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/*
Ray
Copyright (C) 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 _EdgePurger_H
#define _EdgePurger_H
#include "EdgePurgerWorker.h"
#include <code/Mock/Parameters.h>
#include <code/VerticesExtractor/GridTable.h>
#include <code/VerticesExtractor/GridTableIterator.h>
#include <RayPlatform/memory/RingAllocator.h>
#include <RayPlatform/structures/StaticVector.h>
#include <RayPlatform/communication/VirtualCommunicator.h>
#include <RayPlatform/profiling/Profiler.h>
#include <RayPlatform/profiling/Derivative.h>
#include <RayPlatform/scheduling/TaskCreator.h>
#include <RayPlatform/core/ComputeCore.h>
#include <map>
#include <set>
#include <vector>
#include <stdint.h>
using namespace std;
__DeclarePlugin(EdgePurger);
__DeclareSlaveModeAdapter(EdgePurger,RAY_SLAVE_MODE_PURGE_NULL_EDGES);
/**
* VerticesExtractor.cpp adds k-mers and ingoing and outgoing edges
* for everything found in reads. However, GridTable.cpp only considers those with
* enough coverage in the KmerAcademy.cpp.
* Thus, there will be some edges that point to nothing in the GridTable.cpp.
* EdgePurger.cpp remove these edges.
* \author Sébastien Boisvert
*/
class EdgePurger : public TaskCreator, public CorePlugin {
__AddAdapter(EdgePurger,RAY_SLAVE_MODE_PURGE_NULL_EDGES);
MessageTag RAY_MPI_TAG_GET_VERTEX_EDGES_COMPACT_REPLY;
MessageTag RAY_MPI_TAG_PURGE_NULL_EDGES_REPLY;
MessageTag RAY_MPI_TAG_REQUEST_VERTEX_COVERAGE;
MasterMode RAY_MASTER_MODE_WRITE_KMERS;
SlaveMode RAY_SLAVE_MODE_PURGE_NULL_EDGES;
Profiler*m_profiler;
/** checkpointing */
bool m_checkedCheckpoint;
Derivative m_derivative;
uint64_t m_SEEDING_i;
GridTable*m_subgraph;
GridTableIterator m_graphIterator;
int m_masterCountFinished;
Parameters*m_parameters;
StaticVector*m_inbox;
StaticVector*m_outbox;
RingAllocator*m_outboxAllocator;
int*m_slaveMode;
VirtualCommunicator*m_virtualCommunicator;
MyAllocator m_workerAllocator;
int*m_masterMode;
bool m_done;
vector<LargeCount> m_graphSizes;
void writeGraphPartition();
public:
void constructor(StaticVector*outbox,StaticVector*inbox,RingAllocator*outboxAllocator,Parameters*parameters,
int*slaveMode,int*masterMode,VirtualCommunicator*vc,GridTable*graph,VirtualProcessor*virtualProcessor);
void call_RAY_SLAVE_MODE_PURGE_NULL_EDGES();
/** initialize the whole thing */
virtual void initializeMethod();
virtual void finalizeMethod();
virtual bool hasUnassignedTask();
virtual Worker* assignNextTask();
virtual void processWorkerResult(Worker*);
virtual void destroyWorker(Worker*);
void setProfiler(Profiler*profiler);
void registerPlugin(ComputeCore*core);
void resolveSymbols(ComputeCore*core);
};
#endif
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