C++ TreeTemplate::getRootNode方法代码示例

string TreeTemplateTools::treeToParenthesis(const TreeTemplate<Node>& tree, bool writeId)
{
  ostringstream s;
  s << "(";
  const Node* node = tree.getRootNode();
  if (node->hasNoSon())
  {
    s << node->getName();
    for (size_t i = 0; i < node->getNumberOfSons(); ++i)
    {
      s << "," << nodeToParenthesis(*node->getSon(i), writeId);
    }
  }
  else
  {
    s << nodeToParenthesis(*node->getSon(0), writeId);
    for (size_t i = 1; i < node->getNumberOfSons(); ++i)
    {
      s << "," << nodeToParenthesis(*node->getSon(i), writeId);
    }
  }
  s << ")";
  if (node->hasDistanceToFather())
    s << ":" << node->getDistanceToFather();
  s << ";" << endl;
  return s.str();
}

double TreeTemplateTools::getRadius(TreeTemplate<Node>& tree)
{
  TreeTemplateTools::midRoot(tree, MIDROOT_SUM_OF_SQUARES, false);
  Moments_ moments = getSubtreeMoments_(tree.getRootNode());
  double radius = moments.sum / moments.numberOfLeaves;
  return radius;
}

RecursiveLikelihoodTree::RecursiveLikelihoodTree(const SubstitutionProcess& process, bool usepatterns) :
  AbstractLikelihoodTree(process),
  vTree_(),
  patternLinks_(),
  usePatterns_(usepatterns),
  initializedAboveLikelihoods_(false)
{
  TreeTemplate<Node> tree = process.getParametrizableTree().getTree();

  RecursiveLikelihoodNode* rCN = TreeTemplateTools::cloneSubtree<RecursiveLikelihoodNode>(*tree.getRootNode());

  TreeTemplate<RecursiveLikelihoodNode>* pTC = new TreeTemplate<RecursiveLikelihoodNode>(rCN);

  for (size_t i = 0; i < nbClasses_; i++)
  {
    TreeTemplate<RecursiveLikelihoodNode>* pTC2 = pTC->clone();
    vTree_.push_back(pTC2);
  }

  delete pTC;
}

void TreeTemplateTools::midRoot(TreeTemplate<Node>& tree, short criterion, bool forceBranchRoot)
{
  if (criterion != MIDROOT_VARIANCE && criterion != MIDROOT_SUM_OF_SQUARES)
    throw Exception("TreeTemplateTools::midRoot(). Illegal criterion value '" + TextTools::toString(criterion) + "'");

  if (tree.isRooted())
    tree.unroot();
  Node* ref_root = tree.getRootNode();
  //
  // The bestRoot object records :
  // -- the current best branch : .first
  // -- the current best value of the criterion : .second["value"]
  // -- the best position of the root on the branch : .second["position"]
  //      0 is toward the original root, 1 is away from it
  //
  pair<Node*, map<string, double> > best_root_branch;
  best_root_branch.first = ref_root; // nota: the root does not correspond to a branch as it has no father
  best_root_branch.second ["position"] = -1;
  best_root_branch.second ["score"] = numeric_limits<double>::max();

  // find the best root
  getBestRootInSubtree_(tree, criterion, ref_root, best_root_branch);
  tree.rootAt(ref_root); // back to the original root

  // reroot
  const double pos = best_root_branch.second["position"];
  if (pos < 1e-6 or pos > 1 - 1e-6)
    // The best root position is on a node (this is often the case with the sum of squares criterion)
    tree.rootAt(pos < 1e-6 ? best_root_branch.first->getFather() : best_root_branch.first);
  else
  // The best root position is somewhere on a branch (a new Node is created)
  {
    Node* new_root = new Node();
    new_root->setId( TreeTools::getMPNUId(tree, tree.getRootId()) );

    double root_branch_length = best_root_branch.first->getDistanceToFather();
    Node* best_root_father = best_root_branch.first->getFather();

    best_root_father->removeSon(best_root_branch.first);
    best_root_father->addSon(new_root);
    new_root->addSon(best_root_branch.first);

    new_root->setDistanceToFather(max(pos * root_branch_length, 1e-6));
    best_root_branch.first->setDistanceToFather(max((1 - pos) * root_branch_length, 1e-6));

    // The two branches leaving the root must have the same branch properties
    const vector<string> branch_properties = best_root_branch.first->getBranchPropertyNames();
    for (vector<string>::const_iterator p = branch_properties.begin(); p != branch_properties.end(); ++p)
    {
      new_root->setBranchProperty(*p, *best_root_branch.first->getBranchProperty(*p));
    }

    tree.rootAt(new_root);
  }

  if (forceBranchRoot) // if we want the root to be on a branch, not on a node
  {
    Node* orig_root = tree.getRootNode();
    vector<Node*> root_sons = orig_root->getSons();
    if (root_sons.size() > 2)
    {
      Node* nearest = root_sons.at(0);
      for (vector<Node*>::iterator n = root_sons.begin(); n !=
           root_sons.end(); ++n)
      {
        if ((**n).getDistanceToFather() < nearest->getDistanceToFather())
          nearest = *n;
      }
      const double d = nearest->getDistanceToFather();
      Node* new_root = new Node();
      new_root->setId( TreeTools::getMPNUId(tree, tree.getRootId()) );
      orig_root->removeSon(nearest);
      orig_root->addSon(new_root);
      new_root->addSon(nearest);
      new_root->setDistanceToFather(d / 2.);
      nearest->setDistanceToFather(d / 2.);
      const vector<string> branch_properties = nearest->getBranchPropertyNames();
      for (vector<string>::const_iterator p = branch_properties.begin(); p != branch_properties.end(); ++p)
      {
        new_root->setBranchProperty(*p, *nearest->getBranchProperty(*p));
      }
      tree.rootAt(new_root);
    }
  }
}

void ClusterTools::computeNormProperties(TreeTemplate<Node>& tree, const ProbabilisticSubstitutionMapping & mapping)
{
  double min;
  computeNormProperties_(tree.getRootNode(), mapping, min);
}

vector<const Node *> ClusterTools::getSubtreesWithSize(const TreeTemplate<Node>& tree, size_t size)
{
  vector<const Node *> subtrees;
  getSubtreesWithSize(tree.getRootNode(), size, subtrees);
  return subtrees;
}