OpenMS
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Abstract base class describing an isobaric quantitation method in terms of the used channels and an isotope correction matrix. More...
#include <OpenMS/ANALYSIS/QUANTITATION/IsobaricQuantitationMethod.h>
Classes | |
struct | IsobaricChannelInformation |
Summary of an isobaric quantitation channel. More... | |
Public Types | |
typedef std::vector< IsobaricChannelInformation > | IsobaricChannelList |
Public Member Functions | |
IsobaricQuantitationMethod () | |
c'tor setting the name for the underlying param handler More... | |
~IsobaricQuantitationMethod () override | |
d'tor More... | |
virtual const String & | getMethodName () const =0 |
Returns a unique name for the quantitation method. More... | |
virtual const IsobaricChannelList & | getChannelInformation () const =0 |
Returns information on the different channels used by the quantitation method. More... | |
virtual Size | getNumberOfChannels () const =0 |
Gives the number of channels available for this quantitation method. More... | |
virtual Matrix< double > | getIsotopeCorrectionMatrix () const =0 |
Returns an isotope correction matrix suitable for the given quantitation method. More... | |
virtual Size | getReferenceChannel () const =0 |
Returns the index of the reference channel in the IsobaricChannelList (see IsobaricQuantitationMethod::getChannelInformation()). 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 | |
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 | |
virtual void | updateMembers_ () |
This method is used to update extra member variables at the end of the setParameters() method. More... | |
void | defaultsToParam_ () |
Updates the parameters after the defaults have been set in the constructor. More... | |
Additional Inherited Members | |
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... | |
Abstract base class describing an isobaric quantitation method in terms of the used channels and an isotope correction matrix.
typedef std::vector<IsobaricChannelInformation> IsobaricChannelList |
c'tor setting the name for the underlying param handler
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override |
d'tor
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pure virtual |
Returns information on the different channels used by the quantitation method.
Implemented in TMTTenPlexQuantitationMethod, TMTSixteenPlexQuantitationMethod, TMTSixPlexQuantitationMethod, TMTElevenPlexQuantitationMethod, TMTEighteenPlexQuantitationMethod, ItraqFourPlexQuantitationMethod, and ItraqEightPlexQuantitationMethod.
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pure virtual |
Returns an isotope correction matrix suitable for the given quantitation method.
Implemented in TMTTenPlexQuantitationMethod, TMTSixteenPlexQuantitationMethod, TMTSixPlexQuantitationMethod, TMTElevenPlexQuantitationMethod, TMTEighteenPlexQuantitationMethod, ItraqFourPlexQuantitationMethod, and ItraqEightPlexQuantitationMethod.
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pure virtual |
Returns a unique name for the quantitation method.
Implemented in TMTTenPlexQuantitationMethod, TMTSixteenPlexQuantitationMethod, TMTSixPlexQuantitationMethod, TMTElevenPlexQuantitationMethod, TMTEighteenPlexQuantitationMethod, ItraqFourPlexQuantitationMethod, and ItraqEightPlexQuantitationMethod.
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pure virtual |
Gives the number of channels available for this quantitation method.
Implemented in TMTTenPlexQuantitationMethod, TMTSixteenPlexQuantitationMethod, TMTSixPlexQuantitationMethod, TMTElevenPlexQuantitationMethod, TMTEighteenPlexQuantitationMethod, ItraqFourPlexQuantitationMethod, and ItraqEightPlexQuantitationMethod.
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pure virtual |
Returns the index of the reference channel in the IsobaricChannelList (see IsobaricQuantitationMethod::getChannelInformation()).
Implemented in TMTTenPlexQuantitationMethod, TMTSixteenPlexQuantitationMethod, TMTSixPlexQuantitationMethod, TMTElevenPlexQuantitationMethod, TMTEighteenPlexQuantitationMethod, ItraqFourPlexQuantitationMethod, and ItraqEightPlexQuantitationMethod.
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protected |
Helper function to convert a string list containing an isotope correction matrix into a Matrix<double>.
stringlist | The StringList to convert. |