MixedTransitionModel.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_MODEL_MIXEDTRANSITIONMODEL_H
#define BPP_PHYL_MODEL_MIXEDTRANSITIONMODEL_H
 
#include <cstring> // C lib for string copy
#include <map>
#include <string>
#include <vector>
 
#include "SubstitutionModel.h"
 
namespace bpp
{
class MixedTransitionModelInterface :
  public virtual TransitionModelInterface
{
public:
  MixedTransitionModelInterface() {}
 
  virtual ~MixedTransitionModelInterface(){}
 
  virtual MixedTransitionModelInterface* clone() const override = 0;
 
public:
  virtual const TransitionModelInterface& nModel(size_t i) const = 0;
 
  virtual std::shared_ptr<const TransitionModelInterface> getNModel(size_t i) const = 0;
 
  virtual double getNProbability(size_t i) const = 0;
 
  virtual const std::vector<double>& getProbabilities() const = 0;
 
  virtual void setNProbability(size_t i, double prob) = 0;
 
  virtual size_t getNumberOfModels() const = 0;
 
  virtual const std::vector<double>& getVRates() const = 0;
 
  virtual double getNRate(size_t i) const = 0;
 
  virtual void setVRates(const Vdouble& vd) = 0;
 
  virtual void normalizeVRates() = 0;
 
  virtual const TransitionModelInterface& model(const std::string& name) const = 0;
 
  virtual Vuint getSubmodelNumbers(const std::string& desc) const = 0;
 
protected:
  virtual TransitionModelInterface& nModel_(size_t i) = 0;
 
  friend class AbstractBiblioMixedTransitionModel;
  friend class InMixedSubstitutionModel;
};
} // end of namespace bpp.
#endif // BPP_PHYL_MODEL_MIXEDTRANSITIONMODEL_H