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/*
Ray -- Parallel genome assemblies for parallel DNA sequencing
Copyright (C) 2010, 2011, 2012, 2013 Sébastien Boisvert
Copyright (C) 2013 Charles Joly Beauparlant
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 _MachineHelper_h
#define _MachineHelper_h
#include <code/Mock/Parameters.h>
#include <code/FusionData/FusionData.h>
#include <code/NetworkTest/NetworkTest.h>
#include <code/Example/Example.h>
#include <code/Partitioner/Partitioner.h>
#include <code/SequencesLoader/SequencesLoader.h>
#include <code/SeedingData/SeedingData.h>
#include <code/Scaffolder/Scaffolder.h>
#include <code/SeedExtender/SeedExtender.h>
#include <code/SeedExtender/ExtensionData.h>
#include <code/SeedExtender/OpenAssemblerChooser.h>
#include <code/SeedExtender/BubbleData.h>
#include <code/Searcher/Searcher.h>
#include <code/SequencesLoader/ArrayOfReads.h>
#include <code/VerticesExtractor/VerticesExtractor.h>
#include <code/EdgePurger/EdgePurger.h>
#include <code/VerticesExtractor/GridTable.h>
#include <code/KmerAcademyBuilder/KmerAcademyBuilder.h>
#include <code/CoverageGatherer/CoverageGatherer.h>
#include <code/SequencesIndexer/SequencesIndexer.h>
#include <RayPlatform/core/ComputeCore.h>
#include <RayPlatform/communication/VirtualCommunicator.h>
#include <RayPlatform/memory/RingAllocator.h>
#include <RayPlatform/structures/StaticVector.h>
#include <RayPlatform/scheduling/SwitchMan.h>
#include <RayPlatform/handlers/MasterModeHandler.h>
#include <RayPlatform/handlers/SlaveModeHandler.h>
#include <RayPlatform/profiling/TimePrinter.h>
#include <RayPlatform/profiling/Profiler.h>
#include <stdint.h>
#include <map>
using namespace std;
__DeclarePlugin(MachineHelper);
__DeclareMasterModeAdapter(MachineHelper,RAY_MASTER_MODE_LOAD_CONFIG);
__DeclareMasterModeAdapter(MachineHelper,RAY_MASTER_MODE_SEND_COVERAGE_VALUES);
__DeclareMasterModeAdapter(MachineHelper,RAY_MASTER_MODE_WRITE_KMERS);
__DeclareMasterModeAdapter(MachineHelper,RAY_MASTER_MODE_LOAD_SEQUENCES);
__DeclareMasterModeAdapter(MachineHelper,RAY_MASTER_MODE_TRIGGER_VERTICE_DISTRIBUTION);
__DeclareMasterModeAdapter(MachineHelper,RAY_MASTER_MODE_TRIGGER_GRAPH_BUILDING);
__DeclareMasterModeAdapter(MachineHelper,RAY_MASTER_MODE_PURGE_NULL_EDGES);
__DeclareMasterModeAdapter(MachineHelper,RAY_MASTER_MODE_TRIGGER_INDEXING);
__DeclareMasterModeAdapter(MachineHelper,RAY_MASTER_MODE_PREPARE_DISTRIBUTIONS);
__DeclareMasterModeAdapter(MachineHelper,RAY_MASTER_MODE_PREPARE_DISTRIBUTIONS_WITH_ANSWERS);
__DeclareMasterModeAdapter(MachineHelper,RAY_MASTER_MODE_PREPARE_SEEDING);
