OpenMS
Loading...
Searching...
No Matches
Public Member Functions | Protected Member Functions | Private Attributes | Static Private Attributes | List of all members
TMTThirtyFivePlexQuantitationMethod Class Reference

TMT 35plex quantitation to be used for the IsobaricQuantitation. Parameters of this class are:

NameTypeDefaultRestrictionsDescription
channel_126_description string  Description for the content of the 126 channel.
channel_127N_description string  Description for the content of the 127N channel.
channel_127C_description string  Description for the content of the 127C channel.
channel_127D_description string  Description for the content of the 127D channel.
channel_128N_description string  Description for the content of the 128N channel.
channel_128C_description string  Description for the content of the 128C channel.
channel_128ND_description string  Description for the content of the 128ND channel.
channel_128CD_description string  Description for the content of the 128CD channel.
channel_129N_description string  Description for the content of the 129N channel.
channel_129C_description string  Description for the content of the 129C channel.
channel_129ND_description string  Description for the content of the 129ND channel.
channel_129CD_description string  Description for the content of the 129CD channel.
channel_130N_description string  Description for the content of the 130N channel.
channel_130C_description string  Description for the content of the 130C channel.
channel_130ND_description string  Description for the content of the 130ND channel.
channel_130CD_description string  Description for the content of the 130CD channel.
channel_131N_description string  Description for the content of the 131N channel.
channel_131C_description string  Description for the content of the 131C channel.
channel_131ND_description string  Description for the content of the 131ND channel.
channel_131CD_description string  Description for the content of the 131CD channel.
channel_132N_description string  Description for the content of the 132N channel.
channel_132C_description string  Description for the content of the 132C channel.
channel_132ND_description string  Description for the content of the 132ND channel.
channel_132CD_description string  Description for the content of the 132CD channel.
channel_133N_description string  Description for the content of the 133N channel.
channel_133C_description string  Description for the content of the 133C channel.
channel_133ND_description string  Description for the content of the 133ND channel.
channel_133CD_description string  Description for the content of the 133CD channel.
channel_134N_description string  Description for the content of the 134N channel.
channel_134C_description string  Description for the content of the 134C channel.
channel_134ND_description string  Description for the content of the 134ND channel.
channel_134CD_description string  Description for the content of the 134CD channel.
channel_135N_description string  Description for the content of the 135N channel.
channel_135ND_description string  Description for the content of the 135ND channel.
channel_135CD_description string  Description for the content of the 135CD channel.
reference_channel string126 126, 127N, 127C, 127D, 128N, 128C, 128ND, 128CD, 129N, 129C, 129ND, 129CD, 130N, 130C, 130ND, 130CD, 131N, 131C, 131ND, 131CD, 132N, 132C, 132ND, 132CD, 133N, 133C, 133ND, 133CD, 134N, 134C, 134ND, 134CD, 135N, 135ND, 135CDThe reference channel (126, 127N, 127C, 127D, 128N, 128C, 128ND, 128CD, 129N, 129C, 129ND, 129CD, 130N, 130C, 130ND, 130CD, 131N, 131C, 131ND, 131CD, 132N, 132C, 132ND, 132CD, 133N, 133C, 133ND, 133CD, 134N, 134C, 134ND, 134CD, 135N, 135ND, 135CD).
correction_matrix string list[NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA]  Ignored for TMT 35-plex (identity matrix is always used). Isotope correction is not yet supported for this method.

Note: . More...

#include <OpenMS/ANALYSIS/QUANTITATION/TMTThirtyFivePlexQuantitationMethod.h>

Inheritance diagram for TMTThirtyFivePlexQuantitationMethod:
[legend]
Collaboration diagram for TMTThirtyFivePlexQuantitationMethod:
[legend]

Public Member Functions

 TMTThirtyFivePlexQuantitationMethod ()
 Default Constructor.
 
 ~TMTThirtyFivePlexQuantitationMethod () override=default
 Destructor.
 
 TMTThirtyFivePlexQuantitationMethod (const TMTThirtyFivePlexQuantitationMethod &other)
 Copy Constructor.
 
TMTThirtyFivePlexQuantitationMethod & operator= (const TMTThirtyFivePlexQuantitationMethod &rhs)
 Assignment operator.
 
const IsobaricChannelList & getChannelInformation () const override
 Methods to implement from IsobaricQuantitationMethod.
 
Size getNumberOfChannels () const override
 Gives the number of channels available for this quantitation method.
 
Matrix< double > getIsotopeCorrectionMatrix () const override
 Returns an isotope correction matrix suitable for the given quantitation method.
 
Size getReferenceChannel () const override
 Returns the index of the reference channel in the IsobaricChannelList (see IsobaricQuantitationMethod::getChannelInformation()).
 
