OpenMS  2.8.0
SILACLabeler.h
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31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Stephan Aiche$
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34 
35 #pragma once
36 
38 
39 namespace OpenMS
40 {
41 
42 
50  class OPENMS_DLLAPI SILACLabeler :
51  public BaseLabeler
52  {
53 public:
54 
57 
59  ~SILACLabeler() override;
60 
62  static BaseLabeler* create()
63  {
64  return new SILACLabeler();
65  }
66 
68  static const String getProductName()
69  {
70  return "SILAC";
71  }
72 
73  // redeclaration of virtual methods
74  void preCheck(Param& /* param */) const override;
75 
76  void setUpHook(SimTypes::FeatureMapSimVector& /* channels */) override;
77 
78  void postDigestHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */) override;
79 
80  void postRTHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */) override;
81 
82  void postDetectabilityHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */) override;
83 
84  void postIonizationHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */) override;
85 
86  void postRawMSHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */) override;
87 
88  void postRawTandemMSHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */, SimTypes::MSSimExperiment& /* simulated map */) override;
89 
90 protected:
91  void addModificationToPeptideHit_(Feature& feature, const String& modification) const;
92 
93  Feature mergeFeatures_(Feature& labeled_channel_feature, const String& unmodified_sequence, Map<String, Feature>& unlabeled_features_index, Int index_channel_id, Int labeled_channel_id) const;
94 
95  Feature mergeAllChannelFeatures_(Feature& heavy_channel_feature, const String& unmodified_feature_sequence, Map<String, Feature>& light_channel_feature_index, Map<String, Feature>& medium_channel_feature_index) const;
96 
99 
102 
103  bool canModificationBeApplied_(const String& modification_id, const String& aa) const;
104 
105  void applyLabelToProteinHit_(SimTypes::FeatureMapSim& protein_hit, const String& arginine_label, const String& lysine_label) const;
106 
107  void updateMembers_() override;
108 
109  String getUnmodifiedSequence_(const Feature& feature, const String& arginine_label, const String& lysine_label) const;
110 
111 private:
113  static const int LIGHT_FEATURE_MAPID_;
115  static const int MEDIUM_FEATURE_MAPID_;
117  static const int HEAVY_FEATURE_MAPID_;
118  };
119 
120 } // namespace OpenMS
121 
Abstract base class for all kinds of labeling techniques.
Definition: BaseLabeler.h:51
A container for features.
Definition: FeatureMap.h:106
An LC-MS feature.
Definition: Feature.h:72
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:73
Map class based on the STL map (containing several convenience functions)
Definition: Map.h:52
Management and storage of parameters / INI files.
Definition: Param.h:70
Simulate SILAC experiments.
Definition: SILACLabeler.h:52
String medium_channel_arginine_label_
Definition: SILACLabeler.h:98
Feature mergeAllChannelFeatures_(Feature &heavy_channel_feature, const String &unmodified_feature_sequence, Map< String, Feature > &light_channel_feature_index, Map< String, Feature > &medium_channel_feature_index) const
void applyLabelToProteinHit_(SimTypes::FeatureMapSim &protein_hit, const String &arginine_label, const String &lysine_label) const
void postRawTandemMSHook(SimTypes::FeatureMapSimVector &, SimTypes::MSSimExperiment &) override
Labeling after Tandem MS (e.g. iTRAQ)
~SILACLabeler() override
destructor
void addModificationToPeptideHit_(Feature &feature, const String &modification) const
void postIonizationHook(SimTypes::FeatureMapSimVector &) override
Labeling after ionization.
static const int MEDIUM_FEATURE_MAPID_
Map ID for the medium labeled channel.
Definition: SILACLabeler.h:115
static BaseLabeler * create()
create new object (needed by Factory)
Definition: SILACLabeler.h:62
void postRTHook(SimTypes::FeatureMapSimVector &) override
Labeling after rt simulation.
Feature mergeFeatures_(Feature &labeled_channel_feature, const String &unmodified_sequence, Map< String, Feature > &unlabeled_features_index, Int index_channel_id, Int labeled_channel_id) const
bool canModificationBeApplied_(const String &modification_id, const String &aa) const
void postDigestHook(SimTypes::FeatureMapSimVector &) override
Labeling between digestion and rt simulation.
void setUpHook(SimTypes::FeatureMapSimVector &) override
Hook to prepare the simulation process.
String heavy_channel_arginine_label_
Definition: SILACLabeler.h:101
void postRawMSHook(SimTypes::FeatureMapSimVector &) override
Labeling after raw signal generation.
void preCheck(Param &) const override
Checks the (simulation) params passed if they are consistent with the labeling technique.
void postDetectabilityHook(SimTypes::FeatureMapSimVector &) override
Labeling after detectability simulation.
String medium_channel_lysine_label_
Definition: SILACLabeler.h:97
void updateMembers_() override
This method is used to update extra member variables at the end of the setParameters() method.
static const int LIGHT_FEATURE_MAPID_
Map ID for the light/unlabeled channel.
Definition: SILACLabeler.h:113
String heavy_channel_lysine_label_
Definition: SILACLabeler.h:100
SILACLabeler()
default constructor
static const String getProductName()
name of the model (needed by Factory)
Definition: SILACLabeler.h:68
String getUnmodifiedSequence_(const Feature &feature, const String &arginine_label, const String &lysine_label) const
static const int HEAVY_FEATURE_MAPID_
Map ID for the heavy labeled channel.
Definition: SILACLabeler.h:117
A more convenient string class.
Definition: String.h:60
int Int
Signed integer type.
Definition: Types.h:102
std::vector< FeatureMapSim > FeatureMapSimVector
Sim FeatureMap Vector.
Definition: SimTypes.h:99
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47