BinaryAlphabet.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_SEQ_ALPHABET_BINARYALPHABET_H
#define BPP_SEQ_ALPHABET_BINARYALPHABET_H
 
 
#include "AbstractAlphabet.h"
 
namespace bpp
{
class BinaryAlphabet :
  public AbstractAlphabet
{
public:
  // class constructor
  BinaryAlphabet();
 
  BinaryAlphabet(const BinaryAlphabet& bia) : AbstractAlphabet(bia) {}
 
  BinaryAlphabet& operator=(const BinaryAlphabet& bia)
  {
    AbstractAlphabet::operator=(bia);
 
    return *this;
  }
 
  BinaryAlphabet* clone() const
  {
    return new BinaryAlphabet(*this);
  }
 
  // class destructor
  virtual ~BinaryAlphabet() {}
 
public:
  unsigned int getSize() const { return 2; }
  unsigned int getNumberOfTypes() const { return 2; }
  std::string getAlphabetType() const { return "Binary"; }
  int getUnknownCharacterCode() const { return 2; }
  bool isUnresolved(int state) const { return state > 1; }
  bool isUnresolved(const std::string& state) const { return charToInt(state) > 1; }
 
  bool isResolvedIn(int state1, int state2) const;
 
  std::vector<int> getAlias(int state) const;
  std::vector<std::string> getAlias(const std::string& state) const;
};
} // end of namespace bpp.
#endif // BPP_SEQ_ALPHABET_BINARYALPHABET_H