Exponentially modified gaussian distribution model for elution profiles. More...

#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/EmgModel.h>

Inheritance diagram for EmgModel:

Collaboration diagram for EmgModel:

Public Types
typedef InterpolationModel::CoordinateType	CoordinateType

typedef Math::BasicStatistics< CoordinateType >	BasicStatistics

typedef LinearInterpolation::container_type	ContainerType

Public Types inherited from InterpolationModel
typedef double	IntensityType

typedef DPosition< 1 >	PositionType

typedef double	CoordinateType

typedef Math::LinearInterpolation< double >	LinearInterpolation

Public Types inherited from BaseModel< 1 >
typedef double	IntensityType

typedef double	CoordinateType

typedef DPosition< D >	PositionType

typedef DPeak< D >::Type	PeakType

typedef std::vector< PeakType >	SamplesType

Public Member Functions
	EmgModel ()
	Default constructor. More...

	EmgModel (const EmgModel &source)
	copy constructor More...

	~EmgModel () override
	destructor More...

virtual EmgModel &	operator= (const EmgModel &source)
	assignment operator More...

void	setOffset (CoordinateType offset) override
	set offset without being computing all over and without any discrepancy More...

void	setSamples () override
	set sample/supporting points of interpolation More...

CoordinateType	getCenter () const override
	get the center of the Gaussian model i.e. the position of the maximum More...

Public Member Functions inherited from InterpolationModel
	InterpolationModel ()
	Default constructor. More...

	InterpolationModel (const InterpolationModel &source)
	copy constructor More...

	~InterpolationModel () override
	destructor More...

virtual InterpolationModel &	operator= (const InterpolationModel &source)
	assignment operator More...

IntensityType	getIntensity (const PositionType &pos) const override
	access model predicted intensity at position `pos` More...

IntensityType	getIntensity (CoordinateType coord) const
	access model predicted intensity at position `pos` More...

const LinearInterpolation &	getInterpolation () const
	Returns the interpolation class. More...

CoordinateType	getScalingFactor () const
	get the scaling for the model More...

void	getSamples (SamplesType &cont) const override
	get reasonable set of samples from the model (i.e. for printing) More...

void	setInterpolationStep (CoordinateType interpolation_step)
	Set the interpolation step for the linear interpolation of the model. More...

void	setScalingFactor (CoordinateType scaling)

Public Member Functions inherited from BaseModel< 1 >
	BaseModel ()
	Default constructor. More...

	BaseModel (const BaseModel &source)
	copy constructor More...

	~BaseModel () override
	Destructor. More...

virtual BaseModel &	operator= (const BaseModel &source)
	assignment operator More...

void	registerChildren ()

void	registerChildren ()

virtual IntensityType	getIntensity (const PositionType &pos) const=0
	access model predicted intensity at position `pos` More...

virtual bool	isContained (const PositionType &pos) const
	check if position `pos` is part of the model regarding the models cut-off. More...

void	fillIntensity (PeakType &peak) const
	Convenience function to set the intensity of a peak to the predicted intensity at its current position, calling virtual void getIntensity(). More...

void	fillIntensities (PeakIterator begin, PeakIterator end) const
	Convenience function that applies fillIntensity() to an iterator range. More...

virtual IntensityType	getCutOff () const
	get cutoff value More...

virtual void	setCutOff (IntensityType cut_off)
	set cutoff value More...

virtual void	getSamples (std::ostream &os)
	fill stream with reasonable set of samples from the model (i.e. for printing) 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...

Static Public Member Functions
static BaseModel< 1 > *	create ()
	create new EmgModel object (needed by Factory) More...

static const String	getProductName ()
	name of the model (needed by Factory) More...

Static Public Member Functions inherited from BaseModel< 1 >
static void	registerChildren ()
	register all derived classes here (implemented in file BaseModel_impl.h) More...

Static Public Member Functions inherited from DefaultParamHandler
static void	writeParametersToMetaValues (const Param &write_this, MetaInfoInterface &write_here, const String &prefix="")
	Writes all parameters to meta values. More...

Protected Member Functions
void	updateMembers_ () override
	This method is used to update extra member variables at the end of the setParameters() method. More...

Protected Member Functions inherited from InterpolationModel
void	updateMembers_ () override
	This method is used to update extra member variables at the end of the setParameters() method. More...

