OpenMS  2.4.0
Public Member Functions | Protected Member Functions | Protected Attributes | Private Member Functions | Private Attributes | List of all members
RTSimulation Class Reference

Simulates/Predicts retention times for peptides or peptide separation. More...

#include <OpenMS/SIMULATION/RTSimulation.h>

Inheritance diagram for RTSimulation:
DefaultParamHandler

Public Member Functions

RTSimulationoperator= (const RTSimulation &source)
 Assignment operator. More...
 
void predictRT (SimTypes::FeatureMapSim &features)
 Predict retention times for given peptide features based for HPLC or CE. More...
 
void predictContaminantsRT (SimTypes::FeatureMapSim &)
 Set retention times randomly for given contaminants. More...
 
bool isRTColumnOn () const
 Returns true if a RT column was simulated. More...
 
void wrapSVM (std::vector< AASequence > &peptide_sequences, std::vector< double > &predicted_retention_times)
 Wrapper for the SVM RT Prediction (HPLC) using AASequences. More...
 
SimTypes::SimCoordinateType getGradientTime () const
 
void createExperiment (SimTypes::MSSimExperiment &experiment)
 Size experiment and assign retention time grid. More...
 
Constructors and Destructors
 RTSimulation ()
 Default constructor. More...
 
 RTSimulation (SimTypes::MutableSimRandomNumberGeneratorPtr random_generator)
 Constructor taking a random generator. More...
 
 RTSimulation (const RTSimulation &source)
 Copy constructor. More...
 
 ~RTSimulation () override
 Destructor. More...
 
- Public Member Functions inherited from DefaultParamHandler
 DefaultParamHandler (const String &name)
 Constructor with name that is displayed in error messages. More...
 
 DefaultParamHandler (const DefaultParamHandler &rhs)
 Copy constructor. More...
 
virtual ~DefaultParamHandler ()
 Destructor. More...
 
virtual DefaultParamHandleroperator= (const DefaultParamHandler &rhs)
 Assignment operator. More...
 
virtual bool operator== (const DefaultParamHandler &rhs) const
 Equality operator. More...
 
void setParameters (const Param &param)
 Sets the parameters. More...
 
const ParamgetParameters () const
 Non-mutable access to the parameters. More...
 
const ParamgetDefaults () const
 Non-mutable access to the default parameters. More...
 
const StringgetName () const
 Non-mutable access to the name. More...
 
void setName (const String &name)
 Mutable access to the name. More...
 
const std::vector< String > & getSubsections () const
 Non-mutable access to the registered subsections. More...
 

Protected Member Functions

void updateMembers_ () override
 Synchronize members with param class. More...
 
- Protected Member Functions inherited from DefaultParamHandler
void defaultsToParam_ ()
 Updates the parameters after the defaults have been set in the constructor. More...
 

Protected Attributes

SimTypes::MutableSimRandomNumberGeneratorPtr rnd_gen_
 Random number generator. More...
 
- Protected Attributes inherited from DefaultParamHandler
Param param_
 Container for current parameters. More...
 
Param defaults_
 Container for default parameters. This member should be filled in the constructor of derived classes! More...
 
std::vector< Stringsubsections_
 Container for registered subsections. This member should be filled in the constructor of derived classes! More...
 
String error_name_
 Name that is displayed in error messages during the parameter checking. More...
 
bool check_defaults_
 If this member is set to false no checking if parameters in done;. More...
 
bool warn_empty_defaults_
 If this member is set to false no warning is emitted when defaults are empty;. More...
 

Private Member Functions

void setDefaultParams_ ()
 Set default parameters. More...
 
void noRTColumn_ (SimTypes::FeatureMapSim &)
 Simply set all retention times to -1. More...
 
void smoothRTDistortion_ (SimTypes::MSSimExperiment &experiment)
 smoothes the simulated distortion for the elution profiles with a moving average filter of size 3 More...
 
void calculateMT_ (SimTypes::FeatureMapSim &features, std::vector< double > &predicted_retention_times)
 
void getChargeContribution_ (Map< String, double > &q_cterm, Map< String, double > &q_nterm, Map< String, double > &q_aa_basic, Map< String, double > &q_aa_acidic)
 

Private Attributes

OpenMS::String rt_model_file_
 
SimTypes::SimCoordinateType total_gradient_time_
 Total gradient time. More...
 
