/**
 * UGENE - Integrated Bioinformatics Tools.
 * Copyright (C) 2008-2023 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.
 */

#pragma once

#include <U2Core/AnnotationData.h>
#include <U2Core/DNASequence.h>
#include <U2Core/DNATranslation.h>
#include <U2Core/Task.h>

namespace U2 {

struct U2CORE_EXPORT ExtractAnnotatedRegionTaskSettings {
    ExtractAnnotatedRegionTaskSettings()
        : gapSym('-'), gapLength(0), translate(true), complement(true), extLeft(0), extRight(0), splitJoined(false) {
    }
    char gapSym;
    int gapLength;
    bool translate;
    bool complement;
    int extLeft;
    int extRight;
    bool splitJoined;
};

class U2CORE_EXPORT ExtractAnnotatedRegionTask : public Task {
    Q_OBJECT
public:
    ExtractAnnotatedRegionTask(const DNASequence& sequence, const SharedAnnotationData& sd, const ExtractAnnotatedRegionTaskSettings& cfg);
    void prepare();
    void run();
    const QList<DNASequence>& getResultedSequences() const;
    const SharedAnnotationData& getInputAnnotation() const;

private:
    void prepareTranslations();
    void extractLocations(QList<QByteArray>& resParts, QVector<U2Region>& resLocation, const QVector<U2Region>& origLocation);

    DNASequence inputSeq;
    const SharedAnnotationData inputAnn;
    ExtractAnnotatedRegionTaskSettings cfg;

    QVector<U2Region> extendedRegions;
    const DNATranslation* complT;
    const DNATranslation* aminoT;

    QList<DNASequence> resultedSeqList;
};

}  // namespace U2
