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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 GraphSearchResult_Header
#define GraphSearchResult_Header
#include <code/SeedingData/PathHandle.h>
#include <code/SeedingData/GraphPath.h>
#include <RayPlatform/store/CarriageableItem.h>
#include <vector>
using namespace std;
/**
* This stores a graph search result.
*
* Path0 ----------> Path1 ------> Path2 -------> Path3
*
* start start start start
*
* end end end end
*
*
* There are:
*
* * N m_pathNames
* * N-1 m_computedPaths
* * N m_pathStarts
* * N m_pathEnds
*
* if start > end, it means that we must use the other DNA strand.
*
* \author Sébastien Boisvert
*/
class GraphSearchResult: public CarriageableItem {
vector<PathHandle> m_pathHandles;
vector<bool> m_pathOrientations; // false is normal, true is reverse
vector<GraphPath> m_computedPaths;
bool hasPath(PathHandle & handle);
public:
bool addPathHandle(PathHandle handle, bool orientation);
bool addPath(GraphPath & path);
void print();
int load(const char * buffer);
int dump(char * buffer) const;
int getRequiredNumberOfBytes() const;
vector<PathHandle> & getPathHandles();
vector<bool> & getPathOrientations();
vector<GraphPath> & getComputedPaths();
bool addPathOnLeftSide(PathHandle & handle, bool strand, GraphPath & path);
bool addPathOnRightSide(PathHandle & handle, bool strand, GraphPath & path);
string toString() const;
/**
* Rotate the object to obtain a reverse-complement.
*/
void reverseContent();
bool hasData() const;
};
#endif /* GraphSearchResult_Header */
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