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... | |
| virtual | ~IsobaricQuantitationMethod () |
| d'tor More... | |
| virtual const String & | getName () 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... | |
| 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 | |
| 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 | |
| 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 | |
| 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
Abstract base class describing an isobaric quantitation method in terms of the used channels and an isotope correction matrix.
Member Typedef Documentation
◆ IsobaricChannelList
| typedef std::vector<IsobaricChannelInformation> IsobaricChannelList |
Constructor & Destructor Documentation
◆ IsobaricQuantitationMethod()
c'tor setting the name for the underlying param handler
◆ ~IsobaricQuantitationMethod()
|
virtual |
d'tor
Member Function Documentation
◆ getChannelInformation()
|
pure virtual |
Returns information on the different channels used by the quantitation method.
- Returns
- A st::vector containing the channel information for this quantitation method.
Implemented in ItraqEightPlexQuantitationMethod, TMTElevenPlexQuantitationMethod, TMTSixPlexQuantitationMethod, TMTTenPlexQuantitationMethod, and ItraqFourPlexQuantitationMethod.
◆ getIsotopeCorrectionMatrix()
Returns an isotope correction matrix suitable for the given quantitation method.
Implemented in ItraqEightPlexQuantitationMethod, TMTElevenPlexQuantitationMethod, TMTSixPlexQuantitationMethod, TMTTenPlexQuantitationMethod, and ItraqFourPlexQuantitationMethod.
◆ getName()
|
pure virtual |
Returns a unique name for the quantitation method.
- Returns
- The unique name or identifier of the quantitation method.
Implemented in ItraqEightPlexQuantitationMethod, TMTElevenPlexQuantitationMethod, TMTSixPlexQuantitationMethod, TMTTenPlexQuantitationMethod, and ItraqFourPlexQuantitationMethod.
◆ getNumberOfChannels()
|
pure virtual |
Gives the number of channels available for this quantitation method.
- Returns
- The number of channels available for this quantitation method.
Implemented in ItraqEightPlexQuantitationMethod, TMTElevenPlexQuantitationMethod, TMTSixPlexQuantitationMethod, TMTTenPlexQuantitationMethod, and ItraqFourPlexQuantitationMethod.
◆ getReferenceChannel()
|
pure virtual |
Returns the index of the reference channel in the IsobaricChannelList (see IsobaricQuantitationMethod::getChannelInformation()).
Implemented in ItraqEightPlexQuantitationMethod, TMTElevenPlexQuantitationMethod, TMTSixPlexQuantitationMethod, TMTTenPlexQuantitationMethod, and ItraqFourPlexQuantitationMethod.
◆ stringListToIsotopCorrectionMatrix_()
|
protected |
Helper function to convert a string list containing an isotope correction matrix into a Matrix<double>.
- Parameters
-
stringlist The StringList to convert.
- Returns
- An isotope correction matrix as Matrix<double>.