IDConflictResolverAlgorithm Class Reference

Resolves ambiguous annotations of features with peptide identifications. More...

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

Static Public Member Functions
static void	resolve (FeatureMap &features, bool keep_matching=false)
	Resolves ambiguous annotations of features with peptide identifications. The the filtered identifications are added to the vector of unassigned peptides and also reduced to a single best hit. More...
static void	resolve (ConsensusMap &features, bool keep_matching=false)
	Resolves ambiguous annotations of consensus features with peptide identifications. The the filtered identifications are added to the vector of unassigned peptides and also reduced to a single best hit. More...
static void	resolveBetweenFeatures (FeatureMap &features)
	In a single (feature/consensus) map, features with the same (possibly modified) sequence and charge state may appear. This filter removes the peptide sequence annotations from features, if a higher-intensity feature with the same (charge, sequence) combination exists in the map. The total number of features remains unchanged. In the final output, each (charge, sequence) combination appears only once, i.e. no multiplicities. More...
static void	resolveBetweenFeatures (ConsensusMap &features)
	In a single (feature/consensus) map, features with the same (possibly modified) sequence and charge state may appear. This filter removes the peptide sequence annotations from features, if a higher-intensity feature with the same (charge, sequence) combination exists in the map. The total number of features remains unchanged. In the final output, each (charge, sequence) combination appears only once, i.e. no multiplicities. More...

Static Protected Member Functions
template<class T >
static void	resolveConflict_ (T &map, bool keep_matching)
static bool	compareIDsSmallerScores_ (const PeptideIdentification &left, const PeptideIdentification &right)
static void	resolveConflict_ (std::vector< PeptideIdentification > &peptides, std::vector< PeptideIdentification > &removed, UInt64 uid)
static void	resolveConflictKeepMatching_ (std::vector< PeptideIdentification > &peptides, std::vector< PeptideIdentification > &removed, UInt64 uid)
template<class T >
static void	resolveBetweenFeatures_ (T &map)

Detailed Description

Resolves ambiguous annotations of features with peptide identifications.

The peptide identifications are filtered so that only one identification with a single hit (with the best score) is associated to each feature. (If two IDs have the same best score, either one of them may be selected.)

Member Function Documentation

compareIDsSmallerScores_()

static bool compareIDsSmallerScores_ ( const PeptideIdentification &  left, const PeptideIdentification &  right  )

staticprotected

resolve() [1/2]

static void resolve ( ConsensusMap &  features, bool  keep_matching = false  )

static

Resolves ambiguous annotations of consensus features with peptide identifications. The the filtered identifications are added to the vector of unassigned peptides and also reduced to a single best hit.

Parameters

keep_matching

Keeps all IDs that match the modified sequence of the best hit in the feature (e.g. keeps all IDs in a ConsensusMap if id'd same across multiple runs)

resolve() [2/2]

static void resolve ( FeatureMap &  features, bool  keep_matching = false  )

static

Resolves ambiguous annotations of features with peptide identifications. The the filtered identifications are added to the vector of unassigned peptides and also reduced to a single best hit.

Parameters

keep_matching

Keeps all IDs that match the modified sequence of the best hit in the feature (e.g. keeps all IDs in a ConsensusMap if id'd same across multiple runs)

resolveBetweenFeatures() [1/2]

static void resolveBetweenFeatures ( ConsensusMap &  features )

static

In a single (feature/consensus) map, features with the same (possibly modified) sequence and charge state may appear. This filter removes the peptide sequence annotations from features, if a higher-intensity feature with the same (charge, sequence) combination exists in the map. The total number of features remains unchanged. In the final output, each (charge, sequence) combination appears only once, i.e. no multiplicities.

resolveBetweenFeatures() [2/2]

static void resolveBetweenFeatures ( FeatureMap &  features )

static

In a single (feature/consensus) map, features with the same (possibly modified) sequence and charge state may appear. This filter removes the peptide sequence annotations from features, if a higher-intensity feature with the same (charge, sequence) combination exists in the map. The total number of features remains unchanged. In the final output, each (charge, sequence) combination appears only once, i.e. no multiplicities.

resolveBetweenFeatures_()

static void resolveBetweenFeatures_ ( T &  map )

inlinestaticprotected

References PeptideHit::getSequence().

resolveConflict_() [1/2]

static void resolveConflict_ ( std::vector< PeptideIdentification > &  peptides, std::vector< PeptideIdentification > &  removed, UInt64  uid  )

staticprotected

resolveConflict_() [2/2]

static void resolveConflict_ ( T &  map, bool  keep_matching  )

inlinestaticprotected

References OpenMS::Constants::c.

resolveConflictKeepMatching_()

static void resolveConflictKeepMatching_ ( std::vector< PeptideIdentification > &  peptides, std::vector< PeptideIdentification > &  removed, UInt64  uid  )

staticprotected