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annotate 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 /*********************************************************************
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2 * Clustal Omega - Multiple sequence alignment
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3 *
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4 * Copyright (C) 2010 University College Dublin
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5 *
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6 * Clustal-Omega is free software; you can redistribute it and/or
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7 * modify it under the terms of the GNU General Public License as
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8 * published by the Free Software Foundation; either version 2 of the
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9 * License, or (at your option) any later version.
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10 *
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11 * This file is part of Clustal-Omega.
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12 *
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13 ********************************************************************/
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14
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15 /*
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16 * RCS $Id: pair_dist.h 193 2011-02-07 15:45:21Z andreas $
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17 */
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20 #ifndef CLUSTALO_PAIR_DIST_H
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21 #define CLUSTALO_PAIR_DIST_H
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23 #define PAIRDIST_UNKNOWN 0
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24 /* k-tuple distances: Wilbur and Lipman (1983) */
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25 #define PAIRDIST_KTUPLE 1
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26 /* fractional identity between aligned sequences. denominator is
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27 * minimum seq len (see squid:aligneval.c) */
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28 #define PAIRDIST_SQUIDID 2
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29 /* SQUIDID + Kimura correction */
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30 #define PAIRDIST_SQUIDID_KIMURA 3
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32 #include "seq.h"
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33 #include "symmatrix.h"
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35 extern int
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36 PairDistances(symmatrix_t **distmat, mseq_t *mseq, const int pairdist_type,
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37 const int istart, const int iend,
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38 const int jstart, const int jend,
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39 char *fdist_in, char *fdist_out);
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41 #endif
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