OpenMS
ICPLLabeler.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 
50  class OPENMS_DLLAPI ICPLLabeler :
51  public BaseLabeler
52  {
53 public:
54 
57 
59  ~ICPLLabeler() override;
60 
62  static BaseLabeler* create()
63  {
64  return new ICPLLabeler();
65  }
66 
68  static const String getProductName()
69  {
70  return "ICPL";
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  void addLabelToProteinHits_(SimTypes::FeatureMapSim& features, const String& label) const;
94 
95  Feature mergeFeatures_(Feature& labeled_channel_feature, const AASequence& unmodified_sequence, std::map<String, Feature>& unlabeled_features_index) const;
96 
100 
101  void updateMembers_() override;
102 
103  String getUnmodifiedAASequence_(const Feature& feature, const String& label) const;
104 
105 private:
107  static const int LIGHT_FEATURE_MAPID_;
109  static const int MEDIUM_FEATURE_MAPID_;
111  static const int HEAVY_FEATURE_MAPID_;
112  };
113 } // namespace OpenMS
114 
Representation of a peptide/protein sequence.
Definition: AASequence.h:112
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
Simulate ICPL experiments.
Definition: ICPLLabeler.h:52
String medium_channel_label_
Definition: ICPLLabeler.h:98
void postRawTandemMSHook(SimTypes::FeatureMapSimVector &, SimTypes::MSSimExperiment &) override
Labeling after Tandem MS (e.g. iTRAQ)
ICPLLabeler()
default constructor
void addModificationToPeptideHit_(Feature &feature, const String &modification) const
void postIonizationHook(SimTypes::FeatureMapSimVector &) override
Labeling after ionization.
String getUnmodifiedAASequence_(const Feature &feature, const String &label) const
static const int MEDIUM_FEATURE_MAPID_
Map ID for the medium labeled channel.
Definition: ICPLLabeler.h:109
static BaseLabeler * create()
create new object (needed by Factory)
Definition: ICPLLabeler.h:62
void addLabelToProteinHits_(SimTypes::FeatureMapSim &features, const String &label) const
Feature mergeFeatures_(Feature &labeled_channel_feature, const AASequence &unmodified_sequence, std::map< String, Feature > &unlabeled_features_index) const
void postRTHook(SimTypes::FeatureMapSimVector &) override
Labeling after rt simulation.
void postDigestHook(SimTypes::FeatureMapSimVector &) override
Labeling between digestion and rt simulation.
void setUpHook(SimTypes::FeatureMapSimVector &) override
Hook to prepare the simulation process.
void postRawMSHook(SimTypes::FeatureMapSimVector &) override
Labeling after raw signal generation.
String heavy_channel_label_
Definition: ICPLLabeler.h:99
void postDetectabilityHook(SimTypes::FeatureMapSimVector &) override
Labeling after detectability simulation.
~ICPLLabeler() override
destructor
void updateMembers_() override
This method is used to update extra member variables at the end of the setParameters() method.
String light_channel_label_
Definition: ICPLLabeler.h:97
static const int LIGHT_FEATURE_MAPID_
Map ID for the light/unlabeled channel.
Definition: ICPLLabeler.h:107
static const String getProductName()
name of the model (needed by Factory)
Definition: ICPLLabeler.h:68
void preCheck(Param &param) const override
Checks the (simulation) params passed if they are consistent with the labeling technique.
static const int HEAVY_FEATURE_MAPID_
Map ID for the heavy labeled channel.
Definition: ICPLLabeler.h:111
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:72
Management and storage of parameters / INI files.
Definition: Param.h:70
A more convenient string class.
Definition: String.h:60
std::vector< FeatureMapSim > FeatureMapSimVector
Sim FeatureMap Vector.
Definition: SimTypes.h:99
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:48