LexicalAlphabet.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_SEQ_ALPHABET_LEXICALALPHABET_H
#define BPP_SEQ_ALPHABET_LEXICALALPHABET_H
 
 
#include "AbstractAlphabet.h"
 
// From the STL:
#include <string>
#include <vector>
 
namespace bpp
{
class LexicalAlphabet :
  public AbstractAlphabet
{
public:
  // Constructor and destructor.
  LexicalAlphabet(const std::vector<std::string>& vocab);
 
  LexicalAlphabet(const LexicalAlphabet& bia) : AbstractAlphabet(bia) {}
 
  LexicalAlphabet& operator=(const LexicalAlphabet& bia)
  {
    AbstractAlphabet::operator=(bia);
    return *this;
  }
 
  LexicalAlphabet* clone() const
  {
    return new LexicalAlphabet(*this);
  }
 
  virtual ~LexicalAlphabet() {}
 
public:
  unsigned int getSize() const
  {
    return getNumberOfChars() - 2;
  }
 
  unsigned int getNumberOfTypes() const
  {
    return getNumberOfChars() - 1;
  }
 
  std::string getAlphabetType() const;
 
  int getUnknownCharacterCode() const
  {
    return static_cast<int>(getSize());
  }
 
  bool isUnresolved(int state) const { return state == getUnknownCharacterCode(); }
  bool isUnresolved(const std::string& state) const { return charToInt(state) == getUnknownCharacterCode(); }
};
} // end of namespace bpp.
#endif // BPP_SEQ_ALPHABET_LEXICALALPHABET_H