Similarity score of Zhang. More...
#include <OpenMS/COMPARISON/SPECTRA/ZhangSimilarityScore.h>
Inheritance diagram for ZhangSimilarityScore:
Public Member Functions | |
| ZhangSimilarityScore () | |
| default constructor More... | |
| ZhangSimilarityScore (const ZhangSimilarityScore &source) | |
| copy constructor More... | |
| virtual | ~ZhangSimilarityScore () |
| destructor More... | |
| ZhangSimilarityScore & | operator= (const ZhangSimilarityScore &source) |
| assignment operator More... | |
| double | operator() (const PeakSpectrum &spec1, const PeakSpectrum &spec2) const |
| function call operator, calculates the similarity More... | |
| double | operator() (const PeakSpectrum &spec) const |
| calculates self similarity More... | |
 Public Member Functions inherited from PeakSpectrumCompareFunctor | |
| PeakSpectrumCompareFunctor () | |
| default constructor More... | |
| PeakSpectrumCompareFunctor (const PeakSpectrumCompareFunctor &source) | |
| copy constructor More... | |
| virtual | ~PeakSpectrumCompareFunctor () |
| destructor More... | |
| PeakSpectrumCompareFunctor & | operator= (const PeakSpectrumCompareFunctor &source) |
| assignment operator 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... | |
Static Public Member Functions | |
| static PeakSpectrumCompareFunctor * | create () |
| static const String | getProductName () |
| Static Public Member Functions inherited from PeakSpectrumCompareFunctor | |
| static void | registerChildren () |
| registers all derived products More... | |
| static const String | getProductName () |
Protected Member Functions | |
| double | getFactor_ (double mz_tolerance, double mz_difference, bool is_gaussian=false) const |
| returns the factor associated with the m/z tolerance and m/z difference of the peaks 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... | |
Additional Inherited Members | |
| 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
Similarity score of Zhang.
The details of the score can be found in: Z. Zhang, Prediction of Low-Energy Collision-Induced Dissociation Spectra of Peptides, Anal. Chem., 76 (14), 3908 - 3922, 2004
Parameters of this class are:| Name | Type | Default | Restrictions | Description |
|---|---|---|---|---|
| tolerance | float | 0.2 | defines the absolute (in Da) or relative (in ppm) tolerance | |
| is_relative_tolerance | string | false | true, false | If set to true, the tolerance is interpreted as relative |
| use_linear_factor | string | false | true, false | if true, the intensities are weighted with the relative m/z difference |
| use_gaussian_factor | string | false | true, false | if true, the intensities are weighted with the relative m/z difference using a gaussian |
Note:
- If a section name is documented, the documentation is displayed as tooltip.
- Advanced parameter names are italic.
Constructor & Destructor Documentation
◆ ZhangSimilarityScore() [1/2]
default constructor
◆ ZhangSimilarityScore() [2/2]
| ZhangSimilarityScore | ( | const ZhangSimilarityScore & | source | ) |
copy constructor
◆ ~ZhangSimilarityScore()
|
virtual |
destructor
Member Function Documentation
◆ create()
|
inlinestatic |
◆ getFactor_()
|
protected |
returns the factor associated with the m/z tolerance and m/z difference of the peaks
◆ getProductName()
|
inlinestatic |
◆ operator()() [1/2]
|
virtual |
function call operator, calculates the similarity
Implements PeakSpectrumCompareFunctor.
◆ operator()() [2/2]
|
virtual |
calculates self similarity
Implements PeakSpectrumCompareFunctor.
◆ operator=()
| ZhangSimilarityScore& operator= | ( | const ZhangSimilarityScore & | source | ) |
assignment operator