Creates a new Protein ID run into which other runs can be inserted. Creates union of protein hits but concatenates PSMs. Checks search engine consistency of all inserted runs. It differs from the IDMerger tool, in that it is an algorithm class and it allows inserting multiple peptide hits per peptide sequence (not only the first occurrence). More...

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

Inheritance diagram for IDMergerAlgorithm:

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Collaboration diagram for IDMergerAlgorithm:

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Public Member Functions
	IDMergerAlgorithm (const String &runIdentifier="merged")

void	insertRuns (std::vector< ProteinIdentification > &&prots, std::vector< PeptideIdentification > &&peps)

void	insertRuns (const std::vector< ProteinIdentification > &prots, const std::vector< PeptideIdentification > &peps)

void	returnResultsAndClear (ProteinIdentification &prots, std::vector< PeptideIdentification > &peps)
	Return the merged results and reset/clear all internal data. 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...

Public Member Functions inherited from ProgressLogger
	ProgressLogger ()
	Constructor. More...

virtual	~ProgressLogger ()
	Destructor. More...

	ProgressLogger (const ProgressLogger &other)
	Copy constructor. More...

ProgressLogger &	operator= (const ProgressLogger &other)
	Assignment Operator. More...

void	setLogType (LogType type) const
	Sets the progress log that should be used. The default type is NONE! More...

LogType	getLogType () const
	Returns the type of progress log being used. More...

void	startProgress (SignedSize begin, SignedSize end, const String &label) const
	Initializes the progress display. More...

void	setProgress (SignedSize value) const
	Sets the current progress. More...

void	endProgress () const
	Ends the progress display. More...

void	nextProgress () const
	increment progress by 1 (according to range begin-end) More...

Private Types
using	hash_type = std::size_t(*)(const ProteinHit &)

using	equal_type = bool(*)(const ProteinHit &, const ProteinHit &)

Private Member Functions
String	getNewIdentifier_ () const
	Returns the new identifier. The initial identifier plus a timestamp. More...

bool	checkOldRunConsistency_ (const std::vector< ProteinIdentification > &protRuns, const String &experiment_type) const

bool	checkOldRunConsistency_ (const std::vector< ProteinIdentification > &protRuns, const ProteinIdentification &ref, const String &experiment_type) const

void	insertProteinIDs_ (std::vector< ProteinIdentification > &&old_protRuns)

void	updateAndMovePepIDs_ (std::vector< PeptideIdentification > &&pepIDs, const std::map< String, Size > &runID_to_runIdx, const std::vector< StringList > &originFiles, bool annotate_origin)

void	movePepIDsAndRefProteinsToResultFaster_ (std::vector< PeptideIdentification > &&pepIDs, std::vector< ProteinIdentification > &&old_protRuns)

Static Private Member Functions
static void	copySearchParams_ (const ProteinIdentification &from, ProteinIdentification &to)
	Copies over search parameters. More...

static size_t	accessionHash_ (const ProteinHit &p)

static bool	accessionEqual_ (const ProteinHit &p1, const ProteinHit &p2)

Private Attributes
ProteinIdentification	prot_result_
	the resulting new Protein IDs More...

std::vector< PeptideIdentification >	pep_result_
	the resulting new Peptide IDs More...

std::unordered_set< ProteinHit, hash_type, equal_type >	collected_protein_hits_

bool	filled_ = false
	is the resulting protein ID already filled? More...

std::map< String, Size >	file_origin_to_idx_
	to keep track of the mzML origins of spectra More...

String	id_
	the new identifier string More...

Additional Inherited Members
Public Types inherited from ProgressLogger
enum	LogType { CMD , GUI , NONE }
	Possible log types. More...

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...

Static Protected Member Functions inherited from ProgressLogger
static String	logTypeToFactoryName_ (LogType type)
	Return the name of the factory product used for this log type. 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...

Protected Attributes inherited from ProgressLogger
LogType	type_

time_t	last_invoke_

ProgressLoggerImpl *	current_logger_

Static Protected Attributes inherited from ProgressLogger
static int	recursion_depth_

Detailed Description

Creates a new Protein ID run into which other runs can be inserted. Creates union of protein hits but concatenates PSMs. Checks search engine consistency of all inserted runs. It differs from the IDMerger tool, in that it is an algorithm class and it allows inserting multiple peptide hits per peptide sequence (not only the first occurrence).

Todo:: allow filtering for peptide sequence to supersede the IDMerger tool. Make it keep the best PSMs though.

Member Typedef Documentation

◆ equal_type

using equal_type = bool (*)(const ProteinHit&, const ProteinHit&)

private

◆ hash_type

using hash_type = std::size_t (*)(const ProteinHit&)

private

Constructor & Destructor Documentation

◆ IDMergerAlgorithm()

IDMergerAlgorithm ( const String & runIdentifier = "merged" )

explicit

Member Function Documentation

◆ accessionEqual_()

static bool accessionEqual_	(	const ProteinHit &	p1,
		const ProteinHit &	p2
	)

inlinestaticprivate

References ProteinHit::getAccession().

