Simple protein inference by aggregation of per-peptide PSM scores. More...

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

Inheritance diagram for BasicProteinInferenceAlgorithm:

Collaboration diagram for BasicProteinInferenceAlgorithm:

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.

void	run (PeptideIdentificationList &pep_ids, std::vector< ProteinIdentification > &prot_ids) const
	Run inference per protein-ID run, iterating each `prot_ids` entry separately.

void	run (PeptideIdentificationList &pep_ids, ProteinIdentification &prot_id) const
	Run inference for a single protein-ID run.

void	run (ConsensusMap &cmap, ProteinIdentification &prot_id, bool include_unassigned) const
	Run inference over a ConsensusMap, treating every peptide identification it carries as evidence for the proteins in `prot_id`.

Public Member Functions inherited from DefaultParamHandler
	DefaultParamHandler (const std::string &name)
	Constructor with name that is displayed in error messages.

	DefaultParamHandler (const DefaultParamHandler &rhs)
	Copy constructor.

virtual	~DefaultParamHandler ()
	Destructor.

DefaultParamHandler &	operator= (const DefaultParamHandler &rhs)
	Assignment operator.

virtual bool	operator== (const DefaultParamHandler &rhs) const
	Equality operator.

void	setParameters (const Param &param)
	Sets the parameters.

const Param &	getParameters () const
	Non-mutable access to the parameters.

const Param &	getDefaults () const
	Non-mutable access to the default parameters.

const std::string &	getName () const
	Non-mutable access to the name.

void	setName (const std::string &name)
	Mutable access to the name.

const std::vector< std::string > &	getSubsections () const
	Non-mutable access to the registered subsections.

Public Member Functions inherited from ProgressLogger
	ProgressLogger ()
	Constructor.

virtual	~ProgressLogger ()
	Destructor.

	ProgressLogger (const ProgressLogger &other)
	Copy constructor.

ProgressLogger &	operator= (const ProgressLogger &other)
	Assignment Operator.

void	setLogType (LogType type) const
	Sets the progress log that should be used. The default type is NONE!

LogType	getLogType () const
	Returns the type of progress log being used.

void	setLogger (ProgressLoggerImpl *logger)
	Sets the logger to be used for progress logging.

void	startProgress (SignedSize begin, SignedSize end, const std::string &label) const
	Initializes the progress display.

void	setProgress (SignedSize value) const
	Sets the current progress.

void	endProgress (UInt64 bytes_processed=0) const

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

Private Types
typedef double(*	fptr) (double, double)
	Function-pointer type for a two-argument score accumulator.

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, PeptideIdentificationList &pep_ids) const
	Performs simple aggregation-based inference on one protein run.

void	aggregatePeptideScores_ (SequenceToChargeToPSM &best_pep, PeptideIdentificationList &pep_ids, const std::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)

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`

AggregationMethod	aggFromString_ (const std::string &method_string) const
	Map a `score_aggregation_method` parameter string to the AggregationMethod enum.

void	checkCompat_ (const std::string &score_type, const AggregationMethod &aggregation_method) const
	Reject score-type / aggregation-method combinations that don't make statistical sense.

void	checkCompat_ (const IDScoreSwitcherAlgorithm::ScoreType &score_type, const AggregationMethod &aggregation_method) const
	Same as the string overload, but takes a typed IDScoreSwitcherAlgorithm::ScoreType so the check can be done after the score-switcher has classified the score.

double	getInitScoreForAggMethod_ (const AggregationMethod &aggregation_method, bool higher_better) const
	Return the identity-element initial score for the chosen aggregation method.

fptr	aggFunFromEnum_ (const BasicProteinInferenceAlgorithm::AggregationMethod &agg_method, bool higher_better) const
	Pick the two-argument accumulator function matching the chosen aggregation method.

Additional Inherited Members
Static Public Member Functions inherited from DefaultParamHandler
static void	writeParametersToMetaValues (const Param &write_this, MetaInfoInterface &write_here, const std::string &key_prefix="")
	Writes all parameters to meta values.

