libbpp-phyl-dev 2.1.0-1 / usr / include / Bpp / Phyl / TreeTemplate.h

//
// File: TreeTemplate.h
// Created by: Julien Dutheil
//             Celine Scornavacca
// Created on: Thu Mar 13 12:03:18 2003
//

/*
   Copyright or © or Copr. Bio++ Development Team, (November 16, 2004)

   This software is a computer program whose purpose is to provide classes
   for phylogenetic data analysis.

   This software is governed by the CeCILL  license under French law and
   abiding by the rules of distribution of free software.  You can  use,
   modify and/ or redistribute the software under the terms of the CeCILL
   license as circulated by CEA, CNRS and INRIA at the following URL
   "http://www.cecill.info".

   As a counterpart to the access to the source code and  rights to copy,
   modify and redistribute granted by the license, users are provided only
   with a limited warranty  and the software's author,  the holder of the
   economic rights,  and the successive licensors  have only  limited
   liability.

   In this respect, the user's attention is drawn to the risks associated
   with loading,  using,  modifying and/or developing or reproducing the
   software by the user in light of its specific status of free software,
   that may mean  that it is complicated to manipulate,  and  that  also
   therefore means  that it is reserved for developers  and  experienced
   professionals having in-depth computer knowledge. Users are therefore
   encouraged to load and test the software's suitability as regards their
   requirements in conditions enabling the security of their systems and/or
   data to be ensured and,  more generally, to use and operate it in the
   same conditions as regards security.

   The fact that you are presently reading this means that you have had
   knowledge of the CeCILL license and that you accept its terms.
 */

#ifndef _TREETEMPLATE_H_
#define _TREETEMPLATE_H_

#include "TreeExceptions.h"
#include "TreeTemplateTools.h"
#include "Tree.h"

// From the STL:
#include <string>
#include <vector>
#include <map>

namespace bpp
{
/**
 * @brief The phylogenetic tree class.
 *
 * This class is part of the object implementation of phylogenetic trees. Tree are made
 * made of nodes, instances of the class Node. It is possible to use a tree with more
 * complexe Node classes, but currently all nodes of a tree have to be of the same class.
 *
 * Trees are oriented (rooted), i.e. each node has one <i>father node</i> and possibly
 * many <i>son nodes</i>. Leaves are nodes without descendant and root is defined has the without
 * father. Inner nodes will generally contain two descendants (the tree is then called
 * <i>bifurcating</i>), but mutlifurcating trees are also allowed with this kind of description.
 * In the rooted case, each inner node also defines a <i>subtree</i>.
 * This allows to work recursively on trees, which is very convenient in most cases.
 * To deal with non-rooted trees, we place an artificial root at a particular node:
 * hence the root node appears to be trifurcated. This is the way unrooted trees are
 * described in the parenthetic description, the so called Newick format.
 *
 * To clone a tree from from another tree with a different template,
 * consider using the TreeTools::cloneSutree<N>() method:
 * @code
 * Tree * t = new Tree<Node>(...)
 * NodeTemplate<int> * newRoot = TreeTools::cloneSubtree< NodeTemplate<int> >(* (t -> getRootNode()))
 * Tree< NodeTemplate<int> > * tt = new Tree< NodeTemplate<int> >(* newRoot);
 * @endcode
 *
 * The getNextId() method sends a id value which is not used in the tree.
 * In the current implementation, it uses the TreeTools::getMPNUId() method.
 * This avoids to use duplicated ids, but is time consuming.
 * In most cases, it is of better efficiency if the user deal with the ids himself, by using the Node::setId() method.
 * The TreeTools::getMaxId() method may also prove useful in this respect.
 * The resetNodesId() method can also be used to re-initialize all ids.
 *
 * @see Node
 * @see NodeTemplate
 * @see TreeTools
 */
template<class N>
class TreeTemplate :
  public Tree
{
  /**
   * Fields:
   */

private:
  N* root_;
  std::string name_;

public:
  // Constructors and destructor:
  TreeTemplate() : root_(0),
    name_() {}

  TreeTemplate(const TreeTemplate<N>& t) :
    root_(0),
    name_(t.name_)
  {
    // Perform a hard copy of the nodes:
    root_ = TreeTemplateTools::cloneSubtree<N>(*t.getRootNode());
  }

  TreeTemplate(const Tree& t) :
    root_(0),
    name_(t.getName())
  {
    // Create new nodes from an existing tree:
    root_ = TreeTemplateTools::cloneSubtree<N>(t, t.getRootId());
  }

  TreeTemplate(N* root) : root_(root),
    name_()
  {
    root_->removeFather(); // In case this is a subtree from somewhere else...
  }

