| OpenMS 2.5.0

Protected Member Functions | List of all members
ZhangSimilarityScore Class Reference
Spectrum Comparison

Similarity score of Zhang. More...

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

Inheritance diagram for ZhangSimilarityScore:

## Public Member Functions

| ZhangSimilarityScore ()
| default constructor More...
| ZhangSimilarityScore (const ZhangSimilarityScore &source)
| copy constructor More...
| ~ZhangSimilarityScore () override
| destructor More...
ZhangSimilarityScore & | operator= (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...
PeakSpectrumCompareFunctor & | operator= (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...
virtual DefaultParamHandler & | operator= (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 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 PeakSpectrumCompareFunctor * | create ()
static const String | getProductName ()
Static Public Member Functions inherited from PeakSpectrumCompareFunctor
static void | registerChildren ()
| registers all derived products More...
static const String | getProductName ()

## 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< 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

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:

Name | Type | Default | Restrictions | Description
--- | --- | --- | --- | ---
tolerance | float | 0.2 |  | defines the absolute (in Da) or relative (in ppm) tolerance
is_relative_tolerance | string | false | true, false | If set to true, the tolerance is interpreted as relative
use_linear_factor | string | false | true, false | if true, the intensities are weighted with the relative m/z difference
use_gaussian_factor | string | false | true, false | if 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]

ZhangSimilarityScore | ( |  | ) |

default constructor

## ◆ ZhangSimilarityScore() [2/2]

ZhangSimilarityScore | ( | const ZhangSimilarityScore & | source | ) |

copy constructor

## ◆ ~ZhangSimilarityScore()

~ZhangSimilarityScore | ( |  | ) |

override

destructor

## Member Function Documentation

## ◆ create()

static PeakSpectrumCompareFunctor* create | ( |  | ) |

inline static

## ◆ 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 | ( |  | ) |

inline static

## ◆ operator()() [1/2]

double operator() | ( | const PeakSpectrum & | a,
|  | const PeakSpectrum & | b
| ) |  | const

override virtual

function call operator, calculates the similarity

Implements PeakSpectrumCompareFunctor.

## ◆ operator()() [2/2]

double operator() | ( | const PeakSpectrum & | a | ) | const

override virtual

calculates self similarity

Implements PeakSpectrumCompareFunctor.

## ◆ operator=()

ZhangSimilarityScore& operator= | ( | const ZhangSimilarityScore & | source | ) |

assignment operator