alnfn.h File Reference

#include "seqaln.h"

Go to the source code of this file.

Functions
int	results_init (struct SEQALN_SEQUENCE *seq1, struct SEQALN_SEQUENCE *seq2, struct SEQALN_CONSTANTS *scoring, struct SEQALN_RESULTS *results, struct SEQALN_IO *io)
void	localS (struct SEQALN_SEQUENCE *seq1, struct SEQALN_SEQUENCE *seq2, struct SEQALN_CONSTANTS *scoring, struct SEQALN_RESULTS *results, struct SEQALN_IO *io)
void	trace (struct SEQALN_SEQUENCE *seq1, struct SEQALN_SEQUENCE *seq2, struct SEQALN_CONSTANTS *scoring, struct SEQALN_RESULTS *results, struct SEQALN_IO *io)
void	gen_align (struct SEQALN_SEQUENCE *seq1, struct SEQALN_SEQUENCE *seq2, struct SEQALN_CONSTANTS *scoring, struct SEQALN_RESULTS *results, struct SEQALN_IO *io)
void	lsdeclump (struct SEQALN_SEQUENCE *seq1, struct SEQALN_SEQUENCE *seq2, struct SEQALN_CONSTANTS *scoring, struct SEQALN_RESULTS *results, struct SEQALN_IO *io)

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Function Documentation

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

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

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

References SEQALN_CONSTANTS::alpha, SEQALN_RESULTS::bestS, SEQALN_RESULTS::bestSi, SEQALN_RESULTS::bestSj, SEQALN_CONSTANTS::beta, SEQALN_SEQUENCE::code, SEQALN_CONSTANTS::deltafn, E, SEQALN_RESULTS::F, SEQALN_SEQUENCE::len, LINEAR, max3(), SEQALN_CONSTANTS::memuse, rpt_row(), SEQALN_CONSTANTS::rptmat, and SEQALN_RESULTS::S.

void lsdeclump	(	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::code, SEQALN_CONSTANTS::Debug, SEQALN_CONSTANTS::deltafn, E, SEQALN_RESULTS::F, F, gap(), getmaxS(), SEQALN_SEQUENCE::len, markdiag(), max, max3(), SEQALN_RESULTS::S, SEQALN_SEQUENCE::seq, and SEQALN_IO::STDOUT.

int results_init	(	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_RESULTS::best, SEQALN_RESULTS::bestS, SEQALN_RESULTS::bestSi, SEQALN_RESULTS::bestSj, SEQALN_CONSTANTS::beta, SEQALN_CONSTANTS::btype, SEQALN_PVALUE::coeff, DISTANCE, SEQALN_RESULTS::F, FIT, SEQALN_PVALUE::gamma, gap(), GLOBAL, SEQALN_PVALUE::hist, SEQALN_PVALUE::lambda, SEQALN_SEQUENCE::len, SEQALN_RESULTS::linbits, LINEAR, LOCAL, SEQALN_RESULTS::maxentry, SEQALN_CONSTANTS::memuse, min, SEQALN_CONSTANTS::mtype, SEQALN_CONSTANTS::naligns, SEQALN_RESULTS::naligns, SEQALN_PVALUE::ndeclumps, SEQALN_CONSTANTS::ndeclumps, SEQALN_PVALUE::nhist, SEQALN_PVALUE::npvals, SEQALN_PVALUE::nsims, SEQALN_CONSTANTS::nsims, OVER, SEQALN_PVALUE::p, SEQALN_CONSTANTS::palpha, SEQALN_CONSTANTS::pbeta, PROFILE, SEQALN_CONSTANTS::ptype, SEQALN_PVALUE::pvalue, SEQALN_RESULTS::pvalue, PVALUE, SEQALN_SEQUENCE::resized, SEQALN_RESULTS::S, SELF, SEQALN_CONSTANTS::stats, SEQALN_IO::STDERR, SEQALN_CONSTANTS::stype, TANDEM, and topscore().

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.