AlignedPhyloLikelihoodProduct.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_LIKELIHOOD_PHYLOLIKELIHOODS_PRODUCTOFALIGNEDPHYLOLIKELIHOOD_H
#define BPP_PHYL_LIKELIHOOD_PHYLOLIKELIHOODS_PRODUCTOFALIGNEDPHYLOLIKELIHOOD_H
 
 
// From bpp-seq:
#include <Bpp/Seq/Alphabet/Alphabet.h>
#include <Bpp/Seq/Container/AlignmentData.h>
 
#include "AlignedPhyloLikelihoodSet.h"
 
namespace bpp
{
class AlignedPhyloLikelihoodProduct :
  public AbstractAlignedPhyloLikelihoodSet
{
  mutable std::shared_ptr<AlignedLikelihoodCalculation> likCal_;
 
public:
  AlignedPhyloLikelihoodProduct(
      Context& context,
      std::shared_ptr<PhyloLikelihoodContainer> pC,
      bool inCollection = true);
 
  AlignedPhyloLikelihoodProduct(
      Context& context,
      std::shared_ptr<PhyloLikelihoodContainer> pC,
      const std::vector<size_t>& nPhylo,
      bool inCollection = true);
 
  virtual ~AlignedPhyloLikelihoodProduct() {}
 
protected:
  AlignedPhyloLikelihoodProduct(const AlignedPhyloLikelihoodProduct& sd) :
    AbstractPhyloLikelihood(sd),
    AbstractParametrizable(""),
    AbstractPhyloLikelihoodSet(sd),
    AbstractAlignedPhyloLikelihood(sd),
    AbstractAlignedPhyloLikelihoodSet(sd),
    likCal_(sd.likCal_)
  {}
 
  AlignedPhyloLikelihoodProduct& operator=(const AlignedPhyloLikelihoodProduct& sd)
  {
    AbstractAlignedPhyloLikelihoodSet::operator=(sd);
    likCal_ = sd.likCal_;
    return *this;
  }
 
  AlignedPhyloLikelihoodProduct* clone() const
  {
    return new AlignedPhyloLikelihoodProduct(*this);
  }
 
public:
  LikelihoodCalculation& likelihoodCalculation () const
  {
    return *likCal_;
  }
 
  std::shared_ptr<LikelihoodCalculation> getLikelihoodCalculation () const
  {
    return likCal_;
  }
 
  AlignedLikelihoodCalculation& alignedLikelihoodCalculation () const
  {
    return *likCal_;
  }
 
  std::shared_ptr<AlignedLikelihoodCalculation> getAlignedLikelihoodCalculation () const
  {
    return likCal_;
  }
};
} // end of namespace bpp.
#endif // BPP_PHYL_LIKELIHOOD_PHYLOLIKELIHOODS_PRODUCTOFALIGNEDPHYLOLIKELIHOOD_H