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);
}
}
