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 final void collectSettings() {
dataList.simulationsCount = simulationsNumberField.getValue();
if (dataList.setSeed) {
dataList.startingSeed = startingSeedNumberField.getValue();
}
dataList.outputFormat =
SimpleAlignment.OutputType.parseFromString(outputFormat.getSelectedItem().toString());
} // END: collectSettings
/**
* Sets the components up according to the partition model - but does not layout the top level
* options panel.
*/
public void setOptions() {
if (SiteModelsPanel.DEBUG) {
String modelName = (model == null) ? "null" : model.getName();
Logger.getLogger("dr.app.beauti").info("ModelsPanel.setModelOptions(" + modelName + ")");
}
if (model == null) {
return;
}
int dataType = model.getDataType().getType();
switch (dataType) {
case DataType.NUCLEOTIDES:
nucSubstCombo.setSelectedItem(model.getNucSubstitutionModel());
frequencyCombo.setSelectedItem(model.getFrequencyPolicy());
break;
case DataType.AMINO_ACIDS:
aaSubstCombo.setSelectedItem(model.getAaSubstitutionModel());
break;
case DataType.TWO_STATES:
case DataType.COVARION:
binarySubstCombo.setSelectedItem(model.getBinarySubstitutionModel());
useAmbiguitiesTreeLikelihoodCheck.setSelected(model.isUseAmbiguitiesTreeLikelihood());
break;
case DataType.GENERAL:
discreteTraitSiteModelCombo.setSelectedItem(model.getDiscreteSubstType());
activateBSSVS.setSelected(model.isActivateBSSVS());
break;
case DataType.CONTINUOUS:
continuousTraitSiteModelCombo.setSelectedItem(model.getContinuousSubstModelType());
ContinuousComponentOptions component =
(ContinuousComponentOptions)
model.getOptions().getComponentOptions(ContinuousComponentOptions.class);
latLongCheck.setSelected(model.isLatitudeLongitude());
latLongCheck.setEnabled(model.getContinuousTraitCount() == 2);
useLambdaCheck.setSelected(component.useLambda(model));
break;
case DataType.MICRO_SAT:
microsatName.setText(model.getMicrosatellite().getName());
microsatMax.setText(Integer.toString(model.getMicrosatellite().getMax()));
microsatMin.setText(Integer.toString(model.getMicrosatellite().getMin()));
shareMicroSatCheck.setSelected(model.getOptions().shareMicroSat);
rateProportionCombo.setSelectedItem(model.getRatePorportion());
mutationBiasCombo.setSelectedItem(model.getMutationBias());
phaseCombo.setSelectedItem(model.getPhase());
shareMicroSatCheck.setEnabled(
model.getOptions().getPartitionSubstitutionModels(Microsatellite.INSTANCE).size() > 1);
break;
default:
throw new IllegalArgumentException("Unknown data type");
}
if (model.isGammaHetero() && !model.isInvarHetero()) {
heteroCombo.setSelectedIndex(1);
} else if (!model.isGammaHetero() && model.isInvarHetero()) {
heteroCombo.setSelectedIndex(2);
} else if (model.isGammaHetero() && model.isInvarHetero()) {
heteroCombo.setSelectedIndex(3);
} else {
heteroCombo.setSelectedIndex(0);
}
gammaCatCombo.setSelectedIndex(model.getGammaCategories() - 4);
if (model.getCodonHeteroPattern() == null) {
codingCombo.setSelectedIndex(0);
} else if (model.getCodonHeteroPattern().equals("112")) {
codingCombo.setSelectedIndex(1);
} else {
codingCombo.setSelectedIndex(2);
}
substUnlinkCheck.setSelected(model.isUnlinkedSubstitutionModel());
heteroUnlinkCheck.setSelected(model.isUnlinkedHeterogeneityModel());
freqsUnlinkCheck.setSelected(model.isUnlinkedFrequencyModel());
dolloCheck.setSelected(model.isDolloModel());
}
public PartitionModelPanel(final PartitionSubstitutionModel partitionModel) {
