OpenMS  2.7.0
Public Member Functions | Private Member Functions | Private Attributes | List of all members
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:
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Collaboration diagram for ConsensusIDAlgorithmPEPMatrix:
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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 DefaultParamHandleroperator= (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 ParamgetParameters () const
 Non-mutable access to the parameters. More...
 
const ParamgetDefaults () const
 Non-mutable access to the default parameters. More...
 
const StringgetName () 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

 ConsensusIDAlgorithmPEPMatrix (const ConsensusIDAlgorithmPEPMatrix &)
 Not implemented. More...
 
ConsensusIDAlgorithmPEPMatrixoperator= (const ConsensusIDAlgorithmPEPMatrix &)
 Not implemented. More...
 
double getSimilarity_ (AASequence seq1, AASequence seq2) override
 Sequence similarity based on substitution matrix (ignores PTMs) More...
 
void updateMembers_ () override
 Docu in base class. More...
 

Private Attributes

NeedlemanWunsch alignment_
 object for alignment score calculation 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, HitInfoSequenceGrouping
 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< Stringsubsections_
 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:

NameTypeDefaultRestrictionsDescription
matrix stringPAM30MS identity, PAM30MSSubstitution matrix to use for alignment-based similarity scoring
penalty int5 min: 1Alignment gap penalty (the same value is used for gap opening and extension)
filter:considered_hits int0 min: 0The number of top hits in each ID run that are considered for consensus scoring ('0' for all hits).
filter:min_support float0.0 min: 0.0 max: 1.0For 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 stringfalse true, falseCount empty ID runs (i.e. those containing no peptide hit for the current spectrum) when calculating 'min_support'?
filter:keep_old_scores stringfalse true, falseif set, keeps the original scores as user params

Note:

Constructor & Destructor Documentation

◆ ConsensusIDAlgorithmPEPMatrix() [1/2]

Default constructor.

◆ ConsensusIDAlgorithmPEPMatrix() [2/2]

Not implemented.

Member Function Documentation

◆ getSimilarity_()

double getSimilarity_ ( AASequence  seq1,
AASequence  seq2 
)
overrideprivatevirtual

Sequence similarity based on substitution matrix (ignores PTMs)

Implements ConsensusIDAlgorithmSimilarity.

◆ operator=()

Not implemented.

◆ updateMembers_()

void updateMembers_ ( )
overrideprivatevirtual

Docu in base class.

Reimplemented from ConsensusIDAlgorithm.

Member Data Documentation

◆ alignment_

NeedlemanWunsch alignment_
private

object for alignment score calculation