helper.h File Reference

#include "seqaln.h"

Go to the source code of this file.

Functions
void	code2seq (struct SEQALN_SEQUENCE *seq)
int	delta (char a, char b, struct SEQALN_CONSTANTS *scoring)
int	mdelta (char a, char b, struct SEQALN_CONSTANTS *scoring)
int	pdelta (int a, char b, struct SEQALN_PROFILE *pro)
int	gap (int k, struct SEQALN_CONSTANTS *scoring)
int	pgap (int k, struct SEQALN_PROFILE *pro)
int	revcomp (struct SEQALN_SEQUENCE *seq)
int	revseq (struct SEQALN_SEQUENCE *seq)
int	compseq (struct SEQALN_SEQUENCE *seq)
void	rpt_version (char *prog, struct SEQALN_IO *io)
void	reverse_list (SEQALN_TRACE **list)
void	memfree (struct SEQALN_SEQUENCE *seq1, struct SEQALN_SEQUENCE *seq2, struct SEQALN_CONSTANTS *scoring, struct SEQALN_RESULTS *results, struct SEQALN_IO *io)
int	xlate (struct SEQALN_SEQUENCE *seq)
void	freeTraceList (struct SEQALN_RESULTS *rslt)

---

Function Documentation

void code2seq

(

struct SEQALN_SEQUENCE *

seq

)

References SEQALN_SEQUENCE::code, SEQALN_SEQUENCE::len, newmem(), and SEQALN_SEQUENCE::seq.

int compseq

(

struct SEQALN_SEQUENCE *

seq

)

References asc2num(), SEQALN_SEQUENCE::code, complement, SEQALN_SEQUENCE::complement, SEQALN_SEQUENCE::len, and SEQALN_SEQUENCE::seq.

int delta	(	char	a,
		char	b,
		struct SEQALN_CONSTANTS *	scoring
	)

References SEQALN_CONSTANTS::match, and SEQALN_CONSTANTS::mismatch.

void freeTraceList

(

struct SEQALN_RESULTS *

rslt

)

References SEQALN_LSTRUCT::next, and SEQALN_RESULTS::trace.

int gap	(	int	k,
		struct SEQALN_CONSTANTS *	scoring
	)

References SEQALN_CONSTANTS::alpha, and SEQALN_CONSTANTS::beta.

int mdelta	(	char	a,
		char	b,
		struct SEQALN_CONSTANTS *	scoring
	)

References SEQALN_CONSTANTS::xmatrix.

void memfree	(	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::cutoff, SEQALN_CONSTANTS::naligns, and SEQALN_RESULTS::S.

int pdelta	(	int	a,
		char	b,
		struct SEQALN_PROFILE *	pro
	)

References SEQALN_PROFILE::profile.

int pgap	(	int	k,
		struct SEQALN_PROFILE *	pro
	)

References SEQALN_PROFILE::alpha, and SEQALN_PROFILE::beta.

int revcomp

(

struct SEQALN_SEQUENCE *

seq

)

References SEQALN_SEQUENCE::complement, compseq(), SEQALN_SEQUENCE::revcomp, SEQALN_SEQUENCE::reverse, and revseq().

void reverse_list

(

SEQALN_TRACE **

list

)

References SEQALN_LSTRUCT::next.

int revseq

(

struct SEQALN_SEQUENCE *

seq

)

References SEQALN_SEQUENCE::code, SEQALN_SEQUENCE::len, SEQALN_SEQUENCE::reverse, and SEQALN_SEQUENCE::seq.

void rpt_version	(	char *	prog,
		struct SEQALN_IO *	io
	)

References SEQALN_VERSION, and SEQALN_IO::STDOUT.

int xlate

(

struct SEQALN_SEQUENCE *

seq

)

References asc2num(), SEQALN_SEQUENCE::code, SEQALN_SEQUENCE::fstart, SEQALN_SEQUENCE::len, nuc_to_4, SEQALN_SEQUENCE::seq, and SEQALN_SEQUENCE::xlated.