OpenMS  2.5.0
ICPLLabeler.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 ICPLLabeler :
50  public BaseLabeler
51  {
52 public:
53 
55  ICPLLabeler();
56 
58  ~ICPLLabeler() override;
59 
61  static BaseLabeler* create()
62  {
63  return new ICPLLabeler();
64  }
65 
67  static const String getProductName()
68  {
69  return "ICPL";
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  void addLabelToProteinHits_(SimTypes::FeatureMapSim& features, const String& label) const;
93 
94  Feature mergeFeatures_(Feature& labeled_channel_feature, const AASequence& unmodified_sequence, Map<String, Feature>& unlabeled_features_index) const;
95 
99 
100  void updateMembers_() override;
101 
102  String getUnmodifiedAASequence_(const Feature& feature, const String& label) const;
103 
104 private:
106  static const int LIGHT_FEATURE_MAPID_;
108  static const int MEDIUM_FEATURE_MAPID_;
110  static const int HEAVY_FEATURE_MAPID_;
111  };
112 } // namespace OpenMS
113 
OpenMS::ICPLLabeler::LIGHT_FEATURE_MAPID_
static const int LIGHT_FEATURE_MAPID_
Map ID for the light/unlabeled channel.
Definition: ICPLLabeler.h:106
OpenMS::ICPLLabeler::create
static BaseLabeler * create()
create new object (needed by Factory)
Definition: ICPLLabeler.h:61
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
BaseLabeler.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::ICPLLabeler::MEDIUM_FEATURE_MAPID_
static const int MEDIUM_FEATURE_MAPID_
Map ID for the medium labeled channel.
Definition: ICPLLabeler.h:108
OpenMS::ICPLLabeler
Simulate ICPL experiments.
Definition: ICPLLabeler.h:49
OpenMS::SimTypes::FeatureMapSimVector
std::vector< FeatureMapSim > FeatureMapSimVector
Sim FeatureMap Vector.
Definition: SimTypes.h:99
OpenMS::FeatureMap
A container for features.
Definition: FeatureMap.h:95
OpenMS::Feature
An LC-MS feature.
Definition: Feature.h:70
OpenMS::ICPLLabeler::heavy_channel_label_
String heavy_channel_label_
Definition: ICPLLabeler.h:98
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:73
OpenMS::AASequence
Representation of a peptide/protein sequence.
Definition: AASequence.h:113
OpenMS::Map
Map class based on the STL map (containing several convenience functions)
Definition: Map.h:50
OpenMS::ICPLLabeler::getProductName
static const String getProductName()
name of the model (needed by Factory)
Definition: ICPLLabeler.h:67
OpenMS::ICPLLabeler::medium_channel_label_
String medium_channel_label_
Definition: ICPLLabeler.h:97
OpenMS::ICPLLabeler::HEAVY_FEATURE_MAPID_
static const int HEAVY_FEATURE_MAPID_
Map ID for the heavy labeled channel.
Definition: ICPLLabeler.h:110
OpenMS::ICPLLabeler::light_channel_label_
String light_channel_label_
Definition: ICPLLabeler.h:96