<commit_before>/*
 * PartitionClockModelPanel.java
 *
 * Copyright (c) 2002-2015 <NAME>, <NAME> and <NAME>
 *
 * This file is part of BEAST.
 * See the NOTICE file distributed with this work for additional
 * information regarding copyright ownership and licensing.
 *
 * BEAST is free software; you can redistribute it and/or modify
 * it under the terms of the GNU Lesser General Public License as
 * published by the Free Software Foundation; either version 2
 * of the License, or (at your option) any later version.
 *
 *  BEAST 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 Lesser General Public License for more details.
 *
 * You should have received a copy of the GNU Lesser General Public
 * License along with BEAST; if not, write to the
 * Free Software Foundation, Inc., 51 Franklin St, Fifth Floor,
 * Boston, MA  02110-1301  USA
 */

package dr.app.beauti.clockmodelspanel;

import dr.app.beauti.options.PartitionClockModel;
import dr.app.beauti.types.ClockDistributionType;
import dr.app.beauti.types.ClockType;
import dr.app.beauti.util.PanelUtils;
import dr.app.util.OSType;
import jam.panels.OptionsPanel;

import javax.swing.*;
import java.awt.event.ItemEvent;
import java.awt.event.ItemListener;
import java.util.EnumSet;

/**
 * @author <NAME>
 */
public class PartitionClockModelPanel extends OptionsPanel {

    // Components
    private static final long serialVersionUID = -1645661616353099424L;

    private JComboBox clockTypeCombo = new JComboBox(EnumSet.range(
            ClockType.STRICT_CLOCK, ClockType.FIXED_LOCAL_CLOCK).toArray());
    private JComboBox clockDistributionCombo = new JComboBox (new ClockDistributionType[] {
            ClockDistributionType.LOGNORMAL,
            ClockDistributionType.GAMMA,
//            ClockDistributionType.CAUCHY,
            ClockDistributionType.EXPONENTIAL,
            ClockDistributionType.MODEL_AVERAGING
    });
    private JCheckBox continuousQuantileCheck = new JCheckBox("Use continuous quantile parameterization.");

    private JLabel modelAveragingInfo = new JLabel(
            "<html>Using the Bayesian Model Averaging (BMA) approach on the<br>" +
                    "available relaxed clock models as described by Li & Drummond (2012)<br>" +
                    " Mol. Biol. Evol. 29:751-761.</html>");

    protected final PartitionClockModel model;

    public PartitionClockModelPanel(final PartitionClockModel partitionModel) {

        super(12, (OSType.isMac() ? 6 : 24));

        this.model = partitionModel;
<commit_msg>remove BMA for now<commit_after>/*
 * PartitionClockModelPanel.java
 *
 * Copyright (c) 2002-2015 <NAME>, <NAME> and <NAME>
 *
 * This file is part of BEAST.
 * See the NOTICE file distributed with this work for additional
 * information regarding copyright ownership and licensing.
 *
 * BEAST is free software; you can redistribute it and/or modify
 * it under the terms of the GNU Lesser General Public License as
 * published by the Free Software Foundation; either version 2
 * of the License, or (at your option) any later version.
 *
 *  BEAST 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 Lesser General Public License for more details.
 *
 * You should have received a copy of the GNU Lesser General Public
 * License along with BEAST; if not, write to the
 * Free Software Foundation, Inc., 51 Franklin St, Fifth Floor,
 * Boston, MA  02110-1301  USA
 */

package dr.app.beauti.clockmodelspanel;

import dr.app.beauti.options.PartitionClockModel;
import dr.app.beauti.types.ClockDistributionType;
import dr.app.beauti.types.ClockType;
import dr.app.beauti.util.PanelUtils;
import dr.app.util.OSType;
import jam.panels.OptionsPanel;

import javax.swing.*;
import java.awt.event.ItemEvent;
import java.awt.event.ItemListener;
import java.util.EnumSet;

/**
 * @author <NAME>
 */
public class PartitionClockModelPanel extends OptionsPanel {

    // Components
    private static final long serialVersionUID = -1645661616353099424L;

    private JComboBox clockTypeCombo = new JComboBox(EnumSet.range(
            ClockType.STRICT_CLOCK, ClockType.FIXED_LOCAL_CLOCK).toArray());
    private JComboBox clockDistributionCombo = new JComboBox (new ClockDistributionType[] {
            ClockDistributionType.LOGNORMAL,
            ClockDistributionType.GAMMA,
//            ClockDistributionType.CAUCHY,
            ClockDistributionType.EXPONENTIAL,
            //ClockDistributionType.MODEL_AVERAGING
    });
    private JCheckBox continuousQuantileCheck = new JCheckBox("Use continuous quantile parameterization.");

    private JLabel modelAveragingInfo = new JLabel(
            "<html>Using the Bayesian Model Averaging (BMA) approach on the<br>" +
                    "available relaxed clock models as described by Li & Drummond (2012)<br>" +
                    " Mol. Biol. Evol. 29:751-761.</html>");

    protected final PartitionClockModel model;

    public PartitionClockModelPanel(final PartitionClockModel partitionModel) {

        super(12, (OSType.isMac() ? 6 : 24));

        this.model = partitionModel;

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