IsobaricQuantitationMethod Class Reference

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:

Collaboration diagram for IsobaricQuantitationMethod:

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

Public Types
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

Public Member Functions
	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.
virtual const IsobaricChannelList &	getChannelInformation () const =0
	Returns information on the different channels used by the quantitation method.
virtual Size	getNumberOfChannels () const =0
	Gives the number of channels available for this quantitation method.
virtual Matrix< double >	getIsotopeCorrectionMatrix () const =0
	Returns an isotope correction matrix suitable for the given quantitation method.
virtual Size	getReferenceChannel () const =0
	Returns the index of the reference channel in the IsobaricChannelList (see IsobaricQuantitationMethod::getChannelInformation()).
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.

Static Public Member Functions
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 Member Functions
	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
virtual void	updateMembers_ ()
	This method is used to update extra member variables at the end of the setParameters() method.
void	defaultsToParam_ ()
	Updates the parameters after the defaults have been set in the constructor.

Private Attributes
MethodType	iso_method_
	The concrete isobaric method this instance represents; set by the c'tor and returned by getMethodType()/getMethodName().

Additional Inherited Members
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

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

Member Enumeration Documentation

MethodType

enum class MethodType

strong

Identifies a concrete isobaric quantitation method. UNKNOWN is used as a sentinel (disabled/none).

Enumerator
UNKNOWN
TMT_6PLEX
TMT_10PLEX
TMT_11PLEX
TMT_16PLEX
TMT_18PLEX
TMT_32PLEX
TMT_35PLEX
ITRAQ_4PLEX
ITRAQ_8PLEX
SIZE_OF_METHODTYPE	keep last

Constructor & Destructor Documentation

IsobaricQuantitationMethod() [1/2]

IsobaricQuantitationMethod ( )

delete

Default c'tor is deleted: a concrete method must be constructed with its MethodType (see the protected c'tor).

~IsobaricQuantitationMethod()

~IsobaricQuantitationMethod ( )

override

d'tor

IsobaricQuantitationMethod() [2/2]

IsobaricQuantitationMethod ( MethodType  method_type )

explicitprotected

c'tor for derived classes: sets the underlying param-handler name and records the concrete method_type.

Member Function Documentation

create()

static std::unique_ptr< IsobaricQuantitationMethod > create ( MethodType  mt )

static

Factory: creates a new instance of the concrete quantitation method identified by mt.

Parameters

mt	The quantitation method to instantiate.

Returns

An owning pointer to the newly created method, or nullptr if mt is MethodType::UNKNOWN (the disabled/none sentinel).

Exceptions

Exception::IllegalArgument

if mt is not a concrete method, i.e. MethodType::SIZE_OF_METHODTYPE or any value outside the enum range.

getChannelInformation()

virtual const IsobaricChannelList & getChannelInformation ( ) const

pure virtual

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

Returns

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

Implemented in ItraqEightPlexQuantitationMethod, ItraqFourPlexQuantitationMethod, TMTEighteenPlexQuantitationMethod, TMTElevenPlexQuantitationMethod, TMTSixPlexQuantitationMethod, TMTSixteenPlexQuantitationMethod, TMTTenPlexQuantitationMethod, TMTThirtyFivePlexQuantitationMethod, and TMTThirtyTwoPlexQuantitationMethod.

getIsotopeCorrectionMatrix()

virtual Matrix< double > getIsotopeCorrectionMatrix ( ) const

pure virtual

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

Implemented in ItraqEightPlexQuantitationMethod, ItraqFourPlexQuantitationMethod, TMTEighteenPlexQuantitationMethod, TMTElevenPlexQuantitationMethod, TMTSixPlexQuantitationMethod, TMTSixteenPlexQuantitationMethod, TMTTenPlexQuantitationMethod, TMTThirtyFivePlexQuantitationMethod, and TMTThirtyTwoPlexQuantitationMethod.

getMethodName()

const std::string & getMethodName

(

)

const

Returns a unique name for the quantitation method (its canonical identifier, e.g. "tmt6plex").

Returns

The unique name or identifier of the quantitation method.

getMethodType()

MethodType getMethodType ( ) const

inline

Returns the MethodType enum value of this quantitation method.

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, ItraqFourPlexQuantitationMethod, TMTEighteenPlexQuantitationMethod, TMTElevenPlexQuantitationMethod, TMTSixPlexQuantitationMethod, TMTSixteenPlexQuantitationMethod, TMTTenPlexQuantitationMethod, TMTThirtyFivePlexQuantitationMethod, and TMTThirtyTwoPlexQuantitationMethod.

getReferenceChannel()

virtual Size getReferenceChannel ( ) const

pure virtual

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

Implemented in ItraqEightPlexQuantitationMethod, ItraqFourPlexQuantitationMethod, TMTEighteenPlexQuantitationMethod, TMTElevenPlexQuantitationMethod, TMTSixPlexQuantitationMethod, TMTSixteenPlexQuantitationMethod, TMTTenPlexQuantitationMethod, TMTThirtyFivePlexQuantitationMethod, and TMTThirtyTwoPlexQuantitationMethod.

methodDisplayName()

static std::string_view methodDisplayName ( MethodType  mt )

static

Returns a human-readable display name for a given MethodType (e.g. "TMT 6-plex"); "none" for MethodType::UNKNOWN.

Exceptions

Exception::IllegalArgument

for an out-of-range value (MethodType::SIZE_OF_METHODTYPE or beyond).

methodTypeFromName()

static MethodType methodTypeFromName ( std::string_view  name )

static

Returns the MethodType corresponding to name (canonical identifier as returned by methodTypeName()), or MethodType::UNKNOWN if not found.

methodTypeName()

static std::string_view methodTypeName ( MethodType  mt )

static

Returns the canonical string identifier for a given MethodType (e.g. "tmt6plex"); "unknown" for MethodType::UNKNOWN.

Exceptions

Exception::IllegalArgument

for an out-of-range value (MethodType::SIZE_OF_METHODTYPE or beyond).

stringListToIsotopeCorrectionMatrix_()

Matrix< double > stringListToIsotopeCorrectionMatrix_ ( const std::vector< std::string > &  stringlist ) const

protected

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

Parameters

[in]

stringlist

The StringList to convert.

Returns

An isotope correction matrix as Matrix<double>.

Member Data Documentation

iso_method_

MethodType iso_method_

private

The concrete isobaric method this instance represents; set by the c'tor and returned by getMethodType()/getMethodName().