OpenMS  2.5.0
Precursor.h
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31 // $Maintainer: Mathias Walzer $
32 // $Authors: Marc Sturm, Mathias Walzer $
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34 
35 #pragma once
36 
37 #include <OpenMS/KERNEL/Peak1D.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 
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 
85  {
86  NONE,
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_;
235  double window_low_;
236  double window_up_;
237  double drift_time_;
242  std::vector<Int> possible_charge_states_;
243  };
244 } // namespace OpenMS
245 
OpenMS::Precursor::MILLISECOND
milliseconds
Definition: Precursor.h:87
OpenMS::Precursor::SORI
Sustained off-resonance irradiation.
Definition: Precursor.h:74
OpenMS::Precursor::window_up_
double window_up_
Definition: Precursor.h:236
OpenMS::Precursor::drift_time_unit_
DriftTimeUnit drift_time_unit_
Definition: Precursor.h:240
OpenMS::Precursor::SID
Surface-induced dissociation.
Definition: Precursor.h:70
OpenMS::Precursor::activation_methods_
std::set< ActivationMethod > activation_methods_
Definition: Precursor.h:233
Peak1D.h
OpenMS::Precursor::BIRD
Blackbody infrared radiative dissociation.
Definition: Precursor.h:71
OpenMS::Precursor::PHD
Photodissociation.
Definition: Precursor.h:77
OpenMS::Constants::c
const double c
OpenMS::Precursor::NONE
No unit.
Definition: Precursor.h:86
OpenMS::Precursor::IMD
Infrared multiphoton dissociation.
Definition: Precursor.h:73
OpenMS::Precursor::CID
Collision-induced dissociation.
Definition: Precursor.h:67
OpenMS::Precursor::ECD
Electron capture dissociation.
Definition: Precursor.h:72
OpenMS::Precursor::ETD
Electron transfer dissociation.
Definition: Precursor.h:78
OpenMS::Constants::PROTON_MASS_U
const double PROTON_MASS_U
Constants.h
OpenMS::Precursor::LCID
Low-energy collision-induced dissociation.
Definition: Precursor.h:76
OpenMS::Precursor
Precursor meta information.
Definition: Precursor.h:57
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
int
OpenMS::Precursor::charge_
Int charge_
Definition: Precursor.h:241
OpenMS::Precursor::drift_window_low_
double drift_window_low_
Definition: Precursor.h:238
OpenMS::Precursor::drift_time_
double drift_time_
Definition: Precursor.h:237
OpenMS::Peak1D
A 1-dimensional raw data point or peak.
Definition: Peak1D.h:54
OpenMS::Precursor::PQD
Pulsed q dissociation.
Definition: Precursor.h:79
OpenMS::CVTermList
Representation of controlled vocabulary term list.
Definition: CVTermList.h:52
OpenMS::Precursor::PSD
Post-source decay.
Definition: Precursor.h:68
OpenMS::Precursor::DriftTimeUnit
DriftTimeUnit
Drift time unit.
Definition: Precursor.h:84
CVTermList.h
OpenMS::Precursor::drift_window_up_
double drift_window_up_
Definition: Precursor.h:239
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::ActivationMethod
ActivationMethod
Method of activation.
Definition: Precursor.h:65
OpenMS::Precursor::VSSC
volt-second per square centimeter
Definition: Precursor.h:88
OpenMS::Precursor::possible_charge_states_
std::vector< Int > possible_charge_states_
Definition: Precursor.h:242
OpenMS::Precursor::HCID
High-energy collision-induced dissociation.
Definition: Precursor.h:75