LetterAlphabet.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_SEQ_ALPHABET_LETTERALPHABET_H
#define BPP_SEQ_ALPHABET_LETTERALPHABET_H
 
 
// From the STL
#include <string>
#include <vector>
#include <iostream>
 
// From Seq
#include "AbstractAlphabet.h"
#include "AlphabetExceptions.h"
 
namespace bpp
{
class LetterAlphabet :
  public AbstractAlphabet
{
private:
  static const int LETTER_UNDEF_VALUE;
  std::vector<int> letters_;
  bool caseSensitive_;
 
public:
  LetterAlphabet(bool caseSensitive = false) : letters_(256, LETTER_UNDEF_VALUE), caseSensitive_(caseSensitive) {}
 
  LetterAlphabet(const LetterAlphabet& bia) : AbstractAlphabet(bia), letters_(bia.letters_), caseSensitive_(bia.caseSensitive_) {}
 
  LetterAlphabet& operator=(const LetterAlphabet& bia)
  {
    AbstractAlphabet::operator=(bia);
    letters_ = bia.letters_;
    caseSensitive_ = bia.caseSensitive_;
 
    return *this;
  }
 
  virtual LetterAlphabet* clone() const = 0;
 
  virtual ~LetterAlphabet() {}
 
public:
  bool isCharInAlphabet(char state) const
  {
    return letters_[static_cast<size_t>(state)] != LETTER_UNDEF_VALUE;
  }
  bool isCharInAlphabet(const std::string& state) const
  {
    return isCharInAlphabet(state[0]);
  }
  int charToInt(const std::string& state) const
  {
    if (!isCharInAlphabet(state))
      throw BadCharException(state, "LetterAlphabet::charToInt: Unknown state", this);
    return letters_[static_cast<unsigned int>(state[0])];
  }
 
protected:
  void registerState(AlphabetState* st)
  {
    AbstractAlphabet::registerState(st);
    if (caseSensitive_)
    {
      letters_[static_cast<size_t>(st->getLetter()[0])] = st->getNum();
    }
    else
    {
      letters_[static_cast<size_t>(tolower(st->getLetter()[0]))] = st->getNum();
      letters_[static_cast<size_t>(toupper(st->getLetter()[0]))] = st->getNum();
    }
  }
 
  void setState(size_t pos, AlphabetState* st)
  {
    AbstractAlphabet::setState(pos, st);
    if (caseSensitive_)
    {
      letters_[static_cast<size_t>(st->getLetter()[0])] = st->getNum();
    }
    else
    {
      letters_[static_cast<size_t>(tolower(st->getLetter()[0]))] = st->getNum();
      letters_[static_cast<size_t>(toupper(st->getLetter()[0]))] = st->getNum();
    }
  }
};
}
#endif // BPP_SEQ_ALPHABET_LETTERALPHABET_H