ProteicAlphabet.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_SEQ_ALPHABET_PROTEICALPHABET_H
#define BPP_SEQ_ALPHABET_PROTEICALPHABET_H
 
 
#include "LetterAlphabet.h"
#include "ProteicAlphabetState.h"
 
namespace bpp
{
class ProteicAlphabet :
  public LetterAlphabet
{
public:
  const ProteicAlphabetState& getState(const std::string& letter) const
  {
    return dynamic_cast<const ProteicAlphabetState&>(
      AbstractAlphabet::getState(letter)
      );
  }
 
  const ProteicAlphabetState& getState(int num) const
  {
    return dynamic_cast<const ProteicAlphabetState&>(
      AbstractAlphabet::getState(num)
      );
  }
 
protected:
  const ProteicAlphabetState& getStateAt(size_t pos) const
  {
    return dynamic_cast<const ProteicAlphabetState&>(
      AbstractAlphabet::getStateAt(pos)
      );
  }
 
  ProteicAlphabetState& getStateAt(size_t pos)
  {
    return dynamic_cast<ProteicAlphabetState&>(
      AbstractAlphabet::getStateAt(pos)
      );
  }
 
public:
  ProteicAlphabet();
 
  ProteicAlphabet(const ProteicAlphabet& bia) : LetterAlphabet(bia) {}
 
  ProteicAlphabet& operator=(const ProteicAlphabet& bia)
  {
    LetterAlphabet::operator=(bia);
    return *this;
  }
 
  ProteicAlphabet* clone() const
  {
    return new ProteicAlphabet(*this);
  }
 
 
  virtual ~ProteicAlphabet() {}
 
public:
  unsigned int getSize() const { return 20; }
  unsigned int getNumberOfTypes() const { return 24; }
  int getUnknownCharacterCode() const { return 23; }
  bool isResolvedIn(int state1, int state2) const;
  std::vector<int> getAlias(int state) const;
  std::vector<std::string> getAlias(const std::string& state) const;
  int getGeneric(const std::vector<int>& states) const;
  std::string getGeneric(const std::vector<std::string>& states) const;
  bool isUnresolved(int state) const { return state > 19; }
  bool isUnresolved(const std::string& state) const { return charToInt(state) > 19; }
  std::string getAlphabetType() const { return "Proteic"; }
 
public:
  std::string getAbbr(const std::string& aa) const;
 
  std::string getAbbr(int aa) const;
};
} // end of namespace bpp.
#endif // BPP_SEQ_ALPHABET_PROTEICALPHABET_H