__DeclareMasterModeAdapter(MachineHelper,RAY_MASTER_MODE_TRIGGER_SEEDING);
__DeclareMasterModeAdapter(MachineHelper,RAY_MASTER_MODE_TRIGGER_DETECTION);
__DeclareMasterModeAdapter(MachineHelper,RAY_MASTER_MODE_ASK_DISTANCES);
__DeclareMasterModeAdapter(MachineHelper,RAY_MASTER_MODE_START_UPDATING_DISTANCES);
__DeclareMasterModeAdapter(MachineHelper,RAY_MASTER_MODE_TRIGGER_EXTENSIONS);
__DeclareMasterModeAdapter(MachineHelper,RAY_MASTER_MODE_TRIGGER_FUSIONS);
__DeclareMasterModeAdapter(MachineHelper,RAY_MASTER_MODE_TRIGGER_FIRST_FUSIONS);
__DeclareMasterModeAdapter(MachineHelper,RAY_MASTER_MODE_START_FUSION_CYCLE);
__DeclareMasterModeAdapter(MachineHelper,RAY_MASTER_MODE_ASK_EXTENSIONS);
__DeclareMasterModeAdapter(MachineHelper,RAY_MASTER_MODE_SCAFFOLDER);
__DeclareMasterModeAdapter(MachineHelper,RAY_MASTER_MODE_KILL_RANKS);
__DeclareMasterModeAdapter(MachineHelper,RAY_MASTER_MODE_KILL_ALL_MPI_RANKS);
__DeclareSlaveModeAdapter(MachineHelper,RAY_SLAVE_MODE_WRITE_KMERS);
__DeclareSlaveModeAdapter(MachineHelper,RAY_SLAVE_MODE_ASSEMBLE_WAVES);
__DeclareSlaveModeAdapter(MachineHelper,RAY_SLAVE_MODE_SEND_EXTENSION_DATA);
__DeclareSlaveModeAdapter(MachineHelper,RAY_SLAVE_MODE_DIE);
__DeclareMessageTagAdapter(MachineHelper,RAY_MPI_TAG_NOTIFY_ERROR);
__DeclareMessageTagAdapter(MachineHelper,RAY_MPI_TAG_COMPUTE_REQUIRED_SPACE_FOR_EXTENSIONS);
__DeclareMessageTagAdapter(MachineHelper,RAY_MPI_TAG_COMPUTE_REQUIRED_SPACE_FOR_EXTENSIONS_REPLY);
__DeclareMessageTagAdapter(MachineHelper,RAY_MPI_TAG_ASK_EXTENSION_DATA);
__DeclareMessageTagAdapter(MachineHelper,RAY_MPI_TAG_EXTENSION_DATA_END);
/**
* This file contains __legacy code__
* Old handlers are here.
* TODO: move them elsewhere ?
* \author Sébastien Boisvert */
class MachineHelper: public CorePlugin{
__AddAdapter(MachineHelper,RAY_MASTER_MODE_LOAD_CONFIG);
__AddAdapter(MachineHelper,RAY_MASTER_MODE_SEND_COVERAGE_VALUES);
__AddAdapter(MachineHelper,RAY_MASTER_MODE_WRITE_KMERS);
__AddAdapter(MachineHelper,RAY_MASTER_MODE_LOAD_SEQUENCES);
__AddAdapter(MachineHelper,RAY_MASTER_MODE_TRIGGER_VERTICE_DISTRIBUTION);
__AddAdapter(MachineHelper,RAY_MASTER_MODE_TRIGGER_GRAPH_BUILDING);
__AddAdapter(MachineHelper,RAY_MASTER_MODE_PURGE_NULL_EDGES);
__AddAdapter(MachineHelper,RAY_MASTER_MODE_TRIGGER_INDEXING);
__AddAdapter(MachineHelper,RAY_MASTER_MODE_PREPARE_DISTRIBUTIONS);
__AddAdapter(MachineHelper,RAY_MASTER_MODE_PREPARE_DISTRIBUTIONS_WITH_ANSWERS);
__AddAdapter(MachineHelper,RAY_MASTER_MODE_PREPARE_SEEDING);
__AddAdapter(MachineHelper,RAY_MASTER_MODE_TRIGGER_SEEDING);
__AddAdapter(MachineHelper,RAY_MASTER_MODE_TRIGGER_DETECTION);
