| OpenMS 2.5.0

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:

## 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 &param)
| 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()

IsobaricQuantitationMethod | ( |  | ) |

c'tor setting the name for the underlying param handler

## ◆ ~IsobaricQuantitationMethod()

~IsobaricQuantitationMethod | ( |  | ) |

override

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

## ◆ getIsotopeCorrectionMatrix()

virtual Matrix<double> getIsotopeCorrectionMatrix | ( |  | ) | const

pure virtual

Returns an isotope correction matrix suitable for the given quantitation method.

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

## ◆ 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 ItraqEightPlexQuantitationMethod, TMTElevenPlexQuantitationMethod, TMTSixPlexQuantitationMethod, TMTSixteenPlexQuantitationMethod, TMTTenPlexQuantitationMethod, and ItraqFourPlexQuantitationMethod.

## ◆ 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 ItraqEightPlexQuantitationMethod, TMTElevenPlexQuantitationMethod, TMTSixPlexQuantitationMethod, TMTSixteenPlexQuantitationMethod, TMTTenPlexQuantitationMethod, and ItraqFourPlexQuantitationMethod.

## ◆ getReferenceChannel()

virtual Size getReferenceChannel | ( |  | ) | const

pure virtual

Returns the index of the reference channel in the IsobaricChannelList (see IsobaricQuantitationMethod::getChannelInformation()).

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

## ◆ stringListToIsotopCorrectionMatrix_()

Matrix<double> stringListToIsotopCorrectionMatrix_ | ( | const StringList & | stringlist | ) | const

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>.