MixtureOfTransitionModels.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_MODEL_MIXTUREOFTRANSITIONMODELS_H
#define BPP_PHYL_MODEL_MIXTUREOFTRANSITIONMODELS_H
 
#include <Bpp/Numeric/VectorTools.h>
#include <cstring> // C lib for string copy
#include <map>
#include <string>
#include <vector>
 
#include "AbstractMixedTransitionModel.h"
 
namespace bpp
{
class MixtureOfTransitionModels :
  public AbstractMixedTransitionModel
{
public:
  MixtureOfTransitionModels(
      std::shared_ptr<const Alphabet> alpha,
      std::vector<std::unique_ptr<TransitionModelInterface>>& vpModel);
 
  MixtureOfTransitionModels(
      std::shared_ptr<const Alphabet> alpha,
      std::vector<std::unique_ptr<TransitionModelInterface>>& vpModel,
      Vdouble& vproba, Vdouble& vrate);
 
  MixtureOfTransitionModels(const MixtureOfTransitionModels&);
 
  MixtureOfTransitionModels& operator=(const MixtureOfTransitionModels&);
 
  virtual ~MixtureOfTransitionModels();
 
  MixtureOfTransitionModels* clone() const override
  {
    return new MixtureOfTransitionModels(*this);
  }
 
public:
  std::string getName() const override { return "Mixture"; }
 
  const TransitionModelInterface& model(const std::string& name) const override;
 
  const TransitionModelInterface& model(size_t i) const
  {
    return AbstractMixedTransitionModel::nModel(i);
  }
 
  void updateMatrices_() override;
 
  virtual void setVRates(const Vdouble& vd) override;
 
  Vuint getSubmodelNumbers(const std::string& desc) const override;
 
  void setFreq(std::map<int, double>&) override;
};
} // end of namespace bpp.
#endif // BPP_PHYL_MODEL_MIXTUREOFTRANSITIONMODELS_H