Clustal Omega  1.0.3
src/clustal/pair_dist.h
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00001 /*********************************************************************
00002  * Clustal Omega - Multiple sequence alignment
00003  *
00004  * Copyright (C) 2010 University College Dublin
00005  *
00006  * Clustal-Omega is free software; you can redistribute it and/or
00007  * modify it under the terms of the GNU General Public License as
00008  * published by the Free Software Foundation; either version 2 of the
00009  * License, or (at your option) any later version.
00010  *
00011  * This file is part of Clustal-Omega.
00012  *
00013  ********************************************************************/
00014 
00015 /*
00016  *  RCS $Id: pair_dist.h 193 2011-02-07 15:45:21Z andreas $
00017  */
00018 
00019 
00020 #ifndef CLUSTALO_PAIR_DIST_H
00021 #define CLUSTALO_PAIR_DIST_H
00022 
00023 #define PAIRDIST_UNKNOWN 0
00024 /* k-tuple distances: Wilbur and Lipman (1983) */
00025 #define PAIRDIST_KTUPLE 1
00026 /* fractional identity between aligned sequences. denominator is
00027  * minimum seq len (see squid:aligneval.c) */
00028 #define PAIRDIST_SQUIDID 2
00029 /* SQUIDID + Kimura correction */
00030 #define PAIRDIST_SQUIDID_KIMURA 3
00031 
00032 #include "seq.h"
00033 #include "symmatrix.h"
00034 
00035 extern int
00036 PairDistances(symmatrix_t **distmat, mseq_t *mseq, const int pairdist_type,
00037               const int istart, const int iend,
00038               const int jstart, const int jend,
00039               char *fdist_in, char *fdist_out);
00040 
00041 #endif
00042