Ripping protein/peptide identification according their file origin. More...

#include <OpenMS/ANALYSIS/ID/IDRipper.h>

Inheritance diagram for IDRipper:

Collaboration diagram for IDRipper:

Public Member Functions
	IDRipper ()
	Default constructor. More...

	~IDRipper () override
	Destructor. More...

void	rip (std::map< String, std::pair< std::vector< ProteinIdentification >, std::vector< PeptideIdentification > > > &ripped, std::vector< ProteinIdentification > &proteins, std::vector< PeptideIdentification > &peptides)
	Ripping protein/peptide identification according their file origin. 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...

Private Member Functions
	IDRipper (const IDRipper &rhs)
	Copy constructor. More...

IDRipper &	operator= (const IDRipper &rhs)
	Assignment. More...

void	getProteinHits_ (std::vector< ProteinHit > &result, const std::vector< ProteinHit > &protein_hits, const std::vector< String > &protein_accessions)
	helper function, extracts all protein hits that match the protein accession More...

void	getProteinAccessions_ (std::vector< String > &result, const std::vector< PeptideHit > &peptide_hits)
	helper function, returns the string representation of the peptide hit accession More...

void	getProteinIdentification_ (ProteinIdentification &result, PeptideIdentification pep_ident, std::vector< ProteinIdentification > &prot_idents)
	helper function, returns the protein identification for the given peptide identification based on the same identifier More...

Additional Inherited Members
Static Public Member Functions inherited from DefaultParamHandler
static void	writeParametersToMetaValues (const Param &write_this, MetaInfoInterface &write_here, const String &prefix="")
	Writes all parameters to meta values. 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...

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

Ripping protein/peptide identification according their file origin.

Helper class, which is used by ProteinQuantifier. See there for further documentation.

Constructor & Destructor Documentation

◆ IDRipper() [1/2]

IDRipper ( )

Default constructor.

◆ ~IDRipper()

~IDRipper ( )

override

Destructor.

◆ IDRipper() [2/2]

IDRipper ( const IDRipper & rhs )

private

Copy constructor.

Member Function Documentation

◆ getProteinAccessions_()

void getProteinAccessions_	(	std::vector< String > &	result,
		const std::vector< PeptideHit > &	peptide_hits
	)

private

helper function, returns the string representation of the peptide hit accession

◆ getProteinHits_()

void getProteinHits_	(	std::vector< ProteinHit > &	result,
		const std::vector< ProteinHit > &	protein_hits,
		const std::vector< String > &	protein_accessions
	)

private

helper function, extracts all protein hits that match the protein accession

◆ getProteinIdentification_()

void getProteinIdentification_	(	ProteinIdentification &	result,
		PeptideIdentification	pep_ident,
		std::vector< ProteinIdentification > &	prot_idents
	)

private

helper function, returns the protein identification for the given peptide identification based on the same identifier

◆ operator=()

IDRipper& operator= ( const IDRipper & rhs )

private

Assignment.

◆ rip()

void rip	(	std::map< String, std::pair< std::vector< ProteinIdentification >, std::vector< PeptideIdentification > > > &	ripped,
		std::vector< ProteinIdentification > &	proteins,
		std::vector< PeptideIdentification > &	peptides
	)

Ripping protein/peptide identification according their file origin.

Iteration over all PeptideIdentification. For each annotated file origin create a map entry and store the respective PeptideIdentification and ProteinIdentification.

Parameters

ripped	Contains the protein identification and peptide identification for each file origin annotated in proteins and peptides
proteins	Peptide identification annotated with file origin
peptides	Protein identification

Public Member Functions

Private Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ IDRipper() [1/2]

◆ ~IDRipper()

◆ IDRipper() [2/2]

Member Function Documentation

◆ getProteinAccessions_()

◆ getProteinHits_()

◆ getProteinIdentification_()

◆ operator=()

◆ rip()