/* $Id: realign.h,v 1.1 2003-05-19 17:25:47 lstein Exp $ */
/* Fast implementation of a global dp aligner, used by the Realign.pm module
for realigning short HSPs */
#ifndef REALIGN_H
#define REALIGN_H
#define A_EXTEND 0
#define GAP_SRC 1
#define GAP_TGT 2
typedef struct {
int score;
short event;
} ACell,*ACellPtr;
typedef struct {
short match;
short mismatch;
short wcmatch;
short gap;
short gap_extend;
char wildcard;
} MatchMatrix, *MatchMatrixPtr;
typedef int *AlignmentPtr;
typedef struct {
int score;
int row;
int col;
} bestcelldata;
int realign (const char* src, const char* tgt,
const MatchMatrixPtr matrix,
AlignmentPtr *align_out);
#endif