private void setStatusMessage() {
Tree tree = treesPanel.getTree();
if (tree != null) {
String message = "";
message += "Tree loaded, " + tree.getTaxonCount() + " taxa";
TemporalRooting tr = treesPanel.getTemporalRooting();
if (tr.isContemporaneous()) {
message += ", contemporaneous tips";
} else {
NumberFormatter nf = new NumberFormatter(3);
message += ", dated tips with range " + nf.format(tr.getDateRange());
}
statusLabel.setText(message);
}
}
protected void writeTimeTreeFile(PrintStream ps) throws IOException {
FlexibleTree tree = new FlexibleTree(treesPanel.getTreeAsViewed());
Regression r =
treesPanel.getTemporalRooting().getRootToTipRegression(treesPanel.getTreeAsViewed());
for (int i = 0; i < tree.getInternalNodeCount(); i++) {
NodeRef node = tree.getInternalNode(i);
double height = tree.getNodeHeight(node);
tree.setNodeHeight(node, height / r.getGradient());
}
TreeUtils.setHeightsFromDates(tree);
NexusExporter nexusExporter = new NexusExporter(new PrintStream(ps));
nexusExporter.exportTree(tree);
}
protected void writeTreeFile(PrintStream ps, boolean newickFormat) throws IOException {
Tree tree = treesPanel.getTreeAsViewed();
// if (newickFormat) {
// NewickExporter newickExporter = new NewickExporter(ps);
// newickExporter.exportTree(tree);
// } else {
NexusExporter nexusExporter = new NexusExporter(new PrintStream(ps));
nexusExporter.exportTree(tree);
// }
}
@Override
public void doCopy() {
StringWriter writer = new StringWriter();
PrintWriter pwriter = new PrintWriter(writer);
for (String tip : treesPanel.getSelectedTips()) {
pwriter.println(tip);
}
Clipboard clipboard = Toolkit.getDefaultToolkit().getSystemClipboard();
StringSelection selection = new StringSelection(writer.toString());
clipboard.setContents(selection, selection);
}
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);
}
}
}
public void timeScaleChanged() {
treesPanel.timeScaleChanged();
setStatusMessage();
}