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

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

Inheritance diagram for SpectrumCheapDPCorr:

Public Member Functions

	SpectrumCheapDPCorr ()
	default constructor More...

	SpectrumCheapDPCorr (const SpectrumCheapDPCorr &source)
	copy constructor More...

virtual	~SpectrumCheapDPCorr ()
	destructor More...


SpectrumCheapDPCorr &	operator= (const SpectrumCheapDPCorr &source)
	assignment operator More...

double	operator() (const PeakSpectrum &a, const PeakSpectrum &b) const
	function call operator, calculates the similarity More...

double	operator() (const PeakSpectrum &a) const
	calculates self similarity 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 &param)
	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...

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, UInt >	peak_map_
	last peak map More...

Static Private Attributes
static const String	info_

const PeakSpectrum &	lastconsensus () const
	return consensus spectrum from last function call operator More...

Map< UInt, UInt >	getPeakMap () const

void	setFactor (double f)
	set weighting of the second spectrum for consensus from next function call operator More...

static PeakSpectrumCompareFunctor *	create ()

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< 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...

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:

Name	Type	Default	Description
variation	float	0.001	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	int	0	How the peak heights are used in the score. 0 = product 1 = sqrt(product) 2 = sum 3 = agreeing intensity
keeppeaks	int	0	Flag that states if peaks without alignment partner are kept in the consensus spectrum.

Note:

If a section name is documented, the documentation is displayed as tooltip.
Advanced parameter names are italic.

Constructor & Destructor Documentation

SpectrumCheapDPCorr ( )

default constructor

SpectrumCheapDPCorr ( const SpectrumCheapDPCorr & source )

copy constructor

virtual ~SpectrumCheapDPCorr ( )

virtual

destructor

Member Function Documentation

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

private

similarity of two peaks

static PeakSpectrumCompareFunctor* create ( )

inlinestatic

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

private

O(n^2) dynamical programming.

Map<UInt, UInt> getPeakMap ( ) const

static const String getProductName ( )

inlinestatic

const PeakSpectrum& lastconsensus ( ) const

return consensus spectrum from last function call operator

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

virtual

function call operator, calculates the similarity

Implements PeakSpectrumCompareFunctor.

double operator() ( const PeakSpectrum & a ) const

virtual

calculates self similarity

Implements PeakSpectrumCompareFunctor.

SpectrumCheapDPCorr& operator= ( const SpectrumCheapDPCorr & source )

assignment operator

void setFactor ( double f )

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

Member Data Documentation

double factor_

mutableprivate

weighting factor for the next consensus spectrum

const String info_

staticprivate

bool keeppeaks_

private

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

PeakSpectrum lastconsensus_

mutableprivate

consensus spectrum of the last comparison

Map<UInt, UInt> peak_map_

mutableprivate

last peak map

Public Member Functions

Private Member Functions

Private Attributes

Static Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation