/*
Copyright (C) 2011 Diego Darriba, David Posada
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 3 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., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
*/
package es.uvigo.darwin.jmodeltest.gui;
import java.awt.Component;
import java.awt.Dimension;
import java.awt.Point;
import javax.swing.JButton;
import javax.swing.JCheckBox;
import javax.swing.JLayeredPane;
import javax.swing.JMenuBar;
import javax.swing.JPanel;
import javax.swing.JSlider;
import javax.swing.JTextField;
import javax.swing.border.LineBorder;
import javax.swing.event.ChangeEvent;
import javax.swing.event.ChangeListener;
import javax.swing.plaf.BorderUIResource;
import es.uvigo.darwin.jmodeltest.ApplicationOptions;
import es.uvigo.darwin.jmodeltest.ModelTest;
import es.uvigo.darwin.jmodeltest.selection.BIC;
import es.uvigo.darwin.jmodeltest.utilities.Utilities;
public class Frame_BIC extends JModelTestFrame {
private static final long serialVersionUID = 201104031100L;
private JPanel PanelBICSettings = new JPanel();
private JTextField TextFieldTaxaBIC = new JTextField();
private JTextField TextFieldSizeBIC = new JTextField();
private JButton RunButtonBIC = new JButton();
private JButton CancelButtonBIC = new JButton();
private JButton JButtonDefaultBIC = new JButton();
private JCheckBox jCheckBoxPAUPblock = new JCheckBox();
private JCheckBox jCheckBoxAveraging = new JCheckBox();
private JCheckBox jCheckBoxImportance = new JCheckBox();
private JSlider JSliderInterval = new JSlider();
private BIC myBIC;
public Frame_BIC() {
}
public void initComponents() throws Exception {
PanelBICSettings.setSize(490, 240);
PanelBICSettings
.setBorder(new BorderUIResource.TitledBorderUIResource(
new LineBorder(new java.awt.Color(
153, 153, 153), 1, false), "BIC Settings", 4,
2, new java.awt.Font("Application", 1, 10),
new java.awt.Color(102, 102, 153)));
PanelBICSettings.setLocation(10, 10);
PanelBICSettings.setVisible(true);
PanelBICSettings.setLayout(null);
RunButtonBIC.setVisible(true);
RunButtonBIC.setSize(190, 40);
RunButtonBIC.setText("Do BIC calculations");
RunButtonBIC.setLocation(280, 190);
getRootPane().setDefaultButton(RunButtonBIC);
JButtonDefaultBIC.setVisible(true);
JButtonDefaultBIC.setSize(141, 40);
JButtonDefaultBIC.setText("Default Settings");
JButtonDefaultBIC.setLocation(10, 190);
CancelButtonBIC.setVisible(true);
CancelButtonBIC.setSize(110, 40);
CancelButtonBIC.setText("Cancel");
CancelButtonBIC.setLocation(160, 190);
TextFieldSizeBIC
.setToolTipText("Enter the sample size you want to use for the BIC and click RETURN. By default this is the number of sites in the alignment");
TextFieldSizeBIC
.setBorder(new BorderUIResource.TitledBorderUIResource(
new LineBorder(new java.awt.Color(
153, 153, 153), 1, false), "Sample size", 4, 2,
new java.awt.Font("Application", 1, 10),
new java.awt.Color(102, 102, 153)));
TextFieldSizeBIC.setVisible(true);
TextFieldSizeBIC.setSize(170, 40);
TextFieldSizeBIC.setText(Utilities.format(options.getSampleSize(),10,4,false));
TextFieldSizeBIC.setHorizontalAlignment(JTextField.RIGHT);
TextFieldSizeBIC.setLocation(30, 20);
TextFieldSizeBIC.setEnabled(false);
jCheckBoxImportance.setVisible(true);
jCheckBoxImportance.setSize(260, 20);
jCheckBoxImportance.setText("Calculate parameter importances");
jCheckBoxImportance.setLocation(30, 70);
jCheckBoxImportance.setSelected(true);
jCheckBoxAveraging.setVisible(true);
jCheckBoxAveraging.setSize(260, 20);
jCheckBoxAveraging.setText("Do model averaging");
jCheckBoxAveraging.setLocation(30, 110);
jCheckBoxAveraging.setSelected(true);
jCheckBoxPAUPblock.setVisible(true);
jCheckBoxPAUPblock.setSize(260, 20);
jCheckBoxPAUPblock.setText("Write PAUP* block");
jCheckBoxPAUPblock.setLocation(30, 150);
jCheckBoxPAUPblock.setSelected(false);
jCheckBoxPAUPblock
.setToolTipText("Writes a block of PAUP* commands implementing the selected model");
JSliderInterval.setVisible(true);
JSliderInterval
.setToolTipText("Set the confidence interval for model averaging and/or parameter importance");
JSliderInterval
.setBorder(new BorderUIResource.TitledBorderUIResource(
new LineBorder(new java.awt.Color(
153, 153, 153), 1, false),
"Confidence interval = 100%", 4, 2, new java.awt.Font(
"Application", 1, 10), new java.awt.Color(102,
102, 153)));
JSliderInterval.setSize(170, 70);
JSliderInterval.setLocation(300, 70);
JSliderInterval.setMinimum(0);
JSliderInterval.setMaximum(100);
JSliderInterval.setValue(100);
JSliderInterval.setMajorTickSpacing(20);
JSliderInterval.setMinorTickSpacing(5);
JSliderInterval.setPaintTicks(true);
JSliderInterval.setPaintLabels(true);
JSliderInterval.setEnabled(true);
JSliderInterval.setFont(XManager.FONT_SLIDER);
