OpenMS  2.4.0
DigestionEnzymeProtein.h
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35 
36 #pragma once
37 
39 
40 namespace OpenMS
41 {
42 
48  class OPENMS_DLLAPI DigestionEnzymeProtein: public DigestionEnzyme
49  {
50  public:
51 
57 
60 
62  explicit DigestionEnzymeProtein(const String& name,
63  const String& cleavage_regex,
64  const std::set<String>& synonyms = std::set<String>(),
65  String regex_description = "",
66  EmpiricalFormula n_term_gain = EmpiricalFormula("H"),
67  EmpiricalFormula c_term_gain = EmpiricalFormula("OH"),
68  String psi_id = "",
69  String xtandem_id = "",
70  Int comet_id = -1,
71  String crux_id = "",
72  Int msgf_id = -1,
73  Int omssa_id = -1);
74 
76  ~DigestionEnzymeProtein() override;
78 
82  DigestionEnzymeProtein& operator=(const DigestionEnzymeProtein& enzyme);
85 
89  void setNTermGain(EmpiricalFormula value);
91 
93  EmpiricalFormula getNTermGain() const;
94 
96  void setCTermGain(EmpiricalFormula value);
97 
99  EmpiricalFormula getCTermGain() const;
100 
102  void setPSIID(String value);
103 
105  String getPSIID() const;
106 
108  void setXTandemID(String value);
109 
111  String getXTandemID() const;
112 
114  Int getCometID() const;
115 
117  void setCometID(Int value);
118 
120  String getCruxID() const;
121 
123  void setCruxID(const String& value);
124 
126  void setMSGFID(Int value);
127 
129  Int getMSGFID() const;
130 
132  void setOMSSAID(Int value);
133 
135  Int getOMSSAID() const;
136 
138 
142  bool operator==(const DigestionEnzymeProtein& enzyme) const;
144 
146  bool operator!=(const DigestionEnzymeProtein& enzyme) const;
147 
149  bool operator==(String cleavage_regex) const;
150 
152  bool operator!=(String cleavage_regex) const;
153 
155  bool operator<(const DigestionEnzymeProtein& enzyme) const;
157 
163  bool setValueFromFile(const String& key, const String& value) override;
164 
166  friend OPENMS_DLLAPI std::ostream& operator<<(std::ostream& os, const DigestionEnzymeProtein& enzyme);
167 
168  protected:
170 
172 
174 
176 
178 
180 
182 
184 
185  };
186 
187  OPENMS_DLLAPI std::ostream& operator<<(std::ostream& os, const DigestionEnzymeProtein& enzyme);
188 
190 }
191 
A more convenient string class.
Definition: String.h:57
Int comet_id_
Definition: DigestionEnzymeProtein.h:177
String psi_id_
Definition: DigestionEnzymeProtein.h:173
Abstract base class for digestion enzymes.
Definition: DigestionEnzyme.h:52
DigestionEnzymeProtein Protease
Definition: DigestionEnzymeProtein.h:189
bool operator==(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:806
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
String crux_id_
Definition: DigestionEnzymeProtein.h:179
bool operator<(const MultiplexDeltaMasses &dm1, const MultiplexDeltaMasses &dm2)
Representation of an empirical formula.
Definition: EmpiricalFormula.h:81
Int omssa_id_
Definition: DigestionEnzymeProtein.h:183
std::ostream & operator<<(std::ostream &os, const AccurateMassSearchResult &amsr)
EmpiricalFormula c_term_gain_
Definition: DigestionEnzymeProtein.h:171
bool operator!=(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:824
String xtandem_id_
Definition: DigestionEnzymeProtein.h:175
int Int
Signed integer type.
Definition: Types.h:102
EmpiricalFormula n_term_gain_
Definition: DigestionEnzymeProtein.h:169
Representation of a digestion enzyme for proteins (protease)
Definition: DigestionEnzymeProtein.h:48
Int msgf_id_
Definition: DigestionEnzymeProtein.h:181