-1; mid=(lower+upper)/2; } else { lower=mid+1; mid=(lower+upper)/2; } } if(m_vIndex[mid].scanNum==num) posIndex=mid; } //Read the peaks vector mz, inten; specDP dp; if(posIndex==0){ getData(mz, SpectrumMZ, 0, (hsize_t)m_vIndex[posIndex].offset); getData(inten, SpectrumIntensity, 0, (hsize_t)m_vIndex[posIndex].offset); } else { getData(mz, SpectrumMZ, (hsize_t)m_vIndex[posIndex-1].offset, (hsize_t)m_vIndex[posIndex].offset); getData(inten, SpectrumIntensity, (hsize_t)m_vIndex[posIndex-1].offset, (hsize_t)m_vIndex[posIndex].offset); } for(unsigned int i=0;iaddDP(dp); } spec->setPeaksCount((int)mz.size()); //Read the metadata unsigned long start=m_vIndex[posIndex].cvStart; unsigned long stop=start+m_vIndex[posIndex].cvLen; for(size_t i=start;igetScanNum()!=m_vIndex[posIndex].scanNum) spec->setScanNum(m_vIndex[posIndex].scanNum); spec->setScanIndex(posIndex+1); //set the index, which starts from 1, so offset by 1 return true; } #endif libmstoolkit-77.0.0/src/mzParser/BasicChromatogram.cpp0000644000175000017500000000215212455161024022732 0ustar rusconirusconi#include "mzParser.h" BasicChromatogram::BasicChromatogram(){} BasicChromatogram::BasicChromatogram(const BasicChromatogram& c){ vData.clear(); for(unsigned int i=0;i& BasicChromatogram::getData() { return vData; } int BasicChromatogram::getIDString(char* str){ strcpy(str,idString); return strlen(str); } unsigned int BasicChromatogram::size(){ return vData.size(); } libmstoolkit-77.0.0/src/mzParser/BasicSpectrum.cpp0000644000175000017500000001431312455161024022113 0ustar rusconirusconi/* BasicSpectrum.cpp Copyright (C) 2010-2012, Mike Hoopmann Institute for Systems Biology Version 1.1, Mar. 28, 2012 */ #include "mzParser.h" //------------------------------------------ // Constructors & Destructors //------------------------------------------ BasicSpectrum::BasicSpectrum() { activation=none; basePeakIntensity=0.0; basePeakMZ=0.0; centroid=false; filterLine[0]='\0'; highMZ=0.0; lowMZ=0.0; msLevel=1; peaksCount=0; positiveScan=true; precursorCharge=0; precursorIntensity=0.0; compensationVoltage=0.0; precursorMonoMZ=0.0; precursorMZ=0.0; precursorScanNum=-1; rTime=0.0f; scanIndex=0; scanNum=-1; totalIonCurrent=0.0; idString[0]='\0'; vData.clear(); } BasicSpectrum::BasicSpectrum(const BasicSpectrum& s){ vData.clear(); for(unsigned int i=0;istartElement(el, attr); } static void mzp_endElementCallback(void *data, const XML_Char *el) { ((mzpSAXHandler*) data)->endElement(el); } static void mzp_charactersCallback(void *data, const XML_Char *s, int len) { ((mzpSAXHandler*) data)->characters(s, len); } mzpSAXHandler::mzpSAXHandler() { fptr = NULL; m_bGZCompression = false; fptr = NULL; m_parser = XML_ParserCreate(NULL); XML_SetUserData(m_parser, this); XML_SetElementHandler(m_parser, mzp_startElementCallback, mzp_endElementCallback); XML_SetCharacterDataHandler(m_parser, mzp_charactersCallback); } mzpSAXHandler::~mzpSAXHandler() { if(fptr!=NULL) fclose(fptr); fptr = NULL; XML_ParserFree(m_parser); } void mzpSAXHandler::startElement(const XML_Char *el, const XML_Char **attr) { } void mzpSAXHandler::endElement(const XML_Char *el) { } void mzpSAXHandler::characters(const XML_Char *s, int len) { } bool mzpSAXHandler::open(const char* fileName){ if(fptr!