AlphabetIndex1.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1

#ifndef BPP_SEQ_ALPHABETINDEX_ALPHABETINDEX1_H
#define BPP_SEQ_ALPHABETINDEX_ALPHABETINDEX1_H

#include <Bpp/Clonable.h>

#include "../Alphabet/Alphabet.h"
#include "../Alphabet/AlphabetTools.h"
#include "../Alphabet/ProteicAlphabet.h"

// From the STL:
#include <string>

namespace bpp
{
class AlphabetIndex1 :
  public virtual Clonable
{
public:
  AlphabetIndex1() {}
  virtual ~AlphabetIndex1() {}

public:
  virtual AlphabetIndex1* clone() const override = 0;

  virtual double getIndex(int state) const = 0;

  virtual double getIndex(const std::string& state) const = 0;

  virtual std::shared_ptr<const Alphabet> getAlphabet() const = 0;

  virtual const Alphabet& alphabet() const = 0;

  virtual const std::vector<double>& indexVector() const = 0;
};

/*
 * @brief Virtual AlphabetIndex1 for proteic alphabet
 *
 */

class ProteicAlphabetIndex1 :
  public virtual AlphabetIndex1
{
private:
  std::shared_ptr<const ProteicAlphabet> alpha_;

public:
  ProteicAlphabetIndex1() : alpha_(AlphabetTools::PROTEIN_ALPHABET) {}
  virtual ~ProteicAlphabetIndex1() {}

  virtual ProteicAlphabetIndex1* clone() const override = 0;

  ProteicAlphabetIndex1(const ProteicAlphabetIndex1& pt) :
    alpha_(pt.alpha_)
  {}

  ProteicAlphabetIndex1& operator=(const ProteicAlphabetIndex1& 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_ALPHABETINDEX1_H