AlignedPhyloLikelihoodMixture.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_LIKELIHOOD_PHYLOLIKELIHOODS_MIXTUREOFALIGNEDPHYLOLIKELIHOOD_H
#define BPP_PHYL_LIKELIHOOD_PHYLOLIKELIHOODS_MIXTUREOFALIGNEDPHYLOLIKELIHOOD_H
 
 
#include "AlignedPhyloLikelihoodSet.h"
 
// From SeqLib:
#include <Bpp/Seq/Container/AlignmentData.h>
 
#include "../DataFlow/Simplex_DF.h"
 
namespace bpp
{
class AlignedPhyloLikelihoodMixture :
  public AbstractAlignedPhyloLikelihoodSet
{
private:
  std::shared_ptr<ConfiguredSimplex> simplex_;
 
  mutable std::shared_ptr<AlignedLikelihoodCalculation> likCal_;
 
public:
  AlignedPhyloLikelihoodMixture(
      Context& context,
      std::shared_ptr<PhyloLikelihoodContainer> pC,
      const std::vector<size_t>& nPhylo,
      bool inCollection = true);
 
  virtual ~AlignedPhyloLikelihoodMixture() {}
 
protected:
  AlignedPhyloLikelihoodMixture(const AlignedPhyloLikelihoodMixture& mlc) :
    AbstractPhyloLikelihood(mlc),
    AbstractParametrizable(""),
    AbstractPhyloLikelihoodSet(mlc),
    AbstractAlignedPhyloLikelihood(mlc),
    AbstractAlignedPhyloLikelihoodSet(mlc),
    simplex_(mlc.simplex_),
    likCal_(mlc.likCal_)
  {}
 
  AlignedPhyloLikelihoodMixture& operator=(const AlignedPhyloLikelihoodMixture& mlc)
  {
    AbstractAlignedPhyloLikelihoodSet::operator=(mlc);
    simplex_ = mlc.simplex_;
    likCal_ = mlc.likCal_;
    return *this;
  }
 
  AlignedPhyloLikelihoodMixture* clone() const override
  {
    return new AlignedPhyloLikelihoodMixture(*this);
  }
 
protected:
  void fireParameterChanged(const ParameterList& parameters) override;
 
public:
  LikelihoodCalculation& likelihoodCalculation () const override
  {
    return *likCal_;
  }
 
  std::shared_ptr<LikelihoodCalculation> getLikelihoodCalculation () const override
  {
    return likCal_;
  }
 
  AlignedLikelihoodCalculation& alignedLikelihoodCalculation () const override
  {
    return *likCal_;
  }
 
  std::shared_ptr<AlignedLikelihoodCalculation> getAlignedLikelihoodCalculation () const override
  {
    return likCal_;
  }
 
  Vdouble getPhyloProbabilities() const;
 
  double getPhyloProb(size_t index) const;
 
  void setPhyloProb(Simplex const& simplex);
};
} // end of namespace bpp.
#endif // BPP_PHYL_LIKELIHOOD_PHYLOLIKELIHOODS_MIXTUREOFALIGNEDPHYLOLIKELIHOOD_H