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

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

Inheritance diagram for IDRipper:

Collaboration diagram for IDRipper:

Classes
struct	IdentificationRuns
	Represents a set of IdentificationRuns. More...

struct	RipFileContent
	Represents the content of an IDRipper output file. More...

struct	RipFileIdentifier
	Identifies an IDRipper output file. More...

struct	RipFileIdentifierIdxComparator
	Provides a 'less' operation for RipFileIdentifiers that ignores the out_basename and origin_fullname members. More...

Public Types
enum	OriginAnnotationFormat { FILE_ORIGIN = 0 , MAP_INDEX = 1 , ID_MERGE_INDEX = 2 , UNKNOWN_OAF = 3 , SIZE_OF_ORIGIN_ANNOTATION_FORMAT = 4 }
	Possible input file encodings for the origin as used by different versions of IDMerger. More...

typedef std::map< RipFileIdentifier, RipFileContent, RipFileIdentifierIdxComparator >	RipFileMap
	Represents the result of an IDRipper process, a map assigning file content to output file identifiers. More...

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

	~IDRipper () override
	Destructor. More...

void	rip (RipFileMap &ripped, std::vector< ProteinIdentification > &proteins, std::vector< PeptideIdentification > &peptides, bool numeric_filenames, bool split_ident_runs)
	Ripping protein/peptide identification according their file origin. More...

void	rip (std::vector< RipFileIdentifier > &rfis, std::vector< RipFileContent > &rfcs, std::vector< ProteinIdentification > &proteins, std::vector< PeptideIdentification > &peptides, bool numeric_filenames, bool split_ident_runs)
	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...

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...

Static Public Attributes
static const std::array< std::string, SIZE_OF_ORIGIN_ANNOTATION_FORMAT >	names_of_OriginAnnotationFormat
	String representations for the OriginAnnotationFormat enum. More...

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

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

OriginAnnotationFormat	detectOriginAnnotationFormat_ (std::map< String, UInt > &file_origin_map, const std::vector< PeptideIdentification > &peptide_idents)
	helper function, detects file origin annotation standard from collections of protein and peptide hits More...

void	getProteinHits_ (std::vector< ProteinHit > &result, const std::unordered_map< String, const ProteinHit * > &acc2protein_hits, const std::set< String > &protein_accessions)
	helper function, extracts all protein hits that match the protein accession More...

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

int	getProteinIdentification_ (const PeptideIdentification &pep_ident, const IdentificationRuns &id_runs)
	helper function, returns the index of the protein identification for the given peptide identification based on the same identifier using id_runs as lookup More...

bool	registerBasename_ (std::map< String, std::pair< UInt, UInt > > &basename_to_numeric, const IDRipper::RipFileIdentifier &rfi)
	helper function, register a potential output file basename to detect duplicate output basenames More...

bool	setOriginAnnotationMode_ (short &mode, short const new_value)
	helper function, sets the value of mode to new_value and returns true if the old value was identical or unset (-1) 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 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.

Parameters of this class are:

Name	Type	Default	Restrictions	Description

Note:

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

Member Typedef Documentation

◆ RipFileMap

typedef std::map<RipFileIdentifier, RipFileContent, RipFileIdentifierIdxComparator> RipFileMap

Represents the result of an IDRipper process, a map assigning file content to output file identifiers.

Member Enumeration Documentation

◆ OriginAnnotationFormat

enum OriginAnnotationFormat

Possible input file encodings for the origin as used by different versions of IDMerger.

Enumerator
FILE_ORIGIN
MAP_INDEX
ID_MERGE_INDEX
UNKNOWN_OAF
SIZE_OF_ORIGIN_ANNOTATION_FORMAT

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

◆ detectOriginAnnotationFormat_()

OriginAnnotationFormat detectOriginAnnotationFormat_	(	std::map< String, UInt > &	file_origin_map,
		const std::vector< PeptideIdentification > &	peptide_idents
	)

private

helper function, detects file origin annotation standard from collections of protein and peptide hits

◆ getProteinAccessions_()

std::set<String> getProteinAccessions_ ( 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::unordered_map< String, const ProteinHit * > &	acc2protein_hits,
		const std::set< String > &	protein_accessions
	)

private

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

◆ getProteinIdentification_()

int getProteinIdentification_	(	const PeptideIdentification &	pep_ident,
		const IdentificationRuns &	id_runs
	)

private

helper function, returns the index of the protein identification for the given peptide identification based on the same identifier using id_runs as lookup

◆ operator=()

IDRipper& operator= ( const IDRipper & rhs )

private

Assignment.

◆ registerBasename_()

bool registerBasename_	(	std::map< String, std::pair< UInt, UInt > > &	basename_to_numeric,
		const IDRipper::RipFileIdentifier &	rfi
	)

private

helper function, register a potential output file basename to detect duplicate output basenames

◆ rip() [1/2]

void rip	(	RipFileMap &	ripped,
		std::vector< ProteinIdentification > &	proteins,
		std::vector< PeptideIdentification > &	peptides,
		bool	numeric_filenames,
		bool	split_ident_runs
	)

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	Protein identification
peptides	Peptide identification annotated with file origin
numeric_filenames	If false, deduce output files using basenames of origin annotations. Throws an exception if they are not unique. If true, assemble output files based on numerical IDs only.
split_ident_runs	Split identification runs into different files.

◆ rip() [2/2]

void rip	(	std::vector< RipFileIdentifier > &	rfis,
		std::vector< RipFileContent > &	rfcs,
		std::vector< ProteinIdentification > &	proteins,
		std::vector< PeptideIdentification > &	peptides,
		bool	numeric_filenames,
		bool	split_ident_runs
	)

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	Protein identification
peptides	Peptide identification annotated with file origin
numeric_filenames	If false, deduce output files using basenames of origin annotations. Throws an exception if they are not unique. If true, assemble output files based on numerical IDs only.
split_ident_runs	Split identification runs into different files.

◆ setOriginAnnotationMode_()

bool setOriginAnnotationMode_	(	short &	mode,
		short const	new_value
	)

private

helper function, sets the value of mode to new_value and returns true if the old value was identical or unset (-1)

Member Data Documentation

◆ names_of_OriginAnnotationFormat

const std::array<std::string, SIZE_OF_ORIGIN_ANNOTATION_FORMAT> names_of_OriginAnnotationFormat

static

String representations for the OriginAnnotationFormat enum.

Classes

Public Types

Public Member Functions

Static Public Attributes

Private Member Functions

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ RipFileMap

Member Enumeration Documentation

◆ OriginAnnotationFormat

Constructor & Destructor Documentation

◆ IDRipper() [1/2]

◆ ~IDRipper()

◆ IDRipper() [2/2]

Member Function Documentation

◆ detectOriginAnnotationFormat_()

◆ getProteinAccessions_()

◆ getProteinHits_()

◆ getProteinIdentification_()

◆ operator=()

◆ registerBasename_()

◆ rip() [1/2]

◆ rip() [2/2]

◆ setOriginAnnotationMode_()

Member Data Documentation

◆ names_of_OriginAnnotationFormat