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 Object getValueAt(int row, int col) {
// PartitionData partition = options.getPartitionDataNoSpecies().get(row);
AbstractPartitionData partition = options.dataPartitions.get(row);
switch (col) {
case 0:
return partition.getName();
case 1:
return partition.getFileName();
case 2:
return "" + (partition.getTaxonCount() >= 0 ? partition.getTaxonCount() : "-");
case 3:
return "" + (partition.getSiteCount() >= 0 ? partition.getSiteCount() : "-");
case 4:
return partition.getDataDescription();
case 5:
// return partition.getPloidyType();
// case 6:
return partition.getPartitionSubstitutionModel().getName();
case 6:
return ""
+ (partition.getPartitionClockModel() != null
? partition.getPartitionClockModel().getName()
: "-");
case 7:
return partition.getPartitionTreeModel().getName();
default:
throw new IllegalArgumentException("unknown column, " + col);
}
}
public void unlinkClocks() { // reuse previous PartitionTreePrior
int[] selRows = dataTable.getSelectedRows();
for (int row : selRows) {
AbstractPartitionData partition = options.dataPartitions.get(row);
PartitionClockModel model = partition.getPartitionClockModel();
if (!model.getName().equals(partition.getName())) {
PartitionClockModel newModel = new PartitionClockModel(options, partition.getName(), model);
partition.setPartitionClockModel(newModel);
newModel.setClockModelGroup(model.getClockModelGroup()); // set clock model group
}
}
modelsChanged();
fireDataChanged();
repaint();
}
public void unlinkModels() {
int[] selRows = dataTable.getSelectedRows();
for (int row : selRows) {
AbstractPartitionData partition = options.dataPartitions.get(row);
PartitionSubstitutionModel model = partition.getPartitionSubstitutionModel();
if (!model.getName().equals(partition.getName())) {
PartitionSubstitutionModel newModel =
new PartitionSubstitutionModel(options, partition.getName(), model);
partition.setPartitionSubstitutionModel(newModel);
}
}
modelsChanged();
fireDataChanged();
repaint();
}