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/*
* dist.h
*
* $Id: dist.h,v 1.1 2006/08/25 03:26:44 sheneman Exp $
*
*****************************************************************************
*
* Copyright (c) 2004, Luke Sheneman
* All rights reserved.
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions
* are met:
*
* + Redistributions of source code must retain the above copyright
* notice, this list of conditions and the following disclaimer.
* + Redistributions in binary form must reproduce the above copyright
* notice, this list of conditions and the following disclaimer in
* the documentation and/or other materials provided with the
* distribution.
* + The names of its contributors may not be used to endorse or promote
* products derived from this software without specific prior
* written permission.
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
* ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
* LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
* CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
* SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
* INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
* CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
* ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
* POSSIBILITY OF SUCH DAMAGE.
*
*****************************************************************************
*
* Compute a distance matrix given a set of sequences
*
*****************************************************************************
*
* AUTHOR:
*
* Luke Sheneman
* sheneman@cs.uidaho.edu
*
*/
#ifndef _INC_DIST_H_
#define _INC_DIST_H_ 1
#include "fasta.h"
#include "clearcut.h"
/*
* An arbitrarily large distance to represent distances
* which are too great to accurately correct.
*/
#define NJ_BIGDIST 10.0
/* some function prototypes */
DMAT *
NJ_build_distance_matrix(NJ_ARGS *nj_args);
DMAT *
NJ_compute_dmat(NJ_ARGS *nj_args,
NJ_alignment *alignment);
float
NJ_pw_percentid(NJ_alignment *alignment,
long int x,
long int y);
long int
NJ_pw_differences(NJ_alignment *alignment,
long int x,
long int y,
long int *residues);
void
NJ_no_correction(DMAT *dmat,
NJ_alignment *alignment);
void
NJ_DNA_jc_correction(DMAT *dmat,
NJ_alignment *alignment);
void
NJ_PROTEIN_jc_correction(DMAT *dmat,
NJ_alignment *alignment);
void
NJ_DNA_k2p_correction(DMAT *dmat,
NJ_alignment *alignment);
void
NJ_PROTEIN_kimura_correction(DMAT *dmat,
NJ_alignment *alignment);
void
NJ_DNA_count_tt(NJ_alignment *alignment,
long int x,
long int y,
long int *transitions,
long int *transversions,
long int *residues);
#endif /* _INC_DIST_H_ */
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