PhyloTree.h

Go to the documentation of this file.

// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_TREE_PHYLOTREE_H
#define BPP_PHYL_TREE_PHYLOTREE_H
 
#include <Bpp/Graph/AssociationTreeGraphImplObserver.h>
 
#include "PhyloBranch.h"
#include "PhyloNode.h"
#include "TreeTemplate.h"
 
namespace bpp
{
class ParametrizablePhyloTree;
 
class PhyloTree :
  public AssociationTreeGlobalGraphObserver<PhyloNode, PhyloBranch>
{
private:
  std::string name_;
 
public:
  PhyloTree(bool rooted = false);
 
  PhyloTree(const PhyloTree* tree);
 
  PhyloTree(const ParametrizablePhyloTree& tree);
 
  template<class T, class U>
  PhyloTree(AssociationTreeGlobalGraphObserver<T, U> tree) :
    AssociationTreeGlobalGraphObserver<PhyloNode, PhyloBranch>(tree),
    name_("")
  {}
 
  PhyloTree* clone() const
  {
    return new PhyloTree(*this);
  }
 
  std::string getName() const
  {
    return name_;
  }
 
  void setName(const std::string& name)
  {
    name_ = name;
  }
 
  std::vector<std::string> getAllLeavesNames() const;
 
  /*
   *@brief Get PhyloNode with given name, or null shared_ptr if the
   * name is not present in the PhyloTree.
   *
   */
  std::shared_ptr<PhyloNode> getPhyloNode(const std::string& name) const;
 
  Vdouble getBranchLengths() const;
 
  void resetNodesId();
 
  void setBranchLengths(double l);
 
  void scaleTree(double factor);
 
  void pruneTree(std::vector<std::string> leaves);
 
  void scaleTree(std::shared_ptr<PhyloNode> node, double factor);
 
  PhyloTree& operator+=(const PhyloTree& phylotree);
 
  PhyloTree& operator-=(const PhyloTree& phylotree);
 
  PhyloTree& operator/=(const PhyloTree& phylotree);
 
  PhyloTree& operator*=(const PhyloTree& phylotree);
 
  void addSubTree(std::shared_ptr<PhyloNode> phyloNode, const Node& node);
};
}
 
#endif // BPP_PHYL_TREE_PHYLOTREE_H