RTSimulation Class Reference

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

#include <OpenMS/SIMULATION/RTSimulation.h>

Inheritance diagram for RTSimulation:

Public Member Functions
RTSimulation &	operator= (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...
virtual	~RTSimulation ()
	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 DefaultParamHandler &	operator= (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 Param &	getParameters () const
	Non-mutable access to the parameters. More...
const Param &	getDefaults () const
	Non-mutable access to the default parameters. More...
const String &	getName () 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_ ()
	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< String >	subsections_
	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

(

)

Default constructor.

RTSimulation ( SimTypes::MutableSimRandomNumberGeneratorPtr  random_generator )

explicit

Constructor taking a random generator.

RTSimulation

(

const RTSimulation &

source

)

Copy constructor.

virtual ~RTSimulation ( )

virtual

Destructor.

Member Function Documentation

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

private

Wrapper for the Migration time calculation (CE)

Parameters

features	will get modified with metavalue "RT_CE_width_factor", describing widening of MT shape.
predicted_retention_times	will contain afterwards the predicted retention times.

void createExperiment

(

SimTypes::MSSimExperiment &

experiment

)

Size experiment and assign retention time grid.

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

SimTypes::SimCoordinateType getGradientTime

(

)

const

bool isRTColumnOn

(

)

const

Returns true if a RT column was simulated.

void noRTColumn_ ( SimTypes::FeatureMapSim &  )

private

Simply set all retention times to -1.

RTSimulation& operator=

(

const RTSimulation &

source

)

Assignment operator.

void predictContaminantsRT

(

SimTypes::FeatureMapSim &

)

Set retention times randomly for given contaminants.

void predictRT

(

SimTypes::FeatureMapSim &

features

)

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

Parameters

features

Feature map for which the retention times will be predicted

void setDefaultParams_ ( )

private

Set default parameters.

void smoothRTDistortion_ ( SimTypes::MSSimExperiment &  experiment )

private

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

void updateMembers_ ( )

protectedvirtual

Synchronize members with param class.

Reimplemented from DefaultParamHandler.

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

double egh_tau_location_

private

EGH tau value.

double egh_tau_scale_

private

EGH tau scale parameter of the lorentzian variation.

double egh_variance_location_

private

EGH sigma value.

double egh_variance_scale_

private

EGH sigma scale parameter of the lorentzian variation.

SimTypes::SimCoordinateType gradient_max_

private

Maximal observed gradient time.

SimTypes::SimCoordinateType gradient_min_

private

gradient ranges

Minimal observed gradient time

SimTypes::MutableSimRandomNumberGeneratorPtr rnd_gen_

protected

Random number generator.

OpenMS::String rt_model_file_

private

SimTypes::SimCoordinateType rt_sampling_rate_

private

bin size in rt dimension

SimTypes::SimCoordinateType total_gradient_time_

private

Total gradient time.