ParentPeakMower gets rid of high peaks that could stem from unfragmented precursor ions. More...
#include <OpenMS/FILTERING/TRANSFORMERS/ParentPeakMower.h>
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 ¶m) |
| 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_ |
| DoubleReal | window_size_ |
| bool | reduce_by_factor_ |
| DoubleReal | 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... | |
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. |
| ParentPeakMower | ( | ) |
default constructor
| ParentPeakMower | ( | const ParentPeakMower & | source | ) |
copy constructor
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destructor
| void filterPeakMap | ( | PeakMap & | exp | ) |
| void filterPeakSpectrum | ( | PeakSpectrum & | spectrum | ) |
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| ParentPeakMower& operator= | ( | const ParentPeakMower & | source | ) |
assignment operator
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| OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:30 using doxygen 1.8.5 |