FromMixtureSubstitutionModel.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_MODEL_FROMMIXTURESUBSTITUTIONMODEL_H
#define BPP_PHYL_MODEL_FROMMIXTURESUBSTITUTIONMODEL_H
 
 
#include "AbstractSubstitutionModel.h"
#include "AbstractWrappedModel.h"
#include "MixedTransitionModel.h"
 
namespace bpp
{
class FromMixtureSubstitutionModel :
  public virtual AbstractTotallyWrappedSubstitutionModel
{
private:
  std::unique_ptr<SubstitutionModelInterface> subModel_;
 
  std::string mixtName_;
 
public:
  FromMixtureSubstitutionModel(
      const MixedTransitionModelInterface& mixedModel,
      const std::string& subModelName, const std::string& mixtDesc);
 
  FromMixtureSubstitutionModel(
      const MixedTransitionModelInterface& mixedModel,
      size_t subModelNumber,
      const std::string& mixtDesc);
 
  FromMixtureSubstitutionModel(const FromMixtureSubstitutionModel& fmsm);
 
  FromMixtureSubstitutionModel& operator=(const FromMixtureSubstitutionModel& fmsm);
 
  virtual ~FromMixtureSubstitutionModel() {}
 
  FromMixtureSubstitutionModel* clone() const override { return new FromMixtureSubstitutionModel(*this); }
 
public:
  const SubstitutionModelInterface& substitutionModel() const override
  {
    return *subModel_.get();
  }
 
protected:
  SubstitutionModelInterface& substitutionModel_() override
  {
    return *subModel_;
  }
 
public:
  void fireParameterChanged(const ParameterList& parameters) override
  {
    model_().matchParametersValues(parameters);
  }
 
  virtual void setNamespace(const std::string& name) override
  {
    AbstractParameterAliasable::setNamespace(name);
    model_().setNamespace(name);
  }
 
  virtual void addRateParameter() override
  {
    model_().addRateParameter();
    addParameter_(new Parameter(getNamespace() + "rate", model().getRate(), Parameter::R_PLUS_STAR));
  }
 
  /*
   * @}
   */
  std::string getName() const override
  {
    size_t posp = mixtName_.find("(");
    return mixtName_.substr(0, posp) + "_" + model().getName() + mixtName_.substr(posp);
  }
};
} // end of namespace bpp.
#endif // BPP_PHYL_MODEL_FROMMIXTURESUBSTITUTIONMODEL_H