OpenMS
ZhangSimilarityScore Class Reference

Similarity score of Zhang. More...

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

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

 ZhangSimilarityScore ()
 default constructor More...
 
 ZhangSimilarityScore (const ZhangSimilarityScore &source)
 copy constructor More...
 
 ~ZhangSimilarityScore () override
 destructor More...
 
ZhangSimilarityScoreoperator= (const ZhangSimilarityScore &source)
 assignment operator More...
 
double operator() (const PeakSpectrum &spec1, const PeakSpectrum &spec2) const override
 function call operator, calculates the similarity More...
 
double operator() (const PeakSpectrum &spec) const override
 calculates self similarity More...
 
- Public Member Functions inherited from PeakSpectrumCompareFunctor
 PeakSpectrumCompareFunctor ()
 default constructor More...
 
 PeakSpectrumCompareFunctor (const PeakSpectrumCompareFunctor &source)
 copy constructor More...
 
 ~PeakSpectrumCompareFunctor () override
 destructor More...
 
PeakSpectrumCompareFunctoroperator= (const PeakSpectrumCompareFunctor &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 PeakSpectrumCompareFunctorcreate ()
 
static const String getProductName ()
 
- Static Public Member Functions inherited from PeakSpectrumCompareFunctor
static void registerChildren ()
 registers all derived products More...
 
static const String getProductName ()
 
- 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

double getFactor_ (double mz_tolerance, double mz_difference, bool is_gaussian=false) const
 returns the factor associated with the m/z tolerance and m/z difference of the peaks More...
 
- 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...
 

Additional Inherited Members

- 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

Similarity score of Zhang.

The details of the score can be found in: Z. Zhang, Prediction of Low-Energy Collision-Induced Dissociation Spectra of Peptides, Anal. Chem., 76 (14), 3908 - 3922, 2004

Parameters of this class are:

NameTypeDefaultRestrictionsDescription
tolerance float0.2  defines the absolute (in Da) or relative (in ppm) tolerance
is_relative_tolerance stringfalse true, falseIf set to true, the tolerance is interpreted as relative
use_linear_factor stringfalse true, falseif true, the intensities are weighted with the relative m/z difference
use_gaussian_factor stringfalse true, falseif true, the intensities are weighted with the relative m/z difference using a gaussian

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

Constructor & Destructor Documentation

◆ ZhangSimilarityScore() [1/2]

default constructor

◆ ZhangSimilarityScore() [2/2]

copy constructor

◆ ~ZhangSimilarityScore()

~ZhangSimilarityScore ( )
override

destructor

Member Function Documentation

◆ create()

static PeakSpectrumCompareFunctor* create ( )
inlinestatic

◆ getFactor_()

double getFactor_ ( double  mz_tolerance,
double  mz_difference,
bool  is_gaussian = false 
) const
protected

returns the factor associated with the m/z tolerance and m/z difference of the peaks

◆ getProductName()

static const String getProductName ( )
inlinestatic

◆ operator()() [1/2]

double operator() ( const PeakSpectrum a) const
overridevirtual

calculates self similarity

Implements PeakSpectrumCompareFunctor.

◆ operator()() [2/2]

double operator() ( const PeakSpectrum a,
const PeakSpectrum b 
) const
overridevirtual

function call operator, calculates the similarity

Implements PeakSpectrumCompareFunctor.

◆ operator=()

ZhangSimilarityScore& operator= ( const ZhangSimilarityScore source)

assignment operator