Algorithm for merging multiple protein and peptide identification runs. More...

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

Inheritance diagram for IDMergerAlgorithm:

Collaboration diagram for IDMergerAlgorithm:

Public Member Functions
	IDMergerAlgorithm (const String &runIdentifier="merged", bool addTimeStampToID=true)
	Constructor for the IDMergerAlgorithm. More...

void	insertRuns (std::vector< ProteinIdentification > &&prots, PeptideIdentificationList &&peps)
	Insert runs using move semantics. More...

void	insertRuns (const std::vector< ProteinIdentification > &prots, const PeptideIdentificationList &peps)
	Insert runs using copy semantics. More...

void	returnResultsAndClear (ProteinIdentification &prots, PeptideIdentificationList &peps)
	Return the merged results and reset internal state. 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...

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	setLogger (ProgressLoggerImpl *logger)
	Sets the logger to be used for progress logging. 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 (UInt64 bytes_processed=0) const

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

Private Types
using	hash_type = std::size_t(*)(const ProteinHit &)
	Type alias for the hash function. More...

using	equal_type = bool(*)(const ProteinHit &, const ProteinHit &)
	Type alias for the equality function. More...

Private Member Functions
String	getNewIdentifier_ (bool addTimeStampToID) const
	Generate a new identifier for the merged run. More...

bool	checkOldRunConsistency_ (const std::vector< ProteinIdentification > &protRuns, const String &experiment_type) const
	Check consistency of search engines and settings across runs. More...

bool	checkOldRunConsistency_ (const std::vector< ProteinIdentification > &protRuns, const ProteinIdentification &ref, const String &experiment_type) const
	Check consistency of search engines and settings against a reference. More...

void	insertProteinIDs_ (std::vector< ProteinIdentification > &&old_protRuns)
	Insert protein identifications into the merged result. More...

void	updateAndMovePepIDs_ (PeptideIdentificationList &&pepIDs, const std::map< String, Size > &runID_to_runIdx, const std::vector< StringList > &originFiles, bool annotate_origin)
	Update peptide ID references and move them to the result. More...

void	movePepIDsAndRefProteinsToResultFaster_ (PeptideIdentificationList &&pepIDs, std::vector< ProteinIdentification > &&old_protRuns)
	Optimized method to move peptide IDs and reference proteins to result. More...

Static Private Member Functions
static void	copySearchParams_ (const ProteinIdentification &from, ProteinIdentification &to)
	Copy search parameters between protein identifications. More...

static size_t	accessionHash_ (const ProteinHit &p)
	Hash function for protein hits based on accession. More...

static bool	accessionEqual_ (const ProteinHit &p1, const ProteinHit &p2)
	Equality function for protein hits based on accession. More...

Private Attributes
ProteinIdentification	prot_result_
	The resulting merged protein identification. More...

PeptideIdentificationList	pep_result_
	The resulting merged peptide identifications. More...

std::unordered_set< ProteinHit, hash_type, equal_type >	collected_protein_hits_
	Set of collected protein hits using custom hash and equality functions. More...

bool	filled_ = false
	Flag indicating whether the resulting protein ID is already filled. More...

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

String	id_
	The new identifier string for the merged run. More...

bool	fixed_identifier_
	Flag indicating whether the identifier should be fixed (i.e., not contain a timestamp) 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...

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

Algorithm for merging multiple protein and peptide identification runs.

This class creates a new Protein ID run into which other runs can be inserted. It performs the following operations:

Creates a union of protein hits from all inserted runs
Concatenates Peptide-Spectrum Matches (PSMs) from all runs
Checks search engine consistency across all inserted runs
Maintains references between peptide IDs and their corresponding protein IDs

The algorithm differs from the IDMerger tool in two key aspects:

It is implemented as an algorithm class rather than a tool
It allows inserting multiple peptide hits per peptide sequence (not only the first occurrence)

The class handles the complexity of merging identification data from different sources while ensuring consistency and maintaining proper references between proteins and peptides. It can be used in workflows where identification results from multiple files or runs need to be combined into a single comprehensive result set.

The algorithm can optionally annotate the origin of each identification to maintain traceability of the merged results back to their source files.

See also: IDMerger

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

Type alias for the equality function.

◆ hash_type

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

private

Type alias for the hash function.

Constructor & Destructor Documentation

◆ IDMergerAlgorithm()

IDMergerAlgorithm	(	const String &	runIdentifier = `"merged"`,
		bool	addTimeStampToID = `true`
	)

explicit

Constructor for the IDMergerAlgorithm.

Initializes a new merger with the specified run identifier.

Parameters

runIdentifier	Base identifier for the merged run (default: "merged")
addTimeStampToID	Whether to append a timestamp to the run identifier for uniqueness (default: true)

Member Function Documentation

◆ accessionEqual_()

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

inlinestaticprivate

Equality function for protein hits based on accession.

Parameters

p1	First protein hit to compare
p2	Second protein hit to compare

Returns: True if the accessions are equal, false otherwise

References ProteinHit::getAccession().

◆ accessionHash_()

static size_t accessionHash_ ( const ProteinHit & p )

inlinestaticprivate

Hash function for protein hits based on accession.