setLocation(281, 80);
getContentPane().setLayout(null);
setTitle("Bayesian Information Criterion (BIC) Settings");
PanelBICSettings.add(TextFieldTaxaBIC);
PanelBICSettings.add(TextFieldSizeBIC);
PanelBICSettings.add(jCheckBoxAveraging);
PanelBICSettings.add(jCheckBoxImportance);
PanelBICSettings.add(jCheckBoxPAUPblock);
PanelBICSettings.add(JSliderInterval);
PanelBICSettings.add(JButtonDefaultBIC);
PanelBICSettings.add(CancelButtonBIC);
PanelBICSettings.add(RunButtonBIC);
getContentPane().add(PanelBICSettings);
setSize(510, 280);
setResizable(false);
// event handling
jCheckBoxAveraging
.addChangeListener(new ChangeListener() {
public void stateChanged(ChangeEvent e) {
jCheckBoxAveragingStateChanged(e);
}
});
jCheckBoxImportance
.addChangeListener(new ChangeListener() {
public void stateChanged(ChangeEvent e) {
jCheckBoxImportanceStateChanged(e);
}
});
JSliderInterval
.addChangeListener(new ChangeListener() {
public void stateChanged(ChangeEvent e) {
JSliderIntervalStateChanged(e);
}
});
JButtonDefaultBIC
.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent e) {
JButtonDefaultBICActionPerformed(e);
}
});
CancelButtonBIC.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent e) {
CancelButtonBICActionPerformed(e);
}
});
RunButtonBIC.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent e) {
RunButtonBICActionPerformed(e);
}
});
addWindowListener(new java.awt.event.WindowAdapter() {
public void windowClosing(java.awt.event.WindowEvent e) {
thisWindowClosing(e);
}
});
}
private boolean mShown = false;
public void addNotify() {
super.addNotify();
if (mShown)
return;
// resize frame to account for menubar
JMenuBar jMenuBar = getJMenuBar();
if (jMenuBar != null) {
int jMenuBarHeight = jMenuBar.getPreferredSize().height;
Dimension dimension = getSize();
dimension.height += jMenuBarHeight;
setSize(dimension);
// move down components in layered pane
Component[] components = getLayeredPane().getComponentsInLayer(
JLayeredPane.DEFAULT_LAYER.intValue());
for (int i = 0; i < components.length; i++) {
Point location = components[i].getLocation();
location.move(location.x, location.y + jMenuBarHeight);
components[i].setLocation(location);
}
}
mShown = true;
}
// Close the window when the close box is clicked
void thisWindowClosing(java.awt.event.WindowEvent e) {
setVisible(false);
dispose();
// System.exit(0);
}
public void jCheckBoxImportanceStateChanged(ChangeEvent e) {
if (jCheckBoxImportance.isSelected()) {
JSliderInterval.setEnabled(true);
} else {
if (!jCheckBoxAveraging.isSelected())
JSliderInterval.setEnabled(false);
}
}
public void jCheckBoxAveragingStateChanged(ChangeEvent e) {
if (jCheckBoxAveraging.isSelected()) {
JSliderInterval.setEnabled(true);
} else {
if (!jCheckBoxImportance.isSelected())
JSliderInterval.setEnabled(false);
}
}
public void JSliderIntervalStateChanged(ChangeEvent e) {
JSliderInterval
.setBorder(new BorderUIResource.TitledBorderUIResource(
new LineBorder(new java.awt.Color(
153, 153, 153), 1, false),
"Confidence interval = " + JSliderInterval.getValue()
+ "%", 4, 2, new java.awt.Font("Application",
1, 10), new java.awt.Color(102, 102, 153)));
}
public void JButtonDefaultBICActionPerformed(java.awt.event.ActionEvent e) {
TextFieldSizeBIC.setEnabled(false);
TextFieldSizeBIC.setText(Utilities.format(options.getSampleSize(),10,4,false));
ApplicationOptions.getInstance().countBLasParameters = true;
XManager.getInstance().selectedMenuResultsBLasParameters(true);
jCheckBoxPAUPblock.setSelected(false);
jCheckBoxAveraging.setSelected(true);
jCheckBoxImportance.setSelected(true);
JSliderInterval.setValue(100);
}
public void CancelButtonBICActionPerformed(java.awt.event.ActionEvent e) {
try {
setVisible(false);
dispose();
} catch (Exception f) {
f.printStackTrace();
}
}
public void RunButtonBICActionPerformed(java.awt.event.ActionEvent e) {
boolean writePAUPblock, doImportances, doModelAveraging;
double credibleInterval;
try {
setVisible(false);
dispose();
writePAUPblock = jCheckBoxPAUPblock.isSelected();
options.writePAUPblock |= writePAUPblock;
doImportances = jCheckBoxImportance.isSelected();
doModelAveraging = jCheckBoxAveraging.isSelected();
credibleInterval = JSliderInterval.getValue() / 100.0;
myBIC = new BIC(writePAUPblock, doImportances, doModelAveraging,
credibleInterval);
myBIC.compute();
myBIC.print(ModelTest.getCurrentOutStream());
ModelTest.setMyBIC(myBIC);
options.doBIC = myBIC != null;
XManager.getInstance().resultsFrame.enablePane(FrameResults.TAB_BIC);
XManager.getInstance().resultsFrame.populate(FrameResults.TAB_BIC);
XManager.getInstance().enableMenuAveraging(!options.fixedTopology);
} catch (Exception f) {
f.printStackTrace();
}
}
}