TMT 18plex quantitation to be used with the IsobaricQuantitation. More...

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

Inheritance diagram for TMTEighteenPlexQuantitationMethod:

Collaboration diagram for TMTEighteenPlexQuantitationMethod:

Public Member Functions
	TMTEighteenPlexQuantitationMethod ()
	Default c'tor. More...

	~TMTEighteenPlexQuantitationMethod () override=default
	d'tor More...

	TMTEighteenPlexQuantitationMethod (const TMTEighteenPlexQuantitationMethod &other)
	Copy c'tor. More...

TMTEighteenPlexQuantitationMethod &	operator= (const TMTEighteenPlexQuantitationMethod &rhs)
	Assignment operator. More...


const String &	getMethodName () 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...

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 >	stringListToIsotopeCorrectionMatrix_ (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
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 tmt18plex 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...

static const std::vector< std::string >	channel_names_
	List of available channel names as they are presented to the user. More...

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

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. 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

TMT 18plex quantitation to be used with the IsobaricQuantitation.

Parameters of this class are:

Name	Type	Default	Restrictions	Description
channel_126_description	string			Description for the content of the 126 channel.
channel_127N_description	string			Description for the content of the 127N channel.
channel_127C_description	string			Description for the content of the 127C channel.
channel_128N_description	string			Description for the content of the 128N channel.
channel_128C_description	string			Description for the content of the 128C channel.
channel_129N_description	string			Description for the content of the 129N channel.
channel_129C_description	string			Description for the content of the 129C channel.
channel_130N_description	string			Description for the content of the 130N channel.
channel_130C_description	string			Description for the content of the 130C channel.
channel_131N_description	string			Description for the content of the 131N channel.
channel_131C_description	string			Description for the content of the 131C channel.
channel_132N_description	string			Description for the content of the 132N channel.
channel_132C_description	string			Description for the content of the 132C channel.
channel_133N_description	string			Description for the content of the 133N channel.
channel_133C_description	string			Description for the content of the 133C channel.
channel_134N_description	string			Description for the content of the 134N channel.
channel_134C_description	string			Description for the content of the 134C channel.
channel_135N_description	string			Description for the content of the 135N channel.
reference_channel	string	126	126, 127N, 127C, 128N, 128C, 129N, 129C, 130N, 130C, 131N, 131C, 132N, 132C, 133N, 133C, 134N, 134C, 135N	The reference channel (126, 127N, 127C, 128N, 128C, 129N, 129C, 130N, 130C, 131N, 131C, 132N, 132C, 133N, 133C, 134N, 134C, 135N).
correction_matrix	string list	[NA/NA /NA/NA /0.31/9.09 /0.02/0.32, NA/NA /NA/0.78 /NA/9.41 /NA/0.33, NA/NA /0.93/NA /0.35/8.63 /0.01/0.27, NA/0.00 /0.82/0.65 /NA/8.13 /NA/0.26, 0.00/NA /1.47/NA /0.34/6.91 /0.00/0.15, 0.00/0.00 /1.46/1.28 /NA/6.86 /NA/0.15, 0.13/NA /2.59/NA /0.32/6.07 /0.1/0.09, 0.13/0.00 /2.41/0.27 /NA/5.58 /NA/0.10, 0.04/NA /3.10/NA /0.42/4.82 /0.02/0.06, 0.03/0.00 /2.78/0.63 /NA/4.57 /NA/0.12, 0.08/NA /3.90/NA /0.47/3.57 /0.00/0.04, 0.15/0.01 /3.58/0.72 /NA/1.80 /NA/0.00, 0.11/NA /4.55/NA /0.43/1.86 /0.00/0.00, 0.07/0.01 /3.14/0.73 /NA/3.40 /NA/0.03, 0.22/NA /4.96/NA /0.34/1.03 /0.00/NA, 0.30/0.03 /5.49/0.62 /NA/1.14 /NA/NA, 0.14/NA /5.81/NA /0.31/NA /NA/NA, 0.19/0.02 /5.42/0.36 /NA/NA /NA/NA]		Correction matrix for isotope distributions in percent from the Thermo data sheet (see documentation); Please provide 18 entries (rows), separated by comma, where each entry contains 8 values in the following format: <-2C13>/<-N15-C13>/<-C13>/<-N15>/<+N15>/<+C13>/<+N15+C13>/<+2C13> e.g. one row may look like this: 'NA/0.00 / 0.82/0.65 / NA/8.13 / NA/0.26'. You may use whitespaces at your leisure to ease reading.

Note:

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

Constructor & Destructor Documentation

◆ TMTEighteenPlexQuantitationMethod() [1/2]

TMTEighteenPlexQuantitationMethod ( )

Default c'tor.

◆ ~TMTEighteenPlexQuantitationMethod()

~TMTEighteenPlexQuantitationMethod ( )

overridedefault

d'tor

◆ TMTEighteenPlexQuantitationMethod() [2/2]

TMTEighteenPlexQuantitationMethod ( const TMTEighteenPlexQuantitationMethod & 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 std::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.

◆ getMethodName()

const String& getMethodName ( ) 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=()

TMTEighteenPlexQuantitationMethod& operator= ( const TMTEighteenPlexQuantitationMethod & rhs )

Assignment operator.

◆ setDefaultParams_()

void setDefaultParams_ ( )

protected

implemented for DefaultParamHandler

◆ updateMembers_()

void updateMembers_ ( )

overrideprotectedvirtual

implemented for DefaultParamHandler

Reimplemented from DefaultParamHandler.

Member Data Documentation

◆ channel_names_

const std::vector<std::string> channel_names_

staticprivate

List of available channel names as they are presented to the user.

◆ channels_

IsobaricChannelList channels_

private

the actual information on the different tmt18plex channels.

◆ name_

const String name_

staticprivate

The name of the quantitation method.

◆ reference_channel_

Size reference_channel_

private

The reference channel for this experiment.

Public Member Functions

Protected Member Functions

Private Attributes

Static Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ TMTEighteenPlexQuantitationMethod() [1/2]

◆ ~TMTEighteenPlexQuantitationMethod()

◆ TMTEighteenPlexQuantitationMethod() [2/2]

Member Function Documentation

◆ getChannelInformation()

◆ getIsotopeCorrectionMatrix()

◆ getMethodName()

◆ getNumberOfChannels()

◆ getReferenceChannel()

◆ operator=()

◆ setDefaultParams_()

◆ updateMembers_()

Member Data Documentation

◆ channel_names_

◆ channels_

◆ name_

◆ reference_channel_