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.

void	defaultsToParam_ ()
	Updates the parameters after the defaults have been set in the constructor.

Protected Attributes inherited from DefaultParamHandler
Param	param_
	Container for current parameters.

Param	defaults_
	Container for default parameters. This member should be filled in the constructor of derived classes!

std::vector< std::string >	subsections_
	Container for registered subsections. This member should be filled in the constructor of derived classes!

std::string	error_name_
	Name that is displayed in error messages during the parameter checking.

bool	check_defaults_
	If this member is set to false no checking if parameters in done;.

bool	warn_empty_defaults_
	If this member is set to false no warning is emitted when defaults are empty;.

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

Simple protein inference by aggregation of per-peptide PSM scores.

First takes the best PSM per spectrum, then keeps the best PSM per peptidoform (where "peptidoform" is widened or narrowed by the treat_charge_variants_separately and treat_modification_variants_separately parameters), and finally aggregates the peptide-level scores onto the proteins using one of the methods exposed via the score_aggregation_method parameter.

Configurable behaviour is exposed through DefaultParamHandler — see the defaults installed by the constructor for the full list of supported keys, in particular:

"score_aggregation_method" — one of "best", "product", "sum", "maximum"; maps onto AggregationMethod via aggFromString_. The "best" / "maximum" string both produce the BEST mode.
"treat_charge_variants_separately" — distinguish charge variants of the same modified sequence as distinct peptidoforms (default "true").
"treat_modification_variants_separately" — distinguish modified vs. unmodified variants of the same backbone sequence (default "true").
"use_shared_peptides" — if "true", shared peptides count as evidence for every protein they map to (default "true").
"skip_count_annotation" — if set, the per-peptide count annotation on the protein hits is suppressed (default "false").
"annotate_indistinguishable_groups" — compute and annotate indistinguishable protein groups (default "true").
"greedy_group_resolution" — resolve shared peptides to a single best protein (razor-peptide style; default "false").
"min_peptides_per_protein" — minimum peptide count required for a protein to be reported (default 1).
"score_type" — explicit PSM score type to use; empty falls back to the main score.

The algorithm assumes posteriors or posterior error probabilities; PEPs are converted to posteriors as part of scoring. Multiple runs are supported, each processed independently.

Member Typedef Documentation

◆ fptr

typedef double(* fptr) (double, double)

private

Function-pointer type for a two-argument score accumulator.

◆ SequenceToChargeToPSM

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

Member Enumeration Documentation

◆ AggregationMethod

enum class 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

Map a score_aggregation_method parameter string to the AggregationMethod enum.

Recognised values: "product", "sum", "best", "maximum" ("best" and "maximum" both produce AggregationMethod::BEST).

Parameters

[in] method_string Parameter string.

Returns: Matching AggregationMethod.

◆ aggFunFromEnum_()

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

private

Pick the two-argument accumulator function matching the chosen aggregation method.

Parameters

[in]	agg_method	Aggregation mode chosen via `"score_aggregation_method"`.
[in]	higher_better	Whether higher score values are better (used only for BEST, to pick max vs min).

Returns: Function pointer with signature double(double,double).

◆ aggregatePeptideScores_()

void aggregatePeptideScores_	(	SequenceToChargeToPSM &	best_pep,
		PeptideIdentificationList &	pep_ids,
		const std::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

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

◆ checkCompat_() [1/2]

void checkCompat_	(	const IDScoreSwitcherAlgorithm::ScoreType &	score_type,
		const AggregationMethod &	aggregation_method
	)		const

private

Same as the string overload, but takes a typed IDScoreSwitcherAlgorithm::ScoreType so the check can be done after the score-switcher has classified the score.

Parameters

[in]	score_type	Typed score classification.
[in]	aggregation_method	Aggregation mode chosen via `"score_aggregation_method"`.

