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);
}