Compare functor scoring the sum of agreeing intensities for similarity measurement. More...
#include <OpenMS/COMPARISON/SPECTRA/BinnedSumAgreeingIntensities.h>
 
  
 | Public Member Functions | |
| BinnedSumAgreeingIntensities () | |
| default constructor  More... | |
| BinnedSumAgreeingIntensities (const BinnedSumAgreeingIntensities &source) | |
| copy constructor  More... | |
| virtual | ~BinnedSumAgreeingIntensities () | 
| destructor  More... | |
| BinnedSumAgreeingIntensities & | operator= (const BinnedSumAgreeingIntensities &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 sum of agreeing intensities for similarity measurement.
Transformation and other factors of the peptide mass spectrometry pairwise peak-list comparison process Witold E Wolski , Maciej Lalowski* , Peter Martus* , Ralf Herwig* , Patrick Giavalisco , Johan Gobom , Albert Sickmann , Hans Lehrach and Knut Reinert* BMC Bioinformatics 2005, 6:285 doi:10.1186/1471-2105-6-285
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
| BinnedSumAgreeingIntensities | ( | const BinnedSumAgreeingIntensities & | 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 as a binned representation | 
| spec2 | Second spectrum given as a binned representation | 
| IncompatibleBinning | is thrown if the binning of the two input spectra are not the same | 
Implements BinnedSpectrumCompareFunctor.
| 
 | virtual | 
function call operator, calculates self similarity
Implements BinnedSpectrumCompareFunctor.
| BinnedSumAgreeingIntensities& operator= | ( | const BinnedSumAgreeingIntensities & | source | ) | 
assignment operator
| OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:28 using doxygen 1.8.5 |