/*
 *  Wellcome Trust Sanger Institute
 *  Copyright (C) 2011  Wellcome Trust Sanger Institute
 *  
 *  This program 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.
 *  
 *  You should have received a copy of the GNU General Public License
 *  along with this program; if not, write to the Free Software
 *  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
 */


#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "phylip_of_snp_sites.h"
#include "parse_phylip.h"
#include "string_cat.h"


void create_phylip_of_snp_sites(char filename[], int number_of_snps, char ** bases_for_snps, char ** sequence_names, int number_of_samples, int internal_nodes[])
{
	FILE *fasta_file_pointer;
	int sample_counter;
	int snp_counter;
	char * base_filename;
	
	base_filename = (char *) calloc(1024,sizeof(char));
	memcpy(base_filename, filename, 1024*sizeof(char));
	char extension[8] = {".phylip"};
	concat_strings_created_with_malloc(base_filename,extension);
	fasta_file_pointer = fopen(base_filename, "w");
	
	int number_of_leaves = number_of_samples;
	for(sample_counter=0; sample_counter< number_of_samples; sample_counter++)
	{
		if(internal_nodes[sample_counter] == 1)
		{
			number_of_leaves--;
		}
	}
	
	fprintf( fasta_file_pointer, "%d %d\n", number_of_leaves, number_of_snps);
	
	for(sample_counter=0; sample_counter< number_of_samples; sample_counter++)
	{
		// sequence_name can be more than 10 (relaxed phylip format) and contain [\w\s]
		//TODO check for illegal characters [^\w\s]
		if(internal_nodes[sample_counter] == 1)
		{
			continue;
		}
		fprintf( fasta_file_pointer, "%s\t", sequence_names[sample_counter]);
		
		for(snp_counter=0; snp_counter< number_of_snps; snp_counter++)
		{
			fprintf( fasta_file_pointer, "%c", bases_for_snps[snp_counter][sample_counter]);
		}
		fprintf( fasta_file_pointer, "\n");
	}
  fclose(fasta_file_pointer);
	free(base_filename);
}