public void removeSelection() {
int[] selRows = dataTable.getSelectedRows();
Set<AbstractPartitionData> partitionsToRemove = new HashSet<AbstractPartitionData>();
for (int row : selRows) {
partitionsToRemove.add(options.dataPartitions.get(row));
}
boolean hasIdenticalTaxa =
options.hasIdenticalTaxa(); // need to check this before removing partitions
// TODO: would probably be a good idea to check if the user wants to remove the last partition
options.dataPartitions.removeAll(partitionsToRemove);
if (options.dataPartitions.size() == 0) {
// all data partitions removed so reset the taxa
options.reset();
useStarBEASTCheck.setSelected(false);
frame.setupStarBEAST(false);
frame.statusLabel.setText("");
frame.setAllOptions();
frame.getExportAction().setEnabled(false);
} else if (!hasIdenticalTaxa) {
options.updateTaxonList();
}
dataTableModel.fireTableDataChanged();
fireDataChanged();
}
public void removeSelection() {
int[] selRows = dataTable.getSelectedRows();
Set<PartitionData> partitionsToRemove = new HashSet<PartitionData>();
for (int row : selRows) {
partitionsToRemove.add(options.dataPartitions.get(row));
}
// TODO: would probably be a good idea to check if the user wants to remove the last partition
options.dataPartitions.removeAll(partitionsToRemove);
// if (options.allowDifferentTaxa && options.dataPartitions.size() < 2) {
// uncheckAllowDifferentTaxa();
// }
if (options.getNonTraitsDataList().size() == 0) {
// all data partitions removed so reset the taxa
options.reset();
useStarBEASTCheck.setSelected(false);
frame.statusLabel.setText("");
frame.setAllOptions();
frame.getExportAction().setEnabled(false);
}
dataTableModel.fireTableDataChanged();
fireDataChanged();
}
public void setOptions(BeautiOptions options) {
this.options = options;
modelsChanged();
useStarBEASTCheck.setEnabled(
options.getNonTraitsDataList().size() > 0); // single partition is allowed
createImportTraitButton.setEnabled(options.getNonTraitsDataList().size() > 0);
dataTableModel.fireTableDataChanged();
}
public void linkTrees() { // keep previous PartitionTreePrior for reuse
int[] selRows = dataTable.getSelectedRows();
List<AbstractPartitionData> selectedPartitionData = new ArrayList<AbstractPartitionData>();
for (int row : selRows) {
AbstractPartitionData partition = options.dataPartitions.get(row);
if (!selectedPartitionData.contains(partition)) selectedPartitionData.add(partition);
}
if (selectedPartitionData.size() > 1) {
if (!options.hasIdenticalTaxa(selectedPartitionData)) {
String errMsg = "To share a tree, partitions need to have identical taxa.";
if (selectedPartitionData.get(0).getDataType().getType() == DataType.MICRO_SAT)
errMsg += "\nThe data must be all diploid or all haploid when you want to link the tree.";
JOptionPane.showMessageDialog(
this, errMsg, "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 (AbstractPartitionData partition : selectedPartitionData) {
partition.setPartitionTreeModel(model);
}
for (Taxa taxa :
options.taxonSets) { // Issue 454: all the taxon sets are deleted when link/unlink tree
PartitionTreeModel prevModel = options.taxonSetsTreeModel.get(taxa);
if (prevModel != model) options.taxonSetsTreeModel.put(taxa, model);
}
}
modelsChanged();
fireDataChanged();
repaint();
}
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 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 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 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 boolean createFromTraits(List<TraitData> traits) {
int selRow = -1;
if (selectTraitDialog == null) {
selectTraitDialog = new SelectTraitDialog(frame);
}
if (traits == null || traits.size() == 0) {
int result = selectTraitDialog.showDialog(options.traits, null);
if (result != JOptionPane.CANCEL_OPTION) {
TraitData trait = selectTraitDialog.getTrait();
String name = trait.getName();
if (selectTraitDialog.getMakeCopy()) {
name = selectTraitDialog.getName();
}
selRow = options.createPartitionForTraits(name, trait);
} else {
return false;
}
} else {
if (traits.size() > 1) {
// a set of traits have been passed to the function
int result = selectTraitDialog.showDialog(null, null);
if (result != JOptionPane.CANCEL_OPTION) {
String name = selectTraitDialog.getName();
selRow = options.createPartitionForTraits(name, traits);
} else {
return false;
}
} else {
selRow = options.createPartitionForTraits(traits.get(0).getName(), traits);
}
}
modelsChanged();
dataTableModel.fireTableDataChanged();
if (selRow != -1) {
dataTable.getSelectionModel().setSelectionInterval(selRow, selRow);
}
fireDataChanged();
repaint();
return true;
}
private void modelsChanged() {
TableColumn col = dataTable.getColumnModel().getColumn(5);
col.setCellEditor(new ComboBoxCellEditor());
col = dataTable.getColumnModel().getColumn(6);
col.setCellEditor(new ComboBoxCellEditor());
col = dataTable.getColumnModel().getColumn(7);
col.setCellEditor(
new DefaultCellEditor(new JComboBox(options.getNonTraitPartitionTreeModels().toArray())));
}
private void fireDataChanged() {
// options.updateLinksBetweenPDPCMPSMPTMPTPP();
options.updatePartitionAllLinks();
if (!(options.clockModelOptions.getRateOptionClockModel() == FixRateType.TIP_CALIBRATED
|| options.clockModelOptions.getRateOptionClockModel() == FixRateType.NODE_CALIBRATED
|| options.clockModelOptions.getRateOptionClockModel() == FixRateType.RATE_CALIBRATED)) {
// TODO correct?
options.clockModelOptions.fixRateOfFirstClockPartition();
}
frame.setDirty();
}
private void fireDataChanged() {
options.updatePartitionAllLinks();
frame.setDirty();
}