DetectabilitySimulation Class Reference

Simulates peptide detectability. More...

#include <OpenMS/SIMULATION/DetectabilitySimulation.h>

Inheritance diagram for DetectabilitySimulation:

Collaboration diagram for DetectabilitySimulation:

Constructors and Destructors
double	min_detect_
	Minimum allowed detectability likelihood of a peptide. More...
OpenMS::String	dt_model_file_
	Name of the svm model file. More...
	DetectabilitySimulation ()
	Constructor taking a random generator. More...
	DetectabilitySimulation (const DetectabilitySimulation &source)
	Copy constructor. More...
	~DetectabilitySimulation () override
	Destructor. More...
DetectabilitySimulation &	operator= (const DetectabilitySimulation &source)
	Assignment operator. More...
void	filterDetectability (SimTypes::FeatureMapSim &features)
	Filters the given peptide features for detectability. More...
void	predictDetectabilities (std::vector< String > &peptides_vector, std::vector< double > &labels, std::vector< double > &detectabilities)
void	setDefaultParams_ ()
	Set default parameters. More...
void	updateMembers_ () override
	Synchronize members with param class. More...
void	svmFilter_ (SimTypes::FeatureMapSim &)
	Filter the feature map using a svm model. More...
void	noFilter_ (SimTypes::FeatureMapSim &)
	Do not filter the feature map, just set the detectability to a default value. More...

Additional Inherited Members
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...
Static Public Member Functions inherited from DefaultParamHandler
static void	writeParametersToMetaValues (const Param &write_this, MetaInfoInterface &write_here, const String &key_prefix="")
	Writes all parameters to meta values. More...
Protected Member Functions inherited from DefaultParamHandler
void	defaultsToParam_ ()
	Updates the parameters after the defaults have been set in the constructor. 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...

Detailed Description

Simulates peptide detectability.

The peptide detectability is predicted based on a support-vector machine. Alternatively the detectability can be set to a default value for all peptides if no model is given.

Parameters of this class are:

Name	Type	Default	Restrictions	Description
dt_simulation_on	string	false	true, false	Modelling detectibility enabled? This can serve as a filter to remove peptides which ionize badly, thus reducing peptide count
min_detect	float	0.5		Minimum peptide detectability accepted. Peptides with a lower score will be removed
dt_model_file	string	SIMULATION/DTPredict.model		SVM model for peptide detectability prediction

Note:

• If a section name is documented, the documentation is displayed as tooltip.
• Advanced parameter names are italic.

Constructor & Destructor Documentation

DetectabilitySimulation() [1/2]

DetectabilitySimulation

(

)

Constructor taking a random generator.

DetectabilitySimulation() [2/2]

DetectabilitySimulation

(

const DetectabilitySimulation &

source

)

Copy constructor.

~DetectabilitySimulation()

~DetectabilitySimulation ( )

override

Destructor.

Member Function Documentation

filterDetectability()

void filterDetectability

(

SimTypes::FeatureMapSim &

features

)

Filters the given peptide features for detectability.

Based on the provided method (SVM or simple) all peptide features are removed that do not have a sufficient peptide detectability.

Parameters

features

Feature map that will be filtered for detectability

noFilter_()

void noFilter_ ( SimTypes::FeatureMapSim &  )

protected

Do not filter the feature map, just set the detectability to a default value.

operator=()

DetectabilitySimulation& operator=

(

const DetectabilitySimulation &

source

)

Assignment operator.

predictDetectabilities()

void predictDetectabilities	(	std::vector< String > &	peptides_vector,
		std::vector< double > &	labels,
		std::vector< double > &	detectabilities
	)

setDefaultParams_()

void setDefaultParams_ ( )

private

Set default parameters.

svmFilter_()

void svmFilter_ ( SimTypes::FeatureMapSim &  )

protected

Filter the feature map using a svm model.

updateMembers_()

void updateMembers_ ( )

overrideprivatevirtual

Synchronize members with param class.

Reimplemented from DefaultParamHandler.

Member Data Documentation

dt_model_file_

OpenMS::String dt_model_file_

private

Name of the svm model file.

min_detect_

double min_detect_

private

Minimum allowed detectability likelihood of a peptide.