Compare functor scoring the shared peaks for similarity measurement. More...
#include <OpenMS/COMPARISON/SPECTRA/BinnedSharedPeakCount.h>
Public Member Functions | |
BinnedSharedPeakCount () | |
default constructor More... | |
BinnedSharedPeakCount (const BinnedSharedPeakCount &source) | |
copy constructor More... | |
virtual | ~BinnedSharedPeakCount () |
destructor More... | |
BinnedSharedPeakCount & | operator= (const BinnedSharedPeakCount &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... | |
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BinnedSpectrumCompareFunctor () | |
default constructor More... | |
BinnedSpectrumCompareFunctor (const BinnedSpectrumCompareFunctor &source) | |
copy constructor More... | |
virtual | ~BinnedSpectrumCompareFunctor () |
destructor More... | |
BinnedSpectrumCompareFunctor & | operator= (const BinnedSpectrumCompareFunctor &source) |
assignment operator More... | |
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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... | |
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static void | registerChildren () |
registers all derived products More... | |
static const String | getProductName () |
get the identifier for a DefaultParamHandler More... | |
Additional Inherited Members | |
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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... | |
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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 shared peaks 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 |
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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
BinnedSharedPeakCount | ( | const BinnedSharedPeakCount & | source | ) |
copy constructor
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virtual |
destructor
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inlinestatic |
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inlinestatic |
get the identifier for this DefaultParamHandler
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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.
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virtual |
function call operator, calculates self similarity
Implements BinnedSpectrumCompareFunctor.
BinnedSharedPeakCount& operator= | ( | const BinnedSharedPeakCount & | source | ) |
assignment operator
OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:28 using doxygen 1.8.5 |