ConsensusIDAlgorithmSimilarity Class Reference

Abstract base class for ConsensusID algorithms that take peptide similarity into account. More...

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

Inheritance diagram for ConsensusIDAlgorithmSimilarity:

Collaboration diagram for ConsensusIDAlgorithmSimilarity:

Protected Types
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
	ConsensusIDAlgorithmSimilarity ()
	Default constructor. More...
virtual double	getSimilarity_ (AASequence seq1, AASequence seq2)=0
	Sequence similarity calculation (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...

Protected Attributes
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...

Private Member Functions
	ConsensusIDAlgorithmSimilarity (const ConsensusIDAlgorithmSimilarity &)
	Not implemented. More...
ConsensusIDAlgorithmSimilarity &	operator= (const ConsensusIDAlgorithmSimilarity &)
	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 &key_prefix="")
	Writes all parameters to meta values. More...

Detailed Description

Abstract base class for ConsensusID algorithms that take peptide similarity into account.

Similarity-based algorithms require posterior error probabilities (PEPs) as peptide scores, in order to combine scores and similarities into a consensus score for each peptide. See the following publication for the formula governing this calculation:

Nahnsen et al.: Probabilistic consensus scoring improves tandem mass spectrometry peptide identification (J. Proteome Res., 2011, PMID: 21644507).

Derived classes should implement getSimilarity_(), which defines how similarity of two peptide sequences is quantified.

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.

Member Typedef Documentation

SimilarityCache

typedef std::map<std::pair<AASequence, AASequence>, double> SimilarityCache

protected

Mapping: pair of peptide sequences -> sequence similarity.

Constructor & Destructor Documentation

ConsensusIDAlgorithmSimilarity() [1/2]

ConsensusIDAlgorithmSimilarity ( )

protected

Default constructor.

ConsensusIDAlgorithmSimilarity() [2/2]

ConsensusIDAlgorithmSimilarity ( const ConsensusIDAlgorithmSimilarity &  )

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.

getSimilarity_()

virtual double getSimilarity_ ( AASequence  seq1, AASequence  seq2  )

protectedpure virtual

Sequence similarity calculation (to be implemented by subclasses).

Implementations should use/update the cache of previously computed similarities.

Returns

Similarity between two sequences in the range [0, 1]

Implemented in ConsensusIDAlgorithmPEPMatrix, and ConsensusIDAlgorithmPEPIons.

operator=()

ConsensusIDAlgorithmSimilarity& operator= ( const ConsensusIDAlgorithmSimilarity &  )

private

Not implemented.

Member Data Documentation

similarities_

SimilarityCache similarities_

protected

Cache for already computed sequence similarities.