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/*
Ray -- Parallel genome assemblies for parallel DNA sequencing
Copyright (C) 2010, 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 _ExtensionData
#define _ExtensionData
#include "ExtensionElement.h"
#include <code/SequencesLoader/ReadHandle.h>
#include <code/SequencesIndexer/PairedRead.h>
#include <code/SequencesIndexer/ReadAnnotation.h>
#include <code/SequencesLoader/Read.h>
#include <code/Mock/Parameters.h>
#include <code/Mock/common_functions.h>
#include <code/SeedingData/GraphPath.h>
#include <RayPlatform/structures/SplayTree.h>
#include <RayPlatform/profiling/Profiler.h>
#include <map>
#include <set>
#include <vector>
using namespace std;
/*
* Stores the information for a seed extension.
*
* This class is really just a helper for SeedExtender.
* There are so many things to store to implement the heuristics
* correctly.
*
* \author Sébastien Boisvert
*/
class ExtensionData{
SplayTree<ReadHandle,ExtensionElement>*m_database;
int m_numberOfBins;
Parameters*m_parameters;
MyAllocator m_allocator;
void createStructures();
void destroyStructures(Profiler*m_profiler);
public:
int m_readType;
vector<CoverageDepth> m_EXTENSION_coverages;
GraphPath m_EXTENSION_extension;
vector<CoverageDepth> m_extensionCoverageValues;
vector<int> m_repeatedValues;
// EXTENSION MODE
vector<Kmer> m_enumerateChoices_outgoingEdges;
bool m_doChoice_tips_Detected;
PairedRead m_EXTENSION_pairedRead;
bool m_EXTENSION_pairedSequenceRequested;
bool m_EXTENSION_hasPairedReadAnswer;
bool m_EXTENSION_pairedSequenceReceived;
int m_EXTENSION_edgeIterator;
bool m_EXTENSION_hasPairedReadRequested;
bool m_EXTENSION_hasPairedReadReceived;
vector<PathHandle> m_EXTENSION_identifiers;
/**
* bidirectional flow algorithm using Ray's many heuristics
*/
/** the number of vertices flowed previously */
int m_previouslyFlowedVertices;
/** the current flow number */
int m_flowNumber;
/** TODO could be a pointer to the original thing... */
GraphPath m_EXTENSION_currentSeed;
int m_EXTENSION_numberOfRanksDone;
vector<GraphPath> m_EXTENSION_contigs;
bool m_EXTENSION_checkedIfCurrentVertexIsAssembled;
bool m_EXTENSION_VertexMarkAssembled_requested;
bool m_EXTENSION_reverseComplement_requested;
bool m_EXTENSION_vertexIsAssembledResult;
bool m_EXTENSION_readLength_requested;
bool m_EXTENSION_readLength_received;
bool m_EXTENSION_readLength_done;
bool m_EXTENSION_read_vertex_received;
bool m_EXTENSION_read_vertex_requested;
Kmer m_EXTENSION_receivedReadVertex;
bool m_EXTENSION_currentRankIsDone;
bool m_EXTENSION_currentRankIsSet;
bool m_EXTENSION_currentRankIsStarted;
int m_EXTENSION_rank;
bool m_EXTENSION_initiated;
int m_EXTENSION_currentSeedIndex;
bool m_EXTENSION_VertexAssembled_received;
int m_EXTENSION_currentPosition;
bool m_EXTENSION_VertexMarkAssembled_received;
bool m_EXTENSION_markedCurrentVertexAsAssembled;
bool m_EXTENSION_enumerateChoices;
bool m_EXTENSION_choose;
bool m_EXTENSION_directVertexDone;
bool m_EXTENSION_VertexAssembled_requested;
bool m_EXTENSION_receivedAssembled;
bool m_EXTENSION_reverseComplement_received;
vector<ReadAnnotation> m_EXTENSION_receivedReads;
bool m_EXTENSION_reads_requested;
bool m_EXTENSION_reads_received;
vector<ReadHandle> m_sequencesToFree;
int m_EXTENSION_receivedLength;
bool m_EXTENSION_reverseVertexDone;
// reads used so far
// reads to check (the ones "in range")
bool m_EXTENSION_singleEndResolution;
set<ReadHandle>::iterator m_EXTENSION_readIterator;
map<Kmer,vector<int> > m_EXTENSION_readPositionsForVertices;
map<Kmer,vector<int> > m_EXTENSION_pairedReadPositionsForVertices;
map<Kmer,vector<int> > m_EXTENSION_pairedLibrariesForVertices;
map<Kmer,vector<ReadHandle> > m_EXTENSION_pairedReadsForVertices;
CoverageDepth m_currentCoverage;
set<ReadHandle> m_EXTENSION_readsInRange;
set<ReadHandle> m_pairedReadsWithoutMate;
map<int,vector<ReadHandle> > m_expirations;
void lazyDestructor();
void resetStructures(Profiler*m_profiler);
ExtensionElement*getUsedRead(ReadHandle a);
ExtensionElement*addUsedRead(ReadHandle a);
void removeSequence(ReadHandle a);
void constructor(Parameters*parameters);
void destructor();
MyAllocator*getAllocator();
};
#endif
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