Extended isotope distribution fitter (1-dim.) approximated using linear interpolation. More...

#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/ExtendedIsotopeFitter1D.h>

Inheritance diagram for ExtendedIsotopeFitter1D:

Collaboration diagram for ExtendedIsotopeFitter1D:

Public Member Functions
	ExtendedIsotopeFitter1D ()
	Default constructor. More...

	ExtendedIsotopeFitter1D (const ExtendedIsotopeFitter1D &source)
	copy constructor More...

	~ExtendedIsotopeFitter1D () override
	destructor More...

virtual ExtendedIsotopeFitter1D &	operator= (const ExtendedIsotopeFitter1D &source)
	assignment operator More...

QualityType	fit1d (const RawDataArrayType &range, std::unique_ptr< InterpolationModel > &model) override
	return interpolation model More...

Public Member Functions inherited from MaxLikeliFitter1D
	MaxLikeliFitter1D ()
	default constructor More...

	MaxLikeliFitter1D (const MaxLikeliFitter1D &source)
	copy constructor More...

	~MaxLikeliFitter1D () override
	destructor More...

virtual MaxLikeliFitter1D &	operator= (const MaxLikeliFitter1D &source)
	assignment operator More...

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

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

	~Fitter1D () override
	destructor More...

virtual Fitter1D &	operator= (const Fitter1D &source)
	assignment operator 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 Fitter1D *	create ()
	create new ExtendedIsotopeFitter1D object (function needed by Factory) More...

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

Static Public Member Functions inherited from Fitter1D
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 MaxLikeliFitter1D
QualityType	fitOffset_ (std::unique_ptr< InterpolationModel > &model, const RawDataArrayType &set, const CoordinateType stdev1, const CoordinateType stdev2, const CoordinateType offset_step) const
	fit an offset on the basis of the Pearson correlation coefficient More...

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	charge_
	isotope charge More...

CoordinateType	isotope_stdev_
	standard derivation in isotope More...

CoordinateType	monoisotopic_mz_
	monoisotopic mass More...

Int	max_isotope_
	maximum isotopic rank to be considered More...

Protected Attributes inherited from Fitter1D
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...

Additional Inherited Members
Public Types inherited from Fitter1D
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...

Detailed Description

Extended isotope distribution fitter (1-dim.) approximated using linear interpolation.

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.
charge	int	1	Charge state of the model.
statistics:mean	float	1.0	Centroid position of the model.
statistics:variance	float	1.0	Variance of the model.
isotope:stdev	float	0.1	Standard deviation of gaussian applied to the averagine isotopic pattern to simulate the inaccuracy of the mass spectrometer.
isotope:monoisotopic_mz	float	1.0	Monoisotopic m/z of the model.
isotope:maximum	int	100	Maximum isotopic rank to be considered.

Note:

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

Constructor & Destructor Documentation

◆ ExtendedIsotopeFitter1D() [1/2]

ExtendedIsotopeFitter1D ( )

Default constructor.

◆ ExtendedIsotopeFitter1D() [2/2]

ExtendedIsotopeFitter1D ( const ExtendedIsotopeFitter1D & source )

copy constructor

◆ ~ExtendedIsotopeFitter1D()

~ExtendedIsotopeFitter1D ( )

override

destructor

Member Function Documentation

◆ create()

static Fitter1D* create ( )

inlinestatic

create new ExtendedIsotopeFitter1D object (function needed by Factory)

◆ fit1d()

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

overridevirtual

return interpolation model

Reimplemented from Fitter1D.

◆ getProductName()

static const String getProductName ( )

inlinestatic

name of the model (needed by Factory)

◆ operator=()

virtual ExtendedIsotopeFitter1D& operator= ( const ExtendedIsotopeFitter1D & source )

virtual

assignment operator

◆ 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

◆ charge_

CoordinateType charge_

protected

isotope charge

◆ isotope_stdev_

CoordinateType isotope_stdev_

protected

standard derivation in isotope

◆ max_isotope_

Int max_isotope_

protected

maximum isotopic rank to be considered

◆ monoisotopic_mz_

CoordinateType monoisotopic_mz_

protected

monoisotopic mass

Public Member Functions

Static Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ ExtendedIsotopeFitter1D() [1/2]

◆ ExtendedIsotopeFitter1D() [2/2]

◆ ~ExtendedIsotopeFitter1D()

Member Function Documentation

◆ create()

◆ fit1d()

◆ getProductName()

◆ operator=()

◆ updateMembers_()

Member Data Documentation

◆ charge_

◆ isotope_stdev_

◆ max_isotope_

◆ monoisotopic_mz_