OpenMS  2.8.0
Classes | Public Types | Public Member Functions | Protected Member Functions | List of all members
IsobaricQuantitationMethod Class Referenceabstract

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>

Inheritance diagram for IsobaricQuantitationMethod:
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Collaboration diagram for IsobaricQuantitationMethod:
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Classes

struct  IsobaricChannelInformation
 Summary of an isobaric quantitation channel. More...
 

Public Types

typedef std::vector< IsobaricChannelInformationIsobaricChannelList
 

Public Member Functions

 IsobaricQuantitationMethod ()
 c'tor setting the name for the underlying param handler More...
 
 ~IsobaricQuantitationMethod () override
 d'tor More...
 
virtual const StringgetMethodName () const =0
 Returns a unique name for the quantitation method. More...
 
virtual const IsobaricChannelListgetChannelInformation () 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 DefaultParamHandleroperator= (const DefaultParamHandler &rhs)
 Assignment operator. More...
 
virtual bool operator== (const DefaultParamHandler &rhs) const
 Equality operator. More...
 
void setParameters (const Param &param)
 Sets the parameters. More...
 
const ParamgetParameters () const
 Non-mutable access to the parameters. More...
 
const ParamgetDefaults () const
 Non-mutable access to the default parameters. More...
 
const StringgetName () 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 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< Stringsubsections_
 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

Constructor & Destructor Documentation

◆ IsobaricQuantitationMethod()

c'tor setting the name for the underlying param handler

◆ ~IsobaricQuantitationMethod()

d'tor

Member Function Documentation

◆ getChannelInformation()

virtual const IsobaricChannelList& getChannelInformation ( ) const
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 TMTTenPlexQuantitationMethod, TMTSixteenPlexQuantitationMethod, TMTSixPlexQuantitationMethod, TMTElevenPlexQuantitationMethod, ItraqFourPlexQuantitationMethod, and ItraqEightPlexQuantitationMethod.

◆ getIsotopeCorrectionMatrix()

virtual Matrix<double> getIsotopeCorrectionMatrix ( ) const
pure virtual

◆ getMethodName()

virtual const String& getMethodName ( ) const
pure virtual

Returns a unique name for the quantitation method.

Returns
The unique name or identifier of the quantitation method.

Implemented in TMTTenPlexQuantitationMethod, TMTSixteenPlexQuantitationMethod, TMTSixPlexQuantitationMethod, TMTElevenPlexQuantitationMethod, ItraqFourPlexQuantitationMethod, and ItraqEightPlexQuantitationMethod.

◆ getNumberOfChannels()

virtual Size getNumberOfChannels ( ) const
pure virtual

Gives the number of channels available for this quantitation method.

Returns
The number of channels available for this quantitation method.

Implemented in TMTTenPlexQuantitationMethod, TMTSixteenPlexQuantitationMethod, TMTSixPlexQuantitationMethod, TMTElevenPlexQuantitationMethod, ItraqFourPlexQuantitationMethod, and ItraqEightPlexQuantitationMethod.

◆ getReferenceChannel()

virtual Size getReferenceChannel ( ) const
pure virtual

◆ stringListToIsotopCorrectionMatrix_()

Matrix<double> stringListToIsotopCorrectionMatrix_ ( const std::vector< String > &  stringlist) const
protected

Helper function to convert a string list containing an isotope correction matrix into a Matrix<double>.

Parameters
stringlistThe StringList to convert.
Returns
An isotope correction matrix as Matrix<double>.