| OpenMS 2.5.0

MSSim.h
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2 // OpenMS -- Open-Source Mass Spectrometry
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4 // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
5 // ETH Zurich, and Freie Universitaet Berlin 2002-2020.
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30 // --------------------------------------------------------------------------
31 // $Maintainer: Timo Sachsenberg$
32 // $Authors: Stephan Aiche, Chris Bielow$
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
38 #include <OpenMS/SIMULATION/SimTypes.h>
39 #include <OpenMS/KERNEL/ConsensusMap.h>
40
41 #include <OpenMS/CONCEPT/ProgressLogger.h>
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
90 void simulate(SimTypes::MutableSimRandomNumberGeneratorPtr rnd_gen, SimTypes::SampleChannels& peptides);
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:
154 SimTypes::MSSimExperiment experiment_;
155
157 SimTypes::MSSimExperiment peak_map_;
158
160 SimTypes::FeatureMapSimVector feature_maps_;
161
163 ConsensusMap consensus_map_;
164
166 SimTypes::FeatureMapSim contaminants_map_;
167
169 BaseLabeler* labeler_;
170 };
171
172 }
173
OpenMS::SimTypes::SampleProteins
std::vector< SimProtein > SampleProteins
Container for FASTAEntry & abundance information.
Definition: SimTypes.h:90
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:91
SimTypes.h
OpenMS::MSSim::contaminants_map_
SimTypes::FeatureMapSim contaminants_map_
Holds the ground-truth on generated contaminants.
Definition: MSSim.h:166
OpenMS::SimTypes::SampleChannels
std::vector< SampleProteins > SampleChannels
Container for multiple channels of SampleProteins.
Definition: SimTypes.h:93
OpenMS::SimTypes::FeatureMapSimVector
std::vector< FeatureMapSim > FeatureMapSimVector
Sim FeatureMap Vector.
Definition: SimTypes.h:99
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
OpenMS::FeatureMap
A container for features.
Definition: FeatureMap.h:95
ConsensusMap.h
OpenMS::BaseLabeler
Abstract base class for all kinds of labeling techniques.
Definition: BaseLabeler.h:49
OpenMS::MSSim::consensus_map_
ConsensusMap consensus_map_
Holds consensus ground-truth about the charge associations.
Definition: MSSim.h:163
ProgressLogger.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::ProgressLogger
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:54
DefaultParamHandler.h
OpenMS::Param
Management and storage of parameters / INI files.
Definition: Param.h:73
OpenMS::MSSim
Central class for simulation of mass spectrometry experiments.
Definition: MSSim.h:68
OpenMS::MSSim::feature_maps_
SimTypes::FeatureMapSimVector feature_maps_
Holds the ground-truth on generated features.
Definition: MSSim.h:160
OpenMS::MSSim::experiment_
SimTypes::MSSimExperiment experiment_
Holds the simulated data.
Definition: MSSim.h:154
OpenMS::ConsensusMap
A container for consensus elements.
Definition: ConsensusMap.h:79
OpenMS::MSSim::labeler_
BaseLabeler * labeler_
Labeling functionality.
Definition: MSSim.h:169
OpenMS::SimTypes::MutableSimRandomNumberGeneratorPtr
boost::shared_ptr< SimRandomNumberGenerator > MutableSimRandomNumberGeneratorPtr
Definition: SimTypes.h:174
OpenMS::MSSim::peak_map_
SimTypes::MSSimExperiment peak_map_
Holds the ground-truth on generated peaks positions and intensities.
Definition: MSSim.h:157
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127