HmmEmissionProbabilities_Eigen.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_LIKELIHOOD_HMMEMISSIONPROBABILITIES_EIGEN_H
#define BPP_PHYL_LIKELIHOOD_HMMEMISSIONPROBABILITIES_EIGEN_H
 
#include <Bpp/Numeric/Hmm/HmmExceptions.h>
#include <Bpp/Numeric/Hmm/HmmStateAlphabet.h>
#include <Bpp/Numeric/Parametrizable.h>
 
 
// From the STL:
#include <vector>
 
namespace bpp
{
class HmmEmissionProbabilities_Eigen :
  public virtual Parametrizable
{
public:
  virtual HmmEmissionProbabilities_Eigen* clone() const = 0;
 
  virtual const HmmStateAlphabet* getHmmStateAlphabet() const = 0;
 
  virtual void setHmmStateAlphabet(std::shared_ptr<HmmStateAlphabet> stateAlphabet) = 0;
 
  virtual DataLik operator()(size_t pos, size_t state) const = 0;
 
  virtual VectorLik operator()(size_t pos) const = 0;
 
  virtual size_t getNumberOfPositions() const = 0;
};
} // end of namespace bpp.
#endif // BPP_PHYL_LIKELIHOOD_HMMEMISSIONPROBABILITIES_EIGEN_H