/*
 * Copyright (c) <2008 - 2012>, University of Washington, Simon Fraser University
 * 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.
 * - Neither the names of the University of Washington, Simon Fraser University, 
 *   nor the names of its contributors may 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.
 */

/*
  Authors: 
	Farhad Hormozdiari
        Faraz Hach
	Can Alkan
  Emails: 
	farhadh AT uw DOT edu
	fhach AT cs DOT sfu DOT ca
	calkan AT uw DOT edu
 */


#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <ctype.h>
#include "Common.h"
#include "RefGenome.h"

FILE *_rg_fp;
char *_rg_gen;
char *_rg_name;
int _rg_offset;
int _rg_contGen; 

/**********************************************/
int initLoadingRefGenome(char *fileName)
{
	char ch;
	_rg_fp = fileOpen (fileName, "r");
	if (fscanf(_rg_fp, "%c", &ch))
	{
		if (ch == '>')
		{
			_rg_contGen = 0;
			_rg_offset = 0;
			_rg_gen = getMem(CONTIG_MAX_SIZE);
			_rg_name = getMem(CONTIG_NAME_SIZE);
			return 1;
		}
	}
	return 0;
}
/**********************************************/
void finalizeLoadingRefGenome()
{
	freeMem(_rg_gen, CONTIG_MAX_SIZE);
	freeMem(_rg_name, CONTIG_NAME_SIZE); 
	fclose(_rg_fp);
}
/**********************************************/
int loadRefGenome(char **refGen, char **refGenName, int *refGenOff)
{
	char ch;
	int i;
	int returnVal = 0;
	int actualSize=0;
	int size;
	char *tmp;
	
	// New Conting 
	if (!_rg_contGen)
	{
		size = 0;
		tmp = fgets(_rg_name, SEQ_MAX_LENGTH, _rg_fp);
	}
	else
	{
		size=strlen(_rg_gen);
		for( i = 0 ; i < CONTIG_OVERLAP ; i++ )
		{
			
			_rg_gen[i] = _rg_gen[size-CONTIG_OVERLAP+i];
			if (_rg_gen[i] != 'N')
				actualSize++;
		}
		size = CONTIG_OVERLAP;
	}
	while( fscanf(_rg_fp, "%c", &ch) > 0 )
	{
		if (ch == '>')
		{
			_rg_contGen = 0;
			returnVal = 1;
			break;
		}
		else if (!isspace(ch))
		{
			ch = toupper(ch);
			_rg_gen[size++] = ch;
			if (ch != 'N')
			{
				actualSize++;
			}
			if (actualSize == CONTIG_SIZE || size == CONTIG_MAX_SIZE)
			{
				_rg_contGen = 1;
				returnVal=1;
				break;
			}
		}

	}

	_rg_gen[size] = '\0';
	for (i=strlen(_rg_name)-1; i >= 0; i--)
		if (!isspace(_rg_name[i]))
			break;
	_rg_name[i+1] = '\0';

	*refGenOff = _rg_offset;
	*refGenName = _rg_name;
	*refGen = _rg_gen;

	if (_rg_contGen == 1)
	{
		_rg_offset += size-CONTIG_OVERLAP;
	}
	else
	{
		_rg_offset = 0;
	}
	
	
	return returnVal;
}
/**********************************************/