/**
 * 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 <QObject>

#include <U2Core/global.h>

class QColor;

namespace U2 {

class MultipleAlignmentObject;
class MsaHighlightingSchemeFactory;

class U2ALGORITHM_EXPORT MsaHighlightingScheme : public QObject {
    Q_OBJECT
public:
    MsaHighlightingScheme(QObject* parent, const MsaHighlightingSchemeFactory* factory, MultipleAlignmentObject* maObj);

    virtual void process(const char refChar, char& seqChar, QColor& color, bool& highlight, int refCharColumn, int refCharRow) const;
    const MsaHighlightingSchemeFactory* getFactory() const;

    void setUseDots(bool use);
    bool getUseDots() const;

    virtual void applySettings(const QVariantMap& settings);
    virtual QVariantMap getSettings() const;

    static const QString EMPTY;
    static const QString AGREEMENTS;
    static const QString DISAGREEMENTS;
    static const QString TRANSITIONS;
    static const QString TRANSVERSIONS;
    static const QString GAPS;
    static const QString CONSERVATION;

    static const QString THRESHOLD_PARAMETER_NAME;
    static const QString LESS_THAN_THRESHOLD_PARAMETER_NAME;

protected:
    const MsaHighlightingSchemeFactory* factory;
    MultipleAlignmentObject* maObj;
    bool useDots;
};

class U2ALGORITHM_EXPORT MsaHighlightingSchemeFactory : public QObject {
    Q_OBJECT
public:
    MsaHighlightingSchemeFactory(QObject* parent, const QString& id, const QString& name, const AlphabetFlags& supportedAlphabets, bool refFree = false, bool needThreshold = false);

    virtual MsaHighlightingScheme* create(QObject* parent, MultipleAlignmentObject* maObj) const = 0;

    const QString& getId() const;
    const QString& getName() const;
    bool isRefFree() const;
    bool isNeedThreshold() const;
    bool isAlphabetTypeSupported(DNAAlphabetType alphabetType) const;
    const AlphabetFlags& getSupportedAlphabets() const;

private:
    QString id;
    QString name;
    bool refFree;
    bool needThreshold;
    AlphabetFlags supportedAlphabets;
};

class U2ALGORITHM_EXPORT MsaHighlightingSchemeRegistry : public QObject {
    Q_OBJECT
public:
    MsaHighlightingSchemeRegistry();
    ~MsaHighlightingSchemeRegistry();

    MsaHighlightingSchemeFactory* getSchemeFactoryById(const QString& id) const;
    MsaHighlightingSchemeFactory* getEmptySchemeFactory() const;
    QList<MsaHighlightingSchemeFactory*> getAllSchemes(DNAAlphabetType alphabetType) const;
    QMap<AlphabetFlags, QList<MsaHighlightingSchemeFactory*>> getAllSchemesGrouped() const;

private:
    QList<MsaHighlightingSchemeFactory*> schemes;
};

}  // namespace U2
