massspec/refiner.h

#ifndef _REFINER_
#define _REFINER_

/* 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" 
*/

struct Refiner
{
        PeakFinder              finder;
        char*                   szCurve;
        
        // location filter
        float                   NO_SD_MZ_WINDOW;
        int                             SCAN_WINDOW;

        float                   MZ_OVERLAP_THR;

        // size filter
        float                   dNoSDSizeFilter;

        float                   dAvgSigmaRT;
        float                   dSDSigmaRT;

        float                   dAvgSigmaMZ;
        float                   dSDSigmaMZ;
};

typedef struct Refiner Refiner;

extern RestrictionStatistics REFINER_SIGMA_MZ[MAX_NO_OF_STRING_NUMBERS + 1];

extern int REFINER_EVAL_SIGMA_MZ_SET;
extern int REFINER_SDEV_SIGMA_MZ_SET;
extern int REFINER_EVAL_SIGMA_RT_SET;
extern int REFINER_SDEV_SIGMA_RT_SET;

extern float EVAL_SIGMA_MZ;
extern float SDEV_SIGMA_MZ;     
extern float EVAL_SIGMA_RT;     
extern float SDEV_SIGMA_RT;

enum {  REFINER_EVAL_SIGMA_MZ_PARAMETER, 
                REFINER_SDEV_SIGMA_MZ_PARAMETER,
                REFINER_EVAL_SIGMA_RT_PARAMETER,
                REFINER_SDEV_SIGMA_RT_PARAMETER};

#define MQ_REFINING_STRING "--------------- REFINING PEAKGROUP ---------------\n"

int                     Refiner_init(Refiner* refiner);
void            Refiner_fprintf(FILE* fp, Refiner* refiner);
void            Refiner_setParameter(int parameter, float value);
Insets4f        Refiner_calculatePeakGroupBoundaries(Refiner* refiner, PeakGroup* peakgroup);
FPeakFilter Refiner_calculateSizeFilter(Refiner* refiner);

int Refiner_refinerPeakGroup7(Refiner* refiner,
                                                          PeakGroup* peakgroup,  Map2D* map, 
                                                          FPeak2i*   pFPeaksOut, int nFPeaksOut);

float   Map2D_subtractFPeak2i(Map2D* map, FPeak2i* fpeak);
float   Map2D_subtractFPeak2iArray(Map2D* map, FPeak2i* parray, int nsize);

void    FPeak2iArray_validatePositivePeaks(FPeak2i* array, int size);
int             FPeak2iArray_checkSize(FPeak2i* array, int size, Experiment* expmnt);
FPeak2i FPeak2iArray_popFirstValid(FPeak2i* pWorking, int nWorking);
void    FPeak2iArray_calcScanStat(FPeak2i* array, int size, float* scan_mean, float* scan_sd);
int             FPeak2i_isInsidePeakGroupBoundaries(FPeak2i* peak, Insets4f* peakgroup_boundaries);

void    PeakGroup_calcScanStat(PeakGroup* pg, float* scan_mean, float* scan_sd);

void    PeakGroup_validatePositivePeaks(PeakGroup* peakgroup);
float PeakGroup_calcAvgRTI(PeakGroup* pg);


/* ************ BELONGSTO FUNCTIONS *************** */

// peakgroup
int             Peak2i_belongsToPeakGroupStrict(Peak2i* peak  , PeakGroup* pg);
int             FPeak2i_belongsToPeakGroupStrict(FPeak2i* peak, PeakGroup* pg);
int             FPeak2i_belongsToPeakGroup(FPeak2i fpk, PeakGroup* pgr, int first_index, int last_index);

// fpeak pointer array
int             Peak2i_belongsToFPeak2iPointerArrayStrict (Peak2i*  peak, FPeak2iPointer* array, int npeaks);
int             FPeak2i_belongsToFPeak2iPointerArrayStrict(FPeak2i* peak, FPeak2iPointer* array, int npeaks);

// fpeak array
int             FPeak2i_belongsToFPeak2iArrayUsingRestrictions(FPeak2i* fpk, FPeak2i* array, int size, 
                                                                                                                int rti_thr, int mzj_thr);
int             FPeak2iArray_doesFPeak2iOverlap(FPeak2i* array, int size, FPeak2i* peak, float mz_thr);
int             FPeak2i_doesMassBinOverlapWithFPeak2iArray(FPeak2i* peak, FPeak2i* array, int size, int mass_bin_thr);

/* ************ REMOVE_FPEAKS_IN FUNCTIONS *************** */

void FPeak2iArray_removeFPeaksInIsocluster              (FPeak2i* pFPeaksAll, int* nFPeaksAll, IsotopicCluster* ic);
int      FPeak2iArray_removeFPeaksInPeakGroupLax        (FPeak2i* pFPeaksAll, int* nFPeaksAll, PeakGroup* peakgroup, int scan_thr);
int      FPeak2iArray_removeFPeaksInPeakGroupStrict     (FPeak2i* pFPeaksAll, int* nFPeaksAll, PeakGroup* peakgroup);

void FPeak2iArray_removePeaksWithNegativeParam(FPeak2i* array, int* npeaks);
void FPeak2i_fprintStat(FILE* fp);

#endif

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