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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 _VerticesExtractor
#define _VerticesExtractor
#include "GridTable.h"
#include <code/Mock/Parameters.h>
#include <code/Mock/common_functions.h>
#include <code/SequencesLoader/ArrayOfReads.h>
#include <code/SequencesLoader/Read.h>
#include <RayPlatform/profiling/Derivative.h>
#include <RayPlatform/profiling/Profiler.h>
#include <RayPlatform/communication/Message.h>
#include <RayPlatform/communication/BufferedData.h>
#include <RayPlatform/memory/RingAllocator.h>
#include <RayPlatform/core/ComputeCore.h>
#include <RayPlatform/structures/StaticVector.h>
#include <set>
#include <vector>
using namespace std;
__DeclarePlugin(VerticesExtractor);
__DeclareSlaveModeAdapter(VerticesExtractor,RAY_SLAVE_MODE_ADD_EDGES);
/*
* Any MPI rank has some reads to process.
* VerticesExtractor extracts k-mers from these reads.
* It also computes arcs between k-mers.
* These bits are then sent (buffered) to
* their respective owners.
*
* \author Sébastien Boisvert
*/
class VerticesExtractor: public CorePlugin{
__AddAdapter(VerticesExtractor,RAY_SLAVE_MODE_ADD_EDGES);
MessageTag RAY_MPI_TAG_VERTEX_INFO_REPLY;
MessageTag RAY_MPI_TAG_BUILD_GRAPH;
MessageTag RAY_MPI_TAG_WRITE_KMERS;
MessageTag RAY_MPI_TAG_WRITE_KMERS_REPLY;
MessageTag RAY_MPI_TAG_IN_EDGES_DATA;
MessageTag RAY_MPI_TAG_OUT_EDGES_DATA;
MessageTag RAY_MPI_TAG_VERTICES_DATA;
MessageTag RAY_MPI_TAG_VERTICES_DISTRIBUTED;
SlaveMode RAY_SLAVE_MODE_ADD_EDGES;
SlaveMode RAY_SLAVE_MODE_WRITE_KMERS;
Derivative m_derivative;
Profiler*m_profiler;
/** checkpointing */
bool m_checkedCheckpoint;
GridTable*m_subgraph;
char m_readSequence[RAY_MAXIMUM_READ_LENGTH];
bool m_distributionIsCompleted;
Parameters*m_parameters;
int m_rank;
RingAllocator*m_outboxAllocator;
StaticVector*m_outbox;
int*m_mode;
int m_mode_send_vertices_sequence_id;
int m_mode_send_vertices_sequence_id_position;
bool m_hasPreviousVertex;
Kmer m_previousVertex;
Kmer m_previousVertexRC;
BufferedData m_bufferedDataForOutgoingEdges;
BufferedData m_bufferedDataForIngoingEdges;
int m_pendingMessages;
ArrayOfReads*m_myReads;
int m_size;
/** useless state, legacy code **/
bool m_reverseComplementVertex;
bool m_finished;
public:
void constructor(int size,Parameters*parameters,GridTable*graph,
StaticVector*outbox,RingAllocator*outboxAllocator,ArrayOfReads*myReads
);
void call_RAY_SLAVE_MODE_ADD_EDGES();
LargeCount getDefaultNumberOfBitsForBloomFilter();
void setReadiness();
bool finished();
void flushAll(RingAllocator*m_outboxAllocator,StaticVector*m_outbox,int rank);
void assertBuffersAreEmpty();
void incrementPendingMessages();
void showBuffers();
void enableReducer();
bool isDistributionCompleted();
void setDistributionAsCompleted();
void setProfiler(Profiler*profiler);
void registerPlugin(ComputeCore*core);
void resolveSymbols(ComputeCore*core);
};
#endif
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