/**
* UGENE - Integrated Bioinformatics Tools.
* Copyright (C) 2008-2017 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_CMDLINE_TASK_H_
#define _U2_PHYLIP_CMDLINE_TASK_H_

#include <U2Algorithm/PhyTreeGeneratorTask.h>

namespace U2 {

class CmdlineInOutTaskRunner;
class MultipleSequenceAlignmentObject;
class PhyTreeObject;
class TmpDbiHandle;

class PhylipCmdlineTask : public PhyTreeGeneratorTask {
    Q_OBJECT
public:
    PhylipCmdlineTask(const MultipleSequenceAlignment &msa, const CreatePhyTreeSettings &settings);
    ~PhylipCmdlineTask();

    void prepare();
    ReportResult report();

    static const QString PHYLIP_CMDLINE;
    static const QString MATRIX_ARG;
    static const QString GAMMA_ARG;
    static const QString ALPHA_ARG;
    static const QString TT_RATIO_ARG;
    static const QString BOOTSTRAP_ARG;
    static const QString REPLICATES_ARG;
    static const QString SEED_ARG;
    static const QString FRACTION_ARG;
    static const QString CONSENSUS_ARG;

private:
    void createCmdlineTask();
    void prepareTempDbi();

private:
    CmdlineInOutTaskRunner *cmdlineTask;
    MultipleSequenceAlignmentObject *msaObject;
    PhyTreeObject *treeObject;
    QString dbiPath;
    U2DbiRef dbiRef;
};

} // U2

#endif // _U2_PHYLIP_CMDLINE_TASK_H_
