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O18Labeler.h
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34 
35 #ifndef OPENMS_SIMULATION_LABELING_O18LABELER_H
36 #define OPENMS_SIMULATION_LABELING_O18LABELER_H
37 
39 
40 namespace OpenMS
41 {
42 
50  class OPENMS_DLLAPI O18Labeler :
51  public BaseLabeler
52  {
53 public:
54 
56  O18Labeler();
57 
59  virtual ~O18Labeler();
60 
62  static BaseLabeler* create()
63  {
64  return new O18Labeler();
65  }
66 
68  static const String getProductName()
69  {
70  return "o18";
71  }
72 
73  // redeclaration of virtual methods
74  void preCheck(Param& param) const;
75 
76  void setUpHook(SimTypes::FeatureMapSimVector& /* channels */);
77 
78  void postDigestHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */);
79 
80  void postRTHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */);
81 
82  void postDetectabilityHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */);
83 
84  void postIonizationHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */);
85 
86  void postRawMSHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */);
87 
88  void postRawTandemMSHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */, SimTypes::MSSimExperiment& /* simulated map */);
89 
90 protected:
91  void addModificationToPeptideHit_(Feature& feature, const String& modification) const;
92 
93  Feature mergeFeatures_(Feature& labeled_channel_feature, const AASequence& unmodified_sequence, std::map<AASequence, Feature>& unlabeled_features_index) const;
94 
95 private:
97  static const int LIGHT_CHANNEL_ID_;
99  static const int MEDIUM_CHANNEL_ID_;
101  static const int HEAVY_CHANNEL_ID_;
102  };
103 } // namespace OpenMS
104 
105 #endif //#ifndef OPENMS_SIMULATION_LABELING_O18LABELER_H
A more convenient string class.
Definition: String.h:57
Representation of a peptide/protein sequence.
Definition: AASequence.h:108
static const String getProductName()
name of the model (needed by Factory)
Definition: O18Labeler.h:68
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
static const int HEAVY_CHANNEL_ID_
Map ID for the heavy/bi-labeled channel.
Definition: O18Labeler.h:101
static const int MEDIUM_CHANNEL_ID_
Map ID for the medium/mono-labeled channel.
Definition: O18Labeler.h:99
Simulate O-18 experiments.
Definition: O18Labeler.h:50
An LC-MS feature.
Definition: Feature.h:70
static const int LIGHT_CHANNEL_ID_
Map ID for the light/unlabeled channel.
Definition: O18Labeler.h:97
Management and storage of parameters / INI files.
Definition: Param.h:75
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:82
std::vector< FeatureMapSim > FeatureMapSimVector
Sim FeatureMap Vector.
Definition: SimTypes.h:100
Abstract base class for all kinds of labeling techniques.
Definition: BaseLabeler.h:50
static BaseLabeler * create()
create new object (needed by Factory)
Definition: O18Labeler.h:62

OpenMS / TOPP release 2.3.0 Documentation generated on Tue Jan 9 2018 18:22:02 using doxygen 1.8.13