Abstract base class for ConsensusID algorithms that compare only identical sequences. More...

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

Inheritance diagram for ConsensusIDAlgorithmIdentity:

Collaboration diagram for ConsensusIDAlgorithmIdentity:

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

virtual void	preprocess_ (std::vector< PeptideIdentification > &ids)
	Preprocessing of peptide IDs (in the beginning of "apply_"). More...

virtual double	getAggregateScore_ (std::vector< double > &scores, bool higher_better)=0
	Aggregate peptide scores into one final score (to be implemented by subclasses). More...

Protected Member Functions inherited from ConsensusIDAlgorithm
	ConsensusIDAlgorithm ()
	Default constructor. 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...

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

ConsensusIDAlgorithmIdentity &	operator= (const ConsensusIDAlgorithmIdentity &)
	Not implemented. More...

void	apply_ (std::vector< PeptideIdentification > &ids, const std::map< String, String > &se_info, SequenceGrouping &results) override
	Consensus scoring. More...

Additional Inherited Members
Public Member Functions inherited from ConsensusIDAlgorithm
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...

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

Protected Attributes inherited from ConsensusIDAlgorithm
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...

Detailed Description

Abstract base class for ConsensusID algorithms that compare only identical sequences.

Search engine scores are grouped by peptide sequence in apply_(). For each sequence, getAggregateScore_() is called to produce a consensus score from the list of search engine scores.

All derived classes should implement getAggregateScore_(). They may re-implement preprocess_() if required.

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.

Constructor & Destructor Documentation

◆ ConsensusIDAlgorithmIdentity() [1/2]

ConsensusIDAlgorithmIdentity ( )

protected

Default constructor.

◆ ConsensusIDAlgorithmIdentity() [2/2]

ConsensusIDAlgorithmIdentity ( const ConsensusIDAlgorithmIdentity & )

private

Not implemented.

Member Function Documentation

◆ apply_()

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

overrideprivatevirtual

Consensus scoring.

Implements ConsensusIDAlgorithm.

◆ getAggregateScore_()

virtual double getAggregateScore_	(	std::vector< double > &	scores,
		bool	higher_better
	)

protectedpure virtual

Aggregate peptide scores into one final score (to be implemented by subclasses).

Parameters

scores	List of scores for the same peptide by different search engines
higher_better	Whether higher or lower scores are better

Returns: Final score for the respective peptide

Implemented in ConsensusIDAlgorithmRanks, ConsensusIDAlgorithmAverage, ConsensusIDAlgorithmBest, and ConsensusIDAlgorithmWorst.

◆ operator=()

ConsensusIDAlgorithmIdentity& operator= ( const ConsensusIDAlgorithmIdentity & )

private

Not implemented.

◆ preprocess_()

virtual void preprocess_ ( std::vector< PeptideIdentification > & ids )

protectedvirtual

Preprocessing of peptide IDs (in the beginning of "apply_").

Checks whether the score types are the same (warns if not) and whether the score orientations agree (error if not).

Parameters

ids	Input/output peptide identifications

Exceptions

Exception::InvalidValue Score orientations do not agree

Reimplemented in ConsensusIDAlgorithmRanks.

Protected Member Functions

Private Member Functions

Additional Inherited Members