◆ accessionHash_()

static size_t accessionHash_ ( const ProteinHit & p )

inlinestaticprivate

References ProteinHit::getAccession().

◆ checkOldRunConsistency_() [1/2]

bool checkOldRunConsistency_	(	const std::vector< ProteinIdentification > &	protRuns,
		const ProteinIdentification &	ref,
		const String &	experiment_type
	)		const

private

Same as above, if you want to use a specific reference

Parameters

protRuns	The runs to check (first = reference)
ref	A possibly external protein run reference
experiment_type	allow some mismatches in case of other experiment types (e.g. SILAC)

Returns: all same? TODO: a merged RunDescription about what to put in the new runs (e.g. for SILAC)

Exceptions

BaseException for disagreeing settings

◆ checkOldRunConsistency_() [2/2]

bool checkOldRunConsistency_	(	const std::vector< ProteinIdentification > &	protRuns,
		const String &	experiment_type
	)		const

private

Checks consistency of search engines and settings across runs before merging.

Parameters

protRuns	The runs to check (first = implicit reference)
experiment_type	allow some mismatches in case of other experiment types (e.g. SILAC)

Returns: all same? TODO: a merged RunDescription about what to put in the new runs (e.g. for SILAC)

Exceptions

BaseException for disagreeing settings

◆ copySearchParams_()

static void copySearchParams_	(	const ProteinIdentification &	from,
		ProteinIdentification &	to
	)

staticprivate

Copies over search parameters.

◆ getNewIdentifier_()

String getNewIdentifier_ ( ) const

private

Returns the new identifier. The initial identifier plus a timestamp.

◆ insertProteinIDs_()

void insertProteinIDs_ ( std::vector< ProteinIdentification > && old_protRuns )

private

moves and inserts protein IDs if not yet present then clears the input

◆ insertRuns() [1/2]

void insertRuns	(	const std::vector< ProteinIdentification > &	prots,
		const std::vector< PeptideIdentification > &	peps
	)

◆ insertRuns() [2/2]

void insertRuns	(	std::vector< ProteinIdentification > &&	prots,
		std::vector< PeptideIdentification > &&	peps
	)

Insert (=move and clear) a run with its peptide IDs into the internal merged data structures, based on the initial mapping from fileorigins to new run

◆ movePepIDsAndRefProteinsToResultFaster_()

void movePepIDsAndRefProteinsToResultFaster_	(	std::vector< PeptideIdentification > &&	pepIDs,
		std::vector< ProteinIdentification > &&	old_protRuns
	)

private

◆ returnResultsAndClear()

void returnResultsAndClear	(	ProteinIdentification &	prots,
		std::vector< PeptideIdentification > &	peps
	)

Return the merged results and reset/clear all internal data.

◆ updateAndMovePepIDs_()

void updateAndMovePepIDs_	(	std::vector< PeptideIdentification > &&	pepIDs,
		const std::map< String, Size > &	runID_to_runIdx,
		const std::vector< StringList > &	originFiles,
		bool	annotate_origin
	)

private

updates the references in pepIDs to the new protein ID run then moves the peptide IDs based on the mapping in

Member Data Documentation

◆ collected_protein_hits_

std::unordered_set<ProteinHit, hash_type, equal_type> collected_protein_hits_

private

◆ file_origin_to_idx_

std::map<String, Size> file_origin_to_idx_

private

to keep track of the mzML origins of spectra

◆ filled_

bool filled_ = false

private

is the resulting protein ID already filled?

◆ id_

String id_

private

the new identifier string

◆ pep_result_

std::vector<PeptideIdentification> pep_result_

private

the resulting new Peptide IDs

◆ prot_result_

ProteinIdentification prot_result_

private

the resulting new Protein IDs

Public Member Functions

Private Types

Private Member Functions

Static Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ equal_type

◆ hash_type

Constructor & Destructor Documentation

◆ IDMergerAlgorithm()

Member Function Documentation

◆ accessionEqual_()

◆ accessionHash_()

◆ checkOldRunConsistency_() [1/2]

◆ checkOldRunConsistency_() [2/2]

◆ copySearchParams_()

◆ getNewIdentifier_()

◆ insertProteinIDs_()

◆ insertRuns() [1/2]

◆ insertRuns() [2/2]

◆ movePepIDsAndRefProteinsToResultFaster_()

◆ returnResultsAndClear()

◆ updateAndMovePepIDs_()

Member Data Documentation

◆ collected_protein_hits_

◆ file_origin_to_idx_

◆ filled_

◆ id_

◆ pep_result_

◆ prot_result_