/**
 * UGENE - Integrated Bioinformatics Tools.
 * Copyright (C) 2008-2024 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/ExternalToolRunTask.h>
#include <U2Core/GUrl.h>

namespace U2 {

class StringTieTaskSettings {
public:
    StringTieTaskSettings();

    QString inputBam;

    QString referenceAnnotations;  // 1
    QString readOrientation;  // 2 --fr or --rf values, enum?
    QString label;  // 3
    double minIsoformFraction;  // 4
    int minTransciptLen;  // 5

    int minAnchorLen;  // 6
    double minJunctionCoverage;  // 7
    bool trimTranscript;  // 8
    double minCoverage;  // 9
    int minLocusSeparation;  // 10

    double multiHitFraction;  // 11
    QString skipSequences;  // 12 - a list of sequence names comma separated
    bool refOnlyAbudance;  // 13
    bool multiMappingCorrection;  // 14
    bool verboseLog;  // 15

    int threadNum;  // 16

    QString primaryOutputFile;  // 17
    bool geneAbundanceOutput;  // 18
    QString geneAbundanceOutputFile;  // 19
    bool coveredRefOutput;  // 20
    QString coveredRefOutputFile;  // 21
    bool ballgownOutput;  // 22
    QString ballgowmOutputFolder;  // 23
};

class StringTieTask : public ExternalToolSupportTask {
    Q_OBJECT
    Q_DISABLE_COPY(StringTieTask)
public:
    StringTieTask(const StringTieTaskSettings& settings);

    void prepare();
    const StringTieTaskSettings& getSettings() const;

private:
    QStringList getArguments() const;

private:
    ExternalToolRunTask* stringTieTask;
    StringTieTaskSettings settings;
};

}  // namespace U2
