ParentPeakMower Class Reference

ParentPeakMower gets rid of high peaks that could stem from unfragmented precursor ions. More...

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

Inheritance diagram for ParentPeakMower:

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

Private Attributes
Size	default_charge_
bool	clean_all_charge_states_
bool	consider_NH3_loss_
bool	consider_H2O_loss_
double	window_size_
bool	reduce_by_factor_
double	factor_
bool	set_to_zero_

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

ParentPeakMower gets rid of high peaks that could stem from unfragmented precursor ions.

Parameters of this class are:

Name	Type	Default	Restrictions	Description
window_size	float	2		The size of the m/z window where the peaks are removed, +/- window_size.
default_charge	int	2		If the precursor has no charge set, the default charge is assumed.
clean_all_charge_states	int	1		Set to 1 if precursor ions of all possible charge states should be removed.
consider_NH3_loss	int	1		Whether NH3 loss peaks from the precursor should be removed.
consider_H2O_loss	int	1		Whether H2O loss peaks from the precursor should be removed.
reduce_by_factor	int	0		Reduce the intensities of the precursor and related ions by a given factor (set 'set_to_zero' to 0).
factor	float	1000		Factor which is used to reduce the intensities if 'reduce_by_factor' is selected.
set_to_zero	int	1		Reduce the intensities of the precursor and related ions to zero.

Note:

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

Constructor & Destructor Documentation

ParentPeakMower() [1/2]

ParentPeakMower

(

)

default constructor

ParentPeakMower() [2/2]

ParentPeakMower

(

const ParentPeakMower &

source

)

copy constructor

~ParentPeakMower()

virtual ~ParentPeakMower ( )

virtual

destructor

Member Function Documentation

filterPeakMap()

void filterPeakMap

(

PeakMap &

exp

)

filterPeakSpectrum()

void filterPeakSpectrum

(

PeakSpectrum &

spectrum

)

filterSpectrum()

void filterSpectrum ( SpectrumType &  spectrum )

inline

References MSSpectrum::getMSLevel(), and SpectrumSettings::getPrecursors().

operator=()

ParentPeakMower& operator=

(

const ParentPeakMower &

source

)

assignment operator

Member Data Documentation

clean_all_charge_states_

bool clean_all_charge_states_

private

consider_H2O_loss_

bool consider_H2O_loss_

private

consider_NH3_loss_

bool consider_NH3_loss_

private

default_charge_

Size default_charge_

private

factor_

double factor_

private

reduce_by_factor_

bool reduce_by_factor_

private

set_to_zero_

bool set_to_zero_

private

window_size_

double window_size_

private