aln_input.c File Reference

#include "aln_input.h"
#include "helper.h"
#include "util.h"
#include "seqaln.h"

Functions
int	load_distrib (char *fn, double *freq, struct SEQALN_IO *io)
int	load_mat (char *fn, struct SEQALN_CONSTANTS *scoring, struct SEQALN_IO *io)
int	load_pro (struct SEQALN_PROFILE *pro, struct SEQALN_CONSTANTS *scoring, struct SEQALN_IO *io)
int	load_seq (struct SEQALN_SEQUENCE *sequence, struct SEQALN_CONSTANTS *scoring, struct SEQALN_IO *io)
int	load_seq_fromstr (struct SEQALN_SEQUENCE *sequence, struct SEQALN_CONSTANTS *scoring, const char *seqname, const char *seqstring)
int	load_seq_lite (struct SEQALN_SEQUENCE *sequence)
void	parseargs (struct SEQALN_SEQUENCE *seq1, struct SEQALN_SEQUENCE *seq2, struct SEQALN_CONSTANTS *scoring, struct SEQALN_RESULTS *results, struct SEQALN_IO *io, int argc, char *argv[])
void	parseargs_str (struct SEQALN_SEQUENCE *seq1, struct SEQALN_SEQUENCE *seq2, struct SEQALN_CONSTANTS *scoring, struct SEQALN_RESULTS *results, char *seq1name, char *seq2name, char *seq1str, char *seq2str)
void	parseargs_str_new (struct SEQALN_SEQUENCE *seq1, struct SEQALN_SEQUENCE *seq2, struct SEQALN_CONSTANTS *scoring, struct SEQALN_RESULTS *results, char *seq1name, char *seq2name, char *seq1str, char *seq2str, struct SEQALN_IO *io)
void	loadDeltaFunction (struct SEQALN_CONSTANTS *scoring)

---

Function Documentation

int load_distrib	(	char *	fn,
		double *	freq,
		struct SEQALN_IO *	io
	)

References length, MAXPATH, newmem(), SEQALN_IO::STDERR, and value.

Referenced by parseargs(), parseargs_str_new(), and dyaln::setup().

int load_mat	(	char *	fn,
		struct SEQALN_CONSTANTS *	scoring,
		struct SEQALN_IO *	io
	)

depends on the ENV MATDIR for locating the fn (matrix file)

References asc2num(), SEQALN_CONSTANTS::Debug, DISTANCE, MAXLINE, MAXPATH, SEQALN_CONSTANTS::mtype, SEQALN_CONSTANTS::offset, SEQALN_IO::STDERR, toupper(), and SEQALN_CONSTANTS::xmatrix.

Referenced by parseargs(), parseargs_str_new(), dyaln::setMatrix(), aln::setMatrix(), and dyaln::setup().

int load_pro	(	struct SEQALN_PROFILE *	pro,
		struct SEQALN_CONSTANTS *	scoring,
		struct SEQALN_IO *	io
	)

References SEQALN_PROFILE::alpha, SEQALN_PROFILE::beta, SEQALN_PROFILE::fname, SEQALN_PROFILE::len, MAXPATH, MAXSEQNAME, SEQALN_PROFILE::name, newmem(), SEQALN_CONSTANTS::palpha, SEQALN_CONSTANTS::pbeta, SEQALN_PROFILE::profile, and SEQALN_IO::STDERR.

Referenced by parseargs().

int load_seq	(	struct SEQALN_SEQUENCE *	sequence,
		struct SEQALN_CONSTANTS *	scoring,
		struct SEQALN_IO *	io
	)

int load_seq_fromstr	(	struct SEQALN_SEQUENCE *	sequence,
		struct SEQALN_CONSTANTS *	scoring,
		const char *	seqname,
		const char *	seqstring
	)

References asc2num(), SEQALN_SEQUENCE::code, SEQALN_SEQUENCE::fend, SEQALN_SEQUENCE::fname, SEQALN_SEQUENCE::fstart, SEQALN_SEQUENCE::len, SEQALN_SEQUENCE::maxlen, MAXSEQNAME, SEQALN_SEQUENCE::name, newmem(), SEQALN_SEQUENCE::resized, SEQALN_SEQUENCE::seq, and toupper().

Referenced by dyaln::align(), main(), and parseargs_str_new().

int load_seq_lite

(

struct SEQALN_SEQUENCE *

sequence

)

References load_seq(), newmem(), SEQALN_IO::STDERR, SEQALN_IO::STDIN, and SEQALN_IO::STDOUT.

void loadDeltaFunction

(

struct SEQALN_CONSTANTS *

scoring

)

References delta(), SEQALN_CONSTANTS::deltafn, MATRIX, mdelta(), pdelta(), PROFILE, and SEQALN_CONSTANTS::stype.

