NeighborJoining.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_DISTANCE_NEIGHBORJOINING_H
#define BPP_PHYL_DISTANCE_NEIGHBORJOINING_H
 
 
#include "AbstractAgglomerativeDistanceMethod.h"
 
namespace bpp
{
class NeighborJoining :
  public AbstractAgglomerativeDistanceMethod
{
protected:
  std::vector<double> sumDist_;
  bool positiveLengths_;
 
public:
  NeighborJoining(bool rooted = false, bool positiveLengths = false, bool verbose = true) :
    AbstractAgglomerativeDistanceMethod(verbose, rooted),
    sumDist_(),
    positiveLengths_(false)
  {}
 
  NeighborJoining(const DistanceMatrix& matrix, bool rooted = false, bool positiveLengths = false, bool verbose = true) :
    AbstractAgglomerativeDistanceMethod(matrix, verbose, rooted),
    sumDist_(),
    positiveLengths_(positiveLengths)
  {
    sumDist_.resize(matrix.size());
    computeTree();
  }
 
  virtual ~NeighborJoining() {}
 
  NeighborJoining* clone() const { return new NeighborJoining(*this); }
 
public:
  std::string getName() const { return "NJ"; }
 
  virtual void setDistanceMatrix(const DistanceMatrix& matrix)
  {
    AbstractAgglomerativeDistanceMethod::setDistanceMatrix(matrix);
    sumDist_.resize(matrix.size());
  }
 
  virtual void outputPositiveLengths(bool yn) { positiveLengths_ = yn; }
 
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);
};
} // end of namespace bpp.
#endif // BPP_PHYL_DISTANCE_NEIGHBORJOINING_H