SpectrumAlignmentScore Class Reference

Similarity score via spectra alignment. More...

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

Inheritance diagram for SpectrumAlignmentScore:

Collaboration diagram for SpectrumAlignmentScore:

Public Member Functions
	SpectrumAlignmentScore ()
	default constructor More...
	SpectrumAlignmentScore (const SpectrumAlignmentScore &source)
	copy constructor More...
	~SpectrumAlignmentScore () override
	destructor More...
SpectrumAlignmentScore &	operator= (const SpectrumAlignmentScore &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...
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 &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 via spectra alignment.

This class implements a simple scoring based on the alignment of spectra. This alignment is implemented in the SpectrumAlignment class and performs a dynamic programming alignment of the peaks, minimizing the distances between the aligned peaks and maximizing the number of peak pairs.

The scoring is done via the simple formula score = sum / (sqrt(sum1 * sum2)). sum is the product of the intensities of the aligned peaks, with the given exponent (default is 2). sum1 and sum2 are the sum of the intensities squared for each peak of both spectra respectively.

A binned version of this scoring is implemented in the ZhangSimilarityScoring class.

Parameters of this class are:

Name	Type	Default	Restrictions	Description
tolerance	float	0.3		Defines the absolute (in Da) or relative (in ppm) tolerance
is_relative_tolerance	string	false	true, false	if true, the tolerance value is interpreted as ppm
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

SpectrumAlignmentScore() [1/2]

SpectrumAlignmentScore

(

)

default constructor

SpectrumAlignmentScore() [2/2]

SpectrumAlignmentScore

(

const SpectrumAlignmentScore &

source

)

copy constructor

~SpectrumAlignmentScore()

~SpectrumAlignmentScore ( )

override

destructor

Member Function Documentation

create()

static PeakSpectrumCompareFunctor* create ( )

inlinestatic

getProductName()

static const String getProductName ( )

inlinestatic

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=()

SpectrumAlignmentScore& operator=

(

const SpectrumAlignmentScore &

source

)

assignment operator