HmmTransitionMatrix.h

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

#ifndef BPP_NUMERIC_HMM_HMMTRANSITIONMATRIX_H
#define BPP_NUMERIC_HMM_HMMTRANSITIONMATRIX_H


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

// Fron the STL:
#include <vector>

namespace bpp
{
class HmmTransitionMatrix :
  public virtual Parametrizable
{
public:
  virtual HmmTransitionMatrix* 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 size_t getNumberOfStates() const = 0;

  virtual double Pij(size_t i, size_t j) const = 0;

  virtual const Matrix<double>& getPij() const = 0;

  virtual const std::vector<double>& getEquilibriumFrequencies() const = 0;
};
} // end of namespace bpp
#endif // BPP_NUMERIC_HMM_HMMTRANSITIONMATRIX_H