Calculates a consensus from multiple ID runs based on PEPs and shared ions. More...

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

Inheritance diagram for ConsensusIDAlgorithmPEPIons:

Collaboration diagram for ConsensusIDAlgorithmPEPIons:

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

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...

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

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

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

double	getSimilarity_ (AASequence seq1, AASequence seq2) override
	Sequence similarity based on matching ions. More...

Private Attributes
double	mass_tolerance_
	Fragment mass tolerance (for "PEPIons_") More...

Size	min_shared_
	Min. number of shared fragments (for "PEPIons") More...

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 Types inherited from ConsensusIDAlgorithmSimilarity
typedef std::map< std::pair< AASequence, AASequence >, double >	SimilarityCache
	Mapping: pair of peptide sequences -> sequence similarity. More...

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

Protected Member Functions inherited from ConsensusIDAlgorithmSimilarity
	ConsensusIDAlgorithmSimilarity ()
	Default constructor. More...

Protected Member Functions inherited from ConsensusIDAlgorithm
	ConsensusIDAlgorithm ()
	Default constructor. 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 inherited from ConsensusIDAlgorithmSimilarity
SimilarityCache	similarities_
	Cache for already computed sequence similarities. 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

Calculates a consensus from multiple ID runs based on PEPs and shared ions.

Parameters of this class are:

Name	Type	Default	Restrictions	Description
mass_tolerance	float	0.5	min: 0.0	Maximum difference between fragment masses (in Da) for fragments to be considered 'shared' between peptides .
min_shared	int	2	min: 1	The minimal number of 'shared' fragments (between two suggested peptides) that is necessary to evaluate the similarity based on shared peak count (SPC).
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

◆ ConsensusIDAlgorithmPEPIons() [1/2]

ConsensusIDAlgorithmPEPIons ( )

Default constructor.

◆ ConsensusIDAlgorithmPEPIons() [2/2]

ConsensusIDAlgorithmPEPIons ( const ConsensusIDAlgorithmPEPIons & )

private

Not implemented.

Member Function Documentation

◆ getSimilarity_()

double getSimilarity_	(	AASequence	seq1,
		AASequence	seq2
	)

overrideprivatevirtual

Sequence similarity based on matching ions.

Implements ConsensusIDAlgorithmSimilarity.

◆ operator=()

ConsensusIDAlgorithmPEPIons& operator= ( const ConsensusIDAlgorithmPEPIons & )

private

Not implemented.

◆ updateMembers_()

void updateMembers_ ( )

overrideprivatevirtual

Docu in base class.

Reimplemented from ConsensusIDAlgorithm.

Member Data Documentation

◆ mass_tolerance_

double mass_tolerance_

private

Fragment mass tolerance (for "PEPIons_")

◆ min_shared_

Size min_shared_

private

Min. number of shared fragments (for "PEPIons")

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ ConsensusIDAlgorithmPEPIons() [1/2]

◆ ConsensusIDAlgorithmPEPIons() [2/2]

Member Function Documentation

◆ getSimilarity_()

◆ operator=()

◆ updateMembers_()

Member Data Documentation

◆ mass_tolerance_

◆ min_shared_