Similarity score based of Stein & Scott. More...

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

Inheritance diagram for SteinScottImproveScore:

Collaboration diagram for SteinScottImproveScore:

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

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

	~SteinScottImproveScore () override
	destructor More...

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

double	operator() (const PeakSpectrum &spec1, const PeakSpectrum &spec2) const override
	Similarity pairwise score. More...

double	operator() (const PeakSpectrum &spec) const override
	Similarity pairwise score itself. More...

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

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

	~PeakSpectrumCompareFunctor () override
	destructor More...

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

static const String	getProductName ()

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

static const String	getProductName ()

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...

Additional Inherited Members
Protected Member Functions inherited from DefaultParamHandler
virtual void	updateMembers_ ()
	This method is used to update extra member variables at the end of the setParameters() method. More...

void	defaultsToParam_ ()
	Updates the parameters after the defaults have been set in the constructor. 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

Similarity score based of Stein & Scott.

This is a pairwise based score function. The spectrum contains peaks, and each peak can be defined by two values (mz and the intensity). The score function takes the sum of the product of the peak intensities from Spectrum 1 and Spectrum 2, only if the mz-ratio distance between the two spectra is smaller than a given window size. In the default status, the window size is (accuracy of the mass spectrometer). This sum is normalised by dividing it with a distance function. sqrt(sum of the Intensity of square Spectrum1 sum of the Intensity of square Spectrum2). This is all based on SteinScott score. To distinguish the close from the distant spectra an additional term is calculated. It denotes the expected value of both Spectra under the random placement of all peaks, within the given mass-to-charge range. The probability that two peaks with randomized intensity values lie within two epsilon of each other is a constant. This constant is proportional to epsilon. So the additional term is the sum over all peaks of Spectrum 1 and Spectrum 2 of the products of their intensities multiplied with the constant.

The details of the score can be found in: Signal Maps for Mass Spectrometry-based Comparative Proteomics Amol Prakash, Parag Mallick , Jeffrey Whiteaker, Heidi Zhang, Amanda Paulovich, Mark Flory, Hookeun Lee, Ruedi Aebersold, and Benno Schwikowski

Parameters of this class are:

Name	Type	Default	Restrictions	Description
tolerance	float	0.2		defines the absolute error of the mass spectrometer
threshold	float	0.2		if the calculated score is smaller than the threshold, a zero is given back

Note:

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

Constructor & Destructor Documentation

◆ SteinScottImproveScore() [1/2]

SteinScottImproveScore ( )

default constructor

◆ SteinScottImproveScore() [2/2]

SteinScottImproveScore ( const SteinScottImproveScore & source )

copy constructor

◆ ~SteinScottImproveScore()

~SteinScottImproveScore ( )

override

destructor

Member Function Documentation

◆ create()

static PeakSpectrumCompareFunctor* create ( )

inlinestatic

◆ getProductName()

static const String getProductName ( )

inlinestatic

◆ operator()() [1/2]

double operator() ( const PeakSpectrum & spec ) const

overridevirtual

Similarity pairwise score itself.

This function return the similarity score of itself based on SteinScott.

Implements PeakSpectrumCompareFunctor.

◆ operator()() [2/2]

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

overridevirtual

Similarity pairwise score.

This function return the similarity score of two Spectra based on SteinScott.

Implements PeakSpectrumCompareFunctor.

◆ operator=()

SteinScottImproveScore& operator= ( const SteinScottImproveScore & source )

assignment operator

Public Member Functions

Static Public Member Functions

Additional Inherited Members