public void setValueAt(Object aValue, int row, int col) {
// PartitionData partition = options.getPartitionDataNoSpecies().get(row);
PartitionData partition = options.getNonTraitsDataList().get(row);
switch (col) {
case 0:
String name = ((String) aValue).trim();
if (name.length() > 0) {
partition.setName(name);
}
break;
case 5:
// partition.setPloidyType((PloidyType) aValue);
// break;
// case 6:
partition.setPartitionSubstitutionModel((PartitionSubstitutionModel) aValue);
break;
case 6:
partition.setPartitionClockModel((PartitionClockModel) aValue);
break;
case 7:
partition.setPartitionTreeModel((PartitionTreeModel) aValue);
break;
}
fireDataChanged();
}
public void linkClocks() { // keep previous PartitionTreePrior for reuse
int[] selRows = dataTable.getSelectedRows();
List<PartitionData> selectedPartitionData = new ArrayList<PartitionData>();
for (int row : selRows) {
PartitionData partition = options.dataPartitions.get(row);
if (!selectedPartitionData.contains(partition)) selectedPartitionData.add(partition);
}
Object[] modelArray = options.getPartitionClockModels(selectedPartitionData).toArray();
if (selectClockDialog == null) {
selectClockDialog = new SelectClockDialog(frame);
}
int result = selectClockDialog.showDialog(modelArray);
if (result != JOptionPane.CANCEL_OPTION) {
PartitionClockModel model = selectClockDialog.getModel();
if (selectClockDialog.getMakeCopy()) {
model.setName(selectClockDialog.getName());
}
for (PartitionData partition : selectedPartitionData) {
partition.setPartitionClockModel(model);
}
}
modelsChanged();
fireDataChanged();
repaint();
}
public void unlinkTrees() { // reuse previous PartitionTreePrior
int[] selRows = dataTable.getSelectedRows();
for (int row : selRows) {
PartitionData partition = options.dataPartitions.get(row);
PartitionTreeModel model = partition.getPartitionTreeModel();
if (!model.getName().equals(partition.getName())
&& partition.getTraitType() == null) { // not a trait
PartitionTreeModel newTree = new PartitionTreeModel(options, partition);
// this prevents partition not broken, and used for unsharing tree prior only,
// because sharing uses shareSameTreePrior, unsharing uses getPartitionTreePrior
// newTree.setPartitionTreePrior(newPrior); // important
partition.setPartitionTreeModel(newTree);
}
}
options.linkTreePriors(frame.getCurrentPartitionTreePrior());
modelsChanged();
fireDataChanged();
options.taxonSets.clear();
options.taxonSetsMono.clear();
repaint();
}
public Object getValueAt(int row, int col) {
// PartitionData partition = options.getPartitionDataNoSpecies().get(row);
PartitionData partition = options.getNonTraitsDataList().get(row);
switch (col) {
case 0:
return partition.getName();
case 1:
return partition.getFileName();
case 2:
return "" + partition.getTaxaCount();
case 3:
return "" + partition.getSiteCount(); // sequence length
case 4:
return partition.getDataType();
case 5:
// return partition.getPloidyType();
// case 6:
return partition.getPartitionSubstitutionModel().getName();
case 6:
return partition.getPartitionClockModel().getName();
case 7:
return partition.getPartitionTreeModel().getName();
default:
throw new IllegalArgumentException("unknown column, " + col);
}
}
public void linkTrees() { // keep previous PartitionTreePrior for reuse
int[] selRows = dataTable.getSelectedRows();
List<PartitionData> selectedPartitionData = new ArrayList<PartitionData>();
for (int row : selRows) {
PartitionData partition = options.dataPartitions.get(row);
if (!selectedPartitionData.contains(partition)) selectedPartitionData.add(partition);
}
if (options.allowDifferentTaxa) { // BEAST cannot handle multi <taxa> ref for 1 tree
if (selectedPartitionData.size() > 1) {
if (!options.validateDiffTaxa(selectedPartitionData)) {
JOptionPane.showMessageDialog(
this,
"To accommodate different taxa for each partition trees cannot be linked.",
"Illegal Configuration",
JOptionPane.ERROR_MESSAGE);
return;
}
}
}
Object[] treeArray = options.getPartitionTreeModels(selectedPartitionData).toArray();
if (selectTreeDialog == null) {
selectTreeDialog = new SelectTreeDialog(frame);
