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 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 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);
}
}