OpenMS
RTSimulation.h
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31 // $Maintainer: Timo Sachsenberg$
32 // $Authors: Stephan Aiche, Chris Bielow$
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34 
35 #pragma once
36 
39 
40 namespace OpenMS
41 {
53  class OPENMS_DLLAPI RTSimulation :
54  public DefaultParamHandler
55  {
56 
57 
58 public:
62 
65 
68 
70  RTSimulation(const RTSimulation& source);
71 
73  ~RTSimulation() override;
75 
78 
85 
90 
94  bool isRTColumnOn() const;
95 
97  void wrapSVM(std::vector<AASequence>& peptide_sequences, std::vector<double>& predicted_retention_times);
98 
100 
103 
104 private:
107 
110 
113 
121  void calculateMT_(SimTypes::FeatureMapSim& features, std::vector<double>& predicted_retention_times);
122 
123  void getChargeContribution_(std::map<String, double>& q_cterm,
124  std::map<String, double>& q_nterm,
125  std::map<String, double>& q_aa_basic,
126  std::map<String, double>& q_aa_acidic);
127 
128  // MEMBERS:
129 
130  // Name of the svm model file
132 
135 
137 
142 
145 
150 
155 
156 protected:
159 
161  void updateMembers_() override;
162 
163  };
164 
165 }
166 
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92
A container for features.
Definition: FeatureMap.h:106
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:72
Simulates/Predicts retention times for peptides or peptide separation.
Definition: RTSimulation.h:55
void wrapSVM(std::vector< AASequence > &peptide_sequences, std::vector< double > &predicted_retention_times)
Wrapper for the SVM RT Prediction (HPLC) using AASequences.
void calculateMT_(SimTypes::FeatureMapSim &features, std::vector< double > &predicted_retention_times)
void getChargeContribution_(std::map< String, double > &q_cterm, std::map< String, double > &q_nterm, std::map< String, double > &q_aa_basic, std::map< String, double > &q_aa_acidic)
SimTypes::SimCoordinateType gradient_min_
gradient ranges
Definition: RTSimulation.h:139
void predictContaminantsRT(SimTypes::FeatureMapSim &)
Set retention times randomly for given contaminants.
double egh_tau_location_
EGH tau value.
Definition: RTSimulation.h:147
RTSimulation()
Default constructor.
bool isRTColumnOn() const
Returns true if a RT column was simulated.
OpenMS::String rt_model_file_
Definition: RTSimulation.h:131
SimTypes::SimCoordinateType gradient_max_
Maximal observed gradient time.
Definition: RTSimulation.h:141
RTSimulation(const RTSimulation &source)
Copy constructor.
double egh_variance_location_
EGH sigma value.
Definition: RTSimulation.h:152
void setDefaultParams_()
Set default parameters.
void noRTColumn_(SimTypes::FeatureMapSim &)
Simply set all retention times to -1.
void predictRT(SimTypes::FeatureMapSim &features)
Predict retention times for given peptide features based for HPLC or CE.
~RTSimulation() override
Destructor.
SimTypes::SimCoordinateType rt_sampling_rate_
bin size in rt dimension
Definition: RTSimulation.h:144
void smoothRTDistortion_(SimTypes::MSSimExperiment &experiment)
smoothes the simulated distortion for the elution profiles with a moving average filter of size 3
double egh_tau_scale_
EGH tau scale parameter of the lorentzian variation.
Definition: RTSimulation.h:149
double egh_variance_scale_
EGH sigma scale parameter of the lorentzian variation.
Definition: RTSimulation.h:154
void createExperiment(SimTypes::MSSimExperiment &experiment)
Size experiment and assign retention time grid.
SimTypes::SimCoordinateType getGradientTime() const
RTSimulation & operator=(const RTSimulation &source)
Assignment operator.
void updateMembers_() override
Synchronize members with param class.
SimTypes::MutableSimRandomNumberGeneratorPtr rnd_gen_
Random number generator.
Definition: RTSimulation.h:158
RTSimulation(SimTypes::MutableSimRandomNumberGeneratorPtr random_generator)
Constructor taking a random generator.
SimTypes::SimCoordinateType total_gradient_time_
Total gradient time.
Definition: RTSimulation.h:134
A more convenient string class.
Definition: String.h:60
boost::shared_ptr< SimRandomNumberGenerator > MutableSimRandomNumberGeneratorPtr
Definition: SimTypes.h:174
Peak2D::CoordinateType SimCoordinateType
Coordinate type in mz and rt dimension.
Definition: SimTypes.h:59
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:48