DNA.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_SEQ_ALPHABET_DNA_H
#define BPP_SEQ_ALPHABET_DNA_H
 
 
#include "NucleicAlphabet.h"
 
// From the STL:
#include <string>
#include <vector>
 
namespace bpp
{
class DNA :
  public NucleicAlphabet
{
public:
  DNA(bool exclamationMarkCountsAsGap = false);
 
  DNA(const DNA& bia) : NucleicAlphabet(bia) {}
 
  DNA& operator=(const DNA& bia)
  {
    NucleicAlphabet::operator=(bia);
    return *this;
  }
 
  DNA* clone() const
  {
    return new DNA(*this);
  }
 
  virtual ~DNA() {}
 
public:
  bool isResolvedIn(int state1, int state2) const;
 
  std::vector<int> getAlias(int state) const;
  std::vector<std::string> getAlias(const std::string& state) const;
  int getGeneric(const std::vector<int>& states) const;
  std::string getGeneric(const std::vector<std::string>& states) const;
  std::string getAlphabetType() const { return "DNA"; }
};
} // end of namespace bpp.
#endif // BPP_SEQ_ALPHABET_DNA_H