RibonucleotideDB.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
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// $Maintainer: Hendrik Weisser $
// $Authors: Hendrik Weisser $
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#pragma once

#include <OpenMS/CHEMISTRY/Ribonucleotide.h>
#include <OpenMS/DATASTRUCTURES/String.h>
#include <memory>
#include <unordered_map>

namespace OpenMS
{
  class OPENMS_DLLAPI RibonucleotideDB final
  {
  public:
    using ConstRibonucleotidePtr = const Ribonucleotide *;

    typedef std::vector<std::unique_ptr<Ribonucleotide>>::const_iterator ConstIterator;

    static RibonucleotideDB* getInstance();

    ~RibonucleotideDB() = default;

    RibonucleotideDB(const RibonucleotideDB& other) = delete;

    RibonucleotideDB& operator=(const RibonucleotideDB& other) = delete;

    inline ConstIterator begin() const
    {
      return ribonucleotides_.begin();
    }

    inline ConstIterator end() const
    {
      return ribonucleotides_.end();
    }

    ConstRibonucleotidePtr getRibonucleotide(const std::string& code);

    ConstRibonucleotidePtr getRibonucleotidePrefix(const std::string& seq);

    std::pair<ConstRibonucleotidePtr, ConstRibonucleotidePtr> getRibonucleotideAlternatives(const std::string& code);


  protected:
    RibonucleotideDB();

    void readFromFile_(const std::string& path);

    void readFromJSON_(const std::string& path);

    const std::unique_ptr<Ribonucleotide>  parseRow_(const std::string& row, Size line_count);

    std::vector<std::unique_ptr<Ribonucleotide>> ribonucleotides_;

    std::unordered_map<std::string, Size> code_map_;

    std::map<std::string, std::pair<ConstRibonucleotidePtr, ConstRibonucleotidePtr>> ambiguity_map_;

    Size max_code_length_;
  };
}