| OpenMS 2.5.0

BaseLabeler.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
39 #include <OpenMS/KERNEL/ConsensusMap.h>
40
41 #include <OpenMS/SIMULATION/SimTypes.h>
42
43 namespace OpenMS
44 {
45
49 class OPENMS_DLLAPI BaseLabeler :
50 public DefaultParamHandler
51 {
52 public:
53
55 BaseLabeler();
56
58 ~BaseLabeler() override;
59
61 static void registerChildren();
62
68 virtual Param getDefaultParameters() const;
69
76 virtual void setRnd(SimTypes::MutableSimRandomNumberGeneratorPtr rng);
77
85 virtual void preCheck(Param& param) const = 0;
86
91
93 virtual void setUpHook(SimTypes::FeatureMapSimVector& /* features */) = 0;
94
96 virtual void postDigestHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */) = 0;
97
99 virtual void postRTHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */) = 0;
100
102 virtual void postDetectabilityHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */) = 0;
103
105 virtual void postIonizationHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */) = 0;
106
108 virtual void postRawMSHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */) = 0;
109
111 virtual void postRawTandemMSHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */, SimTypes::MSSimExperiment& /* simulated map */) = 0;
112
114
115 ConsensusMap& getConsensus();
116
122 const String& getDescription() const;
123
130 String getChannelIntensityName(const Size channel_index) const;
131
132
133 protected:
141 SimTypes::FeatureMapSim mergeProteinIdentificationsMaps_(const SimTypes::FeatureMapSimVector& maps);
142
152 void mergeProteinAccessions_(Feature& target, const Feature& source) const;
153
161 void recomputeConsensus_(const SimTypes::FeatureMapSim& simulated_features);
162
163
164 ConsensusMap consensus_;
165
166 SimTypes::MutableSimRandomNumberGeneratorPtr rng_;
167
168 String channel_description_;
169
170 };
171 } // namespace OpenMS
172
OpenMS::Feature
An LC-MS feature.
Definition: Feature.h:70
OpenMS::BaseLabeler::channel_description_
String channel_description_
Definition: BaseLabeler.h:168
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::BaseLabeler::consensus_
ConsensusMap consensus_
Definition: BaseLabeler.h:164
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:91
SimTypes.h
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::BaseLabeler::rng_
SimTypes::MutableSimRandomNumberGeneratorPtr rng_
Definition: BaseLabeler.h:166
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
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
DefaultParamHandler.h
OpenMS::Param
Management and storage of parameters / INI files.
Definition: Param.h:73
OpenMS::ConsensusMap
A container for consensus elements.
Definition: ConsensusMap.h:79
OpenMS::SimTypes::MutableSimRandomNumberGeneratorPtr
boost::shared_ptr< SimRandomNumberGenerator > MutableSimRandomNumberGeneratorPtr
Definition: SimTypes.h:174
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127