MixtureOfSubstitutionModels.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_MODEL_MIXTUREOFSUBSTITUTIONMODELS_H
#define BPP_PHYL_MODEL_MIXTUREOFSUBSTITUTIONMODELS_H
 
#include <Bpp/Numeric/VectorTools.h>
#include <cstring> // C lib for string copy
#include <map>
#include <string>
#include <vector>
 
#include "MixtureOfTransitionModels.h"
 
namespace bpp
{
class MixtureOfSubstitutionModels :
  public MixtureOfTransitionModels
{
public:
  MixtureOfSubstitutionModels(
      std::shared_ptr<const Alphabet> alpha,
      std::vector< std::unique_ptr<TransitionModelInterface>>& vpModel) :
    AbstractParameterAliasable("Mixture."),
    AbstractTransitionModel(alpha, vpModel.size() ? vpModel[0]->getStateMap() : 0, "Mixture."),
    MixtureOfTransitionModels(alpha, vpModel)
  {
    // Check that all models are substitutionmodels
    for (const auto& model : modelsContainer_)
    {
      if (!dynamic_cast<const SubstitutionModelInterface*>(model.get()))
        throw Exception("MixtureOfSubstitutionModels can only be built with SubstitutionModels, not " + model->getName());
    }
  }
 
  MixtureOfSubstitutionModels(
      std::shared_ptr<const Alphabet> alpha,
      std::vector< std::unique_ptr<TransitionModelInterface>>& vpModel,
      Vdouble& vproba, Vdouble& vrate) :
    AbstractParameterAliasable("Mixture."),
    AbstractTransitionModel(alpha, vpModel.size() ? vpModel[0]->getStateMap() : 0, "Mixture."),
    MixtureOfTransitionModels(alpha, vpModel, vproba, vrate)
  {
    /*
     * Check that all models are substitutionmodels
     */
 
    for (const auto& model : modelsContainer_)
    {
      if (!dynamic_cast<const SubstitutionModelInterface*>(model.get()))
        throw Exception("MixtureOfSubstitutionModels can only be built with SubstitutionModels, not " + model->getName());
    }
  }
 
 
  MixtureOfSubstitutionModels(const MixtureOfSubstitutionModels& model) :
    AbstractParameterAliasable(model),
    AbstractTransitionModel(model),
    MixtureOfTransitionModels(model)
  {}
 
 
  MixtureOfSubstitutionModels& operator=(const MixtureOfSubstitutionModels& model)
  {
    MixtureOfTransitionModels::operator=(model);
    return *this;
  }
 
  MixtureOfSubstitutionModels* clone() const override { return new MixtureOfSubstitutionModels(*this); }
 
public:
  const SubstitutionModelInterface& subModel(const std::string& name) const
  {
    return dynamic_cast<const SubstitutionModelInterface&>(model(name));
  }
};
} // end of namespace bpp.
#endif // BPP_PHYL_MODEL_MIXTUREOFSUBSTITUTIONMODELS_H