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/*
* Ray -- Parallel genome assemblies for parallel DNA sequencing
* Copyright (C) 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/>
*/
#include "AnnotationFetcher.h"
void AnnotationFetcher::initialize(Parameters*parameters, VirtualCommunicator*virtualCommunicator,
WorkerHandle identifier, RingAllocator * outboxAllocator,
MessageTag RAY_MPI_TAG_ASK_VERTEX_PATHS_SIZE,
MessageTag RAY_MPI_TAG_ASK_VERTEX_PATH
){
m_virtualCommunicator = virtualCommunicator;
m_parameters = parameters;
m_identifier = identifier;
m_outboxAllocator = outboxAllocator;
m_rank = m_parameters->getRank();
this->RAY_MPI_TAG_ASK_VERTEX_PATHS_SIZE = RAY_MPI_TAG_ASK_VERTEX_PATHS_SIZE;
this->RAY_MPI_TAG_ASK_VERTEX_PATH = RAY_MPI_TAG_ASK_VERTEX_PATH;
reset();
}
void AnnotationFetcher::reset(){
m_initializedDirectionFetcher = false;
}
bool AnnotationFetcher::fetchDirections(Kmer*kmer){
if(!m_initializedDirectionFetcher){
m_initializedDirectionFetcher = true;
m_fetchedCount = false;
m_queryWasSent = false;
m_directions.clear();
}else if(!m_fetchedCount){
if(!m_queryWasSent){
MessageTag tag = RAY_MPI_TAG_ASK_VERTEX_PATHS_SIZE;
int elementsPerQuery=m_virtualCommunicator->getElementsPerQuery(tag);
#ifdef DEBUG_LEFT_EXPLORATION
cout << "Sending message for count" << endl;
#endif
Rank destination = m_parameters->vertexRank(kmer);
MessageUnit*message=(MessageUnit*)m_outboxAllocator->allocate(elementsPerQuery*sizeof(MessageUnit));
int bufferPosition=0;
kmer->pack(message,&bufferPosition);
Message aMessage(message, elementsPerQuery,
destination, tag, m_rank);
m_virtualCommunicator->pushMessage(m_identifier, &aMessage);
m_queryWasSent = true;
}else if(m_virtualCommunicator->isMessageProcessed(m_identifier)){
vector<MessageUnit> elements;
m_virtualCommunicator->getMessageResponseElements(m_identifier, &elements);
m_numberOfPaths = elements[0];
m_fetchedCount = true;
#ifdef DEBUG_LEFT_EXPLORATION
cout<<"Paths: "<<m_numberOfPaths << endl;
#endif
m_pathIndex = 0;
m_queryWasSent = false;
m_reverseStrand = false;
}
}else if(m_pathIndex < m_numberOfPaths){
if(!m_queryWasSent){
Kmer theKmer=*kmer;
if(m_reverseStrand)
theKmer = theKmer.complementVertex(m_parameters->getWordSize(),m_parameters->getColorSpaceMode());
Rank destination = m_parameters->vertexRank(&theKmer);
int elementsPerQuery=m_virtualCommunicator->getElementsPerQuery(RAY_MPI_TAG_ASK_VERTEX_PATH);
MessageUnit*message=(MessageUnit*)m_outboxAllocator->allocate(elementsPerQuery);
int outputPosition=0;
theKmer.pack(message,&outputPosition);
message[outputPosition++]=m_pathIndex;
Message aMessage(message, elementsPerQuery, destination,
RAY_MPI_TAG_ASK_VERTEX_PATH, m_parameters->getRank());
m_virtualCommunicator->pushMessage(m_identifier, &aMessage);
m_queryWasSent = true;
}else if(m_virtualCommunicator->isMessageProcessed(m_identifier)){
vector<MessageUnit> response;
m_virtualCommunicator->getMessageResponseElements(m_identifier, &response);
int bufferPosition=0;
/* skip the k-mer because we don't need it */
bufferPosition += kmer->getNumberOfU64();
PathHandle otherPathIdentifier=response[bufferPosition++];
int progression=response[bufferPosition++];
Direction direction;
direction.constructor(otherPathIdentifier, progression, m_reverseStrand);
m_directions.push_back(direction);
m_queryWasSent = false;
m_pathIndex ++;
}
/*
}else if(!m_reverseStrand){
// fetch also reverse-complement entries.
m_reverseStrand = true;
m_pathIndex = 0;
m_queryWasSent = false;
*/
}else{
return true;
}
return false;
}
vector<Direction>* AnnotationFetcher::getDirections(){
return &m_directions;
}
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