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();
}
public int showDialog() {
options = new OptionsPanel(6, 6);
options.addComponent(autoScaleCheck);
JPanel panel = new JPanel();
panel.setLayout(new FlowLayout());
panel.add(fromLabel);
panel.add(fromNumberField);
panel.add(toLabel);
panel.add(toNumberField);
options.addComponent(panel);
JPanel panel1 = new JPanel();
panel1.setLayout(new FlowLayout());
panel1.add(new JLabel("Width from:"));
panel1.add(fromWidthField);
panel1.add(new JLabel("to:"));
panel1.add(toWidthField);
options.addComponent(panel1);
JOptionPane optionPane =
new JOptionPane(
options, JOptionPane.QUESTION_MESSAGE, JOptionPane.OK_CANCEL_OPTION, null, null, null);
optionPane.setBorder(new EmptyBorder(12, 12, 12, 12));
final JDialog dialog = optionPane.createDialog(frame, "Setup colour range");
dialog.pack();
autoScaleCheck.addItemListener(
new ItemListener() {
public void itemStateChanged(ItemEvent e) {
boolean enabled = !autoScaleCheck.isSelected();
fromLabel.setEnabled(enabled);
fromNumberField.setEnabled(enabled);
toLabel.setEnabled(enabled);
toNumberField.setEnabled(enabled);
}
});
dialog.setVisible(true);
int result = JOptionPane.CANCEL_OPTION;
Integer value = (Integer) optionPane.getValue();
if (value != null && value.intValue() != -1) {
result = value.intValue();
}
return result;
}
@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 TreePanel(final BeagleSequenceSimulatorFrame frame, final PartitionDataList dataList) {
super();
this.frame = frame;
this.dataList = dataList;
setOpaque(false);
setLayout(new BorderLayout());
optionPanel = new OptionsPanel(12, 12, SwingConstants.CENTER);
add(optionPanel, BorderLayout.NORTH);
treeFileNameText.setEditable(false);
treeFileButton.addActionListener(new ListenTreeFileButton());
JPanel tmpPanel = new JPanel(new BorderLayout(0, 0));
tmpPanel.setOpaque(false);
tmpPanel.add(treeFileNameText, BorderLayout.CENTER);
tmpPanel.add(treeFileButton, BorderLayout.EAST);
optionPanel.addComponentWithLabel("Input Tree File: ", tmpPanel);
} // END: Constructor
private void setupComponents() {
panel.removeAll();
JScrollPane scrollPane1 =
new JScrollPane(
parametersTable,
JScrollPane.VERTICAL_SCROLLBAR_ALWAYS,
JScrollPane.HORIZONTAL_SCROLLBAR_ALWAYS);
scrollPane1.setOpaque(false);
ActionPanel actionPanel1 = new ActionPanel(false);
actionPanel1.setAddAction(addParameterAction);
actionPanel1.setRemoveAction(removeParameterAction);
actionPanel1.setAddToolTipText("Use this button to add an existing parameter to the prior");
actionPanel1.setRemoveToolTipText("Use this button to remove a parameter from the prior");
removeParameterAction.setEnabled(false);
JPanel controlPanel1 = new JPanel(new FlowLayout(FlowLayout.LEFT));
controlPanel1.setOpaque(false);
controlPanel1.add(actionPanel1);
JPanel panel1 = new JPanel(new BorderLayout(0, 0));
panel1.setOpaque(false);
panel1.add(new JLabel("Linked parameters:"), BorderLayout.NORTH);
panel1.add(scrollPane1, BorderLayout.CENTER);
// removing the control panel for now. Not sure whether we really want adding and
// removing of parameteres in this dialog.
