ConsensusIDAlgorithmPEPMatrix Class Reference

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

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

Inheritance diagram for ConsensusIDAlgorithmPEPMatrix:

Collaboration diagram for ConsensusIDAlgorithmPEPMatrix:

Public Member Functions
	ConsensusIDAlgorithmPEPMatrix ()
	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 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
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 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 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	0.0	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

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.