| OpenMS 2.5.0

RibonucleotideDB.h
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2 // OpenMS -- Open-Source Mass Spectrometry
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5 // ETH Zurich, and Freie Universitaet Berlin 2002-2020.
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30 // --------------------------------------------------------------------------
31 // $Maintainer: Hendrik Weisser $
32 // $Authors: Hendrik Weisser $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/CHEMISTRY/Ribonucleotide.h>
38 #include <OpenMS/DATASTRUCTURES/String.h>
39 #include <unordered_map>
40
41 namespace OpenMS
42 {
50 class OPENMS_DLLAPI RibonucleotideDB
51 {
52 public:
53 using ConstRibonucleotidePtr = const Ribonucleotide *;
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:
106 RibonucleotideDB();
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
123 Size max_code_length_;
124 };
125 }
OpenMS::Ribonucleotide
Representation of a ribonucleotide (modified or unmodified)
Definition: Ribonucleotide.h:51
Ribonucleotide.h
OpenMS::RibonucleotideDB::max_code_length_
Size max_code_length_
Definition: RibonucleotideDB.h:123
OpenMS::RibonucleotideDB::begin
ConstIterator begin() const
Const iterator to beginning of database.
Definition: RibonucleotideDB.h:71
OpenMS::RibonucleotideDB
Database of ribonucleotides (modified and unmodified)
Definition: RibonucleotideDB.h:50
OpenMS::RibonucleotideDB::ConstIterator
std::vector< ConstRibonucleotidePtr >::const_iterator ConstIterator
const iterator type definition
Definition: RibonucleotideDB.h:56
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
String.h
OpenMS::RibonucleotideDB::ribonucleotides_
std::vector< ConstRibonucleotidePtr > ribonucleotides_
list of known (modified) nucleotides
Definition: RibonucleotideDB.h:115
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
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
OpenMS::RibonucleotideDB::end
ConstIterator end() const
Const iterator to end of database.
Definition: RibonucleotideDB.h:77
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127