HierarchicalClustering.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_DISTANCE_HIERARCHICALCLUSTERING_H
#define BPP_PHYL_DISTANCE_HIERARCHICALCLUSTERING_H
 
 
#include "AbstractAgglomerativeDistanceMethod.h"
 
namespace bpp
{
class ClusterInfos
{
public:
  size_t numberOfLeaves;
  double length;
 
public:
  ClusterInfos() : numberOfLeaves(0),
    length(0) {}
};
 
class HierarchicalClustering :
  public AbstractAgglomerativeDistanceMethod
{
public:
  static const std::string COMPLETE;
  static const std::string SINGLE;
  static const std::string AVERAGE;
  static const std::string MEDIAN;
  static const std::string WARD;
  static const std::string CENTROID;
 
protected:
  std::string method_;
 
public:
  HierarchicalClustering(const std::string& method, bool verbose = false) :
    AbstractAgglomerativeDistanceMethod(verbose),
    method_(method) {}
  HierarchicalClustering(const std::string& method, const DistanceMatrix& matrix, bool verbose = false) :
    AbstractAgglomerativeDistanceMethod(matrix, verbose, true),
    method_(method)
  {
    computeTree();
  }
 
  virtual ~HierarchicalClustering() {}
 
  HierarchicalClustering* clone() const { return new HierarchicalClustering(*this); }
 
public:
  std::string getName() const { return "Hierarchical clustering: " + method_; }
 
protected:
  std::vector<size_t> getBestPair();
  std::vector<double> computeBranchLengthsForPair(const std::vector<size_t>& pair);
  double computeDistancesFromPair(const std::vector<size_t>& pair, const std::vector<double>& branchLengths, size_t pos);
  void finalStep(int idRoot);
  virtual Node* getLeafNode(int id, const std::string& name);
  virtual Node* getParentNode(int id, Node* son1, Node* son2);
};
} // end of namespace bpp.
#endif // BPP_PHYL_DISTANCE_HIERARCHICALCLUSTERING_H