How to use

equalsNode

method

in

phylo.tree.model.TreeNode

/**
 * method returns the intersection size of two leaf sets
 *
 * @param leavesSubTree
 * @param leavesSubCompareTree
 * @return intersectionSize
 */
public static int countCommonLeaves(TreeNode[] leavesSubTree, TreeNode[] leavesSubCompareTree) {
  int intersectionSize = 0;
  for (int i = 0; i < leavesSubTree.length; i++) {
    for (int j = 0; j < leavesSubCompareTree.length; j++) {
      if (leavesSubTree[i].equalsNode(leavesSubCompareTree[j])) {
        intersectionSize++;
        break;
      }
    }
  }
  return intersectionSize;
}

  private boolean findLeaf(TreeNode node, int index) {
//      boolean isIn = false;

//        if(leaves.contains(node)) return true;
//        else return false;

    for (TreeNode leave : leaves) {
      if (leave.equalsNode(node)) return true;
    }
    return false;


//      try{
//          TreeNode l = (TreeNode)leaves.get(index); //   elementAt(index);
//                                          
//          if(l.equals(node)){
//             isIn = true;
//             return isIn;
//          }               
//      }catch (ClassCastException e){
//          isIn = false;
//          index+=1;          
//          if(index<leaves.size()){
//              if(findLeaf(node,index))
//              return true;
//          }           
//      }
//      return isIn;            
  }

/**
 * Indicates, if this node is a child of the given node.
 *
 * @param node: the node, that may be parent of this node
 * @return true, if this node is a child of the given node, false otherwise
 */
public boolean isChildOf(TreeNode node) {
  if (this.getParent().equalsNode(node)) {
    return true;
  } else {
    return false;
  }
}

/**
 * Computes the number of the given child for this node.
 * This number is 0 {@literal <=} childNum {@literal <} 'number of children', if the child is a real child of this node.
 * It is childNum = 'number of children', if the given child is parent of this node.
 *
 * @param child: the child, for that its number has to be computed
 * @return the child number for the  given node
 */
public int getChildNumber(TreeNode child) {
  if (this.getParent().equalsNode(child)) {
    return childCount();
  } else if (child.isChildOf(this)) {
    int num = 0;
    for (TreeNode nodesChild : this.children()) {
      if (!nodesChild.equalsNode(child)) {
        num++;
      } else {
        break;
      }
    }
    return num;
  } else {
    throw new RuntimeException("Given child is no child of this node!");
  }
}

  if (leaf.equalsNode(a)) posA = x;
  if (leaf.equalsNode(b)) posB = x;
if (node.equalsNode(a)) posA = x;
if (node.equalsNode(b)) posB = x;