Alphabet.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_SEQ_ALPHABET_ALPHABET_H
#define BPP_SEQ_ALPHABET_ALPHABET_H
 
#include <Bpp/Clonable.h>
#include <string>
#include <vector>
#include <memory>
 
#include "AlphabetState.h"
 
namespace bpp
{
#pragma GCC diagnostic push
#pragma GCC diagnostic ignored "-Wnon-virtual-dtor" // Disable warning coming from the STL because of std::enable_shared_from_this
class Alphabet :
  public virtual Clonable,
  public std::enable_shared_from_this<Alphabet>
{
public:
  Alphabet() {}
  virtual ~Alphabet() = default;
 
  Alphabet* clone() const = 0;
#pragma GCC diagnostic pop
 
public:
  virtual std::string getName(int state) const = 0;
 
  virtual std::string getName(const std::string& state) const = 0;
 
  virtual int getIntCodeAt(size_t stateIndex) const = 0;
 
  virtual const std::string& getCharCodeAt(size_t stateIndex) const = 0;
 
  virtual size_t getStateIndex(int state) const = 0;
 
  virtual size_t getStateIndex(const std::string& state) const = 0;
 
  virtual bool isIntInAlphabet(int state) const = 0;
 
  virtual bool isCharInAlphabet(const std::string& state) const = 0;
  virtual const AlphabetState& getStateAt(size_t stateIndex) const = 0;
 
  virtual const AlphabetState& getState(int state) const = 0;
 
  virtual const AlphabetState& getState(const std::string& state) const = 0;
 
  virtual std::string intToChar(int state) const = 0;
 
  virtual int charToInt(const std::string& state) const = 0;
  virtual size_t getNumberOfStates() const = 0;
 
  virtual unsigned int getNumberOfChars() const = 0;
 
  virtual unsigned int getNumberOfTypes() const = 0;
 
  virtual unsigned int getSize() const = 0;
 
  virtual bool isResolvedIn(int state1, int state2) const = 0;
 
  virtual std::vector<int> getAlias(int state) const = 0;
 
  virtual std::vector<std::string> getAlias(const std::string& state) const = 0;
 
  virtual int getGeneric(const std::vector<int>& states) const = 0;
 
  virtual std::string getGeneric(const std::vector<std::string>& states) const = 0;
 
  virtual const std::vector<int>& getSupportedInts() const = 0;
 
  virtual const std::vector<std::string>& getSupportedChars() const = 0;
 
  virtual const std::vector<std::string>& getResolvedChars() const = 0;
 
  virtual int getUnknownCharacterCode() const = 0;
 
  virtual int getGapCharacterCode() const = 0;
 
  virtual bool isGap(int state) const = 0;
 
  virtual bool isGap(const std::string& state) const = 0;
 
  virtual bool isUnresolved(int state) const = 0;
 
  virtual bool isUnresolved(const std::string& state) const = 0;
 
  virtual std::string getAlphabetType() const = 0;
 
  virtual unsigned int getStateCodingSize() const = 0;
 
  virtual bool equals(const Alphabet& alphabet) const = 0;
};
} // end of namespace bpp.
#endif // BPP_SEQ_ALPHABET_ALPHABET_H