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);
}
/** Initializes and binds the components related to modeling codon positions. */
private void initCodonPartitionComponents() {
PanelUtils.setupComponent(substUnlinkCheck);
substUnlinkCheck.addItemListener(
new ItemListener() {
public void itemStateChanged(ItemEvent ev) {
model.setUnlinkedSubstitutionModel(substUnlinkCheck.isSelected());
}
});
substUnlinkCheck.setEnabled(false);
substUnlinkCheck.setToolTipText(
""
+ "<html>Gives each codon position partition different<br>"
+ "substitution model parameters.</html>");
PanelUtils.setupComponent(heteroUnlinkCheck);
heteroUnlinkCheck.addItemListener(
new ItemListener() {
public void itemStateChanged(ItemEvent ev) {
model.setUnlinkedHeterogeneityModel(heteroUnlinkCheck.isSelected());
}
});
heteroUnlinkCheck.setEnabled(heteroCombo.getSelectedIndex() != 0);
heteroUnlinkCheck.setToolTipText(
"<html>Gives each codon position partition different<br>rate heterogeneity model parameters.</html>");
PanelUtils.setupComponent(freqsUnlinkCheck);
freqsUnlinkCheck.addItemListener(
new ItemListener() {
public void itemStateChanged(ItemEvent ev) {
model.setUnlinkedFrequencyModel(freqsUnlinkCheck.isSelected());
}
});
freqsUnlinkCheck.setEnabled(false);
freqsUnlinkCheck.setToolTipText(
"<html>Gives each codon position partition different<br>nucleotide frequency parameters.</html>");
PanelUtils.setupComponent(codingCombo);
codingCombo.setToolTipText("<html>Select how to partition the codon positions.</html>");
codingCombo.addItemListener(
new ItemListener() {
public void itemStateChanged(ItemEvent ev) {
switch (codingCombo.getSelectedIndex()) {
case 0:
model.setCodonHeteroPattern(null);
break;
case 1:
model.setCodonHeteroPattern("112");
break;
default:
model.setCodonHeteroPattern("123");
break;
}
if (codingCombo.getSelectedIndex() != 0) {
// codon position partitioning
substUnlinkCheck.setEnabled(true);
heteroUnlinkCheck.setEnabled(heteroCombo.getSelectedIndex() != 3);
freqsUnlinkCheck.setEnabled(true);
substUnlinkCheck.setSelected(true);
heteroUnlinkCheck.setSelected(heteroCombo.getSelectedIndex() != 0);
freqsUnlinkCheck.setSelected(true);
} else {
substUnlinkCheck.setEnabled(false);
substUnlinkCheck.setSelected(false);
heteroUnlinkCheck.setEnabled(false);
heteroUnlinkCheck.setSelected(false);
freqsUnlinkCheck.setEnabled(false);
freqsUnlinkCheck.setSelected(false);
}
}
});
}
public DataPanel(
BeautiFrame parent,
Action importDataAction,
Action removeDataAction /*, Action importTraitsAction*/) {
this.frame = parent;
dataTableModel = new DataTableModel();
dataTable = new JTable(dataTableModel);
dataTable.getTableHeader().setReorderingAllowed(false);
dataTable
.getTableHeader()
.setDefaultRenderer(new HeaderRenderer(SwingConstants.LEFT, new Insets(0, 4, 0, 4)));
TableColumn col = dataTable.getColumnModel().getColumn(5);
ComboBoxRenderer comboBoxRenderer = new ComboBoxRenderer();
comboBoxRenderer.putClientProperty("JComboBox.isTableCellEditor", Boolean.TRUE);
col.setCellRenderer(comboBoxRenderer);
// col = dataTable.getColumnModel().getColumn(5);
// comboBoxRenderer = new ComboBoxRenderer();
// comboBoxRenderer.putClientProperty("JComboBox.isTableCellEditor", Boolean.TRUE);
// col.setCellRenderer(comboBoxRenderer);
col = dataTable.getColumnModel().getColumn(6);
comboBoxRenderer = new ComboBoxRenderer();
comboBoxRenderer.putClientProperty("JComboBox.isTableCellEditor", Boolean.TRUE);