  TreeTemplate<N>& operator=(const TreeTemplate<N>& t)
  {
    // Perform a hard copy of the nodes:
    if (root_) { TreeTemplateTools::deleteSubtree(root_); delete root_; }
    root_ = TreeTemplateTools::cloneSubtree<N>(*t.getRootNode());
    name_ = t.name_;
    return *this;
  }

  TreeTemplate<N>* cloneSubtree(int newRootId) const
  {
    N* newRoot = TreeTemplateTools::cloneSubtree<N>(*this, newRootId);
    return new TreeTemplate<N>(newRoot);
  }

  virtual ~TreeTemplate()
  {
    TreeTemplateTools::deleteSubtree(root_);
    delete root_;
  }

  TreeTemplate<N>* clone() const { return new TreeTemplate<N>(*this); }

  /**
   * Methods:
   */

public:
  std::string getName() const { return name_; }

  void setName(const std::string& name) { name_ = name; }

  int getRootId() const { return root_->getId(); }

  size_t getNumberOfLeaves() const { return TreeTemplateTools::getNumberOfLeaves(*root_); }

  size_t getNumberOfNodes() const { return TreeTemplateTools::getNumberOfNodes(*root_); }

  int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }

  std::vector<int> getLeavesId() const { return TreeTemplateTools::getLeavesId(*root_); }

  std::vector<int> getNodesId() const { return TreeTemplateTools::getNodesId(*root_); }

  std::vector<int> getInnerNodesId() const { return TreeTemplateTools::getInnerNodesId(*root_); }

  std::vector<int> getBranchesId() const { return TreeTemplateTools::getBranchesId(*root_); }

  std::vector<double> getBranchLengths() const { return TreeTemplateTools::getBranchLengths(*root_); }

  std::vector<std::string> getLeavesNames() const { return TreeTemplateTools::getLeavesNames(*const_cast<const N*>( root_)); }

  std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException)  { return getNode(parentId)->getSonsId(); }

  std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }

  int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }

  bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }

  std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }

  bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }

  void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }

  void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }

  bool hasNode(int nodeId) const { return TreeTemplateTools::hasNodeWithId(*root_, nodeId); }

  bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }

  bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }

  double getDistanceToFather(int nodeId) const { return getNode(nodeId)->getDistanceToFather(); }

  void setDistanceToFather(int nodeId, double length) { getNode(nodeId)->setDistanceToFather(length); }

  void deleteDistanceToFather(int nodeId) { getNode(nodeId)->deleteDistanceToFather(); }

  bool hasDistanceToFather(int nodeId) const { return getNode(nodeId)->hasDistanceToFather(); }

  bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }

  void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }

  Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }

  const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }

  Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }

  std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }

  bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }

  void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }

  Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }

  const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }

  Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }

  std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }

  void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }

  void newOutGroup(int nodeId) throw (NodeNotFoundException) {  newOutGroup(getNode(nodeId)); }

  bool isRooted() const { return root_->getNumberOfSons() == 2; }

  bool unroot() throw (UnrootedTreeException)
  {
    if (!isRooted()) throw UnrootedTreeException("Tree::unroot", this);
    else
    {
      N* son1 = root_->getSon(0);
      N* son2 = root_->getSon(1);
      if (son1->isLeaf() && son2->isLeaf()) return false;  // We can't unroot a single branch!

      // We manage to have a subtree in position 0:
      if (son1->isLeaf())
      {
        root_->swap(0, 1);
        son1 = root_->getSon(0);
        son2 = root_->getSon(1);
      }

      // Take care of branch lengths:
      if (son1->hasDistanceToFather())
      {
        if (son2->hasDistanceToFather())
        {
          // Both nodes have lengths, we sum them:
          son2->setDistanceToFather(son1->getDistanceToFather() + son2->getDistanceToFather());
        }
        else
        {
          // Only node 1 has length, we set it to node 2:
          son2->setDistanceToFather(son1->getDistanceToFather());
        }
        son1->deleteDistanceToFather();
      } // Else node 2 may or may not have a branch length, we do not care!

      // Remove the root:
      root_->removeSons();
      son1->addSon(son2);
      delete root_;
      setRootNode(son1);
      return true;
    }
  }

  void resetNodesId()
  {
    std::vector<N*> nodes = getNodes();
    for (size_t i = 0; i < nodes.size(); i++)
    {
      nodes[i]->setId(static_cast<int>(i));
    }
  }

  bool isMultifurcating() const
  {
    if (root_->getNumberOfSons() > 3) return true;
    for (size_t i = 0; i < root_->getNumberOfSons(); i++)
      if (TreeTemplateTools::isMultifurcating(*root_->getSon(i)))
        return true;
    return false;
  }

