Mercurial > repos > clustalomega > clustalomega
comparison clustalomega/clustal-omega-1.0.2/src/clustal/pair_dist.h @ 1:bc707542e5de
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author | clustalomega |
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date | Thu, 21 Jul 2011 13:35:08 -0400 |
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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 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 |