/** Lays out the appropriate components in the panel for this partition model. */
private void setupPanel() {
switch (model.getDataType().getType()) {
case DataType.NUCLEOTIDES:
addComponentWithLabel("Substitution Model:", nucSubstCombo);
addComponentWithLabel("Base frequencies:", frequencyCombo);
addComponentWithLabel("Site Heterogeneity Model:", heteroCombo);
heteroCombo.setSelectedIndex(0);
gammaCatLabel = addComponentWithLabel("Number of Gamma Categories:", gammaCatCombo);
gammaCatCombo.setEnabled(false);
addSeparator();
addComponentWithLabel("Partition into codon positions:", codingCombo);
JPanel panel2 = new JPanel();
panel2.setOpaque(false);
panel2.setLayout(new BoxLayout(panel2, BoxLayout.PAGE_AXIS));
panel2.setBorder(BorderFactory.createTitledBorder("Link/Unlink parameters:"));
panel2.add(substUnlinkCheck);
panel2.add(heteroUnlinkCheck);
panel2.add(freqsUnlinkCheck);
addComponent(panel2);
addComponent(setYang96Button);
addComponent(setSRD06Button);
break;
case DataType.AMINO_ACIDS:
addComponentWithLabel("Substitution Model:", aaSubstCombo);
addComponentWithLabel("Citation:", citationText);
addComponentWithLabel("Site Heterogeneity Model:", heteroCombo);
heteroCombo.setSelectedIndex(0);
gammaCatLabel = addComponentWithLabel("Number of Gamma Categories:", gammaCatCombo);
gammaCatCombo.setEnabled(false);
break;
case DataType.TWO_STATES:
case DataType.COVARION:
addComponentWithLabel("Substitution Model:", binarySubstCombo);
addComponentWithLabel("Base frequencies:", frequencyCombo);
addComponentWithLabel("Site Heterogeneity Model:", heteroCombo);
heteroCombo.setSelectedIndex(0);
gammaCatLabel = addComponentWithLabel("Number of Gamma Categories:", gammaCatCombo);
gammaCatCombo.setEnabled(false);
addSeparator();
addComponentWithLabel("", useAmbiguitiesTreeLikelihoodCheck);
// Easy XML specification is currently only available for binary models
if (ENABLE_STOCHASTIC_DOLLO) {
addSeparator();
addComponent(dolloCheck);
}
break;
case DataType.GENERAL:
addComponentWithLabel("Discrete Trait Substitution Model:", discreteTraitSiteModelCombo);
addComponent(activateBSSVS);
break;
case DataType.CONTINUOUS:
addComponentWithLabel("Continuous Trait Model:", continuousTraitSiteModelCombo);
addComponent(latLongCheck);
addSeparator();
addComponent(useLambdaCheck);
break;
case DataType.MICRO_SAT:
addComponentWithLabel("Microsatellite Name:", microsatName);
addComponentWithLabel("Max of Length:", microsatMax);
addComponentWithLabel("Min of Length:", microsatMin);
addComponent(shareMicroSatCheck);
addSeparator();
addComponentWithLabel("Rate Proportionality:", rateProportionCombo);
addComponentWithLabel("Mutational Bias:", mutationBiasCombo);
addComponentWithLabel("Phase:", phaseCombo);
break;
default:
throw new IllegalArgumentException("Unknown data type");
}
setOptions();
}
/**
* 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());
}