Abstract class for 1D-models that are approximated using linear interpolation. More...

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

Inheritance diagram for InterpolationModel:

Public Types
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
	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...

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

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

virtual CoordinateType	getCenter () const
	"center" of the model, particular definition (depends on the derived model) More...

virtual void	setSamples ()
	set sample/supporting points of interpolation wrt params. 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...

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 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
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...

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

Detailed Description

Abstract class for 1D-models that are approximated using linear interpolation.

Model wrapping LinearInterpolation for speed-up in calculation of predicted intensities Derived classes have to implement setSamples()

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

Note:

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

Member Typedef Documentation

◆ CoordinateType

typedef double CoordinateType

◆ IntensityType

typedef double IntensityType

◆ LinearInterpolation

typedef Math::LinearInterpolation<double> LinearInterpolation

◆ PositionType

typedef DPosition<1> PositionType

Constructor & Destructor Documentation

◆ InterpolationModel() [1/2]

InterpolationModel ( )

inline

Default constructor.

◆ InterpolationModel() [2/2]

InterpolationModel ( const InterpolationModel & source )

inline

copy constructor

◆ ~InterpolationModel()

~InterpolationModel ( )

inlineoverride

destructor

Member Function Documentation

◆ getCenter()

virtual CoordinateType getCenter ( ) const

inlinevirtual

"center" of the model, particular definition (depends on the derived model)

Reimplemented in IsotopeModel, ExtendedIsotopeModel, EGHModel, BiGaussModel, GaussModel, and EmgModel.

◆ getIntensity() [1/2]

IntensityType getIntensity ( const PositionType & pos ) const

inlineoverride

access model predicted intensity at position pos

Referenced by MaxLikeliFitter1D::fitOffset_().

◆ getIntensity() [2/2]

IntensityType getIntensity ( CoordinateType coord ) const

inline

access model predicted intensity at position pos

◆ getInterpolation()

const LinearInterpolation& getInterpolation ( ) const

inline

Returns the interpolation class.

Referenced by MaxLikeliFitter1D::fitOffset_().

◆ getSamples()

void getSamples ( SamplesType & cont ) const

inlineoverridevirtual

get reasonable set of samples from the model (i.e. for printing)

Implements BaseModel< 1 >.

◆ getScalingFactor()

CoordinateType getScalingFactor ( ) const

inline

get the scaling for the model

A scaling factor of scaling means that the area under the model equals scaling. Default is 1.

◆ operator=()

virtual InterpolationModel& operator= ( const InterpolationModel & source )

inlinevirtual

assignment operator

References InterpolationModel::interpolation_, InterpolationModel::interpolation_step_, BaseModel< D >::operator=(), and InterpolationModel::scaling_.

◆ setInterpolationStep()

void setInterpolationStep ( CoordinateType interpolation_step )

inline

Set the interpolation step for the linear interpolation of the model.

For setting to take affect, call setSamples().

◆ setOffset()

virtual void setOffset ( CoordinateType offset )

inlinevirtual

set the offset of the model

The whole model will be shifted to the new offset without being recomputed all over. Setting takes affect immediately.

Reimplemented in IsotopeModel, ExtendedIsotopeModel, EGHModel, BiGaussModel, GaussModel, and EmgModel.

Referenced by MaxLikeliFitter1D::fitOffset_().

◆ setSamples()

virtual void setSamples ( )

inlinevirtual

set sample/supporting points of interpolation wrt params.

Reimplemented in ExtendedIsotopeModel, EGHModel, BiGaussModel, GaussModel, and EmgModel.

◆ setScalingFactor()

void setScalingFactor ( CoordinateType scaling )

inline

◆ updateMembers_()

void updateMembers_ ( )

inlineoverrideprotectedvirtual

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.

Reimplemented in IsotopeModel.

References BaseModel< D >::updateMembers_().

Member Data Documentation

◆ interpolation_

LinearInterpolation interpolation_

protected

Referenced by InterpolationModel::operator=().

◆ interpolation_step_

CoordinateType interpolation_step_

protected

Referenced by InterpolationModel::operator=().

◆ scaling_

CoordinateType scaling_

protected

Referenced by InterpolationModel::operator=().

Public Types

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ CoordinateType

◆ IntensityType

◆ LinearInterpolation

◆ PositionType

Constructor & Destructor Documentation

◆ InterpolationModel() [1/2]

◆ InterpolationModel() [2/2]

◆ ~InterpolationModel()

Member Function Documentation

◆ getCenter()

◆ getIntensity() [1/2]

◆ getIntensity() [2/2]

◆ getInterpolation()

◆ getSamples()

◆ getScalingFactor()

◆ operator=()

◆ setInterpolationStep()

◆ setOffset()

◆ setSamples()

◆ setScalingFactor()

◆ updateMembers_()

Member Data Documentation

◆ interpolation_

◆ interpolation_step_

◆ scaling_