Examples with PriorType dr.app.beauti.types.PriorType used on opensource projects

Example 1 with PriorType

use of dr.app.beauti.types.PriorType in project beast-mcmc by beast-dev.

the class HierarchicalPriorDialog method showDialog.

public int showDialog(final java.util.List<Parameter> parameterList) {
    this.parameterList = parameterList;
    this.parameter = parameterList.get(0);
    PriorType priorType = parameter.priorType;
    // Set-up combo box depending on parameters
    priorCombo.removeAllItems();
    if (parameter.isNonNegative) {
        priorCombo.addItem(PriorType.LOGNORMAL_HPM_PRIOR);
    }
    priorCombo.addItem(PriorType.NORMAL_HPM_PRIOR);
    priorCombo.setSelectedItem(priorType);
    double lower = Double.NEGATIVE_INFINITY;
    double upper = Double.POSITIVE_INFINITY;
    if (parameter.isZeroOne) {
        lower = 0.0;
        upper = 1.0;
    } else if (parameter.isNonNegative) {
        lower = 0.0;
    }
    initialField.setRange(lower, upper);
    initialField.setValue(parameter.getInitial());
    panel = new JPanel(new GridBagLayout());
    setupComponents();
    JScrollPane scrollPane = new JScrollPane(panel, JScrollPane.VERTICAL_SCROLLBAR_AS_NEEDED, JScrollPane.HORIZONTAL_SCROLLBAR_NEVER);
    scrollPane.setBorder(null);
    scrollPane.getViewport().setOpaque(false);
    JOptionPane optionPane = new JOptionPane(scrollPane, JOptionPane.PLAIN_MESSAGE, JOptionPane.OK_CANCEL_OPTION, null, null, null);
    optionPane.setBorder(new EmptyBorder(12, 12, 12, 12));
    final JDialog dialog = optionPane.createDialog(frame, "Phylogenetic Hierarchical Model Setup");
    priorCombo.addItemListener(new ItemListener() {

        public void itemStateChanged(ItemEvent e) {
            setupComponents();
            dialog.validate();
            dialog.repaint();
            dialog.pack();
        }
    });
    for (PriorOptionsPanel optionsPanel : optionsPanels.values()) {
        optionsPanel.addListener(new PriorOptionsPanel.Listener() {

            public void optionsPanelChanged() {
                setupChart();
                dialog.validate();
                dialog.repaint();
            }
        });
    }
    dialog.pack();
    if (OSType.isMac()) {
        dialog.setMinimumSize(new Dimension(dialog.getBounds().width, 300));
    } else {
        Toolkit tk = Toolkit.getDefaultToolkit();
        Dimension d = tk.getScreenSize();
        if (d.height < 700 && panel.getHeight() > 450) {
            dialog.setSize(new Dimension(panel.getWidth() + 100, 550));
        } else {
            // setSize because optionsPanel is shrunk in dialog
            dialog.setSize(new Dimension(panel.getWidth() + 100, panel.getHeight() + 100));
        }
    //            System.out.println("panel width = " + panel.getWidth());
    //            System.out.println("panel height = " + panel.getHeight());
    }
    dialog.setResizable(true);
    dialog.setVisible(true);
    int result = JOptionPane.CANCEL_OPTION;
    Integer value = (Integer) optionPane.getValue();
    if (value != null && value != -1) {
        result = value;
    }
    return result;
}

Example 2 with PriorType

use of dr.app.beauti.types.PriorType in project beast-mcmc by beast-dev.

the class PriorSettingsPanel method setParameter.

/**
     * Set the parameter to be controlled
     *                                                                                                       q
     * @param parameter
     */
public void setParameter(final Parameter parameter) {
    this.parameter = parameter;
    priorCombo = new JComboBox();
    for (PriorType priorType : PriorType.getPriorTypes(parameter)) {
        priorCombo.addItem(priorType);
    }
    if (parameter.priorType != null) {
        priorCombo.setSelectedItem(parameter.priorType);
    }
    // setArguments here
    setupComponents();
    priorCombo.addItemListener(new ItemListener() {

        public void itemStateChanged(ItemEvent e) {
            setupComponents();
            dialog.pack();
            dialog.repaint();
        }
    });
    for (PriorOptionsPanel optionsPanel : optionsPanels.values()) {
        optionsPanel.removeAllListeners();
        optionsPanel.addListener(new PriorOptionsPanel.Listener() {

            public void optionsPanelChanged() {
                setupChart();
                dialog.pack();
                dialog.repaint();
            }
        });
    }
}

Example 3 with PriorType

use of dr.app.beauti.types.PriorType in project beast-mcmc by beast-dev.

the class PriorSettingsPanel method setupComponents.