__AddAdapter(MachineHelper,RAY_MASTER_MODE_ASK_DISTANCES);
__AddAdapter(MachineHelper,RAY_MASTER_MODE_START_UPDATING_DISTANCES);
__AddAdapter(MachineHelper,RAY_MASTER_MODE_TRIGGER_EXTENSIONS);
__AddAdapter(MachineHelper,RAY_MASTER_MODE_TRIGGER_FUSIONS);
__AddAdapter(MachineHelper,RAY_MASTER_MODE_TRIGGER_FIRST_FUSIONS);
__AddAdapter(MachineHelper,RAY_MASTER_MODE_START_FUSION_CYCLE);
__AddAdapter(MachineHelper,RAY_MASTER_MODE_ASK_EXTENSIONS);
__AddAdapter(MachineHelper,RAY_MASTER_MODE_SCAFFOLDER);
__AddAdapter(MachineHelper,RAY_MASTER_MODE_KILL_RANKS);
__AddAdapter(MachineHelper,RAY_MASTER_MODE_KILL_ALL_MPI_RANKS);
__AddAdapter(MachineHelper,RAY_SLAVE_MODE_WRITE_KMERS);
__AddAdapter(MachineHelper,RAY_SLAVE_MODE_ASSEMBLE_WAVES);
__AddAdapter(MachineHelper,RAY_SLAVE_MODE_SEND_EXTENSION_DATA);
__AddAdapter(MachineHelper,RAY_SLAVE_MODE_DIE);
__AddAdapter(MachineHelper,RAY_MPI_TAG_NOTIFY_ERROR);
__AddAdapter(MachineHelper,RAY_MPI_TAG_COMPUTE_REQUIRED_SPACE_FOR_EXTENSIONS);
__AddAdapter(MachineHelper,RAY_MPI_TAG_COMPUTE_REQUIRED_SPACE_FOR_EXTENSIONS_REPLY);
__AddAdapter(MachineHelper,RAY_MPI_TAG_ASK_EXTENSION_DATA);
__AddAdapter(MachineHelper,RAY_MPI_TAG_EXTENSION_DATA_END);
MessageTag RAY_MPI_TAG_NOTIFY_ERROR;
MessageTag RAY_MPI_TAG_FINISH_FUSIONS;
MessageTag RAY_MPI_TAG_GET_CONTIG_CHUNK;
MessageTag RAY_MPI_TAG_GET_CONTIG_CHUNK_REPLY;
MessageTag RAY_MPI_TAG_GET_COVERAGE_AND_DIRECTION;
MessageTag RAY_MPI_TAG_GET_COVERAGE_AND_DIRECTION_REPLY;
MessageTag RAY_MPI_TAG_GET_COVERAGE_AND_PATHS;
MessageTag RAY_MPI_TAG_GET_COVERAGE_AND_PATHS_REPLY;
MessageTag RAY_MPI_TAG_GET_PATH_LENGTH;
MessageTag RAY_MPI_TAG_GET_PATH_LENGTH_REPLY;
MessageTag RAY_MPI_TAG_GET_PATH_VERTEX;
MessageTag RAY_MPI_TAG_GET_PATH_VERTEX_REPLY;
MessageTag RAY_MPI_TAG_GET_READ_MARKERS;
MessageTag RAY_MPI_TAG_GET_READ_MARKERS_REPLY;
MessageTag RAY_MPI_TAG_GET_READ_MATE;
MessageTag RAY_MPI_TAG_GET_READ_MATE_REPLY;
MessageTag RAY_MPI_TAG_GET_VERTEX_EDGES_COMPACT;
MessageTag RAY_MPI_TAG_GET_VERTEX_EDGES_COMPACT_REPLY;
MessageTag RAY_MPI_TAG_GOOD_JOB_SEE_YOU_SOON;
MessageTag RAY_MPI_TAG_GOOD_JOB_SEE_YOU_SOON_REPLY;
MessageTag RAY_MPI_TAG_HAS_PAIRED_READ;
MessageTag RAY_MPI_TAG_HAS_PAIRED_READ_REPLY;
MessageTag RAY_MPI_TAG_LOAD_SEQUENCES;
MessageTag RAY_MPI_TAG_PREPARE_COVERAGE_DISTRIBUTION;
MessageTag RAY_MPI_TAG_PREPARE_COVERAGE_DISTRIBUTION_QUESTION;
MessageTag RAY_MPI_TAG_PURGE_NULL_EDGES;
MessageTag RAY_MPI_TAG_REQUEST_READ_SEQUENCE;
MessageTag RAY_MPI_TAG_REQUEST_READ_SEQUENCE_REPLY;
MessageTag RAY_MPI_TAG_REQUEST_SEED_LENGTHS;
MessageTag RAY_MPI_TAG_REQUEST_VERTEX_COVERAGE;
