| OpenMS 2.5.0

Precursor.h
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30 // --------------------------------------------------------------------------
31 // $Maintainer: Mathias Walzer $
32 // $Authors: Marc Sturm, Mathias Walzer $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/KERNEL/Peak1D.h>
38 #include <OpenMS/METADATA/CVTermList.h>
39 #include <OpenMS/CONCEPT/Constants.h>
40
41 #include <set>
42
43 namespace OpenMS
44 {
57 class OPENMS_DLLAPI Precursor :
58 public CVTermList,
59 public Peak1D
60 {
61
62 public:
63
65 enum ActivationMethod
66 {
67 CID,
68 PSD,
69 PD,
70 SID,
71 BIRD,
72 ECD,
73 IMD,
74 SORI,
75 HCID,
76 LCID,
77 PHD,
78 ETD,
79 PQD,
80 SIZE_OF_ACTIVATIONMETHOD
81 };
82
84 enum DriftTimeUnit
85 {
86 NONE,
87 MILLISECOND,
88 VSSC,
89 SIZE_OF_DRIFTTIMEUNIT
90 };
91
92
94 static const std::string NamesOfActivationMethod[SIZE_OF_ACTIVATIONMETHOD];
95 static const std::string NamesOfActivationMethodShort[SIZE_OF_ACTIVATIONMETHOD];
96
98 Precursor();
100 Precursor(const Precursor &) = default;
101
102 // note: we implement the move constructor ourselves due to a bug in MSVS
103 // 2015/2017 which cannot produce a default move constructor for classes
104 // that contain STL containers (other than vector).
105
107 Precursor(Precursor&&) noexcept;
109 ~Precursor() override;
110
112 Precursor & operator=(const Precursor &) = default;
114 Precursor& operator=(Precursor&&) & = default;
115
117 bool operator==(const Precursor & rhs) const;
119 bool operator!=(const Precursor & rhs) const;
120
122 const std::set<ActivationMethod> & getActivationMethods() const;
124 std::set<ActivationMethod> & getActivationMethods();
126 void setActivationMethods(const std::set<ActivationMethod> & activation_methods);
127
129 double getActivationEnergy() const;
131 void setActivationEnergy(double activation_energy);
132
143 double getIsolationWindowLowerOffset() const;
145 void setIsolationWindowLowerOffset(double bound);
146
157 double getIsolationWindowUpperOffset() const;
159 void setIsolationWindowUpperOffset(double bound);
160
168 double getDriftTime() const;
170 void setDriftTime(double drift_time);
171
175 DriftTimeUnit getDriftTimeUnit() const;
176
180 void setDriftTimeUnit(DriftTimeUnit dt);
181
182
193 double getDriftTimeWindowLowerOffset() const;
195 void setDriftTimeWindowLowerOffset(double drift_time);
196
207 double getDriftTimeWindowUpperOffset() const;
209 void setDriftTimeWindowUpperOffset(double drift_time);
210
212 Int getCharge() const;
214 void setCharge(Int charge);
215
217 std::vector<Int> & getPossibleChargeStates();
219 const std::vector<Int> & getPossibleChargeStates() const;
221 void setPossibleChargeStates(const std::vector<Int> & possible_charge_states);
222
224 inline double getUnchargedMass() const
225 {
226 int c = charge_;
227 (c == 0) ? c = 2 : c = charge_;
228 return getMZ() * c - c * Constants::PROTON_MASS_U;
229 }
230
231 protected:
232
233 std::set<ActivationMethod> activation_methods_;
234 double activation_energy_;
235 double window_low_;
236 double window_up_;
237 double drift_time_;
238 double drift_window_low_;
239 double drift_window_up_;
240 DriftTimeUnit drift_time_unit_;
241 Int charge_;
242 std::vector<Int> possible_charge_states_;
243 };
244 } // namespace OpenMS
245
OpenMS::CVTermList
Representation of controlled vocabulary term list.
Definition: CVTermList.h:52
OpenMS::Precursor::CID
Collision-induced dissociation.
Definition: Precursor.h:67
Constants.h
OpenMS::Precursor::possible_charge_states_
std::vector< Int > possible_charge_states_
Definition: Precursor.h:242
OpenMS::Precursor::BIRD
Blackbody infrared radiative dissociation.
Definition: Precursor.h:71
OpenMS::Precursor::HCID
High-energy collision-induced dissociation.
Definition: Precursor.h:75
OpenMS::Precursor::window_low_
double window_low_
Definition: Precursor.h:235
OpenMS::Precursor::activation_energy_
double activation_energy_
Definition: Precursor.h:234
OpenMS::Precursor::PD
Plasma desorption.
Definition: Precursor.h:69
OpenMS::Precursor::SID
Surface-induced dissociation.
Definition: Precursor.h:70
OpenMS::Precursor
Precursor meta information.
Definition: Precursor.h:57
OpenMS::Precursor::drift_time_unit_
DriftTimeUnit drift_time_unit_
Definition: Precursor.h:240
OpenMS::Precursor::drift_window_up_
double drift_window_up_
Definition: Precursor.h:239
OpenMS::Constants::PROTON_MASS_U
const double PROTON_MASS_U
OpenMS::Precursor::drift_time_
double drift_time_
Definition: Precursor.h:237
OpenMS::Precursor::PSD
Post-source decay.
Definition: Precursor.h:68
std
STL namespace.
Peak1D.h
OpenMS::Precursor::ActivationMethod
ActivationMethod
Method of activation.
Definition: Precursor.h:65
OpenMS::Precursor::ETD
Electron transfer dissociation.
Definition: Precursor.h:78
OpenMS::Precursor::VSSC
volt-second per square centimeter
Definition: Precursor.h:88
OpenMS::Precursor::IMD
Infrared multiphoton dissociation.
Definition: Precursor.h:73
OpenMS::Precursor::PHD
Photodissociation.
Definition: Precursor.h:77
OpenMS::Precursor::MILLISECOND
milliseconds
Definition: Precursor.h:87
OpenMS::Peak1D
A 1-dimensional raw data point or peak.
Definition: Peak1D.h:54
OpenMS::Precursor::NONE
No unit.
Definition: Precursor.h:86
OpenMS::Precursor::activation_methods_
std::set< ActivationMethod > activation_methods_
Definition: Precursor.h:233
OpenMS::Precursor::LCID
Low-energy collision-induced dissociation.
Definition: Precursor.h:76
OpenMS::Precursor::SORI
Sustained off-resonance irradiation.
Definition: Precursor.h:74
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::Precursor::ECD
Electron capture dissociation.
Definition: Precursor.h:72
CVTermList.h
OpenMS::Constants::c
const double c
int
OpenMS::Precursor::charge_
Int charge_
Definition: Precursor.h:241
OpenMS::Precursor::PQD
Pulsed q dissociation.
Definition: Precursor.h:79
OpenMS::Precursor::DriftTimeUnit
DriftTimeUnit
Drift time unit.
Definition: Precursor.h:84
OpenMS::Precursor::window_up_
double window_up_
Definition: Precursor.h:236
OpenMS::Precursor::drift_window_low_
double drift_window_low_
Definition: Precursor.h:238