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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 _SequencesLoader
#define _SequencesLoader
#include "Read.h"
#include <code/Mock/Parameters.h>
#include <code/SequencesLoader/Loader.h>
#include <code/SeedExtender/BubbleData.h>
#include <RayPlatform/memory/RingAllocator.h>
#include <RayPlatform/memory/MyAllocator.h>
#include <RayPlatform/structures/StaticVector.h>
#include <RayPlatform/communication/Message.h>
#include <RayPlatform/core/ComputeCore.h>
#include <time.h>
#include <vector>
using namespace std;
__DeclarePlugin(SequencesLoader);
__DeclareSlaveModeAdapter(SequencesLoader,RAY_SLAVE_MODE_LOAD_SEQUENCES);
__DeclareMessageTagAdapter(SequencesLoader,RAY_MPI_TAG_LOAD_SEQUENCES);
__DeclareMessageTagAdapter(SequencesLoader,RAY_MPI_TAG_SET_FILE_ENTRIES);
/*
* Computes the partition on reads (MASTER_RANK).
* Loads the appropriate slice of reads (all MPI ranks).
*
* \author Sébastien Boisvert
*/
class SequencesLoader : public CorePlugin{
__AddAdapter(SequencesLoader,RAY_SLAVE_MODE_LOAD_SEQUENCES);
__AddAdapter(MessageProcessor,RAY_MPI_TAG_LOAD_SEQUENCES);
__AddAdapter(MessageProcessor,RAY_MPI_TAG_SET_FILE_ENTRIES);
MessageTag RAY_MPI_TAG_SEQUENCES_READY;
MessageTag RAY_MPI_TAG_SET_FILE_ENTRIES_REPLY;
MessageTag RAY_MPI_TAG_LOAD_SEQUENCES;
MessageTag RAY_MPI_TAG_SET_FILE_ENTRIES;
SlaveMode RAY_SLAVE_MODE_LOAD_SEQUENCES;
SlaveMode RAY_SLAVE_MODE_DO_NOTHING;
MyAllocator*m_persistentAllocator;
ArrayOfReads*m_myReads;
Parameters*m_parameters;
LargeIndex m_distribution_currentSequenceId;
LargeCount m_totalNumberOfSequences;
int m_distribution_file_id;
LargeIndex m_distribution_sequence_id;
bool m_LOADER_isLeftFile;
bool m_LOADER_isRightFile;
Loader m_loader;
bool m_isInterleavedFile;
Rank m_rank;
int m_size;
StaticVector*m_outbox;
SlaveMode*m_mode;
void registerSequence();
public:
bool call_RAY_SLAVE_MODE_LOAD_SEQUENCES();
void call_RAY_MPI_TAG_LOAD_SEQUENCES(Message*message);
void call_RAY_MPI_TAG_SET_FILE_ENTRIES(Message*message);
bool writeSequencesToAMOSFile(int rank,int size,StaticVector*m_outbox,
RingAllocator*m_outboxAllocator,
bool*m_loadSequenceStep,
BubbleData*m_bubbleData,
time_t*m_lastTime,
Parameters*m_parameters,int*m_master_mode,int*m_mode);
void constructor(int size,MyAllocator*m_persistentAllocator,ArrayOfReads*m_myReads,
Parameters*parameters,StaticVector*outbox,SlaveMode*mode);
void registerPlugin(ComputeCore*core);
void resolveSymbols(ComputeCore*core);
};
#endif
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