OpenMS  2.4.0
ElementDB.h
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31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Andreas Bertsch, Timo Sachsenberg $
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34 //
35 
36 #pragma once
37 
42 
43 namespace OpenMS
44 {
45 
69  class OPENMS_DLLAPI ElementDB
70  {
71 public:
72 
76  inline static const ElementDB * getInstance()
78  {
79  static ElementDB * db_ = nullptr;
80  if (db_ == nullptr)
81  {
82  db_ = new ElementDB;
83  }
84  return db_;
85  }
86 
88  const Map<String, const Element *> & getNames() const;
89 
91  const Map<String, const Element *> & getSymbols() const;
92 
94  const Map<UInt, const Element *> & getAtomicNumbers() const;
95 
100  const Element * getElement(const String & name) const;
101 
103  const Element * getElement(UInt atomic_number) const;
104 
106 
110  bool hasElement(const String & name) const;
112 
114  bool hasElement(UInt atomic_number) const;
116 
117 protected:
118 
119  /*_ parses a Histogram given as a OpenMS String and return the distribution
120 
121  @throw throws exception ParseError
122  */
123  IsotopeDistribution parseIsotopeDistribution_(const Map<UInt, double>& Z_to_abundance, const Map<UInt, double>& Z_to_mass);
124 
125  /*_ calculates the average weight based on isotope abundance and mass
126  */
127  double calculateAvgWeight_(const Map<UInt, double> & Z_to_abundance, const Map<UInt, double> & Z_to_mass);
128 
129  /*_ calculates the mono weight based on the smallest isotope mass
130  */
131  double calculateMonoWeight_(const Map<UInt, double> & Z_to_mass);
132 
133  /*_ read elements from a XML file, formatted as a Param file.
134 
135  @throw throws ParseError if the file cannot be parsed
136  @throw throws FileNotFound if the file could not be found
137  */
138  void readFromFile_(const String & file_name);
139 
140  /*_ resets all containers
141  */
142  void clear_();
143 
145 
147 
149 
150 private:
151 
152  ElementDB();
153 
154  ElementDB(const ElementDB & db);
155 
156  ElementDB & operator=(const ElementDB & db);
157 
158  virtual ~ElementDB();
159  };
160 
161 } // namespace OpenMS
A more convenient string class.
Definition: String.h:57
Map< String, const Element * > symbols_
Definition: ElementDB.h:146
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
Definition: IsotopeDistribution.h:72
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
Representation of an element.
Definition: Element.h:53
Map< UInt, const Element * > atomic_numbers_
Definition: ElementDB.h:148
Map< String, const Element * > names_
Definition: ElementDB.h:144
Stores elements.
Definition: ElementDB.h:69
Map class based on the STL map (containing several convenience functions)
Definition: Map.h:50