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SpectrumAlignmentScore Class Reference
[Spectrum Comparison]

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

Inheritance diagram for SpectrumAlignmentScore:

PeakSpectrumCompareFunctor FactoryProduct DefaultParamHandler

List of all members.


Detailed Description

Similarity score via spectra alignment.

This class implements a simple scoring based on the alignment of spectra. This alignment is implemented in the SpectrumAlignment class and performs a dynamic programming alignment of the peaks, minimizing the distances between the aligned peaks and maximizing the number of peak pairs.

The scoring is done via the simple formula score = sum / (sqrt(sum1 * sum2)). sum is the product of the intensities of the aligned peaks, with the given exponent (default is 2). sum1 and sum2 are the sum of the intensities squared for each peak of both spectra respectively.

A binned version of this scoring is implemented in the ZhangSimilarityScoring class.

SpectrumAlignmentScore Parameters are explained on a separate page.

Public Member Functions

 SpectrumAlignmentScore ()
 default constructor
 SpectrumAlignmentScore (const SpectrumAlignmentScore &source)
 copy constructor
virtual ~SpectrumAlignmentScore ()
 destructor
SpectrumAlignmentScoreoperator= (const SpectrumAlignmentScore &source)
 assignment operator
double operator() (const PeakSpectrum &spec1, const PeakSpectrum &spec2) const
 function call operator, calculates the similarity
double operator() (const PeakSpectrum &spec) const
 calculates self similarity

Static Public Member Functions

static PeakSpectrumCompareFunctorcreate ()
static const String getProductName ()


Constructor & Destructor Documentation

SpectrumAlignmentScore (  ) 

default constructor

SpectrumAlignmentScore ( const SpectrumAlignmentScore source  ) 

copy constructor

virtual ~SpectrumAlignmentScore (  )  [virtual]

destructor


Member Function Documentation

SpectrumAlignmentScore& operator= ( const SpectrumAlignmentScore source  ) 

assignment operator

double operator() ( const PeakSpectrum a,
const PeakSpectrum b 
) const [virtual]

function call operator, calculates the similarity

Implements PeakSpectrumCompareFunctor.

double operator() ( const PeakSpectrum a  )  const [virtual]

calculates self similarity

Implements PeakSpectrumCompareFunctor.

static PeakSpectrumCompareFunctor* create (  )  [inline, static]

static const String getProductName (  )  [inline, static]

Reimplemented from PeakSpectrumCompareFunctor.


The documentation for this class was generated from the following file:
Generated Tue Apr 1 15:36:43 2008 -- using doxygen 1.5.4 OpenMS / TOPP 1.1