FullHmmTransitionMatrix.h

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

#ifndef BPP_NUMERIC_HMM_FULLHMMTRANSITIONMATRIX_H
#define BPP_NUMERIC_HMM_FULLHMMTRANSITIONMATRIX_H


#include "../AbstractParameterAliasable.h"
#include "../Prob/Simplex.h"
#include "AbstractHmmTransitionMatrix.h"

namespace bpp
{
class FullHmmTransitionMatrix :
  public virtual AbstractHmmTransitionMatrix,
  public AbstractParametrizable
{
private:
  std::vector<Simplex> vSimplex_;

public:
  FullHmmTransitionMatrix(std::shared_ptr<const HmmStateAlphabet> alph, const std::string& prefix = "");

  FullHmmTransitionMatrix(const FullHmmTransitionMatrix& hptm);

  FullHmmTransitionMatrix& operator=(const FullHmmTransitionMatrix& hptm);

  FullHmmTransitionMatrix* clone() const { return new FullHmmTransitionMatrix(*this);}

  void setTransitionProbabilities(const Matrix<double>& mat);

  double Pij(size_t i, size_t j) const
  {
    return vSimplex_[i].prob(j);
  }

  const Matrix<double>& getPij() const;

  const std::vector<double>& getEquilibriumFrequencies() const;


  void fireParameterChanged(const ParameterList& parameters);
};
} // end of namespace bpp
#endif // BPP_NUMERIC_HMM_FULLHMMTRANSITIONMATRIX_H