Similarity score of SpectraST. More...

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

Inheritance diagram for SpectraSTSimilarityScore:

Collaboration diagram for SpectraSTSimilarityScore:

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

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

	~SpectraSTSimilarityScore () override
	destructor More...

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

double	operator() (const PeakSpectrum &spec1, const PeakSpectrum &spec2) const override
	: calculates the dot product of the two spectra More...

double	operator() (const BinnedSpectrum &bin1, const BinnedSpectrum &bin2) const
	: calculates the dot product of the two spectra More...

double	operator() (const PeakSpectrum &spec) const override
	: calculates the dot product of itself More...

bool	preprocess (PeakSpectrum &spec, float remove_peak_intensity_threshold=2.01, UInt cut_peaks_below=1000, Size min_peak_number=5, Size max_peak_number=150)
	Preprocesses the spectrum. More...

BinnedSpectrum	transform (const PeakSpectrum &spec)
	spectrum is transformed into a binned spectrum with bin size 1 and spread 1 and the intensities are normalized. More...

double	dot_bias (const BinnedSpectrum &bin1, const BinnedSpectrum &bin2, double dot_product=-1) const
	Calculates how much of the dot product is dominated by a few peaks. More...

double	delta_D (double top_hit, double runner_up)
	calculates the normalized distance between top_hit and runner_up. More...

double	compute_F (double dot_product, double delta_D, double dot_bias)
	computes the overall all score 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...

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 ()
	Reimplemented from PeakSpectrumCompareFunctor. More...

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 &key_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 of SpectraST.

Unlike the other similarity scores this score is used for matching a spectrum against a whole library, although the dot product seems to be an effective method for scoring on its own. For calculating the SpectraST score, first preprocess the spectra if not already done. Transform them and calculate the dot product and the dot bias. Afterwards get the best two hits and calculate delta_D. Now for every spectrum from the library you can calculate the final score.

The details of the score can be found in: H. Lam et al., Development and validation of a spectral library searching method for peptide identification from MS/MS, Proteomics, 7 , 655-667, 2007

Constructor & Destructor Documentation

◆ SpectraSTSimilarityScore() [1/2]

SpectraSTSimilarityScore ( )

default constructor

◆ SpectraSTSimilarityScore() [2/2]

SpectraSTSimilarityScore ( const SpectraSTSimilarityScore & source )

copy constructor

◆ ~SpectraSTSimilarityScore()

~SpectraSTSimilarityScore ( )

override

destructor

Member Function Documentation

◆ compute_F()

double compute_F	(	double	dot_product,
		double	delta_D,
		double	dot_bias
	)

computes the overall all score

Parameters

dot_product	of a match
delta_D	should be calculated after all dot products for a unidentified spectrum are computed
dot_bias

Returns: the SpectraST similarity score

◆ create()

static PeakSpectrumCompareFunctor* create ( )

inlinestatic

◆ delta_D()

double delta_D	(	double	top_hit,
		double	runner_up
	)

calculates the normalized distance between top_hit and runner_up.

Parameters

top_hit	is the best score for a given match.
runner_up	a match with a worse score than top_hit, e.g. the second best score.

Returns: normalized distance

Exceptions

DividedByZero exception if top_hit is 0.

Note: Range of the dot products is between 0 and 1.

◆ dot_bias()

double dot_bias	(	const BinnedSpectrum &	bin1,
		const BinnedSpectrum &	bin2,
		double	dot_product = `-1`
	)		const

Calculates how much of the dot product is dominated by a few peaks.

Parameters

dot_product	if -1 this value will be calculated as well.
bin1	first spectrum in binned representation
bin2	second spectrum in binned representation

◆ getProductName()

static const String getProductName ( )

inlinestatic

Reimplemented from PeakSpectrumCompareFunctor.

◆ operator()() [1/3]

double operator()	(	const BinnedSpectrum &	bin1,
		const BinnedSpectrum &	bin2
	)		const

: calculates the dot product of the two spectra

◆ operator()() [2/3]

double operator() ( const PeakSpectrum & spec ) const

overridevirtual

: calculates the dot product of itself

Implements PeakSpectrumCompareFunctor.

◆ operator()() [3/3]

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

overridevirtual

: calculates the dot product of the two spectra

Implements PeakSpectrumCompareFunctor.

◆ operator=()

SpectraSTSimilarityScore& operator= ( const SpectraSTSimilarityScore & source )

assignment operator

◆ preprocess()

bool preprocess	(	PeakSpectrum &	spec,
		float	remove_peak_intensity_threshold = `2.01`,
		UInt	cut_peaks_below = `1000`,
		Size	min_peak_number = `5`,
		Size	max_peak_number = `150`
	)

Preprocesses the spectrum.

The preprocessing removes peak below a intensity threshold, reject spectra that does not have enough peaks, and cuts peaks exceeding the max_peak_number most intense peaks.

Returns: true if spectrum passes filtering

◆ transform()

BinnedSpectrum transform ( const PeakSpectrum & spec )

spectrum is transformed into a binned spectrum with bin size 1 and spread 1 and the intensities are normalized.

Public Member Functions

Static Public Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ SpectraSTSimilarityScore() [1/2]

◆ SpectraSTSimilarityScore() [2/2]

◆ ~SpectraSTSimilarityScore()

Member Function Documentation

◆ compute_F()

◆ create()

◆ delta_D()

◆ dot_bias()

◆ getProductName()

◆ operator()() [1/3]

◆ operator()() [2/3]

◆ operator()() [3/3]

◆ operator=()

◆ preprocess()

◆ transform()