}
int result = selectTreeDialog.showDialog(treeArray);
if (result != JOptionPane.CANCEL_OPTION) {
PartitionTreeModel model = selectTreeDialog.getTree();
if (selectTreeDialog.getMakeCopy()) {
model.setName(selectTreeDialog.getName());
}
PartitionTreePrior prior = model.getPartitionTreePrior();
options.linkTreePriors(prior);
for (PartitionData partition : selectedPartitionData) {
partition.setPartitionTreeModel(model);
}
}
modelsChanged();
fireDataChanged();
options.taxonSets.clear();
options.taxonSetsMono.clear();
repaint();
}
public void unlinkClocks() { // reuse previous PartitionTreePrior
int[] selRows = dataTable.getSelectedRows();
for (int row : selRows) {
PartitionData partition = options.dataPartitions.get(row);
PartitionClockModel model = partition.getPartitionClockModel();
if (!model.getName().equals(partition.getName())) {
PartitionClockModel newModel = new PartitionClockModel(options, partition);
partition.setPartitionClockModel(newModel);
}
}
modelsChanged();
fireDataChanged();
repaint();
}
public void linkModels() {
int[] selRows = dataTable.getSelectedRows();
List<PartitionData> selectedPartitionData = new ArrayList<PartitionData>();
DataType dateType = null;
for (int row : selRows) {
PartitionData partition = options.dataPartitions.get(row);
if (dateType == null) {
dateType = partition.getPartitionSubstitutionModel().getDataType();
} else {
if (partition.getPartitionSubstitutionModel().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);
}
}
if (!selectedPartitionData.contains(partition)) selectedPartitionData.add(partition);
}
Object[] modelArray =
options.getPartitionSubstitutionModels(dateType, 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 (PartitionData partition : selectedPartitionData) {
partition.setPartitionSubstitutionModel(model);
}
}
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();
}
private void showAlignment() {
int[] selRows = dataTable.getSelectedRows();
for (int row : selRows) {
JFrame frame = new JFrame();
frame.setSize(800, 600);
PartitionData partition = options.dataPartitions.get(row);
Alignment alignment = partition.getAlignment();
// alignment == null if partition is trait
// http://code.google.com/p/beast-mcmc/issues/detail?id=343
if (alignment == null) {
JOptionPane.showMessageDialog(
this,
"Cannot display traits currently. Use the traits panel to view and edit these.",
"Illegal Argument Exception",
JOptionPane.ERROR_MESSAGE);
return;
}
AlignmentViewer viewer = new AlignmentViewer();
if (alignment.getDataType().getType() == DataType.NUCLEOTIDES) {
viewer.setCellDecorator(new StateCellDecorator(new NucleotideDecorator(), false));
} else if (alignment.getDataType().getType() == DataType.AMINO_ACIDS) {
viewer.setCellDecorator(new StateCellDecorator(new AminoAcidDecorator(), false));
} else {
// no colouring
}
viewer.setAlignmentBuffer(new BeautiAlignmentBuffer(alignment));
JPanel panel = new JPanel(new BorderLayout());
panel.setOpaque(false);
panel.add(viewer, BorderLayout.CENTER);
JPanel infoPanel = new JPanel(new BorderLayout());
infoPanel.setOpaque(false);
panel.add(infoPanel, BorderLayout.SOUTH);
frame.setContentPane(panel);
frame.setVisible(true);
}
}
/**
* write tree log to file
*
* @param writer XMLWriter
*/
public void writeTreeLogToFile(XMLWriter writer) {
writer.writeComment("write tree log to file");
if (options.useStarBEAST) { // species
// species tree log
writer.writeOpenTag(
TreeLoggerParser.LOG_TREE,
new Attribute[] {
new Attribute.Default<String>(
XMLParser.ID, TraitData.TRAIT_SPECIES + "." + TREE_FILE_LOG), // speciesTreeFileLog
new Attribute.Default<String>(TreeLoggerParser.LOG_EVERY, options.logEvery + ""),
new Attribute.Default<String>(TreeLoggerParser.NEXUS_FORMAT, "true"),
new Attribute.Default<String>(
TreeLoggerParser.FILE_NAME,
options.fileNameStem + "." + options.starBEASTOptions.SPECIES_TREE_FILE_NAME),
new Attribute.Default<String>(TreeLoggerParser.SORT_TRANSLATION_TABLE, "true")
});
writer.writeIDref(SpeciesTreeModelParser.SPECIES_TREE, SP_TREE);
if (options.hasData()) {
// we have data...
