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/*
* fasta.h
*
* $Id: fasta.h,v 1.3 2007/11/27 18:33:59 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.
*
*****************************************************************************
*
* AUTHOR:
*
* Luke Sheneman
* sheneman@cs.uidaho.edu
*
*/
#ifndef _INC_NJ_FASTA_H_
#define _INC_NJ_FASTA_H_ 1
#include "clearcut.h"
#define NJ_INITIAL_BUFFER_SIZE 512
#define NJ_INITIAL_NSEQS 64
#define NJ_FASTA_MODE_TITLE 100
#define NJ_FASTA_MODE_SEQUENCE 101
#define NJ_FASTA_MODE_NEWLINE 102
#define NJ_FASTA_MODE_UNKNOWN 103
typedef struct _STRUCT_NJ_ALIGNMENT {
long int nseq;
long int length;
char **titles;
char *data;
} NJ_alignment;
NJ_alignment *
NJ_read_fasta(NJ_ARGS *nj_args);
void
NJ_print_alignment(NJ_alignment *alignment);
void
NJ_free_alignment(NJ_alignment *alignment);
int
NJ_taxaname_unique(NJ_alignment *alignment);
#endif /* _INC_NJ_FASTA_H_ */
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