/**
 * 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_CREATE_PHYTREE_SETTINGS_H
#define _U2_CREATE_PHYTREE_SETTINGS_H

#include <QList>
#include <QString>
#include <QStringList>

#include <U2Core/GUrl.h>
#include <U2Core/global.h>

namespace U2 {

class U2ALGORITHM_EXPORT CreatePhyTreeSettings {
public:
    CreatePhyTreeSettings();
    QString algorithm;
    QString matrixId;
    bool displayWithAlignmentEditor;
    bool syncAlignmentWithTree;
    GUrl fileUrl;
    bool useGammaDistributionRates;
    double alphaFactor;
    double ttRatio;    // transition transversion ratio
    bool bootstrap;
    int replicates;
    int seed;
    double fraction;
    QString consensusID;
    int mb_ngen;
    QStringList rowsOrder;

    QString mrBayesSettingsScript;
    QStringList extToolArguments;
};

}    // namespace U2

#endif