Parameters

p	Protein hit to hash

Returns: Hash value for the protein hit

References ProteinHit::getAccession().

◆ checkOldRunConsistency_() [1/2]

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

private

Check consistency of search engines and settings against a reference.

Verifies that all runs have compatible search engine settings before merging, using an explicitly provided reference run.

Parameters

protRuns	The runs to check
ref	An external protein run to use as reference
experiment_type	Experiment type to allow certain mismatches (e.g., "SILAC")

Returns: True if all runs are consistent with the reference, false otherwise

Exceptions

BaseException for disagreeing settings

Todo:: Return a merged RunDescription about what to put in the new runs (e.g., for SILAC)

◆ checkOldRunConsistency_() [2/2]

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

private

Check consistency of search engines and settings across runs.

Verifies that all runs have compatible search engine settings before merging. Uses the first run as an implicit reference.

Parameters

protRuns	The runs to check (first = implicit reference)
experiment_type	Experiment type to allow certain mismatches (e.g., "SILAC")

Returns: True if all runs are consistent, false otherwise

Exceptions

BaseException for disagreeing settings

Todo:: Return a merged RunDescription about what to put in the new runs (e.g., for SILAC)

◆ copySearchParams_()

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

staticprivate

Copy search parameters between protein identifications.

Transfers search parameters from one protein identification to another.

Parameters

from	Source protein identification
to	Destination protein identification

◆ getNewIdentifier_()

String getNewIdentifier_ ( bool addTimeStampToID ) const

private

Generate a new identifier for the merged run.

Creates a new identifier by combining the base identifier with a timestamp if requested.

Parameters

addTimeStampToID Whether to append a timestamp to the identifier

Returns: The generated identifier string

◆ insertProteinIDs_()

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

private

Insert protein identifications into the merged result.

Moves and inserts protein IDs if not yet present, then clears the input.

Parameters

old_protRuns Vector of protein identifications to insert

◆ insertRuns() [1/2]

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

Insert runs using copy semantics.

Inserts (copies) protein and peptide identifications into the internal merged data structures. This version preserves the source data. Note:

Only inserts PeptideIdentifications from existing runs in prots (noop if prots is empty)
Duplicates file origins if multiple (compatible) protein runs from the same spectrumfile are merged

Parameters

prots	Vector of protein identifications to be merged
peps	Vector of peptide identifications to be merged

◆ insertRuns() [2/2]

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

Insert runs using move semantics.

Inserts (moves and clears) protein and peptide identifications into the internal merged data structures. This version uses move semantics for better performance when the source data is no longer needed. Note:

Only inserts PeptideIdentifications from existing runs in prots (noop if prots is empty)
Duplicates file origins if multiple (compatible) protein runs from the same spectrumfile are merged

Parameters

prots	Vector of protein identifications to be merged
peps	Vector of peptide identifications to be merged

◆ movePepIDsAndRefProteinsToResultFaster_()

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

private

Optimized method to move peptide IDs and reference proteins to result.

A faster implementation for moving peptide IDs and their referenced proteins to the result data structures.

Parameters

pepIDs	Vector of peptide identifications to move
old_protRuns	Vector of protein identifications to reference

◆ returnResultsAndClear()

void returnResultsAndClear	(	ProteinIdentification &	prots,
		PeptideIdentificationList &	peps
	)

Return the merged results and reset internal state.

Retrieves the merged protein and peptide identifications and clears all internal data structures, preparing the algorithm instance for potential reuse.

This method should be called after all desired runs have been inserted to obtain the final merged result.

Parameters

prots	[out] The merged protein identification containing the union of all protein hits
peps	[out] The merged peptide identifications containing all PSMs from the inserted runs

Note: After calling this method, the internal state is reset, and the algorithm can be reused for a new merging operation.

◆ updateAndMovePepIDs_()

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

private

Update peptide ID references and move them to the result.

Updates the references in peptide IDs to point to the new protein ID run, then moves the peptide IDs based on the provided mapping.

Parameters

pepIDs	Vector of peptide identifications to update and move
runID_to_runIdx	Mapping from run IDs to run indices
originFiles	List of origin files for each run
annotate_origin	Whether to annotate peptide IDs with their origin

Member Data Documentation

◆ collected_protein_hits_

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

private

Set of collected protein hits using custom hash and equality functions.

◆ file_origin_to_idx_

std::map<String, Size> file_origin_to_idx_

private

Mapping to keep track of the mzML origins of spectra.

◆ filled_

bool filled_ = false

private

Flag indicating whether the resulting protein ID is already filled.

◆ fixed_identifier_

bool fixed_identifier_

private

Flag indicating whether the identifier should be fixed (i.e., not contain a timestamp)

◆ id_

String id_

private

The new identifier string for the merged run.

◆ pep_result_

PeptideIdentificationList pep_result_

private

The resulting merged peptide identifications.

◆ prot_result_

ProteinIdentification prot_result_

private

The resulting merged protein identification.

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_

◆ fixed_identifier_

◆ id_

◆ pep_result_

◆ prot_result_