proteome/speptide.h

#ifndef _SPEPTIDE_H_
#define _SPEPTIDE_H_

struct SPeptide
{
        float mw;
        int       aminoacid_start;
        int       aminoacid_stop;
        int   proteinID;
};

typedef struct SPeptide SPeptide;

int             loadSPeptideLibrary(char* name, SPeptide** speplib);
void    loadPeptideLibraryFromFile(PeptideLibrary* library, char* peplibname);
void    sortSPeptideLibraryByMW(SPeptide* peptideLibrary, long nSizePepLib);
void    printSPeptideLibrary(SPeptide* peptideLibrary, long nSizePepLibrary);
void    printSPeptide(SPeptide spep);
void    fprintSPeptide(FILE* fp, SPeptide spep);


long    createSPeptideLibrary   (char pep[], 
                                                                 int nProteinIndex, 
                                                                 SPeptide** peptideLibrary, long* nSizePepLibrary);
long    createSPeptideLibraryFromString(char pep[], 
                                                                                int nProteinIndex, SPeptide** peptideLibrary, long* nSizePepLibrary, int options);

int             createSPeptideLibraryFromProteinList(char* szProteinListName, SPeptide** peptideLibrary, long* nSizePepLibrary);

void            printSPeptideLibraryField(SPeptide* peptideLibrary, long nSizePepLibrary, int field);
char*           SPeptide_getSequence(SPeptide* spep, LProtein* library);


SPeptide*       SPeptideArray_createFromLProteinArray(LProtein*  proteinLibrary, int   nProteins, long* nPeptides);
SPeptide*       SPeptideArray_createFromString  (char protein[], int nProteinIndex, long* nSizePepLibrary, int skipped_sites);
SPeptide*       SPeptideArray_createFromString_MWLimits_NoEnzyme(char protein[], int nProteinIndex, long* nSizePepLibrary, float min_mw, float max_mw);

int             SPeptideArray_appendTo(SPeptide* peptideLibrary, long MAX_SIZE, long* nCurrentAvailableIndex, char protein[], int nProteinIndex);

#include "speptide_array_search.h"

#endif

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