CodonAdHocSubstitutionModel.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_MODEL_CODON_CODONADHOCSUBSTITUTIONMODEL_H
#define BPP_PHYL_MODEL_CODON_CODONADHOCSUBSTITUTIONMODEL_H
 
 
#include "AbstractCodonSubstitutionModel.h"
 
namespace bpp
{
class CodonAdHocSubstitutionModel :
  public AbstractCodonSubstitutionModel
{
private:
  std::vector< std::unique_ptr<CoreCodonSubstitutionModelInterface>> vModel_;
 
  std::string name_;
 
  std::unique_ptr<CodonFrequencySetInterface> freqSet_;
 
public:
  CodonAdHocSubstitutionModel(
      std::shared_ptr<const GeneticCode> gCode,
      std::unique_ptr<NucleotideSubstitutionModelInterface> pmod,
      std::vector<std::unique_ptr<CoreCodonSubstitutionModelInterface>>& vpmodel,
      const std::string& name);
 
  CodonAdHocSubstitutionModel(
      std::shared_ptr<const GeneticCode> gCode,
      std::unique_ptr<NucleotideSubstitutionModelInterface> pmod1,
      std::unique_ptr<NucleotideSubstitutionModelInterface> pmod2,
      std::unique_ptr<NucleotideSubstitutionModelInterface> pmod3,
      std::vector<std::unique_ptr<CoreCodonSubstitutionModelInterface>>& vpmodel,
      const std::string& name);
 
  CodonAdHocSubstitutionModel(const CodonAdHocSubstitutionModel& model);
 
  CodonAdHocSubstitutionModel& operator=(const CodonAdHocSubstitutionModel& model);
 
  virtual ~CodonAdHocSubstitutionModel() {}
 
  CodonAdHocSubstitutionModel* clone() const override
  {
    return new CodonAdHocSubstitutionModel(*this);
  }
 
public:
  void fireParameterChanged(const ParameterList& parameterlist) override;
 
  std::string getName() const override
  {
    return name_;
  }
 
  void setNamespace(const std::string& prefix) override
  {
    AbstractCodonSubstitutionModel::setNamespace(prefix);
    for (auto& model : vModel_)
    {
      model->setNamespace(prefix);
    }
  }
 
  size_t getNumberOfModels() const
  {
    return vModel_.size();
  }
 
  const CoreCodonSubstitutionModelInterface& layerModel(size_t i) const
  {
    return *vModel_[i];
  }
 
  double getCodonsMulRate(size_t i, size_t j) const override;
 
  void setFreq(std::map<int, double>& frequencies) override;
 
  const CodonFrequencySetInterface& codonFrequencySet() const override
  {
    return *freqSet_;
  }
 
  bool hasCodonFrequencySet() const override
  {
    return freqSet_ != nullptr;
  }
};
} // end of namespace bpp.
#endif // BPP_PHYL_MODEL_CODON_CODONADHOCSUBSTITUTIONMODEL_H