ItraqFourPlexQuantitationMethod Class Reference

iTRAQ 4 plex quantitation to be used with the IsobaricQuantitation. More...

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

Inheritance diagram for ItraqFourPlexQuantitationMethod:

Public Member Functions
	ItraqFourPlexQuantitationMethod ()
	Default c'tor. More...
	~ItraqFourPlexQuantitationMethod ()
	d'tor More...
	ItraqFourPlexQuantitationMethod (const ItraqFourPlexQuantitationMethod &other)
	Copy c'tor. More...
ItraqFourPlexQuantitationMethod &	operator= (const ItraqFourPlexQuantitationMethod &rhs)
	Assignment operator. More...
const String &	getName () const
	Methods to implement from IsobaricQuantitationMethod. More...
const IsobaricChannelList &	getChannelInformation () const
	Returns information on the different channels used by the quantitation method. More...
Size	getNumberOfChannels () const
	Gives the number of channels available for this quantitation method. More...
virtual Matrix< double >	getIsotopeCorrectionMatrix () const
	Returns an isotope correction matrix suitable for the given quantitation method. More...
Size	getReferenceChannel () const
	Returns the index of the reference channel in the IsobaricChannelList (see IsobaricQuantitationMethod::getChannelInformation()). More...
Public Member Functions inherited from IsobaricQuantitationMethod
	IsobaricQuantitationMethod ()
	c'tor setting the name for the underlying param handler More...
virtual	~IsobaricQuantitationMethod ()
	d'tor 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
void	setDefaultParams_ ()
	implemented for DefaultParamHandler More...
void	updateMembers_ ()
	implemented for DefaultParamHandler More...
Protected Member Functions inherited from IsobaricQuantitationMethod
Matrix< double >	stringListToIsotopCorrectionMatrix_ (const StringList &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
void	defaultsToParam_ ()
	Updates the parameters after the defaults have been set in the constructor. More...

Private Attributes
IsobaricChannelList	channels_
	the actual information on the different itraq4plex channels. More...
Size	reference_channel_
	The reference channel for this experiment. More...

Static Private Attributes
static const String	name_
	The name of the quantitation method. More...

Additional Inherited Members
Public Types inherited from IsobaricQuantitationMethod
typedef std::vector< IsobaricChannelInformation >	IsobaricChannelList
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

iTRAQ 4 plex quantitation to be used with the IsobaricQuantitation.

Constructor & Destructor Documentation

ItraqFourPlexQuantitationMethod

(

)

Default c'tor.

~ItraqFourPlexQuantitationMethod

(

)

d'tor

ItraqFourPlexQuantitationMethod

(

const ItraqFourPlexQuantitationMethod &

other

)

Copy c'tor.

Member Function Documentation

const IsobaricChannelList& getChannelInformation ( ) const

virtual

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

Returns

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

Implements IsobaricQuantitationMethod.

virtual Matrix<double> getIsotopeCorrectionMatrix ( ) const

virtual

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

Implements IsobaricQuantitationMethod.

const String& getName ( ) const

virtual

Methods to implement from IsobaricQuantitationMethod.

Implements IsobaricQuantitationMethod.

Size getNumberOfChannels ( ) const

virtual

Gives the number of channels available for this quantitation method.

Returns

The number of channels available for this quantitation method.

Implements IsobaricQuantitationMethod.

Size getReferenceChannel ( ) const

virtual

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

Implements IsobaricQuantitationMethod.

ItraqFourPlexQuantitationMethod& operator=

(

const ItraqFourPlexQuantitationMethod &

rhs

)

Assignment operator.

void setDefaultParams_ ( )

protected

implemented for DefaultParamHandler

void updateMembers_ ( )

protectedvirtual

implemented for DefaultParamHandler

Reimplemented from DefaultParamHandler.

Member Data Documentation

IsobaricChannelList channels_

private

the actual information on the different itraq4plex channels.

const String name_

staticprivate

The name of the quantitation method.

Size reference_channel_

private

The reference channel for this experiment.