Abstract base class describing an isobaric quantitation method in terms of the used channels and an isotope correction matrix. More...

#include <OpenMS/ANALYSIS/QUANTITATION/IsobaricQuantitationMethod.h>

Inheritance diagram for IsobaricQuantitationMethod:

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Collaboration diagram for IsobaricQuantitationMethod:

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Classes
struct	IsobaricChannelInformation
	Summary of an isobaric quantitation channel. More...

Public Types
typedef std::vector< IsobaricChannelInformation >	IsobaricChannelList

Public Member Functions
	IsobaricQuantitationMethod ()
	c'tor setting the name for the underlying param handler More...

	~IsobaricQuantitationMethod () override
	d'tor More...

virtual const String &	getMethodName () const =0
	Returns a unique name for the quantitation method. More...

virtual const IsobaricChannelList &	getChannelInformation () const =0
	Returns information on the different channels used by the quantitation method. More...

virtual Size	getNumberOfChannels () const =0
	Gives the number of channels available for this quantitation method. More...

virtual Matrix< double >	getIsotopeCorrectionMatrix () const =0
	Returns an isotope correction matrix suitable for the given quantitation method. More...

virtual Size	getReferenceChannel () const =0
	Returns the index of the reference channel in the IsobaricChannelList (see IsobaricQuantitationMethod::getChannelInformation()). 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...

Protected Member Functions
Matrix< double >	stringListToIsotopCorrectionMatrix_ (const std::vector< String > &stringlist) const
	Helper function to convert a string list containing an isotope correction matrix into a Matrix<double>. 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...

Additional Inherited Members
Static Public Member Functions inherited from DefaultParamHandler
static void	writeParametersToMetaValues (const Param &write_this, MetaInfoInterface &write_here, const String &prefix="")
	Writes all parameters to meta values. 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

Abstract base class describing an isobaric quantitation method in terms of the used channels and an isotope correction matrix.

Member Typedef Documentation

◆ IsobaricChannelList

typedef std::vector<IsobaricChannelInformation> IsobaricChannelList

Constructor & Destructor Documentation

◆ IsobaricQuantitationMethod()

IsobaricQuantitationMethod ( )

c'tor setting the name for the underlying param handler

◆ ~IsobaricQuantitationMethod()

~IsobaricQuantitationMethod ( )

override

d'tor

Member Function Documentation

◆ getChannelInformation()

virtual const IsobaricChannelList& getChannelInformation ( ) const

pure virtual

Returns information on the different channels used by the quantitation method.

Returns: A st::vector containing the channel information for this quantitation method.

Implemented in TMTTenPlexQuantitationMethod, TMTSixteenPlexQuantitationMethod, TMTSixPlexQuantitationMethod, TMTElevenPlexQuantitationMethod, ItraqFourPlexQuantitationMethod, and ItraqEightPlexQuantitationMethod.

◆ getIsotopeCorrectionMatrix()

virtual Matrix<double> getIsotopeCorrectionMatrix ( ) const

pure virtual

Returns an isotope correction matrix suitable for the given quantitation method.

Implemented in TMTTenPlexQuantitationMethod, TMTSixteenPlexQuantitationMethod, TMTSixPlexQuantitationMethod, TMTElevenPlexQuantitationMethod, ItraqFourPlexQuantitationMethod, and ItraqEightPlexQuantitationMethod.

◆ getMethodName()

virtual const String& getMethodName ( ) const

pure virtual

Returns a unique name for the quantitation method.

Returns: The unique name or identifier of the quantitation method.

Implemented in TMTTenPlexQuantitationMethod, TMTSixteenPlexQuantitationMethod, TMTSixPlexQuantitationMethod, TMTElevenPlexQuantitationMethod, ItraqFourPlexQuantitationMethod, and ItraqEightPlexQuantitationMethod.

◆ getNumberOfChannels()

virtual Size getNumberOfChannels ( ) const

pure virtual

Gives the number of channels available for this quantitation method.

Returns: The number of channels available for this quantitation method.

Implemented in TMTTenPlexQuantitationMethod, TMTSixteenPlexQuantitationMethod, TMTSixPlexQuantitationMethod, TMTElevenPlexQuantitationMethod, ItraqFourPlexQuantitationMethod, and ItraqEightPlexQuantitationMethod.

◆ getReferenceChannel()

virtual Size getReferenceChannel ( ) const

pure virtual

Returns the index of the reference channel in the IsobaricChannelList (see IsobaricQuantitationMethod::getChannelInformation()).

Implemented in TMTTenPlexQuantitationMethod, TMTSixteenPlexQuantitationMethod, TMTSixPlexQuantitationMethod, TMTElevenPlexQuantitationMethod, ItraqFourPlexQuantitationMethod, and ItraqEightPlexQuantitationMethod.

◆ stringListToIsotopCorrectionMatrix_()

Matrix<double> stringListToIsotopCorrectionMatrix_ ( const std::vector< String > & stringlist ) const

protected

Helper function to convert a string list containing an isotope correction matrix into a Matrix<double>.

Parameters

stringlist The StringList to convert.

Returns: An isotope correction matrix as Matrix<double>.

Classes

Public Types

Public Member Functions

Protected Member Functions

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ IsobaricChannelList

Constructor & Destructor Documentation

◆ IsobaricQuantitationMethod()

◆ ~IsobaricQuantitationMethod()

Member Function Documentation

◆ getChannelInformation()

◆ getIsotopeCorrectionMatrix()

◆ getMethodName()

◆ getNumberOfChannels()

◆ getReferenceChannel()

◆ stringListToIsotopCorrectionMatrix_()