POMO.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_MODEL_POMO_H
#define BPP_PHYL_MODEL_POMO_H
 
 
#include "FrequencySet/FrequencySet.h"
#include "AbstractSubstitutionModel.h"
 
#include <Bpp/Seq/Alphabet/AllelicAlphabet.h>
 
namespace bpp
{
class POMO :
  public AbstractSubstitutionModel
{
private:
  uint nbAlleles_;
 
  std::unique_ptr<SubstitutionModelInterface> pmodel_;
  std::unique_ptr<FrequencySetInterface> pfitness_;
 
public:
  POMO(std::shared_ptr<const AllelicAlphabet> allAlph,
      std::unique_ptr<SubstitutionModelInterface> pmodel,
      std::unique_ptr<FrequencySetInterface> pfitness);
 
  POMO(const POMO& model) :
    AbstractParameterAliasable(model),
    AbstractSubstitutionModel(model),
    nbAlleles_(model.nbAlleles_),
    pmodel_(model.pmodel_->clone()),
    pfitness_(model.pfitness_ ? model.pfitness_->clone() : nullptr)
  {}
 
  POMO& operator=(const POMO& model)
  {
    AbstractParameterAliasable::operator=(model);
    nbAlleles_ = model.nbAlleles_;
    pmodel_.reset(model.pmodel_->clone());
    pfitness_.reset(model.pfitness_ ? model.pfitness_->clone() : nullptr);
    return *this;
  }
 
  POMO* clone() const override
  {
    return new POMO(*this);
  }
 
  void fireParameterChanged(const ParameterList& parameters) override;
 
  void setFreq(std::map<int, double>& frequencies) override;
 
  void setNamespace(const std::string& prefix) override
  {
    AbstractParameterAliasable::setNamespace(prefix);
    pmodel_->setNamespace(prefix + pmodel_->getNamespace());
    if (pfitness_)
      pfitness_->setNamespace(prefix + pfitness_->getNamespace());
  }
 
  std::shared_ptr<const AllelicAlphabet> getAllelicAlphabet() const
  {
    return std::dynamic_pointer_cast<const AllelicAlphabet>(alphabet_);
  }
 
  const AllelicAlphabet& allelicAlphabet() const
  {
    return dynamic_cast<const AllelicAlphabet&>(*alphabet_);
  }
 
  uint getNbAlleles() const
  {
    return nbAlleles_;
  }
 
  bool hasFitness() const
  {
    return pfitness_ != nullptr;
  }
 
  const FrequencySetInterface& fitness() const
  {
    return *pfitness_;
  }
 
  const SubstitutionModelInterface& mutationModel() const
  {
    return *pmodel_;
  }
 
  std::string getName() const override
  {
    return "POMO";
  }
 
protected:
  void updateMatrices_() override;
};
} // end of namespace bpp.
#endif // BPP_PHYL_MODEL_POMO_H