/**
 * UGENE - Integrated Bioinformatics Tools.
 * Copyright (C) 2008-2025 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 <QFile>
#include <QStringList>

#include <U2Algorithm/SplicedAlignmentTask.h>

#include <U2Core/AnnotationTableObject.h>
#include <U2Core/DNASequenceObject.h>
#include <U2Core/ExternalToolRunTask.h>

#include <U2Formats/StreamSequenceReader.h>
#include <U2Formats/StreamSequenceWriter.h>

#include <U2Gui/CreateAnnotationWidgetController.h>

namespace U2 {

class PrepareInputForSpideyTask : public Task {
    Q_OBJECT
public:
    PrepareInputForSpideyTask(const U2SequenceObject* dna,
                              const U2SequenceObject* mRna,
                              const QString& outputDirPath);
    void run();
    const QStringList& getArgumentsList() {
        return argumentList;
    }
    const QString& getResultPath() {
        return resultPath;
    }

private:
    const U2SequenceObject* dnaObj;
    const U2SequenceObject* mRnaObj;
    QStringList argumentList;
    StreamSequenceReader seqReader;
    QString outputDir;
    QString resultPath;
};

class SpideyAlignmentTask : public SplicedAlignmentTask {
    Q_OBJECT
public:
    SpideyAlignmentTask(const SplicedAlignmentTaskConfig& config, const QString& annDescription);
    void prepare();
    QList<SharedAnnotationData> getAlignmentResult() {
        return resultAnnotations;
    }
    Task::ReportResult report();
    QList<Task*> onSubTaskFinished(Task* subTask);

private:
    QList<SharedAnnotationData> resultAnnotations;
    QString tmpDirUrl;
    QString tmpOutputUrl;
    const QString annDescription;
    PrepareInputForSpideyTask* prepareDataForSpideyTask;
    ExternalToolRunTask* spideyTask;
};

class SpideyAlignmentTaskFactory : public SplicedAlignmentTaskFactory {
    virtual SplicedAlignmentTask* createTaskInstance(const SplicedAlignmentTaskConfig& config) {
        return new SpideyAlignmentTask(config, "");
    }
};

class SpideyLogParser : public ExternalToolLogParser {
public:
    SpideyLogParser();
    int getProgress();
};

class SpideySupportTask : public Task {
    Q_OBJECT
public:
    SpideySupportTask(const SplicedAlignmentTaskConfig& cfg,
                      AnnotationTableObject* aobj,
                      const QString& annDescription);
    void prepare();
    QList<Task*> onSubTaskFinished(Task* subTask);

private:
    SplicedAlignmentTaskConfig settings;
    SpideyAlignmentTask* spideyAlignmentTask;
    QPointer<AnnotationTableObject> aObj;
};

}  // namespace U2