- Public Member Functions inherited from IsobaricQuantitationMethod
 IsobaricQuantitationMethod ()=delete
 Default c'tor is deleted: a concrete method must be constructed with its MethodType (see the protected c'tor).
 
 ~IsobaricQuantitationMethod () override
 d'tor
 
const std::string & getMethodName () const
 Returns a unique name for the quantitation method (its canonical identifier, e.g. "tmt6plex").
 
MethodType getMethodType () const
 Returns the MethodType enum value of this quantitation method.
 
- Public Member Functions inherited from DefaultParamHandler
 DefaultParamHandler (const std::string &name)
 Constructor with name that is displayed in error messages.
 
 DefaultParamHandler (const DefaultParamHandler &rhs)
 Copy constructor.
 
virtual ~DefaultParamHandler ()
 Destructor.
 
DefaultParamHandler & operator= (const DefaultParamHandler &rhs)
 Assignment operator.
 
virtual bool operator== (const DefaultParamHandler &rhs) const
 Equality operator.
 
void setParameters (const Param &param)
 Sets the parameters.
 
const Param & getParameters () const
 Non-mutable access to the parameters.
 
const Param & getDefaults () const
 Non-mutable access to the default parameters.
 
const std::string & getName () const
 Non-mutable access to the name.
 
void setName (const std::string &name)
 Mutable access to the name.
 
const std::vector< std::string > & getSubsections () const
 Non-mutable access to the registered subsections.
 

Protected Member Functions

void setDefaultParams_ ()
 implemented for DefaultParamHandler
 
void updateMembers_ () override
 implemented for DefaultParamHandler
 
- Protected Member Functions inherited from IsobaricQuantitationMethod
 IsobaricQuantitationMethod (MethodType method_type)
 c'tor for derived classes: sets the underlying param-handler name and records the concrete method_type.
 
Matrix< double > stringListToIsotopeCorrectionMatrix_ (const std::vector< std::string > &stringlist) const
 Helper function to convert a string list containing an isotope correction matrix into a Matrix<double>.
 
- Protected Member Functions inherited from DefaultParamHandler
void defaultsToParam_ ()
 Updates the parameters after the defaults have been set in the constructor.
 

Private Attributes

IsobaricChannelList channels_
 The actual information on the different TMT 35plex channels.
 
Size reference_channel_
 The reference channel for this experiment.
 

Static Private Attributes

static const std::vector< std::string > channel_names_
 List of available channel names as they are presented to the user.
 

Additional Inherited Members

- Public Types inherited from IsobaricQuantitationMethod
enum class  MethodType {
  UNKNOWN = 0 , TMT_6PLEX , TMT_10PLEX , TMT_11PLEX ,
  TMT_16PLEX , TMT_18PLEX , TMT_32PLEX , TMT_35PLEX ,
  ITRAQ_4PLEX , ITRAQ_8PLEX , SIZE_OF_METHODTYPE
}
 Identifies a concrete isobaric quantitation method. UNKNOWN is used as a sentinel (disabled/none). More...
 
typedef std::vector< IsobaricChannelInformation > IsobaricChannelList
 
- Static Public Member Functions inherited from IsobaricQuantitationMethod
static std::string_view methodTypeName (MethodType mt)
 
static std::string_view methodDisplayName (MethodType mt)
 
static MethodType methodTypeFromName (std::string_view name)
 Returns the MethodType corresponding to name (canonical identifier as returned by methodTypeName()), or MethodType::UNKNOWN if not found.
 
static std::unique_ptr< IsobaricQuantitationMethod > create (MethodType mt)
 Factory: creates a new instance of the concrete quantitation method identified by mt.
 
- Static Public Member Functions inherited from DefaultParamHandler
static void writeParametersToMetaValues (const Param &write_this, MetaInfoInterface &write_here, const std::string &key_prefix="")
 Writes all parameters to meta values.
 
- Protected Attributes inherited from DefaultParamHandler
Param param_
 Container for current parameters.
 
Param defaults_
 Container for default parameters. This member should be filled in the constructor of derived classes!
 
std::vector< std::string > subsections_
 Container for registered subsections. This member should be filled in the constructor of derived classes!
 
std::string error_name_
 Name that is displayed in error messages during the parameter checking.
 
bool check_defaults_
 If this member is set to false no checking if parameters in done;.
 
bool warn_empty_defaults_
 If this member is set to false no warning is emitted when defaults are empty;.
 

