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/*
Ray
Copyright (C) 2010, 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 "ExportLoader.h"
#include <code/Mock/constants.h>
#include <fstream>
#include <stdlib.h>
using namespace std;
ExportLoader::ExportLoader() {
addExtension("export.txt");
addExtension("qseq.txt");
}
int ExportLoader::open(string file){
m_f=fopen(file.c_str(),"r");
m_size=0;
m_loaded=0;
char buffer[RAY_MAXIMUM_READ_LENGTH];
while(NULL!=fgets(buffer,RAY_MAXIMUM_READ_LENGTH,m_f)){
m_size++;
}
fclose(m_f);
m_f=fopen(file.c_str(),"r");
return EXIT_SUCCESS;
}
void ExportLoader::load(int maxToLoad,ArrayOfReads*reads,MyAllocator*seqMyAllocator){
char buffer[RAY_MAXIMUM_READ_LENGTH];
int loadedSequences=0;
while(loadedSequences<maxToLoad && NULL!=fgets(buffer,RAY_MAXIMUM_READ_LENGTH,m_f)){
// find the 9th column
// index 8 if 0-based
// 1 -> 1 \t
// 2 -> 2 \t
// 8 -> 8 \t
//
// find the 8th \t
// then find the 9th \t
int theLength=strlen(buffer);
int positionFor8thTabulation=0;
int positionFor9thTabulation=0;
int tabulations=0;
int position=0;
while(position<theLength){
if(buffer[position]=='\t')
tabulations++;
if(tabulations==8 && positionFor8thTabulation==0)
positionFor8thTabulation=position;
if(tabulations==9 && positionFor9thTabulation==0)
positionFor9thTabulation=position;
position++;
}
buffer[positionFor9thTabulation]='\0';
char*dnaSequence=buffer+positionFor8thTabulation+1;
#ifdef DEBUG_EXPORT_FORMAT
cout<<" ExportLoader -> <sequence>"<<dnaSequence<<"</sequence>"<<endl;
#endif
Read t;
t.constructor(dnaSequence,seqMyAllocator,true);
reads->push_back(&t);
loadedSequences++;
m_loaded++;
}
if(m_loaded==m_size){
fclose(m_f);
}
}
int ExportLoader::getSize(){
return m_size;
}
void ExportLoader::close(){
}
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