peakgroupfile.h

#ifndef _PEAK_GROUP_FILE_H_
#define _PEAK_GROUP_FILE_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" 
*/

#define PEAK_GROUP_FILE_CURRENT_VERSION 2.0

struct PEAK_GROUP_FILE
{
    unsigned isMultiple     : 1;
    unsigned isTile         : 1;

    float               dVersion;

    MQExperiment*       experiment;
    char*               szSession;
    char*               szType;
    PeakRestrictions    restr;

    char*               ps;
    ProcScript          procscript;             // was used int the clustring
    int                 curve;
    
    PeakGroup*          pPeakGroups;            //Array of peak groups
    int                 nPeakGroups;

    FPeak2i*            pFPeaks;
    Map2DPosition*      pPositions;
    int                 nFPeaks;

    char*               szFPeakSource;          // Filename of the fpeaks file that 
    char*               szPeakGroupSource;      // Filename of the fpeaks file that 

    // Algorithim related

    float               dLinkageRTThreshold;
    float               dLinkageMZThreshold;

    MQTextFile          deconvolverBoundsFile;

    //MQClusterer           clusterer;
    //Deconvolver           deconv;

};

typedef struct PEAK_GROUP_FILE PeakGroupFile;

enum {PEAKGROUP_FILE_TYPE_PLAIN, PEAKGROUP_FILE_TYPE_DECONVOLVED};

void PeakGroupFile_init(PeakGroupFile* pgf);
void PeakGroupFile_destroy(PeakGroupFile* pgf);

void PeakGroupFile_setExperiment(PeakGroupFile* pgf, MQExperiment* epxmnt);
void PeakGroupFile_setSession(PeakGroupFile* pgf, char* session);
void PeakGroupFile_setProcScript(PeakGroupFile* pgf, char* string, ProcScript* script);
void PeakGroupFile_setZDeconvolverBounds(PeakGroupFile* pgf);
void PeakGroupFile_setSourceFiles(PeakGroupFile* pgf, char* szFPeakSource, char* szPeakGroupSource);

PeakGroup*  PeakGroupFile_getPeakGroupArray(PeakGroupFile pgr_file, int* nPeakGroups);
FPeak2i*    PeakGroupFile_getFPeak2iArray(PeakGroupFile pgr_file, int* nFPeaks);

int     PeakGroupFile_loadHeader(PeakGroupFile* pgf, char* szFilename);
int     PeakGroupFile_load(char* szFilename, PeakGroupFile* pgf);

void    PeakGroupFile_fprintHeader(FILE* fp, PeakGroupFile* pgf, int pgf_type);
void    PeakGroupFile_save(PeakGroupFile* pgf, char* szOutFilename);
int     PeakGroupFile_saveHeader(PeakGroupFile* pgf, char* filename, int pgf_type);

//void PeakGroupFile_create             (PeakGroupFile* pgf,        FPeakFile* fpkfile,     MQClusterer* clust,
//                                                                                      PeakRestrictions* restr,
//                                                                                      int   nIsMultiple);

//void PeakGroupFile_clusterEachPeakGroup   (PeakGroupFile* pgf_out,    PeakGroupFile* pgf_in,  MQClusterer* clust);

//void PeakGroupFile_createAndSaveUsingTiles(FPeakFile*     fpkfile, MQClusterer*       clust, int nIsMultiple);

#endif 

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