C++ TreeTemplate::resetNodesId方法代码示例

TreeTemplate<Node>* TreeTemplateTools::parenthesisToTree(const string& description, bool bootstrap, const string& propertyName, bool withId, bool verbose) throw (Exception)
{
  string::size_type semi = description.rfind(';');
  if (semi == string::npos)
    throw Exception("TreeTemplateTools::parenthesisToTree(). Bad format: no semi-colon found.");
  string content = description.substr(0, semi);
  unsigned int nodeCounter = 0;
  Node* node = parenthesisToNode(content, nodeCounter, bootstrap, propertyName, withId, verbose);
  TreeTemplate<Node>* tree = new TreeTemplate<Node>();
  tree->setRootNode(node);
  if (!withId)
  {
    tree->resetNodesId();
  }
  if (verbose) {
    (*ApplicationTools::message) << " nodes loaded.";
    ApplicationTools::message->endLine();
  }
  return tree;
}

TreeTemplate<Node>* TreeTemplateTools::getRandomTree(vector<string>& leavesNames, bool rooted)
{
  if (leavesNames.size() == 0)
    return 0;                                // No taxa.
  // This vector will contain all nodes.
  // Start with all leaves, and then group nodes randomly 2 by 2.
  // Att the end, contains only the root node of the tree.
  vector<Node*> nodes(leavesNames.size());
  // Create all leaves nodes:
  for (size_t i = 0; i < leavesNames.size(); ++i)
  {
    nodes[i] = new Node(leavesNames[i]);
  }
  // Now group all nodes:
  while (nodes.size() > (rooted ? 2 : 3))
  {
    // Select random nodes:
    size_t pos1 = RandomTools::giveIntRandomNumberBetweenZeroAndEntry<size_t>(nodes.size());
    Node* node1 = nodes[pos1];
    nodes.erase(nodes.begin() + static_cast<ptrdiff_t>(pos1));
    size_t pos2 = RandomTools::giveIntRandomNumberBetweenZeroAndEntry<size_t>(nodes.size());
    Node* node2 = nodes[pos2];
    nodes.erase(nodes.begin() + static_cast<ptrdiff_t>(pos2));
    // Add new node:
    Node* parent = new Node();
    parent->addSon(node1);
    parent->addSon(node2);
    nodes.push_back(parent);
  }
  // Return tree with last node as root node:
  Node* root = new Node();
  for (size_t i = 0; i < nodes.size(); ++i)
  {
    root->addSon(nodes[i]);
  }
  TreeTemplate<Node>* tree = new TreeTemplate<Node>(root);
  tree->resetNodesId();
  return tree;
}

TreeTemplate<Node>* BipartitionList::toTree() const throw (Exception)
{
  BipartitionList* sortedBipL;
  vector<int*> sortedBitBipL;
  int* bip;
  vector<Node*> vecNd, sonNd;
  vector<bool> alive;
  size_t lword, nbword, nbint, ii;

  /* check, copy and prepare bipartition list */

  if (!BipartitionList::areAllCompatible())
    throw Exception("Trying to build a tree from incompatible bipartitions");

  sortedBipL = dynamic_cast<BipartitionList*>(clone());
  for (size_t i = 0; i < sortedBipL->getNumberOfBipartitions(); i++)
  {
    if (sortedBipL->getPartitionSize(i) > sortedBipL->getNumberOfElements() / 2)
      sortedBipL->flip(i);
  }
  sortedBipL->sortByPartitionSize();
  sortedBipL->removeRedundantBipartitions();
  sortedBitBipL = sortedBipL->getBitBipartitionList();

  for (size_t i = 0; i < sortedBipL->getNumberOfBipartitions(); i++)
  {
    alive.push_back(true);
  }
  vecNd.resize(sortedBipL->getNumberOfBipartitions() + 1);
  lword  = static_cast<size_t>(BipartitionTools::LWORD);
  nbword = (elements_.size() + lword - 1) / lword;
  nbint  = nbword * lword / (CHAR_BIT * sizeof(int));
  bip    = new int[1]; bip[0] = 0;

  /* main loop: create one node per bipartition */
  for (size_t i = 0; i < sortedBipL->getNumberOfBipartitions(); i++)
  {
    if (sortedBipL->getPartitionSize(i) == 1)
    { // terminal
      for (size_t j = 0; j < sortedBipL->getNumberOfElements(); j++)
      {
        if (BipartitionTools::testBit(sortedBitBipL[i], static_cast<int>(j)))
        {
          vecNd[i] = new Node(elements_[j]);
          break;
        }
      }
    }
    else
    { // internal
      sonNd.clear();
      for (size_t j = 0; j < i; j++)
      {
        if (alive[j])
        {
          for (ii = 0; ii < nbint; ii++)
          {
            BipartitionTools::bitOr(bip, sortedBitBipL[j] + ii, sortedBitBipL[i] + ii, 1);
            if (bip[0] != sortedBitBipL[i][ii])
              break;
          }
          if (ii == nbint)
          {
            sonNd.push_back(vecNd[j]);
            alive[j] = false;
          }
        }
      }
      vecNd[i] = new Node();
      for (size_t k = 0; k < sonNd.size(); k++)
      {
        vecNd[i]->addSon(sonNd[k]);
      }
    }
  }

  /* create last node, which joins alive bipartitions = fatherless nodes */
  Node* rootNd = new Node();
  for (size_t i = 0; i < sortedBipL->getNumberOfBipartitions(); i++)
  {
    if (alive[i])
      rootNd->addSon(vecNd[i]);
  }

  /* construct tree and return */
  TreeTemplate<Node>* tr = new TreeTemplate<Node>(rootNd);
  tr->resetNodesId();
  delete sortedBipL;
  return tr;
}