Algorithm class that implements simple protein inference by aggregation of peptide scores. It has multiple parameter options like the aggregation method, when to distinguish peptidoforms, and if you want to use shared peptides ("use_shared_peptides"). First, the best PSM per spectrum is used, then only the best PSM per peptidoform is aggregated. Peptidoforms can optionally be distinguished via the treat_X_separate parameters: More...

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

Inheritance diagram for BasicProteinInferenceAlgorithm:

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Collaboration diagram for BasicProteinInferenceAlgorithm:

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Public Types
enum class	AggregationMethod { PROD , SUM , MAXIMUM }
	The aggregation method. More...

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

Public Member Functions
	BasicProteinInferenceAlgorithm ()
	Default constructor. More...

void	run (std::vector< PeptideIdentification > &pep_ids, std::vector< ProteinIdentification > &prot_ids) const

void	run (std::vector< PeptideIdentification > &pep_ids, ProteinIdentification &prot_id) 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...

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 Member Functions
void	processRun_ (std::unordered_map< std::string, std::pair< ProteinHit , Size >> &acc_to_protein_hitP_and_count, std::unordered_map< std::string, std::map< Int, PeptideHit >> &best_pep, ProteinIdentification &prot_run, std::vector< PeptideIdentification > &pep_ids, Size min_peptides_per_protein) const
	Performs simple inference on one protein run. More...

Additional Inherited Members
Static Public Member Functions inherited from DefaultParamHandler
static void	writeParametersToMetaValues (const Param &write_this, MetaInfoInterface &write_here, const String &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

Algorithm class that implements simple protein inference by aggregation of peptide scores. It has multiple parameter options like the aggregation method, when to distinguish peptidoforms, and if you want to use shared peptides ("use_shared_peptides"). First, the best PSM per spectrum is used, then only the best PSM per peptidoform is aggregated. Peptidoforms can optionally be distinguished via the treat_X_separate parameters:

Modifications (modified sequence string)
Charge states The algorithm assumes posteriors or posterior error probabilities and converts to posteriors initially. Possible aggregation methods that can be set via the parameter "aggregation_method" are:
"maximum" (default)
"sum"
"product" (ignoring zeroes) Annotation of the number of peptides used for aggregation can be disabled (see parameters). Supports multiple runs but goes through them one by one iterating over the full PeptideIdentification vector.

Member Enumeration Documentation

◆ AggregationMethod

enum AggregationMethod

strong

The aggregation method.

Enumerator
PROD	aggregate by product (ignore zeroes)
SUM	aggregate by summing
MAXIMUM	aggregate by maximum

Constructor & Destructor Documentation

◆ BasicProteinInferenceAlgorithm()

BasicProteinInferenceAlgorithm ( )

Default constructor.

Member Function Documentation

◆ processRun_()

void processRun_	(	std::unordered_map< std::string, std::pair< ProteinHit *, Size >> &	acc_to_protein_hitP_and_count,
		std::unordered_map< std::string, std::map< Int, PeptideHit * >> &	best_pep,
		ProteinIdentification &	prot_run,
		std::vector< PeptideIdentification > &	pep_ids,
		Size	min_peptides_per_protein
	)		const

private

Performs simple inference on one protein run.

Parameters

acc_to_protein_hitP_and_count	Maps Accessions to a pair of ProteinHit pointers and number of peptidoforms encountered @Todo could use member as hash to save strings
best_pep	Maps (un)modified peptide sequence to a map from charge (0 when unconsidered) to the best PeptideHit pointer
prot_run	The current run to process
pep_ids	Peptides for the current run to process

◆ run() [1/2]

void run	(	std::vector< PeptideIdentification > &	pep_ids,
		ProteinIdentification &	prot_id
	)		const

◆ run() [2/2]

void run	(	std::vector< PeptideIdentification > &	pep_ids,
		std::vector< ProteinIdentification > &	prot_ids
	)		const

main method of BasicProteinInferenceAlgorithm inputs are not const, since it will get annotated with results annotation of protein groups is currently only possible for a single protein ID run

Public Types

Public Member Functions

Private Member Functions

Additional Inherited Members