Example #1
0
  /**
   * Root source by creating a new internal node whose children are (the adjacent) left and right.
   *
   * @param source
   * @param left
   * @param right
   * @param fromLeft branch from new root to left node.
   */
  public RootedFromUnrooted(
      @Param(name = "source", description = "auto converted jebl2 parameter") Tree source,
      @Param(name = "left", description = "auto converted jebl2 parameter") Node left,
      @Param(name = "right", description = "auto converted jebl2 parameter") Node right,
      @Param(name = "fromLeft", description = "auto converted jebl2 parameter") Double fromLeft) {
    this.source = source;
    intentUnrooted = false;
    topLeft = left;
    topRight = right;
    rootToLeft = fromLeft;
    try {
      rootToRight = source.getEdgeLength(left, right) - rootToLeft;
    } catch (NoEdgeException e) {
      // bug
    }
    parents = new LinkedHashMap<>();

    // This is just a handle used to refer to the root so create the simplest possible
    // implementation...
    root =
        new BaseNode() {
          @Override
          public int getDegree() {
            return 2;
          }
        };

    parents.put(root, null);
    setParent(left, root);
    setParent(right, root);
    this.left = left;
    this.right = right;
    this.fromLeft = fromLeft;
  }
Example #2
0
 @Override
 public double getLength(Node node) {
   if (node == root) return 0.0;
   if (node == topLeft) return rootToLeft;
   if (node == topRight) return rootToRight;
   double l = 0.0;
   try {
     l = source.getEdgeLength(node, getParent(node));
   } catch (NoEdgeException e) {
     // bug, should not happen
   }
   return l;
 }
Example #3
0
 @Override
 public double getEdgeLength(Node node1, Node node2) throws NoEdgeException {
   // special case when syntetic root
   if (topLeft != null) {
     if (node2 == root) {
       Node tmp = node1;
       node1 = node2;
       node2 = tmp;
     }
     if (node1 == root) {
       if (!(node2 == topLeft || node2 == topRight)) {
         throw new NoEdgeException();
       }
       return node2 == topLeft ? rootToLeft : rootToRight;
     }
   }
   return source.getEdgeLength(node1, node2);
 }