OpenMS  3.0.0
BaseLabeler.h
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31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Stephan Aiche, Chris Bielow $
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34 
35 #pragma once
36 
38 
40 
42 
43 namespace OpenMS
44 {
45 
49  class OPENMS_DLLAPI BaseLabeler :
50  public DefaultParamHandler
51  {
52 public:
53 
55  BaseLabeler();
56 
58  ~BaseLabeler() override;
59 
61  static void registerChildren();
62 
68  virtual Param getDefaultParameters() const;
69 
76  virtual void setRnd(SimTypes::MutableSimRandomNumberGeneratorPtr rng);
77 
85  virtual void preCheck(Param& param) const = 0;
86 
91 
93  virtual void setUpHook(SimTypes::FeatureMapSimVector& /* features */) = 0;
94 
96  virtual void postDigestHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */) = 0;
97 
99  virtual void postRTHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */) = 0;
100 
102  virtual void postDetectabilityHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */) = 0;
103 
105  virtual void postIonizationHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */) = 0;
106 
108  virtual void postRawMSHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */) = 0;
109 
111  virtual void postRawTandemMSHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */, SimTypes::MSSimExperiment& /* simulated map */) = 0;
112 
114 
115  ConsensusMap& getConsensus();
116 
122  const String& getDescription() const;
123 
130  String getChannelIntensityName(const Size channel_index) const;
131 
132 
133 protected:
141  SimTypes::FeatureMapSim mergeProteinIdentificationsMaps_(const SimTypes::FeatureMapSimVector& maps);
142 
152  void mergeProteinAccessions_(Feature& target, const Feature& source) const;
153 
161  void recomputeConsensus_(const SimTypes::FeatureMapSim& simulated_features);
162 
163 
165 
167 
169 
170  };
171 } // namespace OpenMS
172 
DefaultParamHandler.h
SimTypes.h
OpenMS::String
A more convenient string class.
Definition: String.h:58
ConsensusMap.h
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:70
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
OpenMS::SimTypes::MutableSimRandomNumberGeneratorPtr
boost::shared_ptr< SimRandomNumberGenerator > MutableSimRandomNumberGeneratorPtr
Definition: SimTypes.h:174
OpenMS::BaseLabeler::consensus_
ConsensusMap consensus_
Definition: BaseLabeler.h:164
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::BaseLabeler::rng_
SimTypes::MutableSimRandomNumberGeneratorPtr rng_
Definition: BaseLabeler.h:166
OpenMS::ConsensusMap
A container for consensus elements.
Definition: ConsensusMap.h:82
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::channel_description_
String channel_description_
Definition: BaseLabeler.h:168
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