BernNorm Class Reference

BernNorm scales the peaks by ranking them and then scaling them according to rank. More...

#include <OpenMS/FILTERING/TRANSFORMERS/BernNorm.h>

Inheritance diagram for BernNorm:

Public Member Functions
	BernNorm ()
	default constructor More...
	BernNorm (const BernNorm &source)
	copy constructor More...
virtual	~BernNorm ()
	destructor More...
BernNorm &	operator= (const BernNorm &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...
double	c1_
double	c2_
double	th_
template<typename SpectrumType >
void	filterSpectrum (SpectrumType &spectrum)
void	filterPeakSpectrum (PeakSpectrum &spectrum)
void	filterPeakMap (PeakMap &exp)

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

BernNorm scales the peaks by ranking them and then scaling them according to rank.

For exact formula look in Bioinformatics, Aug 2004; 20: i49 - i54

Improvement:

read paper and try to confirm implementation (Andreas)

Parameters of this class are:

Name	Type	Default	Restrictions	Description
C1	float	28		C1 value of the normalization.
C2	float	400		C2 value of the normalization.
threshold	float	0.1		Threshold of the Bern et al. normalization.

Note:

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

Constructor & Destructor Documentation

BernNorm() [1/2]

BernNorm

(

)

default constructor

BernNorm() [2/2]

BernNorm

(

const BernNorm &

source

)

copy constructor

~BernNorm()

virtual ~BernNorm ( )

virtual

destructor

Member Function Documentation

filterPeakMap()

void filterPeakMap

(

PeakMap &

exp

)

filterPeakSpectrum()

void filterPeakSpectrum

(

PeakSpectrum &

spectrum

)

filterSpectrum()

void filterSpectrum ( SpectrumType &  spectrum )

inline

References MSSpectrum::sortByPosition().

operator=()

BernNorm& operator=

(

const BernNorm &

source

)

assignment operator

Member Data Documentation

c1_

double c1_

private

c2_

double c2_

private

th_

double th_

private