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();
}
});
}
