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())));
}
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 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 Component getTableCellEditorComponent(
JTable table, Object value, boolean isSelected, int row, int column) {
((JComboBox) editorComponent).removeAllItems();
if (options.containTrait(table.getValueAt(row, 0).toString())) {
if (column == 5) {
for (Object ob : options.getPartitionTraitsSubstitutionModels()) {
((JComboBox) editorComponent).addItem(ob);
}
} else if (column == 6) {
for (Object ob : options.getPartitionTraitsClockModels()) {
((JComboBox) editorComponent).addItem(ob);
}
}
} else {
if (column == 5) {
for (Object ob : options.getPartitionNonTraitsSubstitutionModels()) {
((JComboBox) editorComponent).addItem(ob);
}
} else if (column == 6) {
for (Object ob : options.getPartitionNonTraitsClockModels()) {
((JComboBox) editorComponent).addItem(ob);
}
}
}
// if (((JComboBox) editorComponent).contains(value)) // todo need validate whether
// value in the editorComponent
((JComboBox) editorComponent).setSelectedItem(value);
delegate.setValue(value);
return editorComponent;
}
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();
}
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 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 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();
}
public void selectionChanged() {
int[] selRows = dataTable.getSelectedRows();
boolean hasSelection = (selRows != null && selRows.length != 0);
frame.dataSelectionChanged(hasSelection);
boolean canUnlink = options.dataPartitions.size() > 1 && hasSelection;
boolean canLink = options.dataPartitions.size() > 1 && hasSelection && selRows.length > 1;
unlinkModelsAction.setEnabled(canUnlink);
linkModelsAction.setEnabled(canLink);
unlinkClocksAction.setEnabled(canUnlink);
linkClocksAction.setEnabled(canLink);
unlinkTreesAction.setEnabled(canUnlink);
linkTreesAction.setEnabled(canLink);
}
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 showAlignment() {
int[] selRows = dataTable.getSelectedRows();
for (int row : selRows) {
AbstractPartitionData partition = options.dataPartitions.get(row);
Alignment alignment = null;
if (partition instanceof PartitionData)
alignment = ((PartitionData) partition).getAlignment();
// alignment == null if partition is trait or microsat
// http://code.google.com/p/beast-mcmc/issues/detail?id=343
if (alignment == null) {
JOptionPane.showMessageDialog(
this,
"Cannot display traits or microsatellite data currently.\nUse the traits panel to view and edit traits.",
"Illegal Argument Exception",
JOptionPane.ERROR_MESSAGE);
return;
}
JFrame frame = new JFrame();
frame.setSize(800, 600);
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);
}
}
public DataPanel(
BeautiFrame parent,
Action importDataAction,
Action removeDataAction /*, Action importTraitsAction*/) {
this.frame = parent;
dataTableModel = new DataTableModel();
dataTable = new JTable(dataTableModel);
dataTable.getTableHeader().setReorderingAllowed(false);
dataTable
.getTableHeader()
.setDefaultRenderer(new HeaderRenderer(SwingConstants.LEFT, new Insets(0, 4, 0, 4)));
TableColumn col = dataTable.getColumnModel().getColumn(5);
ComboBoxRenderer comboBoxRenderer = new ComboBoxRenderer();
comboBoxRenderer.putClientProperty("JComboBox.isTableCellEditor", Boolean.TRUE);
col.setCellRenderer(comboBoxRenderer);
// col = dataTable.getColumnModel().getColumn(5);
// comboBoxRenderer = new ComboBoxRenderer();
// comboBoxRenderer.putClientProperty("JComboBox.isTableCellEditor", Boolean.TRUE);
// col.setCellRenderer(comboBoxRenderer);
