TwoParameterBinarySubstitutionModel.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_MODEL_TWOPARAMETERBINARYSUBSTITUTIONMODEL_H
#define BPP_PHYL_MODEL_TWOPARAMETERBINARYSUBSTITUTIONMODEL_H
 
#include <Bpp/Seq/Alphabet/BinaryAlphabet.h>
 
#include "AbstractSubstitutionModel.h"
 
namespace bpp
{
class TwoParameterBinarySubstitutionModel :
  public AbstractReversibleSubstitutionModel
{
private:
  double mu_;
  double pi0_;
 
protected:
  mutable double lambda_, exp_;
  mutable RowMatrix<double> p_;
 
public:
  TwoParameterBinarySubstitutionModel(std::shared_ptr<const BinaryAlphabet> alpha, double mu = 1., double pi0 = 0.5);
 
  virtual ~TwoParameterBinarySubstitutionModel() {}
 
  TwoParameterBinarySubstitutionModel* clone() const { return new TwoParameterBinarySubstitutionModel(*this); }
 
public:
  // the inherited functions don't do the work - need to override them with the correct computation
  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 "TwoParameterBinary"; }
 
  size_t getNumberOfStates() const { return 2; }
 
  void setMuBounds(double lb, double ub);
 
protected:
  void updateMatrices_();
};
} // end of namespace bpp.
#endif // BPP_PHYL_MODEL_TWOPARAMETERBINARYSUBSTITUTIONMODEL_H