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/*
Ray -- Parallel genome assemblies for parallel DNA sequencing
Copyright (C) 2011, 2012, 2013 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 _Scaffolder_h
#define _Scaffolder_h
#include "ScaffoldingLink.h"
#include "SummarizedLink.h"
#include <code/SeedExtender/ReadFetcher.h>
#include <code/Mock/Parameters.h>
#include <code/Mock/constants.h>
#include <code/SeedingData/GraphPath.h>
#include <RayPlatform/structures/StaticVector.h>
#include <RayPlatform/memory/RingAllocator.h>
#include <RayPlatform/communication/VirtualCommunicator.h>
#include <RayPlatform/scheduling/SwitchMan.h>
#include <RayPlatform/profiling/TimePrinter.h>
#include <RayPlatform/handlers/SlaveModeHandler.h>
#include <RayPlatform/handlers/MasterModeHandler.h>
#include <RayPlatform/plugins/CorePlugin.h>
#include <vector>
#include <sstream>
using namespace std;
__DeclarePlugin(Scaffolder);
__DeclareMasterModeAdapter(Scaffolder,RAY_MASTER_MODE_WRITE_SCAFFOLDS);
__DeclareSlaveModeAdapter(Scaffolder,RAY_SLAVE_MODE_SCAFFOLDER);
__DeclareMessageTagAdapter(Scaffolder,RAY_MPI_TAG_GET_CONTIG_CHUNK);
__DeclareMessageTagAdapter(Scaffolder,RAY_MPI_TAG_GET_CONTIG_PACKED_CHUNK);
/**
* Scaffolder class, it uses MPI through the virtual communicator.
*
* \author Sébastien Boisvert
*/
class Scaffolder : public CorePlugin{
__AddAdapter(Scaffolder,RAY_MASTER_MODE_WRITE_SCAFFOLDS);
__AddAdapter(Scaffolder,RAY_SLAVE_MODE_SCAFFOLDER);
__AddAdapter(Scaffolder,RAY_MPI_TAG_GET_CONTIG_CHUNK);
__AddAdapter(Scaffolder,RAY_MPI_TAG_GET_CONTIG_PACKED_CHUNK);
ostringstream m_operationBuffer;
MessageTag RAY_MPI_TAG_SCAFFOLDING_LINKS_REPLY;
MessageTag RAY_MPI_TAG_START_SCAFFOLDER;
MessageTag RAY_MPI_TAG_REQUEST_VERTEX_READS;
MessageTag RAY_MPI_TAG_CONTIG_INFO;
MessageTag RAY_MPI_TAG_GET_CONTIG_CHUNK;
MessageTag RAY_MPI_TAG_GET_CONTIG_CHUNK_REPLY;
MessageTag RAY_MPI_TAG_GET_CONTIG_PACKED_CHUNK;
MessageTag RAY_MPI_TAG_GET_CONTIG_PACKED_CHUNK_REPLY;
MessageTag RAY_MPI_TAG_GET_COVERAGE_AND_DIRECTION;
MessageTag RAY_MPI_TAG_GET_PATH_LENGTH;
MessageTag RAY_MPI_TAG_GET_READ_MARKERS;
MessageTag RAY_MPI_TAG_GET_READ_MATE;
MessageTag RAY_MPI_TAG_GET_VERTEX_EDGES_COMPACT;
MessageTag RAY_MPI_TAG_HAS_PAIRED_READ;
MessageTag RAY_MPI_TAG_I_FINISHED_SCAFFOLDING;
MessageTag RAY_MPI_TAG_SCAFFOLDING_LINKS;
MasterMode RAY_MASTER_MODE_WRITE_SCAFFOLDS;
MasterMode RAY_MASTER_MODE_CONTIG_BIOLOGICAL_ABUNDANCES;
MasterMode RAY_MASTER_MODE_COUNT_SEARCH_ELEMENTS;
SlaveMode RAY_SLAVE_MODE_DO_NOTHING;
SlaveMode RAY_SLAVE_MODE_SCAFFOLDER;
bool m_coverageWasComputedWithJustice;
int m_skippedRepeatedObjects;
SwitchMan*m_switchMan;
TimePrinter*m_timePrinter;
/**
* Added to skip scaffolding in case of unpaired reads
*/
bool m_skipScaffolding;
int m_rankIdForContig;
bool m_hasContigSequence_Initialised;
ofstream m_fp;
bool m_hasContigSequence;
string m_contigSequence;
map<PathHandle,int> m_contigLengths;
int m_position;
int m_theLength;
GraphPath m_contigPath;
bool m_requestedContigChunk;
vector<int> m_allScaffoldLengths;
vector<int> m_allContigLengths;
/* coverage values for the current path */
vector<int> m_vertexCoverageValues;
int m_scaffoldId;
int m_positionOnScaffold;
bool m_writeContigRequested;
vector<vector<PathHandle> > m_scaffoldContigs;
vector<vector<char> >m_scaffoldStrands;
vector<vector<int> >m_scaffoldGaps;
bool m_sentContigInfo;
bool m_sentContigMeta;
vector<PathHandle> m_masterContigs;
vector<int> m_masterLengths;
vector<SummarizedLink>m_masterLinks;
int m_summaryIterator;
bool m_summarySent;
vector<SummarizedLink>m_summary;
bool m_summaryPerformed;
bool m_entrySent;
