|
1
|
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 193 2011-02-07 15:45:21Z andreas $
|
|
|
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,
|
|
|
37 const int istart, const int iend,
|
|
|
38 const int jstart, const int jend,
|
|
|
39 char *fdist_in, char *fdist_out);
|
|
|
40
|
|
|
41 #endif
|
|
|
42
|
