make a PeakAlignment of two PeakSpectra More...
#include <OpenMS/COMPARISON/SPECTRA/PeakAlignment.h>
Inheritance diagram for PeakAlignment:
Public Member Functions | |
| PeakAlignment () | |
| default constructor | |
| PeakAlignment (const PeakAlignment &source) | |
| copy constructor | |
| virtual | ~PeakAlignment () |
| destructor | |
| PeakAlignment & | operator= (const PeakAlignment &source) |
| assignment operator | |
| double | operator() (const PeakSpectrum &spec1, const PeakSpectrum &spec2) const |
| double | operator() (const PeakSpectrum &spec) const |
| function call operator, calculates self similarity | |
| std::vector< std::pair< Size, Size > > | getAlignmentTraceback (const PeakSpectrum &spec1, const PeakSpectrum &spec2) const |
| make alignment and get the traceback | |
Static Public Member Functions | |
| static PeakSpectrumCompareFunctor * | create () |
| static const String | getProductName () |
| get the identifier for this DefaultParamHandler | |
Private Member Functions | |
| double | peakPairScore_ (double &pos1, double &intens1, double &pos2, double &intens2, const double &sigma) const |
| calculates the score for aligning two peaks | |
Detailed Description
make a PeakAlignment of two PeakSpectra
The alignment is done according to the Needleman-Wunsch Algorithm (local alignment considering gaps).
Parameters of this class are:| Name | Type | Default | Restrictions | Description |
|---|---|---|---|---|
| epsilon | float | 0.2 | defines the absolute error of the mass spectrometer | |
| normalized | int | 1 | is set 1 if the similarity-measurement is normalized to the range [0,1] | |
| heuristic_level | int | 0 | set 0 means no heuristic is applied otherwise the given value is interpreted as unsigned integer, the number of strongest peaks considered for heurisitcs - in those sets of peaks has to be at least one match to conduct comparison | |
| precursor_mass_tolerance | float | 3 | Mass tolerance of the precursor peak, defines the distance of two PrecursorPeaks for which they are supposed to be from different peptides |
Note:
- If a section name is documented, the documentation is displayed as tooltip.
- Advanced parameter names are italic.
Constructor & Destructor Documentation
| PeakAlignment | ( | ) |
default constructor
| PeakAlignment | ( | const PeakAlignment & | source | ) |
copy constructor
| virtual ~PeakAlignment | ( | ) | [virtual] |
destructor
Member Function Documentation
| static PeakSpectrumCompareFunctor* create | ( | ) | [inline, static] |
| std::vector<std::pair<Size, Size> > getAlignmentTraceback | ( | const PeakSpectrum & | spec1, | |
| const PeakSpectrum & | spec2 | |||
| ) | const |
make alignment and get the traceback
| static const String getProductName | ( | ) | [inline, static] |
get the identifier for this DefaultParamHandler
Reimplemented from PeakSpectrumCompareFunctor.
| double operator() | ( | const PeakSpectrum & | spec1, | |
| const PeakSpectrum & | spec2 | |||
| ) | const [virtual] |
function call operator, calculates the similarity of the given arguments
- Parameters:
-
spec1 First spectrum given in a binned representation spec2 Second spectrum ginve in a binned representation
Implements PeakSpectrumCompareFunctor.
| double operator() | ( | const PeakSpectrum & | spec | ) | const [virtual] |
function call operator, calculates self similarity
Implements PeakSpectrumCompareFunctor.
| PeakAlignment& operator= | ( | const PeakAlignment & | source | ) |
assignment operator
| OpenMS / TOPP release 1.10.0 | Documentation generated on Thu Mar 7 2013 09:42:51 using doxygen 1.7.1 |