helper.h

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#ifndef HELPER_H
#define HELPER_H
// helper functions for sequence alignments

#include "seqaln.h"

/* convert integer code to char with the fomular
 * int + 'A'
 */
void code2seq(struct SEQALN_SEQUENCE *seq);
/* non-matrix based comparison 
 * return match and mismatch scores repectively, depnding
 * on the a == b or not*/
int delta(char a, char b, struct SEQALN_CONSTANTS *scoring);
/* for matrix look up
 * use a<<5 + b to find the element faster
 * each row has 32 elements, this is faster
 */
int mdelta(char a, char b, struct SEQALN_CONSTANTS *scoring);
int pdelta(int a, char b, struct SEQALN_PROFILE *pro);
int gap(int k, struct SEQALN_CONSTANTS *scoring);
int pgap(int k, struct SEQALN_PROFILE *pro);
int revcomp(struct SEQALN_SEQUENCE *seq);
int revseq(struct SEQALN_SEQUENCE *seq);
int compseq(struct SEQALN_SEQUENCE *seq);
void rpt_version(char *prog, struct SEQALN_IO *io);
void reverse_list(SEQALN_TRACE **list);
void memfree(struct SEQALN_SEQUENCE *seq1, struct SEQALN_SEQUENCE *seq2, 
                 struct SEQALN_CONSTANTS *scoring, struct SEQALN_RESULTS *results,
                struct SEQALN_IO *io);
/*
   Header file for codon to protein translation, from the USC sequence
   alignment library.
   Paul Hardy, USC, November 1996
*/
//char nuc2prot[64]={ /* AAA */  'K', /* AAC */  'N', /* AAG */  'K',
//     /* AAU */  'N', /* ACA */  'T', /* ACC */  'T', /* ACG */  'T',
//     /* ACU */  'T', /* AGA */  'R', /* AGC */  'S', /* AGG */  'R',
//     /* AGU */  'S', /* AUA */  'I', /* AUC */  'I', /* AUG */  'M',
//     /* AUU */  'I', /* CAA */  'Q', /* CAC */  'H', /* CAG */  'Q',
//     /* CAU */  'H', /* CCA */  'P', /* CCC */  'P', /* CCG */  'P',
//     /* CCU */  'P', /* CGA */  'R', /* CGC */  'R', /* CGG */  'R',
//     /* CGU */  'R', /* CUA */  'L', /* CUC */  'L', /* CUG */  'L',
//     /* CUU */  'L', /* GAA */  'E', /* GAC */  'D', /* GAG */  'E',
//     /* GAU */  'D', /* GCA */  'A', /* GCC */  'A', /* GCG */  'A',
//     /* GCU */  'A', /* GGA */  'G', /* GGC */  'G', /* GGG */  'G',
//     /* GGU */  'G', /* GUA */  'V', /* GUC */  'V', /* GUG */  'V',
//     /* GUU */  'V', /* UAA */  '*', /* UAC */  'Y', /* UAG */  '*',
//     /* UAU */  'Y', /* UCA */  'S', /* UCC */  'S', /* UCG */  'S',
//     /* UCU */  'S', /* UGA */  '*', /* UGC */  'C', /* UGG */  'W',
//     /* UGU */  'C', /* UUA */  'L', /* UUC */  'F', /* UUG */  'L',
//     /* UUU */  'F'};
int xlate(struct SEQALN_SEQUENCE *seq);
void freeTraceList(struct SEQALN_RESULTS *rslt);
#endif