OpenMS
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iTRAQ 8 plex quantitation to be used with the IsobaricQuantitation. More...
#include <OpenMS/ANALYSIS/QUANTITATION/ItraqEightPlexQuantitationMethod.h>
Public Member Functions | |
ItraqEightPlexQuantitationMethod () | |
Default c'tor. More... | |
~ItraqEightPlexQuantitationMethod () override | |
d'tor More... | |
ItraqEightPlexQuantitationMethod (const ItraqEightPlexQuantitationMethod &other) | |
Copy c'tor. More... | |
ItraqEightPlexQuantitationMethod & | operator= (const ItraqEightPlexQuantitationMethod &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 ¶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_ () 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 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 |
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... | |
iTRAQ 8 plex quantitation to be used with the IsobaricQuantitation.
Parameters of this class are:Name | Type | Default | Restrictions | Description |
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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' |
Default c'tor.
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override |
d'tor
ItraqEightPlexQuantitationMethod | ( | const ItraqEightPlexQuantitationMethod & | other | ) |
Copy c'tor.
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overridevirtual |
Returns information on the different channels used by the quantitation method.
Implements IsobaricQuantitationMethod.
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overridevirtual |
Returns an isotope correction matrix suitable for the given quantitation method.
Implements IsobaricQuantitationMethod.
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overridevirtual |
Methods to implement from IsobaricQuantitationMethod.
Implements IsobaricQuantitationMethod.
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overridevirtual |
Gives the number of channels available for this quantitation method.
Implements IsobaricQuantitationMethod.
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overridevirtual |
Returns the index of the reference channel in the IsobaricChannelList (see IsobaricQuantitationMethod::getChannelInformation()).
Implements IsobaricQuantitationMethod.
ItraqEightPlexQuantitationMethod& operator= | ( | const ItraqEightPlexQuantitationMethod & | rhs | ) |
Assignment operator.
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protected |
implemented for DefaultParamHandler
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overrideprotectedvirtual |
implemented for DefaultParamHandler
Reimplemented from DefaultParamHandler.
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private |
the actual information on the different itraq8plex channels.
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staticprivate |
The name of the quantitation method.
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private |
The reference channel for this experiment.