#include <OpenMS/COMPARISON/SPECTRA/SpectrumAlignmentScore.h>
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 | |
SpectrumAlignmentScore & | operator= (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 PeakSpectrumCompareFunctor * | create () |
static const String | getProductName () |
default constructor
SpectrumAlignmentScore | ( | const SpectrumAlignmentScore & | source | ) |
copy constructor
virtual ~SpectrumAlignmentScore | ( | ) | [virtual] |
destructor
SpectrumAlignmentScore& operator= | ( | const SpectrumAlignmentScore & | source | ) |
assignment operator
double operator() | ( | const PeakSpectrum & | a, | |
const PeakSpectrum & | b | |||
) | const [virtual] |
double operator() | ( | const PeakSpectrum & | a | ) | const [virtual] |
static PeakSpectrumCompareFunctor* create | ( | ) | [inline, static] |
static const String getProductName | ( | ) | [inline, static] |
Reimplemented from PeakSpectrumCompareFunctor.
Generated Tue Apr 1 15:36:43 2008 -- using doxygen 1.5.4 | OpenMS / TOPP 1.1 |