LGL08_CAT.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_MODEL_PROTEIN_LGL08_CAT_H
#define BPP_PHYL_MODEL_PROTEIN_LGL08_CAT_H
 
 
#include "../AbstractBiblioMixedTransitionModel.h"
#include "../AbstractSubstitutionModel.h"
#include "../MixtureOfSubstitutionModels.h"
#include "ProteinSubstitutionModel.h"
 
namespace bpp
{
class LGL08_CAT :
  public AbstractBiblioMixedTransitionModel
{
public:
  class EmbeddedModel :
    public AbstractReversibleProteinSubstitutionModel
  {
private:
    double proportion_;
    std::string name_;
 
public:
    EmbeddedModel(
        std::shared_ptr<const ProteicAlphabet> alpha,
        std::string name,
        unsigned int nbCat = 10);
 
    virtual ~EmbeddedModel() {}
 
    EmbeddedModel* clone() const override { return new EmbeddedModel(*this); }
 
    std::string getName() const override { return name_; }
 
    double getProportion() const { return proportion_; }
  };
 
public:
  LGL08_CAT(std::shared_ptr<const ProteicAlphabet> alpha, unsigned int nbCat = 10);
 
  LGL08_CAT* clone() const override { return new LGL08_CAT(*this); }
 
  LGL08_CAT(const LGL08_CAT& mod2) :
    AbstractParameterAliasable(mod2),
    AbstractWrappedModel(mod2),
    AbstractWrappedTransitionModel(mod2),
    AbstractTotallyWrappedTransitionModel(mod2),
    AbstractBiblioTransitionModel(mod2),
    AbstractBiblioMixedTransitionModel(mod2)
  {}
 
  LGL08_CAT& operator=(const LGL08_CAT& mod2)
  {
    AbstractBiblioMixedTransitionModel::operator=(mod2);
    return *this;
  }
 
  uint getNumberOfCategories() const
  {
    return static_cast<uint>(mixedModelPtr_->getNumberOfModels());
  }
 
  std::string getName() const override { return "LGL08_CAT";}
};
} // end of namespace bpp.
#endif // BPP_PHYL_MODEL_PROTEIN_LGL08_CAT_H