Exemplo 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);
        }
      }
    }
  }
Exemplo n.º 2
0
 public void backwardIBD(NodeRef node) {
   int stateCount = substitutionModel.getStateCount();
   if (node == null) {
     node = treeModel.getRoot();
     int nodeId = node.getNumber();
     for (int state = 0; state < stateCount; ++state) {
       ibdBackward[nodeId][state] = 0;
     }
   }
   getDiagonalRates(diag);
   int childCount = treeModel.getChildCount(node);
   int nodeId = node.getNumber();
   for (int child = 0; child < childCount; ++child) {
     NodeRef childNode = treeModel.getChild(node, child);
     int childNodeId = childNode.getNumber();
     double branchTime =
         branchRateModel.getBranchRate(treeModel, childNode)
             * (treeModel.getNodeHeight(node) - treeModel.getNodeHeight(childNode));
     for (int state = 0; state < stateCount; ++state) {
       ibdBackward[childNodeId][state] = ibdBackward[nodeId][state];
       for (int sibling = 0; sibling < childCount; ++sibling) {
         if (sibling != child) {
           int siblingId = treeModel.getChild(node, sibling).getNumber();
           ibdBackward[childNodeId][state] += ibdForward[siblingId][state];
         }
       }
       ibdBackward[childNodeId][state] *= Math.exp(-diag[state] * branchTime);
     }
   }
   for (int child = 0; child < childCount; ++child) {
     NodeRef childNode = treeModel.getChild(node, child);
     backwardIBD(childNode);
   }
 }