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 , BEST }
	The aggregation method. More...

typedef std::unordered_map< std::string, std::map< Int, PeptideHit * > >	SequenceToChargeToPSM

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

void	run (ConsensusMap &cmap, ProteinIdentification &prot_id, bool include_unassigned) 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	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
typedef double(*	fptr) (double, double)
	get lambda function to aggregate scores More...

Private Member Functions
void	processRun_ (std::unordered_map< std::string, std::pair< ProteinHit *, Size >> &acc_to_protein_hitP_and_count, SequenceToChargeToPSM &best_pep, ProteinIdentification &prot_run, std::vector< PeptideIdentification > &pep_ids) const
	Performs simple aggregation-based inference on one protein run. More...

void	aggregatePeptideScores_ (SequenceToChargeToPSM &best_pep, std::vector< PeptideIdentification > &pep_ids, const String &overall_score_type, bool higher_better, const std::string &run_id) const
	fills and updates the map of best peptide scores `best_pep` (by sequence or modified sequence, depending on algorithm settings) More...

void	updateProteinScores_ (std::unordered_map< std::string, std::pair< ProteinHit *, Size >> &acc_to_protein_hitP_and_count, const SequenceToChargeToPSM &best_pep, bool pep_scores, bool higher_better) const
	aggregates and updates protein scores based on aggregation settings and aggregated peptide level results in prefilled `best_pep` More...

AggregationMethod	aggFromString_ (const std::string &method_string) const
	get the AggregationMethod enum from a `method_string` More...

void	checkCompat_ (const String &score_type, const AggregationMethod &aggregation_method) const

double	getInitScoreForAggMethod_ (const AggregationMethod &aggregation_method, bool higher_better) const
	get the initial score value based on the chosen `aggregation_method`, `higher_better` is needed for "best" score More...

fptr	aggFunFromEnum_ (const BasicProteinInferenceAlgorithm::AggregationMethod &agg_method, bool higher_better) const

Additional Inherited Members
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

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 Typedef Documentation

◆ fptr

typedef double(* fptr) (double, double)

private

get lambda function to aggregate scores

◆ SequenceToChargeToPSM

typedef std::unordered_map<std::string, std::map<Int, PeptideHit*> > SequenceToChargeToPSM

Member Enumeration Documentation

◆ AggregationMethod

enum AggregationMethod

strong

The aggregation method.

Enumerator
PROD	aggregate by product (ignore zeroes)
SUM	aggregate by summing
BEST	aggregate by maximum/minimum

Constructor & Destructor Documentation

◆ BasicProteinInferenceAlgorithm()

BasicProteinInferenceAlgorithm ( )

Default constructor.

Member Function Documentation

◆ aggFromString_()

AggregationMethod aggFromString_ ( const std::string & method_string ) const

private

get the AggregationMethod enum from a method_string

◆ aggFunFromEnum_()

fptr aggFunFromEnum_	(	const BasicProteinInferenceAlgorithm::AggregationMethod &	agg_method,
		bool	higher_better
	)		const

private

◆ aggregatePeptideScores_()

void aggregatePeptideScores_	(	SequenceToChargeToPSM &	best_pep,
		std::vector< PeptideIdentification > &	pep_ids,
		const String &	overall_score_type,
		bool	higher_better,
		const std::string &	run_id
	)		const

private

fills and updates the map of best peptide scores best_pep (by sequence or modified sequence, depending on algorithm settings)

Parameters

best_pep	(mod.) sequence to charge to pointer of best PSM (PeptideHit*)
pep_ids	the spectra with PSMs
overall_score_type	the pre-determined type name to raise an error if mixed types occur
higher_better	if for this score type higher is better
run_id	only process peptides associated with this run_id (e.g. proteinID run getIdentifier())

◆ checkCompat_()

void checkCompat_	(	const String &	score_type,
		const AggregationMethod &	aggregation_method
	)		const

private

check if a score_type is compatible to the chosen aggregation_method I.e. only probabilities can be used for multiplication

◆ getInitScoreForAggMethod_()

double getInitScoreForAggMethod_	(	const AggregationMethod &	aggregation_method,
		bool	higher_better
	)		const

private

get the initial score value based on the chosen aggregation_method, higher_better is needed for "best" score

◆ processRun_()

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

private

Performs simple aggregation-based 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
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() [1/3]

void run	(	ConsensusMap &	cmap,
		ProteinIdentification &	prot_id,
		bool	include_unassigned
	)		const

Performs the actual inference based on best psm per peptide in cmap for proteins from prot_id. Ideally prot_id is the union of proteins in all runs of cmap. Sorts and filters psms in pep_ids. Annotates results in prot_id. Associations (via getIdentifier) for peptides to protein runs ARE IGNORED and all pep_ids used.

Todo:: allow checking matching IDs

◆ run() [2/3]

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

Performs the actual inference based on best psm per peptide in pep_ids per run in prot_id. Sorts and filters psms in pep_ids. Annotates results in prot_id. Associations (via getIdentifier) for peptides to protein runs need to be correct.

◆ run() [3/3]

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

Performs the actual inference based on best psm per peptide in pep_ids per run in prot_ids. Sorts and filters psms in pep_ids. Annotates results in prot_ids. Associations (via getIdentifier) for peptides to protein runs need to be correct.

◆ updateProteinScores_()

void updateProteinScores_	(	std::unordered_map< std::string, std::pair< ProteinHit *, Size >> &	acc_to_protein_hitP_and_count,
		const SequenceToChargeToPSM &	best_pep,
		bool	pep_scores,
		bool	higher_better
	)		const

private

aggregates and updates protein scores based on aggregation settings and aggregated peptide level results in prefilled best_pep

Parameters

acc_to_protein_hitP_and_count	the results to fill
best_pep	best psm per peptide to read the score
pep_scores	if the score is a posterior error probability -> Auto-converts to posterior probability
higher_better	if for the score higher is better. Assume score is unconverted.

Public Types

Public Member Functions

Private Types

Private Member Functions

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ fptr

◆ SequenceToChargeToPSM

Member Enumeration Documentation

◆ AggregationMethod

Constructor & Destructor Documentation

◆ BasicProteinInferenceAlgorithm()

Member Function Documentation

◆ aggFromString_()

◆ aggFunFromEnum_()

◆ aggregatePeptideScores_()

◆ checkCompat_()

◆ getInitScoreForAggMethod_()

◆ processRun_()

◆ run() [1/3]

◆ run() [2/3]

◆ run() [3/3]

◆ updateProteinScores_()