Ejemplo n.º 1
0
  public void forwardIBD() {
    int numNodes = treeModel.getNodeCount();
    int stateCount = substitutionModel.getStateCount();
    getDiagonalRates(diag);
    for (int nodeId = 0; nodeId < numNodes; ++nodeId) {
      NodeRef node = treeModel.getNode(nodeId);
      NodeRef parent = treeModel.getParent(node);
      if (parent == null) { // handle the root

      } else if (treeModel.isExternal(node)) { // Handle the tip
        double branchTime =
            branchRateModel.getBranchRate(treeModel, node)
                * (treeModel.getNodeHeight(parent) - treeModel.getNodeHeight(node));

        for (int state = 0; state < stateCount; ++state) {
          ibdForward[nodeId][state] = Math.exp(-diag[state] * branchTime);
        }
      } else { // Handle internal node
        double branchTime =
            branchRateModel.getBranchRate(treeModel, node)
                * (treeModel.getNodeHeight(parent) - treeModel.getNodeHeight(node));

        int childCount = treeModel.getChildCount(node);
        for (int state = 0; state < stateCount; ++state) {
          ibdForward[nodeId][state] = 0;
          for (int child = 0; child < childCount; ++child) {
            int childNodeId = treeModel.getChild(node, child).getNumber();
            ibdForward[nodeId][state] += ibdForward[childNodeId][state];
          }
          ibdForward[nodeId][state] *= Math.exp(-diag[state] * branchTime);
        }
      }
    }
  }
Ejemplo n.º 2
0
  private boolean eligibleForMove(NodeRef node, TreeModel tree, BranchMapModel branchMap) {
    // to be eligible for this move, the node's parent and grandparent, or parent and other child,
    // must be in the same partition (so removing the parent has no effect on the remaining links of
    // the TT),
    // and the node and its parent must be in different partitions (such that the move does not
    // disconnect anything)

    return ((tree.getParent(tree.getParent(node)) != null
                && branchMap.get(tree.getParent(node).getNumber())
                    == branchMap.get(tree.getParent(tree.getParent(node)).getNumber()))
            || branchMap.get(tree.getParent(node).getNumber())
                == branchMap.get(getOtherChild(tree, tree.getParent(node), node).getNumber()))
        && branchMap.get(tree.getParent(node).getNumber()) != branchMap.get(node.getNumber());
  }
Ejemplo n.º 3
0
  public static void checkTree(TreeModel treeModel) {

    // todo Should only be run if there exists a zero-length interval

    //        TreeModel treeModel = (TreeModel) tree;
    for (int i = 0; i < treeModel.getInternalNodeCount(); i++) {
      NodeRef node = treeModel.getInternalNode(i);
      if (node != treeModel.getRoot()) {
        double parentHeight = treeModel.getNodeHeight(treeModel.getParent(node));
        double childHeight0 = treeModel.getNodeHeight(treeModel.getChild(node, 0));
        double childHeight1 = treeModel.getNodeHeight(treeModel.getChild(node, 1));
        double maxChild = childHeight0;
        if (childHeight1 > maxChild) maxChild = childHeight1;
        double newHeight = maxChild + MathUtils.nextDouble() * (parentHeight - maxChild);
        treeModel.setNodeHeight(node, newHeight);
      }
    }
    treeModel.pushTreeChangedEvent();
  }
Ejemplo n.º 4
0
  private void setup() {

    DataType dataType = baseSubstitutionModel.getDataType();
    FrequencyModel freqModel = baseSubstitutionModel.getFrequencyModel();
    Parameter kappaParameter = new Parameter.Default("kappa", 1, baseSubstitutionModel.getKappa());

    substitutionModels = new LinkedList<SubstitutionModel>();
    branchAssignmentMap = new LinkedHashMap<NodeRef, Integer>();

    int branchClass = 0;
    for (NodeRef node : treeModel.getNodes()) {
      if (!treeModel.isRoot(node)) {

        double nodeHeight = treeModel.getNodeHeight(node);
        double parentHeight = treeModel.getNodeHeight(treeModel.getParent(node));

        double time = 0.5 * (parentHeight + nodeHeight);

        double baseOmega = baseSubstitutionModel.getOmega();

        double fixed = baseOmega * time;

        double epsilon =
            (Math.log(1 - random.nextDouble())
                / (-rate)); // Math.exp((random.nextGaussian() * stdev + mean));

        double value = fixed + epsilon;

