AbstractFromSubstitutionModelTransitionModel.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_MODEL_ABSTRACTFROMSUBSTITUTIONMODELTRANSITIONMODEL_H
#define BPP_PHYL_MODEL_ABSTRACTFROMSUBSTITUTIONMODELTRANSITIONMODEL_H
 
 
#include "AbstractWrappedModel.h"
 
namespace bpp
{
class AbstractFromSubstitutionModelTransitionModel :
  public virtual AbstractWrappedTransitionModel
{
protected:
  std::unique_ptr<SubstitutionModelInterface> subModel_;
 
  size_t size_;
 
  mutable RowMatrix<double> pij_t;
  mutable RowMatrix<double> dpij_t;
  mutable RowMatrix<double> d2pij_t;
 
  std::string nestedPrefix_;
 
public:
  AbstractFromSubstitutionModelTransitionModel(
      std::unique_ptr<SubstitutionModelInterface> subModel,
      const std::string& prefix);
 
  AbstractFromSubstitutionModelTransitionModel(const AbstractFromSubstitutionModelTransitionModel& fmsm);
 
  AbstractFromSubstitutionModelTransitionModel& operator=(const AbstractFromSubstitutionModelTransitionModel& fmsm);
 
  virtual ~AbstractFromSubstitutionModelTransitionModel() {}
 
public:
  const SubstitutionModelInterface& substitutionModel() const
  {
    return *subModel_;
  }
 
  const TransitionModelInterface& transitionModel() const override
  {
    return *subModel_;
  }
 
  const BranchModelInterface& model() const override
  {
    return *subModel_;
  }
 
  bool computeFrequencies() const override
  {
    return subModel_->computeFrequencies();
  }
 
  void computeFrequencies(bool yn) override
  {
    subModel_->computeFrequencies(yn);
  }
 
protected:
  Vdouble& getFrequencies_() override
  {
    return subModel_->getFrequencies_();
  }
 
  SubstitutionModelInterface& substitutionModel_()
  {
    return *subModel_;
  }
 
 
  TransitionModelInterface& transitionModel_() override
  {
    return *subModel_;
  }
 
  BranchModelInterface& model_()
  {
    return *subModel_;
  }
 
public:
  virtual void addRateParameter() override
  {
    model_().addRateParameter();
    addParameter_(new Parameter(getNamespace() + "rate", model().getRate(), Parameter::R_PLUS_STAR));
  }
 
  virtual void fireParameterChanged(const ParameterList& parameters) override
  {
    AbstractParameterAliasable::fireParameterChanged(parameters);
    model_().matchParametersValues(parameters);
  }
 
  virtual void setNamespace(const std::string& prefix) override
  {
    AbstractParameterAliasable::setNamespace(prefix + nestedPrefix_);
    model_().setNamespace(prefix + nestedPrefix_);
  }
};
} // end of namespace bpp.
#endif // BPP_PHYL_MODEL_ABSTRACTFROMSUBSTITUTIONMODELTRANSITIONMODEL_H