AutoCorrelationTransitionMatrix.h

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

#ifndef BPP_NUMERIC_HMM_AUTOCORRELATIONTRANSITIONMATRIX_H
#define BPP_NUMERIC_HMM_AUTOCORRELATIONTRANSITIONMATRIX_H


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

namespace bpp
{
class AutoCorrelationTransitionMatrix :
  public virtual AbstractHmmTransitionMatrix,
  public AbstractParametrizable
{
private:
  std::vector<double> vAutocorrel_;

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

  AutoCorrelationTransitionMatrix(const AutoCorrelationTransitionMatrix& hptm);

  AutoCorrelationTransitionMatrix& operator=(const AutoCorrelationTransitionMatrix& hptm);

  AutoCorrelationTransitionMatrix* clone() const override { return new AutoCorrelationTransitionMatrix(*this);}

  double Pij(size_t i, size_t j) const override
  {
    return (i == j) ? vAutocorrel_[i] : (1 - vAutocorrel_[i]) / static_cast<double>(getNumberOfStates() - 1);
  }

  const Matrix<double>& getPij() const override;

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


  /*
   * @brief From AbstractParametrizable interface
   *
   */

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