trrpt_alignment.c File Reference

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

Defines
#define	align(i0, j0, i1, j1)
#define	delseq1(i0, j0, i1, j1)
#define	delseq2(i0, j0, i1, j1)   (i0 < i1 && j0 == j1)
#define	previ(i0)   (i0 == 0 ? 0 : i0 - 1)
#define	prevj(j0)   (j0 == 0 ? jmax : j0 - 1)
#define	nexti(i0)   (i0 + 1)
#define	nextj(j0)   (j0 == jmax ? 0 : j0 + 1)
Functions
	trrpt_alignment (struct SEQALN_SEQUENCE *seq1, struct SEQALN_SEQUENCE *seq2, struct SEQALN_CONSTANTS *scoring, struct SEQALN_RESULTS *results, struct SEQALN_IO *io)

---

Define Documentation

#define align	(	i0,
		j0,
		i1,
		j1		)

Value:

(i1 == nexti(i0) && j1 == nextj(j0) &&  \
              results->S[i1][j1] == results->S[i0][j0] +           \
              scoring->deltafn(seq1->code[i1],seq2->code[j1+1],scoring))

#define delseq1	(	i0,
		j0,
		i1,
		j1		)

Value:

(i0 == i1 && \
               (j0 < j1 || (j0 == jmax && j1 == 0 && !align(i0,j0,i1,j1))))

Referenced by trrpt_alignment().

#define delseq2	(	i0,
		j0,
		i1,
		j1		)	(i0 < i1 && j0 == j1)

Referenced by trrpt_alignment().

#define nexti

(

i0

)

(i0 + 1)

Referenced by markdiag(), markseq(), ptrace(), scanup(), trace(), trrpt_alignment(), and trtrace().

#define nextj

(

j0

)

(j0 == jmax ? 0 : j0 + 1)

Referenced by markdiag(), markseq(), ptrace(), scanleft(), trace(), trrpt_alignment(), and trtrace().

#define previ

(

i0

)

(i0 == 0 ? 0 : i0 - 1)

Referenced by trrpt_alignment().

#define prevj

(

j0

)

(j0 == 0 ? jmax : j0 - 1)

Referenced by trrpt_alignment().

---

Function Documentation

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

References SEQALN_RESULTS::bestS, SEQALN_RESULTS::bestSi, SEQALN_RESULTS::bestSj, SEQALN_CONSTANTS::Debug, delseq1, delseq2, FIT, SEQALN_LSTRUCT::i, SEQALN_LSTRUCT::j, LOCAL, name, SEQALN_LSTRUCT::next, nexti, nextj, OVER, previ, prevj, PROFILE, SEQALN_CONSTANTS::ptype, SEQALN_CONSTANTS::rptalign, SEQALN_CONSTANTS::rptscore, SEQALN_CONSTANTS::showmmatch, SEQALN_IO::STDERR, SEQALN_IO::STDOUT, SEQALN_CONSTANTS::stype, SEQALN_RESULTS::trace, trace(), SEQALN_CONSTANTS::width, and SEQALN_CONSTANTS::window.