OpenMS  3.0.0
MSSim.h
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31 // $Maintainer: Timo Sachsenberg$
32 // $Authors: Stephan Aiche, Chris Bielow$
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34 
35 #pragma once
36 
40 
42 
43 namespace OpenMS
44 {
45 
46  class BaseLabeler;
47 
68  class OPENMS_DLLAPI MSSim :
69  public DefaultParamHandler,
70  public ProgressLogger
71  {
72 
73 public:
77  MSSim();
79 
81  ~MSSim() override;
83 
91 
93  const SimTypes::MSSimExperiment& getExperiment() const;
94 
96  const SimTypes::FeatureMapSim& getSimulatedFeatures() const;
97 
99  ConsensusMap& getChargeConsensus();
100 
102  const SimTypes::FeatureMapSim& getContaminants() const;
103 
105  ConsensusMap& getLabelingConsensus();
106 
108  const SimTypes::MSSimExperiment& getPeakMap() const;
109 
121  void getIdentifications(std::vector<ProteinIdentification>& proteins, std::vector<PeptideIdentification>& peptides) const;
122 
129  void getMS2Identifications(std::vector<ProteinIdentification>& proteins, std::vector<PeptideIdentification>& peptides) const;
130 
137  void getFeatureIdentifications(std::vector<ProteinIdentification>& proteins, std::vector<PeptideIdentification>& peptides) const;
138 
140  Param getParameters() const;
141 
142 protected:
144  void syncParams_(Param& p, bool to_outer);
145 
147  void createFeatureMap_(const SimTypes::SampleProteins& peptides, SimTypes::FeatureMapSim& features, Size map_index);
148 
150  void updateMembers_() override;
151 
152 private:
155 
158 
161 
164 
167 
170  };
171 
172 }
173 
DefaultParamHandler.h
OpenMS::MSSim::peak_map_
SimTypes::MSSimExperiment peak_map_
Holds the ground-truth on generated peaks positions and intensities.
Definition: MSSim.h:157
SimTypes.h
OpenMS::MSSim::feature_maps_
SimTypes::FeatureMapSimVector feature_maps_
Holds the ground-truth on generated features.
Definition: MSSim.h:160
OpenMS::MSSim
Central class for simulation of mass spectrometry experiments.
Definition: MSSim.h:68
ConsensusMap.h
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:70
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
OpenMS::MSSim::experiment_
SimTypes::MSSimExperiment experiment_
Holds the simulated data.
Definition: MSSim.h:154
OpenMS::SimTypes::SampleProteins
std::vector< SimProtein > SampleProteins
Container for FASTAEntry & abundance information.
Definition: SimTypes.h:90
OpenMS::SimTypes::MutableSimRandomNumberGeneratorPtr
boost::shared_ptr< SimRandomNumberGenerator > MutableSimRandomNumberGeneratorPtr
Definition: SimTypes.h:174
OpenMS::SimTypes::SampleChannels
std::vector< SampleProteins > SampleChannels
Container for multiple channels of SampleProteins.
Definition: SimTypes.h:93
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::ProgressLogger
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:52
ProgressLogger.h
OpenMS::MSSim::consensus_map_
ConsensusMap consensus_map_
Holds consensus ground-truth about the charge associations.
Definition: MSSim.h:163
OpenMS::ConsensusMap
A container for consensus elements.
Definition: ConsensusMap.h:82
OpenMS::SimTypes::FeatureMapSimVector
std::vector< FeatureMapSim > FeatureMapSimVector
Sim FeatureMap Vector.
Definition: SimTypes.h:99
OpenMS::FeatureMap
A container for features.
Definition: FeatureMap.h:98
OpenMS::MSSim::labeler_
BaseLabeler * labeler_
Labeling functionality.
Definition: MSSim.h:169
OpenMS::BaseLabeler
Abstract base class for all kinds of labeling techniques.
Definition: BaseLabeler.h:49
OpenMS::Param
Management and storage of parameters / INI files.
Definition: Param.h:69
OpenMS::MSSim::contaminants_map_
SimTypes::FeatureMapSim contaminants_map_
Holds the ground-truth on generated contaminants.
Definition: MSSim.h:166