massspec/isocluster.h

#ifndef _ISOCLUSTER_H_
#define _ISOCLUSTER_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 CARBON_RICH     16.34
#define CARBON_POOR     34.34

#define MAX_NO_MS2_SCANS_PER_PEAK 50

extern int ISOCLUSTER_SCORE_RT_SD_WIDTH;
extern int ISOCLUSTER_SCORE_DELTA_MZ_SD_WIDTH;
extern int ISOCLUSTER_SCORE_RT_SD_DECIMAL_PLACES;
extern int ISOCLUSTER_SCORE_DELTA_MZ_SD_DECIMAL_PLACES;

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

        char*                           szSession;
        int                                     peakgroup;
        int                                     fpeak;

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

        float                           dCharge;

        float                           ab_avg;
        float                           ab_sd;

        float                           rt_avg;
        float                           rt_sd;

        float                           mz_avg;
        float                           mz_sd;

        float                           delta_mz_avg;
        float                           delta_mz_sd;

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


        Experiment*                     ms2exp;
        int                                     ms2indices[MAX_NO_MS2_SCANS_PER_PEAK+1];        
};

typedef struct ISOTOPIC_CLUSTER ISOTOPIC_CLUSTER;
typedef ISOTOPIC_CLUSTER IsotopicCluster;
typedef IsotopicCluster* IsotopicClusterPointer;

int                                             findSubsetClusters(PeakGroup* PG);
int                                             isClusterSubsetOfSubset(ISOTOPIC_CLUSTER IC1, ISOTOPIC_CLUSTER IC2);
int                                             doesFPeak2iBelongToCluster(FPeak2iPointer pfpeak, ISOTOPIC_CLUSTER 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_NPEAKS_SD            0x00000200
#define IC_MZ                           0x00000400

enum {IC_TABLE, IC_WITH_HEADER};

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_cmpByNPeaksSD         (const void *p1, const void *p2);

void IsotopicClusterArray_sortByField(ISOTOPIC_CLUSTER *ICArray, int nic, int field);

int     cmpIsotopicClusterPointerByPrimaryPeak2i(const void *p1, const void *p2);

void                                    sortIsotopicClusterPointerArrayByPrimaryPeak2i(IsotopicClusterPointer* ICPArray, int nicp);
void                                    IsotopicCluster_destroy(ISOTOPIC_CLUSTER *cluster);
void                                    IsotopicCluster_fprint     (FILE* fp, int index, ISOTOPIC_CLUSTER cluster,   int format);
void                                    IsotopicCluster_init            (IsotopicCluster* isc, int npeaks);
void                                    IsotopicClusterArray_fprint(FILE* fp, ISOTOPIC_CLUSTER *clusters, int nclusters, int format);
void                                    IsotopicClusterArray_fprintWithIndex(FILE* fp, ISOTOPIC_CLUSTER *clusters, int nclusters, int start_index);
IsotopicCluster*                IsotopicClusterArray_convertFromPeakGroupFile(PeakGroupFile* file, RestrictionStatistics* pRestr, int nRestr, int *nIsoclusters);

void                                    IsotopicClusterArray_destroy(ISOTOPIC_CLUSTER **cluster,  int nclusters);
IsotopicClusterPointer* createIsoclusterPointerArrayFromPeakGroupFile(PEAK_GROUP_FILE PGF, int* nicp);

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

void IsotopicCluster_setPeakGroup(IsotopicCluster* IC, int peakgroup);
float guessAbundance(IsotopicCluster* ic, int index);

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

IsotopicCluster* IsotopicClusterArray_create(int size);
IsotopicCluster* IsotopicClusterArray_linkMS2Scans(IsotopicCluster* ica, int* nIsoclusters, Map2D* map);
void IsotopicCluster_rectangleQuantitation(IsotopicCluster* ic, Map2D* map, Rectangle4i rect);

void tprintIC(FILE* fp, IsotopicCluster* ic, int nsize);

int FPeak2iArray_getHighestScoringIsotopicCluster(FPeak2i* pArray, int nArray, 
                                                                                                  IsotopicCluster* out);

#endif

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