MixtureProcessPhyloLikelihood.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_LIKELIHOOD_PHYLOLIKELIHOODS_MIXTUREPROCESSPHYLOLIKELIHOOD_H
#define BPP_PHYL_LIKELIHOOD_PHYLOLIKELIHOODS_MIXTUREPROCESSPHYLOLIKELIHOOD_H
 
 
#include "../DataFlow/Simplex_DF.h"
#include "../MixtureSequenceEvolution.h"
#include "MultiProcessSequencePhyloLikelihood.h"
 
// From SeqLib:
#include <Bpp/Seq/Container/AlignmentData.h>
 
 
namespace bpp
{
class MixtureProcessPhyloLikelihood :
  public MultiProcessSequencePhyloLikelihood
{
private:
  std::shared_ptr<MixtureSequenceEvolution> mSeqEvol_;
 
  std::shared_ptr<ConfiguredSimplex> simplex_;
 
  mutable std::shared_ptr<AlignedLikelihoodCalculation> likCal_;
 
public:
  MixtureProcessPhyloLikelihood(
      std::shared_ptr<const AlignmentDataInterface> data,
      std::shared_ptr<MixtureSequenceEvolution> processSeqEvol,
      std::shared_ptr<CollectionNodes> collNodes,
      size_t nSeqEvol = 0,
      size_t nData = 0);
 
protected:
  MixtureProcessPhyloLikelihood(const MixtureProcessPhyloLikelihood& mlc) :
    AbstractPhyloLikelihood(mlc),
    AbstractAlignedPhyloLikelihood(mlc),
    AbstractSingleDataPhyloLikelihood(mlc),
    AbstractSequencePhyloLikelihood(mlc),
    AbstractParametrizable(mlc),
    MultiProcessSequencePhyloLikelihood(mlc),
    mSeqEvol_(mlc.mSeqEvol_),
    likCal_(mlc.likCal_)
  {}
 
  MixtureProcessPhyloLikelihood& operator=(const MixtureProcessPhyloLikelihood& mlc)
  {
    MultiProcessSequencePhyloLikelihood::operator=(mlc);
    mSeqEvol_ = mlc.mSeqEvol_;
    likCal_ = mlc.likCal_;
    return *this;
  }
 
  MixtureProcessPhyloLikelihood* clone() const override
  {
    return new MixtureProcessPhyloLikelihood(*this);
  }
 
public:
  double getSubProcessProb(size_t i) const
  {
    return simplex_->targetValue()->prob(i);
  }
 
  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_;
  }
 
  VVdouble getPosteriorProbabilitiesPerSitePerProcess() const override;
 
};
} // end of namespace bpp.
#endif // BPP_PHYL_LIKELIHOOD_PHYLOLIKELIHOODS_MIXTUREPROCESSPHYLOLIKELIHOOD_H