Normalizes the peak intensities spectrum-wise. More...

#include <OpenMS/PROCESSING/SCALING/Normalizer.h>

Inheritance diagram for Normalizer:

Collaboration diagram for Normalizer:

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

	~Normalizer () override
	destructor More...

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

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

template<typename SpectrumType >
void	filterSpectrum (SpectrumType &spectrum) const
	Workhorse of this class. More...

void	filterPeakSpectrum (PeakSpectrum &spectrum) const

void	filterPeakMap (PeakMap &exp) const

void	updateMembers_ () override
	This method is used to update extra member variables at the end of the setParameters() method. 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 Attributes
String	method_

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
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

Normalizes the peak intensities spectrum-wise.

Either to a total intensity-sum of one (i.e. to total-ion-count; TIC) or to a maximum intensity of one.

Parameters of this class are:

Name	Type	Default	Restrictions	Description
method	string	to_one	to_one, to_TIC	Normalize via dividing by TIC ('to_TIC') per spectrum (i.e. all peaks sum to 1) or normalize to max. intensity to one ('to_one') per spectrum.

Note:

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

Constructor & Destructor Documentation

◆ Normalizer() [1/2]

Normalizer ( )

default constructor

◆ ~Normalizer()

~Normalizer ( )

override

destructor

◆ Normalizer() [2/2]

Normalizer ( const Normalizer & source )

copy constructor

Member Function Documentation

◆ filterPeakMap()

void filterPeakMap ( PeakMap & exp ) const

Referenced by NucleicAcidSearchEngine::preprocessSpectra_().

◆ filterPeakSpectrum()

void filterPeakSpectrum ( PeakSpectrum & spectrum ) const

◆ filterSpectrum()

void filterSpectrum ( SpectrumType & spectrum ) const

inline

Workhorse of this class.

Parameters

spectrum Input/output spectrum containing peaks

Exceptions

Exception::InvalidValue if 'method_' has unknown value

◆ operator=()

Normalizer& operator= ( const Normalizer & source )

assignment operator

◆ updateMembers_()

void updateMembers_ ( )

overridevirtual

This method is used to update extra member variables at the end of the setParameters() method.

Also call it at the end of the derived classes' copy constructor and assignment operator.

The default implementation is empty.

Reimplemented from DefaultParamHandler.

Member Data Documentation

◆ method_

String method_

private

Public Member Functions

Private Attributes

Additional Inherited Members