PhyloLikelihood.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_LIKELIHOOD_PHYLOLIKELIHOODS_PHYLOLIKELIHOOD_H
#define BPP_PHYL_LIKELIHOOD_PHYLOLIKELIHOODS_PHYLOLIKELIHOOD_H
 
#include <Bpp/Numeric/Function/Functions.h>
#include <Bpp/Numeric/ParameterList.h>
 
#include "../DataFlow/LikelihoodCalculation.h"
 
namespace bpp
{
class PhyloLikelihoodInterface :
  public virtual SecondOrderDerivable
{
public:
  PhyloLikelihoodInterface() {}
  virtual ~PhyloLikelihoodInterface() {}
 
  PhyloLikelihoodInterface* clone() const = 0;
 
public:
  virtual bool isInitialized() const = 0;
 
  virtual const Context& context() const = 0;
 
  virtual Context& context() = 0;
 
  virtual ValueRef<DataLik> getLikelihoodNode() const = 0;
 
  double getLogLikelihood() const
  {
    return -getValue();
  }
 
  // virtual double getDLogLikelihood(const std::string& variable) const = 0;
 
  // virtual double getD2LogLikelihood(const std::string& variable) const = 0;
 
  virtual ParameterList getNonDerivableParameters() const = 0;
 
  virtual ParameterList getDerivableParameters() const = 0;
 
  virtual ParameterList getBranchLengthParameters() const = 0;
 
  virtual ParameterList getSubstitutionModelParameters() const = 0;
 
  virtual ParameterList getRateDistributionParameters() const = 0;
 
  virtual ParameterList getRootFrequenciesParameters() const = 0;
 
  virtual LikelihoodCalculation& likelihoodCalculation() const = 0;
 
  virtual std::shared_ptr<LikelihoodCalculation> getLikelihoodCalculation() const = 0;
};
} // end of namespace bpp.
#endif // BPP_PHYL_LIKELIHOOD_PHYLOLIKELIHOODS_PHYLOLIKELIHOOD_H