isotopiccluster.h

#ifndef _ISOTOPIC_CLUSTER_H_
#define _ISOTOPIC_CLUSTER_H_

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

#define CARBON_RICH 16.34
#define CARBON_POOR 34.34

#define ISOTOPIC_CLUSTER_ARRAY_FITTED_MAX_SIZE 5


extern int ISOTOPIC_CLUSTER_ARRAY_MAX_SIZE;

extern int ISOCLUSTER_SCORE_RT_SD_WIDTH;
extern int ISOCLUSTER_SCORE_RT_SD_DECIMAL_PLACES;

extern int ISOCLUSTER_SCORE_DELTA_MZ_SD_WIDTH;
extern int ISOCLUSTER_SCORE_DELTA_MZ_SD_DECIMAL_PLACES;

extern int ISOCLUSTER_SCORE_DELTA_MZ_WIDTH;
extern int ISOCLUSTER_SCORE_DELTA_MZ_DECIMAL_PLACES;

extern int ISOCLUSTER_SCORE_NORM_ABU_WIDTH;
extern int ISOCLUSTER_SCORE_NORM_ABU_DECIMAL_PLACES;

struct IsotopicCluster
{
    unsigned            isSubset: 1;
    
    unsigned int        isValid;

    char*               szSession;
    int                 peakgroup;

    int                *index_array;
    FPeak2iPointer     *pPFPeaks;       //Array of pointers of FPeak
    FPeak2i            *pFPeaks;
    int                 nFPeaks;
    
    int                *zarray;

    float               dCharge;

    float               ab_avg;
    float               norm_abu;

    float               rt_avg;
    float               rt_sd;

    float               mz_avg;

    float               delta_mz_avg;
    float               delta_mz_sd;
    float               delta_mz_score;

    int                 ncupper;
    int                 nclower;
    int                 ncarbons;       
    int                 mip;
    float               dev;

    float               score;
};

typedef struct IsotopicCluster IsotopicCluster;

typedef IsotopicCluster* IsotopicClusterPointer;

int                     findSubsetClusters(PeakGroup* PG);
int                     isClusterSubsetOfSubset(IsotopicCluster IC1, IsotopicCluster IC2);
int                     doesFPeak2iBelongToCluster(FPeak2iPointer pfpeak, IsotopicCluster IC);

// Enumeration of properties

#define IC_NPEAKS           0x00000001
#define IC_ABUNDANCE        0x00000002
#define IC_CHARGE           0x00000004
#define IC_PEAKGROUP        0x00000008
#define IC_CARBONS          0x00000010
#define IC_FUNDAMENTAL      0x00000020
#define IC_PRIMARY_PEAK2I   0x00000040
#define IC_RT               0x00000080
#define IC_MS2              0x00000100
#define IC_SCORE            0x00000200
#define IC_MZ               0x00000400

enum {ISOTOPIC_CLUSTER_FORMAT_TABLE, ISOTOPIC_CLUSTER_FORMAT_WITH_HEADER};

void IsotopicCluster_destroy(IsotopicCluster *cluster);
void IsotopicCluster_fprint(FILE* fp, IsotopicCluster* cluster, int index, int format);
void IsotopicCluster_init       (IsotopicCluster* isc, int npeaks);

int IsotopicCluster_cmpByCharge       (const void *p1, const void *p2);
int IsotopicCluster_cmpByRT           (const void *p1, const void *p2);
int IsotopicCluster_cmpByMZ           (const void *p1, const void *p2); 
int IsotopicCluster_cmpByAbundance    (const void *p1, const void *p2);
int IsotopicCluster_cmpByNPeaks       (const void *p1, const void *p2);
int IsotopicCluster_cmpByPrimaryPeak2i(const void *p1, const void *p2);
int IsotopicCluster_cmpByScore        (const void *p1, const void *p2);

int     IsotopicCluster_calcCarbonBounds(IsotopicCluster* cluster);
void    IsotopicCluster_calcRT(IsotopicCluster* IC);
void    IsotopicCluster_calcDeltaMZ (IsotopicCluster* IC);
void    IsotopicCluster_calcTotalAbu(IsotopicCluster* IC);
float   IsotopicCluster_calcAvgSigmaMZ(IsotopicCluster* IC);

void    IsotopicCluster_setPeakGroup(IsotopicCluster* ic, int peakgroup);
void    IsotopicCluster_fixCharge(IsotopicCluster* IC, int charge);
void    IsotopicCluster_createFromFPeak2i(IsotopicCluster* IC, FPeak2i* pFPeak);

void    IsotopicCluster_rectangleQuantitation(IsotopicCluster* ic, Map2D* map, Rectangle4i rect);

int     IsotopicClusterPointer_cmpByPrimaryPeak2i(const void *p1, const void *p2);
void    IsotopicClusterPointerArray_sortByPrimaryPeak2i(IsotopicClusterPointer* ICPArray, int nicp);

#endif

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