OpenMS
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 
56 
58  ~BaseLabeler() override;
59 
61  static void registerChildren();
62 
68  virtual Param getDefaultParameters() const;
69 
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 
116 
122  const String& getDescription() const;
123 
130  String getChannelIntensityName(const Size channel_index) const;
131 
132 
133 protected:
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 
Abstract base class for all kinds of labeling techniques.
Definition: BaseLabeler.h:51
~BaseLabeler() override
destructor
virtual void postRawMSHook(SimTypes::FeatureMapSimVector &)=0
Labeling after raw signal generation.
virtual void postRTHook(SimTypes::FeatureMapSimVector &)=0
Labeling after rt simulation.
virtual void setRnd(SimTypes::MutableSimRandomNumberGeneratorPtr rng)
Set the random number generator.
ConsensusMap consensus_
Definition: BaseLabeler.h:164
virtual void preCheck(Param &param) const =0
Checks the (simulation) params passed if they are consistent with the labeling technique.
SimTypes::FeatureMapSim mergeProteinIdentificationsMaps_(const SimTypes::FeatureMapSimVector &maps)
Creates an empty FeatureMap with the merged ProteinIdentifications from all FeatureMaps contained in ...
virtual void postRawTandemMSHook(SimTypes::FeatureMapSimVector &, SimTypes::MSSimExperiment &)=0
Labeling after Tandem MS (e.g. iTRAQ)
BaseLabeler()
constructor
ConsensusMap & getConsensus()
String channel_description_
Definition: BaseLabeler.h:168
SimTypes::MutableSimRandomNumberGeneratorPtr rng_
Definition: BaseLabeler.h:166
void mergeProteinAccessions_(Feature &target, const Feature &source) const
join all protein references of two features
virtual void postDetectabilityHook(SimTypes::FeatureMapSimVector &)=0
Labeling after detectability simulation.
const String & getDescription() const
Get short description of the labeler (e.g., channels used)
virtual void setUpHook(SimTypes::FeatureMapSimVector &)=0
Hook to prepare the simulation process.
void recomputeConsensus_(const SimTypes::FeatureMapSim &simulated_features)
Based on the stored consensus recompute the associations for the passed features, assuming that the f...
virtual void postDigestHook(SimTypes::FeatureMapSimVector &)=0
Labeling between digestion and rt simulation.
virtual Param getDefaultParameters() const
Returns the default parameters. Re-implement.
virtual void postIonizationHook(SimTypes::FeatureMapSimVector &)=0
Labeling after ionization.
String getChannelIntensityName(const Size channel_index) const
to ensure standardized meta value names across labelers for channel intensity
A container for consensus elements.
Definition: ConsensusMap.h:92
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92
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:72
Management and storage of parameters / INI files.
Definition: Param.h:70
A more convenient string class.
Definition: String.h:60
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
boost::shared_ptr< SimRandomNumberGenerator > MutableSimRandomNumberGeneratorPtr
Definition: SimTypes.h:174
std::vector< FeatureMapSim > FeatureMapSimVector
Sim FeatureMap Vector.
Definition: SimTypes.h:99
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:48