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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 "SeedFilteringWorkflow.h"
#include "AnnihilationWorker.h"
/*
* Methods to implement for the TaskCreator interface.
*
* The TaskCreator stack is used in the handler
* RAY_SLAVE_MODE_FILTER_SEEDS.
*/
/** initialize the whole thing */
void SeedFilteringWorkflow::initializeMethod(){
m_seedIndex=0;
m_states.resize(m_seeds->size());
for(int i=0;i<(int)m_states.size(); i++)
m_states[i] = true;
#ifdef CONFIG_ASSERT
assert(m_states.size() == m_seeds->size());
#endif
m_finished = 0 ;
}
/** finalize the whole thing */
void SeedFilteringWorkflow::finalizeMethod(){
vector<GraphPath> newPaths;
for(int i=0;i< (int) m_seeds->size() ; i++){
if(!m_states[i])
continue;
newPaths.push_back(m_seeds->at(i));
}
(*m_seeds) = newPaths;
m_core->getSwitchMan()->closeSlaveModeLocally(m_core->getOutbox(),m_core->getRank());
}
/** has an unassigned task left to compute */
bool SeedFilteringWorkflow::hasUnassignedTask(){
return m_seedIndex < (int) m_seeds->size () ;
}
/** assign the next task to a worker and return this worker */
Worker*SeedFilteringWorkflow::assignNextTask(){
#ifdef CONFIG_ASSERT
assert(m_seedIndex < (int)m_seeds->size());
#endif
if(m_seedIndex % m_period == 0)
cout<<"Rank "<<m_rank<< " assignNextTask "<<m_seedIndex<< "/" << m_seeds->size()<<endl;
AnnihilationWorker*worker=new AnnihilationWorker();
worker->initialize(m_seedIndex, &((*m_seeds)[m_seedIndex]), m_parameters,
m_virtualCommunicator,
m_core->getOutboxAllocator(),
RAY_MPI_TAG_GET_VERTEX_EDGES_COMPACT,
RAY_MPI_TAG_ASK_VERTEX_PATHS_SIZE,
RAY_MPI_TAG_ASK_VERTEX_PATH
);
m_seedIndex++;
return worker;
}
/** get the result of a worker */
void SeedFilteringWorkflow::processWorkerResult(Worker*worker){
bool result = ((AnnihilationWorker*)worker)->isValid();
int seedIndex = worker->getWorkerIdentifier();
m_states[seedIndex] = result;
if(m_finished % m_period == 0){
cout<<"Rank " << m_rank << " processWorkerResult "<<m_finished<<"/" <<m_seeds->size()<<endl;
}
m_finished++;
}
/** destroy a worker */
void SeedFilteringWorkflow::destroyWorker(Worker*worker){
delete worker;
worker = NULL;
}
void SeedFilteringWorkflow::initialize(vector<GraphPath>*seeds, VirtualCommunicator*virtualCommunicator,
VirtualProcessor * virtualProcessor,ComputeCore * core, Parameters * parameters,
MessageTag RAY_MPI_TAG_GET_VERTEX_EDGES_COMPACT,
MessageTag RAY_MPI_TAG_ASK_VERTEX_PATHS_SIZE,
MessageTag RAY_MPI_TAG_ASK_VERTEX_PATH){
m_rank = core->getRank();
m_seeds = seeds;
m_virtualCommunicator = virtualCommunicator;
m_virtualProcessor = virtualProcessor;
m_core = core;
m_parameters = parameters;
this->RAY_MPI_TAG_GET_VERTEX_EDGES_COMPACT = RAY_MPI_TAG_GET_VERTEX_EDGES_COMPACT;
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;
m_period = 100;
}
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