tables/icpep_table.h

#ifndef _ICPEP_TABLE_H_
#define _ICPEP_TABLE_H_

#include "massspec/MS.rc.h"
#include "proteome/proteome.h"
#include "sequence/sequence.h"

typedef struct
{
        IsotopicCluster  ic;
        MassFilterResult mfr;
        MS2MatchResult   mmr;
} TableRow;

typedef struct 
{
        char* osp_format;
        int   ab_column;
        int   mz_column;
        int   rt_column;
        char* mfr_format;
        int   mfr_column;
        char* mmr_format;
        int   mmr_column;
} TableRowFormat;

typedef struct
{
        int nRowIndex;
        int nDTAIndex;
        int nSeqChargeIndex;
} TableIndices;


typedef struct
{
        DTAFile*                pDTAFile;
        TableIndices    indices;

} DTAFileToTableIndices;

typedef struct
{
        SequestScoringPeptide*  ssp;
        TableIndices                    indices;

} ScoringPeptideToTableIndices;


typedef struct
{
        TableRow*                                               pRows;  // starts with 1
        int                                                             nRows;
        DTAFileToTableIndices*                  DTA_INDICES;
        int                                                             nDTAIndices;
        ScoringPeptideToTableIndices*   SPEP_INDICES;
        int                                                             nPSEQIndices;

        unsigned char*                                  pFlags;

} PeptideTable;

enum {TB_IC, SEQ_IC, TABLE_TYPE_IC_MFR, TABLE_TYPE_IC_MMR};
enum {PEPTIDE_TABLE_QUERY_SSP, PEPTIDE_TABLE_QUERY_SSP_SEQ_ONLY};

TableRow*       PeptideTable_readFromFile(int* nRows, int table_type);

int                     PeptideTable_countRows(char* tb_filename);

void            PeptideTable_fprint(FILE* fp, TableRow* rows, int nsize);

void            PeptideTable_fprint_IC_MFR(FILE* fp, 
                                                                                IsotopicCluster* ic, 
                                                                                MassFilterResult* mfr, 
                                                                                int nsize,  int score_model);

void            PeptideTable_fprint_IC_MMR(FILE* fp, 
                                                                                 IsotopicCluster*  ic, 
                                                                                 MS2MatchResult*   mmr,
                                                                                 int nsize);

int                     PeptideTable_countDTAFiles(TableRow* rows, int nRows);

MS2MatchResult* PeptideTable_getMS2MatchPointer(PeptideTable table, int row);
IsotopicCluster* PeptideTable_getIsotopicClusterPointer(PeptideTable table, int row);

ScoringPeptideToTableIndices*   PeptideTable_createScoringPeptideIndex(PeptideTable table, int* nScoringPeptideIndices);
DTAFileToTableIndices*                  PeptideTable_createDTAFileIndex(PeptideTable table, int* nDTAIndices);
TableIndices*                                   PeptideTable_queryDTAFile(PeptideTable table, 
                                                                                                                  DTAFile query, 
                                                                                                                  int* nMatches);

void PeptideTable_queryScoringPeptide(PeptideTable table, 
                                                                                 SequestScoringPeptide* query, 
                                                                                 int nFlag,
                                                                                 TableIndices* indices,
                                                                                 int *nMatches);

void FPeak2iArray_fprintWithMassFilterResults(  FILE* fp, 
                                                                                                FPeak2i* peaks, 
                                                                                                MassFilterResult* mfr, 
                                                                                                int nsize);


#endif

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