massspec/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

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

        float                           dVersion;

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

        char*                           szFPeakSource;                  // Filename of the fpeaks file that                                                                                     // was used int the clustring
        int                                     curve;
        
        PeakGroup*                      pPeakGroups;                    //Array of peak groups
        int                                     nPeakGroups;

        FPeak2i*                        pFPeaks;
        Map2DPosition*          pPositions;
        int                                     nFPeaks;

        // Algorithim related

        Clusterer                       clusterer;
        //Deconvolver                   deconv;

} PEAK_GROUP_FILE;

typedef 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, Experiment* epxmnt);
void PeakGroupFile_setSession(PeakGroupFile* pgf, char* session);

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_save(PeakGroupFile* pgf, char* szOutFilename);
int             PeakGroupFile_saveHeader(PeakGroupFile* pgf, char* filename, int pgf_type);

void PeakGroupFile_create                               (PeakGroupFile* pgf,            FPeakFile* fpkfile,             Clusterer* clust,
                                                                                                                                                                                PeakRestrictions* restr,
                                                                                                                                                                                int   nIsMultiple);
void PeakGroupFile_clusterEachPeakGroup (PeakGroupFile* pgf_out,        PeakGroupFile* pgf_in,  Clusterer* clust);

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

#endif 

---