SimTypes::SimCoordinateType gradient_min_
 gradient ranges More...
 
SimTypes::SimCoordinateType gradient_max_
 Maximal observed gradient time. More...
 
SimTypes::SimCoordinateType rt_sampling_rate_
 bin size in rt dimension More...
 
double egh_tau_location_
 EGH tau value. More...
 
double egh_tau_scale_
 EGH tau scale parameter of the lorentzian variation. More...
 
double egh_variance_location_
 EGH sigma value. More...
 
double egh_variance_scale_
 EGH sigma scale parameter of the lorentzian variation. More...
 

Detailed Description

Simulates/Predicts retention times for peptides or peptide separation.

The retention times for the different peptides are determined based on a SVM model or are all set to -1 in case of simulations without a HPLC column.

Constructor & Destructor Documentation

◆ RTSimulation() [1/3]

Default constructor.

◆ RTSimulation() [2/3]

Constructor taking a random generator.

◆ RTSimulation() [3/3]

RTSimulation ( const RTSimulation source)

Copy constructor.

◆ ~RTSimulation()

~RTSimulation ( )
override

Destructor.

Member Function Documentation

◆ calculateMT_()

void calculateMT_ ( SimTypes::FeatureMapSim features,
std::vector< double > &  predicted_retention_times 
)
private

Wrapper for the Migration time calculation (CE)

Parameters
featureswill get modified with metavalue "RT_CE_width_factor", describing widening of MT shape.
predicted_retention_timeswill contain afterwards the predicted retention times.

◆ createExperiment()

void createExperiment ( SimTypes::MSSimExperiment experiment)

Size experiment and assign retention time grid.

◆ getChargeContribution_()

void getChargeContribution_ ( Map< String, double > &  q_cterm,
Map< String, double > &  q_nterm,
Map< String, double > &  q_aa_basic,
Map< String, double > &  q_aa_acidic 
)
private

◆ getGradientTime()

SimTypes::SimCoordinateType getGradientTime ( ) const

◆ isRTColumnOn()

bool isRTColumnOn ( ) const

Returns true if a RT column was simulated.

◆ noRTColumn_()

void noRTColumn_ ( SimTypes::FeatureMapSim )
private

Simply set all retention times to -1.

◆ operator=()

RTSimulation& operator= ( const RTSimulation source)

Assignment operator.

◆ predictContaminantsRT()

void predictContaminantsRT ( SimTypes::FeatureMapSim )

Set retention times randomly for given contaminants.

◆ predictRT()

void predictRT ( SimTypes::FeatureMapSim features)

Predict retention times for given peptide features based for HPLC or CE.

Parameters
featuresFeature map for which the retention times will be predicted

◆ setDefaultParams_()

void setDefaultParams_ ( )
private

Set default parameters.

◆ smoothRTDistortion_()

void smoothRTDistortion_ ( SimTypes::MSSimExperiment experiment)
private

smoothes the simulated distortion for the elution profiles with a moving average filter of size 3

◆ updateMembers_()

void updateMembers_ ( )
overrideprotectedvirtual

Synchronize members with param class.

Reimplemented from DefaultParamHandler.

◆ wrapSVM()

void wrapSVM ( std::vector< AASequence > &  peptide_sequences,
std::vector< double > &  predicted_retention_times 
)

Wrapper for the SVM RT Prediction (HPLC) using AASequences.

Member Data Documentation

◆ egh_tau_location_

double egh_tau_location_
private

EGH tau value.

◆ egh_tau_scale_

double egh_tau_scale_
private

EGH tau scale parameter of the lorentzian variation.

◆ egh_variance_location_

double egh_variance_location_
private

EGH sigma value.

◆ egh_variance_scale_

double egh_variance_scale_
private

EGH sigma scale parameter of the lorentzian variation.

◆ gradient_max_

SimTypes::SimCoordinateType gradient_max_
private

Maximal observed gradient time.

◆ gradient_min_

SimTypes::SimCoordinateType gradient_min_
private

gradient ranges

Minimal observed gradient time

◆ rnd_gen_

Random number generator.

◆ rt_model_file_

OpenMS::String rt_model_file_
private

◆ rt_sampling_rate_

SimTypes::SimCoordinateType rt_sampling_rate_
private

bin size in rt dimension

◆ total_gradient_time_

SimTypes::SimCoordinateType total_gradient_time_
private

Total gradient time.