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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/>
*/
#ifndef GraphExplorer_header
#define GraphExplorer_header
#include "AttributeFetcher.h"
#include "AnnotationFetcher.h"
#include "GraphSearchResult.h"
#include <code/Mock/Parameters.h>
#include <code/Mock/Parameters.h>
#include <RayPlatform/core/ComputeCore.h>
#include <RayPlatform/communication/VirtualCommunicator.h>
#include <stack>
using namespace std;
#define EXPLORER_LEFT 0x89
#define EXPLORER_RIGHT 0x452
/**
* This class is an explorer to find paths leading to new paths.
*
* \author Sébastien Boisvert
*/
class GraphExplorer {
int m_searchDepthForFirstResult;
bool m_debug;
vector<GraphSearchResult> m_searchResults;
stack<Kmer> m_verticesToVisit;
stack<int> m_depths;
int m_maximumVisitedDepth;
AnnotationFetcher m_annotationFetcher;
AnnotationFetcher m_annotationFetcherReverse;
AttributeFetcher m_attributeFetcher;
WorkerHandle m_key;
int m_direction;
PathHandle m_seedName;
map<Kmer, vector<Kmer> > m_parents;
map<Kmer, int> m_vertexDepths;
CoverageDepth m_coverage1;
Kmer m_start;
MessageTag RAY_MPI_TAG_GET_VERTEX_EDGES_COMPACT;
MessageTag RAY_MPI_TAG_ASK_VERTEX_PATHS_SIZE;
MessageTag RAY_MPI_TAG_ASK_VERTEX_PATH;
bool m_haveAttributes;
bool m_haveAnnotations;
bool m_haveAnnotationsReverse;
bool m_stopAtFirstHit;
bool m_done;
int m_maximumDepth;
VirtualCommunicator * m_virtualCommunicator;
Parameters * m_parameters;
int m_maximumVisitedVertices;
int m_visitedVertices;
RingAllocator*m_outboxAllocator;
GraphPath * m_seed;
bool backtrackPath(vector<Kmer> * path, Kmer * vertex);
bool getBestParent(Kmer * parent, Kmer kmer);
bool processAnnotations(AnnotationFetcher & annotationFetcher, int currentDepth, Kmer & object);
public:
void start(WorkerHandle worker, Kmer * start, GraphPath * seed, int direction, 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,
PathHandle seedName
);
bool work();
vector<GraphSearchResult> & getSearchResults();
bool isValid() const ;
};
#endif /* GraphExplorer_header */
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