make a PeakAlignment of two PeakSpectra More...

#include <OpenMS/COMPARISON/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...

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...

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
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 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

◆ getAlignmentTraceback()

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

make alignment and get the traceback

◆ 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

Private Member Functions

Additional Inherited Members