OpenMS
ItraqFourPlexQuantitationMethod Class Reference

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

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

Inheritance diagram for ItraqFourPlexQuantitationMethod:
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Collaboration diagram for ItraqFourPlexQuantitationMethod:
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Public Member Functions

 ItraqFourPlexQuantitationMethod ()
 Default c'tor. More...
 
 ~ItraqFourPlexQuantitationMethod () override
 d'tor More...
 
 ItraqFourPlexQuantitationMethod (const ItraqFourPlexQuantitationMethod &other)
 Copy c'tor. More...
 
ItraqFourPlexQuantitationMethodoperator= (const ItraqFourPlexQuantitationMethod &rhs)
 Assignment operator. More...
 
const StringgetMethodName () const override
 Methods to implement from IsobaricQuantitationMethod. More...
 
const IsobaricChannelListgetChannelInformation () 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...
 
DefaultParamHandleroperator= (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 ParamgetParameters () const
 Non-mutable access to the parameters. More...
 
const ParamgetDefaults () const
 Non-mutable access to the default parameters. More...
 
const StringgetName () 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 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< IsobaricChannelInformationIsobaricChannelList
 
- 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< Stringsubsections_
 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.

Parameters of this class are:

NameTypeDefaultRestrictionsDescription
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.
reference_channel int114 min: 114 max: 117Number of the reference channel (114-117).
correction_matrix string list[0.0/1.0/5.9/0.2, 0.0/2.0/5.6/0.1, 0.0/3.0/4.5/0.1, 0.1/4.0/3.5/0.1]  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

◆ ItraqFourPlexQuantitationMethod() [1/2]

Default c'tor.

◆ ~ItraqFourPlexQuantitationMethod()

d'tor

◆ ItraqFourPlexQuantitationMethod() [2/2]

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=()

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 itraq4plex channels.

◆ name_

const String name_
staticprivate

The name of the quantitation method.

◆ reference_channel_

Size reference_channel_
private

The reference channel for this experiment.