OpenMS
2.6.0
|
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... | |
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 | |
Static Public Member Functions inherited from DefaultParamHandler | |
static void | writeParametersToMetaValues (const Param &write_this, MetaInfoInterface &write_here, const String &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
|
override |
d'tor
|
pure virtual |
Returns information on the different channels used by the quantitation method.
Implemented in ItraqEightPlexQuantitationMethod, TMTElevenPlexQuantitationMethod, TMTSixPlexQuantitationMethod, TMTSixteenPlexQuantitationMethod, TMTTenPlexQuantitationMethod, and ItraqFourPlexQuantitationMethod.
Returns an isotope correction matrix suitable for the given quantitation method.
Implemented in ItraqEightPlexQuantitationMethod, TMTElevenPlexQuantitationMethod, TMTSixPlexQuantitationMethod, TMTSixteenPlexQuantitationMethod, TMTTenPlexQuantitationMethod, and ItraqFourPlexQuantitationMethod.
|
pure virtual |
Returns a unique name for the quantitation method.
Implemented in ItraqEightPlexQuantitationMethod, TMTElevenPlexQuantitationMethod, TMTSixPlexQuantitationMethod, TMTSixteenPlexQuantitationMethod, TMTTenPlexQuantitationMethod, and ItraqFourPlexQuantitationMethod.
|
pure virtual |
Gives the number of channels available for this quantitation method.
Implemented in ItraqEightPlexQuantitationMethod, TMTElevenPlexQuantitationMethod, TMTSixPlexQuantitationMethod, TMTSixteenPlexQuantitationMethod, TMTTenPlexQuantitationMethod, and ItraqFourPlexQuantitationMethod.
|
pure virtual |
Returns the index of the reference channel in the IsobaricChannelList (see IsobaricQuantitationMethod::getChannelInformation()).
Implemented in ItraqEightPlexQuantitationMethod, TMTElevenPlexQuantitationMethod, TMTSixPlexQuantitationMethod, TMTSixteenPlexQuantitationMethod, TMTTenPlexQuantitationMethod, and ItraqFourPlexQuantitationMethod.
|
protected |
Helper function to convert a string list containing an isotope correction matrix into a Matrix<double>.
stringlist | The StringList to convert. |