Abstract base class for all 1D-dimensional model fitter. More...

#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/Fitter1D.h>

Inheritance diagram for Fitter1D:

Collaboration diagram for Fitter1D:

Public Types
typedef IsotopeCluster::IndexSet	IndexSet
	IndexSet. More...

typedef IsotopeCluster::ChargedIndexSet	ChargedIndexSet
	IndexSet with charge information. More...

typedef Feature::CoordinateType	CoordinateType
	Single coordinate. More...

typedef Feature::QualityType	QualityType
	Quality of a feature. More...

typedef Peak1D	PeakType
	Peak type data point type. More...

typedef std::vector< PeakType >	RawDataArrayType
	Peak type data container type using for the temporary storage of the input data. More...

typedef RawDataArrayType::iterator	PeakIterator
	Peak type data iterator. More...

Public Types inherited from FeatureFinderDefs
enum	Flag { UNUSED , USED }
	Flags that indicate if a peak is already used in a feature. More...

typedef IsotopeCluster::IndexPair	IndexPair
	Index to peak consisting of two UInts (scan index / peak index) More...

typedef IsotopeCluster::ChargedIndexSet	ChargedIndexSet
	Index to peak consisting of two UInts (scan index / peak index) with charge information. More...

typedef IsotopeCluster::IndexSet	IndexSet
	A set of peak indices. More...

Public Member Functions
	Fitter1D ()
	Default constructor. More...

	Fitter1D (const Fitter1D &source)
	copy constructor More...

	~Fitter1D () override
	destructor More...

virtual Fitter1D &	operator= (const Fitter1D &source)
	assignment operator More...

virtual QualityType	fit1d (const RawDataArrayType &, std::unique_ptr< InterpolationModel > &)
	return interpolation model 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 void	registerChildren ()
	register all derived classes here 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 DefaultParamHandler
void	defaultsToParam_ ()
	Updates the parameters after the defaults have been set in the constructor. More...

Protected Attributes
CoordinateType	tolerance_stdev_box_
	standard derivation in bounding box More...

Math::BasicStatistics	statistics_
	basic statistics More...

CoordinateType	interpolation_step_
	interpolation step size 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

Abstract base class for all 1D-dimensional model fitter.

Every derived class has to implement the static functions "T* create()" and "const String getProductName()" (see DefaultParamHandler for details)

Parameters of this class are:

Name	Type	Default	Description
interpolation_step	float	0.2	Sampling rate for the interpolation of the model function.
tolerance_stdev_bounding_box	float	3.0	Bounding box has range [minimim of data, maximum of data] enlarged by tolerance_stdev_bounding_box times the standard deviation of the data.
statistics:mean	float	1.0	Centroid position of the model.
statistics:variance	float	1.0	The variance of the model.

Note:

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

Member Typedef Documentation

◆ ChargedIndexSet

typedef IsotopeCluster::ChargedIndexSet ChargedIndexSet

IndexSet with charge information.

◆ CoordinateType

typedef Feature::CoordinateType CoordinateType

Single coordinate.

◆ IndexSet

typedef IsotopeCluster::IndexSet IndexSet

IndexSet.

◆ PeakIterator

typedef RawDataArrayType::iterator PeakIterator

Peak type data iterator.

◆ PeakType

typedef Peak1D PeakType

Peak type data point type.

◆ QualityType

typedef Feature::QualityType QualityType

Quality of a feature.

◆ RawDataArrayType

typedef std::vector<PeakType> RawDataArrayType

Peak type data container type using for the temporary storage of the input data.

Constructor & Destructor Documentation

◆ Fitter1D() [1/2]

Fitter1D ( )

Default constructor.

◆ Fitter1D() [2/2]

Fitter1D ( const Fitter1D & source )

copy constructor

◆ ~Fitter1D()

~Fitter1D ( )

override

destructor

Member Function Documentation

◆ fit1d()

virtual QualityType fit1d	(	const RawDataArrayType &	,
		std::unique_ptr< InterpolationModel > &
	)

virtual

return interpolation model

Reimplemented in IsotopeFitter1D, GaussFitter1D, ExtendedIsotopeFitter1D, EmgFitter1D, BiGaussFitter1D, and EGHFitter1D.

◆ operator=()

virtual Fitter1D& operator= ( const Fitter1D & source )

virtual

assignment operator

Referenced by LevMarqFitter1D::operator=(), and MaxLikeliFitter1D::operator=().

◆ registerChildren()

static void registerChildren ( )

static

register all derived classes here

◆ 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.

Reimplemented in MaxLikeliFitter1D, LevMarqFitter1D, IsotopeFitter1D, and GaussFitter1D.

Referenced by MaxLikeliFitter1D::updateMembers_().

Member Data Documentation

◆ interpolation_step_

CoordinateType interpolation_step_

protected

interpolation step size

◆ statistics_

Math::BasicStatistics statistics_

protected

basic statistics

◆ tolerance_stdev_box_

CoordinateType tolerance_stdev_box_

protected

standard derivation in bounding box

Public Types

Public Member Functions

Static Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Member Typedef Documentation

◆ ChargedIndexSet

◆ CoordinateType

◆ IndexSet

◆ PeakIterator

◆ PeakType

◆ QualityType

◆ RawDataArrayType

Constructor & Destructor Documentation

◆ Fitter1D() [1/2]

◆ Fitter1D() [2/2]

◆ ~Fitter1D()

Member Function Documentation

◆ fit1d()

◆ operator=()

◆ registerChildren()

◆ updateMembers_()

Member Data Documentation

◆ interpolation_step_

◆ statistics_

◆ tolerance_stdev_box_