AbstractCodonFrequenciesSubstitutionModel.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_MODEL_CODON_ABSTRACTCODONFREQUENCIESSUBSTITUTIONMODEL_H
#define BPP_PHYL_MODEL_CODON_ABSTRACTCODONFREQUENCIESSUBSTITUTIONMODEL_H
 
 
#include "../FrequencySet/CodonFrequencySet.h"
#include "CodonSubstitutionModel.h"
 
namespace bpp
{
class AbstractCodonFrequenciesSubstitutionModel :
  public virtual CoreCodonSubstitutionModelInterface,
  public virtual AbstractParameterAliasable
{
private:
  std::unique_ptr<CodonFrequencySetInterface> pfreqset_;
  std::string freqName_;
 
public:
  AbstractCodonFrequenciesSubstitutionModel(
      std::unique_ptr<CodonFrequencySetInterface> pfreq,
      const std::string& prefix);
 
  AbstractCodonFrequenciesSubstitutionModel(const AbstractCodonFrequenciesSubstitutionModel& model) :
    AbstractParameterAliasable(model),
    pfreqset_(model.pfreqset_->clone()),
    freqName_(model.freqName_)
  {}
 
  AbstractCodonFrequenciesSubstitutionModel& operator=(const AbstractCodonFrequenciesSubstitutionModel& model)
  {
    AbstractParameterAliasable::operator=(model);
    pfreqset_   = std::unique_ptr<CodonFrequencySetInterface>(model.pfreqset_->clone());
    freqName_   = model.freqName_;
    return *this;
  }
 
  AbstractCodonFrequenciesSubstitutionModel* clone() const override
  {
    return new AbstractCodonFrequenciesSubstitutionModel(*this);
  }
 
  virtual ~AbstractCodonFrequenciesSubstitutionModel();
 
  void fireParameterChanged(const ParameterList& parameters) override;
 
  void setFreq(std::map<int, double>& frequencies) override;
 
  void setNamespace(const std::string& prefix) override
  {
    AbstractParameterAliasable::setNamespace(prefix);
    pfreqset_->setNamespace(prefix + freqName_);
  }
 
  double getCodonsMulRate(size_t, size_t) const override;
 
  const CodonFrequencySetInterface& codonFrequencySet() const override
  {
    return *pfreqset_;
  }
 
  const FrequencySetInterface& frequencySet() const
  {
    return *pfreqset_;
  }
 
  bool hasCodonFrequencySet() const override
  {
    return pfreqset_ != nullptr;
  }
};
} // end of namespace bpp.
#endif // BPP_PHYL_MODEL_CODON_ABSTRACTCODONFREQUENCIESSUBSTITUTIONMODEL_H