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.

Public Member Functions
	IDRipper ()
	Default constructor.

	~IDRipper () override
	Destructor.

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

void	rip (std::vector< RipFileIdentifier > &rfis, std::vector< RipFileContent > &rfcs, std::vector< ProteinIdentification > &proteins, PeptideIdentificationList &peptides, bool numeric_filenames, bool split_ident_runs)
	Ripping protein/peptide identification according their file origin.

Public Member Functions inherited from DefaultParamHandler
	DefaultParamHandler (const 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 String &	getName () const
	Non-mutable access to the name.

void	setName (const String &name)
	Mutable access to the name.

const std::vector< String > &	getSubsections () const
	Non-mutable access to the registered subsections.

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

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

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

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

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

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

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

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

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)

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.

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.

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< String >	subsections_
	Container for registered subsections. This member should be filled in the constructor of derived classes!

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

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 PeptideIdentificationList &	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,
		PeptideIdentificationList &	peptides,
		bool	numeric_filenames,
		bool	split_ident_runs
	)

Ripping protein/peptide identification according their file origin.

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

Parameters

[in]	ripped	Contains the protein identification and peptide identification for each file origin annotated in proteins and peptides
[in]	proteins	Protein identification
[in]	peptides	Peptide identification annotated with file origin
[out]	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.
[in]	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,
		PeptideIdentificationList &	peptides,
		bool	numeric_filenames,
		bool	split_ident_runs
	)

Ripping protein/peptide identification according their file origin.

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

Parameters

[out]	rfis	File info relating to `rfcs`
[out]	rfcs	Contains the protein identification and peptide identification for each file origin annotated in proteins and peptides
[in]	proteins	Protein identification
[in]	peptides	Peptide identification annotated with file origin
[out]	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.
[in]	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