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BaseLabeler.h
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34 
35 #ifndef OPENMS_SIMULATION_LABELING_BASELABELER_H
36 #define OPENMS_SIMULATION_LABELING_BASELABELER_H
37 
39 
41 
43 
44 namespace OpenMS
45 {
46 
50  class OPENMS_DLLAPI BaseLabeler :
51  public DefaultParamHandler
52  {
53 public:
54 
56  BaseLabeler();
57 
59  virtual ~BaseLabeler();
60 
62  static void registerChildren();
63 
69  virtual Param getDefaultParameters() const;
70 
77  virtual void setRnd(SimTypes::MutableSimRandomNumberGeneratorPtr rng);
78 
86  virtual void preCheck(Param& param) const = 0;
87 
92 
94  virtual void setUpHook(SimTypes::FeatureMapSimVector& /* features */) = 0;
95 
97  virtual void postDigestHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */) = 0;
98 
100  virtual void postRTHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */) = 0;
101 
103  virtual void postDetectabilityHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */) = 0;
104 
106  virtual void postIonizationHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */) = 0;
107 
109  virtual void postRawMSHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */) = 0;
110 
112  virtual void postRawTandemMSHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */, SimTypes::MSSimExperiment& /* simulated map */) = 0;
113 
115 
116  ConsensusMap& getConsensus();
117 
123  const String& getDescription() const;
124 
131  String getChannelIntensityName(const Size channel_index) const;
132 
133 
134 protected:
142  SimTypes::FeatureMapSim mergeProteinIdentificationsMaps_(const SimTypes::FeatureMapSimVector& maps);
143 
153  void mergeProteinAccessions_(Feature& target, const Feature& source) const;
154 
162  void recomputeConsensus_(const SimTypes::FeatureMapSim& simulated_features);
163 
164 
166 
168 
170 
171  };
172 } // namespace OpenMS
173 
174 #endif //#ifndef OPENMS_SIMULATION_LABELING_BASELABELER_H
A more convenient string class.
Definition: String.h:57
SimTypes::MutableSimRandomNumberGeneratorPtr rng_
Definition: BaseLabeler.h:167
ConsensusMap consensus_
Definition: BaseLabeler.h:165
A container for features.
Definition: FeatureMap.h:94
boost::shared_ptr< SimRandomNumberGenerator > MutableSimRandomNumberGeneratorPtr
Definition: SimTypes.h:175
A container for consensus elements.
Definition: ConsensusMap.h:72
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
String channel_description_
Definition: BaseLabeler.h:169
An LC-MS feature.
Definition: Feature.h:70
Management and storage of parameters / INI files.
Definition: Param.h:75
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:82
std::vector< FeatureMapSim > FeatureMapSimVector
Sim FeatureMap Vector.
Definition: SimTypes.h:100
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:128
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92
Abstract base class for all kinds of labeling techniques.
Definition: BaseLabeler.h:50

OpenMS / TOPP release 2.3.0 Documentation generated on Tue Jan 9 2018 18:21:59 using doxygen 1.8.13