AlphabetIndex2.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_SEQ_ALPHABETINDEX_ALPHABETINDEX2_H
#define BPP_SEQ_ALPHABETINDEX_ALPHABETINDEX2_H
 
#include <Bpp/Clonable.h>
#include <Bpp/Numeric/Matrix/Matrix.h>
 
#include "../Alphabet/Alphabet.h"
#include "../Alphabet/AlphabetTools.h"
#include "../Alphabet/ProteicAlphabet.h"
 
// From the STL:
#include <string>
 
namespace bpp
{
class AlphabetIndex2 : public Clonable
{
public:
  AlphabetIndex2() {}
  virtual ~AlphabetIndex2() {}
 
public:
  virtual AlphabetIndex2* clone() const = 0;
 
  virtual double getIndex(int state1, int state2) const = 0;
 
  virtual double getIndex(const std::string& state1, const std::string& state2) const = 0;
 
  virtual std::shared_ptr<const Alphabet> getAlphabet() const = 0;
 
  virtual const Alphabet& alphabet() const = 0;
 
  virtual const Matrix<double>& getIndexMatrix() const = 0;
 
  virtual bool isSymmetric() const = 0;
};
 
class ProteicAlphabetIndex2 :
  virtual public AlphabetIndex2
{
private:
  std::shared_ptr<const ProteicAlphabet> alpha_;
 
public:
  ProteicAlphabetIndex2() : alpha_(AlphabetTools::PROTEIN_ALPHABET) {}
  virtual ~ProteicAlphabetIndex2() {}
 
  virtual ProteicAlphabetIndex2* clone() const override = 0;
 
  ProteicAlphabetIndex2(const ProteicAlphabetIndex2& pt) :
    alpha_(pt.alpha_)
  {}
 
  ProteicAlphabetIndex2& operator=(const ProteicAlphabetIndex2& pt)
  {
    alpha_ = pt.alpha_;
    return *this;
  }
 
  std::shared_ptr<const Alphabet> getAlphabet() const override { return alpha_; }
  
  const Alphabet& alphabet() const override { return *alpha_; }
};
} // end of namespace bpp.
#endif // BPP_SEQ_ALPHABETINDEX_ALPHABETINDEX2_H