TMTThirtyTwoPlexQuantitationMethod Class Reference

TMT 32plex quantitation to be used for 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_127D_description	string			Description for the content of the 127D 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_128ND_description	string			Description for the content of the 128ND channel.
channel_128CD_description	string			Description for the content of the 128CD 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_129ND_description	string			Description for the content of the 129ND channel.
channel_129CD_description	string			Description for the content of the 129CD 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_130ND_description	string			Description for the content of the 130ND channel.
channel_130CD_description	string			Description for the content of the 130CD 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_131ND_description	string			Description for the content of the 131ND channel.
channel_131CD_description	string			Description for the content of the 131CD 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_132ND_description	string			Description for the content of the 132ND channel.
channel_132CD_description	string			Description for the content of the 132CD 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_133ND_description	string			Description for the content of the 133ND channel.
channel_133CD_description	string			Description for the content of the 133CD channel.
channel_134N_description	string			Description for the content of the 134N channel.
channel_134ND_description	string			Description for the content of the 134ND channel.
channel_134CD_description	string			Description for the content of the 134CD channel.
channel_135ND_description	string			Description for the content of the 135ND channel.
reference_channel	string	126	126, 127N, 127C, 127D, 128N, 128C, 128ND, 128CD, 129N, 129C, 129ND, 129CD, 130N, 130C, 130ND, 130CD, 131N, 131C, 131ND, 131CD, 132N, 132C, 132ND, 132CD, 133N, 133C, 133ND, 133CD, 134N, 134ND, 134CD, 135ND	The reference channel (126, 127N, 127C, 127D, 128N, 128C, 128ND, 128CD, 129N, 129C, 129ND, 129CD, 130N, 130C, 130ND, 130CD, 131N, 131C, 131ND, 131CD, 132N, 132C, 132ND, 132CD, 133N, 133C, 133ND, 133CD, 134N, 134ND, 134CD, 135ND).
correction_matrix	string list	[NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA]		Ignored for TMT 32-plex (identity matrix is always used). Isotope correction is not yet supported for this method.

Note:

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

. More...

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

Inheritance diagram for TMTThirtyTwoPlexQuantitationMethod:

Collaboration diagram for TMTThirtyTwoPlexQuantitationMethod:

Public Member Functions
	TMTThirtyTwoPlexQuantitationMethod ()
	Default Constructor.
	~TMTThirtyTwoPlexQuantitationMethod () override=default
	Destructor.
	TMTThirtyTwoPlexQuantitationMethod (const TMTThirtyTwoPlexQuantitationMethod &other)
	Copy Constructor.
TMTThirtyTwoPlexQuantitationMethod &	operator= (const TMTThirtyTwoPlexQuantitationMethod &rhs)
	Assignment operator.
const String &	getMethodName () const override
	Methods to implement from IsobaricQuantitationMethod.
const IsobaricChannelList &	getChannelInformation () const override
	Returns information on the different channels used by the quantitation method.
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 ()
	c'tor setting the name for the underlying param handler
	~IsobaricQuantitationMethod () override
	d'tor
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
void	setDefaultParams_ ()
	implemented for DefaultParamHandler
void	updateMembers_ () override
	implemented for DefaultParamHandler
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>.
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 TMT 32plex channels.
Size	reference_channel_
	The reference channel for this experiment.

Static Private Attributes
static const String	name_
	The name of the quantitation method.
static const std::vector< std::string >	channel_names_
	List of available channel names as they are presented to the user.

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.
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

TMT 32plex quantitation to be used for 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_127D_description	string			Description for the content of the 127D 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_128ND_description	string			Description for the content of the 128ND channel.
channel_128CD_description	string			Description for the content of the 128CD 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_129ND_description	string			Description for the content of the 129ND channel.
channel_129CD_description	string			Description for the content of the 129CD 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_130ND_description	string			Description for the content of the 130ND channel.
channel_130CD_description	string			Description for the content of the 130CD 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_131ND_description	string			Description for the content of the 131ND channel.
channel_131CD_description	string			Description for the content of the 131CD 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_132ND_description	string			Description for the content of the 132ND channel.
channel_132CD_description	string			Description for the content of the 132CD 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_133ND_description	string			Description for the content of the 133ND channel.
channel_133CD_description	string			Description for the content of the 133CD channel.
channel_134N_description	string			Description for the content of the 134N channel.
channel_134ND_description	string			Description for the content of the 134ND channel.
channel_134CD_description	string			Description for the content of the 134CD channel.
channel_135ND_description	string			Description for the content of the 135ND channel.
reference_channel	string	126	126, 127N, 127C, 127D, 128N, 128C, 128ND, 128CD, 129N, 129C, 129ND, 129CD, 130N, 130C, 130ND, 130CD, 131N, 131C, 131ND, 131CD, 132N, 132C, 132ND, 132CD, 133N, 133C, 133ND, 133CD, 134N, 134ND, 134CD, 135ND	The reference channel (126, 127N, 127C, 127D, 128N, 128C, 128ND, 128CD, 129N, 129C, 129ND, 129CD, 130N, 130C, 130ND, 130CD, 131N, 131C, 131ND, 131CD, 132N, 132C, 132ND, 132CD, 133N, 133C, 133ND, 133CD, 134N, 134ND, 134CD, 135ND).
correction_matrix	string list	[NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA]		Ignored for TMT 32-plex (identity matrix is always used). Isotope correction is not yet supported for this method.

Note:

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

.

Constructor & Destructor Documentation

TMTThirtyTwoPlexQuantitationMethod() [1/2]

TMTThirtyTwoPlexQuantitationMethod

(

)

Default Constructor.

~TMTThirtyTwoPlexQuantitationMethod()

~TMTThirtyTwoPlexQuantitationMethod ( )

overridedefault

Destructor.

TMTThirtyTwoPlexQuantitationMethod() [2/2]

TMTThirtyTwoPlexQuantitationMethod

(

const TMTThirtyTwoPlexQuantitationMethod &

other

)

Copy Constructor.

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=()

TMTThirtyTwoPlexQuantitationMethod & operator=

(

const TMTThirtyTwoPlexQuantitationMethod &

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 TMT 32plex channels.

name_

const String name_

staticprivate

The name of the quantitation method.

reference_channel_

Size reference_channel_

private

The reference channel for this experiment.