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comparison clustalomega/clustal-omega-0.2.0/src/clustal/pair_dist.h @ 0:ff1768533a07

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Migrated tool version 0.2 from old tool shed archive to new tool shed repository
author clustalomega
date Tue, 07 Jun 2011 17:04:25 -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