NonHomogeneousTreeLikelihood.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_LEGACY_LIKELIHOOD_NONHOMOGENEOUSTREELIKELIHOOD_H
#define BPP_PHYL_LEGACY_LIKELIHOOD_NONHOMOGENEOUSTREELIKELIHOOD_H
 
 
#include "../Model/SubstitutionModelSet.h"
#include "TreeLikelihood.h"
 
namespace bpp
{
class NonHomogeneousTreeLikelihood :
  public virtual TreeLikelihoodInterface
{
public:
  NonHomogeneousTreeLikelihood* clone() const override = 0;
 
public:
  std::shared_ptr<const TransitionModelInterface> getModelForSite(int nodeId, size_t siteIndex) const override
  {
    return getModelForNode(nodeId);
  }
 
  std::shared_ptr<TransitionModelInterface> getModelForSite(int nodeId, size_t siteIndex) override
  {
    return getModelForNode(nodeId);
  }
 
  virtual std::shared_ptr<const TransitionModelInterface> getModelForNode(int nodeId) const = 0;
 
  virtual std::shared_ptr<TransitionModelInterface> getModelForNode(int nodeId) = 0;
 
  virtual std::shared_ptr<const SubstitutionModelSet> getSubstitutionModelSet() const = 0;
 
  virtual const SubstitutionModelSet& substitutionModelSet() const = 0;
 
  virtual std::shared_ptr<SubstitutionModelSet> getSubstitutionModelSet() = 0;
 
  virtual SubstitutionModelSet& substitutionModelSet() = 0;
 
  virtual void setSubstitutionModelSet(std::shared_ptr<SubstitutionModelSet> model) = 0;
 
  virtual ParameterList getRootFrequenciesParameters() const = 0;
};
} // end of namespace bpp.
#endif // BPP_PHYL_LEGACY_LIKELIHOOD_NONHOMOGENEOUSTREELIKELIHOOD_H