Normalizes the peak intensities spectrum-wise. More...
#include <OpenMS/FILTERING/TRANSFORMERS/Normalizer.h>
Inheritance diagram for Normalizer:
Public Member Functions | |
| Normalizer () | |
| default constructor More... | |
| virtual | ~Normalizer () |
| destructor More... | |
| Normalizer & | operator= (const Normalizer &source) |
| assignment operator More... | |
| Normalizer (const Normalizer &source) | |
| copy constructor More... | |
| template<typename SpectrumType > | |
| void | filterSpectrum (SpectrumType &spectrum) const |
| void | filterPeakSpectrum (PeakSpectrum &spectrum) const |
| void | filterPeakMap (PeakMap &exp) const |
| virtual void | updateMembers_ () |
| This method is used to update extra member variables at the end of the setParameters() method. 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 ¶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 | |
| String | method_ |
Additional Inherited Members | |
| Protected Member Functions inherited from DefaultParamHandler | |
| 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
Normalizes the peak intensities spectrum-wise.
Either to a total intensity-sum of one (i.e. to total-ion-count; TIC) or to a maximum intensity of one.
Parameters of this class are:| Name | Type | Default | Restrictions | Description |
|---|---|---|---|---|
| method | string | to_one | to_one, to_TIC | Normalize via dividing by TIC ('to_TIC') per spectrum or normalize to max. intensity of one ('to_one') per spectrum. |
Note:
- If a section name is documented, the documentation is displayed as tooltip.
- Advanced parameter names are italic.
Constructor & Destructor Documentation
◆ Normalizer() [1/2]
| Normalizer | ( | ) |
default constructor
◆ ~Normalizer()
|
virtual |
destructor
◆ Normalizer() [2/2]
| Normalizer | ( | const Normalizer & | source | ) |
copy constructor
Member Function Documentation
◆ filterPeakMap()
| void filterPeakMap | ( | PeakMap & | exp | ) | const |
Referenced by SimpleSearchEngine::preprocessSpectra_(), and RNPxlSearch::preprocessSpectra_().
◆ filterPeakSpectrum()
| void filterPeakSpectrum | ( | PeakSpectrum & | spectrum | ) | const |
◆ filterSpectrum()
|
inline |
Workhorse of this class.
- Parameters
-
spectrum Input/output spectrum containing peaks
- Exceptions
-
Exception::InvalidValue if 'method_' has unknown value
◆ operator=()
| Normalizer& operator= | ( | const Normalizer & | source | ) |
assignment operator
◆ updateMembers_()
|
virtual |
This method is used to update extra member variables at the end of the setParameters() method.
Also call it at the end of the derived classes' copy constructor and assignment operator.
The default implementation is empty.
Reimplemented from DefaultParamHandler.
Member Data Documentation
◆ method_
|
private |