map<PathHandle,map<char,map<PathHandle,map<char,vector<ScaffoldingLink> > > > > m_scaffoldingSummary;
bool m_reverseDirectionsReceived;
bool m_reverseDirectionLengthReceived;
PathHandle m_pairedReverseDirectionName;
int m_pairedReverseDirectionPosition;
CoverageDepth m_pairedReverseMarkerCoverage;
bool m_pairedReverseHasDirection;
bool m_reverseDirectionLengthRequested;
int m_pairedReverseDirectionLength;
// these are mostly flags for sends/receives
bool m_forwardDirectionLengthRequested;
bool m_forwardDirectionLengthReceived;
int m_pairedForwardDirectionLength;
bool m_forwardDirectionsRequested;
bool m_forwardDirectionsReceived;
CoverageDepth m_pairedForwardMarkerCoverage;
bool m_pairedForwardHasDirection;
PathHandle m_pairedForwardDirectionName;
int m_pairedForwardDirectionPosition;
bool m_reverseDirectionsRequested;
int m_readLength;
bool m_markersRequested;
bool m_markersReceived;
int m_pairedForwardOffset;
int m_pairedReverseOffset;
Kmer m_pairedForwardMarker;
Kmer m_pairedReverseMarker;
bool m_pairReceived;
int m_pairedReadRank;
int m_pairedReadIndex;
int m_pairedReadLibrary;
int m_pairedReadLength;
bool m_pairRequested;
bool m_hasPairReceived;
bool m_hasPairRequested;
bool m_hasPair;
bool m_initialisedFetcher;
int m_readAnnotationId;
ReadFetcher m_readFetcher;
vector<WorkerHandle> m_activeWorkers;
WorkerHandle m_workerId;
VirtualCommunicator*m_virtualCommunicator;
bool m_coverageRequested;
bool m_coverageReceived;
CoverageDepth m_receivedCoverage;
bool m_reverseDone;
bool m_forwardDone;
int m_contigId;
int m_positionOnContig;
vector<GraphPath>*m_contigs;
vector<PathHandle>*m_contigNames;
Parameters*m_parameters;
StaticVector*m_inbox;
StaticVector*m_outbox;
RingAllocator*m_outboxAllocator;
bool m_ready;
/**
* gets a contig sequence by receiving several MPI messages
*/
map<PathHandle,int>*m_contigNameIndex;
void getContigSequence(PathHandle id);
void getContigSequenceFromKmers(PathHandle id);
void getContigSequenceFromPackedObjects(PathHandle id);
void processContig();
void processContigPosition();
void processVertex(Kmer*vertex);
void processAnnotations();
void processAnnotation();
void performSummary();
void sendSummary();
void sendContigInfo();
void extractScaffolds(char state,map<PathHandle,int>*colors,PathHandle vertex,
map<PathHandle,map<char,vector<vector<PathHandle> > > >*parents,
map<PathHandle,map<char,vector<vector<PathHandle> > > >*children,set<int>*completedColours);
void computeStatistics(vector<int>*lengths,int minimumLength,ostream*outputStream);
void printInStream(ostream*outputStream);
void getCoverageOfBlockOfLife();
Rank m_rank;
/*
* Variables for fetching remote paths.
*/
int m_theLengthInNucleotides;
ostringstream m_contigPathBuffer;
public:
bool m_initialised;
/**
* Number of ranks that have finished scaffolding
*/
int m_numberOfRanksFinished;
/**
* Constructor of the scaffolder
*/
void constructor(StaticVector*outbox,StaticVector*inbox,RingAllocator*outboxAllocator,Parameters*parameters,
VirtualCommunicator*vc,SwitchMan*switchMan);
void setContigPaths(vector<PathHandle>*names,vector<GraphPath>*paths);
void addMasterLink(SummarizedLink*link);
void solve();
void addMasterContig(PathHandle name,int length);
void call_RAY_MASTER_MODE_WRITE_SCAFFOLDS();
void call_RAY_SLAVE_MODE_SCAFFOLDER();
void call_RAY_MPI_TAG_GET_CONTIG_CHUNK(Message*message);
void call_RAY_MPI_TAG_GET_CONTIG_PACKED_CHUNK(Message*message);
void printFinalMessage();
void setTimePrinter(TimePrinter*a);
void registerPlugin(ComputeCore*core);
void resolveSymbols(ComputeCore*core);
};
#endif
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