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BinnedSumAgreeingIntensities Class Reference

Compare functor scoring the sum of agreeing intensities for similarity measurement. More...

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

Inheritance diagram for BinnedSumAgreeingIntensities:
BinnedSpectrumCompareFunctor DefaultParamHandler

Public Member Functions

 BinnedSumAgreeingIntensities ()
 default constructor More...
 
 BinnedSumAgreeingIntensities (const BinnedSumAgreeingIntensities &source)
 copy constructor More...
 
virtual ~BinnedSumAgreeingIntensities ()
 destructor More...
 
BinnedSumAgreeingIntensitiesoperator= (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...
 
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...
 
virtual 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
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< 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

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:

NameTypeDefaultRestrictionsDescription
normalized int1  is set 1 if the similarity-measurement is normalized to the range [0,1]
precursor_mass_tolerance float3  Mass tolerance of the precursor peak, defines the distance of two PrecursorPeaks for which they are supposed to be from different peptides

Note:
See Also
BinnedSpectrumCompareFunctor
BinnedSpectrum

Constructor & Destructor Documentation

default constructor

copy constructor

virtual ~BinnedSumAgreeingIntensities ( )
virtual

destructor

Member Function Documentation

static BinnedSpectrumCompareFunctor* create ( )
inlinestatic
static const String getProductName ( )
inlinestatic

get the identifier for this DefaultParamHandler

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

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.

double operator() ( const BinnedSpectrum spec) const
virtual

function call operator, calculates self similarity

Implements BinnedSpectrumCompareFunctor.

assignment operator


OpenMS / TOPP release 1.11.1 Documentation generated on Thu Nov 14 2013 11:19:28 using doxygen 1.8.5