OpenMS
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TMT 10plex quantitation to be used with the IsobaricQuantitation. More...
#include <OpenMS/ANALYSIS/QUANTITATION/TMTTenPlexQuantitationMethod.h>
Public Member Functions | |
TMTTenPlexQuantitationMethod () | |
Default c'tor. More... | |
~TMTTenPlexQuantitationMethod () override=default | |
d'tor More... | |
TMTTenPlexQuantitationMethod (const TMTTenPlexQuantitationMethod &other) | |
Copy c'tor. More... | |
TMTTenPlexQuantitationMethod & | operator= (const TMTTenPlexQuantitationMethod &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 tmt10plex 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... | |
TMT 10plex quantitation to be used with the IsobaricQuantitation.
Parameters of this class are:Name | Type | Default | Restrictions | Description |
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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_131_description | string | Description for the content of the 131 channel. | ||
reference_channel | string | 126 | 126, 127N, 127C, 128N, 128C, 129N, 129C, 130N, 130C, 131 | The reference channel (126, 127N, 127C, 128N, 128C, 129N, 129C, 130N, 130C, 131). |
correction_matrix | string list | [0.0/0.0/5.09/0.0, 0.0/0.25/5.27/0.0, 0.0/0.37/5.36/0.15, 0.0/0.65/4.17/0.1, 0.08/0.49/3.06/0.0, 0.01/0.71/3.07/0.0, 0.0/1.32/2.62/0.0, 0.02/1.28/2.75/2.53, 0.03/2.08/2.23/0.0, 0.08/1.99/1.65/0.0] | 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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overridedefault |
d'tor
TMTTenPlexQuantitationMethod | ( | const TMTTenPlexQuantitationMethod & | 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.
TMTTenPlexQuantitationMethod& operator= | ( | const TMTTenPlexQuantitationMethod & | 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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staticprivate |
List of available channel names as they are presented to the user.
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private |
the actual information on the different tmt10plex channels.
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staticprivate |
The name of the quantitation method.
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private |
The reference channel for this experiment.