super(12, (OSType.isMac() ? 6 : 24));
this.model = partitionModel;
initCodonPartitionComponents();
PanelUtils.setupComponent(nucSubstCombo);
nucSubstCombo.addItemListener(
new ItemListener() {
public void itemStateChanged(ItemEvent ev) {
model.setNucSubstitutionModel((NucModelType) nucSubstCombo.getSelectedItem());
}
});
nucSubstCombo.setToolTipText("<html>Select the type of nucleotide substitution model.</html>");
PanelUtils.setupComponent(aaSubstCombo);
aaSubstCombo.addItemListener(
new ItemListener() {
public void itemStateChanged(ItemEvent ev) {
AminoAcidModelType type = (AminoAcidModelType) aaSubstCombo.getSelectedItem();
model.setAaSubstitutionModel(type);
citationText.setText(type.getCitation().toString());
}
});
aaSubstCombo.setToolTipText("<html>Select the type of amino acid substitution model.</html>");
PanelUtils.setupComponent(binarySubstCombo);
binarySubstCombo.addItemListener(
new ItemListener() {
public void itemStateChanged(ItemEvent ev) {
model.setBinarySubstitutionModel((BinaryModelType) binarySubstCombo.getSelectedItem());
useAmbiguitiesTreeLikelihoodCheck.setSelected(
binarySubstCombo.getSelectedItem() == BinaryModelType.BIN_COVARION);
useAmbiguitiesTreeLikelihoodCheck.setEnabled(
binarySubstCombo.getSelectedItem() != BinaryModelType.BIN_COVARION);
}
});
binarySubstCombo.setToolTipText("<html>Select the type of binary substitution model.</html>");
PanelUtils.setupComponent(useAmbiguitiesTreeLikelihoodCheck);
useAmbiguitiesTreeLikelihoodCheck.addItemListener(
new ItemListener() {
public void itemStateChanged(ItemEvent ev) {
model.setUseAmbiguitiesTreeLikelihood(useAmbiguitiesTreeLikelihoodCheck.isSelected());
}
});
useAmbiguitiesTreeLikelihoodCheck.setToolTipText(
"<html>Detemine useAmbiguities in < treeLikelihood > .</html>");
PanelUtils.setupComponent(frequencyCombo);
frequencyCombo.addItemListener(
new ItemListener() {
public void itemStateChanged(ItemEvent ev) {
model.setFrequencyPolicy((FrequencyPolicyType) frequencyCombo.getSelectedItem());
}
});
frequencyCombo.setToolTipText(
"<html>Select the policy for determining the base frequencies.</html>");
PanelUtils.setupComponent(heteroCombo);
heteroCombo.setToolTipText(
"<html>Select the type of site-specific rate<br>heterogeneity model.</html>");
heteroCombo.addItemListener(
new ItemListener() {
public void itemStateChanged(ItemEvent ev) {
boolean gammaHetero =
heteroCombo.getSelectedIndex() == 1 || heteroCombo.getSelectedIndex() == 3;
model.setGammaHetero(gammaHetero);
model.setInvarHetero(
heteroCombo.getSelectedIndex() == 2 || heteroCombo.getSelectedIndex() == 3);
if (gammaHetero) {
gammaCatLabel.setEnabled(true);
gammaCatCombo.setEnabled(true);
} else {
gammaCatLabel.setEnabled(false);
gammaCatCombo.setEnabled(false);
}
if (codingCombo.getSelectedIndex() != 0) {
heteroUnlinkCheck.setEnabled(heteroCombo.getSelectedIndex() != 0);
heteroUnlinkCheck.setSelected(heteroCombo.getSelectedIndex() != 0);
}
}
});
PanelUtils.setupComponent(gammaCatCombo);
gammaCatCombo.setToolTipText(
"<html>Select the number of categories to use for<br>the discrete gamma rate heterogeneity model.</html>");
gammaCatCombo.addItemListener(
new ItemListener() {
public void itemStateChanged(ItemEvent ev) {
model.setGammaCategories(gammaCatCombo.getSelectedIndex() + 4);
}
});
setYang96Button = new JButton("Use Yang96 model");
setYang96Button.addActionListener(
new ActionListener() {
public void actionPerformed(ActionEvent ev) {
