gen_align.c File Reference

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

Defines
#define	tandalign(i0, j0, i1, j1)
#define	tanddelseq1(i0, j0, i1, j1)
#define	tanddelseq2(i0, j0, i1, j1)   (i0 < i1 && j0 == j1)
#define	tandprevi(i0)   (i0 == 0 ? 0 : i0 - 1)
#define	tandprevj(j0)   (j0 == 0 ? jmax : j0 - 1)
#define	tandnexti(i0)   (i0 + 1)
#define	tandnextj(j0)   (j0 == jmax ? 0 : j0 + 1)
Functions
void	gen_align (SEQALN_SEQUENCE *seq1, SEQALN_SEQUENCE *seq2, SEQALN_CONSTANTS *scoring, SEQALN_RESULTS *results, SEQALN_IO *io)
void	norm_gen (SEQALN_SEQUENCE *seq1, SEQALN_SEQUENCE *seq2, SEQALN_CONSTANTS *scoring, SEQALN_RESULTS *results, SEQALN_IO *io)
void	tandem_gen (struct SEQALN_SEQUENCE *seq1, struct SEQALN_SEQUENCE *seq2, struct SEQALN_CONSTANTS *scoring, struct SEQALN_RESULTS *results, struct SEQALN_IO *io)

---

Define Documentation

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

Value:

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

Referenced by tandem_gen().

#define tanddelseq1	(	i0,
		j0,
		i1,
		j1		)

Value:

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

#define tanddelseq2	(	i0,
		j0,
		i1,
		j1		)	(i0 < i1 && j0 == j1)

#define tandnexti

(

i0

)

(i0 + 1)

Referenced by tandem_gen().

#define tandnextj

(

j0

)

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

Referenced by tandem_gen().

#define tandprevi

(

i0

)

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

#define tandprevj

(

j0

)

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

---

Function Documentation

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

References SEQALN_CONSTANTS::btype, norm_gen(), TANDEM, and tandem_gen().

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

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

References SEQALN_RESULTS::align0, SEQALN_RESULTS::align1, SEQALN_RESULTS::align2, SEQALN_RESULTS::align_len, SEQALN_SEQUENCE::code, SEQALN_CONSTANTS::csub, SEQALN_CONSTANTS::Debug, SEQALN_CONSTANTS::deltafn, FIT, SEQALN_LSTRUCT::i, SEQALN_RESULTS::iden_count, SEQALN_LSTRUCT::j, LINEAR, LOCAL, SEQALN_RESULTS::match_freq1, SEQALN_RESULTS::match_freq2, SEQALN_RESULTS::max_align_len, SEQALN_CONSTANTS::memuse, SEQALN_CONSTANTS::mtype, newmem(), SEQALN_LSTRUCT::next, SEQALN_RESULTS::nogap_len, OVER, PROFILE, SEQALN_CONSTANTS::ptype, SEQALN_SEQUENCE::seq, SEQALN_CONSTANTS::showmmatch, SIMILARITY, SEQALN_RESULTS::siml_count, SEQALN_RESULTS::start1, SEQALN_RESULTS::start2, SEQALN_IO::STDOUT, SEQALN_CONSTANTS::stype, and SEQALN_RESULTS::trace.

Referenced by gen_align().

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

References SEQALN_RESULTS::align0, SEQALN_RESULTS::align1, SEQALN_RESULTS::align2, SEQALN_RESULTS::align_len, SEQALN_CONSTANTS::Debug, SEQALN_CONSTANTS::deltafn, SEQALN_LSTRUCT::i, SEQALN_LSTRUCT::j, LINEAR, SEQALN_CONSTANTS::memuse, SEQALN_CONSTANTS::mtype, newmem(), SEQALN_LSTRUCT::next, PROFILE, SEQALN_CONSTANTS::showmmatch, SIMILARITY, SEQALN_RESULTS::start1, SEQALN_RESULTS::start2, SEQALN_IO::STDOUT, SEQALN_CONSTANTS::stype, tandalign, tandnexti, tandnextj, and SEQALN_RESULTS::trace.

Referenced by gen_align().