RibonucleotideDB.h

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// Copyright (c) 2002-2023, The OpenMS Team -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Hendrik Weisser $
// $Authors: Hendrik Weisser $
// --------------------------------------------------------------------------
 
#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_;
  };
}