YpR.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_MODEL_NUCLEOTIDE_YPR_H
#define BPP_PHYL_MODEL_NUCLEOTIDE_YPR_H
 
#include <Bpp/Seq/Alphabet/RNY.h>
 
#include "../AbstractSubstitutionModel.h"
#include "NucleotideSubstitutionModel.h"
 
// From Utils:
#include <Bpp/Exceptions.h>
 
using namespace std;
 
namespace bpp
{
class YpR :
  public AbstractSubstitutionModel
{
protected:
  std::unique_ptr<NucleotideSubstitutionModelInterface> pmodel_;
 
  // Prefix of the native pmodel_
  std::string nestedPrefix_;
 
protected:
  YpR(
      std::shared_ptr<const RNY>,
      std::unique_ptr<NucleotideSubstitutionModelInterface> const,
      const std::string& prefix);
 
  YpR(const YpR& ypr);
 
  YpR& operator=(const YpR& ypr)
  {
    AbstractParameterAliasable::operator=(ypr);
    AbstractSubstitutionModel::operator=(ypr);
    nestedPrefix_ = ypr.nestedPrefix_;
    pmodel_.reset(ypr.pmodel_->clone());
    return *this;
  }
 
public:
  virtual ~YpR() {}
 
protected:
  void updateMatrices_(double, double, double, double,
      double, double, double, double);
 
  virtual void updateMatrices_() override;
 
  string getNestedPrefix() const
  {
    return nestedPrefix_;
  }
 
public:
  //  virtual std::string getName() const;
 
  const NucleotideSubstitutionModelInterface& nestedModel() const { return *pmodel_; }
 
  size_t getNumberOfStates() const override { return 36; }
 
  virtual void setNamespace(const std::string&) override;
 
  void fireParameterChanged(const ParameterList& parameters) override
  {
    AbstractSubstitutionModel::fireParameterChanged(parameters);
    pmodel_->matchParametersValues(parameters);
    updateMatrices_();
  }
 
  // Check that the model is good for YpR
  void checkModel(const SubstitutionModelInterface& model) const;
};
}
 
 
// //////////////////////////////////////
// //////// YpR_symetrical
 
namespace bpp
{
class YpR_Sym :
  public YpR
{
public:
  YpR_Sym(
      std::shared_ptr<const RNY> alph,
      std::unique_ptr<NucleotideSubstitutionModelInterface> pm,
      double CgT = 0., double TgC = 0.,
      double CaT = 0., double TaC = 0.);
 
  YpR_Sym(const YpR_Sym&);
 
  virtual ~YpR_Sym() {}
 
  YpR_Sym* clone() const override { return new YpR_Sym(*this); }
 
  std::string getName() const override;
 
protected:
  void updateMatrices_() override;
};
 
// //////////////////////////////////////
// //////// YpR_general
 
class YpR_Gen :
  public YpR
{
public:
  YpR_Gen(
      std::shared_ptr<const RNY> alph,
      std::unique_ptr<NucleotideSubstitutionModelInterface> pm,
      double CgT = 0., double cGA = 0.,
      double TgC = 0., double tGA = 0.,
      double CaT = 0., double cAG = 0.,
      double TaC = 0., double tAG = 0.);
 
  YpR_Gen(const YpR_Gen&);
 
  virtual ~YpR_Gen() {}
 
  YpR_Gen* clone() const override { return new YpR_Gen(*this); }
 
  std::string getName() const override;
 
protected:
  void updateMatrices_() override;
};
}
#endif // BPP_PHYL_MODEL_NUCLEOTIDE_YPR_H