public void linkModels() {
int[] selRows = dataTable.getSelectedRows();
List<AbstractPartitionData> selectedPartitionData = new ArrayList<AbstractPartitionData>();
DataType dateType = null;
for (int row : selRows) {
AbstractPartitionData partition = options.dataPartitions.get(row);
if (dateType == null) {
dateType = partition.getDataType();
} else {
if (partition.getDataType() != dateType) {
JOptionPane.showMessageDialog(
this,
"Can only link the models for data partitions \n"
+ "of the same data type (e.g., nucleotides)",
"Unable to link models",
JOptionPane.ERROR_MESSAGE);
return;
}
}
if (!selectedPartitionData.contains(partition)) selectedPartitionData.add(partition);
}
Object[] modelArray = options.getPartitionSubstitutionModels(selectedPartitionData).toArray();
if (selectModelDialog == null) {
selectModelDialog = new SelectModelDialog(frame);
}
int result = selectModelDialog.showDialog(modelArray);
if (result != JOptionPane.CANCEL_OPTION) {
PartitionSubstitutionModel model = selectModelDialog.getModel();
if (selectModelDialog.getMakeCopy()) {
model.setName(selectModelDialog.getName());
}
for (AbstractPartitionData partition : selectedPartitionData) {
partition.setPartitionSubstitutionModel(model);
}
}
if (options.getPartitionSubstitutionModels(Microsatellite.INSTANCE).size() <= 1) {
options.shareMicroSat = true;
}
modelsChanged();
fireDataChanged();
repaint();
}
public void unlinkModels() {
int[] selRows = dataTable.getSelectedRows();
for (int row : selRows) {
PartitionData partition = options.dataPartitions.get(row);
PartitionSubstitutionModel model = partition.getPartitionSubstitutionModel();
if (!model.getName().equals(partition.getName())) {
PartitionSubstitutionModel newModel = new PartitionSubstitutionModel(options, partition);
partition.setPartitionSubstitutionModel(newModel);
}
}
modelsChanged();
fireDataChanged();
repaint();
}
/** 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());
}
/**
* write log to file
*
* @param writer XMLWriter
* @param treePriorGenerator TreePriorGenerator
* @param branchRatesModelGenerator BranchRatesModelGenerator
* @param substitutionModelGenerator SubstitutionModelGenerator
* @param treeLikelihoodGenerator TreeLikelihoodGenerator
* @param generalTraitGenerator
*/
public void writeLogToFile(
XMLWriter writer,
TreePriorGenerator treePriorGenerator,
BranchRatesModelGenerator branchRatesModelGenerator,
SubstitutionModelGenerator substitutionModelGenerator,
TreeLikelihoodGenerator treeLikelihoodGenerator,
GeneralTraitGenerator generalTraitGenerator) {
writer.writeComment("write log to file");
if (options.logFileName == null) {
options.logFileName = options.fileNameStem + ".log";
}
writer.writeOpenTag(
LoggerParser.LOG,
new Attribute[] {
new Attribute.Default<String>(XMLParser.ID, "fileLog"),
new Attribute.Default<String>(LoggerParser.LOG_EVERY, options.logEvery + ""),
new Attribute.Default<String>(LoggerParser.FILE_NAME, options.logFileName),
new Attribute.Default<Boolean>(
LoggerParser.ALLOW_OVERWRITE_LOG, options.allowOverwriteLog)
});
if (options.hasData()) {
writer.writeIDref(CompoundLikelihoodParser.POSTERIOR, "posterior");
}
writer.writeIDref(CompoundLikelihoodParser.PRIOR, "prior");
if (options.hasData()) {
writer.writeIDref(CompoundLikelihoodParser.LIKELIHOOD, "likelihood");
}
if (options.useStarBEAST) { // species
// coalescent prior
writer.writeIDref(
MultiSpeciesCoalescentParser.SPECIES_COALESCENT,
TraitData.TRAIT_SPECIES + "." + COALESCENT);
// prior on population sizes
// if (options.speciesTreePrior == TreePriorType.SPECIES_YULE) {
writer.writeIDref(MixedDistributionLikelihoodParser.DISTRIBUTION_LIKELIHOOD, SPOPS);
// } else {
// writer.writeIDref(SpeciesTreeBMPrior.STPRIOR, STP);
// }
// prior on species tree
writer.writeIDref(SpeciationLikelihoodParser.SPECIATION_LIKELIHOOD, SPECIATION_LIKE);
writer.writeIDref(
ParameterParser.PARAMETER,
TraitData.TRAIT_SPECIES + "." + options.starBEASTOptions.POP_MEAN);
writer.writeIDref(
ParameterParser.PARAMETER, SpeciesTreeModelParser.SPECIES_TREE + "." + SPLIT_POPS);
if (options.getPartitionTreePriors().get(0).getNodeHeightPrior()
== TreePriorType.SPECIES_BIRTH_DEATH) {
writer.writeIDref(
ParameterParser.PARAMETER,
TraitData.TRAIT_SPECIES + "." + BirthDeathModelParser.MEAN_GROWTH_RATE_PARAM_NAME);
writer.writeIDref(
ParameterParser.PARAMETER,
TraitData.TRAIT_SPECIES + "." + BirthDeathModelParser.RELATIVE_DEATH_RATE_PARAM_NAME);
} else if (options.getPartitionTreePriors().get(0).getNodeHeightPrior()
== TreePriorType.SPECIES_YULE) {
writer.writeIDref(
ParameterParser.PARAMETER,
TraitData.TRAIT_SPECIES
+ "."
