OpenMS  2.4.0
DigestionEnzyme.h
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35 
36 #pragma once
37 
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& enzyme);
61 
63  explicit DigestionEnzyme(const String& name,
64  const String& cleavage_regex,
65  const std::set<String>& synonyms = std::set<String>(),
66  String regex_description = "");
67 
69  virtual ~DigestionEnzyme();
71 
75  DigestionEnzyme& operator=(const DigestionEnzyme& enzyme);
78 
82  void setName(const String& name);
84 
86  String getName() const;
87 
89  void setSynonyms(const std::set<String>& synonyms);
90 
92  void addSynonym(const String& synonym);
93 
95  const std::set<String>& getSynonyms() const;
96 
98  void setRegEx(const String& cleavage_regex);
99 
101  String getRegEx() const;
102 
104  void setRegExDescription(const String& value);
105 
107  String getRegExDescription() const;
109 
113  bool operator==(const DigestionEnzyme& enzyme) const;
115 
117  bool operator!=(const DigestionEnzyme& enzyme) const;
118 
120  bool operator==(const String& cleavage_regex) const;
121 
123  bool operator!=(const String& cleavage_regex) const;
124 
126  bool operator<(const DigestionEnzyme& enzyme) const;
128 
134  virtual bool setValueFromFile(const String& key, const String& value);
135 
137  friend OPENMS_DLLAPI std::ostream& operator<<(std::ostream& os, const DigestionEnzyme& enzyme);
138 
139  protected:
141  DigestionEnzyme();
142 
143  // basic
145 
147 
148  std::set<String> synonyms_;
149 
151  };
152 
153  OPENMS_DLLAPI std::ostream& operator<<(std::ostream& os, const DigestionEnzyme& enzyme);
154 }
155 
A more convenient string class.
Definition: String.h:57
Abstract base class for digestion enzymes.
Definition: DigestionEnzyme.h:52
bool operator==(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:806
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
bool operator<(const MultiplexDeltaMasses &dm1, const MultiplexDeltaMasses &dm2)
String cleavage_regex_
Definition: DigestionEnzyme.h:146
String name_
Definition: DigestionEnzyme.h:144
std::ostream & operator<<(std::ostream &os, const AccurateMassSearchResult &amsr)
std::set< String > synonyms_
Definition: DigestionEnzyme.h:148
bool operator!=(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:824
String regex_description_
Definition: DigestionEnzyme.h:150