OpenMS  2.7.0
Public Member Functions | Private Member Functions | Private Attributes | List of all members
ConsensusIDAlgorithmPEPIons Class Reference

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

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

Inheritance diagram for ConsensusIDAlgorithmPEPIons:
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Collaboration diagram for ConsensusIDAlgorithmPEPIons:
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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 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

 ConsensusIDAlgorithmPEPIons (const ConsensusIDAlgorithmPEPIons &)
 Not implemented. More...
 
ConsensusIDAlgorithmPEPIonsoperator= (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 &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 shared ions.

Parameters of this class are:

NameTypeDefaultRestrictionsDescription
mass_tolerance float0.5 min: 0.0Maximum difference between fragment masses (in Da) for fragments to be considered 'shared' between peptides .
min_shared int2 min: 1The 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 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

◆ ConsensusIDAlgorithmPEPIons() [1/2]

Default constructor.

◆ ConsensusIDAlgorithmPEPIons() [2/2]

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")