/**
 * 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_TCOFFEE_SUPPORT_TASK_H
#define _U2_TCOFFEE_SUPPORT_TASK_H

#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 {

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

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

class LoadDocumentTask;

class TCoffeeSupportTask : public ExternalToolSupportTask {
    Q_OBJECT
    Q_DISABLE_COPY(TCoffeeSupportTask)
public:
    TCoffeeSupportTask(const MultipleSequenceAlignment &_inputMsa, const GObjectReference &_objRef, const TCoffeeSupportTaskSettings &_settings);
    ~TCoffeeSupportTask();

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

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

    MultipleSequenceAlignment resultMA;

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

    SaveMSA2SequencesTask *saveTemporaryDocumentTask;
    ExternalToolRunTask *tCoffeeTask;
    LoadDocumentTask *loadTmpDocumentTask;
    TCoffeeSupportTaskSettings settings;
    QPointer<StateLock> lock;
};

class MultipleSequenceAlignmentObject;

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

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

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

    SaveDocumentTask *saveDocumentTask;
    LoadDocumentTask *loadDocumentTask;
    TCoffeeSupportTask *tCoffeeSupportTask;
    TCoffeeSupportTaskSettings settings;
};

class TCoffeeLogParser : public ExternalToolLogParser {
public:
    TCoffeeLogParser();

    int getProgress();
    void parseOutput(const QString &partOfLog);
    void parseErrOutput(const QString &partOfLog);

private:
    QString lastErrLine;
    int progress;
};

}    // namespace U2
#endif    // _U2_TCOFFEE_SUPPORT_TASK_H
