AbstractHmmTransitionMatrix.h

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//
// File: AbstractHmmTransitionMatrix.h
// Authors:
//   Laurent Guéguen
// Created: lundi 10 février 2014, à 10h 55
//
 
/*
  Copyright or © or Copr. Bio++Development Team, (November 16, 2004)
  
  This software is a computer program whose purpose is to provide classes
  for phylogenetic data analysis.
  
  This software is governed by the CeCILL license under French law and
  abiding by the rules of distribution of free software. You can use,
  modify and/ or redistribute the software under the terms of the CeCILL
  license as circulated by CEA, CNRS and INRIA at the following URL
  "http://www.cecill.info".
  
  As a counterpart to the access to the source code and rights to copy,
  modify and redistribute granted by the license, users are provided only
  with a limited warranty and the software's author, the holder of the
  economic rights, and the successive licensors have only limited
  liability.
  
  In this respect, the user's attention is drawn to the risks associated
  with loading, using, modifying and/or developing or reproducing the
  software by the user in light of its specific status of free software,
  that may mean that it is complicated to manipulate, and that also
  therefore means that it is reserved for developers and experienced
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*/
 
#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:
  const HmmStateAlphabet* alph_;
 
protected:
  mutable RowMatrix<double> pij_, tmpmat_;
 
  mutable Vdouble eqFreq_;
 
  mutable bool upToDate_;
 
public:
  AbstractHmmTransitionMatrix(const HmmStateAlphabet* alph, const std::string& prefix = "");
 
  AbstractHmmTransitionMatrix(const AbstractHmmTransitionMatrix& hptm);
 
  AbstractHmmTransitionMatrix& operator=(const AbstractHmmTransitionMatrix& hptm);
 
  const HmmStateAlphabet* getHmmStateAlphabet() const
  {
    return alph_;
  }
 
  void setHmmStateAlphabet(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