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

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

Inheritance diagram for ItraqEightPlexQuantitationMethod:

Collaboration diagram for ItraqEightPlexQuantitationMethod:

Public Member Functions
	ItraqEightPlexQuantitationMethod ()
	Default c'tor.

	~ItraqEightPlexQuantitationMethod () override
	d'tor

	ItraqEightPlexQuantitationMethod (const ItraqEightPlexQuantitationMethod &other)
	Copy c'tor.

ItraqEightPlexQuantitationMethod &	operator= (const ItraqEightPlexQuantitationMethod &rhs)
	Assignment operator.


const IsobaricChannelList &	getChannelInformation () const override
	Methods to implement from IsobaricQuantitationMethod.

Size	getNumberOfChannels () const override
	Gives the number of channels available for this quantitation method.

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

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

Public Member Functions inherited from IsobaricQuantitationMethod
	IsobaricQuantitationMethod ()=delete
	Default c'tor is deleted: a concrete method must be constructed with its MethodType (see the protected c'tor).

	~IsobaricQuantitationMethod () override
	d'tor

const std::string &	getMethodName () const
	Returns a unique name for the quantitation method (its canonical identifier, e.g. "tmt6plex").

MethodType	getMethodType () const
	Returns the MethodType enum value of this quantitation method.

Public Member Functions inherited from DefaultParamHandler
	DefaultParamHandler (const std::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 std::string &	getName () const
	Non-mutable access to the name.

void	setName (const std::string &name)
	Mutable access to the name.

const std::vector< std::string > &	getSubsections () const
	Non-mutable access to the registered subsections.

Protected Member Functions
void	setDefaultParams_ ()
	implemented for DefaultParamHandler

void	updateMembers_ () override

Protected Member Functions inherited from IsobaricQuantitationMethod
	IsobaricQuantitationMethod (MethodType method_type)
	c'tor for derived classes: sets the underlying param-handler name and records the concrete `method_type`.

Matrix< double >	stringListToIsotopeCorrectionMatrix_ (const std::vector< std::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
void	defaultsToParam_ ()
	Updates the parameters after the defaults have been set in the constructor.

Private Attributes
IsobaricChannelList	channels_
	the actual information on the different itraq8plex channels.

Size	reference_channel_
	The reference channel for this experiment.

Additional Inherited Members
Public Types inherited from IsobaricQuantitationMethod
enum class	MethodType { UNKNOWN = 0 , TMT_6PLEX , TMT_10PLEX , TMT_11PLEX , TMT_16PLEX , TMT_18PLEX , TMT_32PLEX , TMT_35PLEX , ITRAQ_4PLEX , ITRAQ_8PLEX , SIZE_OF_METHODTYPE }
	Identifies a concrete isobaric quantitation method. UNKNOWN is used as a sentinel (disabled/none). More...

typedef std::vector< IsobaricChannelInformation >	IsobaricChannelList

Static Public Member Functions inherited from IsobaricQuantitationMethod
static std::string_view	methodTypeName (MethodType mt)

static std::string_view	methodDisplayName (MethodType mt)

static MethodType	methodTypeFromName (std::string_view name)
	Returns the MethodType corresponding to `name` (canonical identifier as returned by methodTypeName()), or MethodType::UNKNOWN if not found.

static std::unique_ptr< IsobaricQuantitationMethod >	create (MethodType mt)
	Factory: creates a new instance of the concrete quantitation method identified by `mt`.

Static Public Member Functions inherited from DefaultParamHandler
static void	writeParametersToMetaValues (const Param &write_this, MetaInfoInterface &write_here, const std::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< std::string >	subsections_
	Container for registered subsections. This member should be filled in the constructor of derived classes!

std::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

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

Methods to implement from IsobaricQuantitationMethod.

Implements IsobaricQuantitationMethod.

◆ getIsotopeCorrectionMatrix()

Matrix< double > getIsotopeCorrectionMatrix ( ) const

overridevirtual

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

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

Exceptions

Exception::InvalidParameter if the 'reference_channel' parameter is not a valid 8-plex channel (valid: 113-119, 121; 120 is not a valid channel)

Reimplemented from DefaultParamHandler.

Member Data Documentation

◆ channels_

IsobaricChannelList channels_

private

the actual information on the different itraq8plex channels.

◆ reference_channel_

Size reference_channel_

private

The reference channel for this experiment.

Public Member Functions

Protected Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ ItraqEightPlexQuantitationMethod() [1/2]

◆ ~ItraqEightPlexQuantitationMethod()

◆ ItraqEightPlexQuantitationMethod() [2/2]

Member Function Documentation

◆ getChannelInformation()

◆ getIsotopeCorrectionMatrix()

◆ getNumberOfChannels()

◆ getReferenceChannel()

◆ operator=()

◆ setDefaultParams_()

◆ updateMembers_()

Member Data Documentation

◆ channels_

◆ reference_channel_