        Parameter omegaParameter = new Parameter.Default("omega", 1, value);

        GY94CodonModel gy94 =
            new GY94CodonModel((Codons) dataType, omegaParameter, kappaParameter, freqModel);

        substitutionModels.add(gy94);
        branchAssignmentMap.put(node, branchClass);
        branchClass++;
      } // END: root check
    } // END: nodes loop
  } // END: setup
Ejemplo n.º 5
0
  public void proposeTree() throws OperatorFailedException {
    TreeModel tree = c2cLikelihood.getTreeModel();
    BranchMapModel branchMap = c2cLikelihood.getBranchMap();
    NodeRef i;
    double oldMinAge, newMinAge, newRange, oldRange, newAge, q;
    // choose a random node avoiding root, and nodes that are ineligible for this move because they
    // have nowhere to
    // go
    final int nodeCount = tree.getNodeCount();
    do {
      i = tree.getNode(MathUtils.nextInt(nodeCount));
    } while (tree.getRoot() == i || !eligibleForMove(i, tree, branchMap));
    final NodeRef iP = tree.getParent(i);

    // this one can go anywhere

    NodeRef j = tree.getNode(MathUtils.nextInt(tree.getNodeCount()));
    NodeRef k = tree.getParent(j);

    while ((k != null && tree.getNodeHeight(k) <= tree.getNodeHeight(i)) || (i == j)) {
      j = tree.getNode(MathUtils.nextInt(tree.getNodeCount()));
      k = tree.getParent(j);
    }

    if (iP == tree.getRoot() || j == tree.getRoot()) {
      throw new OperatorFailedException("Root changes not allowed!");
    }

    if (k == iP || j == iP || k == i) throw new OperatorFailedException("move failed");

    final NodeRef CiP = getOtherChild(tree, iP, i);
    NodeRef PiP = tree.getParent(iP);

    newMinAge = Math.max(tree.getNodeHeight(i), tree.getNodeHeight(j));
    newRange = tree.getNodeHeight(k) - newMinAge;
    newAge = newMinAge + (MathUtils.nextDouble() * newRange);
    oldMinAge = Math.max(tree.getNodeHeight(i), tree.getNodeHeight(CiP));
    oldRange = tree.getNodeHeight(PiP) - oldMinAge;
    q = newRange / Math.abs(oldRange);

    // need to account for the random repainting of iP

    if (branchMap.get(PiP.getNumber()) != branchMap.get(CiP.getNumber())) {
      q *= 0.5;
    }

    if (branchMap.get(k.getNumber()) != branchMap.get(j.getNumber())) {
      q *= 2;
    }

    tree.beginTreeEdit();

    if (j == tree.getRoot()) {

      // 1. remove edges <iP, CiP>
      tree.removeChild(iP, CiP);
      tree.removeChild(PiP, iP);

      // 2. add edges <k, iP>, <iP, j>, <PiP, CiP>
      tree.addChild(iP, j);
      tree.addChild(PiP, CiP);

      // iP is the new root
      tree.setRoot(iP);

    } else if (iP == tree.getRoot()) {

      // 1. remove edges <k, j>, <iP, CiP>, <PiP, iP>
      tree.removeChild(k, j);
      tree.removeChild(iP, CiP);

      // 2. add edges <k, iP>, <iP, j>, <PiP, CiP>
      tree.addChild(iP, j);
      tree.addChild(k, iP);

      // CiP is the new root
      tree.setRoot(CiP);

    } else {
      // 1. remove edges <k, j>, <iP, CiP>, <PiP, iP>
      tree.removeChild(k, j);
      tree.removeChild(iP, CiP);
      tree.removeChild(PiP, iP);

      // 2. add edges <k, iP>, <iP, j>, <PiP, CiP>
      tree.addChild(iP, j);
      tree.addChild(k, iP);
      tree.addChild(PiP, CiP);
    }

    tree.setNodeHeight(iP, newAge);

    tree.endTreeEdit();

    //
    logq = Math.log(q);

    // repaint the parent to match either its new parent or its new child (50% chance of each).

    if (MathUtils.nextInt(2) == 0) {
      branchMap.set(iP.getNumber(), branchMap.get(k.getNumber()), true);
    } else {
      branchMap.set(iP.getNumber(), branchMap.get(j.getNumber()), true);
    }

    if (DEBUG) {
      c2cLikelihood.checkPartitions();
    }
  }