// panel1.add(controlPanel1, BorderLayout.SOUTH);
panel1.setSize(new Dimension(PREFERRED_TABLE_WIDTH, PREFERRED_TABLE_HEIGHT));
panel1.setPreferredSize(new Dimension(PREFERRED_TABLE_WIDTH, PREFERRED_TABLE_HEIGHT));
panel1.setMinimumSize(new Dimension(MINIMUM_TABLE_WIDTH, MINIMUM_TABLE_HEIGHT));
OptionsPanel optionsPanel = new OptionsPanel(0, 6);
if (parameter.getName() != null) {
nameField.setText(parameter.getName());
} else {
nameField.setText("Untitled");
}
optionsPanel.addComponentWithLabel("Unique Name: ", nameField);
// optionsPanel.addComponentWithLabel("Initial Value: ", initialField);
panel.setOpaque(false);
panel.setBorder(new BorderUIResource.EmptyBorderUIResource(new Insets(12, 12, 12, 12)));
GridBagConstraints c = new GridBagConstraints();
c.gridx = 0;
c.gridy = 0;
c.weightx = 0;
c.weighty = 0;
c.anchor = GridBagConstraints.PAGE_START;
c.fill = GridBagConstraints.HORIZONTAL;
c.gridwidth = 2;
panel.add(optionsPanel, c);
c.gridx = 0;
c.gridy = 1;
c.anchor = GridBagConstraints.PAGE_START;
c.fill = GridBagConstraints.VERTICAL;
c.gridwidth = 1;
panel.add(panel1, c);
c.gridx = 1;
c.gridy = 1;
c.weightx = 1;
c.weighty = 1;
c.fill = GridBagConstraints.BOTH;
c.anchor = GridBagConstraints.PAGE_START;
c.gridwidth = GridBagConstraints.REMAINDER;
panel.add(priorSettingsPanel, c);
}
public ChartSetupDialog(
final JFrame frame,
boolean canLogXAxis,
boolean canLogYAxis,
int defaultMinXAxisFlag,
int defaultMaxXAxisFlag,
int defaultMinYAxisFlag,
int defaultMaxYAxisFlag) {
this.frame = frame;
this.canLogXAxis = canLogXAxis;
this.canLogYAxis = canLogYAxis;
this.defaultMinXAxisFlag = defaultMinXAxisFlag;
this.defaultMaxXAxisFlag = defaultMaxXAxisFlag;
this.defaultMinYAxisFlag = defaultMinYAxisFlag;
this.defaultMaxYAxisFlag = defaultMaxYAxisFlag;
logXAxis = new JCheckBox("Log axis");
manualXAxis = new JCheckBox("Manual range");
minXValue = new RealNumberField();
minXValue.setColumns(12);
maxXValue = new RealNumberField();
maxXValue.setColumns(12);
logYAxis = new JCheckBox("Log axis");
manualYAxis = new JCheckBox("Manual range");
minYValue = new RealNumberField();
minYValue.setColumns(12);
maxYValue = new RealNumberField();
maxYValue.setColumns(12);
optionPanel = new OptionsPanel(12, 12);
optionPanel.addSpanningComponent(new JLabel("X Axis"));
if (canLogXAxis) {
optionPanel.addComponent(logXAxis);
}
optionPanel.addComponent(manualXAxis);
final JLabel minXLabel = new JLabel("Minimum Value:");
optionPanel.addComponents(minXLabel, minXValue);
final JLabel maxXLabel = new JLabel("Maximum Value:");
optionPanel.addComponents(maxXLabel, maxXValue);
manualXAxis.addChangeListener(
new ChangeListener() {
public void stateChanged(ChangeEvent changeEvent) {
final boolean xaSelected = manualXAxis.isSelected();
minXLabel.setEnabled(xaSelected);
minXValue.setEnabled(xaSelected);
maxXLabel.setEnabled(xaSelected);
maxXValue.setEnabled(xaSelected);
}
});
manualXAxis.setSelected(true);
manualXAxis.setSelected(false);
optionPanel.addSeparator();
optionPanel.addSpanningComponent(new JLabel("Y Axis"));
if (canLogYAxis) {
optionPanel.addComponent(logYAxis);
}
optionPanel.addComponent(manualYAxis);
final JLabel minYLabel = new JLabel("Minimum Value:");
optionPanel.addComponents(minYLabel, minYValue);
final JLabel maxYLabel = new JLabel("Maximum Value:");
optionPanel.addComponents(maxYLabel, maxYValue);
manualYAxis.addChangeListener(
new ChangeListener() {
public void stateChanged(ChangeEvent changeEvent) {
final boolean yaSelected = manualYAxis.isSelected();
minYLabel.setEnabled(yaSelected);
minYValue.setEnabled(yaSelected);
maxYLabel.setEnabled(yaSelected);
maxYValue.setEnabled(yaSelected);
}
});
manualYAxis.setSelected(true);
manualYAxis.setSelected(false);
}
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 BeastDialog(final JFrame frame, final String titleString, final Icon icon) {
this.frame = frame;
optionPanel = new OptionsPanel(12, 12);
// this.frame = frame;
JPanel panel = new JPanel(new BorderLayout());
panel.setOpaque(false);
final OptionsPanel optionPanel3 = new OptionsPanel(0, 3);
final JLabel titleIcon = new JLabel();
titleIcon.setIcon(icon);
final JLabel titleText = new JLabel(titleString);
optionPanel3.addComponent(titleText);
// final JButton aboutButton = new JButton("About BEAST...");
// //aboutButton.setAction();
// optionPanel3.addComponent(aboutButton);
optionPanel.addComponents(titleIcon, optionPanel3);
final JButton inputFileButton = new JButton("Choose File...");
final JTextField inputFileNameText = new JTextField("not selected", 16);
inputFileButton.addActionListener(
new ActionListener() {
public void actionPerformed(ActionEvent ae) {
FileDialog dialog = new FileDialog(frame, "Select target file...", FileDialog.LOAD);
dialog.setVisible(true);
if (dialog.getFile() == null) {
// the dialog was cancelled...
