KroneckerCodonDistanceFrequenciesSubstitutionModel.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_MODEL_CODON_KRONECKERCODONDISTANCEFREQUENCIESSUBSTITUTIONMODEL_H
#define BPP_PHYL_MODEL_CODON_KRONECKERCODONDISTANCEFREQUENCIESSUBSTITUTIONMODEL_H
 
 
#include "AbstractCodonDistanceSubstitutionModel.h"
#include "AbstractCodonFrequenciesSubstitutionModel.h"
#include "AbstractKroneckerCodonSubstitutionModel.h"
 
namespace bpp
{
class KroneckerCodonDistanceFrequenciesSubstitutionModel :
  public AbstractKroneckerCodonSubstitutionModel,
  public AbstractCodonDistanceSubstitutionModel,
  public AbstractCodonFrequenciesSubstitutionModel
{
public:
  KroneckerCodonDistanceFrequenciesSubstitutionModel(
      std::shared_ptr<const GeneticCode> gCode,
      std::unique_ptr<NucleotideSubstitutionModelInterface> pmod,
      std::unique_ptr<CodonFrequencySetInterface> pfreq,
      std::shared_ptr<const AlphabetIndex2> pdist = nullptr);
 
  KroneckerCodonDistanceFrequenciesSubstitutionModel(
      std::shared_ptr<const GeneticCode> gCode,
      std::unique_ptr<NucleotideSubstitutionModelInterface> pmod,
      const std::vector<std::set< size_t>>& vPos,
      std::unique_ptr<CodonFrequencySetInterface> pfreq,
      std::shared_ptr<const AlphabetIndex2> pdist = nullptr);
 
  KroneckerCodonDistanceFrequenciesSubstitutionModel(
      std::shared_ptr<const GeneticCode> gCode,
      std::unique_ptr<NucleotideSubstitutionModelInterface> pmod1,
      std::unique_ptr<NucleotideSubstitutionModelInterface> pmod2,
      std::unique_ptr<NucleotideSubstitutionModelInterface> pmod3,
      std::unique_ptr<CodonFrequencySetInterface> pfreq,
      std::shared_ptr<const AlphabetIndex2> pdist = nullptr);
 
  KroneckerCodonDistanceFrequenciesSubstitutionModel(
      std::shared_ptr<const GeneticCode> gCode,
      std::unique_ptr<NucleotideSubstitutionModelInterface> pmod1,
      std::unique_ptr<NucleotideSubstitutionModelInterface> pmod2,
      std::unique_ptr<NucleotideSubstitutionModelInterface> pmod3,
      const std::vector<std::set< size_t>>& vPos,
      std::unique_ptr<CodonFrequencySetInterface> pfreq,
      std::shared_ptr<const AlphabetIndex2> pdist = nullptr);
 
  virtual ~KroneckerCodonDistanceFrequenciesSubstitutionModel() {}
 
  KroneckerCodonDistanceFrequenciesSubstitutionModel* clone() const override
  {
    return new KroneckerCodonDistanceFrequenciesSubstitutionModel(*this);
  }
 
public:
  void fireParameterChanged(const ParameterList& parameterlist) override;
 
  std::string getName() const override;
 
  double getCodonsMulRate(size_t i, size_t j) const override;
 
  void setNamespace(const std::string&) override;
 
  void setFreq(std::map<int, double>& frequencies) override;
 
  const CodonFrequencySetInterface& codonFrequencySet() const override
  {
    return AbstractCodonFrequenciesSubstitutionModel::codonFrequencySet();
  }
 
  bool hasCodonFrequencySet() const override
  {
    return AbstractCodonFrequenciesSubstitutionModel::hasCodonFrequencySet();
  }
};
} // end of namespace bpp.
#endif // BPP_PHYL_MODEL_CODON_KRONECKERCODONDISTANCEFREQUENCIESSUBSTITUTIONMODEL_H