OpenMS  2.6.0
ElementDB.h
Go to the documentation of this file.
1 // --------------------------------------------------------------------------
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.
6 //
7 // This software is released under a three-clause BSD license:
8 // * Redistributions of source code must retain the above copyright
9 // notice, this list of conditions and the following disclaimer.
10 // * Redistributions in binary form must reproduce the above copyright
11 // notice, this list of conditions and the following disclaimer in the
12 // documentation and/or other materials provided with the distribution.
13 // * Neither the name of any author or any participating institution
14 // may be used to endorse or promote products derived from this software
15 // without specific prior written permission.
16 // For a full list of authors, refer to the file AUTHORS.
17 // --------------------------------------------------------------------------
18 // THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
19 // AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
20 // IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
21 // ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
22 // INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
23 // EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
24 // PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
25 // OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
26 // WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
27 // OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
28 // ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
29 //
30 // --------------------------------------------------------------------------
31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Andreas Bertsch, Timo Sachsenberg, Chris Bielow $
33 // --------------------------------------------------------------------------
34 //
35 
36 #pragma once
37 
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 
143 
145 
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::ElementDB
Stores elements.
Definition: ElementDB.h:69
OpenMS::Element
Representation of an element.
Definition: Element.h:53
OpenMS::String
A more convenient string class.
Definition: String.h:59
OpenMS::ElementDB::symbols_
Map< String, const Element * > symbols_
Definition: ElementDB.h:144
OpenMS::ElementDB::atomic_numbers_
Map< UInt, const Element * > atomic_numbers_
Definition: ElementDB.h:146
Map.h
Element.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
IsotopeDistribution.h
OpenMS::UInt
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
OpenMS::IsotopeDistribution
Definition: IsotopeDistribution.h:64
String.h
OpenMS::Map
Map class based on the STL map (containing several convenience functions)
Definition: Map.h:50
OpenMS::ElementDB::names_
Map< String, const Element * > names_
Definition: ElementDB.h:142