sequence/sequest_summary_entry.h

#ifndef _SEQUEST_SUMMARY_ENTRY_H_
#define _SEQUEST_SUMMARY_ENTRY_H_

struct SequestSummaryEntry
{
        unsigned                                isValid:1;
        SequestScoringPeptide   ssp;
        DTAFile                                 dtafile;
};

typedef struct SequestSummaryEntry SequestSummaryEntry;

void                                    SequestSummaryEntry_init(SequestSummaryEntry* sse);
SequestSummaryEntry*    SequestSummaryEntry_createArray(int size);

void    SequestSummaryEntry_setScoringPeptide(SequestSummaryEntry* entry, SequestScoringPeptide* spep);
void    SequestSummaryEntry_setDTAFile(SequestSummaryEntry* entry, char* filename);
void    SequestSummaryEntry_fprint(FILE* fp, SequestSummaryEntry* sse, int index);

Peak2i  SequestSummaryEntry_getPeak2i(SequestSummaryEntry* sse, Experiment* q_expmnt);
Peak2f  SequestSummaryEntry_getRealPeak2f(SequestSummaryEntry* sse);
int             SequestSummaryEntry_getMS2EventBoundaryCoordinates(SequestSummaryEntry* sse, float* mz, float* rt_start, float* rt_stop);
Peak2f  SequestSummaryEntry_getMS2EventCoordinates(SequestSummaryEntry* sse, int x_axis_units);

int SequestSummaryEntry_cmpBySequenceAndCharge(const void *p1, const void *p2);
int SequestSummaryEntry_cmpByScanBoundsAndXCorr(const void *p1, const void *p2);

void SequestSummaryEntry_fprintWithMS2ToFPeak2iArrayUsingAligner(FILE* fp, 
                                                                                                                                 SequestSummaryEntry* sse, 
                                                                                                                                 MS2ToFPeak2i* ms2toms1, 
                                                                                                                                 float scale, int displacement);
 
void SequestSummaryEntry_fprintWithMS2ToFPeak2iArrayUsingCommonRTSampling(      FILE* fp, 
                                                                                                                                                        SequestSummaryEntry* sse, 
                                                                                                                                                        MS2ToFPeak2i* ms2toms1, 
                                                                                                                                                        Experiment* q_expmnt);

void SequestSummaryEntry_fprintTabDelimitedWithFPeak2iArrayUsingCommonRTSampling(       FILE* fp,
                                                                                                                                                                        SequestSummaryEntry* sse, 
                                                                                                                                                                        int index,
                                                                                                                                                                        MS2ToFPeak2i* ms2toms1, 
                                                                                                                                                                        Experiment* q_expmnt);

void SequestSummaryEntry_applyMZFilter(SequestSummaryEntry* entry, Insets4f* borders);
void SequestSummaryEntry_applyXCorrFilter(SequestSummaryEntry* entry, SequestXCorrFilter* filter);
void SequestSummaryEntry_populate(SequestSummaryEntry* entry, char* line);

void SequestSummaryEntry_fprintTabDelimitedWithFPeak2iArrayII(  FILE* fp,       
                                                                                                                                SequestSummaryEntry* sse, 
                                                                                                                                int index,
                                                                                                                                int x_axis_dimension_unit,
                                                                                                                                int y_axis_dimension_unit,
                                                                                                                                Peak2f* speak2f,
                                                                                                                                MS2ToFPeak2i* ms2toms1);

void SequestSummaryEntry_fprintTabDelimitedWithFPeak2iArrayIII( FILE* fp,       
                                                                                                                                SequestSummaryEntry* sse, 
                                                                                                                                int index,
                                                                                                                                int x_axis_dimension_unit,
                                                                                                                                int y_axis_dimension_unit,
                                                                                                                                Peak2f* speak2f,
                                                                                                                                MS2ToFPeak2i* ms2toms1);

// 1. DTA
// 2. MH+
// 3. XCorr
// 4. dCn
// 5. ProtName
// 6. PepSeq

#define SEQUEST_SUMMARY_FILE_DTA_FILE_COLUMN    1
#define SEQUEST_SUMMARY_FILE_MH_COLUMN                  2
#define SEQUEST_SUMMARY_FILE_XCORR_COLUMN               3
#define SEQUEST_SUMMARY_FILE_DCN_COLUMN                 4
#define SEQUEST_SUMMARY_FILE_PROT_NAME_COLUMN   5
#define SEQUEST_SUMMARY_FILE_PEP_SEQ_COLUMN             6

#endif

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