MessageTag RAY_MPI_TAG_REQUEST_VERTEX_COVERAGE_REPLY;
MessageTag RAY_MPI_TAG_REQUEST_VERTEX_OUTGOING_EDGES;
MessageTag RAY_MPI_TAG_REQUEST_VERTEX_OUTGOING_EDGES_REPLY;
MessageTag RAY_MPI_TAG_REQUEST_VERTEX_READS;
MessageTag RAY_MPI_TAG_REQUEST_VERTEX_READS_REPLY;
MessageTag RAY_MPI_TAG_SCAFFOLDING_LINKS;
MessageTag RAY_MPI_TAG_SCAFFOLDING_LINKS_REPLY;
MessageTag RAY_MPI_TAG_SEND_COVERAGE_VALUES;
MessageTag RAY_MPI_TAG_SEQUENCE_BIOLOGICAL_ABUNDANCES;
MessageTag RAY_MPI_TAG_SET_WORD_SIZE;
MessageTag RAY_MPI_TAG_START_FUSION;
MessageTag RAY_MPI_TAG_START_INDEXING_SEQUENCES;
MessageTag RAY_MPI_TAG_START_SCAFFOLDER;
MessageTag RAY_MPI_TAG_START_SEEDING;
MessageTag RAY_MPI_TAG_START_VERTICES_DISTRIBUTION;
MessageTag RAY_MPI_TAG_TEST_NETWORK;
MessageTag RAY_MPI_TAG_TEST_NETWORK_MESSAGE;
MessageTag RAY_MPI_TAG_TEST_NETWORK_MESSAGE_REPLY;
MessageTag RAY_MPI_TAG_VERTEX_INFO;
MessageTag RAY_MPI_TAG_VERTEX_INFO_REPLY;
MessageTag RAY_MPI_TAG_WRITE_AMOS;
MessageTag RAY_MPI_TAG_WRITE_KMERS;
MessageTag RAY_MPI_TAG_WRITE_KMERS_REPLY;
MessageTag RAY_MPI_TAG_ACTIVATE_RELAY_CHECKER;
MessageTag RAY_MPI_TAG_ACTIVATE_RELAY_CHECKER_REPLY;
MessageTag RAY_MPI_TAG_ADD_COLORS;
MessageTag RAY_MPI_TAG_ADD_KMER_COLOR;
MessageTag RAY_MPI_TAG_ASK_EXTENSION;
MessageTag RAY_MPI_TAG_ASK_EXTENSION_DATA;
MessageTag RAY_MPI_TAG_ASK_LIBRARY_DISTANCES;
MessageTag RAY_MPI_TAG_ASK_READ_LENGTH;
MessageTag RAY_MPI_TAG_ASK_READ_LENGTH_REPLY;
MessageTag RAY_MPI_TAG_ASK_VERTEX_PATH;
MessageTag RAY_MPI_TAG_ASK_VERTEX_PATH_REPLY;
MessageTag RAY_MPI_TAG_ASK_VERTEX_PATHS_SIZE;
MessageTag RAY_MPI_TAG_ASK_VERTEX_PATHS_SIZE_REPLY;
MessageTag RAY_MPI_TAG_ASSEMBLE_WAVES;
MessageTag RAY_MPI_TAG_ASSEMBLE_WAVES_DONE;
MessageTag RAY_MPI_TAG_ATTACH_SEQUENCE;
MessageTag RAY_MPI_TAG_ATTACH_SEQUENCE_REPLY;
MessageTag RAY_MPI_TAG_AUTOMATIC_DISTANCE_DETECTION;
MessageTag RAY_MPI_TAG_BUILD_GRAPH;
MessageTag RAY_MPI_TAG_CLEAR_DIRECTIONS;
MessageTag RAY_MPI_TAG_CONTIG_ABUNDANCE;
MessageTag RAY_MPI_TAG_CONTIG_ABUNDANCE_REPLY;
MessageTag RAY_MPI_TAG_CONTIG_BIOLOGICAL_ABUNDANCES;
MessageTag RAY_MPI_TAG_CONTIG_INFO;
MessageTag RAY_MPI_TAG_CONTIG_INFO_REPLY;
MessageTag RAY_MPI_TAG_COUNT_FILE_ENTRIES;
MessageTag RAY_MPI_TAG_COUNT_SEARCH_ELEMENTS;
MessageTag RAY_MPI_TAG_DISTRIBUTE_FUSIONS;
MessageTag RAY_MPI_TAG_EXTENSION_DATA_END;
MessageTag RAY_MPI_TAG_COMPUTE_REQUIRED_SPACE_FOR_EXTENSIONS;
MessageTag RAY_MPI_TAG_COMPUTE_REQUIRED_SPACE_FOR_EXTENSIONS_REPLY;
int m_ranksThatComputedStorage;
vector<uint64_t> m_rankStorage;
uint64_t m_offsetForContigs;
int m_ranksThatWroteContigs;
bool m_authorized;
/*
* Stuff for sending entries in files.
