make a PeakAlignment of two PeakSpectra More...
#include <OpenMS/COMPARISON/SPECTRA/PeakAlignment.h>
 
  
 | Public Member Functions | |
| PeakAlignment () | |
| default constructor  More... | |
| PeakAlignment (const PeakAlignment &source) | |
| copy constructor  More... | |
| virtual | ~PeakAlignment () | 
| destructor  More... | |
| PeakAlignment & | operator= (const PeakAlignment &source) | 
| assignment operator  More... | |
| double | operator() (const PeakSpectrum &spec1, const PeakSpectrum &spec2) const | 
| double | operator() (const PeakSpectrum &spec) const | 
| function call operator, calculates self similarity  More... | |
| std::vector< std::pair< Size, Size > > | getAlignmentTraceback (const PeakSpectrum &spec1, const PeakSpectrum &spec2) const | 
| make alignment and get the traceback  More... | |
|  Public Member Functions inherited from PeakSpectrumCompareFunctor | |
| PeakSpectrumCompareFunctor () | |
| default constructor  More... | |
| PeakSpectrumCompareFunctor (const PeakSpectrumCompareFunctor &source) | |
| copy constructor  More... | |
| virtual | ~PeakSpectrumCompareFunctor () | 
| 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 ¶m) | 
| 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 () | 
| get the identifier for this DefaultParamHandler  More... | |
|  Static Public Member Functions inherited from PeakSpectrumCompareFunctor | |
| static void | registerChildren () | 
| registers all derived products  More... | |
| static const String | getProductName () | 
| Private Member Functions | |
| double | peakPairScore_ (double &pos1, double &intens1, double &pos2, double &intens2, const double &sigma) const | 
| calculates the score for aligning two peaks  More... | |
| Additional Inherited Members | |
|  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... | |
|  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... | |
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 | 
| PeakAlignment | ( | ) | 
default constructor
| PeakAlignment | ( | const PeakAlignment & | source | ) | 
copy constructor
| 
 | virtual | 
destructor
| 
 | inlinestatic | 
| std::vector<std::pair<Size, Size> > getAlignmentTraceback | ( | const PeakSpectrum & | spec1, | 
| const PeakSpectrum & | spec2 | ||
| ) | const | 
make alignment and get the traceback
| 
 | inlinestatic | 
get the identifier for this DefaultParamHandler
| 
 | virtual | 
function call operator, calculates the similarity of the given arguments
| spec1 | First spectrum given in a binned representation | 
| spec2 | Second spectrum ginve in a binned representation | 
Implements PeakSpectrumCompareFunctor.
| 
 | virtual | 
function call operator, calculates self similarity
Implements PeakSpectrumCompareFunctor.
| PeakAlignment& operator= | ( | const PeakAlignment & | source | ) | 
assignment operator
| OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:28 using doxygen 1.8.5 |