trace.c File Reference

#include <stdio.h>
#include "seqaln.h"

Defines
#define	append_score(X, Y)
#define	scandiag()
Functions
void	scanup ()
void	scanleft ()
void	trace (struct SEQALN_SEQUENCE *seq1, struct SEQALN_SEQUENCE *seq2, struct SEQALN_CONSTANTS *scoring, struct SEQALN_RESULTS *results, struct SEQALN_IO *io)

---

Define Documentation

#define append_score	(	X,
		Y		)

Value:

(scorel = \
        (SEQALN_TRACE *)newmem(1, sizeof(SEQALN_TRACE)), \
   scorel->i = i,                                   \
        scorel->j = j,                                   \
   scorel->next = results->trace,                   \
        results->trace = scorel)

 

#define scandiag

(

)

Value:

if ((!results->aligned || !results->aligned[i][j]) &&     \
      i>0 && j>0 && results->S[i][j]==results->S[i-1][j-1]+ \
           scoring->deltafn(seq1->code[i],seq2->code[j],scoring)){\
                results->align_len++; i--; j--; foundalign=1; }

---

Function Documentation

void scanleft

(

)

References nextj.

void scanup

(

)

References nexti.

void trace	(	struct SEQALN_SEQUENCE *	seq1,
		struct SEQALN_SEQUENCE *	seq2,
		struct SEQALN_CONSTANTS *	scoring,
		struct SEQALN_RESULTS *	results,
		struct SEQALN_IO *	io
	)

References SEQALN_RESULTS::align_len, SEQALN_RESULTS::aligned, SEQALN_CONSTANTS::alpha, append_score, SEQALN_RESULTS::bestS, SEQALN_RESULTS::bestSi, SEQALN_RESULTS::bestSj, SEQALN_CONSTANTS::beta, SEQALN_SEQUENCE::code, SEQALN_CONSTANTS::Debug, SEQALN_CONSTANTS::deltafn, SEQALN_CONSTANTS::envelope, FIT, GLOBAL, LOCAL, nexti, nextj, OVER, print_trace(), SEQALN_CONSTANTS::ptype, SEQALN_RESULTS::S, scandiag, scanleft, scanup, SEQALN_RESULTS::start1, SEQALN_RESULTS::start2, SEQALN_IO::STDERR, SEQALN_IO::STDOUT, SEQALN_RESULTS::trace, and SEQALN_CONSTANTS::traceupper.

Referenced by main(), dyaln::outputAln(), pvlocalS(), pvsrlocalS(), trrpt_alignment(), and mgsaln::while().