public void setValueAt(Object aValue, int row, int col) {
AbstractPartitionData partition = options.dataPartitions.get(row);
switch (col) {
case 0:
String name = ((String) aValue).trim();
if (options.hasPartitionData(name)) {
JOptionPane.showMessageDialog(
frame,
"Duplicate partition name.",
"Illegal Argument Exception",
JOptionPane.ERROR_MESSAGE);
return;
}
if (name.length() > 0) {
options.renamePartition(partition, name);
}
break;
case 5:
// partition.setPloidyType((PloidyType) aValue);
// break;
// case 6:
if (((PartitionSubstitutionModel) aValue).getDataType().equals(partition.getDataType())) {
partition.setPartitionSubstitutionModel((PartitionSubstitutionModel) aValue);
}
break;
case 6:
partition.setPartitionClockModel((PartitionClockModel) aValue);
break;
case 7:
partition.setPartitionTreeModel((PartitionTreeModel) aValue);
break;
}
fireDataChanged();
}
public void unlinkTrees() { // reuse previous PartitionTreePrior
int[] selRows = dataTable.getSelectedRows();
for (int row : selRows) {
AbstractPartitionData partition = options.dataPartitions.get(row);
PartitionTreeModel model = partition.getPartitionTreeModel();
if (!model.getName().equals(partition.getName())
&& partition.getTraits() == null) { // not a trait
PartitionTreeModel newTree = new PartitionTreeModel(options, partition.getName(), model);
// 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();
repaint();
}
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();
}