OpenMS
BinnedSumAgreeingIntensities Class Reference

Sum of agreeing intensities for similarity measurement. More...

#include <OpenMS/COMPARISON/SPECTRA/BinnedSumAgreeingIntensities.h>

Inheritance diagram for BinnedSumAgreeingIntensities:
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Collaboration diagram for BinnedSumAgreeingIntensities:
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Public Member Functions

 BinnedSumAgreeingIntensities ()
 default constructor More...
 
 BinnedSumAgreeingIntensities (const BinnedSumAgreeingIntensities &source)
 copy constructor More...
 
 ~BinnedSumAgreeingIntensities () override
 destructor More...
 
BinnedSumAgreeingIntensitiesoperator= (const BinnedSumAgreeingIntensities &source)
 assignment operator More...
 
double operator() (const BinnedSpectrum &spec1, const BinnedSpectrum &spec2) const override
 
double operator() (const BinnedSpectrum &spec) const override
 function call operator, calculates self similarity More...
 
- Public Member Functions inherited from BinnedSpectrumCompareFunctor
 BinnedSpectrumCompareFunctor ()
 default constructor More...
 
 BinnedSpectrumCompareFunctor (const BinnedSpectrumCompareFunctor &source)
 copy constructor More...
 
 ~BinnedSpectrumCompareFunctor () override
 destructor More...
 
BinnedSpectrumCompareFunctoroperator= (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...
 
DefaultParamHandleroperator= (const DefaultParamHandler &rhs)
 Assignment operator. More...
 
virtual bool operator== (const DefaultParamHandler &rhs) const
 Equality operator. More...
 
void setParameters (const Param &param)
 Sets the parameters. More...
 
const ParamgetParameters () const
 Non-mutable access to the parameters. More...
 
const ParamgetDefaults () const
 Non-mutable access to the default parameters. More...
 
const StringgetName () 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 BinnedSpectrumCompareFunctorcreate ()
 
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...
 
- Static Public Member Functions inherited from DefaultParamHandler
static void writeParametersToMetaValues (const Param &write_this, MetaInfoInterface &write_here, const String &key_prefix="")
 Writes all parameters to meta values. More...
 

Protected Member Functions

void updateMembers_ () override
 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< Stringsubsections_
 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

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

Bins whose intensity differences are larger than their average intensity receive a weight of zero.

Prefect agreement results in a similarity score of 1.0

Parameters of this class are:

NameTypeDefaultRestrictionsDescription

Note:
  • If a section name is documented, the documentation is displayed as tooltip.
  • Advanced parameter names are italic.
See also
BinnedSpectrumCompareFunctor
BinnedSpectrum

Constructor & Destructor Documentation

◆ BinnedSumAgreeingIntensities() [1/2]

default constructor

◆ BinnedSumAgreeingIntensities() [2/2]

copy constructor

◆ ~BinnedSumAgreeingIntensities()

destructor

Member Function Documentation

◆ create()

static BinnedSpectrumCompareFunctor* create ( )
inlinestatic

◆ getProductName()

static const String getProductName ( )
inlinestatic

get the identifier for this DefaultParamHandler

◆ operator()() [1/2]

double operator() ( const BinnedSpectrum spec) const
overridevirtual

function call operator, calculates self similarity

Implements BinnedSpectrumCompareFunctor.

◆ operator()() [2/2]

double operator() ( const BinnedSpectrum spec1,
const BinnedSpectrum spec2 
) const
overridevirtual

function call operator, calculates the similarity of the given arguments

Parameters
spec1First spectrum given as a binned representation
spec2Second spectrum given as a binned representation
Exceptions
IncompatibleBinningis thrown if the binning of the two input spectra are not the same

Implements BinnedSpectrumCompareFunctor.

◆ operator=()

assignment operator

◆ updateMembers_()

void updateMembers_ ( )
overrideprotectedvirtual

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_

double precursor_mass_tolerance_
protected