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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 _SeedingData
#define _SeedingData
class SeedExtender;
#include "SeedWorker.h"
#include <code/KmerAcademyBuilder/Kmer.h>
#include <code/SeedExtender/SeedExtender.h>
#include <code/SeedingData/GraphPath.h>
#include <code/VerticesExtractor/GridTableIterator.h>
#include <code/VerticesExtractor/Vertex.h>
#include <code/Mock/common_functions.h>
#include <RayPlatform/communication/VirtualCommunicator.h>
#include <RayPlatform/structures/SplayTreeIterator.h>
#include <RayPlatform/structures/SplayNode.h>
#include <RayPlatform/core/ComputeCore.h>
#include <set>
using namespace std;
__DeclarePlugin(SeedingData);
__DeclareSlaveModeAdapter(SeedingData,RAY_SLAVE_MODE_START_SEEDING);
__DeclareSlaveModeAdapter(SeedingData,RAY_SLAVE_MODE_SEND_SEED_LENGTHS);
/*
* Computes seeds in the k-mer graph.
* The computation is not done actually by
* this class. It is a pool of workers that does the job.
* These workers push messages on the virtual
* communicator and the later groups messages.
* \author Sébastien Boisvert
*/
class SeedingData : public CorePlugin{
__AddAdapter(SeedingData,RAY_SLAVE_MODE_START_SEEDING);
__AddAdapter(SeedingData,RAY_SLAVE_MODE_SEND_SEED_LENGTHS);
/**
* the minimum seed coverage allowed
*/
CoverageDepth m_minimumSeedCoverageDepth;
MessageTag RAY_MPI_TAG_IS_DONE_SENDING_SEED_LENGTHS;
MessageTag RAY_MPI_TAG_SEEDING_IS_OVER;
MessageTag RAY_MPI_TAG_SEND_SEED_LENGTHS;
MessageTag RAY_MPI_TAG_SEND_SEED_LENGTHS_REPLY;
MessageTag RAY_MPI_TAG_GET_VERTEX_EDGES_COMPACT;
MessageTag RAY_MPI_TAG_REQUEST_VERTEX_COVERAGE;
SlaveMode RAY_SLAVE_MODE_DO_NOTHING;
SlaveMode RAY_SLAVE_MODE_START_SEEDING;
SlaveMode RAY_SLAVE_MODE_SEND_SEED_LENGTHS;
/*
* Some counters for sorting objects.
*/
int m_skippedObjectsWithDeadEndForHead;
int m_skippedObjectsWithDeadEndForTail;
int m_skippedObjectsWithTwoDeadEnds;
int m_skippedObjectsWithBubbleWeakComponent;
int m_skippedNotMine;
int m_skippedTooShort;
int m_skippedNotEnoughCoverage;
int m_eligiblePaths;
bool m_debugSeeds;
/** checkpointing */
bool m_checkedCheckpoint;
map<int,int>::iterator m_iterator;
bool m_flushAllMode;
VirtualCommunicator*m_virtualCommunicator;
bool m_initiatedIterator;
Rank m_rank;
int m_size;
RingAllocator*m_outboxAllocator;
StaticVector*m_outbox;
StaticVector*m_inbox;
int*m_seedCoverage;
int*m_mode;
set<WorkerHandle> m_activeWorkers;
set<WorkerHandle>::iterator m_activeWorkerIterator;
map<WorkerHandle,SeedWorker> m_aliveWorkers;
bool m_communicatorWasTriggered;
vector<WorkerHandle> m_workersDone;
vector<WorkerHandle> m_waitingWorkers;
vector<WorkerHandle> m_activeWorkersToRestore;
Parameters*m_parameters;
GridTable*m_subgraph;
GridTableIterator m_splayTreeIterator;
int m_wordSize;
int m_completedJobs;
int m_maximumAliveWorkers;
int m_maximumWorkers;
time_t m_last;
void loadCheckpoint();
void writeCheckpoints();
public:
// TODO: move these attributes in the private zone
map<int,int> m_masterSeedLengths;
map<int,int> m_slaveSeedLengths;
bool m_SEEDING_edgesRequested;
int m_SEEDING_ingoingEdgeIndex;
vector<Kmer> m_SEEDING_receivedOutgoingEdges;
Kmer m_SEEDING_currentVertex;
int m_SEEDING_receivedVertexCoverage;
vector<Kmer> m_SEEDING_receivedIngoingEdges;
bool m_SEEDING_InedgesReceived;
int m_SEEDING_outgoingEdgeIndex;
bool m_SEEDING_vertexCoverageRequested;
bool m_SEEDING_vertexCoverageReceived;
SplayTreeIterator<uint64_t,Vertex>*m_SEEDING_iterator;
SplayNode<Kmer,Vertex>*m_SEEDING_node;
uint64_t m_SEEDING_receivedKey;
bool m_SEEDING_vertexKeyAndCoverageReceived;
int m_SEEDING_currentChildRank;
bool m_SEEDING_edge_initiated;
bool m_SEEDING_NodeInitiated;
bool m_SEEDING_passedCoverageTest;
bool m_SEEDING_passedParentsTest;
bool m_SEEDING_Extended;
bool m_SEEDING_edgesReceived;
LargeIndex m_SEEDING_i;
int m_SEEDING_outgoing_index;
bool m_SEEDING_outgoing_choice_done;
int m_SEEDING_currentRank;
vector<GraphPath> m_SEEDING_seeds;
vector<int> m_SEEDING_outgoingCoverages;
vector<uint64_t> m_SEEDING_outgoingKeys;
bool m_SEEDING_vertexKeyAndCoverageRequested;
int m_SEEDING_currentParentRank;
SeedExtender*m_seedExtender;
int getRank();
int getSize();
void call_RAY_SLAVE_MODE_START_SEEDING();
void constructor(SeedExtender*seedExtender,int rank,int size,StaticVector*outbox,RingAllocator*outboxAllocator,
int*mode,Parameters*parameters,GridTable*subgraph,
StaticVector*inbox,VirtualCommunicator*vc);
void updateStates();
void call_RAY_SLAVE_MODE_SEND_SEED_LENGTHS();
bool m_initialized;
void registerPlugin(ComputeCore*core);
void resolveSymbols(ComputeCore*core);
};
#endif
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