StandardGeneticCode.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_SEQ_GENETICCODE_STANDARDGENETICCODE_H
#define BPP_SEQ_GENETICCODE_STANDARDGENETICCODE_H
 
 
#include "../Alphabet/NucleicAlphabet.h"
#include "GeneticCode.h"
 
namespace bpp
{
class StandardGeneticCode :
  public virtual GeneticCode
{
public:
  StandardGeneticCode(std::shared_ptr<const NucleicAlphabet> alphabet) :
    GeneticCode(alphabet)
  {
    init_();
  }
 
  virtual ~StandardGeneticCode() {}
 
  virtual StandardGeneticCode* clone() const
  {
    return new StandardGeneticCode(*this);
  }
 
public:
  size_t getNumberOfStopCodons() const { return 3; }
 
  std::vector<int> getStopCodonsAsInt() const
  {
    return std::vector<int>({48, 50, 56});
  }
 
  std::vector<std::string> getStopCodonsAsChar() const
  {
    return std::vector<std::string>({"TAA", "TAG", "TGA"});
  }
 
  bool isStop(int state) const
  {
    // Test:
    codonAlphabet_->intToChar(state); // throw exception if invalid state!
    return state == 48 || state == 50 || state == 56;
  }
 
  bool isStop(const std::string& state) const
  {
    int i = codonAlphabet_->charToInt(state);
    return i == 48 || i == 50 || i == 56;
  }
 
  bool isAltStart(int state) const
  {
    // Test:
    codonAlphabet_->intToChar(state); // throw exception if invalid state!
    return state == 62 || state == 30;
  }
 
  bool isAltStart(const std::string& state) const
  {
    int i = codonAlphabet_->charToInt(state);
    return i == 62 || i == 30;
  }
 
private:
  void init_();
};
} // end of namespace bpp.
#endif // BPP_SEQ_GENETICCODE_STANDARDGENETICCODE_H