HmmProcessPhyloLikelihood.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_LIKELIHOOD_PHYLOLIKELIHOODS_HMMPROCESSPHYLOLIKELIHOOD_H
#define BPP_PHYL_LIKELIHOOD_PHYLOLIKELIHOODS_HMMPROCESSPHYLOLIKELIHOOD_H
 
 
#include "../HmmSequenceEvolution.h"
#include "HmmPhyloEmissionProbabilities.h"
#include "MultiProcessSequencePhyloLikelihood.h"
 
// From SeqLib:
#include <Bpp/Seq/Container/AlignmentData.h>
 
 
#include "HmmLikelihood_DF.h"
#include <Bpp/Numeric/Hmm/HmmTransitionMatrix.h>
 
 
namespace bpp
{
class HmmProcessPhyloLikelihood :
  public MultiProcessSequencePhyloLikelihood
{
private:
  std::shared_ptr<HmmPhyloEmissionProbabilities> Hpep_;
 
  mutable std::shared_ptr<HmmLikelihood_DF> hmm_;
 
public:
  HmmProcessPhyloLikelihood(
      std::shared_ptr<const AlignmentDataInterface> data,
      std::shared_ptr<HmmSequenceEvolution> processSeqEvol,
      std::shared_ptr<CollectionNodes> collNodes,
      size_t nSeqEvol = 0,
      size_t nData = 0);
 
protected:
  HmmProcessPhyloLikelihood(const HmmProcessPhyloLikelihood& mlc) :
    AbstractPhyloLikelihood(mlc),
    AbstractAlignedPhyloLikelihood(mlc),
    AbstractSingleDataPhyloLikelihood(mlc),
    AbstractSequencePhyloLikelihood(mlc),
    AbstractParametrizable(mlc),
    MultiProcessSequencePhyloLikelihood(mlc),
    Hpep_(std::shared_ptr<HmmPhyloEmissionProbabilities>(mlc.Hpep_->clone())),
    hmm_(std::shared_ptr<HmmLikelihood_DF>(mlc.hmm_->clone())) {}
 
  HmmProcessPhyloLikelihood* clone() const override { return new HmmProcessPhyloLikelihood(*this); }
 
public:
  virtual ~HmmProcessPhyloLikelihood() {}
 
public:
  void setNamespace(const std::string& nameSpace) override;
 
  void fireParameterChanged(const ParameterList& parameters) override;
 
  LikelihoodCalculation& likelihoodCalculation () const override
  {
    return *hmm_;
  }
 
  std::shared_ptr<LikelihoodCalculation> getLikelihoodCalculation () const override
  {
    return hmm_;
  }
 
  AlignedLikelihoodCalculation& alignedLikelihoodCalculation () const override
  {
    return *hmm_;
  }
 
  std::shared_ptr<AlignedLikelihoodCalculation> getAlignedLikelihoodCalculation () const override
  {
    return hmm_;
  }
 
  /*
   *@brief return the posterior probabilities of subprocess on each site.
   *
   *@return MatrixXd sites x states
   */
  VVdouble getPosteriorProbabilitiesPerSitePerProcess() const override
  {
    VVdouble pp;
    auto mat = hmm_->getHiddenStatesPosteriorProbabilities().transpose();
    copyEigenToBpp(mat, pp);
    return pp;
  }
 
  const Eigen::MatrixXd& getHmmTransitionMatrix() const
  {
    return hmm_->getHmmTransitionMatrix();
  }
};
} // end of namespace bpp.
#endif // BPP_PHYL_LIKELIHOOD_PHYLOLIKELIHOODS_HMMPROCESSPHYLOLIKELIHOOD_H