writer.writeIDref("posterior", "posterior");
}
writer.writeCloseTag(TreeLoggerParser.LOG_TREE);
}
// gene tree log
// TODO make code consistent to MCMCPanel
for (PartitionTreeModel tree : options.getPartitionTreeModels()) {
String treeFileName;
if (options.substTreeLog) {
treeFileName =
options.fileNameStem
+ "."
+ tree.getPrefix()
+ "(time)."
+ STARBEASTOptions.TREE_FILE_NAME;
} else {
treeFileName =
options.fileNameStem
+ "."
+ tree.getPrefix()
+ STARBEASTOptions.TREE_FILE_NAME; // stem.partitionName.tree
}
if (options.treeFileName.get(0).endsWith(".txt")) {
treeFileName += ".txt";
}
List<Attribute> attributes = new ArrayList<Attribute>();
attributes.add(
new Attribute.Default<String>(
XMLParser.ID, tree.getPrefix() + TREE_FILE_LOG)); // partionName.treeFileLog
attributes.add(
new Attribute.Default<String>(TreeLoggerParser.LOG_EVERY, options.logEvery + ""));
attributes.add(new Attribute.Default<String>(TreeLoggerParser.NEXUS_FORMAT, "true"));
attributes.add(new Attribute.Default<String>(TreeLoggerParser.FILE_NAME, treeFileName));
attributes.add(
new Attribute.Default<String>(TreeLoggerParser.SORT_TRANSLATION_TABLE, "true"));
// if (options.clockModelOptions.getRateOptionClockModel() == FixRateType.RElATIVE_TO &&
// tree.containsUncorrelatedRelaxClock()) { //TODO: Sibon's discretized branch length stuff
// double aveFixedRate =
// options.clockModelOptions.getSelectedRate(options.getPartitionClockModels());
// attributes.add(new Attribute.Default<String>(TreeLoggerParser.NORMALISE_MEAN_RATE_TO,
// Double.toString(aveFixedRate)));
// }
// generate <logTree>
writer.writeOpenTag(TreeLoggerParser.LOG_TREE, attributes);
// writer.writeOpenTag(TreeLoggerParser.LOG_TREE,
// new Attribute[]{
// new Attribute.Default<String>(XMLParser.ID, tree.getPrefix() +
// TREE_FILE_LOG), // partionName.treeFileLog
// new Attribute.Default<String>(TreeLoggerParser.LOG_EVERY,
// options.logEvery + ""),
// new Attribute.Default<String>(TreeLoggerParser.NEXUS_FORMAT,
// "true"),
// new Attribute.Default<String>(TreeLoggerParser.FILE_NAME,
// treeFileName),
// new
// Attribute.Default<String>(TreeLoggerParser.SORT_TRANSLATION_TABLE, "true")
// });
writer.writeIDref(TreeModel.TREE_MODEL, tree.getPrefix() + TreeModel.TREE_MODEL);
for (PartitionClockModel model :
options.getPartitionClockModels(options.getAllPartitionData(tree))) {
if (options.getAllPartitionData(model).get(0).getTraitType() == null) {
switch (model.getClockType()) {
case STRICT_CLOCK:
writer.writeIDref(
StrictClockBranchRatesParser.STRICT_CLOCK_BRANCH_RATES,
model.getPrefix() + BranchRateModel.BRANCH_RATES);
break;
case UNCORRELATED_EXPONENTIAL:
case UNCORRELATED_LOGNORMAL:
writer.writeIDref(
DiscretizedBranchRatesParser.DISCRETIZED_BRANCH_RATES,
options.noDuplicatedPrefix(model.getPrefix(), tree.getPrefix())
+ BranchRateModel.BRANCH_RATES);
break;
case RANDOM_LOCAL_CLOCK:
writer.writeIDref(
RandomLocalClockModelParser.LOCAL_BRANCH_RATES,
model.getPrefix() + BranchRateModel.BRANCH_RATES);
break;
case AUTOCORRELATED_LOGNORMAL:
writer.writeIDref(
ACLikelihoodParser.AC_LIKELIHOOD,
options.noDuplicatedPrefix(model.getPrefix(), tree.getPrefix())
+ BranchRateModel.BRANCH_RATES);
break;
default:
throw new IllegalArgumentException("Unknown clock model");
}
}
}
if (options.hasData()) {
// we have data...
