/**
 * 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/DNASequence.h>
#include <U2Core/U2Region.h>

#include <U2Lang/QDScheme.h>
#include <U2Lang/QueryDesignerRegistry.h>

namespace U2 {

class DNATranslation;

class FindGcRegionsSettings {
public:
    U2Region gcRangeInPercents;
    qint64 minLen;
    qint64 offset;
    DNATranslation* complTT;
    QDStrandOption strand;
    FindGcRegionsSettings()
        : gcRangeInPercents(20, 40), minLen(0), offset(0), complTT(nullptr) {
    }
};

class FindGcRegionsTask : public Task {
    Q_OBJECT
public:
    FindGcRegionsTask(const FindGcRegionsSettings& settings, const DNASequence& sequence)
        : Task(tr("Find base content task"), TaskFlag_None), settings_(settings), sequence_(sequence) {
    }
    void run();
    QList<SharedAnnotationData> getResultAsAnnotations() const;

private:
    void find(const char* seq,
              qint64 seqLen,
              U2Region gcRangeInPercents,
              qint64 len,
              QVector<U2Region>& result);
    static QList<SharedAnnotationData> createAnnotations(const QVector<U2Region>& regions, qint64 offset, U2Strand::Direction strand);

private:
    FindGcRegionsSettings settings_;
    DNASequence sequence_;
    QVector<U2Region> directResults;
    QVector<U2Region> compResults;
};

class QDFindGcRegionsActor : public QDActor {
    Q_OBJECT
public:
    QDFindGcRegionsActor(QDActorPrototype const* proto);
    int getMinResultLen() const;
    int getMaxResultLen() const;
    QString getText() const;
    Task* getAlgorithmTask(const QVector<U2Region>& location);
    QColor defaultColor() const {
        return QColor(0xc6, 0xc6, 0x55);
    }
private slots:
    void sl_onTaskFinished(Task*);
};

class QDFindGcActorPrototype : public QDActorPrototype {
public:
    QDFindGcActorPrototype();
    virtual QDActor* createInstance() const {
        return new QDFindGcRegionsActor(this);
    }
};

}  // namespace U2
