/**
 * 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 <U2Algorithm/PhyTreeGeneratorTask.h>

#include <U2Core/ExternalToolRunTask.h>
#include <U2Core/PhyTreeObject.h>

#include <U2View/CreatePhyTreeDialogController.h>

#include "MrBayesSupport.h"
#include "utils/ExportTasks.h"

namespace U2 {

class LoadDocumentTask;

class MrBayesPrepareDataForCalculation : public Task {
    Q_OBJECT
public:
    MrBayesPrepareDataForCalculation(const Msa& _ma, const CreatePhyTreeSettings& s, const QString& url);
    void prepare();
    QList<Task*> onSubTaskFinished(Task* subTask);
    QString getInputFileUrl() {
        return inputFileForMrBayes;
    }

private:
    const Msa& ma;
    CreatePhyTreeSettings settings;
    QString tmpDirUrl;
    SaveAlignmentTask* saveDocumentTask;
    QString inputFileForMrBayes;
};

class MrBayesLogParser : public ExternalToolLogParser {
public:
    MrBayesLogParser(int _nchains);
    int getProgress();
    void parseOutput(const QString& partOfLog);
    void parseErrOutput(const QString& partOfLog);

private:
    QString lastLine;
    QString lastErrLine;
    int nchains;
    bool isMCMCRunning;
    int curProgress;
};

class MrBayesGetCalculatedTreeTask : public Task {
    Q_OBJECT
public:
    MrBayesGetCalculatedTreeTask(const QString& url);
    void prepare();
    QList<Task*> onSubTaskFinished(Task* subTask);
    PhyTreeObject* getPhyObject() {
        return phyObject;
    }

private:
    QString baseFileName;
    LoadDocumentTask* loadTmpDocumentTask;
    PhyTreeObject* phyObject;
};

class MrBayesSupportTask : public PhyTreeGeneratorTask {
    Q_OBJECT
public:
    MrBayesSupportTask(const Msa& _ma, const CreatePhyTreeSettings& s);
    void prepare() override;
    Task::ReportResult report() override;
    QList<Task*> onSubTaskFinished(Task* subTask) override;

private:
    QString tmpDirUrl;
    QString tmpNexusFile;
    MrBayesPrepareDataForCalculation* prepareDataTask;
    ExternalToolRunTask* mrBayesTask;
    MrBayesGetCalculatedTreeTask* getTreeTask;
};

}  // namespace U2