+ YuleModelParser.YULE
+ "."
+ YuleModelParser.BIRTH_RATE);
} else {
throw new IllegalArgumentException(
"Get wrong species tree prior using *BEAST : "
+ options.getPartitionTreePriors().get(0).getNodeHeightPrior().toString());
}
// Species Tree: tmrcaStatistic
writer.writeIDref(
TMRCAStatisticParser.TMRCA_STATISTIC,
SpeciesTreeModelParser.SPECIES_TREE + "." + TreeModelParser.ROOT_HEIGHT);
}
for (PartitionTreeModel model : options.getPartitionTreeModels()) {
writer.writeIDref(
ParameterParser.PARAMETER,
model.getPrefix() + TreeModel.TREE_MODEL + "." + TreeModelParser.ROOT_HEIGHT);
}
for (Taxa taxa : options.taxonSets) {
// make tmrca(tree.name) eay to read in log for Tracer
writer.writeIDref(
TMRCAStatisticParser.TMRCA_STATISTIC,
"tmrca(" + taxa.getTreeModel().getPrefix() + taxa.getId() + ")");
}
// if ( options.shareSameTreePrior ) { // Share Same Tree Prior
// treePriorGenerator.setModelPrefix("");
// treePriorGenerator.writeParameterLog(options.activedSameTreePrior, writer);
// } else { // no species
for (PartitionTreePrior prior : options.getPartitionTreePriors()) {
// treePriorGenerator.setModelPrefix(prior.getPrefix()); // priorName.treeModel
treePriorGenerator.writeParameterLog(prior, writer);
}
// }
for (PartitionSubstitutionModel model : options.getPartitionSubstitutionModels()) {
substitutionModelGenerator.writeLog(writer, model);
if (model.hasCodon()) {
writer.writeIDref(CompoundParameterParser.COMPOUND_PARAMETER, model.getPrefix() + "allMus");
}
}
if (options.clockModelOptions.getRateOptionClockModel() == FixRateType.FIX_MEAN) {
writer.writeIDref(ParameterParser.PARAMETER, "allClockRates");
for (PartitionClockModel model : options.getPartitionClockModels()) {
if (model.getClockType() == ClockType.UNCORRELATED_LOGNORMAL)
writer.writeIDref(ParameterParser.PARAMETER, model.getPrefix() + ClockType.UCLD_STDEV);
}
} else {
for (PartitionClockModel model : options.getPartitionClockModels()) {
branchRatesModelGenerator.writeLog(model, writer);
}
}
for (PartitionClockModel model : options.getPartitionClockModels()) {
branchRatesModelGenerator.writeLogStatistic(model, writer);
}
generateInsertionPoint(ComponentGenerator.InsertionPoint.IN_FILE_LOG_PARAMETERS, writer);
if (options.hasData()) {
treeLikelihoodGenerator.writeTreeLikelihoodReferences(writer);
}
generateInsertionPoint(ComponentGenerator.InsertionPoint.IN_FILE_LOG_LIKELIHOODS, writer);
// coalescentLikelihood
for (PartitionTreeModel model : options.getPartitionTreeModels()) {
PartitionTreePrior prior = model.getPartitionTreePrior();
treePriorGenerator.writePriorLikelihoodReferenceLog(prior, model, writer);
writer.writeText("");
}
for (PartitionTreePrior prior : options.getPartitionTreePriors()) {
if (prior.getNodeHeightPrior() == TreePriorType.EXTENDED_SKYLINE)
writer.writeIDref(
CoalescentLikelihoodParser.COALESCENT_LIKELIHOOD,
prior.getPrefix() + COALESCENT); // only 1 coalescent
}
if (options.hasDiscreteIntegerTraitsExcludeSpecies()) {
generalTraitGenerator.writeAncestralTreeLikelihoodReferences(writer);
}
writer.writeCloseTag(LoggerParser.LOG);
generateInsertionPoint(ComponentGenerator.InsertionPoint.AFTER_FILE_LOG, writer);
}
