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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 _SequencesIndexer
#define _SequencesIndexer
#include "IndexerWorker.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/core/ComputeCore.h>
#include <RayPlatform/communication/Message.h>
#include <RayPlatform/memory/MyAllocator.h>
#include <RayPlatform/memory/RingAllocator.h>
#include <RayPlatform/structures/SplayTree.h>
#include <RayPlatform/structures/SplayTreeIterator.h>
#include <RayPlatform/structures/StaticVector.h>
#include <RayPlatform/communication/BufferedData.h>
#include <RayPlatform/communication/VirtualCommunicator.h>
#include <map>
#include <vector>
#include <fstream>
using namespace std;
__DeclarePlugin(SequencesIndexer);
__DeclareSlaveModeAdapter(SequencesIndexer,RAY_SLAVE_MODE_INDEX_SEQUENCES);
/*
* Computes optimal read markers using workers.
* \author Sébastien Boisvert
*/
class SequencesIndexer: public CorePlugin{
__AddAdapter(SequencesIndexer,RAY_SLAVE_MODE_INDEX_SEQUENCES);
MessageTag RAY_MPI_TAG_GET_READ_MARKERS_REPLY;
MessageTag RAY_MPI_TAG_GET_READ_MATE_REPLY;
MessageTag RAY_MPI_TAG_REQUEST_VERTEX_READS_REPLY;
MessageTag RAY_MPI_TAG_VERTEX_READS_FROM_LIST_REPLY;
MessageTag RAY_MPI_TAG_VERTEX_READS_REPLY;
MessageTag RAY_MPI_TAG_MASTER_IS_DONE_ATTACHING_READS_REPLY;
MessageTag RAY_MPI_TAG_ATTACH_SEQUENCE;
MessageTag RAY_MPI_TAG_REQUEST_VERTEX_COVERAGE;
SlaveMode RAY_SLAVE_MODE_INDEX_SEQUENCES;
SlaveMode RAY_SLAVE_MODE_DO_NOTHING;
Derivative m_derivative;
ofstream m_readMarkerFile;
map<int,map<int,int> >m_forwardStatistics;
map<int,map<int,int> >m_reverseStatistics;
/** for checkpointing */
bool m_checkedCheckpoint;
int m_rank;
int m_size;
Parameters*m_parameters;
MyAllocator m_allocator;
MyAllocator m_workAllocator;
int m_pendingMessages;
int m_completedJobs;
int m_maximumAliveWorkers;
int m_maximumWorkers;
SlaveMode*m_mode;
StaticVector*m_outbox;
VirtualCommunicator*m_virtualCommunicator;
SplayTree<WorkerHandle,char> m_activeWorkers;
SplayTreeIterator<WorkerHandle,char> m_activeWorkerIterator;
SplayTree<WorkerHandle,IndexerWorker> m_aliveWorkers;
bool m_communicatorWasTriggered;
vector<WorkerHandle> m_workersDone;
vector<WorkerHandle> m_waitingWorkers;
vector<WorkerHandle> m_activeWorkersToRestore;
ArrayOfReads*m_myReads;
RingAllocator*m_outboxAllocator;
bool m_initiatedIterator;
int m_theSequenceId;
void updateStates();
public:
void call_RAY_SLAVE_MODE_INDEX_SEQUENCES();
void constructor(Parameters*parameters,RingAllocator*outboxAllocator,StaticVector*inbox,StaticVector*outbox,
VirtualCommunicator*vc,SlaveMode*mode,ArrayOfReads*myReads);
void setReadiness();
MyAllocator*getAllocator();
void registerPlugin(ComputeCore*core);
void resolveSymbols(ComputeCore*core);
};
#endif
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