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 () | |
| d'tor More... | |
| ItraqEightPlexQuantitationMethod (const ItraqEightPlexQuantitationMethod &other) | |
| Copy c'tor. More... | |
| ItraqEightPlexQuantitationMethod & | operator= (const ItraqEightPlexQuantitationMethod &rhs) |
| Assignment operator. More... | |
| const String & | getName () const |
| Methods to implement from IsobaricQuantitationMethod. More... | |
| const IsobaricChannelList & | getChannelInformation () const |
| Returns information on the different channels used by the quantitation method. More... | |
| Size | getNumberOfChannels () const |
| Gives the number of channels available for this quantitation method. More... | |
| virtual Matrix< double > | getIsotopeCorrectionMatrix () const |
| Returns an isotope correction matrix suitable for the given quantitation method. More... | |
| Size | getReferenceChannel () const |
| 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... | |
| virtual | ~IsobaricQuantitationMethod () |
| 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 ¶m) |
| 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_ () |
| 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]
Default c'tor.
◆ ~ItraqEightPlexQuantitationMethod()
d'tor
◆ ItraqEightPlexQuantitationMethod() [2/2]
| ItraqEightPlexQuantitationMethod | ( | const ItraqEightPlexQuantitationMethod & | other | ) |
Copy c'tor.
Member Function Documentation
◆ getChannelInformation()
|
virtual |
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()
Returns an isotope correction matrix suitable for the given quantitation method.
Implements IsobaricQuantitationMethod.
◆ getName()
|
virtual |
Methods to implement from IsobaricQuantitationMethod.
Implements IsobaricQuantitationMethod.
◆ getNumberOfChannels()
|
virtual |
Gives the number of channels available for this quantitation method.
- Returns
- The number of channels available for this quantitation method.
Implements IsobaricQuantitationMethod.
◆ getReferenceChannel()
|
virtual |
Returns the index of the reference channel in the IsobaricChannelList (see IsobaricQuantitationMethod::getChannelInformation()).
Implements IsobaricQuantitationMethod.
◆ operator=()
| ItraqEightPlexQuantitationMethod& operator= | ( | const ItraqEightPlexQuantitationMethod & | rhs | ) |
Assignment operator.
◆ setDefaultParams_()
|
protected |
implemented for DefaultParamHandler
◆ updateMembers_()
|
protectedvirtual |
implemented for DefaultParamHandler
Reimplemented from DefaultParamHandler.
Member Data Documentation
◆ channels_
|
private |
the actual information on the different itraq8plex channels.
◆ name_
|
staticprivate |
The name of the quantitation method.
◆ reference_channel_
|
private |
The reference channel for this experiment.