Sum of agreeing intensities for similarity measurement. More...

#include <OpenMS/COMPARISON/SPECTRA/BinnedSumAgreeingIntensities.h>

Inheritance diagram for BinnedSumAgreeingIntensities:

Collaboration diagram for BinnedSumAgreeingIntensities:

Public Member Functions
	BinnedSumAgreeingIntensities ()
	default constructor More...

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

	~BinnedSumAgreeingIntensities () override
	destructor More...

BinnedSumAgreeingIntensities &	operator= (const BinnedSumAgreeingIntensities &source)
	assignment operator More...

double	operator() (const BinnedSpectrum &spec1, const BinnedSpectrum &spec2) const override

double	operator() (const BinnedSpectrum &spec) const override
	function call operator, calculates self similarity More...

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

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

	~BinnedSpectrumCompareFunctor () override
	destructor More...

BinnedSpectrumCompareFunctor &	operator= (const BinnedSpectrumCompareFunctor &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 BinnedSpectrumCompareFunctor *	create ()

static const String	getProductName ()
	get the identifier for this DefaultParamHandler More...

Static Public Member Functions inherited from BinnedSpectrumCompareFunctor
static void	registerChildren ()
	registers all derived products More...

static const String	getProductName ()
	get the identifier for a DefaultParamHandler 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
double	precursor_mass_tolerance_

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

Sum of agreeing intensities for similarity measurement.

Transformation and other factors of the peptide mass spectrometry pairwise peak-list comparison process Witold E Wolski , Maciej Lalowski* , Peter Martus* , Ralf Herwig* , Patrick Giavalisco , Johan Gobom , Albert Sickmann , Hans Lehrach and Knut Reinert* BMC Bioinformatics 2005, 6:285 doi:10.1186/1471-2105-6-285

Bins whose intensity differences are larger than their average intensity receive a weight of zero.

Prefect agreement results in a similarity score of 1.0

Parameters of this class are:

Name	Type	Default	Restrictions	Description

Note:

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

See also: BinnedSpectrumCompareFunctor; BinnedSpectrum

Constructor & Destructor Documentation

◆ BinnedSumAgreeingIntensities() [1/2]

BinnedSumAgreeingIntensities ( )

default constructor

◆ BinnedSumAgreeingIntensities() [2/2]

BinnedSumAgreeingIntensities ( const BinnedSumAgreeingIntensities & source )

copy constructor

◆ ~BinnedSumAgreeingIntensities()

~BinnedSumAgreeingIntensities ( )

override

destructor

Member Function Documentation

◆ create()

static BinnedSpectrumCompareFunctor* create ( )

inlinestatic

◆ getProductName()

static const String getProductName ( )

inlinestatic

get the identifier for this DefaultParamHandler

◆ operator()() [1/2]

double operator() ( const BinnedSpectrum & spec ) const

overridevirtual

function call operator, calculates self similarity

Implements BinnedSpectrumCompareFunctor.

◆ operator()() [2/2]

double operator()	(	const BinnedSpectrum &	spec1,
		const BinnedSpectrum &	spec2
	)		const

overridevirtual

function call operator, calculates the similarity of the given arguments

Parameters

spec1	First spectrum given as a binned representation
spec2	Second spectrum given as a binned representation

Exceptions

IncompatibleBinning is thrown if the binning of the two input spectra are not the same

Implements BinnedSpectrumCompareFunctor.

◆ operator=()

BinnedSumAgreeingIntensities& operator= ( const BinnedSumAgreeingIntensities & source )

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

◆ precursor_mass_tolerance_

double precursor_mass_tolerance_

protected

Public Member Functions

Static Public Member Functions

Protected Member Functions

Protected Attributes