AbstractCodonAARateSubstitutionModel.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_MODEL_CODON_ABSTRACTCODONAARATESUBSTITUTIONMODEL_H
#define BPP_PHYL_MODEL_CODON_ABSTRACTCODONAARATESUBSTITUTIONMODEL_H
 
 
#include "../Protein/ProteinSubstitutionModel.h"
#include "CodonSubstitutionModel.h"
 
// From bpp-seq:
#include <Bpp/Seq/GeneticCode/GeneticCode.h>
#include <Bpp/Seq/AlphabetIndex/AlphabetIndex2.h>
 
namespace bpp
{
class AbstractCodonAARateSubstitutionModel :
  public virtual CoreCodonSubstitutionModelInterface,
  public virtual AbstractParameterAliasable
{
private:
  std::shared_ptr<ProteinSubstitutionModelInterface> pAAmodel_;
 
  std::shared_ptr<const GeneticCode> pgencode_;
 
  double beta_;
 
  double gamma_;
 
  std::shared_ptr<const StateMapInterface> stateMap_;
 
public:
  AbstractCodonAARateSubstitutionModel(
      std::shared_ptr<ProteinSubstitutionModelInterface> pmodel,
      std::shared_ptr<const GeneticCode> pgencode,
      const std::string& prefix,
      bool paramSynRate = false);
 
 
  AbstractCodonAARateSubstitutionModel(const AbstractCodonAARateSubstitutionModel& model) :
    AbstractParameterAliasable(model),
    pAAmodel_(model.pAAmodel_),
    pgencode_(model.pgencode_),
    beta_(model.beta_),
    gamma_(model.gamma_),
    stateMap_(model.stateMap_)
  {}
 
  AbstractCodonAARateSubstitutionModel& operator=(
      const AbstractCodonAARateSubstitutionModel& model)
  {
    AbstractParameterAliasable::operator=(model);
    pAAmodel_ = model.pAAmodel_;
    pgencode_ = model.pgencode_;
    beta_ = model.beta_;
    gamma_ = model.gamma_;
    stateMap_ = model.stateMap_;
 
    return *this;
  }
 
  AbstractCodonAARateSubstitutionModel* clone() const override
  {
    return new AbstractCodonAARateSubstitutionModel(*this);
  }
 
  virtual ~AbstractCodonAARateSubstitutionModel() {}
 
public:
  void fireParameterChanged(const ParameterList& parameters) override;
 
  double getCodonsMulRate(size_t i, size_t j) const override;
 
  void setNamespace(const std::string& prefix) override
  {
    AbstractParameterAliasable::setNamespace(prefix);
    pAAmodel_->setNamespace(prefix + pAAmodel_->getNamespace());
  }
 
  /*
   * @brief links to a new AA model
   *
   */
  void setAAModel(std::shared_ptr<ProteinSubstitutionModelInterface> model)
  {
    pAAmodel_ = model;
  }
 
  const ProteinSubstitutionModelInterface& aaModel() const
  {
    return *pAAmodel_;
  }
 
  const std::shared_ptr<ProteinSubstitutionModelInterface> getAAModel() const
  {
    return pAAmodel_;
  }
 
  const CodonFrequencySetInterface& codonFrequencySet() const override
  {
    throw NullPointerException("AbstractCodonAARateSubstitutionModel::frequencySet. No associated FrequencySet.");
  }
 
  bool hasCodonFrequencySet() const override
  {
    return false;
  }
 
  void setFreq(std::map<int, double>& frequencies) override {}
};
} // end of namespace bpp.
#endif // BPP_PHYL_MODEL_CODON_ABSTRACTCODONAARATESUBSTITUTIONMODEL_H