| OpenMS 2.5.0

ElementDB.h
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2 // OpenMS -- Open-Source Mass Spectrometry
3 // --------------------------------------------------------------------------
4 // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
5 // ETH Zurich, and Freie Universitaet Berlin 2002-2020.
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30 // --------------------------------------------------------------------------
31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Andreas Bertsch, Timo Sachsenberg, Chris Bielow $
33 // --------------------------------------------------------------------------
34 //
35
36 #pragma once
37
38 #include <OpenMS/DATASTRUCTURES/String.h>
39 #include <OpenMS/DATASTRUCTURES/Map.h>
40 #include <OpenMS/CHEMISTRY/ISOTOPEDISTRIBUTION/IsotopeDistribution.h>
41 #include <OpenMS/CHEMISTRY/Element.h>
42
43 namespace OpenMS
44 {
45
69 class OPENMS_DLLAPI ElementDB
70 {
71 public:
72
76 static const ElementDB* getInstance();
80
82 const Map<String, const Element *> & getNames() const;
83
85 const Map<String, const Element *> & getSymbols() const;
86
88 const Map<UInt, const Element *> & getAtomicNumbers() const;
89
94 const Element * getElement(const String & name) const;
95
97 const Element * getElement(UInt atomic_number) const;
98
100
104 bool hasElement(const String & name) const;
106
108 bool hasElement(UInt atomic_number) const;
110
111 protected:
112
113 /*_ parses a Histogram given as a OpenMS String and return the distribution
114
115 @throw throws exception ParseError
116 */
117 IsotopeDistribution parseIsotopeDistribution_(const Map<UInt, double>& Z_to_abundance, const Map<UInt, double>& Z_to_mass);
118
119 /*_ calculates the average weight based on isotope abundance and mass
120 */
121 double calculateAvgWeight_(const Map<UInt, double> & Z_to_abundance, const Map<UInt, double> & Z_to_mass);
122
123 /*_ calculates the mono weight based on the smallest isotope mass
124 */
125 double calculateMonoWeight_(const Map<UInt, double> & Z_to_mass);
126
127 /*_ read elements from a XML file, formatted as a Param file.
128
129 @throw throws ParseError if the file cannot be parsed
130 @throw throws FileNotFound if the file could not be found
131 */
132 void readFromFile_(const String & file_name);
133
134
136 void storeElement_(const UInt an, const String& name, const String& symbol, const Map<UInt, double>& Z_to_abundancy, const Map<UInt, double>& Z_to_mass);
137
138 /*_ resets all containers
139 */
140 void clear_();
141
142 Map<String, const Element *> names_;
143
144 Map<String, const Element *> symbols_;
145
146 Map<UInt, const Element *> atomic_numbers_;
147
148 private:
149 ElementDB();
150 ~ElementDB();
151 ElementDB(const ElementDB& db) = delete;
152 ElementDB(const ElementDB&& db) = delete;
153 ElementDB& operator=(const ElementDB& db) = delete;
154
155 };
156
157 } // namespace OpenMS
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::IsotopeDistribution
Definition: IsotopeDistribution.h:64
OpenMS::ElementDB::atomic_numbers_
Map< UInt, const Element * > atomic_numbers_
Definition: ElementDB.h:146
IsotopeDistribution.h
OpenMS::ElementDB
Stores elements.
Definition: ElementDB.h:69
String.h
OpenMS::Map
Map class based on the STL map (containing several convenience functions)
Definition: Map.h:50
OpenMS::Element
Representation of an element.
Definition: Element.h:53
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
Map.h
OpenMS::UInt
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
OpenMS::ElementDB::symbols_
Map< String, const Element * > symbols_
Definition: ElementDB.h:144
Element.h
OpenMS::ElementDB::names_
Map< String, const Element * > names_
Definition: ElementDB.h:142