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RTSimulation.h
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31 // $Maintainer: Timo Sachsenberg$
32 // $Authors: Stephan Aiche, Chris Bielow$
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34 
35 #ifndef OPENMS_SIMULATION_RTSIMULATION_H
36 #define OPENMS_SIMULATION_RTSIMULATION_H
37 
41 
42 namespace OpenMS
43 {
55  class OPENMS_DLLAPI RTSimulation :
56  public DefaultParamHandler
57  {
58 
59 
60 public:
64 
66  RTSimulation();
67 
70 
72  RTSimulation(const RTSimulation& source);
73 
75  virtual ~RTSimulation();
77 
79  RTSimulation& operator=(const RTSimulation& source);
80 
86  void predictRT(SimTypes::FeatureMapSim& features);
87 
91  void predictContaminantsRT(SimTypes::FeatureMapSim&);
92 
96  bool isRTColumnOn() const;
97 
99  void wrapSVM(std::vector<AASequence>& peptide_sequences, std::vector<double>& predicted_retention_times);
100 
101  SimTypes::SimCoordinateType getGradientTime() const;
102 
104  void createExperiment(SimTypes::MSSimExperiment& experiment);
105 
106 private:
108  void setDefaultParams_();
109 
111  void noRTColumn_(SimTypes::FeatureMapSim&);
112 
114  void smoothRTDistortion_(SimTypes::MSSimExperiment& experiment);
115 
123  void calculateMT_(SimTypes::FeatureMapSim& features, std::vector<double>& predicted_retention_times);
124 
125  void getChargeContribution_(Map<String, double>& q_cterm,
126  Map<String, double>& q_nterm,
127  Map<String, double>& q_aa_basic,
128  Map<String, double>& q_aa_acidic);
129 
130  // MEMBERS:
131 
132  // Name of the svm model file
134 
137 
139 
144 
147 
152 
157 
158 protected:
161 
163  void updateMembers_();
164 
165  };
166 
167 }
168 
169 #endif
A more convenient string class.
Definition: String.h:57
OpenMS::String rt_model_file_
Definition: RTSimulation.h:133
A container for features.
Definition: FeatureMap.h:94
SimTypes::MutableSimRandomNumberGeneratorPtr rnd_gen_
Random number generator.
Definition: RTSimulation.h:160
boost::shared_ptr< SimRandomNumberGenerator > MutableSimRandomNumberGeneratorPtr
Definition: SimTypes.h:175
double egh_variance_scale_
EGH sigma scale parameter of the lorentzian variation.
Definition: RTSimulation.h:156
Simulates/Predicts retention times for peptides or peptide separation.
Definition: RTSimulation.h:55
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
SimTypes::SimCoordinateType gradient_min_
gradient ranges
Definition: RTSimulation.h:141
double egh_tau_location_
EGH tau value.
Definition: RTSimulation.h:149
double egh_variance_location_
EGH sigma value.
Definition: RTSimulation.h:154
SimTypes::SimCoordinateType rt_sampling_rate_
bin size in rt dimension
Definition: RTSimulation.h:146
SimTypes::SimCoordinateType gradient_max_
Maximal observed gradient time.
Definition: RTSimulation.h:143
SimTypes::SimCoordinateType total_gradient_time_
Total gradient time.
Definition: RTSimulation.h:136
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:82
double egh_tau_scale_
EGH tau scale parameter of the lorentzian variation.
Definition: RTSimulation.h:151
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92
Map class based on the STL map (containing several convenience functions)
Definition: Map.h:51

OpenMS / TOPP release 2.3.0 Documentation generated on Tue Jan 9 2018 18:22:03 using doxygen 1.8.13