示例#1
0
  @Override
  protected Double modifyARG()
      throws InvalidParameterValueException, IllegalModificationException,
          ModificationImpossibleException {

    List<ARGNode> internalNodes = arg.getInternalNodes();

    int nodeNum = RandomSource.getNextIntFromTo(0, internalNodes.size() - 1);
    ARGNode node = internalNodes.get(nodeNum);

    if (internalNodes.size() == 1) // Must be two tips, no recomb nodes
    throw new ModificationImpossibleException("No internal nodes to modify");

    // Pick a node that is not the root
    while (node.getParent(0) == null) {
      node = internalNodes.get(RandomSource.getNextIntFromTo(0, internalNodes.size() - 1));
    }

    double hr;
    if (node instanceof CoalNode) {
      hr = swapCoalNode((CoalNode) node);
    } else {
      hr = swapRecombNode((RecombNode) node);
    }

    return hr;
  }
示例#2
0
  protected double swapCoalNode(CoalNode node)
      throws ModificationImpossibleException, IllegalModificationException {

    List<ARGNode> branches = arg.getBranchesCrossingTime(node.getHeight());
    ARGNode newChild =
        branches.get(
            RandomSource.getNextIntFromTo(
                0, branches.size() - 1)); // This will be new child of coal node
    ARGNode newParent = findDisplaceableParent(newChild, node.getHeight()); // New parent of node
    int oldChildIndex = RandomSource.getNextIntFromTo(0, 1);
    ARGNode oldChild =
        node.getOffspring(oldChildIndex); // Child that will be attached to node's parent
    ARGNode oldParent = node.getParent();

    // Attach the old child we are leaving to the old parent
    int pIndex = whichChild(node, oldParent);
    oldChild.proposeParent(whichParent(oldChild, node), oldParent);
    oldParent.proposeOffspring(pIndex, oldChild);

    // Insert the new node between newChild and newParent
    int cIndex = whichParent(newChild, newParent);
    int cpIndex = whichChild(newChild, newParent);
    node.proposeParent(newParent);
    newParent.proposeOffspring(cpIndex, node);
    newChild.proposeParent(cIndex, node);
    node.proposeOffspring(oldChildIndex, newChild);

    propogateRangeProposals(oldChild);
    propogateRangeProposals(node);

    if (verbose)
      System.out.println(
          "Swapping coal node  "
              + node
              + " to branch connecting parent "
              + newParent
              + " to offspring "
              + newChild);
    return 1.0;
  }