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/*
* Ray -- Parallel genome assemblies for parallel DNA sequencing
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/>
*/
#ifndef _Loader
#define _Loader
#include "LoaderInterface.h"
#include "LoaderFactory.h"
#include "Read.h"
#include "ArrayOfReads.h"
#include <code/Mock/common_functions.h>
#include <RayPlatform/memory/MyAllocator.h>
#include <string>
#include <fstream>
#include <vector>
using namespace std;
/*
* Loader loads data files. Data can be formated as SFF, FASTA, and FASTQ.
* Ray makes no use of quality values, so Their encoding is irrelevant.
* \author Sébastien Boisvert
*/
class Loader{
LoaderFactory m_factory;
LoaderInterface*m_interface;
Rank m_rank;
bool m_show;
int DISTRIBUTION_ALLOCATOR_CHUNK_SIZE;
ArrayOfReads m_reads;
MyAllocator m_allocator;
LargeIndex m_currentOffset;
int m_maxToLoad;
LargeCount m_size;
void loadSequences();
public:
void constructor(const char*prefix,bool show,Rank rank);
int load(string file,bool isGenome);
LargeCount size();
Read*at(LargeIndex i);
void clear();
void reset();
};
#endif
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