OpenMS
RibonucleotideDB.h
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1 // Copyright (c) 2002-2023, The OpenMS Team -- EKU Tuebingen, ETH Zurich, and FU Berlin
2 // SPDX-License-Identifier: BSD-3-Clause
3 //
4 // --------------------------------------------------------------------------
5 // $Maintainer: Hendrik Weisser $
6 // $Authors: Hendrik Weisser $
7 // --------------------------------------------------------------------------
8 
9 #pragma once
10 
13 #include <memory>
14 #include <unordered_map>
15 
16 namespace OpenMS
17 {
25  class OPENMS_DLLAPI RibonucleotideDB final
26  {
27  public:
29 
31  typedef std::vector<std::unique_ptr<Ribonucleotide>>::const_iterator ConstIterator;
32 
35 
37  ~RibonucleotideDB() = default;
38 
40  RibonucleotideDB(const RibonucleotideDB& other) = delete;
41 
43  RibonucleotideDB& operator=(const RibonucleotideDB& other) = delete;
44 
46  inline ConstIterator begin() const
47  {
48  return ribonucleotides_.begin();
49  }
50 
52  inline ConstIterator end() const
53  {
54  return ribonucleotides_.end();
55  }
56 
62  ConstRibonucleotidePtr getRibonucleotide(const std::string& code);
63 
70 
76  std::pair<ConstRibonucleotidePtr, ConstRibonucleotidePtr> getRibonucleotideAlternatives(const std::string& code);
77 
78 
79  protected:
82 
84  void readFromFile_(const std::string& path);
85 
87  void readFromJSON_(const std::string& path);
88 
90  const std::unique_ptr<Ribonucleotide> parseRow_(const std::string& row, Size line_count);
91 
93  std::vector<std::unique_ptr<Ribonucleotide>> ribonucleotides_;
94 
96  std::unordered_map<std::string, Size> code_map_;
97 
99  std::map<std::string, std::pair<ConstRibonucleotidePtr, ConstRibonucleotidePtr>> ambiguity_map_;
100 
102  };
103 }
Database of ribonucleotides (modified and unmodified)
Definition: RibonucleotideDB.h:26
RibonucleotideDB()
default constructor
static RibonucleotideDB * getInstance()
replacement for constructor (singleton pattern)
std::vector< std::unique_ptr< Ribonucleotide > > ribonucleotides_
list of known (modified) nucleotides
Definition: RibonucleotideDB.h:93
std::pair< ConstRibonucleotidePtr, ConstRibonucleotidePtr > getRibonucleotideAlternatives(const std::string &code)
Get the alternatives for an ambiguous modification code.
RibonucleotideDB & operator=(const RibonucleotideDB &other)=delete
assignment operator not available
RibonucleotideDB(const RibonucleotideDB &other)=delete
copy constructor not available
ConstRibonucleotidePtr getRibonucleotide(const std::string &code)
Get a ribonucleotide by its code (short name)
ConstIterator end() const
Const iterator to end of database.
Definition: RibonucleotideDB.h:52
std::vector< std::unique_ptr< Ribonucleotide > >::const_iterator ConstIterator
const iterator type definition
Definition: RibonucleotideDB.h:31
void readFromJSON_(const std::string &path)
read from a newer version of Modomics that uses a JSON file
std::unordered_map< std::string, Size > code_map_
mapping of codes (short names) to indexes into ribonucleotides_
Definition: RibonucleotideDB.h:96
const std::unique_ptr< Ribonucleotide > parseRow_(const std::string &row, Size line_count)
create a (modified) nucleotide from an input row
Size max_code_length_
Definition: RibonucleotideDB.h:101
ConstIterator begin() const
Const iterator to beginning of database.
Definition: RibonucleotideDB.h:46
ConstRibonucleotidePtr getRibonucleotidePrefix(const std::string &seq)
Get the ribonucleotide with the longest code that matches a prefix of seq.
void readFromFile_(const std::string &path)
read (modified) nucleotides from input file
std::map< std::string, std::pair< ConstRibonucleotidePtr, ConstRibonucleotidePtr > > ambiguity_map_
mapping of ambiguity codes to the alternatives they represent
Definition: RibonucleotideDB.h:99
~RibonucleotideDB()=default
destructor
Representation of a ribonucleotide (modified or unmodified)
Definition: Ribonucleotide.h:26
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:101
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:22