private static void renameTreeLeavesLeftToRight(Phylogeny tree) {
PhylogenyNodeIterator iterator = tree.iteratorPreorder();
int i = 0;
while (iterator.hasNext()) {
PhylogenyNode currentNode = iterator.next();
if (currentNode.isExternal()) {
currentNode.setName(i + "");
i++;
}
}
}
private final String printProgressNodeToString(final PhylogenyNode n) {
if (n.isExternal()) {
if (ForesterUtil.isEmpty(n.getName())) {
return Long.toString(n.getId());
}
return n.getName();
}
return n.getId()
+ " ("
+ (ForesterUtil.isEmpty(n.getChildNode1().getName())
? n.getChildNode1().getId()
: n.getChildNode1().getName())
+ "+"
+ (ForesterUtil.isEmpty(n.getChildNode2().getName())
? n.getChildNode2().getId()
: n.getChildNode2().getName())
+ ")";
}
public static void renameTreeLeavesRandomly(Phylogeny tree) {
Random random = new Random();
List<PhylogenyNode> leaves = new ArrayList();
PhylogenyNodeIterator iterator = tree.iteratorPostorder();
while (iterator.hasNext()) {
PhylogenyNode node = iterator.next();
if (node.isExternal()) {
leaves.add(node);
}
}
int i = 0;
while (!leaves.isEmpty()) {
int leafIndex = random.nextInt(leaves.size());
PhylogenyNode currentLeaf = leaves.get(leafIndex);
currentLeaf.setName(i + "");
leaves.remove(leafIndex);
i++;
}
}