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//Copyright 2017 Ryan Wick
//This file is part of Bandage
//Bandage 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, either version 3 of the License, or
//(at your option) any later version.
//Bandage 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 should have received a copy of the GNU General Public License
//along with Bandage. If not, see <http://www.gnu.org/licenses/>.
#ifndef PATH_H
#define PATH_H
#include <QByteArray>
#include <QList>
#include <vector>
#include <QString>
#include <QStringList>
#include "../program/globals.h"
#include "graphlocation.h"
class DeBruijnNode;
class DeBruijnEdge;
class Path
{
public:
//CREATORS
Path() {}
static Path makeFromUnorderedNodes(QList<DeBruijnNode *> nodes,
bool strandSpecific);
static Path makeFromUnorderedNodes(std::vector<DeBruijnNode *> nodes,
bool strandSpecific);
static Path makeFromOrderedNodes(QList<DeBruijnNode *> nodes,
bool circular);
static Path makeFromString(QString pathString, bool circular,
QString * pathStringFailure);
//ACCESSORS
QList<DeBruijnNode *> getNodes() const {return m_nodes;}
QList<DeBruijnEdge *> getEdges() const {return m_edges;}
bool isEmpty() const {return m_nodes.empty();}
bool isCircular() const;
bool haveSameNodes(Path other) const;
bool hasNodeSubset(Path other) const;
QByteArray getPathSequence() const;
QString getFasta() const;
QString getString(bool spaces) const;
int getLength() const;
QList<Path> extendPathInAllPossibleWays() const;
bool canNodeFitOnEnd(DeBruijnNode * node, Path * extendedPath) const;
bool canNodeFitAtStart(DeBruijnNode * node, Path * extendedPath) const;
double getMeanDepth() const;
bool containsNode(DeBruijnNode * node) const;
bool containsEntireNode(DeBruijnNode * node) const;
bool isInMiddleOfPath(DeBruijnNode * node) const;
int numberOfOccurrencesInMiddleOfPath(DeBruijnNode * node) const;
bool isStartingNode(DeBruijnNode * node) const;
bool isEndingNode(DeBruijnNode * node) const;
double getStartFraction() const;
double getEndFraction() const;
int getNodeCount() const;
GraphLocation getStartLocation() const {return m_startLocation;}
GraphLocation getEndLocation() const {return m_endLocation;}
bool operator==(Path const &other) const;
//MODIFERS
bool addNode(DeBruijnNode * newNode, bool strandSpecific, bool makeCircularIfPossible);
void extendPathToIncludeEntirityOfNodes();
//STATIC
static QList<Path> getAllPossiblePaths(GraphLocation startLocation,
GraphLocation endLocation,
int nodeSearchDepth,
int minDistance, int maxDistance);
private:
GraphLocation m_startLocation;
GraphLocation m_endLocation;
QList<DeBruijnNode *> m_nodes;
QList<DeBruijnEdge *> m_edges;
void buildUnambiguousPathFromNodes(QList<DeBruijnNode *> nodes,
bool strandSpecific);
QByteArray modifySequenceUsingOverlap(QByteArray sequence, int overlap) const;
bool checkForOtherEdges();
};
#endif // PATH_H
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