ItraqEightPlexQuantitationMethod Class Reference

iTRAQ 8 plex quantitation to be used with the IsobaricQuantitation. More...

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

Inheritance diagram for ItraqEightPlexQuantitationMethod:

Public Member Functions
	ItraqEightPlexQuantitationMethod ()
	Default c'tor. More...
	~ItraqEightPlexQuantitationMethod () override
	d'tor More...
	ItraqEightPlexQuantitationMethod (const ItraqEightPlexQuantitationMethod &other)
	Copy c'tor. More...
ItraqEightPlexQuantitationMethod &	operator= (const ItraqEightPlexQuantitationMethod &rhs)
	Assignment operator. More...
const String &	getName () const override
	Methods to implement from IsobaricQuantitationMethod. More...
const IsobaricChannelList &	getChannelInformation () const override
	Returns information on the different channels used by the quantitation method. More...
Size	getNumberOfChannels () const override
	Gives the number of channels available for this quantitation method. More...
Matrix< double >	getIsotopeCorrectionMatrix () const override
	Returns an isotope correction matrix suitable for the given quantitation method. More...
Size	getReferenceChannel () const override
	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...
	~IsobaricQuantitationMethod () override
	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_ () override
	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 itraq8plex 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 8 plex quantitation to be used with the IsobaricQuantitation.

Parameters of this class are:

Name	Type	Default	Restrictions	Description
channel_113_description	string			Description for the content of the 113 channel.
channel_114_description	string			Description for the content of the 114 channel.
channel_115_description	string			Description for the content of the 115 channel.
channel_116_description	string			Description for the content of the 116 channel.
channel_117_description	string			Description for the content of the 117 channel.
channel_118_description	string			Description for the content of the 118 channel.
channel_119_description	string			Description for the content of the 119 channel.
channel_121_description	string			Description for the content of the 121 channel.
reference_channel	int	113	min: 113 max: 121	Number of the reference channel (113-121). Please note that 120 is not valid.
correction_matrix	string list	[0.00/0.00/6.89/0.22, 0.00/0.94/5.90/0.16, 0.00/1.88/4.90/0.10, 0.00/2.82/3.90/0.07, 0.06/3.77/2.99/0.00, 0.09/4.71/1.88/0.00, 0.14/5.66/0.87/0.00, 0.27/7.44/0.18/0.00]		Correction matrix for isotope distributions (see documentation); use the following format: <-2Da>/<-1Da>/<+1Da>/<+2Da>; e.g. '0/0.3/4/0', '0.1/0.3/3/0.2'

Note:

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

Constructor & Destructor Documentation

ItraqEightPlexQuantitationMethod() [1/2]

ItraqEightPlexQuantitationMethod

(

)

Default c'tor.

~ItraqEightPlexQuantitationMethod()

~ItraqEightPlexQuantitationMethod ( )

override

d'tor

ItraqEightPlexQuantitationMethod() [2/2]

ItraqEightPlexQuantitationMethod

(

const ItraqEightPlexQuantitationMethod &

other

)

Copy c'tor.

Member Function Documentation

getChannelInformation()

const IsobaricChannelList& getChannelInformation ( ) const

overridevirtual

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.

getIsotopeCorrectionMatrix()

Matrix<double> getIsotopeCorrectionMatrix ( ) const

overridevirtual

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

Implements IsobaricQuantitationMethod.

getName()

const String& getName ( ) const

overridevirtual

Methods to implement from IsobaricQuantitationMethod.

Implements IsobaricQuantitationMethod.

getNumberOfChannels()

Size getNumberOfChannels ( ) const

overridevirtual

Gives the number of channels available for this quantitation method.

Returns

The number of channels available for this quantitation method.

Implements IsobaricQuantitationMethod.

getReferenceChannel()

Size getReferenceChannel ( ) const

overridevirtual

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

Implements IsobaricQuantitationMethod.

operator=()

ItraqEightPlexQuantitationMethod& operator=

(

const ItraqEightPlexQuantitationMethod &

rhs

)

Assignment operator.

setDefaultParams_()

void setDefaultParams_ ( )

protected

implemented for DefaultParamHandler

updateMembers_()

void updateMembers_ ( )

overrideprotectedvirtual

implemented for DefaultParamHandler

Reimplemented from DefaultParamHandler.

Member Data Documentation

channels_

IsobaricChannelList channels_

private

the actual information on the different itraq8plex channels.

name_

const String name_

staticprivate

The name of the quantitation method.

reference_channel_

Size reference_channel_

private

The reference channel for this experiment.