OpenMS
PeakAlignment Class Reference

make a PeakAlignment of two PeakSpectra More...

#include <OpenMS/COMPARISON/PeakAlignment.h>

Inheritance diagram for PeakAlignment:
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Collaboration diagram for PeakAlignment:
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Public Member Functions

 PeakAlignment ()
 default constructor More...
 
 PeakAlignment (const PeakAlignment &source)
 copy constructor More...
 
 ~PeakAlignment () override
 destructor More...
 
PeakAlignmentoperator= (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...
 
PeakSpectrumCompareFunctoroperator= (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...
 
DefaultParamHandleroperator= (const DefaultParamHandler &rhs)
 Assignment operator. More...
 
virtual bool operator== (const DefaultParamHandler &rhs) const
 Equality operator. More...
 
void setParameters (const Param &param)
 Sets the parameters. More...
 
const ParamgetParameters () const
 Non-mutable access to the parameters. More...
 
const ParamgetDefaults () const
 Non-mutable access to the default parameters. More...
 
const StringgetName () 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...
 

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

- Static Public Member Functions inherited from DefaultParamHandler
static void writeParametersToMetaValues (const Param &write_this, MetaInfoInterface &write_here, const String &key_prefix="")
 Writes all parameters to meta values. More...
 
- 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< Stringsubsections_
 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...
 

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:

NameTypeDefaultRestrictionsDescription
epsilon float0.2  defines the absolute error of the mass spectrometer
normalized int1  is set 1 if the similarity-measurement is normalized to the range [0,1]
heuristic_level int0  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 float3.0  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() [1/2]

default constructor

◆ PeakAlignment() [2/2]

PeakAlignment ( const PeakAlignment source)

copy constructor

◆ ~PeakAlignment()

~PeakAlignment ( )
override

destructor

Member Function Documentation

◆ getAlignmentTraceback()

std::vector<std::pair<Size, Size> > getAlignmentTraceback ( const PeakSpectrum spec1,
const PeakSpectrum spec2 
) const

make alignment and get the traceback

◆ operator()() [1/2]

double operator() ( const PeakSpectrum spec) const
overridevirtual

function call operator, calculates self similarity

Implements PeakSpectrumCompareFunctor.

◆ operator()() [2/2]

double operator() ( const PeakSpectrum spec1,
const PeakSpectrum spec2 
) const
overridevirtual

function call operator, calculates the similarity of the given arguments

Parameters
spec1First spectrum given in a binned representation
spec2Second spectrum given in a binned representation

Implements PeakSpectrumCompareFunctor.

◆ operator=()

PeakAlignment& operator= ( const PeakAlignment source)

assignment operator

◆ peakPairScore_()

double peakPairScore_ ( double &  pos1,
double &  intens1,
double &  pos2,
double &  intens2,
const double &  sigma 
) const
private

calculates the score for aligning two peaks