OpenMS  2.8.0
Public Member Functions | Private Attributes | List of all members
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:
[legend]
Collaboration diagram for ParentPeakMower:
[legend]

Public Member Functions

 ParentPeakMower ()
 default constructor More...
 
 ParentPeakMower (const ParentPeakMower &source)
 copy constructor More...
 
 ~ParentPeakMower () override
 destructor More...
 
ParentPeakMoweroperator= (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 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

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

- 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< 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

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

Parameters of this class are:

NameTypeDefaultRestrictionsDescription
window_size float2.0  The size of the m/z window where the peaks are removed, +/- window_size.
default_charge int2  If the precursor has no charge set, the default charge is assumed.
clean_all_charge_states int1  Set to 1 if precursor ions of all possible charge states should be removed.
consider_NH3_loss int1  Whether NH3 loss peaks from the precursor should be removed.
consider_H2O_loss int1  Whether H2O loss peaks from the precursor should be removed.
reduce_by_factor int0  Reduce the intensities of the precursor and related ions by a given factor (set 'set_to_zero' to 0).
factor float1000.0  Factor which is used to reduce the intensities if 'reduce_by_factor' is selected.
set_to_zero int1  Reduce the intensities of the precursor and related ions to zero.

Note:

Constructor & Destructor Documentation

◆ ParentPeakMower() [1/2]

default constructor

◆ ParentPeakMower() [2/2]

ParentPeakMower ( const ParentPeakMower source)

copy constructor

◆ ~ParentPeakMower()

~ParentPeakMower ( )
override

destructor

Member Function Documentation

◆ filterPeakMap()

void filterPeakMap ( PeakMap exp)

◆ filterPeakSpectrum()

void filterPeakSpectrum ( PeakSpectrum spectrum)

◆ filterSpectrum()

void filterSpectrum ( SpectrumType spectrum)
inline

◆ 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