Similarity score of Zhang. More...

#include <OpenMS/COMPARISON/ZhangSimilarityScore.h>

Inheritance diagram for ZhangSimilarityScore:

Collaboration diagram for ZhangSimilarityScore:

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

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

	~ZhangSimilarityScore () override
	destructor More...

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

double	operator() (const PeakSpectrum &spec1, const PeakSpectrum &spec2) const override
	function call operator, calculates the similarity More...

double	operator() (const PeakSpectrum &spec) const override
	calculates self similarity 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...

Protected Member Functions
double	getFactor_ (double mz_tolerance, double mz_difference, bool is_gaussian=false) const
	returns the factor associated with the m/z tolerance and m/z difference of the peaks More...

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...

Additional Inherited Members
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...

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 Zhang.

The details of the score can be found in: Z. Zhang, Prediction of Low-Energy Collision-Induced Dissociation Spectra of Peptides, Anal. Chem., 76 (14), 3908 - 3922, 2004

Parameters of this class are:

Name	Type	Default	Restrictions	Description
tolerance	float	0.2		defines the absolute (in Da) or relative (in ppm) tolerance
is_relative_tolerance	string	false	true, false	If set to true, the tolerance is interpreted as relative
use_linear_factor	string	false	true, false	if true, the intensities are weighted with the relative m/z difference
use_gaussian_factor	string	false	true, false	if true, the intensities are weighted with the relative m/z difference using a gaussian

Note:

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

Constructor & Destructor Documentation

◆ ZhangSimilarityScore() [1/2]

ZhangSimilarityScore ( )

default constructor

◆ ZhangSimilarityScore() [2/2]

ZhangSimilarityScore ( const ZhangSimilarityScore & source )

copy constructor

◆ ~ZhangSimilarityScore()

~ZhangSimilarityScore ( )

override

destructor

Member Function Documentation

◆ getFactor_()

double getFactor_	(	double	mz_tolerance,
		double	mz_difference,
		bool	is_gaussian = `false`
	)		const

protected

returns the factor associated with the m/z tolerance and m/z difference of the peaks

◆ operator()() [1/2]

double operator() ( const PeakSpectrum & a ) const

overridevirtual

calculates self similarity

Implements PeakSpectrumCompareFunctor.

◆ operator()() [2/2]

double operator()	(	const PeakSpectrum &	a,
		const PeakSpectrum &	b
	)		const

overridevirtual

function call operator, calculates the similarity

Implements PeakSpectrumCompareFunctor.

◆ operator=()

ZhangSimilarityScore& operator= ( const ZhangSimilarityScore & source )

assignment operator

Public Member Functions

Protected Member Functions

Additional Inherited Members