F84.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_MODEL_NUCLEOTIDE_F84_H
#define BPP_PHYL_MODEL_NUCLEOTIDE_F84_H
 
#include <Bpp/Numeric/Constraints.h>
 
#include "NucleotideSubstitutionModel.h"
 
// From bpp-seq:
#include <Bpp/Seq/Alphabet/NucleicAlphabet.h>
 
namespace bpp
{
class F84 :
  public AbstractReversibleNucleotideSubstitutionModel
{
private:
  double kappa_, piA_, piC_, piG_, piT_, piY_, piR_, r_, k1_, k2_, theta_, theta1_, theta2_;
  mutable double l_, exp1_, exp2_;
  mutable RowMatrix<double> p_;
 
public:
  F84(
      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 ~F84() {}
 
  F84* clone() const { return new F84(*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 "F84"; }
 
  void setFreq(std::map<int, double>&);
 
protected:
  void updateMatrices_();
};
} // end of namespace bpp.
#endif // BPP_PHYL_MODEL_NUCLEOTIDE_F84_H