OpenMS
2.4.0
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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... | |
~PeakAlignment () override | |
destructor More... | |
PeakAlignment & | operator= (const PeakAlignment &source) |
assignment operator More... | |
double | operator() (const PeakSpectrum &spec1, const PeakSpectrum &spec2) const override |
double | operator() (const PeakSpectrum &spec) const override |
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... | |
~PeakSpectrumCompareFunctor () override | |
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 |
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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
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override |
destructor
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inlinestatic |
std::vector<std::pair<Size, Size> > getAlignmentTraceback | ( | const PeakSpectrum & | spec1, |
const PeakSpectrum & | spec2 | ||
) | const |
make alignment and get the traceback
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inlinestatic |
get the identifier for this DefaultParamHandler
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overridevirtual |
function call operator, calculates the similarity of the given arguments
spec1 | First spectrum given in a binned representation |
spec2 | Second spectrum given in a binned representation |
Implements PeakSpectrumCompareFunctor.
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overridevirtual |
function call operator, calculates self similarity
Implements PeakSpectrumCompareFunctor.
PeakAlignment& operator= | ( | const PeakAlignment & | source | ) |
assignment operator