setYang96Model();
}
});
PanelUtils.setupComponent(setYang96Button);
setYang96Button.setToolTipText(
"<html>Sets a 3 codon-position model with independent GTR and Gamma as described in<br>"
+ "Yang (1996) <i>J Mol Evol</i> <b>42</b>: 587–596. This model is named 3' in this paper.</html>");
setSRD06Button = new JButton("Use SRD06 model");
setSRD06Button.addActionListener(
new ActionListener() {
public void actionPerformed(ActionEvent ev) {
setSRD06Model();
}
});
PanelUtils.setupComponent(setSRD06Button);
setSRD06Button.setToolTipText(
"<html>Sets the SRD06 model as described in<br>"
+ "Shapiro, Rambaut & Drummond (2006) <i>MBE</i> <b>23</b>: 7-9.</html>");
citationText = new JTextArea(1, 40);
citationText.setLineWrap(true);
citationText.setWrapStyleWord(true);
citationText.setEditable(false);
citationText.setFont(this.getFont());
citationText.setOpaque(false);
AminoAcidModelType type = (AminoAcidModelType) aaSubstCombo.getSelectedItem();
citationText.setText(type.getCitation().toString());
dolloCheck.addActionListener(
new ActionListener() {
public void actionPerformed(ActionEvent actionEvent) {
if (dolloCheck.isSelected()) {
binarySubstCombo.setSelectedIndex(0);
binarySubstCombo.setEnabled(false);
useAmbiguitiesTreeLikelihoodCheck.setSelected(true);
useAmbiguitiesTreeLikelihoodCheck.setEnabled(false);
frequencyCombo.setEnabled(false);
frequencyCombo.setSelectedItem(FrequencyPolicyType.EMPIRICAL);
heteroCombo.setSelectedIndex(0);
heteroCombo.setEnabled(false);
model.setBinarySubstitutionModel(BinaryModelType.BIN_DOLLO);
model.setDolloModel(true);
DolloComponentOptions comp =
(DolloComponentOptions)
model.getOptions().getComponentOptions(DolloComponentOptions.class);
comp.createParameters(model.getOptions());
comp.setActive(true);
} else {
binarySubstCombo.setEnabled(true);
useAmbiguitiesTreeLikelihoodCheck.setEnabled(true);
frequencyCombo.setEnabled(true);
heteroCombo.setEnabled(true);
model.setBinarySubstitutionModel(
(BinaryModelType) binarySubstCombo.getSelectedItem());
model.setDolloModel(false);
}
}
});
PanelUtils.setupComponent(dolloCheck);
// dolloCheck.addChangeListener(new ChangeListener() {
// public void stateChanged(ChangeEvent e) {
// model.setDolloModel(true);
// }
// });
dolloCheck.setEnabled(true);
dolloCheck.setToolTipText(
"<html>Activates a Stochastic Dollo model as described in<br>"
+ "Alekseyenko, Lee & Suchard (2008) <i>Syst Biol</i> <b>57</b>: 772-784.</html>");
PanelUtils.setupComponent(discreteTraitSiteModelCombo);
discreteTraitSiteModelCombo.addItemListener(
new ItemListener() {
public void itemStateChanged(ItemEvent ev) {
model.setDiscreteSubstType(
(DiscreteSubstModelType) discreteTraitSiteModelCombo.getSelectedItem());
}
});
PanelUtils.setupComponent(continuousTraitSiteModelCombo);
continuousTraitSiteModelCombo.setToolTipText(
"<html>Select the model of continuous random walk, either homogenous<br>"
+ "or relaxed random walk (RRW) with a choice of distributions.</html>");
continuousTraitSiteModelCombo.addItemListener(
new ItemListener() {
public void itemStateChanged(ItemEvent ev) {
model.setContinuousSubstModelType(
(ContinuousSubstModelType) continuousTraitSiteModelCombo.getSelectedItem());
}
});
PanelUtils.setupComponent(latLongCheck);
latLongCheck.setToolTipText(
"<html>Specify whether this is a geographical trait representing <br>"
+ "latitude and longitude. Provides appropriate statistics to log file.</html>");
latLongCheck.addItemListener(
