align.cpp File Reference

#include <stdio.h>
#include <stdlib.h>
#include "psublast.h"
#include "sim4.h"
#include "sim4b1.h"
#include "Xtend1.h"
#include "align.h"

Functions
static int	snake (int k, int x, int endx, int endy)
static int	rsnake (int k, int x, int startx, int starty, int M)
void	align_path (int i1, int j1, int i2, int j2, int dist, edit_script **head, edit_script **tail)
int	align_get_dist (int i1, int j1, int i2, int j2, int limit)
void	Condense_script (edit_script *head)
void	Condense_both_Ends (edit_script **head, edit_script **tail, edit_script **prev)
void	Flip_script (struct edit_script **script)
void	S2A (edit_script *head, int *S, int flag)
void	align_reverse (int *S)
void	IDISPLAY (const char A[], const char B[], int M, int N, int S[], int AP, int BP, int est_strand, const exon *exons)
void	Free_script (edit_script *head)
Variables
static const char	rcsid [] = "$Id: align.cpp,v 1.1.1.1 2007-07-13 03:44:06 kzhou Exp $"
static char	ALINE [51]
static char	BLINE [51]
static char	CLINE [51]

---

Function Documentation

int align_get_dist	(	int	i1,
		int	j1,
		int	i2,
		int	j2,
		int	limit
	)

References ckalloc(), max, min, MININT, snake(), and upper().

Referenced by pluri_align().

void align_path	(	int	i1,
		int	j1,
		int	i2,
		int	j2,
		int	dist,
		edit_script **	head,
		edit_script **	tail
	)

References align_path(), ckalloc(), DELETE, FALSE, INSERT, M, max, min, edit_script::next, edit_script::num, edit_script::op_type, rsnake(), snake(), SUBSTITUTE, TRUE, and upper().

Referenced by align_path(), and pluri_align().

void align_reverse

(

int *

S

)

Referenced by print_align_blk(), and print_align_lat().

void Condense_both_Ends	(	edit_script **	head,
		edit_script **	tail,
		edit_script **	prev
	)

References edit_script::next, edit_script::num, and edit_script::op_type.

Referenced by pluri_align().

void Condense_script

(

edit_script *

head

)

References edit_script::next, edit_script::num, and edit_script::op_type.

void Flip_script

(

struct edit_script **

script

)

References edit_script::next.

void Free_script

(

edit_script *

head

)

References edit_script::next.

Referenced by free_align(), print_align_blk(), and print_align_lat().

void IDISPLAY	(	const char	A[],
		const char	B[],
		int	M,
		int	N,
		int	S[],
		int	AP,
		int	BP,
		int	est_strand,
		const exon *	exons
	)

References fatal(), exon::from1, exon::from2, exon::next_exon, exon::ori, and exon::to1.

Referenced by print_align_lat().

static int rsnake	(	int	k,
		int	x,
		int	startx,
		int	starty,
		int	M
	)			[static]

References seq1, and seq2.

Referenced by align_path().

void S2A	(	edit_script *	head,
		int *	S,
		int	flag
	)

References INSERT, edit_script::next, edit_script::num, edit_script::op_type, and SUBSTITUTE.

Referenced by print_align_blk(), and print_align_lat().

static int snake	(	int	k,
		int	x,
		int	endx,
		int	endy
	)			[static]

References seq1, and seq2.

Referenced by align_get_dist(), and align_path().

---

Variable Documentation

char ALINE[51] [static]

char BLINE[51] [static]

char CLINE[51] [static]

const char rcsid[] = "$Id: align.cpp,v 1.1.1.1 2007-07-13 03:44:06 kzhou Exp $" [static]