| OpenMS 2.5.0

Private Attributes | List of all members
ParentPeakMower Class Reference
Spectrum filters » Spectra Preprocessors

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...
| ~ParentPeakMower () override
| 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 | 2.0 |  | 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 | 1000.0 |  | 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()

~ParentPeakMower | ( |  | ) |

override

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