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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 BLASTQUERYPATH_H
#define BLASTQUERYPATH_H
#include "../graph/path.h"
#include <QList>
#include "blasthit.h"
#include "../program/scinot.h"
class BlastQuery;
class BlastQueryPath
{
public:
//CREATORS
BlastQueryPath(Path path, BlastQuery * query);
//ACCESSORS
Path getPath() const {return m_path;}
QList<BlastHit *> getHits() const {return m_hits;}
SciNot getEvalueProduct() const;
double getMeanHitPercIdentity() const;
double getRelativeLengthDiscrepancy() const;
double getRelativePathLength() const;
int getAbsolutePathLengthDifference() const;
QString getAbsolutePathLengthDifferenceString(bool commas) const;
double getPathQueryCoverage() const;
double getHitsQueryCoverage() const;
int getTotalHitMismatches() const;
int getTotalHitGapOpens() const;
bool operator<(BlastQueryPath const &other) const;
private:
Path m_path;
BlastQuery * m_query;
QList<BlastHit *> m_hits;
int getHitQueryLength() const;
int getHitOverlap(BlastHit * hit1, BlastHit * hit2) const;
};
#endif // BLASTQUERYPATH_H
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