CodonSameAARateSubstitutionModel.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_MODEL_CODON_CODONSAMEAARATESUBSTITUTIONMODEL_H
#define BPP_PHYL_MODEL_CODON_CODONSAMEAARATESUBSTITUTIONMODEL_H
 
 
#include "../FrequencySet/CodonFrequencySet.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 CodonSameAARateSubstitutionModel :
  public virtual CodonSubstitutionModelInterface,
  public AbstractSubstitutionModel
{
private:
  std::unique_ptr<ProteinSubstitutionModelInterface> pAAmodel_;
 
  std::unique_ptr<CodonSubstitutionModelInterface> pCodonModel_;
 
  std::unique_ptr<CodonFrequencySetInterface> pFreq_;
 
  std::shared_ptr<const GeneticCode> pgencode_;
 
  RowMatrix<double> X_;
 
  Vdouble phi_;
 
public:
  CodonSameAARateSubstitutionModel(
      std::unique_ptr<ProteinSubstitutionModelInterface> pAAmodel,
      std::unique_ptr<CodonSubstitutionModelInterface> pCodonModel,
      std::unique_ptr<CodonFrequencySetInterface> pFreq,
      std::shared_ptr<const GeneticCode> pgencode);
 
  CodonSameAARateSubstitutionModel(
      const CodonSameAARateSubstitutionModel& model) :
    AbstractParameterAliasable(model),
    AbstractSubstitutionModel(model),
    pAAmodel_ (model.pAAmodel_->clone()),
    pCodonModel_ (model.pCodonModel_->clone()),
    pFreq_ (model.pFreq_ ? model.pFreq_->clone() : nullptr),
    pgencode_ (model.pgencode_),
    X_ (model.X_),
    phi_ (model.phi_)
  {
    compute_();
    updateMatrices_();
  }
 
  CodonSameAARateSubstitutionModel& operator=(
      const CodonSameAARateSubstitutionModel& model)
  {
    AbstractSubstitutionModel::operator=(model);
 
    pAAmodel_.reset(model.pAAmodel_->clone());
    pCodonModel_.reset(model.pCodonModel_->clone());
    pFreq_.reset(model.pFreq_ ? model.pFreq_->clone() : nullptr);
 
    pgencode_ = model.pgencode_;
 
    X_ = model.X_;
    phi_  = model.phi_;
 
    return *this;
  }
 
  CodonSameAARateSubstitutionModel* clone() const override
  {
    return new CodonSameAARateSubstitutionModel(*this);
  }
 
  virtual ~CodonSameAARateSubstitutionModel() {}
 
public:
  std::string getName() const override
  {
    return "SameAARate";
  }
 
  const ProteinSubstitutionModelInterface& proteinModel() const
  {
    return *pAAmodel_;
  }
 
  const CodonSubstitutionModelInterface& codonModel() const
  {
    return *pCodonModel_;
  }
 
  void fireParameterChanged(const ParameterList& parameters) override;
 
  void setNamespace(const std::string& prefix) override
  {
    AbstractParameterAliasable::setNamespace(prefix);
 
    pAAmodel_->setNamespace(prefix + pAAmodel_->getNamespace());
    pCodonModel_->setNamespace(prefix + pCodonModel_->getNamespace());
 
    if (pFreq_)
      pFreq_->setNamespace(prefix + pFreq_->getNamespace());
  }
 
  const CodonFrequencySetInterface& codonFrequencySet() const override
  {
    return pCodonModel_->codonFrequencySet();
  }
 
  bool hasCodonFrequencySet() const override
  {
    return pCodonModel_->hasCodonFrequencySet();
  }
 
  std::shared_ptr<const GeneticCode> getGeneticCode() const override
  {
    return pCodonModel_->getGeneticCode();
  }
 
  void setFreq(std::map<int, double>& frequencies) override
  {
    dynamic_cast<CoreCodonSubstitutionModelInterface&>(*pCodonModel_).setFreq(frequencies);
    matchParametersValues(pCodonModel_->getParameters());
  }
 
  double getCodonsMulRate(size_t i, size_t j) const override
  {
    return 1.;
  }
 
private:
  void compute_();
};
} // end of namespace bpp.
#endif // BPP_PHYL_MODEL_CODON_CODONSAMEAARATESUBSTITUTIONMODEL_H