DiscreteRatesAcrossSitesTreeLikelihood.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_LEGACY_LIKELIHOOD_DISCRETERATESACROSSSITESTREELIKELIHOOD_H
#define BPP_PHYL_LEGACY_LIKELIHOOD_DISCRETERATESACROSSSITESTREELIKELIHOOD_H
 
#include <Bpp/Numeric/ParameterList.h>
#include <Bpp/Numeric/Prob/DiscreteDistribution.h>
 
#include "TreeLikelihood.h"
 
namespace bpp
{
class DiscreteRatesAcrossSitesTreeLikelihoodInterface :
  public virtual TreeLikelihoodInterface
{
public:
  DiscreteRatesAcrossSitesTreeLikelihoodInterface() {}
  virtual ~DiscreteRatesAcrossSitesTreeLikelihoodInterface() {}
 
public:
  virtual std::shared_ptr<const DiscreteDistributionInterface> getRateDistribution() const = 0;
 
  virtual std::shared_ptr<DiscreteDistributionInterface> getRateDistribution() = 0;
 
  virtual const DiscreteDistributionInterface& rateDistribution() const = 0;
 
  virtual DiscreteDistributionInterface& rateDistribution() = 0;
 
  virtual double getLikelihoodForASiteForARateClass(size_t site, size_t rateClass) const = 0;
 
  virtual double getLogLikelihoodForASiteForARateClass(size_t site, size_t rateClass) const = 0;
 
  virtual double getLikelihoodForASiteForARateClassForAState(size_t site, size_t rateClass, int state) const = 0;
 
  virtual double getLogLikelihoodForASiteForARateClassForAState(size_t site, size_t rateClass, int state) const = 0;
 
  virtual VVdouble getLikelihoodPerSitePerRateClass() const = 0;
 
  virtual VVdouble getLogLikelihoodPerSitePerRateClass() const = 0;
 
  virtual VVVdouble getLikelihoodPerSitePerRateClassPerState() const = 0;
 
  virtual VVVdouble getLogLikelihoodPerSitePerRateClassPerState() const = 0;
 
  virtual VVdouble getPosteriorProbabilitiesPerRate() const = 0;
 
  virtual std::vector<size_t> getRateClassWithMaxPostProbPerSite() const = 0;
 
  virtual Vdouble getRateWithMaxPostProbPerSite() const = 0;
 
  virtual Vdouble getPosteriorRatePerSite() const = 0;
 
  virtual ParameterList getRateDistributionParameters() const = 0;
 
  virtual size_t getNumberOfClasses() const = 0;
 
  virtual VVVdouble getTransitionProbabilitiesPerRateClass(int nodeId, size_t siteIndex) const = 0;
};
} // end of namespace bpp.
#endif // BPP_PHYL_LEGACY_LIKELIHOOD_DISCRETERATESACROSSSITESTREELIKELIHOOD_H