*/
int m_numberOfRanksThatReplied;
bool m_theEntriesForFileWasSent;
int m_fileIndex;
bool m_startedToSendCounts;
MessageTag RAY_MPI_TAG_SET_FILE_ENTRIES;
MessageTag RAY_MPI_TAG_SET_FILE_ENTRIES_REPLY;
MessageTag RAY_MPI_TAG_SEND_AUTHORIZATION;
MasterMode RAY_MASTER_MODE_ADD_COLORS;
MasterMode RAY_MASTER_MODE_AMOS;
MasterMode RAY_MASTER_MODE_ASK_DISTANCES;
MasterMode RAY_MASTER_MODE_ASK_EXTENSIONS;
MasterMode RAY_MASTER_MODE_CONTIG_BIOLOGICAL_ABUNDANCES;
MasterMode RAY_MASTER_MODE_COUNT_FILE_ENTRIES;
MasterMode RAY_MASTER_MODE_COUNT_SEARCH_ELEMENTS;
MasterMode RAY_MASTER_MODE_DO_NOTHING;
MasterMode RAY_MASTER_MODE_KILL_ALL_MPI_RANKS;
MasterMode RAY_MASTER_MODE_KILL_RANKS;
MasterMode RAY_MASTER_MODE_LOAD_CONFIG;
MasterMode RAY_MASTER_MODE_LOAD_SEQUENCES;
MasterMode RAY_MASTER_MODE_PREPARE_DISTRIBUTIONS;
MasterMode RAY_MASTER_MODE_PREPARE_DISTRIBUTIONS_WITH_ANSWERS;
MasterMode RAY_MASTER_MODE_PREPARE_SEEDING;
MasterMode RAY_MASTER_MODE_PURGE_NULL_EDGES;
MasterMode RAY_MASTER_MODE_SCAFFOLDER;
MasterMode RAY_MASTER_MODE_SEND_COVERAGE_VALUES;
MasterMode RAY_MASTER_MODE_SEQUENCE_BIOLOGICAL_ABUNDANCES;
MasterMode RAY_MASTER_MODE_START_FUSION_CYCLE;
MasterMode RAY_MASTER_MODE_START_UPDATING_DISTANCES;
MasterMode RAY_MASTER_MODE_TEST_NETWORK;
MasterMode RAY_MASTER_MODE_TRIGGER_DETECTION;
MasterMode RAY_MASTER_MODE_TRIGGER_EXTENSIONS;
MasterMode RAY_MASTER_MODE_TRIGGER_FIRST_FUSIONS;
MasterMode RAY_MASTER_MODE_TRIGGER_FUSIONS;
MasterMode RAY_MASTER_MODE_TRIGGER_GRAPH_BUILDING;
MasterMode RAY_MASTER_MODE_TRIGGER_INDEXING;
MasterMode RAY_MASTER_MODE_TRIGGER_SEEDING;
MasterMode RAY_MASTER_MODE_TRIGGER_VERTICE_DISTRIBUTION;
MasterMode RAY_MASTER_MODE_UPDATE_DISTANCES;
MasterMode RAY_MASTER_MODE_WRITE_KMERS;
MasterMode RAY_MASTER_MODE_WRITE_SCAFFOLDS;
MasterMode RAY_MASTER_MODE_STEP_A;
MasterMode RAY_MASTER_MODE_EVALUATE_PATHS;
SlaveMode RAY_SLAVE_MODE_EXTENSION;
SlaveMode RAY_SLAVE_MODE_ADD_COLORS;
SlaveMode RAY_SLAVE_MODE_AMOS;
SlaveMode RAY_SLAVE_MODE_ASSEMBLE_WAVES;
SlaveMode RAY_SLAVE_MODE_AUTOMATIC_DISTANCE_DETECTION;
SlaveMode RAY_SLAVE_MODE_ADD_VERTICES;
SlaveMode RAY_SLAVE_MODE_CONTIG_BIOLOGICAL_ABUNDANCES;
SlaveMode RAY_SLAVE_MODE_COUNT_FILE_ENTRIES;
SlaveMode RAY_SLAVE_MODE_COUNT_SEARCH_ELEMENTS;
SlaveMode RAY_SLAVE_MODE_DIE;
SlaveMode RAY_SLAVE_MODE_DISTRIBUTE_FUSIONS;
SlaveMode RAY_SLAVE_MODE_DO_NOTHING;
SlaveMode RAY_SLAVE_MODE_ADD_EDGES;
SlaveMode RAY_SLAVE_MODE_FINISH_FUSIONS;
SlaveMode RAY_SLAVE_MODE_FUSION;
SlaveMode RAY_SLAVE_MODE_INDEX_SEQUENCES;
SlaveMode RAY_SLAVE_MODE_LOAD_SEQUENCES;
SlaveMode RAY_SLAVE_MODE_SCAFFOLDER;
