| OpenMS 2.5.0

DigestionEnzyme.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: Xiao Liang $
32 // $Authors: Xiao Liang $
33 // --------------------------------------------------------------------------
34 //
35
36 #pragma once
37
38 #include <OpenMS/CHEMISTRY/EmpiricalFormula.h>
39 #include <OpenMS/DATASTRUCTURES/String.h>
40
41 #include <iosfwd>
42 #include <set>
43 #include <vector>
44
45 namespace OpenMS
46 {
52 class OPENMS_DLLAPI DigestionEnzyme
53 {
54 public:
55
59 DigestionEnzyme(const DigestionEnzyme&) = default;
61
63 DigestionEnzyme(DigestionEnzyme&&) = default;
64
66 explicit DigestionEnzyme(const String& name,
67 const String& cleavage_regex,
68 const std::set<String>& synonyms = std::set<String>(),
69 String regex_description = "");
70
72 virtual ~DigestionEnzyme();
74
78 DigestionEnzyme& operator=(const DigestionEnzyme&) = default;
80
82 DigestionEnzyme& operator=(DigestionEnzyme&&) & = default;
84
88 void setName(const String& name);
90
92 String getName() const;
93
95 void setSynonyms(const std::set<String>& synonyms);
96
98 void addSynonym(const String& synonym);
99
101 const std::set<String>& getSynonyms() const;
102
104 void setRegEx(const String& cleavage_regex);
105
107 String getRegEx() const;
108
110 void setRegExDescription(const String& value);
111
113 String getRegExDescription() const;
115
119 bool operator==(const DigestionEnzyme& enzyme) const;
121
123 bool operator!=(const DigestionEnzyme& enzyme) const;
124
126 bool operator==(const String& cleavage_regex) const;
127
129 bool operator!=(const String& cleavage_regex) const;
130
132 bool operator<(const DigestionEnzyme& enzyme) const;
134
140 virtual bool setValueFromFile(const String& key, const String& value);
141
143 friend OPENMS_DLLAPI std::ostream& operator<<(std::ostream& os, const DigestionEnzyme& enzyme);
144
145 protected:
146
148 DigestionEnzyme();
149
150 // basic
151 String name_;
152
153 String cleavage_regex_;
154
155 std::set<String> synonyms_;
156
157 String regex_description_;
158 };
159
160 OPENMS_DLLAPI std::ostream& operator<<(std::ostream& os, const DigestionEnzyme& enzyme);
161 }
162
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::operator<
bool operator<(const MultiplexDeltaMasses &dm1, const MultiplexDeltaMasses &dm2)
KDTree::operator!=
bool operator!=(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:824
OpenMS::DigestionEnzyme::name_
String name_
Definition: DigestionEnzyme.h:151
OpenMS::DigestionEnzyme
Abstract base class for digestion enzymes.
Definition: DigestionEnzyme.h:52
OpenMS::DigestionEnzyme::cleavage_regex_
String cleavage_regex_
Definition: DigestionEnzyme.h:153
String.h
OpenMS::operator<<
std::ostream & operator<<(std::ostream &os, const AccurateMassSearchResult &amsr)
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::DigestionEnzyme::synonyms_
std::set< String > synonyms_
Definition: DigestionEnzyme.h:155
EmpiricalFormula.h
OpenMS::DigestionEnzyme::regex_description_
String regex_description_
Definition: DigestionEnzyme.h:157
KDTree::operator==
bool operator==(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:806