BioNJ.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_DISTANCE_BIONJ_H
#define BPP_PHYL_DISTANCE_BIONJ_H
 
 
#include "NeighborJoining.h"
 
namespace bpp
{
class BioNJ :
  public NeighborJoining
{
private:
  DistanceMatrix variance_;
  double lambda_;
 
public:
  BioNJ(bool rooted = false, bool positiveLengths = false, bool verbose = true) :
    NeighborJoining(rooted, positiveLengths, verbose),
    variance_(0),
    lambda_(0) {}
 
  BioNJ(const DistanceMatrix& matrix, bool rooted = false, bool positiveLengths = false, bool verbose = true) :
    NeighborJoining(rooted, positiveLengths, verbose),
    // Use the default constructor, because the other one call computeTree.
    variance_(matrix),
    lambda_(0)
  {
    setDistanceMatrix(matrix);
    outputPositiveLengths(positiveLengths);
    computeTree();
  }
 
  BioNJ* clone() const { return new BioNJ(*this); }
 
  virtual ~BioNJ() {}
 
public:
  std::string getName() const { return "BioNJ"; }
 
  void setDistanceMatrix(const DistanceMatrix& matrix)
  {
    NeighborJoining::setDistanceMatrix(matrix);
    variance_ = matrix;
  }
  void computeTree();
  double computeDistancesFromPair(const std::vector<size_t>& pair, const std::vector<double>& branchLengths, size_t pos);
};
} // end of namespace bpp.
#endif // BPP_PHYL_DISTANCE_BIONJ_H