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MSSim.h
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31 // $Maintainer: Timo Sachsenberg$
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 
122  void getIdentifications(std::vector<ProteinIdentification>& proteins, std::vector<PeptideIdentification>& peptides) const;
123 
130  void getMS2Identifications(std::vector<ProteinIdentification>& proteins, std::vector<PeptideIdentification>& peptides) const;
131 
138  void getFeatureIdentifications(std::vector<ProteinIdentification>& proteins, std::vector<PeptideIdentification>& peptides) const;
139 
141  Param getParameters() const;
142 
143 protected:
145  void syncParams_(Param& p, bool to_outer);
146 
148  void createFeatureMap_(const SimTypes::SampleProteins& peptides, SimTypes::FeatureMapSim& features, Size map_index);
149 
151  void updateMembers_();
152 
153 private:
156 
159 
162 
165 
168 
171  };
172 
173 }
174 
175 #endif
SimTypes::FeatureMapSimVector feature_maps_
Holds the ground-truth on generated features.
Definition: MSSim.h:161
Central class for simulation of mass spectrometry experiments.
Definition: MSSim.h:69
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
std::vector< SimProtein > SampleProteins
Container for FASTAEntry & abundance information.
Definition: SimTypes.h:91
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
SimTypes::FeatureMapSim contaminants_map_
Holds the ground-truth on generated contaminants.
Definition: MSSim.h:167
std::vector< SampleProteins > SampleChannels
Container for multiple channels of SampleProteins.
Definition: SimTypes.h:94
SimTypes::MSSimExperiment experiment_
Holds the simulated data.
Definition: MSSim.h:155
SimTypes::MSSimExperiment peak_map_
Holds the ground-truth on generated peaks positions and intensities.
Definition: MSSim.h:158
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
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:55
BaseLabeler * labeler_
Labeling functionality.
Definition: MSSim.h:170
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:164
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 18:22:02 using doxygen 1.8.13