OpenMS  2.5.0
Public Member Functions | Static Public Member Functions | 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...
 
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...
 
- 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...
 

Static Public Member Functions

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

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_
 

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< 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
overridevirtual

calculates self similarity

Implements PeakSpectrumCompareFunctor.

◆ operator()() [2/2]

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

function call operator, calculates the 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