Isobaric quantification for Top down proteomics. The report ion ratios from multiple MS2 are merged when their precursor masses belong to the same deconvolved features (MassFeature instances). More...

#include <OpenMS/ANALYSIS/TOPDOWN/TopDownIsobaricQuantification.h>

Inheritance diagram for TopDownIsobaricQuantification:

[legend]

Collaboration diagram for TopDownIsobaricQuantification:

[legend]

Public Member Functions
	TopDownIsobaricQuantification ()
	constructor More...

	~TopDownIsobaricQuantification () override=default
	destructor More...

	TopDownIsobaricQuantification (const TopDownIsobaricQuantification &)
	copy constructor More...

	TopDownIsobaricQuantification (TopDownIsobaricQuantification &&other)=default
	move constructor More...

TopDownIsobaricQuantification &	operator= (const TopDownIsobaricQuantification &other)
	assignment operator More...

void	quantify (const MSExperiment &exp, std::vector< DeconvolvedSpectrum > &deconvolved_spectra, const std::vector< FLASHHelperClasses::MassFeature > &mass_features)

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...

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	updateMembers_ () override
	This method is used to update extra member variables at the end of the setParameters() method. More...

void	setDefaultParams_ ()
	implemented for DefaultParamHandler More...

Protected Member Functions inherited from DefaultParamHandler
void	defaultsToParam_ ()
	Updates the parameters after the defaults have been set in the constructor. More...

Private Member Functions
void	addMethod_ (std::unique_ptr< IsobaricQuantitationMethod > ptr)

Private Attributes
std::map< String, std::unique_ptr< IsobaricQuantitationMethod > >	quant_methods_
	The quantification method used for the dataset to be analyzed. More...

bool	only_fully_quantified_ = false
	retain only fully quantified ratios 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< 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

Isobaric quantification for Top down proteomics. The report ion ratios from multiple MS2 are merged when their precursor masses belong to the same deconvolved features (MassFeature instances).

Constructor & Destructor Documentation

◆ TopDownIsobaricQuantification() [1/3]

TopDownIsobaricQuantification ( )

constructor

◆ ~TopDownIsobaricQuantification()

~TopDownIsobaricQuantification ( )

overridedefault

destructor

◆ TopDownIsobaricQuantification() [2/3]

TopDownIsobaricQuantification ( const TopDownIsobaricQuantification & )

copy constructor

◆ TopDownIsobaricQuantification() [3/3]

TopDownIsobaricQuantification ( TopDownIsobaricQuantification && other )

default

move constructor

Member Function Documentation

◆ addMethod_()

void addMethod_ ( std::unique_ptr< IsobaricQuantitationMethod > ptr )

inlineprivate

◆ operator=()

TopDownIsobaricQuantification& operator= ( const TopDownIsobaricQuantification & other )

assignment operator

◆ quantify()

void quantify	(	const MSExperiment &	exp,
		std::vector< DeconvolvedSpectrum > &	deconvolved_spectra,
		const std::vector< FLASHHelperClasses::MassFeature > &	mass_features
	)

Run quantification

Parameters

exp	the MS experiment
deconvolved_spectra	deconvolved spectra for which the quantification will be carried out
mass_features	mass features that are used to merge quantification results for the MS2 spectra from the same precursor mass

◆ setDefaultParams_()

void setDefaultParams_ ( )

protected

implemented for DefaultParamHandler

◆ updateMembers_()

void updateMembers_ ( )

overrideprotectedvirtual

This method is used to update extra member variables at the end of the setParameters() method.

Also call it at the end of the derived classes' copy constructor and assignment operator.

The default implementation is empty.

Reimplemented from DefaultParamHandler.

Member Data Documentation

◆ only_fully_quantified_

bool only_fully_quantified_ = false

private

retain only fully quantified ratios

◆ quant_methods_

std::map<String, std::unique_ptr<IsobaricQuantitationMethod> > quant_methods_