예제 #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);
        }
      }
    }
  }
예제 #2
0
  // compute scale factor
  private void computeFactor() {

    // scale mean rate to 1.0 or separate parameter

    double treeRate = 0.0;
    double treeTime = 0.0;

    // normalizeBranchRateTo = 1.0;
    for (int i = 0; i < treeModel.getNodeCount(); i++) {
      NodeRef node = treeModel.getNode(i);
      if (!treeModel.isRoot(node)) {
        // d                int rateCategory = (int)
        // Math.round(rateCategories.getNodeValue(treeModel, node));
        // d                 treeRate += rates[rateCategory] * treeModel.getBranchLength(node);
        treeTime += treeModel.getBranchLength(node);

        // d              System.out.println("rates and time\t" + rates[rateCategory] + "\t" +
        // treeModel.getBranchLength(node));
      }
    }
    // treeRate /= treeTime;

    scaleFactor = normalizeBranchRateTo / (treeRate / treeTime);
    System.out.println("scaleFactor\t\t\t\t\t" + scaleFactor);
  }
예제 #3
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();
    }
  }