HKY85.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_MODEL_NUCLEOTIDE_HKY85_H
#define BPP_PHYL_MODEL_NUCLEOTIDE_HKY85_H
 
#include <Bpp/Numeric/Constraints.h>
 
#include "../AbstractSubstitutionModel.h"
#include "NucleotideSubstitutionModel.h"
 
// From SeqLib:
#include <Bpp/Seq/Alphabet/NucleicAlphabet.h>
 
namespace bpp
{
class HKY85 :
  public AbstractReversibleNucleotideSubstitutionModel
{
private:
  double kappa_, k1_, k2_, r_, piA_, piC_, piG_, piT_, piY_, piR_, theta_, theta1_, theta2_;
  mutable double exp1_, exp21_, exp22_, l_;
  mutable RowMatrix<double> p_;
 
public:
  HKY85(
      std::shared_ptr<const NucleicAlphabet> alpha,
      double kappa = 1.,
      double piA = 0.25,
      double piC = 0.25,
      double piG = 0.25,
      double piT = 0.25);
 
  virtual ~HKY85() {}
 
  HKY85* clone() const { return new HKY85(*this); }
 
public:
  double Pij_t    (size_t i, size_t j, double d) const;
  double dPij_dt  (size_t i, size_t j, double d) const;
  double d2Pij_dt2(size_t i, size_t j, double d) const;
  const Matrix<double>& getPij_t    (double d) const;
  const Matrix<double>& getdPij_dt  (double d) const;
  const Matrix<double>& getd2Pij_dt2(double d) const;
 
  std::string getName() const { return "HKY85"; }
 
  void setFreq(std::map<int, double>& freqs);
 
  void updateMatrices_();
};
} // end of namespace bpp.
#endif // BPP_PHYL_MODEL_NUCLEOTIDE_HKY85_H