MiyataAAChemicalDistance.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_SEQ_ALPHABETINDEX_MIYATAAACHEMICALDISTANCE_H
#define BPP_SEQ_ALPHABETINDEX_MIYATAAACHEMICALDISTANCE_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 MiyataAAChemicalDistance :
  public ProteicAlphabetIndex2
{
private:
  LinearMatrix<double> distanceMatrix_;
  LinearMatrix<double> indexMatrix_;
  bool sym_;
 
public:
  MiyataAAChemicalDistance();
 
  MiyataAAChemicalDistance(const MiyataAAChemicalDistance& md) :
    ProteicAlphabetIndex2(md),
    distanceMatrix_(md.distanceMatrix_),
    indexMatrix_(md.indexMatrix_),
    sym_(md.sym_)
  {}
 
  MiyataAAChemicalDistance& operator=(const MiyataAAChemicalDistance& md)
  {
    ProteicAlphabetIndex2::operator=(*this);
 
    distanceMatrix_ = md.distanceMatrix_;
    indexMatrix_ = md.indexMatrix_;
    sym_ = md.sym_;
    return *this;
  }
 
  virtual ~MiyataAAChemicalDistance() {}
 
  MiyataAAChemicalDistance* clone() const override { return new MiyataAAChemicalDistance(); }
 
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 { return indexMatrix_; }
protected:
  void computeIndexMatrix_();
 
public:
  void setSymmetric(bool yn)
  {
    sym_ = yn;
    computeIndexMatrix_();
  }
  bool isSymmetric() const override { return sym_; }
};
} // end of namespace bpp.
#endif // BPP_SEQ_ALPHABETINDEX_MIYATAAACHEMICALDISTANCE_H