AbstractBiblioMixedTransitionModel.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_MODEL_ABSTRACTBIBLIOMIXEDTRANSITIONMODEL_H
#define BPP_PHYL_MODEL_ABSTRACTBIBLIOMIXEDTRANSITIONMODEL_H
 
 
#include "AbstractBiblioSubstitutionModel.h"
#include "MixedTransitionModel.h"
 
namespace bpp
{
class AbstractBiblioMixedTransitionModel :
  public virtual MixedTransitionModelInterface,
  public virtual AbstractBiblioTransitionModel
{
protected:
  std::unique_ptr<MixedTransitionModelInterface> mixedModelPtr_;
 
public:
  AbstractBiblioMixedTransitionModel(const std::string& prefix);
 
  AbstractBiblioMixedTransitionModel(const AbstractBiblioMixedTransitionModel& model);
 
  AbstractBiblioMixedTransitionModel& operator=(const AbstractBiblioMixedTransitionModel& model);
 
  virtual ~AbstractBiblioMixedTransitionModel();
 
public:
  const TransitionModelInterface& nModel(size_t i) const override
  {
    return mixedModel().nModel(i);
  }
 
  std::shared_ptr<const TransitionModelInterface> getNModel(size_t i) const override
  {
    return mixedModel().getNModel(i);
  }
 
  double getNProbability(size_t i) const override
  {
    return mixedModel().getNProbability(i);
  }
 
  const std::vector<double>& getProbabilities() const override
  {
    return mixedModel().getProbabilities();
  }
 
  void setNProbability(size_t i, double prob) override
  {
    mixedModel_().setNProbability(i, prob);
  }
 
  size_t getNumberOfModels() const override
  {
    return mixedModel().getNumberOfModels();
  }
 
  void setVRates(const Vdouble& vd) override
  {
    mixedModel_().setVRates(vd);
  }
 
  void normalizeVRates() override
  {
    mixedModel_().normalizeVRates();
  }
 
  const std::vector<double>& getVRates() const override
  {
    return mixedModel().getVRates();
  }
 
  double getNRate(size_t i) const override
  {
    return mixedModel().getNRate(i);
  }
 
  using AbstractWrappedModel::model;
  const TransitionModelInterface& model(const std::string& name) const override
  {
    return mixedModel().model(name);
  }
 
  Vuint getSubmodelNumbers(const std::string& desc) const override;
 
  const TransitionModelInterface& transitionModel() const override { return *mixedModelPtr_; }
 
  const MixedTransitionModelInterface& mixedModel() const { return *mixedModelPtr_; }
 
  const FrequencySetInterface& frequencySet() const override
  {
    return mixedModelPtr_->nModel(0).frequencySet();
  }
 
protected:
  TransitionModelInterface& transitionModel_() override
  {
    return *mixedModelPtr_;
  }
 
  MixedTransitionModelInterface& mixedModel_() { return *mixedModelPtr_; }
 
  TransitionModelInterface& nModel_(size_t i) override
  {
    return mixedModel_().nModel_(i);
  }
};
} // end of namespace bpp.
#endif // BPP_PHYL_MODEL_ABSTRACTBIBLIOMIXEDTRANSITIONMODEL_H