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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 _Amos
#define _Amos
#include <code/Mock/Parameters.h>
#include <code/FusionData/FusionData.h>
#include <code/Scaffolder/Scaffolder.h>
#include <code/SeedExtender/ExtensionData.h>
#include <code/SeedExtender/ReadFetcher.h>
#include <RayPlatform/structures/StaticVector.h>
#include <RayPlatform/memory/RingAllocator.h>
#include <RayPlatform/communication/VirtualCommunicator.h>
#include <RayPlatform/core/ComputeCore.h>
#include <stdio.h>
#include <stdint.h>
#include <vector>
using namespace std;
__DeclarePlugin(Amos);
__DeclareMasterModeAdapter(Amos,RAY_MASTER_MODE_AMOS);
__DeclareSlaveModeAdapter(Amos,RAY_SLAVE_MODE_AMOS);
/**
* AMOS specification is available : http://sourceforge.net/apps/mediawiki/amos/index.php?title=AMOS
* \see http://sourceforge.net/apps/mediawiki/amos/index.php?title=Message_Types
* \author Sébastien Boisvert
*/
class Amos : public CorePlugin{
__AddAdapter(Amos,RAY_MASTER_MODE_AMOS);
__AddAdapter(Amos,RAY_SLAVE_MODE_AMOS);
MessageTag RAY_MPI_TAG_REQUEST_VERTEX_READS;
MessageTag RAY_MPI_TAG_ASK_READ_LENGTH;
MessageTag RAY_MPI_TAG_WRITE_AMOS;
MessageTag RAY_MPI_TAG_WRITE_AMOS_REPLY;
MasterMode RAY_MASTER_MODE_AMOS;
MasterMode RAY_MASTER_MODE_SCAFFOLDER;
SlaveMode RAY_SLAVE_MODE_AMOS;
SlaveMode RAY_SLAVE_MODE_DO_NOTHING;
VirtualCommunicator*m_virtualCommunicator;
StaticVector*m_inbox;
WorkerHandle m_workerId;
ReadFetcher m_readFetcher;
int*m_master_mode;
int*m_slave_mode;
Scaffolder*m_scaffolder;
FusionData*m_fusionData;
FILE*m_amosFile;
Parameters*m_parameters;
RingAllocator*m_outboxAllocator;
StaticVector*m_outbox;
int m_contigId;
int m_sequence_id;
ExtensionData*m_ed;
int m_mode_send_vertices_sequence_id_position;
vector<WorkerHandle> m_activeWorkers;
public:
void call_RAY_MASTER_MODE_AMOS();
void call_RAY_SLAVE_MODE_AMOS();
void constructor(Parameters*parameters,RingAllocator*outboxAllocator,StaticVector*outbox,
FusionData*fusionData,ExtensionData*extensionData,int*masterMode,int*slaveMode,Scaffolder*scaffolder,
StaticVector*inbox,VirtualCommunicator*virtualCommunicator);
void registerPlugin(ComputeCore*core);
void resolveSymbols(ComputeCore*core);
};
#endif
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