OpenMS  2.4.0
Private Member Functions | Private Attributes | Static Private Attributes | List of all members
SpectrumCheapDPCorr Class Reference

SpectrumCheapDPCorr calculates an optimal alignment on stick spectra. More...

#include <OpenMS/COMPARISON/SPECTRA/SpectrumCheapDPCorr.h>

Inheritance diagram for SpectrumCheapDPCorr:
PeakSpectrumCompareFunctor DefaultParamHandler

Public Member Functions

 SpectrumCheapDPCorr ()
 default constructor More...
 
 SpectrumCheapDPCorr (const SpectrumCheapDPCorr &source)
 copy constructor More...
 
 ~SpectrumCheapDPCorr () override
 destructor More...
 
SpectrumCheapDPCorroperator= (const SpectrumCheapDPCorr &source)
 assignment operator More...
 
double operator() (const PeakSpectrum &a, const PeakSpectrum &b) const override
 function call operator, calculates the similarity More...
 
double operator() (const PeakSpectrum &a) const override
 calculates self similarity 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...
 
virtual 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 dynprog_ (const PeakSpectrum &, const PeakSpectrum &, int, int, int, int) const
 O(n^2) dynamical programming. More...
 
double comparepeaks_ (double posa, double posb, double inta, double intb) const
 similarity of two peaks More...
 

Private Attributes

PeakSpectrum lastconsensus_
 consensus spectrum of the last comparison More...
 
bool keeppeaks_
 should peaks with no alignment partner be kept in the consensus? More...
 
double factor_
 weighting factor for the next consensus spectrum More...
 
Map< UInt, UIntpeak_map_
 last peak map More...
 

Static Private Attributes

static const String info_
 
const PeakSpectrumlastconsensus () const
 return consensus spectrum from last function call operator More...
 
Map< UInt, UIntgetPeakMap () const
 
void setFactor (double f)
 set weighting of the second spectrum for consensus from next function call operator More...
 
static PeakSpectrumCompareFunctorcreate ()
 
static const String getProductName ()
 

Additional Inherited Members

- Static Public Member Functions inherited from PeakSpectrumCompareFunctor
static void registerChildren ()
 registers all derived products More...
 
static const String getProductName ()
 
- 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

SpectrumCheapDPCorr calculates an optimal alignment on stick spectra.

to save computing time only Peak Pairs that could get a score > 0 are considered which Peak Pairs could get scores > 0 ?
Peaks get a score depending on the difference in position and the heights of the peaks
pairs with positions that differ more than some limit get score 0

Parameters of this class are:

NameTypeDefaultRestrictionsDescription
variation float0.001  Maximum difference in position (in percent of the current m/z).
Note that big values of variation ( 1 being the maximum ) result in consideration of all possible pairings which has a running time of O(n*n)
int_cnt int0  How the peak heights are used in the score.
0 = product
1 = sqrt(product)
2 = sum
3 = agreeing intensity
keeppeaks int0  Flag that states if peaks without alignment partner are kept in the consensus spectrum.

Note:

Constructor & Destructor Documentation

◆ SpectrumCheapDPCorr() [1/2]

default constructor

◆ SpectrumCheapDPCorr() [2/2]

copy constructor

◆ ~SpectrumCheapDPCorr()

~SpectrumCheapDPCorr ( )
override

destructor

Member Function Documentation

◆ comparepeaks_()

double comparepeaks_ ( double  posa,
double  posb,
double  inta,
double  intb 
) const
private

similarity of two peaks

◆ create()

static PeakSpectrumCompareFunctor* create ( )
inlinestatic

◆ dynprog_()

double dynprog_ ( const PeakSpectrum ,
const PeakSpectrum ,
int  ,
int  ,
int  ,
int   
) const
private

O(n^2) dynamical programming.

◆ getPeakMap()

Map<UInt, UInt> getPeakMap ( ) const

◆ getProductName()

static const String getProductName ( )
inlinestatic

◆ lastconsensus()

const PeakSpectrum& lastconsensus ( ) const

return consensus spectrum from last function call operator

◆ operator()() [1/2]

double operator() ( const PeakSpectrum a,
const PeakSpectrum b 
) const
overridevirtual

function call operator, calculates the similarity

Implements PeakSpectrumCompareFunctor.

◆ operator()() [2/2]

double operator() ( const PeakSpectrum a) const
overridevirtual

calculates self similarity

Implements PeakSpectrumCompareFunctor.

◆ operator=()

SpectrumCheapDPCorr& operator= ( const SpectrumCheapDPCorr source)

assignment operator

◆ setFactor()

void setFactor ( double  f)

set weighting of the second spectrum for consensus from next function call operator

Member Data Documentation

◆ factor_

double factor_
mutableprivate

weighting factor for the next consensus spectrum

◆ info_

const String info_
staticprivate

◆ keeppeaks_

bool keeppeaks_
private

should peaks with no alignment partner be kept in the consensus?

◆ lastconsensus_

PeakSpectrum lastconsensus_
mutableprivate

consensus spectrum of the last comparison

◆ peak_map_

Map<UInt, UInt> peak_map_
mutableprivate

last peak map