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

Inheritance diagram for IDMergerAlgorithm:

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

void	insertRun (std::vector< ProteinIdentification > &prots, 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...

	~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 Member Functions
String	getNewIdentifier_ () const

void	copySearchParams_ (ProteinIdentification &from, ProteinIdentification &to)

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	movePepIDsAndRefProteinsToResult_ (std::vector< PeptideIdentification > &pepIDs, std::vector< ProteinIdentification > &oldProtRuns)

Private Attributes
ProteinIdentification	protResult

std::vector< PeptideIdentification >	pepResult

std::unordered_set< std::string >	proteinsCollected

bool	filled = false

std::map< String, Size >	fileOriginToIdx

String	id

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

Constructor & Destructor Documentation

◆ IDMergerAlgorithm()

IDMergerAlgorithm ( const String & runIdentifier = "merged" )

explicit

Member Function Documentation

◆ checkOldRunConsistency_() [1/2]

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

◆ checkOldRunConsistency_() [2/2]

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

◆ copySearchParams_()

void copySearchParams_	(	ProteinIdentification &	from,
		ProteinIdentification &	to
	)

private

◆ getNewIdentifier_()

String getNewIdentifier_ ( ) const

private

◆ insertRun()

void insertRun	(	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

◆ movePepIDsAndRefProteinsToResult_()

void movePepIDsAndRefProteinsToResult_	(	std::vector< PeptideIdentification > &	pepIDs,
		std::vector< ProteinIdentification > &	oldProtRuns
	)

private

◆ returnResultsAndClear()

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

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

Member Data Documentation

◆ fileOriginToIdx

std::map<String, Size> fileOriginToIdx

private

◆ filled

bool filled = false

private

◆ id

String id

private

◆ pepResult

std::vector<PeptideIdentification> pepResult

private

◆ proteinsCollected

std::unordered_set<std::string> proteinsCollected

private

◆ protResult

ProteinIdentification protResult

private

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ IDMergerAlgorithm()

Member Function Documentation

◆ checkOldRunConsistency_() [1/2]

◆ checkOldRunConsistency_() [2/2]

◆ copySearchParams_()

◆ getNewIdentifier_()

◆ insertRun()

◆ movePepIDsAndRefProteinsToResult_()

◆ returnResultsAndClear()

Member Data Documentation

◆ fileOriginToIdx

◆ filled

◆ id

◆ pepResult

◆ proteinsCollected

◆ protResult