/**
 * UGENE - Integrated Bioinformatics Tools.
 * Copyright (C) 2008-2021 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.
 */

#ifndef _U2_PHYML_TASK_H
#define _U2_PHYML_TASK_H

#include <U2Algorithm/PhyTreeGenerator.h>
#include <U2Algorithm/PhyTreeGeneratorTask.h>

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

#include <U2View/CreatePhyTreeDialogController.h>

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

namespace U2 {

class LoadDocumentTask;

class PhyMLPrepareDataForCalculation : public Task {
    Q_OBJECT
public:
    PhyMLPrepareDataForCalculation(const MultipleSequenceAlignment &ma, const CreatePhyTreeSettings &s, const QString &url);
    void prepare();
    QList<Task *> onSubTaskFinished(Task *subTask);
    const QString &getInputFileUrl() {
        return inputFileForPhyML;
    }

private:
    const MultipleSequenceAlignment &ma;
    CreatePhyTreeSettings settings;
    QString tmpDirUrl;
    SaveAlignmentTask *saveDocumentTask;
    QString inputFileForPhyML;
};

class PhyMLSupportTask;
class PhyMLLogParser : public ExternalToolLogParser {
    Q_OBJECT
public:
    PhyMLLogParser(PhyMLSupportTask *parentTask, int sequencesNumber);
    int getProgress();
    void parseOutput(const QString &partOfLog);
    void parseErrOutput(const QString &partOfLog);

private:
    PhyMLSupportTask *parentTask;
    QString lastLine;
    QString lastErrLine;
    bool isMCMCRunning;
    int curProgress;
    int processedBranches;
    int sequencesNumber;
};

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

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

class PhyMLSupportTask : public PhyTreeGeneratorTask {
    Q_OBJECT
public:
    PhyMLSupportTask(const MultipleSequenceAlignment &ma, const CreatePhyTreeSettings &s);
    void prepare();
    Task::ReportResult report();
    void onExternalToolFailed(const QString &err);
    QList<Task *> onSubTaskFinished(Task *subTask);

    static const QString TMP_FILE_NAME;
    static const QString RESULT_BOOTSTRAP_EXT;
    static const QString RESULT_TREE_EXT;

private:
    QString tmpDirUrl;
    QString tmpPhylipFile;
    PhyMLPrepareDataForCalculation *prepareDataTask;
    ExternalToolRunTask *phyMlTask;
    PhyMLGetCalculatedTreeTask *getTreeTask;
    int sequencesNumber;
};

}    // namespace U2

#endif    // _U2_PHYML_TASK_H
