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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 _ReadFetcher
#define _ReadFetcher
#include <code/SequencesIndexer/ReadAnnotation.h>
#include <code/Mock/Parameters.h>
#include <RayPlatform/structures/StaticVector.h>
#include <RayPlatform/memory/RingAllocator.h>
#include <RayPlatform/communication/VirtualCommunicator.h>
#include <vector>
#include <stdint.h>
using namespace std;
/**
* A class that fetches reads for a Kmer
* Pretty simple stuff.
*
* \author Sébastien Boisvert
*/
class ReadFetcher{
MessageTag RAY_MPI_TAG_REQUEST_VERTEX_READS;
WorkerHandle m_workerId;
VirtualCommunicator*m_virtualCommunicator;
Parameters*m_parameters;
RingAllocator*m_outboxAllocator;
StaticVector*m_outbox;
StaticVector*m_inbox;
vector<ReadAnnotation> m_reads;
Kmer m_vertex;
bool m_readsRequested;
void*m_pointer;
bool m_done;
public:
/**
* Initiate the object with a Kmer
*/
void constructor(Kmer*vertex,RingAllocator*outboxAllocator,StaticVector*inbox,StaticVector*outbox,Parameters*parameters,VirtualCommunicator*vc,WorkerHandle workerId,
MessageTag RAY_MPI_TAG_REQUEST_VERTEX_READS
);
/**
* Returns true if done
*/
bool isDone();
/**
* Advance the work to be done
*/
void work();
/**
* Get the requested information.
*/
vector<ReadAnnotation>*getResult();
};
#endif
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