splice.cpp File Reference

#include "libc.h"
#include "sim4.h"
#include "psublast.h"
#include "splice.h"

Functions
static void	splice_donor (const char *xseq, const char *yseq, int M, int N, int *gt_score, int *ct_score, int **max_Gf, int **max_Cf, int **start_Gi, int **start_Ci)
static void	splice_donor_uni (const char *xseq, const char *yseq, int M, int N, int *It_score, int **max_IF, int **end_Ii)
static void	splice_acceptor (const char *xseq, const char *yseq, int M, int N, int *ag_score, int *ac_score, int **max_Gb, int **max_Cb, int **end_Gi, int **end_Ci)
static void	splice_acceptor_uni (const char *xseq, const char *yseq, int M, int N, int *aI_score, int **max_Ib, int **end_Ii)
static int	stepct (int n)
void	splice (const char *in_seqx, int ls, int us, int le, int ue, const char *in_seqy, int ys, int ye, splice_t **gcell, splice_t **ccell, int ori)
splice_t *	new_splice (char c, int xs, int xe, int ys, int ye, int score, splice_t *next)
Variables
static const char	rcsid []
int	encoding [NACHARS]
signal_t	gt = {{0, 0, 0, 2},{0, 0, 0, 2},{2, 2, 2, 5},{0, 0, 0, 2}}
signal_t	ct = {{0, 0, 0, 2},{2, 2, 2, 5},{0, 0, 0, 2},{0, 0, 0, 2}}
signal_t	ag = {{2, 2, 5, 2},{0, 0, 2, 0},{0, 0, 2, 0},{0, 0, 2, 0}}
signal_t	ac = {{2, 5, 2, 2},{0, 2, 0, 0},{0, 2, 0, 0},{0, 2, 0, 0}}

---

Function Documentation

splice_t* new_splice	(	char	c,
		int	xs,
		int	xe,
		int	ys,
		int	ye,
		int	score,
		splice_t *	next
	)

References ckalloc(), spliced::next, spliced::score, spliced::type, spliced::xe, spliced::xs, spliced::ye, and spliced::ys.

Referenced by splice(), and sync_slide_intron().

void splice	(	const char *	in_seqx,
		int	ls,
		int	us,
		int	le,
		int	ue,
		const char *	in_seqy,
		int	ys,
		int	ye,
		splice_t **	gcell,
		splice_t **	ccell,
		int	ori
	)

References ac, ag, BOTH, BWD, ckalloc(), ct, encoding, FWD, gt, new_splice(), splice_acceptor(), splice_acceptor_uni(), splice_donor(), and splice_donor_uni().

Referenced by slide_intron(), and sync_slide_intron().

static void splice_acceptor	(	const char *	xseq,
		const char *	yseq,
		int	M,
		int	N,
		int *	ag_score,
		int *	ac_score,
		int **	max_Gb,
		int **	max_Cb,
		int **	end_Gi,
		int **	end_Ci
	)			[static]

References ckalloc(), min, stepct(), and X.

Referenced by splice().

static void splice_acceptor_uni	(	const char *	xseq,
		const char *	yseq,
		int	M,
		int	N,
		int *	aI_score,
		int **	max_Ib,
		int **	end_Ii
	)			[static]

References ckalloc(), min, stepct(), and X.

Referenced by splice().

static void splice_donor	(	const char *	xseq,
		const char *	yseq,
		int	M,
		int	N,
		int *	gt_score,
		int *	ct_score,
		int **	max_Gf,
		int **	max_Cf,
		int **	start_Gi,
		int **	start_Ci
	)			[static]

References ckalloc(), min, stepct(), and X.

Referenced by splice().

static void splice_donor_uni	(	const char *	xseq,
		const char *	yseq,
		int	M,
		int	N,
		int *	It_score,
		int **	max_IF,
		int **	end_Ii
	)			[static]

References ckalloc(), min, stepct(), and X.

Referenced by splice().

static int stepct

(

int

n

)

[static]

References fatal().

Referenced by splice_acceptor(), splice_acceptor_uni(), splice_donor(), and splice_donor_uni().

---

Variable Documentation

signal_t ac = {{2, 5, 2, 2},{0, 2, 0, 0},{0, 2, 0, 0},{0, 2, 0, 0}}

Referenced by splice().

signal_t ag = {{2, 2, 5, 2},{0, 0, 2, 0},{0, 0, 2, 0},{0, 0, 2, 0}}

Referenced by main(), splice(), and trainer::train().

signal_t ct = {{0, 0, 0, 2},{2, 2, 2, 5},{0, 0, 0, 2},{0, 0, 0, 2}}

Referenced by splice(), and translate().

int encoding[NACHARS]

Referenced by bld_table(), and splice().

signal_t gt = {{0, 0, 0, 2},{0, 0, 0, 2},{2, 2, 2, 5},{0, 0, 0, 2}}

Referenced by splice().

const char rcsid[] [static]

Initial value:

"$Id: splice.cpp,v 1.1.1.1 2007-07-13 03:44:06 kzhou Exp $"