=NULL) fclose(fptr); if(m_bGZCompression) fptr=fopen(fileName,"rb"); else fptr=fopen(fileName,"r"); if(fptr==NULL){ cerr << "Failed to open input file '" << fileName << "'.\n"; return false; } setFileName(fileName); //Build the index if gz compressed if(m_bGZCompression){ gzObj.free_index(); int len; len = gzObj.build_index(fptr, SPAN); if (len < 0) { fclose(fptr); switch (len) { case Z_MEM_ERROR: fprintf(stderr, "Error reading .gz file: out of memory\n"); break; case Z_DATA_ERROR: fprintf(stderr, "Error reading .gz file: compressed data error in %s\n", fileName); break; case Z_ERRNO: fprintf(stderr, "Error reading .gz file: read error on %s\n", fileName); break; default: fprintf(stderr, "Error reading .gz file: error %d while building index\n", len); } fptr=NULL; return false; } } return true; } bool mzpSAXHandler::parse() { if (fptr == NULL){ cerr << "Error parse(): No open file." << endl; return false; } char buffer[CHUNK]; //CHUNK=16384 int readBytes = 0; bool success = true; int chunk=0; if(m_bGZCompression){ while (success && (readBytes = gzObj.extract(fptr, 0+chunk*CHUNK, (unsigned char*)buffer, CHUNK))>0) { success = (XML_Parse(m_parser, buffer, readBytes, false) != 0); chunk++; } } else { while (success && (readBytes = (int) fread(buffer, 1, sizeof(buffer), fptr)) != 0){ success = (XML_Parse(m_parser, buffer, readBytes, false) != 0); } } success = success && (XML_Parse(m_parser, buffer, 0, true) != 0); if (!success) { XML_Error error = XML_GetErrorCode(m_parser); cerr << m_strFileName << "(" << XML_GetCurrentLineNumber(m_parser) << ")" << " : error " << (int) error << ": "; switch (error) { case XML_ERROR_SYNTAX: case XML_ERROR_INVALID_TOKEN: case XML_ERROR_UNCLOSED_TOKEN: cerr << "Syntax error parsing XML."; break; // TODO: Add more descriptive text for interesting errors. default: cerr << "XML Parsing error."; break; } cerr << "\n"; return false; } return true; } //This function operates similarly to the parse() function. //However, it accepts a file offset to begin parsing at a specific point. //The parser will halt file reading when stop flag is triggered. bool mzpSAXHandler::parseOffset(f_off offset){ if (fptr == NULL){ cerr << "Error parseOffset(): No open file." << endl; return false; } char buffer[CHUNK]; //CHUNK=16384 int readBytes = 0; bool success = true; int chunk=0; XML_ParserReset(m_parser,"ISO-8859-1"); XML_SetUserData(m_parser, this); XML_SetElementHandler(m_parser, mzp_startElementCallback, mzp_endElementCallback); XML_SetCharacterDataHandler(m_parser, mzp_charactersCallback); mzpfseek(fptr,offset,SEEK_SET); m_bStopParse=false; if(m_bGZCompression){ while (success && (readBytes = gzObj.extract(fptr, offset+chunk*CHUNK, (unsigned char*)buffer, CHUNK))>0) { success = (XML_Parse(m_parser, buffer, readBytes, false) != 0); chunk++; if(m_bStopParse) break; } } else { while (success && (readBytes = (int) fread(buffer, 1, sizeof(buffer), fptr)) != 0) { success = (XML_Parse(m_parser, buffer, readBytes, false) != 0); if(m_bStopParse) break; } } if (!success && !m_bStopParse) { XML_Error error = XML_GetErrorCode(m_parser); cerr << m_strFileName << "(" << XML_GetCurrentLineNumber(m_parser) << ")" << " : error " << (int) error << ": "; switch (error) { case XML_ERROR_SYNTAX: case XML_ERROR_INVALID_TOKEN: case XML_ERROR_UNCLOSED_TOKEN: cerr << "Syntax error parsing XML." << endl; break; // TODO: Add more descriptive text for interesting errors. default: cerr << "Spectrum XML Parsing error:\n"; cerr << XML_ErrorString(error) << endl; break; } exit(-7); return false; } return true; } void mzpSAXHandler::setGZCompression(bool b){ m_bGZCompression=b; } libmstoolkit-77.0.0/src/mzParser/PWIZface.cpp0000644000175000017500000000673412455161024020767 0ustar rusconirusconi#include "mzParser.h" Chromatogram::Chromatogram(){ bc = NULL; } Chromatogram::~Chromatogram(){ bc = NULL; } void Chromatogram::getTimeIntensityPairs(vector& v){ if(bc==NULL) cerr << "Null chromatogram" << endl; else v=bc->getData(); } ChromatogramList::ChromatogramList(){ } ChromatogramList::ChromatogramList(mzpSAXMzmlHandler* ml, void* m5, BasicChromatogram* bc){ mzML=ml; #ifdef MZP_MZ5 mz5=(mzpMz5Handler*)m5; #endif chromat=new Chromatogram(); chromat->bc=bc; } ChromatogramList::~ChromatogramList(){ mzML=NULL; vChromatIndex=NULL; #ifdef MZP_MZ5 mz5=NULL; vMz5Index=NULL; #endif delete chromat; } ChromatogramPtr ChromatogramList::chromatogram(int index, bool binaryData) { char str[128]; if(mzML!=NULL) { mzML->readChromatogram(index); chromat->bc->getIDString(str); chromat->id=str; return chromat; #ifdef MZP_MZ5 } else if(mz5!=NULL) { mz5->readChromatogram(index); chromat->bc->getIDString(str); chromat->id=str; return chromat; #endif } return NULL; } bool ChromatogramList::get() { if(mzML!=NULL) vChromatIndex = mzML->getChromatIndex(); #ifdef MZP_MZ5 else if(mz5!=NULL) vMz5Index = mz5->getChromatIndex(); #endif else return false; return true; } unsigned int ChromatogramList::size() { if(vChromatIndex==NULL) { cerr << "Get chromatogram list first." << endl; return 0; } if(mzML!=NULL) return vChromatIndex->size(); #ifdef MZP_MZ5 else if(mz5!=NULL) return vMz5Index->size(); #endif else return 0; } PwizRun::PwizRun(){ chromatogramListPtr = new ChromatogramList(); } PwizRun::PwizRun(mzpSAXMzmlHandler* ml, void* m5, BasicChromatogram* b){ mzML=ml; #ifdef MZP_MZ5 mz5=(mzpMz5Handler*)m5; #endif bc=b; chromatogramListPtr = new ChromatogramList(ml, m5, b); } PwizRun::~PwizRun(){ mzML=NULL; #ifdef MZP_MZ5 mz5=NULL; #endif bc=NULL; delete chromatogramListPtr; } void PwizRun::set(mzpSAXMzmlHandler* ml, void* m5, BasicChromatogram* b){ mzML=ml; #ifdef MZP_MZ5 mz5=(mzpMz5Handler*)m5; #endif bc=b; delete chromatogramListPtr; chromatogramListPtr = new ChromatogramList(ml, m5, b); } MSDataFile::MSDataFile(string s){ int i=checkFileType(&s[0]); if(i==0){ cerr << "Cannot identify file type." << endl; } else { bs = new BasicSpectrum(); bc = new BasicChromatogram(); switch(i){ case 1: //mzML case 3: mzML=new mzpSAXMzmlHandler(bs,bc); if(i==3) mzML->setGZCompression(true); else