PhyloDAG.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_TREE_PHYLODAG_H
#define BPP_PHYL_TREE_PHYLODAG_H
 
#include <Bpp/Graph/AssociationDAGraphImplObserver.h>
 
#include "PhyloBranch.h"
#include "PhyloNode.h"
 
namespace bpp
{
class ParametrizablePhyloDAG;
 
class PhyloDAG :
  public AssociationDAGlobalGraphObserver<PhyloNode, PhyloBranch>
{
private:
  std::string name_;
 
public:
  PhyloDAG();
 
  PhyloDAG(const PhyloDAG* dag);
 
  PhyloDAG(const ParametrizablePhyloDAG& dag);
 
  template<class T, class U>
  PhyloDAG(AssociationDAGlobalGraphObserver<T, U> dag) :
    AssociationDAGlobalGraphObserver<PhyloNode, PhyloBranch>(dag),
    name_("")
  {}
 
  PhyloDAG* clone() const
  {
    return new PhyloDAG(*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 PhyloDAG.
   *
   */
  std::shared_ptr<PhyloNode> getPhyloNode(const std::string& name) const;
 
  Vdouble getBranchLengths() const;
 
  /*
   *@brief set indexes to nodes & edges.
   * For each node, one (arbitrary) edge has the same index.
   */
 
  void resetNodesId();
 
  void setBranchLengths(double l);
 
  void scaleDAG(double factor);
 
  void pruneDAG(std::vector<std::string> leaves);
 
  void scaleDAG(std::shared_ptr<PhyloNode> node, double factor);
 
  PhyloDAG& operator+=(const PhyloDAG& phylotree);
 
  PhyloDAG& operator-=(const PhyloDAG& phylotree);
 
  PhyloDAG& operator/=(const PhyloDAG& phylotree);
 
  PhyloDAG& operator*=(const PhyloDAG& phylotree);
 
  // /**
  //  * @brief Concatenate the subtree under a Node (in a
  //  * DAGTemplate<Node>) to this PhyloTree, under the given phylonode.
  //  */
  // void addSubTree(std::shared_ptr<PhyloNode> phyloNode, const Node& node);
};
}
 
#endif // BPP_PHYL_TREE_PHYLOTREE_H