fpeakfile.h

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#ifndef _FPEAKFILE_H_
#define _FPEAKFILE_H_

/* Copyright (c) Kyriacos Leptos and the President and Fellows of Harvard University
   Release Date: 2004-11-01
   Part of the MapQuant suite library "massspec.lib" 
*/

struct FPeakFile
{
    unsigned int state: 2;
    unsigned int isMultiple: 1; // added 2004-06-14

    FILE*    pFPeakFile;
    fpos_t   datastart;
    fpos_t   curr_pos;

    // *****************************************************
    // ******** Universal Processing Identifiers ***********
    // *****************************************************

    // MQExperiment pointer
    // MQExperiment's name
    // Rectangle  within experiment
    // Processing script
    // Processing script's name

    char*       szPathname;
    char*       szName;
    char*       szSession;
    char*       szNameInSession;

    char*       szSourceMapSubID;
    char*       szMaskMapSubID;

    MQExperiment*   expmnt;
    // char* szExpName  *** NOT IMPLEMENTED ***

    Rectangle4i borders;
    
    // Processing Script
    char*           ps;
    ProcScript      procscript;
    
    // ******************************************************
    // ********* END OF UNIVERSAL PROCESSING IDENTIFIERS ****
    // ******************************************************

    int         curve;

    Map2DPosition*      pFPeakPositions;

    FPeak2i*            pFPeaks;
    int                 nFPeaks;
    int                 nCurrFPeak;

    int                 nFPeaksCutoff;

    struct Segment* pSegments;

    int         nSegments;
    int         nCurrSegment;

    int         nSkippedSegment;
    
};

typedef struct FPeakFile FPeakFile;

int         FPeakFile_load(char* szFilename, FPeakFile *file);
int         FPeakFile_sntLoad(FPeakFile* file,  MQExperiment* expmnt, 
                                                char* session, 
                                                char* name, char* tile);


int         FPeakFile_populateNextSegment(FPeakFile* file);
void        FPeakFile_initIterator(FPeakFile* file);
Segment*    FPeakFile_getNextSegment(FPeakFile* file);

int         FPeakFile_querySegment(char* szFilename, int scan, int bin);



void        FPeakFile_destroy(FPeakFile* file);
int         FPeakFile_countSegments(FPeakFile* file);
void        FPeakFile_init(FPeakFile* file);
void        FPeakFile_fprintStatusTypes(FILE* fp);
void        FPeakFile_fprintHeader2(FILE* fp, FPeakFile* file);
void        FPeakFile_fprintHeader(FILE* fp, char *experiment,
                                      Rectangle4i *rect, 
                                      ProcScript  *PS,
                                      char* source_map_subid,
                                      char* mask_map_subid,
                                      int nSegments,
                                      char* curve,
                                      int npeaks_cutoff);
void        FPeakFile_fprintSegment(FILE* fp, Segment* segment, int index, int ismulti);

FPeak2i*    FPeakFile_getFPeak2iArray(FPeakFile fpkfile, int* nFPeaks);
Peak2f*     FPeakFile_getPeak2fArray(FPeakFile* fpkfile, int* nFPeaks);

int* getSkippedLabels(char* szPath, char* szFilename, int* nsize);

struct Segment MQExperiment_getSegment(MQExperiment expmnt, char* szSession, int nSegment);
struct Segment FPeakFile_getSegment(FPeakFile fpkfile, char* szSession, int nSegment);

void FPeakFile_tile(FPeakFile* fpk, char* fullname);

/* Querying FPeak2iFile */

#endif

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