make a PeakAlignment of two PeakSpectra More...

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

Inheritance diagram for PeakAlignment:

Collaboration diagram for PeakAlignment:

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

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

	~PeakAlignment () override
	destructor More...

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

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

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

std::vector< std::pair< Size, Size > >	getAlignmentTraceback (const PeakSpectrum &spec1, const PeakSpectrum &spec2) const
	make alignment and get the traceback 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 ()
	get the identifier for this DefaultParamHandler 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...

Private Member Functions
double	peakPairScore_ (double &pos1, double &intens1, double &pos2, double &intens2, const double &sigma) const
	calculates the score for aligning two peaks 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

make a PeakAlignment of two PeakSpectra

The alignment is done according to the Needleman-Wunsch Algorithm (local alignment considering gaps).

Parameters of this class are:

Name	Type	Default	Description
epsilon	float	0.2	defines the absolute error of the mass spectrometer
normalized	int	1	is set 1 if the similarity-measurement is normalized to the range [0,1]
heuristic_level	int	0	set 0 means no heuristic is applied otherwise the given value is interpreted as unsigned integer, the number of strongest peaks considered for heurisitcs - in those sets of peaks has to be at least one match to conduct comparison
precursor_mass_tolerance	float	3.0	Mass tolerance of the precursor peak, defines the distance of two PrecursorPeaks for which they are supposed to be from different peptides

Note:

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

Constructor & Destructor Documentation

◆ PeakAlignment() [1/2]

PeakAlignment ( )

default constructor

◆ PeakAlignment() [2/2]

PeakAlignment ( const PeakAlignment & source )

copy constructor

◆ ~PeakAlignment()

~PeakAlignment ( )

override

destructor

Member Function Documentation

◆ create()

static PeakSpectrumCompareFunctor* create ( )

inlinestatic

◆ getAlignmentTraceback()

std::vector<std::pair<Size, Size> > getAlignmentTraceback	(	const PeakSpectrum &	spec1,
		const PeakSpectrum &	spec2
	)		const

make alignment and get the traceback

◆ getProductName()

static const String getProductName ( )

inlinestatic

get the identifier for this DefaultParamHandler

◆ operator()() [1/2]

double operator() ( const PeakSpectrum & spec ) const

overridevirtual

function call operator, calculates self similarity

Implements PeakSpectrumCompareFunctor.

◆ operator()() [2/2]

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

overridevirtual

function call operator, calculates the similarity of the given arguments

Parameters

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

Implements PeakSpectrumCompareFunctor.

◆ operator=()

PeakAlignment& operator= ( const PeakAlignment & source )

assignment operator

◆ peakPairScore_()

double peakPairScore_	(	double &	pos1,
		double &	intens1,
		double &	pos2,
		double &	intens2,
		const double &	sigma
	)		const

private

calculates the score for aligning two peaks

Public Member Functions

Static Public Member Functions

Private Member Functions

Additional Inherited Members