trtrace.c File Reference

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

Defines
#define	append_score(X, Y)
#define	scandiag()
#define	scanup()
#define	scanleft()
Functions
void	trtrace (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->S[i][j] ==                                  \
                         results->S[i-1][j == 0 ? jmax : j-1] +               \
                         scoring->deltafn(seq1->code[i],                      \
                                   seq2->code[j+1],scoring)) &&               \
                       (!results->linbits || !results->linbits[i])) {         \
                       results->align_len++; i--;                             \
                       j = j==0 ? jmax : j-1;                                 \
                       foundalign=1; }

 

#define scanleft

(

)

Value:

if (j==0 && results->S[i][j] ==                       \
                        results->S[i][jmax] + scoring->alpha) { /* wrap */    \
                       j = jmax;                                              \
                       results->align_len++;                                  \
                       foundalign = 1;                                        \
                       }                                                      \
                     else if (j > 0 && results->S[i][j] ==                    \
                              results->S[i][j-1] + scoring->alpha) {          \
                       results->align_len++;                                  \
                       j--;                                                   \
                       foundalign = 1;                                        \
                       }

 

#define scanup

(

)

Value:

if (results->S[i][j] ==                               \
                        results->S[i-1][j] + scoring->alpha) {                \
                       results->align_len++; i--;                             \
                       foundalign = 1;  /* found a deletion */                \
                    }

---

Function Documentation

void trtrace	(	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_CONSTANTS::alpha, append_score, SEQALN_RESULTS::bestS, SEQALN_RESULTS::bestSi, SEQALN_RESULTS::bestSj, SEQALN_CONSTANTS::Debug, SEQALN_CONSTANTS::deltafn, SEQALN_CONSTANTS::envelope, nexti, nextj, print_trace(), SEQALN_RESULTS::S, scandiag, scanleft, scanup, SEQALN_IO::STDERR, SEQALN_IO::STDOUT, SEQALN_RESULTS::trace, and SEQALN_CONSTANTS::traceupper.

Referenced by main().