Protected Member Functions inherited from BaseModel< 1 >
void	updateMembers_ () override
	This method is used to update extra member variables at the end of the setParameters() method. More...

Protected Member Functions inherited from DefaultParamHandler
void	defaultsToParam_ ()
	Updates the parameters after the defaults have been set in the constructor. More...

Protected Attributes
CoordinateType	min_

CoordinateType	max_

BasicStatistics	statistics_

CoordinateType	height_

CoordinateType	width_

CoordinateType	symmetry_

CoordinateType	retention_

Protected Attributes inherited from InterpolationModel
LinearInterpolation	interpolation_

CoordinateType	interpolation_step_

CoordinateType	scaling_

Protected Attributes inherited from BaseModel< 1 >
IntensityType	cut_off_

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

Exponentially modified gaussian distribution model for elution profiles.

Parameters of this class are:

Name	Type	Default	Description
cutoff	float	0.0	Low intensity cutoff of the model. Peaks below this intensity are not considered part of the model.
interpolation_step	float	0.1	Sampling rate for the interpolation of the model function
intensity_scaling	float	1.0	Scaling factor used to adjust the model distribution to the intensities of the data
bounding_box:min	float	0.0	Lower end of bounding box enclosing the data used to fit the model.
bounding_box:max	float	1.0	Upper end of bounding box enclosing the data used to fit the model.
statistics:mean	float	0.0	Centroid position of the model.
statistics:variance	float	1.0	The variance of the model.
emg:height	float	1.0e05	Height of the exponentially modified Gaussian.
emg:width	float	5.0	Width of the exponentially modified Gaussian.
emg:symmetry	float	5.0	Symmetry of the exponentially modified Gaussian.
emg:retention	float	1200.0	Retention time of the exponentially modified Gaussian.

Note:

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

Member Typedef Documentation

◆ BasicStatistics

typedef Math::BasicStatistics<CoordinateType> BasicStatistics

◆ ContainerType

typedef LinearInterpolation::container_type ContainerType

◆ CoordinateType

typedef InterpolationModel::CoordinateType CoordinateType

Constructor & Destructor Documentation

◆ EmgModel() [1/2]

EmgModel ( )

Default constructor.

◆ EmgModel() [2/2]

EmgModel ( const EmgModel & source )

copy constructor

◆ ~EmgModel()

~EmgModel ( )

override

destructor

Member Function Documentation

◆ create()

static BaseModel<1>* create ( )

inlinestatic

create new EmgModel object (needed by Factory)

◆ getCenter()

CoordinateType getCenter ( ) const

overridevirtual

get the center of the Gaussian model i.e. the position of the maximum

Reimplemented from InterpolationModel.

◆ getProductName()

static const String getProductName ( )

inlinestatic

name of the model (needed by Factory)

◆ operator=()

virtual EmgModel& operator= ( const EmgModel & source )

virtual

assignment operator

◆ setOffset()

void setOffset ( CoordinateType offset )

overridevirtual

set offset without being computing all over and without any discrepancy

Reimplemented from InterpolationModel.

◆ setSamples()

void setSamples ( )

overridevirtual

set sample/supporting points of interpolation

Reimplemented from InterpolationModel.

◆ updateMembers_()

void updateMembers_ ( )

overrideprotectedvirtual

This method is used to update extra member variables at the end of the setParameters() method.

Also call it at the end of the derived classes' copy constructor and assignment operator.

The default implementation is empty.

Reimplemented from DefaultParamHandler.

Member Data Documentation

◆ height_

CoordinateType height_

protected

◆ max_

CoordinateType max_

protected

◆ min_

CoordinateType min_

protected

◆ retention_

CoordinateType retention_

protected

◆ statistics_

BasicStatistics statistics_

protected

◆ symmetry_

CoordinateType symmetry_

protected

◆ width_

CoordinateType width_

protected

Public Types

Public Member Functions

Static Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Member Typedef Documentation

◆ BasicStatistics

◆ ContainerType

◆ CoordinateType

Constructor & Destructor Documentation

◆ EmgModel() [1/2]

◆ EmgModel() [2/2]

◆ ~EmgModel()

Member Function Documentation

◆ create()

◆ getCenter()

◆ getProductName()

◆ operator=()

◆ setOffset()

◆ setSamples()

◆ updateMembers_()

Member Data Documentation

◆ height_

◆ max_

◆ min_

◆ retention_

◆ statistics_

◆ symmetry_

◆ width_