col.setCellRenderer(comboBoxRenderer);
col = dataTable.getColumnModel().getColumn(7);
comboBoxRenderer = new ComboBoxRenderer();
comboBoxRenderer.putClientProperty("JComboBox.isTableCellEditor", Boolean.TRUE);
col.setCellRenderer(comboBoxRenderer);
TableEditorStopper.ensureEditingStopWhenTableLosesFocus(dataTable);
dataTable
.getSelectionModel()
.addListSelectionListener(
new ListSelectionListener() {
public void valueChanged(ListSelectionEvent evt) {
selectionChanged();
}
});
dataTable.addMouseListener(
new MouseAdapter() {
public void mouseClicked(MouseEvent e) {
if (e.getClickCount() == 2) {
showAlignment();
}
}
});
scrollPane =
new JScrollPane(
dataTable,
JScrollPane.VERTICAL_SCROLLBAR_ALWAYS,
JScrollPane.HORIZONTAL_SCROLLBAR_ALWAYS);
scrollPane.setOpaque(false);
JToolBar toolBar1 = new JToolBar();
toolBar1.setFloatable(false);
toolBar1.setOpaque(false);
toolBar1.setLayout(new BoxLayout(toolBar1, BoxLayout.X_AXIS));
JButton button = new JButton(unlinkModelsAction);
unlinkModelsAction.setEnabled(false);
PanelUtils.setupComponent(button);
toolBar1.add(button);
button = new JButton(linkModelsAction);
linkModelsAction.setEnabled(false);
PanelUtils.setupComponent(button);
toolBar1.add(button);
toolBar1.addSeparator();
button = new JButton(unlinkClocksAction);
unlinkClocksAction.setEnabled(false);
PanelUtils.setupComponent(button);
toolBar1.add(button);
button = new JButton(linkClocksAction);
linkClocksAction.setEnabled(false);
PanelUtils.setupComponent(button);
toolBar1.add(button);
toolBar1.addSeparator();
button = new JButton(unlinkTreesAction);
unlinkTreesAction.setEnabled(false);
PanelUtils.setupComponent(button);
toolBar1.add(button);
button = new JButton(linkTreesAction);
linkTreesAction.setEnabled(false);
PanelUtils.setupComponent(button);
toolBar1.add(button);
// too crowded on the toolbar - just double click to show
// button = new JButton(showAction);
// showAction.setEnabled(false);
// PanelUtils.setupComponent(button);
// toolBar1.add(button);
ActionPanel actionPanel1 = new ActionPanel(false);
actionPanel1.setAddAction(importDataAction);
actionPanel1.setRemoveAction(removeDataAction);
removeDataAction.setEnabled(false);
JPanel controlPanel1 = new JPanel(new FlowLayout(FlowLayout.LEFT));
controlPanel1.setOpaque(false);
controlPanel1.add(actionPanel1);
controlPanel1.add(new JLabel(" "));
PanelUtils.setupComponent(createImportTraitButton);
controlPanel1.add(createImportTraitButton);
// controlPanel1.add(new JLabel(" or "));
//
// button = new JButton(importTraitsAction);
// PanelUtils.setupComponent(button);
// controlPanel1.add(button);
JPanel panel1 = new JPanel(new BorderLayout());
panel1.setOpaque(false);
panel1.add(useStarBEASTCheck, BorderLayout.NORTH);
panel1.add(toolBar1, BorderLayout.SOUTH);
setOpaque(false);
setBorder(new BorderUIResource.EmptyBorderUIResource(new Insets(12, 12, 12, 12)));
setLayout(new BorderLayout(0, 0));
add(panel1, BorderLayout.NORTH);
add(scrollPane, BorderLayout.CENTER);
add(controlPanel1, BorderLayout.SOUTH);
useStarBEASTCheck.setEnabled(false);
useStarBEASTCheck.setToolTipText(STARBEASTOptions.CITATION);
useStarBEASTCheck.addActionListener(
new java.awt.event.ActionListener() {
public void actionPerformed(
ActionEvent e) { // wrong listener Issue 397: *BEAST in BEAUti is broken
frame.setupStarBEAST(useStarBEASTCheck.isSelected());
dataTableModel.fireTableDataChanged();
}
});
}