aln_output.h File Reference

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

Go to the source code of this file.

Functions
void	rpt_align (struct SEQALN_SEQUENCE *seq1, struct SEQALN_SEQUENCE *seq2, struct SEQALN_CONSTANTS *scoring, struct SEQALN_RESULTS *results, struct SEQALN_IO *io)
void	rpt_alignment (struct SEQALN_SEQUENCE *seq1, struct SEQALN_SEQUENCE *seq2, struct SEQALN_CONSTANTS *scoring, struct SEQALN_RESULTS *results, struct SEQALN_IO *io)
void	rpt_row (struct SEQALN_SEQUENCE *seq1, struct SEQALN_SEQUENCE *seq2, struct SEQALN_CONSTANTS *scoring, struct SEQALN_RESULTS *results, struct SEQALN_IO *io, int i)
void	rpt_scores (struct SEQALN_SEQUENCE *seq1, struct SEQALN_SEQUENCE *seq2, struct SEQALN_CONSTANTS *scoring, struct SEQALN_RESULTS *results, struct SEQALN_IO *io)
void	print_trace (struct SEQALN_CONSTANTS *scoring, struct SEQALN_RESULTS *results, struct SEQALN_IO *io)

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Function Documentation

void print_trace	(	struct SEQALN_CONSTANTS *	scoring,
		struct SEQALN_RESULTS *	results,
		struct SEQALN_IO *	io
	)

References SEQALN_CONSTANTS::envelope, SEQALN_CONSTANTS::flip, SEQALN_LSTRUCT::i, SEQALN_LSTRUCT::j, SEQALN_LSTRUCT::next, SEQALN_IO::STDOUT, SEQALN_RESULTS::trace, and SEQALN_CONSTANTS::traceupper.

void rpt_align	(	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_RESULTS::bestS, SEQALN_RESULTS::bestSi, SEQALN_RESULTS::bestSj, SEQALN_SEQUENCE::complement, SEQALN_SEQUENCE::fstart, SEQALN_LSTRUCT::i, SEQALN_LSTRUCT::j, LINEAR, SEQALN_CONSTANTS::memuse, SEQALN_SEQUENCE::name, name, PROFILE, SEQALN_SEQUENCE::reverse, SEQALN_CONSTANTS::rptalign, SEQALN_CONSTANTS::rptscore, SEQALN_RESULTS::start1, SEQALN_RESULTS::start2, SEQALN_IO::STDERR, SEQALN_IO::STDOUT, SEQALN_CONSTANTS::stype, SEQALN_RESULTS::trace, and SEQALN_CONSTANTS::width.

void rpt_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_SEQUENCE::code, SEQALN_SEQUENCE::complement, SEQALN_CONSTANTS::deltafn, FIT, SEQALN_LSTRUCT::i, SEQALN_LSTRUCT::j, LINEAR, LOCAL, SEQALN_CONSTANTS::memuse, SEQALN_CONSTANTS::mtype, SEQALN_SEQUENCE::name, name, SEQALN_LSTRUCT::next, OVER, PROFILE, SEQALN_CONSTANTS::ptype, SEQALN_SEQUENCE::reverse, SEQALN_CONSTANTS::rptalign, SEQALN_CONSTANTS::rptscore, SEQALN_SEQUENCE::seq, SEQALN_CONSTANTS::showmmatch, SIMILARITY, SEQALN_IO::STDERR, SEQALN_IO::STDOUT, SEQALN_CONSTANTS::stype, SEQALN_RESULTS::trace, and SEQALN_CONSTANTS::width.

void rpt_row	(	struct SEQALN_SEQUENCE *	seq1,
		struct SEQALN_SEQUENCE *	seq2,
		struct SEQALN_CONSTANTS *	scoring,
		struct SEQALN_RESULTS *	results,
		struct SEQALN_IO *	io,
		int	i
	)

References SEQALN_RESULTS::aligned, SEQALN_CONSTANTS::alpha, SEQALN_CONSTANTS::beta, SEQALN_CONSTANTS::btype, SEQALN_SEQUENCE::len, SEQALN_PROFILE::len, SEQALN_RESULTS::linbits, LINEAR, SEQALN_CONSTANTS::memuse, PROFILE, SEQALN_RESULTS::S, SEQALN_SEQUENCE::seq, SEQALN_IO::STDOUT, SEQALN_CONSTANTS::stype, and TANDEM.

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

References SEQALN_RESULTS::aligned, SEQALN_CONSTANTS::alpha, SEQALN_CONSTANTS::beta, SEQALN_SEQUENCE::len, SEQALN_PROFILE::len, PROFILE, SEQALN_CONSTANTS::rptmat, SEQALN_RESULTS::S, SEQALN_SEQUENCE::seq, SEQALN_IO::STDOUT, and SEQALN_CONSTANTS::stype.