◆ checkCompat_() [2/2]

void checkCompat_	(	const std::string &	score_type,
		const AggregationMethod &	aggregation_method
	)		const

private

Reject score-type / aggregation-method combinations that don't make statistical sense.

Multiplication (AggregationMethod::PROD) is only meaningful for probability-typed scores; other combinations either throw or log a warning. Uses the score-type name.

Parameters

[in]	score_type	Name of the PSM score type.
[in]	aggregation_method	Aggregation mode chosen via `"score_aggregation_method"`.

◆ getInitScoreForAggMethod_()

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

private

Return the identity-element initial score for the chosen aggregation method.

For example, 0 for SUM, 1 for PROD, and the worst-possible score (depending on higher_better) for BEST.

Parameters

[in]	aggregation_method	Aggregation mode chosen via `"score_aggregation_method"`.
[in]	higher_better	Whether higher score values are better (used only for BEST).

Returns: Initial accumulator value to start the aggregation from.

◆ processRun_()

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

private

Performs simple aggregation-based inference on one protein run.

Parameters

[in,out]	acc_to_protein_hitP_and_count	Maps Accessions to a pair of ProteinHit pointers and number of peptidoforms encountered
[in,out]	best_pep	Maps (un)modified peptide sequence to a map from charge (0 when unconsidered) to the best PeptideHit pointer
[in,out]	prot_run	The current run to process
[in,out]	pep_ids	Peptides for the current run to process

◆ run() [1/3]

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

Run inference over a ConsensusMap, treating every peptide identification it carries as evidence for the proteins in prot_id.

Differs from the per-run overloads above by ignoring the getIdentifier association between peptides and protein runs — every peptide id in cmap (and optionally in the unassigned list, see include_unassigned) is used. prot_id is expected to be the union of the proteins of all runs in cmap.

Parameters

[in,out]	cmap	Consensus map providing the peptide identifications; PSMs may be sorted/filtered in place.
[in,out]	prot_id	Protein-identification run to annotate with aggregated scores.
[in]	include_unassigned	If true, also include ConsensusMap::getUnassignedPeptideIdentifications.

Exceptions

Exception::InvalidParameter If PSMs of a peptide carry different score types.

Todo:: JuliaP Allow checking that peptide / protein IDs reference the same run identifier.

◆ run() [2/3]

void run	(	PeptideIdentificationList &	pep_ids,
		ProteinIdentification &	prot_id
	)		const

Run inference for a single protein-ID run.

Convenience overload of the multi-run version: only peptides whose getIdentifier matches prot_id.getIdentifier() are processed; the others are ignored.

Parameters

[in,out]	pep_ids	Peptide identifications for this run; sorted/filtered in place.
[in,out]	prot_id	Protein-identification run to annotate with aggregated scores.

Exceptions

Exception::InvalidParameter If PSMs of a peptide carry different score types.

◆ run() [3/3]

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

Run inference per protein-ID run, iterating each prot_ids entry separately.

For every entry in prot_ids, only peptides whose getIdentifier matches that run's getIdentifier are processed (other peptides are ignored for that run). pep_ids is sorted and filtered to best-PSM-per-peptidoform; prot_ids is annotated with the aggregated scores and (unless "skip_count_annotation" is set) with per-protein peptide counts.

Parameters

[in,out]	pep_ids	Peptide identifications across all runs; sorted/filtered in place.
[in,out]	prot_ids	One protein-identification run per entry; scores and per-peptide counts annotated in place.

Exceptions

Exception::InvalidParameter If PSMs of a peptide carry different score types (mixed score types are not supported).

◆ 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

[in,out]	acc_to_protein_hitP_and_count	the results to fill
[in]	best_pep	best psm per peptide to read the score
[in]	pep_scores	if the score is a posterior error probability -> Auto-converts to posterior probability
[in]	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_() [1/2]

◆ checkCompat_() [2/2]

◆ getInitScoreForAggMethod_()

◆ processRun_()

◆ run() [1/3]

◆ run() [2/3]

◆ run() [3/3]

◆ updateProteinScores_()