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MSSim.h
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31 // $Maintainer: Stephan Aiche$
32 // $Authors: Stephan Aiche, Chris Bielow$
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34 
35 #ifndef OPENMS_SIMULATION_MSSIM_H
36 #define OPENMS_SIMULATION_MSSIM_H
37 
43 
44 namespace OpenMS
45 {
46 
47 
68  class OPENMS_DLLAPI MSSim :
69  public DefaultParamHandler,
70  public ProgressLogger
71  {
72 
73 public:
77  MSSim();
79 
81  virtual ~MSSim();
83 
90  void simulate(const SimRandomNumberGenerator & rnd_gen, SampleChannels & peptides);
91 
93  MSSimExperiment const & getExperiment() const;
94 
96  FeatureMapSim const & getSimulatedFeatures() const;
97 
99  ConsensusMap & getChargeConsensus();
100 
102  FeatureMapSim const & getContaminants() const;
103 
105  ConsensusMap & getLabelingConsensus();
106 
108  MSSimExperiment const & getPeakMap() const;
109 
111  Param getParameters() const;
112 
113 protected:
115  void syncParams_(Param & p, bool to_outer);
116 
118  void createFeatureMap_(const SampleProteins & peptides, FeatureMapSim & features, Size map_index);
119 
120 private:
122  void updateMembers_();
123 
125 
127 
129 
131 
133 
136  };
137 
138 }
139 
140 #endif
Central class for simulation of mass spectrometry experiments.
Definition: MSSim.h:68
A container for features.
Definition: FeatureMap.h:111
MSSimExperiment experiment_
Definition: MSSim.h:124
Container for multiple channels of SampleProteins.
Definition: SimTypes.h:74
A container for consensus elements.
Definition: ConsensusMap.h:60
FeatureMapSim contaminants_map_
Definition: MSSim.h:132
Wrapper class for random number generators used by the simulation classes.
Definition: SimTypes.h:99
FeatureMapSimVector feature_maps_
Definition: MSSim.h:128
Management and storage of parameters / INI files.
Definition: Param.h:69
Container for FASTAEntry & abundance information.
Definition: SimTypes.h:71
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
Base class for all classes that want to report their progess.
Definition: ProgressLogger.h:56
BaseLabeler * labeler_
Labeling functionality.
Definition: MSSim.h:135
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:90
ConsensusMap consensus_map_
Definition: MSSim.h:130
Abstract base class for all kinds of labeling techniques.
Definition: BaseLabeler.h:54
MSSimExperiment peak_map_
Definition: MSSim.h:126

OpenMS / TOPP release 1.11.1 Documentation generated on Thu Nov 14 2013 11:19:18 using doxygen 1.8.5