sequence/mass_filter_result.h

#ifndef _MASS_FILTER_RESULT_H_
#define _MASS_FILTER_RESULT_H_


extern char* CURR_RPEPTIDES_FILENAME;

#define MAX_MASS_FILTER_PEPTIDES 100

enum 
{       
                SEQUENCING_METHOD_SEQUEST,
                SEQUENCING_METHOD_AMT
};

typedef struct
{
        MassFilterPeptide* mfp_array;
        int                                nsize;
} MassFilterResult;

enum {MFR_WITHOUT_P_VAL, MFR_WITH_P_VAL}; 
enum {MFR_AMU_THRESHOLD, MFR_PPM_THRESHOLD}; 

typedef struct
{
        unsigned                flag: 1;
        unsigned                nThresholdType: 1; // 0 if in amu or 1 if in ppm

        int                             nMinCharge;
        int                             nMaxCharge;
        float                   dErrorAllowedMin;
        float                   dErrorAllowedMax;

        float*                  pModification;
        int                             nModification;

        PeptideLibrary  peplib;
        LProtein*               pProteinArray;
        SPeptide*               pSPeptideArray;
        int                             nSPeptideArray;

} MassFilterParam;

enum {MFR_DELTA_MZ, MFR_P_VAL, MFR_PPM};

MassFilterResult*       IsotopicClusterArray_getMassFilterResult
                                        (
                                                IsotopicCluster* IC, int nClusters, 
                                                MassFilterParam mfParam
                                        );

char* MassFilterPeptide_toString(MassFilterPeptide mfp, char* format, int score_model);

MassFilterResult*       FPeak2iArray_getMassFilterResult
                                        (
                                                FPeak2i* array, int nPeaks, 
                                                MassFilterParam* mfParam
                                        );

int             MassFilterResultArray_getForFPeak2iArray(MassFilterResult* mfr_array,   MassFilterParam* mfParam, FPeak2i* array, int nPeaks);
int             MassFilterResult_getForFPeak2i                  (MassFilterResult* mfr,                 MassFilterParam* mfParam, FPeak2i* peak);
int             MassFilterResult_getForMZAndZ                   (MassFilterResult* mfr,                 MassFilterParam* mfParam, float dMZ, int nZ);


void    MassFilterResult_fprintCommaDel(FILE* fp, MassFilterResult* mfr, int ncol);
MassFilterResult* MassFilterResultArray_create(int size);
void    MassFilterResultArray_fprintWithFPeak2iArray(   FILE* fp,
                                                                                                                MassFilterResult* mfr,
                                                                                                                LProtein* library,
                                                                                                                FPeak2i* peaks, 
                                                                                                                int nsize);

MassFilterResult* MassFilterResultArray_markUsingSequestMapQuantMapFile(SequestMapQuantMapFile* mqsqmapfile, FPeak2i* pFPeaks, int nFPeaks);

int                             RegressionParam_load(char* filename);
//void                  tprintIC2MFR(FILE* fp, IsotopicCluster* ic, MassFilterResult* mfr, int nsize, int flag);

#endif

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