PGMA.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_DISTANCE_PGMA_H
#define BPP_PHYL_DISTANCE_PGMA_H
 
 
#include "../Tree/Tree.h"
#include "../Tree/TreeTemplate.h"
#include "AbstractAgglomerativeDistanceMethod.h"
 
namespace bpp
{
struct PGMAInfos
{
  size_t numberOfLeaves;
  double time;
};
 
class PGMA :
  public AbstractAgglomerativeDistanceMethod
{
protected:
  bool weighted_;
 
public:
  PGMA(bool weighted = true) :
    AbstractAgglomerativeDistanceMethod(true, true),
    weighted_(weighted) {}
 
  PGMA(const DistanceMatrix& matrix, bool weighted = true, bool verbose = true) :
    AbstractAgglomerativeDistanceMethod(matrix, verbose, true),
    weighted_(weighted)
  {
    computeTree();
  }
  virtual ~PGMA() {}
 
  PGMA* clone() const { return new PGMA(*this); }
 
public:
  std::string getName() const { return std::string(weighted_ ? "W" : "U") + "PGMA"; }
 
  void setDistanceMatrix(const DistanceMatrix& matrix)
  {
    AbstractAgglomerativeDistanceMethod::setDistanceMatrix(matrix);
  }
 
  void setWeighted(bool weighted) { weighted_ = weighted; }
  bool isWeighted() const { return weighted_; }
 
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_PGMA_H