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ConsensusIDAlgorithmSimilarity Class Referenceabstract

Abstract base class for ConsensusID algorithms that take peptide similarity into account. More...

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

Inheritance diagram for ConsensusIDAlgorithmSimilarity:
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Collaboration diagram for ConsensusIDAlgorithmSimilarity:
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Protected Types

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

 ConsensusIDAlgorithmSimilarity ()
 Default constructor. More...
 
virtual double getSimilarity_ (AASequence seq1, AASequence seq2)=0
 Sequence similarity calculation (to be implemented by subclasses). 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

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...
 

Private Member Functions

 ConsensusIDAlgorithmSimilarity (const ConsensusIDAlgorithmSimilarity &)
 Not implemented. More...
 
ConsensusIDAlgorithmSimilarityoperator= (const ConsensusIDAlgorithmSimilarity &)
 Not implemented. More...
 
void apply_ (std::vector< PeptideIdentification > &ids, const std::map< String, String > &se_info, SequenceGrouping &results) override
 Consensus scoring. More...
 

Additional Inherited Members

- 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...
 
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...
 
- Static Public Member Functions inherited from DefaultParamHandler
static void writeParametersToMetaValues (const Param &write_this, MetaInfoInterface &write_here, const String &key_prefix="")
 Writes all parameters to meta values. More...
 

Detailed Description

Abstract base class for ConsensusID algorithms that take peptide similarity into account.

Similarity-based algorithms require posterior error probabilities (PEPs) as peptide scores, in order to combine scores and similarities into a consensus score for each peptide. See the following publication for the formula governing this calculation:

Nahnsen et al.: Probabilistic consensus scoring improves tandem mass spectrometry peptide identification (J. Proteome Res., 2011, PMID: 21644507).

Derived classes should implement getSimilarity_(), which defines how similarity of two peptide sequences is quantified.

Parameters of this class are:

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

Member Typedef Documentation

◆ SimilarityCache

typedef std::map<std::pair<AASequence, AASequence>, double> SimilarityCache
protected

Mapping: pair of peptide sequences -> sequence similarity.

Constructor & Destructor Documentation

◆ ConsensusIDAlgorithmSimilarity() [1/2]

Default constructor.

◆ ConsensusIDAlgorithmSimilarity() [2/2]

Not implemented.

Member Function Documentation

◆ apply_()

void apply_ ( std::vector< PeptideIdentification > &  ids,
const std::map< String, String > &  se_info,
SequenceGrouping results 
)
overrideprivatevirtual

Consensus scoring.

Implements ConsensusIDAlgorithm.

◆ getSimilarity_()

virtual double getSimilarity_ ( AASequence  seq1,
AASequence  seq2 
)
protectedpure virtual

Sequence similarity calculation (to be implemented by subclasses).

Implementations should use/update the cache of previously computed similarities.

Returns
Similarity between two sequences in the range [0, 1]

Implemented in ConsensusIDAlgorithmPEPMatrix, and ConsensusIDAlgorithmPEPIons.

◆ operator=()

Not implemented.

Member Data Documentation

◆ similarities_

SimilarityCache similarities_
protected

Cache for already computed sequence similarities.