/**
 * 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 <U2Algorithm/PhyTreeGenerator.h>

#include <U2Core/ExternalToolRegistry.h>

namespace U2 {

class PhyMLSupport : public ExternalTool {
    Q_OBJECT
public:
    PhyMLSupport();

    static const QString PHYML_ID;
    static const QString ET_PHYML_ALGORITHM_NAME_AND_KEY;
    static const QString PHYML_TEMP_DIR;
};

class PhyMLAdapter : public PhyTreeGenerator {
public:
    Task* createCalculatePhyTreeTask(const MultipleSequenceAlignment& ma, const CreatePhyTreeSettings& s);
    CreatePhyTreeWidget* createPhyTreeSettingsWidget(const MultipleSequenceAlignment& ma, QWidget* parent = nullptr);
};

enum SubstModelTrRatioType {
    ANY_TT_RATIO,
    ONLY_FIXED_TT_RATIO,
    ONLY_ESTIMATED_TT_RATIO,
    WITHOUT_TT_RATIO
};

class PhyMLModelTypes {
public:
    static const QStringList& getAminoAcidModelTypes() {
        return aminoSubstitutionModels;
    }
    static const QStringList& getDnaModelTypes() {
        return dnaSubstitutionModels;
    }
    static SubstModelTrRatioType getTtRatioType(const QString& modelName);

private:
    static const QStringList dnaSubstitutionModels;  // all dna models
    static const QStringList dnaModelsWithFixedTtRatio;  // only fixed Transition / transversion ratio
    static const QStringList dnaModelsWithEstimatedTtRatio;  // only estimated Transition / transversion ratio
    static const QStringList aminoSubstitutionModels;
};

class PhyMLRatioTestsTypes {
public:
    static const QStringList ratioTestsTypes;

    /** Indicates which test type is to use by default. */
    static const int defaultRatioTestsTypeIndex;
};

class TreeSearchingParams {
public:
    static const QStringList& getInputTreeTypes() {
        return inputTreeTypes;
    }
    static const QStringList& getTreeImprovementTypes() {
        return treeImprovementTypes;
    }

private:
    static const QStringList inputTreeTypes;
    static const QStringList treeImprovementTypes;
};

}  // namespace U2
