peakgroup.h

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#ifndef _PEAK_GROUP_H_
#define _PEAK_GROUP_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" 
*/

enum {  PEAKGROUP_FORMAT_WITH_CURVE         = 0x00000001,
        PEAKGROUP_FORMAT_WITH_POSITION      = 0x00000002,
        PEAKGROUP_FORMAT_VALID_ONLY         = 0x00000004,
        PEAKGROUP_FORMAT_WITH_FITTING_PARAM = 0x00000008
};

extern int PEAKGROUP_INDEX_WIDTH;

struct PeakGroup
{
    unsigned                    isValid: 1;
    unsigned                    isFitted: 1;

    int                         nIndex;
    int                         rti;
    
    FPeak2i*                    pFPeaks;

    FPeak2iPointer*             pfpeaks;            //Array of pointers of FPeak
    int                         npeaks;

    Map2DPositionPointer*       pPFPeakPosition;
    int                         nPositions;
    
    struct IsotopicCluster*     IC;
    int                         nic;
    

    int                 nSegments;
    
    MQTileID*           pTileArray;
    int                 nTiles;

    // Fitting arguments
    float               dChiSqr;
    int                 nIter;
    int                 nStatus;
    float               dAreaPeakGroupMap;
    float               dNumberOfSeconds;
};

typedef struct PeakGroup PeakGroup;
typedef PeakGroup PEAK_GROUP;

#define MAX_NO_PG_FPEAKS 1000

// ***************************************************
// *************** PeakGroup Functions ***************
// ***************************************************

void            PeakGroup_destroy           (PeakGroup* peakgroup);
PeakGroup       PeakGroup_copy              (PeakGroup *peakgroup);
void            PeakGroup_init              (PeakGroup* pg);

void            PeakGroup_fprintf           (FILE* fp, PeakGroup* peakgroup, int index, int format);
void            PeakGroup_fprint            (FILE* fp, PeakGroup* peakgroup, int index);
void            PeakGroup_fprintWithCurve   (FILE* fp, PeakGroup* peakgroup, int index);
void            PeakGroup_fprintWithPos     (FILE* fp, PeakGroup* peakgroup, int index);

int             PeakGroup_cmpByTiles(const void *p1, const void *p2);
int             PeakGroup_cmpByNPeaks(const void *p1, const void *p2);

void            PeakGroup_sortFPeaksByMOZ(PeakGroup *peakgroup);
void            PeakGroup_createFromFPeak2iArray      (PeakGroup* PG, FPeak2i* pFPeaks, int size);
Rectangle4i     PeakGroup_getBoundaries(PEAK_GROUP PG);
MQTileID PeakGroup_getSmallestTile(PeakGroup* peakgroup);
int PeakGroup_countSegmentsFromTile(PeakGroup* peakgroup, MQTileID bTile);
int             PeakGroup_isPeak2iInPeakGroup         (PeakGroup  PG, int scan, int bin);


Peak2i*  SegmentArray_getPeaksNotInPeakGroup  (Segment* pSegments, int nSegments, 
                                               PeakGroup peakgroup, 
                                               int* nPeaks);

FPeak2i* SegmentArray_getFPeaksNotInPeakGroupUsingIndexArray(Segment* pSegmentArray, int* index_array, int nSegments, 
                                                            PeakGroup peakgroup, 
                                                            int* nPeaks);

Map2DPositionPointer*   PeakGroup_getMap2DPositionPointerArray(PeakGroup* pg);

// edited 2004-07-28

int* PeakGroup_getSpanningSegmentIndexArrayUsingLabeledMap(PeakGroup* peakgroup, 
                                                           Map2D* mask, 
                                                           int* nSegments);

int* PeakGroup_getSpanningSegmentIndexArrayUsingSegmentArray(   PeakGroup* peakgroup, 
                                                                Segment*   pSegmentArray, int nSegmentArray,
                                                                int* nSegments);

int  PeakGroup_getSpanningMapFPeaks(PeakGroup* peakgroup, Segment* psegments, int nsegments, FPeak2i* pfpeaks, int *nfpeaks);

int         PeakGroup_countSpanningTiles(PeakGroup* peakgroup);
int         PeakGroup_getTileArray(PeakGroup* peakgroup);
//void      PeakGroup_getSmallestTile   (PeakGroup* peakgroup);


#endif 

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