CodonSubstitutionModel.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_MODEL_CODON_CODONSUBSTITUTIONMODEL_H
#define BPP_PHYL_MODEL_CODON_CODONSUBSTITUTIONMODEL_H
 
 
// From bpp-seq:
#include <Bpp/Seq/GeneticCode/GeneticCode.h>
#include "../SubstitutionModel.h"
#include "../FrequencySet/CodonFrequencySet.h"
 
namespace bpp
{
class CoreCodonSubstitutionModelInterface :
  public virtual ParameterAliasable
{
public:
  CoreCodonSubstitutionModelInterface() {}
  virtual ~CoreCodonSubstitutionModelInterface() {}
 
  virtual CoreCodonSubstitutionModelInterface* clone() const override = 0;
 
public:
  virtual double getCodonsMulRate(size_t, size_t) const = 0;
 
  virtual const CodonFrequencySetInterface& codonFrequencySet() const = 0;
 
  virtual bool hasCodonFrequencySet() const = 0;
 
  virtual void setFreq(std::map<int, double>& frequencies) = 0;
};
 
 
class CodonSubstitutionModelInterface :
  public virtual CoreCodonSubstitutionModelInterface,
  public virtual SubstitutionModelInterface
{
public:
  CodonSubstitutionModelInterface() {}
  virtual ~CodonSubstitutionModelInterface() {}
 
  virtual CodonSubstitutionModelInterface* clone() const override = 0;
 
  virtual std::shared_ptr<const GeneticCode> getGeneticCode() const = 0;
};
 
 
class CodonReversibleSubstitutionModelInterface :
  public virtual CodonSubstitutionModelInterface,
  public virtual ReversibleSubstitutionModelInterface
{
public:
  CodonReversibleSubstitutionModelInterface() {}
  virtual ~CodonReversibleSubstitutionModelInterface() {}
 
  virtual CodonReversibleSubstitutionModelInterface* clone() const override = 0;
};
} // end of namespace bpp.
#endif // BPP_PHYL_MODEL_CODON_CODONSUBSTITUTIONMODEL_H