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/*
* njdist.h
*
* $Id: cmdargs.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.
*
*****************************************************************************
*
* AUTHOR:
*
* Luke Sheneman
* sheneman@cs.uidaho.edu
*
*/
#ifndef _INC_NJ_CMDARGS_H_
#define _INC_NJ_CMDARGS_H_ 1
#include "clearcut.h"
/* some datatypes */
typedef struct _STRUCT_NJ_ARGS {
char *infilename; /* the name of the input file */
char *outfilename; /* the name of the output tree */
char *matrixout; /* the name of the distance matrix output file */
int input_mode;
int aligned_flag;
int verbose_flag;
int quiet_flag;
int stdin_flag;
int stdout_flag;
int help;
int version;
int norandom;
int shuffle;
int dna_flag;
int protein_flag;
int seed;
/* correction models for distance */
int correction_model;
int jukes_flag;
int kimura_flag;
/* flag for using traditional neighbor-joining */
int neighbor;
/* number of trees to output */
int ntrees;
/* exponential notation output */
int expblen; /* exp notation for tree branch lengths */
int expdist; /* exp notation for distances in matrix output */
} NJ_ARGS;
/* some function prototypes */
NJ_ARGS *
NJ_handle_args(int argc,
char *argv[]);
void
NJ_print_args(NJ_ARGS *nj_args);
void
NJ_usage(void);
#endif /* _INC_NJ_CMDARGS_H_ */
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