Calculates a consensus from multiple ID runs based on PEPs and sequence similarities. More...

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

Inheritance diagram for ConsensusIDAlgorithmPEPMatrix:

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

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

	~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 Types
typedef ::seqan::Score< int, ::seqan::ScoreMatrix< ::seqan::AminoAcid, ::seqan::Default > >	SeqAnScore
	SeqAn similarity scoring. More...

typedef ::seqan::String< ::seqan::AminoAcid >	SeqAnSequence
	SeqAn amino acid sequence. More...

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

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

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

double	getSimilarity_ (AASequence seq1, AASequence seq2) override
	Sequence similarity based on substitution matrix (ignores PTMs) More...

Private Attributes
SeqAnScore	scoring_method_
	Similarity scoring method. More...

::seqan::Align< SeqAnSequence, ::seqan::ArrayGaps >	alignment_
	Alignment data structure. More...

Additional Inherited Members
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, std::pair< Int, std::vector< double > > >	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...

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 sequence similarities.

Note: The similarity scoring is based on an amino acid substitution matrix. Therefore only the raw amino acid sequences, without post-translational modifications (PTMs), can be considered for similarity scoring - PTMs are ignored during this step. However, PTMs on peptides are retained and separate results are produced for differently-modified peptides.

Parameters of this class are:

Name	Type	Default	Restrictions	Description
matrix	string	identity	identity, PAM30MS	Substitution matrix to use for alignment-based similarity scoring
penalty	int	5	min: 1	Alignment gap penalty (the same value is used for gap opening and extension)
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	min: 0 max: 1	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'?

Note:

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

Member Typedef Documentation

◆ SeqAnScore

typedef ::seqan::Score<int, ::seqan::ScoreMatrix< ::seqan::AminoAcid, ::seqan::Default> > SeqAnScore

private

SeqAn similarity scoring.

◆ SeqAnSequence

typedef ::seqan::String< ::seqan::AminoAcid> SeqAnSequence

private

SeqAn amino acid sequence.

Constructor & Destructor Documentation

◆ ConsensusIDAlgorithmPEPMatrix() [1/2]

ConsensusIDAlgorithmPEPMatrix ( )

Default constructor.

◆ ConsensusIDAlgorithmPEPMatrix() [2/2]

ConsensusIDAlgorithmPEPMatrix ( const ConsensusIDAlgorithmPEPMatrix & )

private

Not implemented.

Member Function Documentation

◆ getSimilarity_()

double getSimilarity_	(	AASequence	seq1,
		AASequence	seq2
	)

overrideprivatevirtual

Sequence similarity based on substitution matrix (ignores PTMs)

Implements ConsensusIDAlgorithmSimilarity.

◆ operator=()

ConsensusIDAlgorithmPEPMatrix& operator= ( const ConsensusIDAlgorithmPEPMatrix & )

private

Not implemented.

◆ updateMembers_()

void updateMembers_ ( )

overrideprivatevirtual

Docu in base class.

Reimplemented from ConsensusIDAlgorithm.

Member Data Documentation

◆ alignment_

::seqan::Align<SeqAnSequence, ::seqan::ArrayGaps> alignment_

private

Alignment data structure.

◆ scoring_method_

SeqAnScore scoring_method_

private

Similarity scoring method.

Public Member Functions

Private Types

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ SeqAnScore

◆ SeqAnSequence

Constructor & Destructor Documentation

◆ ConsensusIDAlgorithmPEPMatrix() [1/2]

◆ ConsensusIDAlgorithmPEPMatrix() [2/2]

Member Function Documentation

◆ getSimilarity_()

◆ operator=()

◆ updateMembers_()

Member Data Documentation

◆ alignment_

◆ scoring_method_