Mercurial > repos > clustalomega > clustalomega
diff 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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/clustalomega/clustal-omega-1.0.2/src/clustal/pair_dist.h Thu Jul 21 13:35:08 2011 -0400 @@ -0,0 +1,42 @@ +/********************************************************************* + * Clustal Omega - Multiple sequence alignment + * + * Copyright (C) 2010 University College Dublin + * + * Clustal-Omega is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License as + * published by the Free Software Foundation; either version 2 of the + * License, or (at your option) any later version. + * + * This file is part of Clustal-Omega. + * + ********************************************************************/ + +/* + * RCS $Id: pair_dist.h 193 2011-02-07 15:45:21Z andreas $ + */ + + +#ifndef CLUSTALO_PAIR_DIST_H +#define CLUSTALO_PAIR_DIST_H + +#define PAIRDIST_UNKNOWN 0 +/* k-tuple distances: Wilbur and Lipman (1983) */ +#define PAIRDIST_KTUPLE 1 +/* fractional identity between aligned sequences. denominator is + * minimum seq len (see squid:aligneval.c) */ +#define PAIRDIST_SQUIDID 2 +/* SQUIDID + Kimura correction */ +#define PAIRDIST_SQUIDID_KIMURA 3 + +#include "seq.h" +#include "symmatrix.h" + +extern int +PairDistances(symmatrix_t **distmat, mseq_t *mseq, const int pairdist_type, + const int istart, const int iend, + const int jstart, const int jend, + char *fdist_in, char *fdist_out); + +#endif +