SlaveMode RAY_SLAVE_MODE_SEND_DISTRIBUTION;
SlaveMode RAY_SLAVE_MODE_SEND_EXTENSION_DATA;
SlaveMode RAY_SLAVE_MODE_SEND_LIBRARY_DISTANCES;
SlaveMode RAY_SLAVE_MODE_SEND_SEED_LENGTHS;
SlaveMode RAY_SLAVE_MODE_SEQUENCE_BIOLOGICAL_ABUNDANCES;
SlaveMode RAY_SLAVE_MODE_START_SEEDING;
SlaveMode RAY_SLAVE_MODE_TEST_NETWORK;
SlaveMode RAY_SLAVE_MODE_WRITE_KMERS;
bool m_oldDirectoryExists;
SequencesLoader*m_sl;
time_t*m_lastTime;
bool*m_writeKmerInitialised;
Partitioner*m_partitioner;
map<int,map<int,LargeCount> > m_edgeDistribution;
VirtualCommunicator*m_virtualCommunicator;
KmerAcademyBuilder*m_kmerAcademyBuilder;
int*m_mode_send_vertices_sequence_id;
CoverageGatherer*m_coverageGatherer;
GridTable*m_subgraph;
SequencesIndexer*m_si;
ArrayOfReads*m_myReads;
int*m_last_value;
VerticesExtractor*m_verticesExtractor;
EdgePurger*m_edgePurger;
int m_coverageRank;
Searcher*m_searcher;
int*m_numberOfRanksDoneSeeding;
int*m_numberOfRanksDoneDetectingDistances;
int*m_numberOfRanksDoneSendingDistances;
bool m_loadSequenceStep;
bool m_cycleStarted;
int*m_CLEAR_n;
int*m_DISTRIBUTE_n;
int*m_FINISH_n;
OpenAssemblerChooser*m_oa;
bool*m_isFinalFusion;
BubbleData*m_bubbleData;
bool*m_alive;
TimePrinter*m_timePrinter;
SeedExtender*m_seedExtender;
Scaffolder*m_scaffolder;
bool m_coverageInitialised;
int m_currentCycleStep;
int m_cycleNumber;
ExtensionData*m_ed;
FusionData*m_fusionData;
Profiler*m_profiler;
NetworkTest*m_networkTest;
SeedingData*m_seedingData;
bool m_mustStop;
bool*m_reductionOccured;
/** indicator of the killer initialization */
bool m_initialisedKiller;
int m_machineRank;
int m_numberOfRanksDone;
int*m_numberOfMachinesDoneSendingVertices;
bool*m_initialisedAcademy;
int*m_repeatedLength;
int*m_readyToSeed;
int*m_ranksDoneAttachingReads;
// SEQUENCE DISTRIBUTION
bool m_reverseComplementVertex;
int m_argc;
char**m_argv;
Parameters*m_parameters;
SwitchMan*m_switchMan;
RingAllocator*m_outboxAllocator;
StaticVector*m_outbox;
StaticVector*m_inbox;
bool*m_aborted;
map<CoverageDepth,LargeCount>*m_coverageDistribution;
int*m_numberOfMachinesDoneSendingCoverage;
int*m_numberOfRanksWithCoverageData;
int getRank();
int getSize();
void performAssemblyWorkflow(ComputeCore*core);
public:
void constructor(int argc,char**argv,Parameters*parameters,
SwitchMan*switchMan,RingAllocator*outboxAllocator,
StaticVector*outbox,bool*aborted,
map<CoverageDepth,LargeCount>*coverageDistribution,
int*numberOfMachinesDoneSendingCoverage,int*numberOfRanksWithCoverageData,
bool*reductionOccured,ExtensionData*ed,FusionData*fusionData,
Profiler*p,NetworkTest*nt,SeedingData*sd,
