OpenMS  3.0.0
SILACLabeler.h
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31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Stephan Aiche$
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34 
35 #pragma once
36 
38 #include <map>
39 
40 namespace OpenMS
41 {
42 
43 
51  class OPENMS_DLLAPI SILACLabeler :
52  public BaseLabeler
53  {
54 public:
55 
57  SILACLabeler();
58 
60  ~SILACLabeler() override;
61 
63  static BaseLabeler* create()
64  {
65  return new SILACLabeler();
66  }
67 
69  static const String getProductName()
70  {
71  return "SILAC";
72  }
73 
74  // redeclaration of virtual methods
75  void preCheck(Param& /* param */) const override;
76 
77  void setUpHook(SimTypes::FeatureMapSimVector& /* channels */) override;
78 
79  void postDigestHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */) override;
80 
81  void postRTHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */) override;
82 
83  void postDetectabilityHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */) override;
84 
85  void postIonizationHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */) override;
86 
87  void postRawMSHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */) override;
88 
89  void postRawTandemMSHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */, SimTypes::MSSimExperiment& /* simulated map */) override;
90 
91 protected:
92  void addModificationToPeptideHit_(Feature& feature, const String& modification) const;
93 
94  Feature mergeFeatures_(Feature& labeled_channel_feature, const String& unmodified_sequence, std::map<String, Feature>& unlabeled_features_index, Int index_channel_id, Int labeled_channel_id) const;
95 
96  Feature mergeAllChannelFeatures_(Feature& heavy_channel_feature, const String& unmodified_feature_sequence, std::map<String, Feature>& light_channel_feature_index, std::map<String, Feature>& medium_channel_feature_index) const;
97 
100 
103 
104  bool canModificationBeApplied_(const String& modification_id, const String& aa) const;
105 
106  void applyLabelToProteinHit_(SimTypes::FeatureMapSim& protein_hit, const String& arginine_label, const String& lysine_label) const;
107 
108  void updateMembers_() override;
109 
110  String getUnmodifiedSequence_(const Feature& feature, const String& arginine_label, const String& lysine_label) const;
111 
112 private:
114  static const int LIGHT_FEATURE_MAPID_;
116  static const int MEDIUM_FEATURE_MAPID_;
118  static const int HEAVY_FEATURE_MAPID_;
119  };
120 
121 } // namespace OpenMS
122 
OpenMS::SILACLabeler::heavy_channel_arginine_label_
String heavy_channel_arginine_label_
Definition: SILACLabeler.h:102
OpenMS::SILACLabeler::MEDIUM_FEATURE_MAPID_
static const int MEDIUM_FEATURE_MAPID_
Map ID for the medium labeled channel.
Definition: SILACLabeler.h:116
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::Int
int Int
Signed integer type.
Definition: Types.h:102
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::SILACLabeler::LIGHT_FEATURE_MAPID_
static const int LIGHT_FEATURE_MAPID_
Map ID for the light/unlabeled channel.
Definition: SILACLabeler.h:114
OpenMS::SILACLabeler::getProductName
static const String getProductName()
name of the model (needed by Factory)
Definition: SILACLabeler.h:69
OpenMS::SILACLabeler::medium_channel_lysine_label_
String medium_channel_lysine_label_
Definition: SILACLabeler.h:98
OpenMS::SILACLabeler::HEAVY_FEATURE_MAPID_
static const int HEAVY_FEATURE_MAPID_
Map ID for the heavy labeled channel.
Definition: SILACLabeler.h:118
OpenMS::SILACLabeler::create
static BaseLabeler * create()
create new object (needed by Factory)
Definition: SILACLabeler.h:63
OpenMS::SimTypes::FeatureMapSimVector
std::vector< FeatureMapSim > FeatureMapSimVector
Sim FeatureMap Vector.
Definition: SimTypes.h:99
OpenMS::FeatureMap
A container for features.
Definition: FeatureMap.h:98
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::SILACLabeler::medium_channel_arginine_label_
String medium_channel_arginine_label_
Definition: SILACLabeler.h:99
OpenMS::Param
Management and storage of parameters / INI files.
Definition: Param.h:69
OpenMS::SILACLabeler
Simulate SILAC experiments.
Definition: SILACLabeler.h:51
OpenMS::SILACLabeler::heavy_channel_lysine_label_
String heavy_channel_lysine_label_
Definition: SILACLabeler.h:101