}
/**
- * DOCUMENT ME!
+ * Generate a string representation of the Tree
*
- * @return DOCUMENT ME!
+ * @return Newick File with all tree data available
*/
public String toString()
{
jalview.io.NewickFile fout = new jalview.io.NewickFile(getTopNode());
- return fout.print(false, true); // distances only
+ return fout.print(isHasBootstrap(),
+ isHasDistances(), isHasRootDistance()); // output all data available for tree
}
/**
}
}
}
+ /**
+ * rename any nodes according to their associated sequence.
+ * This will modify the tree's metadata! (ie the original NewickFile or newly generated BinaryTree's label data)
+ */
+ public void renameAssociatedNodes() {
+ applyToNodes(new NodeTransformI() {
+ @Override
+ public void transform(BinaryNode node)
+ {
+ Object el = node.element();
+ if (el!=null && el instanceof SequenceI)
+ {
+ node.setName(((SequenceI)el).getName());
+ }
+ }
+ });
+ }
/**
* DOCUMENT ME!
*/