| OpenMS 2.5.0

Element.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 $
33 // --------------------------------------------------------------------------
34 //
35
36 #pragma once
37
38 #include <OpenMS/CONCEPT/Types.h>
39 #include <OpenMS/DATASTRUCTURES/String.h>
40 #include <OpenMS/CHEMISTRY/ISOTOPEDISTRIBUTION/IsotopeDistribution.h>
41
42 #define OPENMS_CHEMISTRY_ELEMENT_NAME_DEFAULT "unknown"
43 #define OPENMS_CHEMISTRY_ELEMENT_SYMBOL_DEFAULT "??"
44 #define OPENMS_CHEMISTRY_ELEMENT_WEIGHT_DEFAULT 0.0
45 #define OPENMS_CHEMISTRY_ELEMENT_ATOMICNUMBER_DEFAULT 0
46
47 namespace OpenMS
48 {
53 class OPENMS_DLLAPI Element
54 {
55 public:
56
57
61 Element();
63
65 Element(const Element & element);
66
68 Element(const String & name,
69 const String & symbol,
70 UInt atomic_number,
71 double average_weight,
72 double mono_weight,
73 const IsotopeDistribution & isotopes);
74
76 virtual ~Element();
78
82 void setAtomicNumber(UInt atomic_number);
84
86 UInt getAtomicNumber() const;
87
89 void setAverageWeight(double weight);
90
92 double getAverageWeight() const;
93
95 void setMonoWeight(double weight);
96
98 double getMonoWeight() const;
99
101 void setIsotopeDistribution(const IsotopeDistribution & isotopes);
102
104 const IsotopeDistribution & getIsotopeDistribution() const;
105
107 void setName(const String & name);
108
110 const String & getName() const;
111
113 void setSymbol(const String & symbol);
114
116 const String & getSymbol() const;
118
122 Element & operator=(const Element & element);
125
129 bool operator==(const Element & element) const;
131
133 bool operator!=(const Element & element) const;
134
136 bool operator<(const Element & element) const;
138
140 friend OPENMS_DLLAPI std::ostream & operator<<(std::ostream & os, const Element & element);
141
142 protected:
143
145 String name_;
146
148 String symbol_;
149
151 UInt atomic_number_;
152
154 double average_weight_;
155
157 double mono_weight_;
158
160 IsotopeDistribution isotopes_;
161 };
162
163 OPENMS_DLLAPI std::ostream & operator<<(std::ostream &, const Element &);
164
165 } // namespace OpenMS
166
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::operator<
bool operator<(const MultiplexDeltaMasses &dm1, const MultiplexDeltaMasses &dm2)
OpenMS::Element::symbol_
String symbol_
symbol of the element
Definition: Element.h:148
OpenMS::IsotopeDistribution
Definition: IsotopeDistribution.h:64
KDTree::operator!=
bool operator!=(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:824
Types.h
IsotopeDistribution.h
String.h
OpenMS::Element::isotopes_
IsotopeDistribution isotopes_
distribution of the isotopes
Definition: Element.h:160
OpenMS::Element
Representation of an element.
Definition: Element.h:53
OpenMS::operator<<
std::ostream & operator<<(std::ostream &os, const AccurateMassSearchResult &amsr)
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::Element::mono_weight_
double mono_weight_
mono isotopic weight of the most frequent isotope
Definition: Element.h:157
OpenMS::Element::average_weight_
double average_weight_
average weight over all isotopes
Definition: Element.h:154
OpenMS::UInt
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
OpenMS::Element::atomic_number_
UInt atomic_number_
atomic number of the element
Definition: Element.h:151
OpenMS::Element::name_
String name_
name of the element
Definition: Element.h:145
KDTree::operator==
bool operator==(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:806