IsobaricQuantitationMethod Class Reference

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:

Collaboration diagram for IsobaricQuantitationMethod:

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
	~IsobaricQuantitationMethod () override
	d'tor
virtual const String &	getMethodName () const =0
	Returns a unique name for the quantitation method.
virtual const IsobaricChannelList &	getChannelInformation () const =0
	Returns information on the different channels used by the quantitation method.
virtual Size	getNumberOfChannels () const =0
	Gives the number of channels available for this quantitation method.
virtual Matrix< double >	getIsotopeCorrectionMatrix () const =0
	Returns an isotope correction matrix suitable for the given quantitation method.
virtual Size	getReferenceChannel () const =0
	Returns the index of the reference channel in the IsobaricChannelList (see IsobaricQuantitationMethod::getChannelInformation()).
Public Member Functions inherited from DefaultParamHandler
	DefaultParamHandler (const String &name)
	Constructor with name that is displayed in error messages.
	DefaultParamHandler (const DefaultParamHandler &rhs)
	Copy constructor.
virtual	~DefaultParamHandler ()
	Destructor.
DefaultParamHandler &	operator= (const DefaultParamHandler &rhs)
	Assignment operator.
virtual bool	operator== (const DefaultParamHandler &rhs) const
	Equality operator.
void	setParameters (const Param &param)
	Sets the parameters.
const Param &	getParameters () const
	Non-mutable access to the parameters.
const Param &	getDefaults () const
	Non-mutable access to the default parameters.
const String &	getName () const
	Non-mutable access to the name.
void	setName (const String &name)
	Mutable access to the name.
const std::vector< String > &	getSubsections () const
	Non-mutable access to the registered subsections.

Protected Member Functions
Matrix< double >	stringListToIsotopeCorrectionMatrix_ (const std::vector< String > &stringlist) const
	Helper function to convert a string list containing an isotope correction matrix into a Matrix<double>.
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.
void	defaultsToParam_ ()
	Updates the parameters after the defaults have been set in the constructor.

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.
Protected Attributes inherited from DefaultParamHandler
Param	param_
	Container for current parameters.
Param	defaults_
	Container for default parameters. This member should be filled in the constructor of derived classes!
std::vector< String >	subsections_
	Container for registered subsections. This member should be filled in the constructor of derived classes!
String	error_name_
	Name that is displayed in error messages during the parameter checking.
bool	check_defaults_
	If this member is set to false no checking if parameters in done;.
bool	warn_empty_defaults_
	If this member is set to false no warning is emitted when defaults are empty;.

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 std::vector containing the channel information for this quantitation method.

Implemented in ItraqEightPlexQuantitationMethod, ItraqFourPlexQuantitationMethod, TMTEighteenPlexQuantitationMethod, TMTElevenPlexQuantitationMethod, TMTSixPlexQuantitationMethod, TMTSixteenPlexQuantitationMethod, TMTTenPlexQuantitationMethod, TMTThirtyFivePlexQuantitationMethod, and TMTThirtyTwoPlexQuantitationMethod.

getIsotopeCorrectionMatrix()

virtual Matrix< double > getIsotopeCorrectionMatrix ( ) const

pure virtual

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

Implemented in ItraqEightPlexQuantitationMethod, ItraqFourPlexQuantitationMethod, TMTEighteenPlexQuantitationMethod, TMTElevenPlexQuantitationMethod, TMTSixPlexQuantitationMethod, TMTSixteenPlexQuantitationMethod, TMTTenPlexQuantitationMethod, TMTThirtyFivePlexQuantitationMethod, and TMTThirtyTwoPlexQuantitationMethod.

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 ItraqEightPlexQuantitationMethod, ItraqFourPlexQuantitationMethod, TMTEighteenPlexQuantitationMethod, TMTElevenPlexQuantitationMethod, TMTSixPlexQuantitationMethod, TMTSixteenPlexQuantitationMethod, TMTTenPlexQuantitationMethod, TMTThirtyFivePlexQuantitationMethod, and TMTThirtyTwoPlexQuantitationMethod.

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 ItraqEightPlexQuantitationMethod, ItraqFourPlexQuantitationMethod, TMTEighteenPlexQuantitationMethod, TMTElevenPlexQuantitationMethod, TMTSixPlexQuantitationMethod, TMTSixteenPlexQuantitationMethod, TMTTenPlexQuantitationMethod, TMTThirtyFivePlexQuantitationMethod, and TMTThirtyTwoPlexQuantitationMethod.

getReferenceChannel()

virtual Size getReferenceChannel ( ) const

pure virtual

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

Implemented in ItraqEightPlexQuantitationMethod, ItraqFourPlexQuantitationMethod, TMTEighteenPlexQuantitationMethod, TMTElevenPlexQuantitationMethod, TMTSixPlexQuantitationMethod, TMTSixteenPlexQuantitationMethod, TMTTenPlexQuantitationMethod, TMTThirtyFivePlexQuantitationMethod, and TMTThirtyTwoPlexQuantitationMethod.

stringListToIsotopeCorrectionMatrix_()

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

protected

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

Parameters

[in]

stringlist

The StringList to convert.

Returns

An isotope correction matrix as Matrix<double>.