/**
 * 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 <QByteArray>

#include <U2Algorithm/PairwiseAlignmentTask.h>
#include <U2Algorithm/SmithWatermanSettings.h>
#include <U2Algorithm/SmithWatermanTaskFactory.h>

#include <U2Core/SequenceWalkerTask.h>
#include <U2Core/Task.h>

#include "SWAlgorithmTask.h"

namespace U2 {

class PairwiseAlignmentTask;

class SWTaskFactory : public SmithWatermanTaskFactory {  // for ADV search only
public:
    SWTaskFactory(SW_AlgType _algType);
    virtual ~SWTaskFactory();
    virtual Task* getTaskInstance(const SmithWatermanSettings& config, const QString& taskName) const;

private:
    SW_AlgType algType;
};

class PairwiseAlignmentSmithWatermanTaskFactory : public AbstractAlignmentTaskFactory {  // for pairwise alignment only
public:
    PairwiseAlignmentSmithWatermanTaskFactory(SW_AlgType _algType);
    virtual ~PairwiseAlignmentSmithWatermanTaskFactory();

    virtual AbstractAlignmentTask* getTaskInstance(AbstractAlignmentTaskSettings* settings) const;

private:
    SW_AlgType algType;
};

}  // namespace U2