Referenced by dyaln::initParameter(), and mgsaln().

void parseargs	(	struct SEQALN_SEQUENCE *	seq1,
		struct SEQALN_SEQUENCE *	seq2,
		struct SEQALN_CONSTANTS *	scoring,
		struct SEQALN_RESULTS *	results,
		struct SEQALN_IO *	io,
		int	argc,
		char *	argv[]
	)

References SEQALN_CONSTANTS::allscores, SEQALN_CONSTANTS::alpha, SEQALN_PROFILE::alpha, SEQALN_CONSTANTS::beta, SEQALN_PROFILE::beta, SEQALN_CONSTANTS::btype, SEQALN_SEQUENCE::code, SEQALN_CONSTANTS::csub, SEQALN_CONSTANTS::cutoff, SEQALN_CONSTANTS::Debug, delta(), SEQALN_CONSTANTS::deltafn, SEQALN_CONSTANTS::envelope, SEQALN_CONSTANTS::flip, SEQALN_PROFILE::fname, SEQALN_SEQUENCE::fname, SEQALN_CONSTANTS::gamma, SEQALN_SEQUENCE::len, LINEAR, load_distrib(), load_mat(), load_pro(), load_seq(), SEQALN_CONSTANTS::match, MATRIX, MAX_ARG_LEN, mdelta(), SEQALN_CONSTANTS::memuse, SEQALN_CONSTANTS::mismatch, SEQALN_CONSTANTS::mtype, SEQALN_CONSTANTS::naligns, SEQALN_CONSTANTS::ndeclumps, newmem(), SEQALN_CONSTANTS::nsims, SEQALN_CONSTANTS::overout, SEQALN_CONSTANTS::p, pdelta(), PROFILE, SEQALN_RESULTS::pvalue, PVALUE, SEQALN_CONSTANTS::randfile, revcomp(), SEQALN_CONSTANTS::revcomp, rpt_version(), SEQALN_CONSTANTS::rptalign, SEQALN_CONSTANTS::rptboth, SEQALN_CONSTANTS::rptmat, SEQALN_CONSTANTS::rptptable, SEQALN_CONSTANTS::rptscore, SEQALN_CONSTANTS::rpttrace, SELF, SEQALN_SEQUENCE::seq, SEQALN_PVALUE::seq1dist, SEQALN_PVALUE::seq1len, SEQALN_PVALUE::seq2dist, SEQALN_PVALUE::seq2len, SEQALN_CONSTANTS::showmmatch, SIMILARITY, SEQALN_CONSTANTS::stats, SEQALN_IO::STDERR, SEQALN_IO::STDIN, SEQALN_IO::STDOUT, SEQALN_CONSTANTS::stype, TANDEM, SEQALN_CONSTANTS::traceupper, SEQALN_CONSTANTS::verbose, SEQALN_CONSTANTS::width, SEQALN_CONSTANTS::window, xlate(), and SEQALN_SEQUENCE::xlated.

Referenced by main().

void parseargs_str	(	struct SEQALN_SEQUENCE *	seq1,
		struct SEQALN_SEQUENCE *	seq2,
		struct SEQALN_CONSTANTS *	scoring,
		struct SEQALN_RESULTS *	results,
		char *	seq1name,
		char *	seq2name,
		char *	seq1str,
		char *	seq2str
	)

References parseargs_str_new(), SEQALN_IO::STDERR, SEQALN_IO::STDIN, and SEQALN_IO::STDOUT.

Referenced by main().

void parseargs_str_new	(	struct SEQALN_SEQUENCE *	seq1,
		struct SEQALN_SEQUENCE *	seq2,
		struct SEQALN_CONSTANTS *	scoring,
		struct SEQALN_RESULTS *	results,
		char *	seq1name,
		char *	seq2name,
		char *	seq1str,
		char *	seq2str,
		struct SEQALN_IO *	io
	)

References SEQALN_CONSTANTS::alpha, SEQALN_CONSTANTS::beta, SEQALN_CONSTANTS::btype, SEQALN_CONSTANTS::csub, delta(), SEQALN_CONSTANTS::deltafn, SEQALN_CONSTANTS::envelope, SEQALN_CONSTANTS::flip, SEQALN_SEQUENCE::fname, load_distrib(), load_mat(), load_seq_fromstr(), SEQALN_CONSTANTS::match, MATRIX, mdelta(), SEQALN_CONSTANTS::mismatch, SEQALN_CONSTANTS::mtype, newmem(), pdelta(), PROFILE, SEQALN_RESULTS::pvalue, PVALUE, SEQALN_CONSTANTS::rptalign, SEQALN_CONSTANTS::rptboth, SEQALN_CONSTANTS::rptmat, SEQALN_CONSTANTS::rptscore, SEQALN_CONSTANTS::rpttrace, SELF, SEQALN_PVALUE::seq1dist, SEQALN_PVALUE::seq1len, SEQALN_PVALUE::seq2dist, SEQALN_PVALUE::seq2len, SEQALN_CONSTANTS::showmmatch, SIMILARITY, SEQALN_CONSTANTS::stats, SEQALN_IO::STDERR, SEQALN_IO::STDIN, SEQALN_IO::STDOUT, SEQALN_CONSTANTS::stype, TANDEM, SEQALN_CONSTANTS::traceupper, and SEQALN_CONSTANTS::window.

Referenced by parseargs_str().