Clustal Omega  1.2.4
ktuple_pair.h
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1 /*********************************************************************
2  * Clustal Omega - Multiple sequence alignment
3  *
4  * Copyright (C) 2010 University College Dublin
5  *
6  * Clustal-Omega is free software; you can redistribute it and/or
7  * modify it under the terms of the GNU General Public License as
8  * published by the Free Software Foundation; either version 2 of the
9  * License, or (at your option) any later version.
10  *
11  * This file is part of Clustal-Omega.
12  *
13  ********************************************************************/
14 
15 /*
16  * RCS $Id: ktuple_pair.h 193 2011-02-07 15:45:21Z andreas $
17  */
18 
19 /* K-Tuple code for pairwise alignment (Wilbur and Lipman (1983)
20  * Most code taken from showpair (Clustal 1.83)
21  */
22 
23 
24 #ifndef CLUSTALO_KTUPLE_PAIR_H
25 #define CLUSTALO_KTUPLE_PAIR_H
26 
27 #include "seq.h"
28 #include "symmatrix.h"
29 #include "progress.h"
30 
31 typedef struct {
32  int ktup;
33  int window;
34  int wind_gap;
35  int signif;
37 
38 
39 extern void
40 KTuplePairDist(symmatrix_t *tmat, mseq_t *mseq,
41  int istart, int iend,
42  int jstart, int jend,
43  ktuple_param_t *aln_param,
44  progress_t *prProgress,
45  unsigned long int *ulStepNo, unsigned long int ulTotalStepNo);
46 
47 #endif
ktuple_param_t::signif
int signif
Definition: ktuple_pair.h:35
mseq_t
structure for storing multiple sequences
Definition: seq.h:47
ktuple_param_t
Definition: ktuple_pair.h:31
seq.h
ktuple_param_t::ktup
int ktup
Definition: ktuple_pair.h:32
ktuple_param_t::wind_gap
int wind_gap
Definition: ktuple_pair.h:34
symmatrix.h
progress_t
Definition: progress.h:25
symmatrix_t
symmetric matrix structure
Definition: symmatrix.h:48
KTuplePairDist
void KTuplePairDist(symmatrix_t *tmat, mseq_t *mseq, int istart, int iend, int jstart, int jend, ktuple_param_t *aln_param, progress_t *prProgress, unsigned long int *ulStepNo, unsigned long int ulTotalStepNo)
Definition: ktuple_pair.c:625
progress.h
ktuple_param_t::window
int window
Definition: ktuple_pair.h:33