  /**
   * @brief Tells if this tree has the same topology as the one given for comparison.
   *
   * This method compares recursively all subtrees. The comparison is performed only on the nodes names and the parental relationships.
   * Nodes ids are ignored, and so are branch lengths and any branch/node properties. The default is to ignore the ordering of the descendants,
   * that is (A,B),C) will be considered as having the same topology as (B,A),C). Multifurcations are permited.
   * If ordering is ignored, a copy of the two trees to be compared is performed and are ordered before comparison, making the whole comparison
   * slower and more memory greedy.
   *
   * @param tree The tree to be compared with.
   * @param ordered Should the ordering of the branching be taken into account?
   * @return True if the input tree has the same topology as this one.
   */
  template<class N2>
  bool hasSameTopologyAs(const TreeTemplate<N2>& tree, bool ordered = false) const
  {
    const TreeTemplate<N>* t1 = 0;
    const TreeTemplate<N2>* t2 = 0;
    if (ordered)
    {
      t1 = this;
      t2 = &tree;
    }
    else
    {
      TreeTemplate<N>* t1tmp = this->clone();
      TreeTemplate<N2>* t2tmp = tree.clone();
      TreeTemplateTools::orderTree(*t1tmp->getRootNode(), true, true);
      TreeTemplateTools::orderTree(*t2tmp->getRootNode(), true, true);
      t1 = t1tmp;
      t2 = t2tmp;
    }
    bool test = TreeTemplateTools::haveSameOrderedTopology(*t1->getRootNode(), *t2->getRootNode());
    if (!ordered)
    {
      delete t1;
      delete t2;
    }
    return test;
  }

  std::vector<double> getBranchLengths() throw (NodeException)
  {
    Vdouble brLen(1);
    for (size_t i = 0; i < root_->getNumberOfSons(); i++)
    {
      Vdouble sonBrLen = TreeTemplateTools::getBranchLengths(*root_->getSon(i));
      for (size_t j = 0; j < sonBrLen.size(); j++) { brLen.push_back(sonBrLen[j]); }
    }
    return brLen;
  }

  double getTotalLength() throw (NodeException)
  {
    return TreeTemplateTools::getTotalLength(*root_, false);
  }

  void setBranchLengths(double brLen)
  {
    for (size_t i = 0; i < root_->getNumberOfSons(); i++)
    {
      TreeTemplateTools::setBranchLengths(*root_->getSon(i), brLen);
    }
  }

  void setVoidBranchLengths(double brLen)
  {
    for (size_t i = 0; i < root_->getNumberOfSons(); i++)
    {
      TreeTemplateTools::setVoidBranchLengths(*root_->getSon(i), brLen);
    }
  }

  void scaleTree(double factor) throw (NodeException)
  {
    for (size_t i = 0; i < root_->getNumberOfSons(); i++)
    {
      TreeTemplateTools::scaleTree(*root_->getSon(i), factor);
    }
  }

  int getNextId()
  {
    return TreeTools::getMPNUId(*this, root_->getId());
  }

  void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
  {
    std::vector<N*> nodes = TreeTemplateTools::searchNodeWithId<N>(*root_, parentId);
    if (nodes.size() == 0) throw NodeNotFoundException("TreeTemplate:swapNodes(): Node with id not found.", "" + parentId);
    for (size_t i = 0; i < nodes.size(); i++) { nodes[i]->swap(i1, i2); }
  }


  /**
   * @name Specific methods
   *
   * @{
   */
  virtual void setRootNode(N* root) { root_ = root; }

  virtual N* getRootNode() { return root_; }

  virtual const N* getRootNode() const { return root_; }

  virtual std::vector<const N*> getLeaves() const { return TreeTemplateTools::getLeaves(*const_cast<const N*>(root_)); }

  virtual std::vector<N*> getLeaves() { return TreeTemplateTools::getLeaves(*root_); }

  virtual std::vector<const N*> getNodes() const { return TreeTemplateTools::getNodes(*const_cast<const N*>(root_)); }

  virtual std::vector<N*> getNodes() { return TreeTemplateTools::getNodes(*root_); }

  virtual std::vector<const N*> getInnerNodes() const { return TreeTemplateTools::getInnerNodes(*const_cast<const N*>(root_)); }

  virtual std::vector<N*> getInnerNodes() { return TreeTemplateTools::getInnerNodes(*root_); }

  virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
  {
    if (checkId) {
      std::vector<N*> nodes;
      TreeTemplateTools::searchNodeWithId<N>(*root_, id, nodes);
      if (nodes.size() > 1) throw Exception("TreeTemplate::getNode(): Non-unique id! (" + TextTools::toString(id) + ").");
      if (nodes.size() == 0) throw NodeNotFoundException("TreeTemplate::getNode(): Node with id not found.", TextTools::toString(id));
      return nodes[0];
    } else {
      N* node = dynamic_cast<N*>(TreeTemplateTools::searchFirstNodeWithId(*root_, id));
      if (node)
        return node;
      else
        throw NodeNotFoundException("TreeTemplate::getNode(): Node with id not found.", TextTools::toString(id));
    }
  }

  virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
  {
    if (checkId) {
      std::vector<const N*> nodes;
      TreeTemplateTools::searchNodeWithId<const N>(*root_, id, nodes);
      if (nodes.size() > 1) throw Exception("TreeTemplate::getNode(): Non-unique id! (" + TextTools::toString(id) + ").");
      if (nodes.size() == 0) throw NodeNotFoundException("TreeTemplate::getNode(): Node with id not found.", TextTools::toString(id));
      return nodes[0];
    } else {
      const N* node = dynamic_cast<const N*>(TreeTemplateTools::searchFirstNodeWithId(*root_, id));
      if (node)
        return node;
      else
        throw NodeNotFoundException("TreeTemplate::getNode(): Node with id not found.", TextTools::toString(id));
    }
  }

  virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
  {
    std::vector<N*> nodes;
    TreeTemplateTools::searchNodeWithName(*root_, name, nodes);
    if (nodes.size() > 1) throw NodeNotFoundException("TreeTemplate::getNode(): Non-unique name.", "" + name);
    if (nodes.size() == 0) throw NodeNotFoundException("TreeTemplate::getNode(): Node with name not found.", "" + name);
    return nodes[0];
  }

  virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
  {
    std::vector<const N*> nodes;
    TreeTemplateTools::searchNodeWithName<const N>(*root_, name, nodes);
    if (nodes.size() > 1) throw NodeNotFoundException("TreeTemplate::getNode(): Non-unique name.", "" + name);
    if (nodes.size() == 0) throw NodeNotFoundException("TreeTemplate::getNode(): Node with name not found.", "" + name);
    return nodes[0];
  }

  void rootAt(N* newRoot)
  {
    if (root_ == newRoot) return;
    if (isRooted()) unroot();
    std::vector<Node*> path = TreeTemplateTools::getPathBetweenAnyTwoNodes(*root_, *newRoot);

    for (size_t i = 0; i < path.size() - 1; i++)
    {
      // pathMatrix[i] -> _father = pathMatrix[i + 1];
      // pathMatrix[i] -> setDistanceToFather(pathMatrix[i + 1] -> getDistanceToFather());
      // typename vector<Node *>::iterator vec_iter;
      // vec_iter = remove(pathMatrix[i] -> _sons.begin(), pathMatrix[i] -> _sons.end(), pathMatrix[i + 1]);
      // pathMatrix[i] -> _sons.erase(vec_iter, pathMatrix[i] -> _sons.end()); // pg 1170, primer.
      // pathMatrix[i+1] -> _sons.push_back(pathMatrix[i + 1] -> getFather());
      // pathMatrix[i+1] -> _father = 0;
      path[i]->removeSon(path[i + 1]);
      if (path[i + 1]->hasDistanceToFather()) path[i]->setDistanceToFather(path[i + 1]->getDistanceToFather());
      else path[i]->deleteDistanceToFather();
      path[i + 1]->addSon(path[i]);

      std::vector<std::string> names = path[i + 1]->getBranchPropertyNames();
      for (size_t j = 0; j < names.size(); j++)
      {
        path[i]->setBranchProperty(names[j], *path[i + 1]->getBranchProperty(names[j]));
      }
      path[i + 1]->deleteBranchProperties();
    }
    newRoot->deleteDistanceToFather();
    newRoot->deleteBranchProperties();
    root_ = newRoot;
  }

  void newOutGroup(N* outGroup)
  {
    if (root_ == outGroup) return;
    int rootId;
    if (isRooted())
    {
      for (size_t i = 0; i < root_->getNumberOfSons(); i++)
      {
        if (root_->getSon(i) == outGroup) return;  // This tree is already rooted appropriately.
      }
      rootId = getRootId();
      unroot();
    }
    else
    {
      rootId = getNextId();
    }
    rootAt(outGroup->getFather());
    N* oldRoot = root_;
    oldRoot->removeSon(outGroup);
    root_ = new N();
    root_->setId(rootId);
    root_->addSon(oldRoot);
    root_->addSon(outGroup);
    // Check lengths:
    if (outGroup->hasDistanceToFather())
    {
      double l = outGroup->getDistanceToFather() / 2.;
      outGroup->setDistanceToFather(l);
      oldRoot->setDistanceToFather(l);
    }
  }

  /** @} */
};
} // end of namespace bpp.

#endif  // _TREETEMPLATE_H_