OpenMS  3.0.0
DigestionEnzymeProtein.h
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35 
36 #pragma once
37 
39 
40 namespace OpenMS
41 {
42 
48  class OPENMS_DLLAPI DigestionEnzymeProtein :
49  public DigestionEnzyme
50  {
51  public:
52 
56 
59 
61  explicit DigestionEnzymeProtein(const DigestionEnzyme& d);
62 
65 
68 
70  explicit DigestionEnzymeProtein(const String& name,
71  const String& cleavage_regex,
72  const std::set<String>& synonyms = std::set<String>(),
73  String regex_description = "",
74  EmpiricalFormula n_term_gain = EmpiricalFormula("H"),
75  EmpiricalFormula c_term_gain = EmpiricalFormula("OH"),
76  String psi_id = "",
77  String xtandem_id = "",
78  Int comet_id = -1,
79  String crux_id = "",
80  Int msgf_id = -1,
81  Int omssa_id = -1);
82 
84  ~DigestionEnzymeProtein() override;
86 
90  DigestionEnzymeProtein& operator=(const DigestionEnzymeProtein&) = default;
92 
94  DigestionEnzymeProtein& operator=(DigestionEnzymeProtein&&) & = default;
96 
100  void setNTermGain(const EmpiricalFormula& value);
102 
104  EmpiricalFormula getNTermGain() const;
105 
107  void setCTermGain(const EmpiricalFormula& value);
108 
110  EmpiricalFormula getCTermGain() const;
111 
113  void setPSIID(const String& value);
114 
116  String getPSIID() const;
117 
119  void setXTandemID(const String& value);
120 
122  String getXTandemID() const;
123 
125  void setCometID(Int value);
126 
128  Int getCometID() const;
129 
131  void setCruxID(const String& value);
132 
134  String getCruxID() const;
135 
137  void setMSGFID(Int value);
138 
140  Int getMSGFID() const;
141 
143  void setOMSSAID(Int value);
144 
146  Int getOMSSAID() const;
147 
149 
153  bool operator==(const DigestionEnzymeProtein& enzyme) const;
155 
157  bool operator!=(const DigestionEnzymeProtein& enzyme) const;
158 
159  // Note: comparison operator is not inherited. TODO rename and make virtual
161  bool operator==(const String& cleavage_regex) const;
162 
164  bool operator!=(const String& cleavage_regex) const;
165 
167  bool operator<(const DigestionEnzymeProtein& enzyme) const;
169 
175  bool setValueFromFile(const String& key, const String& value) override;
176 
178  friend OPENMS_DLLAPI std::ostream& operator<<(std::ostream& os, const DigestionEnzymeProtein& enzyme);
179 
180  protected:
182 
184 
186 
188 
190 
192 
194 
196 
197  };
198 
199  OPENMS_DLLAPI std::ostream& operator<<(std::ostream& os, const DigestionEnzymeProtein& enzyme);
200 
202 }
203 
OpenMS::DigestionEnzymeProtein::crux_id_
String crux_id_
Definition: DigestionEnzymeProtein.h:191
OpenMS::DigestionEnzymeProtein::psi_id_
String psi_id_
Definition: DigestionEnzymeProtein.h:185
OpenMS::String
A more convenient string class.
Definition: String.h:58
KDTree::operator!=
bool operator!=(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:824
OpenMS::DigestionEnzymeProtein::comet_id_
Int comet_id_
Definition: DigestionEnzymeProtein.h:189
OpenMS::operator<
bool operator<(const MultiplexDeltaMasses &dm1, const MultiplexDeltaMasses &dm2)
OpenMS::Int
int Int
Signed integer type.
Definition: Types.h:102
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::Protease
DigestionEnzymeProtein Protease
Definition: DigestionEnzymeProtein.h:201
OpenMS::DigestionEnzymeProtein::c_term_gain_
EmpiricalFormula c_term_gain_
Definition: DigestionEnzymeProtein.h:183
OpenMS::DigestionEnzymeProtein
Representation of a digestion enzyme for proteins (protease)
Definition: DigestionEnzymeProtein.h:48
OpenMS::operator<<
std::ostream & operator<<(std::ostream &os, const AccurateMassSearchResult &amsr)
OpenMS::DigestionEnzymeProtein::omssa_id_
Int omssa_id_
Definition: DigestionEnzymeProtein.h:195
OpenMS::DigestionEnzymeProtein::msgf_id_
Int msgf_id_
Definition: DigestionEnzymeProtein.h:193
OpenMS::DigestionEnzymeProtein::xtandem_id_
String xtandem_id_
Definition: DigestionEnzymeProtein.h:187
OpenMS::DigestionEnzyme
Base class for digestion enzymes.
Definition: DigestionEnzyme.h:52
OpenMS::Internal::operator==
bool operator==(const IDBoostGraph::ProteinGroup &lhs, const IDBoostGraph::ProteinGroup &rhs)
OpenMS::EmpiricalFormula
Representation of an empirical formula.
Definition: EmpiricalFormula.h:84
OpenMS::DigestionEnzymeProtein::n_term_gain_
EmpiricalFormula n_term_gain_
Definition: DigestionEnzymeProtein.h:181
DigestionEnzyme.h