/**
 * 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_MSA_UTIL_TASKS
#define _U2_MSA_UTIL_TASKS

#include <U2Core/MultipleSequenceAlignmentObject.h>
#include <U2Core/Task.h>
#include <U2Core/global.h>

namespace U2 {

class DNATranslation;

/**
 Performs in-place translation of multiple sequence alignment object
*/

class U2ALGORITHM_EXPORT TranslateMsa2AminoTask : public Task {
    Q_OBJECT
public:
    TranslateMsa2AminoTask(MultipleSequenceAlignmentObject *obj);
    TranslateMsa2AminoTask(MultipleSequenceAlignmentObject *obj, const QString &trId);
    const MultipleSequenceAlignment &getTaskResult() {
        return resultMA;
    }
    void run();
    ReportResult report();

private:
    MultipleSequenceAlignment resultMA;
    MultipleSequenceAlignmentObject *maObj;
    DNATranslation *translation;
};

/**
 Wrapper for multiple alignment task
*/

class U2ALGORITHM_EXPORT AlignGObjectTask : public Task {
    Q_OBJECT
public:
    AlignGObjectTask(const QString &taskName, TaskFlags f, MultipleSequenceAlignmentObject *maobj)
        : Task(taskName, f), obj(maobj) {
    }
    virtual void setMAObject(MultipleSequenceAlignmentObject *maobj) {
        obj = maobj;
    }
    MultipleSequenceAlignmentObject *getMAObject() {
        return obj;
    }

protected:
    QPointer<MultipleSequenceAlignmentObject> obj;
};

/**
 Multi task converts alignment object to amino representation if possible.
 This allows to:
 1) speed up alignment
 2) avoid errors of inserting gaps within codon boundaries
*/

class U2ALGORITHM_EXPORT AlignInAminoFormTask : public Task {
    Q_OBJECT
    Q_DISABLE_COPY(AlignInAminoFormTask)
public:
    AlignInAminoFormTask(MultipleSequenceAlignmentObject *obj, AlignGObjectTask *alignTask, const QString &traslId);
    ~AlignInAminoFormTask();

    virtual void prepare();
    virtual void run();
    virtual ReportResult report();

protected:
    AlignGObjectTask *alignTask;
    MultipleSequenceAlignmentObject *maObj, *clonedObj;
    QString traslId;
    Document *tmpDoc;
    QMap<qint64, QList<U2MsaGap>> rowsGapModel;
    QMap<qint64, QList<U2MsaGap>> emptyGapModel;
};

}    // namespace U2

#endif    // _U2_MSA_UTIL_TASKS
