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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 "SeedMergingWorkflow.h"
#include "NanoMerger.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 SeedMergingWorkflow::initializeMethod(){
m_seedIndex=0;
m_finished = 0 ;
}
/** finalize the whole thing */
void SeedMergingWorkflow::finalizeMethod(){
//cout << "[DEBUG] number of relations: " << m_searchResults.size() << endl;
m_core->getSwitchMan()->closeSlaveModeLocally(m_core->getOutbox(),m_core->getRank());
}
/** has an unassigned task left to compute */
bool SeedMergingWorkflow::hasUnassignedTask(){
/*
* This code is still buggy. I will do the 2.3.0 release
* without it.
*/
bool enableSeedMerging = m_parameters->hasOption("-merge-seeds");
//enableSeedMerging = true;
if(!enableSeedMerging)
return false;
return m_seedIndex < (int) m_seeds->size () ;
}
/** assign the next task to a worker and return this worker */
Worker*SeedMergingWorkflow::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;
NanoMerger*worker = new NanoMerger();
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 SeedMergingWorkflow::processWorkerResult(Worker*worker){
NanoMerger * theWorker = (NanoMerger*)worker;
vector<GraphSearchResult> & results = theWorker->getResults();
bool runTransaction = true;
if(results.size() == 2) {
// make sure this is not something like
//
// A001 --------B
// | /
// A100 --------
//
// with repeats, both ends of A could link to B...
set<PathHandle> observations;
for(int i = 0 ; i < (int) results.size() ; i++) {
GraphSearchResult & result = results[i];
observations.insert(result.getPathHandles()[0]);
observations.insert(result.getPathHandles()[1]);
}
if(observations.size() != 3)
runTransaction = false;
}
// we must send the results now !!!A
// we will send at most 2 messages...
// here we don't send messages right away because these units are
// not regular.
for(int i = 0 ; i < (int) results.size() ; i ++) {
if(!runTransaction)
break;
m_searchResults.push_back(results[i]);
}
if(m_finished % m_period == 0){
cout<<"Rank " << m_rank << " processWorkerResult "<<m_finished<<"/" <<m_seeds->size()<<endl;
}
m_finished++;
}
/** destroy a worker */
void SeedMergingWorkflow::destroyWorker(Worker*worker){
NanoMerger * concreteWorker = (NanoMerger*)worker;
delete concreteWorker;
worker = NULL; // this does nothing useful
concreteWorker = NULL;
}
void SeedMergingWorkflow::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;
}
vector<GraphSearchResult> & SeedMergingWorkflow::getResults() {
return m_searchResults;
}
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