new ItemListener() {
public void itemStateChanged(ItemEvent ev) {
model.setIsLatitudeLongitude(latLongCheck.isSelected());
}
});
latLongCheck.setEnabled(false);
PanelUtils.setupComponent(useLambdaCheck);
useLambdaCheck.addItemListener(
new ItemListener() {
public void itemStateChanged(ItemEvent ev) {
ContinuousComponentOptions component =
(ContinuousComponentOptions)
model.getOptions().getComponentOptions(ContinuousComponentOptions.class);
component.setUseLambda(model, useLambdaCheck.isSelected());
}
});
useLambdaCheck.setToolTipText(
"<html>Estimate degree of phylogenetic correlation in continuous traits using <br>"
+ "a tree transform. Inspired by Pagel (1999), described in Lemey et al (2013) <i>in prep</i></html>");
PanelUtils.setupComponent(activateBSSVS);
activateBSSVS.addItemListener(
new ItemListener() {
public void itemStateChanged(ItemEvent ev) {
model.setActivateBSSVS(activateBSSVS.isSelected());
}
});
activateBSSVS.setToolTipText(
"<html>Activates Bayesian stochastic search variable selection on the rates as described in<br>"
+ "Lemey, Rambaut, Drummond & Suchard (2009) <i>PLoS Computational Biology</i> <b>5</b>: e1000520</html>");
// ============ micro-sat ================
microsatName.setColumns(30);
microsatName.addKeyListener(
new java.awt.event.KeyListener() {
public void keyTyped(KeyEvent e) {}
public void keyPressed(KeyEvent e) {}
public void keyReleased(KeyEvent e) {
model.getMicrosatellite().setName(microsatName.getText());
}
});
microsatMax.setColumns(10);
microsatMax.addKeyListener(
new java.awt.event.KeyListener() {
public void keyTyped(KeyEvent e) {}
public void keyPressed(KeyEvent e) {}
public void keyReleased(KeyEvent e) {
model.getMicrosatellite().setMax(Integer.parseInt(microsatMax.getText()));
}
});
microsatMin.setColumns(10);
microsatMin.addKeyListener(
new java.awt.event.KeyListener() {
public void keyTyped(KeyEvent e) {}
public void keyPressed(KeyEvent e) {}
public void keyReleased(KeyEvent e) {
model.getMicrosatellite().setMin(Integer.parseInt(microsatMin.getText()));
}
});
PanelUtils.setupComponent(shareMicroSatCheck);
shareMicroSatCheck.addActionListener(
new ActionListener() {
public void actionPerformed(ActionEvent e) {
model.getOptions().shareMicroSat = shareMicroSatCheck.isSelected();
if (shareMicroSatCheck.isSelected()) {
model.getOptions().shareMicroSat();
} else {
model.getOptions().unshareMicroSat();
}
setOptions();
}
});
PanelUtils.setupComponent(rateProportionCombo);
rateProportionCombo.addItemListener(
new ItemListener() {
public void itemStateChanged(ItemEvent ev) {
model.setRatePorportion(
(MicroSatModelType.RateProportionality) rateProportionCombo.getSelectedItem());
}
});
// rateProportionCombo.setToolTipText("<html>Select the type of microsatellite substitution
// model.</html>");
PanelUtils.setupComponent(mutationBiasCombo);
mutationBiasCombo.addItemListener(
new ItemListener() {
public void itemStateChanged(ItemEvent ev) {
model.setMutationBias(
(MicroSatModelType.MutationalBias) mutationBiasCombo.getSelectedItem());
}
});
PanelUtils.setupComponent(phaseCombo);
phaseCombo.addItemListener(
new ItemListener() {
public void itemStateChanged(ItemEvent ev) {
model.setPhase((MicroSatModelType.Phase) phaseCombo.getSelectedItem());
}
});
setupPanel();
setOpaque(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");
}
public void setSeed(long seed) {
seedText.setValue(seed);
}
public long getSeed() {
return seedText.getLongValue();
}