AbstractHmmTransitionMatrix.h

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

#ifndef BPP_NUMERIC_HMM_ABSTRACTHMMTRANSITIONMATRIX_H
#define BPP_NUMERIC_HMM_ABSTRACTHMMTRANSITIONMATRIX_H


#include "../VectorTools.h"
#include "HmmStateAlphabet.h"
#include "HmmTransitionMatrix.h"

namespace bpp
{
class AbstractHmmTransitionMatrix :
  public virtual HmmTransitionMatrix
{
private:
  std::shared_ptr<const HmmStateAlphabet> alph_;

protected:
  mutable RowMatrix<double> pij_, tmpmat_;

  mutable Vdouble eqFreq_;

  mutable bool upToDate_;

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

  AbstractHmmTransitionMatrix(const AbstractHmmTransitionMatrix& hptm);

  AbstractHmmTransitionMatrix& operator=(const AbstractHmmTransitionMatrix& hptm);

  std::shared_ptr<const HmmStateAlphabet> getHmmStateAlphabet() const
  {
    return alph_;
  }

  const HmmStateAlphabet& hmmStateAlphabet() const
  {
    return *alph_;
  }

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

  size_t getNumberOfStates() const
  {
    return alph_->getNumberOfStates();
  }

  std::vector<size_t> sample(size_t size) const;
};
} // end of namespace bpp
#endif // BPP_NUMERIC_HMM_ABSTRACTHMMTRANSITIONMATRIX_H