Calculates a consensus from multiple ID runs by taking the worst search score (conservative approach). More...
#include <OpenMS/ANALYSIS/ID/ConsensusIDAlgorithmWorst.h>
Inheritance diagram for ConsensusIDAlgorithmWorst:
Public Member Functions | |
| ConsensusIDAlgorithmWorst () | |
| 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... | |
| virtual | ~ConsensusIDAlgorithm () |
| 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 ¶m) |
| 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 Member Functions | |
| ConsensusIDAlgorithmWorst (const ConsensusIDAlgorithmWorst &) | |
| Not implemented. More... | |
| ConsensusIDAlgorithmWorst & | operator= (const ConsensusIDAlgorithmWorst &) |
| Not implemented. More... | |
| virtual double | getAggregateScore_ (std::vector< double > &scores, bool higher_better) |
| Aggregate peptide scores into one final score (by taking the worst score) More... | |
Additional Inherited Members | |
| 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 ConsensusIDAlgorithmIdentity | |
| ConsensusIDAlgorithmIdentity () | |
| Default constructor. More... | |
| virtual void | preprocess_ (std::vector< PeptideIdentification > &ids) |
| Preprocessing of peptide IDs (in the beginning of "apply_"). More... | |
| Protected Member Functions inherited from ConsensusIDAlgorithm | |
| ConsensusIDAlgorithm () | |
| Default constructor. More... | |
| virtual void | updateMembers_ () |
| 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 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 by taking the worst search score (conservative approach).
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 | 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.
Constructor & Destructor Documentation
◆ ConsensusIDAlgorithmWorst() [1/2]
Default constructor.
◆ ConsensusIDAlgorithmWorst() [2/2]
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private |
Not implemented.
Member Function Documentation
◆ getAggregateScore_()
|
privatevirtual |
Aggregate peptide scores into one final score (by taking the worst score)
Implements ConsensusIDAlgorithmIdentity.
◆ operator=()
|
private |
Not implemented.