| OpenMS 2.5.0

Static Public Member Functions | Static Protected Member Functions | List of all members
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
| ) |  |

static protected

## ◆ resolve() [1/2]

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)

Referenced by UTILProteomicsLFQ::quantifyFraction_().

## ◆ resolve() [2/2]

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)

## ◆ resolveBetweenFeatures() [1/2]

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() [2/2]

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_()

static void resolveBetweenFeatures_ | ( | T & | map | ) |

inline static protected

References PeptideHit::getSequence().

## ◆ resolveConflict_() [1/2]

static void resolveConflict_ | ( | T & | map,
|  | bool | keep_matching
| ) |  |

inline static protected

References OpenMS::Constants::c.

## ◆ resolveConflict_() [2/2]

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

static protected

## ◆ resolveConflictKeepMatching_()

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

static protected