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/*
* Ray -- Parallel genome assemblies for parallel DNA sequencing
* Copyright (C) 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 _AnnotationFetcher_h
#define _AnnotationFetcher_h
#include <code/SeedExtender/Direction.h>
#include <code/KmerAcademyBuilder/Kmer.h>
#include <code/Mock/Parameters.h>
#include <RayPlatform/communication/VirtualCommunicator.h>
#include <RayPlatform/scheduling/Worker.h>
#include <vector>
using namespace std;
/**
* This is a building block to fetch annotations.
* This is compatible with seeds and contigs.
*
* \author Sébastien Boisvert
*/
class AnnotationFetcher{
Rank m_rank;
Parameters*m_parameters;
VirtualCommunicator*m_virtualCommunicator;
WorkerHandle m_identifier;
RingAllocator * m_outboxAllocator;
bool m_queryWasSent;
bool m_initializedDirectionFetcher;
bool m_fetchedCount;
int m_pathIndex;
int m_numberOfPaths;
vector<Direction> m_directions;
bool m_reverseStrand;
MessageTag RAY_MPI_TAG_ASK_VERTEX_PATHS_SIZE;
MessageTag RAY_MPI_TAG_ASK_VERTEX_PATH;
public:
void initialize(Parameters*parameters, VirtualCommunicator*virtualCommunicator,
WorkerHandle identifier, RingAllocator * outboxAllocator,
MessageTag RAY_MPI_TAG_ASK_VERTEX_PATHS_SIZE,
MessageTag RAY_MPI_TAG_ASK_VERTEX_PATH);
bool fetchDirections(Kmer*kmer);
void reset();
vector<Direction>* getDirections();
};
#endif
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