public void setOptions(BeautiOptions options) {
this.options = options;
chainLengthField.setValue(options.chainLength);
echoEveryField.setValue(options.echoEvery);
logEveryField.setValue(options.logEvery);
if (options.fileNameStem != null) {
fileNameStemField.setText(options.fileNameStem);
} else {
fileNameStemField.setText(DEFAULT_FILE_NAME_STEM);
fileNameStemField.setEnabled(false);
}
operatorAnalaysisCheck.setSelected(options.operatorAnalysis);
updateOtherFileNames(options);
if (options.contains(Microsatellite.INSTANCE)) {
samplePriorCheckBox.setSelected(false);
samplePriorCheckBox.setVisible(false);
} else {
samplePriorCheckBox.setVisible(true);
samplePriorCheckBox.setSelected(options.samplePriorOnly);
}
optionsPanel.validate();
optionsPanel.repaint();
}
@SuppressWarnings({"unchecked"})
public SimulationPanel(final MainFrame frame, final PartitionDataList dataList) {
this.frame = frame;
this.dataList = dataList;
optionPanel = new OptionsPanel(12, 12, SwingConstants.CENTER);
simulationsNumberField = new WholeNumberField(1, Integer.MAX_VALUE);
simulationsNumberField.setColumns(10);
simulationsNumberField.setValue(dataList.simulationsCount);
optionPanel.addComponentWithLabel("Number of simulations:", simulationsNumberField);
setSeed = new JCheckBox();
setSeed.addItemListener(new SetSeedCheckBoxListener());
setSeed.setSelected(dataList.setSeed);
optionPanel.addComponentWithLabel("Set seed:", setSeed);
startingSeedNumberField = new WholeNumberField(1, Long.MAX_VALUE);
startingSeedNumberField.setColumns(10);
startingSeedNumberField.setValue(dataList.startingSeed);
startingSeedNumberField.setEnabled(dataList.setSeed);
optionPanel.addComponentWithLabel("Starting seed:", startingSeedNumberField);
outputFormat = new JComboBox();
optionPanel.addComponentWithLabel("Output format:", outputFormat);
outputFormatModel = new DefaultComboBoxModel(SimpleAlignment.OutputType.values());
outputFormat.setModel(outputFormatModel);
outputAncestralSequences = new JCheckBox();
outputAncestralSequences.addItemListener(new outputAncestralSequencesCheckBoxListener());
outputAncestralSequences.setSelected(dataList.useParallel);
optionPanel.addComponentWithLabel("Output ancestral sequences:", outputAncestralSequences);
useParallel = new JCheckBox();
useParallel.addItemListener(new UseParallelCheckBoxListener());
useParallel.setSelected(dataList.useParallel);
optionPanel.addComponentWithLabel("Use parallel implementation:", useParallel);
// Buttons holder
JPanel buttonsHolder = new JPanel();
buttonsHolder.setOpaque(false);
// simulate button
simulate = new JButton("Simulate", Utils.createImageIcon(Utils.BIOHAZARD_ICON));
simulate.addActionListener(new ListenSimulate());
buttonsHolder.add(simulate);
generateXML = new JButton("Generate XML", Utils.createImageIcon(Utils.HAMMER_ICON));
generateXML.addActionListener(new ListenGenerateXML());
buttonsHolder.add(generateXML);
setOpaque(false);
setLayout(new BorderLayout());
add(optionPanel, BorderLayout.NORTH);
add(buttonsHolder, BorderLayout.SOUTH);
} // END: SimulationPanel
public MCMCPanel(BeautiFrame parent) {
setLayout(new BorderLayout());
// Mac OS X components have more spacing round them already
optionsPanel = new OptionsPanel(12, (OSType.isMac() ? 6 : 24));
this.frame = parent;
setOpaque(false);
optionsPanel.setOpaque(false);
chainLengthField.setValue(100000);
chainLengthField.setColumns(10);
optionsPanel.addComponentWithLabel("Length of chain:", chainLengthField);
chainLengthField.addKeyListener(
new java.awt.event.KeyListener() {
public void keyTyped(KeyEvent e) {}
public void keyPressed(KeyEvent e) {}
public void keyReleased(KeyEvent e) {
options.chainLength = chainLengthField.getValue();
frame.setDirty();
}
});
optionsPanel.addSeparator();
echoEveryField.setValue(1000);
echoEveryField.setColumns(10);
optionsPanel.addComponentWithLabel("Echo state to screen every:", echoEveryField);
echoEveryField.addKeyListener(
new java.awt.event.KeyListener() {
public void keyTyped(KeyEvent e) {}
public void keyPressed(KeyEvent e) {}
public void keyReleased(KeyEvent e) {
options.echoEvery = echoEveryField.getValue();
frame.setDirty();
}
});
logEveryField.setValue(100);
logEveryField.setColumns(10);
optionsPanel.addComponentWithLabel("Log parameters every:", logEveryField);
