OpenMS
Normalizer Class Reference

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

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

Inheritance diagram for Normalizer:
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Collaboration diagram for Normalizer:
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Public Member Functions

 Normalizer ()
 default constructor More...
 
 ~Normalizer () override
 destructor More...
 
Normalizeroperator= (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...
 
DefaultParamHandleroperator= (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 ParamgetParameters () const
 Non-mutable access to the parameters. More...
 
const ParamgetDefaults () const
 Non-mutable access to the default parameters. More...
 
const StringgetName () 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< Stringsubsections_
 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:

NameTypeDefaultRestrictionsDescription
method stringto_one to_one, to_TICNormalize 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]

default constructor

◆ ~Normalizer()

~Normalizer ( )
override

destructor

◆ Normalizer() [2/2]

Normalizer ( const Normalizer source)

copy constructor

Member Function Documentation

◆ filterPeakMap()

void filterPeakMap ( PeakMap exp) const

◆ filterPeakSpectrum()

void filterPeakSpectrum ( PeakSpectrum spectrum) const

◆ filterSpectrum()

void filterSpectrum ( SpectrumType spectrum) const
inline

Workhorse of this class.

Parameters
spectrumInput/output spectrum containing peaks
Exceptions
Exception::InvalidValueif '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