Detailed Description

TMT 35plex quantitation to be used for the IsobaricQuantitation. Parameters of this class are:

NameTypeDefaultRestrictionsDescription
channel_126_description string  Description for the content of the 126 channel.
channel_127N_description string  Description for the content of the 127N channel.
channel_127C_description string  Description for the content of the 127C channel.
channel_127D_description string  Description for the content of the 127D channel.
channel_128N_description string  Description for the content of the 128N channel.
channel_128C_description string  Description for the content of the 128C channel.
channel_128ND_description string  Description for the content of the 128ND channel.
channel_128CD_description string  Description for the content of the 128CD channel.
channel_129N_description string  Description for the content of the 129N channel.
channel_129C_description string  Description for the content of the 129C channel.
channel_129ND_description string  Description for the content of the 129ND channel.
channel_129CD_description string  Description for the content of the 129CD channel.
channel_130N_description string  Description for the content of the 130N channel.
channel_130C_description string  Description for the content of the 130C channel.
channel_130ND_description string  Description for the content of the 130ND channel.
channel_130CD_description string  Description for the content of the 130CD channel.
channel_131N_description string  Description for the content of the 131N channel.
channel_131C_description string  Description for the content of the 131C channel.
channel_131ND_description string  Description for the content of the 131ND channel.
channel_131CD_description string  Description for the content of the 131CD channel.
channel_132N_description string  Description for the content of the 132N channel.
channel_132C_description string  Description for the content of the 132C channel.
channel_132ND_description string  Description for the content of the 132ND channel.
channel_132CD_description string  Description for the content of the 132CD channel.
channel_133N_description string  Description for the content of the 133N channel.
channel_133C_description string  Description for the content of the 133C channel.
channel_133ND_description string  Description for the content of the 133ND channel.
channel_133CD_description string  Description for the content of the 133CD channel.
channel_134N_description string  Description for the content of the 134N channel.
channel_134C_description string  Description for the content of the 134C channel.
channel_134ND_description string  Description for the content of the 134ND channel.
channel_134CD_description string  Description for the content of the 134CD channel.
channel_135N_description string  Description for the content of the 135N channel.
channel_135ND_description string  Description for the content of the 135ND channel.
channel_135CD_description string  Description for the content of the 135CD channel.
reference_channel string126 126, 127N, 127C, 127D, 128N, 128C, 128ND, 128CD, 129N, 129C, 129ND, 129CD, 130N, 130C, 130ND, 130CD, 131N, 131C, 131ND, 131CD, 132N, 132C, 132ND, 132CD, 133N, 133C, 133ND, 133CD, 134N, 134C, 134ND, 134CD, 135N, 135ND, 135CDThe reference channel (126, 127N, 127C, 127D, 128N, 128C, 128ND, 128CD, 129N, 129C, 129ND, 129CD, 130N, 130C, 130ND, 130CD, 131N, 131C, 131ND, 131CD, 132N, 132C, 132ND, 132CD, 133N, 133C, 133ND, 133CD, 134N, 134C, 134ND, 134CD, 135N, 135ND, 135CD).
correction_matrix string list[NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA]  Ignored for TMT 35-plex (identity matrix is always used). Isotope correction is not yet supported for this method.

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

Constructor & Destructor Documentation

◆ TMTThirtyFivePlexQuantitationMethod() [1/2]

TMTThirtyFivePlexQuantitationMethod ( )

Default Constructor.

◆ ~TMTThirtyFivePlexQuantitationMethod()

~TMTThirtyFivePlexQuantitationMethod ( )
overridedefault

Destructor.

◆ TMTThirtyFivePlexQuantitationMethod() [2/2]

TMTThirtyFivePlexQuantitationMethod ( const TMTThirtyFivePlexQuantitationMethod &  other)

Copy Constructor.

Member Function Documentation

◆ getChannelInformation()

const IsobaricChannelList & getChannelInformation ( ) const
overridevirtual

Methods to implement from IsobaricQuantitationMethod.

Implements IsobaricQuantitationMethod.

◆ getIsotopeCorrectionMatrix()

Matrix< double > getIsotopeCorrectionMatrix ( ) const
overridevirtual

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

Implements IsobaricQuantitationMethod.

◆ getNumberOfChannels()

Size getNumberOfChannels ( ) const
overridevirtual

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
overridevirtual

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

Implements IsobaricQuantitationMethod.

◆ operator=()

TMTThirtyFivePlexQuantitationMethod & operator= ( const TMTThirtyFivePlexQuantitationMethod &  rhs)

Assignment operator.

◆ setDefaultParams_()

void setDefaultParams_ ( )
protected

implemented for DefaultParamHandler

◆ updateMembers_()

void updateMembers_ ( )
overrideprotectedvirtual

implemented for DefaultParamHandler

Reimplemented from DefaultParamHandler.

Member Data Documentation

◆ channel_names_

const std::vector<std::string> channel_names_
staticprivate

List of available channel names as they are presented to the user.

◆ channels_

IsobaricChannelList channels_
private

The actual information on the different TMT 35plex channels.

◆ reference_channel_

Size reference_channel_
private

The reference channel for this experiment.