col = dataTable.getColumnModel().getColumn(6);
comboBoxRenderer = new ComboBoxRenderer();
comboBoxRenderer.putClientProperty("JComboBox.isTableCellEditor", Boolean.TRUE);
col.setCellRenderer(comboBoxRenderer);
col = dataTable.getColumnModel().getColumn(7);
comboBoxRenderer = new ComboBoxRenderer();
comboBoxRenderer.putClientProperty("JComboBox.isTableCellEditor", Boolean.TRUE);
col.setCellRenderer(comboBoxRenderer);
TableEditorStopper.ensureEditingStopWhenTableLosesFocus(dataTable);
dataTable
.getSelectionModel()
.addListSelectionListener(
new ListSelectionListener() {
public void valueChanged(ListSelectionEvent evt) {
selectionChanged();
}
});
dataTable.addMouseListener(
new MouseAdapter() {
public void mouseClicked(MouseEvent e) {
if (e.getClickCount() == 2) {
showAlignment();
}
}
});
scrollPane =
new JScrollPane(
dataTable,
JScrollPane.VERTICAL_SCROLLBAR_ALWAYS,
JScrollPane.HORIZONTAL_SCROLLBAR_ALWAYS);
scrollPane.setOpaque(false);
JToolBar toolBar1 = new JToolBar();
toolBar1.setFloatable(false);
toolBar1.setOpaque(false);
toolBar1.setLayout(new BoxLayout(toolBar1, BoxLayout.X_AXIS));
JButton button = new JButton(unlinkModelsAction);
unlinkModelsAction.setEnabled(false);
PanelUtils.setupComponent(button);
toolBar1.add(button);
button = new JButton(linkModelsAction);
linkModelsAction.setEnabled(false);
PanelUtils.setupComponent(button);
toolBar1.add(button);
toolBar1.addSeparator();
button = new JButton(unlinkClocksAction);
unlinkClocksAction.setEnabled(false);
PanelUtils.setupComponent(button);
toolBar1.add(button);
button = new JButton(linkClocksAction);
linkClocksAction.setEnabled(false);
PanelUtils.setupComponent(button);
toolBar1.add(button);
toolBar1.addSeparator();
button = new JButton(unlinkTreesAction);
unlinkTreesAction.setEnabled(false);
PanelUtils.setupComponent(button);
toolBar1.add(button);
button = new JButton(linkTreesAction);
linkTreesAction.setEnabled(false);
PanelUtils.setupComponent(button);
toolBar1.add(button);
// too crowded on the toolbar - just double click to show
// button = new JButton(showAction);
// showAction.setEnabled(false);
// PanelUtils.setupComponent(button);
// toolBar1.add(button);
ActionPanel actionPanel1 = new ActionPanel(false);
actionPanel1.setAddAction(importDataAction);
actionPanel1.setRemoveAction(removeDataAction);
removeDataAction.setEnabled(false);
JPanel controlPanel1 = new JPanel(new FlowLayout(FlowLayout.LEFT));
controlPanel1.setOpaque(false);
controlPanel1.add(actionPanel1);
controlPanel1.add(new JLabel(" "));
PanelUtils.setupComponent(createImportTraitButton);
controlPanel1.add(createImportTraitButton);
// controlPanel1.add(new JLabel(" or "));
//
// button = new JButton(importTraitsAction);
// PanelUtils.setupComponent(button);
// controlPanel1.add(button);
JPanel panel1 = new JPanel(new BorderLayout());
panel1.setOpaque(false);
panel1.add(useStarBEASTCheck, BorderLayout.NORTH);
panel1.add(toolBar1, BorderLayout.SOUTH);
setOpaque(false);
setBorder(new BorderUIResource.EmptyBorderUIResource(new Insets(12, 12, 12, 12)));
setLayout(new BorderLayout(0, 0));
add(panel1, BorderLayout.NORTH);
add(scrollPane, BorderLayout.CENTER);
add(controlPanel1, BorderLayout.SOUTH);
useStarBEASTCheck.setEnabled(false);
useStarBEASTCheck.setToolTipText(STARBEASTOptions.CITATION);
useStarBEASTCheck.addActionListener(
new java.awt.event.ActionListener() {
public void actionPerformed(
ActionEvent e) { // wrong listener Issue 397: *BEAST in BEAUti is broken
frame.setupStarBEAST(useStarBEASTCheck.isSelected());
dataTableModel.fireTableDataChanged();
}
});
}
public void selectAll() {
dataTable.selectAll();
}