OpenMS
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
featuresFeatures to work on
keep_matchingKeeps 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
featuresFeatures to work on
keep_matchingKeeps 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

◆ 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