#ifndef _SP_H_
#define _SP_H_

#define Nsp 3949


typedef struct SP {

	char* _seq;		// the amino acid sequence of the specific peptide
	int* _table;	// the KMP table
	int* _sr;		// the index of the sr where hit(s) of aSP where found
	int* _frame;	// the index of the frame of the sr where hit(s) of aSP where found
	int _length;	// size of the word (of the SP)
	int _count;		// how many times it appears


} SP;


// read the SPs file(s) and intialize the fields
void initSP(SP*, char**);
// take a word (SP, arg1) and create a Table for the KMP search (arg2)
void KMPTable (char* , int*, int);
// free the array of SPs
void freeSP(SP*);
// print stuff about the SPs
void printSP(SP*, char**);


#endif