TimePrinter*timePrinter,SeedExtender*seedExtender,Scaffolder*scaffolder,
StaticVector*inbox, OpenAssemblerChooser*oa, bool*isFinalFusion, BubbleData*bubbleData, bool*alive,
int*CLEAR_n,int*DISTRIBUTE_n,int*FINISH_n,Searcher*searcher,
int*numberOfRanksDoneSeeding, int*numberOfRanksDoneDetectingDistances, int*numberOfRanksDoneSendingDistances,
ArrayOfReads*myReads, int*last_value, VerticesExtractor*verticesExtractor, EdgePurger*edgePurger,
int*mode_send_vertices_sequence_id,CoverageGatherer*coverageGatherer,GridTable*m_subgraph,SequencesIndexer*m_si,
VirtualCommunicator*virtualCommunicator,KmerAcademyBuilder*kmerAcademyBuilder,
int*numberOfMachinesDoneSendingVertices,
bool*initialisedAcademy,
int*repeatedLength,
int*readyToSeed,
int*ranksDoneAttachingReads,
SequencesLoader*sl,time_t*lastTime,bool*writeKmerInitialised,Partitioner*partitioner
);
void call_RAY_MASTER_MODE_LOAD_CONFIG();
void call_RAY_MASTER_MODE_SEND_COVERAGE_VALUES();
void call_RAY_MASTER_MODE_WRITE_KMERS();
void call_RAY_MASTER_MODE_LOAD_SEQUENCES();
void call_RAY_MASTER_MODE_TRIGGER_VERTICE_DISTRIBUTION();
void call_RAY_MASTER_MODE_TRIGGER_GRAPH_BUILDING();
void call_RAY_MASTER_MODE_PURGE_NULL_EDGES();
void call_RAY_MASTER_MODE_TRIGGER_INDEXING();
void call_RAY_MASTER_MODE_PREPARE_DISTRIBUTIONS();
void call_RAY_MASTER_MODE_PREPARE_DISTRIBUTIONS_WITH_ANSWERS();
void call_RAY_MASTER_MODE_PREPARE_SEEDING();
void call_RAY_MASTER_MODE_TRIGGER_SEEDING();
void call_RAY_MASTER_MODE_TRIGGER_DETECTION();
void call_RAY_MASTER_MODE_ASK_DISTANCES();
void call_RAY_MASTER_MODE_START_UPDATING_DISTANCES();
void call_RAY_MASTER_MODE_TRIGGER_EXTENSIONS();
void call_RAY_MASTER_MODE_TRIGGER_FUSIONS();
void call_RAY_MASTER_MODE_TRIGGER_FIRST_FUSIONS();
void call_RAY_MASTER_MODE_START_FUSION_CYCLE();
void call_RAY_MASTER_MODE_ASK_EXTENSIONS();
void call_RAY_MASTER_MODE_SCAFFOLDER();
void call_RAY_MASTER_MODE_KILL_RANKS();
void call_RAY_MASTER_MODE_KILL_ALL_MPI_RANKS();
void call_RAY_SLAVE_MODE_WRITE_KMERS();
void call_RAY_SLAVE_MODE_ASSEMBLE_WAVES();
void call_RAY_SLAVE_MODE_SEND_EXTENSION_DATA();
void call_RAY_SLAVE_MODE_DIE();
void call_RAY_MPI_TAG_NOTIFY_ERROR(Message*message);
void call_RAY_MPI_TAG_COMPUTE_REQUIRED_SPACE_FOR_EXTENSIONS(Message*message);
void call_RAY_MPI_TAG_COMPUTE_REQUIRED_SPACE_FOR_EXTENSIONS_REPLY(Message*message);
void call_RAY_MPI_TAG_ASK_EXTENSION_DATA(Message*message);
void call_RAY_MPI_TAG_EXTENSION_DATA_END(Message*message);
void notifyThatOldDirectoryExists();
void registerPlugin(ComputeCore*core);
void resolveSymbols(ComputeCore*core);
};
#endif
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