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/*
Ray
Copyright (C) 2010, 2011, 2012 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 _DepthFirstSearchData
#define _DepthFirstSearchData
#include <code/Mock/Parameters.h>
#include <code/Mock/common_functions.h>
#include <code/SeedingData/SeedingData.h>
#include <RayPlatform/memory/RingAllocator.h>
#include <RayPlatform/structures/StaticVector.h>
#include <RayPlatform/structures/MyStack.h>
#include <vector>
#include <map>
#include <set>
using namespace std;
class SeedingData;
/*
* Data for depth first search.
*
* \author Sébastien Boisvert
*/
class DepthFirstSearchData{
MessageTag RAY_MPI_TAG_REQUEST_VERTEX_COVERAGE;
MessageTag RAY_MPI_TAG_REQUEST_VERTEX_EDGES;
MessageTag RAY_MPI_TAG_REQUEST_VERTEX_OUTGOING_EDGES;
bool m_outgoingEdgesDone;
map<Kmer,vector<Kmer> > m_outgoingEdges;
map<Kmer,vector<Kmer> > m_ingoingEdges;
public:
void setTags(
MessageTag RAY_MPI_TAG_REQUEST_VERTEX_COVERAGE,
MessageTag RAY_MPI_TAG_REQUEST_VERTEX_EDGES,
MessageTag RAY_MPI_TAG_REQUEST_VERTEX_OUTGOING_EDGES
);
bool m_maxDepthReached;
bool m_doChoice_tips_dfs_initiated;
// depth first search
bool m_doChoice_tips_Initiated;
bool m_doChoice_tips_dfs_done;
int m_depthFirstSearch_maxDepth;
MyStack<int> m_depthFirstSearchDepths;
int m_doChoice_tips_i;
vector<int> m_doChoice_tips_newEdges;
set<Kmer> m_depthFirstSearchVisitedVertices;
MyStack<Kmer> m_depthFirstSearchVerticesToVisit;
vector<Kmer> m_depthFirstSearchVisitedVertices_vector;
vector<int> m_depthFirstSearchVisitedVertices_depths;
map<Kmer,int> m_coverages;
void depthFirstSearch(Kmer root,Kmer a,int maxDepth,
bool*edgesRequested,bool*vertexCoverageRequested,bool*vertexCoverageReceived,
RingAllocator*outboxAllocator,int size,int theRank,StaticVector*outbox,
int*receivedVertexCoverage,vector<Kmer>*receivedOutgoingEdges,
int minimumCoverage,bool*edgesReceived,int wordSize,Parameters*parameters);
void depthFirstSearchBidirectional(Kmer a,int maxDepth,
bool*edgesRequested,bool*vertexCoverageRequested,bool*vertexCoverageReceived,
RingAllocator*outboxAllocator,int size,int theRank,StaticVector*outbox,
int*receivedVertexCoverage,SeedingData*seedingData,
int minimumCoverage,bool*edgesReceived,Parameters*parameters);
map<Kmer,vector<Kmer> >*getIngoingEdges();
map<Kmer,vector<Kmer> >*getOutgoingEdges();
};
#endif
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