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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 _VertexMessenger
#define _VertexMessenger
#include <code/SequencesLoader/ReadHandle.h>
#include <code/SequencesIndexer/ReadAnnotation.h>
#include <code/KmerAcademyBuilder/Kmer.h>
#include <code/Mock/Parameters.h>
#include <RayPlatform/structures/StaticVector.h>
#include <RayPlatform/memory/RingAllocator.h>
#include <stdint.h>
#include <vector>
#include <set>
using namespace std;
/*
* Get the markers for a Kmer and also send progression
* information to the appropriate MPI rank.
* \author Sébastien Boisvert
*/
class VertexMessenger{
MessageTag RAY_MPI_TAG_VERTEX_INFO;
MessageTag RAY_MPI_TAG_VERTEX_INFO_REPLY;
MessageTag RAY_MPI_TAG_VERTEX_READS;
MessageTag RAY_MPI_TAG_VERTEX_READS_FROM_LIST;
MessageTag RAY_MPI_TAG_VERTEX_READS_FROM_LIST_REPLY;
MessageTag RAY_MPI_TAG_VERTEX_READS_REPLY;
CoverageDepth m_peakCoverage;
set<ReadHandle>::iterator m_mateIterator;
Parameters*m_parameters;
StaticVector*m_inbox;
StaticVector*m_outbox;
RingAllocator*m_outboxAllocator;
uint8_t m_edges;
CoverageDepth m_coverageValue;
vector<ReadAnnotation> m_annotations;
bool m_isDone;
Kmer m_vertex;
PathHandle m_waveId;
int m_wavePosition;
set<ReadHandle>*m_matesToMeet;
bool m_receivedBasicInfo;
bool m_requestedBasicInfo;
int m_numberOfAnnotations;
bool m_getReads;
void*m_pointer;
bool m_requestedReads;
Rank m_destination;
bool m_receivedReads;
void getReadsForUniqueVertex();
void getReadsForRepeatedVertex();
public:
void constructor(Kmer vertex,PathHandle wave,int pos,
set<ReadHandle>*matesToMeet,StaticVector*inbox,StaticVector*outbox,
RingAllocator*outboxAllocator,Parameters*parameters,bool getReads,CoverageDepth peakCoverage,
MessageTag RAY_MPI_TAG_VERTEX_INFO,
MessageTag RAY_MPI_TAG_VERTEX_INFO_REPLY,
MessageTag RAY_MPI_TAG_VERTEX_READS,
MessageTag RAY_MPI_TAG_VERTEX_READS_FROM_LIST,
MessageTag RAY_MPI_TAG_VERTEX_READS_FROM_LIST_REPLY,
MessageTag RAY_MPI_TAG_VERTEX_READS_REPLY
);
bool isDone();
void work();
CoverageDepth getCoverageValue();
uint8_t getEdges();
vector<ReadAnnotation>getReadAnnotations();
};
#endif
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