OpenMS  3.0.0
RibonucleotideDB.h
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31 // $Maintainer: Hendrik Weisser $
32 // $Authors: Hendrik Weisser $
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34 
35 #pragma once
36 
39 #include <unordered_map>
40 
41 namespace OpenMS
42 {
50  class OPENMS_DLLAPI RibonucleotideDB
51  {
52  public:
54 
56  typedef std::vector<ConstRibonucleotidePtr>::const_iterator ConstIterator;
57 
59  static RibonucleotideDB* getInstance();
60 
62  virtual ~RibonucleotideDB();
63 
65  RibonucleotideDB(const RibonucleotideDB& other) = delete;
66 
68  RibonucleotideDB& operator=(const RibonucleotideDB& other) = delete;
69 
71  inline ConstIterator begin() const
72  {
73  return ribonucleotides_.begin();
74  }
75 
77  inline ConstIterator end() const
78  {
79  return ribonucleotides_.end();
80  }
81 
87  ConstRibonucleotidePtr getRibonucleotide(const std::string& code);
88 
94  ConstRibonucleotidePtr getRibonucleotidePrefix(const std::string& seq);
95 
101  std::pair<ConstRibonucleotidePtr, ConstRibonucleotidePtr> getRibonucleotideAlternatives(const std::string& code);
102 
103 
104  protected:
107 
109  void readFromFile_(const std::string& path);
110 
112  ConstRibonucleotidePtr parseRow_(const std::string& row, Size line_count);
113 
115  std::vector<ConstRibonucleotidePtr> ribonucleotides_;
116 
118  std::unordered_map<std::string, Size> code_map_;
119 
121  std::map<std::string, std::pair<ConstRibonucleotidePtr, ConstRibonucleotidePtr>> ambiguity_map_;
122 
124  };
125 }
OpenMS::RibonucleotideDB::ribonucleotides_
std::vector< ConstRibonucleotidePtr > ribonucleotides_
list of known (modified) nucleotides
Definition: RibonucleotideDB.h:115
OpenMS::Ribonucleotide
Representation of a ribonucleotide (modified or unmodified)
Definition: Ribonucleotide.h:51
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
OpenMS::RibonucleotideDB::ConstIterator
std::vector< ConstRibonucleotidePtr >::const_iterator ConstIterator
const iterator type definition
Definition: RibonucleotideDB.h:56
Ribonucleotide.h
OpenMS::RibonucleotideDB::begin
ConstIterator begin() const
Const iterator to beginning of database.
Definition: RibonucleotideDB.h:71
OpenMS::RibonucleotideDB::max_code_length_
Size max_code_length_
Definition: RibonucleotideDB.h:123
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::RibonucleotideDB::code_map_
std::unordered_map< std::string, Size > code_map_
mapping of codes (short names) to indexes into ribonucleotides_
Definition: RibonucleotideDB.h:118
OpenMS::RibonucleotideDB
Database of ribonucleotides (modified and unmodified)
Definition: RibonucleotideDB.h:50
OpenMS::RibonucleotideDB::end
ConstIterator end() const
Const iterator to end of database.
Definition: RibonucleotideDB.h:77
String.h
OpenMS::RibonucleotideDB::ambiguity_map_
std::map< std::string, std::pair< ConstRibonucleotidePtr, ConstRibonucleotidePtr > > ambiguity_map_
mapping of ambiguity codes to the alternatives they represent
Definition: RibonucleotideDB.h:121