helper.c File Reference

#include "helper.h"

Defines
#define	nuc_to_4(X)   (X == 'A' ? 0 : (X == 'C' ? 1 : (X == 'G' ? 2 : 3)))
Functions
void	code2seq (struct SEQALN_SEQUENCE *seq)
INLINE int	delta (char a, char b, struct SEQALN_CONSTANTS *scoring)
INLINE int	mdelta (char a, char b, struct SEQALN_CONSTANTS *scoring)
INLINE int	pdelta (int a, char b, struct SEQALN_PROFILE *pro)
INLINE int	gap (int k, struct SEQALN_CONSTANTS *scoring)
INLINE 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)
Variables
char	complement [128]

---

Define Documentation

#define nuc_to_4

(

X

)

(X == 'A' ? 0 : (X == 'C' ? 1 : (X == 'G' ? 2 : 3)))

Referenced by xlate().

---

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.

Referenced by revcomp().

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

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

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

void freeTraceList

(

struct SEQALN_RESULTS *

rslt

)

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

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

INLINE int gap	(	int	k,
		struct SEQALN_CONSTANTS *	scoring
	)

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

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

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

References SEQALN_CONSTANTS::xmatrix.

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
	)

References SEQALN_RESULTS::aligned, SEQALN_CONSTANTS::cutoff, SEQALN_CONSTANTS::naligns, and SEQALN_RESULTS::S.

Referenced by dyaln::~dyaln().

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

References SEQALN_PROFILE::profile.

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

INLINE int pgap	(	int	k,
		struct SEQALN_PROFILE *	pro
	)

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

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

int revcomp

(

struct SEQALN_SEQUENCE *

seq

)

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

Referenced by parseargs().

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.

Referenced by revcomp().

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

References SEQALN_VERSION, and SEQALN_IO::STDOUT.

Referenced by parseargs().

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.

Referenced by parseargs().

---

Variable Documentation

char complement[128]

Initial value:

{
   0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
   0,0,0,0,0,0,0,0,0,0,0,0,0,0,'.',0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
   0,'T','V','G','H',0,0,'C','D',0,0,0,0,'K','X',
   0,0,0,'Y','S','A','A','B','W','X','R',0,0,0,0,0,0,
   0,'t','v','g','h',0,0,'c','d',0,0,0,0,'k','x',
   0,0,0,'y','s','a','a','b','w','x','r',0,0,0,0,0,0
   }

Referenced by compseq().