aln_input.h File Reference

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

Go to the source code of this file.

Defines
#define	MAX_ARG_LEN   2048
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_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	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	loadDeltaFunction (struct SEQALN_CONSTANTS *scoring)

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Define Documentation

#define MAX_ARG_LEN   2048

Referenced by parseargs().

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Function Documentation

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

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)

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
	)

Referenced by parseargs().

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

Referenced by load_seq_lite(), main(), parseargs(), and mgsaln::while().

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

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

int load_seq_lite

(

struct SEQALN_SEQUENCE *

sequence

)

void loadDeltaFunction

(

struct SEQALN_CONSTANTS *

scoring

)

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[]
	)

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
	)

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
	)

Referenced by parseargs_str().