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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 "NanoMerger.h"
#include <stack>
using namespace std;
/**
* Here, we want to do a depth first search
* on the left and on the right to find
* nearby paths.
*
* Local arbitration will deal with ownership.
*
* \author Sébastien Boisvert
*/
void NanoMerger::work(){
//m_done = true;
if(!m_startedFirst) {
m_explorer.start(m_identifier, &m_first, m_seed, EXPLORER_LEFT, m_parameters,
m_virtualCommunicator,
m_outboxAllocator,
RAY_MPI_TAG_GET_VERTEX_EDGES_COMPACT,
RAY_MPI_TAG_ASK_VERTEX_PATHS_SIZE, RAY_MPI_TAG_ASK_VERTEX_PATH,
m_seedName
);
m_startedFirst = true;
} else if(m_startedFirst && !m_startedLast && m_explorer.work()) {
#ifdef DEBUG_EXPLORER_PATHS
cout << "[DEBUG] NanoMerger processed first, seed length is " << m_seed->size() << endl;
#endif
#ifdef DEBUG_EXPLORER_PATHS
cout << "[DEBUG] path " << m_seedName << " EXPLORER_LEFT " << m_explorer.getSearchResults().size() << " paths found" << endl;
#endif
if(m_explorer.isValid() && m_explorer.getSearchResults().size() == 1) {
m_results.push_back(m_explorer.getSearchResults()[0]);
#ifdef DEBUG_EXPLORER_PATHS
cout << "[DEBUG]";
m_explorer.getSearchResults()[0].print();
cout << endl;
#endif
}
// now do the last one.
m_explorer.start(m_identifier, &m_last, m_seed, EXPLORER_RIGHT, m_parameters,
m_virtualCommunicator,
m_outboxAllocator,
RAY_MPI_TAG_GET_VERTEX_EDGES_COMPACT,
RAY_MPI_TAG_ASK_VERTEX_PATHS_SIZE, RAY_MPI_TAG_ASK_VERTEX_PATH,
m_seedName
);
m_startedLast = true;
} else if(m_startedLast && m_explorer.work()) {
#ifdef DEBUG_EXPLORER_PATHS
cout << "[DEBUG] path " << m_seedName << " EXPLORER_RIGHT " << m_explorer.getSearchResults().size() << " paths found" << endl;
#endif
if(m_explorer.isValid() && m_explorer.getSearchResults().size() == 1) {
m_results.push_back(m_explorer.getSearchResults()[0]);
#ifdef DEBUG_EXPLORER_PATHS
cout << "[DEBUG]";
m_explorer.getSearchResults()[0].print();
cout << endl;
#endif
}
#ifdef DEBUG_EXPLORER_PATHS
cout << "[DEBUG] NanoMerger processed last, seed length is " << m_seed->size() << endl;
#endif
m_done = true;
}
}
bool NanoMerger::isDone(){
return m_done;
}
WorkerHandle NanoMerger::getWorkerIdentifier(){
return m_identifier;
}
/**
* RAY_MPI_TAG_ASK_VERTEX_PATHS_SIZE
* RAY_MPI_TAG_ASK_VERTEX_PATH
*/
void NanoMerger::initialize(WorkerHandle identifier,GraphPath*seed, Parameters * parameters,
VirtualCommunicator * virtualCommunicator, RingAllocator*outboxAllocator,
MessageTag RAY_MPI_TAG_GET_VERTEX_EDGES_COMPACT,
MessageTag RAY_MPI_TAG_ASK_VERTEX_PATHS_SIZE, MessageTag RAY_MPI_TAG_ASK_VERTEX_PATH
){
//cout << "[DEBUG] configuring nano merger now." << endl;
m_identifier = identifier;
m_done = false;
m_seed = seed;
m_virtualCommunicator = virtualCommunicator;
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_rank = m_parameters->getRank();
m_outboxAllocator = outboxAllocator;
int index1 = 0;
m_seed->at(index1, &m_first);
int index2 = m_seed->size() - 1;
m_seed->at(index2, &m_last);
#ifdef CONFIG_ASSERT
assert(index1 == 0);
assert(index2 >= 0);
#endif
//cout << "[DEBUG] achieved with RayPlatform." << endl;
m_startedFirst = false;
m_startedLast = false;
m_seedName = getPathUniqueId(m_parameters->getRank(), identifier);
}
vector<GraphSearchResult> & NanoMerger::getResults() {
return m_results;
}
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