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BaseLabeler.h
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31 // $Maintainer: Stephan Aiche $
32 // $Authors: Stephan Aiche, Chris Bielow $
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34 
35 #ifndef OPENMS_SIMULATION_LABELING_BASELABELER_H
36 #define OPENMS_SIMULATION_LABELING_BASELABELER_H
37 
39 
41 
43 
44 // GSL includes (random number generation)
45 #include <gsl/gsl_rng.h>
46 #include <gsl/gsl_randist.h>
47 
48 namespace OpenMS
49 {
50 
54  class OPENMS_DLLAPI BaseLabeler :
55  public DefaultParamHandler
56  {
57 public:
58 
60  BaseLabeler();
61 
63  virtual ~BaseLabeler();
64 
66  static void registerChildren();
67 
73  virtual Param getDefaultParameters() const;
74 
81  virtual void setRnd(const SimRandomNumberGenerator & rng);
82 
90  virtual void preCheck(Param & param) const = 0;
91 
96 
98  virtual void setUpHook(FeatureMapSimVector & /* features */) = 0;
99 
101  virtual void postDigestHook(FeatureMapSimVector & /* features_to_simulate */) = 0;
102 
104  virtual void postRTHook(FeatureMapSimVector & /* features_to_simulate */) = 0;
105 
107  virtual void postDetectabilityHook(FeatureMapSimVector & /* features_to_simulate */) = 0;
108 
110  virtual void postIonizationHook(FeatureMapSimVector & /* features_to_simulate */) = 0;
111 
113  virtual void postRawMSHook(FeatureMapSimVector & /* features_to_simulate */) = 0;
114 
116  virtual void postRawTandemMSHook(FeatureMapSimVector & /* features_to_simulate */, MSSimExperiment & /* simulated map */) = 0;
117 
119 
120  ConsensusMap & getConsensus();
121 
127  const String & getDescription() const;
128 
135  String getChannelIntensityName(const Size channel_index) const;
136 
137 
138 protected:
146  FeatureMapSim mergeProteinIdentificationsMaps_(const FeatureMapSimVector & maps);
147 
157  void mergeProteinAccessions_(Feature & target, const Feature & source) const;
158 
166  void recomputeConsensus_(const FeatureMapSim & simulated_features);
167 
168 
170 
172 
174 
175  };
176 } // namespace OpenMS
177 
178 #endif //#ifndef OPENMS_SIMULATION_LABELING_BASELABELER_H
A more convenient string class.
Definition: String.h:56
ConsensusMap consensus_
Definition: BaseLabeler.h:169
A container for features.
Definition: FeatureMap.h:111
A container for consensus elements.
Definition: ConsensusMap.h:60
SimRandomNumberGenerator const * rng_
Definition: BaseLabeler.h:171
String channel_description_
Definition: BaseLabeler.h:173
An LC-MS feature.
Definition: Feature.h:66
Wrapper class for random number generators used by the simulation classes.
Definition: SimTypes.h:99
Management and storage of parameters / INI files.
Definition: Param.h:69
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:144
std::vector< FeatureMapSim > FeatureMapSimVector
Sim FeatureMap Vector.
Definition: SimTypes.h:80
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:90
Abstract base class for all kinds of labeling techniques.
Definition: BaseLabeler.h:54

OpenMS / TOPP release 1.11.1 Documentation generated on Thu Nov 14 2013 11:19:11 using doxygen 1.8.5