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 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();
}
