public void initializeComponents() {
samplesPanel = new SamplesPanel(this, taxa);
treesPanel = new TreesPanel(this, trees.get(0));
tabbedPane.addTab("Sample Dates", samplesPanel);
tabbedPane.addTab("Analysis", treesPanel);
JPanel panel = new JPanel(new BorderLayout(6, 6));
panel.setBorder(new BorderUIResource.EmptyBorderUIResource(new Insets(12, 12, 12, 12)));
panel.add(tabbedPane, BorderLayout.CENTER);
panel.add(statusLabel, BorderLayout.SOUTH);
getContentPane().setLayout(new BorderLayout(0, 0));
getContentPane().add(panel, BorderLayout.CENTER);
setSize(new Dimension(1024, 768));
setStatusMessage();
}
protected boolean readFromFile(File file) throws IOException {
Reader reader = new FileReader(file);
BufferedReader bufferedReader = new BufferedReader(reader);
String line = bufferedReader.readLine();
while (line != null && line.length() == 0) {
line = bufferedReader.readLine();
}
boolean isNexus = (line != null && line.toUpperCase().contains("#NEXUS"));
reader = new FileReader(file);
Tree tree = null;
try {
if (isNexus) {
NexusImporter importer = new NexusImporter(reader);
tree = importer.importTree(taxa);
} else {
NewickImporter importer = new NewickImporter(reader);
tree = importer.importTree(taxa);
}
} catch (Importer.ImportException ime) {
JOptionPane.showMessageDialog(
this,
"Error parsing imported file: " + ime,
"Error reading file",
JOptionPane.ERROR_MESSAGE);
ime.printStackTrace();
return false;
} catch (IOException ioex) {
JOptionPane.showMessageDialog(
this, "File I/O Error: " + ioex, "File I/O Error", JOptionPane.ERROR_MESSAGE);
ioex.printStackTrace();
return false;
} catch (Exception ex) {
JOptionPane.showMessageDialog(
this, "Fatal exception: " + ex, "Error reading file", JOptionPane.ERROR_MESSAGE);
ex.printStackTrace();
return false;
}
if (tree == null) {
JOptionPane.showMessageDialog(
this,
"The file is not in a suitable format or contains no trees.",
"Error reading file",
JOptionPane.ERROR_MESSAGE);
return false;
}
FlexibleTree binaryTree = new FlexibleTree(tree, true);
binaryTree.resolveTree();
trees.add(binaryTree);
if (taxa == null) {
taxa = binaryTree;
}
getExportTreeAction().setEnabled(true);
getExportDataAction().setEnabled(true);
return true;
}