/**
 * UGENE - Integrated Bioinformatics Tools.
 * Copyright (C) 2008-2021 UniPro <ugene@unipro.ru>
 * http://ugene.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; either version 2
 * of the License, or (at your option) any later version.
 *
 * 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 should have received a copy of the GNU General Public License
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
 * MA 02110-1301, USA.
 */

#ifndef _U2_FIND_HIGH_FLEX_REGIONS_ALGORITHM_H_
#define _U2_FIND_HIGH_FLEX_REGIONS_ALGORITHM_H_

#include <QMap>

#include <U2Core/Task.h>

#include "FindHighFlexRegions.h"
#include "HighFlexResult.h"

namespace U2 {

class FindHighFlexRegionsListener;

class FindHighFlexRegionsAlgorithm : public Task {
public:
    static void find(FindHighFlexRegionsListener *resultsListener,
                     const HighFlexSettings &settings,
                     const QByteArray sequence,
                     const int seqLength,
                     int &stopFlag,
                     int &percentsCompleted);

    static double flexibilityAngle(char firstNucleotide, char secondNucleotide);

private:
    static void addToResults(FindHighFlexRegionsListener *listener, const HighFlexResult &result);
};

}    // namespace U2

#endif
