Abstract base class for all ConsensusID algorithms (that calculate a consensus from multiple ID runs). More...

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

Inheritance diagram for ConsensusIDAlgorithm:

Collaboration diagram for ConsensusIDAlgorithm:

Classes
struct	HitInfo

Public Member Functions
void	apply (std::vector< PeptideIdentification > &ids, const std::map< String, String > &se_info, Size number_of_runs=0)
	Calculates the consensus ID for a set of peptide identifications of one spectrum or (consensus) feature. More...

void	apply (std::vector< PeptideIdentification > &ids, Size number_of_runs=0)

	~ConsensusIDAlgorithm () override
	Virtual destructor. 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...

Protected Types
typedef std::map< AASequence, HitInfo >	SequenceGrouping
	Mapping: peptide sequence -> (charge, scores) More...

Protected Member Functions
	ConsensusIDAlgorithm ()
	Default constructor. More...

virtual void	apply_ (std::vector< PeptideIdentification > &ids, const std::map< String, String > &se_info, SequenceGrouping &results)=0
	Consensus computation (to be implemented by subclasses). More...

void	updateMembers_ () override
	Docu in base class. More...

void	compareChargeStates_ (Int &recorded_charge, Int new_charge, const AASequence &peptide)
	Compare (and possibly update) charge state information. More...

Protected Member Functions inherited from DefaultParamHandler
void	defaultsToParam_ ()
	Updates the parameters after the defaults have been set in the constructor. More...

Protected Attributes
Size	considered_hits_
	Number of peptide hits considered per ID run (input parameter) More...

Size	number_of_runs_
	Number of ID runs. More...

double	min_support_
	Fraction of required support by other ID runs (input parameter) More...

bool	count_empty_
	Count empty runs in "min_support" calculation? (input parameter) More...

bool	keep_old_scores_
	Keep old scores? 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...

Private Member Functions
	ConsensusIDAlgorithm (const ConsensusIDAlgorithm &)
	Not implemented. More...

ConsensusIDAlgorithm &	operator= (const ConsensusIDAlgorithm &)
	Not implemented. 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...

Detailed Description

Abstract base class for all ConsensusID algorithms (that calculate a consensus from multiple ID runs).

The main function is apply(), which aggregates several peptide identifications into one.

Derived classes should implement apply_(), which takes a list of peptide identifications and produces a map of peptide sequences with accompanying scores (and charge states). Currently there are two derived classes, OpenMS::ConsensusIDAlgorithmIdentity and OpenMS::ConsensusIDAlgorithmSimilarity. They serve as abstract base classes for algorithms that score only identical peptide sequences together and algorithms that take similarities between peptides into account, respectively.

See also the documentation of the TOPP tool, ConsensusID, for more information (e.g. on the filter: parameters).

Parameters of this class are:

Name	Type	Default	Restrictions	Description
filter:considered_hits	int	0	min: 0	The number of top hits in each ID run that are considered for consensus scoring ('0' for all hits).
filter:min_support	float	0.0	min: 0.0 max: 1.0	For each peptide hit from an ID run, the fraction of other ID runs that must support that hit (otherwise it is removed).
filter:count_empty	string	false	true, false	Count empty ID runs (i.e. those containing no peptide hit for the current spectrum) when calculating 'min_support'?
filter:keep_old_scores	string	false	true, false	if set, keeps the original scores as user params

Note:

If a section name is documented, the documentation is displayed as tooltip.
Advanced parameter names are italic.

Class Documentation

◆ OpenMS::ConsensusIDAlgorithm::HitInfo

struct OpenMS::ConsensusIDAlgorithm::HitInfo

Collaboration diagram for ConsensusIDAlgorithm::HitInfo:

[legend]

Class Members
Int	charge
set< PeptideEvidence >	evidence
double	final_score
vector< double >	scores
double	support
String	target_decoy
vector< String >	types

Member Typedef Documentation

◆ SequenceGrouping

typedef std::map<AASequence, HitInfo> SequenceGrouping

protected

Mapping: peptide sequence -> (charge, scores)

Constructor & Destructor Documentation

◆ ~ConsensusIDAlgorithm()

~ConsensusIDAlgorithm ( )

override

Virtual destructor.

