Tree.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_TREE_TREE_H
#define BPP_PHYL_TREE_TREE_H
 
 
#include "TreeExceptions.h"
 
// From Utils:
#include <Bpp/Clonable.h>
 
// From the STL:
#include <string>
#include <vector>
#include <map>
 
namespace bpp
{
class Tree :
  public virtual Clonable
{
public:
  // Constructors and destructor:
 
  Tree() {}
  virtual ~Tree() {}
 
  Tree* clone() const = 0;
 
  virtual Tree* cloneSubtree(int newRootId) const = 0;
 
public:
  virtual std::string getName() const = 0;
 
  virtual void setName(const std::string& name) = 0;
  virtual size_t getNumberOfLeaves() const = 0;
 
  virtual size_t getNumberOfNodes() const = 0;
 
  virtual size_t getNumberOfBranches() const = 0;
 
  virtual std::vector<double> getBranchLengths() const = 0;
 
  virtual std::vector<std::string> getLeavesNames() const = 0;
 
  virtual int getRootId() const = 0;
 
  virtual int getLeafId(const std::string& name) const = 0;
 
  virtual std::vector<int> getLeavesId() const = 0;
 
  virtual std::vector<int> getNodesId() const = 0;
 
  virtual std::vector<int> getInnerNodesId() const = 0;
 
  virtual std::vector<int> getBranchesId() const = 0;
 
  virtual std::vector<int> getSonsId(int parentId) const = 0;
 
  virtual std::vector<int> getAncestorsId(int nodeId) const = 0;
 
  virtual int getFatherId(int parentId) const = 0;
 
  virtual bool hasFather(int nodeId) const = 0;
 
  virtual std::string getNodeName(int nodeId) const = 0;
 
  virtual void setNodeName(int nodeId, const std::string& name) = 0;
 
  virtual void deleteNodeName(int nodeId) = 0;
 
  virtual bool hasNodeName(int nodeId) const = 0;
  virtual bool hasNode(int nodeId) const = 0;
 
  virtual bool isLeaf(int nodeId) const = 0;
 
  virtual bool hasNoSon(int nodeId) const = 0;
 
  virtual bool isRoot(int nodeId) const = 0;
  void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1);
 
  virtual double getDistanceToFather(int nodeId) const = 0;
 
  virtual void setDistanceToFather(int nodeId, double length) = 0;
 
  virtual void deleteDistanceToFather(int nodeId) = 0;
 
  virtual bool hasDistanceToFather(int nodeId) const = 0;
  virtual bool hasNodeProperty(int nodeId, const std::string& name) const = 0;
 
  virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) = 0;
 
  virtual Clonable* getNodeProperty(int nodeId, const std::string& name) = 0;
 
  virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const = 0;
 
  virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) = 0;
 
  virtual std::vector<std::string> getNodePropertyNames(int nodeId) const = 0;
  virtual bool hasBranchProperty(int nodeId, const std::string& name) const = 0;
 
  virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) = 0;
 
  virtual Clonable* getBranchProperty(int nodeId, const std::string& name) = 0;
 
  virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const = 0;
 
  virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) = 0;
 
  virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const = 0;
  virtual void rootAt(int nodeId) = 0;
 
  virtual void newOutGroup(int nodeId) = 0;
 
  virtual bool isRooted() const = 0;
 
  virtual bool unroot() = 0;
 
  virtual void resetNodesId() = 0;
 
  // Works on (multi)furcations:
 
  virtual bool isMultifurcating() const = 0;
 
  virtual std::vector<double> getBranchLengths() = 0;
 
  virtual double getTotalLength() = 0;
 
  virtual void setBranchLengths(double brLen) = 0;
 
  virtual void setVoidBranchLengths(double brLen) = 0;
 
  virtual void scaleTree(double factor) = 0;
 
  virtual int getNextId() = 0;
};
} // end of namespace bpp.
#endif // BPP_PHYL_TREE_TREE_H