RNY.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_SEQ_ALPHABET_RNY_H
#define BPP_SEQ_ALPHABET_RNY_H
 
#include <string>
 
#include "AbstractAlphabet.h"
#include "NucleicAlphabet.h"
 
namespace bpp
{
class RNY : public AbstractAlphabet
{
private:
  std::shared_ptr<const NucleicAlphabet>  nuclalph_;
 
public:
  RNY(std::shared_ptr<const NucleicAlphabet> na);
 
  RNY(const RNY& bia) : AbstractAlphabet(bia), nuclalph_(bia.nuclalph_) {}
 
  RNY& operator=(const RNY& bia)
  {
    AbstractAlphabet::operator=(bia);
    return *this;
  }
 
  RNY* clone() const
  {
    return new RNY(*this);
  }
 
  ~RNY() {}
 
public:
  int charToInt(const std::string& state) const;
  std::string intToChar(int state) const;
 
  bool containsGap(const std::string& state) const;
 
  unsigned int getSize() const { return 36; }
  unsigned int getNumberOfTypes() const { return 80; }
  int getUnknownCharacterCode() const { return 350; }
  bool isGap(int state) const;
  bool isResolvedIn(int state1, int state2) const;
  std::vector<int> getAlias(int state) const;
  std::vector<std::string> getAlias(const std::string& state) const;
  bool isUnresolved(int state) const;
  bool isUnresolved(const std::string& state) const;
 
  std::string getAlphabetType() const { return "RNY(letter=" + nuclalph_->getAlphabetType() + ")"; }
 
  std::shared_ptr<const NucleicAlphabet> getLetterAlphabet() const
  {
    return nuclalph_;
  }
 
public:
  std::string getRNY(const std::string&, const std::string&, const std::string&) const;
 
  int getRNY(int, int, int, const Alphabet&) const;
};
}
#endif // BPP_SEQ_ALPHABET_RNY_H