HmmEmissionProbabilities.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1

#ifndef BPP_NUMERIC_HMM_HMMEMISSIONPROBABILITIES_H
#define BPP_NUMERIC_HMM_HMMEMISSIONPROBABILITIES_H


#include "../Parametrizable.h"
#include "HmmExceptions.h"
#include "HmmStateAlphabet.h"

// From the STL:
#include <vector>

namespace bpp
{
class HmmEmissionProbabilities :
  public virtual Parametrizable
{
public:
  virtual HmmEmissionProbabilities* clone() const override = 0;

  virtual const HmmStateAlphabet& hmmStateAlphabet() const = 0;

  virtual std::shared_ptr<const HmmStateAlphabet> getHmmStateAlphabet() const = 0;

  virtual void setHmmStateAlphabet(std::shared_ptr<const HmmStateAlphabet> stateAlphabet) = 0;

  virtual double operator()(size_t pos, size_t state) const = 0;

  virtual void computeDEmissionProbabilities(std::string& variable) const
  {
    throw (NotImplementedException("HmmEmissionProbabilities::computeDEmissionProbabilities is not overdefined."));
  }

  virtual void computeD2EmissionProbabilities(std::string& variable) const
  {
    throw (NotImplementedException("HmmEmissionProbabilities::computeD2EmissionProbabilities is not overdefined."));
  }

  virtual const std::vector<double>& getDEmissionProbabilities(size_t pos) const
  {
    throw (NotImplementedException("HmmEmissionProbabilities::getDEmissionProbability is not overdefined."));
  }

  virtual const std::vector<double>& getD2EmissionProbabilities(size_t pos) const
  {
    throw (NotImplementedException("HmmEmissionProbabilities::getD2EmissionProbability is not overdefined."));
  }

  virtual const std::vector<double>& operator()(size_t pos) const = 0;

  virtual size_t getNumberOfPositions() const = 0;
};
} // end of namespace bpp.
#endif // BPP_NUMERIC_HMM_HMMEMISSIONPROBABILITIES_H