sequence/ms_ms_spectrum_header.h

#ifndef _MS_MS_SPEC_HEADER_H_
#define _MS_MS_SPEC_HEADER_H_


enum {MS2_SCAN, MS2_PARENT_SCAN, MS2_PARENT_MOZ};

struct MS_MS_SpectrumHeader
{
        unsigned                        isEmpty :1;
        unsigned                        hasScored :1;   
        
        int                                     scan;
        int                                     nSize;
        LPeak2f                         parent;

        int                                     nParentScan;
        float                           dParentRT;
        float                           dParentMOZ;
        
        float                           dBasepeak;      
        float                           dTIC;
        struct Experiment       *expmnt;
} ;

typedef struct MS_MS_SpectrumHeader MS_MS_SpectrumHeader;


int                                       MSMSSpectrumHeader_loadUsingPath(MS_MS_SpectrumHeader* sh, char* path_name,  char* file_name);
MS_MS_SpectrumHeader* MSMSSpectrumHeaderArray_load(char* filename, int* nscans);

void MSMSSpectrumHeader_init(MS_MS_SpectrumHeader* sh, short empty, 
                                                                                                           short scored, 
                                                                                                           int   scan, 
                                                                                                           int   parentscan, 
                                                                                                                 float parentrt, 
                                                                                                                 float parentmoz, 
                                                                                                                 int   nsize,
                                                                                                                 float basepeak,
                                                                                                                 float dTIC);


void    MSMSSpectrumHeader_fprint(FILE* fp, MS_MS_SpectrumHeader sh);

// ARRAY FUNCTIONS
MS_MS_SpectrumHeader* MSMSSpectrumHeaderArray_create(int size);
IndexArray   MSMSSpectrumHeaderArray_getIndicesOfScansInRect(MS_MS_SpectrumHeader* ms2array, int size, Rectangle4i rect);
void    MSMSSpectrumHeaderArray_fprint(FILE* fp, MS_MS_SpectrumHeader* MSMSARRAY, int start, int stop);
int*    MSMSHeaderArray_getFieldArrayFromIndexArray(MS_MS_SpectrumHeader* array, 
                                                                                                        int* index_array, 
                                                                                                        int npeaks,
                                                                                                        int field);


void MSMSSpectrumHeaderArray_fprintAsTabDelimitedTable(FILE* fp, MS_MS_SpectrumHeader* MSMSARRAY, int start, int stop);

void    MSMSSpectrumHeaderArray_sortByParentMOZ(MS_MS_SpectrumHeader* msmsarray, long nPeaks);
char**  MSMSSpectrumHeaderArray_toStringArray(MS_MS_SpectrumHeader* ms2array, int size, const char* format, int field);

struct Peak2i* MSMSHeaderArray_getPeak2iArray(MS_MS_SpectrumHeader* array, int size);

struct Peak2f* MSMSHeaderArray_getMS2Peaks2fForMassChrom(struct Experiment expmnt, struct Map2D* map, int bin, int* nPeaks);

#endif

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