/**
 * 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.
 */

#ifndef _U2_PHYLIP_TASK_H_
#define _U2_PHYLIP_TASK_H_

#include <U2Algorithm/CreatePhyTreeSettings.h>

#include <U2Core/CmdlineTaskRunner.h>
#include <U2Core/U2Type.h>

namespace U2 {

class NeighborJoinCalculateTreeTask;

class PhylipTask : public CmdlineTask {
    Q_OBJECT
public:
    PhylipTask(const U2EntityRef& msaRef, const U2DbiRef& outDbiRef, const CreatePhyTreeSettings& settings);

    void prepare();
    ReportResult report();

private:
    U2DataId saveTree();

private:
    U2EntityRef msaRef;
    U2DbiRef outDbiRef;
    CreatePhyTreeSettings settings;

    NeighborJoinCalculateTreeTask* treeTask;
};

}  // namespace U2

#endif  // _U2_PHYLIP_TASK_H_
