AbstractDiscreteRatesAcrossSitesTreeLikelihood.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_LEGACY_LIKELIHOOD_ABSTRACTDISCRETERATESACROSSSITESTREELIKELIHOOD_H
#define BPP_PHYL_LEGACY_LIKELIHOOD_ABSTRACTDISCRETERATESACROSSSITESTREELIKELIHOOD_H
 
 
#include "../../Model/SubstitutionModel.h"
#include "AbstractTreeLikelihood.h"
#include "DiscreteRatesAcrossSitesTreeLikelihood.h"
 
namespace bpp
{
class AbstractDiscreteRatesAcrossSitesTreeLikelihood :
  public AbstractTreeLikelihood,
  public virtual DiscreteRatesAcrossSitesTreeLikelihoodInterface
{
protected:
  std::shared_ptr<DiscreteDistributionInterface> rateDistribution_;
 
public:
  AbstractDiscreteRatesAcrossSitesTreeLikelihood(
      std::shared_ptr<DiscreteDistributionInterface> rDist,
      bool verbose = true
      );
 
  AbstractDiscreteRatesAcrossSitesTreeLikelihood(
      const AbstractDiscreteRatesAcrossSitesTreeLikelihood& tl) :
    AbstractTreeLikelihood(tl),
    rateDistribution_(tl.rateDistribution_)
  {}
 
  AbstractDiscreteRatesAcrossSitesTreeLikelihood& operator=(
      const AbstractDiscreteRatesAcrossSitesTreeLikelihood& tl)
  {
    AbstractTreeLikelihood::operator=(tl);
    rateDistribution_ = tl.rateDistribution_;
    return *this;
  }
 
  virtual ~AbstractDiscreteRatesAcrossSitesTreeLikelihood() {}
 
public:
  double getLikelihoodForASiteForAState (size_t site, int state) const;
  double getLogLikelihoodForASiteForAState(size_t site, int state) const;
  ParameterList getDerivableParameters() const;
  ParameterList getNonDerivableParameters() const;
  VVdouble getTransitionProbabilities(int nodeId, size_t siteIndex) const;
  std::shared_ptr<const DiscreteDistributionInterface> getRateDistribution() const
  {
    return rateDistribution_;
  }
 
  std::shared_ptr<DiscreteDistributionInterface> getRateDistribution()
  {
    return rateDistribution_;
  }
 
  const DiscreteDistributionInterface& rateDistribution() const
  {
    return *rateDistribution_;
  }
 
  DiscreteDistributionInterface& rateDistribution()
  {
    return *rateDistribution_;
  }
 
  size_t getNumberOfClasses() const
  {
    return rateDistribution_->getNumberOfCategories();
  }
 
  ParameterList getRateDistributionParameters() const;
  VVdouble getLikelihoodPerSitePerRateClass() const;
  VVdouble getLogLikelihoodPerSitePerRateClass() const;
  VVVdouble getLikelihoodPerSitePerRateClassPerState() const;
  VVVdouble getLogLikelihoodPerSitePerRateClassPerState() const;
  VVdouble getPosteriorProbabilitiesPerRate() const;
  Vdouble getRateWithMaxPostProbPerSite() const;
  std::vector<size_t> getRateClassWithMaxPostProbPerSite() const;
  Vdouble getPosteriorRatePerSite() const;
  static void resetLikelihoodArray(VVVdouble& likelihoodArray);
 
  static void displayLikelihoodArray(const VVVdouble& likelihoodArray);
 
};
} // end of namespace bpp.
#endif // BPP_PHYL_LEGACY_LIKELIHOOD_ABSTRACTDISCRETERATESACROSSSITESTREELIKELIHOOD_H