mzML->setGZCompression(false); if(!mzML->load(&s[0])){ cerr << "Failed to load file." << endl; delete mzML; delete bs; delete bc; } run.chromatogramListPtr->vChromatIndex=mzML->getChromatIndex(); break; case 2: //mzXML case 4: cerr << "mzXML not supported in this interface." << endl; delete bs; delete bc; break; #ifdef MZP_MZ5 case 5: //mz5 mz5Config = new mzpMz5Config(); mz5=new mzpMz5Handler(mz5Config, bs, bc); if(!mz5->readFile(&s[0])){ cerr << "Failed to load file." << endl; delete mz5; delete mz5Config; delete bs; delete bc; } break; #endif default: break; } #ifdef MZP_MZ5 run.set(mzML,mz5,bc); #else run.set(mzML,NULL,bc); #endif } } MSDataFile::~MSDataFile(){ if(mzML!=NULL) delete mzML; #ifdef MZP_MZ5 if(mz5!=NULL){ delete mz5; delete mz5Config; } #endif delete bs; delete bc; } libmstoolkit-77.0.0/MSToolkit.sln0000644000175000017500000000553612455161024016663 0ustar rusconirusconi Microsoft Visual Studio Solution File, Format Version 10.00 # Visual C++ Express 2008 Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "MSToolkit", "MSToolkit.vcproj", "{D2646DE9-A31A-4C6E-99C6-B81885C17A93}" EndProject Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "MSToolkitCLR", "MSToolkitCLR.vcproj", "{48702313-7D61-4679-BF85-FBF1A1C34C52}" EndProject Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "MSToolkitLite", "MSToolkitLite.vcproj", "{8093FAFA-4AA1-4E88-A83E-1B433A96AAE5}" EndProject Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "MSToolkitLiteCLR", "MSToolkitLiteCLR.vcproj", "{0B0E7480-5938-4388-B57D-66A262E601C8}" EndProject Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "MSSingleScan", "MSSingleScan\MSSingleScan.vcproj", "{24C852FB-C978-4957-BC4D-92F27FD031AE}" ProjectSection(ProjectDependencies) = postProject {8093FAFA-4AA1-4E88-A83E-1B433A96AAE5} = {8093FAFA-4AA1-4E88-A83E-1B433A96AAE5} EndProjectSection EndProject Global GlobalSection(SolutionConfigurationPlatforms) = preSolution Debug|Win32 = Debug|Win32 Release|Win32 = Release|Win32 EndGlobalSection GlobalSection(ProjectConfigurationPlatforms) = postSolution {D2646DE9-A31A-4C6E-99C6-B81885C17A93}.Debug|Win32.ActiveCfg = Debug|Win32 {D2646DE9-A31A-4C6E-99C6-B81885C17A93}.Debug|Win32.Build.0 = Debug|Win32 {D2646DE9-A31A-4C6E-99C6-B81885C17A93}.Release|Win32.ActiveCfg = Release|Win32 {D2646DE9-A31A-4C6E-99C6-B81885C17A93}.Release|Win32.Build.0 = Release|Win32 {48702313-7D61-4679-BF85-FBF1A1C34C52}.Debug|Win32.ActiveCfg = Debug|Win32 {48702313-7D61-4679-BF85-FBF1A1C34C52}.Debug|Win32.Build.0 = Debug|Win32 {48702313-7D61-4679-BF85-FBF1A1C34C52}.Release|Win32.ActiveCfg = Release|Win32 {48702313-7D61-4679-BF85-FBF1A1C34C52}.Release|Win32.Build.0 = Release|Win32 {8093FAFA-4AA1-4E88-A83E-1B433A96AAE5}.Debug|Win32.ActiveCfg = Debug|Win32 {8093FAFA-4AA1-4E88-A83E-1B433A96AAE5}.Debug|Win32.Build.0 = Debug|Win32 {8093FAFA-4AA1-4E88-A83E-1B433A96AAE5}.Release|Win32.ActiveCfg = Release|Win32 {8093FAFA-4AA1-4E88-A83E-1B433A96AAE5}.Release|Win32.Build.0 = Release|Win32 {0B0E7480-5938-4388-B57D-66A262E601C8}.Debug|Win32.ActiveCfg = Debug|Win32 {0B0E7480-5938-4388-B57D-66A262E601C8}.Debug|Win32.Build.0 = Debug|Win32 {0B0E7480-5938-4388-B57D-66A262E601C8}.Release|Win32.ActiveCfg = Release|Win32 {0B0E7480-5938-4388-B57D-66A262E601C8}.Release|Win32.Build.0 = Release|Win32 {24C852FB-C978-4957-BC4D-92F27FD031AE}.Debug|Win32.ActiveCfg = Debug|Win32 {24C852FB-C978-4957-BC4D-92F27FD031AE}.Debug|Win32.Build.0 = Debug|Win32 {24C852FB-C978-4957-BC4D-92F27FD031AE}.Release|Win32.ActiveCfg = Release|Win32 {24C852FB-C978-4957-BC4D-92F27FD031AE}.Release|Win32.Build.0 = Release|Win32 EndGlobalSection GlobalSection(SolutionProperties) = preSolution HideSolutionNode = FALSE EndGlobalSection EndGlobal libmstoolkit-77.0.0/Makefile0000644000175000017500000000745012455161025015716 0ustar rusconirusconi#Set your paths here. ZLIB_PATH = ./src/zLib-1.2.5 MZPARSER_PATH = ./src/mzParser EXPAT_PATH = ./src/expat-2.0.1 SQLITE_PATH = ./src/sqlite-3.7.7.1 MST_PATH = ./src/MSToolkit HEADER_PATH = ./include MZPARSER = mzp.MSNumpress.o mzp.mzp_base64.o mzp.BasicSpectrum.o mzp.mzParser.o mzp.RAMPface.o mzp.saxhandler.o mzp.saxmzmlhandler.o \ mzp.saxmzxmlhandler.o mzp.Czran.o mzp.mz5handler.o mzp.mzpMz5Config.o mzp.mzpMz5Structs.o mzp.BasicChromatogram.o mzp.PWIZface.o MZPARSERLITE = mzp.MSNumpress.o mzp.mzp_base64_lite.o mzp.BasicSpectrum_lite.o mzp.mzParser_lite.o mzp.RAMPface_lite.o mzp.saxhandler_lite.o mzp.saxmzmlhandler_lite.o \ mzp.saxmzxmlhandler_lite.o mzp.Czran_lite.o mzp.mz5handler_lite.o mzp.mzpMz5Config_lite.o mzp.mzpMz5Structs_lite.o mzp.BasicChromatogram_lite.o mzp.PWIZface_lite.o EXPAT = xmlparse.o xmlrole.o xmltok.o ZLIB = adler32.o compress.o crc32.o deflate.o inffast.o inflate.o infback.o inftrees.o trees.o uncompr.o zutil.o MSTOOLKIT = Spectrum.o MSObject.o READER = MSReader.o READERLITE = MSReaderLite.o SQLITE = sqlite3.o CC = g++ GCC = gcc NOSQLITE = -D_NOSQLITE CFLAGS = -O3 -static -I. -I$(HEADER_PATH) -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DGCC -DHAVE_EXPAT_CONFIG_H LIBS = -lm -lpthread -ldl all: $(ZLIB) $(MZPARSER) $(MZPARSERLITE) $(MSTOOLKIT) $(READER) $(READERLITE) $(EXPAT) $(SQLITE) ar rcs libmstoolkitlite.a $(ZLIB) $(EXPAT) $(MZPARSERLITE) $(MSTOOLKIT) $(READERLITE) ar rcs libmstoolkit.a $(ZLIB) $(EXPAT) $(MZPARSER) $(MSTOOLKIT) $(READER) $(SQLITE) # $(CC) $(CFLAGS) MSTDemo.cpp -L. -lmstoolkitlite -o MSTDemo $(CC) $(CFLAGS) -I./include MSSingleScan/MSSingleScan.cpp -L. -lmstoolkitlite -o msSingleScan # $(CC) $(CFLAGS) MSConvertFile.cpp -L. -lmstoolkitlite -o MSConvertFile lite: $(ZLIB) $(MZPARSERLITE) $(MSTOOLKIT) $(READERLITE) $(EXPAT) ar rcs libmstoolkitlite.a $(ZLIB) $(EXPAT) $(MZPARSERLITE) $(MSTOOLKIT) $(READERLITE) $(CC) $(CFLAGS) -I./include MSSingleScan/MSSingleScan.cpp -L. -lmstoolkitlite -o msSingleScan clean: rm -f *.o libmstoolkitlite.a libmstoolkit.a msSingleScan # zLib objects adler32.o : $(ZLIB_PATH)/adler32.c $(GCC) $(CFLAGS) $(ZLIB_PATH)/adler32.c -c compress.o : $(ZLIB_PATH)/compress.c $(GCC) $(CFLAGS) $(ZLIB_PATH)/compress.c -c crc32.o : $(ZLIB_PATH)/crc32.c $(GCC) $(CFLAGS) $(ZLIB_PATH)/crc32.c -c deflate.o : $(ZLIB_PATH)/deflate.c $(GCC) $(CFLAGS) $(ZLIB_PATH)/deflate.c -c inffast.o : $(ZLIB_PATH)/inffast.c $(GCC) $(CFLAGS) $(ZLIB_PATH)/inffast.c -c inflate.o : $(ZLIB_PATH)/inflate.c $(GCC) $(CFLAGS) $(ZLIB_PATH)/inflate.c -c infback.o : $(ZLIB_PATH)/infback.c $(GCC) $(CFLAGS) $(ZLIB_PATH)/infback.c -c inftrees.o : $(ZLIB_PATH)/inftrees.c $(GCC) $(CFLAGS) $(ZLIB_PATH)/inftrees.c -c trees.o : $(ZLIB_PATH)/trees.c $(GCC) $(CFLAGS) $(ZLIB_PATH)/trees.c -c uncompr.o : $(ZLIB_PATH)/uncompr.c $(GCC) $(CFLAGS) $(ZLIB_PATH)/uncompr.c -c zutil.o : $(ZLIB_PATH)/zutil.c $(GCC) $(CFLAGS) $(ZLIB_PATH)/zutil.c -c #mzParser objects mzp.%.o : $(MZPARSER_PATH)/%.cpp $(CC) $(CFLAGS) $(MZ5) $< -c -o $@ #mzParserLite objects mzp.%_lite.o : $(MZPARSER_PATH)/%.cpp $(CC) $(CFLAGS) $< -c -o $@ #expat objects xmlparse.o : $(EXPAT_PATH)/xmlparse.c $(GCC) $(CFLAGS) $(EXPAT_PATH)/xmlparse.c -c xmlrole.o : $(EXPAT_PATH)/xmlrole.c $(GCC) $(CFLAGS) $(EXPAT_PATH)/xmlrole.c -c xmltok.o : $(EXPAT_PATH)/xmltok.c $(GCC) $(CFLAGS) $(EXPAT_PATH)/xmltok.c -c #SQLite object sqlite3.o : $(SQLITE_PATH)/sqlite3.c $(GCC) $(CFLAGS) $(SQLITE_PATH)/sqlite3.c -c #MSToolkit objects Spectrum.o : $(MST_PATH)/Spectrum.cpp $(CC) $(CFLAGS) $(MST_PATH)/Spectrum.cpp -c MSReader.o : $(MST_PATH)/MSReader.cpp $(CC) $(CFLAGS) $(MZ5) $(MST_PATH)/MSReader.cpp -c MSReaderLite.o : $(MST_PATH)/MSReader.cpp $(CC) $(CFLAGS) $(NOSQLITE) $(MST_PATH)/MSReader.cpp -c -o MSReaderLite.o MSObject.o : $(MST_PATH)/MSObject.cpp $(CC) $(CFLAGS) $(MST_PATH)/MSObject.cpp -c libmstoolkit-77.0.0/MSSingleScan/0000755000175000017500000000000012455161024016535 5ustar rusconirusconilibmstoolkit-77.0.0/MSSingleScan/MSSingleScan.vcproj0000644000175000017500000001023212455161024022246 0ustar rusconirusconi libmstoolkit-77.0.0/MSSingleScan/MSSingleScan.cpp0000644000175000017500000000333112455161024021527 0ustar rusconirusconi#include #include #include #include "MSToolkitTypes.h" #include "MSReader.h" #include "MSObject.h" #include "Spectrum.h" using namespace std; using namespace MSToolkit; int main(int argc, char *argv[]){ //Here are all the variable we are going to need MSReader r; Spectrum s; int j; if(argc==1){ printf("DESCRIPTION: Reads an MS/MS spectrum from any MSToolkit supported file type and outputs to screen in MS2 format.\n\n"); printf("USAGE: MSSingleScan [scan number] [file]\n"); exit(0); } r.setFilter(MS1); r.addFilter(MS2); r.addFilter(MSX); r.addFilter(SRM); char nativeID[256]; r.readFile(argv[2],s,atoi(argv[1])); if(s.getScanNumber()==0) exit(-1); char szNativeID[128]; if (s.getNativeID(szNativeID, 128)) printf("success: scan %d nativeID: %s\n", s.getScanNumber(), szNativeID); else printf("failure: scan %d\n", s.getScanNumber()); s.getNativeID(nativeID, 256); printf("%s\n",nativeID); printf("S\t%d\t%d",s.getScanNumber(),s.getScanNumber()); for(j=0;j0) printf("I\tRTime\t%.*f\n",4,s.getRTime()); //printf("I\tConvA\t%.6lf\n",s.getConversionA()); //printf("I\tConvB\t%.6lf\n",s.getConversionB()); //printf("I\tConvC\t%.6lf\n",s.getConversionC()); //printf("I\tConvD\t%.6lf\n",s.getConversionD()); //printf("I\tConvE\t%.6lf\n",s.getConversionE()); //printf("I\tConvI\t%.6lf\n",s.getConversionI()); for(j=0;j