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

)

int compseq

(

struct SEQALN_SEQUENCE *

seq

)

Referenced by revcomp().

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

Referenced by mRNAModel::growCDS3Prime(), loadDeltaFunction(), main(), parseargs(), parseargs_str_new(), sumNumber(), sumnumN(), and mRNAModel::trimCDSTail().

void freeTraceList

(

struct SEQALN_RESULTS *

rslt

)

Referenced by dyaln::freeTrace(), and aln::freeTrace().

int gap	(	int	k,
		struct SEQALN_CONSTANTS *	scoring
	)

Referenced by fddeclump(), fitD(), fitS(), fsdeclump(), globalD(), globalS(), lsdeclump(), overS(), pfitS(), pfsdeclump(), processAll(), prpt_row(), results_init(), srlocalS(), srlsdeclump(), topscore(), trlocalS(), and trlsdeclump().

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

Referenced by loadDeltaFunction(), parseargs(), and parseargs_str_new().

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

Referenced by dyaln::~dyaln().

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

Referenced by loadDeltaFunction(), parseargs(), and parseargs_str_new().

int pgap	(	int	k,
		struct SEQALN_PROFILE *	pro
	)

Referenced by pfitS(), pfsdeclump(), and prpt_row().

int revcomp

(

struct SEQALN_SEQUENCE *

seq

)

Referenced by parseargs().

void reverse_list

(

SEQALN_TRACE **

list

)

int revseq

(

struct SEQALN_SEQUENCE *

seq

)

Referenced by revcomp().

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

Referenced by parseargs().

int xlate

(

struct SEQALN_SEQUENCE *

seq

)

Referenced by parseargs().