private void doExportTimeTree() {
FileDialog dialog = new FileDialog(this, "Export Time Tree File...", FileDialog.SAVE);
dialog.setVisible(true);
if (dialog.getFile() != null) {
File file = new File(dialog.getDirectory(), dialog.getFile());
PrintStream ps = null;
try {
ps = new PrintStream(file);
writeTimeTreeFile(ps);
ps.close();
} catch (IOException ioe) {
JOptionPane.showMessageDialog(
this,
"Error writing tree file: " + ioe.getMessage(),
"Export Error",
JOptionPane.ERROR_MESSAGE);
}
}
}
protected void doExportData() {
FileDialog dialog = new FileDialog(this, "Export Data File...", FileDialog.SAVE);
dialog.setVisible(true);
if (dialog.getFile() != null) {
File file = new File(dialog.getDirectory(), dialog.getFile());
Writer writer = null;
try {
writer = new PrintWriter(file);
treesPanel.writeDataFile(writer);
writer.close();
} catch (IOException ioe) {
JOptionPane.showMessageDialog(
this,
"Error writing data file: " + ioe.getMessage(),
"Export Error",
JOptionPane.ERROR_MESSAGE);
}
}
}
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;
}