HmmPhyloEmissionProbabilities.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_LIKELIHOOD_PHYLOLIKELIHOODS_HMMPHYLOEMISSIONPROBABILITIES_H
#define BPP_PHYL_LIKELIHOOD_PHYLOLIKELIHOODS_HMMPHYLOEMISSIONPROBABILITIES_H
 
#include <Bpp/Numeric/AbstractParametrizable.h>
 
#include "../DataFlow/DataFlowCWise.h"
#include "../HmmEmissionProbabilities_Eigen.h"
#include "HmmPhyloAlphabet.h"
 
namespace bpp
{
using EmissionLogk = CWiseCompound<MatrixLik, ReductionOf<RowLik>>;
 
class HmmPhyloEmissionProbabilities :
  public virtual HmmEmissionProbabilities_Eigen,
  public AbstractParametrizable
{
private:
  Context& context_;
 
  std::shared_ptr<HmmPhyloAlphabet> phylAlph_;
 
  /*
   *@brief Emission likelihoods are stored in a Matrix from a set of
   * RowVectors.
   *
   */
 
  ValueRef<MatrixLik> emProb_;
 
  size_t nbSites_;
 
public:
  HmmPhyloEmissionProbabilities(std::shared_ptr<HmmPhyloAlphabet> alphabet);
 
  HmmPhyloEmissionProbabilities(const HmmPhyloEmissionProbabilities& hEP) :
    AbstractParametrizable(hEP),
    context_(hEP.context_),
    phylAlph_(hEP.phylAlph_),
    emProb_(hEP.emProb_),
    nbSites_(hEP.nbSites_)
  {}
 
  HmmPhyloEmissionProbabilities* clone() const { return new HmmPhyloEmissionProbabilities(*this);}
 
  const HmmStateAlphabet* getHmmStateAlphabet() const
  {
    return phylAlph_.get();
  }
 
  size_t getNumberOfStates() const
  {
    return phylAlph_->getNumberOfStates();
  }
 
  size_t getNumberOfSites() const
  {
    return nbSites_;
  }
 
  void setHmmStateAlphabet(std::shared_ptr<HmmStateAlphabet> stateAlphabet);
 
  DataLik operator()(size_t pos, size_t state) const
  {
    return (emProb_->targetValue())(Eigen::Index(state), Eigen::Index(pos));
  }
 
  ValueRef<MatrixLik> getEmissionProbabilities()
  {
    return emProb_;
  }
 
  VectorLik operator()(size_t pos) const
  {
    return emProb_->targetValue().col(Eigen::Index(pos));
  }
 
  size_t getNumberOfPositions() const
  {
    return nbSites_;
  }
};
} // end of namespace bpp.
#endif // BPP_PHYL_LIKELIHOOD_PHYLOLIKELIHOODS_HMMPHYLOEMISSIONPROBABILITIES_H