| OpenMS 2.5.0

RTSimulation.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/Map.h>
38 #include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
39 #include <OpenMS/SIMULATION/SimTypes.h>
40
41 namespace OpenMS
42 {
54 class OPENMS_DLLAPI RTSimulation :
55 public DefaultParamHandler
56 {
57
58
59 public:
63
65 RTSimulation();
66
68 explicit RTSimulation(SimTypes::MutableSimRandomNumberGeneratorPtr random_generator);
69
71 RTSimulation(const RTSimulation& source);
72
74 ~RTSimulation() override;
76
78 RTSimulation& operator=(const RTSimulation& source);
79
85 void predictRT(SimTypes::FeatureMapSim& features);
86
90 void predictContaminantsRT(SimTypes::FeatureMapSim&);
91
95 bool isRTColumnOn() const;
96
98 void wrapSVM(std::vector<AASequence>& peptide_sequences, std::vector<double>& predicted_retention_times);
99
100 SimTypes::SimCoordinateType getGradientTime() const;
101
103 void createExperiment(SimTypes::MSSimExperiment& experiment);
104
105 private:
107 void setDefaultParams_();
108
110 void noRTColumn_(SimTypes::FeatureMapSim&);
111
113 void smoothRTDistortion_(SimTypes::MSSimExperiment& experiment);
114
122 void calculateMT_(SimTypes::FeatureMapSim& features, std::vector<double>& predicted_retention_times);
123
124 void getChargeContribution_(Map<String, double>& q_cterm,
125 Map<String, double>& q_nterm,
126 Map<String, double>& q_aa_basic,
127 Map<String, double>& q_aa_acidic);
128
129 // MEMBERS:
130
131 // Name of the svm model file
132 OpenMS::String rt_model_file_;
133
135 SimTypes::SimCoordinateType total_gradient_time_;
136
138
140 SimTypes::SimCoordinateType gradient_min_;
142 SimTypes::SimCoordinateType gradient_max_;
143
145 SimTypes::SimCoordinateType rt_sampling_rate_;
146
148 double egh_tau_location_;
150 double egh_tau_scale_;
151
153 double egh_variance_location_;
155 double egh_variance_scale_;
156
157 protected:
159 SimTypes::MutableSimRandomNumberGeneratorPtr rnd_gen_;
160
162 void updateMembers_() override;
163
164 };
165
166 }
167
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::RTSimulation::egh_tau_scale_
double egh_tau_scale_
EGH tau scale parameter of the lorentzian variation.
Definition: RTSimulation.h:150
OpenMS::RTSimulation::total_gradient_time_
SimTypes::SimCoordinateType total_gradient_time_
Total gradient time.
Definition: RTSimulation.h:135
OpenMS::RTSimulation::gradient_min_
SimTypes::SimCoordinateType gradient_min_
gradient ranges
Definition: RTSimulation.h:140
OpenMS::RTSimulation
Simulates/Predicts retention times for peptides or peptide separation.
Definition: RTSimulation.h:54
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:91
SimTypes.h
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
OpenMS::FeatureMap
A container for features.
Definition: FeatureMap.h:95
OpenMS::RTSimulation::rt_model_file_
OpenMS::String rt_model_file_
Definition: RTSimulation.h:132
OpenMS::RTSimulation::egh_variance_location_
double egh_variance_location_
EGH sigma value.
Definition: RTSimulation.h:153
OpenMS::RTSimulation::gradient_max_
SimTypes::SimCoordinateType gradient_max_
Maximal observed gradient time.
Definition: RTSimulation.h:142
OpenMS::Map
Map class based on the STL map (containing several convenience functions)
Definition: Map.h:50
OpenMS::RTSimulation::egh_variance_scale_
double egh_variance_scale_
EGH sigma scale parameter of the lorentzian variation.
Definition: RTSimulation.h:155
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::RTSimulation::rt_sampling_rate_
SimTypes::SimCoordinateType rt_sampling_rate_
bin size in rt dimension
Definition: RTSimulation.h:145
DefaultParamHandler.h
Map.h
double
OpenMS::RTSimulation::egh_tau_location_
double egh_tau_location_
EGH tau value.
Definition: RTSimulation.h:148
OpenMS::RTSimulation::rnd_gen_
SimTypes::MutableSimRandomNumberGeneratorPtr rnd_gen_
Random number generator.
Definition: RTSimulation.h:159
OpenMS::SimTypes::MutableSimRandomNumberGeneratorPtr
boost::shared_ptr< SimRandomNumberGenerator > MutableSimRandomNumberGeneratorPtr
Definition: SimTypes.h:174