private void setupComponents() {
    removeAll();
    OptionsPanel optionsPanel = new OptionsPanel(12, (OSType.isMac() ? 6 : 24));
    JPanel panel1 = new JPanel(new FlowLayout(FlowLayout.CENTER));
    panel1.add(optionsPanel);
    GridBagConstraints gbc = new GridBagConstraints();
    gbc.gridx = 0;
    gbc.gridy = 0;
    gbc.gridwidth = 1;
    gbc.weightx = 1.0;
    gbc.weighty = 0.0;
    gbc.fill = GridBagConstraints.HORIZONTAL;
    gbc.anchor = GridBagConstraints.PAGE_START;
    gbc.gridwidth = GridBagConstraints.REMAINDER;
    add(panel1, gbc);
    PriorType priorType = (PriorType) priorCombo.getSelectedItem();
    if (!parameter.isPriorFixed) {
        optionsPanel.addComponentWithLabel("Prior Distribution: ", priorCombo);
    } else {
        optionsPanel.addComponentWithLabel("Prior Distribution: ", new JLabel(priorType.toString()));
    }
    PriorOptionsPanel panel3 = optionsPanels.get(priorType);
    if (panel3 != null) {
        // important to make init field appear during switch
        panel3.setArguments(parameter, priorType);
        optionsPanel.addSpanningComponent(panel3);
    }
    if (priorType == PriorType.CTMC_RATE_REFERENCE_PRIOR) {
        optionsPanel.addSpanningComponent(citationText);
    }
    if (priorType == PriorType.ONE_OVER_X_PRIOR) {
        optionsPanel.addSpanningComponent(oneOverXCaution);
    }
    if (priorType == PriorType.NONE_IMPROPER) {
        optionsPanel.addSpanningComponent(improperCaution);
    }
    if (priorType.isPlottable()) {
        optionsPanel.addSeparator();
        setupChart();
        chart.setMinimumSize(new Dimension(120, 120));
        chart.setPreferredSize(new Dimension(300, 200));
        chart.setFontSize(8);
        gbc.gridy = 1;
        gbc.weighty = 1.0;
        gbc.fill = GridBagConstraints.BOTH;
        add(chart, gbc);
        gbc.gridy = 2;
        gbc.weighty = 0.0;
        gbc.anchor = GridBagConstraints.PAGE_END;
        gbc.fill = GridBagConstraints.HORIZONTAL;
        add(quantilePanel, gbc);
    }
    repaint();
}

Example 4 with PriorType

use of dr.app.beauti.types.PriorType in project beast-mcmc by beast-dev.

the class PriorSettingsPanel method hasInvalidInput.

public boolean hasInvalidInput(boolean showError) {
    PriorType priorType = (PriorType) priorCombo.getSelectedItem();
    PriorOptionsPanel panel = optionsPanels.get(priorType);
    if (panel != null) {
        if (panel.hasInvalidInput(priorType)) {
            if (showError)
                JOptionPane.showMessageDialog(frame, panel.error, "Invalid input", JOptionPane.ERROR_MESSAGE);
            return true;
        } else {
            return false;
        }
    }
    // if there is no panel for this prior type then assume it is valid
    return false;
//            throw new IllegalComponentStateException("Cannot get PriorOptionsPanel");
}

Example 5 with PriorType

use of dr.app.beauti.types.PriorType in project beast-mcmc by beast-dev.

the class PriorSettingsPanel method setupChart.

void setupChart() {
    chart.removeAllPlots();
    if (hasInvalidInput(false)) {
        quantileText.setText("Invalid input");
        return;
    }
    PriorType priorType = (PriorType) priorCombo.getSelectedItem();
    if (priorType == null) {
        priorType = parameter.priorType;
        priorCombo.setSelectedItem(priorType);
    }
    // ExponentialDistribution(1.0 / mean)
    //        if (priorType == PriorType.EXPONENTIAL_PRIOR && parameter.mean == 0) parameter.mean = 1;
    PriorOptionsPanel priorOptionsPanel = optionsPanels.get(priorType);
    // TODO is this used or duplicated to OffsetPositiveDistribution?
    double offset = 0.0;
    // this does not refresh dist from parameter truncation lower/upper, it get them from GUI
    Distribution distribution = priorOptionsPanel.getDistribution(parameter);
    chart.addPlot(new PDFPlot(distribution, offset));
    if (distribution != null) {
        quantileText.setText(formatter.format(distribution.quantile(0.025)) + "\n" + formatter.format(distribution.quantile(0.05)) + "\n" + formatter.format(distribution.quantile(0.5)) + "\n" + formatter.format(distribution.quantile(0.95)) + "\n" + formatter.format(distribution.quantile(0.975)));
    }
}