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
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