return;
}
inputFile = new File(dialog.getDirectory(), dialog.getFile());
inputFileNameText.setText(inputFile.getName());
}
});
inputFileNameText.setEditable(false);
JPanel panel1 = new JPanel(new BorderLayout(0, 0));
panel1.add(inputFileNameText, BorderLayout.CENTER);
panel1.add(inputFileButton, BorderLayout.EAST);
inputFileNameText.setToolTipText(
"<html>Drag a BEAST XML file here or use the button to<br>"
+ "select one from a file dialog box.</html>");
inputFileButton.setToolTipText(
"<html>Drag a BEAST XML file here or use the button to<br>"
+ "select one from a file dialog box.</html>");
optionPanel.addComponentWithLabel("BEAST XML File: ", panel1);
Color focusColor = UIManager.getColor("Focus.color");
Border focusBorder = BorderFactory.createMatteBorder(2, 2, 2, 2, focusColor);
new FileDrop(
null,
inputFileNameText,
focusBorder,
new FileDrop.Listener() {
public void filesDropped(java.io.File[] files) {
inputFile = files[0];
inputFileNameText.setText(inputFile.getName());
} // end filesDropped
}); // end FileDrop.Listener
overwriteCheckBox.setToolTipText(
"<html>Specify whether BEAST will overwrite existing log files<br>"
+ "with the same name.</html>");
optionPanel.addComponent(overwriteCheckBox);
optionPanel.addSeparator();
seedText.setColumns(12);
seedText.setToolTipText(
"<html>Specify a particular random number seed to replicate<br>"
+ "precisely the sequence of steps in the MCMC chain. By<br>"
+ "default this uses system information to provide a new<br>"
+ "seed each run.</html>");
optionPanel.addComponentWithLabel("Random number seed: ", seedText);
threadsCombo.setToolTipText(
"<html>Specify how large a thread pool to use.<br>"
+ "In most circumstances this should be set to 'automatic'<br>"
+ "but in some circumstances it may be desirable to restict<br>"
+ "the number of cores being used. 0 will turn off threading</html>");
optionPanel.addComponentWithLabel("Thread pool size: ", threadsCombo);
optionPanel.addSeparator();
optionPanel.addSpanningComponent(beagleCheckBox);
beagleCheckBox.setSelected(true);
final OptionsPanel optionPanel1 = new OptionsPanel(0, 6);
// optionPanel1.setBorder(BorderFactory.createEmptyBorder());
optionPanel1.setBorder(new TitledBorder(""));
OptionsPanel optionPanel2 = new OptionsPanel(0, 3);
optionPanel2.setBorder(BorderFactory.createEmptyBorder());
final JLabel label1 =
optionPanel2.addComponentWithLabel("Prefer use of: ", beagleResourceCombo);
optionPanel2.addComponent(beagleSSECheckBox);
beagleSSECheckBox.setSelected(true);
final JLabel label2 =
optionPanel2.addComponentWithLabel("Prefer precision: ", beaglePrecisionCombo);
final JLabel label3 =
optionPanel2.addComponentWithLabel("Rescaling scheme: ", beagleScalingCombo);
optionPanel2.addComponent(beagleInfoCheckBox);
optionPanel2.setBorder(BorderFactory.createEmptyBorder());
optionPanel1.addComponent(optionPanel2);
final JEditorPane beagleInfo =
new JEditorPane(
"text/html",
"<html><div style=\"font-family:'helvetica neue light',helvetica,sans-serif;font-size:12;\"><p>BEAGLE is a high-performance phylogenetic library that can make use of<br>"
+ "additional computational resources such as graphics boards. It must be<br>"
+ "downloaded and installed independently of BEAST:</p>"
+ "<pre><a href=\"http://beagle-lib.googlecode.com/\">http://beagle-lib.googlecode.com/</a></pre></div>");
beagleInfo.setOpaque(false);
beagleInfo.setEditable(false);
beagleInfo.addHyperlinkListener(new SimpleLinkListener());
optionPanel1.addComponent(beagleInfo);
optionPanel1.setBorder(BorderFactory.createEmptyBorder());
optionPanel.addSpanningComponent(optionPanel1);
beagleInfoCheckBox.setEnabled(false);
beagleCheckBox.addChangeListener(
new ChangeListener() {
public void stateChanged(ChangeEvent e) {
beagleInfo.setEnabled(beagleCheckBox.isSelected());
beagleInfoCheckBox.setEnabled(beagleCheckBox.isSelected());
label1.setEnabled(beagleCheckBox.isSelected());
beagleResourceCombo.setEnabled(beagleCheckBox.isSelected());
beagleSSECheckBox.setEnabled(beagleCheckBox.isSelected());
label2.setEnabled(beagleCheckBox.isSelected());
beaglePrecisionCombo.setEnabled(beagleCheckBox.isSelected());
label3.setEnabled(beagleCheckBox.isSelected());
beagleScalingCombo.setEnabled(beagleCheckBox.isSelected());
}
});
beagleCheckBox.setSelected(false);
beagleResourceCombo.setSelectedItem("CPU");
}
