Clustal Omega  1.0.3
src/clustal/ktuple_pair.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: ktuple_pair.h 193 2011-02-07 15:45:21Z andreas $
00017  */
00018 
00019 /* K-Tuple code for pairwise alignment (Wilbur and Lipman (1983)
00020  * Most code taken from showpair (Clustal 1.83)
00021  */
00022 
00023 
00024 #ifndef CLUSTALO_KTUPLE_PAIR_H
00025 #define CLUSTALO_KTUPLE_PAIR_H
00026 
00027 #include "seq.h"
00028 #include "symmatrix.h"
00029 #include "progress.h"
00030 
00031 typedef struct {
00032     int ktup;
00033     int window;
00034     int wind_gap;
00035     int signif;
00036 } ktuple_param_t;
00037 
00038 
00039 extern void
00040 KTuplePairDist(symmatrix_t *tmat, mseq_t *mseq,
00041                int istart, int iend,
00042                int jstart, int jend,
00043                ktuple_param_t *aln_param,
00044                progress_t *prProgress, 
00045                unsigned long int *ulStepNo, unsigned long int ulTotalStepNo);
00046 
00047 #endif