Compare functor scoring the spectral contrast angle for similarity measurement. More...
#include <OpenMS/COMPARISON/SPECTRA/BinnedSpectralContrastAngle.h>
 
  
 | Public Member Functions | |
| BinnedSpectralContrastAngle () | |
| default constructor  More... | |
| BinnedSpectralContrastAngle (const BinnedSpectralContrastAngle &source) | |
| copy constructor  More... | |
| virtual | ~BinnedSpectralContrastAngle () | 
| destructor  More... | |
| BinnedSpectralContrastAngle & | operator= (const BinnedSpectralContrastAngle &source) | 
| assignment operator  More... | |
| double | operator() (const BinnedSpectrum &spec1, const BinnedSpectrum &spec2) const | 
| double | operator() (const BinnedSpectrum &spec) const | 
| function call operator, calculates self similarity  More... | |
|  Public Member Functions inherited from BinnedSpectrumCompareFunctor | |
| BinnedSpectrumCompareFunctor () | |
| default constructor  More... | |
| BinnedSpectrumCompareFunctor (const BinnedSpectrumCompareFunctor &source) | |
| copy constructor  More... | |
| virtual | ~BinnedSpectrumCompareFunctor () | 
| destructor  More... | |
| BinnedSpectrumCompareFunctor & | operator= (const BinnedSpectrumCompareFunctor &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 BinnedSpectrumCompareFunctor * | create () | 
| static const String | getProductName () | 
| get the identifier for this DefaultParamHandler  More... | |
|  Static Public Member Functions inherited from BinnedSpectrumCompareFunctor | |
| static void | registerChildren () | 
| registers all derived products  More... | |
| static const String | getProductName () | 
| get the identifier for a DefaultParamHandler  More... | |
| 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... | |
Compare functor scoring the spectral contrast angle for similarity measurement.
The details of the score can be found in: K. Wan, I. Vidavsky, and M. Gross. Comparing similar spectra: from similarity index to spectral contrast angle. Journal of the American Society for Mass Spectrometry, 13(1):85-88, January 2002.
Parameters of this class are:| Name | Type | Default | Restrictions | Description | 
|---|---|---|---|---|
| normalized | int | 1 | is set 1 if the similarity-measurement is normalized to the range [0,1] | |
| precursor_mass_tolerance | float | 3 | Mass tolerance of the precursor peak, defines the distance of two PrecursorPeaks for which they are supposed to be from different peptides | 
default constructor
| BinnedSpectralContrastAngle | ( | const BinnedSpectralContrastAngle & | source | ) | 
copy constructor
| 
 | virtual | 
destructor
| 
 | inlinestatic | 
| 
 | inlinestatic | 
get the identifier for this DefaultParamHandler
| 
 | virtual | 
function call operator, calculates the similarity of the given arguments
| spec1 | First spectrum given in a binned representation | 
| spec2 | Second spectrum ginve in a binned representation | 
| IncompatibleBinning | is thrown if the binnings of the spectra are not the same | 
Implements BinnedSpectrumCompareFunctor.
| 
 | virtual | 
function call operator, calculates self similarity
Implements BinnedSpectrumCompareFunctor.
| BinnedSpectralContrastAngle& operator= | ( | const BinnedSpectralContrastAngle & | source | ) | 
assignment operator
| OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:28 using doxygen 1.8.5 |