| OpenMS 2.5.0

Public Member Functions | Protected Member Functions | Private Attributes | Static Private Attributes | List of all members
TMTSixPlexQuantitationMethod Class Reference

TMT 6plex quantitation to be used with the IsobaricQuantitation. More...

`#include <OpenMS/ANALYSIS/QUANTITATION/TMTSixPlexQuantitationMethod.h>`

Inheritance diagram for TMTSixPlexQuantitationMethod:

## Public Member Functions

| TMTSixPlexQuantitationMethod ()
| Default c'tor. More...
| ~TMTSixPlexQuantitationMethod ()=default
| d'tor More...
| TMTSixPlexQuantitationMethod (const TMTSixPlexQuantitationMethod &other)
| Copy c'tor. More...
TMTSixPlexQuantitationMethod & | operator= (const TMTSixPlexQuantitationMethod &rhs)
| Assignment operator. More...
const String & | getMethodName () const override
| Methods to implement from IsobaricQuantitationMethod. More...
const IsobaricChannelList & | getChannelInformation () const override
| Returns information on the different channels used by the quantitation method. More...
Size | getNumberOfChannels () const override
| Gives the number of channels available for this quantitation method. More...
Matrix< double > | getIsotopeCorrectionMatrix () const override
| Returns an isotope correction matrix suitable for the given quantitation method. More...
Size | getReferenceChannel () const override
| Returns the index of the reference channel in the IsobaricChannelList (see IsobaricQuantitationMethod::getChannelInformation()). More...
Public Member Functions inherited from IsobaricQuantitationMethod
| IsobaricQuantitationMethod ()
| c'tor setting the name for the underlying param handler More...
| ~IsobaricQuantitationMethod () override
| d'tor 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

void | setDefaultParams_ ()
| implemented for DefaultParamHandler More...
void | updateMembers_ () override
| implemented for DefaultParamHandler More...
Protected Member Functions inherited from IsobaricQuantitationMethod
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
void | defaultsToParam_ ()
| Updates the parameters after the defaults have been set in the constructor. More...

## Private Attributes

IsobaricChannelList | channels_
| the actual information on the different tmt 6plex channels. More...
Size | reference_channel_
| The reference channel for this experiment. More...

## Static Private Attributes

static const String | name_
| The name of the quantitation method. More...

## Additional Inherited Members

Public Types inherited from IsobaricQuantitationMethod
typedef std::vector< IsobaricChannelInformation > | IsobaricChannelList
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

TMT 6plex quantitation to be used with the IsobaricQuantitation.

Parameters of this class are:

Name | Type | Default | Restrictions | Description
--- | --- | --- | --- | ---
channel_126_description | string |  |  | Description for the content of the 126 channel.
channel_127_description | string |  |  | Description for the content of the 127 channel.
channel_128_description | string |  |  | Description for the content of the 128 channel.
channel_129_description | string |  |  | Description for the content of the 129 channel.
channel_130_description | string |  |  | Description for the content of the 130 channel.
channel_131_description | string |  |  | Description for the content of the 131 channel.
reference_channel | int | 126 | min: 126 max: 131 | Number of the reference channel (126-131).
correction_matrix | string list | [0.0/0.0/0.0/0.0, 0.0/0.0/0.0/0.0, 0.0/0.0/0.0/0.0, 0.0/0.0/0.0/0.0, 0.0/0.0/0.0/0.0, 0.0/0.0/0.0/0.0] |  | Correction matrix for isotope distributions (see documentation); use the following format: <-2Da>/<-1Da>/<+1Da>/<+2Da>; e.g. '0/0.3/4/0', '0.1/0.3/3/0.2'

Note:

- If a section name is documented, the documentation is displayed as tooltip.
- Advanced parameter names are italic.

## Constructor & Destructor Documentation

## ◆ TMTSixPlexQuantitationMethod() [1/2]

TMTSixPlexQuantitationMethod | ( |  | ) |

Default c'tor.

## ◆ ~TMTSixPlexQuantitationMethod()

~TMTSixPlexQuantitationMethod | ( |  | ) |

default

d'tor

## ◆ TMTSixPlexQuantitationMethod() [2/2]

TMTSixPlexQuantitationMethod | ( | const TMTSixPlexQuantitationMethod & | other | ) |

Copy c'tor.

## Member Function Documentation

## ◆ getChannelInformation()

const IsobaricChannelList& getChannelInformation | ( |  | ) | const

override virtual

Returns information on the different channels used by the quantitation method.

Returns
  A st::vector containing the channel information for this quantitation method.

Implements IsobaricQuantitationMethod.

## ◆ getIsotopeCorrectionMatrix()

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

override virtual

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

Implements IsobaricQuantitationMethod.

## ◆ getMethodName()

const String& getMethodName | ( |  | ) | const

override virtual

Methods to implement from IsobaricQuantitationMethod.

Implements IsobaricQuantitationMethod.

## ◆ getNumberOfChannels()

Size getNumberOfChannels | ( |  | ) | const

override virtual

Gives the number of channels available for this quantitation method.

Returns
  The number of channels available for this quantitation method.

Implements IsobaricQuantitationMethod.

## ◆ getReferenceChannel()

Size getReferenceChannel | ( |  | ) | const

override virtual

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

Implements IsobaricQuantitationMethod.

## ◆ operator=()

TMTSixPlexQuantitationMethod& operator= | ( | const TMTSixPlexQuantitationMethod & | rhs | ) |

Assignment operator.

## ◆ setDefaultParams_()

void setDefaultParams_ | ( |  | ) |

protected

implemented for DefaultParamHandler

## ◆ updateMembers_()

void updateMembers_ | ( |  | ) |

override protected virtual

implemented for DefaultParamHandler

Reimplemented from DefaultParamHandler.

## Member Data Documentation

## ◆ channels_

IsobaricChannelList channels_

private

the actual information on the different tmt 6plex channels.

## ◆ name_

const String name_

static private

The name of the quantitation method.

## ◆ reference_channel_

Size reference_channel_

private

The reference channel for this experiment.