CaseMaskedAlphabet.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_SEQ_ALPHABET_CASEMASKEDALPHABET_H
#define BPP_SEQ_ALPHABET_CASEMASKEDALPHABET_H
 
 
#include "LetterAlphabet.h"
 
// From the STL:
#include <string>
 
namespace bpp
{
class CaseMaskedAlphabet :
  public LetterAlphabet
{
public:
  std::shared_ptr<const LetterAlphabet> nocaseAlphabet_;
 
public:
  CaseMaskedAlphabet(std::shared_ptr<const LetterAlphabet> nocaseAlphabet);
 
  CaseMaskedAlphabet(const CaseMaskedAlphabet& cma) :
    LetterAlphabet(cma), nocaseAlphabet_(cma.nocaseAlphabet_) {}
 
  CaseMaskedAlphabet& operator=(const CaseMaskedAlphabet& cma)
  {
    LetterAlphabet::operator=(cma);
    nocaseAlphabet_ = cma.nocaseAlphabet_;
    return *this;
  }
 
  CaseMaskedAlphabet* clone() const override
  {
    return new CaseMaskedAlphabet(*this);
  }
 
public:
  unsigned int getSize() const override { return nocaseAlphabet_->getSize(); }
  unsigned int getNumberOfTypes() const override { return nocaseAlphabet_->getNumberOfTypes(); }
  std::string getAlphabetType() const override { return "CaseMasked"; }
  int getUnknownCharacterCode() const override { return nocaseAlphabet_->getUnknownCharacterCode(); }
  bool isUnresolved(int state) const override { return nocaseAlphabet_->isUnresolved(state); }
  bool isUnresolved(const std::string& state) const override { return nocaseAlphabet_->isUnresolved(state); }
 
  std::shared_ptr<const Alphabet> getUnmaskedAlphabet() const { return nocaseAlphabet_; }
 
  bool isMasked(int state) const { return state >= 100; }
  bool isMasked(const std::string& state) const
  {
    char c = state.c_str()[0];
    return isMasked(c);
  }
  bool isMasked(char state) const
  {
    return isalpha(state) && !isupper(state);
  }
 
  int getMaskedEquivalentState(int state) const;
  const std::string getMaskedEquivalentState(const std::string& state) const;
};
} // end of namespace bpp
#endif // BPP_SEQ_ALPHABET_CASEMASKEDALPHABET_H