| OpenMS 2.5.0

DigestionEnzymeProtein.h
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2 // OpenMS -- Open-Source Mass Spectrometry
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4 // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
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/DigestionEnzyme.h>
39
40 namespace OpenMS
41 {
42
48 class OPENMS_DLLAPI DigestionEnzymeProtein :
49 public DigestionEnzyme
50 {
51 public:
52
56
58 DigestionEnzymeProtein();
59
61 DigestionEnzymeProtein(const DigestionEnzymeProtein&) = default;
62
64 DigestionEnzymeProtein(DigestionEnzymeProtein&&) = default;
65
67 explicit DigestionEnzymeProtein(const String& name,
68 const String& cleavage_regex,
69 const std::set<String>& synonyms = std::set<String>(),
70 String regex_description = "",
71 EmpiricalFormula n_term_gain = EmpiricalFormula("H"),
72 EmpiricalFormula c_term_gain = EmpiricalFormula("OH"),
73 String psi_id = "",
74 String xtandem_id = "",
75 Int comet_id = -1,
76 String crux_id = "",
77 Int msgf_id = -1,
78 Int omssa_id = -1);
79
81 ~DigestionEnzymeProtein() override;
83
87 DigestionEnzymeProtein& operator=(const DigestionEnzymeProtein&) = default;
89
91 DigestionEnzymeProtein& operator=(DigestionEnzymeProtein&&) & = default;
93
97 void setNTermGain(const EmpiricalFormula& value);
99
101 EmpiricalFormula getNTermGain() const;
102
104 void setCTermGain(const EmpiricalFormula& value);
105
107 EmpiricalFormula getCTermGain() const;
108
110 void setPSIID(const String& value);
111
113 String getPSIID() const;
114
116 void setXTandemID(const String& value);
117
119 String getXTandemID() const;
120
122 Int getCometID() const;
123
125 void setCometID(Int value);
126
128 String getCruxID() const;
129
131 void setCruxID(const String& value);
132
134 void setMSGFID(Int value);
135
137 Int getMSGFID() const;
138
140 void setOMSSAID(Int value);
141
143 Int getOMSSAID() const;
144
146
150 bool operator==(const DigestionEnzymeProtein& enzyme) const;
152
154 bool operator!=(const DigestionEnzymeProtein& enzyme) const;
155
156 // Note: comparison operator is not inherited. TODO rename and make virtual
158 bool operator==(const String& cleavage_regex) const;
159
161 bool operator!=(const String& cleavage_regex) const;
162
164 bool operator<(const DigestionEnzymeProtein& enzyme) const;
166
172 bool setValueFromFile(const String& key, const String& value) override;
173
175 friend OPENMS_DLLAPI std::ostream& operator<<(std::ostream& os, const DigestionEnzymeProtein& enzyme);
176
177 protected:
178 EmpiricalFormula n_term_gain_;
179
180 EmpiricalFormula c_term_gain_;
181
182 String psi_id_;
183
184 String xtandem_id_;
185
186 Int comet_id_;
187
188 String crux_id_;
189
190 Int msgf_id_;
191
192 Int omssa_id_;
193
194 };
195
196 OPENMS_DLLAPI std::ostream& operator<<(std::ostream& os, const DigestionEnzymeProtein& enzyme);
197
198 typedef DigestionEnzymeProtein Protease;
199 }
200
OpenMS::DigestionEnzymeProtein::c_term_gain_
EmpiricalFormula c_term_gain_
Definition: DigestionEnzymeProtein.h:180
DigestionEnzyme.h
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::operator<
bool operator<(const MultiplexDeltaMasses &dm1, const MultiplexDeltaMasses &dm2)
OpenMS::DigestionEnzymeProtein::crux_id_
String crux_id_
Definition: DigestionEnzymeProtein.h:188
KDTree::operator!=
bool operator!=(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:824
OpenMS::DigestionEnzyme
Abstract base class for digestion enzymes.
Definition: DigestionEnzyme.h:52
OpenMS::DigestionEnzymeProtein
Representation of a digestion enzyme for proteins (protease)
Definition: DigestionEnzymeProtein.h:48
OpenMS::DigestionEnzymeProtein::omssa_id_
Int omssa_id_
Definition: DigestionEnzymeProtein.h:192
OpenMS::operator<<
std::ostream & operator<<(std::ostream &os, const AccurateMassSearchResult &amsr)
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::EmpiricalFormula
Representation of an empirical formula.
Definition: EmpiricalFormula.h:82
OpenMS::DigestionEnzymeProtein::comet_id_
Int comet_id_
Definition: DigestionEnzymeProtein.h:186
int
OpenMS::DigestionEnzymeProtein::xtandem_id_
String xtandem_id_
Definition: DigestionEnzymeProtein.h:184
OpenMS::Protease
DigestionEnzymeProtein Protease
Definition: DigestionEnzymeProtein.h:198
OpenMS::DigestionEnzymeProtein::msgf_id_
Int msgf_id_
Definition: DigestionEnzymeProtein.h:190
OpenMS::DigestionEnzymeProtein::psi_id_
String psi_id_
Definition: DigestionEnzymeProtein.h:182
KDTree::operator==
bool operator==(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:806
OpenMS::DigestionEnzymeProtein::n_term_gain_
EmpiricalFormula n_term_gain_
Definition: DigestionEnzymeProtein.h:178