| OpenMS 2.5.0

Public Member Functions | Private Member Functions | List of all members
ConsensusIDAlgorithmWorst Class Reference
Analysis » Identification

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...
| ~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 Member Functions

| ConsensusIDAlgorithmWorst (const ConsensusIDAlgorithmWorst &)
| Not implemented. More...
ConsensusIDAlgorithmWorst & | operator= (const ConsensusIDAlgorithmWorst &)
| Not implemented. More...
double | getAggregateScore_ (std::vector< double > &scores, bool higher_better) override
| 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...
void | updateMembers_ () override
| 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 | 0.0 | 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'?

Note:

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

## Constructor & Destructor Documentation

## ◆ ConsensusIDAlgorithmWorst() [1/2]

ConsensusIDAlgorithmWorst | ( |  | ) |

Default constructor.

## ◆ ConsensusIDAlgorithmWorst() [2/2]

ConsensusIDAlgorithmWorst | ( | const ConsensusIDAlgorithmWorst & |  | ) |

private

Not implemented.

## Member Function Documentation

## ◆ getAggregateScore_()

double getAggregateScore_ | ( | std::vector< double > & | scores,
|  | bool | higher_better
| ) |  |

override private virtual

Aggregate peptide scores into one final score (by taking the worst score)

Implements ConsensusIDAlgorithmIdentity.

## ◆ operator=()

ConsensusIDAlgorithmWorst& operator= | ( | const ConsensusIDAlgorithmWorst & |  | ) |

private

Not implemented.