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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 
41 
43 
44 namespace OpenMS
45 {
46 
47  class BaseLabeler;
48 
69  class OPENMS_DLLAPI MSSim :
70  public DefaultParamHandler,
71  public ProgressLogger
72  {
73 
74 public:
78  MSSim();
80 
82  virtual ~MSSim();
84 
92 
94  const SimTypes::MSSimExperiment& getExperiment() const;
95 
97  const SimTypes::FeatureMapSim& getSimulatedFeatures() const;
98 
100  ConsensusMap& getChargeConsensus();
101 
103  const SimTypes::FeatureMapSim& getContaminants() const;
104 
106  ConsensusMap& getLabelingConsensus();
107 
109  const SimTypes::MSSimExperiment& getPeakMap() const;
110 
117  void getMS2Identifications(std::vector<ProteinIdentification>& proteins, std::vector<PeptideIdentification>& peptides) const;
118 
120  Param getParameters() const;
121 
122 protected:
124  void syncParams_(Param& p, bool to_outer);
125 
127  void createFeatureMap_(const SimTypes::SampleProteins& peptides, SimTypes::FeatureMapSim& features, Size map_index);
128 
130  void updateMembers_();
131 
132 private:
135 
138 
141 
144 
147 
150  };
151 
152 }
153 
154 #endif
SimTypes::FeatureMapSimVector feature_maps_
Holds the ground-truth on generated features.
Definition: MSSim.h:140
Central class for simulation of mass spectrometry experiments.
Definition: MSSim.h:69
A container for features.
Definition: FeatureMap.h:93
boost::shared_ptr< SimRandomNumberGenerator > MutableSimRandomNumberGeneratorPtr
Definition: SimTypes.h:178
A container for consensus elements.
Definition: ConsensusMap.h:72
std::vector< SimProtein > SampleProteins
Container for FASTAEntry & abundance information.
Definition: SimTypes.h:94
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
SimTypes::FeatureMapSim contaminants_map_
Holds the ground-truth on generated contaminants.
Definition: MSSim.h:146
std::vector< SampleProteins > SampleChannels
Container for multiple channels of SampleProteins.
Definition: SimTypes.h:97
SimTypes::MSSimExperiment experiment_
Holds the simulated data.
Definition: MSSim.h:134
SimTypes::MSSimExperiment peak_map_
Holds the ground-truth on generated peaks positions and intensities.
Definition: MSSim.h:137
Management and storage of parameters / INI files.
Definition: Param.h:75
std::vector< FeatureMapSim > FeatureMapSimVector
Sim FeatureMap Vector.
Definition: SimTypes.h:103
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:55
BaseLabeler * labeler_
Labeling functionality.
Definition: MSSim.h:149
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92
ConsensusMap consensus_map_
Holds consensus ground-truth about the charge associations.
Definition: MSSim.h:143
Abstract base class for all kinds of labeling techniques.
Definition: BaseLabeler.h:50

OpenMS / TOPP release 2.0.0 Documentation generated on Thu Aug 20 2015 01:44:26 using doxygen 1.8.9.1