DefaultNucleotideScore.h

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