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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 "Loader.h"
#include "Read.h"
#include <sstream>
#include <iostream>
#include <assert.h>
#include <string>
#include <vector>
#include <stdlib.h>
using namespace std;
void Loader::constructor(const char*prefix,bool show,Rank rank){
m_rank=rank;
m_maxToLoad=500000;
m_currentOffset=0;
//m_type=FORMAT_NULL;
ostringstream prefixFull;
prefixFull<<prefix<<"_Loader";
m_show=show;
m_allocator.constructor(4194304,"RAY_MALLOC_TYPE_LOADER_ALLOCATOR",m_show);
m_reads.constructor(&m_allocator);
}
int Loader::load(string file,bool isGenome){
ifstream f(file.c_str());
bool exists=!(f.fail());
f.close();
if(!exists){
cout<<"Ray: cannot access '"<<file<<"': No such file or directory"<<endl;
return EXIT_FAILURE;// ERROR
}
if(file.length()<4){
(cout)<<"Error: "<<file<<endl;
return EXIT_FAILURE;
}
#if 0
if(isGenome){
m_fasta.load(file,&m_reads,&m_allocator);
m_size=m_reads.size();
return EXIT_SUCCESS;
}
#endif
cout<<"Rank "<<m_rank<<" is fetching file "<<file<<" with lazy loading (please wait...)"<<endl;
m_interface=m_factory.makeLoader(file);
if(m_interface!=NULL){
m_interface->open(file);
m_size=m_interface->getSize();
return EXIT_SUCCESS;
}
cout<<"Error: "<<file<<": unknown extension, exiting. (see Ray --help for valid extensions)"<<endl;
return EXIT_FAILURE;
}
Read*Loader::at(LargeIndex i){
#ifdef CONFIG_ASSERT
assert(i<m_size);
#endif
if(i>=m_currentOffset+m_reads.size()){
loadSequences();
}
#ifdef CONFIG_ASSERT
if(i>=m_currentOffset+m_reads.size()){
cout<<"i= "<<i<<" m_currentOffset= " << m_currentOffset<<" m_reads.size: " << m_reads.size()<<endl;
}
assert(i<m_currentOffset+m_reads.size());
#endif
return m_reads.at(i-m_currentOffset);
}
LargeCount Loader::size(){
return m_size;
}
void Loader::clear(){
m_reads.clear();
m_allocator.clear();
m_size=0;
m_currentOffset=0;
//m_type=FORMAT_NULL;
#ifdef CONFIG_ASSERT
assert(m_reads.size()==0);
#endif
}
void Loader::loadSequences(){
//cout << "[DEBUG] loadSequences." << endl;
m_currentOffset += m_reads.size();
m_allocator.reset();
m_reads.reset();
if(m_interface==NULL) {
//cout << "[DEBUG] no interface found" << endl;
return;
}
m_interface->load(m_maxToLoad,&m_reads,&m_allocator);
//cout << "[DEBUG] loaded " << m_reads.size() << " entries into memory" << endl;
}
void Loader::reset(){
m_allocator.reset();
m_reads.reset();
m_size=0;
m_currentOffset=0;
if(m_interface!=NULL){
m_interface->close();
m_interface=NULL;
}
//m_type=FORMAT_NULL;
#ifdef CONFIG_ASSERT
assert(m_reads.size()==0);
#endif
}
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