nexus_common.h

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/* 
 * This file is part of biomcmc-lib, a low-level library for phylogenomic analysis.
 * Copyright (C) 2019-today  Leonardo de Oliveira Martins [ leomrtns at gmail.com;  http://www.leomartins.org ]
 *
 * biomcmc is free software; you can redistribute it and/or modify it under the terms of the GNU General Public
 * License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later
 * version.
 *
 * This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied 
 * warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more 
 * details (file "COPYING" or http://www.gnu.org/copyleft/gpl.html).
 */

#ifndef _biomcmc_nexus_common_h_
#define _biomcmc_nexus_common_h_

#include "char_vector.h"
#include "empirical_frequency.h"

#define MAX_NAME_LENGTH 4096 

char_vector new_char_vector_from_file (char *filename);

char* remove_nexus_comments (char **string, size_t *stringsize, FILE *stream);
char* lowercase_string (char *string);
char* uppercase_string (char *string);
char* remove_space_from_string (char *string);
bool nonempty_string (char *string);
bool nonempty_fasta_line (char *string);

#endif