logEveryField.addKeyListener(
new java.awt.event.KeyListener() {
public void keyTyped(KeyEvent e) {}
public void keyPressed(KeyEvent e) {}
public void keyReleased(KeyEvent e) {
options.logEvery = logEveryField.getValue();
frame.setDirty();
}
});
optionsPanel.addSeparator();
fileNameStemField.setColumns(32);
optionsPanel.addComponentWithLabel("File name stem:", fileNameStemField);
fileNameStemField.setEditable(true);
fileNameStemField.addKeyListener(
new java.awt.event.KeyListener() {
public void keyTyped(KeyEvent e) {}
public void keyPressed(KeyEvent e) {}
public void keyReleased(KeyEvent e) {
options.fileNameStem = fileNameStemField.getText();
updateOtherFileNames(options);
frame.setDirty();
}
});
optionsPanel.addComponent(addTxt);
if (OSType.isWindows()) {
addTxt.setSelected(true);
} else {
addTxt.setSelected(false);
}
addTxt.addChangeListener(
new ChangeListener() {
public void stateChanged(ChangeEvent changeEvent) {
setOptions(options);
frame.setDirty();
}
});
optionsPanel.addSeparator();
logFileNameField.setColumns(32);
optionsPanel.addComponentWithLabel("Log file name:", logFileNameField);
logFileNameField.setEditable(false);
// optionsPanel.addComponent(allowOverwriteLogCheck);
// allowOverwriteLogCheck.setSelected(false);
// allowOverwriteLogCheck.addChangeListener(new ChangeListener() {
// public void stateChanged(ChangeEvent changeEvent) {
// options.allowOverwriteLog = allowOverwriteLogCheck.isSelected();
// }
// });
treeFileNameField.setColumns(32);
optionsPanel.addComponentWithLabel("Trees file name:", treeFileNameField);
treeFileNameField.setEditable(false);
// addComponent(mapTreeLogCheck);
// mapTreeLogCheck.setOpaque(false);
// mapTreeLogCheck.addActionListener(new java.awt.event.ActionListener() {
// public void actionPerformed(ActionEvent e) {
// mapTreeFileNameField.setEnabled(mapTreeLogCheck.isSelected());
// }
// });
//
// mapTreeFileNameField.setColumns(32);
// addComponentWithLabel("MAP tree file name:", mapTreeFileNameField);
optionsPanel.addComponent(substTreeLogCheck);
substTreeLogCheck.setOpaque(false);
substTreeLogCheck.addActionListener(
new java.awt.event.ActionListener() {
public void actionPerformed(ActionEvent e) {
options.substTreeLog = substTreeLogCheck.isSelected();
updateTreeFileNameList();
substTreeFileNameField.setEnabled(substTreeLogCheck.isSelected());
if (substTreeLogCheck.isSelected()) {
substTreeFileNameField.setText(displayTreeList(options.substTreeFileName));
} else {
substTreeFileNameField.setText("");
}
frame.setDirty();
}
});
substTreeFileNameField.setColumns(32);
substTreeFileNameField.setEditable(false);
substTreeFileNameField.setEnabled(false);
optionsPanel.addComponentWithLabel("Substitutions trees file name:", substTreeFileNameField);
optionsPanel.addComponent(operatorAnalaysisCheck);
operatorAnalaysisCheck.addActionListener(
new java.awt.event.ActionListener() {
public void actionPerformed(ActionEvent e) {
options.operatorAnalysis = operatorAnalaysisCheck.isSelected();
updateOtherFileNames(options);
frame.setDirty();
}
});
operatorAnalaysisFileNameField.setColumns(32);
operatorAnalaysisFileNameField.setEditable(false);
operatorAnalaysisFileNameField.setEnabled(false);
optionsPanel.addComponentWithLabel(
"Operator analysis file name:", operatorAnalaysisFileNameField);
optionsPanel.addSeparator();
optionsPanel.addComponent(samplePriorCheckBox);
samplePriorCheckBox.setOpaque(false);
samplePriorCheckBox.addChangeListener(
new ChangeListener() {
public void stateChanged(ChangeEvent changeEvent) {
frame.setDirty();
}
});
// logFileNameField.addKeyListener(listener);
// treeFileNameField.addKeyListener(listener);
// mapTreeFileNameField.addKeyListener(listener);
// substTreeFileNameField.addKeyListener(listener);
// optionsPanel.setPreferredSize(new java.awt.Dimension(500, 600));
JPanel panel = new JPanel(new FlowLayout(FlowLayout.CENTER));
panel.add(optionsPanel, BorderLayout.CENTER);
panel.setOpaque(false);
JScrollPane scrollPane =
new JScrollPane(
panel,
JScrollPane.VERTICAL_SCROLLBAR_AS_NEEDED,
JScrollPane.HORIZONTAL_SCROLLBAR_NEVER);
scrollPane.setOpaque(false);
scrollPane.setBorder(null);
scrollPane.getViewport().setOpaque(false);
add(scrollPane, BorderLayout.CENTER);
}
public void setSeed(long seed) {
seedText.setValue(seed);
}
