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);
// }
}