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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 _ScaffoldingAlgorithm_h
#define _ScaffoldingAlgorithm_h
#include "ScaffoldingEdge.h"
#include "ScaffoldingVertex.h"
#include <code/SeedingData/PathHandle.h>
#include <vector>
#include <set>
#include <map>
using namespace std;
class ScaffoldingAlgorithm{
vector<ScaffoldingVertex>*m_vertices;
vector<ScaffoldingEdge>*m_edges;
map<PathHandle,map<PathHandle,ScaffoldingEdge> > m_addedEdges;
int m_numberOfEdges;
map<PathHandle,int> m_lengths;
map<int,map<int,int> > m_conflicts;
public:
ScaffoldingAlgorithm();
void setVertices(vector<ScaffoldingVertex>*vertices);
void setEdges(vector<ScaffoldingEdge>*edges);
void addEdge(ScaffoldingEdge*edge);
bool hasConflictWithEdgeAroundContig(ScaffoldingEdge*edgeToBeAdded,ScaffoldingEdge*alreadyAcceptedEdge,PathHandle contigToCheck);
bool hasConflictWithEdge(ScaffoldingEdge*edgeToBeAdded,ScaffoldingEdge*alreadyAcceptedEdge);
bool hasConflictWithContig(ScaffoldingEdge*edge,PathHandle contig);
bool hasConflict(ScaffoldingEdge*edge);
void solve(
vector<vector<PathHandle> >*m_scaffoldContigs,
vector<vector<char> >*m_scaffoldStrands,
vector<vector<int> >*m_scaffoldGaps
);
void extractScaffolds(char state,map<PathHandle,int>*colors,PathHandle vertex,
map<PathHandle,map<char,vector<vector<uint64_t> > > >*parents,
map<PathHandle,map<char,vector<vector<uint64_t> > > >*children,set<int>*completedColours,
vector<vector<PathHandle> >*scaffoldContigs,
vector<vector<char> >*scaffoldStrands,
vector<vector<int> >*scaffoldGaps
);
};
#endif
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