BLOSUM50.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_SEQ_ALPHABETINDEX_BLOSUM50_H
#define BPP_SEQ_ALPHABETINDEX_BLOSUM50_H
 
 
// from the STL:
#include <string>
 
#include "AlphabetIndex2.h"
#include "../Alphabet/AlphabetExceptions.h"
#include <Bpp/Exceptions.h>
#include <Bpp/Numeric/Matrix/Matrix.h>
 
namespace bpp
{
class BLOSUM50 :
  public ProteicAlphabetIndex2
{
private:
  LinearMatrix<double> distanceMatrix_;
 
public:
  BLOSUM50();
 
  BLOSUM50(const BLOSUM50& blosum) :
    ProteicAlphabetIndex2(blosum),
    distanceMatrix_(blosum.distanceMatrix_)
  {}
 
  BLOSUM50& operator=(const BLOSUM50& blosum)
  {
    ProteicAlphabetIndex2::operator=(*this);
    distanceMatrix_ = blosum.distanceMatrix_;
    return *this;
  }
 
  BLOSUM50* clone() const override { return new BLOSUM50(); }
 
  virtual ~BLOSUM50() {}
 
public:
  double getIndex(int state1, int state2) const override;
  double getIndex(const std::string& state1, const std::string& state2) const override;
  const Matrix<double>& getIndexMatrix() const override;
  bool isSymmetric() const override { return true; }
};
} // end of namespace bpp.
#endif // BPP_SEQ_ALPHABETINDEX_BLOSUM50_H