Merges identification data in ConsensusMaps. More...

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

Inheritance diagram for ConsensusMapMergerAlgorithm:

Collaboration diagram for ConsensusMapMergerAlgorithm:

Public Member Functions
	ConsensusMapMergerAlgorithm ()

void	mergeProteinsAcrossFractionsAndReplicates (ConsensusMap &cmap, const ExperimentalDesign &exp_design) const

void	mergeAllIDRuns (ConsensusMap &cmap) const

void	mergeProteinIDRuns (ConsensusMap &cmap, const std::map< unsigned, unsigned > &mapIdx_to_new_protIDRun) const

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 &)

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

Private Member Functions
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
	Same as above but with specific reference run. More...

Static Private Member Functions
static size_t	accessionHash_ (const ProteinHit &p)

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

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

Merges identification data in ConsensusMaps.

Todo:

This could be merged in the future with the general IDMergerAlgorithm since it shares a lot. IDMergerAlgorithm needs additional methods to have multiple runs as output. It also needs to store an extended mapping internally to distribute the PeptideIDs to the right output run according to origin and label. And should have non-copying/moving overloads for inserting PeptideIDs since we probably do not want to distribute the PeptideIDs to the features again. In general detaching IDs from features would be of great help here.

Untested for TMT/iTraq data where you usually have one Identification run per File but in one File you might have multiple conditions multiplexed, that you might want to split for inference. Problem: There is only one PeptideIdentification object per Feature that is representative for all "sub maps" (in this case the labels/reporter ions). -> A lookup is necessary if the reporter ion had non-zero intensity and if so, the peptide ID needs to be duplicated for every new (condition-based) IdentificationRun it is supposed to be used in, according to the mapping.

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

◆ ConsensusMapMergerAlgorithm()

ConsensusMapMergerAlgorithm ( )

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 but with specific reference run.

◆ 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. Uses the first run as reference and compares all to it.

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

Exceptions

BaseException for disagreeing settings

◆ mergeAllIDRuns()

void mergeAllIDRuns ( ConsensusMap & cmap ) const

Similar to above, merges every ID Run into one big run. Proteins get only inserted once but Peptides stay unfiltered i.e. might occur in several PeptideIdentifications afterwards

Note: Groups are not carried over during merging.

Exceptions

MissingInformationException for e.g. missing map_indices in PeptideIDs

◆ mergeProteinIDRuns()

void mergeProteinIDRuns	(	ConsensusMap &	cmap,
		const std::map< unsigned, unsigned > &	mapIdx_to_new_protIDRun
	)		const

Takes a ConsensusMap and a mapping between ConsensusMap column index (sub map index in the map_index meta value) and the new ProteinIdentification run index and merges them based on this.

Exceptions

MissingInformationException for e.g. missing map_indices in PeptideIDs

Todo:: Do we need to consider the old IDRun identifier in addition to the sub map index

◆ mergeProteinsAcrossFractionsAndReplicates()

void mergeProteinsAcrossFractionsAndReplicates	(	ConsensusMap &	cmap,
		const ExperimentalDesign &	exp_design
	)		const

Takes a ConsensusMap (with usually one IdentificationRun per column [= sub map] and merges them to one IdentificationRun per Condition (unique entries in Sample section when removing replicate columns) while reassociating the PeptideHits accordingly. It just does not make sense to have every protein duplicated. And IdentificationRuns are used to guide inference methods on what identifications to perform inference on

Note: Constructs the mapping based on the exp. design and then uses mergeProteinIDRuns; Groups are not carried over during merging.

Exceptions

MissingInformationException for e.g. missing map_indices in PeptideIDs

Public Member Functions

Private Types

Private Member Functions

Static Private Member Functions

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ equal_type

◆ hash_type

Constructor & Destructor Documentation

◆ ConsensusMapMergerAlgorithm()

Member Function Documentation

◆ accessionEqual_()

◆ accessionHash_()

◆ checkOldRunConsistency_() [1/2]

◆ checkOldRunConsistency_() [2/2]

◆ mergeAllIDRuns()

◆ mergeProteinIDRuns()

◆ mergeProteinsAcrossFractionsAndReplicates()