AlignedPhyloLikelihood.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_LIKELIHOOD_PHYLOLIKELIHOODS_ALIGNEDPHYLOLIKELIHOOD_H
#define BPP_PHYL_LIKELIHOOD_PHYLOLIKELIHOODS_ALIGNEDPHYLOLIKELIHOOD_H
 
 
// From bpp-seq:
#include <Bpp/Seq/Alphabet/Alphabet.h>
 
// from bpp-core
 
#include <Bpp/Numeric/AbstractParametrizable.h>
 
#include "PhyloLikelihood.h"
#include "AbstractPhyloLikelihood.h"
 
namespace bpp
{
class AlignedPhyloLikelihoodInterface :
  public virtual PhyloLikelihoodInterface
{
public:
  AlignedPhyloLikelihoodInterface() {}
  virtual ~AlignedPhyloLikelihoodInterface() {}
 
  virtual AlignedPhyloLikelihoodInterface* clone() const = 0;
 
public:
  virtual size_t getNumberOfSites() const = 0;
 
  virtual AlignedLikelihoodCalculation& alignedLikelihoodCalculation() const = 0;
 
  virtual std::shared_ptr<AlignedLikelihoodCalculation> getAlignedLikelihoodCalculation() const = 0;
 
  virtual DataLik getLikelihoodForASite(size_t site) const = 0;
 
  virtual double getLogLikelihoodForASite(size_t site) const = 0;
 
  virtual VDataLik getLikelihoodPerSite() const = 0;
 
  friend class AlignedPhyloLikelihoodSet;
};
 
 
class AbstractAlignedPhyloLikelihood :
  public virtual AlignedPhyloLikelihoodInterface,
  public virtual AbstractPhyloLikelihood
{
protected:
  size_t nbSites_;
 
public:
  AbstractAlignedPhyloLikelihood(Context& context, size_t nbSites) :
    AbstractPhyloLikelihood(context),
    nbSites_(nbSites)
  {}
 
protected:
  AbstractAlignedPhyloLikelihood(const AbstractAlignedPhyloLikelihood& aasd) :
    AbstractPhyloLikelihood(aasd),
    nbSites_(aasd.nbSites_)
  {}
 
  AbstractAlignedPhyloLikelihood& operator=(const AbstractAlignedPhyloLikelihood& aasd)
  {
    AbstractPhyloLikelihood::operator=(aasd);
    nbSites_ = aasd.nbSites_;
    return *this;
  }
 
public:
  virtual ~AbstractAlignedPhyloLikelihood() {}
 
  size_t getNumberOfSites() const { return nbSites_; }
 
  DataLik getLikelihoodForASite(size_t site) const
  {
    return alignedLikelihoodCalculation().getLikelihoodForASite(site);
  }
 
  double getLogLikelihoodForASite(size_t site) const
  {
    using namespace numeric;
 
    return convert(getAlignedLikelihoodCalculation()->getLogLikelihoodForASite(site));
  }
 
  VDataLik getLikelihoodPerSite() const
  {
    return getAlignedLikelihoodCalculation()->getLikelihoodPerSite();
  }
 
protected:
  void setNumberOfSites(size_t nbSites)
  {
    nbSites_ = nbSites;
  }
};
} // end of namespace bpp.
#endif // BPP_PHYL_LIKELIHOOD_PHYLOLIKELIHOODS_ALIGNEDPHYLOLIKELIHOOD_H