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RTSimulation.h
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31 // $Maintainer: Stephan Aiche$
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 public:
63 
65  RTSimulation(const SimRandomNumberGenerator & random_generator);
66 
68  RTSimulation(const RTSimulation & source);
69 
71  virtual ~RTSimulation();
73 
75  RTSimulation & operator=(const RTSimulation & source);
76 
82  void predictRT(FeatureMapSim & features);
83 
87  void predictContaminantsRT(FeatureMapSim &);
88 
92  bool isRTColumnOn() const;
93 
95  void wrapSVM(std::vector<AASequence> & peptide_sequences, std::vector<DoubleReal> & predicted_retention_times);
96 
97  SimCoordinateType getGradientTime() const;
98 
100  void createExperiment(MSSimExperiment & experiment);
101 
102 private:
104  RTSimulation();
105 
107  void setDefaultParams_();
108 
110  void noRTColumn_(FeatureMapSim &);
111 
113  void smoothRTDistortion_(MSSimExperiment & experiment);
114 
122  void calculateMT_(FeatureMapSim & features, std::vector<DoubleReal> & 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
133 
136 
138 
143 
146 
151 
156 
157 protected:
160 
162  void updateMembers_();
163 
164  };
165 
166 }
167 
168 #endif
SimRandomNumberGenerator const * rnd_gen_
Random number generator.
Definition: RTSimulation.h:159
A more convenient string class.
Definition: String.h:56
OpenMS::String rt_model_file_
Definition: RTSimulation.h:132
SimCoordinateType gradient_max_
Maximal observed gradient time.
Definition: RTSimulation.h:142
A container for features.
Definition: FeatureMap.h:111
Simulates/Predicts retention times for peptides or peptide separation.
Definition: RTSimulation.h:55
SimCoordinateType gradient_min_
gradient ranges
Definition: RTSimulation.h:140
DoubleReal egh_variance_scale_
EGH sigma scale parameter of the lorentzian variation.
Definition: RTSimulation.h:155
SimCoordinateType rt_sampling_rate_
bin size in rt dimension
Definition: RTSimulation.h:145
Wrapper class for random number generators used by the simulation classes.
Definition: SimTypes.h:99
DoubleReal egh_variance_location_
EGH sigma value.
Definition: RTSimulation.h:153
DoubleReal egh_tau_location_
EGH tau value.
Definition: RTSimulation.h:148
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:90
Map class based on the STL map (containing serveral convenience functions)
Definition: Map.h:50
DoubleReal egh_tau_scale_
EGH tau scale parameter of the lorentzian variation.
Definition: RTSimulation.h:150
SimCoordinateType total_gradient_time_
Total gradient time.
Definition: RTSimulation.h:135

OpenMS / TOPP release 1.11.1 Documentation generated on Thu Nov 14 2013 11:19:20 using doxygen 1.8.5