Compare functor scoring the sum of agreeing intensities for similarity measurement. More...
#include <OpenMS/COMPARISON/SPECTRA/BinnedSumAgreeingIntensities.h>
Inheritance diagram for BinnedSumAgreeingIntensities:
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... | |
Protected Member Functions | |
| void | updateMembers_ () |
| This method is used to update extra member variables at the end of the setParameters() method. More... | |
| Protected Member Functions inherited from DefaultParamHandler | |
| void | defaultsToParam_ () |
| Updates the parameters after the defaults have been set in the constructor. More... | |
Protected Attributes | |
| double | precursor_mass_tolerance_ |
| 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
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 |
Note:
- If a section name is documented, the documentation is displayed as tooltip.
- Advanced parameter names are italic.
Constructor & Destructor Documentation
◆ BinnedSumAgreeingIntensities() [1/2]
default constructor
◆ BinnedSumAgreeingIntensities() [2/2]
| BinnedSumAgreeingIntensities | ( | const BinnedSumAgreeingIntensities & | source | ) |
copy constructor
◆ ~BinnedSumAgreeingIntensities()
|
virtual |
destructor
Member Function Documentation
◆ create()
|
inlinestatic |
◆ getProductName()
|
inlinestatic |
get the identifier for this DefaultParamHandler
◆ operator()() [1/2]
|
virtual |
function call operator, calculates the similarity of the given arguments
- Parameters
-
spec1 First spectrum given as a binned representation spec2 Second spectrum given as a binned representation
- Exceptions
-
IncompatibleBinning is thrown if the binning of the two input spectra are not the same
Implements BinnedSpectrumCompareFunctor.
◆ operator()() [2/2]
|
virtual |
function call operator, calculates self similarity
Implements BinnedSpectrumCompareFunctor.
◆ operator=()
| BinnedSumAgreeingIntensities& operator= | ( | const BinnedSumAgreeingIntensities & | source | ) |
assignment operator
◆ updateMembers_()
|
protectedvirtual |
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
◆ precursor_mass_tolerance_
|
protected |