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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 _FusionData
#define _FusionData
#include <code/Mock/Parameters.h>
#include <code/SeedingData/SeedingData.h>
#include <code/SeedExtender/Direction.h>
#include <code/SeedExtender/ExtensionData.h>
#include <RayPlatform/structures/StaticVector.h>
#include <RayPlatform/memory/RingAllocator.h>
#include <RayPlatform/communication/BufferedData.h>
#include <RayPlatform/profiling/TimePrinter.h>
#include <RayPlatform/handlers/SlaveModeHandler.h>
#include <RayPlatform/core/ComputeCore.h>
#include <vector>
#include <map>
#include <set>
using namespace std;
class SeedingData;
__DeclarePlugin(FusionData);
__DeclareSlaveModeAdapter(FusionData,RAY_SLAVE_MODE_DISTRIBUTE_FUSIONS);
/*
* Contains information regarding fusion of extensions.
* This is a legacy class with public attributes,
* TODO: make attributes private..
*
* \author Sébastien Boisvert
*/
class FusionData : public CorePlugin {
__AddAdapter(FusionData,RAY_SLAVE_MODE_DISTRIBUTE_FUSIONS);
MessageTag RAY_MPI_TAG_ASK_VERTEX_PATHS;
MessageTag RAY_MPI_TAG_DISTRIBUTE_FUSIONS_FINISHED;
MessageTag RAY_MPI_TAG_FINISH_FUSIONS_FINISHED;
MessageTag RAY_MPI_TAG_GET_PATH_LENGTH;
MessageTag RAY_MPI_TAG_GET_PATH_VERTEX;
MessageTag RAY_MPI_TAG_SAVE_WAVE_PROGRESSION_WITH_REPLY;
SlaveMode RAY_SLAVE_MODE_DO_NOTHING;
SlaveMode RAY_SLAVE_MODE_DISTRIBUTE_FUSIONS;
/** debug fusion code */
bool m_debugFusionCode;
/* indicator for checkpoint */
bool m_processedCheckpoint;
SplayTree<Kmer ,Direction*>m_cacheForRepeatedVertices;
MyAllocator m_cacheAllocator;
bool m_mappingConfirmed;
int m_validationPosition;
bool m_checkedValidity;
int*m_mode;
SeedingData*m_seedingData;
int m_wordSize;
bool m_FINISH_vertex_requested;
int m_size;
int m_rank;
ExtensionData*m_ed;
StaticVector*m_outbox;
RingAllocator*m_outboxAllocator;
BufferedData m_buffers;
int m_ready;
vector<vector<Direction> >*m_FINISH_pathsForPosition;
int m_FINISH_positionStart;
bool m_FINISH_hasHit;
PathHandle m_selectedPath;
int m_selectedPosition;
void processCheckpoints();
public:
bool m_FINISH_vertex_received;
bool m_FINISH_fusionOccured;
vector<GraphPath> m_FINISH_newFusions;
vector<int> m_FINISH_coverages;
map<PathHandle,int> m_FINISH_pathLengths;
Kmer m_FINISH_received_vertex;
bool m_Machine_getPaths_INITIALIZED;
bool m_Machine_getPaths_DONE;
vector<Direction> m_Machine_getPaths_result;
// FUSION
bool m_fusionStarted;
bool m_FUSION_direct_fusionDone;
bool m_FUSION_first_done;
int m_FUSION_numberOfRanksDone;
bool m_FUSION_last_done;
int m_FUSION_path_id;
int m_FUSION_numberOfPaths;
bool m_FUSION_paths_requested;
bool m_FUSION_paths_received;
vector<Direction> m_FUSION_firstPaths;
bool m_FUSION_path_received;
int m_FUSION_receivedLength;
bool m_FUSION_reverse_fusionDone;
vector<Direction> m_FUSION_lastPaths;
vector<uint64_t> m_FUSION_matches;
bool m_FUSION_matches_done;
bool m_FUSION_pathLengthReceived;
bool m_FUSION_matches_length_done;
int m_FUSION_match_index;
bool m_FUSION_pathLengthRequested;
vector<Direction> m_FUSION_receivedPaths;
bool m_FUSION_path_requested;
Direction m_FUSION_receivedPath;
Parameters*m_parameters;
map<PathHandle,int> m_FUSION_identifier_map;
set<PathHandle> m_FUSION_eliminated;
void call_RAY_SLAVE_MODE_DISTRIBUTE_FUSIONS();
void constructor(int size,int maxSize,int rank,StaticVector*m_outbox,
RingAllocator*m_outboxAllocator,int wordSize,
ExtensionData*ed,SeedingData*seedingData,int*m_mode,Parameters*parameters);
void setReadiness();
bool isReady();
FusionData();
int getRank();
int getSize();
void finishFusions();
void readyBuffers();
void getPaths(Kmer vertex);
void initialise();
void registerPlugin(ComputeCore*core);
void resolveSymbols(ComputeCore*core);
};
#endif
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