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/*
Ray
Copyright (C) 2010, 2011, 2012 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 _IndexerWorker
#define _IndexerWorker
#include "DynamicVector.h"
#include <code/Mock/Parameters.h>
#include <code/SequencesLoader/ArrayOfReads.h>
#include <RayPlatform/memory/RingAllocator.h>
#include <RayPlatform/memory/MyAllocator.h>
#include <RayPlatform/communication/VirtualCommunicator.h>
#include <RayPlatform/scheduling/Worker.h>
#include <stdint.h>
#include <fstream>
using namespace std;
/**
* this class is a worker for sequence indexing
* Optimal read markers are selected by IndexerWorker
* \author Sébastien Boisvert
*/
// TODO: convert this to Worker
class IndexerWorker /*: public Worker*/{
MessageTag RAY_MPI_TAG_ATTACH_SEQUENCE;
MessageTag RAY_MPI_TAG_REQUEST_VERTEX_COVERAGE;
map<int,map<int,int> >*m_forwardStatistics;
map<int,map<int,int> >*m_reverseStatistics;
ofstream*m_readMarkerFile;
ArrayOfReads*m_reads;
int m_sequenceId;
bool m_done;
int m_position;
VirtualCommunicator*m_virtualCommunicator;
bool m_indexedTheVertex;
Parameters*m_parameters;
int m_workerId;
bool m_checkedCoverage;
RingAllocator*m_outboxAllocator;
bool m_forwardIndexed;
bool m_reverseIndexed;
bool m_vertexInitiated;
bool m_vertexIsDone;
bool m_coverageRequested;
bool m_fetchedCoverageValues;
MyAllocator*m_allocator;
DynamicVector<Kmer> m_vertices;
DynamicVector<int> m_coverages;
int getThreshold(vector<int>*data);
public:
void constructor(int sequenceId,Parameters*parameters,RingAllocator*outboxAllocator,
VirtualCommunicator*vc,WorkerHandle workerId,ArrayOfReads*a,MyAllocator*allocator,
ofstream*f,
map<int,map<int,int> >*forwardStatistics,
map<int,map<int,int> >*reverseStatistics,
MessageTag RAY_MPI_TAG_ATTACH_SEQUENCE,
MessageTag RAY_MPI_TAG_REQUEST_VERTEX_COVERAGE
);
/** work a little bit
* the class Worker provides no implementation for that
*/
void work();
/** is the worker done doing its things */
bool isDone();
/** get the worker number */
WorkerHandle getWorkerIdentifier();
};
#endif
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