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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 _SeedWorker
#define _SeedWorker
#include <code/SeedingData/GraphPath.h>
#include <code/Mock/Parameters.h>
#include <RayPlatform/memory/RingAllocator.h>
#include <RayPlatform/communication/VirtualCommunicator.h>
#include <RayPlatform/scheduling/Worker.h>
#include <stdint.h>
#include <vector>
using namespace std;
/*
* Given a Kmer, SeedWorker determines if it spawns a seed.
* If yes, it computes the seed.
*
* \author Sébastien Boisvert
*/
class SeedWorker : public Worker {
MessageTag RAY_MPI_TAG_GET_VERTEX_EDGES_COMPACT;
MessageTag RAY_MPI_TAG_REQUEST_VERTEX_COVERAGE;
int m_mainVertexCoverage;
bool m_hasDeadEnd;
bool m_debugSeeds;
bool m_elongationMode;
map<Kmer,int> m_cache;
WorkerHandle m_workerIdentifier;
bool m_finished;
Kmer m_SEEDING_currentChildVertex;
bool m_SEEDING_InedgesReceived;
Kmer m_SEEDING_currentParentVertex;
bool m_SEEDING_ingoingEdgesDone;
int m_SEEDING_numberOfOutgoingEdgesWithSeedCoverage;
Kmer m_SEEDING_currentVertex;
int m_SEEDING_numberOfIngoingEdges;
bool m_SEEDING_vertexCoverageRequested;
bool m_SEEDING_edgesReceived;
bool m_SEEDING_testInitiated;
int m_SEEDING_ingoingEdgeIndex;
int m_SEEDING_outgoingEdgeIndex;
vector<Kmer> m_SEEDING_receivedIngoingEdges;
vector<int> m_ingoingCoverages;
vector<int> m_outgoingCoverages;
Parameters*m_parameters;
bool m_SEEDING_vertexCoverageReceived;
vector<Kmer> m_SEEDING_receivedOutgoingEdges;
int m_SEEDING_numberOfOutgoingEdges;
int m_SEEDING_numberOfIngoingEdgesWithSeedCoverage;
bool m_SEEDING_outgoingEdgesDone;
bool m_SEEDING_InedgesRequested;
bool m_outgoingEdgesReceived;
bool m_SEEDING_edgesRequested;
bool m_ingoingEdgesReceived;
int m_wordSize;
GraphPath m_SEEDING_seed;
bool m_SEEDING_firstVertexParentTestDone;
/*
* Store visited vertices.
*/
set<Kmer> m_SEEDING_vertices;
Kmer m_SEEDING_first;
bool m_SEEDING_firstVertexTestDone;
int m_SEEDING_numberOfSeedCoverageCandidates;
int m_rank;
int m_size;
RingAllocator*m_outboxAllocator;
int m_SEEDING_receivedVertexCoverage;
bool m_SEEDING_1_1_test_result;
int getRank();
int getSize();
bool m_SEEDING_1_1_test_done;
VirtualCommunicator*m_virtualCommunicator;
/*
* Additional quality control tests.
*/
bool m_checkedHead;
bool m_checkedTail;
bool m_endChecksModeStarted;
bool m_endChecksMode;
bool m_vertexFetcherStarted;
vector<Kmer> m_vertexFetcherParents;
vector<Kmer> m_vertexFetcherChildren;
CoverageDepth m_vertexFetcherCoverage;
bool m_vertexFetcherReceivedData;
bool m_vertexFetcherRequestedData;
bool m_headIsDeadEnd;
bool m_tailIsDeadEnd;
// topological algorithm for graphs
vector<Kmer> m_verticesBefore;
vector<Kmer> m_verticesAfter;
void performChecksOnPathEnds();
bool fetchVertexData(Kmer*kmer);
bool getPathBefore(Kmer*kmer,int depth);
bool getPathAfter(Kmer*kmer,int depth);
public:
void constructor(Kmer*vertex,Parameters*parameters,RingAllocator*outboxAllocator,
VirtualCommunicator*vc,WorkerHandle workerId,
MessageTag RAY_MPI_TAG_GET_VERTEX_EDGES_COMPACT,
MessageTag RAY_MPI_TAG_REQUEST_VERTEX_COVERAGE
);
GraphPath*getSeed();
void do_1_1_test();
/** 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();
bool isHeadADeadEnd();
bool isTailADeadEnd();
void enableDebugMode();
bool isBubbleWeakComponent();
};
#endif
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