/**
 * 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_MAFFT_SUPPORT_TASK_H
#define _U2_MAFFT_SUPPORT_TASK_H

#include <QFile>

#include <U2Core/ExternalToolRunTask.h>
#include <U2Core/GObjectReference.h>
#include <U2Core/IOAdapter.h>
#include <U2Core/MultipleSequenceAlignment.h>
#include <U2Core/SaveDocumentTask.h>
#include <U2Core/Task.h>

#include "utils/ExportTasks.h"

namespace U2 {

/*Options for MAFFT
+ --op # :         Gap opening penalty, default: 1.53
+ --ep # :         Offset (works like gap extension penalty), default: 0.0
+ --maxiterate # : Maximum number of iterative refinement, default: 0
? --clustalout :   Output: clustal format, default: fasta // With this option bad output clustal file is generated.(dkandrov)
? --reorder :      Outorder: aligned, default: input order
? --quiet :        Do not report progress
? --thread # :     Number of threads. (# must be <= number of physical cores - 1)

*/

class LoadDocumentTask;
class MAFFTLogParser;

class MAFFTSupportTaskSettings {
public:
    MAFFTSupportTaskSettings() {
        reset();
    }
    void reset();

    float gapOpenPenalty;
    float gapExtenstionPenalty;
    int maxNumberIterRefinement;
    QString inputFilePath;
    QString outputFilePath;
};

class MAFFTSupportTask : public ExternalToolSupportTask {
    Q_OBJECT
    Q_DISABLE_COPY(MAFFTSupportTask)
public:
    MAFFTSupportTask(const MultipleSequenceAlignment &_inputMsa, const GObjectReference &_objRef, const MAFFTSupportTaskSettings &settings);
    ~MAFFTSupportTask();

    void prepare();
    Task::ReportResult report();

    QList<Task *> onSubTaskFinished(Task *subTask);

    MultipleSequenceAlignment resultMA;

private slots:
    void sl_progressUndefined();

private:
    MultipleSequenceAlignment inputMsa;
    GObjectReference objRef;
    QPointer<Document> tmpDoc;
    QString url;
    MAFFTLogParser *logParser;

    SaveMSA2SequencesTask *saveTemporaryDocumentTask;
    ExternalToolRunTask *mAFFTTask;
    LoadDocumentTask *loadTmpDocumentTask;
    MAFFTSupportTaskSettings settings;
    QPointer<StateLock> lock;
};

class MultipleSequenceAlignmentObject;

class MAFFTWithExtFileSpecifySupportTask : public Task {
    Q_OBJECT
    Q_DISABLE_COPY(MAFFTWithExtFileSpecifySupportTask)
public:
    MAFFTWithExtFileSpecifySupportTask(const MAFFTSupportTaskSettings &settings);
    ~MAFFTWithExtFileSpecifySupportTask();
    void prepare();
    Task::ReportResult report();

    QList<Task *> onSubTaskFinished(Task *subTask);

private:
    MultipleSequenceAlignmentObject *mAObject;
    Document *currentDocument;
    bool cleanDoc;

    SaveDocumentTask *saveDocumentTask;
    LoadDocumentTask *loadDocumentTask;
    MAFFTSupportTask *mAFFTSupportTask;
    MAFFTSupportTaskSettings settings;
};

class MAFFTLogParser : public ExternalToolLogParser {
    Q_OBJECT
    Q_DISABLE_COPY(MAFFTLogParser)
public:
    MAFFTLogParser(int countSequencesInMSA, int countRefinementIter, const QString &outputFileName);
    ~MAFFTLogParser() {
        cleanup();
    }
    int getProgress();
    void parseOutput(const QString &partOfLog);
    void parseErrOutput(const QString &partOfLog);

    bool isOutFileCreated() {
        return isOutputFileCreated;
    }
    void cleanup();

signals:
    void si_progressUndefined();

private:
    int countSequencesInMSA;
    int countRefinementIter;
    QString outputFileName;
    QFile outFile;
    bool isOutputFileCreated;
    QString lastErrLine;

    bool isMemSaveModeEnabled;    // there is no progress in the memsave mode
    bool firstDistanceMatrix;
    bool secondDistanceMatrix;
    bool firstUPGMATree;
    bool secondUPGMATree;
    bool firstProAlign;
    bool secondProAlign;
    int progress;

    static const QString MEM_SAVE_MODE_MESSAGE;
};

}    // namespace U2
#endif    // _U2_MAFFT_SUPPORT_TASK_H
