Clustal Omega  1.2.4
pair_dist.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: pair_dist.h 302 2016-06-13 13:35:50Z fabian $
17  */
18 
19 
20 #ifndef CLUSTALO_PAIR_DIST_H
21 #define CLUSTALO_PAIR_DIST_H
22 
23 #define PAIRDIST_UNKNOWN 0
24 /* k-tuple distances: Wilbur and Lipman (1983) */
25 #define PAIRDIST_KTUPLE 1
26 /* fractional identity between aligned sequences. denominator is
27  * minimum seq len (see squid:aligneval.c) */
28 #define PAIRDIST_SQUIDID 2
29 /* SQUIDID + Kimura correction */
30 #define PAIRDIST_SQUIDID_KIMURA 3
31 
32 #include "seq.h"
33 #include "symmatrix.h"
34 
35 extern int
36 PairDistances(symmatrix_t **distmat, mseq_t *mseq, const int pairdist_type, bool bPercID,
37  const int istart, const unsigned long int iend,
38  const int jstart, const unsigned long int jend,
39  char *fdist_in, char *fdist_out);
40 
41 #endif
42 
mseq_t
structure for storing multiple sequences
Definition: seq.h:46
seq.h
PairDistances
int PairDistances(symmatrix_t **distmat, mseq_t *mseq, const int pairdist_type, bool bPercID, const int istart, const unsigned long int iend, const int jstart, const unsigned long int jend, char *fdist_in, char *fdist_out)
compute or read precomputed distances for given sequences
Definition: pair_dist.c:276
symmatrix.h
symmatrix_t
symmetric matrix structure
Definition: symmatrix.h:47