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/*
Ray -- Parallel genome assemblies for parallel DNA sequencing
Copyright (C) 2011, 2012, 2013 Sébastien Boisvert
http://DeNovoAssembler.SourceForge.Net/
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, version 3 of the License.
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 have received a copy of the GNU General Public License
along with this program (gpl-3.0.txt).
see <http://www.gnu.org/licenses/>
*/
#include "ColorSpaceLoader.h"
#include <code/Mock/common_functions.h>
#include <stdlib.h>
#include <fstream>
#include <iostream>
#include <string.h>
#include <assert.h>
using namespace std;
ColorSpaceLoader::ColorSpaceLoader() {
addExtension(".csfasta");
addExtension(".csfa");
}
int ColorSpaceLoader::open(string file){
m_f=fopen(file.c_str(),"r");
m_size=0;
m_loaded=0;
char bufferForLine[RAY_MAXIMUM_READ_LENGTH];
while(NULL!=fgets(bufferForLine,RAY_MAXIMUM_READ_LENGTH,m_f)){
if(bufferForLine[0]=='#'){
continue;// skip csfasta comment
}
if(bufferForLine[0]=='>'){
char*returnValue=fgets(bufferForLine,RAY_MAXIMUM_READ_LENGTH,m_f);
assert(returnValue != NULL);
m_size++;
}
}
fclose(m_f);
m_f=fopen(file.c_str(),"r");
return EXIT_SUCCESS;
}
void ColorSpaceLoader::load(int maxToLoad,ArrayOfReads*reads,MyAllocator*seqMyAllocator){
char bufferForLine[RAY_MAXIMUM_READ_LENGTH];
int loadedSequences=0;
while(m_loaded<m_size&& loadedSequences<maxToLoad){
if(NULL==fgets(bufferForLine,RAY_MAXIMUM_READ_LENGTH,m_f))
continue;
if(bufferForLine[0]=='#'){
continue;// skip csfasta comment
}
// read two lines
if(bufferForLine[0]=='>'){
char*returnValue=fgets(bufferForLine,RAY_MAXIMUM_READ_LENGTH,m_f);
assert(returnValue != NULL);
for(int j=0;j<(int)strlen(bufferForLine);j++){
if(bufferForLine[j]==DOUBLE_ENCODING_A_COLOR){
bufferForLine[j]=SYMBOL_A;
}else if(bufferForLine[j]==DOUBLE_ENCODING_T_COLOR){
bufferForLine[j]=SYMBOL_T;
}else if(bufferForLine[j]==DOUBLE_ENCODING_C_COLOR){
bufferForLine[j]=SYMBOL_C;
}else if(bufferForLine[j]==DOUBLE_ENCODING_G_COLOR){
bufferForLine[j]=SYMBOL_G;
}
}
Read t;
// remove the leading T & first color
t.constructor(bufferForLine+2,seqMyAllocator,true);
reads->push_back(&t);
loadedSequences++;
m_loaded++;
}
}
if(m_loaded==m_size){
fclose(m_f);
}
}
int ColorSpaceLoader::getSize(){
return m_size;
}
void ColorSpaceLoader::close(){
}
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