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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 "PathEvaluator.h"
#include <fstream>
using namespace std;
__CreatePlugin(PathEvaluator);
__CreateMasterModeAdapter(PathEvaluator,RAY_MASTER_MODE_EVALUATE_PATHS);
__CreateSlaveModeAdapter(PathEvaluator,RAY_SLAVE_MODE_EVALUATE_PATHS);
void PathEvaluator::call_RAY_MASTER_MODE_EVALUATE_PATHS(){
if(!m_masterModeStarted){
m_core->getSwitchMan()->openMasterMode(m_core->getOutbox(),m_core->getRank());
m_masterModeStarted=true;
}else if(m_core->getSwitchMan()->allRanksAreReady()){
m_core->getSwitchMan()->closeMasterMode();
}
}
void PathEvaluator::call_RAY_SLAVE_MODE_EVALUATE_PATHS(){
writeCheckpointForContigPaths();
m_core->getSwitchMan()->closeSlaveModeLocally(m_core->getOutbox(),m_core->getRank());
}
void PathEvaluator::writeCheckpointForContigPaths(){
/** possibly write the checkpoint */
if(m_parameters->writeCheckpoints() && !m_parameters->hasCheckpoint("ContigPaths")){
cout<<"Rank "<<m_parameters->getRank()<<" is writing checkpoint ContigPaths"<<endl;
ofstream f(m_parameters->getCheckpointFile("ContigPaths").c_str());
ostringstream buffer;
int theSize=m_contigs->size();
buffer.write((char*)&theSize, sizeof(int));
/* write each path with its name and vertices */
for(int i=0;i<theSize;i++){
PathHandle name=(*m_contigNames)[i];
int vertices=(*m_contigs)[i].size();
buffer.write((char*)&name, sizeof(PathHandle));
buffer.write((char*)&vertices, sizeof(int));
for(int j=0;j<vertices;j++){
Kmer kmer;
(*m_contigs)[i].at(j,&kmer);
kmer.write(&buffer);
}
flushFileOperationBuffer(false, &buffer, &f, CONFIG_FILE_IO_BUFFER_SIZE);
}
flushFileOperationBuffer(true, &buffer, &f, CONFIG_FILE_IO_BUFFER_SIZE);
f.close();
}
}
void PathEvaluator::registerPlugin(ComputeCore*core){
PluginHandle plugin=core->allocatePluginHandle();
m_plugin=plugin;
m_core=core;
core->setPluginName(plugin,"PathEvaluator");
core->setPluginDescription(plugin,"Post-processing of paths.");
core->setPluginAuthors(plugin,"Sébastien Boisvert");
core->setPluginLicense(plugin,"GNU General Public License version 3");
__ConfigureMasterModeHandler(PathEvaluator, RAY_MASTER_MODE_EVALUATE_PATHS);
__ConfigureSlaveModeHandler(PathEvaluator, RAY_SLAVE_MODE_EVALUATE_PATHS);
RAY_MPI_TAG_EVALUATE_PATHS=core->allocateMessageTagHandle(plugin);
core->setMessageTagSymbol(plugin,RAY_MPI_TAG_EVALUATE_PATHS,"RAY_MPI_TAG_EVALUATE_PATHS");
__BindPlugin(PathEvaluator);
}
void PathEvaluator::resolveSymbols(ComputeCore*core){
RAY_MASTER_MODE_EVALUATE_PATHS=core->getMasterModeFromSymbol(m_plugin,"RAY_MASTER_MODE_EVALUATE_PATHS");
RAY_MASTER_MODE_ASK_EXTENSIONS=core->getMasterModeFromSymbol(m_plugin,"RAY_MASTER_MODE_ASK_EXTENSIONS");
core->setMasterModeNextMasterMode(m_plugin,RAY_MASTER_MODE_EVALUATE_PATHS,RAY_MASTER_MODE_ASK_EXTENSIONS);
core->setMasterModeToMessageTagSwitch(m_plugin,RAY_MASTER_MODE_EVALUATE_PATHS,RAY_MPI_TAG_EVALUATE_PATHS);
core->setMessageTagToSlaveModeSwitch(m_plugin,RAY_MPI_TAG_EVALUATE_PATHS,RAY_SLAVE_MODE_EVALUATE_PATHS);
m_parameters=(Parameters*)core->getObjectFromSymbol(m_plugin,"/RayAssembler/ObjectStore/Parameters.ray");
m_contigs=(vector<GraphPath>*)core->getObjectFromSymbol(m_plugin,"/RayAssembler/ObjectStore/ContigPaths.ray");
m_contigNames=(vector<PathHandle>*)core->getObjectFromSymbol(m_plugin,"/RayAssembler/ObjectStore/ContigNames.ray");
m_masterModeStarted=false;
}
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