OpenMS  3.0.0
O18Labeler.h
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31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Stephan Aiche$
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34 
35 #pragma once
36 
38 
39 namespace OpenMS
40 {
41 
49  class OPENMS_DLLAPI O18Labeler :
50  public BaseLabeler
51  {
52 public:
53 
55  O18Labeler();
56 
58  ~O18Labeler() override;
59 
61  static BaseLabeler* create()
62  {
63  return new O18Labeler();
64  }
65 
67  static const String getProductName()
68  {
69  return "o18";
70  }
71 
72  // redeclaration of virtual methods
73  void preCheck(Param& param) const override;
74 
75  void setUpHook(SimTypes::FeatureMapSimVector& /* channels */) override;
76 
77  void postDigestHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */) override;
78 
79  void postRTHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */) override;
80 
81  void postDetectabilityHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */) override;
82 
83  void postIonizationHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */) override;
84 
85  void postRawMSHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */) override;
86 
87  void postRawTandemMSHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */, SimTypes::MSSimExperiment& /* simulated map */) override;
88 
89 protected:
90  void addModificationToPeptideHit_(Feature& feature, const String& modification) const;
91 
92  Feature mergeFeatures_(Feature& labeled_channel_feature, const AASequence& unmodified_sequence, std::map<AASequence, Feature>& unlabeled_features_index) const;
93 
94 private:
96  static const int LIGHT_CHANNEL_ID_;
98  static const int MEDIUM_CHANNEL_ID_;
100  static const int HEAVY_CHANNEL_ID_;
101  };
102 } // namespace OpenMS
103 
OpenMS::O18Labeler::HEAVY_CHANNEL_ID_
static const int HEAVY_CHANNEL_ID_
Map ID for the heavy/bi-labeled channel.
Definition: O18Labeler.h:100
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:70
BaseLabeler.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::O18Labeler
Simulate O-18 experiments.
Definition: O18Labeler.h:49
OpenMS::O18Labeler::getProductName
static const String getProductName()
name of the model (needed by Factory)
Definition: O18Labeler.h:67
OpenMS::O18Labeler::create
static BaseLabeler * create()
create new object (needed by Factory)
Definition: O18Labeler.h:61
OpenMS::SimTypes::FeatureMapSimVector
std::vector< FeatureMapSim > FeatureMapSimVector
Sim FeatureMap Vector.
Definition: SimTypes.h:99
OpenMS::O18Labeler::LIGHT_CHANNEL_ID_
static const int LIGHT_CHANNEL_ID_
Map ID for the light/unlabeled channel.
Definition: O18Labeler.h:96
OpenMS::Feature
An LC-MS feature.
Definition: Feature.h:70
OpenMS::BaseLabeler
Abstract base class for all kinds of labeling techniques.
Definition: BaseLabeler.h:49
OpenMS::Param
Management and storage of parameters / INI files.
Definition: Param.h:69
OpenMS::AASequence
Representation of a peptide/protein sequence.
Definition: AASequence.h:111
OpenMS::O18Labeler::MEDIUM_CHANNEL_ID_
static const int MEDIUM_CHANNEL_ID_
Map ID for the medium/mono-labeled channel.
Definition: O18Labeler.h:98