◆ ConsensusIDAlgorithm() [1/2]

ConsensusIDAlgorithm ( )

protected

Default constructor.

◆ ConsensusIDAlgorithm() [2/2]

ConsensusIDAlgorithm ( const ConsensusIDAlgorithm & )

private

Not implemented.

Member Function Documentation

◆ apply() [1/2]

void apply	(	std::vector< PeptideIdentification > &	ids,
		const std::map< String, String > &	se_info,
		Size	number_of_runs = `0`
	)

Calculates the consensus ID for a set of peptide identifications of one spectrum or (consensus) feature.

Make sure that the score type (PeptideIdentification::getScoreType()) and the score orientation (PeptideIdentification::isHigherScoreBetter()) are set properly!

Parameters

ids	Peptide identifications (input: more than one, output: one)
number_of_runs	Number of ID runs (default: size of "ids")
se_info	map from run identifiers to search engine infos to retain original search engine information

Todo:: we could pass the score_types that we want to carry over in the map as well (right now it always takes main)

◆ apply() [2/2]

void apply	(	std::vector< PeptideIdentification > &	ids,
		Size	number_of_runs = `0`
	)

◆ apply_()

virtual void apply_	(	std::vector< PeptideIdentification > &	ids,
		const std::map< String, String > &	se_info,
		SequenceGrouping &	results
	)

protectedpure virtual

Consensus computation (to be implemented by subclasses).

Parameters

ids	Peptide identifications (input)
se_info	mapping from run identifier to search engine to carry over infos to result
results	Algorithm results (output). For each peptide sequence, two scores are expected: the actual consensus score and the "support" value, in this order.

Implemented in ConsensusIDAlgorithmSimilarity, and ConsensusIDAlgorithmIdentity.

◆ compareChargeStates_()

void compareChargeStates_	(	Int &	recorded_charge,
		Int	new_charge,
		const AASequence &	peptide
	)

protected

Compare (and possibly update) charge state information.

◆ operator=()

ConsensusIDAlgorithm& operator= ( const ConsensusIDAlgorithm & )

private

Not implemented.

◆ updateMembers_()

void updateMembers_ ( )

overrideprotectedvirtual

Docu in base class.

Reimplemented from DefaultParamHandler.

Reimplemented in ConsensusIDAlgorithmPEPMatrix, and ConsensusIDAlgorithmPEPIons.

Member Data Documentation

◆ considered_hits_

Size considered_hits_

protected

Number of peptide hits considered per ID run (input parameter)

◆ count_empty_

bool count_empty_

protected

Count empty runs in "min_support" calculation? (input parameter)

◆ keep_old_scores_

bool keep_old_scores_

protected

Keep old scores?

◆ min_support_

double min_support_

protected

Fraction of required support by other ID runs (input parameter)

◆ number_of_runs_

Size number_of_runs_

protected

Number of ID runs.

Classes

Public Member Functions

Protected Types

Protected Member Functions

Protected Attributes

Private Member Functions

Additional Inherited Members

Detailed Description

Class Documentation

◆ OpenMS::ConsensusIDAlgorithm::HitInfo

Member Typedef Documentation

◆ SequenceGrouping

Constructor & Destructor Documentation

◆ ~ConsensusIDAlgorithm()

◆ ConsensusIDAlgorithm() [1/2]

◆ ConsensusIDAlgorithm() [2/2]

Member Function Documentation

◆ apply() [1/2]

◆ apply() [2/2]

◆ apply_()

◆ compareChargeStates_()

◆ operator=()

◆ updateMembers_()

Member Data Documentation

◆ considered_hits_

◆ count_empty_

◆ keep_old_scores_

◆ min_support_

◆ number_of_runs_