BiGaussian distribution approximated using linear interpolation. More...

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

Inheritance diagram for BiGaussModel:

Collaboration diagram for BiGaussModel:

Public Types
typedef InterpolationModel::CoordinateType	CoordinateType

Public Types inherited from InterpolationModel
typedef double	IntensityType

typedef DPosition< 1 >	PositionType

typedef double	CoordinateType

using	KeyType = double

typedef Math::LinearInterpolation< KeyType >	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
	BiGaussModel ()
	Default constructor. More...

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

	~BiGaussModel () override
	destructor More...

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

void	setOffset (CoordinateType offset) override
	set the offset of the model More...

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

CoordinateType	getCenter () const override
	get the center of the BiGaussian 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=default
	destructor More...

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...

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...

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 BiGaussModel object (function 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 &key_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_

Math::BasicStatistics	statistics1_

Math::BasicStatistics	statistics2_

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

BiGaussian distribution approximated using linear interpolation.

Asymmetric distribution realized via two normal distributions with different variances combined at the mean.

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, this also separates both halves of the model.
statistics:variance1	float	1.0	Variance of the first gaussian, used for the lower half of the model.
statistics:variance2	float	1.0	Variance of the second gaussian, used for the upper half of the model.

Note:

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

Member Typedef Documentation

◆ CoordinateType

typedef InterpolationModel::CoordinateType CoordinateType

Constructor & Destructor Documentation

◆ BiGaussModel() [1/2]

BiGaussModel ( )

Default constructor.

◆ BiGaussModel() [2/2]

BiGaussModel ( const BiGaussModel & source )

copy constructor

◆ ~BiGaussModel()

~BiGaussModel ( )

override

destructor

Member Function Documentation

◆ create()

static BaseModel<1>* create ( )

inlinestatic

create new BiGaussModel object (function needed by Factory)

◆ getCenter()

CoordinateType getCenter ( ) const

overridevirtual

get the center of the BiGaussian 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 BiGaussModel& operator= ( const BiGaussModel & source )

virtual

assignment operator

◆ setOffset()

void setOffset ( CoordinateType offset )

overridevirtual

set the offset of the model

The whole model will be shifted to the new 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

◆ max_

CoordinateType max_

protected

◆ min_

CoordinateType min_

protected

◆ statistics1_

Math::BasicStatistics statistics1_

protected

◆ statistics2_

Math::BasicStatistics statistics2_

protected

Public Types

Public Member Functions

Static Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Member Typedef Documentation

◆ CoordinateType

Constructor & Destructor Documentation

◆ BiGaussModel() [1/2]

◆ BiGaussModel() [2/2]

◆ ~BiGaussModel()

Member Function Documentation

◆ create()

◆ getCenter()

◆ getProductName()

◆ operator=()

◆ setOffset()

◆ setSamples()

◆ updateMembers_()

Member Data Documentation

◆ max_

◆ min_

◆ statistics1_

◆ statistics2_