OpenMS
2.4.0
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Calculates a consensus from multiple ID runs based on PEPs and shared ions. More...
#include <OpenMS/ANALYSIS/ID/ConsensusIDAlgorithmPEPIons.h>
Public Member Functions | |
ConsensusIDAlgorithmPEPIons () | |
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 ¶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 | |
ConsensusIDAlgorithmPEPIons (const ConsensusIDAlgorithmPEPIons &) | |
Not implemented. More... | |
ConsensusIDAlgorithmPEPIons & | operator= (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 | |
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, std::pair< Int, std::vector< double > > > | 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... | |
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... | |
Calculates a consensus from multiple ID runs based on PEPs and shared ions.
Parameters of this class are:Name | Type | Default | Restrictions | Description |
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mass_tolerance | float | 0.5 | min: 0 | Maximum difference between fragment masses (in Da) for fragments to be considered 'shared' between peptides . |
min_shared | int | 2 | min: 1 | The 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 | 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'? |
Default constructor.
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private |
Not implemented.
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overrideprivatevirtual |
Sequence similarity based on matching ions.
Implements ConsensusIDAlgorithmSimilarity.
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private |
Not implemented.
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overrideprivatevirtual |
Docu in base class.
Reimplemented from ConsensusIDAlgorithm.
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private |
Fragment mass tolerance (for "PEPIons_")
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private |
Min. number of shared fragments (for "PEPIons")