AbstractCodonPhaseFrequenciesSubstitutionModel.h

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