| OpenMS 2.5.0

Public Member Functions | Static Public Member Functions | Protected Member Functions | Protected Attributes | List of all members
BinnedSharedPeakCount Class Reference
Spectrum Comparison

Compare functor scoring the shared peaks for similarity measurement. More...

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

Inheritance diagram for BinnedSharedPeakCount:

## Public Member Functions

| BinnedSharedPeakCount ()
| default constructor More...
| BinnedSharedPeakCount (const BinnedSharedPeakCount &source)
| copy constructor More...
| ~BinnedSharedPeakCount () override
| destructor More...
BinnedSharedPeakCount & | operator= (const BinnedSharedPeakCount &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...
BinnedSpectrumCompareFunctor & | operator= (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 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 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...

## 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< 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

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
--- | --- | --- | --- | ---

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

## ◆ BinnedSharedPeakCount() [1/2]

BinnedSharedPeakCount | ( |  | ) |

default constructor

## ◆ BinnedSharedPeakCount() [2/2]

BinnedSharedPeakCount | ( | const BinnedSharedPeakCount & | source | ) |

copy constructor

## ◆ ~BinnedSharedPeakCount()

~BinnedSharedPeakCount | ( |  | ) |

override

destructor

## Member Function Documentation

## ◆ create()

static BinnedSpectrumCompareFunctor* create | ( |  | ) |

inline static

## ◆ getProductName()

static const String getProductName | ( |  | ) |

inline static

get the identifier for this DefaultParamHandler

## ◆ operator()() [1/2]

double operator() | ( | const BinnedSpectrum & | spec1,
|  | const BinnedSpectrum & | spec2
| ) |  | const

override virtual

function call operator, calculates the similarity of the given arguments

Parameters

  spec1 | First spectrum given as a binned representation
  spec2 | Second spectrum given as a binned representation

Exceptions

  IncompatibleBinning | is thrown if the binning of the two input spectra are not the same

Implements BinnedSpectrumCompareFunctor.

## ◆ operator()() [2/2]

double operator() | ( | const BinnedSpectrum & | spec | ) | const

override virtual

function call operator, calculates self similarity

Implements BinnedSpectrumCompareFunctor.

## ◆ operator=()

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

assignment operator

## ◆ updateMembers_()

void updateMembers_ | ( |  | ) |

override protected virtual

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