/**
* 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;
}
@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;
}
@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);
}