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/*
* segemehl - a read aligner
* Copyright (C) 2008-2017 Steve Hoffmann and Christian Otto
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
#ifndef DPALIGN_H
#define DPALIGN_H
/*
*
* sw.h
*
*
* @author Steve Hoffmann, steve@bioinf.uni-leipzig.de
* @company Bioinformatics, University of Leipzig
* @date 06.02.2010 14:14:53 CET
*
*/
#include "basic-types.h"
#include "alignment.h"
typedef char symtype;
Uint edist(void *, symtype *, Uint, symtype *, Uint, Uint, Uint *, Uint);
int constscr (symtype, symtype, void *);
int constscrIUPAC (symtype, symtype, void *);
int constscr_Nmatch (symtype, symtype, void *);
int* swmatrix (void *, symtype*, Uint, symtype*, Uint, int,
Sint (*sub)(symtype, symtype, void *), void *);
int* splicedmatrix (void *, symtype*, symtype*, Uint, symtype*, Uint, symtype*, Uint,
Uint, Uint, int, Sint (*sub)(symtype, symtype, void *), void *);
int* swgapless (void *, symtype*, Uint, symtype*, Uint,
Sint (*sub)(symtype, symtype, void *), void *);
int* swgaplesstraceback (void *, int *,
symtype *, Uint, symtype *, Uint,
Sint (*sub)(symtype, symtype, void *), void *, int*);
void
swtraceback (void *space, int *M,
symtype *a, Uint m, symtype *b, Uint n, int indel,
Sint (*sub)(symtype, symtype, void *), void *nfo, Alignment *al);
void
splicedtraceback (void *space, int *M, symtype *a1, symtype *a2, Uint m,
symtype *b1, Uint n1, symtype *b2, Uint n2, Uint strand1, Uint strand2, int indel,
Sint (*sub)(symtype, symtype, void *), void *nfo, Alignment *al1, Alignment *al2);
void
swtracebacksplit (void *space, int *L,
symtype *a, symtype *b, Uint m, symtype *s1, symtype *s2, Uint n, int indel,
unsigned char rc,
Sint (*sub)(symtype, symtype, void *), void *nfo, Alignment *al1, Alignment *al2, FILE *dev);
int*
swsplitalign (void *space, symtype *a, symtype *b,
Uint m, symtype *s1, symtype *s2, Uint n, int indel,
unsigned char rc, Sint (*sub)(symtype, symtype, void *), void *nfo);
void
localsplicedtraceback (void *space, int *M, symtype *a1, symtype *a2, Uint m, symtype *b1, Uint n1,
symtype *b2, Uint n2, Uint strand1, Uint strand2, int indel,
Sint (*sub)(symtype, symtype, void *), void *nfo,
Alignment *al1, Alignment *al2, int* lmv, int *lmr);
int*
localsplicedmatrix (void *space, symtype *a1, symtype *a2, Uint m,
symtype *b1, Uint n1, symtype *b2, Uint n2,
Uint strand1, Uint strand2, int indel,
Sint (*sub)(symtype, symtype, void *), void *nfo, int **lv, int **lr);
void
localsplicedtraceback_test (void *space, int *M, symtype *a1, symtype *a2, Uint m, symtype *b1, Uint n1,
symtype *b2, Uint n2, Uint strand1, Uint strand2, int indel,
Sint (*sub)(symtype, symtype, void *), void *nfo,
Alignment *al1, Alignment *al2, int* lmv, int *lmr);
int*
localsplicedmatrix_test (void *space, symtype *a1, symtype *a2, Uint m,
symtype *b1, Uint n1, symtype *b2, Uint n2,
Uint strand1, Uint strand2, int indel,
Sint (*sub)(symtype, symtype, void *), void *nfo, int **lv, int **lr);
int*
localmultisplicedmatrix (void *space, symtype *a1, symtype *a2, Uint m,
symtype **b, Uint *n, Uint *strand, Uint noofseqs, int indel, int trans,
Sint (*sub)(symtype, symtype, void *), void *nfo, int ***lv, int ***lr, int ***lc);
int***
localmultisplicedmatrixopt (void *space, symtype *a1, symtype *a2, Uint qrylen, Uint *m,
symtype **b, Uint *n, Uint *strand, Uint *qstart, Uint *qend, Uint *tstart, Uint *tend, Uint noofseqs, int indel, int trans,
Sint (*sub)(symtype, symtype, void *), void *nfo, int ***lv, int ***lr, int ***lc, PairUint **scr, char ****, PairUint *diag);
void
localmultisplicedtraceback (void *space, int *M, symtype *a1, symtype *a2, Uint m,
symtype **b, Uint* n, Uint *strand, Uint noofseqs, int indel, int trans,
Sint (*sub)(symtype, symtype, void *), void *nfo,
Alignment **al, int **lmv, int **lmr, int **lmc);
char***
localmultisplicedtracebackopt (void *space, int ***M, symtype *a1, symtype *a2, Uint qrylen, Uint *m,
symtype **b, Uint* n, Uint *strand, Uint *qstart, Uint *qend, Uint *tstart, Uint *tend, Uint noofseqs, int indel, int trans,
Sint (*sub)(symtype, symtype, void *), void *nfo,
Alignment **al, int **lmv, int **lmr, int **lmc, PairUint *);
#endif
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