How to use

getGraph

method

in

phylo.tree.model.TreeNode

@Override
public long getEdgeWeight(TreeNode node) {
  Tree t = (Tree)node.getGraph();
  if (scaffoldTree != null && t.equals(scaffoldTree)) {
    return CutGraphCutter.getInfinity();
  } else {
    return 1;
  }
}

Tree sourceTree = (Tree) character.getGraph();
TreeNode[] sourceTreeTaxa = sourceTree.getLeaves();
for (TreeNode taxon : sourceTreeTaxa) {

if (a.getGraph() != t || b.getGraph() != t) return;

/**
 * This method returns the last common ancestor of two nodes of a tree.
 * <p>
 * This eventually returns null if one of the given nodes is null or the given nodes
 * are not in this tree.
 *
 * @param nodeA
 * @param nodeB
 * @return the LCA of nodeA and nodeB or null if no LCA exists
 */
public TreeNode findLeastCommonAncestor(TreeNode nodeA, TreeNode nodeB) {
  if (nodeA == null || nodeB == null) return null;
  if (nodeA.getGraph() != this || nodeB.getGraph() != this) return null;
  /* set nodeA and nodeB to equal level */
  if (nodeA.getLevel() < nodeB.getLevel()) {
    while (nodeA.getLevel() != nodeB.getLevel()) {
      nodeB = (TreeNode) nodeB.getParent();
    }
  } else {
    while (nodeA.getLevel() != nodeB.getLevel()) {
      nodeA = (TreeNode) nodeA.getParent();
    }
  }
  /* set both nodes to their parent, until they are equal */
  while (nodeA != nodeB) {
    nodeA = (TreeNode) nodeA.getParent();
    nodeB = (TreeNode) nodeB.getParent();
  }
  return (nodeA);
}

Tree tree = (Tree) node.getGraph();
if (scaffoldTree != null && tree.equals(scaffoldTree)) {
  return CutGraphCutter.getInfinity();