OpenMS
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:
78  MSSim();
79 
81  ~MSSim() override;
83 
91 
94 
97 
100 
103 
106 
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 
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 
Abstract base class for all kinds of labeling techniques.
Definition: BaseLabeler.h:51
A container for consensus elements.
Definition: ConsensusMap.h:92
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92
A container for features.
Definition: FeatureMap.h:106
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:72
Central class for simulation of mass spectrometry experiments.
Definition: MSSim.h:71
MSSim()
Default constructor.
const SimTypes::FeatureMapSim & getContaminants() const
Access the contaminants feature map of simulated features.
ConsensusMap & getChargeConsensus()
Access the charge consensus map of simulated features.
void simulate(const SimTypes::MutableSimRandomNumberGeneratorPtr &rnd_gen, SimTypes::SampleChannels &peptides)
General purpose function to simulate a mass spectrometry run.
Param getParameters() const
Returns the default parameters for simulation including the labeling technique with name labeling_nam...
void getMS2Identifications(std::vector< ProteinIdentification > &proteins, std::vector< PeptideIdentification > &peptides) const
Access the simulated MS2 identifications (proteins and peptides)
SimTypes::FeatureMapSim contaminants_map_
Holds the ground-truth on generated contaminants.
Definition: MSSim.h:166
void syncParams_(Param &p, bool to_outer)
handle global params
SimTypes::MSSimExperiment experiment_
Holds the simulated data.
Definition: MSSim.h:154
BaseLabeler * labeler_
Labeling functionality.
Definition: MSSim.h:169
const SimTypes::FeatureMapSim & getSimulatedFeatures() const
Access the simulated features.
~MSSim() override
Destructor.
const SimTypes::MSSimExperiment & getPeakMap() const
Access the picked (centroided) experiment.
ConsensusMap consensus_map_
Holds consensus ground-truth about the charge associations.
Definition: MSSim.h:163
void getIdentifications(std::vector< ProteinIdentification > &proteins, std::vector< PeptideIdentification > &peptides) const
Access the simulated identifications (proteins and peptides)
ConsensusMap & getLabelingConsensus()
Access the labeling consensus map of simulated features.
const SimTypes::MSSimExperiment & getExperiment() const
Access the simulated experiment.
void updateMembers_() override
Synchronize members with param class.
SimTypes::MSSimExperiment peak_map_
Holds the ground-truth on generated peaks positions and intensities.
Definition: MSSim.h:157
void getFeatureIdentifications(std::vector< ProteinIdentification > &proteins, std::vector< PeptideIdentification > &peptides) const
Access the simulated identifications (proteins and peptides) from feature annotations.
SimTypes::FeatureMapSimVector feature_maps_
Holds the ground-truth on generated features.
Definition: MSSim.h:160
void createFeatureMap_(const SimTypes::SampleProteins &peptides, SimTypes::FeatureMapSim &features, Size map_index)
Convert a list of peptides with given abundance values into a FeatureMap.
Management and storage of parameters / INI files.
Definition: Param.h:70
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:53
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
boost::shared_ptr< SimRandomNumberGenerator > MutableSimRandomNumberGeneratorPtr
Definition: SimTypes.h:174
std::vector< FeatureMapSim > FeatureMapSimVector
Sim FeatureMap Vector.
Definition: SimTypes.h:99
std::vector< SampleProteins > SampleChannels
Container for multiple channels of SampleProteins.
Definition: SimTypes.h:93
std::vector< SimProtein > SampleProteins
Container for FASTAEntry & abundance information.
Definition: SimTypes.h:90
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:48