writer.writeIDref("posterior", "posterior");
}
if (options.hasDiscreteIntegerTraitsExcludeSpecies()) {
for (PartitionData partitionData :
options.getAllPartitionData(
tree)) { // Each TD except Species has one AncestralTreeLikelihood
if (partitionData.getTraitType() != null
&& (!partitionData.getName().equalsIgnoreCase(TraitData.TRAIT_SPECIES.toString())))
writer.writeIDref(
AncestralStateTreeLikelihoodParser.RECONSTRUCTING_TREE_LIKELIHOOD,
partitionData.getPrefix() + TreeLikelihoodParser.TREE_LIKELIHOOD);
}
}
writer.writeCloseTag(TreeLoggerParser.LOG_TREE);
} // end For loop
generateInsertionPoint(ComponentGenerator.InsertionPoint.IN_TREES_LOG, writer);
if (options.substTreeLog) {
if (options.useStarBEAST) { // species
// TODO: species sub tree
}
// gene tree
for (PartitionTreeModel tree : options.getPartitionTreeModels()) {
// write tree log to file
writer.writeOpenTag(
TreeLoggerParser.LOG_TREE,
new Attribute[] {
new Attribute.Default<String>(XMLParser.ID, tree.getPrefix() + SUB_TREE_FILE_LOG),
new Attribute.Default<String>(TreeLoggerParser.LOG_EVERY, options.logEvery + ""),
new Attribute.Default<String>(TreeLoggerParser.NEXUS_FORMAT, "true"),
new Attribute.Default<String>(
TreeLoggerParser.FILE_NAME,
options.fileNameStem
+ "."
+ tree.getPrefix()
+ "(subst)."
+ STARBEASTOptions.TREE_FILE_NAME),
new Attribute.Default<String>(
TreeLoggerParser.BRANCH_LENGTHS, TreeLoggerParser.SUBSTITUTIONS)
});
writer.writeIDref(TreeModel.TREE_MODEL, tree.getPrefix() + TreeModel.TREE_MODEL);
for (PartitionClockModel model :
options.getPartitionClockModels(options.getAllPartitionData(tree))) {
if (options.getAllPartitionData(model).get(0).getTraitType() == null) {
switch (model.getClockType()) {
case STRICT_CLOCK:
writer.writeIDref(
StrictClockBranchRatesParser.STRICT_CLOCK_BRANCH_RATES,
model.getPrefix() + BranchRateModel.BRANCH_RATES);
break;
case UNCORRELATED_EXPONENTIAL:
case UNCORRELATED_LOGNORMAL:
writer.writeIDref(
DiscretizedBranchRatesParser.DISCRETIZED_BRANCH_RATES,
options.noDuplicatedPrefix(model.getPrefix(), tree.getPrefix())
+ BranchRateModel.BRANCH_RATES);
break;
case RANDOM_LOCAL_CLOCK:
writer.writeIDref(
RandomLocalClockModelParser.LOCAL_BRANCH_RATES,
model.getPrefix() + BranchRateModel.BRANCH_RATES);
break;
case AUTOCORRELATED_LOGNORMAL:
writer.writeIDref(
ACLikelihoodParser.AC_LIKELIHOOD,
options.noDuplicatedPrefix(model.getPrefix(), tree.getPrefix())
+ BranchRateModel.BRANCH_RATES);
break;
default:
throw new IllegalArgumentException("Unknown clock model");
}
}
}
writer.writeCloseTag(TreeLoggerParser.LOG_TREE);
}
}
generateInsertionPoint(ComponentGenerator.InsertionPoint.AFTER_TREES_LOG, writer);
}